PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The regulating effects and mechanism of biochar and maifanite on copper and cadmium in a polluted soil-Lolium perenne L. system
items: Therapeutic effects of astragaloside IV and Astragalus spinosus saponins against bisphenol A-induced neurotoxicity and DNA damage in rats
items: Designing of the N-ethyl-4-(pyridin-4-yl)benzamide based potent ROCK1 inhibitors using docking, molecular dynamics, and 3D-QSAR
items: Klebsiella variicola improves the antioxidant ability of maize seedlings under saline-alkali stress
items: Comparative transcriptome analysis of R3a and Avr3a-mediated defense responses in transgenic tomato
items: Snakes on an African plain: the radiation of Crotaphopeltis and Philothamnus into open habitat (Serpentes: Colubridae)
items: Identification of a circRNA-miRNA-mRNA regulatory network for exploring novel therapeutic options for glioma
items: IdentPMP: identification of moonlighting proteins in plants using sequence-based learning models
items: Identification of miRNA-target gene regulatory networks in liver fibrosis based on bioinformatics analysis
items: A new Andean treefrog (Amphibia: Hyloscirtus bogotensis group) from Ecuador: an example of community involvement for conservation

The regulating effects and mechanism of biochar and maifanite on copper and cadmium in a polluted soil-Lolium perenne L. system
type: item
type: AcademicArticle
description: Arable land polluted by copper (Cu) and cadmium (Cd) is a widespread problem. The use of biochar and/or clay mineral as a soil amendment can effectively solidify heavy metals in the soil. We applied biochar (BC), iron modified biochar (Fe-BC), maifanite (MF, a kind of clay minerals), a combination of BC with MF (BC:MF), and Fe-BC with MF (Fe-BC:MF) at a 2 wt % dose as soil amendments to study their ability to prevent Cu and Cd from accumulating in ryegrass (Lolium perenne L.). We found that after 90 days of cultivation, the Cd and Cu content both significantly decreased in ryegrass shoots from 2.06 and 209.3 mg kg−1 (control) to 1.44–2.01 and 51.50–70.92 mg kg−1, respectively, across treatments (p < 0.05). Similarly, the bioconcentration factor (BCF) for Cd/Cu was significantly smaller (P < 0.05) in all amendments versus control soil. This trend differed among the shoot, BCF, and transportation factor (TF). Combining BC:MF or Fe-BC:MF did not significantly improve the Cd/Cu stabilization in the soil compared to the corresponding single amendment (p > 0.05). Our adsorption balance experiment showed that BC, Fe-BC, and MF physically and chemically adsorbed Cd and Cu by complexation with functional groups (mesoporous nanomaterials) whose porosity measurements ranged from 0.68 to 78.57 m2 g−1. Furthermore, the amorphous crystalline iron oxide binding Cd and Cu was the key to immobilizing these metals in the soil. The amendments applied in our study show promise for enhancing immobilization of Cu and Cd in contaminated paddy soils.
format: application/pdf
format: text/html
creator: Yuan Ding
creator: Weiya Wang
creator: Shiying Ao
subject: Environmental Sciences
subject: Plant Science
subject: Soil Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.11921
publisher: PeerJ Inc.
rights: © 2021 Ding et al.
abstract: Arable land polluted by copper (Cu) and cadmium (Cd) is a widespread problem. The use of biochar and/or clay mineral as a soil amendment can effectively solidify heavy metals in the soil. We applied biochar (BC), iron modified biochar (Fe-BC), maifanite (MF, a kind of clay minerals), a combination of BC with MF (BC:MF), and Fe-BC with MF (Fe-BC:MF) at a 2 wt % dose as soil amendments to study their ability to prevent Cu and Cd from accumulating in ryegrass (Lolium perenne L.). We found that after 90 days of cultivation, the Cd and Cu content both significantly decreased in ryegrass shoots from 2.06 and 209.3 mg kg−1 (control) to 1.44–2.01 and 51.50–70.92 mg kg−1, respectively, across treatments (p < 0.05). Similarly, the bioconcentration factor (BCF) for Cd/Cu was significantly smaller (P < 0.05) in all amendments versus control soil. This trend differed among the shoot, BCF, and transportation factor (TF). Combining BC:MF or Fe-BC:MF did not significantly improve the Cd/Cu stabilization in the soil compared to the corresponding single amendment (p > 0.05). Our adsorption balance experiment showed that BC, Fe-BC, and MF physically and chemically adsorbed Cd and Cu by complexation with functional groups (mesoporous nanomaterials) whose porosity measurements ranged from 0.68 to 78.57 m2 g−1. Furthermore, the amorphous crystalline iron oxide binding Cd and Cu was the key to immobilizing these metals in the soil. The amendments applied in our study show promise for enhancing immobilization of Cu and Cd in contaminated paddy soils.
bibliographic citation: Ding et al. (2021) The regulating effects and mechanism of biochar and maifanite on copper and cadmium in a polluted soil-Lolium perenne L. system. PeerJ 9:e11921 https://doi.org/10.7717/peerj.11921
date submitted: 2021-03-05
date accepted: 2021-07-16
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ding
  given name: Yuan
author list: Agent
  family name: Wang
  given name: Weiya
author list: Agent
  family name: Ao
  given name: Shiying
doi: 10.7717/peerj.11921
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: ©2021 Ding et al.
attribution name: Ding et al.

