PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Isolation, characterization, and cryopreservation of collared peccary skin-derived fibroblast cell lines
items: Identification of DEGs and transcription factors involved in H. pylori-associated inflammation and their relevance with gastric cancer
items: Incorporating reef fish avoidance behavior improves accuracy of species distribution models
items: Addressing initialisation uncertainty for end-to-end ecosystem models: application to the Chatham Rise Atlantis model
items: Identification of gene expression and DNA methylation of SERPINA5 and TIMP1 as novel prognostic markers in lower-grade gliomas
items: Identification of differentially expressed methylated genes in melanoma versus nevi using bioinformatics methods
items: The linkages of plant, litter and soil C:N:P stoichiometry and nutrient stock in different secondary mixed forest types in the Qinling Mountains, China
items: Association of carotid intima-media thickness with the risk of sudden sensorineural hearing loss
items: Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2
items: Ginsenoside panaxatriol reverses TNBC paclitaxel resistance by inhibiting the IRAK1/NF-κB and ERK pathways

Isolation, characterization, and cryopreservation of collared peccary skin-derived fibroblast cell lines
type: item
type: AcademicArticle
description: Background Biobanking of cell lines is a promising tool of support for wildlife conservation. In particular, the ability to preserve fibroblast cell lines derived from collared peccaries is of significance as these wild mammals are unique to the Americas and play a large role in maintaining the ecosystem. We identified collared peccary fibroblasts by immunofluorescence and evaluated their morphology, growth and adherence capacity. Further, we monitored the viability and metabolic activity of the fibroblasts to determine the effects of passage number and cryopreservation on establishment of cell lines. Methods Skin biopsies were collected from the peripheral ear region from five adult animals in captivity. Initially, cells were isolated from fragments and cultured in the Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and 2% antibiotic–antimycotic solution under a controlled atmosphere (38.5 °C, 5% CO2). We evaluated the maintenance of primary cells for morphology, adherence capacity of explants, explants in subconfluence, cell growth and absence of contamination. Moreover, we identified the fibroblast cells by immunofluorescence. Additionally, to evaluate the influence of the number of passages (first, third and tenth passage) and cryopreservation on establishment of cell lines, fibroblasts were analysed for the viability, metabolic activity, population doubling time (PDT), levels of reactive oxygen species (ROS), and mitochondrial membrane potential (ΔΨm). Results All explants (20/20) adhered to the dish in 2.4 days ± 0.5 with growth around the explants in 4.6 days ± 0.7, and subconfluence was observed within 7.8 days ± 1.0. Moreover, by morphology and immunocytochemistry analyses, cells were identified as fibroblasts which presented oval nuclei, a fusiform shape and positive vimentin staining. No contamination was observed after culture without antibiotics and antifungals for 30 days. While there was no difference observed for cell viabil…
format: application/pdf
format: text/html
creator: Alana Azevedo Borges
creator: Gabriela Pereira De Oliveira Lira
creator: Lucas Emanuel Nascimento
creator: Maria Valéria De Oliveira Santos
creator: Moacir Franco De Oliveira
creator: Alexandre Rodrigues Silva
creator: Alexsandra Fernandes Pereira
subject: Cell Biology
subject: Conservation Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.9136
publisher: PeerJ Inc.
rights: © 2020 Borges et al.
abstract: Background Biobanking of cell lines is a promising tool of support for wildlife conservation. In particular, the ability to preserve fibroblast cell lines derived from collared peccaries is of significance as these wild mammals are unique to the Americas and play a large role in maintaining the ecosystem. We identified collared peccary fibroblasts by immunofluorescence and evaluated their morphology, growth and adherence capacity. Further, we monitored the viability and metabolic activity of the fibroblasts to determine the effects of passage number and cryopreservation on establishment of cell lines. Methods Skin biopsies were collected from the peripheral ear region from five adult animals in captivity. Initially, cells were isolated from fragments and cultured in the Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and 2% antibiotic–antimycotic solution under a controlled atmosphere (38.5 °C, 5% CO2). We evaluated the maintenance of primary cells for morphology, adherence capacity of explants, explants in subconfluence, cell growth and absence of contamination. Moreover, we identified the fibroblast cells by immunofluorescence. Additionally, to evaluate the influence of the number of passages (first, third and tenth passage) and cryopreservation on establishment of cell lines, fibroblasts were analysed for the viability, metabolic activity, population doubling time (PDT), levels of reactive oxygen species (ROS), and mitochondrial membrane potential (ΔΨm). Results All explants (20/20) adhered to the dish in 2.4 days ± 0.5 with growth around the explants in 4.6 days ± 0.7, and subconfluence was observed within 7.8 days ± 1.0. Moreover, by morphology and immunocytochemistry analyses, cells were identified as fibroblasts which presented oval nuclei, a fusiform shape and positive vimentin staining. No contamination was observed after culture without antibiotics and antifungals for 30 days. While there was no difference observed for cell viabil…
bibliographic citation: Borges et al. (2020) Isolation, characterization, and cryopreservation of collared peccary skin-derived fibroblast cell lines. PeerJ 8:e9136 https://doi.org/10.7717/peerj.9136
date submitted: 2019-11-20
date accepted: 2020-04-15
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Borges
  given name: Alana Azevedo
author list: Agent
  family name: Lira
  given name: Gabriela Pereira De Oliveira
author list: Agent
  family name: Nascimento
  given name: Lucas Emanuel
author list: Agent
  family name: Santos
  given name: Maria Valéria De Oliveira
author list: Agent
  family name: Oliveira
  given name: Moacir Franco De
author list: Agent
  family name: Silva
  given name: Alexandre Rodrigues
author list: Agent
  family name: Pereira
  given name: Alexsandra Fernandes
doi: 10.7717/peerj.9136
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: © 2020 Borges et al.
attribution name: Borges et al.

