PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Cathepsin S are involved in human carotid atherosclerotic disease progression, mainly by mediating phagosomes: bioinformatics and in vivo and vitro experiments
items: Evaluating the therapeutic effect of tumor treating fields (TTFields) by monitoring the impedance across TTFields electrode arrays
items: Genome-wide identification and functional characterization of CDPK gene family reveal their involvement in response to drought stress in Gossypium barbadense
items: Occurrence of microplastics in edible aquatic insect Pantala sp. (Odonata: Libellulidae) from rice fields
items: Detection of microplastics in Litopenaeus vannamei (Penaeidae) and Macrobrachium rosenbergii (Palaemonidae) in cultured pond
items: Antiviral drug discovery by targeting the SARS-CoV-2 polyprotein processing by inhibition of the main protease
items: Characterization of the bark storage protein gene (JcBSP) family in the perennial woody plant Jatropha curcas and the function of JcBSP1 in Arabidopsis thaliana
items: Cross-sectional study of chromosomal aberrations and immunologic factors in Iraqi couples with recurrent pregnancy loss
items: Using virtual reality for anatomical landmark annotation in geometric morphometrics
items: Temperature and duration of exposure drive infection intensity with the amphibian pathogen Batrachochytrium dendrobatidis

Cathepsin S are involved in human carotid atherosclerotic disease progression, mainly by mediating phagosomes: bioinformatics and in vivo and vitro experiments
type: item
type: AcademicArticle
description: Background Atherosclerosis emerges as a result of multiple dynamic cell processes including endothelial damage, inflammatory and immune cell infiltration, foam cell formation, plaque rupture, and thrombosis. Animal experiments have indicated that cathepsins (CTSs) mediate the antigen transmission and inflammatory response involved in the atherosclerosis process, but the specific signal pathways and target cells of the CTSs involved in atherosclerosis are unknown. Methods We used the GEO query package to download the dataset GSE28829 from the Gene Expression Omnibus (GEO) and filtered the data to check the standardization of the samples through the box chart. We then used the ‘limma’ package to analyze between-group differences and selected the corresponding differentially expressed genes of CTSs from the protein-protein interaction (PPI) network constructed with the STRING database, and then visualized the CTS-target genes. The best matching pathway and target cells were verified by a male mouse ligation experiment, single-sample GSEA (ssGSEA) analysis, and vitro experiment. Results There were 275 differentially expressed genes (DEGs) selected from the GSE28829 dataset, and the DEGs were identified mainly in the PPI network; 58 core genes (APOE, CD74, CP, AIF1, etc.) target three selected CTS family members (CTSS, CTSB, and CTSC). After the enriched analysis, 15 CTS-target genes were markedly enriched in the phagosome signaling pathway. The mouse experiment results revealed that the percentages and numbers of monocytes and neutrophils and the number of CD68+ cells in CTSS deficiency (CatS−/−) group were lower than those in the wildtype (CatS+/+) group. CTSS mediating phagosome via macrophage were further verified by ssGSEA analysis and vitro experiment. Conclusions CTSS are the main target molecules in the CTS family that are involved in atherosclerosis. The molecule participate in the progression of atherosclerosis by mediating the phagosome via macrophage.
format: application/pdf
format: text/html
creator: Hailong Wang
creator: Haiying Jiang
creator: Xian Wu Cheng
subject: Bioinformatics
subject: Genetics
subject: Cardiology
description: doi:10.7717/peerj.12846
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Atherosclerosis emerges as a result of multiple dynamic cell processes including endothelial damage, inflammatory and immune cell infiltration, foam cell formation, plaque rupture, and thrombosis. Animal experiments have indicated that cathepsins (CTSs) mediate the antigen transmission and inflammatory response involved in the atherosclerosis process, but the specific signal pathways and target cells of the CTSs involved in atherosclerosis are unknown. Methods We used the GEO query package to download the dataset GSE28829 from the Gene Expression Omnibus (GEO) and filtered the data to check the standardization of the samples through the box chart. We then used the ‘limma’ package to analyze between-group differences and selected the corresponding differentially expressed genes of CTSs from the protein-protein interaction (PPI) network constructed with the STRING database, and then visualized the CTS-target genes. The best matching pathway and target cells were verified by a male mouse ligation experiment, single-sample GSEA (ssGSEA) analysis, and vitro experiment. Results There were 275 differentially expressed genes (DEGs) selected from the GSE28829 dataset, and the DEGs were identified mainly in the PPI network; 58 core genes (APOE, CD74, CP, AIF1, etc.) target three selected CTS family members (CTSS, CTSB, and CTSC). After the enriched analysis, 15 CTS-target genes were markedly enriched in the phagosome signaling pathway. The mouse experiment results revealed that the percentages and numbers of monocytes and neutrophils and the number of CD68+ cells in CTSS deficiency (CatS−/−) group were lower than those in the wildtype (CatS+/+) group. CTSS mediating phagosome via macrophage were further verified by ssGSEA analysis and vitro experiment. Conclusions CTSS are the main target molecules in the CTS family that are involved in atherosclerosis. The molecule participate in the progression of atherosclerosis by mediating the phagosome via macrophage.
