PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Hepatic nuclear factor 4 alpha promotes the ferroptosis of lung adenocarcinoma via transcriptional activation of cytochrome P450 oxidoreductase
items: Student perceptions toward virtual reality training in dental implant education
items: Identification of key immune-related genes associated with LPS/D-GalN-induced acute liver failure in mice based on transcriptome sequencing
items: Retrospective study of influencing factors on the outcomes of luteal phase stimulation in patients with dual stimulation
items: Reporting inconsistency between published conference abstracts and article abstracts of randomised controlled trials in prosthodontics presented at IADR general sessions
items: Genome-wide transcriptomic analysis identifies candidate genes involved in jasmonic acid-mediated salt tolerance of alfalfa
items: Using DNA metabarcoding to assess insect diversity in citrus orchards
items: Pollination efficacy of stingless bees, Tetragonula pagdeni Schwarz (Apidae: Meliponini), on greenhouse tomatoes (Solanum lycopersicum Linnaeus)
items: Identification of ABF/AREB gene family in tomato (Solanum lycopersicum L.) and functional analysis of ABF/AREB in response to ABA and abiotic stresses
items: Variation of choroidal thickness during the waking period over three consecutive days in different degrees of myopia and emmetropia using optical coherence tomography

Hepatic nuclear factor 4 alpha promotes the ferroptosis of lung adenocarcinoma via transcriptional activation of cytochrome P450 oxidoreductase
type: item
type: AcademicArticle
description: Background Lung adenocarcinoma is one of the most prevalent cancers while ferroptosis is crucial for cancer therapies. This study aims to investigate the function and mechanism of hepatic nuclear factor 4 alpha (HNF4A) in lung adenocarcinomas’ ferroptosis. Materials and Methods HNF4A expression in ferroptotic A549 cells was detected. Then HNF4A was knocked down in A549 cells while overexpressed in H23 cells. Cells with changed HNF4A expression were tested for cytotoxicity and the level of cellular lipid peroxidation. The expression of cytochrome P450 oxidoreductase (POR) expression was examined after HNF4A was knocked down or overexpressed. Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and dual-luciferase assays were performed to validate the regulation of HNF4A on POR. Finally, POR was restored in HNF4A-altered cells to check whether it restores the effect of HNF4A on ferroptosis. Results We found that HNF4A expression significantly decreased in the ferroptosis of A549 cells, and this change can be blocked by deferoxamine, an inhibitor of ferroptosis. Knockdown of HNF4A inhibited ferroptosis in A549 cells while overexpression of HNF4A promoted ferroptosis in H23 cells. We identified a key ferroptosis-related gene, POR serves as a potential target gene of HNF4A, whose expression was significantly changed in lung adenocarcinoma cells knocking down or overexpressing HNF4A. We demonstrated that HNF4A was bound to the POR’s promoter to enhance POR expression, and identified the binding sites via ChIP-qPCR and luciferase assays. Restoration of POR expression blocked the promoting effect of HNF4A on ferroptosis in lung adenocarcinoma. Conclusion HNF4A promotes POR expression through binding to the POR’s promoter, and subsequently promotes the ferroptosis of lung adenocarcinoma.
format: application/pdf
format: text/html
creator: Valeria Besskaya
creator: Huan Zhang
creator: Yunyi Bian
creator: Jiaqi Liang
creator: Guoshu Bi
creator: Guangyao Shan
creator: Cheng Zhan
creator: Zongwu Lin
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.15377
publisher: PeerJ Inc.
rights: © 2023 Besskaya et al.
abstract: Background Lung adenocarcinoma is one of the most prevalent cancers while ferroptosis is crucial for cancer therapies. This study aims to investigate the function and mechanism of hepatic nuclear factor 4 alpha (HNF4A) in lung adenocarcinomas’ ferroptosis. Materials and Methods HNF4A expression in ferroptotic A549 cells was detected. Then HNF4A was knocked down in A549 cells while overexpressed in H23 cells. Cells with changed HNF4A expression were tested for cytotoxicity and the level of cellular lipid peroxidation. The expression of cytochrome P450 oxidoreductase (POR) expression was examined after HNF4A was knocked down or overexpressed. Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and dual-luciferase assays were performed to validate the regulation of HNF4A on POR. Finally, POR was restored in HNF4A-altered cells to check whether it restores the effect of HNF4A on ferroptosis. Results We found that HNF4A expression significantly decreased in the ferroptosis of A549 cells, and this change can be blocked by deferoxamine, an inhibitor of ferroptosis. Knockdown of HNF4A inhibited ferroptosis in A549 cells while overexpression of HNF4A promoted ferroptosis in H23 cells. We identified a key ferroptosis-related gene, POR serves as a potential target gene of HNF4A, whose expression was significantly changed in lung adenocarcinoma cells knocking down or overexpressing HNF4A. We demonstrated that HNF4A was bound to the POR’s promoter to enhance POR expression, and identified the binding sites via ChIP-qPCR and luciferase assays. Restoration of POR expression blocked the promoting effect of HNF4A on ferroptosis in lung adenocarcinoma. Conclusion HNF4A promotes POR expression through binding to the POR’s promoter, and subsequently promotes the ferroptosis of lung adenocarcinoma.
bibliographic citation: Besskaya et al. (2023) Hepatic nuclear factor 4 alpha promotes the ferroptosis of lung adenocarcinoma via transcriptional activation of cytochrome P450 oxidoreductase. PeerJ 11:e15377 https://doi.org/10.7717/peerj.15377
date submitted: 2023-03-22
date accepted: 2023-04-18
issued: 2023-05-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Besskaya
  given name: Valeria
author list: Agent
  family name: Zhang
  given name: Huan
author list: Agent
  family name: Bian
  given name: Yunyi
author list: Agent
  family name: Liang
  given name: Jiaqi
author list: Agent
  family name: Bi
  given name: Guoshu
author list: Agent
  family name: Shan
  given name: Guangyao
author list: Agent
  family name: Zhan
  given name: Cheng
author list: Agent
  family name: Lin
  given name: Zongwu
doi: 10.7717/peerj.15377
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-08
copyright: © 2023 Besskaya et al.
attribution name: Besskaya et al.

