PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Prognostic significance of SH2D5 expression in lung adenocarcinoma and its relation to immune cell infiltration
items: A long non-coding RNA PelncRNA1 is involved in Phyllostachys edulis response to UV-B stress
items: Topological feature generation for link prediction in biological networks
items: Comparison of the chloroplast genomes and phylogenomic analysis of Elaeocarpaceae
items: Botanical characteristics, chemical components, biological activity, and potential applications of mangosteen
items: 24-Epibrassinolide confers zinc stress tolerance in watermelon seedlings through modulating antioxidative capacities and lignin accumulation
items: Molecular analysis of the 14-3-3 genes in Panax ginseng and their responses to heat stress
items: Integrated analysis of lncRNAs, mRNAs, and TFs to identify network modules underlying diterpenoid biosynthesis in Salvia miltiorrhiza
items: Self-reported interoceptive accuracy and interoceptive attention differentially correspond to measures of visual attention and self-regard
items: Prediction of the spread of African swine fever through pig and carcass movements in Thailand using a network analysis and diffusion model

Prognostic significance of SH2D5 expression in lung adenocarcinoma and its relation to immune cell infiltration
type: item
type: AcademicArticle
description: Objective Through analyzing the SH2D5 expression profiles, clinical features, and immune infiltration in lung adenocarcinoma (LUAD), the study was intended to discuss the correlations of SH2D5 with prognosis and immune infiltration in LUAD. Methods We downloaded transcriptome and clinical data of LUAD patients from TCGA, GEO, and CCLE databases. Sangerbox, R language, GEPIA, UALCAN, and Kaplan-Meier Plotter were adopted to analyze the SH2D5 expression patterns, prognosis, and clinical features. Spearman correlation analysis was performed to determine the association between SH2D5 expression and immune cell infiltration and immune checkpoint genes. The miRNA-SH2D5 relations were predicted by miRDB and starbase. Lastly, quantitative PCR, IHC and Western blot were implemented for validation. Results A prominent up-regulation of SH2D5 was noted in the LUAD group relative to the normal group, which was validated by quantitative PCR, IHC and Western blot. SH2D5 expression was inversely related to overall survival (OS) of LUAD patients as well as B cell immune infiltration. Additionally, SH2D5 expression was negatively correlated with dendritic cells resting (p < 0.001), plasma cells (p < 0.001), mast cells resting (p = 0.031) and T cells CD4 memory resting (p = 0.036) in LUAD patients with abundant SH2D5 expression correlated with poor prognosis. Furthermore, enrichment analysis suggested that SH2D5 was associated with lung cancer and immunity. Lastly, we investigated the relationship between the expression of SH2D5 and the use of antitumor drugs. Conclusion High SH2D5 expression shares an association with unfavorable prognosis in LUAD, and SH2D5 may also provide new ideas for immunotherapy as a potential therapeutic target.
format: application/pdf
format: text/html
creator: Hao Zhou
creator: Shengjun Li
creator: Yuansheng Lin
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Medical Genetics
description: doi:10.7717/peerj.15238
publisher: PeerJ Inc.
rights: © 2023 Zhou et al.
abstract: Objective Through analyzing the SH2D5 expression profiles, clinical features, and immune infiltration in lung adenocarcinoma (LUAD), the study was intended to discuss the correlations of SH2D5 with prognosis and immune infiltration in LUAD. Methods We downloaded transcriptome and clinical data of LUAD patients from TCGA, GEO, and CCLE databases. Sangerbox, R language, GEPIA, UALCAN, and Kaplan-Meier Plotter were adopted to analyze the SH2D5 expression patterns, prognosis, and clinical features. Spearman correlation analysis was performed to determine the association between SH2D5 expression and immune cell infiltration and immune checkpoint genes. The miRNA-SH2D5 relations were predicted by miRDB and starbase. Lastly, quantitative PCR, IHC and Western blot were implemented for validation. Results A prominent up-regulation of SH2D5 was noted in the LUAD group relative to the normal group, which was validated by quantitative PCR, IHC and Western blot. SH2D5 expression was inversely related to overall survival (OS) of LUAD patients as well as B cell immune infiltration. Additionally, SH2D5 expression was negatively correlated with dendritic cells resting (p < 0.001), plasma cells (p < 0.001), mast cells resting (p = 0.031) and T cells CD4 memory resting (p = 0.036) in LUAD patients with abundant SH2D5 expression correlated with poor prognosis. Furthermore, enrichment analysis suggested that SH2D5 was associated with lung cancer and immunity. Lastly, we investigated the relationship between the expression of SH2D5 and the use of antitumor drugs. Conclusion High SH2D5 expression shares an association with unfavorable prognosis in LUAD, and SH2D5 may also provide new ideas for immunotherapy as a potential therapeutic target.
bibliographic citation: Zhou et al. (2023) Prognostic significance of SH2D5 expression in lung adenocarcinoma and its relation to immune cell infiltration. PeerJ 11:e15238 https://doi.org/10.7717/peerj.15238
date submitted: 2022-09-21
date accepted: 2023-03-28
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Hao
author list: Agent
  family name: Li
  given name: Shengjun
author list: Agent
  family name: Lin
  given name: Yuansheng
doi: 10.7717/peerj.15238
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Zhou et al.
attribution name: Zhou et al.

