PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Factors regulating growth pattern and condition factor of an amphibious fish Periophthalmus gracilis living in the Mekong Delta
items: An overview of the nutritional value, health properties, and future challenges of Chinese bayberry
items: Hurricane María drives increased indoor proliferation of filamentous fungi in San Juan, Puerto Rico: a two-year culture-based approach
items: Back pain and body posture of non-professional Brazilian Jiu-Jitsu practitioners
items: Titanium dioxide dental implants surfaces related oxidative stress in bone remodeling: a systematic review
items: LncRNA CCAT1 facilitates the proliferation, invasion and migration of human laryngeal squamous cell carcinoma cells via the miR-218-5p/BMI1
items: Transcriptome-wide identification and expression analysis of the KT/HAK/KUP family in Salicornia europaea L. under varied NaCl and KCl treatments
items: East palearctic treefrog past and present habitat suitability using ecological niche models
items: Tracking multiple fish
items: Overexpression of the Tectona grandis TgNAC01 regulates growth, leaf senescence and confer salt stress tolerance in transgenic tobacco plants

Factors regulating growth pattern and condition factor of an amphibious fish Periophthalmus gracilis living in the Mekong Delta
type: item
type: AcademicArticle
description: Growth pattern and condition factor (CF) are essential to fish resource assessment but limited to Periophthalmus gracilis—an amphibious fish living in the mudflats along the Indo-Pacific regions, including the Mekong Delta (MD), Vietnam. This study lasted from April 2020 to March 2021 to verify if their growth pattern and CF change with sex, size, season, month and site. The total length and weight of 486 individuals (236 females and 250 males) were 2.9–5.9 cm and 0.13–1.66 g, respectively. The mudskipper displayed negative allometry as the slope value (b = 2.69 ± 0.06) obtained from length and weight (LWR) was significantly less than 3 (p < 0.01), indicating that most fish specimens were caught in the immature stage. The fish growth pattern did not change with sex as both males and females displayed negative allometry but varied by size since the mudskipper showed negative allometry in the immature group and isometry in the mature group. Likewise, growth type changed with season since fish showed negative allometry in the dry season but isometry in the wet season. As the slope value (b) varied by site and month, the mudskipper displayed spatiotemporal growth patterns, ranging from negative to positive allometry. The CF was impacted by sex as this value of females (1.09 ± 0.02) was higher than that of males (0.96 ± 0.01, p < 0.01). Besides, CF was regulated by fish length since this value was higher in the mature group (1.12 ± 0.03) than in the immature group (1.01 ± 0.01, p < 0.01). Likewise, CF was affected by season as this value was higher in the wet season (1.05 ± 0.02) than in the dry season (0.99 ± 0.01, p < 0.01). Although the CF varied with site and month variables (p < 0.01), this value (1.02 ± 0.01) was generally higher than 1, showing fish adapted well to their habitat. The fish length at first capture should be increased to exploit this species sustainably.
format: application/pdf
format: text/html
creator: Quang Minh Dinh
creator: Ton Huu Duc Nguyen
creator: Ngon Trong Truong
creator: Lam Nguyen-Ngoc
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.13060
publisher: PeerJ Inc.
rights: © 2022 Dinh et al.
abstract: Growth pattern and condition factor (CF) are essential to fish resource assessment but limited to Periophthalmus gracilis—an amphibious fish living in the mudflats along the Indo-Pacific regions, including the Mekong Delta (MD), Vietnam. This study lasted from April 2020 to March 2021 to verify if their growth pattern and CF change with sex, size, season, month and site. The total length and weight of 486 individuals (236 females and 250 males) were 2.9–5.9 cm and 0.13–1.66 g, respectively. The mudskipper displayed negative allometry as the slope value (b = 2.69 ± 0.06) obtained from length and weight (LWR) was significantly less than 3 (p < 0.01), indicating that most fish specimens were caught in the immature stage. The fish growth pattern did not change with sex as both males and females displayed negative allometry but varied by size since the mudskipper showed negative allometry in the immature group and isometry in the mature group. Likewise, growth type changed with season since fish showed negative allometry in the dry season but isometry in the wet season. As the slope value (b) varied by site and month, the mudskipper displayed spatiotemporal growth patterns, ranging from negative to positive allometry. The CF was impacted by sex as this value of females (1.09 ± 0.02) was higher than that of males (0.96 ± 0.01, p < 0.01). Besides, CF was regulated by fish length since this value was higher in the mature group (1.12 ± 0.03) than in the immature group (1.01 ± 0.01, p < 0.01). Likewise, CF was affected by season as this value was higher in the wet season (1.05 ± 0.02) than in the dry season (0.99 ± 0.01, p < 0.01). Although the CF varied with site and month variables (p < 0.01), this value (1.02 ± 0.01) was generally higher than 1, showing fish adapted well to their habitat. The fish length at first capture should be increased to exploit this species sustainably.
bibliographic citation: Dinh et al. (2022) Factors regulating growth pattern and condition factor of an amphibious fish Periophthalmus gracilis living in the Mekong Delta. PeerJ 10:e13060 https://doi.org/10.7717/peerj.13060
date submitted: 2021-10-29
date accepted: 2022-02-13
issued: 2022-03-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dinh
  given name: Quang Minh
author list: Agent
  family name: Nguyen
  given name: Ton Huu Duc
author list: Agent
  family name: Truong
  given name: Ngon Trong
author list: Agent
  family name: Nguyen-Ngoc
  given name: Lam
doi: 10.7717/peerj.13060
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-04
copyright: ©2022 Dinh et al.
attribution name: Dinh et al.

