PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Influence of water availability and temperature on estimates of microbial extracellular enzyme activity
items: Cranial ornamentation in the Late Cretaceous nodosaurid ankylosaur Hungarosaurus
items: Examining long-term natural vegetation dynamics in the Aral Sea Basin applying the linear spectral mixture model
items: Comparative transcriptome analyses of maize seedling root responses to salt stress
items: Comparison of circulating tumor cell (CTC) detection rates with epithelial cell adhesion molecule (EpCAM) and cell surface vimentin (CSV) antibodies in different solid tumors: a retrospective study
items: Residual dynamics and dietary exposure risk of dimethoate and its metabolite in greenhouse celery
items: The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study
items: The regulatory roles and mechanisms of the transcription factor FOXF2 in human diseases
items: Undercarboxylated osteocalcin inhibits the early differentiation of osteoclast mediated by Gprc6a
items: Taxonomic revision of the Malagasy Aphaenogaster swammerdami group (Hymenoptera: Formicidae)

Influence of water availability and temperature on estimates of microbial extracellular enzyme activity
type: item
type: AcademicArticle
description: Soils are highly heterogeneous and support highly diverse microbial communities. Microbial extracellular enzymes breakdown complex polymers into small assimilable molecules representing the limiting step of soil organic matter mineralization. This process occurs on to soil particles although currently it is typically estimated in laboratory aqueous solutions. Herein, estimates of microbial extracellular enzyme activity were obtained over a broad range of temperatures and water availabilities frequently observed at soil upper layers. A Pseudomonas strain presented optimum extracellular enzyme activities at high water activity whereas a desiccation resistant bacterium (Deinococcus) and a soil thermophilic isolate (Parageobacillus) showed optimum extracellular enzyme activity under dried (i.e., water activities ranging 0.5–0.8) rather that wet conditions. Different unamended soils presented a distinctive response of extracellular enzyme activity as a function of temperature and water availability. This study presents a procedure to obtain realistic estimates of microbial extracellular enzyme activity under natural soil conditions of extreme water availability and temperature. Improving estimates of microbial extracellular enzyme activity contribute to better understand the role of microorganisms in soils.
format: application/pdf
format: text/html
creator: Enrique J. Gomez
creator: Jose A. Delgado
creator: Juan M. Gonzalez
subject: Ecology
subject: Ecosystem Science
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.10994
publisher: PeerJ Inc.
rights: © 2021 Gomez et al.
abstract: Soils are highly heterogeneous and support highly diverse microbial communities. Microbial extracellular enzymes breakdown complex polymers into small assimilable molecules representing the limiting step of soil organic matter mineralization. This process occurs on to soil particles although currently it is typically estimated in laboratory aqueous solutions. Herein, estimates of microbial extracellular enzyme activity were obtained over a broad range of temperatures and water availabilities frequently observed at soil upper layers. A Pseudomonas strain presented optimum extracellular enzyme activities at high water activity whereas a desiccation resistant bacterium (Deinococcus) and a soil thermophilic isolate (Parageobacillus) showed optimum extracellular enzyme activity under dried (i.e., water activities ranging 0.5–0.8) rather that wet conditions. Different unamended soils presented a distinctive response of extracellular enzyme activity as a function of temperature and water availability. This study presents a procedure to obtain realistic estimates of microbial extracellular enzyme activity under natural soil conditions of extreme water availability and temperature. Improving estimates of microbial extracellular enzyme activity contribute to better understand the role of microorganisms in soils.
bibliographic citation: Gomez et al. (2021) Influence of water availability and temperature on estimates of microbial extracellular enzyme activity. PeerJ 9:e10994 https://doi.org/10.7717/peerj.10994
date submitted: 2020-09-04
date accepted: 2021-02-01
issued: 2021-03-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gomez
  given name: Enrique J.
author list: Agent
  family name: Delgado
  given name: Jose A.
author list: Agent
  family name: Gonzalez
  given name: Juan M.
doi: 10.7717/peerj.10994
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-03
copyright: © 2021 Gomez et al.
attribution name: Gomez et al.

Cranial ornamentation in the Late Cretaceous nodosaurid ankylosaur Hungarosaurus
type: item
type: AcademicArticle
description: Bony cranial ornamentation is developed by many groups of vertebrates, including ankylosaur dinosaurs. To date, the morphology and ontogenetic origin of ankylosaurian cranial ornamentation has primarily focused on a limited number of species from only one of the two major lineages, Ankylosauridae. For members of the sister group Nodosauridae, less is known. Here, we provide new details of the cranial anatomy of the nodosaurid Hungarosaurus from the Santonian of Europe. Based on a number of previously described and newly identified fragmentary skulls and skull elements, we recognize three different size classes of Hungarosaurus. We interpret these size classes as representing different stages of ontogeny. Cranial ornamentation is already well-developed in the earliest ontogenetic stage represented herein, suggesting that the presence of outgrowths may have played a role in intra- and interspecific recognition. We find no evidence that cranial ornamentation in Hungarosaurus involves the contribution of coossified osteoderms. Instead, available evidence indicates that cranial ornamentation forms as a result of the elaboration of individual elements. Although individual differences and sexual dimorphism cannot be excluded, the observed variation in Hungarosaurus cranial ornamentation appears to be associated with ontogeny.