Therapeutic effects of astragaloside IV and Astragalus spinosus saponins against bisphenol A-induced neurotoxicity and DNA damage in rats
type: item
type: AcademicArticle
description: Background Bisphenol A (BPA) is an endocrine disruptor to which humans are often subjected during daily life. This study aimed to investigate the ameliorative effect of astragaloside IV (ASIV) or saponins extracted from Astragalus spinosus (A. spinosus) against DNA damage and neurotoxic effects induced by BPA in prefrontal cortex (PFC), hippocampal and striatal brain regions of developing male rats. Materials and Methods Juvenile PND20 (pre-weaning; age of 20 days) male Sprague Dawley rats were randomly and equally divided into four groups: control, BPA, BPA+ASIV and BPA+A. spinosus saponins groups. Bisphenol A (125 mg/kg/day) was administrated orally to male rats from day 20 (BPA group) and along with ASIV (80 mg/kg/day) (BPA+ASIV group) or A. spinosus saponin (100 mg/kg/day) (BPA+ A. spinosus saponins group) from day 50 to adult age day 117. Results Increased level of nitric oxide (NO) and decreased level of glutamate (Glu), glutamine (Gln), glutaminase (GA) and glutamine synthetase (GS) were observed in the brain regions of BPA treated rats compared with the control. On the other hand, co-administration of ASIV or A. spinosus saponin with BPA considerably improved levels of these neurochemicals. The current study also revealed restoration of the level of brain derived neurotrophic factor (BDNF) and N-methyl-D-aspartate receptors (NR2A and NR2B) gene expression in BPA+ ASIV and BPA+A. spinosus saponins groups. The co-treatment of BPA group with ASIV or A. spinosus saponin significantly reduced the values of comet parameters as well as the intensity of estrogen receptors (ERs) immunoreactive cells and improved the histological alterations induced by BPA in different brain regions. Conclusion It could be concluded that ASIV or A. spinosus saponins has a promising role in modulating the neurotoxicity and DNA damage elicited by BPA.
format: application/pdf
format: text/html
creator: Amina E. Essawy
creator: Heba-Tallah Abd Elrahim Abd Elkader
creator: Omaima A. Khamiss
creator: Saber Mohamed Eweda
creator: Heba Mohamed Abdou
subject: Biochemistry
subject: Molecular Biology
subject: Neuroscience
subject: Toxicology
subject: Histology
description: doi:10.7717/peerj.11930
publisher: PeerJ Inc.
rights: © 2021 Essawy et al.
abstract: Background Bisphenol A (BPA) is an endocrine disruptor to which humans are often subjected during daily life. This study aimed to investigate the ameliorative effect of astragaloside IV (ASIV) or saponins extracted from Astragalus spinosus (A. spinosus) against DNA damage and neurotoxic effects induced by BPA in prefrontal cortex (PFC), hippocampal and striatal brain regions of developing male rats. Materials and Methods Juvenile PND20 (pre-weaning; age of 20 days) male Sprague Dawley rats were randomly and equally divided into four groups: control, BPA, BPA+ASIV and BPA+A. spinosus saponins groups. Bisphenol A (125 mg/kg/day) was administrated orally to male rats from day 20 (BPA group) and along with ASIV (80 mg/kg/day) (BPA+ASIV group) or A. spinosus saponin (100 mg/kg/day) (BPA+ A. spinosus saponins group) from day 50 to adult age day 117. Results Increased level of nitric oxide (NO) and decreased level of glutamate (Glu), glutamine (Gln), glutaminase (GA) and glutamine synthetase (GS) were observed in the brain regions of BPA treated rats compared with the control. On the other hand, co-administration of ASIV or A. spinosus saponin with BPA considerably improved levels of these neurochemicals. The current study also revealed restoration of the level of brain derived neurotrophic factor (BDNF) and N-methyl-D-aspartate receptors (NR2A and NR2B) gene expression in BPA+ ASIV and BPA+A. spinosus saponins groups. The co-treatment of BPA group with ASIV or A. spinosus saponin significantly reduced the values of comet parameters as well as the intensity of estrogen receptors (ERs) immunoreactive cells and improved the histological alterations induced by BPA in different brain regions. Conclusion It could be concluded that ASIV or A. spinosus saponins has a promising role in modulating the neurotoxicity and DNA damage elicited by BPA.
bibliographic citation: Essawy et al. (2021) Therapeutic effects of astragaloside IV and Astragalus spinosus saponins against bisphenol A-induced neurotoxicity and DNA damage in rats. PeerJ 9:e11930 https://doi.org/10.7717/peerj.11930
date submitted: 2021-04-01
date accepted: 2021-07-18
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Essawy
  given name: Amina E.
author list: Agent
  family name: Abd Elkader
  given name: Heba-Tallah Abd Elrahim
author list: Agent
  family name: Khamiss
  given name: Omaima A.
author list: Agent
  family name: Eweda
  given name: Saber Mohamed
author list: Agent
  family name: Abdou
  given name: Heba Mohamed
doi: 10.7717/peerj.11930
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: ©2021 Essawy et al.
attribution name: Essawy et al.