An overview of the nutritional value, health properties, and future challenges of Chinese bayberry
type: item
type: AcademicArticle
description: Chinese bayberry (CB) is among the most popular and valuable fruits in China owing to its attractive color and unique sweet/sour taste. Recent studies have highlighted the nutritional value and health-related benefits of CB. CB has special biological characteristics of evergreen, special aroma, dioecious, nodulation, nitrogen fixation. Moreover, the fruits, leaves, and bark of CB plants harbor a number of bioactive compounds including proanthocyanidins, flavonoids, vitamin C, phenolic acids, and anthocyanins that have been linked to the anti-cancer, anti-oxidant, anti-inflammatory, anti-obesity, anti-diabetic, and neuroprotective properties and to the treatment of cardiovascular and cerebrovascular diseases. The CB fruits have been used to produce a range of products: beverages, foods, and washing supplies. Future CB-related product development is thus expected to further leverage the health-promoting potential of this valuable ecological resource. The present review provides an overview of the botanical characteristics, processing, nutritional value, health-related properties, and applications of CB in order to provide a foundation for further research and development.
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creator: Shuwen Zhang
creator: Zheping Yu
creator: Li Sun
creator: Haiying Ren
creator: Xiliang Zheng
creator: Senmiao Liang
creator: Xingjiang Qi
subject: Agricultural Science
subject: Biochemistry
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.13070
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Chinese bayberry (CB) is among the most popular and valuable fruits in China owing to its attractive color and unique sweet/sour taste. Recent studies have highlighted the nutritional value and health-related benefits of CB. CB has special biological characteristics of evergreen, special aroma, dioecious, nodulation, nitrogen fixation. Moreover, the fruits, leaves, and bark of CB plants harbor a number of bioactive compounds including proanthocyanidins, flavonoids, vitamin C, phenolic acids, and anthocyanins that have been linked to the anti-cancer, anti-oxidant, anti-inflammatory, anti-obesity, anti-diabetic, and neuroprotective properties and to the treatment of cardiovascular and cerebrovascular diseases. The CB fruits have been used to produce a range of products: beverages, foods, and washing supplies. Future CB-related product development is thus expected to further leverage the health-promoting potential of this valuable ecological resource. The present review provides an overview of the botanical characteristics, processing, nutritional value, health-related properties, and applications of CB in order to provide a foundation for further research and development.
bibliographic citation: Zhang et al. (2022) An overview of the nutritional value, health properties, and future challenges of Chinese bayberry. PeerJ 10:e13070 https://doi.org/10.7717/peerj.13070
date submitted: 2021-10-26
date accepted: 2022-02-15
issued: 2022-03-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shuwen
author list: Agent
  family name: Yu
  given name: Zheping
author list: Agent
  family name: Sun
  given name: Li
author list: Agent
  family name: Ren
  given name: Haiying
author list: Agent
  family name: Zheng
  given name: Xiliang
author list: Agent
  family name: Liang
  given name: Senmiao
author list: Agent
  family name: Qi
  given name: Xingjiang
doi: 10.7717/peerj.13070
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-04
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

Hurricane María drives increased indoor proliferation of filamentous fungi in San Juan, Puerto Rico: a two-year culture-based approach
type: item
type: AcademicArticle
description: Extensive flooding caused by Hurricane María in Puerto Rico (PR) created favorable conditions for indoor growth of filamentous fungi. These conditions represent a public health concern as contamination by environmental fungi is associated with a higher prevalence of inflammatory respiratory conditions. This work compares culturable fungal spore communities present in homes that sustained water damage after Hurricane María to those present in dry, non-flooded homes. We collected air samples from 50 houses in a neighborhood in San Juan, PR, 12 and 22 months after Hurricane María. Self-reported data was used to classify the homes as flooded, water-damage or dry non-flooded. Fungi abundances, composition and diversity were analyzed by culturing on two media. Our results showed no significant differences in indoor fungal concentrations (CFU/m3) one year after the Hurricane in both culture media studied (MEA and G25N). During the second sampling period fungal levels were 2.7 times higher in previously flooded homes (Median = 758) when compared to dry homes (Median = 283), (p-value < 0.005). Fungal profiles showed enrichment of Aspergillus species inside flooded homes compared to outdoor samples during the first sampling period (FDR-adjusted p-value = 0.05). In contrast, 22 months after the storm, indoor fungal composition consisted primarily of non-sporulated fungi, most likely basidiospores, which are characteristic of the outdoor air in PR. Together, this data highlights that homes that suffered water damage not only have higher indoor proliferation of filamentous fungi, but their indoor fungal populations change over time following the Hurricane. Ultimately, after nearly two years, indoor and outdoor fungal communities converged in this sample of naturally ventilated homes.
