PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: G3BP2, a stress granule assembly factor, is dispensable for spermatogenesis in mice
items: Longitudinal study on the effect of keratinized mucosal augmentation surrounding dental implants in preventing peri-implant bone loss
items: Providing choice of feedback affects perceived choice but does not affect performance
items: The potential of CircRNA1002 as a biomarker in hepatitis B virus-related hepatocellular carcinoma
items: High-resolution melting (HRM) curve analysis as a potential tool for the identification of earthworm species and haplotypes
items: Comparative transcriptomics reveals new insights into melatonin-enhanced drought tolerance in naked oat seedlings
items: Happiness, depression, physical activity and cognition among the middle and old-aged population in China: a conditional process analysis
items: Enhanced specialized metabolite, trichome density, and biosynthetic gene expression in Stevia rebaudiana (Bertoni) Bertoni plants inoculated with endophytic bacteria Enterobacter hormaechei
items: Therapeutic targets and signaling pathways of active components of QiLing decoction against castration-resistant prostate cancer based on network pharmacology
items: A combined test for feature selection on sparse metaproteomics data—an alternative to missing value imputation

G3BP2, a stress granule assembly factor, is dispensable for spermatogenesis in mice
type: item
type: AcademicArticle
description: Background Spermatogenesis is a complex process that includes mitosis, meiosis, and spermiogenesis. During spermatogenesis, genetic factors play a vital role inthe formation of properly functioning sperm. GTPase-activating protein (SH3 domain)-binding protein 2 (G3BP2) is known to take part in immune responses, mRNA transport, and stress-granule assembly. However, its role in male fertility is unclear. Here, we generated a G3bp2 conditional knockout (cKO) mouse model to explore the function of G3BP2 in male fertility. Methods Polymerase chain reaction (PCR) and western blotting (WB) were used to confirm testis-specific G3bp2 knockout. Hematoxylin-eosin (HE) staining to observe testicular morphology and epididymal structure. Computer-aided sperm analysis (CASA) to detect sperm concentration and motility. Terminal deoxynucleotidyl transferase-dUTP nick-end labeling (TUNEL) assay was used to detect apoptotic cells. Results We found that cKO male mice are fertile with the normal morphology of the testis and sperm. Additionally, CASA of the semen from cKO mice showed that they all had a similar sperm concentration and motility. In addition, sperm from these mice exhibited a similar morphology. But the tunnel assay revealed increased apoptosis in their testes relative to the level in the wild type (WT). Conclusion Together, our data demonstrate that G3BP2 is dispensable for spermatogenesis and male fertility in mice albeit with the increased germ-cell apoptosis.
format: application/pdf
format: text/html
creator: Damin Yun
creator: Liwei Zhou
creator: Jie Shi
creator: Xinyao Li
creator: Xiaolong Wu
creator: Fei Sun
subject: Cell Biology
subject: Genetics
subject: Microbiology
description: doi:10.7717/peerj.13532
publisher: PeerJ Inc.
rights: © 2022 Yun et al.
abstract: Background Spermatogenesis is a complex process that includes mitosis, meiosis, and spermiogenesis. During spermatogenesis, genetic factors play a vital role inthe formation of properly functioning sperm. GTPase-activating protein (SH3 domain)-binding protein 2 (G3BP2) is known to take part in immune responses, mRNA transport, and stress-granule assembly. However, its role in male fertility is unclear. Here, we generated a G3bp2 conditional knockout (cKO) mouse model to explore the function of G3BP2 in male fertility. Methods Polymerase chain reaction (PCR) and western blotting (WB) were used to confirm testis-specific G3bp2 knockout. Hematoxylin-eosin (HE) staining to observe testicular morphology and epididymal structure. Computer-aided sperm analysis (CASA) to detect sperm concentration and motility. Terminal deoxynucleotidyl transferase-dUTP nick-end labeling (TUNEL) assay was used to detect apoptotic cells. Results We found that cKO male mice are fertile with the normal morphology of the testis and sperm. Additionally, CASA of the semen from cKO mice showed that they all had a similar sperm concentration and motility. In addition, sperm from these mice exhibited a similar morphology. But the tunnel assay revealed increased apoptosis in their testes relative to the level in the wild type (WT). Conclusion Together, our data demonstrate that G3BP2 is dispensable for spermatogenesis and male fertility in mice albeit with the increased germ-cell apoptosis.
bibliographic citation: Yun et al. (2022) G3BP2, a stress granule assembly factor, is dispensable for spermatogenesis in mice. PeerJ 10:e13532 https://doi.org/10.7717/peerj.13532
date submitted: 2022-03-17
date accepted: 2022-05-12
issued: 2022-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yun
  given name: Damin
author list: Agent
  family name: Zhou
  given name: Liwei
author list: Agent
  family name: Shi
  given name: Jie
author list: Agent
  family name: Li
  given name: Xinyao
author list: Agent
  family name: Wu
  given name: Xiaolong
author list: Agent
  family name: Sun
  given name: Fei
doi: 10.7717/peerj.13532
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-28
copyright: © 2022 Yun et al.
attribution name: Yun et al.

