PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Combined effects of body mass index and unhealthy behaviors on disability in older Japanese adults: the Okayama study
items: 1H-NMR spectroscopy identifies potential biomarkers in serum metabolomic signatures for early stage esophageal squamous cell carcinoma
items: Life history response of Echinops gmelinii Turcz. to variation in the rainfall pattern in a temperate desert
items: Screening and identification of key candidate genes and pathways in myelodysplastic syndrome by bioinformatic analysis
items: Polyphenol-rich Trapa quadrispinosa pericarp extract ameliorates high-fat diet induced non-alcoholic fatty liver disease by regulating lipid metabolism and insulin resistance in mice
items: Characterization and expression profiling of the ICE-CBF-COR genes in wheat
items: Does bone preparation impact its shape: consequences for comparative analyses of bone shape
items: Invasions of gladiolus rust in North America are caused by a widely-distributed clone of Uromycestransversalis
items: Long noncoding RNA MEG3 suppresses podocyte injury in diabetic nephropathy by inactivating Wnt/β-catenin signaling
items: Multiple ecosystem services from field margin vegetation for ecological sustainability in agriculture: scientific evidence and knowledge gaps

Combined effects of body mass index and unhealthy behaviors on disability in older Japanese adults: the Okayama study
type: item
type: AcademicArticle
description: Background Body mass index (BMI) is a significant predictor of functional disability in older adults. However, when evaluated, the association between BMI and incident functional disability, considering behaviors only as covariates or not, may not be appropriate. The primary purpose of the study was to investigate the combined effects of BMI and unhealthy behaviors on the risk of incident functional disability. Methods This was a retrospective cohort study that took place in Okayama City, Japan. Data on BMI and unhealthy behaviors were obtained using the health check-up questionnaire. The certification of Long-Term Care Insurance was used to measure functional disability. Cox proportional hazard models were used; adjusted hazard ratios (HRs) with 95% confidence interval (CI) were calculated for incidence of functional disability across categories of BMI and number of unhealthy behaviors. Results The relationship between BMI and incident functional disability was U-shaped (HR = 1.18, 95% CI [1.11–1.25], among the underweight range; and 1.26 [1.19–1.34] among the obesity range), and its risk was significantly higher within the normal-to-overweight range of BMI values with co-occurring unhealthy behaviors (with normal weight range and one, 1.17 [1.01–1.21]; two, 1.29 [1.18–1.41]; and three or four unhealthy behaviors 1.38 [1.24–1.54]; as well as among overweight range and one, 1.16 [1.05–1.27]; two, 1.26 [1.15–1.38]; and three or four unhealthy behaviors, 1.47 [1.31–1.64]). In each BMI category, the risk of incident functional disability increased with increasing number of unhealthy behaviors (p < 0.05 for linear tread), with the highest risk (1.87 [1.58–2.20]) occurring in combination with at least three unhealthy behaviors with BMI ≥ 27.5, for both sexes (2.20 [1.64–2.92] in men and 1.66 [1.35–2.04] in women). Conclusion It is necessary to consider the combined effects of BMI and behaviors on incident functional disability. Furthermore, interventions targeting multip…
format: application/pdf
format: text/html
creator: Yangyang Liu
creator: Toshiharu Mitsuhashi
creator: Michiyo Yamakawa
creator: Megumi Sasai
creator: Toshihide Tsuda
creator: Hiroyuki Doi
creator: Jun Hamada
subject: Epidemiology
subject: Geriatrics
subject: Public Health
description: doi:10.7717/peerj.8146
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Background Body mass index (BMI) is a significant predictor of functional disability in older adults. However, when evaluated, the association between BMI and incident functional disability, considering behaviors only as covariates or not, may not be appropriate. The primary purpose of the study was to investigate the combined effects of BMI and unhealthy behaviors on the risk of incident functional disability. Methods This was a retrospective cohort study that took place in Okayama City, Japan. Data on BMI and unhealthy behaviors were obtained using the health check-up questionnaire. The certification of Long-Term Care Insurance was used to measure functional disability. Cox proportional hazard models were used; adjusted hazard ratios (HRs) with 95% confidence interval (CI) were calculated for incidence of functional disability across categories of BMI and number of unhealthy behaviors. Results The relationship between BMI and incident functional disability was U-shaped (HR = 1.18, 95% CI [1.11–1.25], among the underweight range; and 1.26 [1.19–1.34] among the obesity range), and its risk was significantly higher within the normal-to-overweight range of BMI values with co-occurring unhealthy behaviors (with normal weight range and one, 1.17 [1.01–1.21]; two, 1.29 [1.18–1.41]; and three or four unhealthy behaviors 1.38 [1.24–1.54]; as well as among overweight range and one, 1.16 [1.05–1.27]; two, 1.26 [1.15–1.38]; and three or four unhealthy behaviors, 1.47 [1.31–1.64]). In each BMI category, the risk of incident functional disability increased with increasing number of unhealthy behaviors (p < 0.05 for linear tread), with the highest risk (1.87 [1.58–2.20]) occurring in combination with at least three unhealthy behaviors with BMI ≥ 27.5, for both sexes (2.20 [1.64–2.92] in men and 1.66 [1.35–2.04] in women). Conclusion It is necessary to consider the combined effects of BMI and behaviors on incident functional disability. Furthermore, interventions targeting multip…
bibliographic citation: Liu et al. (2019) Combined effects of body mass index and unhealthy behaviors on disability in older Japanese adults: the Okayama study. PeerJ 7:e8146 https://doi.org/10.7717/peerj.8146
date submitted: 2019-07-09
date accepted: 2019-11-03
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yangyang
author list: Agent
  family name: Mitsuhashi
  given name: Toshiharu
author list: Agent
  family name: Yamakawa
  given name: Michiyo
author list: Agent
  family name: Sasai
  given name: Megumi
author list: Agent
  family name: Tsuda
  given name: Toshihide
author list: Agent
  family name: Doi
  given name: Hiroyuki
author list: Agent
  family name: Hamada
  given name: Jun
doi: 10.7717/peerj.8146
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: © 2019 Liu et al.
