PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Association of ApoE gene polymorphisms with serum lipid levels and the risk of type 2 diabetes mellitus in the Chinese Han population of central China
items: Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat
items: https://peerj.com/articles/15284
items: Effects of two different dual-task training protocols on gait, balance, and cognitive function in community-dwelling older adults: a 24-week randomized controlled trial
items: PAIP1 regulates expression of immune and inflammatory response associated genes at transcript level in liver cancer cell
items: Metabolic shift and the effect of mitochondrial respiration on the osteogenic differentiation of dental pulp stem cells
items: Evaluation of waterlogging tolerance and responses of protective enzymes to waterlogging stress in pumpkin
items: Captive breeding in the endangered alpine tree frog, Litoria verreauxii alpina
items: Exploratory and confirmatory factor analyses identify three structural dimensions for measuring physical function in community-dwelling older adults
items: The influence of climate warming on flowering phenology in relation to historical annual and seasonal temperatures and plant functional traits

Association of ApoE gene polymorphisms with serum lipid levels and the risk of type 2 diabetes mellitus in the Chinese Han population of central China
type: item
type: AcademicArticle
description: Background Apolipoprotein E (ApoE) is involved in lipid transformation and metabolism. Although some studies have examined the association between ApoE polymorphisms and the risk of type 2 diabetes mellitus (T2DM), the findings differ depending on the location and population. Methods A total of 1,738 participants, including 743 patients with T2DM and 995 controls without T2DM, were enrolled from central China, and ApoE polymorphisms, 388T > C (rs429358) and 526C > T (rs7412), were genotyped. The association between ApoE alleles and T2DM and blood lipid levels was analyzed. Logistic regression analysis was performed to evaluate the interactions between ApoE polymorphisms and various factors, such as age, sex, and prevalence of hypertension in patients with T2DM. Results The genotype ɛ3/ɛ4 and ɛ4 alleles of ApoE were associated with T2DM risk in the Chinese Han population in central China. Moreover, in patients with T2DM, participants in the E4 (ɛ3/ɛ4, ɛ4/ɛ4) group had significantly higher lipid profiles than those in the E3 (ɛ3/ɛ3) group, whereas participants in the E2 group (ɛ2/ɛ2, ɛ2/ɛ3) showed lower total cholesterol, low-density lipoprotein cholesterol, and ApoE-A1 levels than those in the E3 (ɛ3/ɛ3) group. The results from the current study may help in understanding ApoE polymorphisms and lipid profiles in the Chinese Han population.
format: application/pdf
format: text/html
creator: Yali Zeng
creator: Shuang Wen
creator: Lijun Huan
creator: Liang Xiong
creator: Botao Zhong
creator: Pengyun Wang
subject: Diabetes and Endocrinology
subject: Global Health
subject: Hematology
subject: Medical Genetics
description: doi:10.7717/peerj.15226
publisher: PeerJ Inc.
rights: © 2023 Zeng et al.
abstract: Background Apolipoprotein E (ApoE) is involved in lipid transformation and metabolism. Although some studies have examined the association between ApoE polymorphisms and the risk of type 2 diabetes mellitus (T2DM), the findings differ depending on the location and population. Methods A total of 1,738 participants, including 743 patients with T2DM and 995 controls without T2DM, were enrolled from central China, and ApoE polymorphisms, 388T > C (rs429358) and 526C > T (rs7412), were genotyped. The association between ApoE alleles and T2DM and blood lipid levels was analyzed. Logistic regression analysis was performed to evaluate the interactions between ApoE polymorphisms and various factors, such as age, sex, and prevalence of hypertension in patients with T2DM. Results The genotype ɛ3/ɛ4 and ɛ4 alleles of ApoE were associated with T2DM risk in the Chinese Han population in central China. Moreover, in patients with T2DM, participants in the E4 (ɛ3/ɛ4, ɛ4/ɛ4) group had significantly higher lipid profiles than those in the E3 (ɛ3/ɛ3) group, whereas participants in the E2 group (ɛ2/ɛ2, ɛ2/ɛ3) showed lower total cholesterol, low-density lipoprotein cholesterol, and ApoE-A1 levels than those in the E3 (ɛ3/ɛ3) group. The results from the current study may help in understanding ApoE polymorphisms and lipid profiles in the Chinese Han population.
bibliographic citation: Zeng et al. (2023) Association of ApoE gene polymorphisms with serum lipid levels and the risk of type 2 diabetes mellitus in the Chinese Han population of central China. PeerJ 11:e15226 https://doi.org/10.7717/peerj.15226
date submitted: 2022-12-29
date accepted: 2023-03-23
issued: 2023-04-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeng
  given name: Yali
author list: Agent
  family name: Wen
  given name: Shuang
author list: Agent
  family name: Huan
  given name: Lijun
author list: Agent
  family name: Xiong
  given name: Liang
author list: Agent
  family name: Zhong
  given name: Botao
author list: Agent
  family name: Wang
  given name: Pengyun
doi: 10.7717/peerj.15226
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-24
copyright: ©2023 Zeng et al.
attribution name: Zeng et al.

Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat
type: item
type: AcademicArticle
description: Sexually dimorphic traits are common in sexually reproducing organisms and can be encoded by differential gene regulation between males and females. Although alternative splicing is common mechanism in generating transcriptional diversity, its role in generating sex differences relative to differential gene expression is less clear. Here, we investigate the relative roles of differential gene expression and alternative splicing between male and female the horseshoe bat species, Rhinolophus sinicus. Horseshoe bats are an excellent model to study acoustic differences between sexes. Using RNA-seq analyses of two somatic tissues (brain and liver) from males and females of the same population, we identified 3,471 and 2,208 differentially expressed genes between the sexes (DEGs) in the brain and liver, respectively. DEGs were enriched with functional categories associated with physiological difference of the sexes (e.g.,gamete generation and energy production for reproduction in females). In addition, we also detected many differentially spliced genes between the sexes (DSGs, 2,231 and 1,027 in the brain and liver, respectively) which were mainly involved in regulation of RNA splicing and mRNA metabolic process. Interestingly, we found a significant enrichment of DEGs on the X chromosome, but not for DSGs. As for the extent of overlap between the two sets of genes, more than expected overlap of DEGs and DSGs was observed in the brain but not in the liver. This suggests that more complex tissues, such as the brain, may require the intricate and simultaneous interplay of both differential gene expression and splicing of genes to govern sex-specific functions. Overall, our results support that variation in gene expression and alternative splicing are important and complementary mechanisms governing sex differences.
format: application/pdf
format: text/html
creator: Wenli Chen
creator: Weiwei Zhou
creator: Qianqian Li
creator: Xiuguang Mao
subject: Evolutionary Studies
subject: Genetics
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.15231
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Sexually dimorphic traits are common in sexually reproducing organisms and can be encoded by differential gene regulation between males and females. Although alternative splicing is common mechanism in generating transcriptional diversity, its role in generating sex differences relative to differential gene expression is less clear. Here, we investigate the relative roles of differential gene expression and alternative splicing between male and female the horseshoe bat species, Rhinolophus sinicus. Horseshoe bats are an excellent model to study acoustic differences between sexes. Using RNA-seq analyses of two somatic tissues (brain and liver) from males and females of the same population, we identified 3,471 and 2,208 differentially expressed genes between the sexes (DEGs) in the brain and liver, respectively. DEGs were enriched with functional categories associated with physiological difference of the sexes (e.g.,gamete generation and energy production for reproduction in females). In addition, we also detected many differentially spliced genes between the sexes (DSGs, 2,231 and 1,027 in the brain and liver, respectively) which were mainly involved in regulation of RNA splicing and mRNA metabolic process. Interestingly, we found a significant enrichment of DEGs on the X chromosome, but not for DSGs. As for the extent of overlap between the two sets of genes, more than expected overlap of DEGs and DSGs was observed in the brain but not in the liver. This suggests that more complex tissues, such as the brain, may require the intricate and simultaneous interplay of both differential gene expression and splicing of genes to govern sex-specific functions. Overall, our results support that variation in gene expression and alternative splicing are important and complementary mechanisms governing sex differences.
bibliographic citation: Chen et al. (2023) Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat. PeerJ 11:e15231 https://doi.org/10.7717/peerj.15231
date submitted: 2022-10-17
date accepted: 2023-03-24
issued: 2023-04-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Wenli
author list: Agent
  family name: Zhou
  given name: Weiwei
author list: Agent
  family name: Li
  given name: Qianqian
author list: Agent
  family name: Mao
  given name: Xiuguang
doi: 10.7717/peerj.15231
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-24
copyright: ©2023 Chen et al.
attribution name: Chen et al.

https://peerj.com/articles/15284
type: item
type: AcademicArticle
title: Uncovering the potential functions of lymph node metastasis-associated aberrant methylation differentially expressed genes and their association with the immune infiltration and prognosis in bladder urothelial carcinoma
description: Background Bladder urothelial carcinoma (BLCA) is a malignant tumor of the urinary system. This study aimed to explore the potential role of lymph node metastasis-associated aberrant methylation differentially expressed genes (DEGs) in BLCA. Methods CHAMP and limma packages were used to identify lymph node metastasis-associated aberrant methylation DEGs. Univariate Cox analysis and Lasso analysis were performed to identify the signature genes, and multivariate Cox analysis was used to construct the risk score. Subsequently, the molecular characteristics of the signature genes and the relationship between risk score and prognosis, clinical characteristics and immune cell infiltration were analyzed. The signature gene AKAP7 was selected for functional verification. Results A novel risk score model was constructed based on 12 signature genes. The risk score had a good ability to predict overall survival (OS). The nomogram constructed based on age, N stage and risk score had a higher value in predicting the prognosis of patients. It was also found that stromal activation in TIME may inhibit the antitumor effects of immune cells. Functional enrichment analysis revealed that ECM receptor interaction and focal adhesion were two important pathways involved in the regulation of BLCA. Immunohistochemistry showed that AKAP7 may be associated with the occurrence, clinical stages and grades, and lymph node metastasis of BLCA. In vitro cell experiments showed that the migration and invasion ability of EJ cells was significantly inhibited after AKAP7 overexpression, while the migration and invasion ability of T24 cells was significantly promoted after AKAP7 knockdown. Conclusion The risk score model based on lymph node metastasis-associated aberrant methylation DEGs has a good ability to predict OS and is an independent prognostic factor for BLCA. It was also found that stromal activation in TIME may inhibit the antitumor effects of immune cells. This implicates aberrant methylati…
format: application/pdf
format: text/html
creator: Wenzhi Gao
creator: Jiafeng Zhang
creator: Tai Tian
creator: Zhixin Fu
creator: Liangliang Bai
creator: Yifei Yang
creator: Qiangqiang Wu
creator: Wei Wang
creator: Yuexian Guo
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.15284
publisher: PeerJ Inc.