Designing of the N-ethyl-4-(pyridin-4-yl)benzamide based potent ROCK1 inhibitors using docking, molecular dynamics, and 3D-QSAR
type: item
type: AcademicArticle
description: Rho-associated kinase-1 (ROCK1) has been recognized for its pivotal role in heart diseases, different types of malignancy, and many neurological disorders. Hyperactivity of ROCK phosphorylates the protein kinase-C (PKC), which ultimately induces smooth muscle cell contraction in the vascular system. Inhibition of ROCK1 has been shown to be a promising therapy for patients with cardiovascular disease. In this study, we have conducted molecular modeling techniques such as docking, molecular dynamics (MD), and 3-Dimensional structure-activity relationship (3D-QSAR) on a series of N-ethyl-4-(pyridin-4-yl)benzamide-based compounds. Docking and MD showed critical interactions and binding affinities between ROCK1 and its inhibitors. To establish the structure-activity relationship (SAR) of the compounds, 3D-QSAR techniques such as Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) were used. The CoMFA (q2 = 0.774, r2 = 0.965, ONC = 6, and ${r}_{pred}^{2}$ r p r e d 2 = 0.703) and CoMSIA (q2 = 0.676, r2 = 0.949, ONC = 6, and ${r}_{pred}^{2}$ r p r e d 2 = 0.548) both models have shown reasonable external predictive activity, and contour maps revealed favorable and unfavorable substitutions for chemical group modifications. Based on the contour maps, we have designed forty new compounds, among which, seven compounds exhibited higher predictive activity (pIC50). Further, we conducted the MD study, ADME/Tox, and SA score prediction using the seven newly designed compounds. The combination of docking, MD, and 3D-QSAR studies helps to understand the coherence modification of existing molecules. Our study may provide valuable insight into the development of more potent ROCK1 inhibitors.
format: application/pdf
format: text/html
creator: Suparna Ghosh
creator: Seketoulie Keretsu
creator: Seung Joo Cho
subject: Bioinformatics
subject: Biophysics
subject: Computational Biology
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.11951
publisher: PeerJ Inc.
rights: © 2021 Ghosh et al.
abstract: Rho-associated kinase-1 (ROCK1) has been recognized for its pivotal role in heart diseases, different types of malignancy, and many neurological disorders. Hyperactivity of ROCK phosphorylates the protein kinase-C (PKC), which ultimately induces smooth muscle cell contraction in the vascular system. Inhibition of ROCK1 has been shown to be a promising therapy for patients with cardiovascular disease. In this study, we have conducted molecular modeling techniques such as docking, molecular dynamics (MD), and 3-Dimensional structure-activity relationship (3D-QSAR) on a series of N-ethyl-4-(pyridin-4-yl)benzamide-based compounds. Docking and MD showed critical interactions and binding affinities between ROCK1 and its inhibitors. To establish the structure-activity relationship (SAR) of the compounds, 3D-QSAR techniques such as Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) were used. The CoMFA (q2 = 0.774, r2 = 0.965, ONC = 6, and ${r}_{pred}^{2}$ r p r e d 2 = 0.703) and CoMSIA (q2 = 0.676, r2 = 0.949, ONC = 6, and ${r}_{pred}^{2}$ r p r e d 2 = 0.548) both models have shown reasonable external predictive activity, and contour maps revealed favorable and unfavorable substitutions for chemical group modifications. Based on the contour maps, we have designed forty new compounds, among which, seven compounds exhibited higher predictive activity (pIC50). Further, we conducted the MD study, ADME/Tox, and SA score prediction using the seven newly designed compounds. The combination of docking, MD, and 3D-QSAR studies helps to understand the coherence modification of existing molecules. Our study may provide valuable insight into the development of more potent ROCK1 inhibitors.
bibliographic citation: Ghosh et al. (2021) Designing of the N-ethyl-4-(pyridin-4-yl)benzamide based potent ROCK1 inhibitors using docking, molecular dynamics, and 3D-QSAR. PeerJ 9:e11951 https://doi.org/10.7717/peerj.11951
date submitted: 2021-05-18
date accepted: 2021-07-20
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ghosh
  given name: Suparna
author list: Agent
  family name: Keretsu
  given name: Seketoulie
author list: Agent
  family name: Cho
  given name: Seung Joo
doi: 10.7717/peerj.11951
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: ©2021 Ghosh et al.
attribution name: Ghosh et al.

Klebsiella variicola improves the antioxidant ability of maize seedlings under saline-alkali stress
type: item
type: AcademicArticle
description: Background Saline-alkali soil is mainly distributed in the northern and coastal areas of China. The Songnen Plain, located in the northeast of China, is a region with a relatively high concentration of saline-alkali soil and is also one of the more at-risk areas in the country. Every year, the increasing spread of saline-alkali soil areas has a serious impact on the growth of agricultural crops. The maize crop is sensitive to saline-alkali stress, which seriously affects its growth and development. Our previous study determined that Klebsiella variicola performs a variety of biological functions, as well as improves the rhizosphere microenvironment and promotes the growth and development of maize seedlings in saline-alkali soil environments. The present study further analyzed the mechanism that enables K. variicola to alleviate saline-alkali stress at the level of the antioxidant system. Methods The accumulation of O2− was observed directly via histochemical staining. The activities of several antioxidant enzymes were determined using the nitro blue tetrazolium and the guaiacol methods. The contents of non-enzymatic antioxidants were determined using the dithionitrobenzoic acid method. Results The contents of the superoxide anion and hydrogen peroxide in leaves and roots of maize seedlings increased under saline-alkali stress conditions. The higher level of reactive oxygen species increased the degree of membrane lipid peroxidation. There were differences in the degree of oxidative damage and performance of the antioxidant defence system in maize seedlings under saline-alkali stress. Following the application of increasing concentrations of K. variicola, the activity of antioxidant enzymes increased by 21.22%–215.46%, and the content of non-enzymatic antioxidants increased as well, the ratios of ASA/DHA and GSH/GSSG in leaves increased by 4.97% and 1.87 times, respectively, and those in roots increased by 3.24% and 1.60 times, respectively. The accumulation of react…
