PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The prevalence and associated factors of sleep deprivation among healthy college students in China: a cross-sectional survey
items: Robustness of genetic diversity measures under spatial sampling and a new frequency-independent measure
items: Expression profiles of circular RNAs and interaction networks of competing endogenous RNAs in neurogenic bladder of rats following suprasacral spinal cord injury
items: A new gnathosaurine (Pterosauria, Archaeopterodactyloidea) from the Late Jurassic of Portugal
items: Performance of multigene testing in cytologically indeterminate thyroid nodules and molecular risk stratification
items: Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides
items: In vitro and ex vitro propagation of Turkish myrtles through conventional and plantform bioreactor systems
items: The mediating roles of coping styles and academic burnout in the relationship between stressors and depressive symptoms among Chinese postgraduates
items: Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19: a retrospective pilot study
items: Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators

The prevalence and associated factors of sleep deprivation among healthy college students in China: a cross-sectional survey
type: item
type: AcademicArticle
description: Background The prevalence of sleep deprivation among college students is increasing and has a few associated factors. Methods The present study analyzed 2,142 college students from 28 provinces in China. The Chinese version of the Pittsburgh Sleep Quality Index (PSQI) was used to assess sleep duration. Binary logistic regression was conducted to explore the sleep deprivation related factors. Age and gender were controlled as covariates. Results Among the 2,142 college students (27.7% male, 72.3% female), 1,620 (75.6%) reported the average sleep duration was below 7 h per day for one month, 49.3% (1,055/2,142) slept 6∼7 h (contains 6 h), 21.0% (449/2,142) slept 5∼6 h (contains 5 h), and 5.4% (116/2,142) slept <5 h. Age increased the risk of sleep deprivation, the adjusted odds ratio = 1.05 (95% CI [1.01∼1.10]). The adjusted odds ratio (A-OR) for sleep deprivation was higher for students of more than 60 min nap duration per day (A-OR = 2.35, 95% CI [1.45∼3.80]), and age growth (A-OR = 1.05, 95% CI [1.01∼1.10]). In contrast, A-ORs were lower among sleeping inconsistency between work and rest days (A-OR = 0.61, 95% CI [0.49∼0.75]), accustomed to staying up late (A-OR = 0.45, 95% CI [0.36∼0.57]), staying up late to work or study (A-OR = 0.62, 95% CI [0.49∼0.78]), stress (A-OR = 0.75, 95% CI [0.58∼0.98]), and repeated thoughts in bed had (A-OR = 0.79, 95% CI [0.62∼0.99]). Conclusions Sleep deprivation is extremely common among healthy college students in China. It is necessary to perform methods maintaining enough sleep due to the current high incidence of sleep deprivation. Controlling the nap duration and getting enough sleep on rest days to replace missing hours of sleep on workdays might improve college students’ sleep.
format: application/pdf
format: text/html
creator: Congcong Guo
creator: Songzhe Piao
creator: Chenyu Wang
creator: Lili Yu
creator: Kejun Wang
creator: Qian Qu
creator: Cuiting Zhang
creator: Xiaofei Yu
subject: Global Health
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.16009
publisher: PeerJ Inc.
rights: © 2023 Guo et al.
abstract: Background The prevalence of sleep deprivation among college students is increasing and has a few associated factors. Methods The present study analyzed 2,142 college students from 28 provinces in China. The Chinese version of the Pittsburgh Sleep Quality Index (PSQI) was used to assess sleep duration. Binary logistic regression was conducted to explore the sleep deprivation related factors. Age and gender were controlled as covariates. Results Among the 2,142 college students (27.7% male, 72.3% female), 1,620 (75.6%) reported the average sleep duration was below 7 h per day for one month, 49.3% (1,055/2,142) slept 6∼7 h (contains 6 h), 21.0% (449/2,142) slept 5∼6 h (contains 5 h), and 5.4% (116/2,142) slept <5 h. Age increased the risk of sleep deprivation, the adjusted odds ratio = 1.05 (95% CI [1.01∼1.10]). The adjusted odds ratio (A-OR) for sleep deprivation was higher for students of more than 60 min nap duration per day (A-OR = 2.35, 95% CI [1.45∼3.80]), and age growth (A-OR = 1.05, 95% CI [1.01∼1.10]). In contrast, A-ORs were lower among sleeping inconsistency between work and rest days (A-OR = 0.61, 95% CI [0.49∼0.75]), accustomed to staying up late (A-OR = 0.45, 95% CI [0.36∼0.57]), staying up late to work or study (A-OR = 0.62, 95% CI [0.49∼0.78]), stress (A-OR = 0.75, 95% CI [0.58∼0.98]), and repeated thoughts in bed had (A-OR = 0.79, 95% CI [0.62∼0.99]). Conclusions Sleep deprivation is extremely common among healthy college students in China. It is necessary to perform methods maintaining enough sleep due to the current high incidence of sleep deprivation. Controlling the nap duration and getting enough sleep on rest days to replace missing hours of sleep on workdays might improve college students’ sleep.
bibliographic citation: Guo et al. (2023) The prevalence and associated factors of sleep deprivation among healthy college students in China: a cross-sectional survey. PeerJ 11:e16009 https://doi.org/10.7717/peerj.16009
date submitted: 2023-02-24
date accepted: 2023-08-09
issued: 2023-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Congcong
author list: Agent
  family name: Piao
  given name: Songzhe
author list: Agent
  family name: Wang
  given name: Chenyu
author list: Agent
  family name: Yu
  given name: Lili
author list: Agent
  family name: Wang
  given name: Kejun
author list: Agent
  family name: Qu
  given name: Qian
author list: Agent
  family name: Zhang
  given name: Cuiting
author list: Agent
  family name: Yu
  given name: Xiaofei
doi: 10.7717/peerj.16009
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-18
copyright: ©2023 Guo et al.
attribution name: Guo et al.

