PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Online e-learning during the COVID-19 lockdown in Trinidad and Tobago: prevalence and associated factors with ocular complaints among schoolchildren aged 11–19 years
items: Cell division cycle associated 2 (CDCA2) upregulation promotes the progression of hepatocellular carcinoma in a p53-dependant manner
items: Association between fibrinogen/albumin ratio and severity of coronary artery calcification in patients with chronic kidney disease: a retrospective study
items: Stable nitrogen and carbon isotope compositions in plant-soil systems under different land-use types in a red soil region, Southeast China
items: Determination of muscle strength and function in plesiosaur limbs: finite element structural analyses of Cryptoclidus eurymerus humerus and femur
items: Quercetin prevents chronic kidney disease on mesangial cells model by regulating inflammation, oxidative stress, and TGF-β1/SMADs pathway
items: Withasomniferol C, a new potential SARS-CoV-2 main protease inhibitor from the Withania somnifera plant proposed by in silico approaches
items: A new hybodontiform shark (Strophodus Agassiz 1838) from the Lower Cretaceous (Valanginian-Hauterivian) of Colombia
items: A new species of deep-sea grunt, Rhonciscus pauco (Lutjaniformes: Haemulidae), from Puerto Rico
items: Calotropin and corotoxigenin 3-O-glucopyranoside from the desert milkweed Asclepias subulata inhibit the Na+/K+-ATPase activity

Online e-learning during the COVID-19 lockdown in Trinidad and Tobago: prevalence and associated factors with ocular complaints among schoolchildren aged 11–19 years
type: item
type: AcademicArticle
description: Background The increase in online learning during the pandemic has been linked to various ocular complaints. This study determined the prevalence and factors associated with ocular complaints among schoolchildren aged 12–19 years during the COVID-19 lockdown in Trinidad and Tobago (T&T). Methods A cross-sectional study was conducted between January and May 2021, during the COVID-19 lockdown in T&T among secondary school students studying remotely. A two-stage cluster sampling method was employed. A modified web-based Computer Vision Syndrome questionnaire was administered to students. Data on demography, duration of digital device use, and ocular complaints were collected, and multilevel logistic regression was used to determine factors associated with ocular complaints among school children, 12–19 years of age in T&T. Results A total of 435 schoolchildren (mean age, standard deviation, 15.2 ± 1.9 years range 12–19 years) responded to the questionnaire. The prevalence of self-reported symptoms of headache, blurred vision, dry eyes, itchy eyes, and double vision were 75.0%, 65.1%; 56.8%; 46.4%; and 33.5%, respectively. Schoolchildren aged 18–19 years, those that used spectacles for correction of their refractive errors, and spent more than 6 h on average on digital devices, reported a high prevalence of any ocular complaints. Analysis also revealed that age (14–15 years) was associated with dry eyes, blurred vision, and headaches, while gender (more prevalently females) was associated with blurred vision and headache. Those that had an eye examination in the last year and schoolchildren that took action to resolve ocular complaints were more likely to experience nearly all ocular complaints. Conclusions During the COVID-19 lockdown, over three in four students in T&T reported ocular complaints from digital devices for online learning. Tailored interventional messages to reduce all forms of ocular complaints should target older students, particularly females, those wh…
format: application/pdf
format: text/html
creator: Kingsley Ekemiri
creator: Ngozika Ezinne
creator: Khadeejah Kamalodeen
creator: Keomi Pierre
creator: Brandon Lalla
creator: Onyekachukwu Amiebenomo
creator: Diane van Staden
creator: Ferial Zeried
creator: Chioma Ekemiri
creator: Kingsley E. Agho
creator: Uchechukwu Levi Osuagwu
subject: Infectious Diseases
subject: Ophthalmology
subject: Pediatrics
subject: Science and Medical Education
subject: COVID-19
description: doi:10.7717/peerj.13334
publisher: PeerJ Inc.
rights: © 2022 Ekemiri et al.
abstract: Background The increase in online learning during the pandemic has been linked to various ocular complaints. This study determined the prevalence and factors associated with ocular complaints among schoolchildren aged 12–19 years during the COVID-19 lockdown in Trinidad and Tobago (T&T). Methods A cross-sectional study was conducted between January and May 2021, during the COVID-19 lockdown in T&T among secondary school students studying remotely. A two-stage cluster sampling method was employed. A modified web-based Computer Vision Syndrome questionnaire was administered to students. Data on demography, duration of digital device use, and ocular complaints were collected, and multilevel logistic regression was used to determine factors associated with ocular complaints among school children, 12–19 years of age in T&T. Results A total of 435 schoolchildren (mean age, standard deviation, 15.2 ± 1.9 years range 12–19 years) responded to the questionnaire. The prevalence of self-reported symptoms of headache, blurred vision, dry eyes, itchy eyes, and double vision were 75.0%, 65.1%; 56.8%; 46.4%; and 33.5%, respectively. Schoolchildren aged 18–19 years, those that used spectacles for correction of their refractive errors, and spent more than 6 h on average on digital devices, reported a high prevalence of any ocular complaints. Analysis also revealed that age (14–15 years) was associated with dry eyes, blurred vision, and headaches, while gender (more prevalently females) was associated with blurred vision and headache. Those that had an eye examination in the last year and schoolchildren that took action to resolve ocular complaints were more likely to experience nearly all ocular complaints. Conclusions During the COVID-19 lockdown, over three in four students in T&T reported ocular complaints from digital devices for online learning. Tailored interventional messages to reduce all forms of ocular complaints should target older students, particularly females, those wh…
bibliographic citation: Ekemiri et al. (2022) Online e-learning during the COVID-19 lockdown in Trinidad and Tobago: prevalence and associated factors with ocular complaints among schoolchildren aged 11–19 years. PeerJ 10:e13334 https://doi.org/10.7717/peerj.13334
date submitted: 2022-01-18
date accepted: 2022-04-04
issued: 2022-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ekemiri
  given name: Kingsley
author list: Agent
  family name: Ezinne
  given name: Ngozika
author list: Agent
  family name: Kamalodeen
  given name: Khadeejah
author list: Agent
  family name: Pierre
  given name: Keomi
author list: Agent
  family name: Lalla
  given name: Brandon
author list: Agent
  family name: Amiebenomo
  given name: Onyekachukwu
author list: Agent
  family name: van Staden
  given name: Diane
author list: Agent
  family name: Zeried
  given name: Ferial
author list: Agent
  family name: Ekemiri
  given name: Chioma
author list: Agent
  family name: Agho
  given name: Kingsley E.
