PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Mesenchymal stem cell exosomes reverse acute lung injury through Nrf-2/ARE and NF-κB signaling pathways
items: Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs
items: Radiolarian assemblages in the shelf area of the East China Sea and Yellow Sea and their ecological indication of the Kuroshio Current derivative branches
items: Development of a noninvasive photograph-based method for the evaluation of body condition in free-ranging brown bears
items: Soil fungal networks are more sensitive to grazing exclusion than bacterial networks
items: Evidence of transfer of miRNAs from the diet to the blood still inconclusive
items: Salinity impairs photosynthetic capacity and enhances carotenoid-related gene expression and biosynthesis in tomato (Solanum lycopersicum L. cv. Micro-Tom)
items: Jatropha curcas ortholog of tomato MADS-box gene 6 (JcTM6) promoter exhibits floral-specific activity in Arabidopsis thaliana
items: Association between serum and dietary antioxidant micronutrients and advanced liver fibrosis in non-alcoholic fatty liver disease: an observational study
items: lcc: an R package to estimate the concordance correlation, Pearson correlation and accuracy over time

Mesenchymal stem cell exosomes reverse acute lung injury through Nrf-2/ARE and NF-κB signaling pathways
type: item
type: AcademicArticle
description: Acute lung injury (ALI) is associated with histopathological diffuse alveolar damage. The potential role of mesenchymal stem cells (MSCs) in the treatment of various clinical disorders have been widely documented, such as those for ALI. Recent evidence has demonstrated that exosomes from endothelial progenitor cells can improve outcomes of the lipopolysaccharide (LPS)-induced ALI. However, there has been no research on the potential role of MSC-exosomes in the treatment of sepsis-induced ALI, which is worth further exploration. Thus, the objective of our study was to identify whether the MSC-exosomes could reverse ALI. The ALI model induced by LPS was established in this study. MTT assay was performed to test cell proliferation. Expression of inflammatory factors (TNF-α, IL-6, and IL-10) in the LPS-treated type II alveolar epithelial cells (AECs) (MLE-12) was detected by ELISA. After co-culture of MSC-exosomes with LPS-treated MLE-12 cells, we found that the cell proliferation of MLE-12 cells gradually increased. Furthermore, we selected five of the Nrf-2/ARE- and NF-κB signaling pathway-related genes to explore if MSC-exosomes could reverse LPS-induced ALI through Nrf-2/ARE and NF-κB signaling pathways. QRT-PCR and western blot experiment results showed that the expression of these five genes were significantly regulated after stimulation with high-concentration LPS and exosome intervention. Taken together, these findings highlighted the fact that MSC-exosomes could reverse ALI through the Nrf-2/ARE and NF-κB signaling pathways. The MSC-exosome may be the potential future therapeutic strategy for the treatment of ALI.
format: application/pdf
format: text/html
creator: Jun Li
creator: Xingqi Deng
creator: Xiangling Ji
creator: Xiaojun Shi
creator: Zhiying Ying
creator: Kan Shen
creator: Dongwei Xu
creator: Zhihui Cheng
subject: Biochemistry
subject: Cell Biology
subject: Respiratory Medicine
description: doi:10.7717/peerj.9928
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Acute lung injury (ALI) is associated with histopathological diffuse alveolar damage. The potential role of mesenchymal stem cells (MSCs) in the treatment of various clinical disorders have been widely documented, such as those for ALI. Recent evidence has demonstrated that exosomes from endothelial progenitor cells can improve outcomes of the lipopolysaccharide (LPS)-induced ALI. However, there has been no research on the potential role of MSC-exosomes in the treatment of sepsis-induced ALI, which is worth further exploration. Thus, the objective of our study was to identify whether the MSC-exosomes could reverse ALI. The ALI model induced by LPS was established in this study. MTT assay was performed to test cell proliferation. Expression of inflammatory factors (TNF-α, IL-6, and IL-10) in the LPS-treated type II alveolar epithelial cells (AECs) (MLE-12) was detected by ELISA. After co-culture of MSC-exosomes with LPS-treated MLE-12 cells, we found that the cell proliferation of MLE-12 cells gradually increased. Furthermore, we selected five of the Nrf-2/ARE- and NF-κB signaling pathway-related genes to explore if MSC-exosomes could reverse LPS-induced ALI through Nrf-2/ARE and NF-κB signaling pathways. QRT-PCR and western blot experiment results showed that the expression of these five genes were significantly regulated after stimulation with high-concentration LPS and exosome intervention. Taken together, these findings highlighted the fact that MSC-exosomes could reverse ALI through the Nrf-2/ARE and NF-κB signaling pathways. The MSC-exosome may be the potential future therapeutic strategy for the treatment of ALI.
bibliographic citation: Li et al. (2020) Mesenchymal stem cell exosomes reverse acute lung injury through Nrf-2/ARE and NF-κB signaling pathways. PeerJ 8:e9928 https://doi.org/10.7717/peerj.9928
date submitted: 2020-01-23
date accepted: 2020-08-21
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jun
author list: Agent
  family name: Deng
  given name: Xingqi
author list: Agent
  family name: Ji
  given name: Xiangling
author list: Agent
  family name: Shi
  given name: Xiaojun
author list: Agent
  family name: Ying
  given name: Zhiying
author list: Agent
  family name: Shen
  given name: Kan
author list: Agent
  family name: Xu
  given name: Dongwei
author list: Agent
  family name: Cheng
  given name: Zhihui
doi: 10.7717/peerj.9928
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Li et al.
attribution name: Li et al.

Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs
type: item
type: AcademicArticle
description: Using the crystal structure of SARS-CoV-2 papain-like protease (PLpro) as a template, we developed a pharmacophore model of functional centers of the PLpro inhibitor-binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. This search identified 147 compounds that can be potential inhibitors of SARS-CoV-2 PLpro. The conformations of these compounds underwent 3D fingerprint similarity clusterization, followed by docking of possible conformers to the binding pocket of PLpro. Docking of random compounds to the binding pocket of protease was also done for comparison. Free energies of the docking interaction for the selected compounds were lower than for random compounds. The drug list obtained includes inhibitors of HIV, hepatitis C, and cytomegalovirus (CMV), as well as a set of drugs that have demonstrated some activity in MERS, SARS-CoV, and SARS-CoV-2 therapy. We recommend testing of the selected compounds for treatment of COVID-19
format: application/pdf
format: text/html
creator: Valentina L. Kouznetsova
creator: Aidan Zhang
creator: Mahidhar Tatineni
creator: Mark A. Miller
creator: Igor F. Tsigelny
subject: Bioinformatics
subject: Biophysics
subject: Computational Biology
subject: Drugs and Devices
subject: Infectious Diseases
description: doi:10.7717/peerj.9965
publisher: PeerJ Inc.
rights: © 2020 Kouznetsova et al.
abstract: Using the crystal structure of SARS-CoV-2 papain-like protease (PLpro) as a template, we developed a pharmacophore model of functional centers of the PLpro inhibitor-binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. This search identified 147 compounds that can be potential inhibitors of SARS-CoV-2 PLpro. The conformations of these compounds underwent 3D fingerprint similarity clusterization, followed by docking of possible conformers to the binding pocket of PLpro. Docking of random compounds to the binding pocket of protease was also done for comparison. Free energies of the docking interaction for the selected compounds were lower than for random compounds. The drug list obtained includes inhibitors of HIV, hepatitis C, and cytomegalovirus (CMV), as well as a set of drugs that have demonstrated some activity in MERS, SARS-CoV, and SARS-CoV-2 therapy. We recommend testing of the selected compounds for treatment of COVID-19
bibliographic citation: Kouznetsova et al. (2020) Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs. PeerJ 8:e9965 https://doi.org/10.7717/peerj.9965
date submitted: 2020-07-01
date accepted: 2020-08-26
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kouznetsova
  given name: Valentina L.
author list: Agent
  family name: Zhang
  given name: Aidan
author list: Agent
  family name: Tatineni
  given name: Mahidhar
author list: Agent
  family name: Miller
  given name: Mark A.
author list: Agent
  family name: Tsigelny
  given name: Igor F.
doi: 10.7717/peerj.9965
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: © 2020 Kouznetsova et al.
attribution name: Kouznetsova et al.

Radiolarian assemblages in the shelf area of the East China Sea and Yellow Sea and their ecological indication of the Kuroshio Current derivative branches
type: item
type: AcademicArticle
description: We analyzed the radiolarian assemblages of 59 surface sediment samples collected from the Yellow Sea and East China Sea of the northwestern Pacific. In the study region, the Kuroshio Current and its derivative branches exerted a crucial impact on radiolarian composition and distribution. Radiolarians in the Yellow Sea shelf showed a quite low abundance as no tests were found in 15 of 25 Yellow Sea samples. Radiolarians in the East China Sea shelf could be divided into three regional groups: the East China Sea north region group, the East China Sea middle region group, and the East China Sea south region group. The results of the redundancy analysis suggested that the Sea Surface Temperature and Sea Surface Salinity were primary environmental variables explaining species-environment relationship. The gradients of temperature, salinity, and species diversity reflect the powerful influence of the Kuroshio Current in the study area.
format: application/pdf
format: text/html
creator: Hanxue Qu
creator: Yong Xu
creator: Jinbao Wang
creator: Xin-Zheng Li
subject: Biodiversity
subject: Marine Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.9976
publisher: PeerJ Inc.
rights: © 2020 Qu et al.