attribution name: Liu et al.

1H-NMR spectroscopy identifies potential biomarkers in serum metabolomic signatures for early stage esophageal squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent types of upper gastrointestinal malignancies. Here, we used 1H nuclear magnetic resonance spectroscopy (1H-NMR) to identify potential serum biomarkers in patients with early stage ESCC. Methods Sixty-five serum samples from early stage ESCC patients (n = 25) and healthy controls (n = 40) were analysed using 1H-NMR spectroscopy. We distinguished between different metabolites through principal component analysis, partial least squares-discriminant analysis, and orthogonal partial least squares-discriminant analysis (OPLS-DA) using SIMCA-P+ version 14.0 software. Receiver operating characteristic (ROC) analysis was conducted to verify potential biomarkers. Results Using OPLS-DA, 31 altered serum metabolites were successfully identified between the groups. Based on the area under the ROC curve (AUROC), and the biomarker panel with AUROC of 0.969, six serum metabolites (α-glucose, choline, glutamine, glutamate, valine, and dihydrothymine) were selected as potential biomarkers for early stage ESCC. Dihydrothymine particularly was selected as a new feasible biomarker associated with tumor occurrence. Conclusions 1H-NMR spectroscopy may be a useful tumour detection approach in identifying useful metabolic ESCC biomarkers for early diagnosis and in the exploration of the molecular pathogenesis of ESCC.
format: application/pdf
format: text/html
creator: Yan-Yan Liu
creator: Zhong-Xian Yang
creator: Li-Min Ma
creator: Xu-Qing Wen
creator: Huan-Lin Ji
creator: Ke Li
subject: Biochemistry
subject: Clinical Trials
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Translational Medicine
description: doi:10.7717/peerj.8151
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Background Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent types of upper gastrointestinal malignancies. Here, we used 1H nuclear magnetic resonance spectroscopy (1H-NMR) to identify potential serum biomarkers in patients with early stage ESCC. Methods Sixty-five serum samples from early stage ESCC patients (n = 25) and healthy controls (n = 40) were analysed using 1H-NMR spectroscopy. We distinguished between different metabolites through principal component analysis, partial least squares-discriminant analysis, and orthogonal partial least squares-discriminant analysis (OPLS-DA) using SIMCA-P+ version 14.0 software. Receiver operating characteristic (ROC) analysis was conducted to verify potential biomarkers. Results Using OPLS-DA, 31 altered serum metabolites were successfully identified between the groups. Based on the area under the ROC curve (AUROC), and the biomarker panel with AUROC of 0.969, six serum metabolites (α-glucose, choline, glutamine, glutamate, valine, and dihydrothymine) were selected as potential biomarkers for early stage ESCC. Dihydrothymine particularly was selected as a new feasible biomarker associated with tumor occurrence. Conclusions 1H-NMR spectroscopy may be a useful tumour detection approach in identifying useful metabolic ESCC biomarkers for early diagnosis and in the exploration of the molecular pathogenesis of ESCC.
bibliographic citation: Liu et al. (2019) 1H-NMR spectroscopy identifies potential biomarkers in serum metabolomic signatures for early stage esophageal squamous cell carcinoma. PeerJ 7:e8151 https://doi.org/10.7717/peerj.8151
date submitted: 2018-12-23
date accepted: 2019-11-04
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yan-Yan
author list: Agent
  family name: Yang
  given name: Zhong-Xian
author list: Agent
  family name: Ma
  given name: Li-Min
author list: Agent
  family name: Wen
  given name: Xu-Qing
author list: Agent
  family name: Ji
  given name: Huan-Lin
author list: Agent
  family name: Li
  given name: Ke
doi: 10.7717/peerj.8151
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: ©2019 Liu et al.
attribution name: Liu et al.

