PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Exploring the spatiotemporal changes in carbon storage under different development scenarios in Jiangsu Province, China
items: Identification of key differential genes in intimal hyperplasia induced by left carotid artery ligation
items: The Microphenotron: a novel method for screening plant growth-promoting rhizobacteria
items: Lipopolysaccharide-activated macrophages regulate the osteogenic differentiation of bone marrow mesenchymal stem cells through exosomes
items: A field test of forest canopy structure measurements with the CanopyCapture smartphone application
items: Soil properties and microbial communities of spring maize filed in response to tillage with straw incorporation and nitrogen fertilization in northeast China
items: Linking multi-level population dynamics: state, role, and population
items: Non-destructive monitoring of 3D cell cultures: new technologies and applications
items: The choice of reference point for computing sagittal plane angular momentum affects inferences about dynamic balance
items: Curcumol alleviates liver fibrosis by inducing endoplasmic reticulum stress-mediated necroptosis of hepatic stellate cells through Sirt1/NICD pathway

Exploring the spatiotemporal changes in carbon storage under different development scenarios in Jiangsu Province, China
type: item
type: AcademicArticle
description: Carbon storage (CS) is closely linked to the global challenge of climate change. Land use/cover (LULC) change is the main factor driving changes in CS, and evaluating the impact of LULC changes on CS is important for carbon balance. Taking Jiangsu Province as an example, we used the Integrated Valuation of Ecosystem Services and Trade-offs model to analyze the spatiotemporal changes in CS during 2000–2015. Then we coupled it with the patch-generating land use simulation model to simulate and predict LULC and CS in 2050 under four different development plans. The results showed that LULC change in Jiangsu Province was manifested mainly as transformation of cropland to construction land (3,485 km2) and cropland to water body (470 km2). The high value area for CS was concentrated mainly in forest land, water body and grassland, whereas the low value area was concentrated mainly in construction land. During 2000–2015, CS decreased by 0.23 Tg, and during 2015–2050, CS was predicted to decrease by 0.16, 1.69, 0.02, and 0.10 Tg under the baseline, fast, slow and harmonious development scenarios. The conversion of a large amount of cropland to construction land was the main cause of CS loss. In all scenarios, the carbon loss was the largest in southern Jiangsu and lowest in central Jiangsu. It is necessary to balance the conflict between economic development and ecological protection during the process of urbanization. This study can provide an important reference for decision makers during the formulation of regional development models and ecological management strategies.
format: application/pdf
format: text/html
creator: Xiaomian Zhang
creator: Jun Wang
creator: Chunlei Yue
creator: Shuai Ma
creator: Liang-Jie Wang
subject: Ecology
subject: Ecosystem Science
subject: Biogeochemistry
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13411
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Carbon storage (CS) is closely linked to the global challenge of climate change. Land use/cover (LULC) change is the main factor driving changes in CS, and evaluating the impact of LULC changes on CS is important for carbon balance. Taking Jiangsu Province as an example, we used the Integrated Valuation of Ecosystem Services and Trade-offs model to analyze the spatiotemporal changes in CS during 2000–2015. Then we coupled it with the patch-generating land use simulation model to simulate and predict LULC and CS in 2050 under four different development plans. The results showed that LULC change in Jiangsu Province was manifested mainly as transformation of cropland to construction land (3,485 km2) and cropland to water body (470 km2). The high value area for CS was concentrated mainly in forest land, water body and grassland, whereas the low value area was concentrated mainly in construction land. During 2000–2015, CS decreased by 0.23 Tg, and during 2015–2050, CS was predicted to decrease by 0.16, 1.69, 0.02, and 0.10 Tg under the baseline, fast, slow and harmonious development scenarios. The conversion of a large amount of cropland to construction land was the main cause of CS loss. In all scenarios, the carbon loss was the largest in southern Jiangsu and lowest in central Jiangsu. It is necessary to balance the conflict between economic development and ecological protection during the process of urbanization. This study can provide an important reference for decision makers during the formulation of regional development models and ecological management strategies.
