PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Assessing knowledge anxiety in researchers: a comprehensive measurement scale
items: Phenotypic diversity and provenance variation of Cupressus funebris: a case study in the Sichuan Basin, China
items: Prognosis and immune landscape of bladder cancer can be predicted using a novel miRNA signature associated with cuproptosis
items: Physiological and molecular response mechanisms of tomato seedlings to cadmium (Cd) and lead (Pb) stress
items: Effect of prognostic nutritional index on laboratory parameters and survival in metastatic colorectal cancer patients treated with fruquintinib: a retrospective study
items: Resistance characterization and transcriptomic analysis of imipenem-induced drug resistance in Escherichia coli
items: Genome-wide identification and expression analysis of the Trihelix transcription factor family in potato (Solanum tuberosum L.) during development
items: Losartan and dapagliflozin combination therapy in reducing uric acid level compared to monotherapy in patients with heart failure
items: Effects of a single bout of exercise on human hemocytes and serum interleukin 3, erythropoietin, and soluble transferrin receptor in a hot and humid environment
items: Assessment of genotype by environment and yield performance of tropical maize hybrids using stability statistics and graphical biplots

Assessing knowledge anxiety in researchers: a comprehensive measurement scale
type: item
type: AcademicArticle
description: Background The rapid pace of knowledge production has introduced a phenomenon termed “knowledge anxiety”, a psychological state where researchers feel inadequate in keeping up with emerging information. This state can negatively affect productivity and mental well-being, yet there is no comprehensive tool to measure knowledge anxiety across different research domains. Methods We employed a mixed-methods approach to develop a multidimensional scale for assessing knowledge anxiety. Initial items were generated through a literature review and qualitative interviews with 313 researchers. After pilot testing, the main study involved 26 participants. The scale was refined through exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) to ensure its structural validity and reliability. Results EFA resulted in a 16-item scale with four distinct factors: cognitive, emotional, behavioral, and capability-related anxieties. CFA confirmed a strong model fit, with standardized factor loadings between 0.549 and 0.887. The scale demonstrated high reliability, with a composite Cronbach’s alpha of 0.883. Conclusions This newly developed scale offers a reliable and valid measure of knowledge anxiety, providing researchers with a valuable tool to assess the psychological impacts of knowledge overload.
format: application/pdf
format: text/html
creator: Yu Zhenlei
creator: Lin Song
creator: Dong Minyi
creator: He Qiang
subject: Psychiatry and Psychology
subject: Data Science
description: doi:10.7717/peerj.18478
publisher: PeerJ Inc.
rights: © 2024 Zhenlei et al.
abstract: Background The rapid pace of knowledge production has introduced a phenomenon termed “knowledge anxiety”, a psychological state where researchers feel inadequate in keeping up with emerging information. This state can negatively affect productivity and mental well-being, yet there is no comprehensive tool to measure knowledge anxiety across different research domains. Methods We employed a mixed-methods approach to develop a multidimensional scale for assessing knowledge anxiety. Initial items were generated through a literature review and qualitative interviews with 313 researchers. After pilot testing, the main study involved 26 participants. The scale was refined through exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) to ensure its structural validity and reliability. Results EFA resulted in a 16-item scale with four distinct factors: cognitive, emotional, behavioral, and capability-related anxieties. CFA confirmed a strong model fit, with standardized factor loadings between 0.549 and 0.887. The scale demonstrated high reliability, with a composite Cronbach’s alpha of 0.883. Conclusions This newly developed scale offers a reliable and valid measure of knowledge anxiety, providing researchers with a valuable tool to assess the psychological impacts of knowledge overload.
bibliographic citation: Zhenlei et al. (2024) Assessing knowledge anxiety in researchers: a comprehensive measurement scale. PeerJ 12:e18478 https://doi.org/10.7717/peerj.18478
date submitted: 2024-07-02
date accepted: 2024-10-16
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhenlei
  given name: Yu
author list: Agent
  family name: Song
  given name: Lin
author list: Agent
  family name: Minyi
  given name: Dong
author list: Agent
  family name: Qiang
  given name: He
doi: 10.7717/peerj.18478
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: ©2024 Zhenlei et al.
attribution name: Zhenlei et al.

Phenotypic diversity and provenance variation of Cupressus funebris: a case study in the Sichuan Basin, China
type: item
type: AcademicArticle
description: Background The species Cupressus funebris holds substantial ecological value and economic potential, particularly in the realms of rehabilitating barren mountain landscapes and advancing urban greening endeavors. However, inadequate attention has been given to research endeavors exploring the genetic diversity and morphological characteristics of Cupressus funebris, a deficiency that could potentially hinder its development, utilization, and conservation of genetic resources. Methods To rectify the shortage of existing basic morphological data, a morphological analysis was conducted in this study on 180 Cupressus funebris germplasm resources sourced from five provenances. Key traits explored included growth characteristics, overall morphology, branch/leaf features, and seed traits. This will facilitate the evaluation of genetic diversity in Cupressus funebris. Results The findings reveal a considerable level of phenotypic variation (PVC of 16.9%) and genetic diversity (1.97 index) in Cupressus funebris germplasm resources. The phenotypic differentiation is observed to be 48% between provenances and 52% within provenances, primarily attributed to variation originating from individual provenances. Based on these morphological characteristics, the germplasm resources have been categorized into four distinct groups: Ecological Restoration Planting, Secondary Reserve Forest, Urban Greening, and Timber Forest. Interestingly, the pattern of variation observed within these groups is irregular, exhibiting no significant correlation with their respective provenances. Furthermore, conifer trees sharing similar growth characteristics tend to display comparable patterns of random variation, suggesting potential underlying genetic mechanisms. This study significantly enriches the phenotypic dataset within the genetic variation research of Cupressus funebris, facilitating development and utilization for ecological construction, timber breeding, and horticultural greening.