bibliographic citation: Wang et al. (2022) Cathepsin S are involved in human carotid atherosclerotic disease progression, mainly by mediating phagosomes: bioinformatics and in vivo and vitro experiments. PeerJ 10:e12846 https://doi.org/10.7717/peerj.12846
date submitted: 2021-08-24
date accepted: 2022-01-07
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hailong
author list: Agent
  family name: Jiang
  given name: Haiying
author list: Agent
  family name: Cheng
  given name: Xian Wu
doi: 10.7717/peerj.12846
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Evaluating the therapeutic effect of tumor treating fields (TTFields) by monitoring the impedance across TTFields electrode arrays
type: item
type: AcademicArticle
description: Background Tumor Treating Fields (TTFields), are a novel, non-invasive tissue ablation technology for treatment of cancer. Tissue ablation is achieved through the continuous delivery of a narrow range of electromagnetic fields across a tumor, for a period of months. TTFields are designed to affect only cells that divide and to interfere with the cell division process. The therapy is monitored with MRI imaging, performed every couple of months. Current technology is unable to assess the treatment effectiveness in real time. Methods We propose that the effect of the treatment can be assessed, in real time, by continuously measuring the change in electrical impedance across the TTFields delivery electrode arrays. An in vitro anatomic skull experimental study, with brain and tumor mimics phantom tissues was conducted to confirm the potential value of the proposed monitoring system. Results Experiments show that measuring the change in the impedance amplitude between opposite TTFields electrode arrays, at a typical TTFields treatment frequency of (200 kHz), can detect changes in the tumor radius with a sensitivity that increases with the radius of the tumor. The study shows that TTFields electrode arrays can be used to assess the effectiveness of TTFields treatment on changes in the tumor dimensions in real time, throughout the treatement. This monitoring system may become a valuable addition to the TTFields cancer treatment technology. It could provide the means to continuously assess the effectiveness of the treatment, and thereby optimize the design of the treatment protocol.
format: application/pdf
format: text/html
creator: Xing Li
creator: Moshe Oziel
creator: Boris Rubinsky
subject: Biochemistry
subject: Bioengineering
subject: Biophysics
subject: Biotechnology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.12877
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background Tumor Treating Fields (TTFields), are a novel, non-invasive tissue ablation technology for treatment of cancer. Tissue ablation is achieved through the continuous delivery of a narrow range of electromagnetic fields across a tumor, for a period of months. TTFields are designed to affect only cells that divide and to interfere with the cell division process. The therapy is monitored with MRI imaging, performed every couple of months. Current technology is unable to assess the treatment effectiveness in real time. Methods We propose that the effect of the treatment can be assessed, in real time, by continuously measuring the change in electrical impedance across the TTFields delivery electrode arrays. An in vitro anatomic skull experimental study, with brain and tumor mimics phantom tissues was conducted to confirm the potential value of the proposed monitoring system. Results Experiments show that measuring the change in the impedance amplitude between opposite TTFields electrode arrays, at a typical TTFields treatment frequency of (200 kHz), can detect changes in the tumor radius with a sensitivity that increases with the radius of the tumor. The study shows that TTFields electrode arrays can be used to assess the effectiveness of TTFields treatment on changes in the tumor dimensions in real time, throughout the treatement. This monitoring system may become a valuable addition to the TTFields cancer treatment technology. It could provide the means to continuously assess the effectiveness of the treatment, and thereby optimize the design of the treatment protocol.
bibliographic citation: Li et al. (2022) Evaluating the therapeutic effect of tumor treating fields (TTFields) by monitoring the impedance across TTFields electrode arrays. PeerJ 10:e12877 https://doi.org/10.7717/peerj.12877
date submitted: 2021-09-24
date accepted: 2022-01-12
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xing
author list: Agent
  family name: Oziel
  given name: Moshe
author list: Agent
  family name: Rubinsky
  given name: Boris
doi: 10.7717/peerj.12877
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Li et al.
attribution name: Li et al.

Genome-wide identification and functional characterization of CDPK gene family reveal their involvement in response to drought stress in Gossypium barbadense
type: item
type: AcademicArticle
description: Background Calcium dependent protein kinases (CDPKs) are a class of important calcium signal sensing response proteins, which play an important regulatory role in response to abiotic stress. However, researchers have not been excavated CDPKs’ role in drought in sea-island cotton(Gossypium barbadense L. ‘H7124’). Results Eighty-four CDPK genes have been identified in G. barbadense. These GbCDPK genes are unevenly distributed on 26 chromosomes, and segmental duplication is the significant way for the extension of CDPK family. Also, members within the same subfamily share a similar gene structure and motif composition. There are a large number of cis-elements involved in plant growth and response to stresses in the promoter regions of GbCDPKs. Additionally, these GbCDPKs show differential expression patterns in cotton tissues. The transcription levels of most genes were markedly altered in cotton under heat, cold, salt and PEG treatments, while the expressions of some GbCDPKs were induced in cotton under drought stress. Among these drought-induced genes, we selected GbCDPK32, GbCDPK68, GbCDPK74, GbCDPK80 and GbCDPK83 for further functional characterization by virus-induced gene silencing (VIGS) method. Conclusions In conclusion, the principal findings of this prospective study are that CDPKs were associated with drought. These findings provide a solid foundation for the development of future molecular mechanism in sea-island cotton.