A long non-coding RNA PelncRNA1 is involved in Phyllostachys edulis response to UV-B stress
type: item
type: AcademicArticle
description: Phyllostachys edulis (moso bamboo) is China’s most widespread bamboo species, with significant economic and ecological values. Long non-coding RNA (lncRNA) is a type of regulatory RNA that is longer than 200 nucleotides and incapable of encoding proteins, and is frequently involved in regulating biotic and abiotic stress and plant development. However, the biological functions of lncRNA in moso bamboo are unknown. In this study, a lncRNA (named PelncRNA1) differentially expressed following UV-B treatment was discovered in the whole transcriptome sequencing database of moso bamboo. The target genes were filtered and defined by correlation analysis of PelncRNA1 and gene expression pattern. The expression levels of PelncRNA1 and its target genes were verified using qRT-PCR. The results demonstrated that the expression levels of PelncRNA1 and its target genes increased during UV-B treatment. In Arabidopsis transgenic seedlings and moso bamboo protoplasts, PelncRNA1 was discovered to influence the expression of its target genes when overexpressed. In addition, transgenic Arabidopsis showed higher tolerance to UV-B stress. These results suggest that PelncRNA1 and its target genes are involved in the response of moso bamboo to UV-B stress. The novel findings would contribute to our understanding of how lncRNAs regulate the response to abiotic stresses in moso bamboo.
format: application/pdf
format: text/html
creator: Lu Yu
creator: Yiqian Ding
creator: Mingbing Zhou
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15243
publisher: PeerJ Inc.
rights: © 2023 Yu et al.
abstract: Phyllostachys edulis (moso bamboo) is China’s most widespread bamboo species, with significant economic and ecological values. Long non-coding RNA (lncRNA) is a type of regulatory RNA that is longer than 200 nucleotides and incapable of encoding proteins, and is frequently involved in regulating biotic and abiotic stress and plant development. However, the biological functions of lncRNA in moso bamboo are unknown. In this study, a lncRNA (named PelncRNA1) differentially expressed following UV-B treatment was discovered in the whole transcriptome sequencing database of moso bamboo. The target genes were filtered and defined by correlation analysis of PelncRNA1 and gene expression pattern. The expression levels of PelncRNA1 and its target genes were verified using qRT-PCR. The results demonstrated that the expression levels of PelncRNA1 and its target genes increased during UV-B treatment. In Arabidopsis transgenic seedlings and moso bamboo protoplasts, PelncRNA1 was discovered to influence the expression of its target genes when overexpressed. In addition, transgenic Arabidopsis showed higher tolerance to UV-B stress. These results suggest that PelncRNA1 and its target genes are involved in the response of moso bamboo to UV-B stress. The novel findings would contribute to our understanding of how lncRNAs regulate the response to abiotic stresses in moso bamboo.
bibliographic citation: Yu et al. (2023) A long non-coding RNA PelncRNA1 is involved in Phyllostachys edulis response to UV-B stress. PeerJ 11:e15243 https://doi.org/10.7717/peerj.15243
date submitted: 2022-12-15
date accepted: 2023-03-28
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Lu
author list: Agent
  family name: Ding
  given name: Yiqian
author list: Agent
  family name: Zhou
  given name: Mingbing
doi: 10.7717/peerj.15243
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Yu et al.
attribution name: Yu et al.

Topological feature generation for link prediction in biological networks
type: item
type: AcademicArticle
description: Graph or network embedding is a powerful method for extracting missing or potential information from interactions between nodes in biological networks. Graph embedding methods learn representations of nodes and interactions in a graph with low-dimensional vectors, which facilitates research to predict potential interactions in networks. However, most graph embedding methods suffer from high computational costs in the form of high computational complexity of the embedding methods and learning times of the classifier, as well as the high dimensionality of complex biological networks. To address these challenges, in this study, we use the Chopper algorithm as an alternative approach to graph embedding, which accelerates the iterative processes and thus reduces the running time of the iterative algorithms for three different (nervous system, blood, heart) undirected protein-protein interaction (PPI) networks. Due to the high dimensionality of the matrix obtained after the embedding process, the data are transformed into a smaller representation by applying feature regularization techniques. We evaluated the performance of the proposed method by comparing it with state-of-the-art methods. Extensive experiments demonstrate that the proposed approach reduces the learning time of the classifier and performs better in link prediction. We have also shown that the proposed embedding method is faster than state-of-the-art methods on three different PPI datasets.
format: application/pdf
format: text/html
creator: Mustafa Temiz
creator: Burcu Bakir-Gungor
creator: Pınar Güner Şahan
creator: Mustafa Coskun
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.15313
publisher: PeerJ Inc.
rights: © 2023 Temiz et al.
