PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Expression of connexin-43 in surgical resections of primary tumor and lymph node metastases of squamous cell carcinoma and adenocarcinoma of the lung: a retrospective study
items: Environmental enrichment changes rabbits’ behavior, serum hormone level and further affects cecal microbiota
items: Long-term consumption of artificial sweeteners does not affect cardiovascular health and survival in rats
items: Full-length transcriptome analysis of Adiantum flabellulatum gametophyte
items: Immunogenicity mechanism of mRNA vaccines and their limitations in promoting adaptive protection against SARS-CoV-2
items: Distinct metabolic profiling is correlated with bisexual flowers formation resulting from exogenous ethephon induction in melon (Cucumis melo L.)
items: A bZIP transcription factor, PqbZIP1, is involved in the plant defense response of American ginseng
items: Associations between the rs5498 (A > G) and rs281432 (C > G) polymorphisms of the ICAM1 gene and atherosclerotic cardiovascular disease risk, including hypercholesterolemia
items: Microbial community spatial structures in Luzhou-flavored liquor pit muds with different brewing materials
items: Abubidentin A, New Oleanane-type Triterpene Ester from Abutilon bidentatum and its antioxidant, cholinesterase and antimicrobial activities

Expression of connexin-43 in surgical resections of primary tumor and lymph node metastases of squamous cell carcinoma and adenocarcinoma of the lung: a retrospective study
type: item
type: AcademicArticle
description: Background Connexins are transmembrane proteins forming gap junctions between the cells, which allow intercellular communication. Significance of gap junctions and connexins in lung carcinoma is not yet understood. The objective of the study was to investigate immunohistochemical expression and the localization of connexin-43 (Cx43) in primary lung carcinoma and its lymphatic metastases. Methods Surgical specimens of excised tumors from 88 patients (45 men and 43 women, 61.9 ± 7.4 years) with lung carcinoma (52 adenocarcinoma (AC), 36 squamous cell carcinoma (SqCC)) who were operated on at the University Hospital “Bezanijska Kosa” in a five-year period (2012–2016) were used. We conducted immunohistochemical staining for Cx43 and measured the degree of expression (percentage of positive cells and staining intensity) as well as localization of Cx43 in primary tumor and in lymphatic metastases. Results Immunohistochemical analysis of the primary tumors revealed that SqCC showed significantly higher percentage of tumor cells expressing Cx43 as well as higher staining intensity than AC (p < 0.001). Almost 70% of samples with SqCC showed high Cx43 expression, whereas AC showed no expression in more than 50% of cases. Localization of Cx43 expression was most often cytoplasmic (AC and SqCC) and combined membranous and cytoplasmic (SqCC) with very rare instances of nuclear localization (AC). Almost the same pattern in distribution, intensity, and localization of Cx43 expression was observed in the lymph node metastases; however, almost a third of AC cases changed the pattern of Cx43 expression in the metastasis compared to primary tumor. Conclusion The results of this study showed that lung carcinomas express Cx43 in more than 65% of cases and that it was aberrantly localized (not membranous localization). We highlighted that SqCC expressed Cx43 more than did AC, both in primary tumor and lymphatic metastases. Further research is needed to establish whether Cx43 could be use…
format: application/pdf
format: text/html
creator: Ivana Savic
creator: Petar Milovanovic
creator: Svetlana Opric
creator: Nebojsa Ivanovic
creator: Dejan Oprić
subject: Oncology
subject: Pathology
subject: Respiratory Medicine
subject: Histology
description: doi:10.7717/peerj.13055
publisher: PeerJ Inc.
rights: © 2022 Savic et al.
abstract: Background Connexins are transmembrane proteins forming gap junctions between the cells, which allow intercellular communication. Significance of gap junctions and connexins in lung carcinoma is not yet understood. The objective of the study was to investigate immunohistochemical expression and the localization of connexin-43 (Cx43) in primary lung carcinoma and its lymphatic metastases. Methods Surgical specimens of excised tumors from 88 patients (45 men and 43 women, 61.9 ± 7.4 years) with lung carcinoma (52 adenocarcinoma (AC), 36 squamous cell carcinoma (SqCC)) who were operated on at the University Hospital “Bezanijska Kosa” in a five-year period (2012–2016) were used. We conducted immunohistochemical staining for Cx43 and measured the degree of expression (percentage of positive cells and staining intensity) as well as localization of Cx43 in primary tumor and in lymphatic metastases. Results Immunohistochemical analysis of the primary tumors revealed that SqCC showed significantly higher percentage of tumor cells expressing Cx43 as well as higher staining intensity than AC (p < 0.001). Almost 70% of samples with SqCC showed high Cx43 expression, whereas AC showed no expression in more than 50% of cases. Localization of Cx43 expression was most often cytoplasmic (AC and SqCC) and combined membranous and cytoplasmic (SqCC) with very rare instances of nuclear localization (AC). Almost the same pattern in distribution, intensity, and localization of Cx43 expression was observed in the lymph node metastases; however, almost a third of AC cases changed the pattern of Cx43 expression in the metastasis compared to primary tumor. Conclusion The results of this study showed that lung carcinomas express Cx43 in more than 65% of cases and that it was aberrantly localized (not membranous localization). We highlighted that SqCC expressed Cx43 more than did AC, both in primary tumor and lymphatic metastases. Further research is needed to establish whether Cx43 could be use…
bibliographic citation: Savic et al. (2022) Expression of connexin-43 in surgical resections of primary tumor and lymph node metastases of squamous cell carcinoma and adenocarcinoma of the lung: a retrospective study. PeerJ 10:e13055 https://doi.org/10.7717/peerj.13055
date submitted: 2020-07-22
date accepted: 2022-02-12
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Savic
  given name: Ivana
author list: Agent
  family name: Milovanovic
  given name: Petar
author list: Agent
  family name: Opric
  given name: Svetlana
author list: Agent
  family name: Ivanovic
  given name: Nebojsa
author list: Agent
  family name: Oprić
  given name: Dejan
doi: 10.7717/peerj.13055
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Savic et al.
attribution name: Savic et al.