author list: Agent
  family name: Osuagwu
  given name: Uchechukwu Levi
doi: 10.7717/peerj.13334
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-06
copyright: © 2022 Ekemiri et al.
attribution name: Ekemiri et al.

Cell division cycle associated 2 (CDCA2) upregulation promotes the progression of hepatocellular carcinoma in a p53-dependant manner
type: item
type: AcademicArticle
description: Background Elevated expression and oncogenic functions of cell division cycle associated 2 (CDCA2), an important mitotic regulator, have been demonstrated in several cancer types, however their involvement in hepatocellular carcinoma (HCC) has not been elucidated, and the underlying molecular mechanism remains unclear. This study aims to determine the role of CDCA2 in HCC and the underlying molecular mechanism. Methods The expression of CDCA2 in HCC was studied in 40 pairs of frozen and 48 pairs of paraffin-embedded HCC samples and paracancerous normal samples by qRT-PCR and immunohistochemistry, respectively, and using The Cancer Genome Atlas (TCGA) datasets. The cellular function of CDCA2 was studied in vitro in the HepG2, Huh7 and SK-Hep1 HCC cell lines. Results We found significantly upregulated CDCA2 expression in HCC, which was correlated with higher clinical stage, tumor grade and Glypican-3 (+). High CDCA2 expression was correlated with worse overall survival. CDCA2 promoted the proliferation of HCC cells by promoting G1/S transition through the upregulation and activation of CCND1/CDK4/6 and CCNE1/CDK2, enhanced the clonogenic ability, inhibited apoptosis in a p53/p21-dependent manner by inhibiting the p38 MAPK pathway and activating the JNK/c-Jun pathway, and promoted the migration of p53-mutant Huh7 cells by activating the epithelial-mesenchymal transition. Targeting CDCA2 reduced the chemoresistance of HCC cells to cisplatin. CDCA2 expression was also regulated by cyclophilin J. Conclusions This study revealed elevated expression of CDCA2 in HCC, possibly as a result of p53 dysregulation, which was associated with worse prognosis of patients. We confirmed the oncogenic role of CDCA2 in HCC in vitro and revealed some of the underlying molecular mechanisms. This study indicated the potential value of CDCA2 as a future target for the treatment of HCC.
format: application/pdf
format: text/html
creator: Jiahui Wang
creator: Xin Liu
creator: Hongjin Chu
creator: Jian Chen
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.13535
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Elevated expression and oncogenic functions of cell division cycle associated 2 (CDCA2), an important mitotic regulator, have been demonstrated in several cancer types, however their involvement in hepatocellular carcinoma (HCC) has not been elucidated, and the underlying molecular mechanism remains unclear. This study aims to determine the role of CDCA2 in HCC and the underlying molecular mechanism. Methods The expression of CDCA2 in HCC was studied in 40 pairs of frozen and 48 pairs of paraffin-embedded HCC samples and paracancerous normal samples by qRT-PCR and immunohistochemistry, respectively, and using The Cancer Genome Atlas (TCGA) datasets. The cellular function of CDCA2 was studied in vitro in the HepG2, Huh7 and SK-Hep1 HCC cell lines. Results We found significantly upregulated CDCA2 expression in HCC, which was correlated with higher clinical stage, tumor grade and Glypican-3 (+). High CDCA2 expression was correlated with worse overall survival. CDCA2 promoted the proliferation of HCC cells by promoting G1/S transition through the upregulation and activation of CCND1/CDK4/6 and CCNE1/CDK2, enhanced the clonogenic ability, inhibited apoptosis in a p53/p21-dependent manner by inhibiting the p38 MAPK pathway and activating the JNK/c-Jun pathway, and promoted the migration of p53-mutant Huh7 cells by activating the epithelial-mesenchymal transition. Targeting CDCA2 reduced the chemoresistance of HCC cells to cisplatin. CDCA2 expression was also regulated by cyclophilin J. Conclusions This study revealed elevated expression of CDCA2 in HCC, possibly as a result of p53 dysregulation, which was associated with worse prognosis of patients. We confirmed the oncogenic role of CDCA2 in HCC in vitro and revealed some of the underlying molecular mechanisms. This study indicated the potential value of CDCA2 as a future target for the treatment of HCC.
