PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma
items: Serum metabolomic profiling reveals an increase in homocitrulline in Chinese patients with nonalcoholic fatty liver disease: a retrospective study
items: Sphenofontis velserae gen. et sp. nov., a new rhynchocephalian from the Late Jurassic of Brunn (Solnhofen Archipelago, southern Germany)
items: Ecosystem services show variable responses to future climate conditions in the Colombian páramos
items: DXA reference values of the humanoid sheep model in preclinical studies
items: Response of net primary productivity to grassland phenological changes in Xinjiang, China
items: Downregulation of both mismatch repair and non-homologous end-joining pathways in hypoxic brain tumour cell lines
items: A Toll-like receptor identified in Gigantidas platifrons and its potential role in the immune recognition of endosymbiotic methane oxidation bacteria
items: Continuous bubble streams for controlling marine biofouling on static artificial structures
items: Cinnamaldehyde inhibits the growth of Phytophthora capsici through disturbing metabolic homoeostasis

Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Hepatocellular carcinoma (HCC) is one of the deadliest tumors. The majority of HCC is detected in the late stage, and the clinical results for HCC patients are poor. There is an urgent need to discover early diagnostic biomarkers and potential therapeutic targets for HCC. Methods The GSE87630 and GSE112790 datasets from the Gene Expression Omnibus (GEO) database were downloaded to analyze the differentially expressed genes (DEGs) between HCC and normal tissues. R packages were used for Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses of the DEGs. A Search Tool for Retrieval of Interacting Genes (STRING) database was used to develop a protein-protein interaction (PPI) network, and also cytoHubba, Molecular Complex Detection (MCODE), EMBL-EBI, CCLE, Gene Expression Profiling Interactive Analysis (GEPIA), and Oncomine analyses were performed to identify hub genes. Gene expression was verified with a third GEO dataset, GSE25097. The Cancer Genome Atlas (TCGA) database was used to explore the correlations between the hub genes and clinical indexes of HCC patients. The functions of the hub genes were enriched by gene set enrichment analysis (GSEA), and the biological significance of the hub genes was explored by real-time polymerase chain reaction (qRT-PCR), western blot, immunofluorescence, CCK-8, colony formation, Transwell and flow cytometry assays with loss-of-function experiments in vitro. Results Centromere protein N (CENPN) was screened as a hub gene affecting HCC tumorigenesis. Evaluation by Cox regression showed that a high level of CENPN expression was an independent danger variable for poor prognosis of HCC. GSEA showed that high CENPN expression was linked to the following pathways: liver cancer subclass proliferation, cell cycle, p53 signaling pathway, Rb1 pathway, positive regulation of cell cycle G1/S phase transition, and DNA damage response signal transduction by p53 class moderators. Further cell experi…
format: application/pdf
format: text/html
creator: Qingqing Wang
creator: Xiaoyan Yu
creator: Zhewen Zheng
creator: Fengxia Chen
creator: Ningning Yang
creator: Yunfeng Zhou
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.11342
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background Hepatocellular carcinoma (HCC) is one of the deadliest tumors. The majority of HCC is detected in the late stage, and the clinical results for HCC patients are poor. There is an urgent need to discover early diagnostic biomarkers and potential therapeutic targets for HCC. Methods The GSE87630 and GSE112790 datasets from the Gene Expression Omnibus (GEO) database were downloaded to analyze the differentially expressed genes (DEGs) between HCC and normal tissues. R packages were used for Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses of the DEGs. A Search Tool for Retrieval of Interacting Genes (STRING) database was used to develop a protein-protein interaction (PPI) network, and also cytoHubba, Molecular Complex Detection (MCODE), EMBL-EBI, CCLE, Gene Expression Profiling Interactive Analysis (GEPIA), and Oncomine analyses were performed to identify hub genes. Gene expression was verified with a third GEO dataset, GSE25097. The Cancer Genome Atlas (TCGA) database was used to explore the correlations between the hub genes and clinical indexes of HCC patients. The functions of the hub genes were enriched by gene set enrichment analysis (GSEA), and the biological significance of the hub genes was explored by real-time polymerase chain reaction (qRT-PCR), western blot, immunofluorescence, CCK-8, colony formation, Transwell and flow cytometry assays with loss-of-function experiments in vitro. Results Centromere protein N (CENPN) was screened as a hub gene affecting HCC tumorigenesis. Evaluation by Cox regression showed that a high level of CENPN expression was an independent danger variable for poor prognosis of HCC. GSEA showed that high CENPN expression was linked to the following pathways: liver cancer subclass proliferation, cell cycle, p53 signaling pathway, Rb1 pathway, positive regulation of cell cycle G1/S phase transition, and DNA damage response signal transduction by p53 class moderators. Further cell experi…
bibliographic citation: Wang et al. (2021) Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma. PeerJ 9:e11342 https://doi.org/10.7717/peerj.11342
date submitted: 2021-01-04
date accepted: 2021-04-03
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Qingqing