bibliographic citation: Zhang et al. (2022) Exploring the spatiotemporal changes in carbon storage under different development scenarios in Jiangsu Province, China. PeerJ 10:e13411 https://doi.org/10.7717/peerj.13411
date submitted: 2022-02-16
date accepted: 2022-04-19
issued: 2022-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiaomian
author list: Agent
  family name: Wang
  given name: Jun
author list: Agent
  family name: Yue
  given name: Chunlei
author list: Agent
  family name: Ma
  given name: Shuai
author list: Agent
  family name: Wang
  given name: Liang-Jie
doi: 10.7717/peerj.13411
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-13
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

Identification of key differential genes in intimal hyperplasia induced by left carotid artery ligation
type: item
type: AcademicArticle
description: Background Intimal hyperplasia is a common pathological process of restenosis following angioplasty, atherosclerosis, pulmonary hypertension, vein graft stenosis, and other proliferative diseases. This study aims to screen for potential novel gene targets and mechanisms related to vascular intimal hyperplasia through an integrated microarray analysis of the Gene Expression Omnibus Database (GEO) database. Material and Methods The gene expression profile of the GSE56143 dataset was downloaded from the Gene Expression Omnibus database. Functional enrichment analysis, protein-protein interaction (PPI) network analysis, and the transcription factor (TF)-target gene regulatory network were used to reveal the biological functions of differential genes (DEGs). Furthermore, the expression levels of the top 10 key DEGs were verified at the mRNA and protein level in the carotid artery 7 days after ligation. Results A total of 373 DEGs (199 upregulated DEGs and 174 downregulated DEGs) were screened. These DEGs were significantly enriched in biological processes, including immune system process, cell adhesion, and several pathways, which were mainly associated with cell adhesion molecules and the regulation of the actin cytoskeleton. The top 10 key DEGs (Ptprc, Fn1, Tyrobp, Emr1, Itgb2, Itgax, CD44, Ctss, Ly86, and Aif1) acted as key genes in the PPI network. The verification of these key DEGs at the mRNA and protein levels was consistent with the results of the above-mentioned bioinformatics analysis. Conclusion The present study identified key genes and pathways involved in intimal hyperplasia induced by carotid artery ligation. These results improved our understanding of the mechanisms underlying the development of intimal hyperplasia and provided candidate targets.
format: application/pdf
format: text/html
creator: Lina Zhang
creator: Jianjun Gu
creator: Sichuan Wang
creator: Fuming He
creator: Kaizheng Gong
subject: Biochemistry
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.13436
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Intimal hyperplasia is a common pathological process of restenosis following angioplasty, atherosclerosis, pulmonary hypertension, vein graft stenosis, and other proliferative diseases. This study aims to screen for potential novel gene targets and mechanisms related to vascular intimal hyperplasia through an integrated microarray analysis of the Gene Expression Omnibus Database (GEO) database. Material and Methods The gene expression profile of the GSE56143 dataset was downloaded from the Gene Expression Omnibus database. Functional enrichment analysis, protein-protein interaction (PPI) network analysis, and the transcription factor (TF)-target gene regulatory network were used to reveal the biological functions of differential genes (DEGs). Furthermore, the expression levels of the top 10 key DEGs were verified at the mRNA and protein level in the carotid artery 7 days after ligation. Results A total of 373 DEGs (199 upregulated DEGs and 174 downregulated DEGs) were screened. These DEGs were significantly enriched in biological processes, including immune system process, cell adhesion, and several pathways, which were mainly associated with cell adhesion molecules and the regulation of the actin cytoskeleton. The top 10 key DEGs (Ptprc, Fn1, Tyrobp, Emr1, Itgb2, Itgax, CD44, Ctss, Ly86, and Aif1) acted as key genes in the PPI network. The verification of these key DEGs at the mRNA and protein levels was consistent with the results of the above-mentioned bioinformatics analysis. Conclusion The present study identified key genes and pathways involved in intimal hyperplasia induced by carotid artery ligation. These results improved our understanding of the mechanisms underlying the development of intimal hyperplasia and provided candidate targets.
bibliographic citation: Zhang et al. (2022) Identification of key differential genes in intimal hyperplasia induced by left carotid artery ligation. PeerJ 10:e13436 https://doi.org/10.7717/peerj.13436
date submitted: 2021-09-07
date accepted: 2022-04-22
issued: 2022-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Lina
author list: Agent
  family name: Gu
  given name: Jianjun
author list: Agent
  family name: Wang
  given name: Sichuan
author list: Agent
  family name: He
  given name: Fuming
author list: Agent
  family name: Gong
  given name: Kaizheng
doi: 10.7717/peerj.13436
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-13
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

The Microphenotron: a novel method for screening plant growth-promoting rhizobacteria
type: item
type: AcademicArticle
description: Background The ‘Microphenotron’ is an automated screening platform that uses 96-well microtiter plates to test the response of seedlings to natural products. This system allows monitoring the phenotypic effect of a large number of small molecules. Here, this model system was used to study the effect of phytohormones produced by plant growth-promoting rhizobacteria (PGPR) on the growth of wild-type and mutant lines of Arabidopsis thaliana. Methods In the present study, high-throughput screening based on ‘Microphenotron’ was used to screen PGPRs. Rhizobacteria were isolated from the rhizosphere of Acacia Arabica, which was growing in saline habitats. The phylogeny of these rhizobacteria was determined by 16S rRNA gene sequencing. Strains were screened for plant growth-promoting traits such as auxin production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and phosphate solubilization. Ultra-Performance Liquid Chromatography (UPLC) was used to detect the presence of different indolic compounds. Finally, PGPR were evaluated to enhance the growth of A. thaliana in the ‘Microphenotron’ system and pot trials. Results Selected rhizobacteria strains showed positive results for multiple plant-growth promoting traits. For instance, strain (S-6) of Bacillus endophyticus exhibited the highest ACC-deaminase activity. UPLC analysis indicated the presence of different indolic compounds in bacterial extracts that included indole lactic acid (ILA), indole carboxylic acid (ICA), and indole-3-acetic acid (IAA). Two strains (S-7 and S-11) of Psychrobacter alimentarius produced the most IAA, ICA and ILA. A screening bioassay through 96-well microtiter plates with wild-type Col. N6000 showed an increase in root growth and proliferation. The highest twofold increase was recorded in root growth with B. thuringiensis S-26 and B. thuringiensis S-50. In pot trials, mutant lines of A. thaliana impaired for auxin signaling showed that B. endophyticus S-6, Psy. alimenterius S-11, En…
format: application/pdf
format: text/html
creator: Asif Raheem
creator: Basharat Ali
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13438
publisher: PeerJ Inc.