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format: text/html
creator: Lorraine N. Vélez-Torres
creator: Benjamín Bolaños-Rosero
creator: Filipa Godoy-Vitorino
creator: Felix E. Rivera-Mariani
creator: Juan P. Maestre
creator: Kerry Kinney
creator: Humberto Cavallin
subject: Biodiversity
subject: Microbiology
subject: Climate Change Biology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.12730
publisher: PeerJ Inc.
rights: © 2022 Vélez-Torres et al.
abstract: Extensive flooding caused by Hurricane María in Puerto Rico (PR) created favorable conditions for indoor growth of filamentous fungi. These conditions represent a public health concern as contamination by environmental fungi is associated with a higher prevalence of inflammatory respiratory conditions. This work compares culturable fungal spore communities present in homes that sustained water damage after Hurricane María to those present in dry, non-flooded homes. We collected air samples from 50 houses in a neighborhood in San Juan, PR, 12 and 22 months after Hurricane María. Self-reported data was used to classify the homes as flooded, water-damage or dry non-flooded. Fungi abundances, composition and diversity were analyzed by culturing on two media. Our results showed no significant differences in indoor fungal concentrations (CFU/m3) one year after the Hurricane in both culture media studied (MEA and G25N). During the second sampling period fungal levels were 2.7 times higher in previously flooded homes (Median = 758) when compared to dry homes (Median = 283), (p-value < 0.005). Fungal profiles showed enrichment of Aspergillus species inside flooded homes compared to outdoor samples during the first sampling period (FDR-adjusted p-value = 0.05). In contrast, 22 months after the storm, indoor fungal composition consisted primarily of non-sporulated fungi, most likely basidiospores, which are characteristic of the outdoor air in PR. Together, this data highlights that homes that suffered water damage not only have higher indoor proliferation of filamentous fungi, but their indoor fungal populations change over time following the Hurricane. Ultimately, after nearly two years, indoor and outdoor fungal communities converged in this sample of naturally ventilated homes.
bibliographic citation: Vélez-Torres et al. (2022) Hurricane María drives increased indoor proliferation of filamentous fungi in San Juan, Puerto Rico: a two-year culture-based approach. PeerJ 10:e12730 https://doi.org/10.7717/peerj.12730
date submitted: 2021-10-07
date accepted: 2021-12-11
issued: 2022-03-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vélez-Torres
  given name: Lorraine N.
author list: Agent
  family name: Bolaños-Rosero
  given name: Benjamín
author list: Agent
  family name: Godoy-Vitorino
  given name: Filipa
author list: Agent
  family name: Rivera-Mariani
  given name: Felix E.
author list: Agent
  family name: Maestre
  given name: Juan P.
author list: Agent
  family name: Kinney
  given name: Kerry
author list: Agent
  family name: Cavallin
  given name: Humberto
doi: 10.7717/peerj.12730
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-03
copyright: ©2022 Vélez-Torres et al.
attribution name: Vélez-Torres et al.

Back pain and body posture of non-professional Brazilian Jiu-Jitsu practitioners
type: item
type: AcademicArticle
description: Background The aim of the study was to assess the prevalence of back pain in non-professional Brazilian Jiu-Jitsu practitioners (NP-BJJ practitioners), and to assess the relationship between their back pain and postural disorders. Methods The study involved 61 subjects (age: 30.7 ± 4.9 years old; body mass: 79.4 ± 12.9 kg; body height: 179.6 ± 8.4 cm; 8 woman and 53 man), 31 who trained Brazilian Jiu-Jitsu (BJJ) and 30 subjects who had never trained any combat sport. The mean time of training BJJ in the study population was 3.9 ± 4.1 years. Postural assessments were conducted with the use of the photogrammetric method. The assessment of back pain and injuries was conducted with the Oswestry Disability Index (ODI) and with our proprietary questionnaire. Results Among both populations, 37 subjects reported back pain. There were no differences in back pain location between the two groups or in functional state on the ODI. Significant differences between the groups in the values of the postural parameters (spinal height, length of kyphosis, length of lordosis, pelvis inclination angle) were observed. Statistically significant differences between the NP-BJJ practitioners with and without back pain in the length of the thoracic kyphosis and the differences in the height of the waist triangles were found. Conclusions Both in the study population and in the control group the spinal pain was minimal or moderate on the ODI. BJJ practitioners who reported back pain had characteristic postural changes in some of the analysed postural parameters in comparison to BJJ practitioners who did not report back pain.
