PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Development of a novel in vitro insulin resistance model in primary human tenocytes for diabetic tendinopathy research
items: A systematic review of the direct and indirect effects of herbivory on plant reproduction mediated by pollination
items: Age-dependent differences in iris colouration of passerines during autumn migration in Central Europe
items: Temporal and spatial variability of terrestrial diatoms at the catchment scale: controls on productivity and comparison with other soil algae
items: Muscle activation varies between high-bar and low-bar back squat
items: Multiple immunity-related genes control susceptibility of Arabidopsis thaliana to the parasitic weed Phelipanche aegyptiaca
items: Lycopene alleviates oxidative stress via the PI3K/Akt/Nrf2pathway in a cell model of Alzheimer’s disease
items: A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology
items: Reconstruction of past distribution for the Mongolian toad, Strauchbufo raddei (Anura: Bufonidae) using environmental modeling
items: Nebulized dexmedetomidine improves pulmonary shunt and lung mechanics during one-lung ventilation: a randomized clinical controlled trial

Development of a novel in vitro insulin resistance model in primary human tenocytes for diabetic tendinopathy research
type: item
type: AcademicArticle
description: Background Type 2 diabetes mellitus (T2DM) had been reported to be associated with tendinopathy. However, the underlying mechanisms of diabetic tendinopathy still remain largely to be discovered. The purpose of this study was to develop insulin resistance (IR) model on primary human tenocytes (hTeno) culture with tumour necrosis factor-alpha (TNF-α) treatment to study tenocytes homeostasis as an implication for diabetic tendinopathy. Methods hTenowere isolated from human hamstring tendon. Presence of insulin receptor beta (INSR-β) on normal tendon tissues and the hTeno monolayer culture were analyzed by immunofluorescence staining. The presence of Glucose Transporter Type 1 (GLUT1) and Glucose Transporter Type 4 (GLUT4) on the hTeno monolayer culture were also analyzed by immunofluorescence staining. Primary hTeno were treated with 0.008, 0.08, 0.8 and 8.0 µM of TNF-α, with and without insulin supplement. Outcome measures include 2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl) amino]-2-deoxy-d-glucose (2-NBDG) assay to determine the glucose uptake activity; colourimetric total collagen assay to quantify the total collagen expression levels; COL-I ELISA assay to measure the COL-I expression levels and real-time qPCR to analyze the mRNA gene expressions levels of Scleraxis (SCX), Mohawk (MKX), type I collagen (COL1A1), type III collagen (COL3A1), matrix metalloproteinases (MMP)-9 and MMP-13 in hTeno when treated with TNF-α. Apoptosis assay for hTeno induced with TNF-α was conducted using Annexin-V FITC flow cytometry analysis. Results Immunofluorescence imaging showed the presence of INSR-β on the hTeno in the human Achilles tendon tissues and in the hTeno in monolayer culture. GLUT1 and GLUT4 were both positively expressed in the hTeno. TNF-α significantly reduced the insulin-mediated 2-NBDG uptake in all the tested concentrations, especially at 0.008 µM. Total collagen expression levels and COL-I expression levels in hTeno were also significantly reduced in hTeno treated w…
format: application/pdf
format: text/html
creator: Hui Yee Tan
creator: Sik Loo Tan
creator: Seow Hui Teo
creator: Margaret M. Roebuck
creator: Simon P. Frostick
creator: Tunku Kamarul
subject: Biotechnology
subject: Cell Biology
subject: Anatomy and Physiology
subject: Diabetes and Endocrinology
subject: Orthopedics
description: doi:10.7717/peerj.8740
publisher: PeerJ Inc.
rights: © 2020 Tan et al.
