PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Beneficial effects of an intergenerational exercise intervention on health-related physical and psychosocial outcomes in Swiss preschool children and residential seniors: a clinical trial
items: Transcriptomics analysis reveals the effect of Broussonetia papyrifera L. fermented feed on meat quality traits in fattening lamb
items: Identification of key genes and biological processes contributing to colitis associated dysplasia in ulcerative colitis
items: Ambient ozone pollution at a coal chemical industry city in the border of Loess Plateau and Mu Us Desert: characteristics, sensitivity analysis and control strategies
items: Comparative transcriptome analysis reveals key insights into male sterility in Salvia miltiorrhiza Bunge
items: Genome-wide identification, classification, and expression analysis of the HSF gene family in pineapple (Ananas comosus)
items: Association between gonadal hormones and osteoporosis in schizophrenia patients undergoing risperidone monotherapy: a cross-sectional study
items: Identification of potential genes in upper tract urothelial carcinoma using next-generation sequencing with bioinformatics and in vitro analyses
items: Variation in purple sea urchin (Strongylocentrotus purpuratus) morphological traits in relation to resource availability
items: Comparison of morphology, development and expression patterns of hsf and hsp11.0 of Cotesia chilonis under normal and high temperature

Beneficial effects of an intergenerational exercise intervention on health-related physical and psychosocial outcomes in Swiss preschool children and residential seniors: a clinical trial
type: item
type: AcademicArticle
description: Background Intergenerational exercise possesses the potential to becoming an innovative strategy for promoting physical activity in seniors and children. Although this approach has gained attraction within the last decade, controlled trials on physical and psychosocial effects have not been performed yet. Methods Sixty-eight healthy preschool children (age: 4.9 y (SD 0.7)) and 47 residential seniors (age: 81.7 y (7.1)) participated in this five-armed intervention study. All participants were assigned to either an intergenerational (IG), peer (PG) or a control group (CON). Children were tested on gross motor skills (TGMD-2), jump performance and handgrip strength. Social-emotional skills questionnaires (KOMPIK) were assessed by kindergarten teachers. Seniors performed the Short Physical Performance Battery (SPPB), including gait speed. Arterial stiffness parameters were also examined. Questionnaires assessing psychosocial wellbeing were filled in with staff. IG and PG received one comparable exercise session a week lasting 45 minutes for 25-weeks. CON received no intervention. Measurements were performed before and after the intervention. Results In children: IG improved all measured physical parameters. When adjusted for baseline values, large effects were observed in favor of IG compared to CON in TGMD-2 (Cohen’s d=0.78 [0.33;1.24]) and in handgrip strength (d = 1.07 [0.63;1.51]). No relevant differences were found in KOMPIK between groups (−0.38<d≤0.14). In seniors: IG showed moderate to very large improvements in all main physical performance (0.61<d≤2.53) and psychosocial parameters (0.89<d≤1.20) compared to CON. Conclusion IG children showed large benefits in motor skills compared to CON while IG seniors benefit especially in psychosocial wellbeing and functional mobility necessary for everyday life. Intergenerational exercise is comparable and in certain dimensions superior to peer group exercise and a promising strategy to integratively improve mental health …
format: application/pdf
format: text/html
creator: Alice Minghetti
creator: Lars Donath
creator: Lukas Zahner
creator: Henner Hanssen
creator: Oliver Faude
subject: Geriatrics
subject: Kinesiology
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11292
publisher: PeerJ Inc.
rights: © 2021 Minghetti et al.
abstract: Background Intergenerational exercise possesses the potential to becoming an innovative strategy for promoting physical activity in seniors and children. Although this approach has gained attraction within the last decade, controlled trials on physical and psychosocial effects have not been performed yet. Methods Sixty-eight healthy preschool children (age: 4.9 y (SD 0.7)) and 47 residential seniors (age: 81.7 y (7.1)) participated in this five-armed intervention study. All participants were assigned to either an intergenerational (IG), peer (PG) or a control group (CON). Children were tested on gross motor skills (TGMD-2), jump performance and handgrip strength. Social-emotional skills questionnaires (KOMPIK) were assessed by kindergarten teachers. Seniors performed the Short Physical Performance Battery (SPPB), including gait speed. Arterial stiffness parameters were also examined. Questionnaires assessing psychosocial wellbeing were filled in with staff. IG and PG received one comparable exercise session a week lasting 45 minutes for 25-weeks. CON received no intervention. Measurements were performed before and after the intervention. Results In children: IG improved all measured physical parameters. When adjusted for baseline values, large effects were observed in favor of IG compared to CON in TGMD-2 (Cohen’s d=0.78 [0.33;1.24]) and in handgrip strength (d = 1.07 [0.63;1.51]). No relevant differences were found in KOMPIK between groups (−0.38<d≤0.14). In seniors: IG showed moderate to very large improvements in all main physical performance (0.61<d≤2.53) and psychosocial parameters (0.89<d≤1.20) compared to CON. Conclusion IG children showed large benefits in motor skills compared to CON while IG seniors benefit especially in psychosocial wellbeing and functional mobility necessary for everyday life. Intergenerational exercise is comparable and in certain dimensions superior to peer group exercise and a promising strategy to integratively improve mental health …
bibliographic citation: Minghetti et al. (2021) Beneficial effects of an intergenerational exercise intervention on health-related physical and psychosocial outcomes in Swiss preschool children and residential seniors: a clinical trial. PeerJ 9:e11292 https://doi.org/10.7717/peerj.11292
date submitted: 2020-12-17
date accepted: 2021-03-26
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Minghetti
  given name: Alice
author list: Agent
  family name: Donath
  given name: Lars
author list: Agent
  family name: Zahner
  given name: Lukas
author list: Agent
  family name: Hanssen
  given name: Henner
author list: Agent
  family name: Faude
  given name: Oliver
doi: 10.7717/peerj.11292
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Minghetti et al.
attribution name: Minghetti et al.