format: application/pdf
format: text/html
creator: Wang Yan
creator: Yongqi Xiang
creator: Mei Gao
creator: Ruoyu Deng
creator: Yan Sun
creator: Renping Wan
creator: Xianyi Pan
creator: Wanzhen Li
creator: Yu Zhong
subject: Agricultural Science
subject: Biodiversity
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.18494
publisher: PeerJ Inc.
rights: © 2024 Yan et al.
abstract: Background The species Cupressus funebris holds substantial ecological value and economic potential, particularly in the realms of rehabilitating barren mountain landscapes and advancing urban greening endeavors. However, inadequate attention has been given to research endeavors exploring the genetic diversity and morphological characteristics of Cupressus funebris, a deficiency that could potentially hinder its development, utilization, and conservation of genetic resources. Methods To rectify the shortage of existing basic morphological data, a morphological analysis was conducted in this study on 180 Cupressus funebris germplasm resources sourced from five provenances. Key traits explored included growth characteristics, overall morphology, branch/leaf features, and seed traits. This will facilitate the evaluation of genetic diversity in Cupressus funebris. Results The findings reveal a considerable level of phenotypic variation (PVC of 16.9%) and genetic diversity (1.97 index) in Cupressus funebris germplasm resources. The phenotypic differentiation is observed to be 48% between provenances and 52% within provenances, primarily attributed to variation originating from individual provenances. Based on these morphological characteristics, the germplasm resources have been categorized into four distinct groups: Ecological Restoration Planting, Secondary Reserve Forest, Urban Greening, and Timber Forest. Interestingly, the pattern of variation observed within these groups is irregular, exhibiting no significant correlation with their respective provenances. Furthermore, conifer trees sharing similar growth characteristics tend to display comparable patterns of random variation, suggesting potential underlying genetic mechanisms. This study significantly enriches the phenotypic dataset within the genetic variation research of Cupressus funebris, facilitating development and utilization for ecological construction, timber breeding, and horticultural greening.
bibliographic citation: Yan et al. (2024) Phenotypic diversity and provenance variation of Cupressus funebris: a case study in the Sichuan Basin, China. PeerJ 12:e18494 https://doi.org/10.7717/peerj.18494
date submitted: 2024-08-02
date accepted: 2024-10-17
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Wang
author list: Agent
  family name: Xiang
  given name: Yongqi
author list: Agent
  family name: Gao
  given name: Mei
author list: Agent
  family name: Deng
  given name: Ruoyu
author list: Agent
  family name: Sun
  given name: Yan
author list: Agent
  family name: Wan
  given name: Renping
author list: Agent
  family name: Pan
  given name: Xianyi
author list: Agent
  family name: Li
  given name: Wanzhen
author list: Agent
  family name: Zhong
  given name: Yu
doi: 10.7717/peerj.18494
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Yan et al.
attribution name: Yan et al.

Prognosis and immune landscape of bladder cancer can be predicted using a novel miRNA signature associated with cuproptosis
type: item
type: AcademicArticle
description: Background Bladder cancer is characterized by a high recurrence rate and mortality, posing a significant challenge to clinical management. Recently, cuproptosis, a novel form of regulated cell death, has been identified as a potential target for therapeutic intervention in various diseases. The contribution of cuproptosis-related microRNAs (miRNAs) in bladder cancer pathogenesis, however, remains largely unexplored. Therefore, the current study aims to construct a miRNA signature related to cuproptosis for predicting the prognosis and facilitating personalized therapeutic strategies in bladder cancer patients. Methods In this study, we retrieved transcriptomic data and clinical information pertaining to bladder cancer from publicly available databases, including the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). We identified a set of 19 cuproptosis-related genes through a comprehensive review of relevant literature. Using multivariate Cox regression and LASSO analysis, we constructed a cuproptosis-related miRNA prognostic signature. The Kaplan-Meier (K-M) and receiver operating characteristic (ROC) curves were used to validate the accuracy of prediction. Additionally, we developed a nomogram incorporating clinical characteristics and the miRNA signature to further assess its prognostic value. We evaluated the tumor microenvironment (TME) of every patient using immune ESTIMATE, CIBERSORT, and ssGSEA algorithms. We also investigated the differences in tumor mutation burden (TMB) and drug sensitivity between two groups. Finally, we validated the prognostic value of this miRNA signature using the OncomiR dataset. Results We developed a panel of eight cuproptosis-associated miRNAs to serve as a prognostic signature. The predictive validity of this signature was determined using Kaplan-Meier and ROC curves, and was found to be acceptable in both the TCGA training, test and total dataset. The prognostic value of this signature was confirmed by univariate an…
format: application/pdf
format: text/html
creator: Zhilei Zhang
creator: Fang Liu
creator: Yongbo Yu
creator: Fei Xie
creator: Tao Zhu
subject: Bioinformatics
subject: Genetics
subject: Immunology
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.18530