rights: © 2023 Gao et al.
abstract: Background Bladder urothelial carcinoma (BLCA) is a malignant tumor of the urinary system. This study aimed to explore the potential role of lymph node metastasis-associated aberrant methylation differentially expressed genes (DEGs) in BLCA. Methods CHAMP and limma packages were used to identify lymph node metastasis-associated aberrant methylation DEGs. Univariate Cox analysis and Lasso analysis were performed to identify the signature genes, and multivariate Cox analysis was used to construct the risk score. Subsequently, the molecular characteristics of the signature genes and the relationship between risk score and prognosis, clinical characteristics and immune cell infiltration were analyzed. The signature gene AKAP7 was selected for functional verification. Results A novel risk score model was constructed based on 12 signature genes. The risk score had a good ability to predict overall survival (OS). The nomogram constructed based on age, N stage and risk score had a higher value in predicting the prognosis of patients. It was also found that stromal activation in TIME may inhibit the antitumor effects of immune cells. Functional enrichment analysis revealed that ECM receptor interaction and focal adhesion were two important pathways involved in the regulation of BLCA. Immunohistochemistry showed that AKAP7 may be associated with the occurrence, clinical stages and grades, and lymph node metastasis of BLCA. In vitro cell experiments showed that the migration and invasion ability of EJ cells was significantly inhibited after AKAP7 overexpression, while the migration and invasion ability of T24 cells was significantly promoted after AKAP7 knockdown. Conclusion The risk score model based on lymph node metastasis-associated aberrant methylation DEGs has a good ability to predict OS and is an independent prognostic factor for BLCA. It was also found that stromal activation in TIME may inhibit the antitumor effects of immune cells. This implicates aberrant methylati…
bibliographic citation: Gao et al. (2023) Uncovering the potential functions of lymph node metastasis-associated aberrant methylation differentially expressed genes and their association with the immune infiltration and prognosis in bladder urothelial carcinoma. PeerJ 11:e15284 https://doi.org/10.7717/peerj.15284
date submitted: 2023-01-19
date accepted: 2023-04-03
issued: 2023-04-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Wenzhi
author list: Agent
  family name: Zhang
  given name: Jiafeng
author list: Agent
  family name: Tian
  given name: Tai
author list: Agent
  family name: Fu
  given name: Zhixin
author list: Agent
  family name: Bai
  given name: Liangliang
author list: Agent
  family name: Yang
  given name: Yifei
author list: Agent
  family name: Wu
  given name: Qiangqiang
author list: Agent
  family name: Wang
  given name: Wei
author list: Agent
  family name: Guo
  given name: Yuexian
doi: 10.7717/peerj.15284
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-24
copyright: © 2023 Gao et al.
attribution name: Gao et al.

Effects of two different dual-task training protocols on gait, balance, and cognitive function in community-dwelling older adults: a 24-week randomized controlled trial
type: item
type: AcademicArticle
description: Background Although alternating dual-task (ADT) training is functionally easier for older adults, a large part of the motor and cognitive tasks is simultaneously performed, especially during activities of daily living that require maintaining body balance. Objective To evaluate the effects of mixed dual-task training on mobility, cognitive function, and balance in community-dwelling older adults. Methods Sixty participants were randomly allocated at a 1:1 ratio into the experimental group—single motor task (SMT) and simultaneous dual task (SDT) interchangeably in stage 1 (for 12 weeks) and after strictly with SDT in stage 2 (the last 12 weeks)—or into the control group—only SMT and SDT interchangeably in stages 1 and 2. Gait parameters were acquired by two inertial sensors. Physical and cognitive performance were acquired by specific questionnaires. Generalized linear mixed models were used for analyzing interaction and main effects. Results No between-group difference was observed for gait performance. Both protocols improved mobility (mean change ((MC) = 0.74)), dual-task effect (MC = −13.50), lower limb function (MC = 4.44), static (MC = −0.61), and dynamic balance (MC = −0.23), body sway (MC = 4.80), and cognitive function (MC = 41.69). Conclusion Both dual-task training protocols improved these outcomes.
format: application/pdf
format: text/html
creator: Francis Trombini-Souza
creator: Vitória Thaysa Gomes de Moura
creator: Lucas Willian Nunes da Silva
creator: Iara dos Santos Leal
creator: Cleber Anderson Nascimento
creator: Paloma Sthefane Teles Silva
creator: Monica Rodrigues Perracini
creator: Isabel CN Sacco
creator: Rodrigo Cappato de Araújo
creator: Marcelo de Maio Nascimento
subject: Clinical Trials
subject: Cognitive Disorders
subject: Geriatrics
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.15030
publisher: PeerJ Inc.
rights: © 2023 Trombini-Souza et al.
