PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Cephalopod species identification using integrated analysis of machine learning and deep learning approaches
items: Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters
items: Expression of cyanobacterial genes enhanced CO2 assimilation and biomass production in transgenic Arabidopsis thaliana
items: Physiological changes and transcript identification in Coreopsis tinctoria Nutt. in early stages of salt stress
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)

Cephalopod species identification using integrated analysis of machine learning and deep learning approaches
type: item
type: AcademicArticle
description: Background Despite the high commercial fisheries value and ecological importance as prey item for higher marine predators, very limited taxonomic work has been done on cephalopods in Malaysia. Due to the soft-bodied nature of cephalopods, the identification of cephalopod species based on the beak hard parts can be more reliable and useful than conventional body morphology. Since the traditional method for species classification was time-consuming, this study aimed to develop an automated identification model that can identify cephalopod species based on beak images. Methods A total of 174 samples of seven cephalopod species were collected from the west coast of Peninsular Malaysia. Both upper and lower beaks were extracted from the samples and the left lateral views of upper and lower beak images were acquired. Three types of traditional morphometric features were extracted namely grey histogram of oriented gradient (HOG), colour HOG, and morphological shape descriptor (MSD). In addition, deep features were extracted by using three pre-trained convolutional neural networks (CNN) models which are VGG19, InceptionV3, and Resnet50. Eight machine learning approaches were used in the classification step and compared for model performance. Results The results showed that the Artificial Neural Network (ANN) model achieved the best testing accuracy of 91.14%, using the deep features extracted from the VGG19 model from lower beak images. The results indicated that the deep features were more accurate than the traditional features in highlighting morphometric differences from the beak images of cephalopod species. In addition, the use of lower beaks of cephalopod species provided better results compared to the upper beaks, suggesting that the lower beaks possess more significant morphological differences between the studied cephalopod species. Future works should include more cephalopod species and sample size to enhance the identification accuracy and comprehensiveness of th…
format: application/pdf
format: text/html
creator: Hui Yuan Tan
creator: Zhi Yun Goh
creator: Kar-Hoe Loh
creator: Amy Yee-Hui Then
creator: Hasmahzaiti Omar
creator: Siow-Wee Chang
subject: Computational Biology
subject: Marine Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.11825
publisher: PeerJ Inc.
rights: © 2021 Tan et al.
abstract: Background Despite the high commercial fisheries value and ecological importance as prey item for higher marine predators, very limited taxonomic work has been done on cephalopods in Malaysia. Due to the soft-bodied nature of cephalopods, the identification of cephalopod species based on the beak hard parts can be more reliable and useful than conventional body morphology. Since the traditional method for species classification was time-consuming, this study aimed to develop an automated identification model that can identify cephalopod species based on beak images. Methods A total of 174 samples of seven cephalopod species were collected from the west coast of Peninsular Malaysia. Both upper and lower beaks were extracted from the samples and the left lateral views of upper and lower beak images were acquired. Three types of traditional morphometric features were extracted namely grey histogram of oriented gradient (HOG), colour HOG, and morphological shape descriptor (MSD). In addition, deep features were extracted by using three pre-trained convolutional neural networks (CNN) models which are VGG19, InceptionV3, and Resnet50. Eight machine learning approaches were used in the classification step and compared for model performance. Results The results showed that the Artificial Neural Network (ANN) model achieved the best testing accuracy of 91.14%, using the deep features extracted from the VGG19 model from lower beak images. The results indicated that the deep features were more accurate than the traditional features in highlighting morphometric differences from the beak images of cephalopod species. In addition, the use of lower beaks of cephalopod species provided better results compared to the upper beaks, suggesting that the lower beaks possess more significant morphological differences between the studied cephalopod species. Future works should include more cephalopod species and sample size to enhance the identification accuracy and comprehensiveness of th…
bibliographic citation: Tan et al. (2021) Cephalopod species identification using integrated analysis of machine learning and deep learning approaches. PeerJ 9:e11825 https://doi.org/10.7717/peerj.11825
date submitted: 2020-11-13
date accepted: 2021-06-30
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Hui Yuan
author list: Agent
  family name: Goh
  given name: Zhi Yun
author list: Agent
  family name: Loh
  given name: Kar-Hoe
author list: Agent
  family name: Then
  given name: Amy Yee-Hui
author list: Agent
  family name: Omar
  given name: Hasmahzaiti
author list: Agent
  family name: Chang
  given name: Siow-Wee
doi: 10.7717/peerj.11825
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: ©2021 Tan et al.
attribution name: Tan et al.

Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters
type: item
type: AcademicArticle
description: Environmental DNA (eDNA) detection of aquatic invasive species is currently at the forefront of aquatic conservation efforts because the methodology provides a cost effective and sensitive means to detect animals at low densities. Developments in eDNA technologies have improved detection probabilities for rare, indicator, and invasive species over the past decade. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are required for mitigation. Here, we investigated the performance of a real-time quantitative PCR system for on-site eDNA detection of New Zealand mud snails (Potamopyrgus antipodarum). Six sites in western Washington, USA were sampled using the rapid eDNA technique and traditional methods, with five samples per site. On-site eDNA detection of mud snails resulted in a 10% increase in positive sites (16/30 = 53% positive) relative to visual surveys (13/30 = 43% positive). In addition, positive associations were observed between mud snail eDNA concentration (eDNA copies per reaction) and the number of mud snail individuals at each site (R2 = 0.78). We show that the rapid on-site eDNA technology can be effective for detection and quantification of New Zealand mud snails in freshwaters. This on-site eDNA detection approach could possibly be used to initiate management protocols that allow for more rapid responses during the onset of biological invasions.
format: application/pdf
format: text/html
creator: Jake J. Ponce
creator: Ivan Arismendi
creator: Austen Thomas
subject: Ecology
subject: Molecular Biology
subject: Freshwater Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.11835
publisher: PeerJ Inc.
rights: © 2021 Ponce et al.
abstract: Environmental DNA (eDNA) detection of aquatic invasive species is currently at the forefront of aquatic conservation efforts because the methodology provides a cost effective and sensitive means to detect animals at low densities. Developments in eDNA technologies have improved detection probabilities for rare, indicator, and invasive species over the past decade. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are required for mitigation. Here, we investigated the performance of a real-time quantitative PCR system for on-site eDNA detection of New Zealand mud snails (Potamopyrgus antipodarum). Six sites in western Washington, USA were sampled using the rapid eDNA technique and traditional methods, with five samples per site. On-site eDNA detection of mud snails resulted in a 10% increase in positive sites (16/30 = 53% positive) relative to visual surveys (13/30 = 43% positive). In addition, positive associations were observed between mud snail eDNA concentration (eDNA copies per reaction) and the number of mud snail individuals at each site (R2 = 0.78). We show that the rapid on-site eDNA technology can be effective for detection and quantification of New Zealand mud snails in freshwaters. This on-site eDNA detection approach could possibly be used to initiate management protocols that allow for more rapid responses during the onset of biological invasions.
bibliographic citation: Ponce et al. (2021) Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters. PeerJ 9:e11835 https://doi.org/10.7717/peerj.11835
date submitted: 2021-01-11
date accepted: 2021-07-01
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ponce
  given name: Jake J.
author list: Agent
  family name: Arismendi
  given name: Ivan
author list: Agent
  family name: Thomas
  given name: Austen
doi: 10.7717/peerj.11835
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: ©2021 Ponce et al.
attribution name: Ponce et al.