Robustness of genetic diversity measures under spatial sampling and a new frequency-independent measure
type: item
type: AcademicArticle
description: The genetic diversity of a taxon has often been estimated by genetic diversity measures. However, they assume random sampling of individuals which is often inapplicable. Except when the distribution of the taxon is limited, researchers conventionally choose several sampling locations from the known distribution and then collect individuals from each location. Spatial sampling is a formalized version of the conventional sampling, which objectively provides geographically even sampling locations to cover genetic variation in a taxon assuming isolation by distance. To evaluate the validity of the spatial sampling in estimating genetic diversity, we conducted coalescent simulation experiments. The sampling locations were selected by spatial sampling and one sample was collected from each location for the sake of theoretical simplicity. We also devised a new measure of genetic diversity, ς, which assumes spatial sampling and is independent of allele frequency. This new measure places an emphasis on rare and phylogenetically distant alleles which have relatively small effect on nucleotide diversity. Therefore, it can complementarily serve for conservation studies although it cannot be used to estimate population mutation rate. We compared ς with the other diversity measures in the experiments. Nucleotide diversity, expected heterozygosity and ς showed within 3% relative biases on average while Watterson’s theta was 31% overestimation on average. Thus, genetic diversities other than Watterson’s theta held good robustness under the spatial sampling.
format: application/pdf
format: text/html
creator: Satoshi Aoki
creator: Fumiko Ishihama
creator: Keita Fukasawa
subject: Biodiversity
subject: Biogeography
subject: Bioinformatics
subject: Ecology
subject: Genomics
description: doi:10.7717/peerj.16027
publisher: PeerJ Inc.
rights: © 2023 Aoki et al.
abstract: The genetic diversity of a taxon has often been estimated by genetic diversity measures. However, they assume random sampling of individuals which is often inapplicable. Except when the distribution of the taxon is limited, researchers conventionally choose several sampling locations from the known distribution and then collect individuals from each location. Spatial sampling is a formalized version of the conventional sampling, which objectively provides geographically even sampling locations to cover genetic variation in a taxon assuming isolation by distance. To evaluate the validity of the spatial sampling in estimating genetic diversity, we conducted coalescent simulation experiments. The sampling locations were selected by spatial sampling and one sample was collected from each location for the sake of theoretical simplicity. We also devised a new measure of genetic diversity, ς, which assumes spatial sampling and is independent of allele frequency. This new measure places an emphasis on rare and phylogenetically distant alleles which have relatively small effect on nucleotide diversity. Therefore, it can complementarily serve for conservation studies although it cannot be used to estimate population mutation rate. We compared ς with the other diversity measures in the experiments. Nucleotide diversity, expected heterozygosity and ς showed within 3% relative biases on average while Watterson’s theta was 31% overestimation on average. Thus, genetic diversities other than Watterson’s theta held good robustness under the spatial sampling.
bibliographic citation: Aoki et al. (2023) Robustness of genetic diversity measures under spatial sampling and a new frequency-independent measure. PeerJ 11:e16027 https://doi.org/10.7717/peerj.16027
date submitted: 2022-11-16
date accepted: 2023-08-13
issued: 2023-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aoki
  given name: Satoshi
author list: Agent
  family name: Ishihama
  given name: Fumiko
author list: Agent
  family name: Fukasawa
  given name: Keita
doi: 10.7717/peerj.16027
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-18
copyright: ©2023 Aoki et al.
attribution name: Aoki et al.