rights: © 2022 Raheem and Ali
abstract: Background The ‘Microphenotron’ is an automated screening platform that uses 96-well microtiter plates to test the response of seedlings to natural products. This system allows monitoring the phenotypic effect of a large number of small molecules. Here, this model system was used to study the effect of phytohormones produced by plant growth-promoting rhizobacteria (PGPR) on the growth of wild-type and mutant lines of Arabidopsis thaliana. Methods In the present study, high-throughput screening based on ‘Microphenotron’ was used to screen PGPRs. Rhizobacteria were isolated from the rhizosphere of Acacia Arabica, which was growing in saline habitats. The phylogeny of these rhizobacteria was determined by 16S rRNA gene sequencing. Strains were screened for plant growth-promoting traits such as auxin production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and phosphate solubilization. Ultra-Performance Liquid Chromatography (UPLC) was used to detect the presence of different indolic compounds. Finally, PGPR were evaluated to enhance the growth of A. thaliana in the ‘Microphenotron’ system and pot trials. Results Selected rhizobacteria strains showed positive results for multiple plant-growth promoting traits. For instance, strain (S-6) of Bacillus endophyticus exhibited the highest ACC-deaminase activity. UPLC analysis indicated the presence of different indolic compounds in bacterial extracts that included indole lactic acid (ILA), indole carboxylic acid (ICA), and indole-3-acetic acid (IAA). Two strains (S-7 and S-11) of Psychrobacter alimentarius produced the most IAA, ICA and ILA. A screening bioassay through 96-well microtiter plates with wild-type Col. N6000 showed an increase in root growth and proliferation. The highest twofold increase was recorded in root growth with B. thuringiensis S-26 and B. thuringiensis S-50. In pot trials, mutant lines of A. thaliana impaired for auxin signaling showed that B. endophyticus S-6, Psy. alimenterius S-11, En…
bibliographic citation: Raheem et al. (2022) The Microphenotron: a novel method for screening plant growth-promoting rhizobacteria. PeerJ 10:e13438 https://doi.org/10.7717/peerj.13438
date submitted: 2020-09-28
date accepted: 2022-04-22
issued: 2022-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Raheem
  given name: Asif
author list: Agent
  family name: Ali
  given name: Basharat
doi: 10.7717/peerj.13438
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-13
copyright: © 2022 Raheem and Ali
attribution name: Raheem and Ali

Lipopolysaccharide-activated macrophages regulate the osteogenic differentiation of bone marrow mesenchymal stem cells through exosomes
type: item
type: AcademicArticle
description: Background Periodontal tissue regeneration is the ultimate goal of periodontitis treatment. Exosomes are nanoscale vesicles secreted by cells that participate in and regulate the physiological activities between cells. However, the relationship between inflammatory macrophage-derived exosomes and osteoblast differentiation in periodontitis has not been thoroughly reported. Here, we attempt to explore the role of inflammatory macrophage-derived exosomes in crosstalk with osteoblasts. Methods Porphyromonas gingivalis lipopolysaccharide was used to stimulate macrophages and inflate their inflammatory cellular state. Exosomes were extracted from inflammatory macrophages using supercentrifugation, and their characteristics were detected by transmission electron microscopy, particle size analysis, and Western blotting. Exosome uptake bybone marrow mesenchymal stem cells (BMSCs) was observed by fluorescence microscopy. The effects of exosomes on the BMSC inflammatory response and on osteogenic differentiation were detected by quantitative polymerase chain reaction and Western blot analysis. Alkaline phosphatase activity was tested for verification. Results We successfully extracted and identified inflammatory macrophage-derived exosomes and observed that BMSCs successfully took up exosomes. Inflammatory macrophage-derived exosomes upregulated the expression levels of the inflammatory factors interleukin-6 and tumour necrosis factor-alpha in BMSCs and mediated inflammatory stimulation. Additionally, they inhibited the transcription levels of the osteogenic genes alkaline phosphatase, type I collagen, and Runt-related transcription factor 2 as well as the alkaline phosphatase activity, while the use of the exosome inhibitor GW4869 attenuated this effect. Conclusion Our study shows that macrophages in periodontitis can mediate inflammatory stimulation and inhibit the osteogenic differentiation of bone marrow mesenchymal stem cells through the exosome pathway. Interference wit…
format: application/pdf
format: text/html
creator: Xiao Song
creator: Yiwen Xue
creator: Siyu Fan
creator: Jing Hao
creator: Runzhi Deng
subject: Cell Biology
subject: Molecular Biology
subject: Dentistry
description: doi:10.7717/peerj.13442
publisher: PeerJ Inc.