format: application/pdf
format: text/html
creator: Guangzhen Shi
creator: Xinxia Zhu
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12883
publisher: PeerJ Inc.
rights: © 2022 Shi and Zhu
abstract: Background Calcium dependent protein kinases (CDPKs) are a class of important calcium signal sensing response proteins, which play an important regulatory role in response to abiotic stress. However, researchers have not been excavated CDPKs’ role in drought in sea-island cotton(Gossypium barbadense L. ‘H7124’). Results Eighty-four CDPK genes have been identified in G. barbadense. These GbCDPK genes are unevenly distributed on 26 chromosomes, and segmental duplication is the significant way for the extension of CDPK family. Also, members within the same subfamily share a similar gene structure and motif composition. There are a large number of cis-elements involved in plant growth and response to stresses in the promoter regions of GbCDPKs. Additionally, these GbCDPKs show differential expression patterns in cotton tissues. The transcription levels of most genes were markedly altered in cotton under heat, cold, salt and PEG treatments, while the expressions of some GbCDPKs were induced in cotton under drought stress. Among these drought-induced genes, we selected GbCDPK32, GbCDPK68, GbCDPK74, GbCDPK80 and GbCDPK83 for further functional characterization by virus-induced gene silencing (VIGS) method. Conclusions In conclusion, the principal findings of this prospective study are that CDPKs were associated with drought. These findings provide a solid foundation for the development of future molecular mechanism in sea-island cotton.
bibliographic citation: Shi et al. (2022) Genome-wide identification and functional characterization of CDPK gene family reveal their involvement in response to drought stress in Gossypium barbadense. PeerJ 10:e12883 https://doi.org/10.7717/peerj.12883
date submitted: 2021-11-04
date accepted: 2022-01-13
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Guangzhen
author list: Agent
  family name: Zhu
  given name: Xinxia
doi: 10.7717/peerj.12883
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Shi and Zhu
attribution name: Shi and Zhu

Occurrence of microplastics in edible aquatic insect Pantala sp. (Odonata: Libellulidae) from rice fields
type: item
type: AcademicArticle
description: Background Microplastic (MP) contamination has been discovered in aquatic systems throughout the world. They are well known as contaminants in aquatic species, but there is a gap in understanding about pathways of MP contamination into humans (i.e., through aquatic animals). The goal of this study is to assess MP contamination in an edible aquatic insect (Pantala sp.) living in rice fields. Methods A dragonfly larva, Pantala sp. (Odonata: Libellulidae), was tested for MPs. The study concentrated on three distinct anatomical compartments (whole body, gastrointestinal tract, and body without gastrointestinal tract), each of which was examined separately. For the physical identification and chemical analysis of MPs, a stereomicroscope and a Fourier transformed infrared spectroscope (FT-IR) were used, respectively. Results and Discussion The microplastics content was 121 in the whole body, 95 in the gastrointestinal tract, and 66 in the body without the gastrointestinal tract, with an average of 1.34 ± 1.11, 1.06 ± 0.77, and 0.73 ± 0.51 abundance/ individual, respectively. The most common MPs discovered during this study were fragments, followed by fibers and rods. The chemical analysis by FT-IR confirmed three different polymers, including polymethyl methacrylate (PMMA), polyethylene terephthalate (PET), and polypropylene (PP). There was no significant difference in MP abundances among the sample types (Kruskal-Wallis chi-squared = 2.774, df = 2, p = 0.250). The findings suggest that eating an edible aquatic insect (Odonata: Pantala sp.) could be one way for humans to ingest MPs.
format: application/pdf
format: text/html
creator: Witwisitpong Maneechan
creator: Taeng On Prommi
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Freshwater Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.12902
publisher: PeerJ Inc.
rights: © 2022 Maneechan and Prommi
abstract: Background Microplastic (MP) contamination has been discovered in aquatic systems throughout the world. They are well known as contaminants in aquatic species, but there is a gap in understanding about pathways of MP contamination into humans (i.e., through aquatic animals). The goal of this study is to assess MP contamination in an edible aquatic insect (Pantala sp.) living in rice fields. Methods A dragonfly larva, Pantala sp. (Odonata: Libellulidae), was tested for MPs. The study concentrated on three distinct anatomical compartments (whole body, gastrointestinal tract, and body without gastrointestinal tract), each of which was examined separately. For the physical identification and chemical analysis of MPs, a stereomicroscope and a Fourier transformed infrared spectroscope (FT-IR) were used, respectively. Results and Discussion The microplastics content was 121 in the whole body, 95 in the gastrointestinal tract, and 66 in the body without the gastrointestinal tract, with an average of 1.34 ± 1.11, 1.06 ± 0.77, and 0.73 ± 0.51 abundance/ individual, respectively. The most common MPs discovered during this study were fragments, followed by fibers and rods. The chemical analysis by FT-IR confirmed three different polymers, including polymethyl methacrylate (PMMA), polyethylene terephthalate (PET), and polypropylene (PP). There was no significant difference in MP abundances among the sample types (Kruskal-Wallis chi-squared = 2.774, df = 2, p = 0.250). The findings suggest that eating an edible aquatic insect (Odonata: Pantala sp.) could be one way for humans to ingest MPs.