Expression profiles of circular RNAs and interaction networks of competing endogenous RNAs in neurogenic bladder of rats following suprasacral spinal cord injury
type: item
type: AcademicArticle
description: Background Neurogenic bladder (NB) following suprasacral spinal cord injury (SSCI) is an interstitial disease with the structural remodeling of bladder tissue and matrix over-deposition. Circular RNAs (circRNAs) are involved in fibrotic disease development through their post-transcriptional regulatory functions. This study aimed to use transcriptome high-throughput sequencing to investigate the process of NB and bladder fibrosis after SSCI. Methods Spinal cord transection at the T10–T11 level was used to construct the SSCI model in rats (10–week–old female Wistar rats, weighing 200 ± 20 g). The bladders were collected without (sham group) and with (SSCI 1–3 groups) NB status. Morphological examination was conducted to assess the extent of bladder fibrosis. Additionally, RNA sequencing was utilized to determine mRNAs and circRNAs expression patterns. The dynamic changes of differentially expressed mRNAs (DEMs) and circRNAs (DECs) in different periods of SSCI were further analyzed. Results Bladder weight, smooth muscle cell hypertrophy, and extracellular matrix gradually increased after SSCI. Compared with the sham group, 3,255 DEMs and 1,339 DECs, 3,449 DEMs and 1,324 DECs, 884 DEMs, and 1,151 DECs were detected in the SSCI 1–3 groups, respectively. Specifically, circRNA3621, circRNA0617, circRNA0586, and circRNA4426 were significant DECs common to SSCI 1–3 groups compared with the sham group. Moreover, Gene Ontology (GO) enrichment suggested that inflammatory and chronic inflammatory responses were the key events in NB progression following SSCI. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment associated with the “Chemokine signaling pathway”, the “IL-17 signaling pathway”, and the “TGF-beta signaling pathway” suggests their potential involvement in regulating biological processes. The circRNA–miRNA–mRNA interaction networks of DECs revealed rno-circ-2239 (micu2) as the largest node, indicating that the rno-circ-2239–miRNA–mRNA–mediated network ma…
format: application/pdf
format: text/html
creator: Jimeng Ruan
creator: Xin Cui
creator: Hao Yan
creator: Chunsong Jia
creator: Tongwen Ou
creator: Zhenhua Shang
subject: Bioinformatics
subject: Genomics
subject: Urology
description: doi:10.7717/peerj.16042
publisher: PeerJ Inc.
rights: © 2023 Ruan et al.
abstract: Background Neurogenic bladder (NB) following suprasacral spinal cord injury (SSCI) is an interstitial disease with the structural remodeling of bladder tissue and matrix over-deposition. Circular RNAs (circRNAs) are involved in fibrotic disease development through their post-transcriptional regulatory functions. This study aimed to use transcriptome high-throughput sequencing to investigate the process of NB and bladder fibrosis after SSCI. Methods Spinal cord transection at the T10–T11 level was used to construct the SSCI model in rats (10–week–old female Wistar rats, weighing 200 ± 20 g). The bladders were collected without (sham group) and with (SSCI 1–3 groups) NB status. Morphological examination was conducted to assess the extent of bladder fibrosis. Additionally, RNA sequencing was utilized to determine mRNAs and circRNAs expression patterns. The dynamic changes of differentially expressed mRNAs (DEMs) and circRNAs (DECs) in different periods of SSCI were further analyzed. Results Bladder weight, smooth muscle cell hypertrophy, and extracellular matrix gradually increased after SSCI. Compared with the sham group, 3,255 DEMs and 1,339 DECs, 3,449 DEMs and 1,324 DECs, 884 DEMs, and 1,151 DECs were detected in the SSCI 1–3 groups, respectively. Specifically, circRNA3621, circRNA0617, circRNA0586, and circRNA4426 were significant DECs common to SSCI 1–3 groups compared with the sham group. Moreover, Gene Ontology (GO) enrichment suggested that inflammatory and chronic inflammatory responses were the key events in NB progression following SSCI. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment associated with the “Chemokine signaling pathway”, the “IL-17 signaling pathway”, and the “TGF-beta signaling pathway” suggests their potential involvement in regulating biological processes. The circRNA–miRNA–mRNA interaction networks of DECs revealed rno-circ-2239 (micu2) as the largest node, indicating that the rno-circ-2239–miRNA–mRNA–mediated network ma…
bibliographic citation: Ruan et al. (2023) Expression profiles of circular RNAs and interaction networks of competing endogenous RNAs in neurogenic bladder of rats following suprasacral spinal cord injury. PeerJ 11:e16042 https://doi.org/10.7717/peerj.16042
date submitted: 2023-05-30
date accepted: 2023-08-15
issued: 2023-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ruan
  given name: Jimeng
author list: Agent
  family name: Cui
  given name: Xin
author list: Agent
  family name: Yan
  given name: Hao
author list: Agent
  family name: Jia
  given name: Chunsong
author list: Agent
  family name: Ou
  given name: Tongwen
author list: Agent
  family name: Shang
  given name: Zhenhua
doi: 10.7717/peerj.16042
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-18
copyright: ©2023 Ruan et al.
attribution name: Ruan et al.

A new gnathosaurine (Pterosauria, Archaeopterodactyloidea) from the Late Jurassic of Portugal
type: item
type: AcademicArticle
description: An incomplete, yet remarkably-sized dentated rostrum and associated partial cervical vertebrae of a pterosaur (ML 2554) were recently discovered from the Late Jurassic (Late Kimmeridgian-Early Tithonian) Lourinhã Formation of Praia do Caniçal, of central west Portugal. This specimen exhibits features such as a spatulated anterior expansion of the rostrum, robust comb-like dentition, and pronounced rims of the tooth alveoli, indicating gnathosaurine affinities. Based on its further unique tooth and dentary morphology, a new genus and species, Lusognathus almadrava gen. et spec. nov., is proposed, making this the first named pterosaur species found within Portugal. The presence of this taxon adds yet another element to the fluvio-deltaic lagoonal environment that has been suggested as representative of the Lourinhã Formation in the Late Jurassic, further contributing to the diversity and distribution of gnathosaurines worldwide.
format: application/pdf
format: text/html
creator: Alexandra E. Fernandes
creator: Victor Beccari
creator: Alexander W. A. Kellner
creator: Octávio Mateus
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.16048
publisher: PeerJ Inc.
