PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Development of a single-chain fragment variable fused-mutant HALT-1 recombinant immunotoxin against G12V mutated KRAS colorectal cancer cells
items: Bioinformatics analysis for the identification of differentially expressed genes and related signaling pathways in H. pylori-CagA transfected gastric cancer cells
items: Identification and characterization of melon circular RNAs involved in powdery mildew responses through comparative transcriptome analysis
items: Ectomycorrhizal fungal communities associated with Larix gemelinii Rupr. in the Great Khingan Mountains, China
items: Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China
items: Melatonin ameliorates myocardial injury by reducing apoptosis and autophagy of cardiomyocytes in a rat cardiopulmonary bypass model
items: Explorations of avoidance and approach coping and perceived stress with a computer-based avatar task: detrimental effects of resignation and withdrawal
items: Conjuring up creativity: the effect of performing magic tricks on divergent thinking
items: Morphological grounds for the obligate aerial respiration of an aquatic snail: functional and evolutionary perspectives
items: Unraveling the genetic diversity and structure of Quercus liaotungensis population through analysis of microsatellite markers

Development of a single-chain fragment variable fused-mutant HALT-1 recombinant immunotoxin against G12V mutated KRAS colorectal cancer cells
type: item
type: AcademicArticle
description: Background KRAS oncogenes harboring codon G12 and G13 substitutions are considered gatekeeper mutations which drive oncogenesis in many cancers. To date, there are still no target-specific vaccines or drugs available against this genotype, thus reinforcing the need towards the development of targeted therapies such as immunotoxins. Methods This study aims to develop a recombinant anti-mKRAS scFv-fused mutant Hydra actinoporin-like-toxin-1 (mHALT-1) immunotoxin that is capable of recognizing and eradicating codon-12 mutated k-ras antigen abnormal cells. One G13D peptide mimotope (164-D) and one G12V peptide mimotope (68-V) were designed to elicit antigen specific IgG titres against mutated K-ras antigens in immunised Balb/c mice. The RNA was extracted from splenocytes following ELISA confirmation on post-immunized mice sera and was reverse transcribed into cDNA. The scFv combinatorial library was constructed from cDNA repertoire of variable regions of heavy chain (VH) and light chain (VL) fusions connected by a flexible glycine-serine linker, using splicing by overlap extension PCR (SOE-PCR). Anti-mKRAS G12V and G13D scFvs were cloned in pCANTAB5E phagemid and superinfected with helper phage. After few rounds of bio-panning, a specific mKRAS G12V and G13D scFv antibody against G12V and G13D control mimotope was identified and confirmed using ELISA without any cross-reactivity with other mimotopes or controls. Subsequently, the anti-mKRAS scFv was fused to mHALT-1 using SOE-PCR and cloned in pET22b vector. Expressed recombinant immunotoxins were analyzed for their effects on cell proliferation by the MTT assay and targeted specificity by cell-based ELISA on KRAS-positive and KRAS-negative cancer cells. Results The VH and VL genes from spleen RNA of mice immunized with 164-D and 68-V were amplified and randomly linked together, using SOE-PCR producing band sizes about 750 bp. Anti-mKRAS G12V and G13D scFvs were constructed in phagemid pCANTAB5E vectors with a library c…
format: application/pdf
format: text/html
creator: Michelle Yee Mun Teo
creator: Jeremy Jeack Ceen Ng
creator: Jung Yin Fong
creator: Jung Shan Hwang
creator: Adelene Ai-Lian Song
creator: Renee Lay Hong Lim
creator: Lionel Lian Aun In
subject: Biotechnology
subject: Cell Biology
subject: Molecular Biology
subject: Toxicology
subject: Oncology
description: doi:10.7717/peerj.11063
publisher: PeerJ Inc.
rights: © 2021 Teo et al.
abstract: Background KRAS oncogenes harboring codon G12 and G13 substitutions are considered gatekeeper mutations which drive oncogenesis in many cancers. To date, there are still no target-specific vaccines or drugs available against this genotype, thus reinforcing the need towards the development of targeted therapies such as immunotoxins. Methods This study aims to develop a recombinant anti-mKRAS scFv-fused mutant Hydra actinoporin-like-toxin-1 (mHALT-1) immunotoxin that is capable of recognizing and eradicating codon-12 mutated k-ras antigen abnormal cells. One G13D peptide mimotope (164-D) and one G12V peptide mimotope (68-V) were designed to elicit antigen specific IgG titres against mutated K-ras antigens in immunised Balb/c mice. The RNA was extracted from splenocytes following ELISA confirmation on post-immunized mice sera and was reverse transcribed into cDNA. The scFv combinatorial library was constructed from cDNA repertoire of variable regions of heavy chain (VH) and light chain (VL) fusions connected by a flexible glycine-serine linker, using splicing by overlap extension PCR (SOE-PCR). Anti-mKRAS G12V and G13D scFvs were cloned in pCANTAB5E phagemid and superinfected with helper phage. After few rounds of bio-panning, a specific mKRAS G12V and G13D scFv antibody against G12V and G13D control mimotope was identified and confirmed using ELISA without any cross-reactivity with other mimotopes or controls. Subsequently, the anti-mKRAS scFv was fused to mHALT-1 using SOE-PCR and cloned in pET22b vector. Expressed recombinant immunotoxins were analyzed for their effects on cell proliferation by the MTT assay and targeted specificity by cell-based ELISA on KRAS-positive and KRAS-negative cancer cells. Results The VH and VL genes from spleen RNA of mice immunized with 164-D and 68-V were amplified and randomly linked together, using SOE-PCR producing band sizes about 750 bp. Anti-mKRAS G12V and G13D scFvs were constructed in phagemid pCANTAB5E vectors with a library c…
bibliographic citation: Teo et al. (2021) Development of a single-chain fragment variable fused-mutant HALT-1 recombinant immunotoxin against G12V mutated KRAS colorectal cancer cells. PeerJ 9:e11063 https://doi.org/10.7717/peerj.11063
date submitted: 2020-07-27
date accepted: 2021-02-14
issued: 2021-04-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Teo
  given name: Michelle Yee Mun
author list: Agent
  family name: Ng
  given name: Jeremy Jeack Ceen
author list: Agent
  family name: Fong
  given name: Jung Yin
author list: Agent
  family name: Hwang
  given name: Jung Shan
author list: Agent
  family name: Song
  given name: Adelene Ai-Lian
author list: Agent
  family name: Lim
  given name: Renee Lay Hong
author list: Agent
  family name: In
  given name: Lionel Lian Aun
doi: 10.7717/peerj.11063
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-15
copyright: © 2021 Teo et al.