Transcriptomics analysis reveals the effect of Broussonetia papyrifera L. fermented feed on meat quality traits in fattening lamb
type: item
type: AcademicArticle
description: To date, utilization of feed grains is increasing, which competes for human food. It is imperative to develop and utilize unconventional feed materials. Broussonetia papyrifera L. (B. papyrifera) is a good feeding material with high crude protein, crude fat, and low crude fiber, which is widely distributed in China. In this study, 12 Dorper ♂×Hu ♀ crossbred weaned male lambs were seleted into four groups based on the feed that ratio of the B. papyrifera fermented feed in the total mixed diet (0%, 6%, 18%, and 100%), to character the lambs’ longissimus dorsi (LD) fatty acids, morphology and transcriptome. Results showed that the muscle fiber’s diameter and area were the smallest in the 100% group. The highest content of beneficial fatty acids and the lowest content of harmful fatty acids in group 18%. RNA-seq identified 443 differentially expressed genes (DEGs) in the LD of lambs from 4 groups. Among these genes, 169 (38.1%) were up-regulated and 274 (61.9%) were down-regulated. The DEGs were mostly enriched in in fatty acid metabolism, arginine and proline metabolism, and PPAR signaling pathways. Our results provide knowledge to understand effect of different ratios of B. papyrifera fermented feed on sheep meat quality traits, also a basis for understanding of the molecular regulation mechanism of B. papyrifera fermented feed affecting on sheep meat quality.
format: application/pdf
format: text/html
creator: Xuejiao An
creator: Shengwei Zhang
creator: Taotao Li
creator: Nana Chen
creator: Xia Wang
creator: Baojun Zhang
creator: Youji Ma
subject: Agricultural Science
subject: Food Science and Technology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.11295
publisher: PeerJ Inc.
rights: © 2021 An et al.
abstract: To date, utilization of feed grains is increasing, which competes for human food. It is imperative to develop and utilize unconventional feed materials. Broussonetia papyrifera L. (B. papyrifera) is a good feeding material with high crude protein, crude fat, and low crude fiber, which is widely distributed in China. In this study, 12 Dorper ♂×Hu ♀ crossbred weaned male lambs were seleted into four groups based on the feed that ratio of the B. papyrifera fermented feed in the total mixed diet (0%, 6%, 18%, and 100%), to character the lambs’ longissimus dorsi (LD) fatty acids, morphology and transcriptome. Results showed that the muscle fiber’s diameter and area were the smallest in the 100% group. The highest content of beneficial fatty acids and the lowest content of harmful fatty acids in group 18%. RNA-seq identified 443 differentially expressed genes (DEGs) in the LD of lambs from 4 groups. Among these genes, 169 (38.1%) were up-regulated and 274 (61.9%) were down-regulated. The DEGs were mostly enriched in in fatty acid metabolism, arginine and proline metabolism, and PPAR signaling pathways. Our results provide knowledge to understand effect of different ratios of B. papyrifera fermented feed on sheep meat quality traits, also a basis for understanding of the molecular regulation mechanism of B. papyrifera fermented feed affecting on sheep meat quality.
bibliographic citation: An et al. (2021) Transcriptomics analysis reveals the effect of Broussonetia papyrifera L. fermented feed on meat quality traits in fattening lamb. PeerJ 9:e11295 https://doi.org/10.7717/peerj.11295
date submitted: 2020-09-11
date accepted: 2021-03-27
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: An
  given name: Xuejiao
author list: Agent
  family name: Zhang
  given name: Shengwei
author list: Agent
  family name: Li
  given name: Taotao
author list: Agent
  family name: Chen
  given name: Nana
author list: Agent
  family name: Wang
  given name: Xia
author list: Agent
  family name: Zhang
  given name: Baojun
author list: Agent
  family name: Ma
  given name: Youji
doi: 10.7717/peerj.11295
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 An et al.
attribution name: An et al.