Student perceptions toward virtual reality training in dental implant education
type: item
type: AcademicArticle
description: Objectives Both the shortage of professional teaching resources and the expensive dental implant supplies impede the effective training of dental undergraduate in implantology. Virtual reality (VR) technology may provide solutions to solve these problems. This pilot study was implemented to explore the usability and acceptance of a VR application in the training of dental implant among dental students at the Jinan University School of Stomatology. Methods We designed and developed a VR system with head-mounted displays (HMDs) to assist dental implant training. Undergraduate dental students were invited to experience a 30-minute “Introduction to dental implants” VR-HMDs training module. A total of 119 dental students participated the training. Firstly, the VR interactive training on dental implant was described, illustrated and practiced. Next, a system usability scale (SUS) survey was used to verify the usability and feasibility of the VR application on training dental students. Finally, the participants were given a questionnaire to provide their perceptions and feedback of the usefulness of the VR application for training dental implant skills. Results The SUS score was 82.00 ± 10.79, indicating a top 10 percentage ranking of the system’s usabilitys. The participants’ answers to the questionnaire reflected most of them exhibited strong interests in the VR system, with a tendency that the female students were more confident than the male in manipulating the VR system. The participants generally acknowledged the usefulness of VR dental implants, ranking VR value above the traditional laboratory operations, and a preference for using the VR system on learning other skills. They also gave valuable suggestions on VR dental implants for substantial improvement. However, some students were not strongly positive about the VR training in this study, the reason might lie in a more theoretical module was selected for testing, which impacted the students’ ratings. Conclusions…
format: application/pdf
format: text/html
creator: Yue Huang
creator: Yingwen Hu
creator: Unman Chan
creator: Pengyu Lai
creator: Yueting Sun
creator: Jun Dai
creator: Xin Cheng
creator: Xuesong Yang
subject: Dentistry
subject: Surgery and Surgical Specialties
subject: Science and Medical Education
description: doi:10.7717/peerj.14857
publisher: PeerJ Inc.
rights: © 2023 Huang et al.
abstract: Objectives Both the shortage of professional teaching resources and the expensive dental implant supplies impede the effective training of dental undergraduate in implantology. Virtual reality (VR) technology may provide solutions to solve these problems. This pilot study was implemented to explore the usability and acceptance of a VR application in the training of dental implant among dental students at the Jinan University School of Stomatology. Methods We designed and developed a VR system with head-mounted displays (HMDs) to assist dental implant training. Undergraduate dental students were invited to experience a 30-minute “Introduction to dental implants” VR-HMDs training module. A total of 119 dental students participated the training. Firstly, the VR interactive training on dental implant was described, illustrated and practiced. Next, a system usability scale (SUS) survey was used to verify the usability and feasibility of the VR application on training dental students. Finally, the participants were given a questionnaire to provide their perceptions and feedback of the usefulness of the VR application for training dental implant skills. Results The SUS score was 82.00 ± 10.79, indicating a top 10 percentage ranking of the system’s usabilitys. The participants’ answers to the questionnaire reflected most of them exhibited strong interests in the VR system, with a tendency that the female students were more confident than the male in manipulating the VR system. The participants generally acknowledged the usefulness of VR dental implants, ranking VR value above the traditional laboratory operations, and a preference for using the VR system on learning other skills. They also gave valuable suggestions on VR dental implants for substantial improvement. However, some students were not strongly positive about the VR training in this study, the reason might lie in a more theoretical module was selected for testing, which impacted the students’ ratings. Conclusions…
bibliographic citation: Huang et al. (2023) Student perceptions toward virtual reality training in dental implant education. PeerJ 11:e14857 https://doi.org/10.7717/peerj.14857
date submitted: 2022-08-09
date accepted: 2023-01-15
issued: 2023-05-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Yue
author list: Agent
  family name: Hu
  given name: Yingwen
author list: Agent
  family name: Chan
  given name: Unman
author list: Agent
  family name: Lai
  given name: Pengyu
author list: Agent
  family name: Sun
  given name: Yueting
author list: Agent
  family name: Dai
  given name: Jun
author list: Agent
  family name: Cheng
  given name: Xin
author list: Agent
  family name: Yang
  given name: Xuesong
doi: 10.7717/peerj.14857
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-05
copyright: ©2023 Huang et al.
attribution name: Huang et al.