rights: © 2023 Fernandes et al.
abstract: An incomplete, yet remarkably-sized dentated rostrum and associated partial cervical vertebrae of a pterosaur (ML 2554) were recently discovered from the Late Jurassic (Late Kimmeridgian-Early Tithonian) Lourinhã Formation of Praia do Caniçal, of central west Portugal. This specimen exhibits features such as a spatulated anterior expansion of the rostrum, robust comb-like dentition, and pronounced rims of the tooth alveoli, indicating gnathosaurine affinities. Based on its further unique tooth and dentary morphology, a new genus and species, Lusognathus almadrava gen. et spec. nov., is proposed, making this the first named pterosaur species found within Portugal. The presence of this taxon adds yet another element to the fluvio-deltaic lagoonal environment that has been suggested as representative of the Lourinhã Formation in the Late Jurassic, further contributing to the diversity and distribution of gnathosaurines worldwide.
bibliographic citation: Fernandes et al. (2023) A new gnathosaurine (Pterosauria, Archaeopterodactyloidea) from the Late Jurassic of Portugal. PeerJ 11:e16048 https://doi.org/10.7717/peerj.16048
date submitted: 2023-06-13
date accepted: 2023-08-16
issued: 2023-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fernandes
  given name: Alexandra E.
author list: Agent
  family name: Beccari
  given name: Victor
author list: Agent
  family name: Kellner
  given name: Alexander W. A.
author list: Agent
  family name: Mateus
  given name: Octávio
doi: 10.7717/peerj.16048
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-18
copyright: © 2023 Fernandes et al.
attribution name: Fernandes et al.

Performance of multigene testing in cytologically indeterminate thyroid nodules and molecular risk stratification
type: item
type: AcademicArticle
description: Objective Thyroid cancer is the third most prevalent cancer among females. Genetic testing based on next-generation sequencing may provide an auxiliary diagnosis to reduce cytologically diagnostic uncertainty. However, commercial multigene tests are not widely available and are not well-tested in the Chinese population. Methods In this study, we designed a multigene testing panel and evaluated its performance in 529 cytologically indeterminate thyroid nodules (Bethesda III, IV and V). The molecular data of the DNA mutations and RNA fusions of fine needle aspiration samples were reviewed in conjunction with a clinical diagnosis, pathological reports, and definitive surgery for retrospective analysis. Then, the molecular risk stratification was investigated for its accuracy in malignant risk prediction. Results The overall combined consistency revealed substantial agreement (Kappa = 0.726) with the sensitivity, specificity, positive predictive value, and negative predictive values of 97.80%, 82.14%, 98.99%, and 67.65%, respectively. The most common aberration was BRAFV600E (82.59%), followed by NRAS mutants (4.07%), RET fusions (3.70%), and KRAS mutants (3.15%). Two cases (0.44%) were categorized into a high-risk group, 426 cases (94.67%) were categorized into a BRAF-like group with totally histopathologic papillary patterned tumors, and 22 cases (4.89%) were categorized into a RAS-like group with 14 papillary and eight follicular patterned tumors when the cohort concurrent aberrations were excluded. Potentially aggressive features may be related to concurrent molecular alterations of BRAFV600E with TERTQ302R, and AKT1L52R, NRASG12C, NRASQ61R, and CCDC6-RET fusions. Conclusions This study provided a multigene panel for identifying benign nodules from cytologically indeterminate thyroid nodules to avoid unnecessary surgery. We provide further evidence for using molecular risk stratification as a promising predictor of disease outcomes. The results of this study may be …
format: application/pdf
format: text/html
creator: Yuanyuan Zhou
creator: Xinping Wu
creator: Yuzhi Zhang
creator: Zhiqiang Li
creator: Xia Ge
creator: Hao Chen
creator: Yuan Mao
creator: Wenbo Ding
subject: Biotechnology
subject: Oncology
subject: Pathology
subject: Medical Genetics
description: doi:10.7717/peerj.16054
publisher: PeerJ Inc.
rights: © 2023 Zhou et al.