Identification of key genes and biological processes contributing to colitis associated dysplasia in ulcerative colitis
type: item
type: AcademicArticle
description: Background Ulcerative colitis-associated colorectal cancer (UC-CRC) is a life-threatening complication of ulcerative colitis (UC). The mechanisms underlying UC-CRC remain to be elucidated. The purpose of this study was to explore the key genes and biological processes contributing to colitis-associated dysplasia (CAD) or carcinogenesis in UC via database mining, thus offering opportunities for early prediction and intervention of UC-CRC. Methods Microarray datasets (GSE47908 and GSE87466) were downloaded from Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) between groups of GSE47908 were identified using the “limma” R package. Weighted gene co-expression network analysis (WGCNA) based on DEGs between the CAD and control groups was conducted subsequently. Functional enrichment analysis was performed, and hub genes of selected modules were identified using the “clusterProfiler” R package. Single-gene gene set enrichment analysis (GSEA) was conducted to predict significant biological processes and pathways associated with the specified gene. Results Six functional modules were identified based on 4929 DEGs. Green and blue modules were selected because of their consistent correlation with UC and CAD, and the highest correlation coefficient with the progress of UC-associated carcinogenesis. Functional enrichment analysis revealed that genes of these two modules were significantly enriched in biological processes, including mitochondrial dysfunction, cell-cell junction, and immune responses. However, GSEA based on differential expression analysis between sporadic colorectal cancer (CRC) and normal controls from The Cancer Genome Atlas (TCGA) indicated that mitochondrial dysfunction may not be the major carcinogenic mechanism underlying sporadic CRC. Thirteen hub genes (SLC25A3, ACO2, AIFM1, ATP5A1, DLD, TFE3, UQCRC1, ADIPOR2, SLC35D1, TOR1AIP1, PRR5L, ATOX1, and DTX3) were identified. Their expression trends were validated in UC patients of GSE87466, …
format: application/pdf
format: text/html
creator: Di Zhang
creator: Pengguang Yan
creator: Taotao Han
creator: Xiaoyun Cheng
creator: Jingnan Li
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Internal Medicine
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.11321
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Background Ulcerative colitis-associated colorectal cancer (UC-CRC) is a life-threatening complication of ulcerative colitis (UC). The mechanisms underlying UC-CRC remain to be elucidated. The purpose of this study was to explore the key genes and biological processes contributing to colitis-associated dysplasia (CAD) or carcinogenesis in UC via database mining, thus offering opportunities for early prediction and intervention of UC-CRC. Methods Microarray datasets (GSE47908 and GSE87466) were downloaded from Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) between groups of GSE47908 were identified using the “limma” R package. Weighted gene co-expression network analysis (WGCNA) based on DEGs between the CAD and control groups was conducted subsequently. Functional enrichment analysis was performed, and hub genes of selected modules were identified using the “clusterProfiler” R package. Single-gene gene set enrichment analysis (GSEA) was conducted to predict significant biological processes and pathways associated with the specified gene. Results Six functional modules were identified based on 4929 DEGs. Green and blue modules were selected because of their consistent correlation with UC and CAD, and the highest correlation coefficient with the progress of UC-associated carcinogenesis. Functional enrichment analysis revealed that genes of these two modules were significantly enriched in biological processes, including mitochondrial dysfunction, cell-cell junction, and immune responses. However, GSEA based on differential expression analysis between sporadic colorectal cancer (CRC) and normal controls from The Cancer Genome Atlas (TCGA) indicated that mitochondrial dysfunction may not be the major carcinogenic mechanism underlying sporadic CRC. Thirteen hub genes (SLC25A3, ACO2, AIFM1, ATP5A1, DLD, TFE3, UQCRC1, ADIPOR2, SLC35D1, TOR1AIP1, PRR5L, ATOX1, and DTX3) were identified. Their expression trends were validated in UC patients of GSE87466, …
bibliographic citation: Zhang et al. (2021) Identification of key genes and biological processes contributing to colitis associated dysplasia in ulcerative colitis. PeerJ 9:e11321 https://doi.org/10.7717/peerj.11321
date submitted: 2020-12-15
date accepted: 2021-03-31
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Di
author list: Agent
  family name: Yan
  given name: Pengguang
author list: Agent
  family name: Han
  given name: Taotao
author list: Agent
  family name: Cheng
  given name: Xiaoyun
author list: Agent
  family name: Li
  given name: Jingnan
doi: 10.7717/peerj.11321
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Zhang et al.
attribution name: Zhang et al.

Ambient ozone pollution at a coal chemical industry city in the border of Loess Plateau and Mu Us Desert: characteristics, sensitivity analysis and control strategies
type: item
type: AcademicArticle
description: In this study, ambient ozone (O3) pollution characteristics and sensitivity analysis were carried out in Yulin, a city in the central area of the Loess Plateau during 2017 to 2019 summer. O3 concentrations increased for 2017 to 2019. Correlation and statistics analysis indicated high temperature (T > 25 °C, low relative humidity (RH < 60%), and low wind speed (WS < 3 m/s) were favorable for O3 formation and accumulation, and the O3 pollution days (MDA8 O3 > 160 µg/m3) were predominantly observed when the wind was traveling from the easterly and southerly. O3 concentration in urban area of Yulin was higher than that in background. The pollution air masses from Fenwei Plain increase the level and duration of O3 pollution. In order to clarify the formation mechanism and source of O3, online measurements of volatile organic compounds (VOCs) were conducted from 7 July to 10 August in 2019. The average of VOCs concentration was 26 ± 12 ppbv, and large amounts of alkenes followed by aromatics, characteristic pollutants of the coal chemical industry, were detected in the ambient air. To further measure the sensitivity, the observation-based model (OBM) simulation was conducted. Empirical Kinetic Modeling Approach (EKMA) plot and relative incremental reactivity (RIR) value indicated Yulin located on VOCs-limited regime. That implied a slight decrease of NOx may increase O3 concentration. When the emission reduction ratio of anthropogenic VOCs/NOx higher than 1:1, the O3 will decrease. O3 control strategies analysis shows that the O3 targets of 5% and 10% O3 concentration reductions are achievable through precursor control, but more effort is needed to reach the 30% and 40% reduction control targets.
format: application/pdf
format: text/html
creator: Manfei Yin
creator: Xin Zhang
creator: Yunfeng Li
creator: Kai Fan
creator: Hong Li
creator: Rui Gao
creator: Jinjuan Li
subject: Atmospheric Chemistry
subject: Environmental Impacts
description: doi:10.7717/peerj.11322
publisher: PeerJ Inc.
rights: © 2021 Yin et al.