Longitudinal study on the effect of keratinized mucosal augmentation surrounding dental implants in preventing peri-implant bone loss
type: item
type: AcademicArticle
description: Background Dental implant therapy is a well-established method of prosthetic rehabilitation of missing teeth. To maintain the health of the surrounding tissue, management of risk factors/indicators and daily maintenance are important. It still remains controversial whether a certain amount of keratinized mucosal width is essential for maintaining the health of peri-implant tissue. The purpose of this multicenter retrospective study was to assess the correlation between bone loss around dental implant and the amount of keratinized tissue width. Methods A total of 1,644 implants were evaluated. Data was collected about participants’ general and dental history, as well as implant details. Bone resorption around implant was calculated from intra-oral radiographs taken after 1 year and more than 3 years of function. Implants were classified into three groups; received free gingival graft or apically repositioned flap surgery for increasing the keratinized mucosa ≥2 mm width (group A), keratinized mucosa width ≥2 mm (group B), and keratinized mucosa width <2 mm (group C). These data were analyzed by propensity score analysis and a generalized linear regression analysis was performed to compare the bone resorption among groups. Results Mean functional time was 55.8 months (SD = 20.5) in group A, 67.6 months (SD = 28.1) in group B, and 74.5 months (SD = 32.9) in group C. Mean bone resorption of groups A, B, and C were 0.08 mm (SD = 0.40), 0.18 mm (SD = 0.66), and 0.44 mm (SD = 0.40). Groups A and B had significantly lower bone resorption than group C. Conclusion The results in this study show the importance of keratinized mucosa in maintaining the peri-implant bone. Our findings also suggest that mucosal transplantation is useful, as opposed to narrowing of the keratinized mucosa.
format: application/pdf
format: text/html
creator: Takeshi Kikuchi
creator: Masahiro Wada
creator: Tomoaki Mameno
creator: Daisuke Hasegawa
creator: Giovanni Serino
creator: Kazunori Ikebe
subject: Anatomy and Physiology
subject: Dentistry
subject: Drugs and Devices
subject: Orthopedics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.13598
publisher: PeerJ Inc.
rights: © 2022 Kikuchi et al.
abstract: Background Dental implant therapy is a well-established method of prosthetic rehabilitation of missing teeth. To maintain the health of the surrounding tissue, management of risk factors/indicators and daily maintenance are important. It still remains controversial whether a certain amount of keratinized mucosal width is essential for maintaining the health of peri-implant tissue. The purpose of this multicenter retrospective study was to assess the correlation between bone loss around dental implant and the amount of keratinized tissue width. Methods A total of 1,644 implants were evaluated. Data was collected about participants’ general and dental history, as well as implant details. Bone resorption around implant was calculated from intra-oral radiographs taken after 1 year and more than 3 years of function. Implants were classified into three groups; received free gingival graft or apically repositioned flap surgery for increasing the keratinized mucosa ≥2 mm width (group A), keratinized mucosa width ≥2 mm (group B), and keratinized mucosa width <2 mm (group C). These data were analyzed by propensity score analysis and a generalized linear regression analysis was performed to compare the bone resorption among groups. Results Mean functional time was 55.8 months (SD = 20.5) in group A, 67.6 months (SD = 28.1) in group B, and 74.5 months (SD = 32.9) in group C. Mean bone resorption of groups A, B, and C were 0.08 mm (SD = 0.40), 0.18 mm (SD = 0.66), and 0.44 mm (SD = 0.40). Groups A and B had significantly lower bone resorption than group C. Conclusion The results in this study show the importance of keratinized mucosa in maintaining the peri-implant bone. Our findings also suggest that mucosal transplantation is useful, as opposed to narrowing of the keratinized mucosa.
bibliographic citation: Kikuchi et al. (2022) Longitudinal study on the effect of keratinized mucosal augmentation surrounding dental implants in preventing peri-implant bone loss. PeerJ 10:e13598 https://doi.org/10.7717/peerj.13598
date submitted: 2022-03-23
date accepted: 2022-05-25
issued: 2022-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kikuchi
  given name: Takeshi
author list: Agent
  family name: Wada
  given name: Masahiro
author list: Agent
  family name: Mameno
  given name: Tomoaki
author list: Agent
  family name: Hasegawa
  given name: Daisuke
author list: Agent
  family name: Serino
  given name: Giovanni
author list: Agent
  family name: Ikebe
  given name: Kazunori
doi: 10.7717/peerj.13598
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-28
copyright: ©2022 Kikuchi et al.
attribution name: Kikuchi et al.