Environmental enrichment changes rabbits’ behavior, serum hormone level and further affects cecal microbiota
type: item
type: AcademicArticle
description: Many studies have shown that stress is associated with gut microbiota. Environmental enrichment (EE) could reduce stress in farm animals; however, limited information is available on the microbial community composition in rabbits raised with or without EE. This study aimed to identify EE influences on the behavior, serum hormonal levels, and cecal microbiota of rabbits. Two hundred Rex rabbits were segregated randomly within four cohorts (n = 50); reared for 76 d within standardized enclosures (non-enriched) or within cages containing a willow-stick (WS), rubber-duck (RD), or a can of beans (CB). The rabbits’ ingestive, rest, locomotion, exploratory, grooming, and abnormal behavior were observed. The serum hormone levels for rabbits were measured, and cecal specimens were sequencedfrom the V3–V4 region using 16S rRNA amplicons. Environmental enrichment increased feeding and drinking time, promoted exploratory behavior, and reduced abnormal behavior in rabbits. Insulin-like growth factor 1(IGF-1) levels of the enriched cohorts were elevated in comparison to the control cohort. Serum cortisol level for CB cohort was markedly reduced in comparison to the control cohort (p < 0.05), while dopamine levels for CB cohort peaked. Further, we found that EE mainly affected the dominant microbiota. Several families, such as Erysipelotrichaceae, Tannerellaceae, Enterobacteriaceae, Burkholderiaceae, and Prevotellaceae were markedly reduced within the CB cohort. Bacteria such as Alloprevotella, Bifidobacterium, Enterobacteriaceae, Parabacteroides, and Erysipelatoclostridium were identified as having negative associations with the presence of serum cortisol. EE influenced rabbit behavior and serum hormonal levels, and CB enrichment was the most suitable for rabbits. Further, cecal microbiota composition and diversity were affected by CB enrichment. These findings suggested that CB could be considered for use in rabbit husbandry.
format: application/pdf
format: text/html
creator: Yang Feng
creator: Huimei Fan
creator: Xue Liang
creator: Xiaofeng Wang
creator: Guoyan Gao
creator: Shuangbao Gun
subject: Animal Behavior
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.13068
publisher: PeerJ Inc.
rights: © 2022 Feng et al.
abstract: Many studies have shown that stress is associated with gut microbiota. Environmental enrichment (EE) could reduce stress in farm animals; however, limited information is available on the microbial community composition in rabbits raised with or without EE. This study aimed to identify EE influences on the behavior, serum hormonal levels, and cecal microbiota of rabbits. Two hundred Rex rabbits were segregated randomly within four cohorts (n = 50); reared for 76 d within standardized enclosures (non-enriched) or within cages containing a willow-stick (WS), rubber-duck (RD), or a can of beans (CB). The rabbits’ ingestive, rest, locomotion, exploratory, grooming, and abnormal behavior were observed. The serum hormone levels for rabbits were measured, and cecal specimens were sequencedfrom the V3–V4 region using 16S rRNA amplicons. Environmental enrichment increased feeding and drinking time, promoted exploratory behavior, and reduced abnormal behavior in rabbits. Insulin-like growth factor 1(IGF-1) levels of the enriched cohorts were elevated in comparison to the control cohort. Serum cortisol level for CB cohort was markedly reduced in comparison to the control cohort (p < 0.05), while dopamine levels for CB cohort peaked. Further, we found that EE mainly affected the dominant microbiota. Several families, such as Erysipelotrichaceae, Tannerellaceae, Enterobacteriaceae, Burkholderiaceae, and Prevotellaceae were markedly reduced within the CB cohort. Bacteria such as Alloprevotella, Bifidobacterium, Enterobacteriaceae, Parabacteroides, and Erysipelatoclostridium were identified as having negative associations with the presence of serum cortisol. EE influenced rabbit behavior and serum hormonal levels, and CB enrichment was the most suitable for rabbits. Further, cecal microbiota composition and diversity were affected by CB enrichment. These findings suggested that CB could be considered for use in rabbit husbandry.
bibliographic citation: Feng et al. (2022) Environmental enrichment changes rabbits’ behavior, serum hormone level and further affects cecal microbiota. PeerJ 10:e13068 https://doi.org/10.7717/peerj.13068
date submitted: 2020-12-15
date accepted: 2022-02-15
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: Yang
author list: Agent
  family name: Fan
  given name: Huimei
author list: Agent
  family name: Liang
  given name: Xue
author list: Agent
  family name: Wang
  given name: Xiaofeng
author list: Agent
  family name: Gao
  given name: Guoyan
author list: Agent
  family name: Gun
  given name: Shuangbao
doi: 10.7717/peerj.13068
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Feng et al.
attribution name: Feng et al.

Long-term consumption of artificial sweeteners does not affect cardiovascular health and survival in rats
type: item
type: AcademicArticle
description: Background Recent epidemiological cohort studies have suggested that consumption of artificial sweeteners (AS) is associated with adverse cardiovascular events and mortality. However, these population association studies cannot establish a causal relationship. In this study we investigated the effect of long-term (1-year) consumption of AS (Equal and Splenda, two commonly used AS) on cardiovascular health and survival in rats. Methods Adult Sprague-Dawley rats (both sexes, 4–5 months old) were randomized into the following 3 groups: control (n = 21), AS Equal (n = 21) and Splenda (n = 18). In the AS groups, Equal or Splenda was added to the drinking water (2-packets/250 ml), while drinking water alone was used in the control rats. The treatment was administered for 12 months. Cardiovascular function and survival were monitored in all animals. Results It was found that rats in the AS groups consistently consumed more sweetened water than those in the control group. AS did not affect body weight, non-fasting blood cholesterol, triglycerides, blood pressure or pulse wave velocity. There were no significant differences in left ventricular wall thicknesses, chamber dimension, cardiac function or survival. AS did not affect heart rate or atrial effective refractory period. However, rats in both Equal and Splenda groups had prolonged PR intervals (63 ± 5ms in Equal, 68 ± 6 ms in Splenda, vs 56 ± 8 ms in control, p < 0.05) and a tendency of increased atrial fibrillation inducibility. Conclusion Long-term consumption of AS does not affect cardiovascular structure, function or survival but may cause some electrophysiological abnormalities with prolonged PR intervals and a tendency of increased atrial fibrillation inducibility in rats.