Expression of cyanobacterial genes enhanced CO2 assimilation and biomass production in transgenic Arabidopsis thaliana
type: item
type: AcademicArticle
description: Background Photosynthesis is a key process in plants that is compromised by the oxygenase activity of Rubisco, which leads to the production of toxic compound phosphoglycolate that is catabolized by photorespiratory pathway. Transformation of plants with photorespiratory bypasses have been shown to reduce photorespiration and enhance plant biomass. Interestingly, engineering of a single gene from such photorespiratory bypasses has also improved photosynthesis and plant productivity. Although single gene transformations may not completely reduce photorespiration, increases in plant biomass accumulation have still been observed indicating an alternative role in regulating different metabolic processes. Therefore, the current study was aimed at evaluating the underlying mechanism (s) associated with the effects of introducing a single cyanobacterial glycolate decarboxylation pathway gene on photosynthesis and plant performance. Methods Transgenic Arabidopsis thaliana plants (GD, HD, OX) expressing independently cyanobacterial decarboxylation pathway genes i.e., glycolate dehydrogenase, hydroxyacid dehydrogenase, and oxalate decarboxylase, respectively, were utilized. Photosynthetic, fluorescence related, and growth parameters were analyzed. Additionally, transcriptomic analysis of GD transgenic plants was also performed. Results The GD plants exhibited a significant increase (16%) in net photosynthesis rate while both HD and OX plants showed a non-significant (11%) increase as compared to wild type plants (WT). The stomatal conductance was significantly higher (24%) in GD and HD plants than the WT plants. The quantum efficiencies of photosystem II, carbon dioxide assimilation and the chlorophyll fluorescence-based photosynthetic electron transport rate were also higher than WT plants. The OX plants displayed significant reductions in the rate of photorespiration relative to gross photosynthesis and increase in the ratio of the photosynthetic electron flow attributable …
format: application/pdf
format: text/html
creator: Anum Zeb Abbasi
creator: Misbah Bilal
creator: Ghazal Khurshid
creator: Charilaos Yiotis
creator: Iftikhar Zeb
creator: Jamshaid Hussain
creator: Ayesha Baig
creator: Mohammad Maroof Shah
creator: Safee Ullah Chaudhary
creator: Bruce Osborne
creator: Raza Ahmad
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.11860
publisher: PeerJ Inc.
rights: © 2021 Abbasi et al.
abstract: Background Photosynthesis is a key process in plants that is compromised by the oxygenase activity of Rubisco, which leads to the production of toxic compound phosphoglycolate that is catabolized by photorespiratory pathway. Transformation of plants with photorespiratory bypasses have been shown to reduce photorespiration and enhance plant biomass. Interestingly, engineering of a single gene from such photorespiratory bypasses has also improved photosynthesis and plant productivity. Although single gene transformations may not completely reduce photorespiration, increases in plant biomass accumulation have still been observed indicating an alternative role in regulating different metabolic processes. Therefore, the current study was aimed at evaluating the underlying mechanism (s) associated with the effects of introducing a single cyanobacterial glycolate decarboxylation pathway gene on photosynthesis and plant performance. Methods Transgenic Arabidopsis thaliana plants (GD, HD, OX) expressing independently cyanobacterial decarboxylation pathway genes i.e., glycolate dehydrogenase, hydroxyacid dehydrogenase, and oxalate decarboxylase, respectively, were utilized. Photosynthetic, fluorescence related, and growth parameters were analyzed. Additionally, transcriptomic analysis of GD transgenic plants was also performed. Results The GD plants exhibited a significant increase (16%) in net photosynthesis rate while both HD and OX plants showed a non-significant (11%) increase as compared to wild type plants (WT). The stomatal conductance was significantly higher (24%) in GD and HD plants than the WT plants. The quantum efficiencies of photosystem II, carbon dioxide assimilation and the chlorophyll fluorescence-based photosynthetic electron transport rate were also higher than WT plants. The OX plants displayed significant reductions in the rate of photorespiration relative to gross photosynthesis and increase in the ratio of the photosynthetic electron flow attributable …
bibliographic citation: Abbasi et al. (2021) Expression of cyanobacterial genes enhanced CO2 assimilation and biomass production in transgenic Arabidopsis thaliana. PeerJ 9:e11860 https://doi.org/10.7717/peerj.11860
date submitted: 2021-02-28
date accepted: 2021-07-05
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abbasi
  given name: Anum Zeb
author list: Agent
  family name: Bilal
  given name: Misbah
author list: Agent
  family name: Khurshid
  given name: Ghazal
author list: Agent
  family name: Yiotis
  given name: Charilaos
author list: Agent
  family name: Zeb
  given name: Iftikhar
author list: Agent
  family name: Hussain
  given name: Jamshaid
author list: Agent
  family name: Baig
  given name: Ayesha
author list: Agent
  family name: Shah
  given name: Mohammad Maroof
author list: Agent
  family name: Chaudhary
  given name: Safee Ullah
author list: Agent
  family name: Osborne
  given name: Bruce
author list: Agent
  family name: Ahmad
  given name: Raza
doi: 10.7717/peerj.11860
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: © 2021 Abbasi et al.
attribution name: Abbasi et al.