bibliographic citation: Wang et al. (2022) Cell division cycle associated 2 (CDCA2) upregulation promotes the progression of hepatocellular carcinoma in a p53-dependant manner. PeerJ 10:e13535 https://doi.org/10.7717/peerj.13535
date submitted: 2022-02-14
date accepted: 2022-05-13
issued: 2022-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jiahui
author list: Agent
  family name: Liu
  given name: Xin
author list: Agent
  family name: Chu
  given name: Hongjin
author list: Agent
  family name: Chen
  given name: Jian
doi: 10.7717/peerj.13535
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-06
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Association between fibrinogen/albumin ratio and severity of coronary artery calcification in patients with chronic kidney disease: a retrospective study
type: item
type: AcademicArticle
description: Aim Previous studies have shown that the fibrinogen to albumin ratio (FAR) is closely related to the severity and prognosis of coronary atherosclerosis. In this study, we sought to evaluate the association between FAR and the degree of coronary artery calcification (CAC) in patients with chronic kidney disease (CKD). Methods In this retrospective study, 218 patients with CKD were stratified into low, medium and high FAR groups according to the tertiles of the FAR values. The CAC scores, clinical information and laboratory test results of the three FAR groups were compared. To explore the relationship between FAR and CAC we conducted binary logistic regression and correlation analyses. Results In the low FAR group, the CAC scores were significantly lower than those in the medium and high FAR groups (P < 0.001). There was a significant correlation between the FAR and CAC scores (r = 0.510, P < 0.001). The FAR was an independent predictor of CAC (OR = 1.106, 95% CI [1.004–1.218], P = 0.042). Conclusion In patients with CKD, the FAR can be considered as an effective predictor of CAC.
format: application/pdf
format: text/html
creator: Yuyu Zhu
creator: Shuman Tao
creator: Danfeng Zhang
creator: Jianping Xiao
creator: Xuerong Wang
creator: Liang Yuan
creator: Haifeng Pan
creator: Deguang Wang
subject: Cardiology
subject: Epidemiology
subject: Hematology
subject: Nephrology
description: doi:10.7717/peerj.13550
publisher: PeerJ Inc.
rights: © 2022 Zhu et al.
abstract: Aim Previous studies have shown that the fibrinogen to albumin ratio (FAR) is closely related to the severity and prognosis of coronary atherosclerosis. In this study, we sought to evaluate the association between FAR and the degree of coronary artery calcification (CAC) in patients with chronic kidney disease (CKD). Methods In this retrospective study, 218 patients with CKD were stratified into low, medium and high FAR groups according to the tertiles of the FAR values. The CAC scores, clinical information and laboratory test results of the three FAR groups were compared. To explore the relationship between FAR and CAC we conducted binary logistic regression and correlation analyses. Results In the low FAR group, the CAC scores were significantly lower than those in the medium and high FAR groups (P < 0.001). There was a significant correlation between the FAR and CAC scores (r = 0.510, P < 0.001). The FAR was an independent predictor of CAC (OR = 1.106, 95% CI [1.004–1.218], P = 0.042). Conclusion In patients with CKD, the FAR can be considered as an effective predictor of CAC.
bibliographic citation: Zhu et al. (2022) Association between fibrinogen/albumin ratio and severity of coronary artery calcification in patients with chronic kidney disease: a retrospective study. PeerJ 10:e13550 https://doi.org/10.7717/peerj.13550
date submitted: 2021-10-12
date accepted: 2022-05-17
issued: 2022-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhu
  given name: Yuyu
author list: Agent
  family name: Tao
  given name: Shuman
author list: Agent
  family name: Zhang
  given name: Danfeng
author list: Agent
  family name: Xiao
  given name: Jianping
author list: Agent
  family name: Wang
  given name: Xuerong
author list: Agent
  family name: Yuan
  given name: Liang
author list: Agent
  family name: Pan
  given name: Haifeng
author list: Agent
  family name: Wang
  given name: Deguang
doi: 10.7717/peerj.13550
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-06
copyright: ©2022 Zhu et al.
attribution name: Zhu et al.

Stable nitrogen and carbon isotope compositions in plant-soil systems under different land-use types in a red soil region, Southeast China
type: item
type: AcademicArticle
description: Background Stable N isotope compositions in plant-soil systems have been widely used to indicate soil N transformation and translocation processes in ecosystems. However, soil N processes and nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ) loss potential under different land-use types are short of systematic comparison in the red soil region of Southeast China. Methods In the present study, the stable N and C isotope compositions (δ15N and δ13C) of soil and leaf were analyzed to indicate soil N transformation processes, and the soil to plant 15N enrichment factor (EF) was used to compare soil ${\mathrm{NO}}_{3}^{-}$ NO 3 − loss potential under different land-use types, including an abandoned agricultural land, a natural pure forest without understory, and a natural pure forest with a simple understory. Results The foliar δ15N value (−0.8‰) in the abandoned agricultural land was greater than those of the forest lands (ranged from −2.2‰ to −10.8‰). In the abandoned agricultural land, δ15N values of soil organic nitrogen (SON) increased from 0.8‰ to 5.7‰ and δ13C values of soil organic carbon (SOC) decreased from −22.7‰ to −25.9‰ with increasing soil depth from 0–70 cm, mainly resulting from SON mineralization, soil organic matter (SOM) decomposition, and C4 plant input. In the soils below 70 cm depth, δ15N values of SON (mean 4.9‰) were likely affected by microbial assimilation of 15N-depleted ${\mathrm{NO}}_{3}^{-}$ NO 3 − . The variations in δ15N values of soil profiles under the two forests were similar, but the EF values were significant different between the pure forest with a simple understory (−10.0‰) and the forest without understory (−5.5‰). Conclusions These results suggest that soil to plant 15N enrichment factor have a great promise to compare soil ${\mathrm{NO}}_{3}^{-}$ NO 3 − loss potential among different ecosystems.