abstract: Background Although alternating dual-task (ADT) training is functionally easier for older adults, a large part of the motor and cognitive tasks is simultaneously performed, especially during activities of daily living that require maintaining body balance. Objective To evaluate the effects of mixed dual-task training on mobility, cognitive function, and balance in community-dwelling older adults. Methods Sixty participants were randomly allocated at a 1:1 ratio into the experimental group—single motor task (SMT) and simultaneous dual task (SDT) interchangeably in stage 1 (for 12 weeks) and after strictly with SDT in stage 2 (the last 12 weeks)—or into the control group—only SMT and SDT interchangeably in stages 1 and 2. Gait parameters were acquired by two inertial sensors. Physical and cognitive performance were acquired by specific questionnaires. Generalized linear mixed models were used for analyzing interaction and main effects. Results No between-group difference was observed for gait performance. Both protocols improved mobility (mean change ((MC) = 0.74)), dual-task effect (MC = −13.50), lower limb function (MC = 4.44), static (MC = −0.61), and dynamic balance (MC = −0.23), body sway (MC = 4.80), and cognitive function (MC = 41.69). Conclusion Both dual-task training protocols improved these outcomes.
bibliographic citation: Trombini-Souza et al. (2023) Effects of two different dual-task training protocols on gait, balance, and cognitive function in community-dwelling older adults: a 24-week randomized controlled trial. PeerJ 11:e15030 https://doi.org/10.7717/peerj.15030
date submitted: 2022-10-31
date accepted: 2023-02-19
issued: 2023-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Trombini-Souza
  given name: Francis
author list: Agent
  family name: de Moura
  given name: Vitória Thaysa Gomes
author list: Agent
  family name: da Silva
  given name: Lucas Willian Nunes
author list: Agent
  family name: Leal
  given name: Iara dos Santos
author list: Agent
  family name: Nascimento
  given name: Cleber Anderson
author list: Agent
  family name: Silva
  given name: Paloma Sthefane Teles
author list: Agent
  family name: Perracini
  given name: Monica Rodrigues
author list: Agent
  family name: Sacco
  given name: Isabel CN
author list: Agent
  family name: de Araújo
  given name: Rodrigo Cappato
author list: Agent
  family name: Nascimento
  given name: Marcelo de Maio
doi: 10.7717/peerj.15030
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-21
copyright: © 2023 Trombini-Souza et al.
attribution name: Trombini-Souza et al.

PAIP1 regulates expression of immune and inflammatory response associated genes at transcript level in liver cancer cell
type: item
type: AcademicArticle
description: Poly(A) binding protein interacting protein 1 (PAIP1) is a translation regulator and also regulate the decay of mRNA. PAIP1 has also been reported to be a marker of increased invasive potential of liver cancer. However, the roles and underlying molecular mechanism of PAIP1 in liver cancer is still unclear. Here, cell viability and the gene expression profile of liver cancer line HepG2 transfected with PAIP1 siRNA was compared with cells transfected with non-targeting control siRNA. The results showed that PAIP1 knockdown inhibited cell viability, and extensively affects expression of 893 genes at transcriptional level in HepG2 cells. Gene function analysis showed that a large number of PAIP1 up-regulated genes were enriched in term of DNA-dependent transcription and the down-regulated genes were enriched in some pathways including immune response and inflammatory response. qPCR confirmed that PAIP1 knockdown positively regulated the expression of selected immune and inflammatory factor genes in HepG2 cells. Expression analysis of TCGA revealed that PAIP1 had positive correlations with two immune associated genes IL1R2 and PTAFR in liver tumor tissue. Taken together, our results demonstrated that PAIP1 was not only a translation regulator, but also a transcription regulator in liver cancer. Moreover, PAIP1 could function as a regulatory factor of immune and inflammatory genes in liver cancer. Thus, our study provides important cues for further study on the regulatory mechanism of PAIP1 in liver cancer.
format: application/pdf
format: text/html
creator: Jianfeng Zheng
creator: Weiwei Fan
creator: Xiaoyu Zhang
creator: Weili Quan
creator: Yunfei Wu
creator: Mengni Shu
creator: Moyang Chen
creator: Ming Liang
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.15070
publisher: PeerJ Inc.
rights: © 2023 Zheng et al.
abstract: Poly(A) binding protein interacting protein 1 (PAIP1) is a translation regulator and also regulate the decay of mRNA. PAIP1 has also been reported to be a marker of increased invasive potential of liver cancer. However, the roles and underlying molecular mechanism of PAIP1 in liver cancer is still unclear. Here, cell viability and the gene expression profile of liver cancer line HepG2 transfected with PAIP1 siRNA was compared with cells transfected with non-targeting control siRNA. The results showed that PAIP1 knockdown inhibited cell viability, and extensively affects expression of 893 genes at transcriptional level in HepG2 cells. Gene function analysis showed that a large number of PAIP1 up-regulated genes were enriched in term of DNA-dependent transcription and the down-regulated genes were enriched in some pathways including immune response and inflammatory response. qPCR confirmed that PAIP1 knockdown positively regulated the expression of selected immune and inflammatory factor genes in HepG2 cells. Expression analysis of TCGA revealed that PAIP1 had positive correlations with two immune associated genes IL1R2 and PTAFR in liver tumor tissue. Taken together, our results demonstrated that PAIP1 was not only a translation regulator, but also a transcription regulator in liver cancer. Moreover, PAIP1 could function as a regulatory factor of immune and inflammatory genes in liver cancer. Thus, our study provides important cues for further study on the regulatory mechanism of PAIP1 in liver cancer.
bibliographic citation: Zheng et al. (2023) PAIP1 regulates expression of immune and inflammatory response associated genes at transcript level in liver cancer cell. PeerJ 11:e15070 https://doi.org/10.7717/peerj.15070
date submitted: 2021-10-28
date accepted: 2023-02-23
issued: 2023-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Jianfeng
author list: Agent
  family name: Fan
  given name: Weiwei
author list: Agent
  family name: Zhang
  given name: Xiaoyu
author list: Agent
  family name: Quan
  given name: Weili
author list: Agent
  family name: Wu
  given name: Yunfei
author list: Agent
  family name: Shu
  given name: Mengni
author list: Agent
  family name: Chen
  given name: Moyang
author list: Agent
  family name: Liang
  given name: Ming
doi: 10.7717/peerj.15070
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-21
copyright: ©2023 Zheng et al.
attribution name: Zheng et al.