format: application/pdf
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creator: Attila Ősi
creator: János Magyar
creator: Károly Rosta
creator: Matthew Vickaryous
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.11010
publisher: PeerJ Inc.
rights: © 2021 Ősi et al.
abstract: Bony cranial ornamentation is developed by many groups of vertebrates, including ankylosaur dinosaurs. To date, the morphology and ontogenetic origin of ankylosaurian cranial ornamentation has primarily focused on a limited number of species from only one of the two major lineages, Ankylosauridae. For members of the sister group Nodosauridae, less is known. Here, we provide new details of the cranial anatomy of the nodosaurid Hungarosaurus from the Santonian of Europe. Based on a number of previously described and newly identified fragmentary skulls and skull elements, we recognize three different size classes of Hungarosaurus. We interpret these size classes as representing different stages of ontogeny. Cranial ornamentation is already well-developed in the earliest ontogenetic stage represented herein, suggesting that the presence of outgrowths may have played a role in intra- and interspecific recognition. We find no evidence that cranial ornamentation in Hungarosaurus involves the contribution of coossified osteoderms. Instead, available evidence indicates that cranial ornamentation forms as a result of the elaboration of individual elements. Although individual differences and sexual dimorphism cannot be excluded, the observed variation in Hungarosaurus cranial ornamentation appears to be associated with ontogeny.
bibliographic citation: Ősi et al. (2021) Cranial ornamentation in the Late Cretaceous nodosaurid ankylosaur Hungarosaurus. PeerJ 9:e11010 https://doi.org/10.7717/peerj.11010
date submitted: 2020-10-30
date accepted: 2021-02-04
issued: 2021-03-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ősi
  given name: Attila
author list: Agent
  family name: Magyar
  given name: János
author list: Agent
  family name: Rosta
  given name: Károly
author list: Agent
  family name: Vickaryous
  given name: Matthew
doi: 10.7717/peerj.11010
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-03
copyright: ©2021 Ősi et al.
attribution name: Ősi et al.

Examining long-term natural vegetation dynamics in the Aral Sea Basin applying the linear spectral mixture model
type: item
type: AcademicArticle
description: Background Associated with the significant decrease in water resources, natural vegetation degradation has also led to many widespread environmental problems in the Aral Sea Basin. However, few studies have examined long-term vegetation dynamics in the Aral Sea Basin or distinguished between natural vegetation and cultivated land when calculating the fractional vegetation cover. Methods Based on the multi-temporal Moderate Resolution Imaging Spectroradiometer, this study examined the natural vegetation coverage by introducing the Linear Spectral Mixture Model to the Google Earth Engine platform, which greatly reduces the experimental time. Further, trend line analysis, Sen trend analysis, and Mann–Kendall trend test methods were employed to explore the characteristics of natural vegetation cover change in the Aral Sea Basin from 2000 to 2018. Results Analyses of the results suggest three major conclusions. First, the development of irrigated agriculture in the desert area is the main reason for the decrease in downstream water. Second, with the reduction of water, the natural vegetation coverage in the Aral Sea Basin showed an upward trend of 17.77% from 2000 to 2018. Finally, the main driving factor of vegetation cover changes in the Aral Sea Basin is the migration of cultivated land to the desert.
format: application/pdf
format: text/html
creator: Yiting Su
creator: Dongchuan Wang
creator: Shuang Zhao
creator: Jiancong Shi
creator: Yanqing Shi
creator: Dongying Wei
subject: Ecosystem Science
subject: Plant Science
subject: Environmental Impacts
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10747
publisher: PeerJ Inc.
rights: © 2021 Su et al.
abstract: Background Associated with the significant decrease in water resources, natural vegetation degradation has also led to many widespread environmental problems in the Aral Sea Basin. However, few studies have examined long-term vegetation dynamics in the Aral Sea Basin or distinguished between natural vegetation and cultivated land when calculating the fractional vegetation cover. Methods Based on the multi-temporal Moderate Resolution Imaging Spectroradiometer, this study examined the natural vegetation coverage by introducing the Linear Spectral Mixture Model to the Google Earth Engine platform, which greatly reduces the experimental time. Further, trend line analysis, Sen trend analysis, and Mann–Kendall trend test methods were employed to explore the characteristics of natural vegetation cover change in the Aral Sea Basin from 2000 to 2018. Results Analyses of the results suggest three major conclusions. First, the development of irrigated agriculture in the desert area is the main reason for the decrease in downstream water. Second, with the reduction of water, the natural vegetation coverage in the Aral Sea Basin showed an upward trend of 17.77% from 2000 to 2018. Finally, the main driving factor of vegetation cover changes in the Aral Sea Basin is the migration of cultivated land to the desert.