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Background Bladder cancer is characterized by a high recurrence rate and mortality, posing a significant challenge to clinical management. Recently, cuproptosis, a novel form of regulated cell death, has been identified as a potential target for therapeutic intervention in various diseases. The contribution of cuproptosis-related microRNAs (miRNAs) in bladder cancer pathogenesis, however, remains largely unexplored. Therefore, the current study aims to construct a miRNA signature related to cuproptosis for predicting the prognosis and facilitating personalized therapeutic strategies in bladder cancer patients. Methods In this study, we retrieved transcriptomic data and clinical information pertaining to bladder cancer from publicly available databases, including the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). We identified a set of 19 cuproptosis-related genes through a comprehensive review of relevant literature. Using multivariate Cox regression and LASSO analysis, we constructed a cuproptosis-related miRNA prognostic signature. The Kaplan-Meier (K-M) and receiver operating characteristic (ROC) curves were used to validate the accuracy of prediction. Additionally, we developed a nomogram incorporating clinical characteristics and the miRNA signature to further assess its prognostic value. We evaluated the tumor microenvironment (TME) of every patient using immune ESTIMATE, CIBERSORT, and ssGSEA algorithms. We also investigated the differences in tumor mutation burden (TMB) and drug sensitivity between two groups. Finally, we validated the prognostic value of this miRNA signature using the OncomiR dataset. Results We developed a panel of eight cuproptosis-associated miRNAs to serve as a prognostic signature. The predictive validity of this signature was determined using Kaplan-Meier and ROC curves, and was found to be acceptable in both the TCGA training, test and total dataset. The prognostic value of this signature was confirmed by univariate an…
bibliographic citation: Zhang et al. (2024) Prognosis and immune landscape of bladder cancer can be predicted using a novel miRNA signature associated with cuproptosis. PeerJ 12:e18530 https://doi.org/10.7717/peerj.18530
date submitted: 2024-05-30
date accepted: 2024-10-24
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Zhilei
author list: Agent
  family name: Liu
  given name: Fang
author list: Agent
  family name: Yu
  given name: Yongbo
author list: Agent
  family name: Xie
  given name: Fei
author list: Agent
  family name: Zhu
  given name: Tao
doi: 10.7717/peerj.18530
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

Physiological and molecular response mechanisms of tomato seedlings to cadmium (Cd) and lead (Pb) stress
type: item
type: AcademicArticle
description: Heavy metal contamination, particularly from cadmium (Cd) and lead (Pb), poses significant risks to soil and water resources and leads to severe damage in plants. This study investigated the physiological and molecular mechanisms of the responses of tomato (Solanum lycopersicum L.) seedlings to Cd and Pb stress by applying 50 mg/L Cd, 100 mg/L Pb, and a combination of 50 mg/L Cd + 100 mg/L Pb. The goal was to understand how these heavy metals impact the growth, antioxidant systems, and secondary metabolic pathways in tomato seedlings. The results showed that compared with the control, Cd + Pb stress significantly increased the content of soluble sugar by 37.40% and 33.46% on days 5 and 15, respectively, and the content of proline by 77.91% to 93.91% during the entire period in tomato seedlings. It also elevated electrical leakage by 110.52% on day 15, maintained the levels of malondialdehyde close to the control, enhanced the activities of superoxide dismutase by 33.32% on day 10 and 11.22% on day 15, peroxidase by 42.15% on day 10, and catalase by 90.78% on day 10. Additionally, it reduced the contents of hydrogen peroxide by 15.47% to 29.64% and the rate of formation of superoxide anions by 26.34% to 53.47% during the entire period of treatment. The transcriptomic analysis revealed a significant differential expression of the genes involved in pathways, such as phenylalanine, glutathione, arginine and proline, and nitrogen metabolism. These genes included PALs, HDCs, GGCT, ODC1, LAPs, SMS, and SAMDC. Notably, transcription factors, such as ERF109, ARF9, GRF3, GRF4, GRF7, and GRF9, were also significantly regulated. The study concluded that Cd and Pb stress enhanced the osmoregulatory and antioxidant defense systems in tomato seedlings, which may contribute to their tolerance to heavy metal stress. Future research could explore the application of these findings to develop strategies to improve the resistance of plants to contamination with heavy metals.
format: application/pdf
format: text/html
creator: Yan Zhou
creator: Jinyu Fu
creator: Yuqi Ye
creator: Qibo Xu
creator: Jinjie Liang
creator: Yanyan Chen
creator: Yuxing Mo
creator: Kaidong Liu
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.18533
publisher: PeerJ Inc.
rights: © 2024 Zhou et al.
abstract: Heavy metal contamination, particularly from cadmium (Cd) and lead (Pb), poses significant risks to soil and water resources and leads to severe damage in plants. This study investigated the physiological and molecular mechanisms of the responses of tomato (Solanum lycopersicum L.) seedlings to Cd and Pb stress by applying 50 mg/L Cd, 100 mg/L Pb, and a combination of 50 mg/L Cd + 100 mg/L Pb. The goal was to understand how these heavy metals impact the growth, antioxidant systems, and secondary metabolic pathways in tomato seedlings. The results showed that compared with the control, Cd + Pb stress significantly increased the content of soluble sugar by 37.40% and 33.46% on days 5 and 15, respectively, and the content of proline by 77.91% to 93.91% during the entire period in tomato seedlings. It also elevated electrical leakage by 110.52% on day 15, maintained the levels of malondialdehyde close to the control, enhanced the activities of superoxide dismutase by 33.32% on day 10 and 11.22% on day 15, peroxidase by 42.15% on day 10, and catalase by 90.78% on day 10. Additionally, it reduced the contents of hydrogen peroxide by 15.47% to 29.64% and the rate of formation of superoxide anions by 26.34% to 53.47% during the entire period of treatment. The transcriptomic analysis revealed a significant differential expression of the genes involved in pathways, such as phenylalanine, glutathione, arginine and proline, and nitrogen metabolism. These genes included PALs, HDCs, GGCT, ODC1, LAPs, SMS, and SAMDC. Notably, transcription factors, such as ERF109, ARF9, GRF3, GRF4, GRF7, and GRF9, were also significantly regulated. The study concluded that Cd and Pb stress enhanced the osmoregulatory and antioxidant defense systems in tomato seedlings, which may contribute to their tolerance to heavy metal stress. Future research could explore the application of these findings to develop strategies to improve the resistance of plants to contamination with heavy metals.
