PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Cinnamtannin B1 attenuates rosacea-like signs via inhibition of pro-inflammatory cytokine production and down-regulation of the MAPK pathway
items: Responses of branching reef corals Acropora digitifera and Montipora digitata to elevated temperature and pCO2
items: Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia
items: Dnajb8, a target gene of SOX30, is dispensable for male fertility in mice
items: Estimating salt content of vegetated soil at different depths with Sentinel-2 data
items: Sevoflurane preconditioning attenuates hypoxia/reoxygenation injury of H9c2 cardiomyocytes by activation of the HIF-1/PDK-1 pathway
items: Improved plaque assay for human coronaviruses 229E and OC43
items: Uncovering the hidden diversity of Mississippian crinoids (Crinoidea, Echinodermata) from Poland
items: Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes
items: Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species

Cinnamtannin B1 attenuates rosacea-like signs via inhibition of pro-inflammatory cytokine production and down-regulation of the MAPK pathway
type: item
type: AcademicArticle
description: Background Rosacea is a common inflammatory disease of facial skin. Dysregulation of innate immunity with enhanced inflammation and increased abundance of LL-37 at the epidermal site is a characteristic feature of rosacea. Cinnamtannin B1 (CB1) is a condensed tannin with anti-inflammatory and anti-microbial activities. The aims of the study were to evaluate the potential of CB1 as a therapy for rosacea and to characterize the potential mechanisms of action. Methods We intraperitoneally administered 20 mg/kg CB1 once daily for 2 days into the LL-37-induced mouse model of rosacea. The effects of CB1 in vivo were evaluated by the observations of lesions, histology, immunohistochemistry, and the transcription and translation of pro-inflammatory cytokines and chemokines. Human keratinocyte HaCaT and monocyte THP-1 were used to characterize the effects of CB1 on LL-37-induced inflammation in vitro. The changes in pro-inflammatory chemokine interleukin-8 (IL-8) were quantitated by enzyme-linked immunosorbent assay (ELISA), and the expressions of genes involved were determined by Western blotting. Results CB1 attenuated local redness, inflammation, and neutrophil recruitment in the mouse model of rosacea in vivo. CB1 suppressed myeloperoxidase (MPO) and macrophage inflammatory protein 2 (MIP-2) production, a functional homolog of interleukin-8 (IL-8), at the lesions. In vitro experiments confirmed that CB1 reversed the LL-37-induced IL-8 production in human keratinocytes HaCaT and monocyte THP-1 cells. CB1 inhibited IL-8 production through downregulating the phosphorylation of extracellular signal-regulated kinase (ERK) in the mitogen-activated protein kinase (MAPK) pathway. Conclusion CB1 attenuated LL-37-induced inflammation, specifically IL-8 production, through inhibiting the phosphorylation of ERK. CB1 has potential as a treatment for rosacea.
format: application/pdf
format: text/html
creator: Hung-Lin Kan
creator: Chia-Chi Wang
creator: Yin-Hua Cheng
creator: Chi-Lung Yang
creator: Hsun-Shuo Chang
creator: Ih-Sheng Chen
creator: Ying-Chi Lin
subject: Biochemistry
subject: Cell Biology
subject: Dermatology
subject: Immunology
subject: Pharmacology
description: doi:10.7717/peerj.10548
publisher: PeerJ Inc.
rights: © 2020 Kan et al.
abstract: Background Rosacea is a common inflammatory disease of facial skin. Dysregulation of innate immunity with enhanced inflammation and increased abundance of LL-37 at the epidermal site is a characteristic feature of rosacea. Cinnamtannin B1 (CB1) is a condensed tannin with anti-inflammatory and anti-microbial activities. The aims of the study were to evaluate the potential of CB1 as a therapy for rosacea and to characterize the potential mechanisms of action. Methods We intraperitoneally administered 20 mg/kg CB1 once daily for 2 days into the LL-37-induced mouse model of rosacea. The effects of CB1 in vivo were evaluated by the observations of lesions, histology, immunohistochemistry, and the transcription and translation of pro-inflammatory cytokines and chemokines. Human keratinocyte HaCaT and monocyte THP-1 were used to characterize the effects of CB1 on LL-37-induced inflammation in vitro. The changes in pro-inflammatory chemokine interleukin-8 (IL-8) were quantitated by enzyme-linked immunosorbent assay (ELISA), and the expressions of genes involved were determined by Western blotting. Results CB1 attenuated local redness, inflammation, and neutrophil recruitment in the mouse model of rosacea in vivo. CB1 suppressed myeloperoxidase (MPO) and macrophage inflammatory protein 2 (MIP-2) production, a functional homolog of interleukin-8 (IL-8), at the lesions. In vitro experiments confirmed that CB1 reversed the LL-37-induced IL-8 production in human keratinocytes HaCaT and monocyte THP-1 cells. CB1 inhibited IL-8 production through downregulating the phosphorylation of extracellular signal-regulated kinase (ERK) in the mitogen-activated protein kinase (MAPK) pathway. Conclusion CB1 attenuated LL-37-induced inflammation, specifically IL-8 production, through inhibiting the phosphorylation of ERK. CB1 has potential as a treatment for rosacea.