Metabolic shift and the effect of mitochondrial respiration on the osteogenic differentiation of dental pulp stem cells
type: item
type: AcademicArticle
description: Background Metabolism shifts from glycolysis to mitochondrial oxidative phosphorylation are vital during the differentiation of stem cells. Mitochondria have a direct function in differentiation. However, the metabolic shift and the effect of mitochondria in regulating the osteogenic differentiation of human dental pulp stem cells (hDPSCs) remain unclear. Methods Human dental pulp stem cells were collected from five healthy donors. Osteogenic differentiation was induced by osteogenic induction medium. The activities of alkaline phosphatase, hexokinase, pyruvate kinase, and lactate dehydrogenase were analyzed by enzymatic activity kits. The extracellular acidification rate and the mitochondrial oxygen consumption rate were measured. The mRNA levels of COL-1, ALP, TFAM, and NRF1 were analyzed. The protein levels of p-AMPK and AMPK were detected by western blotting. Results Glycolysis decreased after a slight increase, while mitochondrial oxidative phosphorylation continued to increase when cells grew in osteogenic induction medium. Therefore, the metabolism of differentiating cells switched to mitochondrial respiration. Next, inhibiting mitochondrial respiration with carbonyl cyanide-chlorophenylhydrazone, a mitochondrial uncoupler inhibited hDPSCs differentiation with less ALP activity and decreased ALP and COL-1 mRNA expression. Furthermore, mitochondrial uncoupling led to AMPK activation. 5-Aminoimidazole-4-carboxamide ribonucleotide, an AMPK activator, simulated the effect of mitochondrial uncoupling by inhibiting osteogenic differentiation, mitochondrial biogenesis, and mitochondrial morphology. Mitochondrial uncoupling and activation of AMPK depressed mitochondrial oxidative phosphorylation and inhibited differentiation, suggesting that they may serve as regulators to halt osteogenic differentiation from impaired mitochondrial oxidative phosphorylation.
format: application/pdf
format: text/html
creator: Lingyun Wan
creator: Linyan Wang
creator: Ran Cheng
creator: Li Cheng
creator: Tao Hu
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Dentistry
description: doi:10.7717/peerj.15164
publisher: PeerJ Inc.
rights: © 2023 Wan et al.
abstract: Background Metabolism shifts from glycolysis to mitochondrial oxidative phosphorylation are vital during the differentiation of stem cells. Mitochondria have a direct function in differentiation. However, the metabolic shift and the effect of mitochondria in regulating the osteogenic differentiation of human dental pulp stem cells (hDPSCs) remain unclear. Methods Human dental pulp stem cells were collected from five healthy donors. Osteogenic differentiation was induced by osteogenic induction medium. The activities of alkaline phosphatase, hexokinase, pyruvate kinase, and lactate dehydrogenase were analyzed by enzymatic activity kits. The extracellular acidification rate and the mitochondrial oxygen consumption rate were measured. The mRNA levels of COL-1, ALP, TFAM, and NRF1 were analyzed. The protein levels of p-AMPK and AMPK were detected by western blotting. Results Glycolysis decreased after a slight increase, while mitochondrial oxidative phosphorylation continued to increase when cells grew in osteogenic induction medium. Therefore, the metabolism of differentiating cells switched to mitochondrial respiration. Next, inhibiting mitochondrial respiration with carbonyl cyanide-chlorophenylhydrazone, a mitochondrial uncoupler inhibited hDPSCs differentiation with less ALP activity and decreased ALP and COL-1 mRNA expression. Furthermore, mitochondrial uncoupling led to AMPK activation. 5-Aminoimidazole-4-carboxamide ribonucleotide, an AMPK activator, simulated the effect of mitochondrial uncoupling by inhibiting osteogenic differentiation, mitochondrial biogenesis, and mitochondrial morphology. Mitochondrial uncoupling and activation of AMPK depressed mitochondrial oxidative phosphorylation and inhibited differentiation, suggesting that they may serve as regulators to halt osteogenic differentiation from impaired mitochondrial oxidative phosphorylation.
bibliographic citation: Wan et al. (2023) Metabolic shift and the effect of mitochondrial respiration on the osteogenic differentiation of dental pulp stem cells. PeerJ 11:e15164 https://doi.org/10.7717/peerj.15164
date submitted: 2022-11-09
date accepted: 2023-03-13
issued: 2023-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wan
  given name: Lingyun
author list: Agent
  family name: Wang
  given name: Linyan
author list: Agent
  family name: Cheng
  given name: Ran
author list: Agent
  family name: Cheng
  given name: Li
author list: Agent
  family name: Hu
  given name: Tao
doi: 10.7717/peerj.15164
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-21
copyright: ©2023 Wan et al.
attribution name: Wan et al.