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creator: Katarzyna Sędek
creator: Aleksandra Truszczyńska-Baszak
creator: Anna Katarzyna Cygańska
creator: Justyna Drzał-Grabiec
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.12838
publisher: PeerJ Inc.
rights: © 2022 Sędek et al.
abstract: Background The aim of the study was to assess the prevalence of back pain in non-professional Brazilian Jiu-Jitsu practitioners (NP-BJJ practitioners), and to assess the relationship between their back pain and postural disorders. Methods The study involved 61 subjects (age: 30.7 ± 4.9 years old; body mass: 79.4 ± 12.9 kg; body height: 179.6 ± 8.4 cm; 8 woman and 53 man), 31 who trained Brazilian Jiu-Jitsu (BJJ) and 30 subjects who had never trained any combat sport. The mean time of training BJJ in the study population was 3.9 ± 4.1 years. Postural assessments were conducted with the use of the photogrammetric method. The assessment of back pain and injuries was conducted with the Oswestry Disability Index (ODI) and with our proprietary questionnaire. Results Among both populations, 37 subjects reported back pain. There were no differences in back pain location between the two groups or in functional state on the ODI. Significant differences between the groups in the values of the postural parameters (spinal height, length of kyphosis, length of lordosis, pelvis inclination angle) were observed. Statistically significant differences between the NP-BJJ practitioners with and without back pain in the length of the thoracic kyphosis and the differences in the height of the waist triangles were found. Conclusions Both in the study population and in the control group the spinal pain was minimal or moderate on the ODI. BJJ practitioners who reported back pain had characteristic postural changes in some of the analysed postural parameters in comparison to BJJ practitioners who did not report back pain.
bibliographic citation: Sędek et al. (2022) Back pain and body posture of non-professional Brazilian Jiu-Jitsu practitioners. PeerJ 10:e12838 https://doi.org/10.7717/peerj.12838
date submitted: 2021-05-21
date accepted: 2022-01-05
issued: 2022-03-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sędek
  given name: Katarzyna
author list: Agent
  family name: Truszczyńska-Baszak
  given name: Aleksandra
author list: Agent
  family name: Cygańska
  given name: Anna Katarzyna
author list: Agent
  family name: Drzał-Grabiec
  given name: Justyna
doi: 10.7717/peerj.12838
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-03
copyright: ©2022 Sędek et al.
attribution name: Sędek et al.

Titanium dioxide dental implants surfaces related oxidative stress in bone remodeling: a systematic review
type: item
type: AcademicArticle
description: Background Titanium dioxide dental implants have a controversial effect on reactive oxygen species (ROS) production. ROS is necessary for cellular signal transmission and proper metabolism, but also has the ability to cause cell death as well as DNA, RNA, and proteins damage by excessive oxidative stress. This study aimed to systematically review the effect of titanium dioxide dental implant-induced oxidative stress and its role on the osteogenesis-angiogenesis coupling in bone remodeling. Methods This systematic review was performed conforming to preferred reporting items for systematic review and meta-analysis (PRISMA) model. Four different databases (PubMed, Science Direct, Scopus and Medline databases) as well as manual searching were adopted. Relevant studies from January 2000 till September 2021 were retrieved. Critical Appraisal Skills Programme (CASP) was used to assess the quality of the selected studies. Results Out of 755 articles, only 14 which met the eligibility criteria were included. Six studies found that titanium dioxide nanotube (TNT) reduced oxidative stress and promoted osteoblastic activity through its effect on Wnt, mitogen-activated protein kinase (MAPK) and forkhead box protein O1 (FoxO1) signaling pathways. On the other hand, three studies confirmed that titanium dioxide nanoparticles (TiO2NPs) induce oxidative stress, reduce ostegenesis and impair antioxidant defense system as a significant negative correlation was found between decreased SIR3 protein level and increased superoxide (O2•-). Moreover, five studies proved that titanium implant alloy enhances the generation of ROS and induces cytotoxicity of osteoblast cells via its effect on NOX pathway. Conclusion TiO2NPs stimulate a wide array of oxidative stress related pathways. Scientific evidence are in favor to support the use of TiO2 nanotube-coated titanium implants to reduce oxidative stress and promote osteogenesis in bone remodeling. To validate the cellular and molecular cross ta…
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creator: Elaf Akram Abdulhameed
creator: Natheer H. Al-Rawi
creator: Marzuki Omar
creator: Nadia Khalifa
creator: A.B. Rani Samsudin
subject: Dentistry
subject: Drugs and Devices
subject: Public Health
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.12951
publisher: PeerJ Inc.
rights: © 2022 Abdulhameed et al.
abstract: Background Titanium dioxide dental implants have a controversial effect on reactive oxygen species (ROS) production. ROS is necessary for cellular signal transmission and proper metabolism, but also has the ability to cause cell death as well as DNA, RNA, and proteins damage by excessive oxidative stress. This study aimed to systematically review the effect of titanium dioxide dental implant-induced oxidative stress and its role on the osteogenesis-angiogenesis coupling in bone remodeling. Methods This systematic review was performed conforming to preferred reporting items for systematic review and meta-analysis (PRISMA) model. Four different databases (PubMed, Science Direct, Scopus and Medline databases) as well as manual searching were adopted. Relevant studies from January 2000 till September 2021 were retrieved. Critical Appraisal Skills Programme (CASP) was used to assess the quality of the selected studies. Results Out of 755 articles, only 14 which met the eligibility criteria were included. Six studies found that titanium dioxide nanotube (TNT) reduced oxidative stress and promoted osteoblastic activity through its effect on Wnt, mitogen-activated protein kinase (MAPK) and forkhead box protein O1 (FoxO1) signaling pathways. On the other hand, three studies confirmed that titanium dioxide nanoparticles (TiO2NPs) induce oxidative stress, reduce ostegenesis and impair antioxidant defense system as a significant negative correlation was found between decreased SIR3 protein level and increased superoxide (O2•-). Moreover, five studies proved that titanium implant alloy enhances the generation of ROS and induces cytotoxicity of osteoblast cells via its effect on NOX pathway. Conclusion TiO2NPs stimulate a wide array of oxidative stress related pathways. Scientific evidence are in favor to support the use of TiO2 nanotube-coated titanium implants to reduce oxidative stress and promote osteogenesis in bone remodeling. To validate the cellular and molecular cross ta…
bibliographic citation: Abdulhameed et al. (2022) Titanium dioxide dental implants surfaces related oxidative stress in bone remodeling: a systematic review. PeerJ 10:e12951 https://doi.org/10.7717/peerj.12951
date submitted: 2021-10-28
date accepted: 2022-01-26
issued: 2022-03-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdulhameed
  given name: Elaf Akram
author list: Agent
  family name: Al-Rawi
  given name: Natheer H.