Providing choice of feedback affects perceived choice but does not affect performance
type: item
type: AcademicArticle
description: Background Autonomy or choice can lead to improved learning in various educational domains. The purpose of this online study was to examine whether giving participants a choice regarding the frequency of their received feedback (either after each individual trial or after a block of trials) in a computerized alternate task-switching task, will affect their performance. Methods Participants (n = 148) were randomly assigned to three groups: choice group (n = 49), online feedback group (n = 51), and summary feedback group (n = 48). From those three groups we created two groups: a choice group and a no-choice group (n = 49 in each group). All participants performed eight familiarization trials, a pre-test of 24 trials, five blocks of 24 trials for practice, and a post-test of 24 trials. After completing the task, the participants were asked about their perceived feeling of choice and completed the short form of the International Positive and Negative Affect Schedule. Results The participants in the choice group had higher perceived choice compared with the participants in the no-choice group (8.41 vs 5.47 out of 10, respectively). However, this higher perceived choice did not materialize into better performance during practice or in the post-test.
format: application/pdf
format: text/html
creator: Gal Ziv
creator: Ronnie Lidor
creator: Oron Levin
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.13631
publisher: PeerJ Inc.
rights: © 2022 Ziv et al.
abstract: Background Autonomy or choice can lead to improved learning in various educational domains. The purpose of this online study was to examine whether giving participants a choice regarding the frequency of their received feedback (either after each individual trial or after a block of trials) in a computerized alternate task-switching task, will affect their performance. Methods Participants (n = 148) were randomly assigned to three groups: choice group (n = 49), online feedback group (n = 51), and summary feedback group (n = 48). From those three groups we created two groups: a choice group and a no-choice group (n = 49 in each group). All participants performed eight familiarization trials, a pre-test of 24 trials, five blocks of 24 trials for practice, and a post-test of 24 trials. After completing the task, the participants were asked about their perceived feeling of choice and completed the short form of the International Positive and Negative Affect Schedule. Results The participants in the choice group had higher perceived choice compared with the participants in the no-choice group (8.41 vs 5.47 out of 10, respectively). However, this higher perceived choice did not materialize into better performance during practice or in the post-test.
bibliographic citation: Ziv et al. (2022) Providing choice of feedback affects perceived choice but does not affect performance. PeerJ 10:e13631 https://doi.org/10.7717/peerj.13631
date submitted: 2022-02-21
date accepted: 2022-06-03
issued: 2022-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ziv
  given name: Gal
author list: Agent
  family name: Lidor
  given name: Ronnie
author list: Agent
  family name: Levin
  given name: Oron
doi: 10.7717/peerj.13631
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-28
copyright: © 2022 Ziv et al.
attribution name: Ziv et al.

The potential of CircRNA1002 as a biomarker in hepatitis B virus-related hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Although hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, there is a lack of effective diagnostic measures. Circular RNAs (circRNAs) can be used as biomarkers for monitoring the occurrence and development of HCC. However, a convenient and reliable serum circRNA biomarker is not currently available. Materials & Methods CircRNA expression profiles were explored using high-throughput sequencing technology, and targeted circRNAs and mRNAs were validated by quantitative reverse transcription PCR (RT-qPCR). The biological functions of circRNAs were investigated using Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Downstream miRNAs and mRNAs of dysregulated circRNAs were predicted using TargetScan, miRanda, and miRDB; then circRNA-miRNA-mRNA interaction networks were constructed based on sequencing data and the Cancer Genome Atlas (TCGA). Results A total of 50,327 circRNAs were identified, with 1,187 circRNAs significantly differentially expressed between hepatitis B virus (HBV)-related HCC and HBV asymptomatic carriers. Among these circRNAs, four (circRNA1002, circRNA7941, circRNA 39338, and circRNA44142) were validated by RT-qPCR as being statistically different either in HCC tissue or serum samples. circRNA1002 was significantly down-regulated in both HCC serum and tissue, indicating its reliability. Bioinformatics analysis showed that circRNA1002-associated genes were enriched in GO terms relating to hormone pathway and cell-cell interaction processes, which are involved in the progression of HCC. Conclusion Our circRNA analysis of HCC patients and HBV asymptomatic carriers showed that circRNA1002 may be a reliable serum biomarker for HCC. These results could provide an improved assay for the early detection of HCC.