abstract: We analyzed the radiolarian assemblages of 59 surface sediment samples collected from the Yellow Sea and East China Sea of the northwestern Pacific. In the study region, the Kuroshio Current and its derivative branches exerted a crucial impact on radiolarian composition and distribution. Radiolarians in the Yellow Sea shelf showed a quite low abundance as no tests were found in 15 of 25 Yellow Sea samples. Radiolarians in the East China Sea shelf could be divided into three regional groups: the East China Sea north region group, the East China Sea middle region group, and the East China Sea south region group. The results of the redundancy analysis suggested that the Sea Surface Temperature and Sea Surface Salinity were primary environmental variables explaining species-environment relationship. The gradients of temperature, salinity, and species diversity reflect the powerful influence of the Kuroshio Current in the study area.
bibliographic citation: Qu et al. (2020) Radiolarian assemblages in the shelf area of the East China Sea and Yellow Sea and their ecological indication of the Kuroshio Current derivative branches. PeerJ 8:e9976 https://doi.org/10.7717/peerj.9976
date submitted: 2019-12-23
date accepted: 2020-08-26
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qu
  given name: Hanxue
author list: Agent
  family name: Xu
  given name: Yong
author list: Agent
  family name: Wang
  given name: Jinbao
author list: Agent
  family name: Li
  given name: Xin-Zheng
doi: 10.7717/peerj.9976
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Qu et al.
attribution name: Qu et al.

Development of a noninvasive photograph-based method for the evaluation of body condition in free-ranging brown bears
type: item
type: AcademicArticle
description: Body condition is an important determinant of health, and its evaluation has practical applications for the conservation and management of mammals. We developed a noninvasive method that uses photographs to assess the body condition of free-ranging brown bears (Ursus arctos) in the Shiretoko Peninsula, Hokkaido, Japan. First, we weighed and measured 476 bears captured during 1998–2017 and calculated their body condition index (BCI) based on residuals from the regression of body mass against body length. BCI showed seasonal changes and was lower in spring and summer than in autumn. The torso height:body length ratio was strongly correlated with BCI, which suggests that it can be used as an indicator of body condition. Second, we examined the precision of photograph-based measurements using an identifiable bear in the Rusha area, a special wildlife protection area on the peninsula. A total of 220 lateral photographs of this bear were taken September 24–26, 2017, and classified according to bear posture. The torso height:body/torso length ratio was calculated with four measurement methods and compared among bear postures in the photographs. The results showed torso height:horizontal torso length (TH:HTL) to be the indicator that could be applied to photographs of the most diverse postures, and its coefficient of variation for measurements was <5%. In addition, when analyzing photographs of this bear taken from June to October during 2016–2018, TH:HTL was significantly higher in autumn than in spring/summer, which indicates that this ratio reflects seasonal changes in body condition in wild bears. Third, we calculated BCI from actual measurements of seven females captured in the Rusha area and TH:HTL from photographs of the same individuals. We found a significant positive relationship between TH:HTL and BCI, which suggests that the body condition of brown bears can be estimated with high accuracy based on photographs. Our simple and accurate method is useful for monito…
format: application/pdf
format: text/html
creator: Yuri Shirane
creator: Fumihiko Mori
creator: Masami Yamanaka
creator: Masanao Nakanishi
creator: Tsuyoshi Ishinazaka
creator: Tsutomu Mano
creator: Mina Jimbo
creator: Mariko Sashika
creator: Toshio Tsubota
creator: Michito Shimozuru
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.9982
publisher: PeerJ Inc.
rights: © 2020 Shirane et al.
abstract: Body condition is an important determinant of health, and its evaluation has practical applications for the conservation and management of mammals. We developed a noninvasive method that uses photographs to assess the body condition of free-ranging brown bears (Ursus arctos) in the Shiretoko Peninsula, Hokkaido, Japan. First, we weighed and measured 476 bears captured during 1998–2017 and calculated their body condition index (BCI) based on residuals from the regression of body mass against body length. BCI showed seasonal changes and was lower in spring and summer than in autumn. The torso height:body length ratio was strongly correlated with BCI, which suggests that it can be used as an indicator of body condition. Second, we examined the precision of photograph-based measurements using an identifiable bear in the Rusha area, a special wildlife protection area on the peninsula. A total of 220 lateral photographs of this bear were taken September 24–26, 2017, and classified according to bear posture. The torso height:body/torso length ratio was calculated with four measurement methods and compared among bear postures in the photographs. The results showed torso height:horizontal torso length (TH:HTL) to be the indicator that could be applied to photographs of the most diverse postures, and its coefficient of variation for measurements was <5%. In addition, when analyzing photographs of this bear taken from June to October during 2016–2018, TH:HTL was significantly higher in autumn than in spring/summer, which indicates that this ratio reflects seasonal changes in body condition in wild bears. Third, we calculated BCI from actual measurements of seven females captured in the Rusha area and TH:HTL from photographs of the same individuals. We found a significant positive relationship between TH:HTL and BCI, which suggests that the body condition of brown bears can be estimated with high accuracy based on photographs. Our simple and accurate method is useful for monito…
bibliographic citation: Shirane et al. (2020) Development of a noninvasive photograph-based method for the evaluation of body condition in free-ranging brown bears. PeerJ 8:e9982 https://doi.org/10.7717/peerj.9982
date submitted: 2020-06-10
date accepted: 2020-08-27
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shirane
  given name: Yuri
author list: Agent
  family name: Mori
  given name: Fumihiko
author list: Agent
  family name: Yamanaka
  given name: Masami
author list: Agent
  family name: Nakanishi
  given name: Masanao
author list: Agent
  family name: Ishinazaka
  given name: Tsuyoshi
author list: Agent
  family name: Mano
  given name: Tsutomu
author list: Agent
  family name: Jimbo
  given name: Mina
author list: Agent
  family name: Sashika
  given name: Mariko
author list: Agent
  family name: Tsubota
  given name: Toshio
author list: Agent
  family name: Shimozuru
  given name: Michito
doi: 10.7717/peerj.9982
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Shirane et al.