attribution name: Teo et al.

Bioinformatics analysis for the identification of differentially expressed genes and related signaling pathways in H. pylori-CagA transfected gastric cancer cells
type: item
type: AcademicArticle
description: Aim Helicobacter pylori cytotoxin-associated protein A (CagA) is an important virulence factor known to induce gastric cancer development. However, the cause and the underlying molecular events of CagA induction remain unclear. Here, we applied integrated bioinformatics to identify the key genes involved in the process of CagA-induced gastric epithelial cell inflammation and can ceration to comprehend the potential molecular mechanisms involved. Materials and Methods AGS cells were transected with pcDNA3.1 and pcDNA3.1::CagA for 24 h. The transfected cells were subjected to transcriptome sequencing to obtain the expressed genes. Differentially expressed genes (DEG) with adjusted P value < 0.05, — logFC —> 2 were screened, and the R package was applied for gene ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The differential gene protein–protein interaction (PPI) network was constructed using the STRING Cytoscape application, which conducted visual analysis to create the key function networks and identify the key genes. Next, the Kaplan–Meier plotter survival analysis tool was employed to analyze the survival of the key genes derived from the PPI network. Further analysis of the key gene expressions in gastric cancer and normal tissues were performed based on The Cancer Genome Atlas (TCGA) database and RT-qPCR verification. Results After transfection of AGS cells, the cell morphology changes in a hummingbird shape and causes the level of CagA phosphorylation to increase. Transcriptomics identified 6882 DEG, of which 4052 were upregulated and 2830 were downregulated, among which q-value < 0.05, FC > 2, and FC under the condition of ≤2. Accordingly, 1062 DEG were screened, of which 594 were upregulated and 468 were downregulated. The DEG participated in a total of 151 biological processes, 56 cell components, and 40 molecular functions. The KEGG pathway analysis revealed that the DEG were involved in 21 pathways. The PP…
format: application/pdf
format: text/html
creator: Dingyu Chen
creator: Chao Li
creator: Yan Zhao
creator: Jianjiang Zhou
creator: Qinrong Wang
creator: Yuan Xie
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.11203
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Aim Helicobacter pylori cytotoxin-associated protein A (CagA) is an important virulence factor known to induce gastric cancer development. However, the cause and the underlying molecular events of CagA induction remain unclear. Here, we applied integrated bioinformatics to identify the key genes involved in the process of CagA-induced gastric epithelial cell inflammation and can ceration to comprehend the potential molecular mechanisms involved. Materials and Methods AGS cells were transected with pcDNA3.1 and pcDNA3.1::CagA for 24 h. The transfected cells were subjected to transcriptome sequencing to obtain the expressed genes. Differentially expressed genes (DEG) with adjusted P value < 0.05, — logFC —> 2 were screened, and the R package was applied for gene ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The differential gene protein–protein interaction (PPI) network was constructed using the STRING Cytoscape application, which conducted visual analysis to create the key function networks and identify the key genes. Next, the Kaplan–Meier plotter survival analysis tool was employed to analyze the survival of the key genes derived from the PPI network. Further analysis of the key gene expressions in gastric cancer and normal tissues were performed based on The Cancer Genome Atlas (TCGA) database and RT-qPCR verification. Results After transfection of AGS cells, the cell morphology changes in a hummingbird shape and causes the level of CagA phosphorylation to increase. Transcriptomics identified 6882 DEG, of which 4052 were upregulated and 2830 were downregulated, among which q-value < 0.05, FC > 2, and FC under the condition of ≤2. Accordingly, 1062 DEG were screened, of which 594 were upregulated and 468 were downregulated. The DEG participated in a total of 151 biological processes, 56 cell components, and 40 molecular functions. The KEGG pathway analysis revealed that the DEG were involved in 21 pathways. The PP…
bibliographic citation: Chen et al. (2021) Bioinformatics analysis for the identification of differentially expressed genes and related signaling pathways in H. pylori-CagA transfected gastric cancer cells. PeerJ 9:e11203 https://doi.org/10.7717/peerj.11203
date submitted: 2020-08-20
date accepted: 2021-03-11
issued: 2021-04-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Dingyu
author list: Agent
  family name: Li
  given name: Chao
author list: Agent
  family name: Zhao
  given name: Yan
author list: Agent
  family name: Zhou
  given name: Jianjiang
author list: Agent
  family name: Wang
  given name: Qinrong
author list: Agent
  family name: Xie
  given name: Yuan
doi: 10.7717/peerj.11203
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-15
copyright: ©2021 Chen et al.
attribution name: Chen et al.

