PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Multidimensional evaluation of the TRMM 3B43V7 satellite-based precipitation product in mainland China from 1998–2016
items: Upregulated expression of pyruvate kinase M2 mRNA predicts poor prognosis in lung adenocarcinoma
items: Single nucleotide polymorphism of MTHFR rs1801133 associated with elevated Hcy levels affects susceptibility to cerebral small vessel disease
items: Endoplasmic reticulum stress and the protein degradation system in ophthalmic diseases
items: Engrailed-2 promotes a malignant phenotype of esophageal squamous cell carcinoma through upregulating the expression of pro-oncogenic genes
items: Reassessment of the Triassic archosauriform Scleromochlus taylori: neither runner nor biped, but hopper
items: Mutant dlx3b disturbs normal tooth mineralization and bone formation in zebrafish
items: Invasive vegetation affects amphibian skin microbiota and body condition
items: The E2F family as potential biomarkers and therapeutic targets in colon cancer
items: Facilitating open-science with realistic fMRI simulation: validation and application

Multidimensional evaluation of the TRMM 3B43V7 satellite-based precipitation product in mainland China from 1998–2016
type: item
type: AcademicArticle
description: This study evaluates the applicability of the Tropical Rain Measurement Mission (TRMM) 3B43V7 product for use throughout mainland China. Four statistical metrics were used based on the observations made by rain gauges; these metrics were the correlation coefficient (R), the relative bias (RB), the root mean square error (RMSE) and Nash-Sutcliffe efficiency (NSE), and they were chosen to evaluate the performance of the 3B43V7 product at temporal and spatial scales. The results revealed that 3B43V7 performed satisfactorily on all timescales (R > 0.9 and NSE > 0.86); however, it overestimated the results when compared with the rain gauge observations in certain circumstances (RB = 9.7%). Monthly estimates from 3B43V7 were in agreement with rain gauge observations. 3B43V7 can effectively capture the seasonal patterns of precipitation characteristics over mainland China. However, 3B43V7 tends to register a greater overestimation of precipitation in the winter (RB = 14%) than in other seasons while showing greater consistency with the observations made by rain gauges during dry periods. The 3B43V7 product performs well in the eastern part of mainland China, while its performance is poor in the western part of mainland China. In terms of altitude, 3B43V7 performs satisfactorily in areas with moderate to low altitudes (when altitude < 3,500 m, R > 0.9, NSE > 0.8 and RB < 10.2%) but RB values increase with altitude. Overall, 3B43V7 had a favorable performance throughout mainland China.
format: application/pdf
format: text/html
creator: Ziteng Zhou
creator: Bin Guo
creator: Youzhe Su
creator: Zhongsheng Chen
creator: Juan Wang
subject: Natural Resource Management
subject: Food, Water and Energy Nexus
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.8615
publisher: PeerJ Inc.
rights: © 2020 Zhou et al.
abstract: This study evaluates the applicability of the Tropical Rain Measurement Mission (TRMM) 3B43V7 product for use throughout mainland China. Four statistical metrics were used based on the observations made by rain gauges; these metrics were the correlation coefficient (R), the relative bias (RB), the root mean square error (RMSE) and Nash-Sutcliffe efficiency (NSE), and they were chosen to evaluate the performance of the 3B43V7 product at temporal and spatial scales. The results revealed that 3B43V7 performed satisfactorily on all timescales (R > 0.9 and NSE > 0.86); however, it overestimated the results when compared with the rain gauge observations in certain circumstances (RB = 9.7%). Monthly estimates from 3B43V7 were in agreement with rain gauge observations. 3B43V7 can effectively capture the seasonal patterns of precipitation characteristics over mainland China. However, 3B43V7 tends to register a greater overestimation of precipitation in the winter (RB = 14%) than in other seasons while showing greater consistency with the observations made by rain gauges during dry periods. The 3B43V7 product performs well in the eastern part of mainland China, while its performance is poor in the western part of mainland China. In terms of altitude, 3B43V7 performs satisfactorily in areas with moderate to low altitudes (when altitude < 3,500 m, R > 0.9, NSE > 0.8 and RB < 10.2%) but RB values increase with altitude. Overall, 3B43V7 had a favorable performance throughout mainland China.
bibliographic citation: Zhou et al. (2020) Multidimensional evaluation of the TRMM 3B43V7 satellite-based precipitation product in mainland China from 1998–2016. PeerJ 8:e8615 https://doi.org/10.7717/peerj.8615
date submitted: 2019-09-26
date accepted: 2020-01-21
issued: 2020-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Ziteng
author list: Agent
  family name: Guo
  given name: Bin
author list: Agent
  family name: Su
  given name: Youzhe
author list: Agent
  family name: Chen
  given name: Zhongsheng
author list: Agent
  family name: Wang
  given name: Juan
doi: 10.7717/peerj.8615
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-20
copyright: ©2020 Zhou et al.
attribution name: Zhou et al.