format: application/pdf
format: text/html
creator: Lijuan Yang
creator: Yufeng Wang
creator: Kejun Yang
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
subject: Histology
description: doi:10.7717/peerj.11963
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Background Saline-alkali soil is mainly distributed in the northern and coastal areas of China. The Songnen Plain, located in the northeast of China, is a region with a relatively high concentration of saline-alkali soil and is also one of the more at-risk areas in the country. Every year, the increasing spread of saline-alkali soil areas has a serious impact on the growth of agricultural crops. The maize crop is sensitive to saline-alkali stress, which seriously affects its growth and development. Our previous study determined that Klebsiella variicola performs a variety of biological functions, as well as improves the rhizosphere microenvironment and promotes the growth and development of maize seedlings in saline-alkali soil environments. The present study further analyzed the mechanism that enables K. variicola to alleviate saline-alkali stress at the level of the antioxidant system. Methods The accumulation of O2− was observed directly via histochemical staining. The activities of several antioxidant enzymes were determined using the nitro blue tetrazolium and the guaiacol methods. The contents of non-enzymatic antioxidants were determined using the dithionitrobenzoic acid method. Results The contents of the superoxide anion and hydrogen peroxide in leaves and roots of maize seedlings increased under saline-alkali stress conditions. The higher level of reactive oxygen species increased the degree of membrane lipid peroxidation. There were differences in the degree of oxidative damage and performance of the antioxidant defence system in maize seedlings under saline-alkali stress. Following the application of increasing concentrations of K. variicola, the activity of antioxidant enzymes increased by 21.22%–215.46%, and the content of non-enzymatic antioxidants increased as well, the ratios of ASA/DHA and GSH/GSSG in leaves increased by 4.97% and 1.87 times, respectively, and those in roots increased by 3.24% and 1.60 times, respectively. The accumulation of react…
bibliographic citation: Yang et al. (2021) Klebsiella variicola improves the antioxidant ability of maize seedlings under saline-alkali stress. PeerJ 9:e11963 https://doi.org/10.7717/peerj.11963
date submitted: 2021-04-19
date accepted: 2021-07-21
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Lijuan
author list: Agent
  family name: Wang
  given name: Yufeng
author list: Agent
  family name: Yang
  given name: Kejun
doi: 10.7717/peerj.11963
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: ©2021 Yang et al.
attribution name: Yang et al.

Comparative transcriptome analysis of R3a and Avr3a-mediated defense responses in transgenic tomato
type: item
type: AcademicArticle
description: Late blight caused by Phytophthora infestans is one of the most devastating diseases in potatoes and tomatoes. At present, several late blight resistance genes have been mapped and cloned. To better understand the transcriptome changes during the incompatible interaction process between R3a and Avr3a, in this study, after spraying DEX, the leaves of MM-R3a-Avr3a and MM-Avr3a transgenic plants at different time points were used for comparative transcriptome analysis. A total of 7,324 repeated DEGs were detected in MM-R3a-Avr3a plants at 2-h and 6-h, and 729 genes were differentially expressed at 6-h compared with 2-h. Only 1,319 repeated DEGs were found in MM-Avr3a at 2-h and 6-h, of which 330 genes have the same expression pattern. Based on GO, KEGG and WCGNA analysis of DEGs, the phenylpropanoid biosynthesis, plant-pathogen interaction, and plant hormone signal transduction pathways were significantly up-regulated. Parts of the down-regulated DEGs were enriched in carbon metabolism and the photosynthesis process. Among these DEGs, most of the transcription factors, such as WRKY, MYB, and NAC, related to disease resistance or endogenous hormones SA and ET pathways, as well as PR, CML, SGT1 gene were also significantly induced. Our results provide transcriptome-wide insights into R3a and Avr3a-mediated incompatibility interaction.
format: application/pdf
format: text/html
creator: Dongqi Xue
creator: Han Liu
creator: Dong Wang
creator: Yanna Gao
creator: Zhiqi Jia
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11965
publisher: PeerJ Inc.
rights: © 2021 Xue et al.
abstract: Late blight caused by Phytophthora infestans is one of the most devastating diseases in potatoes and tomatoes. At present, several late blight resistance genes have been mapped and cloned. To better understand the transcriptome changes during the incompatible interaction process between R3a and Avr3a, in this study, after spraying DEX, the leaves of MM-R3a-Avr3a and MM-Avr3a transgenic plants at different time points were used for comparative transcriptome analysis. A total of 7,324 repeated DEGs were detected in MM-R3a-Avr3a plants at 2-h and 6-h, and 729 genes were differentially expressed at 6-h compared with 2-h. Only 1,319 repeated DEGs were found in MM-Avr3a at 2-h and 6-h, of which 330 genes have the same expression pattern. Based on GO, KEGG and WCGNA analysis of DEGs, the phenylpropanoid biosynthesis, plant-pathogen interaction, and plant hormone signal transduction pathways were significantly up-regulated. Parts of the down-regulated DEGs were enriched in carbon metabolism and the photosynthesis process. Among these DEGs, most of the transcription factors, such as WRKY, MYB, and NAC, related to disease resistance or endogenous hormones SA and ET pathways, as well as PR, CML, SGT1 gene were also significantly induced. Our results provide transcriptome-wide insights into R3a and Avr3a-mediated incompatibility interaction.
bibliographic citation: Xue et al. (2021) Comparative transcriptome analysis of R3a and Avr3a-mediated defense responses in transgenic tomato. PeerJ 9:e11965 https://doi.org/10.7717/peerj.11965
date submitted: 2021-04-09
date accepted: 2021-07-21
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xue
  given name: Dongqi
author list: Agent
  family name: Liu
  given name: Han
author list: Agent
  family name: Wang
  given name: Dong
author list: Agent
  family name: Gao
  given name: Yanna
author list: Agent
  family name: Jia
  given name: Zhiqi
doi: 10.7717/peerj.11965
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: ©2021 Xue et al.
attribution name: Xue et al.