abstract: Objective Thyroid cancer is the third most prevalent cancer among females. Genetic testing based on next-generation sequencing may provide an auxiliary diagnosis to reduce cytologically diagnostic uncertainty. However, commercial multigene tests are not widely available and are not well-tested in the Chinese population. Methods In this study, we designed a multigene testing panel and evaluated its performance in 529 cytologically indeterminate thyroid nodules (Bethesda III, IV and V). The molecular data of the DNA mutations and RNA fusions of fine needle aspiration samples were reviewed in conjunction with a clinical diagnosis, pathological reports, and definitive surgery for retrospective analysis. Then, the molecular risk stratification was investigated for its accuracy in malignant risk prediction. Results The overall combined consistency revealed substantial agreement (Kappa = 0.726) with the sensitivity, specificity, positive predictive value, and negative predictive values of 97.80%, 82.14%, 98.99%, and 67.65%, respectively. The most common aberration was BRAFV600E (82.59%), followed by NRAS mutants (4.07%), RET fusions (3.70%), and KRAS mutants (3.15%). Two cases (0.44%) were categorized into a high-risk group, 426 cases (94.67%) were categorized into a BRAF-like group with totally histopathologic papillary patterned tumors, and 22 cases (4.89%) were categorized into a RAS-like group with 14 papillary and eight follicular patterned tumors when the cohort concurrent aberrations were excluded. Potentially aggressive features may be related to concurrent molecular alterations of BRAFV600E with TERTQ302R, and AKT1L52R, NRASG12C, NRASQ61R, and CCDC6-RET fusions. Conclusions This study provided a multigene panel for identifying benign nodules from cytologically indeterminate thyroid nodules to avoid unnecessary surgery. We provide further evidence for using molecular risk stratification as a promising predictor of disease outcomes. The results of this study may be …
bibliographic citation: Zhou et al. (2023) Performance of multigene testing in cytologically indeterminate thyroid nodules and molecular risk stratification. PeerJ 11:e16054 https://doi.org/10.7717/peerj.16054
date submitted: 2023-03-20
date accepted: 2023-08-16
issued: 2023-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Yuanyuan
author list: Agent
  family name: Wu
  given name: Xinping
author list: Agent
  family name: Zhang
  given name: Yuzhi
author list: Agent
  family name: Li
  given name: Zhiqiang
author list: Agent
  family name: Ge
  given name: Xia
author list: Agent
  family name: Chen
  given name: Hao
author list: Agent
  family name: Mao
  given name: Yuan
author list: Agent
  family name: Ding
  given name: Wenbo
doi: 10.7717/peerj.16054
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-18
copyright: ©2023 Zhou et al.
attribution name: Zhou et al.

Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides
type: item
type: AcademicArticle
description: Background Gardenia jasminoides is a species of Chinese medicinal plant, which has high medicinal and economic value and rich genetic diversity, but the study on its genetic diversity is far not enough. Methods In this study, one wild and one cultivated gardenia materials were resequenced using IlluminaHiSeq sequencing platform and the data were evaluated to understand the genomic characteristics of G. jasminoides. Results After data analysis, the results showed that clean data of 11.77G, Q30 reached 90.96%. The average comparison rate between the sample and reference genome was 96.08%, the average coverage depth was 15X, and the genome coverage was 85.93%. The SNPs of FD and YP1 were identified, and 3,087,176 and 3,241,416 SNPs were developed, respectively. In addition, SNP non-synonymous mutation, InDel mutation, SV mutation and CNV mutation were also detected between the sample and the reference genome, and KEGG, GO and COG database annotations were made for genes with DNA level variation. The structural gene variation in the biosynthetic pathway of crocin and gardenia, the main medicinal substance of G. jasminoides was further explored, which provided basic data for molecular breeding and genetic diversity of G. jasminoides in the future.
format: application/pdf
format: text/html
creator: Xinyu Xu
creator: Bihua Chen
creator: Juan Zhang
creator: Siren Lan
creator: Shasha Wu
subject: Agricultural Science
subject: Bioinformatics
subject: Developmental Biology
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.16056
publisher: PeerJ Inc.
rights: © 2023 Xu et al.
abstract: Background Gardenia jasminoides is a species of Chinese medicinal plant, which has high medicinal and economic value and rich genetic diversity, but the study on its genetic diversity is far not enough. Methods In this study, one wild and one cultivated gardenia materials were resequenced using IlluminaHiSeq sequencing platform and the data were evaluated to understand the genomic characteristics of G. jasminoides. Results After data analysis, the results showed that clean data of 11.77G, Q30 reached 90.96%. The average comparison rate between the sample and reference genome was 96.08%, the average coverage depth was 15X, and the genome coverage was 85.93%. The SNPs of FD and YP1 were identified, and 3,087,176 and 3,241,416 SNPs were developed, respectively. In addition, SNP non-synonymous mutation, InDel mutation, SV mutation and CNV mutation were also detected between the sample and the reference genome, and KEGG, GO and COG database annotations were made for genes with DNA level variation. The structural gene variation in the biosynthetic pathway of crocin and gardenia, the main medicinal substance of G. jasminoides was further explored, which provided basic data for molecular breeding and genetic diversity of G. jasminoides in the future.
bibliographic citation: Xu et al. (2023) Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides. PeerJ 11:e16056 https://doi.org/10.7717/peerj.16056
date submitted: 2023-06-27
date accepted: 2023-08-17
issued: 2023-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Xinyu
author list: Agent
  family name: Chen
  given name: Bihua
author list: Agent
  family name: Zhang
  given name: Juan
author list: Agent
  family name: Lan
  given name: Siren
author list: Agent
  family name: Wu
  given name: Shasha
doi: 10.7717/peerj.16056
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-18
copyright: ©2023 Xu et al.
attribution name: Xu et al.