Evaluation of waterlogging tolerance and responses of protective enzymes to waterlogging stress in pumpkin
type: item
type: AcademicArticle
description: Waterlogging caused by short and severe, or prolonged precipitation can be attributed to global warming. Pumpkin plants are drought-tolerant but not tolerate to waterlogging stress. Under frequent rain and waterlogging conditions, the production of pumpkins is of lower quality, sometimes rotten, and harvest failure occurs in severe cases. Therefore, it is of great significance to assess the waterlogging tolerance mechanism of pumpkin plants. In this study, 10 novel pumpkin varieties from Baimi series were used. The waterlogging tolerance level of pumpkin plants was evaluated by measuring waterlogging tolerance coefficient of biomass and physiological indices using waterlogging stress simulation method. The criteria to evaluate the waterlogging tolerance capacities of pumpkin plants were also explored. Using principal component and membership function analysis, waterlogging tolerance levels of the pumpkin varieties were ranked as follows: Baimi No. 10>; Baimi No. 5>; Baimi No. 1>; Baimi No. 2>; Baimi No. 3>; Baimi No. 7>; Baimi No. 9>; Baimi No. 6>; Baimi No. 4>; Baimi No. 8. Based on the results, Baimi No. 10 was identified with strong waterlogging tolerance and Baimi No. 8 with weak waterlogging tolerance. The responses of malondialdehyde (MDA), proline, key enzymes responsible for anaerobic respiration, and antioxidant enzymes to waterlogging stress were studied in pumpkin plants. The relative expression levels of related genes were determined using real-time fluorescence quantitative PCR technique. The aim of our study was to assess the waterlogging tolerance mechanism of pumpkin plants, thus laying a theoretical foundation for breeding waterlogging-tolerant varieties in the future. After flooding stress treatment, the antioxidant enzyme activities, contents of proline and alcohol dehydrogenases of Baimi No. 10 and Baimi No. 8 displayed an increase followed by a decrease. All indices of Baimi No. 10 were higher than Baimi No. 8. MDA contents gradually increased, …
format: application/pdf
format: text/html
creator: Zhenwei Liu
creator: Dandan Qiao
creator: Zhenyu Liu
creator: Pengwei Wang
creator: Li Sun
creator: Xinzheng Li
subject: Agricultural Science
subject: Genetics
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15177
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Waterlogging caused by short and severe, or prolonged precipitation can be attributed to global warming. Pumpkin plants are drought-tolerant but not tolerate to waterlogging stress. Under frequent rain and waterlogging conditions, the production of pumpkins is of lower quality, sometimes rotten, and harvest failure occurs in severe cases. Therefore, it is of great significance to assess the waterlogging tolerance mechanism of pumpkin plants. In this study, 10 novel pumpkin varieties from Baimi series were used. The waterlogging tolerance level of pumpkin plants was evaluated by measuring waterlogging tolerance coefficient of biomass and physiological indices using waterlogging stress simulation method. The criteria to evaluate the waterlogging tolerance capacities of pumpkin plants were also explored. Using principal component and membership function analysis, waterlogging tolerance levels of the pumpkin varieties were ranked as follows: Baimi No. 10>; Baimi No. 5>; Baimi No. 1>; Baimi No. 2>; Baimi No. 3>; Baimi No. 7>; Baimi No. 9>; Baimi No. 6>; Baimi No. 4>; Baimi No. 8. Based on the results, Baimi No. 10 was identified with strong waterlogging tolerance and Baimi No. 8 with weak waterlogging tolerance. The responses of malondialdehyde (MDA), proline, key enzymes responsible for anaerobic respiration, and antioxidant enzymes to waterlogging stress were studied in pumpkin plants. The relative expression levels of related genes were determined using real-time fluorescence quantitative PCR technique. The aim of our study was to assess the waterlogging tolerance mechanism of pumpkin plants, thus laying a theoretical foundation for breeding waterlogging-tolerant varieties in the future. After flooding stress treatment, the antioxidant enzyme activities, contents of proline and alcohol dehydrogenases of Baimi No. 10 and Baimi No. 8 displayed an increase followed by a decrease. All indices of Baimi No. 10 were higher than Baimi No. 8. MDA contents gradually increased, …
bibliographic citation: Liu et al. (2023) Evaluation of waterlogging tolerance and responses of protective enzymes to waterlogging stress in pumpkin. PeerJ 11:e15177 https://doi.org/10.7717/peerj.15177
date submitted: 2022-12-15
date accepted: 2023-03-13
issued: 2023-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Zhenwei
author list: Agent
  family name: Qiao
  given name: Dandan
author list: Agent
  family name: Liu
  given name: Zhenyu
author list: Agent
  family name: Wang
  given name: Pengwei
author list: Agent
  family name: Sun
  given name: Li
author list: Agent
  family name: Li
  given name: Xinzheng
doi: 10.7717/peerj.15177
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-21
copyright: ©2023 Liu et al.
attribution name: Liu et al.