abstract: Background Type 2 diabetes mellitus (T2DM) had been reported to be associated with tendinopathy. However, the underlying mechanisms of diabetic tendinopathy still remain largely to be discovered. The purpose of this study was to develop insulin resistance (IR) model on primary human tenocytes (hTeno) culture with tumour necrosis factor-alpha (TNF-α) treatment to study tenocytes homeostasis as an implication for diabetic tendinopathy. Methods hTenowere isolated from human hamstring tendon. Presence of insulin receptor beta (INSR-β) on normal tendon tissues and the hTeno monolayer culture were analyzed by immunofluorescence staining. The presence of Glucose Transporter Type 1 (GLUT1) and Glucose Transporter Type 4 (GLUT4) on the hTeno monolayer culture were also analyzed by immunofluorescence staining. Primary hTeno were treated with 0.008, 0.08, 0.8 and 8.0 µM of TNF-α, with and without insulin supplement. Outcome measures include 2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl) amino]-2-deoxy-d-glucose (2-NBDG) assay to determine the glucose uptake activity; colourimetric total collagen assay to quantify the total collagen expression levels; COL-I ELISA assay to measure the COL-I expression levels and real-time qPCR to analyze the mRNA gene expressions levels of Scleraxis (SCX), Mohawk (MKX), type I collagen (COL1A1), type III collagen (COL3A1), matrix metalloproteinases (MMP)-9 and MMP-13 in hTeno when treated with TNF-α. Apoptosis assay for hTeno induced with TNF-α was conducted using Annexin-V FITC flow cytometry analysis. Results Immunofluorescence imaging showed the presence of INSR-β on the hTeno in the human Achilles tendon tissues and in the hTeno in monolayer culture. GLUT1 and GLUT4 were both positively expressed in the hTeno. TNF-α significantly reduced the insulin-mediated 2-NBDG uptake in all the tested concentrations, especially at 0.008 µM. Total collagen expression levels and COL-I expression levels in hTeno were also significantly reduced in hTeno treated w…
bibliographic citation: Tan et al. (2020) Development of a novel in vitro insulin resistance model in primary human tenocytes for diabetic tendinopathy research. PeerJ 8:e8740 https://doi.org/10.7717/peerj.8740
date submitted: 2019-08-21
date accepted: 2020-02-12
issued: 2020-06-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Hui Yee
author list: Agent
  family name: Tan
  given name: Sik Loo
author list: Agent
  family name: Teo
  given name: Seow Hui
author list: Agent
  family name: Roebuck
  given name: Margaret M.
author list: Agent
  family name: Frostick
  given name: Simon P.
author list: Agent
  family name: Kamarul
  given name: Tunku
doi: 10.7717/peerj.8740
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-08
copyright: ©2020 Tan et al.
attribution name: Tan et al.

A systematic review of the direct and indirect effects of herbivory on plant reproduction mediated by pollination
type: item
type: AcademicArticle
description: Background Plant reproduction is influenced by the net outcome of plant–herbivore and plant–pollinator interactions. While both herbivore impacts and pollinator impacts on plant reproduction have been widely studied, few studies examine them in concert. Methodology Here, we review the contemporary literature that examines the net outcomes of herbivory and pollination on plant reproduction and the impacts of herbivores on pollination through damage to shared host plants using systematic review tools. The direct or indirect effects of herbivores on floral tissue and reported mechanisms were compiled including the taxonomic breadth of herbivores, plants and pollinators. Results A total of 4,304 studies were examined producing 59 relevant studies for synthesis that reported both pollinator and herbivore measures. A total of 49% of studies examined the impact of direct damage to floral tissue through partial florivory while 36% of studies also examined the impact of vegetative damage on pollination through folivory, root herbivory, and stem damage. Only three studies examined the effects of both direct and indirect damage to pollination outcomes within the same study. Conclusions It is not unreasonable to assume that plants often sustain simultaneous forms of damage to different tissues and that the net effects can be assessed through differences in reproductive output. Further research that controls for other relative drivers of reproductive output but examines more than one pathway of damage simultaneously will inform our understanding of the mechanistic relevance of herbivore impacts on pollination and also highlight interactions between herbivores and pollinators through plants. It is clear that herbivory can impact plant fitness through pollination; however, the relative importance of direct and indirect damage to floral tissue on plant reproduction is still largely unknown.
format: application/pdf
format: text/html
creator: Stephanie M. Haas
creator: Christopher J. Lortie
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.9049
publisher: PeerJ Inc.
rights: © 2020 Haas and Lortie
abstract: Background Plant reproduction is influenced by the net outcome of plant–herbivore and plant–pollinator interactions. While both herbivore impacts and pollinator impacts on plant reproduction have been widely studied, few studies examine them in concert. Methodology Here, we review the contemporary literature that examines the net outcomes of herbivory and pollination on plant reproduction and the impacts of herbivores on pollination through damage to shared host plants using systematic review tools. The direct or indirect effects of herbivores on floral tissue and reported mechanisms were compiled including the taxonomic breadth of herbivores, plants and pollinators. Results A total of 4,304 studies were examined producing 59 relevant studies for synthesis that reported both pollinator and herbivore measures. A total of 49% of studies examined the impact of direct damage to floral tissue through partial florivory while 36% of studies also examined the impact of vegetative damage on pollination through folivory, root herbivory, and stem damage. Only three studies examined the effects of both direct and indirect damage to pollination outcomes within the same study. Conclusions It is not unreasonable to assume that plants often sustain simultaneous forms of damage to different tissues and that the net effects can be assessed through differences in reproductive output. Further research that controls for other relative drivers of reproductive output but examines more than one pathway of damage simultaneously will inform our understanding of the mechanistic relevance of herbivore impacts on pollination and also highlight interactions between herbivores and pollinators through plants. It is clear that herbivory can impact plant fitness through pollination; however, the relative importance of direct and indirect damage to floral tissue on plant reproduction is still largely unknown.