In vitro and ex vitro propagation of Turkish myrtles through conventional and plantform bioreactor systems
type: item
type: AcademicArticle
description: The myrtle (Myrtus communis) plant naturally grows in the temperate Mediterranean and subtropical regions and is used for various purposes; thus, it is among the promising species of horticultural crops. This study aimed to evaluate and compare the performance of different propagation systems, including rooting, solid media propagation, rooting, and with the Plantform bioreactor system, in achieving healthy and rapid growth of four myrtle genotypes with diverse genetic origins and well-regional adaptation. The selection of myrtle genotypes with distinct genetic backgrounds and proven adaptability to specific regions allowed for a comprehensive assessment of the propagation systems under investigation. Present findings proved that the Plantform system, the new-generation tissue culture system, was quite successful in micropropagation and rooting myrtle genotypes. We succeeded in vitro micropropagation and rooting of diverse wild myrtle genotypes, enabling year-round propagation without reliance on specific seasons or environmental conditions. The process involved initiating cultures from explants and multiplying them through shoot proliferation in a controlled environment. This contributes to sustainable plant propagation, preserving and utilizing genetic resources for conservation and agriculture.
format: application/pdf
format: text/html
creator: Özhan Şimşek
creator: Dicle Dönmez
creator: Mehmet Ali Sarıdaş
creator: Emine Acar
creator: Yıldız Aka Kaçar
creator: Sevgi Paydaş Kargı
creator: Tolga İzgü
subject: Agricultural Science
subject: Biodiversity
subject: Biotechnology
subject: Plant Science
description: doi:10.7717/peerj.16061
publisher: PeerJ Inc.
rights: © 2023 Şimşek et al.
abstract: The myrtle (Myrtus communis) plant naturally grows in the temperate Mediterranean and subtropical regions and is used for various purposes; thus, it is among the promising species of horticultural crops. This study aimed to evaluate and compare the performance of different propagation systems, including rooting, solid media propagation, rooting, and with the Plantform bioreactor system, in achieving healthy and rapid growth of four myrtle genotypes with diverse genetic origins and well-regional adaptation. The selection of myrtle genotypes with distinct genetic backgrounds and proven adaptability to specific regions allowed for a comprehensive assessment of the propagation systems under investigation. Present findings proved that the Plantform system, the new-generation tissue culture system, was quite successful in micropropagation and rooting myrtle genotypes. We succeeded in vitro micropropagation and rooting of diverse wild myrtle genotypes, enabling year-round propagation without reliance on specific seasons or environmental conditions. The process involved initiating cultures from explants and multiplying them through shoot proliferation in a controlled environment. This contributes to sustainable plant propagation, preserving and utilizing genetic resources for conservation and agriculture.
bibliographic citation: Şimşek et al. (2023) In vitro and ex vitro propagation of Turkish myrtles through conventional and plantform bioreactor systems. PeerJ 11:e16061 https://doi.org/10.7717/peerj.16061
date submitted: 2023-01-11
date accepted: 2023-08-17
issued: 2023-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Şimşek
  given name: Özhan
author list: Agent
  family name: Dönmez
  given name: Dicle
author list: Agent
  family name: Sarıdaş
  given name: Mehmet Ali
author list: Agent
  family name: Acar
  given name: Emine
author list: Agent
  family name: Aka Kaçar
  given name: Yıldız
author list: Agent
  family name: Paydaş Kargı
  given name: Sevgi
author list: Agent
  family name: İzgü
  given name: Tolga
doi: 10.7717/peerj.16061
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-18
copyright: ©2023 Şimşek et al.
attribution name: Şimşek et al.

The mediating roles of coping styles and academic burnout in the relationship between stressors and depressive symptoms among Chinese postgraduates
type: item
type: AcademicArticle
description: Background Since few studies have incorporated factors like stressors, coping styles, and academic burnout into the same model to analyze their impacts on depressive symptoms, this research attempts to establish an optimal structural model to explore the direct and indirect effects of these factors on depressive symptoms. Methods A total of 266 postgraduates completed questionnaires regarding coping styles, academic burnout, stressors, and depressive symptoms. The path analysis was applied for investigating the roles of coping styles and academic burnout in mediating the relationship between stressors and depressive symptoms. Results The total and direct effects of stressors on depressive symptoms were 0.53 and 0.31, respectively. The proportion of the direct effect of stressors on depressive symptoms to its total effect amounted to 58.50%. The indirect effects of academic burnout, positive coping style, and negative coping style on the association between stressors and depressive symptoms were 0.11, 0.04, and 0.03, taking up 20.75%, 7.55%, and 5.66% of the total effect, respectively. The serial indirect effect of positive coping style and academic burnout was 0.02, accounting for 3.77% of the total effect, while that of negative coping style and academic burnout was 0.02, taking up 3.77% of the total effect. Conclusions Coping styles and academic burnout chain jointly mediate the relationship between stressors and depressive symptoms among postgraduates. Thus, encouraging postgraduates to tackle stress positively may reduce the likelihood of the development of academic burnout and further reduce depressive symptoms.
format: application/pdf
format: text/html
creator: Hong Shi
creator: Hanfang Zhao
creator: Minfu He
creator: Zheng Ren
creator: Shixun Wang
creator: Li Cui
creator: Jieyu Zhao
creator: Wenjun Li
creator: Yachen Wei
creator: Wenjing Zhang
creator: Ziqiang Chen
creator: Hongjian Liu
creator: Xiumin Zhang
subject: Psychiatry and Psychology
subject: Science and Medical Education
subject: Mental Health
description: doi:10.7717/peerj.16064
publisher: PeerJ Inc.
rights: © 2023 Shi et al.