Identification of DEGs and transcription factors involved in H. pylori-associated inflammation and their relevance with gastric cancer
type: item
type: AcademicArticle
description: Background Previous studies have indicated that chronic inflammation linked to H. pylori infection is the leading causes for gastric cancer (GC). However, the exact mechanism is not entirely clear until now. Purpose To identify the key molecules and TFs involved in H. pylori infection and to provide new insights into H. pylori-associated carcinogenesis and lay the groundwork for the prevention of GC. Results GO and KEGG analysis revealed that the DEGs of Hp+-NAG were mainly associated with the immune response, chemokine activity, extracellular region and rheumatoid arthritis pathway. The DEGs of Hp+-AG-IM were related to the apical plasma membrane, intestinal cholesterol absorption, transporter activity and fat digestion and absorption pathway. In Hp+-NAG network, the expression of TNF, CXCL8, MMP9, CXCL9, CXCL1, CCL20, CTLA4, CXCL2, C3, SAA1 and FOXP3, JUN had statistical significance between normal and cancer in TCGA database. In Hp+-AG-IM network the expression of APOA4, GCG, CYP3A4, XPNPEP2 and FOXP3, JUN were statistically different in the comparison of normal and cancer in TCGA database. FOXP3 were negatively associated with overall survival, and the association for JUN was positive. Conclusion The current study identified key DEGs and their transcriptional regulatory networks involved in H. pylori-associated NAG, AG-IM and GC and found that patients with higher expressed FOXP3 or lower expressed JUN had shorter overall survival time. Our study provided new directions for inflammation-associated oncogenic transformation involved in H. pylori infection.
format: application/pdf
format: text/html
creator: Honghao Yin
creator: Aining Chu
creator: Songyi Liu
creator: Yuan Yuan
creator: Yuehua Gong
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
subject: Oncology
description: doi:10.7717/peerj.9223
publisher: PeerJ Inc.
rights: © 2020 Yin et al.
abstract: Background Previous studies have indicated that chronic inflammation linked to H. pylori infection is the leading causes for gastric cancer (GC). However, the exact mechanism is not entirely clear until now. Purpose To identify the key molecules and TFs involved in H. pylori infection and to provide new insights into H. pylori-associated carcinogenesis and lay the groundwork for the prevention of GC. Results GO and KEGG analysis revealed that the DEGs of Hp+-NAG were mainly associated with the immune response, chemokine activity, extracellular region and rheumatoid arthritis pathway. The DEGs of Hp+-AG-IM were related to the apical plasma membrane, intestinal cholesterol absorption, transporter activity and fat digestion and absorption pathway. In Hp+-NAG network, the expression of TNF, CXCL8, MMP9, CXCL9, CXCL1, CCL20, CTLA4, CXCL2, C3, SAA1 and FOXP3, JUN had statistical significance between normal and cancer in TCGA database. In Hp+-AG-IM network the expression of APOA4, GCG, CYP3A4, XPNPEP2 and FOXP3, JUN were statistically different in the comparison of normal and cancer in TCGA database. FOXP3 were negatively associated with overall survival, and the association for JUN was positive. Conclusion The current study identified key DEGs and their transcriptional regulatory networks involved in H. pylori-associated NAG, AG-IM and GC and found that patients with higher expressed FOXP3 or lower expressed JUN had shorter overall survival time. Our study provided new directions for inflammation-associated oncogenic transformation involved in H. pylori infection.
bibliographic citation: Yin et al. (2020) Identification of DEGs and transcription factors involved in H. pylori-associated inflammation and their relevance with gastric cancer. PeerJ 8:e9223 https://doi.org/10.7717/peerj.9223
date submitted: 2019-12-11
date accepted: 2020-04-29
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Honghao
author list: Agent
  family name: Chu
  given name: Aining
author list: Agent
  family name: Liu
  given name: Songyi
author list: Agent
  family name: Yuan
  given name: Yuan
author list: Agent
  family name: Gong
  given name: Yuehua
doi: 10.7717/peerj.9223
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: ©2020 Yin et al.
attribution name: Yin et al.