attribution name: Shirane et al.

Soil fungal networks are more sensitive to grazing exclusion than bacterial networks
type: item
type: AcademicArticle
description: Soil microbial communities play a crucial role in ecological restoration, but it is unknown how co-occurrence networks within these communities respond to grazing exclusion. This lack of information was addressed by investigating the effects of eight years of grazing exclusion on microbial networks in an area of Stipa glareosa P. Smirn desert steppe in northern China. Here, we show that fungal networks were more sensitive to grazing exclusion than bacterial networks. Eight years of grazing exclusion decreased the soil fungal community stability via changes in plant composition and reductions in soil total organic carbon, in this case triggering negative effects on the S. glareosa desert steppe. The results provide new insights into the response mechanisms of soil microbes to grazing exclusion and offer possible solutions for management issues in the restoration of degraded desert steppe.
format: application/pdf
format: text/html
creator: Lingling Chen
creator: Jiajia Shi
creator: Zhihua Bao
creator: Taogetao Baoyin
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Mycology
subject: Soil Science
description: doi:10.7717/peerj.9986
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Soil microbial communities play a crucial role in ecological restoration, but it is unknown how co-occurrence networks within these communities respond to grazing exclusion. This lack of information was addressed by investigating the effects of eight years of grazing exclusion on microbial networks in an area of Stipa glareosa P. Smirn desert steppe in northern China. Here, we show that fungal networks were more sensitive to grazing exclusion than bacterial networks. Eight years of grazing exclusion decreased the soil fungal community stability via changes in plant composition and reductions in soil total organic carbon, in this case triggering negative effects on the S. glareosa desert steppe. The results provide new insights into the response mechanisms of soil microbes to grazing exclusion and offer possible solutions for management issues in the restoration of degraded desert steppe.
bibliographic citation: Chen et al. (2020) Soil fungal networks are more sensitive to grazing exclusion than bacterial networks. PeerJ 8:e9986 https://doi.org/10.7717/peerj.9986
date submitted: 2020-04-30
date accepted: 2020-08-27
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Lingling
author list: Agent
  family name: Shi
  given name: Jiajia
author list: Agent
  family name: Bao
  given name: Zhihua
author list: Agent
  family name: Baoyin
  given name: Taogetao
doi: 10.7717/peerj.9986
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Chen et al.
attribution name: Chen et al.

Evidence of transfer of miRNAs from the diet to the blood still inconclusive
type: item
type: AcademicArticle
description: MicroRNAs (miRNAs) are short, non-coding, single-strand RNA molecules that act as regulators of gene expression in plants and animals. In 2012, the first evidence was found that plant miRNAs could enter the bloodstream through the digestive tract. Since then, there has been an ongoing discussion about whether miRNAs from the diet are transferred to blood, accumulate in tissues, and regulate gene expression. Different research groups have tried to replicate these findings, using both plant and animal sources. Here, we review the evidence for and against the transfer of diet-derived miRNAs from plants, meat, milk and exosome and their assimilation and putative molecular regulation role in the consuming organism. Some groups using both miRNAs from plant and animal sources have claimed success, whereas others have not shown transfer. In spite of the biological barriers that may limit miRNA transference, several diet-derived miRNAs can transfer into the circulating system and targets genes for transcription regulation, which adds arguments that miRNAs can be absorbed from the diet and target specific genes by regulating their expression. However, many other studies show that cross-kingdom transfer of exogenous miRNAs appears to be insignificant and not biologically relevant. The main source of controversy in plant studies is the lack of reproducibility of the findings. For meat-derived miRNAs, studies concluded that the miRNAs can survive the cooking process; nevertheless, our evidence shows that the bovine miRNAs are not transferred to human bloodstream. The most important contributions and promising evidence in this controversial field is the transference of milk miRNAs in exosomes and the finding that plant miRNAs in beebread regulate honeybee caste development, and cause similar changes when fed to Drosophila. MiRNAs encapsulated in exosomes ensure their stability and resistance in the harsh conditions presented in milk, bloodstream, and gastrointestinaltract to rein…
format: application/pdf
format: text/html
creator: Fermín Mar-Aguilar
creator: Alejandra Arreola-Triana
creator: Daniela Mata-Cardona
creator: Vianey Gonzalez-Villasana
creator: Cristina Rodríguez-Padilla
creator: Diana Reséndez-Pérez
subject: Molecular Biology
subject: Nutrition
description: doi:10.7717/peerj.9567
publisher: PeerJ Inc.