Identification of key immune-related genes associated with LPS/D-GalN-induced acute liver failure in mice based on transcriptome sequencing
type: item
type: AcademicArticle
description: Background The aim of this study was to identify key immune-related genes in acute liver failure (ALF) by constructing an ALF mouse model for transcriptome sequencing. Methods The C57BL/6 mouse with ALF model was induced by lipopolysaccharide (LPS)/ D-galactosamine (D-GalN). After successful modelling, the liver tissues of all mice were obtained for transcriptome sequencing. The key immune-related genes in mice with ALF were identified by differential expression analysis, immune infiltration analysis, weighted gene co-expression network analysis (WGCNA), enrichment analysis, and protein-protein interaction (PPI) analysis. Results An LPS/D-GalN-induced ALF mouse model was successfully constructed, and transcriptome sequencing was performed. Significant differences in the proportions of monocytes, macrophages M0, macrophages M1 and neutrophils were shown by immune infiltration analysis, and 5255 genes highly associated with these four immune cells were identified by WGCNA. These immune genes were found to be significantly enriched in the TNF signalling pathway by enrichment analysis. Finally, PPI analysis was performed on genes enriched in this pathway and three key genes (CXCL1, CXCL10 and IL1B) were screened out and revealed to be significantly upregulated in ALF. Conclusions Key immune-related genes in ALF were identified in this study, which may provide not only potential therapeutic targets for treating ALF and improving its prognosis, but also a reliable scientific basis for the immunotherapy of the disease.
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format: text/html
creator: Ling Chen
creator: Li Yuan
creator: Jingle Yang
creator: Yizhi Pan
creator: Hong Wang
subject: Bioinformatics
subject: Cell Biology
subject: Computational Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.15241
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Background The aim of this study was to identify key immune-related genes in acute liver failure (ALF) by constructing an ALF mouse model for transcriptome sequencing. Methods The C57BL/6 mouse with ALF model was induced by lipopolysaccharide (LPS)/ D-galactosamine (D-GalN). After successful modelling, the liver tissues of all mice were obtained for transcriptome sequencing. The key immune-related genes in mice with ALF were identified by differential expression analysis, immune infiltration analysis, weighted gene co-expression network analysis (WGCNA), enrichment analysis, and protein-protein interaction (PPI) analysis. Results An LPS/D-GalN-induced ALF mouse model was successfully constructed, and transcriptome sequencing was performed. Significant differences in the proportions of monocytes, macrophages M0, macrophages M1 and neutrophils were shown by immune infiltration analysis, and 5255 genes highly associated with these four immune cells were identified by WGCNA. These immune genes were found to be significantly enriched in the TNF signalling pathway by enrichment analysis. Finally, PPI analysis was performed on genes enriched in this pathway and three key genes (CXCL1, CXCL10 and IL1B) were screened out and revealed to be significantly upregulated in ALF. Conclusions Key immune-related genes in ALF were identified in this study, which may provide not only potential therapeutic targets for treating ALF and improving its prognosis, but also a reliable scientific basis for the immunotherapy of the disease.
bibliographic citation: Chen et al. (2023) Identification of key immune-related genes associated with LPS/D-GalN-induced acute liver failure in mice based on transcriptome sequencing. PeerJ 11:e15241 https://doi.org/10.7717/peerj.15241
date submitted: 2022-11-10
date accepted: 2023-03-28
issued: 2023-05-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Ling
author list: Agent
  family name: Yuan
  given name: Li
author list: Agent
  family name: Yang
  given name: Jingle
author list: Agent
  family name: Pan
  given name: Yizhi
author list: Agent
  family name: Wang
  given name: Hong
doi: 10.7717/peerj.15241
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-05
copyright: ©2023 Chen et al.
attribution name: Chen et al.

Retrospective study of influencing factors on the outcomes of luteal phase stimulation in patients with dual stimulation
type: item
type: AcademicArticle
description: Background Dual/double stimulation (DS) is an ovarian stimulation strategy that has emerged in recent years; it is characterized by two rounds of ovarian stimulation and oocyte retrieval in the same menstrual cycle. DS can greatly shorten the time required to obtain valid embryos in assisted reproduction. For fertility preservation, DS can speed up oocyte storage process. However, factors influencing luteal phase ovarian stimulation (LPS) outcomes in DS have not been elucidated. Methods A total of 156 cycles from 78 cases were studied. Patients were grouped and analyzed according to their follicular phase ovarian stimulation (FPS) types. Female ages, ovarian stimulation protocols, number of oocytes retrieved, embryo quality were recorded. Comparisons of outcomes were conducted between different groups. Results Our study found that LPS obtained similar outcomes to follicular phase stimulation (FPS), and that the choice of FPS protocol affected the efficiency of LPS, the antagonist protocol and progestin-primed ovarian stimulation (PPOS) protocol resulted in better embryo outcomes in LPS. In LPS of DS, sufficient stimulation duration was the guarantee of embryo quality (number of available embryos: β = 0.145, 95% CI [0.078–0.211], P = 0.000; number of high-quality embryos: β = 0.114, 95% CI [0.057–0.171], P = 0.000). Discussion This study provided ideas for the precise use of DS. We suggest to further expand the sample size of DS in the future, conduct prospective controlled studies, unify the sample size of each subgroup, include the ovarian reserve of patients in the grouping basis, and exclude the influence of male factors. We hope that this study will help further refinement of DS so as to maximize patient benefits from it. Conclusion When the DS strategy is considered in the follicular phase, the antagonist protocol and PPOS protocol are more recommended for better embryo outcomes in LPS. During LPS, adequate ovarian stimulation duration is the most important gua…
format: application/pdf
format: text/html
creator: Yuanyuan Chen
creator: Hong Ye
creator: Junhua Bao
creator: Yanping Cai
creator: Yuanbo Hu
creator: Hongli Yan
subject: Gynecology and Obstetrics
subject: Internal Medicine
subject: Public Health