Upregulated expression of pyruvate kinase M2 mRNA predicts poor prognosis in lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Pyruvate kinase M2 (PKM2) is critical regulator contributing to Warburg effect. However, the expression pattern and prognostic value of PKM2 remain unknown in lung adenocarcinoma (LUAD). The aim of this study is to clarify the prognostic value of PKM2 via intergrated bioinformatics analysis. Methods Firstly, mRNA expression levels of PKM2 in LUAD were systematically analyzed using the ONCOMINE and TCGA databases. Then, the association between PKM2 expression and clinical parameters was investigated by UALCAN. The Kaplan–Meier Plotter was used to assess the prognostic significance of PKM2. Finally, the relationship between PKM2 expression and its genetic and epigenetic changes was evaluated with MEXPRESS and MethHC database. Results Pooled analysis showed that PKM2 is frequently upregulated expression in LUAD. Subsequently, PKM2 expression was identified to be positively associated with tumor stage and lymph node metastasis and also strongly correlated with worse OS (P = 2.80e−14), PPS (P = 0.022), FP (P = 1.30e−6) and RFS (P = 3.41e−8). Importantly, our results demonstrated that over-expressed PKM2 is associated with PKM2 hypomethylation and copy number variations (CNVs). Conclusion This study confirms that over-expressed PKM2 in LUAD is associated with poor prognosis, suggesting that PKM2 might act as a promising prognostic biomarker and novel therapeutic target for LUAD.
format: application/pdf
format: text/html
creator: Guiping Wang
creator: Yingying Zhong
creator: Jiecong Liang
creator: Zhibin Li
creator: Yun Ye
subject: Bioinformatics
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.8625
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background Pyruvate kinase M2 (PKM2) is critical regulator contributing to Warburg effect. However, the expression pattern and prognostic value of PKM2 remain unknown in lung adenocarcinoma (LUAD). The aim of this study is to clarify the prognostic value of PKM2 via intergrated bioinformatics analysis. Methods Firstly, mRNA expression levels of PKM2 in LUAD were systematically analyzed using the ONCOMINE and TCGA databases. Then, the association between PKM2 expression and clinical parameters was investigated by UALCAN. The Kaplan–Meier Plotter was used to assess the prognostic significance of PKM2. Finally, the relationship between PKM2 expression and its genetic and epigenetic changes was evaluated with MEXPRESS and MethHC database. Results Pooled analysis showed that PKM2 is frequently upregulated expression in LUAD. Subsequently, PKM2 expression was identified to be positively associated with tumor stage and lymph node metastasis and also strongly correlated with worse OS (P = 2.80e−14), PPS (P = 0.022), FP (P = 1.30e−6) and RFS (P = 3.41e−8). Importantly, our results demonstrated that over-expressed PKM2 is associated with PKM2 hypomethylation and copy number variations (CNVs). Conclusion This study confirms that over-expressed PKM2 in LUAD is associated with poor prognosis, suggesting that PKM2 might act as a promising prognostic biomarker and novel therapeutic target for LUAD.
bibliographic citation: Wang et al. (2020) Upregulated expression of pyruvate kinase M2 mRNA predicts poor prognosis in lung adenocarcinoma. PeerJ 8:e8625 https://doi.org/10.7717/peerj.8625
date submitted: 2019-09-18
date accepted: 2020-01-23
issued: 2020-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Guiping
author list: Agent
  family name: Zhong
  given name: Yingying
author list: Agent
  family name: Liang
  given name: Jiecong
author list: Agent
  family name: Li
  given name: Zhibin
author list: Agent
  family name: Ye
  given name: Yun
doi: 10.7717/peerj.8625
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-20
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Single nucleotide polymorphism of MTHFR rs1801133 associated with elevated Hcy levels affects susceptibility to cerebral small vessel disease
type: item
type: AcademicArticle
description: Background Methylenetetrahydrofolate reductase (MTHFR) is indispensable for the conversion of homocysteine (Hcy) to methionine. The single nucleotide polymorphism (SNP) of MTHFR gene (rs1801133, C667T) is correlated with decreased enzyme activity that eventually results in elevated plasma Hcy levels. Hyperhomocysteinemia has been confirmed to be involved in the pathogenesis of stroke, cerebral small vessel disease (CSVD), various metabolic disorders and so on. However, the relationship between the MTHFR gene polymorphisms, Hcy, and CSVD has not been investigated. In this study, the relationship between SNPs of MTHFR gene and CSVD was determined after adjusting for cardiovascular risk factors, and the potential mechanism based on Hcy levels was explored. Methods A total of 163 consecutive CSVD patients were collected as the case group. In the corresponding period, 326 healthy people were selected as the control group, who were matched to these cases according to age (±2 years) and gender at a ratio of 2:1. SNPs of MTHFR rs1801133, rs1801131, rs2274976, rs4846048, rs4846049, rs13306561 and rs3737964, were genotyped with TaqMan Pre-Designed SNP Genotyping Assays. Plasma Hcy levels were detected using Hcy reagent through enzymatic cycling assay. Multivariate analysis was used to identify the SNPs associated with CSVD susceptibility. Plasma Hcy levels were compared between different genotypes. Results The MTHFR rs1801133 TT and CT genotype had increased risk for CSVD, and the OR was higher in the TT genotype than in the CT genotype (2.307 vs 1.473). The plasma Hcy levels of different genotypes showed the tendency of the TT genotype > CT genotype > CC genotype (19.91 ± 8.73 pg/ml vs 17.04 ± 5.68 pg/ml vs 14.96 ± 4.85 pg/ml). Conclusions The SNP of MTHFR rs1801133 was correlated with CSVD, and the TT and CT genotypes had increased risk for CSVD compared to the CC genotype. The potential mechanism was associated with elevated Hcy levels.