abstract: In this study, ambient ozone (O3) pollution characteristics and sensitivity analysis were carried out in Yulin, a city in the central area of the Loess Plateau during 2017 to 2019 summer. O3 concentrations increased for 2017 to 2019. Correlation and statistics analysis indicated high temperature (T > 25 °C, low relative humidity (RH < 60%), and low wind speed (WS < 3 m/s) were favorable for O3 formation and accumulation, and the O3 pollution days (MDA8 O3 > 160 µg/m3) were predominantly observed when the wind was traveling from the easterly and southerly. O3 concentration in urban area of Yulin was higher than that in background. The pollution air masses from Fenwei Plain increase the level and duration of O3 pollution. In order to clarify the formation mechanism and source of O3, online measurements of volatile organic compounds (VOCs) were conducted from 7 July to 10 August in 2019. The average of VOCs concentration was 26 ± 12 ppbv, and large amounts of alkenes followed by aromatics, characteristic pollutants of the coal chemical industry, were detected in the ambient air. To further measure the sensitivity, the observation-based model (OBM) simulation was conducted. Empirical Kinetic Modeling Approach (EKMA) plot and relative incremental reactivity (RIR) value indicated Yulin located on VOCs-limited regime. That implied a slight decrease of NOx may increase O3 concentration. When the emission reduction ratio of anthropogenic VOCs/NOx higher than 1:1, the O3 will decrease. O3 control strategies analysis shows that the O3 targets of 5% and 10% O3 concentration reductions are achievable through precursor control, but more effort is needed to reach the 30% and 40% reduction control targets.
bibliographic citation: Yin et al. (2021) Ambient ozone pollution at a coal chemical industry city in the border of Loess Plateau and Mu Us Desert: characteristics, sensitivity analysis and control strategies. PeerJ 9:e11322 https://doi.org/10.7717/peerj.11322
date submitted: 2021-01-12
date accepted: 2021-03-31
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Manfei
author list: Agent
  family name: Zhang
  given name: Xin
author list: Agent
  family name: Li
  given name: Yunfeng
author list: Agent
  family name: Fan
  given name: Kai
author list: Agent
  family name: Li
  given name: Hong
author list: Agent
  family name: Gao
  given name: Rui
author list: Agent
  family name: Li
  given name: Jinjuan
doi: 10.7717/peerj.11322
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Yin et al.
attribution name: Yin et al.

Comparative transcriptome analysis reveals key insights into male sterility in Salvia miltiorrhiza Bunge
type: item
type: AcademicArticle
description: Background Large-scale heterosis breeding depends upon stable, inherited male sterility lines. We accidentally discovered a male sterility line (SW-S) in the F1progeny of a Salvia miltiorrhiza Bunge from Shandong, China (purple flowers) crossed with a S. miltiorrhiza f. alba from Sichuan, China (white flowers). We sought to provide insights into the pollen development for male sterility in S. miltiorrhiza. Methods The phenotypic and cytological features of the SW-S and fertile control SW-F were observed using scanning electron microscopy and paraffin sections to identify the key stage of male sterility. Transcriptome profiles were recorded for anthers at the tetrad stage of SW-S and SW-F using Illumina RNA-Seq. Results The paraffin sections showed that sterility mainly occurred at the tetrad stage of microspore development, during which the tapetum cells in the anther compartment completely fell off and gradually degraded in the sterile line. There was little-to-no callose deposited around the microspore cells. The tetrad microspore was shriveled and had abnormal morphology. Therefore, anthers at the tetrad stage of SW-S and fertile control SW-F were selected for comparative transcriptome analysis. In total, 266,722,270 clean reads were obtained from SW-S and SW-F, which contained 36,534 genes. There were 2,571 differentially expressed genes (DEGs) in SW-S and SW-F, of which 63.5% were downregulated. Gene Ontology (GO) enrichment analysis indicated that the differentially expressed genes were enriched in 56 functional groups (GO terms); of these, all DEGs involved in microgametogenesis and developmental maturation were downregulated in SW-S. These results were confirmed by quantitative RT-PCR. The two GO terms contained 18 DEGs, among which eight DEGs (namely: GPAT3, RHF1A, phosphatidylinositol, PFAS, MYB96, MYB78, Cals5, and LAT52) were related to gamete development. There were 10 DEGs related to development and maturation, among which three genes were directly rel…
format: application/pdf
format: text/html
creator: Yan Yu
creator: Yuanyuan Jiang
creator: Long Wang
creator: Yichao Wu
creator: Jinqiu Liao
creator: Mingzhi Zhong
creator: Ruiwu Yang
creator: Xingfu Chen
creator: Qingmiao Li
creator: Li Zhang
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11326
publisher: PeerJ Inc.
rights: © 2021 Yu et al.