Life history response of Echinops gmelinii Turcz. to variation in the rainfall pattern in a temperate desert
type: item
type: AcademicArticle
description: Background Current and future changes in rainfall amount and frequency may particularly impact annual plants in desert ecosystems. The winter annual Echinops gmelinii Turcz. is widely distributed in the desert habitats of northern China and is a dominant pioneer annual plant following sand stabilization in the Tengger Desert. This species plays a vital role in dune stabilization during spring and early summer, when wind erosion is the most severe and frequent. However, seedling emergence and regeneration in sandy soil are mainly determined by rainfall patterns. Therefore, understanding the life history response of this species to rainfall variation is necessary for understanding the change of population dynamics under the future climate change. Methods A field simulation rainfall pot experiment using rainout shelter was conducted that included five amounts and five frequencies of rainfall based on historical and predicted values to monitor the life history responses of E. gmelinii in a near-natural habitat. Results We found that rainfall amount and frequency significantly affected seedling survival, growth and reproduction. The plant height, biomass, capitula number, seed number, seed mass and reproductive effort, but not the root/shoot ratio, significantly increased with increasing rainfall. Further, these traits exhibited the greatest response to low-frequency and larger rainfall events, especially the optimal rainfall frequency of 10-day intervals. Offspring seed germination showed increasing trends with decreasing rainfall, suggesting that the maternal effects may have occurred. Conclusions Our study shows that the plasticity in growth and reproduction of E. gmelinii in response to rainfall variations may help it to gain dominance in the harsh and unpredictable desert environment. Furthermore, population development of this winter annual species should be promoted under the likely future scenarios of large rainfall events and increasing cool-season precipitation…
format: application/pdf
format: text/html
creator: Yanli Wang
creator: Xinrong Li
creator: Lichao Liu
creator: Jiecai Zhao
creator: Jingyao Sun
subject: Ecology
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.8159
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Current and future changes in rainfall amount and frequency may particularly impact annual plants in desert ecosystems. The winter annual Echinops gmelinii Turcz. is widely distributed in the desert habitats of northern China and is a dominant pioneer annual plant following sand stabilization in the Tengger Desert. This species plays a vital role in dune stabilization during spring and early summer, when wind erosion is the most severe and frequent. However, seedling emergence and regeneration in sandy soil are mainly determined by rainfall patterns. Therefore, understanding the life history response of this species to rainfall variation is necessary for understanding the change of population dynamics under the future climate change. Methods A field simulation rainfall pot experiment using rainout shelter was conducted that included five amounts and five frequencies of rainfall based on historical and predicted values to monitor the life history responses of E. gmelinii in a near-natural habitat. Results We found that rainfall amount and frequency significantly affected seedling survival, growth and reproduction. The plant height, biomass, capitula number, seed number, seed mass and reproductive effort, but not the root/shoot ratio, significantly increased with increasing rainfall. Further, these traits exhibited the greatest response to low-frequency and larger rainfall events, especially the optimal rainfall frequency of 10-day intervals. Offspring seed germination showed increasing trends with decreasing rainfall, suggesting that the maternal effects may have occurred. Conclusions Our study shows that the plasticity in growth and reproduction of E. gmelinii in response to rainfall variations may help it to gain dominance in the harsh and unpredictable desert environment. Furthermore, population development of this winter annual species should be promoted under the likely future scenarios of large rainfall events and increasing cool-season precipitation…
bibliographic citation: Wang et al. (2019) Life history response of Echinops gmelinii Turcz. to variation in the rainfall pattern in a temperate desert. PeerJ 7:e8159 https://doi.org/10.7717/peerj.8159
date submitted: 2019-06-05
date accepted: 2019-11-04
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yanli
author list: Agent
  family name: Li
  given name: Xinrong
author list: Agent
  family name: Liu
  given name: Lichao
author list: Agent
  family name: Zhao
  given name: Jiecai
author list: Agent
  family name: Sun
  given name: Jingyao
doi: 10.7717/peerj.8159
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Screening and identification of key candidate genes and pathways in myelodysplastic syndrome by bioinformatic analysis
type: item
type: AcademicArticle
description: Myelodysplastic syndrome (MDS) is a heterogeneous hematologic malignancy derived from hematopoietic stem cells and the molecular mechanism of MDS remains unclear. This study aimed to elucidate potential markers of diagnosis and prognosis of MDS. The gene expression profiles GSE19429 and GSE58831 were obtained and downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in MDS were screened using GEO2R and overlapped DEGs were obtained with Venn Diagrams. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway functional enrichment analyses, protein–protein interaction network establishment and survival analyses were performed. Functional enrichment analysis indicated that these DEGs were significantly enriched in the interferon signaling pathway, immune response, hematopoietic cell lineage and the FOXO signaling pathway. Four hub genes and four significant modules including 25 module genes were obtained via Cytoscape MCODE. Survival analysis showed that the overall survival of MDS patients having BLNK, IRF4, IFITM1, IFIT1, ISG20, IFI44L alterations were worse than that without alterations. In conclusion, the identification of these genes and pathways helps understand the underlying molecular mechanisms of MDS and provides candidate targets for the diagnosis and prognosis of MDS.