bibliographic citation: Kan et al. (2020) Cinnamtannin B1 attenuates rosacea-like signs via inhibition of pro-inflammatory cytokine production and down-regulation of the MAPK pathway. PeerJ 8:e10548 https://doi.org/10.7717/peerj.10548
date submitted: 2020-06-19
date accepted: 2020-11-20
issued: 2020-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kan
  given name: Hung-Lin
author list: Agent
  family name: Wang
  given name: Chia-Chi
author list: Agent
  family name: Cheng
  given name: Yin-Hua
author list: Agent
  family name: Yang
  given name: Chi-Lung
author list: Agent
  family name: Chang
  given name: Hsun-Shuo
author list: Agent
  family name: Chen
  given name: Ih-Sheng
author list: Agent
  family name: Lin
  given name: Ying-Chi
doi: 10.7717/peerj.10548
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-21
copyright: ©2020 Kan et al.
attribution name: Kan et al.

Responses of branching reef corals Acropora digitifera and Montipora digitata to elevated temperature and pCO2
type: item
type: AcademicArticle
description: Anthropogenic emission of CO2 into the atmosphere has been increasing exponentially, causing ocean acidification (OA) and ocean warming (OW). The “business-as-usual” scenario predicts that the atmospheric concentration of CO2 may exceed 1,000 µatm and seawater temperature may increase by up to 3 °C by the end of the 21st century. Increases in OA and OW may negatively affect the growth and survival of reef corals. In the present study, we separately examined the effects of OW and OA on the corals Acropora digitifera and Montipora digitata, which are dominant coral species occurring along the Ryukyu Archipelago, Japan, at three temperatures (28 °C, 30 °C, and 32 °C) and following four pCO2 treatments (400, 600, 800, and 1,000 µatm) in aquarium experiments. In the OW experiment, the calcification rate (p = 0.02), endosymbiont density, and maximum photosynthetic efficiency (Fv/Fm) (both p < 0.0001) decreased significantly at the highest temperature (32 °C) compared to those at the lower temperatures (28 °C and 30 °C) in both species. In the OA experiment, the calcification rate decreased significantly as pCO2 increased (p < 0.0001), whereas endosymbiont density, chlorophyll content, and Fv/Fm were not affected. The calcification rate of A. digitifera showed greater decreases from 30 °C to 32 °C than that of M. digitata. The calcification of the two species responded differently to OW and OA. These results suggest that A. digitifera is more sensitive to OW than M. digitata, whereas M. digitata is more sensitive to OA. Thus, differences in the sensitivity of the two coral species to OW and OA might be attributed to differences in the endosymbiont species and high calcification rates, respectively.
format: application/pdf
format: text/html
creator: Cristiana Manullang
creator: Intan Herwindra Millyaningrum
creator: Akira Iguchi
creator: Aika Miyagi
creator: Yasuaki Tanaka
creator: Yukihiro Nojiri
creator: Kazuhiko Sakai
subject: Conservation Biology
subject: Marine Biology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.10562
publisher: PeerJ Inc.
rights: © 2020 Manullang et al.
abstract: Anthropogenic emission of CO2 into the atmosphere has been increasing exponentially, causing ocean acidification (OA) and ocean warming (OW). The “business-as-usual” scenario predicts that the atmospheric concentration of CO2 may exceed 1,000 µatm and seawater temperature may increase by up to 3 °C by the end of the 21st century. Increases in OA and OW may negatively affect the growth and survival of reef corals. In the present study, we separately examined the effects of OW and OA on the corals Acropora digitifera and Montipora digitata, which are dominant coral species occurring along the Ryukyu Archipelago, Japan, at three temperatures (28 °C, 30 °C, and 32 °C) and following four pCO2 treatments (400, 600, 800, and 1,000 µatm) in aquarium experiments. In the OW experiment, the calcification rate (p = 0.02), endosymbiont density, and maximum photosynthetic efficiency (Fv/Fm) (both p < 0.0001) decreased significantly at the highest temperature (32 °C) compared to those at the lower temperatures (28 °C and 30 °C) in both species. In the OA experiment, the calcification rate decreased significantly as pCO2 increased (p < 0.0001), whereas endosymbiont density, chlorophyll content, and Fv/Fm were not affected. The calcification rate of A. digitifera showed greater decreases from 30 °C to 32 °C than that of M. digitata. The calcification of the two species responded differently to OW and OA. These results suggest that A. digitifera is more sensitive to OW than M. digitata, whereas M. digitata is more sensitive to OA. Thus, differences in the sensitivity of the two coral species to OW and OA might be attributed to differences in the endosymbiont species and high calcification rates, respectively.