Snakes on an African plain: the radiation of Crotaphopeltis and Philothamnus into open habitat (Serpentes: Colubridae)
type: item
type: AcademicArticle
description: Background The African continent is comprised of several different biomes, although savanna is the most prevalent. The current heterogeneous landscape was formed through long-term vegetation shifts as a result of the global cooling trend since the Oligocene epoch. The overwhelming trend was a shift from primarily forest, to primarily savanna. As such, faunal groups that emerged during the Paleogene/Neogene period and have species distributed in both forest and savanna habitat should show a genetic signature of the possible evolutionary impact of these biome developments. Crotaphopeltis and Philothamnus (Colubridae) are excellent taxa to investigate the evolutionary impact of these biome developments on widespread African colubrid snakes, and whether timing and patterns of radiation are synchronous with biome reorganisation. Methods A phylogenetic framework was used to investigate timing of lineage diversification. Phylogenetic analysis included both genera as well as other Colubridae to construct a temporal framework in order to estimate radiation times for Crotaphopeltis and Philothamnus. Lineage diversification was estimated in Bayesian Evolutionary Analysis Sampling Trees (BEAST), using two mitochondrial markers (cyt–b, ND4), one nuclear marker (c–mos), and incorporating one fossil and two biogeographical calibration points. Vegetation layers were used to classify and confirm species association with broad biome types (‘closed’ = forest, ‘open’ = savanna/other), and the ancestral habitat state for each genus was estimated. Results Philothamnus showed an ancestral state of closed habitat, but the ancestral habitat type for Crotaphopeltis was equivocal. Both genera showed similar timing of lineage diversification diverging from their sister genera during the Oligocene/Miocene transition (ca. 25 Mya), with subsequent species radiation in the Mid-Miocene. Philothamnus appeared to have undergone allopatric speciation during Mid-Miocene forest fragmentation. Habitat ge…
format: application/pdf
format: text/html
creator: Hanlie M. Engelbrecht
creator: William R. Branch
creator: Krystal A. Tolley
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.11728
publisher: PeerJ Inc.
rights: © 2021 Engelbrecht et al.
abstract: Background The African continent is comprised of several different biomes, although savanna is the most prevalent. The current heterogeneous landscape was formed through long-term vegetation shifts as a result of the global cooling trend since the Oligocene epoch. The overwhelming trend was a shift from primarily forest, to primarily savanna. As such, faunal groups that emerged during the Paleogene/Neogene period and have species distributed in both forest and savanna habitat should show a genetic signature of the possible evolutionary impact of these biome developments. Crotaphopeltis and Philothamnus (Colubridae) are excellent taxa to investigate the evolutionary impact of these biome developments on widespread African colubrid snakes, and whether timing and patterns of radiation are synchronous with biome reorganisation. Methods A phylogenetic framework was used to investigate timing of lineage diversification. Phylogenetic analysis included both genera as well as other Colubridae to construct a temporal framework in order to estimate radiation times for Crotaphopeltis and Philothamnus. Lineage diversification was estimated in Bayesian Evolutionary Analysis Sampling Trees (BEAST), using two mitochondrial markers (cyt–b, ND4), one nuclear marker (c–mos), and incorporating one fossil and two biogeographical calibration points. Vegetation layers were used to classify and confirm species association with broad biome types (‘closed’ = forest, ‘open’ = savanna/other), and the ancestral habitat state for each genus was estimated. Results Philothamnus showed an ancestral state of closed habitat, but the ancestral habitat type for Crotaphopeltis was equivocal. Both genera showed similar timing of lineage diversification diverging from their sister genera during the Oligocene/Miocene transition (ca. 25 Mya), with subsequent species radiation in the Mid-Miocene. Philothamnus appeared to have undergone allopatric speciation during Mid-Miocene forest fragmentation. Habitat ge…
bibliographic citation: Engelbrecht et al. (2021) Snakes on an African plain: the radiation of Crotaphopeltis and Philothamnus into open habitat (Serpentes: Colubridae). PeerJ 9:e11728 https://doi.org/10.7717/peerj.11728
date submitted: 2020-11-17
date accepted: 2021-06-15
issued: 2021-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Engelbrecht
  given name: Hanlie M.
author list: Agent
  family name: Branch
  given name: William R.
author list: Agent
  family name: Tolley
  given name: Krystal A.
doi: 10.7717/peerj.11728
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-06
copyright: ©2021 Engelbrecht et al.
attribution name: Engelbrecht et al.

Identification of a circRNA-miRNA-mRNA regulatory network for exploring novel therapeutic options for glioma
type: item
type: AcademicArticle
description: Background Glioma is the most common brain neoplasm with a poor prognosis. Circular RNA (circRNA) and their associated competing endogenous RNA (ceRNA) network play critical roles in the pathogenesis of glioma. However, the alteration of the circRNA-miRNA-mRNA regulatory network and its correlation with glioma therapy haven’t been systematically analyzed. Methods With GEO, GEPIA2, circBank, CSCD, CircInteractome, mirWalk 2.0, and mirDIP 4.1, we constructed a circRNA–miRNA–mRNA network in glioma. LASSO regression and multivariate Cox regression analysis established a hub mRNA signature to assess the prognosis. GSVA was used to estimate the immune infiltration level. Potential anti-glioma drugs were forecasted using the cMap database and evaluated with GSEA using GEO data. Results A ceRNA network of seven circRNAs (hsa_circ_0030788/0034182/0000227/ 0018086/0000229/0036592/0002765), 15 miRNAs(hsa-miR-1200/1205/1248/ 1303/3925-5p/5693/581/586/599/607/640/647/6867-5p/767-3p/935), and 46 mRNAs (including 11 hub genes of ARHGAP11A, DRP2, HNRNPA3, IGFBP5, IP6K2, KLF10, KPNA4, NRP2, PAIP1, RCN1, and SEMA5A) was constructed. Functional enrichment showed they influenced majority of the hallmarks of tumors. Eleven hub genes were proven to be decent prognostic signatures for glioma in both TCGA and CGGA datasets. Forty-six LASSO regression significant genes were closely related to immune infiltration. Finally, five compounds (fulvestrant, tanespimycin, mifepristone, tretinoin, and harman) were predicted as potential treatments for glioma. Among them, mifepristone and tretinoin were proven to inhibit the cell cycle and DNA repair in glioma. Conclusion This study highlights the potential pathogenesis of the circRNA-miRNA-mRNA regulatory network and identifies novel therapeutic options for glioma.