format: application/pdf
format: text/html
creator: Satvinder K. Guru
creator: Ying Li
creator: Olga V. Savinova
creator: Youhua Zhang
subject: Cardiology
subject: Nutrition
subject: Translational Medicine
description: doi:10.7717/peerj.13071
publisher: PeerJ Inc.
rights: © 2022 Guru et al.
abstract: Background Recent epidemiological cohort studies have suggested that consumption of artificial sweeteners (AS) is associated with adverse cardiovascular events and mortality. However, these population association studies cannot establish a causal relationship. In this study we investigated the effect of long-term (1-year) consumption of AS (Equal and Splenda, two commonly used AS) on cardiovascular health and survival in rats. Methods Adult Sprague-Dawley rats (both sexes, 4–5 months old) were randomized into the following 3 groups: control (n = 21), AS Equal (n = 21) and Splenda (n = 18). In the AS groups, Equal or Splenda was added to the drinking water (2-packets/250 ml), while drinking water alone was used in the control rats. The treatment was administered for 12 months. Cardiovascular function and survival were monitored in all animals. Results It was found that rats in the AS groups consistently consumed more sweetened water than those in the control group. AS did not affect body weight, non-fasting blood cholesterol, triglycerides, blood pressure or pulse wave velocity. There were no significant differences in left ventricular wall thicknesses, chamber dimension, cardiac function or survival. AS did not affect heart rate or atrial effective refractory period. However, rats in both Equal and Splenda groups had prolonged PR intervals (63 ± 5ms in Equal, 68 ± 6 ms in Splenda, vs 56 ± 8 ms in control, p < 0.05) and a tendency of increased atrial fibrillation inducibility. Conclusion Long-term consumption of AS does not affect cardiovascular structure, function or survival but may cause some electrophysiological abnormalities with prolonged PR intervals and a tendency of increased atrial fibrillation inducibility in rats.
bibliographic citation: Guru et al. (2022) Long-term consumption of artificial sweeteners does not affect cardiovascular health and survival in rats. PeerJ 10:e13071 https://doi.org/10.7717/peerj.13071
date submitted: 2021-12-09
date accepted: 2022-02-15
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guru
  given name: Satvinder K.
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Savinova
  given name: Olga V.
author list: Agent
  family name: Zhang
  given name: Youhua
doi: 10.7717/peerj.13071
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Guru et al.
attribution name: Guru et al.

Full-length transcriptome analysis of Adiantum flabellulatum gametophyte
type: item
type: AcademicArticle
description: Ferns are important components of plant communities on earth, but their genomes are generally very large, with many redundant genes, making whole genome sequencing of ferns prohibitively expensive and time-consuming. This means there is a significant lack of fern reference genomes, making molecular biology research difficult. The gametophytes of ferns can survive independently, are responsible for sexual reproduction and the feeding of young sporophytes, and play an important role in the alternation of generations. For this study, we selected Adiantum flabellulatum as it has both ornamental and medicinal value and is also an indicator plant of acidic soil. The full-length transcriptome sequencing of its gametophytes was carried out using PacBio three-generation sequencing technology. A total of 354,228 transcripts were obtained, and 231,705 coding sequences (CDSs) were predicted, including 5,749 transcription factors (TFs), 2,214 transcription regulators (TRs) and 4,950 protein kinases (PKs). The transcripts annotated by non-redundant protein sequence database (NR), Kyoto encyclopedia of genes and genomes (KEGG), eukaryotic ortholog groups (KOG), Swissprot, protein family (Pfma), nucleotide sequence database (NT) and gene ontology (GO) were 251,501, 197,474, 193,630, 194,639, 195,956, 113,069 and 197,883, respectively. In addition, 138,995 simple sequence repeats (SSRs) and 111,793 long non-coding RNAs (lncRNAs) were obtained. We selected nine chlorophyll synthase genes for qRT-PCR, and the results showed that the full-length transcript sequences and the annotation information were reliable. This study can provide a reference gene set for subsequent gene expression quantification.
format: application/pdf
format: text/html
creator: Zeping Cai
creator: Zhenyu Xie
creator: Luyao Huang
creator: Zixuan Wang
creator: Min Pan
creator: Xudong Yu
creator: Shitao Xu
creator: Jiajia Luo
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13079
publisher: PeerJ Inc.
rights: © 2022 Cai et al.
abstract: Ferns are important components of plant communities on earth, but their genomes are generally very large, with many redundant genes, making whole genome sequencing of ferns prohibitively expensive and time-consuming. This means there is a significant lack of fern reference genomes, making molecular biology research difficult. The gametophytes of ferns can survive independently, are responsible for sexual reproduction and the feeding of young sporophytes, and play an important role in the alternation of generations. For this study, we selected Adiantum flabellulatum as it has both ornamental and medicinal value and is also an indicator plant of acidic soil. The full-length transcriptome sequencing of its gametophytes was carried out using PacBio three-generation sequencing technology. A total of 354,228 transcripts were obtained, and 231,705 coding sequences (CDSs) were predicted, including 5,749 transcription factors (TFs), 2,214 transcription regulators (TRs) and 4,950 protein kinases (PKs). The transcripts annotated by non-redundant protein sequence database (NR), Kyoto encyclopedia of genes and genomes (KEGG), eukaryotic ortholog groups (KOG), Swissprot, protein family (Pfma), nucleotide sequence database (NT) and gene ontology (GO) were 251,501, 197,474, 193,630, 194,639, 195,956, 113,069 and 197,883, respectively. In addition, 138,995 simple sequence repeats (SSRs) and 111,793 long non-coding RNAs (lncRNAs) were obtained. We selected nine chlorophyll synthase genes for qRT-PCR, and the results showed that the full-length transcript sequences and the annotation information were reliable. This study can provide a reference gene set for subsequent gene expression quantification.