Physiological changes and transcript identification in Coreopsis tinctoria Nutt. in early stages of salt stress
type: item
type: AcademicArticle
description: Coreopsis tinctoria Nutt. (C. tinctoria) is a special tea ingredient that adapts to certain salt stresses and shares the functions of chrysanthemum. With annual expansion of the cultivation area of C. tinctoria in Xinjiang (China), soil salinity may become a constraint for chrysanthemum cultivation. To investigate the response of C. tinctoria to salt stress, physiological and transcriptional changes in C. tinctoria in the early stages of low (50 mM NaCl) and high (200 mM NaCl) salt stress were analyzed and identified. The results showed that the contents of osmotic regulators (free proline, soluble sugar, and soluble protein) and antioxidant enzymes (catalase and peroxidase) under salt stress increased to various extents compared with those of the control (CK) within 72 h, and the increase was higher under 200 mM NaCl treatments. De novo RNA-seq was used to analyze changes in the transcripts under 50 and 200 mM NaCl treatments for up to 48 h. In total, 8,584, 3,760, 7,833, 19,341, 13,233, and 9,224 differentially expressed genes (DEGs) were detected under 12 h, 24 h, and 48 h for 50 and 200 mM NaCl treatments, respectively. Weighted correlation network analysis (WGCNA) was used to analyze the correlations between all DEGs and physiological indexes. We found that the coexpression modules blue2 and Lightskyblue4 highly correlated with osmotic regulators and CAT and identified 20 and 30 hub genes, respectively. The results provide useful data for the further study of salt tolerance in C. tinctoria.
format: application/pdf
format: text/html
creator: Hong Jiang
creator: Zhiyuan Li
creator: Xiumei Jiang
creator: Yong Qin
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.11888
publisher: PeerJ Inc.
rights: © 2021 Jiang et al.
abstract: Coreopsis tinctoria Nutt. (C. tinctoria) is a special tea ingredient that adapts to certain salt stresses and shares the functions of chrysanthemum. With annual expansion of the cultivation area of C. tinctoria in Xinjiang (China), soil salinity may become a constraint for chrysanthemum cultivation. To investigate the response of C. tinctoria to salt stress, physiological and transcriptional changes in C. tinctoria in the early stages of low (50 mM NaCl) and high (200 mM NaCl) salt stress were analyzed and identified. The results showed that the contents of osmotic regulators (free proline, soluble sugar, and soluble protein) and antioxidant enzymes (catalase and peroxidase) under salt stress increased to various extents compared with those of the control (CK) within 72 h, and the increase was higher under 200 mM NaCl treatments. De novo RNA-seq was used to analyze changes in the transcripts under 50 and 200 mM NaCl treatments for up to 48 h. In total, 8,584, 3,760, 7,833, 19,341, 13,233, and 9,224 differentially expressed genes (DEGs) were detected under 12 h, 24 h, and 48 h for 50 and 200 mM NaCl treatments, respectively. Weighted correlation network analysis (WGCNA) was used to analyze the correlations between all DEGs and physiological indexes. We found that the coexpression modules blue2 and Lightskyblue4 highly correlated with osmotic regulators and CAT and identified 20 and 30 hub genes, respectively. The results provide useful data for the further study of salt tolerance in C. tinctoria.
bibliographic citation: Jiang et al. (2021) Physiological changes and transcript identification in Coreopsis tinctoria Nutt. in early stages of salt stress. PeerJ 9:e11888 https://doi.org/10.7717/peerj.11888
date submitted: 2020-10-26
date accepted: 2021-07-09
issued: 2021-08-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Hong
author list: Agent
  family name: Li
  given name: Zhiyuan
author list: Agent
  family name: Jiang
  given name: Xiumei
author list: Agent
  family name: Qin
  given name: Yong
doi: 10.7717/peerj.11888
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-09
copyright: ©2021 Jiang et al.
attribution name: Jiang et al.

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.

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