rights: © 2020 Mar-Aguilar et al.
abstract: MicroRNAs (miRNAs) are short, non-coding, single-strand RNA molecules that act as regulators of gene expression in plants and animals. In 2012, the first evidence was found that plant miRNAs could enter the bloodstream through the digestive tract. Since then, there has been an ongoing discussion about whether miRNAs from the diet are transferred to blood, accumulate in tissues, and regulate gene expression. Different research groups have tried to replicate these findings, using both plant and animal sources. Here, we review the evidence for and against the transfer of diet-derived miRNAs from plants, meat, milk and exosome and their assimilation and putative molecular regulation role in the consuming organism. Some groups using both miRNAs from plant and animal sources have claimed success, whereas others have not shown transfer. In spite of the biological barriers that may limit miRNA transference, several diet-derived miRNAs can transfer into the circulating system and targets genes for transcription regulation, which adds arguments that miRNAs can be absorbed from the diet and target specific genes by regulating their expression. However, many other studies show that cross-kingdom transfer of exogenous miRNAs appears to be insignificant and not biologically relevant. The main source of controversy in plant studies is the lack of reproducibility of the findings. For meat-derived miRNAs, studies concluded that the miRNAs can survive the cooking process; nevertheless, our evidence shows that the bovine miRNAs are not transferred to human bloodstream. The most important contributions and promising evidence in this controversial field is the transference of milk miRNAs in exosomes and the finding that plant miRNAs in beebread regulate honeybee caste development, and cause similar changes when fed to Drosophila. MiRNAs encapsulated in exosomes ensure their stability and resistance in the harsh conditions presented in milk, bloodstream, and gastrointestinaltract to rein…
bibliographic citation: Mar-Aguilar et al. (2020) Evidence of transfer of miRNAs from the diet to the blood still inconclusive. PeerJ 8:e9567 https://doi.org/10.7717/peerj.9567
date submitted: 2020-01-27
date accepted: 2020-06-28
issued: 2020-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mar-Aguilar
  given name: Fermín
author list: Agent
  family name: Arreola-Triana
  given name: Alejandra
author list: Agent
  family name: Mata-Cardona
  given name: Daniela
author list: Agent
  family name: Gonzalez-Villasana
  given name: Vianey
author list: Agent
  family name: Rodríguez-Padilla
  given name: Cristina
author list: Agent
  family name: Reséndez-Pérez
  given name: Diana
doi: 10.7717/peerj.9567
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-17
copyright: ©2020 Mar-Aguilar et al.
attribution name: Mar-Aguilar et al.

Salinity impairs photosynthetic capacity and enhances carotenoid-related gene expression and biosynthesis in tomato (Solanum lycopersicum L. cv. Micro-Tom)
type: item
type: AcademicArticle
description: Carotenoids are essential components of the photosynthetic antenna and reaction center complexes, being also responsible for antioxidant defense, coloration, and many other functions in multiple plant tissues. In tomato, salinity negatively affects the development of vegetative organs and productivity, but according to previous studies it might also increase fruit color and taste, improving its quality, which is a current agricultural challenge. The fruit quality parameters that are increased by salinity are cultivar-specific and include carotenoid, sugar, and organic acid contents. However, the relationship between vegetative and reproductive organs and response to salinity is still poorly understood. Considering this, Solanum lycopersicum cv. Micro-Tom plants were grown in the absence of salt supplementation as well as with increasing concentrations of NaCl for 14 weeks, evaluating plant performance from vegetative to reproductive stages. In response to salinity, plants showed a significant reduction in net photosynthesis, stomatal conductance, PSII quantum yield, and electron transport rate, in addition to an increase in non-photochemical quenching. In line with these responses the number of tomato clusters decreased, and smaller fruits with higher soluble solids content were obtained. Mature-green fruits also displayed a salt-dependent higher induction in the expression of PSY1, PDS, ZDS, and LYCB, key genes of the carotenoid biosynthesis pathway, in correlation with increased lycopene, lutein, β-carotene, and violaxanthin levels. These results suggest a key relationship between photosynthetic plant response and yield, involving impaired photosynthetic capacity, increased carotenoid-related gene expression, and carotenoid biosynthesis.
format: application/pdf
format: text/html
creator: Andrés Leiva-Ampuero
creator: Mario Agurto
creator: José Tomás Matus
creator: Gustavo Hoppe
creator: Camila Huidobro
creator: Claudio Inostroza-Blancheteau
creator: Marjorie Reyes-Díaz
creator: Claudia Stange
creator: Paulo Canessa
creator: Andrea Vega
subject: Agricultural Science
subject: Biotechnology
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9742
publisher: PeerJ Inc.