format: application/pdf
format: text/html
creator: Hongyu Yuan
creator: Man Fu
creator: Xianzhang Yang
creator: Kun Huang
creator: Xiaoyan Ren
subject: Molecular Biology
subject: Neurology
description: doi:10.7717/peerj.8627
publisher: PeerJ Inc.
rights: © 2020 Yuan et al.
abstract: Background Methylenetetrahydrofolate reductase (MTHFR) is indispensable for the conversion of homocysteine (Hcy) to methionine. The single nucleotide polymorphism (SNP) of MTHFR gene (rs1801133, C667T) is correlated with decreased enzyme activity that eventually results in elevated plasma Hcy levels. Hyperhomocysteinemia has been confirmed to be involved in the pathogenesis of stroke, cerebral small vessel disease (CSVD), various metabolic disorders and so on. However, the relationship between the MTHFR gene polymorphisms, Hcy, and CSVD has not been investigated. In this study, the relationship between SNPs of MTHFR gene and CSVD was determined after adjusting for cardiovascular risk factors, and the potential mechanism based on Hcy levels was explored. Methods A total of 163 consecutive CSVD patients were collected as the case group. In the corresponding period, 326 healthy people were selected as the control group, who were matched to these cases according to age (±2 years) and gender at a ratio of 2:1. SNPs of MTHFR rs1801133, rs1801131, rs2274976, rs4846048, rs4846049, rs13306561 and rs3737964, were genotyped with TaqMan Pre-Designed SNP Genotyping Assays. Plasma Hcy levels were detected using Hcy reagent through enzymatic cycling assay. Multivariate analysis was used to identify the SNPs associated with CSVD susceptibility. Plasma Hcy levels were compared between different genotypes. Results The MTHFR rs1801133 TT and CT genotype had increased risk for CSVD, and the OR was higher in the TT genotype than in the CT genotype (2.307 vs 1.473). The plasma Hcy levels of different genotypes showed the tendency of the TT genotype > CT genotype > CC genotype (19.91 ± 8.73 pg/ml vs 17.04 ± 5.68 pg/ml vs 14.96 ± 4.85 pg/ml). Conclusions The SNP of MTHFR rs1801133 was correlated with CSVD, and the TT and CT genotypes had increased risk for CSVD compared to the CC genotype. The potential mechanism was associated with elevated Hcy levels.
bibliographic citation: Yuan et al. (2020) Single nucleotide polymorphism of MTHFR rs1801133 associated with elevated Hcy levels affects susceptibility to cerebral small vessel disease. PeerJ 8:e8627 https://doi.org/10.7717/peerj.8627
date submitted: 2019-09-09
date accepted: 2020-01-23
issued: 2020-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Hongyu
author list: Agent
  family name: Fu
  given name: Man
author list: Agent
  family name: Yang
  given name: Xianzhang
author list: Agent
  family name: Huang
  given name: Kun
author list: Agent
  family name: Ren
  given name: Xiaoyan
doi: 10.7717/peerj.8627
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-20
copyright: ©2020 Yuan et al.
attribution name: Yuan et al.

Endoplasmic reticulum stress and the protein degradation system in ophthalmic diseases
type: item
type: AcademicArticle
description: Objective Endoplasmic reticulum (ER) stress is involved in the pathogenesis of various ophthalmic diseases, and ER stress-mediated degradation systems play an important role in maintaining ER homeostasis during ER stress. The purpose of this review is to explore the potential relationship between them and to find their equilibrium sites. Design This review illustrates the important role of reasonable regulation of the protein degradation system in ER stress-mediated ophthalmic diseases. There were 128 articles chosen for review in this study, and the keywords used for article research are ER stress, autophagy, UPS, ophthalmic disease, and ocular. Data sources The data are from Web of Science, PubMed, with no language restrictions from inception until 2019 Jul. Results The ubiquitin proteasome system (UPS) and autophagy are important degradation systems in ER stress. They can restore ER homeostasis, but if ER stress cannot be relieved in time, cell death may occur. However, they are not independent of each other, and the relationship between them is complementary. Therefore, we propose that ER stability can be achieved by adjusting the balance between them. Conclusion The degradation system of ER stress, UPS and autophagy are interrelated. Because an imbalance between the UPS and autophagy can cause cell death, regulating that balance may suppress ER stress and protect cells against pathological stress damage.
format: application/pdf
format: text/html
creator: Jing-Yao Song
creator: Xue-Guang Wang
creator: Zi-Yuan Zhang
creator: Lin Che
creator: Bin Fan
creator: Guang-Yu Li
subject: Cell Biology
subject: Ophthalmology
description: doi:10.7717/peerj.8638
publisher: PeerJ Inc.
rights: © 2020 Song et al.