description: doi:10.7717/peerj.15296
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Background Dual/double stimulation (DS) is an ovarian stimulation strategy that has emerged in recent years; it is characterized by two rounds of ovarian stimulation and oocyte retrieval in the same menstrual cycle. DS can greatly shorten the time required to obtain valid embryos in assisted reproduction. For fertility preservation, DS can speed up oocyte storage process. However, factors influencing luteal phase ovarian stimulation (LPS) outcomes in DS have not been elucidated. Methods A total of 156 cycles from 78 cases were studied. Patients were grouped and analyzed according to their follicular phase ovarian stimulation (FPS) types. Female ages, ovarian stimulation protocols, number of oocytes retrieved, embryo quality were recorded. Comparisons of outcomes were conducted between different groups. Results Our study found that LPS obtained similar outcomes to follicular phase stimulation (FPS), and that the choice of FPS protocol affected the efficiency of LPS, the antagonist protocol and progestin-primed ovarian stimulation (PPOS) protocol resulted in better embryo outcomes in LPS. In LPS of DS, sufficient stimulation duration was the guarantee of embryo quality (number of available embryos: β = 0.145, 95% CI [0.078–0.211], P = 0.000; number of high-quality embryos: β = 0.114, 95% CI [0.057–0.171], P = 0.000). Discussion This study provided ideas for the precise use of DS. We suggest to further expand the sample size of DS in the future, conduct prospective controlled studies, unify the sample size of each subgroup, include the ovarian reserve of patients in the grouping basis, and exclude the influence of male factors. We hope that this study will help further refinement of DS so as to maximize patient benefits from it. Conclusion When the DS strategy is considered in the follicular phase, the antagonist protocol and PPOS protocol are more recommended for better embryo outcomes in LPS. During LPS, adequate ovarian stimulation duration is the most important gua…
bibliographic citation: Chen et al. (2023) Retrospective study of influencing factors on the outcomes of luteal phase stimulation in patients with dual stimulation. PeerJ 11:e15296 https://doi.org/10.7717/peerj.15296
date submitted: 2022-12-23
date accepted: 2023-04-04
issued: 2023-05-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yuanyuan
author list: Agent
  family name: Ye
  given name: Hong
author list: Agent
  family name: Bao
  given name: Junhua
author list: Agent
  family name: Cai
  given name: Yanping
author list: Agent
  family name: Hu
  given name: Yuanbo
author list: Agent
  family name: Yan
  given name: Hongli
doi: 10.7717/peerj.15296
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-05
copyright: © 2023 Chen et al.
attribution name: Chen et al.

Reporting inconsistency between published conference abstracts and article abstracts of randomised controlled trials in prosthodontics presented at IADR general sessions
type: item
type: AcademicArticle
description: Background There is commonly a discrepancy between conference abstracts and published article abstracts in prosthodontic randomized controlled trials (RCTs), which may mislead the scholars those attend conferences. Objective To identify the characteristics predicting inconsistency between conference abstracts and published article abstracts in prosthodontic RCTs. Methods The conference abstracts of prosthodontic RCTs presented at the IADR general sessions from 2002 to 2015 were searched. Electronic searches of MEDLINE, EMBASE, the Cochrane Library, and Google Scholar databases were conducted to match full-text publications for conference abstracts. Two investigators extracted basic characteristics and assessed the consistency and reporting quality independently and in duplicate. The linear regression model was used to analyze the predictors of inconsistency. Results A total of 147 conference abstracts were matched with published articles. Results for the secondary outcome measure, Statistical analysis, and precision measure were less than 50% consistent, and even nearly 5% of the studies had opposite conclusions. Multiple linear regression analysis showed that three factors were correlated with lower inconsistency, including continent of origin (p = 0.011), presentation type (p = 0.017), and difference in reporting quality (p = 0.013). Conclusion Conference attendees should cautiously treat the findings of the conference abstracts. Researchers should improve the precision of the information delivered at conferences. We recommend the authors of RCTs to explain the primary difference between conference abstracts and article abstracts.
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format: text/html
creator: Guanru Wang
creator: Junsheng Chen
creator: Honglin Li
creator: Cheng Miao
creator: Yubin Cao
creator: Chunjie Li
subject: Dentistry
subject: Evidence Based Medicine
description: doi:10.7717/peerj.15303
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Background There is commonly a discrepancy between conference abstracts and published article abstracts in prosthodontic randomized controlled trials (RCTs), which may mislead the scholars those attend conferences. Objective To identify the characteristics predicting inconsistency between conference abstracts and published article abstracts in prosthodontic RCTs. Methods The conference abstracts of prosthodontic RCTs presented at the IADR general sessions from 2002 to 2015 were searched. Electronic searches of MEDLINE, EMBASE, the Cochrane Library, and Google Scholar databases were conducted to match full-text publications for conference abstracts. Two investigators extracted basic characteristics and assessed the consistency and reporting quality independently and in duplicate. The linear regression model was used to analyze the predictors of inconsistency. Results A total of 147 conference abstracts were matched with published articles. Results for the secondary outcome measure, Statistical analysis, and precision measure were less than 50% consistent, and even nearly 5% of the studies had opposite conclusions. Multiple linear regression analysis showed that three factors were correlated with lower inconsistency, including continent of origin (p = 0.011), presentation type (p = 0.017), and difference in reporting quality (p = 0.013). Conclusion Conference attendees should cautiously treat the findings of the conference abstracts. Researchers should improve the precision of the information delivered at conferences. We recommend the authors of RCTs to explain the primary difference between conference abstracts and article abstracts.