author list: Agent
  family name: Yu
  given name: Xiaoyan
author list: Agent
  family name: Zheng
  given name: Zhewen
author list: Agent
  family name: Chen
  given name: Fengxia
author list: Agent
  family name: Yang
  given name: Ningning
author list: Agent
  family name: Zhou
  given name: Yunfeng
doi: 10.7717/peerj.11342
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Serum metabolomic profiling reveals an increase in homocitrulline in Chinese patients with nonalcoholic fatty liver disease: a retrospective study
type: item
type: AcademicArticle
description: Backgrounds Nonalcoholic fatty liver disease (NAFLD) has multiple causes, is triggered by individual genetic susceptibility, environmental factors, and metabolic disturbances, and may be triggered by acquired metabolic stress. The metabolic profiles of NAFLD show significant ethnic differences, and the metabolic characteristics of NAFLD in Chinese individuals are unclear. Our study aimed to identify the metabolites and pathways associated with NAFLD in a Chinese cohort. Methods One hundred participants, including 50 NAFLD patients and 50 healthy controls, were enrolled in this retrospective observational study at Jinling Hospital in Nanjing; serum samples were collected from the patients and healthy subjects. The metabolome was determined in all samples by liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry (LC-Q/TOF-MS). Univariate and multivariate statistical analyses were used to compare the metabolic profiles between the two groups. Results The comparison indicated that the levels of 89 metabolites were different between the two groups. The glycerophospholipid family of metabolites was the most abundant family of metabolites that demonstrated significant differences. L-acetylcarnitine, L-homocitrulline, and glutamic acid were the top three metabolites ranked by VIP score and had favorable effective functions for diagnosis. Moreover, pathway enrichment analysis suggested 14 potentially different metabolic pathways between NAFLD patients and healthy controls based on their impact value. Biological modules involved in the lipid and carbohydrate metabolism had the highest relevance to the conditions of NAFLD. Glycerophospholipid metabolism had the strongest associations with the conditions of NAFLD. Conclusions Our data suggest that the serum metabolic profiles of NAFLD patients and healthy controls are different. L-Homocitrulline was remarkably increased in NAFLD patients.
format: application/pdf
format: text/html
creator: Yarong Yang
creator: Zexin Huang
creator: Zhao Yang
creator: Ying Qi
creator: Hui Shi
creator: Yifei Zhou
creator: Fangyu Wang
creator: Miaofang Yang
subject: Gastroenterology and Hepatology
subject: Hematology
subject: Metabolic Sciences
description: doi:10.7717/peerj.11346
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Backgrounds Nonalcoholic fatty liver disease (NAFLD) has multiple causes, is triggered by individual genetic susceptibility, environmental factors, and metabolic disturbances, and may be triggered by acquired metabolic stress. The metabolic profiles of NAFLD show significant ethnic differences, and the metabolic characteristics of NAFLD in Chinese individuals are unclear. Our study aimed to identify the metabolites and pathways associated with NAFLD in a Chinese cohort. Methods One hundred participants, including 50 NAFLD patients and 50 healthy controls, were enrolled in this retrospective observational study at Jinling Hospital in Nanjing; serum samples were collected from the patients and healthy subjects. The metabolome was determined in all samples by liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry (LC-Q/TOF-MS). Univariate and multivariate statistical analyses were used to compare the metabolic profiles between the two groups. Results The comparison indicated that the levels of 89 metabolites were different between the two groups. The glycerophospholipid family of metabolites was the most abundant family of metabolites that demonstrated significant differences. L-acetylcarnitine, L-homocitrulline, and glutamic acid were the top three metabolites ranked by VIP score and had favorable effective functions for diagnosis. Moreover, pathway enrichment analysis suggested 14 potentially different metabolic pathways between NAFLD patients and healthy controls based on their impact value. Biological modules involved in the lipid and carbohydrate metabolism had the highest relevance to the conditions of NAFLD. Glycerophospholipid metabolism had the strongest associations with the conditions of NAFLD. Conclusions Our data suggest that the serum metabolic profiles of NAFLD patients and healthy controls are different. L-Homocitrulline was remarkably increased in NAFLD patients.
bibliographic citation: Yang et al. (2021) Serum metabolomic profiling reveals an increase in homocitrulline in Chinese patients with nonalcoholic fatty liver disease: a retrospective study. PeerJ 9:e11346 https://doi.org/10.7717/peerj.11346
date submitted: 2020-10-07
date accepted: 2021-04-03
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yarong
author list: Agent
  family name: Huang
  given name: Zexin
author list: Agent
  family name: Yang
  given name: Zhao
author list: Agent
  family name: Qi
  given name: Ying
author list: Agent
  family name: Shi
  given name: Hui
author list: Agent
  family name: Zhou
  given name: Yifei
author list: Agent
  family name: Wang
  given name: Fangyu
author list: Agent
  family name: Yang
  given name: Miaofang
doi: 10.7717/peerj.11346
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Yang et al.
attribution name: Yang et al.