Incorporating reef fish avoidance behavior improves accuracy of species distribution models
type: item
type: AcademicArticle
description: Species distribution models (SDMs) are used to interpret and map fish distributions based on habitat variables and other drivers. Reef fish avoidance behavior has been shown to vary in the presence of divers and is primarily driven by spearfishing pressure. Diver avoidance behavior or fish wariness may spatially influence counts and other descriptive measures of fish assemblages. Because fish assemblage metrics are response variables for SDMs, measures of fish wariness may be useful as predictors in SDMs of fishes targeted by spearfishing. We used a diver operated stereo-video system to conduct fish surveys and record minimum approach distance (MAD) of targeted reef fishes inside and outside of two marine reserves on the island of Oʻahu in the main Hawaiian Islands. By comparing MAD between sites and management types we tested the assumption that it provides a proxy for fish wariness related to spearfishing pressure. We then compared the accuracy of SDMs which included MAD as a predictor with SDMs that did not. Individual measures of MAD differed between sites though not management types. When included as a predictor, MAD averaged at the transect level greatly improved the accuracy of SDMs of targeted fish biomass.
format: application/pdf
format: text/html
creator: Kostantinos A. Stamoulis
creator: Jade M.S. Delevaux
creator: Ivor D. Williams
creator: Alan M. Friedlander
creator: Jake Reichard
creator: Keith Kamikawa
creator: Euan S. Harvey
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9246
publisher: PeerJ Inc.
rights: © 2020 Stamoulis et al.
abstract: Species distribution models (SDMs) are used to interpret and map fish distributions based on habitat variables and other drivers. Reef fish avoidance behavior has been shown to vary in the presence of divers and is primarily driven by spearfishing pressure. Diver avoidance behavior or fish wariness may spatially influence counts and other descriptive measures of fish assemblages. Because fish assemblage metrics are response variables for SDMs, measures of fish wariness may be useful as predictors in SDMs of fishes targeted by spearfishing. We used a diver operated stereo-video system to conduct fish surveys and record minimum approach distance (MAD) of targeted reef fishes inside and outside of two marine reserves on the island of Oʻahu in the main Hawaiian Islands. By comparing MAD between sites and management types we tested the assumption that it provides a proxy for fish wariness related to spearfishing pressure. We then compared the accuracy of SDMs which included MAD as a predictor with SDMs that did not. Individual measures of MAD differed between sites though not management types. When included as a predictor, MAD averaged at the transect level greatly improved the accuracy of SDMs of targeted fish biomass.
bibliographic citation: Stamoulis et al. (2020) Incorporating reef fish avoidance behavior improves accuracy of species distribution models. PeerJ 8:e9246 https://doi.org/10.7717/peerj.9246
date submitted: 2020-01-14
date accepted: 2020-05-07
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stamoulis
  given name: Kostantinos A.
author list: Agent
  family name: Delevaux
  given name: Jade M.S.
author list: Agent
  family name: Williams
  given name: Ivor D.
author list: Agent
  family name: Friedlander
  given name: Alan M.
author list: Agent
  family name: Reichard
  given name: Jake
author list: Agent
  family name: Kamikawa
  given name: Keith
author list: Agent
  family name: Harvey
  given name: Euan S.
doi: 10.7717/peerj.9246
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: ©2020 Stamoulis et al.
attribution name: Stamoulis et al.

Addressing initialisation uncertainty for end-to-end ecosystem models: application to the Chatham Rise Atlantis model
type: item
type: AcademicArticle
description: Ecosystem models require the specification of initial conditions, and these initial conditions have some level of uncertainty. It is important to allow for uncertainty when presenting model results, because it reduces the risk of errant or non-representative results. It is crucial that model results are presented as an envelope of what is likely, rather than presenting only one instance. We perturbed the initial conditions of the Chatham Rise Atlantis model and analysed the effect of this uncertainty on the model’s dynamics by comparing the model outputs resulting from many initial condition perturbations. At the species group level, we found some species groups were more sensitive than others, with lower trophic level species groups generally more sensitive to perturbations of the initial conditions. We recommend testing for robust system dynamics by assessing the consistency of ecosystem indicators in response to fishing pressure under perturbed initial conditions. In any set of scenarios explored using complex end-to-end ecosystem models, we recommend that associated uncertainty analysis be included with perturbations of the initial conditions.
format: application/pdf
format: text/html
creator: Vidette L. McGregor
creator: Elizabeth A. Fulton
creator: Matthew R. Dunn
subject: Aquaculture, Fisheries and Fish Science
subject: Ecosystem Science
subject: Mathematical Biology
subject: Statistics
subject: Population Biology
description: doi:10.7717/peerj.9254
publisher: PeerJ Inc.
rights: © 2020 McGregor et al.
abstract: Ecosystem models require the specification of initial conditions, and these initial conditions have some level of uncertainty. It is important to allow for uncertainty when presenting model results, because it reduces the risk of errant or non-representative results. It is crucial that model results are presented as an envelope of what is likely, rather than presenting only one instance. We perturbed the initial conditions of the Chatham Rise Atlantis model and analysed the effect of this uncertainty on the model’s dynamics by comparing the model outputs resulting from many initial condition perturbations. At the species group level, we found some species groups were more sensitive than others, with lower trophic level species groups generally more sensitive to perturbations of the initial conditions. We recommend testing for robust system dynamics by assessing the consistency of ecosystem indicators in response to fishing pressure under perturbed initial conditions. In any set of scenarios explored using complex end-to-end ecosystem models, we recommend that associated uncertainty analysis be included with perturbations of the initial conditions.
bibliographic citation: McGregor et al. (2020) Addressing initialisation uncertainty for end-to-end ecosystem models: application to the Chatham Rise Atlantis model. PeerJ 8:e9254 https://doi.org/10.7717/peerj.9254
date submitted: 2019-09-18
date accepted: 2020-05-08
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McGregor
  given name: Vidette L.
author list: Agent
  family name: Fulton
  given name: Elizabeth A.
author list: Agent
  family name: Dunn
  given name: Matthew R.
doi: 10.7717/peerj.9254
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: © 2020 McGregor et al.
attribution name: McGregor et al.