format: application/pdf
format: text/html
creator: Man Liu
creator: Guilin Han
subject: Ecosystem Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.13558
publisher: PeerJ Inc.
rights: © 2022 Liu and Han
abstract: Background Stable N isotope compositions in plant-soil systems have been widely used to indicate soil N transformation and translocation processes in ecosystems. However, soil N processes and nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ) loss potential under different land-use types are short of systematic comparison in the red soil region of Southeast China. Methods In the present study, the stable N and C isotope compositions (δ15N and δ13C) of soil and leaf were analyzed to indicate soil N transformation processes, and the soil to plant 15N enrichment factor (EF) was used to compare soil ${\mathrm{NO}}_{3}^{-}$ NO 3 − loss potential under different land-use types, including an abandoned agricultural land, a natural pure forest without understory, and a natural pure forest with a simple understory. Results The foliar δ15N value (−0.8‰) in the abandoned agricultural land was greater than those of the forest lands (ranged from −2.2‰ to −10.8‰). In the abandoned agricultural land, δ15N values of soil organic nitrogen (SON) increased from 0.8‰ to 5.7‰ and δ13C values of soil organic carbon (SOC) decreased from −22.7‰ to −25.9‰ with increasing soil depth from 0–70 cm, mainly resulting from SON mineralization, soil organic matter (SOM) decomposition, and C4 plant input. In the soils below 70 cm depth, δ15N values of SON (mean 4.9‰) were likely affected by microbial assimilation of 15N-depleted ${\mathrm{NO}}_{3}^{-}$ NO 3 − . The variations in δ15N values of soil profiles under the two forests were similar, but the EF values were significant different between the pure forest with a simple understory (−10.0‰) and the forest without understory (−5.5‰). Conclusions These results suggest that soil to plant 15N enrichment factor have a great promise to compare soil ${\mathrm{NO}}_{3}^{-}$ NO 3 − loss potential among different ecosystems.
bibliographic citation: Liu et al. (2022) Stable nitrogen and carbon isotope compositions in plant-soil systems under different land-use types in a red soil region, Southeast China. PeerJ 10:e13558 https://doi.org/10.7717/peerj.13558
date submitted: 2022-01-13
date accepted: 2022-05-18
issued: 2022-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Man
author list: Agent
  family name: Han
  given name: Guilin
doi: 10.7717/peerj.13558
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-06
copyright: ©2022 Liu and Han
attribution name: Liu and Han

Determination of muscle strength and function in plesiosaur limbs: finite element structural analyses of Cryptoclidus eurymerus humerus and femur
type: item
type: AcademicArticle
description: Background The Plesiosauria (Sauropterygia) are secondary marine diapsids. They are the only tetrapods to have evolved hydrofoil fore- and hindflippers. Once this specialization of locomotion had evolved, it remained essentially unchanged for 135 Ma. It is still controversial whether plesiosaurs flew underwater, rowed, or used a mixture of the two modes of locomotion. The long bones of Tetrapoda are functionally loaded by torsion, bending, compression, and tension during locomotion. Superposition of load cases shows that the bones are loaded mainly by compressive stresses. Therefore, it is possible to use finite element structure analysis (FESA) as a test environment for loading hypotheses. These include muscle reconstructions and muscle lines of action (LOA) when the goal is to obtain a homogeneous compressive stress distribution and to minimize bending in the model. Myological reconstruction revealed a muscle-powered flipper twisting mechanism. The flippers of plesiosaurs were twisted along the flipper length axis by extensors and flexors that originated from the humerus and femur as well as further distal locations. Methods To investigate locomotion in plesiosaurs, the humerus and femur of a mounted skeleton of Cryptoclidus eurymerus (Middle Jurassic Oxford Clay Formation from Britain) were analyzed using FE methods based on the concept of optimization of loading by compression. After limb muscle reconstructions including the flipper twisting muscles, LOA were derived for all humerus and femur muscles of Cryptoclidus by stretching cords along casts of the fore- and hindflippers of the mounted skeleton. LOA and muscle attachments were added to meshed volumetric models of the humerus and femur derived from micro-CT scans. Muscle forces were approximated by stochastic iteration and the compressive stress distribution for the two load cases, “downstroke” and “upstroke”, for each bone were calculated by aiming at a homogeneous compressive stress distribution. Results …
format: application/pdf
format: text/html
creator: Anna Krahl
creator: Andreas Lipphaus
creator: P. Martin Sander
creator: Ulrich Witzel
subject: Environmental Sciences
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.13342
publisher: PeerJ Inc.
rights: © 2022 Krahl et al.