bibliographic citation: Manullang et al. (2020) Responses of branching reef corals Acropora digitifera and Montipora digitata to elevated temperature and pCO2. PeerJ 8:e10562 https://doi.org/10.7717/peerj.10562
date submitted: 2020-06-11
date accepted: 2020-11-22
issued: 2020-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Manullang
  given name: Cristiana
author list: Agent
  family name: Millyaningrum
  given name: Intan Herwindra
author list: Agent
  family name: Iguchi
  given name: Akira
author list: Agent
  family name: Miyagi
  given name: Aika
author list: Agent
  family name: Tanaka
  given name: Yasuaki
author list: Agent
  family name: Nojiri
  given name: Yukihiro
author list: Agent
  family name: Sakai
  given name: Kazuhiko
doi: 10.7717/peerj.10562
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-21
copyright: ©2020 Manullang et al.
attribution name: Manullang et al.

Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia
type: item
type: AcademicArticle
description: Background Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia (n = 60) from March to September 2020 and (3) to perform phylogenetic analysis of SARS-CoV-2 complete genomes from different countries, including Indonesia. Methods Whole genome sequencing (WGS) was performed using next-generation sequencing (NGS) applied in the Illumina MiSeq instrument. Full-length virus genomes were annotated using the reference genome of hCoV-19/Wuhan/Hu-1/2019 (NC_045512.2) and then visualized in UGENE v. 1.30. For phylogenetic analysis, a dataset of 88 available SARS-CoV-2 complete genomes from different countries, including Indonesia, was retrieved from GISAID. Results All patients were hospitalized with various severities of COVID-19. Phylogenetic analysis revealed that one and three virus samples belong to clade L and GH. These three clade GH virus samples (EPI_ISL_525492, EPI_ISL_516800 and EPI_ISL_516829) were not only located in a cluster with SARS-CoV-2 genomes from Asia but also those from Europe, whereas the clade L virus sample (EPI_ISL_516806) was located amongst SARS-CoV-2 genomes from Asia. Using full-length sequences available in the GISAID EpiCoV Database, 39 of 60 SARS-CoV-2 (65%) from Indonesia harbor the D614G mutation. Conclusion These findings indicate that SARS-CoV-2 with the D614G mutation appears to become the major circulating virus in Indonesia, concurrent with the COVID-19 situation worldwide.
format: application/pdf
format: text/html
creator: Gunadi
creator: Hendra Wibawa
creator: Marcellus
creator: Mohamad Saifudin Hakim
creator: Edwin Widyanto Daniwijaya
creator: Ludhang Pradipta Rizki
creator: Endah Supriyati
creator: Dwi Aris Agung Nugrahaningsih
creator: Afiahayati
creator: Siswanto
creator: Kristy Iskandar
creator: Nungki Anggorowati
creator: Alvin Santoso Kalim
creator: Dyah Ayu Puspitarani
creator: Kemala Athollah
creator: Eggi Arguni
creator: Titik Nuryastuti
creator: Tri Wibawa
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Virology
subject: Infectious Diseases
description: doi:10.7717/peerj.10575
publisher: PeerJ Inc.
rights: © 2020 Gunadi et al.
abstract: Background Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia (n = 60) from March to September 2020 and (3) to perform phylogenetic analysis of SARS-CoV-2 complete genomes from different countries, including Indonesia. Methods Whole genome sequencing (WGS) was performed using next-generation sequencing (NGS) applied in the Illumina MiSeq instrument. Full-length virus genomes were annotated using the reference genome of hCoV-19/Wuhan/Hu-1/2019 (NC_045512.2) and then visualized in UGENE v. 1.30. For phylogenetic analysis, a dataset of 88 available SARS-CoV-2 complete genomes from different countries, including Indonesia, was retrieved from GISAID. Results All patients were hospitalized with various severities of COVID-19. Phylogenetic analysis revealed that one and three virus samples belong to clade L and GH. These three clade GH virus samples (EPI_ISL_525492, EPI_ISL_516800 and EPI_ISL_516829) were not only located in a cluster with SARS-CoV-2 genomes from Asia but also those from Europe, whereas the clade L virus sample (EPI_ISL_516806) was located amongst SARS-CoV-2 genomes from Asia. Using full-length sequences available in the GISAID EpiCoV Database, 39 of 60 SARS-CoV-2 (65%) from Indonesia harbor the D614G mutation. Conclusion These findings indicate that SARS-CoV-2 with the D614G mutation appears to become the major circulating virus in Indonesia, concurrent with the COVID-19 situation worldwide.