rights: © 2022 Song et al.
abstract: Background Periodontal tissue regeneration is the ultimate goal of periodontitis treatment. Exosomes are nanoscale vesicles secreted by cells that participate in and regulate the physiological activities between cells. However, the relationship between inflammatory macrophage-derived exosomes and osteoblast differentiation in periodontitis has not been thoroughly reported. Here, we attempt to explore the role of inflammatory macrophage-derived exosomes in crosstalk with osteoblasts. Methods Porphyromonas gingivalis lipopolysaccharide was used to stimulate macrophages and inflate their inflammatory cellular state. Exosomes were extracted from inflammatory macrophages using supercentrifugation, and their characteristics were detected by transmission electron microscopy, particle size analysis, and Western blotting. Exosome uptake bybone marrow mesenchymal stem cells (BMSCs) was observed by fluorescence microscopy. The effects of exosomes on the BMSC inflammatory response and on osteogenic differentiation were detected by quantitative polymerase chain reaction and Western blot analysis. Alkaline phosphatase activity was tested for verification. Results We successfully extracted and identified inflammatory macrophage-derived exosomes and observed that BMSCs successfully took up exosomes. Inflammatory macrophage-derived exosomes upregulated the expression levels of the inflammatory factors interleukin-6 and tumour necrosis factor-alpha in BMSCs and mediated inflammatory stimulation. Additionally, they inhibited the transcription levels of the osteogenic genes alkaline phosphatase, type I collagen, and Runt-related transcription factor 2 as well as the alkaline phosphatase activity, while the use of the exosome inhibitor GW4869 attenuated this effect. Conclusion Our study shows that macrophages in periodontitis can mediate inflammatory stimulation and inhibit the osteogenic differentiation of bone marrow mesenchymal stem cells through the exosome pathway. Interference wit…
bibliographic citation: Song et al. (2022) Lipopolysaccharide-activated macrophages regulate the osteogenic differentiation of bone marrow mesenchymal stem cells through exosomes. PeerJ 10:e13442 https://doi.org/10.7717/peerj.13442
date submitted: 2021-12-14
date accepted: 2022-04-25
issued: 2022-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Xiao
author list: Agent
  family name: Xue
  given name: Yiwen
author list: Agent
  family name: Fan
  given name: Siyu
author list: Agent
  family name: Hao
  given name: Jing
author list: Agent
  family name: Deng
  given name: Runzhi
doi: 10.7717/peerj.13442
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-13
copyright: ©2022 Song et al.
attribution name: Song et al.

A field test of forest canopy structure measurements with the CanopyCapture smartphone application
type: item
type: AcademicArticle
description: Background Several smartphone applications have been developed for the purpose of low-cost and convenient assessments of vegetation canopy structure and understorey illumination. Like standard hemispherical photography, most of these applications require user decisions about image processing, posing challenges for repeatability of measurements. Here I report a test of CanopyCapture, an application that instantaneously estimates percentage canopy gap fraction without any input from the user, and has the added advantage of an intuitive levelling mechanism. Methods Gap fraction estimates by CanopyCapture were compared with gap fraction values computed by the LAI-2200C Canopy Analyzer, in two contrasting evergreen temperate forests in New Zealand: an even-aged southern beech (Nothofagus) stand and an old-growth podocarp/broadleaf forest. These comparisons were repeated using a wide-angle adapter to enhance the smartphone camera’s field of view from 45 to 65°. I also asked if CanopyCapture results depended on sky condition (sunny vs. overcast) and on the type of smartphone used. Results CanopyCapture output was significantly correlated with gap fraction computed by the LAI-2200C (R2 = 0.39), and use of the wide-angle adapter lifted this value to 0.56. However, CanopyCapture output was not significantly correlated with LAI-2200C output in the even-aged Nothofagus stand, where there was less spatial variation in canopy structure. Despite being much less sensitive to variation in gap fraction than the LAI-2200C, CanopyCapture was nevertheless able to detect differences in average gap fraction between the two forests studied. CanopyCapture results beneath intact canopies were not significantly affected by sky condition, but reflection of direct light off tree trunks in sunny weather caused slight overestimation of gap fraction beneath broken canopies and gaps. Uneven or patchy cloud cover can also cause erroneous readings beneath large canopy openings. Three different models…
format: application/pdf
format: text/html
creator: Christopher H. Lusk
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.13450
publisher: PeerJ Inc.