bibliographic citation: Maneechan et al. (2022) Occurrence of microplastics in edible aquatic insect Pantala sp. (Odonata: Libellulidae) from rice fields. PeerJ 10:e12902 https://doi.org/10.7717/peerj.12902
date submitted: 2021-10-13
date accepted: 2022-01-17
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maneechan
  given name: Witwisitpong
author list: Agent
  family name: Prommi
  given name: Taeng On
doi: 10.7717/peerj.12902
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Maneechan and Prommi
attribution name: Maneechan and Prommi

Detection of microplastics in Litopenaeus vannamei (Penaeidae) and Macrobrachium rosenbergii (Palaemonidae) in cultured pond
type: item
type: AcademicArticle
description: Background The presence of plastic particles in freshwater species is becoming a global concern owing to the potential impact on food security and human health. In this study, we investigated the presence microplastics (MPs) in two economically important freshwater species: the giant freshwater prawn (Macrobrachium rosenbergii) and the white leg shrimp (Litopenaeus vannamei) cultured in a polyculture pond in the central part of Thailand. Methods The gastrointestinal tract (GT) of 300 giant freshwater prawn (160 female and 140 male) and 150 white leg shrimp specimens were investigated for the presence of MPs. Results From the pooled samples, a total of 1,166 MP items were identified. Specifically, the GTs of female and male freshwater prawns and white leg shrimps contained an average of 33.31 ± 19.42, 33.43 ± 19.07, and 11.00 ± 4.60 MP items per individual, respectively. Further, their mean MP contents per g of gut material were 32.66 ± 5.10, 32.14 ± 4.85, and 10.28 ± 1.19 MP items, respectively. In the GT of these species, MPs with sizes in the range 500–1000 µm, were predominant, and white/transparent MPs were most prevalent (63.67%). Furthermore, regarding the morphotypes of the MPs, fibers, fragments, films, and spheres were frequently observed, with fibers shows predominance. Specifically, the proportions of fibers in the GTs of female Macrobrachium rosenbergii, male Macrobrachium rosenbergii, and Litopenaeus vannamei were 83.3, 79.91, and 46.06%, respectively. Four MP polymer types, polyethylene, polycaprolactone, polyvinyl alcohol, and acrylonitrile butadiene styrene, were also identified via FTIR spectroscopy, which further confirmed the presence of MPs in the GT of the freshwater-cultured species. Discussion Our findings indicated that consuming shrimps and prawns without first removing the MPs from their GTs is one of the mean by which humans get exposed to MPs. Thus, MPs in freshwater species can be passed down the food chain to humans.
format: application/pdf
format: text/html
creator: Thanya Reunura
creator: Taeng On Prommi
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.12916
publisher: PeerJ Inc.
rights: © 2022 Reunura and Prommi
abstract: Background The presence of plastic particles in freshwater species is becoming a global concern owing to the potential impact on food security and human health. In this study, we investigated the presence microplastics (MPs) in two economically important freshwater species: the giant freshwater prawn (Macrobrachium rosenbergii) and the white leg shrimp (Litopenaeus vannamei) cultured in a polyculture pond in the central part of Thailand. Methods The gastrointestinal tract (GT) of 300 giant freshwater prawn (160 female and 140 male) and 150 white leg shrimp specimens were investigated for the presence of MPs. Results From the pooled samples, a total of 1,166 MP items were identified. Specifically, the GTs of female and male freshwater prawns and white leg shrimps contained an average of 33.31 ± 19.42, 33.43 ± 19.07, and 11.00 ± 4.60 MP items per individual, respectively. Further, their mean MP contents per g of gut material were 32.66 ± 5.10, 32.14 ± 4.85, and 10.28 ± 1.19 MP items, respectively. In the GT of these species, MPs with sizes in the range 500–1000 µm, were predominant, and white/transparent MPs were most prevalent (63.67%). Furthermore, regarding the morphotypes of the MPs, fibers, fragments, films, and spheres were frequently observed, with fibers shows predominance. Specifically, the proportions of fibers in the GTs of female Macrobrachium rosenbergii, male Macrobrachium rosenbergii, and Litopenaeus vannamei were 83.3, 79.91, and 46.06%, respectively. Four MP polymer types, polyethylene, polycaprolactone, polyvinyl alcohol, and acrylonitrile butadiene styrene, were also identified via FTIR spectroscopy, which further confirmed the presence of MPs in the GT of the freshwater-cultured species. Discussion Our findings indicated that consuming shrimps and prawns without first removing the MPs from their GTs is one of the mean by which humans get exposed to MPs. Thus, MPs in freshwater species can be passed down the food chain to humans.