bibliographic citation: Gunadi et al. (2020) Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. PeerJ 8:e10575 https://doi.org/10.7717/peerj.10575
date submitted: 2020-09-22
date accepted: 2020-11-24
issued: 2020-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gunadi
author list: Agent
  family name: Wibawa
  given name: Hendra
author list: Agent
  family name: Marcellus
author list: Agent
  family name: Hakim
  given name: Mohamad Saifudin
author list: Agent
  family name: Daniwijaya
  given name: Edwin Widyanto
author list: Agent
  family name: Rizki
  given name: Ludhang Pradipta
author list: Agent
  family name: Supriyati
  given name: Endah
author list: Agent
  family name: Nugrahaningsih
  given name: Dwi Aris Agung
author list: Agent
  family name: Afiahayati
author list: Agent
  family name: Siswanto
author list: Agent
  family name: Iskandar
  given name: Kristy
author list: Agent
  family name: Anggorowati
  given name: Nungki
author list: Agent
  family name: Kalim
  given name: Alvin Santoso
author list: Agent
  family name: Puspitarani
  given name: Dyah Ayu
author list: Agent
  family name: Athollah
  given name: Kemala
author list: Agent
  family name: Arguni
  given name: Eggi
author list: Agent
  family name: Nuryastuti
  given name: Titik
author list: Agent
  family name: Wibawa
  given name: Tri
doi: 10.7717/peerj.10575
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-21
copyright: © 2020 Gunadi et al.
attribution name: Gunadi et al.

Dnajb8, a target gene of SOX30, is dispensable for male fertility in mice
type: item
type: AcademicArticle
description: Background The DNAJ family of molecular chaperones maintains protein homeostasis in mitotic and postmeiotic cells, especially germ cells. Recently, we found that the transcription factor SOX30 initiates transcription of Dnajb8 during late meiosis and spermiogenesis in mouse testes. Methods We used the CRISPR/Cas9 system to generate Dnajb8 mutant mice and analyze the phenotype of the Dnajb8 mutants. Results AlthoughDnajb8 is an evolutionarily conserved gene, it is not essential for spermatogenesis and male fertility. We provide this phenotypic information, which could prevent duplicative work by other groups.
format: application/pdf
format: text/html
creator: Fengsong Wang
creator: Shuai Kong
creator: Xuechun Hu
creator: Xin Li
creator: Bo Xu
creator: Qiuling Yue
creator: Kaiqiang Fu
creator: Lan Ye
creator: Shun Bai
subject: Developmental Biology
subject: Genetics
subject: Molecular Biology
subject: Andrology
description: doi:10.7717/peerj.10582
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background The DNAJ family of molecular chaperones maintains protein homeostasis in mitotic and postmeiotic cells, especially germ cells. Recently, we found that the transcription factor SOX30 initiates transcription of Dnajb8 during late meiosis and spermiogenesis in mouse testes. Methods We used the CRISPR/Cas9 system to generate Dnajb8 mutant mice and analyze the phenotype of the Dnajb8 mutants. Results AlthoughDnajb8 is an evolutionarily conserved gene, it is not essential for spermatogenesis and male fertility. We provide this phenotypic information, which could prevent duplicative work by other groups.
bibliographic citation: Wang et al. (2020) Dnajb8, a target gene of SOX30, is dispensable for male fertility in mice. PeerJ 8:e10582 https://doi.org/10.7717/peerj.10582
date submitted: 2020-08-18
date accepted: 2020-11-24
issued: 2020-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Fengsong
author list: Agent
  family name: Kong
  given name: Shuai
author list: Agent
  family name: Hu
  given name: Xuechun
author list: Agent
  family name: Li
  given name: Xin
author list: Agent
  family name: Xu
  given name: Bo
author list: Agent
  family name: Yue
  given name: Qiuling
author list: Agent
  family name: Fu
  given name: Kaiqiang
author list: Agent
  family name: Ye
  given name: Lan
author list: Agent
  family name: Bai
  given name: Shun
doi: 10.7717/peerj.10582
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-21
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Estimating salt content of vegetated soil at different depths with Sentinel-2 data
type: item
type: AcademicArticle
description: The accurate and timely monitoring of the soil salt content (SSC) at different depths is the prerequisite for the solution to salinization in the arid and semiarid areas. Sentinel-2 has demonstrated significant superiority in SSC inversion for its higher temporal, spatial and spectral resolution, but previous research on SSC inversion with Sentinel-2 mainly focused on the unvegetated surface soil. Based on Sentinel-2 data, this study aimed to build four machine learning models at five depths (0∼20 cm, 20∼40 cm, 40∼60 cm, 0∼40 cm, and 0∼60 cm) in the vegetated area, and evaluate the sensitivity of Sentinel-2 to SSC at different depths and the inversion capability of the models. Firstly, 117 soil samples were collected from Jiefangzha Irrigation Area (JIA) in Hetao Irrigation District (HID), Inner Mongolia, China during August, 2019. Then a set of independent variables (IVs, including 12 bands and 32 spectral indices) were obtained based on the Sentinel-2 data (released by the European Space Agency), and the full subset selection was used to select the optimal combination of IVs at five depths. Finally, four machine learning algorithms, back propagation neural network (BPNN), support vector machine (SVM), extreme learning machine (ELM) and random forest (RF), were used to build inversion models at each depth. The model performance was assessed using adjusted coefficient of determination (R2adj), root mean square error (RMSE) and mean absolute error (MAE). The results indicated that 20∼40 cm was the optimal depth for SSC inversion. All the models at this depth demonstrated a good fitting (R2adj≈ 0.6) and a good control of the inversion errors (RMSE < 0.16%, MAE < 0.12%). At the depths of 40∼60 cm and 0∼20 cm the inversion performance showed a slight and a great decrease respectively. The sensitivity of Sentinel-2 to SSC at different depths was as follows: 20∼40 cm > 40∼60 cm > 0∼40 cm > 0∼60 cm > 0∼20 cm. All four machine learning models demonstrated good inversion per…