bibliographic citation: Wang et al. (2023) Reporting inconsistency between published conference abstracts and article abstracts of randomised controlled trials in prosthodontics presented at IADR general sessions. PeerJ 11:e15303 https://doi.org/10.7717/peerj.15303
date submitted: 2023-01-06
date accepted: 2023-04-05
issued: 2023-05-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Guanru
author list: Agent
  family name: Chen
  given name: Junsheng
author list: Agent
  family name: Li
  given name: Honglin
author list: Agent
  family name: Miao
  given name: Cheng
author list: Agent
  family name: Cao
  given name: Yubin
author list: Agent
  family name: Li
  given name: Chunjie
doi: 10.7717/peerj.15303
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-05
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Genome-wide transcriptomic analysis identifies candidate genes involved in jasmonic acid-mediated salt tolerance of alfalfa
type: item
type: AcademicArticle
description: Soil salinity imposes a major threat to plant growth and agricultural productivity. Despite being one of the most common fodder crops in saline locations, alfalfa is vulnerable to salt stress. Jasmonic acid (JA) is a phytohormone that influences plant response to abiotic stimuli such as salt stress. However, key genes and pathways by which JA-mediated salt tolerance of alfalfa are little known. A comprehensive transcriptome analysis was performed to elucidate the underlying molecular mechanisms of JA-mediated salt tolerance. The transcripts regulated by salt (S) compared to control (C) and JA+salt (JS) compared to C were investigated. Venn diagram and expression pattern of DEGs indicated that JS further altered a series of genes expression regulated by salt treatment, implying the roles of JA in priming salt tolerance. Enrichment analysis revealed that DEGs exclusively regulated by JS treatment belonged to primary or secondary metabolism, respiratory electron transport chain, and oxidative stress resistance. Alternatively, splicing (AS) was induced by salt alone or JA combined treatment, with skipped exon (SE) events predominately. DEGs undergo exon skipping involving some enriched items mentioned above and transcription factors. Finally, the gene expressions were validated using quantitative polymerase chain reaction (qPCR), which produced results that agreed with the sequencing results. Taken together, these findings suggest that JA modulates the expression of genes related to energy supply and antioxidant capacity at both the transcriptional and post-transcriptional levels, possibly through the involvement of transcription factors and AS events.
format: application/pdf
format: text/html
creator: Tianhui Yang
creator: Mei Tian
creator: Ting Gao
creator: Chuan Wang
creator: Xiaochun Wang
creator: Caijin Chen
creator: Weidi Yang
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15324
publisher: PeerJ Inc.
rights: © 2023 Yang et al.
abstract: Soil salinity imposes a major threat to plant growth and agricultural productivity. Despite being one of the most common fodder crops in saline locations, alfalfa is vulnerable to salt stress. Jasmonic acid (JA) is a phytohormone that influences plant response to abiotic stimuli such as salt stress. However, key genes and pathways by which JA-mediated salt tolerance of alfalfa are little known. A comprehensive transcriptome analysis was performed to elucidate the underlying molecular mechanisms of JA-mediated salt tolerance. The transcripts regulated by salt (S) compared to control (C) and JA+salt (JS) compared to C were investigated. Venn diagram and expression pattern of DEGs indicated that JS further altered a series of genes expression regulated by salt treatment, implying the roles of JA in priming salt tolerance. Enrichment analysis revealed that DEGs exclusively regulated by JS treatment belonged to primary or secondary metabolism, respiratory electron transport chain, and oxidative stress resistance. Alternatively, splicing (AS) was induced by salt alone or JA combined treatment, with skipped exon (SE) events predominately. DEGs undergo exon skipping involving some enriched items mentioned above and transcription factors. Finally, the gene expressions were validated using quantitative polymerase chain reaction (qPCR), which produced results that agreed with the sequencing results. Taken together, these findings suggest that JA modulates the expression of genes related to energy supply and antioxidant capacity at both the transcriptional and post-transcriptional levels, possibly through the involvement of transcription factors and AS events.
bibliographic citation: Yang et al. (2023) Genome-wide transcriptomic analysis identifies candidate genes involved in jasmonic acid-mediated salt tolerance of alfalfa. PeerJ 11:e15324 https://doi.org/10.7717/peerj.15324
date submitted: 2022-12-05
date accepted: 2023-04-10
issued: 2023-05-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Tianhui
author list: Agent
  family name: Tian
  given name: Mei
author list: Agent
  family name: Gao
  given name: Ting
author list: Agent
  family name: Wang
  given name: Chuan
author list: Agent
  family name: Wang
  given name: Xiaochun
author list: Agent
  family name: Chen
  given name: Caijin
author list: Agent
  family name: Yang
  given name: Weidi
doi: 10.7717/peerj.15324
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-05
copyright: © 2023 Yang et al.
attribution name: Yang et al.