Identification of gene expression and DNA methylation of SERPINA5 and TIMP1 as novel prognostic markers in lower-grade gliomas
type: item
type: AcademicArticle
description: Background Lower-grade gliomas (LGGs) is characteristic with great difference in prognosis. Due to limited prognostic biomarkers, it is urgent to identify more molecular markers to provide a more objective and accurate tumor classification system for LGGs. Methods In the current study, we performed an integrated analysis of gene expression data and genome-wide methylation data to determine novel prognostic genes and methylation sites in LGGs. Results To determine genes that differentially expressed between 44 short-term survivors (<2 years) and 48 long-term survivors (≥2 years), we searched LGGs TCGA RNA-seq dataset and identified 106 differentially expressed genes. SERPINA5 and TIMP1 were selected for further study. Kaplan–Meier plots showed that SERPINA5 and TIMP1 expression were significantly correlated with overall survival (OS) and relapse-free survival (RFS) in TCGA LGGs patients. We next validated the correlation between the candidate genes expression and clinical outcome in CGGA LGGs patients. Multivariate analysis showed that TIMP1 mRNA expression had a significant prognostic value independent of other variables (HR = 4.825, 95% CI = 1.370–17.000, P = 0.014). Then, differential methylation sites were identified from differentially candidate gene expression groups, and all four methylation sites were significantly negatively correlated with gene expression (spearman r < − 0.5, P < 0.0001). Moreover, hyper-methylation of four methylation sites indicated better OS (P < 0.05), and three of them also shown statistical significantly association with better RFS, except for SERPINA5 cg15509705 (P = 0.0762). Conclusion Taken together, these findings indicated that the gene expression and methylation of SERPINA5 and TIMP1 may serve as prognostic predictors in LGGs and may help to precise the current histology-based tumors classification system and to provide better stratification for future clinical trials.
format: application/pdf
format: text/html
creator: Wen-Jing Zeng
creator: Yong-Long Yang
creator: Zhi-Peng Wen
creator: Peng Chen
creator: Xiao-Ping Chen
creator: Zhi-Cheng Gong
subject: Genomics
subject: Neurology
subject: Oncology
subject: Translational Medicine
description: doi:10.7717/peerj.9262
publisher: PeerJ Inc.
rights: © 2020 Zeng et al.
abstract: Background Lower-grade gliomas (LGGs) is characteristic with great difference in prognosis. Due to limited prognostic biomarkers, it is urgent to identify more molecular markers to provide a more objective and accurate tumor classification system for LGGs. Methods In the current study, we performed an integrated analysis of gene expression data and genome-wide methylation data to determine novel prognostic genes and methylation sites in LGGs. Results To determine genes that differentially expressed between 44 short-term survivors (<2 years) and 48 long-term survivors (≥2 years), we searched LGGs TCGA RNA-seq dataset and identified 106 differentially expressed genes. SERPINA5 and TIMP1 were selected for further study. Kaplan–Meier plots showed that SERPINA5 and TIMP1 expression were significantly correlated with overall survival (OS) and relapse-free survival (RFS) in TCGA LGGs patients. We next validated the correlation between the candidate genes expression and clinical outcome in CGGA LGGs patients. Multivariate analysis showed that TIMP1 mRNA expression had a significant prognostic value independent of other variables (HR = 4.825, 95% CI = 1.370–17.000, P = 0.014). Then, differential methylation sites were identified from differentially candidate gene expression groups, and all four methylation sites were significantly negatively correlated with gene expression (spearman r < − 0.5, P < 0.0001). Moreover, hyper-methylation of four methylation sites indicated better OS (P < 0.05), and three of them also shown statistical significantly association with better RFS, except for SERPINA5 cg15509705 (P = 0.0762). Conclusion Taken together, these findings indicated that the gene expression and methylation of SERPINA5 and TIMP1 may serve as prognostic predictors in LGGs and may help to precise the current histology-based tumors classification system and to provide better stratification for future clinical trials.
bibliographic citation: Zeng et al. (2020) Identification of gene expression and DNA methylation of SERPINA5 and TIMP1 as novel prognostic markers in lower-grade gliomas. PeerJ 8:e9262 https://doi.org/10.7717/peerj.9262
date submitted: 2019-10-11
date accepted: 2020-05-09
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeng
  given name: Wen-Jing
author list: Agent
  family name: Yang
  given name: Yong-Long
author list: Agent
  family name: Wen
  given name: Zhi-Peng
author list: Agent
  family name: Chen
  given name: Peng
author list: Agent
  family name: Chen
  given name: Xiao-Ping
author list: Agent
  family name: Gong
  given name: Zhi-Cheng
doi: 10.7717/peerj.9262
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: ©2020 Zeng et al.
attribution name: Zeng et al.