abstract: Background Since few studies have incorporated factors like stressors, coping styles, and academic burnout into the same model to analyze their impacts on depressive symptoms, this research attempts to establish an optimal structural model to explore the direct and indirect effects of these factors on depressive symptoms. Methods A total of 266 postgraduates completed questionnaires regarding coping styles, academic burnout, stressors, and depressive symptoms. The path analysis was applied for investigating the roles of coping styles and academic burnout in mediating the relationship between stressors and depressive symptoms. Results The total and direct effects of stressors on depressive symptoms were 0.53 and 0.31, respectively. The proportion of the direct effect of stressors on depressive symptoms to its total effect amounted to 58.50%. The indirect effects of academic burnout, positive coping style, and negative coping style on the association between stressors and depressive symptoms were 0.11, 0.04, and 0.03, taking up 20.75%, 7.55%, and 5.66% of the total effect, respectively. The serial indirect effect of positive coping style and academic burnout was 0.02, accounting for 3.77% of the total effect, while that of negative coping style and academic burnout was 0.02, taking up 3.77% of the total effect. Conclusions Coping styles and academic burnout chain jointly mediate the relationship between stressors and depressive symptoms among postgraduates. Thus, encouraging postgraduates to tackle stress positively may reduce the likelihood of the development of academic burnout and further reduce depressive symptoms.
bibliographic citation: Shi et al. (2023) The mediating roles of coping styles and academic burnout in the relationship between stressors and depressive symptoms among Chinese postgraduates. PeerJ 11:e16064 https://doi.org/10.7717/peerj.16064
date submitted: 2023-03-15
date accepted: 2023-08-18
issued: 2023-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Hong
author list: Agent
  family name: Zhao
  given name: Hanfang
author list: Agent
  family name: He
  given name: Minfu
author list: Agent
  family name: Ren
  given name: Zheng
author list: Agent
  family name: Wang
  given name: Shixun
author list: Agent
  family name: Cui
  given name: Li
author list: Agent
  family name: Zhao
  given name: Jieyu
author list: Agent
  family name: Li
  given name: Wenjun
author list: Agent
  family name: Wei
  given name: Yachen
author list: Agent
  family name: Zhang
  given name: Wenjing
author list: Agent
  family name: Chen
  given name: Ziqiang
author list: Agent
  family name: Liu
  given name: Hongjian
author list: Agent
  family name: Zhang
  given name: Xiumin
doi: 10.7717/peerj.16064
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-18
copyright: ©2023 Shi et al.
attribution name: Shi et al.

Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19: a retrospective pilot study
type: item
type: AcademicArticle
description: Background COVID-19 is a worldwide pandemic caused by the highly infective SARS-CoV-2. There is a need for biomarkers not only for overall prognosis but also for predicting the response to treatments and thus for improvements in the clinical management of patients with COVID-19. Circulating cell-free DNA (cfDNA) has emerged as a promising biomarker in the assessment of various pathological conditions. The aim of this retrospective and observational pilot study was to investigate the range of cfDNA plasma concentrations in hospitalized COVID-19 patients during the first wave of SARS-CoV-2 infection, to relate them to established inflammatory parameters as a correlative biomarker for disease severity, and to compare them with plasma levels in a healthy control group. Methods Lithium-Heparin plasma samples were obtained from COVID-19 patients (n = 21) during hospitalization in the University Medical Centre of Mainz, Germany between March and June 2020, and the cfDNA concentrations were determined by quantitative PCR yielding amplicons of long interspersed nuclear elements (LINE-1). The cfDNA levels were compared with those of an uninfected control group (n = 19). Results Plasma cfDNA levels in COVID-19 patients ranged from 247.5 to 6,346.25 ng/ml and the mean concentration was 1,831 ± 1,388 ng/ml (± standard deviation), which was significantly different from the levels of the uninfected control group (p < 0.001). Regarding clinical complications, the highest correlation was found between cfDNA levels and the myositis (p = 0.049). In addition, cfDNA levels correlated with the “WHO clinical progression scale”. D-Dimer and C-reactive protein (CRP) were the clinical laboratory parameters with the highest correlations with cfDNA levels. Conclusion The results of this observational pilot study show a wide range in cfDNA plasma concentrations in patients with COVID-19 during the first wave of infection and confirm that cfDNA plasma concentrations serve as a predictive biomark…
format: application/pdf
format: text/html
creator: Katharina Hoeter
creator: Elmo Neuberger
creator: Susanne Fischer
creator: Manuel Herbst
creator: Ema Juškevičiūtė
creator: Kira Enders
creator: Heidi Rossmann
creator: Martin F. Sprinzl
creator: Perikles Simon
creator: Marc Bodenstein
creator: Michael Schaefer
subject: Infectious Diseases
subject: Medical Genetics
subject: COVID-19
description: doi:10.7717/peerj.16072
publisher: PeerJ Inc.
rights: © 2023 Hoeter et al.