format: application/pdf
format: text/html
creator: Ying Li
creator: Ronghua Li
creator: Da Cheng
creator: Xiaoyu Fu
creator: Lei Fu
creator: Shifang Peng
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Public Health
subject: Medical Genetics
description: doi:10.7717/peerj.13640
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background Although hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, there is a lack of effective diagnostic measures. Circular RNAs (circRNAs) can be used as biomarkers for monitoring the occurrence and development of HCC. However, a convenient and reliable serum circRNA biomarker is not currently available. Materials & Methods CircRNA expression profiles were explored using high-throughput sequencing technology, and targeted circRNAs and mRNAs were validated by quantitative reverse transcription PCR (RT-qPCR). The biological functions of circRNAs were investigated using Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Downstream miRNAs and mRNAs of dysregulated circRNAs were predicted using TargetScan, miRanda, and miRDB; then circRNA-miRNA-mRNA interaction networks were constructed based on sequencing data and the Cancer Genome Atlas (TCGA). Results A total of 50,327 circRNAs were identified, with 1,187 circRNAs significantly differentially expressed between hepatitis B virus (HBV)-related HCC and HBV asymptomatic carriers. Among these circRNAs, four (circRNA1002, circRNA7941, circRNA 39338, and circRNA44142) were validated by RT-qPCR as being statistically different either in HCC tissue or serum samples. circRNA1002 was significantly down-regulated in both HCC serum and tissue, indicating its reliability. Bioinformatics analysis showed that circRNA1002-associated genes were enriched in GO terms relating to hormone pathway and cell-cell interaction processes, which are involved in the progression of HCC. Conclusion Our circRNA analysis of HCC patients and HBV asymptomatic carriers showed that circRNA1002 may be a reliable serum biomarker for HCC. These results could provide an improved assay for the early detection of HCC.
bibliographic citation: Li et al. (2022) The potential of CircRNA1002 as a biomarker in hepatitis B virus-related hepatocellular carcinoma. PeerJ 10:e13640 https://doi.org/10.7717/peerj.13640
date submitted: 2021-08-09
date accepted: 2022-06-06
issued: 2022-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Li
  given name: Ronghua
author list: Agent
  family name: Cheng
  given name: Da
author list: Agent
  family name: Fu
  given name: Xiaoyu
author list: Agent
  family name: Fu
  given name: Lei
author list: Agent
  family name: Peng
  given name: Shifang
doi: 10.7717/peerj.13640
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-28
copyright: © 2022 Li et al.
attribution name: Li et al.

High-resolution melting (HRM) curve analysis as a potential tool for the identification of earthworm species and haplotypes
type: item
type: AcademicArticle
description: Background Earthworm communities are an important component of soil biodiversity and contribute to a number of ecosystem functions such as soil-nutrient cycling. Taxonomic identification is an essential requirement to assess earthworm biodiversity and functionality. Although morphological identification of species is labour-intensive, it is the most commonly used method due to a lack of cost-efficient alternatives. Molecular approaches to identify earthworms at species and haplotype level such as DNA barcoding are gaining popularity in science but are rarely applied in practice. In contrast to barcoding, the differentiation of PCR products based on their thermal denaturation properties using high-resolution melting (HRM) curve analysis is a fast and cost-efficient molecular closed-tube, post-PCR tool that allows identification of taxa. Methods We developed a HRM curve assay to identify eight earthworm species common to agricultural soils in Central Europe (Allolobophora chlorotica, Aporrectodea caliginosa, Apo. limicola, Apo. longa, Apo. rosea, Lumbricus castaneus, L. rubellus, and L. terrestris). For this, a new primer pair targeting a 158-bp long subregion of the cytochrome c oxidase I (COI) gene was designed. Our HRM assay was further tested for the differentiation of COI haplotypes using 28 individuals of the earthworm species Allo. chlorotica. Furthermore, we developed a novel extraction method for DNA from earthworm tissue that is fast and requires minimal consumables and laboratory equipment. Results The developed HRM curve assay allowed identifying all eight earthworm species. Performing the assay on 28 individuals of the earthworm species Allo. chlorotica enabled the distinction among different COI haplotypes. Furthermore, we successfully developed a rapid, robust, scalable, and inexpensive method for the extraction of earthworm DNA from fresh or frozen tissue. Conclusions HRM curve analysis of COI genes has the potential to identify earthworm species and h…
format: application/pdf
format: text/html
creator: Anna Vaupel
creator: Bernd Hommel
creator: Lukas Beule
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.13661
publisher: PeerJ Inc.
rights: © 2022 Vaupel et al.