Identification and characterization of melon circular RNAs involved in powdery mildew responses through comparative transcriptome analysis
type: item
type: AcademicArticle
description: Circular RNAs (circRNAs) are a class of newly discovered non-coding RNAs that are typically derived from a genome’s exonic, intronic, and intergenic regions. Recent studies of circRNAs in animals and plants have shown that circRNAs are vital in response to various abiotic and biotic stresses. Powdery mildew disease (PM) is a serious fungal disease threatening the melon industry. We performed whole transcriptome sequencing using the leaves of a PM-resistant (M1) and a PM-susceptible (B29) melon to identify circRNAs and determine their molecular functions. A total of 303 circRNAs were identified and >50% circRNAs were derived from exonic regions. Expression levels were significantly altered in 17 and 23 circRNAs after PM infections in B29 and M1, respectively. Melon circRNAs may participate in the response to biotic stimuli, oxidation reduction, metabolic processes, and the regulation of gene expression based on the functional annotation of circRNA parental genes. Furthermore, 27 circRNAs were predicted to be potential targets or ‘sponges’ for 18 microRNAs (miRNAs). Our results are the first to identify and characterize circRNA functions in melon and may contribute to a better understanding of the role and regulatory mechanisms of circRNAs in resisting PM.
format: application/pdf
format: text/html
creator: Jianlei Sun
creator: Yumei Dong
creator: Chongqi Wang
creator: Shouhua Xiao
creator: Zigao Jiao
creator: Chao Gao
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11216
publisher: PeerJ Inc.
rights: © 2021 Sun et al.
abstract: Circular RNAs (circRNAs) are a class of newly discovered non-coding RNAs that are typically derived from a genome’s exonic, intronic, and intergenic regions. Recent studies of circRNAs in animals and plants have shown that circRNAs are vital in response to various abiotic and biotic stresses. Powdery mildew disease (PM) is a serious fungal disease threatening the melon industry. We performed whole transcriptome sequencing using the leaves of a PM-resistant (M1) and a PM-susceptible (B29) melon to identify circRNAs and determine their molecular functions. A total of 303 circRNAs were identified and >50% circRNAs were derived from exonic regions. Expression levels were significantly altered in 17 and 23 circRNAs after PM infections in B29 and M1, respectively. Melon circRNAs may participate in the response to biotic stimuli, oxidation reduction, metabolic processes, and the regulation of gene expression based on the functional annotation of circRNA parental genes. Furthermore, 27 circRNAs were predicted to be potential targets or ‘sponges’ for 18 microRNAs (miRNAs). Our results are the first to identify and characterize circRNA functions in melon and may contribute to a better understanding of the role and regulatory mechanisms of circRNAs in resisting PM.
bibliographic citation: Sun et al. (2021) Identification and characterization of melon circular RNAs involved in powdery mildew responses through comparative transcriptome analysis. PeerJ 9:e11216 https://doi.org/10.7717/peerj.11216
date submitted: 2020-09-10
date accepted: 2021-03-15
issued: 2021-04-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Jianlei
author list: Agent
  family name: Dong
  given name: Yumei
author list: Agent
  family name: Wang
  given name: Chongqi
author list: Agent
  family name: Xiao
  given name: Shouhua
author list: Agent
  family name: Jiao
  given name: Zigao
author list: Agent
  family name: Gao
  given name: Chao
doi: 10.7717/peerj.11216
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-15
copyright: ©2021 Sun et al.
attribution name: Sun et al.

Ectomycorrhizal fungal communities associated with Larix gemelinii Rupr. in the Great Khingan Mountains, China
type: item
type: AcademicArticle
description: Larix gemelinii is an important tree species in the Great Khingan Mountains in Northeast China with a high economic and ecological value for its role in carbon sequestration and as a source of lumber and nuts. However, the ectomycorrhizal (EM) fungal diversity and community composition of this tree remain largely undefined. We examined EM fungal communities associated with L. gemelinii from three sites in the Great Khingan Mountains using Illumina Miseq to sequence the rDNA ITS2 region and evaluated the impact of spatial, soil, and climatic variables on the EM fungal community. A total of 122 EM fungal operational taxonomic units (OTUs) were identified from 21 pooled-root samples, and the dominant EM fungal lineages were /tricholoma, /tomentella-thelephora, /suillus-rhizopogon, and /piloderma. A high proportion of unique EM fungal OTUs were present; some abundant OTUs largely restricted to specific sites. EM fungal richness and community assembly were significantly correlated with spatial distance and climatic and soil variables, with mean annual temperature being the most important predictor for fungal richness and geographic distance as the largest determinant for community turnover. Our findings indicate that L. gemelinii has a rich and distinctive EM fungal community contributing to our understanding of the montane EM fungal community structure from the perspective of a single host plant that has not been previously reported.