abstract: Background The Plesiosauria (Sauropterygia) are secondary marine diapsids. They are the only tetrapods to have evolved hydrofoil fore- and hindflippers. Once this specialization of locomotion had evolved, it remained essentially unchanged for 135 Ma. It is still controversial whether plesiosaurs flew underwater, rowed, or used a mixture of the two modes of locomotion. The long bones of Tetrapoda are functionally loaded by torsion, bending, compression, and tension during locomotion. Superposition of load cases shows that the bones are loaded mainly by compressive stresses. Therefore, it is possible to use finite element structure analysis (FESA) as a test environment for loading hypotheses. These include muscle reconstructions and muscle lines of action (LOA) when the goal is to obtain a homogeneous compressive stress distribution and to minimize bending in the model. Myological reconstruction revealed a muscle-powered flipper twisting mechanism. The flippers of plesiosaurs were twisted along the flipper length axis by extensors and flexors that originated from the humerus and femur as well as further distal locations. Methods To investigate locomotion in plesiosaurs, the humerus and femur of a mounted skeleton of Cryptoclidus eurymerus (Middle Jurassic Oxford Clay Formation from Britain) were analyzed using FE methods based on the concept of optimization of loading by compression. After limb muscle reconstructions including the flipper twisting muscles, LOA were derived for all humerus and femur muscles of Cryptoclidus by stretching cords along casts of the fore- and hindflippers of the mounted skeleton. LOA and muscle attachments were added to meshed volumetric models of the humerus and femur derived from micro-CT scans. Muscle forces were approximated by stochastic iteration and the compressive stress distribution for the two load cases, “downstroke” and “upstroke”, for each bone were calculated by aiming at a homogeneous compressive stress distribution. Results …
bibliographic citation: Krahl et al. (2022) Determination of muscle strength and function in plesiosaur limbs: finite element structural analyses of Cryptoclidus eurymerus humerus and femur. PeerJ 10:e13342 https://doi.org/10.7717/peerj.13342
date submitted: 2021-03-15
date accepted: 2022-04-05
issued: 2022-06-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Krahl
  given name: Anna
author list: Agent
  family name: Lipphaus
  given name: Andreas
author list: Agent
  family name: Sander
  given name: P. Martin
author list: Agent
  family name: Witzel
  given name: Ulrich
doi: 10.7717/peerj.13342
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-03
copyright: © 2022 Krahl et al.
attribution name: Krahl et al.

Quercetin prevents chronic kidney disease on mesangial cells model by regulating inflammation, oxidative stress, and TGF-β1/SMADs pathway
type: item
type: AcademicArticle
description: Background Chronic kidney disease (CKD) happens due to decreasing kidney function. Inflammation and oxidative stress have been shown to result in the progression of CKD. Quercetin is widely known to have various bioactivities including antioxidant, anticancer, and anti-inflammatory activities. Objective To evaluate the activity of quercetin to inhibit inflammation, stress oxidative, and fibrosis on CKD cells model (mouse mesangial cells induced by glucose). Methods and Material The SV40 MES 13 cells were plated in a 6-well plate with cell density at 5,000 cells/well. The medium had been substituted for 3 days with a glucose-induced medium with a concentration of 20 mM. Quercetin was added with 50, 10, and 5 µg/mL concentrations. The negative control was the untreated cell. The levels of TGF-β1, TNF-α, and MDA were determined using ELISA KIT. The gene expressions of the SMAD7, SMAD3, SMAD2, and SMAD4 were analyzed using qRT-PCR. Results Glucose can lead to an increase in inflammatory cytokines TNF-α, TGF-β1, MDA as well as the expressions of the SMAD2, SMAD3, SMAD4, and a decrease in SMAD7. Quercetin caused the reduction of TNF-α, TGF-β1, MDA as well as the expression of the SMAD2, SMAD3, SMAD4, and increased SMAD7. Conclusion Quercetin has anti-inflammation, antioxidant, antifibrosis activity in the CKD cells model. Thus, quercetin is a promising substance for CKD therapy and further research is needed to prove this in CKD animal model.
format: application/pdf
format: text/html
creator: Wahyu Widowati
creator: Sijani Prahastuti
creator: Rita Tjokropranoto
creator: Philips Onggowidjaja
creator: Hanna Sari Widya Kusuma
creator: Ervi Afifah
creator: Seila Arumwardana
creator: Muhamad Aldi Maulana
creator: Rizal Rizal
subject: Cell Biology
subject: Molecular Biology
subject: Immunology
subject: Nephrology
description: doi:10.7717/peerj.13257
publisher: PeerJ Inc.
rights: © 2022 Widowati et al.
abstract: Background Chronic kidney disease (CKD) happens due to decreasing kidney function. Inflammation and oxidative stress have been shown to result in the progression of CKD. Quercetin is widely known to have various bioactivities including antioxidant, anticancer, and anti-inflammatory activities. Objective To evaluate the activity of quercetin to inhibit inflammation, stress oxidative, and fibrosis on CKD cells model (mouse mesangial cells induced by glucose). Methods and Material The SV40 MES 13 cells were plated in a 6-well plate with cell density at 5,000 cells/well. The medium had been substituted for 3 days with a glucose-induced medium with a concentration of 20 mM. Quercetin was added with 50, 10, and 5 µg/mL concentrations. The negative control was the untreated cell. The levels of TGF-β1, TNF-α, and MDA were determined using ELISA KIT. The gene expressions of the SMAD7, SMAD3, SMAD2, and SMAD4 were analyzed using qRT-PCR. Results Glucose can lead to an increase in inflammatory cytokines TNF-α, TGF-β1, MDA as well as the expressions of the SMAD2, SMAD3, SMAD4, and a decrease in SMAD7. Quercetin caused the reduction of TNF-α, TGF-β1, MDA as well as the expression of the SMAD2, SMAD3, SMAD4, and increased SMAD7. Conclusion Quercetin has anti-inflammation, antioxidant, antifibrosis activity in the CKD cells model. Thus, quercetin is a promising substance for CKD therapy and further research is needed to prove this in CKD animal model.