bibliographic citation: Haas et al. (2020) A systematic review of the direct and indirect effects of herbivory on plant reproduction mediated by pollination. PeerJ 8:e9049 https://doi.org/10.7717/peerj.9049
date submitted: 2019-10-17
date accepted: 2020-04-02
issued: 2020-06-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Haas
  given name: Stephanie M.
author list: Agent
  family name: Lortie
  given name: Christopher J.
doi: 10.7717/peerj.9049
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-08
copyright: © 2020 Haas and Lortie
attribution name: Haas and Lortie

Age-dependent differences in iris colouration of passerines during autumn migration in Central Europe
type: item
type: AcademicArticle
description: Avian eye colour changes with age, but many aspects of this transition are still insufficiently understood. We examined if an individual’s sex, age, species and body condition are related to the iris colour in common migratory passerines during their autumn passage through Central Europe. A total of 1,399 individuals from nine numerous species were ringed and examined in late autumn in northern Poland. Each individual was sexed by plumage (if possible) and assigned to one of three classes of the iris colour—typical for immatures, typical for adults and intermediate. We found that the iris was typical in 97.7% cases of immatures and in 75.8% cases of adults and this difference was significant. Species, sex and body mass index (BMI) had no significant influence on the iris colour. We show that iris colour in passerines in late autumn is strongly age-dependent and thus can serve as a reliable feature for ageing in field studies, especially in species difficult to age by plumage.
format: application/pdf
format: text/html
creator: Michał Polakowski
creator: Krzysztof Stępniewski
creator: Joanna Śliwa-Dominiak
creator: Magdalena Remisiewicz
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.9188
publisher: PeerJ Inc.
rights: © 2020 Polakowski et al.
abstract: Avian eye colour changes with age, but many aspects of this transition are still insufficiently understood. We examined if an individual’s sex, age, species and body condition are related to the iris colour in common migratory passerines during their autumn passage through Central Europe. A total of 1,399 individuals from nine numerous species were ringed and examined in late autumn in northern Poland. Each individual was sexed by plumage (if possible) and assigned to one of three classes of the iris colour—typical for immatures, typical for adults and intermediate. We found that the iris was typical in 97.7% cases of immatures and in 75.8% cases of adults and this difference was significant. Species, sex and body mass index (BMI) had no significant influence on the iris colour. We show that iris colour in passerines in late autumn is strongly age-dependent and thus can serve as a reliable feature for ageing in field studies, especially in species difficult to age by plumage.
bibliographic citation: Polakowski et al. (2020) Age-dependent differences in iris colouration of passerines during autumn migration in Central Europe. PeerJ 8:e9188 https://doi.org/10.7717/peerj.9188
date submitted: 2020-01-17
date accepted: 2020-04-23
issued: 2020-06-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Polakowski
  given name: Michał
author list: Agent
  family name: Stępniewski
  given name: Krzysztof
author list: Agent
  family name: Śliwa-Dominiak
  given name: Joanna
author list: Agent
  family name: Remisiewicz
  given name: Magdalena
doi: 10.7717/peerj.9188
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-08
copyright: ©2020 Polakowski et al.
attribution name: Polakowski et al.

Temporal and spatial variability of terrestrial diatoms at the catchment scale: controls on productivity and comparison with other soil algae
type: item
type: AcademicArticle
description: Terrestrial diatoms are an integral component of the soil microbial community. However, their productivity and how it compares to other algal groups remains poorly known. This lack of knowledge hampers their potential use as environmental markers in various applications. As a way forward, we investigated the seasonal and spatial patterns of diatom assemblages and the role of environmental factors on the soil diatom productivity. We collected soil algal samples in 16 sites across the Attert River basin (Luxembourg) every 4 weeks for a period of 12 months. The algal abundances were then derived from pigment analysis using High-Performance Liquid Chromatography. Our results indicate that diatom productivity is mainly controlled by factors related to soil moisture availability leading to seasonal patterns, whereas the concentration of green algae remained stable over the course of the study period. Generally, anthropic disturbed habitats contained less living diatom cells than undisturbed habitats. Also, we learned that diatoms can be the dominant algal group at periods of the year with high soil moisture.
format: application/pdf
format: text/html
creator: Jasper Foets
creator: Carlos E. Wetzel
creator: Adriaan J. Teuling
creator: Laurent Pfister
subject: Ecology
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.9198
publisher: PeerJ Inc.