bibliographic citation: Su et al. (2021) Examining long-term natural vegetation dynamics in the Aral Sea Basin applying the linear spectral mixture model. PeerJ 9:e10747 https://doi.org/10.7717/peerj.10747
date submitted: 2020-08-26
date accepted: 2020-12-18
issued: 2021-03-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Yiting
author list: Agent
  family name: Wang
  given name: Dongchuan
author list: Agent
  family name: Zhao
  given name: Shuang
author list: Agent
  family name: Shi
  given name: Jiancong
author list: Agent
  family name: Shi
  given name: Yanqing
author list: Agent
  family name: Wei
  given name: Dongying
doi: 10.7717/peerj.10747
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-02
copyright: © 2021 Su et al.
attribution name: Su et al.

Comparative transcriptome analyses of maize seedling root responses to salt stress
type: item
type: AcademicArticle
description: Salt stress affects crop yield by limiting growth and delaying development. In this study, we constructed 16 transcriptome libraries from maize seedling roots using two maize lines, with contrasting salt tolerance, that were exposed to salt stress for 0, 6, 18 and 36 h. In total, 6,584 differential expression genes (DEGs; 3,669 upregulated, 2,915 downregulated) were induced in the salt-sensitive line and 6,419 DEGs (3,876 upregulated, 2,543 downregulated) were induced in the salt-tolerant line. Several DEGs common to both lines were enriched in the ABA signaling pathway, which was presumed to coordinate the process of maize salt response. A total of 459 DEGs were specifically induced in the salt-tolerant line and represented candidate genes responsible for high salt-tolerance. Expression pattern analysis for these DEGs indicated that the period between 0 and 6 h was a crucial period for the rapid response of the tolerant genes under salt stress. Among these DEGs, several genes, Aux/IAA, SAUR, and CBL-interacting kinase have been reported to regulate salt tolerance. In addition, the transcription factors WRKY, bZIP and MYB acted as regulators in the salt-responsive regulatory network of maize roots. Our findings will contribute to understanding of the mechanism on salt response and provide references for functional gene revelation in plants.
format: application/pdf
format: text/html
creator: Xiaoxiang Zhang
creator: Peng Liu
creator: Chunyan Qing
creator: Cong Yang
creator: Yaou Shen
creator: Langlang Ma
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10765
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Salt stress affects crop yield by limiting growth and delaying development. In this study, we constructed 16 transcriptome libraries from maize seedling roots using two maize lines, with contrasting salt tolerance, that were exposed to salt stress for 0, 6, 18 and 36 h. In total, 6,584 differential expression genes (DEGs; 3,669 upregulated, 2,915 downregulated) were induced in the salt-sensitive line and 6,419 DEGs (3,876 upregulated, 2,543 downregulated) were induced in the salt-tolerant line. Several DEGs common to both lines were enriched in the ABA signaling pathway, which was presumed to coordinate the process of maize salt response. A total of 459 DEGs were specifically induced in the salt-tolerant line and represented candidate genes responsible for high salt-tolerance. Expression pattern analysis for these DEGs indicated that the period between 0 and 6 h was a crucial period for the rapid response of the tolerant genes under salt stress. Among these DEGs, several genes, Aux/IAA, SAUR, and CBL-interacting kinase have been reported to regulate salt tolerance. In addition, the transcription factors WRKY, bZIP and MYB acted as regulators in the salt-responsive regulatory network of maize roots. Our findings will contribute to understanding of the mechanism on salt response and provide references for functional gene revelation in plants.
bibliographic citation: Zhang et al. (2021) Comparative transcriptome analyses of maize seedling root responses to salt stress. PeerJ 9:e10765 https://doi.org/10.7717/peerj.10765
date submitted: 2020-08-04
date accepted: 2020-12-22
issued: 2021-03-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiaoxiang
author list: Agent
  family name: Liu
  given name: Peng
author list: Agent
  family name: Qing
  given name: Chunyan
author list: Agent
  family name: Yang
  given name: Cong
author list: Agent
  family name: Shen
  given name: Yaou
author list: Agent
  family name: Ma
  given name: Langlang
doi: 10.7717/peerj.10765
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-02
copyright: ©2021 Zhang et al.
attribution name: Zhang et al.