format: application/pdf
format: text/html
creator: Yonglong Wang
creator: Yanling Zhao
creator: Ying Xu
creator: Jianjun Ma
creator: Busayo Joshua Babalola
creator: Yongjun Fan
subject: Biodiversity
subject: Ecology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.11230
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Larix gemelinii is an important tree species in the Great Khingan Mountains in Northeast China with a high economic and ecological value for its role in carbon sequestration and as a source of lumber and nuts. However, the ectomycorrhizal (EM) fungal diversity and community composition of this tree remain largely undefined. We examined EM fungal communities associated with L. gemelinii from three sites in the Great Khingan Mountains using Illumina Miseq to sequence the rDNA ITS2 region and evaluated the impact of spatial, soil, and climatic variables on the EM fungal community. A total of 122 EM fungal operational taxonomic units (OTUs) were identified from 21 pooled-root samples, and the dominant EM fungal lineages were /tricholoma, /tomentella-thelephora, /suillus-rhizopogon, and /piloderma. A high proportion of unique EM fungal OTUs were present; some abundant OTUs largely restricted to specific sites. EM fungal richness and community assembly were significantly correlated with spatial distance and climatic and soil variables, with mean annual temperature being the most important predictor for fungal richness and geographic distance as the largest determinant for community turnover. Our findings indicate that L. gemelinii has a rich and distinctive EM fungal community contributing to our understanding of the montane EM fungal community structure from the perspective of a single host plant that has not been previously reported.
bibliographic citation: Wang et al. (2021) Ectomycorrhizal fungal communities associated with Larix gemelinii Rupr. in the Great Khingan Mountains, China. PeerJ 9:e11230 https://doi.org/10.7717/peerj.11230
date submitted: 2020-07-10
date accepted: 2021-03-16
issued: 2021-04-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yonglong
author list: Agent
  family name: Zhao
  given name: Yanling
author list: Agent
  family name: Xu
  given name: Ying
author list: Agent
  family name: Ma
  given name: Jianjun
author list: Agent
  family name: Babalola
  given name: Busayo Joshua
author list: Agent
  family name: Fan
  given name: Yongjun
doi: 10.7717/peerj.11230
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-15
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China
type: item
type: AcademicArticle
description: Background The rapid expansion of urbanization leads to significant losses of soil ecological functions. Microbes directly participate in key soil processes and play crucial roles in maintaining soil functions. However, we still have a limited understanding of underlying mechanisms shaping microbial communities and the interactions among microbial taxa in park soils. Methods In this study, the community variations of bacteria and fungi in urban and suburban park soils were investigated in Shanghai, China. Real-time PCR and high-throughput Illumina sequencing were used to examine the microbial abundance and community composition, respectively. Results The results showed that soil molecular biomass and fungal abundance in urban park soils were significantly higher than those in suburban park soils, while no significant difference was observed in the bacterial abundance between urban and suburban park soils. The alpha diversity of soil microbes in urban and suburban park soils was similar to each other, except for Chao1 index of fungal communities. The results of similarity analysis (ANOSIM) revealed remarkable differences in the composition of bacterial and fungal communities between urban and suburban park soils. Specifically, park soils in urban areas were enriched with the phyla Methylomirabilota and Verrucomicrobiota, while the relative abundance of Gemmatimonadota was higher in suburban park soils. Moreover, the fungal class Eurotiomycetes was also enriched in urban park soils. Compared with suburban park soils, nodes and average paths of the bacterial and fungal networks were higher in urban park soils, but the number of module hubs and connectors of the bacterial networks and negative interactions among bacterial taxa were lower. Compared with suburban park soils, Acidobacteriota bacterium and Mortierellomycota fungus played more important roles in the ecological networks of urban park soils. Soil available zinc (Zn), available nitrogen (N), pH, and total potas…
format: application/pdf
format: text/html
creator: Weiwei Zhang
creator: Jigang Han
creator: Haibing Wu
creator: Qicheng Zhong
creator: Wen Liu
creator: Shanwen He
creator: Lang Zhang
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
description: doi:10.7717/peerj.11231
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Background The rapid expansion of urbanization leads to significant losses of soil ecological functions. Microbes directly participate in key soil processes and play crucial roles in maintaining soil functions. However, we still have a limited understanding of underlying mechanisms shaping microbial communities and the interactions among microbial taxa in park soils. Methods In this study, the community variations of bacteria and fungi in urban and suburban park soils were investigated in Shanghai, China. Real-time PCR and high-throughput Illumina sequencing were used to examine the microbial abundance and community composition, respectively. Results The results showed that soil molecular biomass and fungal abundance in urban park soils were significantly higher than those in suburban park soils, while no significant difference was observed in the bacterial abundance between urban and suburban park soils. The alpha diversity of soil microbes in urban and suburban park soils was similar to each other, except for Chao1 index of fungal communities. The results of similarity analysis (ANOSIM) revealed remarkable differences in the composition of bacterial and fungal communities between urban and suburban park soils. Specifically, park soils in urban areas were enriched with the phyla Methylomirabilota and Verrucomicrobiota, while the relative abundance of Gemmatimonadota was higher in suburban park soils. Moreover, the fungal class Eurotiomycetes was also enriched in urban park soils. Compared with suburban park soils, nodes and average paths of the bacterial and fungal networks were higher in urban park soils, but the number of module hubs and connectors of the bacterial networks and negative interactions among bacterial taxa were lower. Compared with suburban park soils, Acidobacteriota bacterium and Mortierellomycota fungus played more important roles in the ecological networks of urban park soils. Soil available zinc (Zn), available nitrogen (N), pH, and total potas…
bibliographic citation: Zhang et al. (2021) Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China. PeerJ 9:e11231 https://doi.org/10.7717/peerj.11231
date submitted: 2020-09-21
date accepted: 2021-03-16
issued: 2021-04-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Weiwei
author list: Agent
  family name: Han
  given name: Jigang
author list: Agent
  family name: Wu
  given name: Haibing
author list: Agent
  family name: Zhong
  given name: Qicheng
author list: Agent
  family name: Liu
  given name: Wen
author list: Agent
  family name: He
  given name: Shanwen
author list: Agent
  family name: Zhang
  given name: Lang
doi: 10.7717/peerj.11231
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-15
copyright: © 2021 Zhang et al.
attribution name: Zhang et al.