abstract: Background Large-scale heterosis breeding depends upon stable, inherited male sterility lines. We accidentally discovered a male sterility line (SW-S) in the F1progeny of a Salvia miltiorrhiza Bunge from Shandong, China (purple flowers) crossed with a S. miltiorrhiza f. alba from Sichuan, China (white flowers). We sought to provide insights into the pollen development for male sterility in S. miltiorrhiza. Methods The phenotypic and cytological features of the SW-S and fertile control SW-F were observed using scanning electron microscopy and paraffin sections to identify the key stage of male sterility. Transcriptome profiles were recorded for anthers at the tetrad stage of SW-S and SW-F using Illumina RNA-Seq. Results The paraffin sections showed that sterility mainly occurred at the tetrad stage of microspore development, during which the tapetum cells in the anther compartment completely fell off and gradually degraded in the sterile line. There was little-to-no callose deposited around the microspore cells. The tetrad microspore was shriveled and had abnormal morphology. Therefore, anthers at the tetrad stage of SW-S and fertile control SW-F were selected for comparative transcriptome analysis. In total, 266,722,270 clean reads were obtained from SW-S and SW-F, which contained 36,534 genes. There were 2,571 differentially expressed genes (DEGs) in SW-S and SW-F, of which 63.5% were downregulated. Gene Ontology (GO) enrichment analysis indicated that the differentially expressed genes were enriched in 56 functional groups (GO terms); of these, all DEGs involved in microgametogenesis and developmental maturation were downregulated in SW-S. These results were confirmed by quantitative RT-PCR. The two GO terms contained 18 DEGs, among which eight DEGs (namely: GPAT3, RHF1A, phosphatidylinositol, PFAS, MYB96, MYB78, Cals5, and LAT52) were related to gamete development. There were 10 DEGs related to development and maturation, among which three genes were directly rel…
bibliographic citation: Yu et al. (2021) Comparative transcriptome analysis reveals key insights into male sterility in Salvia miltiorrhiza Bunge. PeerJ 9:e11326 https://doi.org/10.7717/peerj.11326
date submitted: 2020-12-13
date accepted: 2021-03-31
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Yan
author list: Agent
  family name: Jiang
  given name: Yuanyuan
author list: Agent
  family name: Wang
  given name: Long
author list: Agent
  family name: Wu
  given name: Yichao
author list: Agent
  family name: Liao
  given name: Jinqiu
author list: Agent
  family name: Zhong
  given name: Mingzhi
author list: Agent
  family name: Yang
  given name: Ruiwu
author list: Agent
  family name: Chen
  given name: Xingfu
author list: Agent
  family name: Li
  given name: Qingmiao
author list: Agent
  family name: Zhang
  given name: Li
doi: 10.7717/peerj.11326
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Yu et al.
attribution name: Yu et al.

Genome-wide identification, classification, and expression analysis of the HSF gene family in pineapple (Ananas comosus)
type: item
type: AcademicArticle
description: Transcription factors (TFs), such as heat shock transcription factors (HSFs), usually play critical regulatory functions in plant development, growth, and response to environmental cues. However, no HSFs have been characterized in pineapple thus far. Here, we identified 22 AcHSF genes from the pineapple genome. Gene structure, motifs, and phylogenetic analysis showed that AcHSF families were distinctly grouped into three subfamilies (12 in Group A, seven in Group B, and four in Group C). The AcHSF promoters contained various cis-elements associated with stress, hormones, and plant development processes, for instance, STRE, WRKY, and ABRE binding sites. The majority of HSFs were expressed in diverse pineapple tissues and developmental stages. The expression of AcHSF-B4b/AcHSF-B4c and AcHSF-A7b/AcHSF-A1c were enriched in the ovules and fruits, respectively. Six genes (AcHSF-A1a , AcHSF-A2, AcHSF-A9a, AcHSF-B1a, AcHSF-B2a, and AcHSF-C1a) were transcriptionally modified by cold, heat, and ABA. Our results provide an overview and lay the foundation for future functional characterization of the pineapple HSF gene family.
format: application/pdf
format: text/html
creator: Lulu Wang
creator: Yanhui Liu
creator: Mengnan Chai
creator: Huihuang Chen
creator: Mohammad Aslam
creator: Xiaoping Niu
creator: Yuan Qin
creator: Hanyang Cai
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11329
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Transcription factors (TFs), such as heat shock transcription factors (HSFs), usually play critical regulatory functions in plant development, growth, and response to environmental cues. However, no HSFs have been characterized in pineapple thus far. Here, we identified 22 AcHSF genes from the pineapple genome. Gene structure, motifs, and phylogenetic analysis showed that AcHSF families were distinctly grouped into three subfamilies (12 in Group A, seven in Group B, and four in Group C). The AcHSF promoters contained various cis-elements associated with stress, hormones, and plant development processes, for instance, STRE, WRKY, and ABRE binding sites. The majority of HSFs were expressed in diverse pineapple tissues and developmental stages. The expression of AcHSF-B4b/AcHSF-B4c and AcHSF-A7b/AcHSF-A1c were enriched in the ovules and fruits, respectively. Six genes (AcHSF-A1a , AcHSF-A2, AcHSF-A9a, AcHSF-B1a, AcHSF-B2a, and AcHSF-C1a) were transcriptionally modified by cold, heat, and ABA. Our results provide an overview and lay the foundation for future functional characterization of the pineapple HSF gene family.