abstract: Objective Endoplasmic reticulum (ER) stress is involved in the pathogenesis of various ophthalmic diseases, and ER stress-mediated degradation systems play an important role in maintaining ER homeostasis during ER stress. The purpose of this review is to explore the potential relationship between them and to find their equilibrium sites. Design This review illustrates the important role of reasonable regulation of the protein degradation system in ER stress-mediated ophthalmic diseases. There were 128 articles chosen for review in this study, and the keywords used for article research are ER stress, autophagy, UPS, ophthalmic disease, and ocular. Data sources The data are from Web of Science, PubMed, with no language restrictions from inception until 2019 Jul. Results The ubiquitin proteasome system (UPS) and autophagy are important degradation systems in ER stress. They can restore ER homeostasis, but if ER stress cannot be relieved in time, cell death may occur. However, they are not independent of each other, and the relationship between them is complementary. Therefore, we propose that ER stability can be achieved by adjusting the balance between them. Conclusion The degradation system of ER stress, UPS and autophagy are interrelated. Because an imbalance between the UPS and autophagy can cause cell death, regulating that balance may suppress ER stress and protect cells against pathological stress damage.
bibliographic citation: Song et al. (2020) Endoplasmic reticulum stress and the protein degradation system in ophthalmic diseases. PeerJ 8:e8638 https://doi.org/10.7717/peerj.8638
date submitted: 2019-10-08
date accepted: 2020-01-26
issued: 2020-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Jing-Yao
author list: Agent
  family name: Wang
  given name: Xue-Guang
author list: Agent
  family name: Zhang
  given name: Zi-Yuan
author list: Agent
  family name: Che
  given name: Lin
author list: Agent
  family name: Fan
  given name: Bin
author list: Agent
  family name: Li
  given name: Guang-Yu
doi: 10.7717/peerj.8638
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-20
copyright: ©2020 Song et al.
attribution name: Song et al.

Engrailed-2 promotes a malignant phenotype of esophageal squamous cell carcinoma through upregulating the expression of pro-oncogenic genes
type: item
type: AcademicArticle
description: Background A number of homeobox genes have been implicated in the development of various cancers. However, the role of engrailed 2 (EN2), a member of the homeobox gene superfamily, in esophageal squamous cell carcinoma (ESCC) remains unknown. Methods The expression of EN2 was examined using quantitative real-time PCR and immunohistochemistry. A stable cell line was established to express exogenous EN2 using a lentivirus system. The malignant phenotype was analyzed with proliferation, clonogenicity, wound-healing and invasion assays. The CRISPR/Cas9 system was adopted to deplete endogenous EN2. RNA profiling was performed using gene expression microarray. The ShRNA-mediated method was used to knock down the expression of SPARC. The structure-function relationship was determined using site-directed mutagenesis. Results EN2 is highly expressed in ESCC. The malignant phenotype of the ESCC cell line was amplified by an overexpression of EN2 but was attenuated by a disruption of EN2. RNA profiling analysis revealed that distinct sets of genes were modulated by the expression of EN2 in various ESCC cell lines and oncogenes were among these. EN2 greatly increased the expression of SPARC in Eca109. Site-directed mutagenesis revealed that the induction of SPARC was closely correlated with the protumor function of EN2. ShRNA-mediated knockdown of SPARC attenuated the malignant phenotype of EN2-infected cells. These data suggest that SPARC is crucial for mediating the protumor function of EN2. Discussion EN2 has an oncogenic function in ESCC that is mediated by upregulating the expression of pro-oncogenic genes downstream. EN2 may potentially act as a diagnostic marker or therapeutic target for ESCC treatment in the future.
format: application/pdf
format: text/html
creator: Yong Cao
creator: Xiaoyan Wang
creator: Li Tang
creator: Yan Li
creator: Xueqin Song
creator: Xu Liu
creator: Mingying Li
creator: Feng Chen
creator: Haisu Wan
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.8662
publisher: PeerJ Inc.
rights: © 2020 Cao et al.
abstract: Background A number of homeobox genes have been implicated in the development of various cancers. However, the role of engrailed 2 (EN2), a member of the homeobox gene superfamily, in esophageal squamous cell carcinoma (ESCC) remains unknown. Methods The expression of EN2 was examined using quantitative real-time PCR and immunohistochemistry. A stable cell line was established to express exogenous EN2 using a lentivirus system. The malignant phenotype was analyzed with proliferation, clonogenicity, wound-healing and invasion assays. The CRISPR/Cas9 system was adopted to deplete endogenous EN2. RNA profiling was performed using gene expression microarray. The ShRNA-mediated method was used to knock down the expression of SPARC. The structure-function relationship was determined using site-directed mutagenesis. Results EN2 is highly expressed in ESCC. The malignant phenotype of the ESCC cell line was amplified by an overexpression of EN2 but was attenuated by a disruption of EN2. RNA profiling analysis revealed that distinct sets of genes were modulated by the expression of EN2 in various ESCC cell lines and oncogenes were among these. EN2 greatly increased the expression of SPARC in Eca109. Site-directed mutagenesis revealed that the induction of SPARC was closely correlated with the protumor function of EN2. ShRNA-mediated knockdown of SPARC attenuated the malignant phenotype of EN2-infected cells. These data suggest that SPARC is crucial for mediating the protumor function of EN2. Discussion EN2 has an oncogenic function in ESCC that is mediated by upregulating the expression of pro-oncogenic genes downstream. EN2 may potentially act as a diagnostic marker or therapeutic target for ESCC treatment in the future.
bibliographic citation: Cao et al. (2020) Engrailed-2 promotes a malignant phenotype of esophageal squamous cell carcinoma through upregulating the expression of pro-oncogenic genes. PeerJ 8:e8662 https://doi.org/10.7717/peerj.8662
date submitted: 2019-10-06
date accepted: 2020-01-29
issued: 2020-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Yong
author list: Agent
  family name: Wang
  given name: Xiaoyan
author list: Agent
  family name: Tang
  given name: Li
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: Song
  given name: Xueqin
author list: Agent
  family name: Liu
  given name: Xu
author list: Agent
  family name: Li
  given name: Mingying
author list: Agent
  family name: Chen
  given name: Feng
author list: Agent
  family name: Wan
  given name: Haisu
doi: 10.7717/peerj.8662
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-20
copyright: © 2020 Cao et al.
attribution name: Cao et al.