Captive breeding in the endangered alpine tree frog, Litoria verreauxii alpina
type: item
type: AcademicArticle
description: Amphibians are experiencing dramatic worldwide declines and many species are reliant on captive breeding programs to ensure continued survival. However, captive breeding in amphibians is not always successful because many species, especially ones in decline, have particular and specific breeding needs. The endangered alpine tree frog, Litoria verreauxii alpina, has never been bred in captivity before. Due to its dramatic declines across the Australian Alps caused by the global pandemic chytridiomycosis, the species is a potential candidate for captive assurance colonies, which rely on captive breeding. For this study we tested hormone induction using two hormones that have had some success in other amphibian species, to no avail. We then tried outdoor breeding mesocosms during the winter/spring at temperatures similar to their natural breeding season, which was successful. Sixty-five percent of the egg masses laid successfully hatched tadpoles. Females laid more than one clutch over the experiment indicating either a shorter than annual ovulation cycle, or that females are capable of partial ovulation during breeding events. Outdoor breeding mesocosms are a possibility outside the native climate of a species, provided that temperatures overlap with their natural environment. Here, we highlight that troubleshooting is essential before embarking on a captive breeding program of a species that has not been bred before. Hormonal induction of breeding is not always successful; therefore, outdoor mesocosms might be required to achieve healthy tadpoles.
format: application/pdf
format: text/html
creator: Laura A. Brannelly
creator: Preeti Sharma
creator: Danielle K. Wallace
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.15179
publisher: PeerJ Inc.
rights: © 2023 Brannelly et al.
abstract: Amphibians are experiencing dramatic worldwide declines and many species are reliant on captive breeding programs to ensure continued survival. However, captive breeding in amphibians is not always successful because many species, especially ones in decline, have particular and specific breeding needs. The endangered alpine tree frog, Litoria verreauxii alpina, has never been bred in captivity before. Due to its dramatic declines across the Australian Alps caused by the global pandemic chytridiomycosis, the species is a potential candidate for captive assurance colonies, which rely on captive breeding. For this study we tested hormone induction using two hormones that have had some success in other amphibian species, to no avail. We then tried outdoor breeding mesocosms during the winter/spring at temperatures similar to their natural breeding season, which was successful. Sixty-five percent of the egg masses laid successfully hatched tadpoles. Females laid more than one clutch over the experiment indicating either a shorter than annual ovulation cycle, or that females are capable of partial ovulation during breeding events. Outdoor breeding mesocosms are a possibility outside the native climate of a species, provided that temperatures overlap with their natural environment. Here, we highlight that troubleshooting is essential before embarking on a captive breeding program of a species that has not been bred before. Hormonal induction of breeding is not always successful; therefore, outdoor mesocosms might be required to achieve healthy tadpoles.
bibliographic citation: Brannelly et al. (2023) Captive breeding in the endangered alpine tree frog, Litoria verreauxii alpina. PeerJ 11:e15179 https://doi.org/10.7717/peerj.15179
date submitted: 2022-11-10
date accepted: 2023-03-14
issued: 2023-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brannelly
  given name: Laura A.
author list: Agent
  family name: Sharma
  given name: Preeti
author list: Agent
  family name: Wallace
  given name: Danielle K.
doi: 10.7717/peerj.15179
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-21
copyright: ©2023 Brannelly et al.
attribution name: Brannelly et al.

Exploratory and confirmatory factor analyses identify three structural dimensions for measuring physical function in community-dwelling older adults
type: item
type: AcademicArticle
description: Background Physical function is a strong indicator of biological age and quality of life among older adults. However, the results from studies exploring the structural dimensions of physical function are inconsistent, and the measures assessed vary greatly, leading to a lack of comparability among them. This study aimed to construct a model to identify structural dimensions that are suitable and best assess physical function among community-dwelling adults 60–74 years of age in China. Method This study was conducted in 11 communities in Shanghai, China, from May to July 2021. A total of 381 adults 60–74 years of age were included in the study. Measured physical function data were used in factor analyses. Data collected from individuals were randomly assigned to either exploratory factor analysis (EFA) (n = 190) or confirmatory factor analysis (CFA) (n = 191). The statistical software used in the study was SPSS for EFA and AMOS for CFA. To test the properties of the structural dimension model of physical function, various fit indices, convergent validity, and discriminant validity were calculated. Results The EFA results derived seven indicators in three factors, with 58.548% of the total variance explained. The three factors were mobility function (three indicators), which explained 26.380% of the variance, handgrip strength and pulmonary function (two indicators), which explained 19.117% of the variance, and muscle strength (two indicators) which explained 13.050% of the variance. The CFA indicated that this model had an acceptable fit (χ2/df ratio, 2.102; GFI, 0.967; IFI, 0.960; CFI, 0.959; and RMSEA, 0.076), and the criteria for convergent validity and discriminability were also met by the model. Conclusion The constructed structural dimension model of physical function appeared to be a suitable and reliable tool to measure physical function in community-dwelling adults aged 60–74 years in China. The structural dimension indicators identified by this model may he…
format: application/pdf
format: text/html
creator: Guiping Jiang
creator: Xiaohuan Tan
creator: Hailong Wang
creator: Min Xu
creator: Xueping Wu
subject: Geriatrics
subject: Global Health
subject: Kinesiology
subject: Public Health
description: doi:10.7717/peerj.15182
publisher: PeerJ Inc.
rights: © 2023 Jiang et al.