Sphenofontis velserae gen. et sp. nov., a new rhynchocephalian from the Late Jurassic of Brunn (Solnhofen Archipelago, southern Germany)
type: item
type: AcademicArticle
description: The Solnhofen Archipelago is well known for its fossil vertebrates of Late Jurassic age, among which figure numerous rhynchocephalian specimens, representing at least six and up to nine genera. A new taxon, named Sphenofontis velserae gen. et sp. nov., increases rhynchocephalian diversity in the Solnhofen Archipelago and is herein described based on a single, well-preserved specimen originating from the Late Kimmeridgian of the Brunn quarry, near Regensburg. The exquisite preservation of the holotype allowed a detailed description of the animal, revealing a skeletal morphology that includes both plesiomorphic and derived features within rhynchocephalians. Sphenofontis is herein referred to Neosphenodontia and tentatively to sphenodontine sphenodontids. It notably differs from all other rhynchocephalians known from the Jurassic of Europe, showing instead closer resemblance with the Middle Jurassic Cynosphenodon from Mexico and especially the extant Sphenodon. This is evidence for a wide distribution of taxa related to the extant tuatara early in the Mesozoic, and also for the presence of less-specialized rhynchocephalians coexisting with more derived forms during the earliest time in the history of the Solnhofen Archipelago.
format: application/pdf
format: text/html
creator: Andrea Villa
creator: Roel Montie
creator: Martin Röper
creator: Monika Rothgaenger
creator: Oliver W.M. Rauhut
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11363
publisher: PeerJ Inc.
rights: © 2021 Villa et al.
abstract: The Solnhofen Archipelago is well known for its fossil vertebrates of Late Jurassic age, among which figure numerous rhynchocephalian specimens, representing at least six and up to nine genera. A new taxon, named Sphenofontis velserae gen. et sp. nov., increases rhynchocephalian diversity in the Solnhofen Archipelago and is herein described based on a single, well-preserved specimen originating from the Late Kimmeridgian of the Brunn quarry, near Regensburg. The exquisite preservation of the holotype allowed a detailed description of the animal, revealing a skeletal morphology that includes both plesiomorphic and derived features within rhynchocephalians. Sphenofontis is herein referred to Neosphenodontia and tentatively to sphenodontine sphenodontids. It notably differs from all other rhynchocephalians known from the Jurassic of Europe, showing instead closer resemblance with the Middle Jurassic Cynosphenodon from Mexico and especially the extant Sphenodon. This is evidence for a wide distribution of taxa related to the extant tuatara early in the Mesozoic, and also for the presence of less-specialized rhynchocephalians coexisting with more derived forms during the earliest time in the history of the Solnhofen Archipelago.
bibliographic citation: Villa et al. (2021) Sphenofontis velserae gen. et sp. nov., a new rhynchocephalian from the Late Jurassic of Brunn (Solnhofen Archipelago, southern Germany). PeerJ 9:e11363 https://doi.org/10.7717/peerj.11363
date submitted: 2020-12-07
date accepted: 2021-04-06
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Villa
  given name: Andrea
author list: Agent
  family name: Montie
  given name: Roel
author list: Agent
  family name: Röper
  given name: Martin
author list: Agent
  family name: Rothgaenger
  given name: Monika
author list: Agent
  family name: Rauhut
  given name: Oliver W.M.
doi: 10.7717/peerj.11363
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: © 2021 Villa et al.
attribution name: Villa et al.

Ecosystem services show variable responses to future climate conditions in the Colombian páramos
type: item
type: AcademicArticle
description: Background The páramos, the high-elevation ecosystems of the northern Andes, are well-known for their high species richness and provide a variety of ecosystem services to local subsistence-based communities and regional urbanizations. Climate change is expected to negatively affect the provision of these services, but the level of this impact is still unclear. Here we assess future climate change impact on the ecosystem services provided by the critically important páramos of the department of Boyacá in Colombia, of which over 25% of its territory is páramo. Methods We first performed an extensive literature review to identify useful species of Boyacá, and selected 103 key plant species that, based on their uses, support the provision of ecosystem services in the páramos. We collated occurrence information for each key species and using a Mahalanobis distance approach we applied climate niche modelling for current and future conditions. Results We show an overall tendency of reduction in area for all ecosystem services under future climate conditions (mostly a loss of 10% but reaching up to a loss of 40%), but we observe also increases, and responses differ in intensity loss. Services such as Food for animals, Material and Medicinal, show a high range of changes that includes both positive and negative outcomes, while for Food for humans the responses are mostly substantially negative. Responses are less extreme than those projected for individual species but are often complex because a given ecosystem service is provided by several species. As the level of functional or ecological redundancy between species is not yet known, there is an urgency to expand our knowledge on páramos ecosystem services for more species. Our results are crucial for decision-makers, social and conservation organizations to support sustainable strategies to monitor and mitigate the potential consequences of climate change for human livelihoods in mountainous settings.
format: application/pdf
format: text/html
creator: Mauricio Diazgranados
creator: Carolina Tovar
creator: Thomas R. Etherington
creator: Paula A. Rodríguez-Zorro
creator: Carolina Castellanos-Castro
creator: Manuel Galvis Rueda
creator: Suzette G.A. Flantua
subject: Biogeography
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.11370
publisher: PeerJ Inc.
rights: © 2021 Diazgranados et al.