Comparison of circulating tumor cell (CTC) detection rates with epithelial cell adhesion molecule (EpCAM) and cell surface vimentin (CSV) antibodies in different solid tumors: a retrospective study
type: item
type: AcademicArticle
description: Purpose Status of epithelial-mesenchymal transition (EMT) varies from tumors to tumors. Epithelial cell adhesion molecule (EpCAM) and cell surface vimentin (CSV) are the most common used targets for isolating epithelial and mesenchymal CTCs, respectively. This study aimed to identify a suitable CTC capturing antibody for CTC enrichment in each solid tumor by comparing CTC detection rates with EpCAM and CSV antibodies in different solid tumors. Methods Treatment-naive patients with confirmed cancer diagnosis and healthy people who have performed CTC detection between April 2017 and May 2018 were included in this study. CTC detection was performed with CytoSorter® CTC system using either EpCAM or CSV antibody. In total, 853 CTC results from 690 cancer patients and 72 healthy people were collected for analysis. The performance of CTC capturing antibody was determined by the CTC detection rate. Results EpCAM has the highest CTC detection rate of 84.09% in CRC, followed by BCa (78.32%). CTC detection rates with EpCAM antibody are less than 40% in HCC (25%), PDAC (32.5%) and OC (33.33%). CSV has the highest CTC detection rate of 90% in sarcoma, followed by BC (85.71%), UC (84.62%), OC (83.33%) and BCa (81.82%). CTC detection rates with CSV antibody are over 60% in all 14 solid tumors. Except for CRC, CSV has better performances than EpCAM in most solid tumors regarding the CTC detection rates. Conclusion EpCAM can be used as a target to isolate CTCs in CRC, LC, GC, BCa, EC, HNSCC, CC and PCa, especially in CRC, while CSV can be used in most solid tumors for isolating CTCs.
format: application/pdf
format: text/html
creator: Yang Gao
creator: Wan-Hung Fan
creator: Zhengbo Song
creator: Haizhou Lou
creator: Xixong Kang
subject: Hematology
subject: Oncology
description: doi:10.7717/peerj.10777
publisher: PeerJ Inc.
rights: © 2021 Gao et al.
abstract: Purpose Status of epithelial-mesenchymal transition (EMT) varies from tumors to tumors. Epithelial cell adhesion molecule (EpCAM) and cell surface vimentin (CSV) are the most common used targets for isolating epithelial and mesenchymal CTCs, respectively. This study aimed to identify a suitable CTC capturing antibody for CTC enrichment in each solid tumor by comparing CTC detection rates with EpCAM and CSV antibodies in different solid tumors. Methods Treatment-naive patients with confirmed cancer diagnosis and healthy people who have performed CTC detection between April 2017 and May 2018 were included in this study. CTC detection was performed with CytoSorter® CTC system using either EpCAM or CSV antibody. In total, 853 CTC results from 690 cancer patients and 72 healthy people were collected for analysis. The performance of CTC capturing antibody was determined by the CTC detection rate. Results EpCAM has the highest CTC detection rate of 84.09% in CRC, followed by BCa (78.32%). CTC detection rates with EpCAM antibody are less than 40% in HCC (25%), PDAC (32.5%) and OC (33.33%). CSV has the highest CTC detection rate of 90% in sarcoma, followed by BC (85.71%), UC (84.62%), OC (83.33%) and BCa (81.82%). CTC detection rates with CSV antibody are over 60% in all 14 solid tumors. Except for CRC, CSV has better performances than EpCAM in most solid tumors regarding the CTC detection rates. Conclusion EpCAM can be used as a target to isolate CTCs in CRC, LC, GC, BCa, EC, HNSCC, CC and PCa, especially in CRC, while CSV can be used in most solid tumors for isolating CTCs.
bibliographic citation: Gao et al. (2021) Comparison of circulating tumor cell (CTC) detection rates with epithelial cell adhesion molecule (EpCAM) and cell surface vimentin (CSV) antibodies in different solid tumors: a retrospective study. PeerJ 9:e10777 https://doi.org/10.7717/peerj.10777
date submitted: 2020-08-07
date accepted: 2020-12-22
issued: 2021-03-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Yang
author list: Agent
  family name: Fan
  given name: Wan-Hung
author list: Agent
  family name: Song
  given name: Zhengbo
author list: Agent
  family name: Lou
  given name: Haizhou
author list: Agent
  family name: Kang
  given name: Xixong
doi: 10.7717/peerj.10777
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-02
copyright: © 2021 Gao et al.
attribution name: Gao et al.