bibliographic citation: Wang et al. (2021) Genome-wide identification, classification, and expression analysis of the HSF gene family in pineapple (Ananas comosus). PeerJ 9:e11329 https://doi.org/10.7717/peerj.11329
date submitted: 2020-12-16
date accepted: 2021-03-31
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lulu
author list: Agent
  family name: Liu
  given name: Yanhui
author list: Agent
  family name: Chai
  given name: Mengnan
author list: Agent
  family name: Chen
  given name: Huihuang
author list: Agent
  family name: Aslam
  given name: Mohammad
author list: Agent
  family name: Niu
  given name: Xiaoping
author list: Agent
  family name: Qin
  given name: Yuan
author list: Agent
  family name: Cai
  given name: Hanyang
doi: 10.7717/peerj.11329
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Association between gonadal hormones and osteoporosis in schizophrenia patients undergoing risperidone monotherapy: a cross-sectional study
type: item
type: AcademicArticle
description: Objective Patients with schizophrenia are at increased risk of osteoporosis. This study first determined the osteoporosis rate in patients with schizophrenia and then then explored the association between serum gonadal hormone levels and osteoporosis among these patients. Methods A total of 250 patients with schizophrenia and 288 healthy controls were recruited. Osteoporosis was defined by decreased bone mineral density (BMD) of the calcaneus. Serum fasting levels of gonadal hormones (prolactin, estradiol, testosterone, progesterone, follicle-stimulating hormone, luteinizing hormone) were determined. The relationship between osteoporosis and hormone levels was statistically analyzed by binary logistic regression analysis. Results Our results showed that patients with schizophrenia had a markedly higher rate of osteoporosis (24.4% vs. 10.1%) than healthy controls (P < 0.001). Patients with osteoporosis were older, had a longer disease course, and had a lower body mass index (BMI) than patients without osteoporosis (all P < 0.05). Regarding gonadal hormones, we found significantly higher prolactin, but lower estradiol, levels in patients with osteoporosis than in those without osteoporosis (both P < 0.05). The regression analysis revealed that PRL (OR = 1.1, 95% CI [1.08–1.15], P < 0.001) and E2 level (OR = 0.9, 95%CI [0.96–0.99], P = 0.011) were significantly associated with osteoporosis in patients with schizophrenia. Conclusion Our results indicate that patients with schizophrenia who are being treated with risperidone have a high rate of osteoporosis. Increased prolactin and reduced estradiol levels are significantly associated with osteoporosis.
format: application/pdf
format: text/html
creator: Yi Chen
creator: Yaoyao Zhang
creator: Kaili Fan
creator: Weiqian Xu
creator: Chao Teng
creator: Shuangshuang Wang
creator: Wei Tang
creator: Xiaomin Zhu
subject: Drugs and Devices
subject: Neurology
subject: Orthopedics
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.11332
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Objective Patients with schizophrenia are at increased risk of osteoporosis. This study first determined the osteoporosis rate in patients with schizophrenia and then then explored the association between serum gonadal hormone levels and osteoporosis among these patients. Methods A total of 250 patients with schizophrenia and 288 healthy controls were recruited. Osteoporosis was defined by decreased bone mineral density (BMD) of the calcaneus. Serum fasting levels of gonadal hormones (prolactin, estradiol, testosterone, progesterone, follicle-stimulating hormone, luteinizing hormone) were determined. The relationship between osteoporosis and hormone levels was statistically analyzed by binary logistic regression analysis. Results Our results showed that patients with schizophrenia had a markedly higher rate of osteoporosis (24.4% vs. 10.1%) than healthy controls (P < 0.001). Patients with osteoporosis were older, had a longer disease course, and had a lower body mass index (BMI) than patients without osteoporosis (all P < 0.05). Regarding gonadal hormones, we found significantly higher prolactin, but lower estradiol, levels in patients with osteoporosis than in those without osteoporosis (both P < 0.05). The regression analysis revealed that PRL (OR = 1.1, 95% CI [1.08–1.15], P < 0.001) and E2 level (OR = 0.9, 95%CI [0.96–0.99], P = 0.011) were significantly associated with osteoporosis in patients with schizophrenia. Conclusion Our results indicate that patients with schizophrenia who are being treated with risperidone have a high rate of osteoporosis. Increased prolactin and reduced estradiol levels are significantly associated with osteoporosis.
bibliographic citation: Chen et al. (2021) Association between gonadal hormones and osteoporosis in schizophrenia patients undergoing risperidone monotherapy: a cross-sectional study. PeerJ 9:e11332 https://doi.org/10.7717/peerj.11332
date submitted: 2020-10-29
date accepted: 2021-04-01
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yi
author list: Agent
  family name: Zhang
  given name: Yaoyao
author list: Agent
  family name: Fan
  given name: Kaili
author list: Agent
  family name: Xu
  given name: Weiqian
author list: Agent
  family name: Teng
  given name: Chao
author list: Agent
  family name: Wang
  given name: Shuangshuang
author list: Agent
  family name: Tang
  given name: Wei
author list: Agent
  family name: Zhu
  given name: Xiaomin
doi: 10.7717/peerj.11332
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Chen et al.
attribution name: Chen et al.

Identification of potential genes in upper tract urothelial carcinoma using next-generation sequencing with bioinformatics and in vitro analyses
type: item
type: AcademicArticle
description: Background We aimed to identify prognostic biomarkers of upper tract urothelial carcinomas (UTUCs), including microRNAs (miRNAs) and genes which account for only 5% to 10% of all urothelial carcinomas (UCs). In Taiwan, this figure is markedly higher, where it can reach up to 30% of UC cases. Materials and Methods Using next-generation sequencing (NGS), we analyzed two pairs of renal pelvis tumors and adjacent normal urothelial tissues to screen miRNAs and messenger RNAs. By combining bioinformatics analysis from miRmap, Gene Expression Omnibus (GEO), and Oncomine and Ingenuity® Pathway Analysis databases, we identified candidate genes. To search for upstream miRNAs with exact target binding sites, we used miRmap, TargetScan, and miRDB to enforce evidence. Then, we clarified gene and protein expression through an in vitro study using western blot analysis and quantitative real-time reverse transcriptase-PCR. Results Interactions between selected target genes obtained using the NGS and miRmap methods were assessed through a Venn diagram analysis. Six potential genes, namely, PDE5A, RECK, ZEB2, NCALD, PLCXD3 and CYBRD1 showed significant differences. Further analysis of gene expression from the GEO dataset indicated lower expression of PDE5A, RECK, ZEB2, and CYBRD1 in bladder cancer tissue than in normal bladder mucosa, which indicated that PDE5A, RECK, ZEB2, and CYBRD1 may act as tumor suppressors in UTUC. In addition, we compared the expression of these genes in various UC cell lines (RT4, BFTC905, J82, T24, UMUC3, 5637, BFTC 909, UMUC14) and found decreased expression of PDE5A in muscle-invasive UC cells compared with the RT4 cell line. Furthermore, by using paired UTUC and normal tissues from 20 patients, lower PDE5A expression was also demonstrated in tumor specimens. Conclusions Our findings suggest these candidate genes may play some roles in UTUC progression. We propose that these markers may be potential targets clarified by in vitro and in vivo experiments. P…
format: application/pdf
format: text/html
creator: Hsiang-Ying Lee
creator: Ching-Chia Li
creator: Wei-Ming Li
creator: Ya-Ling Hsu
creator: Hsin-Chih Yeh
creator: Hung-Lung Ke
creator: Bi Wen Yeh
creator: Chun-Nung Huang
creator: Chien-Feng Li
creator: Po-Lin Kuo
creator: Wen-Jeng Wu
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.11343
publisher: PeerJ Inc.