abstract: Background Earthworm communities are an important component of soil biodiversity and contribute to a number of ecosystem functions such as soil-nutrient cycling. Taxonomic identification is an essential requirement to assess earthworm biodiversity and functionality. Although morphological identification of species is labour-intensive, it is the most commonly used method due to a lack of cost-efficient alternatives. Molecular approaches to identify earthworms at species and haplotype level such as DNA barcoding are gaining popularity in science but are rarely applied in practice. In contrast to barcoding, the differentiation of PCR products based on their thermal denaturation properties using high-resolution melting (HRM) curve analysis is a fast and cost-efficient molecular closed-tube, post-PCR tool that allows identification of taxa. Methods We developed a HRM curve assay to identify eight earthworm species common to agricultural soils in Central Europe (Allolobophora chlorotica, Aporrectodea caliginosa, Apo. limicola, Apo. longa, Apo. rosea, Lumbricus castaneus, L. rubellus, and L. terrestris). For this, a new primer pair targeting a 158-bp long subregion of the cytochrome c oxidase I (COI) gene was designed. Our HRM assay was further tested for the differentiation of COI haplotypes using 28 individuals of the earthworm species Allo. chlorotica. Furthermore, we developed a novel extraction method for DNA from earthworm tissue that is fast and requires minimal consumables and laboratory equipment. Results The developed HRM curve assay allowed identifying all eight earthworm species. Performing the assay on 28 individuals of the earthworm species Allo. chlorotica enabled the distinction among different COI haplotypes. Furthermore, we successfully developed a rapid, robust, scalable, and inexpensive method for the extraction of earthworm DNA from fresh or frozen tissue. Conclusions HRM curve analysis of COI genes has the potential to identify earthworm species and h…
bibliographic citation: Vaupel et al. (2022) High-resolution melting (HRM) curve analysis as a potential tool for the identification of earthworm species and haplotypes. PeerJ 10:e13661 https://doi.org/10.7717/peerj.13661
date submitted: 2022-04-19
date accepted: 2022-06-10
issued: 2022-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vaupel
  given name: Anna
author list: Agent
  family name: Hommel
  given name: Bernd
author list: Agent
  family name: Beule
  given name: Lukas
doi: 10.7717/peerj.13661
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-28
copyright: ©2022 Vaupel et al.
attribution name: Vaupel et al.

Comparative transcriptomics reveals new insights into melatonin-enhanced drought tolerance in naked oat seedlings
type: item
type: AcademicArticle
description: The growth and development of naked oat (Avena nuda L.) seedlings, a grain recognized as nutritious and healthy, is limited by drought. Melatonin plays a positive role in plants under drought stress. However, its function is unclear in naked oats. This study demonstrated that melatonin enhances drought stress tolerance in oat seedlings. Melatonin application alleviated the declining growth parameters of two naked oat varieties, Huazao No.2 (H2) and Jizhangyou No.15 (J15), under drought stress by increasing the chlorophyll content and photosynthetic rate of leaves. Melatonin pretreatment induced differential gene expression in H2 and J15 under drought stress. Subsequently, the differential gene expression responses to melatonin in the two varieties were further analyzed. The key drought response transcription factors and the regulatory effect of melatonin on drought-related transcription factors were assessed, focusing on genes encoding proteins in the ABA signal transduction pathway, including PYL, PP2C, ABF, SNRK2, and IAA. Taken together, this study provides new insights into the effect and underlying mechanism of melatonin in alleviating drought stress in naked oat seedlings.
format: application/pdf
format: text/html
creator: Xinjun Zhang
creator: Wenting Liu
creator: Yaci Lv
creator: Jing Bai
creator: Tianliang Li
creator: Xiaohong Yang
creator: Liantao Liu
creator: Haitao Zhou
subject: Plant Science
description: doi:10.7717/peerj.13669
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: The growth and development of naked oat (Avena nuda L.) seedlings, a grain recognized as nutritious and healthy, is limited by drought. Melatonin plays a positive role in plants under drought stress. However, its function is unclear in naked oats. This study demonstrated that melatonin enhances drought stress tolerance in oat seedlings. Melatonin application alleviated the declining growth parameters of two naked oat varieties, Huazao No.2 (H2) and Jizhangyou No.15 (J15), under drought stress by increasing the chlorophyll content and photosynthetic rate of leaves. Melatonin pretreatment induced differential gene expression in H2 and J15 under drought stress. Subsequently, the differential gene expression responses to melatonin in the two varieties were further analyzed. The key drought response transcription factors and the regulatory effect of melatonin on drought-related transcription factors were assessed, focusing on genes encoding proteins in the ABA signal transduction pathway, including PYL, PP2C, ABF, SNRK2, and IAA. Taken together, this study provides new insights into the effect and underlying mechanism of melatonin in alleviating drought stress in naked oat seedlings.