Using DNA metabarcoding to assess insect diversity in citrus orchards
type: item
type: AcademicArticle
description: Background DNA metabarcoding is rapidly emerging as a cost-effective approach for large-scale biodiversity assessment and pest monitoring. The current study employed metabarcoding to assess insect diversity in citrus orchards in Ganzhou City, Jiangxi, China in both 2018 and 2019. Insects were sampled using Malaise traps deployed in three citrus orchards producing a total of 43 pooled monthly samples. Methods The Malaise trap samples were sequenced following DNA metabarcoding workflow. Generated sequences were curated and analyzed using two cloud databases and analytical platforms, the barcode of life data system (BOLD) and multiplex barcode research and visualization environment (mBRAVE). Results These platforms assigned the sequences to 2,141 barcode index numbers (BINs), a species proxy. Most (63%) of the BINs were shared among the three sampling sites while BIN sharing between any two sites did not exceed 71%. Shannon diversity index (H′) showed a similar pattern of BIN assortment at the three sampling sites. Beta diversity analysis by Jaccard similarity coefficient (J) and Bray-Curtis distance matrix (BC) revealed a high level of BIN similarity among the three sites (J = 0.67–0.68; BC = 0.19–0.20). Comparison of BIN records against all those on BOLD made it possible to identify 40% of the BINs to a species, 57% to a genus, 97% to a family and 99% to an order. BINs which received a species match on BOLD were placed in one of four categories based on this assignment: pest, parasitoid, predator, or pollinator. As this study provides the first baseline data on insect biodiversity in Chinese citrus plantations, it is a valuable resource for research in a broad range of areas such as pest management and monitoring beneficial insects in citrus gardens.
format: application/pdf
format: text/html
creator: Chenxi Liu
creator: Muhammad Ashfaq
creator: Yanfang Yin
creator: Yanjuan Zhu
creator: Zhen Wang
creator: Hongmei Cheng
creator: Paul Hebert
subject: Biodiversity
subject: Entomology
description: doi:10.7717/peerj.15338
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Background DNA metabarcoding is rapidly emerging as a cost-effective approach for large-scale biodiversity assessment and pest monitoring. The current study employed metabarcoding to assess insect diversity in citrus orchards in Ganzhou City, Jiangxi, China in both 2018 and 2019. Insects were sampled using Malaise traps deployed in three citrus orchards producing a total of 43 pooled monthly samples. Methods The Malaise trap samples were sequenced following DNA metabarcoding workflow. Generated sequences were curated and analyzed using two cloud databases and analytical platforms, the barcode of life data system (BOLD) and multiplex barcode research and visualization environment (mBRAVE). Results These platforms assigned the sequences to 2,141 barcode index numbers (BINs), a species proxy. Most (63%) of the BINs were shared among the three sampling sites while BIN sharing between any two sites did not exceed 71%. Shannon diversity index (H′) showed a similar pattern of BIN assortment at the three sampling sites. Beta diversity analysis by Jaccard similarity coefficient (J) and Bray-Curtis distance matrix (BC) revealed a high level of BIN similarity among the three sites (J = 0.67–0.68; BC = 0.19–0.20). Comparison of BIN records against all those on BOLD made it possible to identify 40% of the BINs to a species, 57% to a genus, 97% to a family and 99% to an order. BINs which received a species match on BOLD were placed in one of four categories based on this assignment: pest, parasitoid, predator, or pollinator. As this study provides the first baseline data on insect biodiversity in Chinese citrus plantations, it is a valuable resource for research in a broad range of areas such as pest management and monitoring beneficial insects in citrus gardens.
bibliographic citation: Liu et al. (2023) Using DNA metabarcoding to assess insect diversity in citrus orchards. PeerJ 11:e15338 https://doi.org/10.7717/peerj.15338
date submitted: 2022-09-23
date accepted: 2023-04-11
issued: 2023-05-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Chenxi
author list: Agent
  family name: Ashfaq
  given name: Muhammad
author list: Agent
  family name: Yin
  given name: Yanfang
author list: Agent
  family name: Zhu
  given name: Yanjuan
author list: Agent
  family name: Wang
  given name: Zhen
author list: Agent
  family name: Cheng
  given name: Hongmei
author list: Agent
  family name: Hebert
  given name: Paul
doi: 10.7717/peerj.15338
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-05
copyright: © 2023 Liu et al.
attribution name: Liu et al.

Pollination efficacy of stingless bees, Tetragonula pagdeni Schwarz (Apidae: Meliponini), on greenhouse tomatoes (Solanum lycopersicum Linnaeus)
type: item
type: AcademicArticle
description: The stingless bee Tetragonula pagdeni is distributed over a vast Southeast Asian territory. This species is commonly used as a commercial insect pollinator. Pollination efficacy of T. pagdeni was investigated with tomato (Solanum lycopersicum L.) cultivated in greenhouse environments. In the first experiment, the number of fruit sets, number of seeds, fresh weight, and fruit height were quantified in the greenhouse with stingless bees, without stingless bees, and with pollination by mechanical vibration by hand. In the second experiment, the treatments were conducted with tomatoes of indeterminate growth in the greenhouse with and without stingless bees to prevent variation among the different tomato plants. The obtained results showed that a greenhouse with stingless bees presented 85 ± 4.24 fruits per 100 flowers, more than a greenhouse with mechanical vibration (79.5 ± 2.12 fruits per 100 flowers) or a greenhouse without stingless bees (15 ± 0.00 fruits per 100 flowers). In addition, fruit produced in a greenhouse with stingless bees showed greater fruit weight and number of seeds than fruit produced in a greenhouse without stingless bees or pollinated by mechanical vibration. According to the obtained results, we suggest that T. pagdeni could be beneficial as an insect pollinator of greenhouse tomatoes in tropical regions, where the use of honeybees and bumblebees would be more difficult.