Residual dynamics and dietary exposure risk of dimethoate and its metabolite in greenhouse celery
type: item
type: AcademicArticle
description: This study aimed to explore the residual dynamics and dietary risk of dimethoate and its metabolite omethoate in celery. Celery was sprayed with 40% dimethoate emulsifiable concentrate (EC) at either a low concentration of 600 g a.i./ha or a high concentration of 900 g a.i./ha. Plants in the seedling, transplanting, or middle growth stages were sprayed once, and the samples were collected 90 days after transplantation. Plants in the harvesting stage were sprayed two or three times. The samples were collected on days 3, 5, 7, 10, 14 and 21 after the last pesticide application. The dimethoate and omethoate compounds were extracted from the celery samples using acetonitrile, and their concentrations were detected using ultra-performance liquid chromatography-tandem mass spectrometry. Also, the dietary risk assessments of dimethoate and omethoate were conducted in various populations and on different foods in China. The metabolism led to the formation of omethoate from dimethoate in the celery. The degradation dynamics of dimethoate and total residues in greenhouse celery followed the first-order kinetic equation. The half-lives of the compounds were 2.42 days and 2.92 days, respectively. The celery which received one application during the harvesting stage had a final residue of dimethoate after 14 days, which was lower than the maximum residue limit (MRL) 0.5 mg kg−1 for Chinese celery. The final deposition of the metabolite omethoate after 28 days was less than the maximum residue limit of 0.02 mg kg−1 for Chinese celery. Furthermore, the risk quotients of dimethoate in celery were less than 1; therefore, the level of chronic risk was acceptable after day 21. Only children aged 2–7 years had an HQ of dimethoate more than 1 (an unacceptable level of acute risk), while the acute dietary risks to other populations were within acceptable levels. It was recommended that any dimethoate applications to celery in greenhouses should happen before the celery reached the harves…
format: application/pdf
format: text/html
creator: Chunjing Guo
creator: Guang Li
creator: Qiujun Lin
creator: Xianxin Wu
creator: Jianzhong Wang
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.10789
publisher: PeerJ Inc.
rights: © 2021 Guo et al.
abstract: This study aimed to explore the residual dynamics and dietary risk of dimethoate and its metabolite omethoate in celery. Celery was sprayed with 40% dimethoate emulsifiable concentrate (EC) at either a low concentration of 600 g a.i./ha or a high concentration of 900 g a.i./ha. Plants in the seedling, transplanting, or middle growth stages were sprayed once, and the samples were collected 90 days after transplantation. Plants in the harvesting stage were sprayed two or three times. The samples were collected on days 3, 5, 7, 10, 14 and 21 after the last pesticide application. The dimethoate and omethoate compounds were extracted from the celery samples using acetonitrile, and their concentrations were detected using ultra-performance liquid chromatography-tandem mass spectrometry. Also, the dietary risk assessments of dimethoate and omethoate were conducted in various populations and on different foods in China. The metabolism led to the formation of omethoate from dimethoate in the celery. The degradation dynamics of dimethoate and total residues in greenhouse celery followed the first-order kinetic equation. The half-lives of the compounds were 2.42 days and 2.92 days, respectively. The celery which received one application during the harvesting stage had a final residue of dimethoate after 14 days, which was lower than the maximum residue limit (MRL) 0.5 mg kg−1 for Chinese celery. The final deposition of the metabolite omethoate after 28 days was less than the maximum residue limit of 0.02 mg kg−1 for Chinese celery. Furthermore, the risk quotients of dimethoate in celery were less than 1; therefore, the level of chronic risk was acceptable after day 21. Only children aged 2–7 years had an HQ of dimethoate more than 1 (an unacceptable level of acute risk), while the acute dietary risks to other populations were within acceptable levels. It was recommended that any dimethoate applications to celery in greenhouses should happen before the celery reached the harves…
bibliographic citation: Guo et al. (2021) Residual dynamics and dietary exposure risk of dimethoate and its metabolite in greenhouse celery. PeerJ 9:e10789 https://doi.org/10.7717/peerj.10789
date submitted: 2020-04-30
date accepted: 2020-12-25
issued: 2021-03-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Chunjing
author list: Agent
  family name: Li
  given name: Guang
author list: Agent
  family name: Lin
  given name: Qiujun
author list: Agent
  family name: Wu
  given name: Xianxin
author list: Agent
  family name: Wang
  given name: Jianzhong
doi: 10.7717/peerj.10789
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-02
copyright: © 2021 Guo et al.
attribution name: Guo et al.

The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study
type: item
type: AcademicArticle
description: Tumor-derived circulating tumor DNA (ctDNA) has demonstrated its excellent potential for cancer diagnosis by DNA methylome; therefore, this study aimed to identify the retinoblastoma (RB) specific methylated CpG loci as the RB diagnostic biomarkers and design a methylation specific assay to detect these biomarker from aqueous humor of RB patients. Through a genome-wide methylation profiling of tissue samples from patients with RB, normal retina and other retinal diseases, we shortlisted two CpG loci were only methylated in RB but not in normal retina or other retinal diseases. Both of these two CpG loci were located in the genome of TFAP2A. Through the screening, a primer and probe set for the two CpG loci were tested in fully methylated standards and RB tissues with a significant differentiation of RB. Our results of this assay tested in aqueous humor from RB revealed an accuracy of 92.7% for RB diagnosis. These results suggested our assay targeting the TFAP2A ctDNA methylation can be utilized for RB diagnosis and cancer monitoring.