abstract: Graph or network embedding is a powerful method for extracting missing or potential information from interactions between nodes in biological networks. Graph embedding methods learn representations of nodes and interactions in a graph with low-dimensional vectors, which facilitates research to predict potential interactions in networks. However, most graph embedding methods suffer from high computational costs in the form of high computational complexity of the embedding methods and learning times of the classifier, as well as the high dimensionality of complex biological networks. To address these challenges, in this study, we use the Chopper algorithm as an alternative approach to graph embedding, which accelerates the iterative processes and thus reduces the running time of the iterative algorithms for three different (nervous system, blood, heart) undirected protein-protein interaction (PPI) networks. Due to the high dimensionality of the matrix obtained after the embedding process, the data are transformed into a smaller representation by applying feature regularization techniques. We evaluated the performance of the proposed method by comparing it with state-of-the-art methods. Extensive experiments demonstrate that the proposed approach reduces the learning time of the classifier and performs better in link prediction. We have also shown that the proposed embedding method is faster than state-of-the-art methods on three different PPI datasets.
bibliographic citation: Temiz et al. (2023) Topological feature generation for link prediction in biological networks. PeerJ 11:e15313 https://doi.org/10.7717/peerj.15313
date submitted: 2022-11-14
date accepted: 2023-04-06
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Temiz
  given name: Mustafa
author list: Agent
  family name: Bakir-Gungor
  given name: Burcu
author list: Agent
  family name: Güner Şahan
  given name: Pınar
author list: Agent
  family name: Coskun
  given name: Mustafa
doi: 10.7717/peerj.15313
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: © 2023 Temiz et al.
attribution name: Temiz et al.

Comparison of the chloroplast genomes and phylogenomic analysis of Elaeocarpaceae
type: item
type: AcademicArticle
description: Background Elaeocarpaceae is a vital family in tropical and subtropical forests. Compared with the important position of Elaeocarpaceae species in forest ecosystem and the concern of medicinal value, the most research on Elaeocarpaceae are classification and taxonomy. Molecular systematics has corrected the morphological misjudgment, and it belongs to Oxalidales. Phylogenetic and divergence time estimates of Elaeocarpaceae is mostly constructed by using chloroplast gene fragments. At present, although there are reports on the chloroplast structure of Elaeocarpaceae, a comprehensive analysis of the chloroplast structure of Elaeocarpaceae is lacking. Methods To understand the variation in chloroplast sequence size and structure in Elaeocarpaceae, the chloroplast genomes of nine species were sequenced using the Illumina HiSeq 2500 platform and further assembled and annotated with Elaeocarpus japonicus and Sloanea sinensis (family Elaeocarpaceae) as references. A phylogenomic tree was constructed based on the complete chloroplast genomes of the 11 species representing five genera of Elaeocarpaceae. Chloroplast genome characteristics were examined by using Circoletto and IRscope software. Results The results revealed the following: (a) The 11 sequenced chloroplast genomes ranged in size from 157,546 to 159,400 bp. (b) The chloroplast genomes of Elaeocarpus, Sloanea, Crinodendron and Vallea lacked the rpl32 gene in the small single-copy (SSC) region. The large single-copy (LSC) region of the chloroplast genomes lacked the ndhK gene in Elaeocarpus, Vallea stipularis, and Aristotelia fruticosa. The LSC region of the chloroplast genomes lacked the infA gene in genus Elaeocarpus and Crinodendron patagua. (c) Through inverted repeat (IR) expansion and contraction analysis, a significant difference was found between the LSC/IRB and IRA/LSC boundaries among these species. Rps3 was detected in the neighboring regions of the LSC and IRb regions in Elaeocarpus. (d) Phylogenomic ana…
format: application/pdf
format: text/html
creator: Yihui Wang
creator: Yifei Xie
creator: Jiayi Jin
creator: Jinyue Li
creator: Xiangdong Qiu
creator: Yang Tong
creator: Zhongyang Li
creator: Zhixiang Zhang
creator: Wenling Lai
subject: Biogeography
subject: Evolutionary Studies
subject: Molecular Biology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.15322
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Background Elaeocarpaceae is a vital family in tropical and subtropical forests. Compared with the important position of Elaeocarpaceae species in forest ecosystem and the concern of medicinal value, the most research on Elaeocarpaceae are classification and taxonomy. Molecular systematics has corrected the morphological misjudgment, and it belongs to Oxalidales. Phylogenetic and divergence time estimates of Elaeocarpaceae is mostly constructed by using chloroplast gene fragments. At present, although there are reports on the chloroplast structure of Elaeocarpaceae, a comprehensive analysis of the chloroplast structure of Elaeocarpaceae is lacking. Methods To understand the variation in chloroplast sequence size and structure in Elaeocarpaceae, the chloroplast genomes of nine species were sequenced using the Illumina HiSeq 2500 platform and further assembled and annotated with Elaeocarpus japonicus and Sloanea sinensis (family Elaeocarpaceae) as references. A phylogenomic tree was constructed based on the complete chloroplast genomes of the 11 species representing five genera of Elaeocarpaceae. Chloroplast genome characteristics were examined by using Circoletto and IRscope software. Results The results revealed the following: (a) The 11 sequenced chloroplast genomes ranged in size from 157,546 to 159,400 bp. (b) The chloroplast genomes of Elaeocarpus, Sloanea, Crinodendron and Vallea lacked the rpl32 gene in the small single-copy (SSC) region. The large single-copy (LSC) region of the chloroplast genomes lacked the ndhK gene in Elaeocarpus, Vallea stipularis, and Aristotelia fruticosa. The LSC region of the chloroplast genomes lacked the infA gene in genus Elaeocarpus and Crinodendron patagua. (c) Through inverted repeat (IR) expansion and contraction analysis, a significant difference was found between the LSC/IRB and IRA/LSC boundaries among these species. Rps3 was detected in the neighboring regions of the LSC and IRb regions in Elaeocarpus. (d) Phylogenomic ana…