bibliographic citation: Zhou et al. (2024) Physiological and molecular response mechanisms of tomato seedlings to cadmium (Cd) and lead (Pb) stress. PeerJ 12:e18533 https://doi.org/10.7717/peerj.18533
date submitted: 2024-06-07
date accepted: 2024-10-24
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Yan
author list: Agent
  family name: Fu
  given name: Jinyu
author list: Agent
  family name: Ye
  given name: Yuqi
author list: Agent
  family name: Xu
  given name: Qibo
author list: Agent
  family name: Liang
  given name: Jinjie
author list: Agent
  family name: Chen
  given name: Yanyan
author list: Agent
  family name: Mo
  given name: Yuxing
author list: Agent
  family name: Liu
  given name: Kaidong
doi: 10.7717/peerj.18533
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Zhou et al.
attribution name: Zhou et al.

Effect of prognostic nutritional index on laboratory parameters and survival in metastatic colorectal cancer patients treated with fruquintinib: a retrospective study
type: item
type: AcademicArticle
description: Objective Fruquintinib, a novel anti-angiogenic targeted drug, has gained widespread application in the treatment of metastatic colorectal cancer. This study aims to investigate the impact of the prognostic nutritional index (PNI) on the safety and survival outcomes of patients undergoing fruquintinib treatment for metastatic colorectal cancer. Methods A cohort of 106 patients with metastatic colorectal cancer, treated with fruquintinib at Zhejiang Cancer Hospital between 2019 and 2023, was included in this study. Clinical and laboratory data were subjected to chi-square and t-tests for analysis. PNI values were calculated using a specific formula. The optimal thresholds (cut-off values) for post-treatment PNI were determined through the ROC curve analysis. Kaplan-Meier analysis and the Log-rank test were employed to evaluate progression-free survival (PFS) and overall survival (OS) based on PNI. Multivariate Cox regression model was used to determine independent prognostic factors which influenced survival time. Results The study enrolled 106 colorectal cancer patients treated with fruquintinib. Stratified PNI analysis revealed significant differences in various indicators between high and low PNI groups after treatment with fruquintinib. Notably, after fruquintinib treatment, the high PNI group demonstrated elevated levels in white blood cells, lymphocytes, basophils, red blood cells, hemoglobin, platelets, total protein, and albumin compared to the low PNI group. The median OS for patients with high PNI values was 467 days, significantly longer than the 182 days observed for patients with low PNI values (P < 0.05). Cox regression analysis identified wild-type total RAS and BRAF, partial response (PR) + stable disease (SD), and high PNI values as influencing factors for OS in colorectal cancer patients. Additionally, PR + SD was an independent influencing factor for PFS in colorectal cancer patients (P < 0.05). Conclusions This study suggests that fuquinitinib can…
format: application/pdf
format: text/html
creator: Zeng Wang
creator: Sining Zhao
creator: Xuan Zhang
creator: Xinyi Mao
creator: Guonong Yang
creator: Meiqin Yuan
creator: Xiaofang Zhou
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.18565
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Objective Fruquintinib, a novel anti-angiogenic targeted drug, has gained widespread application in the treatment of metastatic colorectal cancer. This study aims to investigate the impact of the prognostic nutritional index (PNI) on the safety and survival outcomes of patients undergoing fruquintinib treatment for metastatic colorectal cancer. Methods A cohort of 106 patients with metastatic colorectal cancer, treated with fruquintinib at Zhejiang Cancer Hospital between 2019 and 2023, was included in this study. Clinical and laboratory data were subjected to chi-square and t-tests for analysis. PNI values were calculated using a specific formula. The optimal thresholds (cut-off values) for post-treatment PNI were determined through the ROC curve analysis. Kaplan-Meier analysis and the Log-rank test were employed to evaluate progression-free survival (PFS) and overall survival (OS) based on PNI. Multivariate Cox regression model was used to determine independent prognostic factors which influenced survival time. Results The study enrolled 106 colorectal cancer patients treated with fruquintinib. Stratified PNI analysis revealed significant differences in various indicators between high and low PNI groups after treatment with fruquintinib. Notably, after fruquintinib treatment, the high PNI group demonstrated elevated levels in white blood cells, lymphocytes, basophils, red blood cells, hemoglobin, platelets, total protein, and albumin compared to the low PNI group. The median OS for patients with high PNI values was 467 days, significantly longer than the 182 days observed for patients with low PNI values (P < 0.05). Cox regression analysis identified wild-type total RAS and BRAF, partial response (PR) + stable disease (SD), and high PNI values as influencing factors for OS in colorectal cancer patients. Additionally, PR + SD was an independent influencing factor for PFS in colorectal cancer patients (P < 0.05). Conclusions This study suggests that fuquinitinib can…
bibliographic citation: Wang et al. (2024) Effect of prognostic nutritional index on laboratory parameters and survival in metastatic colorectal cancer patients treated with fruquintinib: a retrospective study. PeerJ 12:e18565 https://doi.org/10.7717/peerj.18565
date submitted: 2024-07-23
date accepted: 2024-10-31
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zeng
author list: Agent
  family name: Zhao
  given name: Sining
author list: Agent
  family name: Zhang
  given name: Xuan
author list: Agent
  family name: Mao
  given name: Xinyi
author list: Agent
  family name: Yang
  given name: Guonong
author list: Agent
  family name: Yuan
  given name: Meiqin
author list: Agent
  family name: Zhou
  given name: Xiaofang
doi: 10.7717/peerj.18565
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Wang et al.
attribution name: Wang et al.