bibliographic citation: Zhang et al. (2022) Comparative transcriptomics reveals new insights into melatonin-enhanced drought tolerance in naked oat seedlings. PeerJ 10:e13669 https://doi.org/10.7717/peerj.13669
date submitted: 2021-09-22
date accepted: 2022-06-10
issued: 2022-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xinjun
author list: Agent
  family name: Liu
  given name: Wenting
author list: Agent
  family name: Lv
  given name: Yaci
author list: Agent
  family name: Bai
  given name: Jing
author list: Agent
  family name: Li
  given name: Tianliang
author list: Agent
  family name: Yang
  given name: Xiaohong
author list: Agent
  family name: Liu
  given name: Liantao
author list: Agent
  family name: Zhou
  given name: Haitao
doi: 10.7717/peerj.13669
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-28
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

Happiness, depression, physical activity and cognition among the middle and old-aged population in China: a conditional process analysis
type: item
type: AcademicArticle
description: Background Happiness is one variable of subjective well-being, which has been increasingly shown to have protective effects on health. Although the association between happiness and cognition has been established, the mechanism by which happiness leads to cognition remains unclear. Since happiness, depression, and physical activity may all be related to cognition, and happiness is related to depression and physical activity, this study explored the effect of depression and physical activity on the relationship between happiness and cognition among middle and old-aged individuals in China. Methods Data on 14,344 participants above 45 years of age were obtained from the 2018 China Family Panel Studies survey. A multiple linear regression analysis was performed to identify the correlation factors of cognition. The conditional process analysis was used to assess the mediatory effect of depression and physical activity on the relationship between happiness and cognition. Results Residence, age, sex, income level, social status, smoking, napping, reading, education, exercise times, satisfaction, happiness, and depression had associations with cognition. When other variables were held constant, cognition score increased by 0.029 standard deviation(SD) for every 1 SD increased in happiness. Mediation analysis showed that happiness had a significant positive total effect on cognition. The direct effect of happiness was significant and accounted for 57.86% of the total effect. The mediatory effect of depression (path of happiness→depression→cognition) accounted for 38.31% of the total effect, whereas that of physical activity (path of happiness→exercise times→cognition) accounted for 3.02% of the total effect. Conclusion Happiness has a positive correlation with cognitive function, and depression and physical activity play mediatory roles in this association. Effective interventions to improve happiness levels of middle and old-aged population will not only improve their subj…
format: application/pdf
format: text/html
creator: Xiaojuan Shi
creator: Xiaoxue He
creator: Degong Pan
creator: Hui Qiao
creator: Jiangping Li
subject: Cognitive Disorders
subject: Geriatrics
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.13673
publisher: PeerJ Inc.
rights: © 2022 Shi et al.
abstract: Background Happiness is one variable of subjective well-being, which has been increasingly shown to have protective effects on health. Although the association between happiness and cognition has been established, the mechanism by which happiness leads to cognition remains unclear. Since happiness, depression, and physical activity may all be related to cognition, and happiness is related to depression and physical activity, this study explored the effect of depression and physical activity on the relationship between happiness and cognition among middle and old-aged individuals in China. Methods Data on 14,344 participants above 45 years of age were obtained from the 2018 China Family Panel Studies survey. A multiple linear regression analysis was performed to identify the correlation factors of cognition. The conditional process analysis was used to assess the mediatory effect of depression and physical activity on the relationship between happiness and cognition. Results Residence, age, sex, income level, social status, smoking, napping, reading, education, exercise times, satisfaction, happiness, and depression had associations with cognition. When other variables were held constant, cognition score increased by 0.029 standard deviation(SD) for every 1 SD increased in happiness. Mediation analysis showed that happiness had a significant positive total effect on cognition. The direct effect of happiness was significant and accounted for 57.86% of the total effect. The mediatory effect of depression (path of happiness→depression→cognition) accounted for 38.31% of the total effect, whereas that of physical activity (path of happiness→exercise times→cognition) accounted for 3.02% of the total effect. Conclusion Happiness has a positive correlation with cognitive function, and depression and physical activity play mediatory roles in this association. Effective interventions to improve happiness levels of middle and old-aged population will not only improve their subj…
bibliographic citation: Shi et al. (2022) Happiness, depression, physical activity and cognition among the middle and old-aged population in China: a conditional process analysis. PeerJ 10:e13673 https://doi.org/10.7717/peerj.13673
date submitted: 2022-04-11
date accepted: 2022-06-13
issued: 2022-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Xiaojuan
author list: Agent
  family name: He
  given name: Xiaoxue
author list: Agent
  family name: Pan
  given name: Degong
author list: Agent
  family name: Qiao
  given name: Hui
author list: Agent
  family name: Li
  given name: Jiangping
doi: 10.7717/peerj.13673
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-28
copyright: ©2022 Shi et al.
attribution name: Shi et al.

Enhanced specialized metabolite, trichome density, and biosynthetic gene expression in Stevia rebaudiana (Bertoni) Bertoni plants inoculated with endophytic bacteria Enterobacter hormaechei
type: item
type: AcademicArticle
description: Stevia rebaudiana (Bertoni) Bertoni is a plant of economic interest in the food and pharmaceutical industries due its steviol glycosides (SG), which are rich in metabolites that are 300 times sweeter than sucrose. In addition, S. rebaudiana plants contain phenolic compounds and flavonoids with antioxidant activity. Endophytic bacteria promote the growth and development and modulate the metabolism of the host plant. However, little is known regarding the role of endophytic bacteria in the growth; synthesis of SG, flavonoids and phenolic compounds; and the relationship between trichome development and specialized metabolites in S. rebaudiana, which was the subject of this study. The 12 bacteria tested did not increase the growth of S. rebaudiana plants; however, the content of SG increased with inoculation with the bacteria Enterobacter hormaechei H2A3 and E. hormaechei H5A2. The SG content in leaves paralleled an increase in the density of glandular, short, and large trichome. The image analysis of S. rebaudiana leaves showed the presence of SG, phenolic compounds, and flavonoids principally in glandular and short trichomes. The increase in the transcript levels of the KO, KAH, UGT74G1, and UGT76G1 genes was related to the SG concentration in plants of S. rebaudiana inoculated with E. hormaechei H2A3 and E. hormaechei H5A2. In conclusion, inoculation with the stimulating endophytes E. hormaechei H2A3 and E. hormaechei H5A2 increased SG synthesis, flavonoid content and flavonoid accumulation in the trichomes of S. rebaudiana plants.