abstract: Background The páramos, the high-elevation ecosystems of the northern Andes, are well-known for their high species richness and provide a variety of ecosystem services to local subsistence-based communities and regional urbanizations. Climate change is expected to negatively affect the provision of these services, but the level of this impact is still unclear. Here we assess future climate change impact on the ecosystem services provided by the critically important páramos of the department of Boyacá in Colombia, of which over 25% of its territory is páramo. Methods We first performed an extensive literature review to identify useful species of Boyacá, and selected 103 key plant species that, based on their uses, support the provision of ecosystem services in the páramos. We collated occurrence information for each key species and using a Mahalanobis distance approach we applied climate niche modelling for current and future conditions. Results We show an overall tendency of reduction in area for all ecosystem services under future climate conditions (mostly a loss of 10% but reaching up to a loss of 40%), but we observe also increases, and responses differ in intensity loss. Services such as Food for animals, Material and Medicinal, show a high range of changes that includes both positive and negative outcomes, while for Food for humans the responses are mostly substantially negative. Responses are less extreme than those projected for individual species but are often complex because a given ecosystem service is provided by several species. As the level of functional or ecological redundancy between species is not yet known, there is an urgency to expand our knowledge on páramos ecosystem services for more species. Our results are crucial for decision-makers, social and conservation organizations to support sustainable strategies to monitor and mitigate the potential consequences of climate change for human livelihoods in mountainous settings.
bibliographic citation: Diazgranados et al. (2021) Ecosystem services show variable responses to future climate conditions in the Colombian páramos. PeerJ 9:e11370 https://doi.org/10.7717/peerj.11370
date submitted: 2020-11-01
date accepted: 2021-04-07
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Diazgranados
  given name: Mauricio
author list: Agent
  family name: Tovar
  given name: Carolina
author list: Agent
  family name: Etherington
  given name: Thomas R.
author list: Agent
  family name: Rodríguez-Zorro
  given name: Paula A.
author list: Agent
  family name: Castellanos-Castro
  given name: Carolina
author list: Agent
  family name: Galvis Rueda
  given name: Manuel
author list: Agent
  family name: Flantua
  given name: Suzette G.A.
doi: 10.7717/peerj.11370
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: © 2021 Diazgranados et al.
attribution name: Diazgranados et al.

DXA reference values of the humanoid sheep model in preclinical studies
type: item
type: AcademicArticle
description: Background Merino land sheep are a popular pre-clinical large animal model in research on systemic skeletal diseases such as osteoporosis. Interpretation of studies is difficult because many reference parameters are missing or not established. This study aims to determine the reference parameters of the skeletal system (peak bone mass = PBM, T-Score). A defined standard allows an easier comparison of the study data of the animal model with human studies (T-Score). Materials and methods A total of 116 Dual Energy X-ray Absorptiometry DXA measurements were performed on 74 untreated sheep. The average age of the animals was 57 months. The BMD, BMC, and fat content of the sheep were determined by the relevant human region of interest (ROI). From this, the PBM and from this the T-score for each of the animals were calculated. Results Using 682 DXA measurements BMD and BMC were determined to provide an indication to PBM. For BMD a significant correlation to the age of the animals was observed (p = 0.043). A significant correlation was also seen for BMC (B) (p ≤ 0.001). In the age-dependent analysis, a widespread of values above the linear regression line was measured for both BMD and BMC between the 50th and 90th months of life. From an age of about 90 months, a wider spread of values below the linear regression line was found, although the average values continued to rise. Discussion The evaluation of the 116 DXA measurements allowed the determination of the PBM for merino land sheep. With the help of the PBM, a T-score was calculated for each animal. The statistical analysis shows significant differences in BMD values between the different animal groups in each of the four ROIs investigated. Individual control or sham groups per study are therefore not sufficient. To improve comparability, an independent reference group should be established. Conclusion An independent reference group for PBM and a T-score was established from four to six-year-old animals. The bone densi…
format: application/pdf
format: text/html
creator: Christoph Biehl
creator: Jakob Schmitt
creator: Sabine Stoetzel
creator: Deeksha Malhan
creator: Fathi Hassan
creator: Gero Knapp
creator: Christian Heiss
creator: Thaqif El Khassawna
subject: Orthopedics
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.11183
publisher: PeerJ Inc.
rights: © 2021 Biehl et al.
abstract: Background Merino land sheep are a popular pre-clinical large animal model in research on systemic skeletal diseases such as osteoporosis. Interpretation of studies is difficult because many reference parameters are missing or not established. This study aims to determine the reference parameters of the skeletal system (peak bone mass = PBM, T-Score). A defined standard allows an easier comparison of the study data of the animal model with human studies (T-Score). Materials and methods A total of 116 Dual Energy X-ray Absorptiometry DXA measurements were performed on 74 untreated sheep. The average age of the animals was 57 months. The BMD, BMC, and fat content of the sheep were determined by the relevant human region of interest (ROI). From this, the PBM and from this the T-score for each of the animals were calculated. Results Using 682 DXA measurements BMD and BMC were determined to provide an indication to PBM. For BMD a significant correlation to the age of the animals was observed (p = 0.043). A significant correlation was also seen for BMC (B) (p ≤ 0.001). In the age-dependent analysis, a widespread of values above the linear regression line was measured for both BMD and BMC between the 50th and 90th months of life. From an age of about 90 months, a wider spread of values below the linear regression line was found, although the average values continued to rise. Discussion The evaluation of the 116 DXA measurements allowed the determination of the PBM for merino land sheep. With the help of the PBM, a T-score was calculated for each animal. The statistical analysis shows significant differences in BMD values between the different animal groups in each of the four ROIs investigated. Individual control or sham groups per study are therefore not sufficient. To improve comparability, an independent reference group should be established. Conclusion An independent reference group for PBM and a T-score was established from four to six-year-old animals. The bone densi…
bibliographic citation: Biehl et al. (2021) DXA reference values of the humanoid sheep model in preclinical studies. PeerJ 9:e11183 https://doi.org/10.7717/peerj.11183
date submitted: 2020-08-10
date accepted: 2021-03-08
issued: 2021-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Biehl
  given name: Christoph
author list: Agent
  family name: Schmitt
  given name: Jakob
author list: Agent
  family name: Stoetzel
  given name: Sabine
author list: Agent
  family name: Malhan
  given name: Deeksha
author list: Agent
  family name: Hassan
  given name: Fathi
author list: Agent
  family name: Knapp
  given name: Gero
author list: Agent
  family name: Heiss
  given name: Christian
author list: Agent
  family name: El Khassawna
  given name: Thaqif
doi: 10.7717/peerj.11183
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-30
copyright: ©2021 Biehl et al.