author list: Agent
  family name: Omar
  given name: Marzuki
author list: Agent
  family name: Khalifa
  given name: Nadia
author list: Agent
  family name: Samsudin
  given name: A.B. Rani
doi: 10.7717/peerj.12951
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-03
copyright: ©2022 Abdulhameed et al.
attribution name: Abdulhameed et al.

LncRNA CCAT1 facilitates the proliferation, invasion and migration of human laryngeal squamous cell carcinoma cells via the miR-218-5p/BMI1
type: item
type: AcademicArticle
description: Long non-coding RNAs (LncRNAs) are vital in the treatment of laryngeal squamous cell carcinoma (LSCC). This study estimated the mechanism of lncRNA CCAT1 (CCAT1) in LSCC cells. The expression of CCAT1 in the human laryngeal mucosal epithelial cells (HLCs) and LSCC cells (Hep-2 and TU177) was detected. CCK-8 and Transwell assays were used to evaluate the cell proliferative, migrative, and invasive abilities, respectively. The subcellular localization of CCAT1 was verified by RNA-FISH and cytoplasmic isolation assays. The targeted relationship among CCAT1, miR-218-5p, and BMI1 was verified by dual-luciferase assay. Expressions of miR-218-5p and BMI1 were detected by RT-qPCR. Our results depicted that CCAT1 was highly-expressed in Hep-2 and TU177 cells. Silencing CCAT1 inhibited the proliferation, migration, and invasion of Hep-2 and TU177 cells. Mechanically, CCAT1 regulated the BMI1 expression by competitively binding to miR-218-5p as a competing endogenous RNA (ceRNA), and thus facilitated the growth of Hep-2 and TU177 cells. Downregulation of miR-218-5p or upregulation of BMI1 inhibited the inhibitory effect of silencing CCAT1 on Hep-2 and TU177 cell proliferation, invasion, and migration. In conclusion, our study elicited that lncRNA CCAT1 facilitated the proliferation, migration, and invasion of Hep-2 and TU177 cells by sponging miR-218-5p and regulating the downstream BMI1.
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format: text/html
creator: Jing Hong
creator: Ali Hong
creator: Houshu Tu
creator: Zhichao Wan
creator: Yuqiao Deng
creator: Chengcheng Deng
creator: Bo Tao
creator: Yanjin Yu
creator: Lanfei Zhou
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.12961
publisher: PeerJ Inc.
rights: © 2022 Hong et al.
abstract: Long non-coding RNAs (LncRNAs) are vital in the treatment of laryngeal squamous cell carcinoma (LSCC). This study estimated the mechanism of lncRNA CCAT1 (CCAT1) in LSCC cells. The expression of CCAT1 in the human laryngeal mucosal epithelial cells (HLCs) and LSCC cells (Hep-2 and TU177) was detected. CCK-8 and Transwell assays were used to evaluate the cell proliferative, migrative, and invasive abilities, respectively. The subcellular localization of CCAT1 was verified by RNA-FISH and cytoplasmic isolation assays. The targeted relationship among CCAT1, miR-218-5p, and BMI1 was verified by dual-luciferase assay. Expressions of miR-218-5p and BMI1 were detected by RT-qPCR. Our results depicted that CCAT1 was highly-expressed in Hep-2 and TU177 cells. Silencing CCAT1 inhibited the proliferation, migration, and invasion of Hep-2 and TU177 cells. Mechanically, CCAT1 regulated the BMI1 expression by competitively binding to miR-218-5p as a competing endogenous RNA (ceRNA), and thus facilitated the growth of Hep-2 and TU177 cells. Downregulation of miR-218-5p or upregulation of BMI1 inhibited the inhibitory effect of silencing CCAT1 on Hep-2 and TU177 cell proliferation, invasion, and migration. In conclusion, our study elicited that lncRNA CCAT1 facilitated the proliferation, migration, and invasion of Hep-2 and TU177 cells by sponging miR-218-5p and regulating the downstream BMI1.
bibliographic citation: Hong et al. (2022) LncRNA CCAT1 facilitates the proliferation, invasion and migration of human laryngeal squamous cell carcinoma cells via the miR-218-5p/BMI1. PeerJ 10:e12961 https://doi.org/10.7717/peerj.12961
date submitted: 2021-09-16
date accepted: 2022-01-27
issued: 2022-03-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hong
  given name: Jing
author list: Agent
  family name: Hong
  given name: Ali
author list: Agent
  family name: Tu
  given name: Houshu
author list: Agent
  family name: Wan
  given name: Zhichao
author list: Agent
  family name: Deng
  given name: Yuqiao
author list: Agent
  family name: Deng
  given name: Chengcheng
author list: Agent
  family name: Tao
  given name: Bo
author list: Agent
  family name: Yu
  given name: Yanjin
author list: Agent
  family name: Zhou
  given name: Lanfei
doi: 10.7717/peerj.12961
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-03
copyright: © 2022 Hong et al.
attribution name: Hong et al.