format: application/pdf
format: text/html
creator: Qi Zeng
creator: Sha Wang
creator: Jia Tan
creator: Lu Chen
creator: Jinwei Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Ophthalmology
subject: Pediatrics
description: doi:10.7717/peerj.10830
publisher: PeerJ Inc.
rights: © 2021 Zeng et al.
abstract: Tumor-derived circulating tumor DNA (ctDNA) has demonstrated its excellent potential for cancer diagnosis by DNA methylome; therefore, this study aimed to identify the retinoblastoma (RB) specific methylated CpG loci as the RB diagnostic biomarkers and design a methylation specific assay to detect these biomarker from aqueous humor of RB patients. Through a genome-wide methylation profiling of tissue samples from patients with RB, normal retina and other retinal diseases, we shortlisted two CpG loci were only methylated in RB but not in normal retina or other retinal diseases. Both of these two CpG loci were located in the genome of TFAP2A. Through the screening, a primer and probe set for the two CpG loci were tested in fully methylated standards and RB tissues with a significant differentiation of RB. Our results of this assay tested in aqueous humor from RB revealed an accuracy of 92.7% for RB diagnosis. These results suggested our assay targeting the TFAP2A ctDNA methylation can be utilized for RB diagnosis and cancer monitoring.
bibliographic citation: Zeng et al. (2021) The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study. PeerJ 9:e10830 https://doi.org/10.7717/peerj.10830
date submitted: 2020-10-13
date accepted: 2021-01-04
issued: 2021-03-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeng
  given name: Qi
author list: Agent
  family name: Wang
  given name: Sha
author list: Agent
  family name: Tan
  given name: Jia
author list: Agent
  family name: Chen
  given name: Lu
author list: Agent
  family name: Wang
  given name: Jinwei
doi: 10.7717/peerj.10830
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-02
copyright: ©2021 Zeng et al.
attribution name: Zeng et al.

The regulatory roles and mechanisms of the transcription factor FOXF2 in human diseases
type: item
type: AcademicArticle
description: Many studies have focused on the relationship between transcription factors and a variety of common pathological conditions, such as diabetes, stroke, and cancer. It has been found that abnormal transcription factor regulation can lead to aberrant expression of downstream genes, which contributes to the occurrence and development of many diseases. The forkhead box (FOX) transcription factor family is encoded by the FOX gene, which mediates gene transcription and follow-up functions during physiological and pathological processes. FOXF2, a member of the FOX transcription family, is expressed in various organs and tissues while maintaining their normal structural and functional development during the embryonic and adult stages. Multiple regulatory pathways that regulate FOXF2 may also be controlled by FOXF2. Abnormal FOXF2 expression induced by uncontrollable regulatory signals mediate the progression of human diseases by interfering with the cell cycle, proliferation, differentiation, invasion, and metastasis. FOXF2 manipulates downstream pathways and targets as both a pro-oncogenic and anti-oncogenic factor across different types of cancer, suggesting it may be a new potential clinical marker or therapeutic target for cancer. However, FOXF2’s biological functions and specific roles in cancer development remain unclear. In this study, we provide an overview of FOXF2’s structure, function, and regulatory mechanisms in the physiological and pathological conditions of human body. We also discussed the possible reasons why FOXF2 performs the opposite function in the same types of cancer.
format: application/pdf
format: text/html
creator: Qiong Wu
creator: Wei Li
creator: Chongge You
subject: Molecular Biology
subject: Oncology
subject: Translational Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.10845
publisher: PeerJ Inc.
rights: © 2021 Wu et al.
abstract: Many studies have focused on the relationship between transcription factors and a variety of common pathological conditions, such as diabetes, stroke, and cancer. It has been found that abnormal transcription factor regulation can lead to aberrant expression of downstream genes, which contributes to the occurrence and development of many diseases. The forkhead box (FOX) transcription factor family is encoded by the FOX gene, which mediates gene transcription and follow-up functions during physiological and pathological processes. FOXF2, a member of the FOX transcription family, is expressed in various organs and tissues while maintaining their normal structural and functional development during the embryonic and adult stages. Multiple regulatory pathways that regulate FOXF2 may also be controlled by FOXF2. Abnormal FOXF2 expression induced by uncontrollable regulatory signals mediate the progression of human diseases by interfering with the cell cycle, proliferation, differentiation, invasion, and metastasis. FOXF2 manipulates downstream pathways and targets as both a pro-oncogenic and anti-oncogenic factor across different types of cancer, suggesting it may be a new potential clinical marker or therapeutic target for cancer. However, FOXF2’s biological functions and specific roles in cancer development remain unclear. In this study, we provide an overview of FOXF2’s structure, function, and regulatory mechanisms in the physiological and pathological conditions of human body. We also discussed the possible reasons why FOXF2 performs the opposite function in the same types of cancer.