format: application/pdf
format: text/html
creator: Ying Le
subject: Bioinformatics
subject: Hematology
subject: Immunology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.8162
publisher: PeerJ Inc.
rights: © 2019 Le
abstract: Myelodysplastic syndrome (MDS) is a heterogeneous hematologic malignancy derived from hematopoietic stem cells and the molecular mechanism of MDS remains unclear. This study aimed to elucidate potential markers of diagnosis and prognosis of MDS. The gene expression profiles GSE19429 and GSE58831 were obtained and downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in MDS were screened using GEO2R and overlapped DEGs were obtained with Venn Diagrams. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway functional enrichment analyses, protein–protein interaction network establishment and survival analyses were performed. Functional enrichment analysis indicated that these DEGs were significantly enriched in the interferon signaling pathway, immune response, hematopoietic cell lineage and the FOXO signaling pathway. Four hub genes and four significant modules including 25 module genes were obtained via Cytoscape MCODE. Survival analysis showed that the overall survival of MDS patients having BLNK, IRF4, IFITM1, IFIT1, ISG20, IFI44L alterations were worse than that without alterations. In conclusion, the identification of these genes and pathways helps understand the underlying molecular mechanisms of MDS and provides candidate targets for the diagnosis and prognosis of MDS.
bibliographic citation: Le (2019) Screening and identification of key candidate genes and pathways in myelodysplastic syndrome by bioinformatic analysis. PeerJ 7:e8162 https://doi.org/10.7717/peerj.8162
date submitted: 2019-08-27
date accepted: 2019-11-04
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Le
  given name: Ying
doi: 10.7717/peerj.8162
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: © 2019 Le
attribution name: Le

Polyphenol-rich Trapa quadrispinosa pericarp extract ameliorates high-fat diet induced non-alcoholic fatty liver disease by regulating lipid metabolism and insulin resistance in mice
type: item
type: AcademicArticle
description: In China, Trapa quadrispinosa (also called water caltrop) has long been used as a function food and folk medicine to treat diabetes mellitus for years. In the present study, the extract of T. quadrispinosa pericarp (TQPE) which mainly contains hydrolysable tannins was prepared to investigate the potential therapeutic action in non-alcoholic fatty liver disease (NAFLD) mice induced by high fat-diet (HFD). After the administration of TQPE (15, 30 mg/kg/day) for 8 weeks, the increased weight of body and liver were significantly suppressed. TQPE also ameliorated liver lipid deposition and reduced lipids parameters of blood in mice. Moreover, TQPE attenuated oxidative stress and showed a hepatoprotective effect in mice. TQPE was also found to decrease the value of homeostatic model assessment for insulin resistance. In addition, TQPE administration increased the phosphorylation of AMP-activated protein kinase (AMPK) and Acetyl-CoA carboxylase (ACC) and inhibited sterol regulatory element-binding protein (SREBP) in the liver tissue. Meanwhile, TQPE elevated insulin receptor substrate-1 (IRs-1) and protein kinase B (Akt) phosphorylation. These results reflected that, as a nature product, TQPE is a potential agent for suppressing the process of NAFLD via regulation of the AMPK/SREBP/ACC and IRs-1/Akt pathways.
format: application/pdf
format: text/html
creator: Tunyu Jian
creator: Han Lü
creator: Xiaoqin Ding
creator: Yuexian Wu
creator: Yuanyuan Zuo
creator: Jiawei Li
creator: Jian Chen
creator: Hong Gu
subject: Diabetes and Endocrinology
subject: Gastroenterology and Hepatology
subject: Pharmacology
description: doi:10.7717/peerj.8165
publisher: PeerJ Inc.
rights: © 2019 Jian et al.
abstract: In China, Trapa quadrispinosa (also called water caltrop) has long been used as a function food and folk medicine to treat diabetes mellitus for years. In the present study, the extract of T. quadrispinosa pericarp (TQPE) which mainly contains hydrolysable tannins was prepared to investigate the potential therapeutic action in non-alcoholic fatty liver disease (NAFLD) mice induced by high fat-diet (HFD). After the administration of TQPE (15, 30 mg/kg/day) for 8 weeks, the increased weight of body and liver were significantly suppressed. TQPE also ameliorated liver lipid deposition and reduced lipids parameters of blood in mice. Moreover, TQPE attenuated oxidative stress and showed a hepatoprotective effect in mice. TQPE was also found to decrease the value of homeostatic model assessment for insulin resistance. In addition, TQPE administration increased the phosphorylation of AMP-activated protein kinase (AMPK) and Acetyl-CoA carboxylase (ACC) and inhibited sterol regulatory element-binding protein (SREBP) in the liver tissue. Meanwhile, TQPE elevated insulin receptor substrate-1 (IRs-1) and protein kinase B (Akt) phosphorylation. These results reflected that, as a nature product, TQPE is a potential agent for suppressing the process of NAFLD via regulation of the AMPK/SREBP/ACC and IRs-1/Akt pathways.