rights: © 2020 Foets et al.
abstract: Terrestrial diatoms are an integral component of the soil microbial community. However, their productivity and how it compares to other algal groups remains poorly known. This lack of knowledge hampers their potential use as environmental markers in various applications. As a way forward, we investigated the seasonal and spatial patterns of diatom assemblages and the role of environmental factors on the soil diatom productivity. We collected soil algal samples in 16 sites across the Attert River basin (Luxembourg) every 4 weeks for a period of 12 months. The algal abundances were then derived from pigment analysis using High-Performance Liquid Chromatography. Our results indicate that diatom productivity is mainly controlled by factors related to soil moisture availability leading to seasonal patterns, whereas the concentration of green algae remained stable over the course of the study period. Generally, anthropic disturbed habitats contained less living diatom cells than undisturbed habitats. Also, we learned that diatoms can be the dominant algal group at periods of the year with high soil moisture.
bibliographic citation: Foets et al. (2020) Temporal and spatial variability of terrestrial diatoms at the catchment scale: controls on productivity and comparison with other soil algae. PeerJ 8:e9198 https://doi.org/10.7717/peerj.9198
date submitted: 2020-01-21
date accepted: 2020-04-24
issued: 2020-06-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Foets
  given name: Jasper
author list: Agent
  family name: Wetzel
  given name: Carlos E.
author list: Agent
  family name: Teuling
  given name: Adriaan J.
author list: Agent
  family name: Pfister
  given name: Laurent
doi: 10.7717/peerj.9198
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-08
copyright: © 2020 Foets et al.
attribution name: Foets et al.

Muscle activation varies between high-bar and low-bar back squat
type: item
type: AcademicArticle
description: Background Differences in the muscular activity between the high-bar back squat (HBBS) and the low-bar back squat (LBBS) on the same representative group of experienced powerlifters are still scarcely investigated. The main purpose of the study was to compare the normalized bioelectrical activity and maximal angles within single homogeneous group between the HBBS and LBBS for 60% one repetition maximum (1RM), 65% 1RM and 70% 1RM. Methods Twelve healthy men (age 24.3 ± 2.8 years, height 178.8 ± 5.6 cm, body mass 88.3 ± 11.5 kg), experienced in powerlifting performed HBBS and LBBS with comparable external loads equal 60% 1RM, 65% 1RM, and 70% 1RM. Electromyography (EMG) signals of muscle groups were synchronously recorded alongside kinematic data (joints angle) by means of a motion capture system. Results EMG activity during eccentric phase of squat motion were significantly higher during LBBS than in HBBS for all selected muscles (60% 1RM and 65% 1RM) (p < 0.05). All examined muscles were more activated during concentric phase of the squat cycle (p < 0.05). In the concentric phase, significant differences between the loads were generally not observed between just 5% 1RM change in load level for LBBS. Conclusions Our results confirmed significant differences in muscles activation between both squat techniques. Muscle activity during eccentric phase of squat motion were significantly higher during LBBS than HBBS. The differences are crucial for posterior muscle chain during eccentric phase of squat cycle.
format: application/pdf
format: text/html
creator: Michal Murawa
creator: Anna Fryzowicz
creator: Jaroslaw Kabacinski
creator: Jakub Jurga
creator: Joanna Gorwa
creator: Manuela Galli
creator: Matteo Zago
subject: Bioengineering
subject: Anatomy and Physiology
subject: Kinesiology
subject: Public Health
description: doi:10.7717/peerj.9256
publisher: PeerJ Inc.
rights: © 2020 Murawa et al.
abstract: Background Differences in the muscular activity between the high-bar back squat (HBBS) and the low-bar back squat (LBBS) on the same representative group of experienced powerlifters are still scarcely investigated. The main purpose of the study was to compare the normalized bioelectrical activity and maximal angles within single homogeneous group between the HBBS and LBBS for 60% one repetition maximum (1RM), 65% 1RM and 70% 1RM. Methods Twelve healthy men (age 24.3 ± 2.8 years, height 178.8 ± 5.6 cm, body mass 88.3 ± 11.5 kg), experienced in powerlifting performed HBBS and LBBS with comparable external loads equal 60% 1RM, 65% 1RM, and 70% 1RM. Electromyography (EMG) signals of muscle groups were synchronously recorded alongside kinematic data (joints angle) by means of a motion capture system. Results EMG activity during eccentric phase of squat motion were significantly higher during LBBS than in HBBS for all selected muscles (60% 1RM and 65% 1RM) (p < 0.05). All examined muscles were more activated during concentric phase of the squat cycle (p < 0.05). In the concentric phase, significant differences between the loads were generally not observed between just 5% 1RM change in load level for LBBS. Conclusions Our results confirmed significant differences in muscles activation between both squat techniques. Muscle activity during eccentric phase of squat motion were significantly higher during LBBS than HBBS. The differences are crucial for posterior muscle chain during eccentric phase of squat cycle.