attribution name: Biehl et al.

Response of net primary productivity to grassland phenological changes in Xinjiang, China
type: item
type: AcademicArticle
description: Determining the relationship between net primary productivity (NPP) and grassland phenology is important for an in-depth understanding of the impact of climate change on ecosystems. In this study, the NPP of grassland in Xinjiang, China, was simulated using the Carnegie-Ames-Stanford approach (CASA) model with Moderate Resolution Imaging Spectroradiometer (MODIS) grassland phenological (MCD12Q2) data to study trends in phenological metrics, grassland NPP, and the relations between these factors from 2001–2014. The results revealed advancement of the start of the growing season (SOS) for grassland in most regions (55.2%) in Xinjiang. The percentage of grassland area in which the end of the growing season (EOS) was delayed (50.9%) was generally the same as that in which the EOS was advanced (49.1%). The percentage of grassland area with an increase in the length of the growing season (LOS) for the grassland area (54.6%) was greater than that with a decrease in the LOS (45.4%). The percentage of grassland area with an increase in NPP (61.6%) was greater than that with a decrease in NPP (38.4%). Warmer regions featured an earlier SOS and a later EOS and thus a longer LOS. Regions with higher precipitation exhibited a later SOS and an earlier EOS and thus a shorter LOS. In most regions, the SOS was earlier, and spring NPP was higher. A linear statistical analysis showed that at various humidity (K) levels, grassland NPP in all regions initially increased but then decreased with increasing LOS. At higher levels of K, when NPP gradually increased, the LOS gradually decreased.
format: application/pdf
format: text/html
creator: Renping Zhang
creator: Jing Guo
creator: Gang Yin
subject: Climate Change Biology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10650
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Determining the relationship between net primary productivity (NPP) and grassland phenology is important for an in-depth understanding of the impact of climate change on ecosystems. In this study, the NPP of grassland in Xinjiang, China, was simulated using the Carnegie-Ames-Stanford approach (CASA) model with Moderate Resolution Imaging Spectroradiometer (MODIS) grassland phenological (MCD12Q2) data to study trends in phenological metrics, grassland NPP, and the relations between these factors from 2001–2014. The results revealed advancement of the start of the growing season (SOS) for grassland in most regions (55.2%) in Xinjiang. The percentage of grassland area in which the end of the growing season (EOS) was delayed (50.9%) was generally the same as that in which the EOS was advanced (49.1%). The percentage of grassland area with an increase in the length of the growing season (LOS) for the grassland area (54.6%) was greater than that with a decrease in the LOS (45.4%). The percentage of grassland area with an increase in NPP (61.6%) was greater than that with a decrease in NPP (38.4%). Warmer regions featured an earlier SOS and a later EOS and thus a longer LOS. Regions with higher precipitation exhibited a later SOS and an earlier EOS and thus a shorter LOS. In most regions, the SOS was earlier, and spring NPP was higher. A linear statistical analysis showed that at various humidity (K) levels, grassland NPP in all regions initially increased but then decreased with increasing LOS. At higher levels of K, when NPP gradually increased, the LOS gradually decreased.
bibliographic citation: Zhang et al. (2021) Response of net primary productivity to grassland phenological changes in Xinjiang, China. PeerJ 9:e10650 https://doi.org/10.7717/peerj.10650
date submitted: 2020-01-08
date accepted: 2020-12-04
issued: 2021-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Renping
author list: Agent
  family name: Guo
  given name: Jing
author list: Agent
  family name: Yin
  given name: Gang
doi: 10.7717/peerj.10650
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-30
copyright: © 2021 Zhang et al.
attribution name: Zhang et al.