Identification of differentially expressed methylated genes in melanoma versus nevi using bioinformatics methods
type: item
type: AcademicArticle
description: Background Melanoma is a highly invasive malignant skin tumor. While melanoma may share some similarities with that of melanocytic nevi, there also exist a number of distinct differences between these conditions. An analysis of these differences may provide a means to more effectively evaluate the etiology and pathogenesis of melanoma. In particular, differences in aberrant methylation expression may prove to represent a critical distinction. Methods Data from gene expression datasets (GSE3189 and GSE46517) and gene methylation datasets (GSE86355 and GSE120878) were downloaded from the GEO database. GEO2R was used to obtain differentially expressed genes (DEGs) and differentially methylation genes (DMGs). Function and pathway enrichment of selected genes were performed using the DAVID database. A protein-protein interaction (PPI) network was constructed by STRING while its visualization was achieved with use of cytoscape. Primary melanoma samples from TCGA were used to identify significant survival genes. Results There was a total of 199 genes in the hypermethylation-low expression group, while 136 genes in the hypomethylation-high expression group were identified. The former were enriched in the biological processes of transcription regulation, RNA metabolism and regulation of cell proliferation. The later were highly involved in cell cycle regulation. 13 genes were screened out after survival analysis and included: ISG20, DTL, TRPV2, PLOD3, KIF3C, DLGAP4, PI4K2A, WIPI1, SHANK2, SLC16A10, GSTA4O, LFML2A and TMEM47. Conclusion These findings reveal some of the methylated differentially expressed genes and pathways that exist between melonoma and melanocytic nevi. Moreover, we have identified some critical genes that may help to improve the diagnosis and treatment of melanoma.
format: application/pdf
format: text/html
creator: Congcong He
creator: Yujing Zhang
creator: Hanghang Jiang
creator: Xueli Niu
creator: Ruiqun Qi
creator: Xinghua Gao
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Dermatology
description: doi:10.7717/peerj.9273
publisher: PeerJ Inc.
rights: © 2020 He et al.
abstract: Background Melanoma is a highly invasive malignant skin tumor. While melanoma may share some similarities with that of melanocytic nevi, there also exist a number of distinct differences between these conditions. An analysis of these differences may provide a means to more effectively evaluate the etiology and pathogenesis of melanoma. In particular, differences in aberrant methylation expression may prove to represent a critical distinction. Methods Data from gene expression datasets (GSE3189 and GSE46517) and gene methylation datasets (GSE86355 and GSE120878) were downloaded from the GEO database. GEO2R was used to obtain differentially expressed genes (DEGs) and differentially methylation genes (DMGs). Function and pathway enrichment of selected genes were performed using the DAVID database. A protein-protein interaction (PPI) network was constructed by STRING while its visualization was achieved with use of cytoscape. Primary melanoma samples from TCGA were used to identify significant survival genes. Results There was a total of 199 genes in the hypermethylation-low expression group, while 136 genes in the hypomethylation-high expression group were identified. The former were enriched in the biological processes of transcription regulation, RNA metabolism and regulation of cell proliferation. The later were highly involved in cell cycle regulation. 13 genes were screened out after survival analysis and included: ISG20, DTL, TRPV2, PLOD3, KIF3C, DLGAP4, PI4K2A, WIPI1, SHANK2, SLC16A10, GSTA4O, LFML2A and TMEM47. Conclusion These findings reveal some of the methylated differentially expressed genes and pathways that exist between melonoma and melanocytic nevi. Moreover, we have identified some critical genes that may help to improve the diagnosis and treatment of melanoma.
bibliographic citation: He et al. (2020) Identification of differentially expressed methylated genes in melanoma versus nevi using bioinformatics methods. PeerJ 8:e9273 https://doi.org/10.7717/peerj.9273
date submitted: 2019-09-30
date accepted: 2020-05-11
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Congcong
author list: Agent
  family name: Zhang
  given name: Yujing
author list: Agent
  family name: Jiang
  given name: Hanghang
author list: Agent
  family name: Niu
  given name: Xueli
author list: Agent
  family name: Qi
  given name: Ruiqun
author list: Agent
  family name: Gao
  given name: Xinghua
doi: 10.7717/peerj.9273
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: ©2020 He et al.
attribution name: He et al.

The linkages of plant, litter and soil C:N:P stoichiometry and nutrient stock in different secondary mixed forest types in the Qinling Mountains, China
type: item
type: AcademicArticle
description: Background Carbon (C), nitrogen (N) and phosphorus (P) stoichiometric ratios are important indicators of ecosystem function and productivity. However, few studies have assessed the nutrient relationship between plant, litter and soil, and the nutrient stock in different secondary mixed forest types. Methods We investigated the C, N and P concentrations and stoichiometric ratios in trees, understory plants, litter and soil layers in three different secondary mixed forest types (broadleaf mixed forests (BM), broadleaf-conifer mixed forests (BCM) and coniferous mixed forests (CM)) in the Qinling Mountains. Results The results showed that significant differences in C:N:P stoichiometry were detected in multiple organs in the vegetation layers in the different forest types. Trees, shrubs and herbs all allocated more N and P in leaves and had a higher N:P ratio in leaves than in other organs. The C concentrations, C:N ratios and C:P ratios of all tree organs showed a decreasing order: BM < BCM < CM, while the N and P concentrations showed an increasing order: BM > BCM > CM. For litter and soil, BM had generally higher N and P concentrations than those of BCM and CM. The highest N and P stock was in tree branches-not in the stem, which had the highest biomass (except for P in CM). Compared with other forest types, CM stored more nutrients in the labile litter layer, while BM stored more nutrients in the stable soil layer. The net ecosystem nutrient element stock in BM was generally higher than that in BCM and CM. The C, N and P concentrations and stoichiometry in the plant organs, litter and soil were significantly correlated. Conclusion Our findings demonstrate that nutrient concentrations in plant organs, litter and soil are tightly linked in secondary mixed forests.