bibliographic citation: Murawa et al. (2020) Muscle activation varies between high-bar and low-bar back squat. PeerJ 8:e9256 https://doi.org/10.7717/peerj.9256
date submitted: 2020-01-31
date accepted: 2020-05-08
issued: 2020-06-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Murawa
  given name: Michal
author list: Agent
  family name: Fryzowicz
  given name: Anna
author list: Agent
  family name: Kabacinski
  given name: Jaroslaw
author list: Agent
  family name: Jurga
  given name: Jakub
author list: Agent
  family name: Gorwa
  given name: Joanna
author list: Agent
  family name: Galli
  given name: Manuela
author list: Agent
  family name: Zago
  given name: Matteo
doi: 10.7717/peerj.9256
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-08
copyright: ©2020 Murawa et al.
attribution name: Murawa et al.

Multiple immunity-related genes control susceptibility of Arabidopsis thaliana to the parasitic weed Phelipanche aegyptiaca
type: item
type: AcademicArticle
description: Parasitic weeds represent a major threat to agricultural production across the world. Little is known about which host genetic pathways determine compatibility for any host–parasitic plant interaction. We developed a quantitative assay to characterize the growth of the parasitic weed Phelipanche aegyptiaca on 46 mutant lines of the host plant Arabidopsis thaliana to identify host genes that are essential for susceptibility to the parasite. A. thaliana host plants with mutations in genes involved in jasmonic acid biosynthesis/signaling or the negative regulation of plant immunity were less susceptible to P. aegyptiaca parasitization. In contrast, A. thaliana plants with a mutant allele of the putative immunity hub gene Pfd6 were more susceptible to parasitization. Additionally, quantitative PCR revealed that P. aegyptiaca parasitization leads to transcriptional reprograming of several hormone signaling pathways. While most tested A. thaliana lines were fully susceptible to P. aegyptiaca parasitization, this work revealed several host genes essential for full susceptibility or resistance to parasitism. Altering these pathways may be a viable approach for limiting host plant susceptibility to parasitism.
format: application/pdf
format: text/html
creator: Christopher R. Clarke
creator: So-Yon Park
creator: Robert Tuosto
creator: Xiaoyan Jia
creator: Amanda Yoder
creator: Jennifer Van Mullekom
creator: James Westwood
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9268
publisher: PeerJ Inc.
rights: © 2020
abstract: Parasitic weeds represent a major threat to agricultural production across the world. Little is known about which host genetic pathways determine compatibility for any host–parasitic plant interaction. We developed a quantitative assay to characterize the growth of the parasitic weed Phelipanche aegyptiaca on 46 mutant lines of the host plant Arabidopsis thaliana to identify host genes that are essential for susceptibility to the parasite. A. thaliana host plants with mutations in genes involved in jasmonic acid biosynthesis/signaling or the negative regulation of plant immunity were less susceptible to P. aegyptiaca parasitization. In contrast, A. thaliana plants with a mutant allele of the putative immunity hub gene Pfd6 were more susceptible to parasitization. Additionally, quantitative PCR revealed that P. aegyptiaca parasitization leads to transcriptional reprograming of several hormone signaling pathways. While most tested A. thaliana lines were fully susceptible to P. aegyptiaca parasitization, this work revealed several host genes essential for full susceptibility or resistance to parasitism. Altering these pathways may be a viable approach for limiting host plant susceptibility to parasitism.
bibliographic citation: Clarke et al. (2020) Multiple immunity-related genes control susceptibility of Arabidopsis thaliana to the parasitic weed Phelipanche aegyptiaca. PeerJ 8:e9268 https://doi.org/10.7717/peerj.9268
date submitted: 2020-02-25
date accepted: 2020-05-10
issued: 2020-06-08
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Clarke
  given name: Christopher R.
