PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genome-wide identification of the Gossypium hirsutum CAD gene family and functional study of GhiCAD23 under drought stress
items: https://peerj.com/articles/18455
items: PSENEN influences the progression of renal clear cell carcinoma by regulating the immune microenvironment and oxidative phosphorylation
items: The effect of carbonic anhydrase on foraminiferal Mg/Ca
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

Genome-wide identification of the Gossypium hirsutum CAD gene family and functional study of GhiCAD23 under drought stress
type: item
type: AcademicArticle
description: Cinnamyl alcohol dehydrogenase (CAD) is a crucial enzyme in the final stage of lignin monomer biosynthesis. This study focuses on the CAD gene family within Gossypium hirsutum. Through comprehensive genomic analysis, we identified 29 GhiCAD genes within the Gossypium hirsutum genome using a bioinformatics approach. Phylogenetic analysis revealed that the GhiCAD family can be categorized into four subgroups, which are closest to the evolutionary relationship with Arabidopsis thaliana. There are multiple cis-acting elements on the promoters of GhiCAD genes associated with abiotic stress responses. Some GhiCAD genes demonstrated high expression in various tissues like root, leaf, and sepal, as well as in fiber and ovule at different developmental stages (10 days post anthesis (DPA), 15 DPA, 20 DPA, 25 DPA). The transcript levels of GhiCAD23 were notably elevated when exposed to PEG treatment and drought stress (DS). GhiCAD23 is also co-expressed with many known drought response genes, suggesting its involvement in the plant’s reaction to DS. Employing virus-induced gene silencing (VIGS) technology to silence the GhiCAD23 gene, it was found that silencing GhiCAD23 reduced the tolerance of cotton to DS. Under DS, the relative leaf water content, superoxide dismutase (SOD), and catalase (CAT) enzyme activities of the GhiCAD23-silenced cotton plants were decreased by 31.84%, 30.22% and 14.19%, respectively, while malondialdehyde (MDA) was increased by 72.16% compared with the control cohort. Drought promotes the accumulation of lignin, and it was found that silencing the GhiCAD23 reduces lignin accumulation in cotton under DS. The analysis of phenotypic and physiological indicators indicates that GhiCAD23 is vital in cotton’s resistance to DS. This investigation provides an important reference for future comprehensive exploration of the GhiCAD23 gene’s function in cotton’s DS response mechanism.
format: application/pdf
format: text/html
creator: Xin Zhang
creator: Ziyu Wang
creator: Xingyue Zhong
creator: Wanwan Fu
creator: Yuanxin Li
creator: Yunhao Liusui
creator: Yanjun Guo
creator: JingBo Zhang
creator: Bo Li
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.18439
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Cinnamyl alcohol dehydrogenase (CAD) is a crucial enzyme in the final stage of lignin monomer biosynthesis. This study focuses on the CAD gene family within Gossypium hirsutum. Through comprehensive genomic analysis, we identified 29 GhiCAD genes within the Gossypium hirsutum genome using a bioinformatics approach. Phylogenetic analysis revealed that the GhiCAD family can be categorized into four subgroups, which are closest to the evolutionary relationship with Arabidopsis thaliana. There are multiple cis-acting elements on the promoters of GhiCAD genes associated with abiotic stress responses. Some GhiCAD genes demonstrated high expression in various tissues like root, leaf, and sepal, as well as in fiber and ovule at different developmental stages (10 days post anthesis (DPA), 15 DPA, 20 DPA, 25 DPA). The transcript levels of GhiCAD23 were notably elevated when exposed to PEG treatment and drought stress (DS). GhiCAD23 is also co-expressed with many known drought response genes, suggesting its involvement in the plant’s reaction to DS. Employing virus-induced gene silencing (VIGS) technology to silence the GhiCAD23 gene, it was found that silencing GhiCAD23 reduced the tolerance of cotton to DS. Under DS, the relative leaf water content, superoxide dismutase (SOD), and catalase (CAT) enzyme activities of the GhiCAD23-silenced cotton plants were decreased by 31.84%, 30.22% and 14.19%, respectively, while malondialdehyde (MDA) was increased by 72.16% compared with the control cohort. Drought promotes the accumulation of lignin, and it was found that silencing the GhiCAD23 reduces lignin accumulation in cotton under DS. The analysis of phenotypic and physiological indicators indicates that GhiCAD23 is vital in cotton’s resistance to DS. This investigation provides an important reference for future comprehensive exploration of the GhiCAD23 gene’s function in cotton’s DS response mechanism.