rights: © 2022 Lusk
abstract: Background Several smartphone applications have been developed for the purpose of low-cost and convenient assessments of vegetation canopy structure and understorey illumination. Like standard hemispherical photography, most of these applications require user decisions about image processing, posing challenges for repeatability of measurements. Here I report a test of CanopyCapture, an application that instantaneously estimates percentage canopy gap fraction without any input from the user, and has the added advantage of an intuitive levelling mechanism. Methods Gap fraction estimates by CanopyCapture were compared with gap fraction values computed by the LAI-2200C Canopy Analyzer, in two contrasting evergreen temperate forests in New Zealand: an even-aged southern beech (Nothofagus) stand and an old-growth podocarp/broadleaf forest. These comparisons were repeated using a wide-angle adapter to enhance the smartphone camera’s field of view from 45 to 65°. I also asked if CanopyCapture results depended on sky condition (sunny vs. overcast) and on the type of smartphone used. Results CanopyCapture output was significantly correlated with gap fraction computed by the LAI-2200C (R2 = 0.39), and use of the wide-angle adapter lifted this value to 0.56. However, CanopyCapture output was not significantly correlated with LAI-2200C output in the even-aged Nothofagus stand, where there was less spatial variation in canopy structure. Despite being much less sensitive to variation in gap fraction than the LAI-2200C, CanopyCapture was nevertheless able to detect differences in average gap fraction between the two forests studied. CanopyCapture results beneath intact canopies were not significantly affected by sky condition, but reflection of direct light off tree trunks in sunny weather caused slight overestimation of gap fraction beneath broken canopies and gaps. Uneven or patchy cloud cover can also cause erroneous readings beneath large canopy openings. Three different models…
bibliographic citation: Lusk (2022) A field test of forest canopy structure measurements with the CanopyCapture smartphone application. PeerJ 10:e13450 https://doi.org/10.7717/peerj.13450
date submitted: 2021-10-18
date accepted: 2022-04-26
issued: 2022-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lusk
  given name: Christopher H.
doi: 10.7717/peerj.13450
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-13
copyright: © 2022 Lusk
attribution name: Lusk

Soil properties and microbial communities of spring maize filed in response to tillage with straw incorporation and nitrogen fertilization in northeast China
type: item
type: AcademicArticle
description: Soil enzymes and microorganisms are both important to maintaining good soil quality and are also sensitive to changes in agricultural management. The individual effects of tillage, straw incorporation and nitrogen (N) fertilization on soil enzymes and microflora have been widely acknowledged, but their interactive effect remains largely unknown. In a 5–year in–situ field study, effects of rotary (RTS) and plow tillage (PTS) practices with straw incorporation combined with three N fertilization levels (0 kg N ha–1, CK; 187 kg N ha–1, MN; 337 kg N ha–1, HN) on soil enzyme activities and microbial communities were assessed. Our results showed that the activities of β–glucosidase (βG), N–acetylglucosaminidase (NAG) and acid phosphatase (APH) were improved in RTS+MN. The bacterial and fungal abundances in RTS+MN and RTS+HN were 1.27–27.51 times higher than those in other treatment groups. However, the bacterial and fungal alpha diversities were enhanced in PTS+MN and PTS+CK compared with other treatments, respectively. Proteobacteria and Basidiomycota were the predominant phylum for the respective bacterial and fungal communities. Moreover, significant interactive effects were found in the fungal community composition, but only minor impacts were observed on the bacterial community composition. Soil water content and penetration resistance contributed more to the soil enzyme activity and microbial community than other soil properties investigated, whereas there was a significant positive correlation between βG and APH activities and microbial abundance. These findings can provide new insights into tillage with straw incorporation and N fertilization on maize cultivation in northeast China.
format: application/pdf
format: text/html
creator: Pengxiang Sui
creator: Ping Tian
creator: Zhengyu Wang
creator: Hongli Lian
creator: Yadong Yang
creator: Ziqi Ma
creator: Ying Jiang
creator: Jinyu Zheng
creator: Hua Qi
subject: Agricultural Science
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.13462
publisher: PeerJ Inc.
rights: © 2022 Sui et al.
abstract: Soil enzymes and microorganisms are both important to maintaining good soil quality and are also sensitive to changes in agricultural management. The individual effects of tillage, straw incorporation and nitrogen (N) fertilization on soil enzymes and microflora have been widely acknowledged, but their interactive effect remains largely unknown. In a 5–year in–situ field study, effects of rotary (RTS) and plow tillage (PTS) practices with straw incorporation combined with three N fertilization levels (0 kg N ha–1, CK; 187 kg N ha–1, MN; 337 kg N ha–1, HN) on soil enzyme activities and microbial communities were assessed. Our results showed that the activities of β–glucosidase (βG), N–acetylglucosaminidase (NAG) and acid phosphatase (APH) were improved in RTS+MN. The bacterial and fungal abundances in RTS+MN and RTS+HN were 1.27–27.51 times higher than those in other treatment groups. However, the bacterial and fungal alpha diversities were enhanced in PTS+MN and PTS+CK compared with other treatments, respectively. Proteobacteria and Basidiomycota were the predominant phylum for the respective bacterial and fungal communities. Moreover, significant interactive effects were found in the fungal community composition, but only minor impacts were observed on the bacterial community composition. Soil water content and penetration resistance contributed more to the soil enzyme activity and microbial community than other soil properties investigated, whereas there was a significant positive correlation between βG and APH activities and microbial abundance. These findings can provide new insights into tillage with straw incorporation and N fertilization on maize cultivation in northeast China.