bibliographic citation: Jian et al. (2019) Polyphenol-rich Trapa quadrispinosa pericarp extract ameliorates high-fat diet induced non-alcoholic fatty liver disease by regulating lipid metabolism and insulin resistance in mice. PeerJ 7:e8165 https://doi.org/10.7717/peerj.8165
date submitted: 2019-09-02
date accepted: 2019-11-05
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jian
  given name: Tunyu
author list: Agent
  family name: Lü
  given name: Han
author list: Agent
  family name: Ding
  given name: Xiaoqin
author list: Agent
  family name: Wu
  given name: Yuexian
author list: Agent
  family name: Zuo
  given name: Yuanyuan
author list: Agent
  family name: Li
  given name: Jiawei
author list: Agent
  family name: Chen
  given name: Jian
author list: Agent
  family name: Gu
  given name: Hong
doi: 10.7717/peerj.8165
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: ©2019 Jian et al.
attribution name: Jian et al.

Characterization and expression profiling of the ICE-CBF-COR genes in wheat
type: item
type: AcademicArticle
description: Cold stress is one of the major abiotic stresses that limit crop production. The ICE-CBF-COR pathway is associated with cold stress response in a wide variety of crop species. However, the ICE-CBF-COR genes has not been well characterized in wheat (Triticum aestivum). This study identified, characterized and examined the expression profiles of the ICE, CBF and COR genes for cold defense in wheat. Five ICE (inducer of CBF expression) genes, 37 CBF (C-repeat binding factor) genes and 11 COR (cold-responsive or cold-regulated) genes were discovered in the wheat genome database. Phylogenetic trees based on all 53 genes revealed that CBF genes were more diverse than ICE and COR genes. Twenty-two of the 53 genes appeared to include 11 duplicated pairs. Twenty rice (Oryza sativa) genes and 21 sorghum (Sorghum bicolor) and maize (Zea mays) genes showed collinearity with the wheat ICE, CBF and COR genes. Transcriptome data and qRT-PCR analyses revealed tissue-specific expression patterns of the ICE, CBF and COR genes, and identified similarities in the expression pattern of genes from the same family when subjected to drought, heat, drought plus heat, and cold stress. These results provide information for better understanding the biological roles of ICE, CBF, COR genes in wheat.
format: application/pdf
format: text/html
creator: Jie Guo
creator: Yongkang Ren
creator: Zhaohui Tang
creator: Weiping Shi
creator: Meixue Zhou
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.8190
publisher: PeerJ Inc.
rights: © 2019 Guo et al.
abstract: Cold stress is one of the major abiotic stresses that limit crop production. The ICE-CBF-COR pathway is associated with cold stress response in a wide variety of crop species. However, the ICE-CBF-COR genes has not been well characterized in wheat (Triticum aestivum). This study identified, characterized and examined the expression profiles of the ICE, CBF and COR genes for cold defense in wheat. Five ICE (inducer of CBF expression) genes, 37 CBF (C-repeat binding factor) genes and 11 COR (cold-responsive or cold-regulated) genes were discovered in the wheat genome database. Phylogenetic trees based on all 53 genes revealed that CBF genes were more diverse than ICE and COR genes. Twenty-two of the 53 genes appeared to include 11 duplicated pairs. Twenty rice (Oryza sativa) genes and 21 sorghum (Sorghum bicolor) and maize (Zea mays) genes showed collinearity with the wheat ICE, CBF and COR genes. Transcriptome data and qRT-PCR analyses revealed tissue-specific expression patterns of the ICE, CBF and COR genes, and identified similarities in the expression pattern of genes from the same family when subjected to drought, heat, drought plus heat, and cold stress. These results provide information for better understanding the biological roles of ICE, CBF, COR genes in wheat.
bibliographic citation: Guo et al. (2019) Characterization and expression profiling of the ICE-CBF-COR genes in wheat. PeerJ 7:e8190 https://doi.org/10.7717/peerj.8190
date submitted: 2019-07-15
date accepted: 2019-11-11
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Jie
author list: Agent
  family name: Ren
  given name: Yongkang
author list: Agent
  family name: Tang
  given name: Zhaohui
author list: Agent
  family name: Shi
  given name: Weiping
author list: Agent
  family name: Zhou
  given name: Meixue
doi: 10.7717/peerj.8190
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: ©2019 Guo et al.
attribution name: Guo et al.

Does bone preparation impact its shape: consequences for comparative analyses of bone shape
type: item
type: AcademicArticle
description: Vertebrate osteological collections provide comparative material for morphological analysis. Before being stored in the collection and studied by researchers, specimens are treated by preparators or curators and are cleaned. The preparation protocol employed ideally should not damage the material. Here, we explore the potential deformation of bones due to preparation using geometric morphometric methods. We focus both on intraspecific and interspecific variability. Our data on the scapular girdle of birds show that, at an intraspecific level, the effect of preparation on bone shape cannot be neglected. Paired and unpaired bones did not respond to the preparation process in the same way, possibly due to differences in function and their anatomical characteristics. Moreover, deformations due to preparation can be estimated by looking at the texture of the bone. At the interspecific level, we found no significant differences as the deformations induced by preparation are relatively small compared to differences among species. This study highlights the importance of carefully selecting preparation methods in order to avoid physical damage that could impact the shape of bones, especially for studies at the intraspecific level.