Downregulation of both mismatch repair and non-homologous end-joining pathways in hypoxic brain tumour cell lines
type: item
type: AcademicArticle
description: Glioblastoma, a grade IV astrocytoma, has a poor survival rate in part due to ineffective treatment options available. These tumours are heterogeneous with areas of low oxygen levels, termed hypoxic regions. Many intra-cellular signalling pathways, including DNA repair, can be altered by hypoxia. Since DNA damage induction and subsequent activation of DNA repair mechanisms is the cornerstone of glioblastoma treatment, alterations to DNA repair mechanisms could have a direct influence on treatment success. Our aim was to elucidate the impact of chronic hypoxia on DNA repair gene expression in a range of glioblastoma cell lines. We adopted a NanoString transcriptomic approach to examine the expression of 180 DNA repair-related genes in four classical glioblastoma cell lines (U87-MG, U251-MG, D566-MG, T98G) exposed to 5 days of normoxia (21% O2), moderate (1% O2) or severe (0.1% O2) hypoxia. We observed altered gene expression in several DNA repair pathways including homologous recombination repair, non-homologous end-joining and mismatch repair, with hypoxia primarily resulting in downregulation of gene expression. The extent of gene expression changes was dependent on hypoxic severity. Some, but not all, of these downregulations were directly under the control of HIF activity. For example, the downregulation of LIG4, a key component of non-homologous end-joining, was reversed upon inhibition of the hypoxia-inducible factor (HIF). In contrast, the downregulation of the mismatch repair gene, PMS2, was not affected by HIF inhibition. This suggests that numerous molecular mechanisms lead to hypoxia-induced reprogramming of the transcriptional landscape of DNA repair. Whilst the global impact of hypoxia on DNA repair gene expression is likely to lead to genomic instability, tumorigenesis and reduced sensitivity to anti-cancer treatment, treatment re-sensitising might require additional approaches to a simple HIF inhibition.
format: application/pdf
format: text/html
creator: Sophie Cowman
creator: Barry Pizer
creator: Violaine Sée
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.11275
publisher: PeerJ Inc.
rights: © 2021 Cowman et al.
abstract: Glioblastoma, a grade IV astrocytoma, has a poor survival rate in part due to ineffective treatment options available. These tumours are heterogeneous with areas of low oxygen levels, termed hypoxic regions. Many intra-cellular signalling pathways, including DNA repair, can be altered by hypoxia. Since DNA damage induction and subsequent activation of DNA repair mechanisms is the cornerstone of glioblastoma treatment, alterations to DNA repair mechanisms could have a direct influence on treatment success. Our aim was to elucidate the impact of chronic hypoxia on DNA repair gene expression in a range of glioblastoma cell lines. We adopted a NanoString transcriptomic approach to examine the expression of 180 DNA repair-related genes in four classical glioblastoma cell lines (U87-MG, U251-MG, D566-MG, T98G) exposed to 5 days of normoxia (21% O2), moderate (1% O2) or severe (0.1% O2) hypoxia. We observed altered gene expression in several DNA repair pathways including homologous recombination repair, non-homologous end-joining and mismatch repair, with hypoxia primarily resulting in downregulation of gene expression. The extent of gene expression changes was dependent on hypoxic severity. Some, but not all, of these downregulations were directly under the control of HIF activity. For example, the downregulation of LIG4, a key component of non-homologous end-joining, was reversed upon inhibition of the hypoxia-inducible factor (HIF). In contrast, the downregulation of the mismatch repair gene, PMS2, was not affected by HIF inhibition. This suggests that numerous molecular mechanisms lead to hypoxia-induced reprogramming of the transcriptional landscape of DNA repair. Whilst the global impact of hypoxia on DNA repair gene expression is likely to lead to genomic instability, tumorigenesis and reduced sensitivity to anti-cancer treatment, treatment re-sensitising might require additional approaches to a simple HIF inhibition.
bibliographic citation: Cowman et al. (2021) Downregulation of both mismatch repair and non-homologous end-joining pathways in hypoxic brain tumour cell lines. PeerJ 9:e11275 https://doi.org/10.7717/peerj.11275
date submitted: 2020-12-08
date accepted: 2021-03-24
issued: 2021-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cowman
  given name: Sophie
author list: Agent
  family name: Pizer
  given name: Barry
author list: Agent
  family name: Sée
  given name: Violaine
doi: 10.7717/peerj.11275
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-30
copyright: © 2021 Cowman et al.
attribution name: Cowman et al.

A Toll-like receptor identified in Gigantidas platifrons and its potential role in the immune recognition of endosymbiotic methane oxidation bacteria
type: item
type: AcademicArticle
description: Symbiosis with chemosynthetic bacteria is an important ecological strategy for the deep-sea megafaunas including mollusks, tubeworms and crustacean to obtain nutrients in hydrothermal vents and cold seeps. How the megafaunas recognize symbionts and establish the symbiosis has attracted much attention. Bathymodiolinae mussels are endemic species in both hydrothermal vents and cold seeps while the immune recognition mechanism underlying the symbiosis is not well understood due to the nonculturable symbionts. In previous study, a lipopolysaccharide (LPS) pull-down assay was conducted in Gigantidas platifrons to screen the pattern recognition receptors potentially involved in the recognition of symbiotic methane-oxidizing bacteria (MOB). Consequently, a total of 208 proteins including GpTLR13 were identified. Here the molecular structure, expression pattern and immune function of GpTLR13 were further analyzed. It was found that GpTLR13 could bind intensively with the lipid A structure of LPS through surface plasmon resonance analysis. The expression alternations of GpTLR13 transcripts during a 28-day of symbiont-depletion assay were investigated by real-time qPCR. As a result, a robust decrease of GpTLR13 transcripts was observed accompanying with the loss of symbionts, implying its participation in symbiosis. In addition, GpTLR13 transcripts were found expressed exclusively in the bacteriocytes of gills of G. platifrons by in situ hybridization. It was therefore speculated that GpTLR13 may be involved in the immune recognition of symbiotic methane-oxidizing bacteria by specifically recognizing the lipid A structure of LPS. However, the interaction between GpTLR13 and symbiotic MOB was failed to be addressed due to the nonculturable symbionts. Nevertheless, the present result has provided with a promising candidate as well as a new approach for the identification of symbiont-related genes in Bathymodiolinae mussels.