bibliographic citation: Wu et al. (2021) The regulatory roles and mechanisms of the transcription factor FOXF2 in human diseases. PeerJ 9:e10845 https://doi.org/10.7717/peerj.10845
date submitted: 2020-07-16
date accepted: 2021-01-05
issued: 2021-03-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Qiong
author list: Agent
  family name: Li
  given name: Wei
author list: Agent
  family name: You
  given name: Chongge
doi: 10.7717/peerj.10845
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-02
copyright: ©2021 Wu et al.
attribution name: Wu et al.

Undercarboxylated osteocalcin inhibits the early differentiation of osteoclast mediated by Gprc6a
type: item
type: AcademicArticle
description: Osteocalcin (OCN) was the most abundant noncollagen protein and considered as an endocrine factor. However, the functions of Undercarboxylated osteocalcin (ucOCN) on osteoclast and bone resorption are not well understood. In the present study, preosteoclast RAW264.7 cells and bone marrow mononuclear cells (BMMs) were treated with ucOCN purified from prokaryotic bacteria. Our results showed that ucOCN attenuated the proliferation of RAW264.7 cells with a concentration dependant manner by MTS assay. Scrape wounding assay revealed the decreased motility of RAW264.7 cells after ucOCN treatment. RT-qPCR results manifested the inhibitory effects of ucOCN on the expression of osteoclastic marker genes in RAW264.7 cells during inducing differentiation of RANKL. It was also observed that ucOCN inhibited the formation of multinucleated cells from RAW264.7 cells and BMMs detected by TRAP staining. The number and area of bone resorb pits were also decreased after treatment with ucOCN during their osteoclast induction by toluidine blue staining. The formation and integrity of the osteoclast actin ring were impaired by ucOCN by immunofluorescent staining. Time dependant treatment of ucOCN during osteoclastic induction demonstrated the inhibitory effects mainly occurred at the early stage of osteoclastogenesis. Signaling analysis of luciferase activity of the CRE or SRE reporter and ERK1/2 phosphorylation showed the selective inhibitor or siRNA of Gprc6a (a presumptive ucOCN receptor) could attenuate the promotion of ucOCN on CRE-luciferase activity. Taken together, we provided the first evidence that ucOCN had negative effects on the early differentiation and bone resorption of osteoclasts via Gprc6a.
format: application/pdf
format: text/html
creator: Hailong Wang
creator: Jinqiao Li
creator: Zihan Xu
creator: Feng Wu
creator: Hongyu Zhang
creator: Chao Yang
creator: Jian Chen
creator: Bai Ding
creator: Xiukun Sui
creator: Zhifeng Guo
creator: Yinghui Li
creator: Zhongquan Dai
subject: Cell Biology
subject: Molecular Biology
subject: Orthopedics
description: doi:10.7717/peerj.10898
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Osteocalcin (OCN) was the most abundant noncollagen protein and considered as an endocrine factor. However, the functions of Undercarboxylated osteocalcin (ucOCN) on osteoclast and bone resorption are not well understood. In the present study, preosteoclast RAW264.7 cells and bone marrow mononuclear cells (BMMs) were treated with ucOCN purified from prokaryotic bacteria. Our results showed that ucOCN attenuated the proliferation of RAW264.7 cells with a concentration dependant manner by MTS assay. Scrape wounding assay revealed the decreased motility of RAW264.7 cells after ucOCN treatment. RT-qPCR results manifested the inhibitory effects of ucOCN on the expression of osteoclastic marker genes in RAW264.7 cells during inducing differentiation of RANKL. It was also observed that ucOCN inhibited the formation of multinucleated cells from RAW264.7 cells and BMMs detected by TRAP staining. The number and area of bone resorb pits were also decreased after treatment with ucOCN during their osteoclast induction by toluidine blue staining. The formation and integrity of the osteoclast actin ring were impaired by ucOCN by immunofluorescent staining. Time dependant treatment of ucOCN during osteoclastic induction demonstrated the inhibitory effects mainly occurred at the early stage of osteoclastogenesis. Signaling analysis of luciferase activity of the CRE or SRE reporter and ERK1/2 phosphorylation showed the selective inhibitor or siRNA of Gprc6a (a presumptive ucOCN receptor) could attenuate the promotion of ucOCN on CRE-luciferase activity. Taken together, we provided the first evidence that ucOCN had negative effects on the early differentiation and bone resorption of osteoclasts via Gprc6a.