format: application/pdf
format: text/html
creator: Yinwen Chen
creator: Yuanlin Qiu
creator: Zhitao Zhang
creator: Junrui Zhang
creator: Ce Chen
creator: Jia Han
creator: Dan Liu
subject: Agricultural Science
subject: Soil Science
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10585
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: The accurate and timely monitoring of the soil salt content (SSC) at different depths is the prerequisite for the solution to salinization in the arid and semiarid areas. Sentinel-2 has demonstrated significant superiority in SSC inversion for its higher temporal, spatial and spectral resolution, but previous research on SSC inversion with Sentinel-2 mainly focused on the unvegetated surface soil. Based on Sentinel-2 data, this study aimed to build four machine learning models at five depths (0∼20 cm, 20∼40 cm, 40∼60 cm, 0∼40 cm, and 0∼60 cm) in the vegetated area, and evaluate the sensitivity of Sentinel-2 to SSC at different depths and the inversion capability of the models. Firstly, 117 soil samples were collected from Jiefangzha Irrigation Area (JIA) in Hetao Irrigation District (HID), Inner Mongolia, China during August, 2019. Then a set of independent variables (IVs, including 12 bands and 32 spectral indices) were obtained based on the Sentinel-2 data (released by the European Space Agency), and the full subset selection was used to select the optimal combination of IVs at five depths. Finally, four machine learning algorithms, back propagation neural network (BPNN), support vector machine (SVM), extreme learning machine (ELM) and random forest (RF), were used to build inversion models at each depth. The model performance was assessed using adjusted coefficient of determination (R2adj), root mean square error (RMSE) and mean absolute error (MAE). The results indicated that 20∼40 cm was the optimal depth for SSC inversion. All the models at this depth demonstrated a good fitting (R2adj≈ 0.6) and a good control of the inversion errors (RMSE < 0.16%, MAE < 0.12%). At the depths of 40∼60 cm and 0∼20 cm the inversion performance showed a slight and a great decrease respectively. The sensitivity of Sentinel-2 to SSC at different depths was as follows: 20∼40 cm > 40∼60 cm > 0∼40 cm > 0∼60 cm > 0∼20 cm. All four machine learning models demonstrated good inversion per…
bibliographic citation: Chen et al. (2020) Estimating salt content of vegetated soil at different depths with Sentinel-2 data. PeerJ 8:e10585 https://doi.org/10.7717/peerj.10585
date submitted: 2020-08-12
date accepted: 2020-11-24
issued: 2020-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yinwen
author list: Agent
  family name: Qiu
  given name: Yuanlin
author list: Agent
  family name: Zhang
  given name: Zhitao
author list: Agent
  family name: Zhang
  given name: Junrui
author list: Agent
  family name: Chen
  given name: Ce
author list: Agent
  family name: Han
  given name: Jia
author list: Agent
  family name: Liu
  given name: Dan
doi: 10.7717/peerj.10585
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-21
copyright: ©2020 Chen et al.
attribution name: Chen et al.

Sevoflurane preconditioning attenuates hypoxia/reoxygenation injury of H9c2 cardiomyocytes by activation of the HIF-1/PDK-1 pathway
type: item
type: AcademicArticle
description: Background Sevoflurane preconditioning (SPC) can provide myocardial protective effects similar to ischemic preconditioning (IPC). However, the underlying molecular mechanism of SPC remains unclear. Studies confirm that hypoxia-inducible factor-1 (HIF-1) can transform cells from aerobic oxidation to anaerobic glycolysis by activating the switch protein pyruvate dehydrogenase kinase-1 (PDK-1), thus providing energy for the normal life activities of cells under hypoxic conditions. The purpose of this study was to investigate whether the cardioprotective effects of SPC are associated with activation of the HIF-1a/PDK-1 signal pathway. Methods The H9c2 cardiomyocytes hypoxia/reoxygenation model was established and treated with 2.4% sevoflurane at the end of equilibration. Lactate dehydrogenase (LDH) level, cell viability, cell apoptosis, mitochondrial membrane potential, key enzymes of glycolysis, ATP concentration of glycolysis were assessed after the intervention. Apoptosis related protein(Bcl-2, Bax), HIF-1a protein, and PDK-1 protein were assessed by western blot. Results Compared with the H/R group, SPC significantly increased the expression of HIF-1a, PDK-1, and Bcl-2 and reduced the protein expression of Bax, which markedly decreased the apoptosis ratio and Lactate dehydrogenase (LDH) level, increasing the cell viability, content of key enzymes of glycolysis, ATP concentration of glycolysis and stabilizing the mitochondrial membrane potential. However, the cardioprotective effects of SPC were disappeared by treatment with a HIF-1a selective inhibitor. Conclusion This study demonstrates that the cardioprotective effects of SPC are associated with the activation of the HIF-1a/PDK-1 signaling pathway. The mechanism may be related to increasing the content of key enzymes and ATP of glycolysis in the early stage of hypoxia.