rights: © 2021 Lee et al.
abstract: Background We aimed to identify prognostic biomarkers of upper tract urothelial carcinomas (UTUCs), including microRNAs (miRNAs) and genes which account for only 5% to 10% of all urothelial carcinomas (UCs). In Taiwan, this figure is markedly higher, where it can reach up to 30% of UC cases. Materials and Methods Using next-generation sequencing (NGS), we analyzed two pairs of renal pelvis tumors and adjacent normal urothelial tissues to screen miRNAs and messenger RNAs. By combining bioinformatics analysis from miRmap, Gene Expression Omnibus (GEO), and Oncomine and Ingenuity® Pathway Analysis databases, we identified candidate genes. To search for upstream miRNAs with exact target binding sites, we used miRmap, TargetScan, and miRDB to enforce evidence. Then, we clarified gene and protein expression through an in vitro study using western blot analysis and quantitative real-time reverse transcriptase-PCR. Results Interactions between selected target genes obtained using the NGS and miRmap methods were assessed through a Venn diagram analysis. Six potential genes, namely, PDE5A, RECK, ZEB2, NCALD, PLCXD3 and CYBRD1 showed significant differences. Further analysis of gene expression from the GEO dataset indicated lower expression of PDE5A, RECK, ZEB2, and CYBRD1 in bladder cancer tissue than in normal bladder mucosa, which indicated that PDE5A, RECK, ZEB2, and CYBRD1 may act as tumor suppressors in UTUC. In addition, we compared the expression of these genes in various UC cell lines (RT4, BFTC905, J82, T24, UMUC3, 5637, BFTC 909, UMUC14) and found decreased expression of PDE5A in muscle-invasive UC cells compared with the RT4 cell line. Furthermore, by using paired UTUC and normal tissues from 20 patients, lower PDE5A expression was also demonstrated in tumor specimens. Conclusions Our findings suggest these candidate genes may play some roles in UTUC progression. We propose that these markers may be potential targets clarified by in vitro and in vivo experiments. P…
bibliographic citation: Lee et al. (2021) Identification of potential genes in upper tract urothelial carcinoma using next-generation sequencing with bioinformatics and in vitro analyses. PeerJ 9:e11343 https://doi.org/10.7717/peerj.11343
date submitted: 2020-11-20
date accepted: 2021-04-03
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Hsiang-Ying
author list: Agent
  family name: Li
  given name: Ching-Chia
author list: Agent
  family name: Li
  given name: Wei-Ming
author list: Agent
  family name: Hsu
  given name: Ya-Ling
author list: Agent
  family name: Yeh
  given name: Hsin-Chih
author list: Agent
  family name: Ke
  given name: Hung-Lung
author list: Agent
  family name: Yeh
  given name: Bi Wen
author list: Agent
  family name: Huang
  given name: Chun-Nung
author list: Agent
  family name: Li
  given name: Chien-Feng
author list: Agent
  family name: Kuo
  given name: Po-Lin
author list: Agent
  family name: Wu
  given name: Wen-Jeng
doi: 10.7717/peerj.11343
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Lee et al.
attribution name: Lee et al.

Variation in purple sea urchin (Strongylocentrotus purpuratus) morphological traits in relation to resource availability
type: item
type: AcademicArticle
description: Flexible resource investment is a risk sensitive reproductive strategy where individuals trade resources spent on reproduction for basic metabolic maintenance and survival. This study examined morphological variation in herbivorous sea urchin grazers across a mosaic landscape of macroalgae dominated habitats interspersed with patches of sea urchin barrens to determine whether sea urchins shift energy allocation in response to food limitation. Extensive underwater surveys of habitat attributes (e.g., sea urchin density, algae cover) were paired with detailed laboratory assays (e.g., sea urchin dissections) to determine how resource abundance affects energy allocation between reproductive capacity and body structure in the purple sea urchin, Strongylocentrotus purpuratus. We found that: (1) sea urchins had a more elongate jaw structure relative to body size in habitats void of macroalgae (i.e., barrens), (2) sea urchin reproductive capacity (i.e., gonad index) was lower in barrens and the barrens habitat was primarily comprised of encrusting algae, and (3) sea urchin jaw morphology (i.e., lantern index) and reproductive capacity (i.e., gonad index) were inversely related. These results suggest that sea urchins respond to macroalgae limited environments by shifting energy allocation between reproductive capacity and modifications of the foraging apparatus, which may explain the ability of sea urchins to acquire food in resource-limited environments.