Melatonin ameliorates myocardial injury by reducing apoptosis and autophagy of cardiomyocytes in a rat cardiopulmonary bypass model
type: item
type: AcademicArticle
description: Background Myocardial injury is a frequent complication after cardiac surgery with cardiopulmonary bypass (CPB). This study aimed to test the hypothesis that melatonin could attenuate myocardial injury in a rat CPB model. Methods Eighteen male Sprague-Dawley rats were randomly divided into three groups, n = 6 for each group: the sham operation (SO) group, CPB group and melatonin group. Rats in the SO group underwent cannulation without CPB, rats in CPB group intraperitoneal injected an equal volume of vehicle daily for 7 days before being subjected to CPB and rats in melatonin group intraperitoneal injected 20 mg/kg of melatonin solution daily for 7 days before being subjected to CPB. After 120 min for CPB, the expression levels of plasma interleukin (IL) -6, IL-1β, superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), malondialdehyde (MDA), creatine kinase (CK) -MB and cardiac troponin T (cTnT) were measured. Reactive oxygen species (ROS) were detected by dihydroethidium (DHE). Apoptosis was detected by terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) staining. Mitochondrial damage and autophagosomes were detected by electron microscopy. Apoptosis inducing factor (AIF) was detected by immunofluorescence. The expression of B cell lymphoma/leukemia2 associated X (Bax), B cell lymphoma/leukemia 2 (Bcl-2), cytochrome C (Cyto-C), cleaved caspase-9, AKT, p-AKT, signal transducer and activator of transcription 3 (STAT3), p-STAT3, LC3, P62, mechanistic target of rapamycin kinase (mTOR), p-mTOR and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were determined using western blotting. Results Melatonin significantly decreased the levels of IL-1β, IL-6, MDA, CK-MB and cTnT and increased the levels of SOD and GSH-Px, all of which were altered by CPB. Melatonin reduced cardiomyocyte superoxide production, the apoptosis index and autophagy in cardiomyocytes induced by CPB. The AKT, STAT3 and mTOR signaling pathways were activated by melatonin during …
format: application/pdf
format: text/html
creator: Xiaolin Huang
creator: Jian Hou
creator: Suiqing Huang
creator: Kangni Feng
creator: Yuan Yue
creator: Huayang Li
creator: Shaojie Huang
creator: Mengya Liang
creator: Guangxian Chen
creator: Zhongkai Wu
subject: Biochemistry
subject: Cell Biology
subject: Zoology
subject: Cardiology
description: doi:10.7717/peerj.11264
publisher: PeerJ Inc.
rights: © 2021 Huang et al.
abstract: Background Myocardial injury is a frequent complication after cardiac surgery with cardiopulmonary bypass (CPB). This study aimed to test the hypothesis that melatonin could attenuate myocardial injury in a rat CPB model. Methods Eighteen male Sprague-Dawley rats were randomly divided into three groups, n = 6 for each group: the sham operation (SO) group, CPB group and melatonin group. Rats in the SO group underwent cannulation without CPB, rats in CPB group intraperitoneal injected an equal volume of vehicle daily for 7 days before being subjected to CPB and rats in melatonin group intraperitoneal injected 20 mg/kg of melatonin solution daily for 7 days before being subjected to CPB. After 120 min for CPB, the expression levels of plasma interleukin (IL) -6, IL-1β, superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), malondialdehyde (MDA), creatine kinase (CK) -MB and cardiac troponin T (cTnT) were measured. Reactive oxygen species (ROS) were detected by dihydroethidium (DHE). Apoptosis was detected by terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) staining. Mitochondrial damage and autophagosomes were detected by electron microscopy. Apoptosis inducing factor (AIF) was detected by immunofluorescence. The expression of B cell lymphoma/leukemia2 associated X (Bax), B cell lymphoma/leukemia 2 (Bcl-2), cytochrome C (Cyto-C), cleaved caspase-9, AKT, p-AKT, signal transducer and activator of transcription 3 (STAT3), p-STAT3, LC3, P62, mechanistic target of rapamycin kinase (mTOR), p-mTOR and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were determined using western blotting. Results Melatonin significantly decreased the levels of IL-1β, IL-6, MDA, CK-MB and cTnT and increased the levels of SOD and GSH-Px, all of which were altered by CPB. Melatonin reduced cardiomyocyte superoxide production, the apoptosis index and autophagy in cardiomyocytes induced by CPB. The AKT, STAT3 and mTOR signaling pathways were activated by melatonin during …
bibliographic citation: Huang et al. (2021) Melatonin ameliorates myocardial injury by reducing apoptosis and autophagy of cardiomyocytes in a rat cardiopulmonary bypass model. PeerJ 9:e11264 https://doi.org/10.7717/peerj.11264
date submitted: 2020-12-21
date accepted: 2021-03-23
issued: 2021-04-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Xiaolin
author list: Agent
  family name: Hou
  given name: Jian
author list: Agent
  family name: Huang
  given name: Suiqing
author list: Agent
  family name: Feng
  given name: Kangni
author list: Agent
  family name: Yue
  given name: Yuan
author list: Agent
  family name: Li
  given name: Huayang
author list: Agent
  family name: Huang
  given name: Shaojie
author list: Agent
  family name: Liang
  given name: Mengya
author list: Agent
  family name: Chen
  given name: Guangxian
author list: Agent
  family name: Wu
  given name: Zhongkai
doi: 10.7717/peerj.11264
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-15
copyright: ©2021 Huang et al.
attribution name: Huang et al.