bibliographic citation: Wang et al. (2023) Comparison of the chloroplast genomes and phylogenomic analysis of Elaeocarpaceae. PeerJ 11:e15322 https://doi.org/10.7717/peerj.15322
date submitted: 2022-10-13
date accepted: 2023-04-10
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yihui
author list: Agent
  family name: Xie
  given name: Yifei
author list: Agent
  family name: Jin
  given name: Jiayi
author list: Agent
  family name: Li
  given name: Jinyue
author list: Agent
  family name: Qiu
  given name: Xiangdong
author list: Agent
  family name: Tong
  given name: Yang
author list: Agent
  family name: Li
  given name: Zhongyang
author list: Agent
  family name: Zhang
  given name: Zhixiang
author list: Agent
  family name: Lai
  given name: Wenling
doi: 10.7717/peerj.15322
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: © 2023 Wang et al.
attribution name: Wang et al.

Botanical characteristics, chemical components, biological activity, and potential applications of mangosteen
type: item
type: AcademicArticle
description: Garcinia mangostana L. (Mangosteen), a functional food, belongs to the Garcinaceae family and has various pharmacological effects, including anti-oxidative, anti-inflammatory, anticancer, antidiabetic, and neuroprotective effects. Mangosteen has abundant chemical constituents with powerful pharmacological effects. After searching scientific literature databases, including PubMed, Science Direct, Research Gate, Web of Science, VIP, Wanfang, and CNKI, we summarized the traditional applications, botanical features, chemical composition, and pharmacological effects of mangosteen. Further, we revealed the mechanism by which it improves health and treats disease. These findings provide a theoretical basis for mangosteen’s future clinical use and will aid doctors and researchers who investigate the biological activity and functions of food.
format: application/pdf
format: text/html
creator: Chenchen Bi
creator: Hang Xu
creator: Jingru Yu
creator: Zhinan Ding
creator: Zheng Liu
subject: Biochemistry
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.15329
publisher: PeerJ Inc.
rights: © 2023 Bi et al.
abstract: Garcinia mangostana L. (Mangosteen), a functional food, belongs to the Garcinaceae family and has various pharmacological effects, including anti-oxidative, anti-inflammatory, anticancer, antidiabetic, and neuroprotective effects. Mangosteen has abundant chemical constituents with powerful pharmacological effects. After searching scientific literature databases, including PubMed, Science Direct, Research Gate, Web of Science, VIP, Wanfang, and CNKI, we summarized the traditional applications, botanical features, chemical composition, and pharmacological effects of mangosteen. Further, we revealed the mechanism by which it improves health and treats disease. These findings provide a theoretical basis for mangosteen’s future clinical use and will aid doctors and researchers who investigate the biological activity and functions of food.
bibliographic citation: Bi et al. (2023) Botanical characteristics, chemical components, biological activity, and potential applications of mangosteen. PeerJ 11:e15329 https://doi.org/10.7717/peerj.15329
date submitted: 2023-01-10
date accepted: 2023-04-10
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bi
  given name: Chenchen
author list: Agent
  family name: Xu
  given name: Hang
author list: Agent
  family name: Yu
  given name: Jingru
author list: Agent
  family name: Ding
  given name: Zhinan
author list: Agent
  family name: Liu
  given name: Zheng
doi: 10.7717/peerj.15329
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Bi et al.
attribution name: Bi et al.

24-Epibrassinolide confers zinc stress tolerance in watermelon seedlings through modulating antioxidative capacities and lignin accumulation
type: item
type: AcademicArticle
description: Zinc (Zn) is an important element in plants, but over-accumulation of Zn is harmful. It is well-known that brassinolide (BR) plays a key role in the regulation of abiotic stress responses in plants. However, the effects of brassinolide on alleviating Zn phytotoxicity in watermelon (Citrullus lanatus L.) seedlings are not clear. The purpose of this study was to study the effect of 24-epibrassinolide (EBR, one of the bioactive BRs) on Zn tolerance of watermelon seedlings and its potential resistance mechanism. Exposure to excessive Zn significantly inhibited shoot and root fresh weight of watermelon, but this could be significantly alleviated by the optimum 0.05 μM EBR. Exogenous spraying EBR increased the pigments and alleviated oxidative damage caused by Zn through reducing Zn accumulation and the levels of reactive oxygen species (ROS) and malonaldehyde (MDA) and increasing the activities of antioxidant enzymes and contents of ascorbic acid (AsA) and glutathione (GSH). Importantly, the relative mRNA levels of antioxidant genesincluding Cu/Zn-superoxidedismutase (Cu-Zn SOD), catalase (CAT), ascorbic acid peroxidase (APX), and glutathione reductase (GR) were significantly induced after EBR treatment. In addition, EBR pre-treatment induced lignin accumulation under Zn stress, and the activity of phenylalanine ammonia-lyase (PAL) and 4-coumaric ligase (4CL), two key enzymes regulating lignin synthesis, also tended to be consistent. Collectively, the present research proves the beneficial effects of EBR in response to Zn stress through enhancing antioxidant defense and lignin accumulation and provides a new insight into the mechanism of BR-enhancing heavy metal tolerance.