Reassessment of the Triassic archosauriform Scleromochlus taylori: neither runner nor biped, but hopper
type: item
type: AcademicArticle
description: The six known specimens of Scleromochlus taylori and casts made from their negative impressions were examined to reassess the osteological evidence that has been used to interpret Scleromochlus’s locomotion and phylogenetic relationships. It was found that the trunk was dorsoventrally compressed. The upper temporal fenestra was on the lateral surface of skull and two-thirds the size of the lower, the jaw joint posteriorly placed with short retroarticular process, and teeth short and subconical, but no evidence of external nares or antorbital fossae was found. The posterior trunk was covered with ~20 rows of closely spaced transversely elongate dorsal osteoderms. The coracoid was robust and elongate. The acetabulum was imperforate and the femoral head hemispherical and only weakly inturned such that the hip joint was unsuited to swinging in a parasagittal plane. The presence of four distal tarsals is confirmed. The marked disparity of tibial and fibular shaft diameters and of proximal tarsal dimensions indicates that the larger proximal tarsal is the astragalus and the significantly smaller tarsal is the calcaneum. The astragalus and calcaneum bear little resemblance to those of Lagosuchus, and the prominent calcaneal tuber confirms that the ankle was crurotarsal. There is no evidence that preserved body and limb postures are unnatural, and most specimens are preserved in what is interpreted as a typical sprawling resting pose. A principal component analysis of skeletal measurements of Scleromochlus and other vertebrates of known locomotor type found Scleromochlus to plot with frogs, and that finding combined with skeletal morphology suggests Scleromochlus was a sprawling quadrupedal hopper. Phylogenetic analyses found that Scleromochlus was not an ornithodiran, but was either within the Doswelliidae or outside the clade consisting of the most recent common ancestor of the Erythrosuchidae and Archosauria and all its descendants.
format: application/pdf
format: text/html
creator: S. Christopher Bennett
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.8418
publisher: PeerJ Inc.
rights: © 2020 Bennett
abstract: The six known specimens of Scleromochlus taylori and casts made from their negative impressions were examined to reassess the osteological evidence that has been used to interpret Scleromochlus’s locomotion and phylogenetic relationships. It was found that the trunk was dorsoventrally compressed. The upper temporal fenestra was on the lateral surface of skull and two-thirds the size of the lower, the jaw joint posteriorly placed with short retroarticular process, and teeth short and subconical, but no evidence of external nares or antorbital fossae was found. The posterior trunk was covered with ~20 rows of closely spaced transversely elongate dorsal osteoderms. The coracoid was robust and elongate. The acetabulum was imperforate and the femoral head hemispherical and only weakly inturned such that the hip joint was unsuited to swinging in a parasagittal plane. The presence of four distal tarsals is confirmed. The marked disparity of tibial and fibular shaft diameters and of proximal tarsal dimensions indicates that the larger proximal tarsal is the astragalus and the significantly smaller tarsal is the calcaneum. The astragalus and calcaneum bear little resemblance to those of Lagosuchus, and the prominent calcaneal tuber confirms that the ankle was crurotarsal. There is no evidence that preserved body and limb postures are unnatural, and most specimens are preserved in what is interpreted as a typical sprawling resting pose. A principal component analysis of skeletal measurements of Scleromochlus and other vertebrates of known locomotor type found Scleromochlus to plot with frogs, and that finding combined with skeletal morphology suggests Scleromochlus was a sprawling quadrupedal hopper. Phylogenetic analyses found that Scleromochlus was not an ornithodiran, but was either within the Doswelliidae or outside the clade consisting of the most recent common ancestor of the Erythrosuchidae and Archosauria and all its descendants.