bibliographic citation: Reunura et al. (2022) Detection of microplastics in Litopenaeus vannamei (Penaeidae) and Macrobrachium rosenbergii (Palaemonidae) in cultured pond. PeerJ 10:e12916 https://doi.org/10.7717/peerj.12916
date submitted: 2021-10-27
date accepted: 2022-01-20
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reunura
  given name: Thanya
author list: Agent
  family name: Prommi
  given name: Taeng On
doi: 10.7717/peerj.12916
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Reunura and Prommi
attribution name: Reunura and Prommi

Antiviral drug discovery by targeting the SARS-CoV-2 polyprotein processing by inhibition of the main protease
type: item
type: AcademicArticle
description: The spread of SARS-CoV-2, the causative agent for COVID-19, has led to a global and deadly pandemic. To date, few drugs have been approved for treating SARS-CoV-2 infections. In this study, a structure-based approach was adopted using the SARS-CoV-2 main protease (Mpro) and a carefully selected dataset of 37,060 compounds comprising Mpro and antiviral protein-specific libraries. The compounds passed two-step docking filtration, starting with standard precision (SP) followed by extra precision (XP) runs. Fourteen compounds with the highest XP docking scores were examined by 20 ns molecular dynamics simulations (MDs). Based on backbone route mean square deviations (RMSD) and molecular mechanics/generalized Born surface area (MM/GBSA) binding energy, four drugs were selected for comprehensive MDs analysis at 100 ns. Results indicated that birinapant, atazanavir, and ritonavir potently bound and stabilized SARS-CoV-2 Mpro structure. Binding energies higher than −102 kcal/mol, RMSD values <0.22 nm, formation of several hydrogen bonds with Mpro, favourable electrostatic contributions, and low radii of gyration were among the estimated factors contributing to the strength of the binding of these three compounds with Mpro. The top two compounds, atazanavir and birinapant, were tested for their ability to prevent SARS-CoV-2 plaque formation. At 10 µM of birinapant concentration, antiviral tests against SARS-CoV-2 demonstrated a 37% reduction of virus multiplication. Antiviral assays demonstrated that birinapant has high anti-SARS-CoV-2 activity in the low micromolar range, with an IC50 value of 18 ± 3.6 µM. Therefore, birinapant is a candidate for further investigation to determine whether it is a feasible therapy option.
format: application/pdf
format: text/html
creator: Mahmoud Kandeel
creator: Jinsoo Kim
creator: Mahmoud Fayez
creator: Yukio Kitade
creator: Hyung-Joo Kwon
subject: Biochemistry
subject: Bioinformatics
subject: Computational Biology
subject: Computational Science
description: doi:10.7717/peerj.12929
publisher: PeerJ Inc.
rights: © 2022 Kandeel et al.
abstract: The spread of SARS-CoV-2, the causative agent for COVID-19, has led to a global and deadly pandemic. To date, few drugs have been approved for treating SARS-CoV-2 infections. In this study, a structure-based approach was adopted using the SARS-CoV-2 main protease (Mpro) and a carefully selected dataset of 37,060 compounds comprising Mpro and antiviral protein-specific libraries. The compounds passed two-step docking filtration, starting with standard precision (SP) followed by extra precision (XP) runs. Fourteen compounds with the highest XP docking scores were examined by 20 ns molecular dynamics simulations (MDs). Based on backbone route mean square deviations (RMSD) and molecular mechanics/generalized Born surface area (MM/GBSA) binding energy, four drugs were selected for comprehensive MDs analysis at 100 ns. Results indicated that birinapant, atazanavir, and ritonavir potently bound and stabilized SARS-CoV-2 Mpro structure. Binding energies higher than −102 kcal/mol, RMSD values <0.22 nm, formation of several hydrogen bonds with Mpro, favourable electrostatic contributions, and low radii of gyration were among the estimated factors contributing to the strength of the binding of these three compounds with Mpro. The top two compounds, atazanavir and birinapant, were tested for their ability to prevent SARS-CoV-2 plaque formation. At 10 µM of birinapant concentration, antiviral tests against SARS-CoV-2 demonstrated a 37% reduction of virus multiplication. Antiviral assays demonstrated that birinapant has high anti-SARS-CoV-2 activity in the low micromolar range, with an IC50 value of 18 ± 3.6 µM. Therefore, birinapant is a candidate for further investigation to determine whether it is a feasible therapy option.
bibliographic citation: Kandeel et al. (2022) Antiviral drug discovery by targeting the SARS-CoV-2 polyprotein processing by inhibition of the main protease. PeerJ 10:e12929 https://doi.org/10.7717/peerj.12929
date submitted: 2021-09-16
date accepted: 2022-01-21
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kandeel
  given name: Mahmoud
author list: Agent
  family name: Kim
  given name: Jinsoo
author list: Agent
  family name: Fayez
  given name: Mahmoud
author list: Agent
  family name: Kitade
  given name: Yukio
author list: Agent
  family name: Kwon
  given name: Hyung-Joo
doi: 10.7717/peerj.12929
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Kandeel et al.
attribution name: Kandeel et al.