abstract: Background Physical function is a strong indicator of biological age and quality of life among older adults. However, the results from studies exploring the structural dimensions of physical function are inconsistent, and the measures assessed vary greatly, leading to a lack of comparability among them. This study aimed to construct a model to identify structural dimensions that are suitable and best assess physical function among community-dwelling adults 60–74 years of age in China. Method This study was conducted in 11 communities in Shanghai, China, from May to July 2021. A total of 381 adults 60–74 years of age were included in the study. Measured physical function data were used in factor analyses. Data collected from individuals were randomly assigned to either exploratory factor analysis (EFA) (n = 190) or confirmatory factor analysis (CFA) (n = 191). The statistical software used in the study was SPSS for EFA and AMOS for CFA. To test the properties of the structural dimension model of physical function, various fit indices, convergent validity, and discriminant validity were calculated. Results The EFA results derived seven indicators in three factors, with 58.548% of the total variance explained. The three factors were mobility function (three indicators), which explained 26.380% of the variance, handgrip strength and pulmonary function (two indicators), which explained 19.117% of the variance, and muscle strength (two indicators) which explained 13.050% of the variance. The CFA indicated that this model had an acceptable fit (χ2/df ratio, 2.102; GFI, 0.967; IFI, 0.960; CFI, 0.959; and RMSEA, 0.076), and the criteria for convergent validity and discriminability were also met by the model. Conclusion The constructed structural dimension model of physical function appeared to be a suitable and reliable tool to measure physical function in community-dwelling adults aged 60–74 years in China. The structural dimension indicators identified by this model may he…
bibliographic citation: Jiang et al. (2023) Exploratory and confirmatory factor analyses identify three structural dimensions for measuring physical function in community-dwelling older adults. PeerJ 11:e15182 https://doi.org/10.7717/peerj.15182
date submitted: 2022-10-27
date accepted: 2023-03-14
issued: 2023-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Guiping
author list: Agent
  family name: Tan
  given name: Xiaohuan
author list: Agent
  family name: Wang
  given name: Hailong
author list: Agent
  family name: Xu
  given name: Min
author list: Agent
  family name: Wu
  given name: Xueping
doi: 10.7717/peerj.15182
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-21
copyright: ©2023 Jiang et al.
attribution name: Jiang et al.

The influence of climate warming on flowering phenology in relation to historical annual and seasonal temperatures and plant functional traits
type: item
type: AcademicArticle
description: Climate warming has the potential to influence plant flowering phenology which in turn can have broader ecological consequences. Herbarium collections offer a source of historical plant data that makes possible the ability to document and better understand how warming climate can influence long-term shifts in flowering phenology. We examined the influence of annual, winter, and spring temperatures on the flowering phenology of herbarium specimens for 36 species collected from 1884–2015. We then compared the response to warming between native and non-native, woody and herbaceous, dry and fleshy fruit, and spring vs summer blooming species. Across all species, plants flowered 2.26 days earlier per 1 °C increase in annual average temperatures and 2.93 days earlier per 1 °C increase in spring onset average temperatures. Winter temperatures did not significantly influence flowering phenology. The relationship of temperature and flowering phenology was not significantly different between native and non-native species. Woody species flowered earlier than herbaceous species only in response to increasing annual temperatures. There was no difference in the phenological response between species with dry fruits and those fleshy fruits for any of the temperature periods. Spring blooming species exhibited a significantly greater phenological response to warming yearly average temperatures than summer blooming species. Although herbarium specimens can reveal climate change impacts on phenology, it is also evident that the phenological responses to warming vary greatly among species due to differences in functional traits such as those considered here, as well as other factors.
format: application/pdf
format: text/html
creator: Cole Geissler
creator: Allison Davidson
creator: Richard A. Niesenbaum
subject: Ecology
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.15188
publisher: PeerJ Inc.
rights: © 2023 Geissler et al.
abstract: Climate warming has the potential to influence plant flowering phenology which in turn can have broader ecological consequences. Herbarium collections offer a source of historical plant data that makes possible the ability to document and better understand how warming climate can influence long-term shifts in flowering phenology. We examined the influence of annual, winter, and spring temperatures on the flowering phenology of herbarium specimens for 36 species collected from 1884–2015. We then compared the response to warming between native and non-native, woody and herbaceous, dry and fleshy fruit, and spring vs summer blooming species. Across all species, plants flowered 2.26 days earlier per 1 °C increase in annual average temperatures and 2.93 days earlier per 1 °C increase in spring onset average temperatures. Winter temperatures did not significantly influence flowering phenology. The relationship of temperature and flowering phenology was not significantly different between native and non-native species. Woody species flowered earlier than herbaceous species only in response to increasing annual temperatures. There was no difference in the phenological response between species with dry fruits and those fleshy fruits for any of the temperature periods. Spring blooming species exhibited a significantly greater phenological response to warming yearly average temperatures than summer blooming species. Although herbarium specimens can reveal climate change impacts on phenology, it is also evident that the phenological responses to warming vary greatly among species due to differences in functional traits such as those considered here, as well as other factors.
bibliographic citation: Geissler et al. (2023) The influence of climate warming on flowering phenology in relation to historical annual and seasonal temperatures and plant functional traits. PeerJ 11:e15188 https://doi.org/10.7717/peerj.15188
date submitted: 2022-10-11
date accepted: 2023-03-15
issued: 2023-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Geissler
  given name: Cole
author list: Agent
  family name: Davidson
  given name: Allison
author list: Agent
  family name: Niesenbaum
  given name: Richard A.
doi: 10.7717/peerj.15188
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-21
copyright: ©2023 Geissler et al.
attribution name: Geissler et al.

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