format: application/pdf
format: text/html
creator: Fanny Pagès
creator: Anne-Claire Fabre
creator: Anick Abourachid
subject: Computational Biology
subject: Conservation Biology
subject: Zoology
subject: Anatomy and Physiology
subject: Orthopedics
description: doi:10.7717/peerj.7932
publisher: PeerJ Inc.
rights: © 2019 Pagès et al.
abstract: Vertebrate osteological collections provide comparative material for morphological analysis. Before being stored in the collection and studied by researchers, specimens are treated by preparators or curators and are cleaned. The preparation protocol employed ideally should not damage the material. Here, we explore the potential deformation of bones due to preparation using geometric morphometric methods. We focus both on intraspecific and interspecific variability. Our data on the scapular girdle of birds show that, at an intraspecific level, the effect of preparation on bone shape cannot be neglected. Paired and unpaired bones did not respond to the preparation process in the same way, possibly due to differences in function and their anatomical characteristics. Moreover, deformations due to preparation can be estimated by looking at the texture of the bone. At the interspecific level, we found no significant differences as the deformations induced by preparation are relatively small compared to differences among species. This study highlights the importance of carefully selecting preparation methods in order to avoid physical damage that could impact the shape of bones, especially for studies at the intraspecific level.
bibliographic citation: Pagès et al. (2019) Does bone preparation impact its shape: consequences for comparative analyses of bone shape. PeerJ 7:e7932 https://doi.org/10.7717/peerj.7932
date submitted: 2019-07-30
date accepted: 2019-09-23
issued: 2019-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pagès
  given name: Fanny
author list: Agent
  family name: Fabre
  given name: Anne-Claire
author list: Agent
  family name: Abourachid
  given name: Anick
doi: 10.7717/peerj.7932
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-28
copyright: © 2019 Pagès et al.
attribution name: Pagès et al.

Invasions of gladiolus rust in North America are caused by a widely-distributed clone of Uromycestransversalis
type: item
type: AcademicArticle
description: Uromyces transversalis, the causal agent of Gladiolus rust, is an invasive plant pathogen in the United States and is regulated as a quarantine pathogen in Europe. The aim of this research was to: (i) determine the origin of introductions of U. transversalis to the United States, (ii) track the movement of genotypes, and (iii) understand the worldwide genetic diversity of the species. To develop molecular markers for genotyping, whole genome sequencing was performed on three isolates collected in the United States. Genomes were assembled de novo and searched for microsatellite regions. Primers were developed and tested on ten isolates from the United States resulting in the identification of 24 polymorphic markers. Among 92 isolates collected from Costa Rica, Mexico, New Zealand, Australia, and the United States there were polymorphisms within isolates with no genotypic diversity detected among isolates; however, missing data among the New Zealand and Australia isolates due to either poor amplification of degraded DNA or null alleles as a result of genetic differences made it difficult to generate conclusions about these populations. The microsatellite loci and flanking regions showed high diversity and two divergent genomes within dikaryotic individuals, yet no diversity among individuals, suggesting that the invasive U. transversalis populations from North America are strictly clonal.
format: application/pdf
format: text/html
creator: Jeffery A. DeLong
creator: Jane E. Stewart
creator: Alberto Valencia-Botín
creator: Kerry F. Pedley
creator: James W. Buck
creator: Marin T. Brewer
subject: Agricultural Science
subject: Mycology
subject: Population Biology
description: doi:10.7717/peerj.7986
publisher: PeerJ Inc.
rights: © 2019 DeLong et al.
abstract: Uromyces transversalis, the causal agent of Gladiolus rust, is an invasive plant pathogen in the United States and is regulated as a quarantine pathogen in Europe. The aim of this research was to: (i) determine the origin of introductions of U. transversalis to the United States, (ii) track the movement of genotypes, and (iii) understand the worldwide genetic diversity of the species. To develop molecular markers for genotyping, whole genome sequencing was performed on three isolates collected in the United States. Genomes were assembled de novo and searched for microsatellite regions. Primers were developed and tested on ten isolates from the United States resulting in the identification of 24 polymorphic markers. Among 92 isolates collected from Costa Rica, Mexico, New Zealand, Australia, and the United States there were polymorphisms within isolates with no genotypic diversity detected among isolates; however, missing data among the New Zealand and Australia isolates due to either poor amplification of degraded DNA or null alleles as a result of genetic differences made it difficult to generate conclusions about these populations. The microsatellite loci and flanking regions showed high diversity and two divergent genomes within dikaryotic individuals, yet no diversity among individuals, suggesting that the invasive U. transversalis populations from North America are strictly clonal.
bibliographic citation: DeLong et al. (2019) Invasions of gladiolus rust in North America are caused by a widely-distributed clone of Uromycestransversalis. PeerJ 7:e7986 https://doi.org/10.7717/peerj.7986
date submitted: 2019-06-17
date accepted: 2019-10-04
issued: 2019-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: DeLong
  given name: Jeffery A.
author list: Agent
  family name: Stewart
  given name: Jane E.
author list: Agent
  family name: Valencia-Botín
  given name: Alberto
author list: Agent
  family name: Pedley
  given name: Kerry F.
author list: Agent
  family name: Buck
  given name: James W.
author list: Agent
  family name: Brewer
  given name: Marin T.
doi: 10.7717/peerj.7986
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-28
copyright: ©2019 DeLong et al.
attribution name: DeLong et al.