bibliographic citation: Cai et al. (2022) Full-length transcriptome analysis of Adiantum flabellulatum gametophyte. PeerJ 10:e13079 https://doi.org/10.7717/peerj.13079
date submitted: 2021-09-24
date accepted: 2022-02-16
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Zeping
author list: Agent
  family name: Xie
  given name: Zhenyu
author list: Agent
  family name: Huang
  given name: Luyao
author list: Agent
  family name: Wang
  given name: Zixuan
author list: Agent
  family name: Pan
  given name: Min
author list: Agent
  family name: Yu
  given name: Xudong
author list: Agent
  family name: Xu
  given name: Shitao
author list: Agent
  family name: Luo
  given name: Jiajia
doi: 10.7717/peerj.13079
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Cai et al.
attribution name: Cai et al.

Immunogenicity mechanism of mRNA vaccines and their limitations in promoting adaptive protection against SARS-CoV-2
type: item
type: AcademicArticle
description: Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) in late 2019, hundreds of millions of people have been infected worldwide. There have been unprecedented efforts in acquiring effective vaccines to confer protection against the disease. mRNA vaccines have emerged as promising alternatives to conventional vaccines due to their high potency with the capacity for rapid development and low manufacturing costs. In this review, we summarize the currently available vaccines against SARS-CoV-2 in development, with the focus on the concepts of mRNA vaccines, their antigen selection, delivery and optimization to increase the immunostimulatory capability of mRNA as well as its stability and translatability. We also discuss the host immune responses to the SARS-CoV-2 infection and expound in detail, the adaptive immune response upon immunization with mRNA vaccines, in which high levels of spike-specific IgG and neutralizing antibodies were detected after two-dose vaccination. mRNA vaccines have been shown to induce a robust CD8+T cell response, with a balanced CD4+ TH1/TH2 response. We further discuss the challenges and limitations of COVID-19 mRNA vaccines, where newly emerging variants of SARS-CoV-2 may render currently deployed vaccines less effective. Imbalanced and inappropriate inflammatory responses, resulting from hyper-activation of pro-inflammatory cytokines, which may lead to vaccine-associated enhanced respiratory disease (VAERD) and rare cases of myocarditis and pericarditis also are discussed.
format: application/pdf
format: text/html
creator: Mohd Zulkifli Salleh
creator: Mohd Nor Norazmi
creator: Zakuan Zainy Deris
subject: Molecular Biology
subject: Immunology
subject: Infectious Diseases
subject: COVID-19
description: doi:10.7717/peerj.13083
publisher: PeerJ Inc.
rights: © 2022 Salleh et al.
abstract: Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) in late 2019, hundreds of millions of people have been infected worldwide. There have been unprecedented efforts in acquiring effective vaccines to confer protection against the disease. mRNA vaccines have emerged as promising alternatives to conventional vaccines due to their high potency with the capacity for rapid development and low manufacturing costs. In this review, we summarize the currently available vaccines against SARS-CoV-2 in development, with the focus on the concepts of mRNA vaccines, their antigen selection, delivery and optimization to increase the immunostimulatory capability of mRNA as well as its stability and translatability. We also discuss the host immune responses to the SARS-CoV-2 infection and expound in detail, the adaptive immune response upon immunization with mRNA vaccines, in which high levels of spike-specific IgG and neutralizing antibodies were detected after two-dose vaccination. mRNA vaccines have been shown to induce a robust CD8+T cell response, with a balanced CD4+ TH1/TH2 response. We further discuss the challenges and limitations of COVID-19 mRNA vaccines, where newly emerging variants of SARS-CoV-2 may render currently deployed vaccines less effective. Imbalanced and inappropriate inflammatory responses, resulting from hyper-activation of pro-inflammatory cytokines, which may lead to vaccine-associated enhanced respiratory disease (VAERD) and rare cases of myocarditis and pericarditis also are discussed.
bibliographic citation: Salleh et al. (2022) Immunogenicity mechanism of mRNA vaccines and their limitations in promoting adaptive protection against SARS-CoV-2. PeerJ 10:e13083 https://doi.org/10.7717/peerj.13083
date submitted: 2021-11-15
date accepted: 2022-02-16
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salleh
  given name: Mohd Zulkifli
author list: Agent
  family name: Norazmi
  given name: Mohd Nor
author list: Agent
  family name: Deris
  given name: Zakuan Zainy
doi: 10.7717/peerj.13083
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Salleh et al.
attribution name: Salleh et al.