rights: © 2020 Leiva-Ampuero et al.
abstract: Carotenoids are essential components of the photosynthetic antenna and reaction center complexes, being also responsible for antioxidant defense, coloration, and many other functions in multiple plant tissues. In tomato, salinity negatively affects the development of vegetative organs and productivity, but according to previous studies it might also increase fruit color and taste, improving its quality, which is a current agricultural challenge. The fruit quality parameters that are increased by salinity are cultivar-specific and include carotenoid, sugar, and organic acid contents. However, the relationship between vegetative and reproductive organs and response to salinity is still poorly understood. Considering this, Solanum lycopersicum cv. Micro-Tom plants were grown in the absence of salt supplementation as well as with increasing concentrations of NaCl for 14 weeks, evaluating plant performance from vegetative to reproductive stages. In response to salinity, plants showed a significant reduction in net photosynthesis, stomatal conductance, PSII quantum yield, and electron transport rate, in addition to an increase in non-photochemical quenching. In line with these responses the number of tomato clusters decreased, and smaller fruits with higher soluble solids content were obtained. Mature-green fruits also displayed a salt-dependent higher induction in the expression of PSY1, PDS, ZDS, and LYCB, key genes of the carotenoid biosynthesis pathway, in correlation with increased lycopene, lutein, β-carotene, and violaxanthin levels. These results suggest a key relationship between photosynthetic plant response and yield, involving impaired photosynthetic capacity, increased carotenoid-related gene expression, and carotenoid biosynthesis.
bibliographic citation: Leiva-Ampuero et al. (2020) Salinity impairs photosynthetic capacity and enhances carotenoid-related gene expression and biosynthesis in tomato (Solanum lycopersicum L. cv. Micro-Tom). PeerJ 8:e9742 https://doi.org/10.7717/peerj.9742
date submitted: 2020-02-10
date accepted: 2020-07-26
issued: 2020-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leiva-Ampuero
  given name: Andrés
author list: Agent
  family name: Agurto
  given name: Mario
author list: Agent
  family name: Matus
  given name: José Tomás
author list: Agent
  family name: Hoppe
  given name: Gustavo
author list: Agent
  family name: Huidobro
  given name: Camila
author list: Agent
  family name: Inostroza-Blancheteau
  given name: Claudio
author list: Agent
  family name: Reyes-Díaz
  given name: Marjorie
author list: Agent
  family name: Stange
  given name: Claudia
author list: Agent
  family name: Canessa
  given name: Paulo
author list: Agent
  family name: Vega
  given name: Andrea
doi: 10.7717/peerj.9742
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-17
copyright: ©2020 Leiva-Ampuero et al.
attribution name: Leiva-Ampuero et al.

Jatropha curcas ortholog of tomato MADS-box gene 6 (JcTM6) promoter exhibits floral-specific activity in Arabidopsis thaliana
type: item
type: AcademicArticle
description: Background Jatropha curcas L., a perennial oilseed plant, is considered as a promising feedstock for biodiesel production. Genetic modification of flowering characteristics is critical for Jatropha breeding. However, analysis of floral-specific promoters in Jatropha is limited. Methods In this study, we isolated the Jatropha ortholog of TM6 (JcTM6) gene from Jatropha flower cDNA library and detected the expression pattern of JcTM6 gene by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We isolated a 1.8-kb fragment from the 5’ region of the JcTM6 gene and evaluated its spatiotemporal expression pattern in Arabidopsis using the β-glucuronidase (GUS) reporter gene and Arabidopsis ATP/ADP isopentenyltransferase 4 (AtIPT4) gene, respectively. Results JcTM6 was identified as a flower-specific gene in Jatropha. As expected, JcTM6 promoter was only active in transgenic Arabidopsis flowers with the strongest activity in stamens. Moreover, JcTM6:AtIPT4 transgenic Arabidopsis showed a phenotype of large flowers without any alterations in other organs. Furthermore, deletion of the region from –1,717 to –876 bp resulted in the disappearance of promoter activity in stamens but an increase in promoter activity in young leaves, sepals, and petals. Deletion analysis suggests that the –1,717- to –876-bp promoter fragment contains regulatory elements that confer promoter activity in stamens and inhibit activity in young leaves, sepals, and petals.