bibliographic citation: Sui et al. (2022) Soil properties and microbial communities of spring maize filed in response to tillage with straw incorporation and nitrogen fertilization in northeast China. PeerJ 10:e13462 https://doi.org/10.7717/peerj.13462
date submitted: 2021-02-09
date accepted: 2022-04-28
issued: 2022-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sui
  given name: Pengxiang
author list: Agent
  family name: Tian
  given name: Ping
author list: Agent
  family name: Wang
  given name: Zhengyu
author list: Agent
  family name: Lian
  given name: Hongli
author list: Agent
  family name: Yang
  given name: Yadong
author list: Agent
  family name: Ma
  given name: Ziqi
author list: Agent
  family name: Jiang
  given name: Ying
author list: Agent
  family name: Zheng
  given name: Jinyu
author list: Agent
  family name: Qi
  given name: Hua
doi: 10.7717/peerj.13462
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-13
copyright: © 2022 Sui et al.
attribution name: Sui et al.

Linking multi-level population dynamics: state, role, and population
type: item
type: AcademicArticle
description: The dynamics of an ecological community can be described at different focal scales of the species, such as individual states or the population level. More detailed descriptions of ecological dynamics offer more information, but produce more complex models that are difficult to analyze. Adequately controlling the model complexity and the availability of multiple descriptions of the concerned dynamics maximizes our understanding of ecological dynamics. One of the central goals of ecological studies is to develop links between multiple descriptions of an ecological community. In this article, starting from a nonlinear state-level description of an ecological community (generalized McKendrick–von Foerster model), role-level and population-level descriptions (Lotka–Volterra model) are derived in a consistent manner. The role-level description covers a wider range of situations than the population-level description. However, using the established connections, it is demonstrated that the population-level description can be used to predict the equilibrium status of the role-level description. This approach connects state-, role-, and population-level dynamics consistently, and offers a justification for the multiple choices of model description.
format: application/pdf
format: text/html
creator: Nao Takashina
subject: Ecology
subject: Mathematical Biology
description: doi:10.7717/peerj.13315
publisher: PeerJ Inc.
rights: © 2022 Takashina
abstract: The dynamics of an ecological community can be described at different focal scales of the species, such as individual states or the population level. More detailed descriptions of ecological dynamics offer more information, but produce more complex models that are difficult to analyze. Adequately controlling the model complexity and the availability of multiple descriptions of the concerned dynamics maximizes our understanding of ecological dynamics. One of the central goals of ecological studies is to develop links between multiple descriptions of an ecological community. In this article, starting from a nonlinear state-level description of an ecological community (generalized McKendrick–von Foerster model), role-level and population-level descriptions (Lotka–Volterra model) are derived in a consistent manner. The role-level description covers a wider range of situations than the population-level description. However, using the established connections, it is demonstrated that the population-level description can be used to predict the equilibrium status of the role-level description. This approach connects state-, role-, and population-level dynamics consistently, and offers a justification for the multiple choices of model description.
bibliographic citation: Takashina (2022) Linking multi-level population dynamics: state, role, and population. PeerJ 10:e13315 https://doi.org/10.7717/peerj.13315
date submitted: 2022-01-06
date accepted: 2022-03-31
issued: 2022-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Takashina
  given name: Nao
doi: 10.7717/peerj.13315
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-12
copyright: © 2022 Takashina
attribution name: Takashina

Non-destructive monitoring of 3D cell cultures: new technologies and applications
type: item
type: AcademicArticle
description: 3D cell cultures are becoming the new standard for cell-based in vitro research, due to their higher transferrability toward in vivo biology. The lack of established techniques for the non-destructive quantification of relevant variables, however, constitutes a major barrier to the adoption of these technologies, as it increases the resources needed for the experimentation and reduces its accuracy. In this review, we aim at addressing this limitation by providing an overview of different non-destructive approaches for the evaluation of biological features commonly quantified in a number of studies and applications. In this regard, we will cover cell viability, gene expression, population distribution, cell morphology and interactions between the cells and the environment. This analysis is expected to promote the use of the showcased technologies, together with the further development of these and other monitoring methods for 3D cell cultures. Overall, an extensive technology shift is required, in order for monolayer cultures to be superseded, but the potential benefit derived from an increased accuracy of in vitro studies, justifies the effort and the investment.