Transcriptome-wide identification and expression analysis of the KT/HAK/KUP family in Salicornia europaea L. under varied NaCl and KCl treatments
type: item
type: AcademicArticle
description: Background The KT/HAK/KUP (KUP) transporters play important roles in potassium (K+) uptake and translocation, regulation of osmotic potential, salt tolerance, root morphogenesis and plant development. However, the KUP family has not been systematically studied in the typical halophyte Salicornia europaea L., and the specific expression patterns of SeKUPs under NaCl condition and K+ deficiency are unknown. Methods In this study, SeKUPs were screened from PacBio transcriptome data of Salicornia europaea L. using bioinformatics. The identification, phylogenetic analysis and prediction of conserved motifs of SeKUPs were extensively explored. Moreover, the expression levels of 24 selected SeKUPs were assayed by real-time quantitative polymerase chain reaction (RT-qPCR). Results In this study, a total of 24 putative SeKUPs were identified in S. europaea. Nineteen SeKUPs with the fixed domain EA[ML]FADL were used to construct the phylogenetic tree, and they were divided into four clusters (clusters I–IV). MEME analysis identified 10 motifs in S. europaea, and the motif analysis suggested that 19 of the identified SeKUPs had at least four K+ transporter motifs existed in all SeKUPs (with the exception of SeKUP-2). The RT-qPCR analysis showed that the expression levels of most SeKUPs were significantly up-regulated in S. europaea when they were exposed to K+ deficiency and high salinity, implying that these SeKUPs may play a key role in the absorption and transport of K+ and Na+ in S. europaea. Discussions Our results laid the foundation for revealing the salt tolerance mechanism of SeKUPs, and provided key candidate genes for further studies on the function of KUP family in S. europaea.
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creator: Jia Wei
creator: Richard John Tiika
creator: Guangxin Cui
creator: Yanjun Ma
creator: Hongshan Yang
creator: Huirong Duan
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.12989
publisher: PeerJ Inc.
rights: © 2022 Wei et al.
abstract: Background The KT/HAK/KUP (KUP) transporters play important roles in potassium (K+) uptake and translocation, regulation of osmotic potential, salt tolerance, root morphogenesis and plant development. However, the KUP family has not been systematically studied in the typical halophyte Salicornia europaea L., and the specific expression patterns of SeKUPs under NaCl condition and K+ deficiency are unknown. Methods In this study, SeKUPs were screened from PacBio transcriptome data of Salicornia europaea L. using bioinformatics. The identification, phylogenetic analysis and prediction of conserved motifs of SeKUPs were extensively explored. Moreover, the expression levels of 24 selected SeKUPs were assayed by real-time quantitative polymerase chain reaction (RT-qPCR). Results In this study, a total of 24 putative SeKUPs were identified in S. europaea. Nineteen SeKUPs with the fixed domain EA[ML]FADL were used to construct the phylogenetic tree, and they were divided into four clusters (clusters I–IV). MEME analysis identified 10 motifs in S. europaea, and the motif analysis suggested that 19 of the identified SeKUPs had at least four K+ transporter motifs existed in all SeKUPs (with the exception of SeKUP-2). The RT-qPCR analysis showed that the expression levels of most SeKUPs were significantly up-regulated in S. europaea when they were exposed to K+ deficiency and high salinity, implying that these SeKUPs may play a key role in the absorption and transport of K+ and Na+ in S. europaea. Discussions Our results laid the foundation for revealing the salt tolerance mechanism of SeKUPs, and provided key candidate genes for further studies on the function of KUP family in S. europaea.
bibliographic citation: Wei et al. (2022) Transcriptome-wide identification and expression analysis of the KT/HAK/KUP family in Salicornia europaea L. under varied NaCl and KCl treatments. PeerJ 10:e12989 https://doi.org/10.7717/peerj.12989
date submitted: 2021-10-05
date accepted: 2022-02-01
issued: 2022-03-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Jia
author list: Agent
  family name: Tiika
  given name: Richard John
author list: Agent
  family name: Cui
  given name: Guangxin
author list: Agent
  family name: Ma
  given name: Yanjun
author list: Agent
  family name: Yang
  given name: Hongshan
author list: Agent
  family name: Duan
  given name: Huirong
doi: 10.7717/peerj.12989
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-03
copyright: ©2022 Wei et al.
attribution name: Wei et al.