Explorations of avoidance and approach coping and perceived stress with a computer-based avatar task: detrimental effects of resignation and withdrawal
type: item
type: AcademicArticle
description: Background Individuals differ in how they react to stress or trauma through different coping styles in which they may deal directly with a stressor by adopting approach coping styles or disengage with a stressor by utilizing avoidant coping styles. Avoidant coping styles have been linked to adverse outcomes including psychological distress, anxiety disorders, and post-traumatic stress disorder (PTSD). Recently, avoidance coping styles as measured by a subset of items on the Brief COPE were found to have a weak positive relationship with performance on a computer-based avatar task which is related to avoidant personality temperaments. This avatar task was developed as an alternative for paper and pencil self-report inventories for measuring avoidant tendencies based on possible response biases of avoidant individuals. In the current study, avoidance and approach coping styles as measured by the Brief Approach/Avoidance Coping Questionnaire (BACQ) were compared to avoidant coping as measured by the Brief COPE and performance on the avatar task. In addition to approach and avoidance coping, the BACQ also measures active avoidance coping (i.e., diversion) and passive avoidance coping (i.e., resignation and withdrawal). The relationships between approach and avoidance coping and performance on the avatar task were also analyzed with the outcome of perceived stress as measured by the Perceived Stress Scale (PSS). Methods One hundred undergraduates voluntarily completed the BACQ, the Brief COPE, and the PSS. Participants also completed a computer-based task in which they guided an avatar through a series of social situations where they indicated how they would interact with or avoid interacting with strangers. Results Approach coping had a weak negative relationship to avoidance coping as measured by the BACQ and the Brief COPE. Performance on the avatar task had a moderate positive relationship with avoidance coping (diversion as well as resignation and withdrawal) as mea…
format: application/pdf
format: text/html
creator: M. Todd Allen
subject: Psychiatry and Psychology
subject: Human-Computer Interaction
description: doi:10.7717/peerj.11265
publisher: PeerJ Inc.
rights: © 2021 Allen
abstract: Background Individuals differ in how they react to stress or trauma through different coping styles in which they may deal directly with a stressor by adopting approach coping styles or disengage with a stressor by utilizing avoidant coping styles. Avoidant coping styles have been linked to adverse outcomes including psychological distress, anxiety disorders, and post-traumatic stress disorder (PTSD). Recently, avoidance coping styles as measured by a subset of items on the Brief COPE were found to have a weak positive relationship with performance on a computer-based avatar task which is related to avoidant personality temperaments. This avatar task was developed as an alternative for paper and pencil self-report inventories for measuring avoidant tendencies based on possible response biases of avoidant individuals. In the current study, avoidance and approach coping styles as measured by the Brief Approach/Avoidance Coping Questionnaire (BACQ) were compared to avoidant coping as measured by the Brief COPE and performance on the avatar task. In addition to approach and avoidance coping, the BACQ also measures active avoidance coping (i.e., diversion) and passive avoidance coping (i.e., resignation and withdrawal). The relationships between approach and avoidance coping and performance on the avatar task were also analyzed with the outcome of perceived stress as measured by the Perceived Stress Scale (PSS). Methods One hundred undergraduates voluntarily completed the BACQ, the Brief COPE, and the PSS. Participants also completed a computer-based task in which they guided an avatar through a series of social situations where they indicated how they would interact with or avoid interacting with strangers. Results Approach coping had a weak negative relationship to avoidance coping as measured by the BACQ and the Brief COPE. Performance on the avatar task had a moderate positive relationship with avoidance coping (diversion as well as resignation and withdrawal) as mea…
bibliographic citation: Allen (2021) Explorations of avoidance and approach coping and perceived stress with a computer-based avatar task: detrimental effects of resignation and withdrawal. PeerJ 9:e11265 https://doi.org/10.7717/peerj.11265
date submitted: 2020-06-26
date accepted: 2021-03-23
issued: 2021-04-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Allen
  given name: M. Todd
doi: 10.7717/peerj.11265
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-15
copyright: ©2021 Allen
attribution name: Allen

Conjuring up creativity: the effect of performing magic tricks on divergent thinking
type: item
type: AcademicArticle
description: Research suggests that learning to perform magic tricks can promote both physical and psychological wellbeing. The current study extended this work by examining the impact of learning magic tricks on divergent thinking. A group of 10- to 11-year-old children completed Guilford’s Alternate Uses Test both before and after participating in either a magic-based, or art-based, activity. As predicted, compared to the art-based activity, the magic-based activity resulted in a significantly greater increase in both AUT Fluency and AUT Originality scores. Rosenberg’s Self-Esteem Scale and Dweck’s Implicit Theories of Intelligence Scale for Children was also completed after each activity, and participants’ self-esteem scores were higher after the art-based activity than the magic-based activity. In an exploratory aspect of the study, the AUT was re-administered to both groups three weeks later, and yielded no significant differences. The practical and theoretical implications of these findings are discussed, along with recommendations for future research.