Distinct metabolic profiling is correlated with bisexual flowers formation resulting from exogenous ethephon induction in melon (Cucumis melo L.)
type: item
type: AcademicArticle
description: Melon (Cucumis melo L.) is an agronomically important vegetable. Most cultivars of melon are andromonoecious and bisexual flowers only emerged from the leaf axil of lateral branches. However, the regulatory mechanism contributing to the occurrence of bisexual flowers were still obscure. In this study, ethephon was applied in two common cultivars of melon. In control without ethephon treatment, no bisexual flower was made in the main stem. However, 6.56 ± 1.42 and 6.63 ± 0.55 bisexual flowers were respectively induced in main stem of ‘Yangjiaocui-QX’ and ‘Lvbao’ after ethephon treatment, and induced bisexual flowers distributed in 12–20 nodes of main stem. During the formation of bisexual flowers, 41 metabolites were significantly up-regulated and 98 metabolites were significantly down-regulated. According to the KEGG enrichment analysis of 139 different metabolites, a total of 30 pathways were mapped and KEGG terms of “Phenylalanine, tyrosine and tryptophan biosynthesis”, “Phenylalanine metabolism” and “Flavone and flavonol biosynthesis” were significantly enriched. In three significantly enriched KEGG terms, shikimic acid, L-tryptophan, L-phenylalanine, and kaempferol were significantly up-regulated while L-tyrosine, 4-hydroxycinnami acid and luteolin were significantly down-regulated in ET compared to CK. Different metabolites were also classified depend on major class features and 14 classes were acquired. The results of metabonomics and endogenous hormone identification indicated that ethylene could enhance the concentration of salicylic acid, methyl jasmonate, ABA and IAA. This study provided an important theoretical foundation for inducing bisexual flowers in main stem and breeding new varieties of melon in future.
format: application/pdf
format: text/html
creator: Siyu Fang
creator: Yaqian Duan
creator: Lanchun Nie
creator: Wensheng Zhao
creator: Jiahao Wang
creator: Jiateng Zhao
creator: Liping Zhao
creator: Lei Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.13088
publisher: PeerJ Inc.
rights: © 2022 Fang et al.
abstract: Melon (Cucumis melo L.) is an agronomically important vegetable. Most cultivars of melon are andromonoecious and bisexual flowers only emerged from the leaf axil of lateral branches. However, the regulatory mechanism contributing to the occurrence of bisexual flowers were still obscure. In this study, ethephon was applied in two common cultivars of melon. In control without ethephon treatment, no bisexual flower was made in the main stem. However, 6.56 ± 1.42 and 6.63 ± 0.55 bisexual flowers were respectively induced in main stem of ‘Yangjiaocui-QX’ and ‘Lvbao’ after ethephon treatment, and induced bisexual flowers distributed in 12–20 nodes of main stem. During the formation of bisexual flowers, 41 metabolites were significantly up-regulated and 98 metabolites were significantly down-regulated. According to the KEGG enrichment analysis of 139 different metabolites, a total of 30 pathways were mapped and KEGG terms of “Phenylalanine, tyrosine and tryptophan biosynthesis”, “Phenylalanine metabolism” and “Flavone and flavonol biosynthesis” were significantly enriched. In three significantly enriched KEGG terms, shikimic acid, L-tryptophan, L-phenylalanine, and kaempferol were significantly up-regulated while L-tyrosine, 4-hydroxycinnami acid and luteolin were significantly down-regulated in ET compared to CK. Different metabolites were also classified depend on major class features and 14 classes were acquired. The results of metabonomics and endogenous hormone identification indicated that ethylene could enhance the concentration of salicylic acid, methyl jasmonate, ABA and IAA. This study provided an important theoretical foundation for inducing bisexual flowers in main stem and breeding new varieties of melon in future.
bibliographic citation: Fang et al. (2022) Distinct metabolic profiling is correlated with bisexual flowers formation resulting from exogenous ethephon induction in melon (Cucumis melo L.). PeerJ 10:e13088 https://doi.org/10.7717/peerj.13088
date submitted: 2021-10-18
date accepted: 2022-02-17
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fang
  given name: Siyu
author list: Agent
  family name: Duan
  given name: Yaqian
author list: Agent
  family name: Nie
  given name: Lanchun
author list: Agent
  family name: Zhao
  given name: Wensheng
author list: Agent
  family name: Wang
  given name: Jiahao
author list: Agent
  family name: Zhao
  given name: Jiateng
author list: Agent
  family name: Zhao
  given name: Liping
author list: Agent
  family name: Wang
  given name: Lei
doi: 10.7717/peerj.13088
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Fang et al.
attribution name: Fang et al.

A bZIP transcription factor, PqbZIP1, is involved in the plant defense response of American ginseng
type: item
type: AcademicArticle
description: American ginseng (Panax quinquefolius L.) is a perennial medicinal plant that has a long usage history in China. However, root rot, which is mainly caused by Fusarium solani can severely reduce the yield and quality of American ginseng, but no disease-resistant variety of American ginseng exists, and the resistance against this disease is not yet well understood. Thus, it is very urgent to analyze the interaction mechanism regulating the interactions between American ginseng and F. solani to mine disease resistance genes. Using transcriptome data and quantitative polymerase chain reaction (qPCR), we screened the transcription factor PqbZIP1 in response to induction by chitin. Yeast self-activation and subcellular localization experiments proved that PqbZIP1 showed transcriptional activity and was localized in the plant nucleus. In addition, qPCR showed that the highest relative expression level was in the roots, wherein chitin and F. solani inhibited and activated the expression of PqbZIP1, respectively, in American ginseng. Additionally, PqbZIP1 significantly inhibited the growth of the Pseudomonas syringae pv. tomato D36E strain in Nicotiana benthamiana, where expressing PqbZIP1 in N. benthamiana increased the jasmonic acid, salicylic acid, and abscisic acid content. Furthermore, PqbZIP1 expression was continually increased upon inoculation with F. solani. Hence, this study revealed that the PqbZIP1 transcription factor might mediate multiple hormonal signaling pathway to modulate root rot disease resistance in American ginseng, and provided important information to breed disease-resistant American ginseng.