format: application/pdf
format: text/html
creator: Tianliang Hou
creator: Haiping Ma
creator: Haixia Wang
creator: Chunling Chen
creator: Jianrong Ye
creator: Ahmed Mohamed Ahmed
creator: Hong Zheng
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: Anesthesiology and Pain Management
subject: Cardiology
description: doi:10.7717/peerj.10603
publisher: PeerJ Inc.
rights: © 2020 Hou et al.
abstract: Background Sevoflurane preconditioning (SPC) can provide myocardial protective effects similar to ischemic preconditioning (IPC). However, the underlying molecular mechanism of SPC remains unclear. Studies confirm that hypoxia-inducible factor-1 (HIF-1) can transform cells from aerobic oxidation to anaerobic glycolysis by activating the switch protein pyruvate dehydrogenase kinase-1 (PDK-1), thus providing energy for the normal life activities of cells under hypoxic conditions. The purpose of this study was to investigate whether the cardioprotective effects of SPC are associated with activation of the HIF-1a/PDK-1 signal pathway. Methods The H9c2 cardiomyocytes hypoxia/reoxygenation model was established and treated with 2.4% sevoflurane at the end of equilibration. Lactate dehydrogenase (LDH) level, cell viability, cell apoptosis, mitochondrial membrane potential, key enzymes of glycolysis, ATP concentration of glycolysis were assessed after the intervention. Apoptosis related protein(Bcl-2, Bax), HIF-1a protein, and PDK-1 protein were assessed by western blot. Results Compared with the H/R group, SPC significantly increased the expression of HIF-1a, PDK-1, and Bcl-2 and reduced the protein expression of Bax, which markedly decreased the apoptosis ratio and Lactate dehydrogenase (LDH) level, increasing the cell viability, content of key enzymes of glycolysis, ATP concentration of glycolysis and stabilizing the mitochondrial membrane potential. However, the cardioprotective effects of SPC were disappeared by treatment with a HIF-1a selective inhibitor. Conclusion This study demonstrates that the cardioprotective effects of SPC are associated with the activation of the HIF-1a/PDK-1 signaling pathway. The mechanism may be related to increasing the content of key enzymes and ATP of glycolysis in the early stage of hypoxia.
bibliographic citation: Hou et al. (2020) Sevoflurane preconditioning attenuates hypoxia/reoxygenation injury of H9c2 cardiomyocytes by activation of the HIF-1/PDK-1 pathway. PeerJ 8:e10603 https://doi.org/10.7717/peerj.10603
date submitted: 2020-09-03
date accepted: 2020-11-28
issued: 2020-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: Tianliang
author list: Agent
  family name: Ma
  given name: Haiping
author list: Agent
  family name: Wang
  given name: Haixia
author list: Agent
  family name: Chen
  given name: Chunling
author list: Agent
  family name: Ye
  given name: Jianrong
author list: Agent
  family name: Ahmed
  given name: Ahmed Mohamed
author list: Agent
  family name: Zheng
  given name: Hong
doi: 10.7717/peerj.10603
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-21
copyright: ©2020 Hou et al.
attribution name: Hou et al.

Improved plaque assay for human coronaviruses 229E and OC43
type: item
type: AcademicArticle
description: In light of the COVID-19 pandemic, studies that work to understand SARS-CoV-2 are urgently needed. In turn, the less severe human coronaviruses such as HCoV-229E and OC43 are drawing newfound attention. These less severe coronaviruses can be used as a model to facilitate our understanding of the host immune response to coronavirus infection. SARS-CoV-2 must be handled under biosafety level 3 (BSL-3) conditions. Therefore, HCoV-229E and OC43, which can be handled at BSL-2 provide an alternative to SARS-CoV-2 for preclinical screening and designing of antivirals. However, to date, there is no published effective and efficient method to titrate HCoVs other than expensive indirect immunostaining. Here we present an improved approach using an agarose-based conventional plaque assay to titrate HCoV 229E and OC43 with mink lung epithelial cells, Mv1Lu. Our results indicate that titration of HCoV 229E and OC43 with Mv1Lu is consistent and reproducible. The titers produced are also comparable to those produced using human rhabdomyosarcoma (RD) cells. More importantly, Mv1Lu cells display a higher tolerance for cell-cell contact stress, decreased temperature sensitivity, and a faster growth rate. We believe that our improved low-cost plaque assay can serve as an easy tool for researchers conducting HCoV research.