East palearctic treefrog past and present habitat suitability using ecological niche models
type: item
type: AcademicArticle
description: Ecological niche modeling is a tool used to determine current potential species’ distribution or habitat suitability models which can then be used to project suitable areas in time. Projections of suitability into past climates can identify locations of climate refugia, or areas with high climatic stability likely to contain the highest levels of genetic diversity and stable populations when climatic conditions are less suitable in other parts of the range. Modeling habitat suitability for closely related species in recent past can also reveal potential periods and regions of contact and possible admixture. In the east palearctic, there are five Dryophytes (Hylid treefrog) clades belonging to two groups: Dryophytes japonicus group: Clades A and B; and Dryophytes immaculatus group: Dryophytes immaculatus, Dryophytes flaviventris, and Dryophytes suweonensis. We used maximum entropy modeling to determine the suitable ranges of these five clades during the present and projected to the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. We also calculated climatic stability for each clade to identify possible areas of climate refugia. Our models indicated suitable range expansion during the LGM for four clades with the exclusion of D. immaculatus. High climatic stability in our models corresponded to areas with the highest numbers of recorded occurrences in the present. The models produced here can additionally serve as baselines for models of suitability under climate change scenarios and indicate species ecological requirements.
format: application/pdf
format: text/html
creator: Desiree Andersen
creator: Irina Maslova
creator: Zoljargal Purevdorj
creator: Jia-Tang Li
creator: Kevin R. Messenger
creator: Jin-Long Ren
creator: Yikweon Jang
creator: Amaël Borzée
subject: Biogeography
subject: Ecology
subject: Zoology
subject: Climate Change Biology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.12999
publisher: PeerJ Inc.
rights: © 2022 Andersen et al.
abstract: Ecological niche modeling is a tool used to determine current potential species’ distribution or habitat suitability models which can then be used to project suitable areas in time. Projections of suitability into past climates can identify locations of climate refugia, or areas with high climatic stability likely to contain the highest levels of genetic diversity and stable populations when climatic conditions are less suitable in other parts of the range. Modeling habitat suitability for closely related species in recent past can also reveal potential periods and regions of contact and possible admixture. In the east palearctic, there are five Dryophytes (Hylid treefrog) clades belonging to two groups: Dryophytes japonicus group: Clades A and B; and Dryophytes immaculatus group: Dryophytes immaculatus, Dryophytes flaviventris, and Dryophytes suweonensis. We used maximum entropy modeling to determine the suitable ranges of these five clades during the present and projected to the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. We also calculated climatic stability for each clade to identify possible areas of climate refugia. Our models indicated suitable range expansion during the LGM for four clades with the exclusion of D. immaculatus. High climatic stability in our models corresponded to areas with the highest numbers of recorded occurrences in the present. The models produced here can additionally serve as baselines for models of suitability under climate change scenarios and indicate species ecological requirements.
bibliographic citation: Andersen et al. (2022) East palearctic treefrog past and present habitat suitability using ecological niche models. PeerJ 10:e12999 https://doi.org/10.7717/peerj.12999
date submitted: 2021-10-15
date accepted: 2022-02-02
issued: 2022-03-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Andersen
  given name: Desiree
author list: Agent
  family name: Maslova
  given name: Irina
author list: Agent
  family name: Purevdorj
  given name: Zoljargal
author list: Agent
  family name: Li
  given name: Jia-Tang
author list: Agent
  family name: Messenger
  given name: Kevin R.
author list: Agent
  family name: Ren
  given name: Jin-Long
author list: Agent
  family name: Jang
  given name: Yikweon
author list: Agent
  family name: Borzée
  given name: Amaël
doi: 10.7717/peerj.12999
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-03
copyright: © 2022 Andersen et al.
attribution name: Andersen et al.

Tracking multiple fish
type: item
type: AcademicArticle
description: Although the Multiple Object Tracking (MOT) task is a widely used experimental method for studying divided attention, tracking objects in the real world usually looks different. For example, in the real world, objects are usually clearly distinguishable from each other and also possess different movement patterns. One such case is tracking groups of creatures, such as tracking fish in an aquarium. We used movies of fish in an aquarium and measured general tracking performance in this task (Experiment 1). In Experiment 2, we compared tracking accuracy within-subjects in fish tracking, tracking typical MOT stimuli, and in a third condition using standard MOT uniform objects which possessed movement patterns similar to the real fish. This third condition was added to further examine the impact of different motion characteristics on tracking performance. Results within a Bayesian framework showed that tracking real fish shares similarities with tracking simple objects in a typical laboratory MOT task. Furthermore, we observed a close relationship between performance in both laboratory MOT tasks (typical and fish-like) and real fish tracking, suggesting that the commonly used laboratory MOT task possesses a good level of ecological validity.
format: application/pdf
format: text/html
creator: Filip Děchtěrenko
creator: Daniela Jakubková
creator: Jiří Lukavský
creator: Christina J. Howard
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.13031
publisher: PeerJ Inc.
rights: © 2022 Děchtěrenko et al.