format: application/pdf
format: text/html
creator: Xuefang Liu
creator: Quanwen Zhu
creator: Wentao Liu
creator: Jun Zhang
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15330
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Zinc (Zn) is an important element in plants, but over-accumulation of Zn is harmful. It is well-known that brassinolide (BR) plays a key role in the regulation of abiotic stress responses in plants. However, the effects of brassinolide on alleviating Zn phytotoxicity in watermelon (Citrullus lanatus L.) seedlings are not clear. The purpose of this study was to study the effect of 24-epibrassinolide (EBR, one of the bioactive BRs) on Zn tolerance of watermelon seedlings and its potential resistance mechanism. Exposure to excessive Zn significantly inhibited shoot and root fresh weight of watermelon, but this could be significantly alleviated by the optimum 0.05 μM EBR. Exogenous spraying EBR increased the pigments and alleviated oxidative damage caused by Zn through reducing Zn accumulation and the levels of reactive oxygen species (ROS) and malonaldehyde (MDA) and increasing the activities of antioxidant enzymes and contents of ascorbic acid (AsA) and glutathione (GSH). Importantly, the relative mRNA levels of antioxidant genesincluding Cu/Zn-superoxidedismutase (Cu-Zn SOD), catalase (CAT), ascorbic acid peroxidase (APX), and glutathione reductase (GR) were significantly induced after EBR treatment. In addition, EBR pre-treatment induced lignin accumulation under Zn stress, and the activity of phenylalanine ammonia-lyase (PAL) and 4-coumaric ligase (4CL), two key enzymes regulating lignin synthesis, also tended to be consistent. Collectively, the present research proves the beneficial effects of EBR in response to Zn stress through enhancing antioxidant defense and lignin accumulation and provides a new insight into the mechanism of BR-enhancing heavy metal tolerance.
bibliographic citation: Liu et al. (2023) 24-Epibrassinolide confers zinc stress tolerance in watermelon seedlings through modulating antioxidative capacities and lignin accumulation. PeerJ 11:e15330 https://doi.org/10.7717/peerj.15330
date submitted: 2022-12-15
date accepted: 2023-04-10
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xuefang
author list: Agent
  family name: Zhu
  given name: Quanwen
author list: Agent
  family name: Liu
  given name: Wentao
author list: Agent
  family name: Zhang
  given name: Jun
doi: 10.7717/peerj.15330
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: © 2023 Liu et al.
attribution name: Liu et al.

Molecular analysis of the 14-3-3 genes in Panax ginseng and their responses to heat stress
type: item
type: AcademicArticle
description: Background Panax Ginseng is a perennial and semi-shady herb with tremendous medicinal value. Due to its unique botanical characteristics, ginseng is vulnerable to various abiotic factors during its growth and development, especially in high temperatures. Proteins encoded by 14-3-3 genes form a highly conserved protein family that widely exists in eukaryotes. The 14-3-3 family regulates the vital movement of cells and plays an essential role in the response of plants to abiotic stresses, including high temperatures. Currently, there is no relevant research on the 14-3-3 genes of ginseng. Methods The identification of the ginseng 14-3-3 gene family was mainly based on ginseng genomic data and Hidden Markov Models (HMM). We used bioinformatics-related databases and tools to analyze the gene structure, physicochemical properties, cis-acting elements, gene ontology (GO), phylogenetic tree, interacting proteins, and transcription factor regulatory networks. We analyzed the transcriptome data of different ginseng tissues to clarify the expression pattern of the 14-3-3 gene family in ginseng. The expression level and modes of 14-3-3 genes under heat stress were analyzed by quantitative real-time PCR (qRT-PCR) technology to determine the genes in the 14-3-3 gene family responding to high-temperature stress. Results In this study, 42 14-3-3 genes were identified from the ginseng genome and renamed PgGF14-1 to PgGF14-42. Gene structure and evolutionary relationship research divided PgGF14s into epsilon (ε) and non-epsilon (non-ε) groups, mainly located in four evolutionary branches. The gene structure and motif remained highly consistent within a subgroup. The physicochemical properties and structure of the predicted PgGF14 proteins conformed to the essential characteristics of 14-3-3 proteins. RNA-seq results indicated that the detected PgGF14s existed in different organs and tissues but differed in abundance; their expression was higher in roots, stems, leaves, and fruits bu…
format: application/pdf
format: text/html