format: application/pdf
format: text/html
creator: Yue Pang
creator: Jing Tian
creator: Xuan Zhao
creator: Zhi Chao
creator: Yuchao Wang
creator: Xinping Zhang
creator: Dexiang Wang
subject: Ecosystem Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.9274
publisher: PeerJ Inc.
rights: © 2020 Pang et al.
abstract: Background Carbon (C), nitrogen (N) and phosphorus (P) stoichiometric ratios are important indicators of ecosystem function and productivity. However, few studies have assessed the nutrient relationship between plant, litter and soil, and the nutrient stock in different secondary mixed forest types. Methods We investigated the C, N and P concentrations and stoichiometric ratios in trees, understory plants, litter and soil layers in three different secondary mixed forest types (broadleaf mixed forests (BM), broadleaf-conifer mixed forests (BCM) and coniferous mixed forests (CM)) in the Qinling Mountains. Results The results showed that significant differences in C:N:P stoichiometry were detected in multiple organs in the vegetation layers in the different forest types. Trees, shrubs and herbs all allocated more N and P in leaves and had a higher N:P ratio in leaves than in other organs. The C concentrations, C:N ratios and C:P ratios of all tree organs showed a decreasing order: BM < BCM < CM, while the N and P concentrations showed an increasing order: BM > BCM > CM. For litter and soil, BM had generally higher N and P concentrations than those of BCM and CM. The highest N and P stock was in tree branches-not in the stem, which had the highest biomass (except for P in CM). Compared with other forest types, CM stored more nutrients in the labile litter layer, while BM stored more nutrients in the stable soil layer. The net ecosystem nutrient element stock in BM was generally higher than that in BCM and CM. The C, N and P concentrations and stoichiometry in the plant organs, litter and soil were significantly correlated. Conclusion Our findings demonstrate that nutrient concentrations in plant organs, litter and soil are tightly linked in secondary mixed forests.
bibliographic citation: Pang et al. (2020) The linkages of plant, litter and soil C:N:P stoichiometry and nutrient stock in different secondary mixed forest types in the Qinling Mountains, China. PeerJ 8:e9274 https://doi.org/10.7717/peerj.9274
date submitted: 2019-12-20
date accepted: 2020-05-11
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pang
  given name: Yue
author list: Agent
  family name: Tian
  given name: Jing
author list: Agent
  family name: Zhao
  given name: Xuan
author list: Agent
  family name: Chao
  given name: Zhi
author list: Agent
  family name: Wang
  given name: Yuchao
author list: Agent
  family name: Zhang
  given name: Xinping
author list: Agent
  family name: Wang
  given name: Dexiang
doi: 10.7717/peerj.9274
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: © 2020 Pang et al.
attribution name: Pang et al.

Association of carotid intima-media thickness with the risk of sudden sensorineural hearing loss
type: item
type: AcademicArticle
description: Cardiovascular factors are associated with the pathophysiological features and risk of sudden sensorineural hearing loss (SSNHL). However, little is known about the link between carotid intima-media thickness (IMT), SSNHL risk, and their respective treatment outcomes. In this study, we retrospectively reviewed 47 SSNHL cases and 33 control subjects from a single medical center and compared their demographic data and clinical characteristics, including their carotid IMT and audiological data. Of the 80 enrolled subjects, the proportion of those with high carotid IMT was greater in the SSNHL group (53.2%) than in the control group (21.2%), with an odds ratio (OR) of 4.22 (95% confidence interval (CI) [1.53–11.61], P = 0.004). Notably, high carotid IMT was more common in female SSNHL patients than females in the control group (54.2% vs. 12.5%; OR, 8.27 (95% CI [1.53–44.62]), P = 0.008), particularly in female patients ≥50 years of age (75% vs. 25%; OR, 9.0 (95% CI [1.27–63.9]), P = 0.032). The multivariate regression analyses showed the association between high carotid IMT and SSNHL with an adjusted OR of 4.655 (95% CI [1.348–16.076], P = 0.015), particularly in female SSNHL patients (adjusted OR, 9.818 (95% CI [1.064–90.587], P = 0.044). The carotid IMT was not associated with the treatment outcomes of SSNHL. Our results indicate that early-stage atherosclerosis may be associated with SSNHL, particularly in female patients more than 50 years old.
format: application/pdf
format: text/html
creator: Chun-Hsien Ho
creator: Teng-Yeow Tan
creator: Chung-Feng Hwang
creator: Wei-Che Lin
creator: Ching-Nung Wu
creator: Chao-Hui Yang
subject: Cardiology
subject: Neurology
subject: Otorhinolaryngology
subject: Women’s Health
description: doi:10.7717/peerj.9276
publisher: PeerJ Inc.
rights: © 2020 Ho et al.