format: application/pdf
format: text/html
creator: Marilisa Cortesi
creator: Emanuele Giordano
subject: Bioengineering
subject: Cell Biology
description: doi:10.7717/peerj.13338
publisher: PeerJ Inc.
rights: © 2022 Cortesi and Giordano
abstract: 3D cell cultures are becoming the new standard for cell-based in vitro research, due to their higher transferrability toward in vivo biology. The lack of established techniques for the non-destructive quantification of relevant variables, however, constitutes a major barrier to the adoption of these technologies, as it increases the resources needed for the experimentation and reduces its accuracy. In this review, we aim at addressing this limitation by providing an overview of different non-destructive approaches for the evaluation of biological features commonly quantified in a number of studies and applications. In this regard, we will cover cell viability, gene expression, population distribution, cell morphology and interactions between the cells and the environment. This analysis is expected to promote the use of the showcased technologies, together with the further development of these and other monitoring methods for 3D cell cultures. Overall, an extensive technology shift is required, in order for monolayer cultures to be superseded, but the potential benefit derived from an increased accuracy of in vitro studies, justifies the effort and the investment.
bibliographic citation: Cortesi et al. (2022) Non-destructive monitoring of 3D cell cultures: new technologies and applications. PeerJ 10:e13338 https://doi.org/10.7717/peerj.13338
date submitted: 2022-01-12
date accepted: 2022-04-05
issued: 2022-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cortesi
  given name: Marilisa
author list: Agent
  family name: Giordano
  given name: Emanuele
doi: 10.7717/peerj.13338
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-12
copyright: ©2022 Cortesi and Giordano
attribution name: Cortesi and Giordano

The choice of reference point for computing sagittal plane angular momentum affects inferences about dynamic balance
type: item
type: AcademicArticle
description: Background Measures of whole-body angular momentum in the sagittal plane are commonly used to characterize dynamic balance during human walking. To compute angular momentum, one must specify a reference point about which momentum is calculated. Although biomechanists primarily compute angular momentum about the center of mass (CoM), momentum-based controllers for humanoid robots often use the center of pressure. Here, we asked if the choice of the reference point influences interpretations of how dynamic balance is controlled in the sagittal plane during perturbed walking. Methods Eleven healthy young individuals walked on a dual-belt treadmill at their self-selected speed. Balance disturbances were generated by treadmill accelerations of varying magnitudes and directions. We computed angular momentum about two reference points: (1) the CoM or (2) the leading edge of the base of support and then projected it along the mediolateral axes that pass through either of the reference points as the sagittal plane angular momentum. We also performed principal component analysis to determine if the choice of reference point influences our interpretations of how intersegmental coordination patterns contribute to perturbation recovery. Results We found that the peak angular momentum was correlated with perturbation amplitude and the slope of this relationship did not differ between reference points. One advantage of using a reference point at the CoM is that one can easily determine how the momenta from contralateral limbs, such as the left and right legs, offset one another to regulate the whole-body angular momentum. Alternatively, analysis of coordination patterns referenced to the leading edge of the base of support may provide more insight into the inverted-pendulum dynamics of walking during responses to sudden losses of balance.
format: application/pdf
format: text/html
creator: Chang Liu
creator: Sungwoo Park
creator: James Finley
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.13371
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Background Measures of whole-body angular momentum in the sagittal plane are commonly used to characterize dynamic balance during human walking. To compute angular momentum, one must specify a reference point about which momentum is calculated. Although biomechanists primarily compute angular momentum about the center of mass (CoM), momentum-based controllers for humanoid robots often use the center of pressure. Here, we asked if the choice of the reference point influences interpretations of how dynamic balance is controlled in the sagittal plane during perturbed walking. Methods Eleven healthy young individuals walked on a dual-belt treadmill at their self-selected speed. Balance disturbances were generated by treadmill accelerations of varying magnitudes and directions. We computed angular momentum about two reference points: (1) the CoM or (2) the leading edge of the base of support and then projected it along the mediolateral axes that pass through either of the reference points as the sagittal plane angular momentum. We also performed principal component analysis to determine if the choice of reference point influences our interpretations of how intersegmental coordination patterns contribute to perturbation recovery. Results We found that the peak angular momentum was correlated with perturbation amplitude and the slope of this relationship did not differ between reference points. One advantage of using a reference point at the CoM is that one can easily determine how the momenta from contralateral limbs, such as the left and right legs, offset one another to regulate the whole-body angular momentum. Alternatively, analysis of coordination patterns referenced to the leading edge of the base of support may provide more insight into the inverted-pendulum dynamics of walking during responses to sudden losses of balance.
bibliographic citation: Liu et al. (2022) The choice of reference point for computing sagittal plane angular momentum affects inferences about dynamic balance. PeerJ 10:e13371 https://doi.org/10.7717/peerj.13371
date submitted: 2021-12-03
date accepted: 2022-04-12
issued: 2022-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Chang
author list: Agent
  family name: Park
  given name: Sungwoo
author list: Agent
  family name: Finley
  given name: James
doi: 10.7717/peerj.13371
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-12
copyright: ©2022 Liu et al.
attribution name: Liu et al.