Resistance characterization and transcriptomic analysis of imipenem-induced drug resistance in Escherichia coli
type: item
type: AcademicArticle
description: Background Bacteria can develop resistance to various antibiotics under selective pressure, leading to multifaceted changes in resistance mechanisms. Transcriptomic sequencing allows for the observation of transcriptional level alterations in cells under antibiotic stress. Understanding the bacterial response to such stress is essential for deciphering their strategy against drug-resistant antibiotics and identifying potential targets for antibiotic development. Methods This study using wild-type (WT) Escherichia coli (E. coli) discovered that continuous in vitro induction screening for imipenem-resistant strains resulted in bacteria with enhanced biofilm-forming ability and mutations in antibiotic target sites. Transcriptomic sequencing of the resistant bacteria revealed significant changes in carbon and amino acid metabolism, nutrient assimilation, substance transport, nucleotide metabolism, protein biosynthesis, and cell wall biosynthesis. The up-regulated drug efflux genes were disrupted using gene knockout technology. Drug sensitivity tests indicated that drug efflux has a minimal effect on imipenem resistance. Results This suggests a strategy for E. coli drug resistance involving the reduction of unnecessary substance synthesis and metabolism, coupled with an increase in activities that aid in resisting foreign threats.
format: application/pdf
format: text/html
creator: Chunyu Tong
creator: Yimin Liang
creator: Qi Liu
creator: Honghao Yu
creator: Wenzhi Feng
creator: Bocui Song
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.18572
publisher: PeerJ Inc.
rights: © 2024 Tong et al.
abstract: Background Bacteria can develop resistance to various antibiotics under selective pressure, leading to multifaceted changes in resistance mechanisms. Transcriptomic sequencing allows for the observation of transcriptional level alterations in cells under antibiotic stress. Understanding the bacterial response to such stress is essential for deciphering their strategy against drug-resistant antibiotics and identifying potential targets for antibiotic development. Methods This study using wild-type (WT) Escherichia coli (E. coli) discovered that continuous in vitro induction screening for imipenem-resistant strains resulted in bacteria with enhanced biofilm-forming ability and mutations in antibiotic target sites. Transcriptomic sequencing of the resistant bacteria revealed significant changes in carbon and amino acid metabolism, nutrient assimilation, substance transport, nucleotide metabolism, protein biosynthesis, and cell wall biosynthesis. The up-regulated drug efflux genes were disrupted using gene knockout technology. Drug sensitivity tests indicated that drug efflux has a minimal effect on imipenem resistance. Results This suggests a strategy for E. coli drug resistance involving the reduction of unnecessary substance synthesis and metabolism, coupled with an increase in activities that aid in resisting foreign threats.
bibliographic citation: Tong et al. (2024) Resistance characterization and transcriptomic analysis of imipenem-induced drug resistance in Escherichia coli. PeerJ 12:e18572 https://doi.org/10.7717/peerj.18572
date submitted: 2024-06-21
date accepted: 2024-11-01
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tong
  given name: Chunyu
author list: Agent
  family name: Liang
  given name: Yimin
author list: Agent
  family name: Liu
  given name: Qi
author list: Agent
  family name: Yu
  given name: Honghao
author list: Agent
  family name: Feng
  given name: Wenzhi
author list: Agent
  family name: Song
  given name: Bocui
doi: 10.7717/peerj.18572
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: ©2024 Tong et al.
attribution name: Tong et al.

Genome-wide identification and expression analysis of the Trihelix transcription factor family in potato (Solanum tuberosum L.) during development
type: item
type: AcademicArticle
description: Trihelix transcription factors (TF) are photoresponsive proteins featuring a characteristic three-helix structure (helix-loop-helix-loop-helix) and contain the Myb/SANT-LIKE (MSL) domain. They perform crucial functions in the development and stress-response of plants. However, the function of the Trihelix TF in potato (Solanum tuberosum L.) remains unknown. In the present study, forty-three StMSLs were characterized in the potato genome and named StMSL1 to StMSL43. Structural domain analysis revealed that motifs 1 and 2 may play a central role in the implementation of trihelix gene functions, and motifs 4 and 9 may be related to specific functions of StMSL. Phylogenetic analysis divided the StMSLs into six groups (SIP1, GT1, GT2, GTγ, SH4 and GT3). The GT3 group, which is rarely identified in the Trihelix TF family, contained three StMSLs. The 43 StMSLs were unevenly distributed on 12 chromosomes in potato and comprised two pairs of tandem duplication and five pairs of segmental duplication genes. Additionally, RNA-Seq analysis found that 36 out of the 43 StMSLs were expressed in at least one of the 12 tissues, with some exhibiting tissue-specific expression patterns. Trihelix transcriptional regulation network analysis identified 387 genes as potential targets of the 36 StMSL genes, and these genes have a wide variety of functions. Furthermore, RNA-Seq analysis revealed that at least 18 StMSLs were upregulated in response to osmotic stress. The induced pattern of eight StMSLs was subsequently validated using qRT-PCR. This study provides a detailed insight into the StMSLs of the potato and lays the foundation for further analysis of the functions of the Trihelix gene in plant development.
format: application/pdf
format: text/html
creator: Chao Mei
creator: Yuwei Liu
creator: Huiyang Song
creator: Jinghao Li
creator: Qianna Song
creator: Yonghong Duan
creator: Ruiyun Feng
subject: Plant Science
description: doi:10.7717/peerj.18578
publisher: PeerJ Inc.
rights: © 2024 Mei et al.