format: application/pdf
format: text/html
creator: Shanshan Yang
creator: Xiaoxiao Zhang
creator: Ximei Zhang
creator: Yanmeng Bi
creator: Weiwei Gao
subject: Agricultural Science
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.12939
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: American ginseng (Panax quinquefolius L.) is a perennial medicinal plant that has a long usage history in China. However, root rot, which is mainly caused by Fusarium solani can severely reduce the yield and quality of American ginseng, but no disease-resistant variety of American ginseng exists, and the resistance against this disease is not yet well understood. Thus, it is very urgent to analyze the interaction mechanism regulating the interactions between American ginseng and F. solani to mine disease resistance genes. Using transcriptome data and quantitative polymerase chain reaction (qPCR), we screened the transcription factor PqbZIP1 in response to induction by chitin. Yeast self-activation and subcellular localization experiments proved that PqbZIP1 showed transcriptional activity and was localized in the plant nucleus. In addition, qPCR showed that the highest relative expression level was in the roots, wherein chitin and F. solani inhibited and activated the expression of PqbZIP1, respectively, in American ginseng. Additionally, PqbZIP1 significantly inhibited the growth of the Pseudomonas syringae pv. tomato D36E strain in Nicotiana benthamiana, where expressing PqbZIP1 in N. benthamiana increased the jasmonic acid, salicylic acid, and abscisic acid content. Furthermore, PqbZIP1 expression was continually increased upon inoculation with F. solani. Hence, this study revealed that the PqbZIP1 transcription factor might mediate multiple hormonal signaling pathway to modulate root rot disease resistance in American ginseng, and provided important information to breed disease-resistant American ginseng.
bibliographic citation: Yang et al. (2022) A bZIP transcription factor, PqbZIP1, is involved in the plant defense response of American ginseng. PeerJ 10:e12939 https://doi.org/10.7717/peerj.12939
date submitted: 2021-08-23
date accepted: 2022-01-24
issued: 2022-03-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Shanshan
author list: Agent
  family name: Zhang
  given name: Xiaoxiao
author list: Agent
  family name: Zhang
  given name: Ximei
author list: Agent
  family name: Bi
  given name: Yanmeng
author list: Agent
  family name: Gao
  given name: Weiwei
doi: 10.7717/peerj.12939
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-08
copyright: © 2022 Yang et al.
attribution name: Yang et al.

Associations between the rs5498 (A > G) and rs281432 (C > G) polymorphisms of the ICAM1 gene and atherosclerotic cardiovascular disease risk, including hypercholesterolemia
type: item
type: AcademicArticle
description: Background Atherosclerotic cardiovascular disease (ASCVD) originates from complex risk factors, including age, gender, dyslipidemia, obesity, race, genetic and genetic variation. ICAM1 gene polymorphisms are a significant risk factor for ASCVD. However, the impact of the rs5498 and rs281432 polymorphisms on the prevalence of hypercholesterolemia (HCL) has not been reported. Therefore, we determine the relationships between single nucleotide polymorphisms (SNPs), including rs5498 and rs281432 on Intercellular adhesion molecule 1 gene (ICAM1) and ASCVD susceptibility in patients with HCL. Methods The clinical characteristics of 278 participants were assessed, and classified to groups having HCL and without HCL. ICAM1 SNPs genotyping was performed by DNA sequencing, and ICAM1 expression was measured using real-time PCR. Results Positive dominant model rs5498 participants had twice the risk of HCL (95% confidence interval (CI): [1.24–3.23], P = 0.005). The frequency of the G allele in rs5498 was 1.69 times higher in participants with HCL than in controls (95% CI [1.15–2.47], P = 0.007). Participants with the rs5498 AG or GG variants and high ICAM1 mRNA expression (≥3.12) had 2.49 times the risk (95% CI [1.42–4.38], P = 0.001), and those with a high LDL-C concentration (≥3.36 mmol/L) had 2.09 times the risk (95% CI [1.19–3.66], P = 0.010) of developing ASCVD compared with those with low ICAM1 mRNA and LDL-C levels. Interestingly, participants carrying the rs5498 AG or GG variants who had tachycardia (resting heart rates (RHRs) >100 beats/min) had a 5.02-times higher risk than those with a lower RHR (95% CI [1.35–18.63], P = 0.016). Conclusions It may consider the G allele in ICAM1 rs5498 is associated with a higher risk of ASCVD in Thai people with HCL, and is also positively associated with ICAM1 mRNA expression, LDL-C concentration, and RHR.
format: application/pdf
format: text/html
creator: Naruemon Wechjakwen
creator: Amornrat Aroonnual
creator: Pattaneeya Prangthip
creator: Ngamphol Soonthornworasiri
creator: Pornpimol Panprathip Phienluphon
creator: Jirayu Lainampetch
creator: Karunee Kwanbunjan
subject: Bioinformatics
subject: Cardiology
subject: Epidemiology
subject: Medical Genetics
subject: Metabolic Sciences
description: doi:10.7717/peerj.12972
publisher: PeerJ Inc.
rights: © 2022 Wechjakwen et al.
abstract: Background Atherosclerotic cardiovascular disease (ASCVD) originates from complex risk factors, including age, gender, dyslipidemia, obesity, race, genetic and genetic variation. ICAM1 gene polymorphisms are a significant risk factor for ASCVD. However, the impact of the rs5498 and rs281432 polymorphisms on the prevalence of hypercholesterolemia (HCL) has not been reported. Therefore, we determine the relationships between single nucleotide polymorphisms (SNPs), including rs5498 and rs281432 on Intercellular adhesion molecule 1 gene (ICAM1) and ASCVD susceptibility in patients with HCL. Methods The clinical characteristics of 278 participants were assessed, and classified to groups having HCL and without HCL. ICAM1 SNPs genotyping was performed by DNA sequencing, and ICAM1 expression was measured using real-time PCR. Results Positive dominant model rs5498 participants had twice the risk of HCL (95% confidence interval (CI): [1.24–3.23], P = 0.005). The frequency of the G allele in rs5498 was 1.69 times higher in participants with HCL than in controls (95% CI [1.15–2.47], P = 0.007). Participants with the rs5498 AG or GG variants and high ICAM1 mRNA expression (≥3.12) had 2.49 times the risk (95% CI [1.42–4.38], P = 0.001), and those with a high LDL-C concentration (≥3.36 mmol/L) had 2.09 times the risk (95% CI [1.19–3.66], P = 0.010) of developing ASCVD compared with those with low ICAM1 mRNA and LDL-C levels. Interestingly, participants carrying the rs5498 AG or GG variants who had tachycardia (resting heart rates (RHRs) >100 beats/min) had a 5.02-times higher risk than those with a lower RHR (95% CI [1.35–18.63], P = 0.016). Conclusions It may consider the G allele in ICAM1 rs5498 is associated with a higher risk of ASCVD in Thai people with HCL, and is also positively associated with ICAM1 mRNA expression, LDL-C concentration, and RHR.