format: application/pdf
format: text/html
creator: Richard Wiseman
creator: Amy Wiles
creator: Caroline Watt
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Science and Medical Education
description: doi:10.7717/peerj.11289
publisher: PeerJ Inc.
rights: © 2021 Wiseman et al.
abstract: Research suggests that learning to perform magic tricks can promote both physical and psychological wellbeing. The current study extended this work by examining the impact of learning magic tricks on divergent thinking. A group of 10- to 11-year-old children completed Guilford’s Alternate Uses Test both before and after participating in either a magic-based, or art-based, activity. As predicted, compared to the art-based activity, the magic-based activity resulted in a significantly greater increase in both AUT Fluency and AUT Originality scores. Rosenberg’s Self-Esteem Scale and Dweck’s Implicit Theories of Intelligence Scale for Children was also completed after each activity, and participants’ self-esteem scores were higher after the art-based activity than the magic-based activity. In an exploratory aspect of the study, the AUT was re-administered to both groups three weeks later, and yielded no significant differences. The practical and theoretical implications of these findings are discussed, along with recommendations for future research.
bibliographic citation: Wiseman et al. (2021) Conjuring up creativity: the effect of performing magic tricks on divergent thinking. PeerJ 9:e11289 https://doi.org/10.7717/peerj.11289
date submitted: 2021-02-25
date accepted: 2021-03-26
issued: 2021-04-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wiseman
  given name: Richard
author list: Agent
  family name: Wiles
  given name: Amy
author list: Agent
  family name: Watt
  given name: Caroline
doi: 10.7717/peerj.11289
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-15
copyright: © 2021 Wiseman et al.
attribution name: Wiseman et al.

Morphological grounds for the obligate aerial respiration of an aquatic snail: functional and evolutionary perspectives
type: item
type: AcademicArticle
description: The freshwater caenogastropod family Ampullariidae is emerging as a model for a variety of studies, among them, the evolution of terrestriality. A common character of the family is that all its members bear a lung while retaining the ancestral gill. This ensures that many ampullariids are able to inhabit poorly oxygenated waters, to bury in the mud during estivation, and to temporarily leave the water, in some species for oviposition. To these characters Pomacea canaliculata (Caenogastropoda, Ampullariidae) adds that is an obligate air-breather. In a recent paper, we showed the gill epithelium of P. canaliculata has a set of characteristics that suggest its role for oxygen uptake may be less significant than its role in ionic/osmotic regulation and immunity. We complement here our morphological investigation on the respiratory organs of P. canaliculata by studying the lung of this species at the anatomical (3D reconstructions of the blood system and nerve supply), histological and ultrastructural levels. The circulation of the gill and the lung are interconnected so that the effluence of blood from the gill goes to the lung where it completes oxygenation. Besides that, we found the lung cavity is lined by a pavement epithelium that encloses an anastomosing network of small blood spaces resting over a fibromuscular layer, which altogether form the respiratory lamina. The pavement cells form a blood-gas barrier that is 80–150 nm thick and thus fulfils the requirements for an efficient gas exchanger. Tufts of ciliary cells, together with some microvillar and secretory cells, are interspersed in the respiratory lamina. Rhogocytes, which have been proposed to partake in metal depuration and in the synthesis of hemocyanin in other gastropods, were found below the respiratory lamina, in close association with the storage cell tissue. In light of these findings, we discuss the functional role of the lung in P. canaliculata and compare it with that of other gastropods. Final…
format: application/pdf
format: text/html
creator: Cristian Rodriguez
creator: Guido I. Prieto
creator: Israel A. Vega
creator: Alfredo Castro-Vazquez
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Zoology
subject: Histology
subject: Freshwater Biology
description: doi:10.7717/peerj.10763
publisher: PeerJ Inc.
rights: © 2021 Rodriguez et al.
abstract: The freshwater caenogastropod family Ampullariidae is emerging as a model for a variety of studies, among them, the evolution of terrestriality. A common character of the family is that all its members bear a lung while retaining the ancestral gill. This ensures that many ampullariids are able to inhabit poorly oxygenated waters, to bury in the mud during estivation, and to temporarily leave the water, in some species for oviposition. To these characters Pomacea canaliculata (Caenogastropoda, Ampullariidae) adds that is an obligate air-breather. In a recent paper, we showed the gill epithelium of P. canaliculata has a set of characteristics that suggest its role for oxygen uptake may be less significant than its role in ionic/osmotic regulation and immunity. We complement here our morphological investigation on the respiratory organs of P. canaliculata by studying the lung of this species at the anatomical (3D reconstructions of the blood system and nerve supply), histological and ultrastructural levels. The circulation of the gill and the lung are interconnected so that the effluence of blood from the gill goes to the lung where it completes oxygenation. Besides that, we found the lung cavity is lined by a pavement epithelium that encloses an anastomosing network of small blood spaces resting over a fibromuscular layer, which altogether form the respiratory lamina. The pavement cells form a blood-gas barrier that is 80–150 nm thick and thus fulfils the requirements for an efficient gas exchanger. Tufts of ciliary cells, together with some microvillar and secretory cells, are interspersed in the respiratory lamina. Rhogocytes, which have been proposed to partake in metal depuration and in the synthesis of hemocyanin in other gastropods, were found below the respiratory lamina, in close association with the storage cell tissue. In light of these findings, we discuss the functional role of the lung in P. canaliculata and compare it with that of other gastropods. Final…
bibliographic citation: Rodriguez et al. (2021) Morphological grounds for the obligate aerial respiration of an aquatic snail: functional and evolutionary perspectives. PeerJ 9:e10763 https://doi.org/10.7717/peerj.10763
date submitted: 2020-06-25
date accepted: 2020-12-22
issued: 2021-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodriguez
  given name: Cristian
author list: Agent
  family name: Prieto
  given name: Guido I.
author list: Agent
  family name: Vega
  given name: Israel A.
author list: Agent
  family name: Castro-Vazquez
  given name: Alfredo
doi: 10.7717/peerj.10763
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-14
copyright: © 2021 Rodriguez et al.
attribution name: Rodriguez et al.