bibliographic citation: Zhang et al. (2024) Genome-wide identification of the Gossypium hirsutum CAD gene family and functional study of GhiCAD23 under drought stress. PeerJ 12:e18439 https://doi.org/10.7717/peerj.18439
date submitted: 2024-08-20
date accepted: 2024-10-11
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhang
  given name: Xin
author list: Agent
  family name: Wang
  given name: Ziyu
author list: Agent
  family name: Zhong
  given name: Xingyue
author list: Agent
  family name: Fu
  given name: Wanwan
author list: Agent
  family name: Li
  given name: Yuanxin
author list: Agent
  family name: Liusui
  given name: Yunhao
author list: Agent
  family name: Guo
  given name: Yanjun
author list: Agent
  family name: Zhang
  given name: JingBo
author list: Agent
  family name: Li
  given name: Bo
doi: 10.7717/peerj.18439
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

https://peerj.com/articles/18455
type: item
type: AcademicArticle
title: Genome-wide identification and expression analysis of C2H2 zinc finger proteins in Chinese jujube (Ziziphus jujuba Mill.) in different fruit development stages and under different levels of water stress
description: The C2H2 type zinc finger proteins (C2H2-ZFPs) are prevalent motifs found widely across the eukaryotic kingdom, playing crucial roles in various biological processes, including stress responses and plant growth and development. To date, C2H2-ZFPs have been identified in many plant systems, but there have been no reports in Chinese jujube (Ziziphus jujuba Mill.). In this study, a total of 77 ZjC2H2-ZFPs were identified in Chinese jujube and classified into three groups, with set A containing 29 genes, set B containing two genes, and set C containing 46 genes. The set A group genes were further divided into three groups: A1, A2, and A4 (with no member of the A3 subgroup found in jujube). The set C C2H2-ZFPs genes were also further divided into three groups: C1 containing 24 genes, C2 with two genes, and C3 with three genes. These ZjC2H2-ZFPs were distributed on 12 chromosomes and one tandem duplicated pair of ZjC2H2-ZFPs was found on chromosome 4 (ZjC2H2-21 with ZjC2H2-22). Notably, the 77 ZjC2H2-ZFPs identified in this study lacked finger clusters comprising 10 or more repeats. The structure and protein motif analysis of ZjC2H2-ZFPs showed that most C1 subgroup members were enriched with ‘QALGGH’ motif zinc finger helices and the A1a ZjC2H2-ZFPs contained highly conserved ‘SATALLQKAAQMGS’ residues in jujube. A unique finding was the discovery of a conserved non-finger domain (PCYCC motif) in A1 group members, absent in other ZjC2H2-ZFPs and unreported in other species. The enzyme activity of jujube leaves under different water stress treatments were measured, and the results showed that as the degree of water stress increased, the activity of SOD enzymes and H2O2 content also increased. The POD enzyme activity levels of different treatment groups were CK>MS>SS>LS. The levels of malondialdehyde (MDA) content observed under various treatments were notably higher and the proline content was lower in comparison to the control group (CK). Differential expression of ZjC2H2…
format: application/pdf
format: text/html
creator: Xie Zhengwan
creator: Ji Qing
creator: Lihu Wang
creator: Ao Zhang
creator: Shengxing Li
creator: Sunyang Li
creator: Mei Chen
creator: Yang Jiayue
creator: Ruifang Wang
subject: Agricultural Science
subject: Cell Biology
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.18455
publisher: PeerJ Inc.
rights: © 2024 Zhengwan et al.