creator: Qi Wang
creator: Wenyue Peng
creator: Junbo Rong
creator: Mengyang Zhang
creator: Wenhao Jia
creator: Xiujuan Lei
creator: Yingping Wang
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15331
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Background Panax Ginseng is a perennial and semi-shady herb with tremendous medicinal value. Due to its unique botanical characteristics, ginseng is vulnerable to various abiotic factors during its growth and development, especially in high temperatures. Proteins encoded by 14-3-3 genes form a highly conserved protein family that widely exists in eukaryotes. The 14-3-3 family regulates the vital movement of cells and plays an essential role in the response of plants to abiotic stresses, including high temperatures. Currently, there is no relevant research on the 14-3-3 genes of ginseng. Methods The identification of the ginseng 14-3-3 gene family was mainly based on ginseng genomic data and Hidden Markov Models (HMM). We used bioinformatics-related databases and tools to analyze the gene structure, physicochemical properties, cis-acting elements, gene ontology (GO), phylogenetic tree, interacting proteins, and transcription factor regulatory networks. We analyzed the transcriptome data of different ginseng tissues to clarify the expression pattern of the 14-3-3 gene family in ginseng. The expression level and modes of 14-3-3 genes under heat stress were analyzed by quantitative real-time PCR (qRT-PCR) technology to determine the genes in the 14-3-3 gene family responding to high-temperature stress. Results In this study, 42 14-3-3 genes were identified from the ginseng genome and renamed PgGF14-1 to PgGF14-42. Gene structure and evolutionary relationship research divided PgGF14s into epsilon (ε) and non-epsilon (non-ε) groups, mainly located in four evolutionary branches. The gene structure and motif remained highly consistent within a subgroup. The physicochemical properties and structure of the predicted PgGF14 proteins conformed to the essential characteristics of 14-3-3 proteins. RNA-seq results indicated that the detected PgGF14s existed in different organs and tissues but differed in abundance; their expression was higher in roots, stems, leaves, and fruits bu…
bibliographic citation: Wang et al. (2023) Molecular analysis of the 14-3-3 genes in Panax ginseng and their responses to heat stress. PeerJ 11:e15331 https://doi.org/10.7717/peerj.15331
date submitted: 2023-02-03
date accepted: 2023-04-10
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Qi
author list: Agent
  family name: Peng
  given name: Wenyue
author list: Agent
  family name: Rong
  given name: Junbo
author list: Agent
  family name: Zhang
  given name: Mengyang
author list: Agent
  family name: Jia
  given name: Wenhao
author list: Agent
  family name: Lei
  given name: Xiujuan
author list: Agent
  family name: Wang
  given name: Yingping
doi: 10.7717/peerj.15331
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: © 2023 Wang et al.
attribution name: Wang et al.

Integrated analysis of lncRNAs, mRNAs, and TFs to identify network modules underlying diterpenoid biosynthesis in Salvia miltiorrhiza
type: item
type: AcademicArticle
description: Long non-coding RNAs (lncRNAs) are transcripts of more than 200 nucleotides (nt) in length, with minimal or no protein-coding capacity. Increasing evidence indicates that lncRNAs play important roles in the regulation of gene expression including in the biosynthesis of secondary metabolites. Salvia miltiorrhiza Bunge is an important medicinal plant in China. Diterpenoid tanshinones are one of the main active components of S. miltiorrhiza. To better understand the role of lncRNAs in regulating diterpenoid biosynthesis in S. miltiorrhiza, we integrated analysis of lncRNAs, mRNAs, and transcription factors (TFs) to identify network modules underlying diterpenoid biosynthesis based on transcriptomic data. In transcriptomic data, we obtained 6,651 candidate lncRNAs, 46 diterpenoid biosynthetic pathway genes, and 11 TFs involved in diterpenoid biosynthesis. Combining the co-expression and genomic location analysis, we obtained 23 candidate lncRNA-mRNA/TF pairs that were both co-expressed and co-located. To further observe the expression patterns of these 23 candidate gene pairs, we analyzed the time-series expression of S. miltiorrhiza induced by methyl jasmonate (MeJA). The results showed that 19 genes were differentially expressed at least a time-point, and four lncRNAs, two mRNAs, and two TFs formed three lncRNA-mRNA and/or TF network modules. This study revealed the relationship among lncRNAs, mRNAs, and TFs and provided new insight into the regulation of the biosynthetic pathway of S. miltiorrhiza diterpenoids.