Characterization of the bark storage protein gene (JcBSP) family in the perennial woody plant Jatropha curcas and the function of JcBSP1 in Arabidopsis thaliana
type: item
type: AcademicArticle
description: Background Bark storage protein (BSP) plays an important role in seasonal nitrogen cycling in perennial deciduous trees. However, there is no report on the function of BSP in the perennial woody oil plant Jatropha curcas. Methods In this study, we identified six members of JcBSP gene family in J. curcas genome. The patterns, seasonal changes, and responses to nitrogen treatment in gene expression of JcBSPs were detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Overexpression of JcBSP1 in transgenic Arabidopsis thaliana was driven by a constitutive cauliflower mosaic virus (CaMV) 35S RNA promoter. Results JcBSP members were found to be expressed in various tissues, except seeds. The seasonal changes in the total protein concentration and JcBSP1 expression in the stems of J. curcas were positively correlated, as both increased in autumn and winter and decreased in spring and summer. In addition, the JcBSP1 expression in J. curcas seedlings treated with different concentrations of an NH4NO3 solution was positively correlated with the NH4NO3 concentration and application duration. Furthermore, JcBSP1 overexpression in Arabidopsis resulted in a phenotype of enlarged rosette leaves, flowers, and seeds, and significantly increased the seed weight and yield in transgenic plants.
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creator: Ming-Jun Zhang
creator: Qiantang Fu
creator: Mao-Sheng Chen
creator: Huiying He
creator: Mingyong Tang
creator: Jun Ni
creator: Yan-Bin Tao
creator: Zeng-Fu Xu
subject: Molecular Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.12938
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Bark storage protein (BSP) plays an important role in seasonal nitrogen cycling in perennial deciduous trees. However, there is no report on the function of BSP in the perennial woody oil plant Jatropha curcas. Methods In this study, we identified six members of JcBSP gene family in J. curcas genome. The patterns, seasonal changes, and responses to nitrogen treatment in gene expression of JcBSPs were detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Overexpression of JcBSP1 in transgenic Arabidopsis thaliana was driven by a constitutive cauliflower mosaic virus (CaMV) 35S RNA promoter. Results JcBSP members were found to be expressed in various tissues, except seeds. The seasonal changes in the total protein concentration and JcBSP1 expression in the stems of J. curcas were positively correlated, as both increased in autumn and winter and decreased in spring and summer. In addition, the JcBSP1 expression in J. curcas seedlings treated with different concentrations of an NH4NO3 solution was positively correlated with the NH4NO3 concentration and application duration. Furthermore, JcBSP1 overexpression in Arabidopsis resulted in a phenotype of enlarged rosette leaves, flowers, and seeds, and significantly increased the seed weight and yield in transgenic plants.
bibliographic citation: Zhang et al. (2022) Characterization of the bark storage protein gene (JcBSP) family in the perennial woody plant Jatropha curcas and the function of JcBSP1 in Arabidopsis thaliana. PeerJ 10:e12938 https://doi.org/10.7717/peerj.12938
date submitted: 2021-11-10
date accepted: 2022-01-24
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Ming-Jun
author list: Agent
  family name: Fu
  given name: Qiantang
author list: Agent
  family name: Chen
  given name: Mao-Sheng
author list: Agent
  family name: He
  given name: Huiying
author list: Agent
  family name: Tang
  given name: Mingyong
author list: Agent
  family name: Ni
  given name: Jun
author list: Agent
  family name: Tao
  given name: Yan-Bin
author list: Agent
  family name: Xu
  given name: Zeng-Fu
doi: 10.7717/peerj.12938
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

Cross-sectional study of chromosomal aberrations and immunologic factors in Iraqi couples with recurrent pregnancy loss
type: item
type: AcademicArticle
description: Background Parental chromosomal aberrations are important causes of recurrent pregnancy loss (RPL). Some immunological factors such as antiphospholipid antibodies and interleukin-6 (IL-6) also contribute to this complication. The aim of this study was to determine the frequency of chromosomal abnormalities and to evaluate some of the immunological factors in couples with RPL from different cities in Iraq. Methods This study was conducted on 25 couples (50 individuals) who had more than two first trimester abortions in the past and 25 healthy females as controls. Karyotyping was performed on peripheral blood of all participants. Anticardiolipin (IgG and IgM), antiphosopholipid (IgG and IgM), lupus anticoagulant, and IL-6 were assayed. Data were analyzed using appropriate statistical tests. Results Chromosomal abnormalities were found in 28.0% (n = 7/25) of RPL couples. Of these five (10.0%) were female and two (4.0%) were male. The types of structural abnormalities were as follows: 45, XX, t(21; 21); 45, XX, rob (14, 15); 46, XX, add (21) (p13); 46 XY, add (21)(p13); 46, XX, 21ps+; 46, XY, per inv (9) (p11q12) and 45, XX, t(13q, 13q). No chromosomal abnormalities were found in the control group. Also, no significant differences were found in the immunological parameters of the couples with RPL and the control group. Conclusion In this study, karyotyping revealed a high number of chromosomal abnormalities associated with the RPL in Iraqi couples. Since identification of genetic causes of miscarriage is important for genetic counseling and educating couples about the risk of future pregnancies, it is recommended that conventional karyotyping be investigated in patients with RPL.
format: application/pdf
format: text/html
creator: Doaa A. Khamees
creator: Mushtak T. S. Al-Ouqaili
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Andrology
subject: Gynecology and Obstetrics
description: doi:10.7717/peerj.12801
publisher: PeerJ Inc.