author list: Agent
  family name: Park
  given name: So-Yon
author list: Agent
  family name: Tuosto
  given name: Robert
author list: Agent
  family name: Jia
  given name: Xiaoyan
author list: Agent
  family name: Yoder
  given name: Amanda
author list: Agent
  family name: Van Mullekom
  given name: Jennifer
author list: Agent
  family name: Westwood
  given name: James
doi: 10.7717/peerj.9268
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-08

Lycopene alleviates oxidative stress via the PI3K/Akt/Nrf2pathway in a cell model of Alzheimer’s disease
type: item
type: AcademicArticle
description: Background & Aims Oxidative stress (OS) plays an important role in neurodegenerative diseases such as Alzheimer’s disease (AD). Lycopene is a pigment with potent antioxidant and anti-tumor effects. However, its potential role in central nervous system is not well-defined. The aim of this study was to investigate the effect of lycopene on the cell model of AD and determine its underlying mechanisms. Methods M146L cell is a double-transfected (human APP gene and presenlin-1 gene) Chinese hamster ovary (CHO) cell line that overexpresses β -amyloid (Aβ) and is an ideal cell model for AD. We treated cells with lycopene, and observed the effect of lycopene on M146L cells. Results Oxidative stress and apoptosis in M146L cells were significantly higher than those in CHO cells, suggesting that Aβ induced OS and apoptosis. Lycopene alleviated OS and apoptosis, activated the PI3K/Akt/Nrf2 signaling pathway, upregulated antioxidant and antiapoptotic proteins and downregulated proapoptotic proteins. Additionally, lycopene inhibited β -secretase (BACE) activity in M146L cells. These results suggest that lycopene inhibits BACE activity and protects M146L cells from oxidative stress and apoptosis by activating the PI3K/Akt/Nrf2 pathway. Conclusion Lycopene possibly prevents Aβ-induced damage by activating the PI3K/Akt/Nrf2 signaling pathway and reducing the expression of BACE in M146L cells.
format: application/pdf
format: text/html
creator: Yinchao Fang
creator: Shanshan Ou
creator: Tong Wu
creator: Lingqi Zhou
creator: Hai Tang
creator: Mei Jiang
creator: Jie Xu
creator: Kaihua Guo
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Geriatrics
description: doi:10.7717/peerj.9308
publisher: PeerJ Inc.
rights: © 2020 Fang et al.
abstract: Background & Aims Oxidative stress (OS) plays an important role in neurodegenerative diseases such as Alzheimer’s disease (AD). Lycopene is a pigment with potent antioxidant and anti-tumor effects. However, its potential role in central nervous system is not well-defined. The aim of this study was to investigate the effect of lycopene on the cell model of AD and determine its underlying mechanisms. Methods M146L cell is a double-transfected (human APP gene and presenlin-1 gene) Chinese hamster ovary (CHO) cell line that overexpresses β -amyloid (Aβ) and is an ideal cell model for AD. We treated cells with lycopene, and observed the effect of lycopene on M146L cells. Results Oxidative stress and apoptosis in M146L cells were significantly higher than those in CHO cells, suggesting that Aβ induced OS and apoptosis. Lycopene alleviated OS and apoptosis, activated the PI3K/Akt/Nrf2 signaling pathway, upregulated antioxidant and antiapoptotic proteins and downregulated proapoptotic proteins. Additionally, lycopene inhibited β -secretase (BACE) activity in M146L cells. These results suggest that lycopene inhibits BACE activity and protects M146L cells from oxidative stress and apoptosis by activating the PI3K/Akt/Nrf2 pathway. Conclusion Lycopene possibly prevents Aβ-induced damage by activating the PI3K/Akt/Nrf2 signaling pathway and reducing the expression of BACE in M146L cells.
bibliographic citation: Fang et al. (2020) Lycopene alleviates oxidative stress via the PI3K/Akt/Nrf2pathway in a cell model of Alzheimer’s disease. PeerJ 8:e9308 https://doi.org/10.7717/peerj.9308
date submitted: 2020-03-20
date accepted: 2020-05-17
issued: 2020-06-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fang
  given name: Yinchao
author list: Agent
  family name: Ou
  given name: Shanshan
author list: Agent
  family name: Wu
  given name: Tong
author list: Agent
  family name: Zhou
  given name: Lingqi
author list: Agent
  family name: Tang
  given name: Hai
author list: Agent
  family name: Jiang
  given name: Mei
author list: Agent
  family name: Xu
  given name: Jie
author list: Agent
  family name: Guo
  given name: Kaihua
doi: 10.7717/peerj.9308
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-08
copyright: ©2020 Fang et al.
attribution name: Fang et al.