format: application/pdf
format: text/html
creator: Mengna Li
creator: Hao Chen
creator: Minxiao Wang
creator: Zhaoshan Zhong
creator: Hao Wang
creator: Li Zhou
creator: Huan Zhang
creator: Chaolun Li
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.11282
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Symbiosis with chemosynthetic bacteria is an important ecological strategy for the deep-sea megafaunas including mollusks, tubeworms and crustacean to obtain nutrients in hydrothermal vents and cold seeps. How the megafaunas recognize symbionts and establish the symbiosis has attracted much attention. Bathymodiolinae mussels are endemic species in both hydrothermal vents and cold seeps while the immune recognition mechanism underlying the symbiosis is not well understood due to the nonculturable symbionts. In previous study, a lipopolysaccharide (LPS) pull-down assay was conducted in Gigantidas platifrons to screen the pattern recognition receptors potentially involved in the recognition of symbiotic methane-oxidizing bacteria (MOB). Consequently, a total of 208 proteins including GpTLR13 were identified. Here the molecular structure, expression pattern and immune function of GpTLR13 were further analyzed. It was found that GpTLR13 could bind intensively with the lipid A structure of LPS through surface plasmon resonance analysis. The expression alternations of GpTLR13 transcripts during a 28-day of symbiont-depletion assay were investigated by real-time qPCR. As a result, a robust decrease of GpTLR13 transcripts was observed accompanying with the loss of symbionts, implying its participation in symbiosis. In addition, GpTLR13 transcripts were found expressed exclusively in the bacteriocytes of gills of G. platifrons by in situ hybridization. It was therefore speculated that GpTLR13 may be involved in the immune recognition of symbiotic methane-oxidizing bacteria by specifically recognizing the lipid A structure of LPS. However, the interaction between GpTLR13 and symbiotic MOB was failed to be addressed due to the nonculturable symbionts. Nevertheless, the present result has provided with a promising candidate as well as a new approach for the identification of symbiont-related genes in Bathymodiolinae mussels.
bibliographic citation: Li et al. (2021) A Toll-like receptor identified in Gigantidas platifrons and its potential role in the immune recognition of endosymbiotic methane oxidation bacteria. PeerJ 9:e11282 https://doi.org/10.7717/peerj.11282
date submitted: 2021-01-04
date accepted: 2021-03-24
issued: 2021-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Mengna
author list: Agent
  family name: Chen
  given name: Hao
author list: Agent
  family name: Wang
  given name: Minxiao
author list: Agent
  family name: Zhong
  given name: Zhaoshan
author list: Agent
  family name: Wang
  given name: Hao
author list: Agent
  family name: Zhou
  given name: Li
author list: Agent
  family name: Zhang
  given name: Huan
author list: Agent
  family name: Li
  given name: Chaolun
doi: 10.7717/peerj.11282
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-30
copyright: © 2021 Li et al.
attribution name: Li et al.

Continuous bubble streams for controlling marine biofouling on static artificial structures
type: item
type: AcademicArticle
description: Biofouling accumulation is not proactively managed on most marine static artificial structures (SAS) due to the lack of effective options presently available. We describe a series of laboratory and field trials that examine the efficacy of continuous bubble streams in maintaining SAS free of macroscopic biofouling and demonstrate that this treatment approach is effective on surface types commonly used in the marine environment. At least two mechanisms were shown to be at play: the disruption of settlement created by the bubble stream, and the scouring of recently settled larvae through shear stress. Field trials conducted over a one-year period identified fouling on diffusers as a major issue to long-term treatment applications. Field measurements suggest that noise associated with surface mounted air blowers and sub-surface diffusers will be highly localised and of low environmental risk. Future studies should aim to develop and test systems at an operational scale.
format: application/pdf
format: text/html
creator: Grant A. Hopkins
creator: Fletcher Gilbertson
creator: Oli Floerl
creator: Paula Casanovas
creator: Matt Pine
creator: Patrick Cahill
subject: Ecology
subject: Marine Biology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.11323
publisher: PeerJ Inc.
rights: © 2021 Hopkins et al.
abstract: Biofouling accumulation is not proactively managed on most marine static artificial structures (SAS) due to the lack of effective options presently available. We describe a series of laboratory and field trials that examine the efficacy of continuous bubble streams in maintaining SAS free of macroscopic biofouling and demonstrate that this treatment approach is effective on surface types commonly used in the marine environment. At least two mechanisms were shown to be at play: the disruption of settlement created by the bubble stream, and the scouring of recently settled larvae through shear stress. Field trials conducted over a one-year period identified fouling on diffusers as a major issue to long-term treatment applications. Field measurements suggest that noise associated with surface mounted air blowers and sub-surface diffusers will be highly localised and of low environmental risk. Future studies should aim to develop and test systems at an operational scale.