abstract: Trihelix transcription factors (TF) are photoresponsive proteins featuring a characteristic three-helix structure (helix-loop-helix-loop-helix) and contain the Myb/SANT-LIKE (MSL) domain. They perform crucial functions in the development and stress-response of plants. However, the function of the Trihelix TF in potato (Solanum tuberosum L.) remains unknown. In the present study, forty-three StMSLs were characterized in the potato genome and named StMSL1 to StMSL43. Structural domain analysis revealed that motifs 1 and 2 may play a central role in the implementation of trihelix gene functions, and motifs 4 and 9 may be related to specific functions of StMSL. Phylogenetic analysis divided the StMSLs into six groups (SIP1, GT1, GT2, GTγ, SH4 and GT3). The GT3 group, which is rarely identified in the Trihelix TF family, contained three StMSLs. The 43 StMSLs were unevenly distributed on 12 chromosomes in potato and comprised two pairs of tandem duplication and five pairs of segmental duplication genes. Additionally, RNA-Seq analysis found that 36 out of the 43 StMSLs were expressed in at least one of the 12 tissues, with some exhibiting tissue-specific expression patterns. Trihelix transcriptional regulation network analysis identified 387 genes as potential targets of the 36 StMSL genes, and these genes have a wide variety of functions. Furthermore, RNA-Seq analysis revealed that at least 18 StMSLs were upregulated in response to osmotic stress. The induced pattern of eight StMSLs was subsequently validated using qRT-PCR. This study provides a detailed insight into the StMSLs of the potato and lays the foundation for further analysis of the functions of the Trihelix gene in plant development.
bibliographic citation: Mei et al. (2024) Genome-wide identification and expression analysis of the Trihelix transcription factor family in potato (Solanum tuberosum L.) during development. PeerJ 12:e18578 https://doi.org/10.7717/peerj.18578
date submitted: 2024-05-20
date accepted: 2024-11-04
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mei
  given name: Chao
author list: Agent
  family name: Liu
  given name: Yuwei
author list: Agent
  family name: Song
  given name: Huiyang
author list: Agent
  family name: Li
  given name: Jinghao
author list: Agent
  family name: Song
  given name: Qianna
author list: Agent
  family name: Duan
  given name: Yonghong
author list: Agent
  family name: Feng
  given name: Ruiyun
doi: 10.7717/peerj.18578
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Mei et al.
attribution name: Mei et al.

Losartan and dapagliflozin combination therapy in reducing uric acid level compared to monotherapy in patients with heart failure
type: item
type: AcademicArticle
description: Background Sodium-Glucose Transport Protein 2 (SGLT2) inhibitors, and Angiotensin II Receptor Antagonists (ARBs) also have the effect of reducing serum uric acid but few studies worldwide assessed. Objective Evaluate the effectiveness of serum uric acid lowering treatment of SGLT2 inhibitors, and ARB in heart failure (HF) patients. Methods We conducted a cross-sectional analysis study with 8 weeks of follow-up on 733 heart failure (HF) patients treated at Can Tho Central General Hospital from January 2023 to March 2024. Patients enrolled in the study were examined and received losartan (Group A) or dapagliflozin (Group B) monotherapy or losartan and dapagliflozin combined therapy (Group C). The uric acid concentration group was defined into three subgroups with tertile 1 from smallest to quartile (Q) 1, tertile 2 from Q2 to Q3, and tertile 3 from Q3 to the largest value. Results After 8 weeks of treatment, the uric acid reduction effect between groups A, B, and C showed that the combination group had the optimal reducing effect compared to losartan and dapagliflozin monotherapy with the mean difference being −229.62 ± 76.65 µmol/L, −217.00 ± 146.17 µmol/L, and −284.43 ± 136.32 µmol/L, respectively. In total, combination therapy showed the best reduction outcome in the population of male, female, patients with type 2 diabetes mellitus (T2DM), and dyslipidemia with the mean difference ranging from −226.21 ± 74.65 µmol/L to −231.85 ± 76.28 µmol/L and −209.62 ± 184.94 µmol/L to −225.75 ± 78.53 µmol/L and −273.02 ± 204.54 µmol/L to −308.93 ± 72.97 µmol/L in group A, B, and C, respectively. Conclusion The optimal therapy for reducing uric acid levels in HF patients was the combination of losartan and dapagliflozin, and the effectiveness did not change through sex, T2DM, and dyslipidemia patients.
format: application/pdf
format: text/html
creator: Tuong Le Trong Huynh
creator: Phong Thanh Pham
creator: Hien Dieu Tran
creator: Nhan Dinh Tran
creator: Duong Van Tran
creator: Bao Lam Thai Tran
creator: Khoa Dang Dang Tran
creator: Toan Hoang Ngo
creator: Son Kim Tran
subject: Cardiology
subject: Internal Medicine
description: doi:10.7717/peerj.18595
publisher: PeerJ Inc.
rights: © 2024 Huynh et al.