A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology
type: item
type: AcademicArticle
description: The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.
format: application/pdf
format: text/html
creator: Jiawei Wang
creator: Weizhen Liu
creator: Dongzi Zhu
creator: Xiang Zhou
creator: Po Hong
creator: Hongjun Zhao
creator: Yue Tan
creator: Xin Chen
creator: Xiaojuan Zong
creator: Li Xu
creator: Lisi Zhang
creator: Hairong Wei
creator: Qingzhong Liu
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.9114
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.
bibliographic citation: Wang et al. (2020) A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology. PeerJ 8:e9114 https://doi.org/10.7717/peerj.9114
date submitted: 2019-09-16
date accepted: 2020-04-10
issued: 2020-06-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jiawei
author list: Agent
  family name: Liu
  given name: Weizhen
author list: Agent
  family name: Zhu
  given name: Dongzi
author list: Agent
  family name: Zhou
  given name: Xiang
author list: Agent
  family name: Hong
  given name: Po
author list: Agent
  family name: Zhao
  given name: Hongjun
author list: Agent
  family name: Tan
  given name: Yue
author list: Agent
  family name: Chen
  given name: Xin
author list: Agent
  family name: Zong
  given name: Xiaojuan
author list: Agent
  family name: Xu
  given name: Li
author list: Agent
  family name: Zhang
  given name: Lisi
author list: Agent
  family name: Wei
  given name: Hairong
author list: Agent
  family name: Liu
  given name: Qingzhong
doi: 10.7717/peerj.9114
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-05
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Reconstruction of past distribution for the Mongolian toad, Strauchbufo raddei (Anura: Bufonidae) using environmental modeling
type: item
type: AcademicArticle
description: The use of ecological models enables determining the current distribution of species, but also their past distribution when matching climatic conditions are available. In specific cases, they can also be used to determine the likelihood of fossils to belong to the same species—under the hypothesis that all individuals of a species have the same ecological requirements. Here, using environmental modeling, we reconstructed the distribution of the Mongolian toad, Strauchbufo raddei, since the Last Glacial Maximum and thus covering the time period between the Late Pleistocene and the Holocene. We found the range of the species to have shifted over time, with the LGM population clustered around the current southern range of the species, before expanding east and north during the Pleistocene, and reaching the current range since the mid-Holocene. Finally, we determined that the ecological conditions during the life-time of the mid-Pleistocene fossils attributed to the species in Europe were too different from the one of the extant species or fossils occurring at the same period in Asia to belong to the same species.
format: application/pdf
format: text/html
creator: Spartak N. Litvinchuk
creator: Natalya A. Schepina
creator: Amaël Borzée
subject: Biodiversity
subject: Biogeography
subject: Zoology
description: doi:10.7717/peerj.9216
publisher: PeerJ Inc.
rights: © 2020 Litvinchuk et al.
abstract: The use of ecological models enables determining the current distribution of species, but also their past distribution when matching climatic conditions are available. In specific cases, they can also be used to determine the likelihood of fossils to belong to the same species—under the hypothesis that all individuals of a species have the same ecological requirements. Here, using environmental modeling, we reconstructed the distribution of the Mongolian toad, Strauchbufo raddei, since the Last Glacial Maximum and thus covering the time period between the Late Pleistocene and the Holocene. We found the range of the species to have shifted over time, with the LGM population clustered around the current southern range of the species, before expanding east and north during the Pleistocene, and reaching the current range since the mid-Holocene. Finally, we determined that the ecological conditions during the life-time of the mid-Pleistocene fossils attributed to the species in Europe were too different from the one of the extant species or fossils occurring at the same period in Asia to belong to the same species.
bibliographic citation: Litvinchuk et al. (2020) Reconstruction of past distribution for the Mongolian toad, Strauchbufo raddei (Anura: Bufonidae) using environmental modeling. PeerJ 8:e9216 https://doi.org/10.7717/peerj.9216
date submitted: 2020-02-17
date accepted: 2020-04-27
issued: 2020-06-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Litvinchuk
  given name: Spartak N.
author list: Agent
  family name: Schepina
  given name: Natalya A.
author list: Agent
  family name: Borzée
  given name: Amaël
doi: 10.7717/peerj.9216
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-05
copyright: ©2020 Litvinchuk et al.
attribution name: Litvinchuk et al.