rights: © 2022 Khamees and Al-Ouqaili
abstract: Background Parental chromosomal aberrations are important causes of recurrent pregnancy loss (RPL). Some immunological factors such as antiphospholipid antibodies and interleukin-6 (IL-6) also contribute to this complication. The aim of this study was to determine the frequency of chromosomal abnormalities and to evaluate some of the immunological factors in couples with RPL from different cities in Iraq. Methods This study was conducted on 25 couples (50 individuals) who had more than two first trimester abortions in the past and 25 healthy females as controls. Karyotyping was performed on peripheral blood of all participants. Anticardiolipin (IgG and IgM), antiphosopholipid (IgG and IgM), lupus anticoagulant, and IL-6 were assayed. Data were analyzed using appropriate statistical tests. Results Chromosomal abnormalities were found in 28.0% (n = 7/25) of RPL couples. Of these five (10.0%) were female and two (4.0%) were male. The types of structural abnormalities were as follows: 45, XX, t(21; 21); 45, XX, rob (14, 15); 46, XX, add (21) (p13); 46 XY, add (21)(p13); 46, XX, 21ps+; 46, XY, per inv (9) (p11q12) and 45, XX, t(13q, 13q). No chromosomal abnormalities were found in the control group. Also, no significant differences were found in the immunological parameters of the couples with RPL and the control group. Conclusion In this study, karyotyping revealed a high number of chromosomal abnormalities associated with the RPL in Iraqi couples. Since identification of genetic causes of miscarriage is important for genetic counseling and educating couples about the risk of future pregnancies, it is recommended that conventional karyotyping be investigated in patients with RPL.
bibliographic citation: Khamees et al. (2022) Cross-sectional study of chromosomal aberrations and immunologic factors in Iraqi couples with recurrent pregnancy loss. PeerJ 10:e12801 https://doi.org/10.7717/peerj.12801
date submitted: 2021-10-25
date accepted: 2021-12-24
issued: 2022-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khamees
  given name: Doaa A.
author list: Agent
  family name: Al-Ouqaili
  given name: Mushtak T. S.
doi: 10.7717/peerj.12801
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-07
copyright: © 2022 Khamees and Al-Ouqaili
attribution name: Khamees and Al-Ouqaili

Using virtual reality for anatomical landmark annotation in geometric morphometrics
type: item
type: AcademicArticle
description: To study the shape of objects using geometric morphometrics, landmarks are oftentimes collected digitally from a 3D scanned model. The expert may annotate landmarks using software that visualizes the 3D model on a flat screen, and interaction is achieved with a mouse and a keyboard. However, landmark annotation of a 3D model on a 2D display is a tedious process and potentially introduces error due to the perception and interaction limitations of the flat interface. In addition, digital landmark placement can be more time-consuming than direct annotation on the physical object using a tactile digitizer arm. Since virtual reality (VR) is designed to more closely resemble the real world, we present a VR prototype for annotating landmarks on 3D models. We study the impact of VR on annotation performance by comparing our VR prototype to Stratovan Checkpoint, a commonly used commercial desktop software. We use an experimental setup, where four operators placed six landmarks on six grey seal (Halichoerus grypus) skulls in six trials for both systems. This enables us to investigate multiple sources of measurement error. We analyse both for the configuration and for single landmarks. Our analysis shows that annotation in VR is a promising alternative to desktop annotation. We find that annotation precision is comparable between the two systems, with VR being significantly more precise for one of the landmarks. We do not find evidence that annotation in VR is faster than on the desktop, but it is accurate.
format: application/pdf
format: text/html
creator: Dolores Messer
creator: Michael Atchapero
creator: Mark B. Jensen
creator: Michelle S. Svendsen
creator: Anders Galatius
creator: Morten T. Olsen
creator: Jeppe R. Frisvad
creator: Vedrana A. Dahl
creator: Knut Conradsen
creator: Anders B. Dahl
creator: Andreas Bærentzen
subject: Zoology
subject: Data Science
description: doi:10.7717/peerj.12869
publisher: PeerJ Inc.
rights: © 2022 Messer et al.
abstract: To study the shape of objects using geometric morphometrics, landmarks are oftentimes collected digitally from a 3D scanned model. The expert may annotate landmarks using software that visualizes the 3D model on a flat screen, and interaction is achieved with a mouse and a keyboard. However, landmark annotation of a 3D model on a 2D display is a tedious process and potentially introduces error due to the perception and interaction limitations of the flat interface. In addition, digital landmark placement can be more time-consuming than direct annotation on the physical object using a tactile digitizer arm. Since virtual reality (VR) is designed to more closely resemble the real world, we present a VR prototype for annotating landmarks on 3D models. We study the impact of VR on annotation performance by comparing our VR prototype to Stratovan Checkpoint, a commonly used commercial desktop software. We use an experimental setup, where four operators placed six landmarks on six grey seal (Halichoerus grypus) skulls in six trials for both systems. This enables us to investigate multiple sources of measurement error. We analyse both for the configuration and for single landmarks. Our analysis shows that annotation in VR is a promising alternative to desktop annotation. We find that annotation precision is comparable between the two systems, with VR being significantly more precise for one of the landmarks. We do not find evidence that annotation in VR is faster than on the desktop, but it is accurate.