Long noncoding RNA MEG3 suppresses podocyte injury in diabetic nephropathy by inactivating Wnt/β-catenin signaling
type: item
type: AcademicArticle
description: Background Diabetic nephropathy (DN) is one of the principal complications of diabetes and podocyte injury plays an important role in the DN pathogenesis. Wnt/β-catenin signaling overactivation confers podocyte injury and promotes multiple types of renal disease. However, the underlying mechanism of Wnt/β-catenin signaling activation in DN progression has not been fully elucidated. Long noncoding RNA (lncRNA) is a large class of endogenous RNA molecules lacking functional code capacity and which participates in the pathogenesis of human disease, including DN. Method A diabetes model was constructed by intraperitoneal injection of Streptozotocin in rats. The MPC5 cells were used to create the in vitro model. Western blot and Quantitative reverse-transcriptase-PCR were used to examine the expression of protein and mRNA. The migrated capacity was analyzed by Transwell migration assay. The cell viability was detected by CCK8. Results In the present study, we revealed the association of lncRNA Maternally Expressed Gene 3 (MEG3) with aberrant activation of Wnt/β-catenin signaling and the role of MEG3/Wnt axis in podocyte injury. We found that high glucose (HG) treatment suppressed MEG3 expression in cultured podocytes, activated Wnt/β-catenin signaling and caused podocyte injury as indicated by the downregulation of podocyte-specific markers (podocin and synaptopodin) and the upregulation of snail1 and α-smooth muscle actin. Overexpression of MEG3 attenuated HG-induced podocyte injury by reducing Wnt/β-catenin activity, repressing cell migration, reactive oxygen species production and increasing the viability of podocytes. Furthermore, we provided evidences that restoration of Wnt/β-catenin signaling by specific agonist impeded the protective effect of MEG3 on podocyte injury. Current results demonstrated that MEG3/Wnt axis plays an important role in fostering podocyte injury and may serve as a potential therapeutic target for the treatment of DN. Conclusion lncRNA MEG3 a…
format: application/pdf
format: text/html
creator: Xiajing Che
creator: Xin Deng
creator: Kewei Xie
creator: Qin Wang
creator: Jiayi Yan
creator: Xinghua Shao
creator: Zhaohui Ni
creator: Liang Ying
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.8016
publisher: PeerJ Inc.
rights: © 2019 Che et al.
abstract: Background Diabetic nephropathy (DN) is one of the principal complications of diabetes and podocyte injury plays an important role in the DN pathogenesis. Wnt/β-catenin signaling overactivation confers podocyte injury and promotes multiple types of renal disease. However, the underlying mechanism of Wnt/β-catenin signaling activation in DN progression has not been fully elucidated. Long noncoding RNA (lncRNA) is a large class of endogenous RNA molecules lacking functional code capacity and which participates in the pathogenesis of human disease, including DN. Method A diabetes model was constructed by intraperitoneal injection of Streptozotocin in rats. The MPC5 cells were used to create the in vitro model. Western blot and Quantitative reverse-transcriptase-PCR were used to examine the expression of protein and mRNA. The migrated capacity was analyzed by Transwell migration assay. The cell viability was detected by CCK8. Results In the present study, we revealed the association of lncRNA Maternally Expressed Gene 3 (MEG3) with aberrant activation of Wnt/β-catenin signaling and the role of MEG3/Wnt axis in podocyte injury. We found that high glucose (HG) treatment suppressed MEG3 expression in cultured podocytes, activated Wnt/β-catenin signaling and caused podocyte injury as indicated by the downregulation of podocyte-specific markers (podocin and synaptopodin) and the upregulation of snail1 and α-smooth muscle actin. Overexpression of MEG3 attenuated HG-induced podocyte injury by reducing Wnt/β-catenin activity, repressing cell migration, reactive oxygen species production and increasing the viability of podocytes. Furthermore, we provided evidences that restoration of Wnt/β-catenin signaling by specific agonist impeded the protective effect of MEG3 on podocyte injury. Current results demonstrated that MEG3/Wnt axis plays an important role in fostering podocyte injury and may serve as a potential therapeutic target for the treatment of DN. Conclusion lncRNA MEG3 a…
bibliographic citation: Che et al. (2019) Long noncoding RNA MEG3 suppresses podocyte injury in diabetic nephropathy by inactivating Wnt/β-catenin signaling. PeerJ 7:e8016 https://doi.org/10.7717/peerj.8016
date submitted: 2019-05-14
date accepted: 2019-10-09
issued: 2019-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Che
  given name: Xiajing
author list: Agent
  family name: Deng
  given name: Xin
author list: Agent
  family name: Xie
  given name: Kewei
author list: Agent
  family name: Wang
  given name: Qin
author list: Agent
  family name: Yan
  given name: Jiayi
author list: Agent
  family name: Shao
  given name: Xinghua
author list: Agent
  family name: Ni
  given name: Zhaohui
author list: Agent
  family name: Ying
  given name: Liang
doi: 10.7717/peerj.8016
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-28
copyright: © 2019 Che et al.
attribution name: Che et al.