format: application/pdf
format: text/html
creator: Yi He
creator: Yihong Chen
creator: Yuxin Tong
creator: Wenyong Long
creator: Qing Liu
subject: Bioinformatics
subject: Neurology
subject: Oncology
subject: Medical Genetics
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.11894
publisher: PeerJ Inc.
rights: © 2021 He et al.
abstract: Background Glioma is the most common brain neoplasm with a poor prognosis. Circular RNA (circRNA) and their associated competing endogenous RNA (ceRNA) network play critical roles in the pathogenesis of glioma. However, the alteration of the circRNA-miRNA-mRNA regulatory network and its correlation with glioma therapy haven’t been systematically analyzed. Methods With GEO, GEPIA2, circBank, CSCD, CircInteractome, mirWalk 2.0, and mirDIP 4.1, we constructed a circRNA–miRNA–mRNA network in glioma. LASSO regression and multivariate Cox regression analysis established a hub mRNA signature to assess the prognosis. GSVA was used to estimate the immune infiltration level. Potential anti-glioma drugs were forecasted using the cMap database and evaluated with GSEA using GEO data. Results A ceRNA network of seven circRNAs (hsa_circ_0030788/0034182/0000227/ 0018086/0000229/0036592/0002765), 15 miRNAs(hsa-miR-1200/1205/1248/ 1303/3925-5p/5693/581/586/599/607/640/647/6867-5p/767-3p/935), and 46 mRNAs (including 11 hub genes of ARHGAP11A, DRP2, HNRNPA3, IGFBP5, IP6K2, KLF10, KPNA4, NRP2, PAIP1, RCN1, and SEMA5A) was constructed. Functional enrichment showed they influenced majority of the hallmarks of tumors. Eleven hub genes were proven to be decent prognostic signatures for glioma in both TCGA and CGGA datasets. Forty-six LASSO regression significant genes were closely related to immune infiltration. Finally, five compounds (fulvestrant, tanespimycin, mifepristone, tretinoin, and harman) were predicted as potential treatments for glioma. Among them, mifepristone and tretinoin were proven to inhibit the cell cycle and DNA repair in glioma. Conclusion This study highlights the potential pathogenesis of the circRNA-miRNA-mRNA regulatory network and identifies novel therapeutic options for glioma.
bibliographic citation: He et al. (2021) Identification of a circRNA-miRNA-mRNA regulatory network for exploring novel therapeutic options for glioma. PeerJ 9:e11894 https://doi.org/10.7717/peerj.11894
date submitted: 2021-05-21
date accepted: 2021-07-12
issued: 2021-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Yi
author list: Agent
  family name: Chen
  given name: Yihong
author list: Agent
  family name: Tong
  given name: Yuxin
author list: Agent
  family name: Long
  given name: Wenyong
author list: Agent
  family name: Liu
  given name: Qing
doi: 10.7717/peerj.11894
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-06
copyright: ©2021 He et al.
attribution name: He et al.

IdentPMP: identification of moonlighting proteins in plants using sequence-based learning models
type: item
type: AcademicArticle
description: Background A moonlighting protein refers to a protein that can perform two or more functions. Since the current moonlighting protein prediction tools mainly focus on the proteins in animals and microorganisms, and there are differences in the cells and proteins between animals and plants, these may cause the existing tools to predict plant moonlighting proteins inaccurately. Hence, the availability of a benchmark data set and a prediction tool specific for plant moonlighting protein are necessary. Methods This study used some protein feature classes from the data set constructed in house to develop a web-based prediction tool. In the beginning, we built a data set about plant protein and reduced redundant sequences. We then performed feature selection, feature normalization and feature dimensionality reduction on the training data. Next, machine learning methods for preliminary modeling were used to select feature classes that performed best in plant moonlighting protein prediction. This selected feature was incorporated into the final plant protein prediction tool. After that, we compared five machine learning methods and used grid searching to optimize parameters, and the most suitable method was chosen as the final model. Results The prediction results indicated that the eXtreme Gradient Boosting (XGBoost) performed best, which was used as the algorithm to construct the prediction tool, called IdentPMP (Identification of Plant Moonlighting Proteins). The results of the independent test set shows that the area under the precision-recall curve (AUPRC) and the area under the receiver operating characteristic curve (AUC) of IdentPMP is 0.43 and 0.68, which are 19.44% (0.43 vs. 0.36) and 13.33% (0.68 vs. 0.60) higher than state-of-the-art non-plant specific methods, respectively. This further demonstrated that a benchmark data set and a plant-specific prediction tool was required for plant moonlighting protein studies. Finally, we implemented the tool into a web versi…
format: application/pdf
format: text/html
creator: Xinyi Liu
creator: Yueyue Shen
creator: Youhua Zhang
creator: Fei Liu
creator: Zhiyu Ma
creator: Zhenyu Yue
creator: Yi Yue
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.11900