bibliographic citation: Wechjakwen et al. (2022) Associations between the rs5498 (A > G) and rs281432 (C > G) polymorphisms of the ICAM1 gene and atherosclerotic cardiovascular disease risk, including hypercholesterolemia. PeerJ 10:e12972 https://doi.org/10.7717/peerj.12972
date submitted: 2021-10-26
date accepted: 2022-01-30
issued: 2022-03-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wechjakwen
  given name: Naruemon
author list: Agent
  family name: Aroonnual
  given name: Amornrat
author list: Agent
  family name: Prangthip
  given name: Pattaneeya
author list: Agent
  family name: Soonthornworasiri
  given name: Ngamphol
author list: Agent
  family name: Phienluphon
  given name: Pornpimol Panprathip
author list: Agent
  family name: Lainampetch
  given name: Jirayu
author list: Agent
  family name: Kwanbunjan
  given name: Karunee
doi: 10.7717/peerj.12972
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-08
copyright: ©2022 Wechjakwen et al.
attribution name: Wechjakwen et al.

Microbial community spatial structures in Luzhou-flavored liquor pit muds with different brewing materials
type: item
type: AcademicArticle
description: Background Although studies have shown that Bacteroidetes, Clostridiales, and Lactobacillales are the main components of the microbial community in pit mud during the brewing of Luzhou-flavored liquor, little is known about the effect of brewing materials on spatial structures of this microbiome. Methods High-throughput sequencing of the V4–V5 region of prokaryotic 16S rRNA gene was performed to analyze the microbial community diversity and spatial heterogeneity in Luzhou-flavored liquor pit muds with different brewing ingredients. The structural characteristics and heterogeneous spatial distribution of the pit mud microbial communities were examined using bioinformatics and multivariate statistical analysis methods. Results Our results showed that Euryarchaeota, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Firmicutes, Proteobacteria, Synergistetes, Tenericutes, and WWE1 were the dominant phyla in the pit mud microbiome. The Shannon and Simpson indices of the pit mud microbiome with three grains (M3G) in the upper layer were significantly lower than those in middle layer and bottom, whereas those of the pit mud microbiome with five grains (M5G) in bottom were significantly lower than those in middle layer (p < 0.05). There were significant differences in the microbial community compositions between the pit muds with different brewing ingredients and locations in the same pit (p < 0.05). T78 of Anaerolinaceae, Butyrivibrio, Dehalobacter_Syntrophobotulus, Desulfosporosinus, Asteroleplasma, and vadinCA02 of Synergistaceae were significantly enriched in M3G, whereas Prevotella, Vagococcus, Caldicoprobacter, Butyrivibrio, Coprococcus, Dorea, Sporanaerobacter, Tepidimicrobium, TissierellaSoehngenia, RFN20 of Erysipelotrichaceae, Sutterella, 125ds10 of Alteromonadales, Vibrio, and Sphaerochaeta were significantly enriched in M5G. This study provides a theoretical basis for exploring the influence of brewing ingredients in pit muds on the production of Luzhou-flavo…
format: application/pdf
format: text/html
creator: Jinjin Li
creator: Hongzhao Sun
creator: Qian Wang
creator: Yunfei Cai
creator: Zhu Shi
creator: Jianlei Jia
creator: Lei Zheng
creator: Ru Jiang
creator: Lingmei Gao
subject: Biochemistry
subject: Biotechnology
subject: Food Science and Technology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.12987
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background Although studies have shown that Bacteroidetes, Clostridiales, and Lactobacillales are the main components of the microbial community in pit mud during the brewing of Luzhou-flavored liquor, little is known about the effect of brewing materials on spatial structures of this microbiome. Methods High-throughput sequencing of the V4–V5 region of prokaryotic 16S rRNA gene was performed to analyze the microbial community diversity and spatial heterogeneity in Luzhou-flavored liquor pit muds with different brewing ingredients. The structural characteristics and heterogeneous spatial distribution of the pit mud microbial communities were examined using bioinformatics and multivariate statistical analysis methods. Results Our results showed that Euryarchaeota, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Firmicutes, Proteobacteria, Synergistetes, Tenericutes, and WWE1 were the dominant phyla in the pit mud microbiome. The Shannon and Simpson indices of the pit mud microbiome with three grains (M3G) in the upper layer were significantly lower than those in middle layer and bottom, whereas those of the pit mud microbiome with five grains (M5G) in bottom were significantly lower than those in middle layer (p < 0.05). There were significant differences in the microbial community compositions between the pit muds with different brewing ingredients and locations in the same pit (p < 0.05). T78 of Anaerolinaceae, Butyrivibrio, Dehalobacter_Syntrophobotulus, Desulfosporosinus, Asteroleplasma, and vadinCA02 of Synergistaceae were significantly enriched in M3G, whereas Prevotella, Vagococcus, Caldicoprobacter, Butyrivibrio, Coprococcus, Dorea, Sporanaerobacter, Tepidimicrobium, TissierellaSoehngenia, RFN20 of Erysipelotrichaceae, Sutterella, 125ds10 of Alteromonadales, Vibrio, and Sphaerochaeta were significantly enriched in M5G. This study provides a theoretical basis for exploring the influence of brewing ingredients in pit muds on the production of Luzhou-flavo…
bibliographic citation: Li et al. (2022) Microbial community spatial structures in Luzhou-flavored liquor pit muds with different brewing materials. PeerJ 10:e12987 https://doi.org/10.7717/peerj.12987
date submitted: 2021-11-26
date accepted: 2022-02-01
issued: 2022-03-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jinjin
author list: Agent
  family name: Sun
  given name: Hongzhao
author list: Agent
  family name: Wang
  given name: Qian
author list: Agent
  family name: Cai
  given name: Yunfei
author list: Agent
  family name: Shi
  given name: Zhu
author list: Agent
  family name: Jia
  given name: Jianlei
author list: Agent
  family name: Zheng
  given name: Lei
author list: Agent
  family name: Jiang
  given name: Ru
author list: Agent
  family name: Gao
  given name: Lingmei
doi: 10.7717/peerj.12987
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-08
copyright: © 2022 Li et al.