format: application/pdf
format: text/html
creator: Jing-Xian Wang
creator: Xin Ming
creator: Yan-Bin Tao
creator: Zeng-Fu Xu
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.9827
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background Jatropha curcas L., a perennial oilseed plant, is considered as a promising feedstock for biodiesel production. Genetic modification of flowering characteristics is critical for Jatropha breeding. However, analysis of floral-specific promoters in Jatropha is limited. Methods In this study, we isolated the Jatropha ortholog of TM6 (JcTM6) gene from Jatropha flower cDNA library and detected the expression pattern of JcTM6 gene by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We isolated a 1.8-kb fragment from the 5’ region of the JcTM6 gene and evaluated its spatiotemporal expression pattern in Arabidopsis using the β-glucuronidase (GUS) reporter gene and Arabidopsis ATP/ADP isopentenyltransferase 4 (AtIPT4) gene, respectively. Results JcTM6 was identified as a flower-specific gene in Jatropha. As expected, JcTM6 promoter was only active in transgenic Arabidopsis flowers with the strongest activity in stamens. Moreover, JcTM6:AtIPT4 transgenic Arabidopsis showed a phenotype of large flowers without any alterations in other organs. Furthermore, deletion of the region from –1,717 to –876 bp resulted in the disappearance of promoter activity in stamens but an increase in promoter activity in young leaves, sepals, and petals. Deletion analysis suggests that the –1,717- to –876-bp promoter fragment contains regulatory elements that confer promoter activity in stamens and inhibit activity in young leaves, sepals, and petals.
bibliographic citation: Wang et al. (2020) Jatropha curcas ortholog of tomato MADS-box gene 6 (JcTM6) promoter exhibits floral-specific activity in Arabidopsis thaliana. PeerJ 8:e9827 https://doi.org/10.7717/peerj.9827
date submitted: 2020-01-20
date accepted: 2020-08-05
issued: 2020-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wang
  given name: Jing-Xian
author list: Agent
  family name: Ming
  given name: Xin
author list: Agent
  family name: Tao
  given name: Yan-Bin
author list: Agent
  family name: Xu
  given name: Zeng-Fu
doi: 10.7717/peerj.9827
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-17
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Association between serum and dietary antioxidant micronutrients and advanced liver fibrosis in non-alcoholic fatty liver disease: an observational study
type: item
type: AcademicArticle
description: Background Despite clinical trials with antioxidant supplementation, few studies have been conducted to evaluate the nutritional status of antioxidant vitamins and minerals, and none have reported on the status of these serum antioxidants associated with the dietary intake of antioxidants by non-alcoholic fatty liver disease (NAFLD) patients. Objective To evaluate association between serum and dietetics antioxidants with liver fibrosis in patients with NAFLD. Methods Across-section analysis with out with 72 patients diagnosed with NAFLD. Hepatic fibrosis was measured by FibroScan®, and liver stiffness ≥7.9 kPa was considered to indicate advanced fibrosis. Retinol, alpha-tocopherol, ascorbic acid, beta-carotene, serum zinc, and selenium were evaluated, as was the dietary intake of these micronutrients in the previous 24 h (using 24-h dietary recall). The Mann–Whitney test was used to compare the fibrosis groups and, a linear regression analysis was performed to determine associated risk factors between age, sex, BMI, hepatic fibrosis, and serum antioxidants. Results A high proportion of inadequate serum retinol (20.8%), vitamin C (27%), and selenium (73.6%) was observed in the patients with NAFLD, in addition to a significant inadequacy of vitamin A (98.3%) and vitamin E (100%) intake. Patients with advanced liver fibrosis had reduced levels of serum retinol (P = 0.002), with liver fibrosis being the independent risk factor associated with serum retinol lower. Conclusion Hepatic fibrosis was associated with a reduction in serum retinol and was reduced in advanced fibrosis. NAFLD patients showed an important serum deficiency and insufficient dietary intake of the evaluated micronutrients.
format: application/pdf
format: text/html
creator: Juliana Moraes Coelho
creator: Katia Cansanção
creator: Renata de Mello Perez
creator: Nathalie Carvalho Leite
creator: Patrícia Padilha
creator: Andrea Ramalho
creator: Wilza Peres
subject: Gastroenterology and Hepatology
subject: Hematology
subject: Nutrition
description: doi:10.7717/peerj.9838
publisher: PeerJ Inc.
rights: © 2020 Coelho et al.
abstract: Background Despite clinical trials with antioxidant supplementation, few studies have been conducted to evaluate the nutritional status of antioxidant vitamins and minerals, and none have reported on the status of these serum antioxidants associated with the dietary intake of antioxidants by non-alcoholic fatty liver disease (NAFLD) patients. Objective To evaluate association between serum and dietetics antioxidants with liver fibrosis in patients with NAFLD. Methods Across-section analysis with out with 72 patients diagnosed with NAFLD. Hepatic fibrosis was measured by FibroScan®, and liver stiffness ≥7.9 kPa was considered to indicate advanced fibrosis. Retinol, alpha-tocopherol, ascorbic acid, beta-carotene, serum zinc, and selenium were evaluated, as was the dietary intake of these micronutrients in the previous 24 h (using 24-h dietary recall). The Mann–Whitney test was used to compare the fibrosis groups and, a linear regression analysis was performed to determine associated risk factors between age, sex, BMI, hepatic fibrosis, and serum antioxidants. Results A high proportion of inadequate serum retinol (20.8%), vitamin C (27%), and selenium (73.6%) was observed in the patients with NAFLD, in addition to a significant inadequacy of vitamin A (98.3%) and vitamin E (100%) intake. Patients with advanced liver fibrosis had reduced levels of serum retinol (P = 0.002), with liver fibrosis being the independent risk factor associated with serum retinol lower. Conclusion Hepatic fibrosis was associated with a reduction in serum retinol and was reduced in advanced fibrosis. NAFLD patients showed an important serum deficiency and insufficient dietary intake of the evaluated micronutrients.