format: application/pdf
format: text/html
creator: Lin Wang
creator: Peijin Zou
creator: Fang Liu
creator: Rui Liu
creator: Zhu-Yun Yan
creator: Xin Chen
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15332
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Long non-coding RNAs (lncRNAs) are transcripts of more than 200 nucleotides (nt) in length, with minimal or no protein-coding capacity. Increasing evidence indicates that lncRNAs play important roles in the regulation of gene expression including in the biosynthesis of secondary metabolites. Salvia miltiorrhiza Bunge is an important medicinal plant in China. Diterpenoid tanshinones are one of the main active components of S. miltiorrhiza. To better understand the role of lncRNAs in regulating diterpenoid biosynthesis in S. miltiorrhiza, we integrated analysis of lncRNAs, mRNAs, and transcription factors (TFs) to identify network modules underlying diterpenoid biosynthesis based on transcriptomic data. In transcriptomic data, we obtained 6,651 candidate lncRNAs, 46 diterpenoid biosynthetic pathway genes, and 11 TFs involved in diterpenoid biosynthesis. Combining the co-expression and genomic location analysis, we obtained 23 candidate lncRNA-mRNA/TF pairs that were both co-expressed and co-located. To further observe the expression patterns of these 23 candidate gene pairs, we analyzed the time-series expression of S. miltiorrhiza induced by methyl jasmonate (MeJA). The results showed that 19 genes were differentially expressed at least a time-point, and four lncRNAs, two mRNAs, and two TFs formed three lncRNA-mRNA and/or TF network modules. This study revealed the relationship among lncRNAs, mRNAs, and TFs and provided new insight into the regulation of the biosynthetic pathway of S. miltiorrhiza diterpenoids.
bibliographic citation: Wang et al. (2023) Integrated analysis of lncRNAs, mRNAs, and TFs to identify network modules underlying diterpenoid biosynthesis in Salvia miltiorrhiza. PeerJ 11:e15332 https://doi.org/10.7717/peerj.15332
date submitted: 2022-10-27
date accepted: 2023-04-11
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lin
author list: Agent
  family name: Zou
  given name: Peijin
author list: Agent
  family name: Liu
  given name: Fang
author list: Agent
  family name: Liu
  given name: Rui
author list: Agent
  family name: Yan
  given name: Zhu-Yun
author list: Agent
  family name: Chen
  given name: Xin
doi: 10.7717/peerj.15332
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Self-reported interoceptive accuracy and interoceptive attention differentially correspond to measures of visual attention and self-regard
type: item
type: AcademicArticle
description: Background Interoception, the perception of bodily functions and sensations, is a crucial contributor to cognition, emotion, and well-being. However, the relationship between these three processes is not well understood. Further, it is increasingly clear that dimensions of interoception differentially corresponds to these processes, yet this is only recently being explored. The present study addresses two important questions: Are subjective interoceptive accuracy and interoceptive attention related to self-regard and well-being? And are they related to exteroceptive (visual) attention? Methods Participants (N = 98; 29% women; aged 23–64 years) completed: a battery of questionnaires to assess subjective accuracy (how well one predicts bodily sensations), interoceptive attention (a tendency to notice bodily signals), self-regard (self-esteem, self-image, life satisfaction), state negative affect (depression, anxiety, and stress), a self-esteem Implicit Association Task (a measure of implicit self-esteem), and a flanker task to assess visual selective attention. Subjective interoceptive accuracy and attention served as dependent variables. Correlations and principal component analysis was used to establish correlations among variables and determine how, or whether, these measures are associated with subjective interoceptive accuracy or attention. Results Greater scores on measures of self-regard, implicit self-esteem, cognition and lower negative affect were broadly associated with greater subjective interoceptive accuracy. Conversely, only explicit self-esteem, satisfaction with life, and self-image corresponded to subjective interoceptive attention. An exploratory analysis with a more inclusive scale of interoceptive attention was conducted. Results of this exploratory analysis showed that the broader measure was a stronger correlate to self-regard than subjective interoceptive accuracy, though it, too, did not correlate with visual attention. In short, both subjecti…
format: application/pdf
format: text/html
creator: Erik M. Benau
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.15348
publisher: PeerJ Inc.
rights: © 2023 Benau
abstract: Background Interoception, the perception of bodily functions and sensations, is a crucial contributor to cognition, emotion, and well-being. However, the relationship between these three processes is not well understood. Further, it is increasingly clear that dimensions of interoception differentially corresponds to these processes, yet this is only recently being explored. The present study addresses two important questions: Are subjective interoceptive accuracy and interoceptive attention related to self-regard and well-being? And are they related to exteroceptive (visual) attention? Methods Participants (N = 98; 29% women; aged 23–64 years) completed: a battery of questionnaires to assess subjective accuracy (how well one predicts bodily sensations), interoceptive attention (a tendency to notice bodily signals), self-regard (self-esteem, self-image, life satisfaction), state negative affect (depression, anxiety, and stress), a self-esteem Implicit Association Task (a measure of implicit self-esteem), and a flanker task to assess visual selective attention. Subjective interoceptive accuracy and attention served as dependent variables. Correlations and principal component analysis was used to establish correlations among variables and determine how, or whether, these measures are associated with subjective interoceptive accuracy or attention. Results Greater scores on measures of self-regard, implicit self-esteem, cognition and lower negative affect were broadly associated with greater subjective interoceptive accuracy. Conversely, only explicit self-esteem, satisfaction with life, and self-image corresponded to subjective interoceptive attention. An exploratory analysis with a more inclusive scale of interoceptive attention was conducted. Results of this exploratory analysis showed that the broader measure was a stronger correlate to self-regard than subjective interoceptive accuracy, though it, too, did not correlate with visual attention. In short, both subjecti…
bibliographic citation: Benau (2023) Self-reported interoceptive accuracy and interoceptive attention differentially correspond to measures of visual attention and self-regard. PeerJ 11:e15348 https://doi.org/10.7717/peerj.15348
date submitted: 2023-01-17
date accepted: 2023-04-13
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Benau
  given name: Erik M.