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background A moonlighting protein refers to a protein that can perform two or more functions. Since the current moonlighting protein prediction tools mainly focus on the proteins in animals and microorganisms, and there are differences in the cells and proteins between animals and plants, these may cause the existing tools to predict plant moonlighting proteins inaccurately. Hence, the availability of a benchmark data set and a prediction tool specific for plant moonlighting protein are necessary. Methods This study used some protein feature classes from the data set constructed in house to develop a web-based prediction tool. In the beginning, we built a data set about plant protein and reduced redundant sequences. We then performed feature selection, feature normalization and feature dimensionality reduction on the training data. Next, machine learning methods for preliminary modeling were used to select feature classes that performed best in plant moonlighting protein prediction. This selected feature was incorporated into the final plant protein prediction tool. After that, we compared five machine learning methods and used grid searching to optimize parameters, and the most suitable method was chosen as the final model. Results The prediction results indicated that the eXtreme Gradient Boosting (XGBoost) performed best, which was used as the algorithm to construct the prediction tool, called IdentPMP (Identification of Plant Moonlighting Proteins). The results of the independent test set shows that the area under the precision-recall curve (AUPRC) and the area under the receiver operating characteristic curve (AUC) of IdentPMP is 0.43 and 0.68, which are 19.44% (0.43 vs. 0.36) and 13.33% (0.68 vs. 0.60) higher than state-of-the-art non-plant specific methods, respectively. This further demonstrated that a benchmark data set and a plant-specific prediction tool was required for plant moonlighting protein studies. Finally, we implemented the tool into a web versi…
bibliographic citation: Liu et al. (2021) IdentPMP: identification of moonlighting proteins in plants using sequence-based learning models. PeerJ 9:e11900 https://doi.org/10.7717/peerj.11900
date submitted: 2020-11-17
date accepted: 2021-07-13
issued: 2021-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xinyi
author list: Agent
  family name: Shen
  given name: Yueyue
author list: Agent
  family name: Zhang
  given name: Youhua
author list: Agent
  family name: Liu
  given name: Fei
author list: Agent
  family name: Ma
  given name: Zhiyu
author list: Agent
  family name: Yue
  given name: Zhenyu
author list: Agent
  family name: Yue
  given name: Yi
doi: 10.7717/peerj.11900
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-06
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Identification of miRNA-target gene regulatory networks in liver fibrosis based on bioinformatics analysis
type: item
type: AcademicArticle
description: Background Liver cirrhosis is one of the leading causes of death worldwide. MicroRNAs (miRNAs) can regulate liver fibrosis, but the underlying mechanisms are not fully understood, and the interactions between miRNAs and mRNAs are not clearly elucidated. Methods miRNA and mRNA expression arrays of cirrhotic samples and control samples were acquired from the Gene Expression Omnibus database. miRNA-mRNA integrated analysis, functional enrichment analysis and protein-protein interaction (PPI) network construction were performed to identify differentially expressed miRNAs (DEMs) and mRNAs (DEGs), miRNA-mRNA interaction networks, enriched pathways and hub genes. Finally, the results were validated with in vitro cell models. Results By bioinformatics analysis, we identified 13 DEMs between cirrhotic samples and control samples. Among these DEMs, six upregulated (hsa-miR-146b-5p, hsa-miR-150-5p, hsa-miR-224-3p, hsa-miR-3135b, hsa-miR-3195, and hsa-miR-4725-3p) and seven downregulated (hsa-miR-1234-3p, hsa-miR-30b-3p, hsa-miR-3162-3p, hsa-miR-548aj-3p, hsa-miR-548x-3p, hsa-miR-548z, and hsa-miR-890) miRNAs were further validated in activated LX2 cells. miRNA-mRNA interaction networks revealed a total of 361 miRNA-mRNA pairs between 13 miRNAs and 245 corresponding target genes. Moreover, PPI network analysis revealed the top 20 hub genes, including COL1A1, FBN1 and TIMP3, which were involved in extracellular matrix (ECM) organization; CCL5, CXCL9, CXCL12, LCK and CD24, which participated in the immune response; and CDH1, PECAM1, SELL and CAV1, which regulated cell adhesion. Functional enrichment analysis of all DEGs as well as hub genes showed similar results, as ECM-associated pathways, cell surface interaction and adhesion, and immune response were significantly enriched in both analyses. Conclusions We identified 13 differentially expressed miRNAs as potential biomarkers of liver cirrhosis. Moreover, we identified 361 regulatory pairs of miRNA-mRNA and 20 hub genes in live…
format: application/pdf
format: text/html
creator: Yang Tai
creator: Chong Zhao
creator: Jinhang Gao
creator: Tian Lan
creator: Huan Tong
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Medical Genetics
description: doi:10.7717/peerj.11910
publisher: PeerJ Inc.
rights: © 2021 Tai et al.