bibliographic citation: Widowati et al. (2022) Quercetin prevents chronic kidney disease on mesangial cells model by regulating inflammation, oxidative stress, and TGF-β1/SMADs pathway. PeerJ 10:e13257 https://doi.org/10.7717/peerj.13257
date submitted: 2021-12-13
date accepted: 2022-03-22
issued: 2022-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Widowati
  given name: Wahyu
author list: Agent
  family name: Prahastuti
  given name: Sijani
author list: Agent
  family name: Tjokropranoto
  given name: Rita
author list: Agent
  family name: Onggowidjaja
  given name: Philips
author list: Agent
  family name: Kusuma
  given name: Hanna Sari Widya
author list: Agent
  family name: Afifah
  given name: Ervi
author list: Agent
  family name: Arumwardana
  given name: Seila
author list: Agent
  family name: Maulana
  given name: Muhamad Aldi
author list: Agent
  family name: Rizal
  given name: Rizal
doi: 10.7717/peerj.13257
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-02
copyright: ©2022 Widowati et al.
attribution name: Widowati et al.

Withasomniferol C, a new potential SARS-CoV-2 main protease inhibitor from the Withania somnifera plant proposed by in silico approaches
type: item
type: AcademicArticle
description: Exploring potent herbal medicine candidates is a promising strategy for combating a pandemic in the present global health crisis. In Ayurveda (a traditional medicine system in India), Withania somnifera (WS) is one of the most important herbs and it has been used for millennia as Rasayana (a type of juice) for its wide-ranging health benefits. WS phytocompounds display a broad spectrum of biological activities (such as antioxidant, anticancer and antimicrobial) modulate detoxifying enzymes, and enhance immunity. Inspired by the numerous biological actions of WS phytocompounds, the present investigation explored the potential of the WS phytocompounds against the SARS-CoV-2 main protease (3CLpro). We selected 11 specific withanolide compounds, such as withaphysalin, withasomniferol, and withafastuosin, through manual literature curation against 3CLpro. A molecular similarity analysis showed their similarity with compounds that have an established inhibitory activity against the SARS-CoV-2. In silico molecular docking and molecular dynamics simulations elucidated withasomniferol C (WS11) as a potential candidate against SARS-CoV-2 3CLpro. Additionally, the present work also presents a new method of validating docking poses using the AlteQ method.
format: application/pdf
format: text/html
creator: Shivananada Kandagalla
creator: Hrvoje Rimac
creator: Krishnamoorthy Gurushankar
creator: Jurica Novak
creator: Maria Grishina
creator: Vladimir Potemkin
subject: Bioinformatics
subject: Biophysics
subject: Computational Biology
subject: COVID-19
description: doi:10.7717/peerj.13374
publisher: PeerJ Inc.
rights: © 2022 Kandagalla et al.
abstract: Exploring potent herbal medicine candidates is a promising strategy for combating a pandemic in the present global health crisis. In Ayurveda (a traditional medicine system in India), Withania somnifera (WS) is one of the most important herbs and it has been used for millennia as Rasayana (a type of juice) for its wide-ranging health benefits. WS phytocompounds display a broad spectrum of biological activities (such as antioxidant, anticancer and antimicrobial) modulate detoxifying enzymes, and enhance immunity. Inspired by the numerous biological actions of WS phytocompounds, the present investigation explored the potential of the WS phytocompounds against the SARS-CoV-2 main protease (3CLpro). We selected 11 specific withanolide compounds, such as withaphysalin, withasomniferol, and withafastuosin, through manual literature curation against 3CLpro. A molecular similarity analysis showed their similarity with compounds that have an established inhibitory activity against the SARS-CoV-2. In silico molecular docking and molecular dynamics simulations elucidated withasomniferol C (WS11) as a potential candidate against SARS-CoV-2 3CLpro. Additionally, the present work also presents a new method of validating docking poses using the AlteQ method.
bibliographic citation: Kandagalla et al. (2022) Withasomniferol C, a new potential SARS-CoV-2 main protease inhibitor from the Withania somnifera plant proposed by in silico approaches. PeerJ 10:e13374 https://doi.org/10.7717/peerj.13374
date submitted: 2021-10-14
date accepted: 2022-04-13
issued: 2022-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kandagalla
  given name: Shivananada
author list: Agent
  family name: Rimac
  given name: Hrvoje
author list: Agent
  family name: Gurushankar
  given name: Krishnamoorthy
author list: Agent
  family name: Novak
  given name: Jurica
author list: Agent
  family name: Grishina
  given name: Maria
author list: Agent
  family name: Potemkin
  given name: Vladimir
doi: 10.7717/peerj.13374
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-02
copyright: ©2022 Kandagalla et al.
attribution name: Kandagalla et al.