bibliographic citation: Wang et al. (2021) Undercarboxylated osteocalcin inhibits the early differentiation of osteoclast mediated by Gprc6a. PeerJ 9:e10898 https://doi.org/10.7717/peerj.10898
date submitted: 2020-08-07
date accepted: 2021-01-13
issued: 2021-03-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hailong
author list: Agent
  family name: Li
  given name: Jinqiao
author list: Agent
  family name: Xu
  given name: Zihan
author list: Agent
  family name: Wu
  given name: Feng
author list: Agent
  family name: Zhang
  given name: Hongyu
author list: Agent
  family name: Yang
  given name: Chao
author list: Agent
  family name: Chen
  given name: Jian
author list: Agent
  family name: Ding
  given name: Bai
author list: Agent
  family name: Sui
  given name: Xiukun
author list: Agent
  family name: Guo
  given name: Zhifeng
author list: Agent
  family name: Li
  given name: Yinghui
author list: Agent
  family name: Dai
  given name: Zhongquan
doi: 10.7717/peerj.10898
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-02
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Taxonomic revision of the Malagasy Aphaenogaster swammerdami group (Hymenoptera: Formicidae)
type: item
type: AcademicArticle
description: Background Madagascar is famous for its extremely rich biodiversity; the island harbors predominantly endemic and threatened communities meriting special attention from biodiversity scientists. Continuing ongoing efforts to inventory the Malagasy ant fauna, we revise the species currently placed in the myrmicine genus Aphaenogaster Mayr. One species described from Madagascar, Aphaenogaster friederichsi Forel, is synonymized with the Palearctic A. subterranea Latreille syn. nov. This species is considered neither native to Madagascar nor established in the region. This revision focuses on the balance of species in the A. swammerdami group which are all endemic to Madagascar. Methods The diversity of the Malagasy Aphaenogaster fauna was assessed via application of multiple lines of evidence involving quantitative morphometric, qualitative morphological, and DNA sequence data. (1) Morphometric investigation was based on hypothesis-free Nest Centroid clustering (NC-clustering) combined with PArtitioning based on Recursive Thresholding (PART) to estimate the number of morphological clusters and determine the most probable boundaries between them. This protocol provides a repeatable and testable approach to find patterns in continuous morphometric data. Species boundaries and the reliability of morphological clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis (LDA). (2) Qualitative, external morphological characteristics (e.g., shape, coloration patterns, setae number) were subjectively evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. (3) Species delimitation analyses based on mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were carried out to test the putative species previously delimited by morphological and morphometric analyses. Results Five species can be inferred based on the integrated evaluation of multiple lines of evidence; o…
format: application/pdf
format: text/html
creator: Sandor Csősz
creator: Ana C. Loss
creator: Brian L. Fisher
subject: Biodiversity
subject: Entomology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10900
publisher: PeerJ Inc.
rights: © 2021 Csősz et al.
abstract: Background Madagascar is famous for its extremely rich biodiversity; the island harbors predominantly endemic and threatened communities meriting special attention from biodiversity scientists. Continuing ongoing efforts to inventory the Malagasy ant fauna, we revise the species currently placed in the myrmicine genus Aphaenogaster Mayr. One species described from Madagascar, Aphaenogaster friederichsi Forel, is synonymized with the Palearctic A. subterranea Latreille syn. nov. This species is considered neither native to Madagascar nor established in the region. This revision focuses on the balance of species in the A. swammerdami group which are all endemic to Madagascar. Methods The diversity of the Malagasy Aphaenogaster fauna was assessed via application of multiple lines of evidence involving quantitative morphometric, qualitative morphological, and DNA sequence data. (1) Morphometric investigation was based on hypothesis-free Nest Centroid clustering (NC-clustering) combined with PArtitioning based on Recursive Thresholding (PART) to estimate the number of morphological clusters and determine the most probable boundaries between them. This protocol provides a repeatable and testable approach to find patterns in continuous morphometric data. Species boundaries and the reliability of morphological clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis (LDA). (2) Qualitative, external morphological characteristics (e.g., shape, coloration patterns, setae number) were subjectively evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. (3) Species delimitation analyses based on mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were carried out to test the putative species previously delimited by morphological and morphometric analyses. Results Five species can be inferred based on the integrated evaluation of multiple lines of evidence; o…
bibliographic citation: Csősz et al. (2021) Taxonomic revision of the Malagasy Aphaenogaster swammerdami group (Hymenoptera: Formicidae). PeerJ 9:e10900 https://doi.org/10.7717/peerj.10900
date submitted: 2020-07-02
date accepted: 2021-01-13
issued: 2021-03-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Csősz
  given name: Sandor
author list: Agent
  family name: Loss
  given name: Ana C.
author list: Agent
  family name: Fisher
  given name: Brian L.
doi: 10.7717/peerj.10900
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-02
copyright: © 2021 Csősz et al.
attribution name: Csősz et al.

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