bibliographic citation: Bennett (2020) Reassessment of the Triassic archosauriform Scleromochlus taylori: neither runner nor biped, but hopper. PeerJ 8:e8418 https://doi.org/10.7717/peerj.8418
date submitted: 2019-07-02
date accepted: 2019-12-17
issued: 2020-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bennett
  given name: S. Christopher
doi: 10.7717/peerj.8418
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-19
copyright: © 2020 Bennett
attribution name: Bennett

Mutant dlx3b disturbs normal tooth mineralization and bone formation in zebrafish
type: item
type: AcademicArticle
description: Background Tricho-dento-osseous (TDO) syndrome is an autosomal dominant disorder characterized by anomalies in hair, teeth and bone (OMIM190320). Various mutations of Distal-Less 3 (DLX3) gene are found to be responsible for human TDO. The aim of this study was to investigate effects of DLX3 on tooth and bone development using a zebrafish model. Methods The dlx3b mutant zebrafish lines were established using the gene targeting tool transcription activator-like effector nuclease (TALEN). Micro-computed tomography was used to render the three-dimensional skeletal structures of mutant fishes. The pharyngeal bone along with connected teeth was isolated and stained by Alizarine Red S, then observed under stereomicroscope. Scanning electron microscopy (SEM) and energy dispersive spectrometer (EDS) were used to examine the tooth surface morphology and mineral composition. Quantitative real-time PCR was used to analyze gene expression. Results A moderate curvature of the spine toward the dorsal side was found at the early larval stages, appearing in 86 out of 100 larvae in dlx3b-/- group as compared to 3 out of 99 in the dlx3b+/+ group. At the adult stage, three of the thirty dlx3b-/- homozygotes exhibited prominent abnormal curvature in the spine. SEM revealed morphological surface changes in pharyngeal teeth enameloid, accompanied by a decrease in the mineral content detected by EDS. Furthermore, specific secretory calcium-binding phosphoprotein (SCPP) genes, including odam, scpp9, spp1, scpp1, and scpp5 were significantly downregulated in dlx3b mutants. Conclusion The findings of this study suggest that dlx3b is critical for enamel mineralization and bone formation in zebrafish. Moreover, the discovery of the downregulation of SCPP genes in dlx3b mutants sheds new light on the molecular mechanisms underlying TDO syndrome.
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format: text/html
creator: Liping Pang
creator: Zhichun Zhang
creator: Yan Shen
creator: Zhenchao Cheng
creator: Xuejun Gao
creator: Bo Zhang
creator: Xiaoyan Wang
creator: Hua Tian
subject: Developmental Biology
subject: Dentistry
description: doi:10.7717/peerj.8515
publisher: PeerJ Inc.
rights: © 2020 Pang et al.
abstract: Background Tricho-dento-osseous (TDO) syndrome is an autosomal dominant disorder characterized by anomalies in hair, teeth and bone (OMIM190320). Various mutations of Distal-Less 3 (DLX3) gene are found to be responsible for human TDO. The aim of this study was to investigate effects of DLX3 on tooth and bone development using a zebrafish model. Methods The dlx3b mutant zebrafish lines were established using the gene targeting tool transcription activator-like effector nuclease (TALEN). Micro-computed tomography was used to render the three-dimensional skeletal structures of mutant fishes. The pharyngeal bone along with connected teeth was isolated and stained by Alizarine Red S, then observed under stereomicroscope. Scanning electron microscopy (SEM) and energy dispersive spectrometer (EDS) were used to examine the tooth surface morphology and mineral composition. Quantitative real-time PCR was used to analyze gene expression. Results A moderate curvature of the spine toward the dorsal side was found at the early larval stages, appearing in 86 out of 100 larvae in dlx3b-/- group as compared to 3 out of 99 in the dlx3b+/+ group. At the adult stage, three of the thirty dlx3b-/- homozygotes exhibited prominent abnormal curvature in the spine. SEM revealed morphological surface changes in pharyngeal teeth enameloid, accompanied by a decrease in the mineral content detected by EDS. Furthermore, specific secretory calcium-binding phosphoprotein (SCPP) genes, including odam, scpp9, spp1, scpp1, and scpp5 were significantly downregulated in dlx3b mutants. Conclusion The findings of this study suggest that dlx3b is critical for enamel mineralization and bone formation in zebrafish. Moreover, the discovery of the downregulation of SCPP genes in dlx3b mutants sheds new light on the molecular mechanisms underlying TDO syndrome.
bibliographic citation: Pang et al. (2020) Mutant dlx3b disturbs normal tooth mineralization and bone formation in zebrafish. PeerJ 8:e8515 https://doi.org/10.7717/peerj.8515
date submitted: 2019-06-25
date accepted: 2020-01-05
issued: 2020-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pang
  given name: Liping
author list: Agent
  family name: Zhang
  given name: Zhichun
author list: Agent
  family name: Shen
  given name: Yan
author list: Agent
  family name: Cheng
  given name: Zhenchao
author list: Agent
  family name: Gao
  given name: Xuejun
author list: Agent
  family name: Zhang
  given name: Bo
author list: Agent
  family name: Wang
  given name: Xiaoyan
author list: Agent
  family name: Tian
  given name: Hua
doi: 10.7717/peerj.8515
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-19
copyright: ©2020 Pang et al.
attribution name: Pang et al.