A new hybodontiform shark (Strophodus Agassiz 1838) from the Lower Cretaceous (Valanginian-Hauterivian) of Colombia
type: item
type: AcademicArticle
description: The vertebrate marine faunas that inhabited northern South America during the Cretaceous are still poorly known. This study is a contribution to a growing wave of new studies on Lower Cretaceous vertebrates from Colombia. Here we report and describe a new species of a hybodontiform shark of the genus Strophodus, which we named Strophodus rebecae sp. nov., based on isolated teeth, that were collected in Valanginian-Hauterivian rocks of the Rosa Blanca Formation (Carrizal and El Sapo Members) near the town of Zapatoca, Santander Department, Andes of Colombia. In addition, we describe two other fragmented teeth assigned to Strophodus sp. from the Rosa Blanca Fm. The new species from Colombia represents the only Cretaceous record of Strophodus from Gondwana, offering new insights into the paleogeographic distribution of the genus, as well as increasing the knowledge about the scarce hybodontiform paleodiversity known from South America. The presence of Strophodus in the Rosa Blanca Formation suggests that these durophagous (shell-crushing) fishes played an important role as predators of the abundant and diverse invertebrate fauna present in these ancient tropical coastal ecosystems of Gondwana.
format: application/pdf
format: text/html
creator: Jorge D. Carrillo-Briceño
creator: Edwin-Alberto Cadena
subject: Biodiversity
subject: Marine Biology
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13496
publisher: PeerJ Inc.
rights: © 2022 Carrillo-Briceño and Cadena
abstract: The vertebrate marine faunas that inhabited northern South America during the Cretaceous are still poorly known. This study is a contribution to a growing wave of new studies on Lower Cretaceous vertebrates from Colombia. Here we report and describe a new species of a hybodontiform shark of the genus Strophodus, which we named Strophodus rebecae sp. nov., based on isolated teeth, that were collected in Valanginian-Hauterivian rocks of the Rosa Blanca Formation (Carrizal and El Sapo Members) near the town of Zapatoca, Santander Department, Andes of Colombia. In addition, we describe two other fragmented teeth assigned to Strophodus sp. from the Rosa Blanca Fm. The new species from Colombia represents the only Cretaceous record of Strophodus from Gondwana, offering new insights into the paleogeographic distribution of the genus, as well as increasing the knowledge about the scarce hybodontiform paleodiversity known from South America. The presence of Strophodus in the Rosa Blanca Formation suggests that these durophagous (shell-crushing) fishes played an important role as predators of the abundant and diverse invertebrate fauna present in these ancient tropical coastal ecosystems of Gondwana.
bibliographic citation: Carrillo-Briceño et al. (2022) A new hybodontiform shark (Strophodus Agassiz 1838) from the Lower Cretaceous (Valanginian-Hauterivian) of Colombia. PeerJ 10:e13496 https://doi.org/10.7717/peerj.13496
date submitted: 2022-01-05
date accepted: 2022-05-05
issued: 2022-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carrillo-Briceño
  given name: Jorge D.
author list: Agent
  family name: Cadena
  given name: Edwin-Alberto
doi: 10.7717/peerj.13496
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-02
copyright: ©2022 Carrillo-Briceño and Cadena
attribution name: Carrillo-Briceño and Cadena

A new species of deep-sea grunt, Rhonciscus pauco (Lutjaniformes: Haemulidae), from Puerto Rico
type: item
type: AcademicArticle
description: A fourth species of the genus Rhonciscus (Lutjaniformes: Haemulidae) is described from various specimens collected by small-scale fishers from the insular upper slope of western Puerto Rico. The new species was molecularly recovered as sister to the Eastern Pacific R. branickii, to which it bears many morphological similarities. It is distinguished from other Rhonciscus species by the number of scale rows between the dorsal fin and the lateral line (7), larger and thus fewer scales along the lateral line (48–50), large eyes (9.4–10.4 times in SL), longer caudal peduncle (15.2–20% of SL), larger sized penultimate (14.7–19.1% in SL) and last (7.4–9.5% in SL) dorsal fin spines which translates to a less deeply notched dorsal fin, and its opalescent silver with golden specks live coloration. This grunt, only now recognized by ichthyologists, but well known by local fishers that target snappers and groupers between 200 and 500 m in depth, occurs in far deeper waters than any western Atlantic grunt.
format: application/pdf
format: text/html
creator: Jose Tavera
creator: Michelle T. Schärer-Umpierre
creator: Arturo Acero P.