abstract: The C2H2 type zinc finger proteins (C2H2-ZFPs) are prevalent motifs found widely across the eukaryotic kingdom, playing crucial roles in various biological processes, including stress responses and plant growth and development. To date, C2H2-ZFPs have been identified in many plant systems, but there have been no reports in Chinese jujube (Ziziphus jujuba Mill.). In this study, a total of 77 ZjC2H2-ZFPs were identified in Chinese jujube and classified into three groups, with set A containing 29 genes, set B containing two genes, and set C containing 46 genes. The set A group genes were further divided into three groups: A1, A2, and A4 (with no member of the A3 subgroup found in jujube). The set C C2H2-ZFPs genes were also further divided into three groups: C1 containing 24 genes, C2 with two genes, and C3 with three genes. These ZjC2H2-ZFPs were distributed on 12 chromosomes and one tandem duplicated pair of ZjC2H2-ZFPs was found on chromosome 4 (ZjC2H2-21 with ZjC2H2-22). Notably, the 77 ZjC2H2-ZFPs identified in this study lacked finger clusters comprising 10 or more repeats. The structure and protein motif analysis of ZjC2H2-ZFPs showed that most C1 subgroup members were enriched with ‘QALGGH’ motif zinc finger helices and the A1a ZjC2H2-ZFPs contained highly conserved ‘SATALLQKAAQMGS’ residues in jujube. A unique finding was the discovery of a conserved non-finger domain (PCYCC motif) in A1 group members, absent in other ZjC2H2-ZFPs and unreported in other species. The enzyme activity of jujube leaves under different water stress treatments were measured, and the results showed that as the degree of water stress increased, the activity of SOD enzymes and H2O2 content also increased. The POD enzyme activity levels of different treatment groups were CK>MS>SS>LS. The levels of malondialdehyde (MDA) content observed under various treatments were notably higher and the proline content was lower in comparison to the control group (CK). Differential expression of ZjC2H2…
bibliographic citation: Zhengwan et al. (2024) Genome-wide identification and expression analysis of C2H2 zinc finger proteins in Chinese jujube (Ziziphus jujuba Mill.) in different fruit development stages and under different levels of water stress. PeerJ 12:e18455 https://doi.org/10.7717/peerj.18455
date submitted: 2023-09-22
date accepted: 2024-10-14
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhengwan
  given name: Xie
author list: Agent
  family name: Qing
  given name: Ji
author list: Agent
  family name: Wang
  given name: Lihu
author list: Agent
  family name: Zhang
  given name: Ao
author list: Agent
  family name: Li
  given name: Shengxing
author list: Agent
  family name: Li
  given name: Sunyang
author list: Agent
  family name: Chen
  given name: Mei
author list: Agent
  family name: Jiayue
  given name: Yang
author list: Agent
  family name: Wang
  given name: Ruifang
doi: 10.7717/peerj.18455
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: ©2024 Zhengwan et al.
attribution name: Zhengwan et al.

PSENEN influences the progression of renal clear cell carcinoma by regulating the immune microenvironment and oxidative phosphorylation
type: item
type: AcademicArticle
description: Background Presenilin enhancer gamma-secretase subunit (PSENEN), the straight target of metformin, is highly expressed in several cancers. The role of PSENEN in kidney renal clear cell carcinoma (KIRC) has not been reported. Methods PSENEN expression in KIRC specimens was investigated in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, as well as by immunohistochemical analysis and qPCR assay. The relationship between PSENEN expression and patient survival was discussed. The biological function of PSENEN in KIRC and its correlation with immune infiltration of KIRC were then investigated, and possible cellular mechanisms were again analyzed. The effects of metformin on KIRC cell proliferation, migration and invasion were discussed in cellular experiments. Results PSENEN was found to be highly expressed in KIRC. The high PSENEN expression was an adverse factor in KIRC. Several immune-related pathways were enriched including immune response, complement and coagulation cascade reactions, and neutrophil extracellular trap formation, as evidenced by enrichment analyses. Immune infiltration analysis revealed that PSENEN expression correlated positively with regulatory T cells. Gene set variation analysis suggested that PSENEN expression correlated positively with oxidative phosphorylation. In addition, a certain concentration of metformin was found to inhibit the proliferation, migration and invasion of KIRC cells, in which PSENEN down-regulation, AMPK up-regulation and mTOR down-regulation were also observed. Conclusions PSENEN may be involved in regulating the immune microenvironment of KIRC, and oxidative phosphorylation may also be a pathway for its involvement in cancer development. PSENEN is a novel prognostic marker for KIRC.
format: application/pdf
format: text/html
creator: Congying Huang
creator: Kaijie Chen
creator: Siyu Zhu
creator: Xin Yang
creator: Jiangang Hou
creator: Xuefeng Gu
subject: Bioinformatics
subject: Nephrology
subject: Oncology
description: doi:10.7717/peerj.18457
publisher: PeerJ Inc.
rights: © 2024 Huang et al.
abstract: Background Presenilin enhancer gamma-secretase subunit (PSENEN), the straight target of metformin, is highly expressed in several cancers. The role of PSENEN in kidney renal clear cell carcinoma (KIRC) has not been reported. Methods PSENEN expression in KIRC specimens was investigated in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, as well as by immunohistochemical analysis and qPCR assay. The relationship between PSENEN expression and patient survival was discussed. The biological function of PSENEN in KIRC and its correlation with immune infiltration of KIRC were then investigated, and possible cellular mechanisms were again analyzed. The effects of metformin on KIRC cell proliferation, migration and invasion were discussed in cellular experiments. Results PSENEN was found to be highly expressed in KIRC. The high PSENEN expression was an adverse factor in KIRC. Several immune-related pathways were enriched including immune response, complement and coagulation cascade reactions, and neutrophil extracellular trap formation, as evidenced by enrichment analyses. Immune infiltration analysis revealed that PSENEN expression correlated positively with regulatory T cells. Gene set variation analysis suggested that PSENEN expression correlated positively with oxidative phosphorylation. In addition, a certain concentration of metformin was found to inhibit the proliferation, migration and invasion of KIRC cells, in which PSENEN down-regulation, AMPK up-regulation and mTOR down-regulation were also observed. Conclusions PSENEN may be involved in regulating the immune microenvironment of KIRC, and oxidative phosphorylation may also be a pathway for its involvement in cancer development. PSENEN is a novel prognostic marker for KIRC.