bibliographic citation: Messer et al. (2022) Using virtual reality for anatomical landmark annotation in geometric morphometrics. PeerJ 10:e12869 https://doi.org/10.7717/peerj.12869
date submitted: 2021-10-27
date accepted: 2022-01-10
issued: 2022-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Messer
  given name: Dolores
author list: Agent
  family name: Atchapero
  given name: Michael
author list: Agent
  family name: Jensen
  given name: Mark B.
author list: Agent
  family name: Svendsen
  given name: Michelle S.
author list: Agent
  family name: Galatius
  given name: Anders
author list: Agent
  family name: Olsen
  given name: Morten T.
author list: Agent
  family name: Frisvad
  given name: Jeppe R.
author list: Agent
  family name: Dahl
  given name: Vedrana A.
author list: Agent
  family name: Conradsen
  given name: Knut
author list: Agent
  family name: Dahl
  given name: Anders B.
author list: Agent
  family name: Bærentzen
  given name: Andreas
doi: 10.7717/peerj.12869
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-07
copyright: © 2022 Messer et al.
attribution name: Messer et al.

Temperature and duration of exposure drive infection intensity with the amphibian pathogen Batrachochytrium dendrobatidis
type: item
type: AcademicArticle
description: The intensity of a pathogen infection plays a key role in determining how the host responds to infection. Hosts with high infections are more likely to transmit infection to others, and are may be more likely to experience progression from infection to disease symptoms, to being physiologically compromised by disease. Understanding how and why hosts exhibit variation in infection intensity therefore plays a major part in developing and implementing measures aimed at controlling infection spread, its effects, and its chance of persisting and circulating within a population of hosts. To track the relative importance of a number of variables in determining the level of infection intensity, we ran field-surveys at two breeding sites over a 12 month period using marked larvae of the common midwife toad (Alyes obstetricans) and their levels of infection with the amphibian pathogen Batrachochytrium dendrobatidis (Bd). At each sampling occasion we measured the density of larvae, the temperature of the water in the 48 h prior to sampling, the period of time the sampled individual had been in the water body, the developmental (Gosner) stage and the intensity of Bd infection of the individual. Overall our data suggest that the temperature and the duration of time spent in the water play a major role in determining the intensity of Bd infection within an individual host. However, although the duration of time spent in the water was clearly associated with infection intensity, the relationship was negative: larvae that had spent less than 3–6 months in the water had significantly higher infection intensities than those that had spent over 12 months, although this infection intensity peaked between 9 and 12 months. This could be due to animals with heavier infections developing more quickly, suffering increased mortality or, more likely, losing their mouthparts (the only part of anuran larvae that can be infected with Bd). Overall, our results identify drivers of infection intens…
format: application/pdf
format: text/html
creator: Jon Bielby
creator: Cristina Sausor
creator: Camino Monsalve-Carcaño
creator: Jaime Bosch
subject: Conservation Biology
subject: Ecology
subject: Parasitology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12889
publisher: PeerJ Inc.
rights: © 2022 Bielby et al.
abstract: The intensity of a pathogen infection plays a key role in determining how the host responds to infection. Hosts with high infections are more likely to transmit infection to others, and are may be more likely to experience progression from infection to disease symptoms, to being physiologically compromised by disease. Understanding how and why hosts exhibit variation in infection intensity therefore plays a major part in developing and implementing measures aimed at controlling infection spread, its effects, and its chance of persisting and circulating within a population of hosts. To track the relative importance of a number of variables in determining the level of infection intensity, we ran field-surveys at two breeding sites over a 12 month period using marked larvae of the common midwife toad (Alyes obstetricans) and their levels of infection with the amphibian pathogen Batrachochytrium dendrobatidis (Bd). At each sampling occasion we measured the density of larvae, the temperature of the water in the 48 h prior to sampling, the period of time the sampled individual had been in the water body, the developmental (Gosner) stage and the intensity of Bd infection of the individual. Overall our data suggest that the temperature and the duration of time spent in the water play a major role in determining the intensity of Bd infection within an individual host. However, although the duration of time spent in the water was clearly associated with infection intensity, the relationship was negative: larvae that had spent less than 3–6 months in the water had significantly higher infection intensities than those that had spent over 12 months, although this infection intensity peaked between 9 and 12 months. This could be due to animals with heavier infections developing more quickly, suffering increased mortality or, more likely, losing their mouthparts (the only part of anuran larvae that can be infected with Bd). Overall, our results identify drivers of infection intens…
bibliographic citation: Bielby et al. (2022) Temperature and duration of exposure drive infection intensity with the amphibian pathogen Batrachochytrium dendrobatidis. PeerJ 10:e12889 https://doi.org/10.7717/peerj.12889
date submitted: 2021-09-17
date accepted: 2022-01-14
issued: 2022-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bielby
  given name: Jon
author list: Agent
  family name: Sausor
  given name: Cristina
author list: Agent
  family name: Monsalve-Carcaño
  given name: Camino
author list: Agent
  family name: Bosch
  given name: Jaime
doi: 10.7717/peerj.12889
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-07
copyright: © 2022 Bielby et al.
attribution name: Bielby et al.

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