format: application/pdf
format: text/html
creator: Nicole Bracci
creator: Han-Chi Pan
creator: Caitlin Lehman
creator: Kylene Kehn-Hall
creator: Shih-Chao Lin
subject: Biotechnology
subject: Virology
description: doi:10.7717/peerj.10639
publisher: PeerJ Inc.
rights: © 2020 Bracci et al.
abstract: In light of the COVID-19 pandemic, studies that work to understand SARS-CoV-2 are urgently needed. In turn, the less severe human coronaviruses such as HCoV-229E and OC43 are drawing newfound attention. These less severe coronaviruses can be used as a model to facilitate our understanding of the host immune response to coronavirus infection. SARS-CoV-2 must be handled under biosafety level 3 (BSL-3) conditions. Therefore, HCoV-229E and OC43, which can be handled at BSL-2 provide an alternative to SARS-CoV-2 for preclinical screening and designing of antivirals. However, to date, there is no published effective and efficient method to titrate HCoVs other than expensive indirect immunostaining. Here we present an improved approach using an agarose-based conventional plaque assay to titrate HCoV 229E and OC43 with mink lung epithelial cells, Mv1Lu. Our results indicate that titration of HCoV 229E and OC43 with Mv1Lu is consistent and reproducible. The titers produced are also comparable to those produced using human rhabdomyosarcoma (RD) cells. More importantly, Mv1Lu cells display a higher tolerance for cell-cell contact stress, decreased temperature sensitivity, and a faster growth rate. We believe that our improved low-cost plaque assay can serve as an easy tool for researchers conducting HCoV research.
bibliographic citation: Bracci et al. (2020) Improved plaque assay for human coronaviruses 229E and OC43. PeerJ 8:e10639 https://doi.org/10.7717/peerj.10639
date submitted: 2020-10-09
date accepted: 2020-12-02
issued: 2020-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bracci
  given name: Nicole
author list: Agent
  family name: Pan
  given name: Han-Chi
author list: Agent
  family name: Lehman
  given name: Caitlin
author list: Agent
  family name: Kehn-Hall
  given name: Kylene
author list: Agent
  family name: Lin
  given name: Shih-Chao
doi: 10.7717/peerj.10639
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-21
copyright: © 2020 Bracci et al.
attribution name: Bracci et al.

Uncovering the hidden diversity of Mississippian crinoids (Crinoidea, Echinodermata) from Poland
type: item
type: AcademicArticle
description: Partial crinoid crowns and aboral cups are reported from the Mississippian of Poland for the first time. Most specimens are partially disarticulated or isolated plates, which prevent identification to genus and species, but regardless these remains indicate a rich diversity of Mississippian crinoids in Poland during the Mississippian, especially during the late Viséan. Lanecrinus? sp. is described from the late Tournaisian of the Dębnik Anticline region. A high crinoid biodiversity occurred during late Viséan of the Holy Cross Mountains, including the camerate crinoids Gilbertsocrinus? sp., Platycrinitidae Indeterminate; one flexible crinoid; and numerous eucladid crinoids, including Cyathocrinites mammillaris (Phillips), three taxa represented by partial cups left in open nomenclature, and numerous additional taxa known only from isolated radial plates, brachial plates, and columnals. To date, the youngest occurrence of Gilbertsocrinus was the early Viséan of the United States, thus the present finding in upper Viséan extends this genus range. Furthermore, the occurrence of Lanecrinus? sp. expands the Western European range of this genus into the Tournaisian. A single partially disarticulated crown, Crinoidea Indeterminate B, is described from the Serpukhovian of the Upper Silesian Coal Basin. In addition, several echinoid test plates and spines are also reported.
format: application/pdf
format: text/html
creator: Mariusz A. Salamon
creator: William I. Ausich
creator: Tomasz Brachaniec
creator: Bartosz J. Płachno
creator: Przemysław Gorzelak
subject: Paleontology
description: doi:10.7717/peerj.10641
publisher: PeerJ Inc.
rights: © 2020 Salamon et al.
abstract: Partial crinoid crowns and aboral cups are reported from the Mississippian of Poland for the first time. Most specimens are partially disarticulated or isolated plates, which prevent identification to genus and species, but regardless these remains indicate a rich diversity of Mississippian crinoids in Poland during the Mississippian, especially during the late Viséan. Lanecrinus? sp. is described from the late Tournaisian of the Dębnik Anticline region. A high crinoid biodiversity occurred during late Viséan of the Holy Cross Mountains, including the camerate crinoids Gilbertsocrinus? sp., Platycrinitidae Indeterminate; one flexible crinoid; and numerous eucladid crinoids, including Cyathocrinites mammillaris (Phillips), three taxa represented by partial cups left in open nomenclature, and numerous additional taxa known only from isolated radial plates, brachial plates, and columnals. To date, the youngest occurrence of Gilbertsocrinus was the early Viséan of the United States, thus the present finding in upper Viséan extends this genus range. Furthermore, the occurrence of Lanecrinus? sp. expands the Western European range of this genus into the Tournaisian. A single partially disarticulated crown, Crinoidea Indeterminate B, is described from the Serpukhovian of the Upper Silesian Coal Basin. In addition, several echinoid test plates and spines are also reported.