format: application/pdf
format: text/html
creator: Kanyanat Wongsa
creator: Orawan Duangphakdee
creator: Atsalek Rattanawannee
subject: Agricultural Science
subject: Ecology
subject: Entomology
subject: Plant Science
subject: Zoology
description: doi:10.7717/peerj.15367
publisher: PeerJ Inc.
rights: © 2023 Wongsa et al.
abstract: The stingless bee Tetragonula pagdeni is distributed over a vast Southeast Asian territory. This species is commonly used as a commercial insect pollinator. Pollination efficacy of T. pagdeni was investigated with tomato (Solanum lycopersicum L.) cultivated in greenhouse environments. In the first experiment, the number of fruit sets, number of seeds, fresh weight, and fruit height were quantified in the greenhouse with stingless bees, without stingless bees, and with pollination by mechanical vibration by hand. In the second experiment, the treatments were conducted with tomatoes of indeterminate growth in the greenhouse with and without stingless bees to prevent variation among the different tomato plants. The obtained results showed that a greenhouse with stingless bees presented 85 ± 4.24 fruits per 100 flowers, more than a greenhouse with mechanical vibration (79.5 ± 2.12 fruits per 100 flowers) or a greenhouse without stingless bees (15 ± 0.00 fruits per 100 flowers). In addition, fruit produced in a greenhouse with stingless bees showed greater fruit weight and number of seeds than fruit produced in a greenhouse without stingless bees or pollinated by mechanical vibration. According to the obtained results, we suggest that T. pagdeni could be beneficial as an insect pollinator of greenhouse tomatoes in tropical regions, where the use of honeybees and bumblebees would be more difficult.
bibliographic citation: Wongsa et al. (2023) Pollination efficacy of stingless bees, Tetragonula pagdeni Schwarz (Apidae: Meliponini), on greenhouse tomatoes (Solanum lycopersicum Linnaeus). PeerJ 11:e15367 https://doi.org/10.7717/peerj.15367
date submitted: 2023-03-06
date accepted: 2023-04-17
issued: 2023-05-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wongsa
  given name: Kanyanat
author list: Agent
  family name: Duangphakdee
  given name: Orawan
author list: Agent
  family name: Rattanawannee
  given name: Atsalek
doi: 10.7717/peerj.15367
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-05
copyright: © 2023 Wongsa et al.
attribution name: Wongsa et al.

Identification of ABF/AREB gene family in tomato (Solanum lycopersicum L.) and functional analysis of ABF/AREB in response to ABA and abiotic stresses
type: item
type: AcademicArticle
description: Abscisic acid (ABA) is a plant hormone that plays an important regulatory role in plant growth and stress response. The AREB (ABA-responsive element binding protein)/ABF (ABRE-binding factor) are important ABA-signaling components that participate in abiotic stress response. However, genome-scale analysis of ABF/AREB has not been systemically investigated in tomato. This study was conducted to identify tomato ABF/AREB family members and analyze their response to ABA and abiotic stresses. The results show that a total of 10 ABF/AREB members were identified in tomato, which are randomly distributed on five chromosomes. Domain analysis showed that these members exhibit high protein similarity, especially in the basic leucine zipper (bZIP) domain region. Subcellular localization analysis indicated that all 10 ABF/AREB members are localized in the nucleus. Phylogenetic tree analysis showed that tomato ABF/AREB genes are divided into two groups, and they are similar with the orthologs of other plants. The analysis of cis-acting elements showed that most tomato ABF/AREB genes contain a variety of hormones and stress-related elements. Expression profiles of different tissues indicated that SlABF2 and SlABF10 play an important role in fruit ripening. Finally, qRT-PCR analysis revealed that 10 tomato ABF/AREB genes respond to ABA, with SlABF3 being the most sensitive. SlABF3, SlABF5 and SlABF10 positively respond to salt and cold stresses. SlABF1, SlABF3 and SlABF10 are significantly induced under UV radiation treatment. SlABF3 and SlABF5 are significantly induced in osmotic stress. Overall, this study may provide insight into the role of tomato ABF/AREB homologues in plant response to abiotic stresses, which laid a foundation for future functional study of ABF/AREB in tomato.
format: application/pdf
format: text/html
creator: Xuejuan Pan
creator: Chunlei Wang
creator: Zesheng Liu
creator: Rong Gao
creator: Li Feng
creator: Ailing Li
creator: Kangding Yao
creator: Weibiao Liao
subject: Agricultural Science
subject: Bioinformatics
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15310
publisher: PeerJ Inc.
rights: © 2023 Pan et al.