bibliographic citation: Coelho et al. (2020) Association between serum and dietary antioxidant micronutrients and advanced liver fibrosis in non-alcoholic fatty liver disease: an observational study. PeerJ 8:e9838 https://doi.org/10.7717/peerj.9838
date submitted: 2020-06-15
date accepted: 2020-08-08
issued: 2020-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coelho
  given name: Juliana Moraes
author list: Agent
  family name: Cansanção
  given name: Katia
author list: Agent
  family name: Perez
  given name: Renata de Mello
author list: Agent
  family name: Leite
  given name: Nathalie Carvalho
author list: Agent
  family name: Padilha
  given name: Patrícia
author list: Agent
  family name: Ramalho
  given name: Andrea
author list: Agent
  family name: Peres
  given name: Wilza
doi: 10.7717/peerj.9838
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-17
copyright: © 2020 Coelho et al.
attribution name: Coelho et al.

lcc: an R package to estimate the concordance correlation, Pearson correlation and accuracy over time
type: item
type: AcademicArticle
description: Background and Objective Observational studies and experiments in medicine, pharmacology and agronomy are often concerned with assessing whether different methods/raters produce similar values over the time when measuring a quantitative variable. This article aims to describe the statistical package lcc, for are, that can be used to estimate the extent of agreement between two (or more) methods over the time, and illustrate the developed methodology using three real examples. Methods The longitudinal concordance correlation, longitudinal Pearson correlation, and longitudinal accuracy functions can be estimated based on fixed effects and variance components of the mixed-effects regression model. Inference is made through bootstrap confidence intervals and diagnostic can be done via plots, and statistical tests. Results The main features of the package are estimation and inference about the extent of agreement using numerical and graphical summaries. Moreover, our approach accommodates both balanced and unbalanced experimental designs or observational studies, and allows for different within-group error structures, while allowing for the inclusion of covariates in the linear predictor to control systematic variations in the response. All examples show that our methodology is flexible and can be applied to many different data types. Conclusions The lcc package, available on the CRAN repository, proved to be a useful tool to describe the agreement between two or more methods over time, allowing the detection of changes in the extent of agreement. The inclusion of different structures for the variance-covariance matrices of random effects and residuals makes the package flexible for working with different types of databases.
format: application/pdf
format: text/html
creator: Thiago P. Oliveira
creator: Rafael A. Moral
creator: Silvio S. Zocchi
creator: Clarice G.B. Demetrio
creator: John Hinde
subject: Bioinformatics
subject: Statistics
description: doi:10.7717/peerj.9850
publisher: PeerJ Inc.
rights: © 2020 Oliveira et al.
abstract: Background and Objective Observational studies and experiments in medicine, pharmacology and agronomy are often concerned with assessing whether different methods/raters produce similar values over the time when measuring a quantitative variable. This article aims to describe the statistical package lcc, for are, that can be used to estimate the extent of agreement between two (or more) methods over the time, and illustrate the developed methodology using three real examples. Methods The longitudinal concordance correlation, longitudinal Pearson correlation, and longitudinal accuracy functions can be estimated based on fixed effects and variance components of the mixed-effects regression model. Inference is made through bootstrap confidence intervals and diagnostic can be done via plots, and statistical tests. Results The main features of the package are estimation and inference about the extent of agreement using numerical and graphical summaries. Moreover, our approach accommodates both balanced and unbalanced experimental designs or observational studies, and allows for different within-group error structures, while allowing for the inclusion of covariates in the linear predictor to control systematic variations in the response. All examples show that our methodology is flexible and can be applied to many different data types. Conclusions The lcc package, available on the CRAN repository, proved to be a useful tool to describe the agreement between two or more methods over time, allowing the detection of changes in the extent of agreement. The inclusion of different structures for the variance-covariance matrices of random effects and residuals makes the package flexible for working with different types of databases.
bibliographic citation: Oliveira et al. (2020) lcc: an R package to estimate the concordance correlation, Pearson correlation and accuracy over time. PeerJ 8:e9850 https://doi.org/10.7717/peerj.9850
date submitted: 2020-03-18
date accepted: 2020-08-11
issued: 2020-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oliveira
  given name: Thiago P.
author list: Agent
  family name: Moral
  given name: Rafael A.
author list: Agent
  family name: Zocchi
  given name: Silvio S.
author list: Agent
  family name: Demetrio
  given name: Clarice G.B.
author list: Agent
  family name: Hinde
  given name: John
doi: 10.7717/peerj.9850
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-17
copyright: © 2020 Oliveira et al.
attribution name: Oliveira et al.

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