Invasive vegetation affects amphibian skin microbiota and body condition
type: item
type: AcademicArticle
description: Invasive plants are major drivers of habitat modification and the scale of their impact is increasing globally as anthropogenic activities facilitate their spread. In California, an invasive plant genus of great concern is Eucalyptus. Eucalyptus leaves can alter soil chemistry and negatively affect underground macro- and microbial communities. Amphibians serve as excellent models to evaluate the effect of Eucalyptus invasion on ground-dwelling species as they predate on soil arthropods and incorporate soil microbes into their microbiotas. The skin microbiota is particularly important to amphibian health, suggesting that invasive plant species could ultimately affect amphibian populations. To investigate the potential for invasive vegetation to induce changes in microbial communities, we sampled microbial communities in the soil and on the skin of local amphibians. Specifically, we compared Batrachoseps attenuatus skin microbiomes in both Eucalyptus globulus (Myrtaceae) and native Quercus agriflolia (Fagaceae) dominated forests in the San Francisco Bay Area. We determined whether changes in microbial diversity and composition in both soil and Batrachoseps attenuatus skin were associated with dominant vegetation type. To evaluate animal health across vegetation types, we compared Batrachoseps attenuatus body condition and the presence/absence of the amphibian skin pathogen Batrachochytrium dendrobatidis. We found that Eucalyptus invasion had no measurable effect on soil microbial community diversity and a relatively small effect (compared to the effect of site identity) on community structure in the microhabitats sampled. In contrast, our results show that Batrachoseps attenuatus skin microbiota diversity was greater in Quercus dominated habitats. One amplicon sequence variant identified in the family Chlamydiaceae was observed in higher relative abundance among salamanders sampled in Eucalyptus dominated habitats. We also observed that Batrachoseps attenuatus body co…
format: application/pdf
format: text/html
creator: Obed Hernández-Gómez
creator: Allison Q. Byrne
creator: Alex R. Gunderson
creator: Thomas S. Jenkinson
creator: Clay F. Noss
creator: Andrew P. Rothstein
creator: Molly C. Womack
creator: Erica B. Rosenblum
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.8549
publisher: PeerJ Inc.
rights: © 2020 Hernández-Gómez et al.
abstract: Invasive plants are major drivers of habitat modification and the scale of their impact is increasing globally as anthropogenic activities facilitate their spread. In California, an invasive plant genus of great concern is Eucalyptus. Eucalyptus leaves can alter soil chemistry and negatively affect underground macro- and microbial communities. Amphibians serve as excellent models to evaluate the effect of Eucalyptus invasion on ground-dwelling species as they predate on soil arthropods and incorporate soil microbes into their microbiotas. The skin microbiota is particularly important to amphibian health, suggesting that invasive plant species could ultimately affect amphibian populations. To investigate the potential for invasive vegetation to induce changes in microbial communities, we sampled microbial communities in the soil and on the skin of local amphibians. Specifically, we compared Batrachoseps attenuatus skin microbiomes in both Eucalyptus globulus (Myrtaceae) and native Quercus agriflolia (Fagaceae) dominated forests in the San Francisco Bay Area. We determined whether changes in microbial diversity and composition in both soil and Batrachoseps attenuatus skin were associated with dominant vegetation type. To evaluate animal health across vegetation types, we compared Batrachoseps attenuatus body condition and the presence/absence of the amphibian skin pathogen Batrachochytrium dendrobatidis. We found that Eucalyptus invasion had no measurable effect on soil microbial community diversity and a relatively small effect (compared to the effect of site identity) on community structure in the microhabitats sampled. In contrast, our results show that Batrachoseps attenuatus skin microbiota diversity was greater in Quercus dominated habitats. One amplicon sequence variant identified in the family Chlamydiaceae was observed in higher relative abundance among salamanders sampled in Eucalyptus dominated habitats. We also observed that Batrachoseps attenuatus body co…
bibliographic citation: Hernández-Gómez et al. (2020) Invasive vegetation affects amphibian skin microbiota and body condition. PeerJ 8:e8549 https://doi.org/10.7717/peerj.8549
date submitted: 2019-10-17
date accepted: 2020-01-12
issued: 2020-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernández-Gómez
  given name: Obed
author list: Agent
  family name: Byrne
  given name: Allison Q.
author list: Agent
  family name: Gunderson
  given name: Alex R.
author list: Agent
  family name: Jenkinson
  given name: Thomas S.
author list: Agent
  family name: Noss
  given name: Clay F.
author list: Agent
  family name: Rothstein
  given name: Andrew P.
author list: Agent
  family name: Womack
  given name: Molly C.
author list: Agent
  family name: Rosenblum
  given name: Erica B.
doi: 10.7717/peerj.8549
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-19
copyright: © 2020 Hernández-Gómez et al.
attribution name: Hernández-Gómez et al.

The E2F family as potential biomarkers and therapeutic targets in colon cancer
type: item
type: AcademicArticle
description: Background The E2F family is a group of genes encoding a series of transcription factors in higher eukaryotes and participating in the regulation of cell cycle and DNA synthesis in mammals. This study was designed to investigate the role of E2F family in colon cancer. Methods In this study, the transcriptional levels of E2F1-8 in patients with colon cancer from GEPIA was examined. Meanwhile, the immunohistochemical data of the eight genes were also obtained in the The Human Protein Atlas website. Additionally, we re-identified the mRNA expression levels of these genes via real time PCR. Furthermore, the association between the levels of E2F family and stage plot as wells overall survival of patients with colon cancer were analyzed. Results We found that the mRNA and protein levels of E2F1, E2F2, E3F3, E2F5, E2F7 and E2F8 were significantly higher in colon cancer tissues than in normal colon tissues while the expression levels of E2F4 and E2F6 displayed no significant difference between colon cancer tissues and normal tissues. Additionally, E2F3, E2F4, E2F7 and E2F8 were significantly associated with the stages of colon cancer. The Kaplan-Meier Plotter showed that the high levels of E2F3 conferred a worse overall survival and disease free survival of patients with colon cancer. Also, high levels of E2F4 resulted in a worse overall survival. Conclusion Our study implied that E2F3, E2F4, E2F7 and E2F8 are potential targets of precision therapy for patients with colon cancer while E2F1, E2F2, E3F3, E2F5, E2F7 and E2F8 are potential biomarkers for the diagnosis of colon cancer.