abstract: Background Sodium-Glucose Transport Protein 2 (SGLT2) inhibitors, and Angiotensin II Receptor Antagonists (ARBs) also have the effect of reducing serum uric acid but few studies worldwide assessed. Objective Evaluate the effectiveness of serum uric acid lowering treatment of SGLT2 inhibitors, and ARB in heart failure (HF) patients. Methods We conducted a cross-sectional analysis study with 8 weeks of follow-up on 733 heart failure (HF) patients treated at Can Tho Central General Hospital from January 2023 to March 2024. Patients enrolled in the study were examined and received losartan (Group A) or dapagliflozin (Group B) monotherapy or losartan and dapagliflozin combined therapy (Group C). The uric acid concentration group was defined into three subgroups with tertile 1 from smallest to quartile (Q) 1, tertile 2 from Q2 to Q3, and tertile 3 from Q3 to the largest value. Results After 8 weeks of treatment, the uric acid reduction effect between groups A, B, and C showed that the combination group had the optimal reducing effect compared to losartan and dapagliflozin monotherapy with the mean difference being −229.62 ± 76.65 µmol/L, −217.00 ± 146.17 µmol/L, and −284.43 ± 136.32 µmol/L, respectively. In total, combination therapy showed the best reduction outcome in the population of male, female, patients with type 2 diabetes mellitus (T2DM), and dyslipidemia with the mean difference ranging from −226.21 ± 74.65 µmol/L to −231.85 ± 76.28 µmol/L and −209.62 ± 184.94 µmol/L to −225.75 ± 78.53 µmol/L and −273.02 ± 204.54 µmol/L to −308.93 ± 72.97 µmol/L in group A, B, and C, respectively. Conclusion The optimal therapy for reducing uric acid levels in HF patients was the combination of losartan and dapagliflozin, and the effectiveness did not change through sex, T2DM, and dyslipidemia patients.
bibliographic citation: Huynh et al. (2024) Losartan and dapagliflozin combination therapy in reducing uric acid level compared to monotherapy in patients with heart failure. PeerJ 12:e18595 https://doi.org/10.7717/peerj.18595
date submitted: 2024-06-10
date accepted: 2024-11-05
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huynh
  given name: Tuong Le Trong
author list: Agent
  family name: Pham
  given name: Phong Thanh
author list: Agent
  family name: Tran
  given name: Hien Dieu
author list: Agent
  family name: Tran
  given name: Nhan Dinh
author list: Agent
  family name: Tran
  given name: Duong Van
author list: Agent
  family name: Tran
  given name: Bao Lam Thai
author list: Agent
  family name: Tran
  given name: Khoa Dang Dang
author list: Agent
  family name: Ngo
  given name: Toan Hoang
author list: Agent
  family name: Tran
  given name: Son Kim
doi: 10.7717/peerj.18595
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Huynh et al.
attribution name: Huynh et al.

Effects of a single bout of exercise on human hemocytes and serum interleukin 3, erythropoietin, and soluble transferrin receptor in a hot and humid environment
type: item
type: AcademicArticle
description: Background Exercise in humid and hot environments (HHEs) may result in decreased perception, motor performance, and memory owing to endogenous heat production and exogenous load. However, whether a single bout of exercise (SBOE) intensity affects the magnitude of changes in the levels of hemocytes remains controversial. In this article, we aimed to investigate the effects of a SBOE of varying intensities on blood cells in HHE. Methods Thirty-two volunteers were randomly divided into a quiet control group (QC), 55% VO2max intensity exercise group (HHE55%), 70% VO2max intensity exercise group (HHE70%), and 85% VO2max intensity exercise group (HHE85%). The participants in the exercise groups were assigned to perform an SBOE on the treadmill under HHE conditions for 30 min, whereas participants in the QC remained still under HHE conditions for 30 min (temperature: 28–32 °C, relative humidity: 85–95%). Results The net body mass (NBM), perfusion index (PI), mean corpuscular volume (MCV), platelet (PLT), and plateletcrit (PCT) values were affected significantly by the exercise intensity (P < 0.01) the hemoglobin (HGB) and neutrophil count (NE) were affected significantly by exercise intensity (P < 0.05). After an SBOE, compared with that before exercise, the sublingual temperature (ST) of all groups, the NBM and MCV of all exercise groups, the PI of the HHE55% and HHE70% groups, the HGB, hematocrit (HCT), and NE of the HHE70% group, the red blood cell count (RBC), PLT, and PCT of the HHE70% and HHE85% groups, and the white blood cell count (WBC) of HHE85% changed very significantly (P < 0.01). The PCT of QC, blood oxygen saturation (SaO2), and soluble transferrin receptor (sTfR) levels in the HHE55% group, the lymphocyte count (LY) in the HHE70% group, and the HGB and HCT in the HHE85% group changed significantly (P < 0.05). Conclusion Low- and moderate-intensity SBOE in HHE could increase the serum EPO and serum sTfR levels and decrease the serum IL-3 levels. Conversely, …
format: application/pdf
format: text/html
creator: Yuhu Lv
creator: Lin Cheng
creator: Xiqian Zhang
creator: Fenglin Peng
creator: Yu Yuan
creator: Xiquan Weng
creator: Wen-Tao Lin
subject: Molecular Biology
subject: Anatomy and Physiology
subject: Hematology
subject: Kinesiology
description: doi:10.7717/peerj.18603
publisher: PeerJ Inc.
rights: © 2024 Lv et al.