Curcumol alleviates liver fibrosis by inducing endoplasmic reticulum stress-mediated necroptosis of hepatic stellate cells through Sirt1/NICD pathway
type: item
type: AcademicArticle
description: Liver fibrosis is a repair response process after chronic liver injury. During this process, activated hepatic stellate cells (HSCs) will migrate to the injury site and secrete extracellular matrix (ECM) to produce fibrous scars. Clearing activated HSCs may be a major strategy for the treatment of liver fibrosis. Curcumol isolated from plants of the genus Curcuma can effectively induce apoptosis of many cancer cells, but whether it can clear activated HSCs remains to be clarified. In the present study, we found that the effect of curcumol in treating liver fibrosis was to clear activated HSCs by inducing necroptosis of HSCs. Receptor-interacting protein kinase 3 (RIP3) silencing could impair necroptosis induced by curcumol. Interestingly, endoplasmic reticulum (ER) stress-induced cellular dysfunction was associated with curcumol-induced cell death. The ER stress inhibitor 4-PBA prevented curcumol-induced ER stress and necroptosis. We proved that ER stress regulated curcumol-induced necroptosis in HSCs via Sirtuin-1(Sirt1)/Notch signaling pathway. Sirt1-mediated deacetylation of the intracellular domain of Notch (NICD) led to degradation of NICD, thereby inhibiting Notch signalling pathway to alleviate liver fibrosis. Specific knockdown of Sirt1 by HSCs in male ICR mice further exacerbated CCl4-induced liver fibrosis. Overall, our study elucidates the anti-fibrotic effect of curcumol and reveals the underlying mechanism between ER stress and necroptosis.
format: application/pdf
format: text/html
creator: Sumin Sun
creator: Sheng Huan
creator: Zhanghao Li
creator: Yue Yao
creator: Ying Su
creator: Siwei Xia
creator: Shijun Wang
creator: Xuefen Xu
creator: Jiangjuan Shao
creator: Zili Zhang
creator: Feng Zhang
creator: Jinbo Fu
creator: Shizhong Zheng
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Histology
description: doi:10.7717/peerj.13376
publisher: PeerJ Inc.
rights: © 2022 Sun et al.
abstract: Liver fibrosis is a repair response process after chronic liver injury. During this process, activated hepatic stellate cells (HSCs) will migrate to the injury site and secrete extracellular matrix (ECM) to produce fibrous scars. Clearing activated HSCs may be a major strategy for the treatment of liver fibrosis. Curcumol isolated from plants of the genus Curcuma can effectively induce apoptosis of many cancer cells, but whether it can clear activated HSCs remains to be clarified. In the present study, we found that the effect of curcumol in treating liver fibrosis was to clear activated HSCs by inducing necroptosis of HSCs. Receptor-interacting protein kinase 3 (RIP3) silencing could impair necroptosis induced by curcumol. Interestingly, endoplasmic reticulum (ER) stress-induced cellular dysfunction was associated with curcumol-induced cell death. The ER stress inhibitor 4-PBA prevented curcumol-induced ER stress and necroptosis. We proved that ER stress regulated curcumol-induced necroptosis in HSCs via Sirtuin-1(Sirt1)/Notch signaling pathway. Sirt1-mediated deacetylation of the intracellular domain of Notch (NICD) led to degradation of NICD, thereby inhibiting Notch signalling pathway to alleviate liver fibrosis. Specific knockdown of Sirt1 by HSCs in male ICR mice further exacerbated CCl4-induced liver fibrosis. Overall, our study elucidates the anti-fibrotic effect of curcumol and reveals the underlying mechanism between ER stress and necroptosis.
bibliographic citation: Sun et al. (2022) Curcumol alleviates liver fibrosis by inducing endoplasmic reticulum stress-mediated necroptosis of hepatic stellate cells through Sirt1/NICD pathway. PeerJ 10:e13376 https://doi.org/10.7717/peerj.13376
date submitted: 2022-01-24
date accepted: 2022-04-13
issued: 2022-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Sumin
author list: Agent
  family name: Huan
  given name: Sheng
author list: Agent
  family name: Li
  given name: Zhanghao
author list: Agent
  family name: Yao
  given name: Yue
author list: Agent
  family name: Su
  given name: Ying
author list: Agent
  family name: Xia
  given name: Siwei
author list: Agent
  family name: Wang
  given name: Shijun
author list: Agent
  family name: Xu
  given name: Xuefen
author list: Agent
  family name: Shao
  given name: Jiangjuan
author list: Agent
  family name: Zhang
  given name: Zili
author list: Agent
  family name: Zhang
  given name: Feng
author list: Agent
  family name: Fu
  given name: Jinbo
author list: Agent
  family name: Zheng
  given name: Shizhong
doi: 10.7717/peerj.13376
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-12
copyright: © 2022 Sun et al.
attribution name: Sun et al.

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