format: application/pdf
format: text/html
creator: Haibo Yao
creator: Fang Lu
creator: Yanfei Shao
subject: Bioinformatics
subject: Oncology
description: doi:10.7717/peerj.8562
publisher: PeerJ Inc.
rights: © 2020 Yao et al.
abstract: Background The E2F family is a group of genes encoding a series of transcription factors in higher eukaryotes and participating in the regulation of cell cycle and DNA synthesis in mammals. This study was designed to investigate the role of E2F family in colon cancer. Methods In this study, the transcriptional levels of E2F1-8 in patients with colon cancer from GEPIA was examined. Meanwhile, the immunohistochemical data of the eight genes were also obtained in the The Human Protein Atlas website. Additionally, we re-identified the mRNA expression levels of these genes via real time PCR. Furthermore, the association between the levels of E2F family and stage plot as wells overall survival of patients with colon cancer were analyzed. Results We found that the mRNA and protein levels of E2F1, E2F2, E3F3, E2F5, E2F7 and E2F8 were significantly higher in colon cancer tissues than in normal colon tissues while the expression levels of E2F4 and E2F6 displayed no significant difference between colon cancer tissues and normal tissues. Additionally, E2F3, E2F4, E2F7 and E2F8 were significantly associated with the stages of colon cancer. The Kaplan-Meier Plotter showed that the high levels of E2F3 conferred a worse overall survival and disease free survival of patients with colon cancer. Also, high levels of E2F4 resulted in a worse overall survival. Conclusion Our study implied that E2F3, E2F4, E2F7 and E2F8 are potential targets of precision therapy for patients with colon cancer while E2F1, E2F2, E3F3, E2F5, E2F7 and E2F8 are potential biomarkers for the diagnosis of colon cancer.
bibliographic citation: Yao et al. (2020) The E2F family as potential biomarkers and therapeutic targets in colon cancer. PeerJ 8:e8562 https://doi.org/10.7717/peerj.8562
date submitted: 2019-07-08
date accepted: 2020-01-13
issued: 2020-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Haibo
author list: Agent
  family name: Lu
  given name: Fang
author list: Agent
  family name: Shao
  given name: Yanfei
doi: 10.7717/peerj.8562
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-19
copyright: ©2020 Yao et al.
attribution name: Yao et al.

Facilitating open-science with realistic fMRI simulation: validation and application
type: item
type: AcademicArticle
description: With advances in methods for collecting and analyzing fMRI data, there is a concurrent need to understand how to reliably evaluate and optimally use these methods. Simulations of fMRI data can aid in both the evaluation of complex designs and the analysis of data. We present fmrisim, a new Python package for standardized, realistic simulation of fMRI data. This package is part of BrainIAK: a recently released open-source Python toolbox for advanced neuroimaging analyses. We describe how to use fmrisim to extract noise properties from real fMRI data and then create a synthetic dataset with matched noise properties and a user-specified signal. We validate the noise generated by fmrisim to show that it can approximate the noise properties of real data. We further show how fmrisim can help researchers find the optimal design in terms of power. The fmrisim package holds promise for improving the design of fMRI experiments, which may facilitate both the pre-registration of such experiments as well as the analysis of fMRI data.
format: application/pdf
format: text/html
creator: Cameron T. Ellis
creator: Christopher Baldassano
creator: Anna C. Schapiro
creator: Ming Bo Cai
creator: Jonathan D. Cohen
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8564
publisher: PeerJ Inc.
rights: © 2020 Ellis et al.
abstract: With advances in methods for collecting and analyzing fMRI data, there is a concurrent need to understand how to reliably evaluate and optimally use these methods. Simulations of fMRI data can aid in both the evaluation of complex designs and the analysis of data. We present fmrisim, a new Python package for standardized, realistic simulation of fMRI data. This package is part of BrainIAK: a recently released open-source Python toolbox for advanced neuroimaging analyses. We describe how to use fmrisim to extract noise properties from real fMRI data and then create a synthetic dataset with matched noise properties and a user-specified signal. We validate the noise generated by fmrisim to show that it can approximate the noise properties of real data. We further show how fmrisim can help researchers find the optimal design in terms of power. The fmrisim package holds promise for improving the design of fMRI experiments, which may facilitate both the pre-registration of such experiments as well as the analysis of fMRI data.
bibliographic citation: Ellis et al. (2020) Facilitating open-science with realistic fMRI simulation: validation and application. PeerJ 8:e8564 https://doi.org/10.7717/peerj.8564
date submitted: 2019-10-16
date accepted: 2020-01-14
issued: 2020-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ellis
  given name: Cameron T.
author list: Agent
  family name: Baldassano
  given name: Christopher
author list: Agent
  family name: Schapiro
  given name: Anna C.
author list: Agent
  family name: Cai
  given name: Ming Bo
author list: Agent
  family name: Cohen
  given name: Jonathan D.
doi: 10.7717/peerj.8564
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-19
copyright: ©2020 Ellis et al.
attribution name: Ellis et al.

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