attribution name: Li et al.

Abubidentin A, New Oleanane-type Triterpene Ester from Abutilon bidentatum and its antioxidant, cholinesterase and antimicrobial activities
type: item
type: AcademicArticle
description: Background This work describes the phytochemical and biological investigation of aerial parts of Abutilon bidentatum Hochst. Of Saudi origin. Methodology Petroleum ether fraction of ethanolic extract A. bidentatum was fractionated on a silica gel column and further purified with different chromatographic procedures for the isolation of chemical compounds. The chemical structures of all the pure isolated compounds were elucidated by the interpretation of their spectral data using IR, UV, 1H, 13C NMR, and MS spectroscopy and chemical methods (alkaline hydrolysis) as well as comparison with data reported in the literature. The extract and isolated compounds were evaluated for antioxidant, cholinesterase inhibitory, and antimicrobial activities. Results A new oleanane-type triterpene ester, namely abubidentin A (3) (α, 3β, 30-trihydroxy-29-carboxy-olean-9(11), 12-diene-3-dotriacontanoate), along with two known compounds: 2-hydroxydocosanoic acid (1) and stigmasta-22-ene-3-β-ol (2) were isolated from the aerial parts of Abutilon bidentatum Hochst. (Malvaceae). Concerning the biological potential, the abubidentinA displayed antioxidant, cholinesterase inhibitory and antimicrobial activities. AbubidentinA possessed strong antioxidant activity against DPPH and ABTS+ radical scavenging assays. This new triterpene exhibited high inhibition against acetylcholinesterase (IC50 38.13 ± 0.07 µgmL−1) and butyrylcholinesterase (IC50 32.68 ± 0.37 µgmL−1). Abubidentin A displayed promising antimicrobial activity against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus (125–150 µgmL−1). Conclusion These findings suggest A. bidentatum can contribute as a source of new biologically active compounds, especially antioxidants and antimicrobial agents.
format: application/pdf
format: text/html
creator: Gadah A. Al-Hamoud
creator: Nawal M. Al-Musayeib
creator: Musarat Amina
creator: Sabrin R.M. Ibrahim
subject: Biochemistry
subject: Biomolecules
subject: Bioorganic Chemistry
subject: Natural Products
description: doi:10.7717/peerj.13040
publisher: PeerJ Inc.
rights: © 2022 Al-Hamoud et al.
abstract: Background This work describes the phytochemical and biological investigation of aerial parts of Abutilon bidentatum Hochst. Of Saudi origin. Methodology Petroleum ether fraction of ethanolic extract A. bidentatum was fractionated on a silica gel column and further purified with different chromatographic procedures for the isolation of chemical compounds. The chemical structures of all the pure isolated compounds were elucidated by the interpretation of their spectral data using IR, UV, 1H, 13C NMR, and MS spectroscopy and chemical methods (alkaline hydrolysis) as well as comparison with data reported in the literature. The extract and isolated compounds were evaluated for antioxidant, cholinesterase inhibitory, and antimicrobial activities. Results A new oleanane-type triterpene ester, namely abubidentin A (3) (α, 3β, 30-trihydroxy-29-carboxy-olean-9(11), 12-diene-3-dotriacontanoate), along with two known compounds: 2-hydroxydocosanoic acid (1) and stigmasta-22-ene-3-β-ol (2) were isolated from the aerial parts of Abutilon bidentatum Hochst. (Malvaceae). Concerning the biological potential, the abubidentinA displayed antioxidant, cholinesterase inhibitory and antimicrobial activities. AbubidentinA possessed strong antioxidant activity against DPPH and ABTS+ radical scavenging assays. This new triterpene exhibited high inhibition against acetylcholinesterase (IC50 38.13 ± 0.07 µgmL−1) and butyrylcholinesterase (IC50 32.68 ± 0.37 µgmL−1). Abubidentin A displayed promising antimicrobial activity against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus (125–150 µgmL−1). Conclusion These findings suggest A. bidentatum can contribute as a source of new biologically active compounds, especially antioxidants and antimicrobial agents.
bibliographic citation: Al-Hamoud et al. (2022) Abubidentin A, New Oleanane-type Triterpene Ester from Abutilon bidentatum and its antioxidant, cholinesterase and antimicrobial activities. PeerJ 10:e13040 https://doi.org/10.7717/peerj.13040
date submitted: 2021-10-25
date accepted: 2022-02-09
issued: 2022-03-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al-Hamoud
  given name: Gadah A.
author list: Agent
  family name: Al-Musayeib
  given name: Nawal M.
author list: Agent
  family name: Amina
  given name: Musarat
author list: Agent
  family name: Ibrahim
  given name: Sabrin R.M.
doi: 10.7717/peerj.13040
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-08
copyright: ©2022 Al-Hamoud et al.
attribution name: Al-Hamoud et al.

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