abstract: Background Liver cirrhosis is one of the leading causes of death worldwide. MicroRNAs (miRNAs) can regulate liver fibrosis, but the underlying mechanisms are not fully understood, and the interactions between miRNAs and mRNAs are not clearly elucidated. Methods miRNA and mRNA expression arrays of cirrhotic samples and control samples were acquired from the Gene Expression Omnibus database. miRNA-mRNA integrated analysis, functional enrichment analysis and protein-protein interaction (PPI) network construction were performed to identify differentially expressed miRNAs (DEMs) and mRNAs (DEGs), miRNA-mRNA interaction networks, enriched pathways and hub genes. Finally, the results were validated with in vitro cell models. Results By bioinformatics analysis, we identified 13 DEMs between cirrhotic samples and control samples. Among these DEMs, six upregulated (hsa-miR-146b-5p, hsa-miR-150-5p, hsa-miR-224-3p, hsa-miR-3135b, hsa-miR-3195, and hsa-miR-4725-3p) and seven downregulated (hsa-miR-1234-3p, hsa-miR-30b-3p, hsa-miR-3162-3p, hsa-miR-548aj-3p, hsa-miR-548x-3p, hsa-miR-548z, and hsa-miR-890) miRNAs were further validated in activated LX2 cells. miRNA-mRNA interaction networks revealed a total of 361 miRNA-mRNA pairs between 13 miRNAs and 245 corresponding target genes. Moreover, PPI network analysis revealed the top 20 hub genes, including COL1A1, FBN1 and TIMP3, which were involved in extracellular matrix (ECM) organization; CCL5, CXCL9, CXCL12, LCK and CD24, which participated in the immune response; and CDH1, PECAM1, SELL and CAV1, which regulated cell adhesion. Functional enrichment analysis of all DEGs as well as hub genes showed similar results, as ECM-associated pathways, cell surface interaction and adhesion, and immune response were significantly enriched in both analyses. Conclusions We identified 13 differentially expressed miRNAs as potential biomarkers of liver cirrhosis. Moreover, we identified 361 regulatory pairs of miRNA-mRNA and 20 hub genes in live…
bibliographic citation: Tai et al. (2021) Identification of miRNA-target gene regulatory networks in liver fibrosis based on bioinformatics analysis. PeerJ 9:e11910 https://doi.org/10.7717/peerj.11910
date submitted: 2021-05-20
date accepted: 2021-07-14
issued: 2021-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tai
  given name: Yang
author list: Agent
  family name: Zhao
  given name: Chong
author list: Agent
  family name: Gao
  given name: Jinhang
author list: Agent
  family name: Lan
  given name: Tian
author list: Agent
  family name: Tong
  given name: Huan
doi: 10.7717/peerj.11910
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-06
copyright: ©2021 Tai et al.
attribution name: Tai et al.

A new Andean treefrog (Amphibia: Hyloscirtus bogotensis group) from Ecuador: an example of community involvement for conservation
type: item
type: AcademicArticle
description: We provide several lines of evidence to delimit a new species of Hyloscirtus and define its phylogenetic position inside the Hyloscirtus bogotensis group. The new species is the sister taxon to Hyloscirtus mashpi and is related to a clade formed by H. alytolylax and a putative new species from the province of El Oro in, southwestern Ecuador. Hyloscirtus conscientia sp. nov. is described from the montane forests of the Mira River basin in the extreme northwestern Ecuador. The new species is characterized as follows: tympanic annulus conspicuous, tip of snout in dorsal view subacuminate, middorsal stripe formed by melanophores larger and less dense, dorsal skin with individual iridophores forming dots, scarcely distributed across dorsum. Our study also highlights the importance of the Mira River Valley as a biogeographic barrier; suggesting research efforts north and south of the valley are likely to reveal additional endemic cryptic diversity. Finally, our partnership with Reserva: The Youth Land Trust, Rainforest Trust and EcoMinga Foundation has produced a novel and meaningful way to connect young people with biodiversity discovery and habitat conservation.
format: application/pdf
format: text/html
creator: Mario H. Yánez-Muñoz
creator: Juan Pablo Reyes-Puig
creator: Diego Batallas-Revelo
creator: Callie Broaddus
creator: Miguel Urgilés-Merchán
creator: Diego F. Cisneros-Heredia
creator: Juan M. Guayasamin
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11914
publisher: PeerJ Inc.
rights: © 2021 Yánez-Muñoz et al.
abstract: We provide several lines of evidence to delimit a new species of Hyloscirtus and define its phylogenetic position inside the Hyloscirtus bogotensis group. The new species is the sister taxon to Hyloscirtus mashpi and is related to a clade formed by H. alytolylax and a putative new species from the province of El Oro in, southwestern Ecuador. Hyloscirtus conscientia sp. nov. is described from the montane forests of the Mira River basin in the extreme northwestern Ecuador. The new species is characterized as follows: tympanic annulus conspicuous, tip of snout in dorsal view subacuminate, middorsal stripe formed by melanophores larger and less dense, dorsal skin with individual iridophores forming dots, scarcely distributed across dorsum. Our study also highlights the importance of the Mira River Valley as a biogeographic barrier; suggesting research efforts north and south of the valley are likely to reveal additional endemic cryptic diversity. Finally, our partnership with Reserva: The Youth Land Trust, Rainforest Trust and EcoMinga Foundation has produced a novel and meaningful way to connect young people with biodiversity discovery and habitat conservation.
bibliographic citation: Yánez-Muñoz et al. (2021) A new Andean treefrog (Amphibia: Hyloscirtus bogotensis group) from Ecuador: an example of community involvement for conservation. PeerJ 9:e11914 https://doi.org/10.7717/peerj.11914
date submitted: 2021-03-19
date accepted: 2021-07-14
issued: 2021-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Yánez-Muñoz
  given name: Mario H.
author list: Agent
  family name: Reyes-Puig
  given name: Juan Pablo
author list: Agent
  family name: Batallas-Revelo
  given name: Diego
author list: Agent
  family name: Broaddus
  given name: Callie
author list: Agent
  family name: Urgilés-Merchán
  given name: Miguel
author list: Agent
  family name: Cisneros-Heredia
  given name: Diego F.
author list: Agent
  family name: Guayasamin
  given name: Juan M.
doi: 10.7717/peerj.11914
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-06
copyright: © 2021 Yánez-Muñoz et al.
attribution name: Yánez-Muñoz et al.

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