format: application/pdf
format: text/html
creator: Dumas G. Oviedo-Pereira
creator: Melina López-Meyer
creator: Silvia Evangelista-Lozano
creator: Luis G. Sarmiento-López
creator: Gabriela Sepúlveda-Jiménez
creator: Mario Rodríguez-Monroy
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13675
publisher: PeerJ Inc.
rights: © 2022 Oviedo-Pereira et al.
abstract: Stevia rebaudiana (Bertoni) Bertoni is a plant of economic interest in the food and pharmaceutical industries due its steviol glycosides (SG), which are rich in metabolites that are 300 times sweeter than sucrose. In addition, S. rebaudiana plants contain phenolic compounds and flavonoids with antioxidant activity. Endophytic bacteria promote the growth and development and modulate the metabolism of the host plant. However, little is known regarding the role of endophytic bacteria in the growth; synthesis of SG, flavonoids and phenolic compounds; and the relationship between trichome development and specialized metabolites in S. rebaudiana, which was the subject of this study. The 12 bacteria tested did not increase the growth of S. rebaudiana plants; however, the content of SG increased with inoculation with the bacteria Enterobacter hormaechei H2A3 and E. hormaechei H5A2. The SG content in leaves paralleled an increase in the density of glandular, short, and large trichome. The image analysis of S. rebaudiana leaves showed the presence of SG, phenolic compounds, and flavonoids principally in glandular and short trichomes. The increase in the transcript levels of the KO, KAH, UGT74G1, and UGT76G1 genes was related to the SG concentration in plants of S. rebaudiana inoculated with E. hormaechei H2A3 and E. hormaechei H5A2. In conclusion, inoculation with the stimulating endophytes E. hormaechei H2A3 and E. hormaechei H5A2 increased SG synthesis, flavonoid content and flavonoid accumulation in the trichomes of S. rebaudiana plants.
bibliographic citation: Oviedo-Pereira et al. (2022) Enhanced specialized metabolite, trichome density, and biosynthetic gene expression in Stevia rebaudiana (Bertoni) Bertoni plants inoculated with endophytic bacteria Enterobacter hormaechei. PeerJ 10:e13675 https://doi.org/10.7717/peerj.13675
date submitted: 2022-02-11
date accepted: 2022-06-13
issued: 2022-06-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oviedo-Pereira
  given name: Dumas G.
author list: Agent
  family name: López-Meyer
  given name: Melina
author list: Agent
  family name: Evangelista-Lozano
  given name: Silvia
author list: Agent
  family name: Sarmiento-López
  given name: Luis G.
author list: Agent
  family name: Sepúlveda-Jiménez
  given name: Gabriela
author list: Agent
  family name: Rodríguez-Monroy
  given name: Mario
doi: 10.7717/peerj.13675
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-28
copyright: ©2022 Oviedo-Pereira et al.
attribution name: Oviedo-Pereira et al.

Therapeutic targets and signaling pathways of active components of QiLing decoction against castration-resistant prostate cancer based on network pharmacology
type: item
type: AcademicArticle
description: QiLing decoction (QLD) is a traditional Chinese medicine compound. This study aims to explore the therapeutic effect of QLD in castration-resistant prostate cancer (CRPC) and its potential bio-targets. A total of 51 active components and QLD 149 targets were identified using bioinformatics analysis. Additionally, five optimal hub target genes were screened including tumor protein P53 (TP53), interleukin-6 (IL-6), vascular endothelial growth factor-A (VEGF-A), caspase-3 (CASP-3), and estrogen receptor-1 (ESR-1). The interrelated network between active components of QLD and their potential targets was constructed. The molecular function, biological processes, and signaling pathways of QLD-against CRPC were identified. Moreover, QLD was found to efficiently exert a repressive effect on CRPC tumor growth mainly by suppressing the activation of HIF-α/VEGFA and TNF-α/IL6 signaling pathways, and increasing the P53 expression level. These results successfully indicated the potential anti-CRPC mechanism of the active components of QLD.
format: application/pdf
format: text/html
creator: Hongwen Cao
creator: Dan Wang
creator: Renjie Gao
creator: Chenggong Li
creator: Yigeng Feng
creator: Lei Chen
subject: Biochemistry
subject: Bioinformatics
subject: Pharmacology
description: doi:10.7717/peerj.13481
publisher: PeerJ Inc.
rights: © 2022 Cao et al.