abstract: Abscisic acid (ABA) is a plant hormone that plays an important regulatory role in plant growth and stress response. The AREB (ABA-responsive element binding protein)/ABF (ABRE-binding factor) are important ABA-signaling components that participate in abiotic stress response. However, genome-scale analysis of ABF/AREB has not been systemically investigated in tomato. This study was conducted to identify tomato ABF/AREB family members and analyze their response to ABA and abiotic stresses. The results show that a total of 10 ABF/AREB members were identified in tomato, which are randomly distributed on five chromosomes. Domain analysis showed that these members exhibit high protein similarity, especially in the basic leucine zipper (bZIP) domain region. Subcellular localization analysis indicated that all 10 ABF/AREB members are localized in the nucleus. Phylogenetic tree analysis showed that tomato ABF/AREB genes are divided into two groups, and they are similar with the orthologs of other plants. The analysis of cis-acting elements showed that most tomato ABF/AREB genes contain a variety of hormones and stress-related elements. Expression profiles of different tissues indicated that SlABF2 and SlABF10 play an important role in fruit ripening. Finally, qRT-PCR analysis revealed that 10 tomato ABF/AREB genes respond to ABA, with SlABF3 being the most sensitive. SlABF3, SlABF5 and SlABF10 positively respond to salt and cold stresses. SlABF1, SlABF3 and SlABF10 are significantly induced under UV radiation treatment. SlABF3 and SlABF5 are significantly induced in osmotic stress. Overall, this study may provide insight into the role of tomato ABF/AREB homologues in plant response to abiotic stresses, which laid a foundation for future functional study of ABF/AREB in tomato.
bibliographic citation: Pan et al. (2023) Identification of ABF/AREB gene family in tomato (Solanum lycopersicum L.) and functional analysis of ABF/AREB in response to ABA and abiotic stresses. PeerJ 11:e15310 https://doi.org/10.7717/peerj.15310
date submitted: 2022-12-15
date accepted: 2023-04-06
issued: 2023-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Xuejuan
author list: Agent
  family name: Wang
  given name: Chunlei
author list: Agent
  family name: Liu
  given name: Zesheng
author list: Agent
  family name: Gao
  given name: Rong
author list: Agent
  family name: Feng
  given name: Li
author list: Agent
  family name: Li
  given name: Ailing
author list: Agent
  family name: Yao
  given name: Kangding
author list: Agent
  family name: Liao
  given name: Weibiao
doi: 10.7717/peerj.15310
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-04
copyright: © 2023 Pan et al.
attribution name: Pan et al.

Variation of choroidal thickness during the waking period over three consecutive days in different degrees of myopia and emmetropia using optical coherence tomography
type: item
type: AcademicArticle
description: Purpose To investigate the diurnal variation in subfoveal choroidal thickness (SFCT) during the waking period over three consecutive days in different degrees of myopia and emmetropia. Methods A total of 60 adult volunteers were grouped into low, moderate, high myopia, and emmetropia subgroups. SFCT, axial length (AL), anterior chamber depth (ACD), and intraocular pressure (IOP) were measured every 2 h from 8 AM to 8 PM for three successive days. Results The mean values of daily change amplitude were 3.18 mmHg (IOP), 0.05 mm (AL), 0.17 mm (ACD), and 13.51 μm (SFCT). The values of AL and ACD increased simultaneously with spherical equivalent refraction (SER), but SFCT was the opposite. IOP had a diurnal variation, and there was no difference among the four groups. AL of the high myopia group, ACD of the emmetropia group, and SFCT of each myopia group had diurnal variation over three consecutive days. AL had a high mean value at noon every day, and SFCT had a low mean value at noon every day. Conclusion The choroid thickness of subjects with different degrees of myopia had a significant diurnal variation. The change of diurnal variation between emmetropic and myopic subjects may be one of the causes of myopia.
format: application/pdf
format: text/html
creator: Xianming Jiang
creator: Ping Xiao
creator: Qian Tan
creator: Yunxiao Zhu
subject: Ophthalmology
description: doi:10.7717/peerj.15317
publisher: PeerJ Inc.
rights: © 2023 Jiang et al.
abstract: Purpose To investigate the diurnal variation in subfoveal choroidal thickness (SFCT) during the waking period over three consecutive days in different degrees of myopia and emmetropia. Methods A total of 60 adult volunteers were grouped into low, moderate, high myopia, and emmetropia subgroups. SFCT, axial length (AL), anterior chamber depth (ACD), and intraocular pressure (IOP) were measured every 2 h from 8 AM to 8 PM for three successive days. Results The mean values of daily change amplitude were 3.18 mmHg (IOP), 0.05 mm (AL), 0.17 mm (ACD), and 13.51 μm (SFCT). The values of AL and ACD increased simultaneously with spherical equivalent refraction (SER), but SFCT was the opposite. IOP had a diurnal variation, and there was no difference among the four groups. AL of the high myopia group, ACD of the emmetropia group, and SFCT of each myopia group had diurnal variation over three consecutive days. AL had a high mean value at noon every day, and SFCT had a low mean value at noon every day. Conclusion The choroid thickness of subjects with different degrees of myopia had a significant diurnal variation. The change of diurnal variation between emmetropic and myopic subjects may be one of the causes of myopia.
bibliographic citation: Jiang et al. (2023) Variation of choroidal thickness during the waking period over three consecutive days in different degrees of myopia and emmetropia using optical coherence tomography. PeerJ 11:e15317 https://doi.org/10.7717/peerj.15317
date submitted: 2023-01-03
date accepted: 2023-04-07
issued: 2023-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Xianming
author list: Agent
  family name: Xiao
  given name: Ping
author list: Agent
  family name: Tan
  given name: Qian
author list: Agent
  family name: Zhu
  given name: Yunxiao
doi: 10.7717/peerj.15317
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-04
copyright: © 2023 Jiang et al.
attribution name: Jiang et al.

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