abstract: Background Exercise in humid and hot environments (HHEs) may result in decreased perception, motor performance, and memory owing to endogenous heat production and exogenous load. However, whether a single bout of exercise (SBOE) intensity affects the magnitude of changes in the levels of hemocytes remains controversial. In this article, we aimed to investigate the effects of a SBOE of varying intensities on blood cells in HHE. Methods Thirty-two volunteers were randomly divided into a quiet control group (QC), 55% VO2max intensity exercise group (HHE55%), 70% VO2max intensity exercise group (HHE70%), and 85% VO2max intensity exercise group (HHE85%). The participants in the exercise groups were assigned to perform an SBOE on the treadmill under HHE conditions for 30 min, whereas participants in the QC remained still under HHE conditions for 30 min (temperature: 28–32 °C, relative humidity: 85–95%). Results The net body mass (NBM), perfusion index (PI), mean corpuscular volume (MCV), platelet (PLT), and plateletcrit (PCT) values were affected significantly by the exercise intensity (P < 0.01) the hemoglobin (HGB) and neutrophil count (NE) were affected significantly by exercise intensity (P < 0.05). After an SBOE, compared with that before exercise, the sublingual temperature (ST) of all groups, the NBM and MCV of all exercise groups, the PI of the HHE55% and HHE70% groups, the HGB, hematocrit (HCT), and NE of the HHE70% group, the red blood cell count (RBC), PLT, and PCT of the HHE70% and HHE85% groups, and the white blood cell count (WBC) of HHE85% changed very significantly (P < 0.01). The PCT of QC, blood oxygen saturation (SaO2), and soluble transferrin receptor (sTfR) levels in the HHE55% group, the lymphocyte count (LY) in the HHE70% group, and the HGB and HCT in the HHE85% group changed significantly (P < 0.05). Conclusion Low- and moderate-intensity SBOE in HHE could increase the serum EPO and serum sTfR levels and decrease the serum IL-3 levels. Conversely, …
bibliographic citation: Lv et al. (2024) Effects of a single bout of exercise on human hemocytes and serum interleukin 3, erythropoietin, and soluble transferrin receptor in a hot and humid environment. PeerJ 12:e18603 https://doi.org/10.7717/peerj.18603
date submitted: 2021-07-09
date accepted: 2024-11-06
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lv
  given name: Yuhu
author list: Agent
  family name: Cheng
  given name: Lin
author list: Agent
  family name: Zhang
  given name: Xiqian
author list: Agent
  family name: Peng
  given name: Fenglin
author list: Agent
  family name: Yuan
  given name: Yu
author list: Agent
  family name: Weng
  given name: Xiquan
author list: Agent
  family name: Lin
  given name: Wen-Tao
doi: 10.7717/peerj.18603
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Lv et al.
attribution name: Lv et al.

Assessment of genotype by environment and yield performance of tropical maize hybrids using stability statistics and graphical biplots
type: item
type: AcademicArticle
description: Background Enhancing maize grain yield in tropical regions faces significant challenges due to variability in agroclimate, soil conditions, and agroecosystems. Understanding genotype (G) by environment (E) interaction (GEI) in plant breeding is crucial for selecting and developing high-yielding genotypes adapted to diverse environments. Methods Ten maize hybrids, including eight candidates and two commercial varieties, were evaluated across ten environments in Indonesia using a randomized complete block design with three replications. The GEI effect and yield stability were assessed using stability statistics, additive main effects and multiplicative interaction model (AMMI), and genotype + genotype × environment (GGE) biplot methods. Results and Discussion Analysis of variance revealed a significant GEI effect, indicating differences in hybrid responses for grain yield (GY), allowing for stability analysis. G01 showed the highest GY based on the best linear unbiased prediction (BLUP) across environments. Correlation analysis indicated strong associations between stability statistics (YSi and S(6)) and GY, aiding in the selection of high-yielding hybrids. The integration of AMMI with the BLUP method, and weighted average of absolute scores (WAASB), enabled precise measurement of genotype stability. Overall, G01 (R0211), G04 (R0105), G05 (R0118), and G07 (R0641) emerged as high-yielding, stable hybrids based on stability statistics, AMMI, GGE biplot, and WAASB rankings. These hybrids offer promising candidates for maize genetic improvement programs in tropical regions.
format: application/pdf
format: text/html
creator: Dedy Supriadi
creator: Yusuf Mufti Bimantara
creator: Yuniel Melvanolo Zendrato
creator: Eko Widaryanto
creator: Kuswanto Kuswanto
creator: Budi Waluyo
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.18624
publisher: PeerJ Inc.
rights: © 2024 Supriadi et al.
abstract: Background Enhancing maize grain yield in tropical regions faces significant challenges due to variability in agroclimate, soil conditions, and agroecosystems. Understanding genotype (G) by environment (E) interaction (GEI) in plant breeding is crucial for selecting and developing high-yielding genotypes adapted to diverse environments. Methods Ten maize hybrids, including eight candidates and two commercial varieties, were evaluated across ten environments in Indonesia using a randomized complete block design with three replications. The GEI effect and yield stability were assessed using stability statistics, additive main effects and multiplicative interaction model (AMMI), and genotype + genotype × environment (GGE) biplot methods. Results and Discussion Analysis of variance revealed a significant GEI effect, indicating differences in hybrid responses for grain yield (GY), allowing for stability analysis. G01 showed the highest GY based on the best linear unbiased prediction (BLUP) across environments. Correlation analysis indicated strong associations between stability statistics (YSi and S(6)) and GY, aiding in the selection of high-yielding hybrids. The integration of AMMI with the BLUP method, and weighted average of absolute scores (WAASB), enabled precise measurement of genotype stability. Overall, G01 (R0211), G04 (R0105), G05 (R0118), and G07 (R0641) emerged as high-yielding, stable hybrids based on stability statistics, AMMI, GGE biplot, and WAASB rankings. These hybrids offer promising candidates for maize genetic improvement programs in tropical regions.
bibliographic citation: Supriadi et al. (2024) Assessment of genotype by environment and yield performance of tropical maize hybrids using stability statistics and graphical biplots. PeerJ 12:e18624 https://doi.org/10.7717/peerj.18624
date submitted: 2024-09-11
date accepted: 2024-11-11
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Supriadi
  given name: Dedy
author list: Agent
  family name: Bimantara
  given name: Yusuf Mufti
author list: Agent
  family name: Zendrato
  given name: Yuniel Melvanolo
author list: Agent
  family name: Widaryanto
  given name: Eko
author list: Agent
  family name: Kuswanto
  given name: Kuswanto
author list: Agent
  family name: Waluyo
  given name: Budi
doi: 10.7717/peerj.18624
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Supriadi et al.
attribution name: Supriadi et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359