Nebulized dexmedetomidine improves pulmonary shunt and lung mechanics during one-lung ventilation: a randomized clinical controlled trial
type: item
type: AcademicArticle
description: Background Dexmedetomidine (Dex), a selective a2-adrenergic receptor agonist, has been previously reported to attenuate intrapulmonary shunt during one-lung ventilation (OLV) and to alleviate bronchoconstriction. However, the therapeutic effects of nebulized Dex on pulmonary shunt and lung mechanics during OLV have not been evaluated. Here we determine whether nebulized dexmedetomidine improved pulmonary shunt and lung mechanics in patients undergoing elective thoracic surgery in a prospective randomized controlled clinical trial. Methods One hundred and twenty-eight patients undergoing elective thoracoscopic surgery were included in this study and randomly divided into four groups: 0.9% saline (Placebo group), 0.5 µg/kg (Dex0.5 group), 1 µg/kg (Dex1 group) and 2 µg/kg (Dex2group) dexmedetomidine. After bronchial intubation, patients received different nebulized doses of dexmedetomidine (0.5 µg/kg, 1 µg/kg and 2 µg/kg) or 0.9% saline placebo during two-lung ventilation(TLV). OLV was initiated 15 min after bronchial intubation. Anesthesia was maintained with intravenous infusion of cisatracurium and propofol. Bispectral Index values were maintained within 40–50 by adjusting the infusion of propofol in all groups. Arterial blood gas samples and central venous blood gas samples were taken as follows: 15 min after bronchial intubation during two-lung ventilation (TLV15), after 30 and 60 min of OLV (OLV30and OLV60, respectively) and 15 min after reinstitution of TLV (ReTLV). Dynamic compliance was also calculated at TLV15, OLV30, OLV60 and ReTLV. Results Dex decreased the requirement of propofol in a dose-dependent manner(P = 0.000). Heart rate (HR) and mean arterial pressure (MAP) displayed no significant difference among groups (P = 0.397 and 0.863). Compared with the placebo group, Dex administered between 0.5 and 2 µg/kg increased partial pressure of oxygen (PaO2) significantly at OLV30 and OLV60(P = 0.000); however, Dex administered between 1 and 2 µg/kg decreased p…
format: application/pdf
format: text/html
creator: Bo Xu
creator: Hong Gao
creator: Dan Li
creator: Chunxiao Hu
creator: Jianping Yang
subject: Anesthesiology and Pain Management
subject: Clinical Trials
subject: Pharmacology
subject: Respiratory Medicine
description: doi:10.7717/peerj.9247
publisher: PeerJ Inc.
rights: © 2020 Xu et al.
abstract: Background Dexmedetomidine (Dex), a selective a2-adrenergic receptor agonist, has been previously reported to attenuate intrapulmonary shunt during one-lung ventilation (OLV) and to alleviate bronchoconstriction. However, the therapeutic effects of nebulized Dex on pulmonary shunt and lung mechanics during OLV have not been evaluated. Here we determine whether nebulized dexmedetomidine improved pulmonary shunt and lung mechanics in patients undergoing elective thoracic surgery in a prospective randomized controlled clinical trial. Methods One hundred and twenty-eight patients undergoing elective thoracoscopic surgery were included in this study and randomly divided into four groups: 0.9% saline (Placebo group), 0.5 µg/kg (Dex0.5 group), 1 µg/kg (Dex1 group) and 2 µg/kg (Dex2group) dexmedetomidine. After bronchial intubation, patients received different nebulized doses of dexmedetomidine (0.5 µg/kg, 1 µg/kg and 2 µg/kg) or 0.9% saline placebo during two-lung ventilation(TLV). OLV was initiated 15 min after bronchial intubation. Anesthesia was maintained with intravenous infusion of cisatracurium and propofol. Bispectral Index values were maintained within 40–50 by adjusting the infusion of propofol in all groups. Arterial blood gas samples and central venous blood gas samples were taken as follows: 15 min after bronchial intubation during two-lung ventilation (TLV15), after 30 and 60 min of OLV (OLV30and OLV60, respectively) and 15 min after reinstitution of TLV (ReTLV). Dynamic compliance was also calculated at TLV15, OLV30, OLV60 and ReTLV. Results Dex decreased the requirement of propofol in a dose-dependent manner(P = 0.000). Heart rate (HR) and mean arterial pressure (MAP) displayed no significant difference among groups (P = 0.397 and 0.863). Compared with the placebo group, Dex administered between 0.5 and 2 µg/kg increased partial pressure of oxygen (PaO2) significantly at OLV30 and OLV60(P = 0.000); however, Dex administered between 1 and 2 µg/kg decreased p…
bibliographic citation: Xu et al. (2020) Nebulized dexmedetomidine improves pulmonary shunt and lung mechanics during one-lung ventilation: a randomized clinical controlled trial. PeerJ 8:e9247 https://doi.org/10.7717/peerj.9247
date submitted: 2019-09-03
date accepted: 2020-05-07
issued: 2020-06-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Bo
author list: Agent
  family name: Gao
  given name: Hong
author list: Agent
  family name: Li
  given name: Dan
author list: Agent
  family name: Hu
  given name: Chunxiao
author list: Agent
  family name: Yang
  given name: Jianping
doi: 10.7717/peerj.9247
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-05
copyright: ©2020 Xu et al.
attribution name: Xu et al.

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