Multiple ecosystem services from field margin vegetation for ecological sustainability in agriculture: scientific evidence and knowledge gaps
type: item
type: AcademicArticle
description: Background Field margin and non-crop vegetation in agricultural systems are potential ecosystem services providers because they offer semi-natural habitats for both below and above ground animal groups such as soil organisms, small mammals, birds and arthropods that are service supplying units. They are considered as a target area for enhancing farm biodiversity. Methodology To explore the multiple potential benefits of these semi-natural habitats and to identify research trends and knowledge gaps globally, a review was carried out following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. A total of 235 publications from the year 2000 to 2016 in the Scopus and Web of Science databases were reviewed. Results The literature showed an increasing trend in the number of published articles over time with European studies leading in the proportion of studies conducted, followed by North America, Asia, South America, Africa and Australia. Several functional groups of organisms were studied from field margin and non-crop vegetation around agricultural lands including natural enemies (37%), insect pests (22%), birds (17%), pollinators (16%), soil macro fauna (4%) and small mammals (4%). Ecosystem services derived from the field margin included natural pest regulation, pollination, nutrient cycling and reduced offsite erosion. Some field margin plants were reported to host detrimental crop pests, a major ecosystem dis-service, potentially leading to increased pest infestation in the field. Conclusion The majority of studies revealed the importance of field margin and non-crop vegetation around arable fields in enhancing ecosystem biodiversity. Promotion of field margin plants that selectively enhance the population of beneficial organisms would support sustainable food security rather than simply boosting plant diversity. Our analyses also highlight that agro-ecological studies remain largely overlooked in some regions.
format: application/pdf
format: text/html
creator: Prisila A. Mkenda
creator: Patrick A. Ndakidemi
creator: Ernest Mbega
creator: Philip C. Stevenson
creator: Sarah E.J. Arnold
creator: Geoff M. Gurr
creator: Steven R. Belmain
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Natural Resource Management
description: doi:10.7717/peerj.8091
publisher: PeerJ Inc.
rights: © 2019 Mkenda et al.
abstract: Background Field margin and non-crop vegetation in agricultural systems are potential ecosystem services providers because they offer semi-natural habitats for both below and above ground animal groups such as soil organisms, small mammals, birds and arthropods that are service supplying units. They are considered as a target area for enhancing farm biodiversity. Methodology To explore the multiple potential benefits of these semi-natural habitats and to identify research trends and knowledge gaps globally, a review was carried out following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. A total of 235 publications from the year 2000 to 2016 in the Scopus and Web of Science databases were reviewed. Results The literature showed an increasing trend in the number of published articles over time with European studies leading in the proportion of studies conducted, followed by North America, Asia, South America, Africa and Australia. Several functional groups of organisms were studied from field margin and non-crop vegetation around agricultural lands including natural enemies (37%), insect pests (22%), birds (17%), pollinators (16%), soil macro fauna (4%) and small mammals (4%). Ecosystem services derived from the field margin included natural pest regulation, pollination, nutrient cycling and reduced offsite erosion. Some field margin plants were reported to host detrimental crop pests, a major ecosystem dis-service, potentially leading to increased pest infestation in the field. Conclusion The majority of studies revealed the importance of field margin and non-crop vegetation around arable fields in enhancing ecosystem biodiversity. Promotion of field margin plants that selectively enhance the population of beneficial organisms would support sustainable food security rather than simply boosting plant diversity. Our analyses also highlight that agro-ecological studies remain largely overlooked in some regions.
bibliographic citation: Mkenda et al. (2019) Multiple ecosystem services from field margin vegetation for ecological sustainability in agriculture: scientific evidence and knowledge gaps. PeerJ 7:e8091 https://doi.org/10.7717/peerj.8091
date submitted: 2019-06-24
date accepted: 2019-10-23
issued: 2019-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mkenda
  given name: Prisila A.
author list: Agent
  family name: Ndakidemi
  given name: Patrick A.
author list: Agent
  family name: Mbega
  given name: Ernest
author list: Agent
  family name: Stevenson
  given name: Philip C.
author list: Agent
  family name: Arnold
  given name: Sarah E.J.
author list: Agent
  family name: Gurr
  given name: Geoff M.
author list: Agent
  family name: Belmain
  given name: Steven R.
doi: 10.7717/peerj.8091
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-28
copyright: © 2019 Mkenda et al.
attribution name: Mkenda et al.

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