format: application/pdf
format: text/html
creator: Joshua G. Smith
creator: Sabrina C. Garcia
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.11352
publisher: PeerJ Inc.
rights: © 2021 Smith and Garcia
abstract: Flexible resource investment is a risk sensitive reproductive strategy where individuals trade resources spent on reproduction for basic metabolic maintenance and survival. This study examined morphological variation in herbivorous sea urchin grazers across a mosaic landscape of macroalgae dominated habitats interspersed with patches of sea urchin barrens to determine whether sea urchins shift energy allocation in response to food limitation. Extensive underwater surveys of habitat attributes (e.g., sea urchin density, algae cover) were paired with detailed laboratory assays (e.g., sea urchin dissections) to determine how resource abundance affects energy allocation between reproductive capacity and body structure in the purple sea urchin, Strongylocentrotus purpuratus. We found that: (1) sea urchins had a more elongate jaw structure relative to body size in habitats void of macroalgae (i.e., barrens), (2) sea urchin reproductive capacity (i.e., gonad index) was lower in barrens and the barrens habitat was primarily comprised of encrusting algae, and (3) sea urchin jaw morphology (i.e., lantern index) and reproductive capacity (i.e., gonad index) were inversely related. These results suggest that sea urchins respond to macroalgae limited environments by shifting energy allocation between reproductive capacity and modifications of the foraging apparatus, which may explain the ability of sea urchins to acquire food in resource-limited environments.
bibliographic citation: Smith et al. (2021) Variation in purple sea urchin (Strongylocentrotus purpuratus) morphological traits in relation to resource availability. PeerJ 9:e11352 https://doi.org/10.7717/peerj.11352
date submitted: 2020-11-12
date accepted: 2021-04-05
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smith
  given name: Joshua G.
author list: Agent
  family name: Garcia
  given name: Sabrina C.
doi: 10.7717/peerj.11352
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: © 2021 Smith and Garcia
attribution name: Smith and Garcia

Comparison of morphology, development and expression patterns of hsf and hsp11.0 of Cotesia chilonis under normal and high temperature
type: item
type: AcademicArticle
description: Cotesia chilonis (Munakata) is the dominant parasitic wasp of the rice pest, Chilo suppressalis (Walker), and is a valuable parasitic wasp for the prevention and control of C. suppressalis. In this study, developmental indicators and expression of Cchsp11.0 (heat shock protein 11.0) and Cchsf (heat shock factor) were compared for C. chilonis at 27 °C and 36 °C. Developmental duration, morphology, emergence rate, and number of C. chilonis offspring were shortened at 36 °C while the ratio of females to males increased. Cchsp11.0 and Cchsf were highly expressed in the 1st instar stage at 36 °C, and Cchsp11.0 expression gradually decreased as C. chilonis matured; Cchsf expression was not correlated with Cchsp11.0 expression. Compared with 27 °C, the expression pattern of Cchsp11.0 and Cchsf was also not consistent, and Cchsp11.0 expression increased significantly at the adult stage. In conclusion, mildly high temperatures impact growth, development and reproduction of C. chilonis and stimulate the expression of Cchsp11.0 and Cchsf, and Cchsp11.0 and Cchsf play different roles in different developmental stages of C. chilonis at normal and high temperature.
format: application/pdf
format: text/html
creator: Fu-Jing He
creator: Feng Zhu
creator: Ming-Xing Lu
creator: Yu-Zhou Du
subject: Agricultural Science
subject: Entomology
description: doi:10.7717/peerj.11353
publisher: PeerJ Inc.
rights: © 2021 He et al.
abstract: Cotesia chilonis (Munakata) is the dominant parasitic wasp of the rice pest, Chilo suppressalis (Walker), and is a valuable parasitic wasp for the prevention and control of C. suppressalis. In this study, developmental indicators and expression of Cchsp11.0 (heat shock protein 11.0) and Cchsf (heat shock factor) were compared for C. chilonis at 27 °C and 36 °C. Developmental duration, morphology, emergence rate, and number of C. chilonis offspring were shortened at 36 °C while the ratio of females to males increased. Cchsp11.0 and Cchsf were highly expressed in the 1st instar stage at 36 °C, and Cchsp11.0 expression gradually decreased as C. chilonis matured; Cchsf expression was not correlated with Cchsp11.0 expression. Compared with 27 °C, the expression pattern of Cchsp11.0 and Cchsf was also not consistent, and Cchsp11.0 expression increased significantly at the adult stage. In conclusion, mildly high temperatures impact growth, development and reproduction of C. chilonis and stimulate the expression of Cchsp11.0 and Cchsf, and Cchsp11.0 and Cchsf play different roles in different developmental stages of C. chilonis at normal and high temperature.
bibliographic citation: He et al. (2021) Comparison of morphology, development and expression patterns of hsf and hsp11.0 of Cotesia chilonis under normal and high temperature. PeerJ 9:e11353 https://doi.org/10.7717/peerj.11353
date submitted: 2021-01-14
date accepted: 2021-04-05
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Fu-Jing
author list: Agent
  family name: Zhu
  given name: Feng
author list: Agent
  family name: Lu
  given name: Ming-Xing
author list: Agent
  family name: Du
  given name: Yu-Zhou
doi: 10.7717/peerj.11353
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: © 2021 He et al.
attribution name: He et al.

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