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13502
publisher: PeerJ Inc.
rights: © 2022 Tavera et al.
abstract: A fourth species of the genus Rhonciscus (Lutjaniformes: Haemulidae) is described from various specimens collected by small-scale fishers from the insular upper slope of western Puerto Rico. The new species was molecularly recovered as sister to the Eastern Pacific R. branickii, to which it bears many morphological similarities. It is distinguished from other Rhonciscus species by the number of scale rows between the dorsal fin and the lateral line (7), larger and thus fewer scales along the lateral line (48–50), large eyes (9.4–10.4 times in SL), longer caudal peduncle (15.2–20% of SL), larger sized penultimate (14.7–19.1% in SL) and last (7.4–9.5% in SL) dorsal fin spines which translates to a less deeply notched dorsal fin, and its opalescent silver with golden specks live coloration. This grunt, only now recognized by ichthyologists, but well known by local fishers that target snappers and groupers between 200 and 500 m in depth, occurs in far deeper waters than any western Atlantic grunt.
bibliographic citation: Tavera et al. (2022) A new species of deep-sea grunt, Rhonciscus pauco (Lutjaniformes: Haemulidae), from Puerto Rico. PeerJ 10:e13502 https://doi.org/10.7717/peerj.13502
date submitted: 2022-03-08
date accepted: 2022-05-05
issued: 2022-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tavera
  given name: Jose
author list: Agent
  family name: Schärer-Umpierre
  given name: Michelle T.
author list: Agent
  family name: Acero P.
  given name: Arturo
doi: 10.7717/peerj.13502
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-02
copyright: © 2022 Tavera et al.
attribution name: Tavera et al.

Calotropin and corotoxigenin 3-O-glucopyranoside from the desert milkweed Asclepias subulata inhibit the Na+/K+-ATPase activity
type: item
type: AcademicArticle
description: Na+/K+-ATPase is an essential transmembrane enzyme found in all mammalian cells with critical functions for cell ion homeostasis. The inhibition of this enzyme by several cardiotonic steroids (CTS) has been associated with the cytotoxic effect on cancer cell lines of phytochemicals such as ouabain and digitoxin. This study evaluated the inhibitory capacity of cardenolides calotropin and corotoxigenin 3-O-glucopyranoside (C3OG) from Asclepias subulata over the Na+/K+-ATPase activity in vitro and silico. The inhibitory assays showed that calotropin and C3OG decreased the Na+/K+-ATPase activity with IC50 values of 0.27 and 0.87 μM, respectively. Furthermore, the molecules presented an uncompetitive inhibition on Na+/K+-ATPase activity, with Ki values of 0.2 μM to calotropin and 0.5 μM to C3OG. Furthermore, the molecular modeling indicated that calotropin and C3OG might interact with the Thr797 and Gln111 residues, considered essential to the interaction with the Na+/K+-ATPase. Besides, these cardenolides can interact with amino acid residues such as Phe783, Leu125, and Ala323, to establish hydrophobic interactions on the binding site. Considering the results, these provide novel evidence about the mechanism of action of cardenolides from A. subulata, proposing that C3OG is a novel cardenolide that deserves further consideration for in vitro cellular antiproliferative assays and in vivo studies as an anticancer molecule.
format: application/pdf
format: text/html
creator: Salvador E. Meneses-Sagrero
creator: Luisa A. Rascón-Valenzuela
creator: Juan C. García-Ramos
creator: Wagner Vilegas
creator: Aldo A. Arvizu-Flores
creator: Rogerio R. Sotelo-Mundo
creator: Ramon E. Robles-Zepeda
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13524
publisher: PeerJ Inc.
rights: © 2022 Meneses-Sagrero et al.
abstract: Na+/K+-ATPase is an essential transmembrane enzyme found in all mammalian cells with critical functions for cell ion homeostasis. The inhibition of this enzyme by several cardiotonic steroids (CTS) has been associated with the cytotoxic effect on cancer cell lines of phytochemicals such as ouabain and digitoxin. This study evaluated the inhibitory capacity of cardenolides calotropin and corotoxigenin 3-O-glucopyranoside (C3OG) from Asclepias subulata over the Na+/K+-ATPase activity in vitro and silico. The inhibitory assays showed that calotropin and C3OG decreased the Na+/K+-ATPase activity with IC50 values of 0.27 and 0.87 μM, respectively. Furthermore, the molecules presented an uncompetitive inhibition on Na+/K+-ATPase activity, with Ki values of 0.2 μM to calotropin and 0.5 μM to C3OG. Furthermore, the molecular modeling indicated that calotropin and C3OG might interact with the Thr797 and Gln111 residues, considered essential to the interaction with the Na+/K+-ATPase. Besides, these cardenolides can interact with amino acid residues such as Phe783, Leu125, and Ala323, to establish hydrophobic interactions on the binding site. Considering the results, these provide novel evidence about the mechanism of action of cardenolides from A. subulata, proposing that C3OG is a novel cardenolide that deserves further consideration for in vitro cellular antiproliferative assays and in vivo studies as an anticancer molecule.
bibliographic citation: Meneses-Sagrero et al. (2022) Calotropin and corotoxigenin 3-O-glucopyranoside from the desert milkweed Asclepias subulata inhibit the Na+/K+-ATPase activity. PeerJ 10:e13524 https://doi.org/10.7717/peerj.13524
date submitted: 2022-02-08
date accepted: 2022-05-10
issued: 2022-06-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meneses-Sagrero
  given name: Salvador E.
author list: Agent
  family name: Rascón-Valenzuela
  given name: Luisa A.
author list: Agent
  family name: García-Ramos
  given name: Juan C.
author list: Agent
  family name: Vilegas
  given name: Wagner
author list: Agent
  family name: Arvizu-Flores
  given name: Aldo A.
author list: Agent
  family name: Sotelo-Mundo
  given name: Rogerio R.
author list: Agent
  family name: Robles-Zepeda
  given name: Ramon E.
doi: 10.7717/peerj.13524
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-02
copyright: © 2022 Meneses-Sagrero et al.
attribution name: Meneses-Sagrero et al.

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