doi: 10.7717/peerj.15348
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Benau
attribution name: Benau

Prediction of the spread of African swine fever through pig and carcass movements in Thailand using a network analysis and diffusion model
type: item
type: AcademicArticle
description: Background African swine fever (ASF) is a serious contagious viral disease of pigs that affects the pig industry. This study aimed to evaluate the possible African swine fever (ASF) distribution using network analysis and a diffusion model through live pig, carcass, and pig product movement data. Material and Methods Empirical movement data from Thailand for the year 2019 were used, and expert opinions were sought to evaluate network properties and the diffusion model. The networks were presented as live pig movement and carcass movement data at the provincial and district levels. For network analysis, a descriptive network analysis was performed using outdegree, indegree, betweenness, fragmentation, and power law distribution, and cutpoints were used to describe movement patterns. For the diffusion model, we simulated each network using spatially different infected locations, patterns, and initial infection sites. Based on expert opinions, the initial infection site, the probability of ASF occurrence, and the probability of the initial infected adopter were selected for the appropriated network. In this study, we also simulated networks under varying network parameters to predict the infection speed. Results and Conclusions The total number of movements recorded was 2,594,364. These were divided into 403,408 (403,408/2,594,364; 15.55%) for live pigs and 2,190,956 (2,190,956/2,594,364; 84.45%) for carcasses. We found that carcass movement at the provincial level showed the highest outdegree (mean = 342.554, standard deviation (SD) = 900.528) and indegree values (mean = 342.554, SD = 665.509). In addition, the outdegree and indegree presented similar mean values and the degree distributions of both district networks followed a power-law function. The network of live pigs at provincial level showed the highest value for betweenness (mean = 0.011, SD = 0.017), and the network of live pigs at provincial level showed the highest value for fragmentation (mean = 0.027, SD …
format: application/pdf
format: text/html
creator: Chaithep Poolkhet
creator: Suwicha Kasemsuwan
creator: Sukanya Thongratsakul
creator: Nattachai Warrasuth
creator: Nuttavadee Pamaranon
creator: Suphachai Nuanualsuwan
subject: Agricultural Science
subject: Veterinary Medicine
subject: Epidemiology
subject: Infectious Diseases
subject: Computational Science
description: doi:10.7717/peerj.15359
publisher: PeerJ Inc.
rights: © 2023 Poolkhet et al.
abstract: Background African swine fever (ASF) is a serious contagious viral disease of pigs that affects the pig industry. This study aimed to evaluate the possible African swine fever (ASF) distribution using network analysis and a diffusion model through live pig, carcass, and pig product movement data. Material and Methods Empirical movement data from Thailand for the year 2019 were used, and expert opinions were sought to evaluate network properties and the diffusion model. The networks were presented as live pig movement and carcass movement data at the provincial and district levels. For network analysis, a descriptive network analysis was performed using outdegree, indegree, betweenness, fragmentation, and power law distribution, and cutpoints were used to describe movement patterns. For the diffusion model, we simulated each network using spatially different infected locations, patterns, and initial infection sites. Based on expert opinions, the initial infection site, the probability of ASF occurrence, and the probability of the initial infected adopter were selected for the appropriated network. In this study, we also simulated networks under varying network parameters to predict the infection speed. Results and Conclusions The total number of movements recorded was 2,594,364. These were divided into 403,408 (403,408/2,594,364; 15.55%) for live pigs and 2,190,956 (2,190,956/2,594,364; 84.45%) for carcasses. We found that carcass movement at the provincial level showed the highest outdegree (mean = 342.554, standard deviation (SD) = 900.528) and indegree values (mean = 342.554, SD = 665.509). In addition, the outdegree and indegree presented similar mean values and the degree distributions of both district networks followed a power-law function. The network of live pigs at provincial level showed the highest value for betweenness (mean = 0.011, SD = 0.017), and the network of live pigs at provincial level showed the highest value for fragmentation (mean = 0.027, SD …
bibliographic citation: Poolkhet et al. (2023) Prediction of the spread of African swine fever through pig and carcass movements in Thailand using a network analysis and diffusion model. PeerJ 11:e15359 https://doi.org/10.7717/peerj.15359
date submitted: 2022-08-04
date accepted: 2023-04-16
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Poolkhet
  given name: Chaithep
author list: Agent
  family name: Kasemsuwan
  given name: Suwicha
author list: Agent
  family name: Thongratsakul
  given name: Sukanya
author list: Agent
  family name: Warrasuth
  given name: Nattachai
author list: Agent
  family name: Pamaranon
  given name: Nuttavadee
author list: Agent
  family name: Nuanualsuwan
  given name: Suphachai
doi: 10.7717/peerj.15359
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: © 2023 Poolkhet et al.
attribution name: Poolkhet et al.

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