bibliographic citation: Huang et al. (2024) PSENEN influences the progression of renal clear cell carcinoma by regulating the immune microenvironment and oxidative phosphorylation. PeerJ 12:e18457 https://doi.org/10.7717/peerj.18457
date submitted: 2024-07-23
date accepted: 2024-10-14
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Congying
author list: Agent
  family name: Chen
  given name: Kaijie
author list: Agent
  family name: Zhu
  given name: Siyu
author list: Agent
  family name: Yang
  given name: Xin
author list: Agent
  family name: Hou
  given name: Jiangang
author list: Agent
  family name: Gu
  given name: Xuefeng
doi: 10.7717/peerj.18457
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Huang et al.
attribution name: Huang et al.

The effect of carbonic anhydrase on foraminiferal Mg/Ca
type: item
type: AcademicArticle
description: Marine biogenic calcium carbonate production plays a role in the exchange of CO2 between ocean and atmosphere. The effect of increased CO2 on calcification and on the resulting chemistry of shells and skeletons, however, is only partly understood. Foraminifera are among the main marine CaCO3 producers and the controls on element partitioning and isotope fractionation is the subject of many recent investigations. The enzyme carbonic anhydrase (CA) was, for example, shown to be vital for CaCO3 deposition in benthic foraminifera and indicates their ability to manipulate their intracellular inorganic carbon chemistry. Here, we tested whether CA affects the partitioning of Na, Mg and Sr in the perforate, large benthic, symbiont-bearing foraminifer Amphistegina lessonii by addition of the inhibitor acetazolamide (AZ). The effect of dissolved CO2 on the effect of CA on element partitioning was also determined using a culturing setup with controlled atmospheric carbon dioxide levels (400–1,600 ppm). Results show that inhibition by AZ reduces calcification greatly and that CO2 has a small, but positive effect on the amount of calcite formed during the incubations. Furthermore, the inhibition of CA activity has a positive effect on element partitioning, most notably Mg. This may be explained by a (n indirect) coupling of inorganic carbon uptake and inward calcium ion pumping.
format: application/pdf
format: text/html
creator: Siham De Goeyse
creator: Chiara Lesuis
creator: Gert-Jan Reichart
creator: Lennart de Nooijer
subject: Aquatic and Marine Chemistry
subject: Biogeochemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.18458
publisher: PeerJ Inc.
rights: © 2024 De Goeyse et al.
abstract: Marine biogenic calcium carbonate production plays a role in the exchange of CO2 between ocean and atmosphere. The effect of increased CO2 on calcification and on the resulting chemistry of shells and skeletons, however, is only partly understood. Foraminifera are among the main marine CaCO3 producers and the controls on element partitioning and isotope fractionation is the subject of many recent investigations. The enzyme carbonic anhydrase (CA) was, for example, shown to be vital for CaCO3 deposition in benthic foraminifera and indicates their ability to manipulate their intracellular inorganic carbon chemistry. Here, we tested whether CA affects the partitioning of Na, Mg and Sr in the perforate, large benthic, symbiont-bearing foraminifer Amphistegina lessonii by addition of the inhibitor acetazolamide (AZ). The effect of dissolved CO2 on the effect of CA on element partitioning was also determined using a culturing setup with controlled atmospheric carbon dioxide levels (400–1,600 ppm). Results show that inhibition by AZ reduces calcification greatly and that CO2 has a small, but positive effect on the amount of calcite formed during the incubations. Furthermore, the inhibition of CA activity has a positive effect on element partitioning, most notably Mg. This may be explained by a (n indirect) coupling of inorganic carbon uptake and inward calcium ion pumping.
bibliographic citation: De Goeyse et al. (2024) The effect of carbonic anhydrase on foraminiferal Mg/Ca. PeerJ 12:e18458 https://doi.org/10.7717/peerj.18458
date submitted: 2023-12-18
date accepted: 2024-10-14
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Goeyse
  given name: Siham
author list: Agent
  family name: Lesuis
  given name: Chiara
author list: Agent
  family name: Reichart
  given name: Gert-Jan
author list: Agent
  family name: de Nooijer
  given name: Lennart
doi: 10.7717/peerj.18458
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 De Goeyse et al.
attribution name: De Goeyse et al.

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.

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