abstract: Background COVID-19 is a worldwide pandemic caused by the highly infective SARS-CoV-2. There is a need for biomarkers not only for overall prognosis but also for predicting the response to treatments and thus for improvements in the clinical management of patients with COVID-19. Circulating cell-free DNA (cfDNA) has emerged as a promising biomarker in the assessment of various pathological conditions. The aim of this retrospective and observational pilot study was to investigate the range of cfDNA plasma concentrations in hospitalized COVID-19 patients during the first wave of SARS-CoV-2 infection, to relate them to established inflammatory parameters as a correlative biomarker for disease severity, and to compare them with plasma levels in a healthy control group. Methods Lithium-Heparin plasma samples were obtained from COVID-19 patients (n = 21) during hospitalization in the University Medical Centre of Mainz, Germany between March and June 2020, and the cfDNA concentrations were determined by quantitative PCR yielding amplicons of long interspersed nuclear elements (LINE-1). The cfDNA levels were compared with those of an uninfected control group (n = 19). Results Plasma cfDNA levels in COVID-19 patients ranged from 247.5 to 6,346.25 ng/ml and the mean concentration was 1,831 ± 1,388 ng/ml (± standard deviation), which was significantly different from the levels of the uninfected control group (p < 0.001). Regarding clinical complications, the highest correlation was found between cfDNA levels and the myositis (p = 0.049). In addition, cfDNA levels correlated with the “WHO clinical progression scale”. D-Dimer and C-reactive protein (CRP) were the clinical laboratory parameters with the highest correlations with cfDNA levels. Conclusion The results of this observational pilot study show a wide range in cfDNA plasma concentrations in patients with COVID-19 during the first wave of infection and confirm that cfDNA plasma concentrations serve as a predictive biomark…
bibliographic citation: Hoeter et al. (2023) Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19: a retrospective pilot study. PeerJ 11:e16072 https://doi.org/10.7717/peerj.16072
date submitted: 2022-12-29
date accepted: 2023-08-20
issued: 2023-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoeter
  given name: Katharina
author list: Agent
  family name: Neuberger
  given name: Elmo
author list: Agent
  family name: Fischer
  given name: Susanne
author list: Agent
  family name: Herbst
  given name: Manuel
author list: Agent
  family name: Juškevičiūtė
  given name: Ema
author list: Agent
  family name: Enders
  given name: Kira
author list: Agent
  family name: Rossmann
  given name: Heidi
author list: Agent
  family name: Sprinzl
  given name: Martin F.
author list: Agent
  family name: Simon
  given name: Perikles
author list: Agent
  family name: Bodenstein
  given name: Marc
author list: Agent
  family name: Schaefer
  given name: Michael
doi: 10.7717/peerj.16072
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-18
copyright: © 2023 Hoeter et al.
attribution name: Hoeter et al.

Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators
type: item
type: AcademicArticle
description: Background Serine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using SMN1/2 minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9. Methods In this study, the effects of these proteins on SMN1/2 exon 7 splicing when tethered at either intron 6 or 7 were evaluated using an MS2-tethering assay. Deletion analysis in four SR proteins and co-overexpression analysis were performed. Results Splicing outcomes varied among all four SR proteins, SRSF1 and SRSF5 function the same at the two sites, acting as repressor and stimulator, respectively; while SRSF6 and SRSF9 promote exon 7 inclusion at only one site. Further, the key domains of each SR proteins were investigated, which identified a potent inhibitory nonapeptide in the C-terminus of SRSF1/9 ribonucleic acid recognition motif-1 (RRM1) and a potent stimulatory heptapeptide at the N-terminus of SRSF5/6 RRM1. Conclusion The insight of the four SR proteins and their domains in affecting SMN gene splicing brings a new perspective on the modes of action of SR proteins; and the functional peptides obtained here offers new ideas for developing splice switching-related therapies.
format: application/pdf
format: text/html
creator: Tao Jiang
creator: Li Wang
creator: Liang Tang
creator: Azhar Zeb
creator: Yanjun Hou
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.16103
publisher: PeerJ Inc.
rights: © 2023 Jiang et al.
abstract: Background Serine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using SMN1/2 minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9. Methods In this study, the effects of these proteins on SMN1/2 exon 7 splicing when tethered at either intron 6 or 7 were evaluated using an MS2-tethering assay. Deletion analysis in four SR proteins and co-overexpression analysis were performed. Results Splicing outcomes varied among all four SR proteins, SRSF1 and SRSF5 function the same at the two sites, acting as repressor and stimulator, respectively; while SRSF6 and SRSF9 promote exon 7 inclusion at only one site. Further, the key domains of each SR proteins were investigated, which identified a potent inhibitory nonapeptide in the C-terminus of SRSF1/9 ribonucleic acid recognition motif-1 (RRM1) and a potent stimulatory heptapeptide at the N-terminus of SRSF5/6 RRM1. Conclusion The insight of the four SR proteins and their domains in affecting SMN gene splicing brings a new perspective on the modes of action of SR proteins; and the functional peptides obtained here offers new ideas for developing splice switching-related therapies.
bibliographic citation: Jiang et al. (2023) Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators. PeerJ 11:e16103 https://doi.org/10.7717/peerj.16103
date submitted: 2023-04-19
date accepted: 2023-08-25
issued: 2023-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Tao
author list: Agent
  family name: Wang
  given name: Li
author list: Agent
  family name: Tang
  given name: Liang
author list: Agent
  family name: Zeb
  given name: Azhar
author list: Agent
  family name: Hou
  given name: Yanjun
doi: 10.7717/peerj.16103
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-18
copyright: © 2023 Jiang et al.
attribution name: Jiang et al.

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