abstract: QiLing decoction (QLD) is a traditional Chinese medicine compound. This study aims to explore the therapeutic effect of QLD in castration-resistant prostate cancer (CRPC) and its potential bio-targets. A total of 51 active components and QLD 149 targets were identified using bioinformatics analysis. Additionally, five optimal hub target genes were screened including tumor protein P53 (TP53), interleukin-6 (IL-6), vascular endothelial growth factor-A (VEGF-A), caspase-3 (CASP-3), and estrogen receptor-1 (ESR-1). The interrelated network between active components of QLD and their potential targets was constructed. The molecular function, biological processes, and signaling pathways of QLD-against CRPC were identified. Moreover, QLD was found to efficiently exert a repressive effect on CRPC tumor growth mainly by suppressing the activation of HIF-α/VEGFA and TNF-α/IL6 signaling pathways, and increasing the P53 expression level. These results successfully indicated the potential anti-CRPC mechanism of the active components of QLD.
bibliographic citation: Cao et al. (2022) Therapeutic targets and signaling pathways of active components of QiLing decoction against castration-resistant prostate cancer based on network pharmacology. PeerJ 10:e13481 https://doi.org/10.7717/peerj.13481
date submitted: 2021-07-22
date accepted: 2022-05-02
issued: 2022-06-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Hongwen
author list: Agent
  family name: Wang
  given name: Dan
author list: Agent
  family name: Gao
  given name: Renjie
author list: Agent
  family name: Li
  given name: Chenggong
author list: Agent
  family name: Feng
  given name: Yigeng
author list: Agent
  family name: Chen
  given name: Lei
doi: 10.7717/peerj.13481
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-27
copyright: ©2022 Cao et al.
attribution name: Cao et al.

A combined test for feature selection on sparse metaproteomics data—an alternative to missing value imputation
type: item
type: AcademicArticle
description: One of the difficulties encountered in the statistical analysis of metaproteomics data is the high proportion of missing values, which are usually treated by imputation. Nevertheless, imputation methods are based on restrictive assumptions regarding missingness mechanisms, namely “at random” or “not at random”. To circumvent these limitations in the context of feature selection in a multi-class comparison, we propose a univariate selection method that combines a test of association between missingness and classes, and a test for difference of observed intensities between classes. This approach implicitly handles both missingness mechanisms. We performed a quantitative and qualitative comparison of our procedure with imputation-based feature selection methods on two experimental data sets, as well as simulated data with various scenarios regarding the missingness mechanisms and the nature of the difference of expression (differential intensity or differential presence). Whereas we observed similar performances in terms of prediction on the experimental data set, the feature ranking and selection from various imputation-based methods were strongly divergent. We showed that the combined test reaches a compromise by correlating reasonably with other methods, and remains efficient in all simulated scenarios unlike imputation-based feature selection methods.
format: application/pdf
format: text/html
creator: Sandra Plancade
creator: Magali Berland
creator: Mélisande Blein-Nicolas
creator: Olivier Langella
creator: Ariane Bassignani
creator: Catherine Juste
subject: Bioinformatics
subject: Molecular Biology
subject: Statistics
description: doi:10.7717/peerj.13525
publisher: PeerJ Inc.
rights: © 2022 Plancade et al.
abstract: One of the difficulties encountered in the statistical analysis of metaproteomics data is the high proportion of missing values, which are usually treated by imputation. Nevertheless, imputation methods are based on restrictive assumptions regarding missingness mechanisms, namely “at random” or “not at random”. To circumvent these limitations in the context of feature selection in a multi-class comparison, we propose a univariate selection method that combines a test of association between missingness and classes, and a test for difference of observed intensities between classes. This approach implicitly handles both missingness mechanisms. We performed a quantitative and qualitative comparison of our procedure with imputation-based feature selection methods on two experimental data sets, as well as simulated data with various scenarios regarding the missingness mechanisms and the nature of the difference of expression (differential intensity or differential presence). Whereas we observed similar performances in terms of prediction on the experimental data set, the feature ranking and selection from various imputation-based methods were strongly divergent. We showed that the combined test reaches a compromise by correlating reasonably with other methods, and remains efficient in all simulated scenarios unlike imputation-based feature selection methods.
bibliographic citation: Plancade et al. (2022) A combined test for feature selection on sparse metaproteomics data—an alternative to missing value imputation. PeerJ 10:e13525 https://doi.org/10.7717/peerj.13525
date submitted: 2021-08-20
date accepted: 2022-05-11
issued: 2022-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Plancade
  given name: Sandra
author list: Agent
  family name: Berland
  given name: Magali
author list: Agent
  family name: Blein-Nicolas
  given name: Mélisande
author list: Agent
  family name: Langella
  given name: Olivier
author list: Agent
  family name: Bassignani
  given name: Ariane
author list: Agent
  family name: Juste
  given name: Catherine
doi: 10.7717/peerj.13525
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-24
copyright: © 2022 Plancade et al.
attribution name: Plancade et al.

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