Unraveling the genetic diversity and structure of Quercus liaotungensis population through analysis of microsatellite markers
type: item
type: AcademicArticle
description: Background Quercus liaotungensis Koidz. is an ecologically and economically important tree species widely distributed in Northern China. However, the effective assessment, utilization, and protection of Q. liaotungensis resources remain unexplored. Methods In total, 120 samples obtained from 12 Q. liaotungensis populations of Northern China were investigated for genetic diversity and structure using 19 simple sequence repeat (SSR) primer pairs. Results The total number of alleles detected was 293, the average number of effective allele (Ne) was 6.084, the genetic differentiation coefficient (Fst) was 0.033, and the mean observed heterozygosity (Ho) and expected heterozygosity (He) were 0.690 and 0.801, respectively. Moreover, analysis of molecular variance (AMOVA) showed a 5.5% genetic variation among 12 Q. liaotungensis populations, indicating that a high level of genetic diversity and a low degree of genetic differentiation among Q. liaotungensis populations. STRUCTURE and cluster analysis divided the 12 Q. liaotungensis populations into the following three subpopulations: Bashang Plateau subpopulation (SH), Liaodong Peninsula subpopulation (NC), and Loess Plateau subpopulation (other 10 populations). The cluster analysis based on 19 climatic factors was consistent with the genetic structure. A positive correlation was found between genetic distance and geographical distance (r = 0.638, p = 0.028) by the Mantel test, and two boundaries were found among the 12 Q. liaotungensis populations by the Barrier analysis, indicating that Q. liaotungensis populations existed isolated by geographical distance and physical barrier. Conclusion This study suggests that geographical isolation, physical barrier, climatic types, and natural hybridization promote the formation of genetic structures, which can contribute to future protection and genetic improvement of Q. liaotungensis.
format: application/pdf
format: text/html
creator: Bin Guo
creator: Xiangchun Hao
creator: Lijun Han
creator: Yu Zhai
creator: Shuai Zhou
creator: Si Chen
creator: Da Ren
creator: Xinmin An
subject: Biodiversity
subject: Genetics
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.10922
publisher: PeerJ Inc.
rights: © 2021 Guo et al.
abstract: Background Quercus liaotungensis Koidz. is an ecologically and economically important tree species widely distributed in Northern China. However, the effective assessment, utilization, and protection of Q. liaotungensis resources remain unexplored. Methods In total, 120 samples obtained from 12 Q. liaotungensis populations of Northern China were investigated for genetic diversity and structure using 19 simple sequence repeat (SSR) primer pairs. Results The total number of alleles detected was 293, the average number of effective allele (Ne) was 6.084, the genetic differentiation coefficient (Fst) was 0.033, and the mean observed heterozygosity (Ho) and expected heterozygosity (He) were 0.690 and 0.801, respectively. Moreover, analysis of molecular variance (AMOVA) showed a 5.5% genetic variation among 12 Q. liaotungensis populations, indicating that a high level of genetic diversity and a low degree of genetic differentiation among Q. liaotungensis populations. STRUCTURE and cluster analysis divided the 12 Q. liaotungensis populations into the following three subpopulations: Bashang Plateau subpopulation (SH), Liaodong Peninsula subpopulation (NC), and Loess Plateau subpopulation (other 10 populations). The cluster analysis based on 19 climatic factors was consistent with the genetic structure. A positive correlation was found between genetic distance and geographical distance (r = 0.638, p = 0.028) by the Mantel test, and two boundaries were found among the 12 Q. liaotungensis populations by the Barrier analysis, indicating that Q. liaotungensis populations existed isolated by geographical distance and physical barrier. Conclusion This study suggests that geographical isolation, physical barrier, climatic types, and natural hybridization promote the formation of genetic structures, which can contribute to future protection and genetic improvement of Q. liaotungensis.
bibliographic citation: Guo et al. (2021) Unraveling the genetic diversity and structure of Quercus liaotungensis population through analysis of microsatellite markers. PeerJ 9:e10922 https://doi.org/10.7717/peerj.10922
date submitted: 2020-10-05
date accepted: 2021-01-19
issued: 2021-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Bin
author list: Agent
  family name: Hao
  given name: Xiangchun
author list: Agent
  family name: Han
  given name: Lijun
author list: Agent
  family name: Zhai
  given name: Yu
author list: Agent
  family name: Zhou
  given name: Shuai
author list: Agent
  family name: Chen
  given name: Si
author list: Agent
  family name: Ren
  given name: Da
author list: Agent
  family name: An
  given name: Xinmin
doi: 10.7717/peerj.10922
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-14
copyright: ©2021 Guo et al.
attribution name: Guo et al.

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