abstract: Cardiovascular factors are associated with the pathophysiological features and risk of sudden sensorineural hearing loss (SSNHL). However, little is known about the link between carotid intima-media thickness (IMT), SSNHL risk, and their respective treatment outcomes. In this study, we retrospectively reviewed 47 SSNHL cases and 33 control subjects from a single medical center and compared their demographic data and clinical characteristics, including their carotid IMT and audiological data. Of the 80 enrolled subjects, the proportion of those with high carotid IMT was greater in the SSNHL group (53.2%) than in the control group (21.2%), with an odds ratio (OR) of 4.22 (95% confidence interval (CI) [1.53–11.61], P = 0.004). Notably, high carotid IMT was more common in female SSNHL patients than females in the control group (54.2% vs. 12.5%; OR, 8.27 (95% CI [1.53–44.62]), P = 0.008), particularly in female patients ≥50 years of age (75% vs. 25%; OR, 9.0 (95% CI [1.27–63.9]), P = 0.032). The multivariate regression analyses showed the association between high carotid IMT and SSNHL with an adjusted OR of 4.655 (95% CI [1.348–16.076], P = 0.015), particularly in female SSNHL patients (adjusted OR, 9.818 (95% CI [1.064–90.587], P = 0.044). The carotid IMT was not associated with the treatment outcomes of SSNHL. Our results indicate that early-stage atherosclerosis may be associated with SSNHL, particularly in female patients more than 50 years old.
bibliographic citation: Ho et al. (2020) Association of carotid intima-media thickness with the risk of sudden sensorineural hearing loss. PeerJ 8:e9276 https://doi.org/10.7717/peerj.9276
date submitted: 2019-10-22
date accepted: 2020-05-11
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ho
  given name: Chun-Hsien
author list: Agent
  family name: Tan
  given name: Teng-Yeow
author list: Agent
  family name: Hwang
  given name: Chung-Feng
author list: Agent
  family name: Lin
  given name: Wei-Che
author list: Agent
  family name: Wu
  given name: Ching-Nung
author list: Agent
  family name: Yang
  given name: Chao-Hui
doi: 10.7717/peerj.9276
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: © 2020 Ho et al.
attribution name: Ho et al.

Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2
type: item
type: AcademicArticle
description: Background Highly sensitive real-time reverse transcription polymerase chain reaction (RT-qPCR) methods have been developed for the detection of SARS-CoV-2. However, they are costly. Loop-mediated isothermal amplification (LAMP) assay has emerged as a novel alternative isothermal amplification method for the detection of nucleic acid. Methods A rapid, sensitive and specific real-time reverse transcription LAMP (RT-LAMP) assay was developed for SARS-CoV-2 detection. Results This assay detected one copy/reaction of SARS-CoV-2 RNA in 30 min. Both the clinical sensitivity and specificity of this assay were 100%. The RT-LAMP showed comparable performance with RT-qPCR. Combining simplicity and cost-effectiveness, this assay is therefore recommended for use in resource resource-limited settings.
format: application/pdf
format: text/html
creator: Yee Ling Lau
creator: Ilyiana Ismail
creator: Nur Izati Mustapa
creator: Meng Yee Lai
creator: Tuan Suhaila Tuan Soh
creator: Afifah Hassan
creator: Kalaiarasu M. Peariasamy
creator: Yee Leng Lee
creator: Yoong Min Chong
creator: I-Ching Sam
creator: Pik Pin Goh
subject: Virology
subject: Drugs and Devices
subject: Emergency and Critical Care
subject: Global Health
subject: Infectious Diseases
description: doi:10.7717/peerj.9278
publisher: PeerJ Inc.
rights: © 2020 Lau et al.
abstract: Background Highly sensitive real-time reverse transcription polymerase chain reaction (RT-qPCR) methods have been developed for the detection of SARS-CoV-2. However, they are costly. Loop-mediated isothermal amplification (LAMP) assay has emerged as a novel alternative isothermal amplification method for the detection of nucleic acid. Methods A rapid, sensitive and specific real-time reverse transcription LAMP (RT-LAMP) assay was developed for SARS-CoV-2 detection. Results This assay detected one copy/reaction of SARS-CoV-2 RNA in 30 min. Both the clinical sensitivity and specificity of this assay were 100%. The RT-LAMP showed comparable performance with RT-qPCR. Combining simplicity and cost-effectiveness, this assay is therefore recommended for use in resource resource-limited settings.
bibliographic citation: Lau et al. (2020) Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2. PeerJ 8:e9278 https://doi.org/10.7717/peerj.9278
date submitted: 2020-03-30
date accepted: 2020-05-12
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lau
  given name: Yee Ling
author list: Agent
  family name: Ismail
  given name: Ilyiana
author list: Agent
  family name: Mustapa
  given name: Nur Izati
author list: Agent
  family name: Lai
  given name: Meng Yee
author list: Agent
  family name: Tuan Soh
  given name: Tuan Suhaila
author list: Agent
  family name: Hassan
  given name: Afifah
author list: Agent
  family name: Peariasamy
  given name: Kalaiarasu M.
author list: Agent
  family name: Lee
  given name: Yee Leng
author list: Agent
  family name: Chong
  given name: Yoong Min
author list: Agent
  family name: Sam
  given name: I-Ching
author list: Agent
  family name: Goh
  given name: Pik Pin
doi: 10.7717/peerj.9278
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: © 2020 Lau et al.
attribution name: Lau et al.