bibliographic citation: Salamon et al. (2020) Uncovering the hidden diversity of Mississippian crinoids (Crinoidea, Echinodermata) from Poland. PeerJ 8:e10641 https://doi.org/10.7717/peerj.10641
date submitted: 2020-10-12
date accepted: 2020-12-03
issued: 2020-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salamon
  given name: Mariusz A.
author list: Agent
  family name: Ausich
  given name: William I.
author list: Agent
  family name: Brachaniec
  given name: Tomasz
author list: Agent
  family name: Płachno
  given name: Bartosz J.
author list: Agent
  family name: Gorzelak
  given name: Przemysław
doi: 10.7717/peerj.10641
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-21
copyright: ©2020 Salamon et al.
attribution name: Salamon et al.

Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes
type: item
type: AcademicArticle
description: Light plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. A total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. Our study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.
format: application/pdf
format: text/html
creator: Tingting Song
creator: Yingyue Shen
creator: Qunli Jin
creator: Weilin Feng
creator: Lijun Fan
creator: Weiming Cai
subject: Agricultural Science
subject: Developmental Biology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.9859
publisher: PeerJ Inc.
rights: © 2020 Song et al.
abstract: Light plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. A total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. Our study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.
bibliographic citation: Song et al. (2020) Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes. PeerJ 8:e9859 https://doi.org/10.7717/peerj.9859
date submitted: 2020-04-02
date accepted: 2020-08-12
issued: 2020-12-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Tingting
author list: Agent
  family name: Shen
  given name: Yingyue
author list: Agent
  family name: Jin
  given name: Qunli
author list: Agent
  family name: Feng
  given name: Weilin
author list: Agent
  family name: Fan
  given name: Lijun
author list: Agent
  family name: Cai
  given name: Weiming
doi: 10.7717/peerj.9859
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-18
copyright: ©2020 Song et al.
attribution name: Song et al.

Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species
type: item
type: AcademicArticle
description: Research on the gut microbiome of host organisms has rapidly advanced with next generation sequencing (NGS) and high-performance computing capabilities. Nonetheless, gut microbiome research has focused on mammalian organisms in laboratory settings, and investigations pertaining to wild fish gut microbiota remain in their infancy. We applied a procedure (available at https://github.com/bngallo1994) for sampling of the fish gut for use in NGS to describe microbial community structure. Our approach allowed for high bacterial OTU diversity coverage (>99.7%, Good’s Coverage) that led to detection of differences in gut microbiota of an invasive (Round Goby) and native (Yellow Bullhead) fish species and collected from the upper St. Lawrence River, an environment where the gut microbiota of fish had not previously been tested. Additionally, results revealed habitat level differences in gut microbiota using two distance metrics (Unifrac, Bray–Curtis) between nearshore littoral and offshore profundal collections of Round Goby. Species and habitat level differences in intestinal microbiota may be of importance in understanding individual and species variation and its importance in regulating fish health and physiology.
format: application/pdf
format: text/html
creator: Benjamin D. Gallo
creator: John M. Farrell
creator: Brian Leydet
subject: Aquaculture, Fisheries and Fish Science
subject: Microbiology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.10237
publisher: PeerJ Inc.
rights: © 2020 Gallo et al.
abstract: Research on the gut microbiome of host organisms has rapidly advanced with next generation sequencing (NGS) and high-performance computing capabilities. Nonetheless, gut microbiome research has focused on mammalian organisms in laboratory settings, and investigations pertaining to wild fish gut microbiota remain in their infancy. We applied a procedure (available at https://github.com/bngallo1994) for sampling of the fish gut for use in NGS to describe microbial community structure. Our approach allowed for high bacterial OTU diversity coverage (>99.7%, Good’s Coverage) that led to detection of differences in gut microbiota of an invasive (Round Goby) and native (Yellow Bullhead) fish species and collected from the upper St. Lawrence River, an environment where the gut microbiota of fish had not previously been tested. Additionally, results revealed habitat level differences in gut microbiota using two distance metrics (Unifrac, Bray–Curtis) between nearshore littoral and offshore profundal collections of Round Goby. Species and habitat level differences in intestinal microbiota may be of importance in understanding individual and species variation and its importance in regulating fish health and physiology.
bibliographic citation: Gallo et al. (2020) Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species. PeerJ 8:e10237 https://doi.org/10.7717/peerj.10237
date submitted: 2020-02-25
date accepted: 2020-10-04
issued: 2020-12-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gallo
  given name: Benjamin D.
author list: Agent
  family name: Farrell
  given name: John M.
author list: Agent
  family name: Leydet
  given name: Brian
doi: 10.7717/peerj.10237
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-18
copyright: © 2020 Gallo et al.
attribution name: Gallo et al.

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