abstract: Although the Multiple Object Tracking (MOT) task is a widely used experimental method for studying divided attention, tracking objects in the real world usually looks different. For example, in the real world, objects are usually clearly distinguishable from each other and also possess different movement patterns. One such case is tracking groups of creatures, such as tracking fish in an aquarium. We used movies of fish in an aquarium and measured general tracking performance in this task (Experiment 1). In Experiment 2, we compared tracking accuracy within-subjects in fish tracking, tracking typical MOT stimuli, and in a third condition using standard MOT uniform objects which possessed movement patterns similar to the real fish. This third condition was added to further examine the impact of different motion characteristics on tracking performance. Results within a Bayesian framework showed that tracking real fish shares similarities with tracking simple objects in a typical laboratory MOT task. Furthermore, we observed a close relationship between performance in both laboratory MOT tasks (typical and fish-like) and real fish tracking, suggesting that the commonly used laboratory MOT task possesses a good level of ecological validity.
bibliographic citation: Děchtěrenko et al. (2022) Tracking multiple fish. PeerJ 10:e13031 https://doi.org/10.7717/peerj.13031
date submitted: 2021-11-26
date accepted: 2022-02-08
issued: 2022-03-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Děchtěrenko
  given name: Filip
author list: Agent
  family name: Jakubková
  given name: Daniela
author list: Agent
  family name: Lukavský
  given name: Jiří
author list: Agent
  family name: Howard
  given name: Christina J.
doi: 10.7717/peerj.13031
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-03
copyright: © 2022 Děchtěrenko et al.
attribution name: Děchtěrenko et al.

Overexpression of the Tectona grandis TgNAC01 regulates growth, leaf senescence and confer salt stress tolerance in transgenic tobacco plants
type: item
type: AcademicArticle
description: NAC transcription factors play critical roles in xylem secondary development and in regulation of stress response in plants. NAC proteins related to secondary cell wall development were recently identified and characterized in Tectona grandis (teak), one of the hardwood trees of highest economic importance in the world. In this work, we characterized the novel TgNAC01 gene, which is involved in signaling pathways that mediate teak response to stress. Abscisic acid (ABA) increases TgNAC01 expression in teak plants. Therefore, this gene may have a role in signaling events that mediate ABA-dependent osmotic stress responsive in this plant species. Stable expression in tobacco plants showed that the TgNAC01 protein is localized in the cell nucleus. Overexpression of TgNAC01 in two out three independent transgenic tobacco lines resulted in increased growth, leaf senescence and salt tolerance compared to wild type (WT) plants. Moreover, the stress tolerance of transgenic plants was affected by levels of TgNAC01 gene expression. Water potential, gas exchange and chlorophyll fluorescence were used to determine salt stress tolerance. The 35S:TgNAC01-6 line under 300 mM NaCl stress responded with a significant increase in photosynthesis rate, stomatal conductance, transpiration and carboxylation efficiency, but lower water potential compared to WT plants. The data indicate that the TgNAC01 transcription factor acts as a transcriptional activator of the ABA-mediated regulation and induces leaf senescence.
format: application/pdf
format: text/html
creator: Fernando Matias
creator: Perla Novais de Oliveira
creator: Olman Gómez-Espinoza
creator: Esteban Galeano
creator: Helaine Carrer
subject: Agricultural Science
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13039
publisher: PeerJ Inc.
rights: © 2022 Matias et al.
abstract: NAC transcription factors play critical roles in xylem secondary development and in regulation of stress response in plants. NAC proteins related to secondary cell wall development were recently identified and characterized in Tectona grandis (teak), one of the hardwood trees of highest economic importance in the world. In this work, we characterized the novel TgNAC01 gene, which is involved in signaling pathways that mediate teak response to stress. Abscisic acid (ABA) increases TgNAC01 expression in teak plants. Therefore, this gene may have a role in signaling events that mediate ABA-dependent osmotic stress responsive in this plant species. Stable expression in tobacco plants showed that the TgNAC01 protein is localized in the cell nucleus. Overexpression of TgNAC01 in two out three independent transgenic tobacco lines resulted in increased growth, leaf senescence and salt tolerance compared to wild type (WT) plants. Moreover, the stress tolerance of transgenic plants was affected by levels of TgNAC01 gene expression. Water potential, gas exchange and chlorophyll fluorescence were used to determine salt stress tolerance. The 35S:TgNAC01-6 line under 300 mM NaCl stress responded with a significant increase in photosynthesis rate, stomatal conductance, transpiration and carboxylation efficiency, but lower water potential compared to WT plants. The data indicate that the TgNAC01 transcription factor acts as a transcriptional activator of the ABA-mediated regulation and induces leaf senescence.
bibliographic citation: Matias et al. (2022) Overexpression of the Tectona grandis TgNAC01 regulates growth, leaf senescence and confer salt stress tolerance in transgenic tobacco plants. PeerJ 10:e13039 https://doi.org/10.7717/peerj.13039
date submitted: 2021-09-20
date accepted: 2022-02-09
issued: 2022-03-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matias
  given name: Fernando
author list: Agent
  family name: Novais de Oliveira
  given name: Perla
author list: Agent
  family name: Gómez-Espinoza
  given name: Olman
author list: Agent
  family name: Galeano
  given name: Esteban
author list: Agent
  family name: Carrer
  given name: Helaine
doi: 10.7717/peerj.13039
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-03
copyright: ©2022 Matias et al.
attribution name: Matias et al.

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