bibliographic citation: Hopkins et al. (2021) Continuous bubble streams for controlling marine biofouling on static artificial structures. PeerJ 9:e11323 https://doi.org/10.7717/peerj.11323
date submitted: 2020-11-24
date accepted: 2021-03-31
issued: 2021-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hopkins
  given name: Grant A.
author list: Agent
  family name: Gilbertson
  given name: Fletcher
author list: Agent
  family name: Floerl
  given name: Oli
author list: Agent
  family name: Casanovas
  given name: Paula
author list: Agent
  family name: Pine
  given name: Matt
author list: Agent
  family name: Cahill
  given name: Patrick
doi: 10.7717/peerj.11323
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-30
copyright: ©2021 Hopkins et al.
attribution name: Hopkins et al.

Cinnamaldehyde inhibits the growth of Phytophthora capsici through disturbing metabolic homoeostasis
type: item
type: AcademicArticle
description: Background Phytophthora capsici Leonian (P. capsici) can cause wilting and roots rotting on pepper and other cash crops. The new fungicide cinnamaldehyde (CA) has high activity against this pathogen. However, its potential mechanism is still unknown. Methods In order to gain insights into the mechanism, isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics was used to analyze P. capsici treated with CA. The iTRAQ results were evaluated by parallel reaction monitoring (PRM) analysis and quantitative real-time PCR (qRT-PCR) analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was used to speculate the biochemical pathways that the agent may act on. Results The results showed that 1502 differentially expressed proteins were identified, annotated and classified into 209 different terms (like metabolic process, cellular process, single-organism process) based on Gene Ontology (GO) functional enrichment analysis and nine different pathways (glyoxylate and dicarboxylate metabolism, fatty acid metabolism and so on) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. This study suggested that CA disordered fatty acid metabolism, polysaccharide metabolism and leucine metabolism. Based on PRM analysis, five proteins including CAMK/CAMK1 protein kinase, glucan 1,3-beta-glucosidase, 1,3-beta-glucanosyltransferase, methylcrotonoyl-CoA carboxylase subunit alpha and isovaleryl-CoA dehydrogenase were down-regulated in P. capsici treated with CA. Furthermore, the qRT-PCR analysis showed that the gene expression level of the interested proteins was consistent with the protein expression level, except for CAMK/CAMK1 protein kinase, acetyl-CoA carboxylase and fatty acid synthase subunit alpha. Conclusions CA destroyed the metabolic homoeostasisof P. capsici, which led to cell death. This is the first proteomic analysis of P. capsici treated with CA, which may provide an important information for …
format: application/pdf
format: text/html
creator: Yinan Wang
creator: Mengke Wang
creator: Min Li
creator: Te Zhao
creator: Lin Zhou
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Toxicology
description: doi:10.7717/peerj.11339
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background Phytophthora capsici Leonian (P. capsici) can cause wilting and roots rotting on pepper and other cash crops. The new fungicide cinnamaldehyde (CA) has high activity against this pathogen. However, its potential mechanism is still unknown. Methods In order to gain insights into the mechanism, isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics was used to analyze P. capsici treated with CA. The iTRAQ results were evaluated by parallel reaction monitoring (PRM) analysis and quantitative real-time PCR (qRT-PCR) analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was used to speculate the biochemical pathways that the agent may act on. Results The results showed that 1502 differentially expressed proteins were identified, annotated and classified into 209 different terms (like metabolic process, cellular process, single-organism process) based on Gene Ontology (GO) functional enrichment analysis and nine different pathways (glyoxylate and dicarboxylate metabolism, fatty acid metabolism and so on) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. This study suggested that CA disordered fatty acid metabolism, polysaccharide metabolism and leucine metabolism. Based on PRM analysis, five proteins including CAMK/CAMK1 protein kinase, glucan 1,3-beta-glucosidase, 1,3-beta-glucanosyltransferase, methylcrotonoyl-CoA carboxylase subunit alpha and isovaleryl-CoA dehydrogenase were down-regulated in P. capsici treated with CA. Furthermore, the qRT-PCR analysis showed that the gene expression level of the interested proteins was consistent with the protein expression level, except for CAMK/CAMK1 protein kinase, acetyl-CoA carboxylase and fatty acid synthase subunit alpha. Conclusions CA destroyed the metabolic homoeostasisof P. capsici, which led to cell death. This is the first proteomic analysis of P. capsici treated with CA, which may provide an important information for …
bibliographic citation: Wang et al. (2021) Cinnamaldehyde inhibits the growth of Phytophthora capsici through disturbing metabolic homoeostasis. PeerJ 9:e11339 https://doi.org/10.7717/peerj.11339
date submitted: 2020-12-08
date accepted: 2021-04-03
issued: 2021-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yinan
author list: Agent
  family name: Wang
  given name: Mengke
author list: Agent
  family name: Li
  given name: Min
author list: Agent
  family name: Zhao
  given name: Te
author list: Agent
  family name: Zhou
  given name: Lin
doi: 10.7717/peerj.11339
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-30
copyright: ©2021 Wang et al.
attribution name: Wang et al.

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