Ginsenoside panaxatriol reverses TNBC paclitaxel resistance by inhibiting the IRAK1/NF-κB and ERK pathways
type: item
type: AcademicArticle
description: Background Paclitaxel (PTX) resistance is a major obstacle in the treatment of triple-negative breast cancer (TNBC). Previously, we have reported that interleukin-1 receptor-associated kinase 1 (IRAK1) and its downstream pathways are associated with PTX resistance in TNBC cells. In this study, we sought to investigate the combination treatment of ginsenoside panaxatriol (GPT), one of the main active components in Panax ginseng, with PTX on viability and apoptosis of TNBC PTX resistant cells, and explore the role of IRAK1 mediated signaling pathways in the therapeutic effects. Methods CellTiter-Glo and colony formation assays were used to assess cell viability. Flow cytometry was used to analyze subG1 and apoptosis. Western blot was used to detect expressions of proteins involved in apoptosis and the IRAK1/NF-κB and ERK pathways. The mRNA expression of inflammatory cytokines, S100A7/8/9 and cancer stem cell (CSC)-related genes were examined by qPCR. Stem cells were identified by tumor sphere assay. Cell invasion ability was examined by transwell assay. Results We show that GPT inhibits MDA-MB-231 PTX resistant (MB231-PR) cell viability in a dose-dependent manner. When combined with PTX, GPT synergistically causes more cell death, induces subG1 accumulation and cell apoptosis. Besides, up-regulation of BAX/BCL-2 ratio, and down-regulation of MCL-1 are also observed. Moreover, this combination inhibits IRAK1, NF-κB and ERK1/2 activation, and leads to down-regulation of inflammatory cytokines (IL6, IL8, CXCL1, CCL2), S100A7/9 and CSC-related genes (OCT4, SOX2, NANOG, ALDH1, CD44) expression. In addition, the combination treatment suppresses MB231-PR cell invasion ability, and impairs tumor sphere growth both in MB231-PR and SUM159 PTX resistant (SUM159-PR) cells. Conclusion Our study demonstrates that GPT can resensitize TNBC PTX resistant cells to PTX by inhibiting the IRAK1/NF-κB and ERK pathways and reducing stem cell characteristics.
format: application/pdf
format: text/html
creator: Panpan Wang
creator: Dan Song
creator: Danhong Wan
creator: Lingyu Li
creator: Wenhui Mei
creator: Xiaoyun Li
creator: Li Han
creator: Xiaofeng Zhu
creator: Li Yang
creator: Yu Cai
creator: Ronghua Zhang
subject: Molecular Biology
subject: Toxicology
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.9281
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background Paclitaxel (PTX) resistance is a major obstacle in the treatment of triple-negative breast cancer (TNBC). Previously, we have reported that interleukin-1 receptor-associated kinase 1 (IRAK1) and its downstream pathways are associated with PTX resistance in TNBC cells. In this study, we sought to investigate the combination treatment of ginsenoside panaxatriol (GPT), one of the main active components in Panax ginseng, with PTX on viability and apoptosis of TNBC PTX resistant cells, and explore the role of IRAK1 mediated signaling pathways in the therapeutic effects. Methods CellTiter-Glo and colony formation assays were used to assess cell viability. Flow cytometry was used to analyze subG1 and apoptosis. Western blot was used to detect expressions of proteins involved in apoptosis and the IRAK1/NF-κB and ERK pathways. The mRNA expression of inflammatory cytokines, S100A7/8/9 and cancer stem cell (CSC)-related genes were examined by qPCR. Stem cells were identified by tumor sphere assay. Cell invasion ability was examined by transwell assay. Results We show that GPT inhibits MDA-MB-231 PTX resistant (MB231-PR) cell viability in a dose-dependent manner. When combined with PTX, GPT synergistically causes more cell death, induces subG1 accumulation and cell apoptosis. Besides, up-regulation of BAX/BCL-2 ratio, and down-regulation of MCL-1 are also observed. Moreover, this combination inhibits IRAK1, NF-κB and ERK1/2 activation, and leads to down-regulation of inflammatory cytokines (IL6, IL8, CXCL1, CCL2), S100A7/9 and CSC-related genes (OCT4, SOX2, NANOG, ALDH1, CD44) expression. In addition, the combination treatment suppresses MB231-PR cell invasion ability, and impairs tumor sphere growth both in MB231-PR and SUM159 PTX resistant (SUM159-PR) cells. Conclusion Our study demonstrates that GPT can resensitize TNBC PTX resistant cells to PTX by inhibiting the IRAK1/NF-κB and ERK pathways and reducing stem cell characteristics.
bibliographic citation: Wang et al. (2020) Ginsenoside panaxatriol reverses TNBC paclitaxel resistance by inhibiting the IRAK1/NF-κB and ERK pathways. PeerJ 8:e9281 https://doi.org/10.7717/peerj.9281
date submitted: 2020-01-27
date accepted: 2020-05-12
issued: 2020-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Panpan
author list: Agent
  family name: Song
  given name: Dan
author list: Agent
  family name: Wan
  given name: Danhong
author list: Agent
  family name: Li
  given name: Lingyu
author list: Agent
  family name: Mei
  given name: Wenhui
author list: Agent
  family name: Li
  given name: Xiaoyun
author list: Agent
  family name: Han
  given name: Li
author list: Agent
  family name: Zhu
  given name: Xiaofeng
author list: Agent
  family name: Yang
  given name: Li
author list: Agent
  family name: Cai
  given name: Yu
author list: Agent
  family name: Zhang
  given name: Ronghua
doi: 10.7717/peerj.9281
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-03
copyright: © 2020 Wang et al.
attribution name: Wang et al.

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