PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Plasma membrane proteomic analysis by TMT-PRM provides insight into mechanisms of aluminum resistance in tamba black soybean roots tips
items: Non-linear responses of net ecosystem productivity to gradient warming in a paddy field in Northeast China
items: Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach
items: Relationship between the average slope in the active commuting to and from school and fitness in adolescents: the mediator role of fatness
items: Plastome of the mycoheterotrophic eudicot Exacum paucisquama (Gentianaceae) exhibits extensive gene loss and a highly expanded inverted repeat region
items: Validation of a general subjective well-being factor using Classical Test Theory
items: Silicon induces hormetic dose-response effects on growth and concentrations of chlorophylls, amino acids and sugars in pepper plants during the early developmental stage
items: Bacterial communities associated with cell phones and shoes
items: Effectiveness of topical antibiotics in treating corals affected by Stony Coral Tissue Loss Disease
items: Within-person structures of daily cognitive performance differ from between-person structures of cognitive abilities

Plasma membrane proteomic analysis by TMT-PRM provides insight into mechanisms of aluminum resistance in tamba black soybean roots tips
type: item
type: AcademicArticle
description: Aluminum (Al) toxicity in acid soil is a worldwide agricultural problem that inhibits crop growth and productivity. However, the signal pathways associated with Al tolerance in plants remain largely unclear. In this study, tandem mass tag (TMT)-based quantitative proteomic methods were used to identify the differentially expressed plasma membrane (PM) proteins in Tamba black soybean (TBS) root tips under Al stress. Data are available via ProteomeXchange with identifier PXD017160. In addition, parallel reaction monitoring (PRM) was used to verify the protein quantitative data. The results showed that 907 PM proteins were identified in Al-treated plants. Among them, compared to untreated plants, 90 proteins were differentially expressed (DEPs) with 46 up-regulated and 44 down-regulated (fold change > 1.3 or < 0.77, p < 0.05). Functional enrichment based on GO, KEGG and protein domain revealed that the DEPs were associated with membrane trafficking and transporters, modifying cell wall composition, defense response and signal transduction. In conclusion, our results highlight the involvement of GmMATE13, GmMATE75, GmMATE87 and H+-ATPase in Al-induced citrate secretion in PM of TBS roots, and ABC transporters and Ca2+ have been implicated in internal detoxification and signaling of Al, respectively. Importantly, our data provides six receptor-like protein kinases (RLKs) as candidate proteins for further investigating Al signal transmembrane mechanisms.
format: application/pdf
format: text/html
creator: Yunmin Wei
creator: Caode Jiang
creator: Rongrong Han
creator: Yonghong Xie
creator: Lusheng Liu
creator: Yongxiong Yu
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.9312
publisher: PeerJ Inc.
rights: © 2020 Wei et al.
abstract: Aluminum (Al) toxicity in acid soil is a worldwide agricultural problem that inhibits crop growth and productivity. However, the signal pathways associated with Al tolerance in plants remain largely unclear. In this study, tandem mass tag (TMT)-based quantitative proteomic methods were used to identify the differentially expressed plasma membrane (PM) proteins in Tamba black soybean (TBS) root tips under Al stress. Data are available via ProteomeXchange with identifier PXD017160. In addition, parallel reaction monitoring (PRM) was used to verify the protein quantitative data. The results showed that 907 PM proteins were identified in Al-treated plants. Among them, compared to untreated plants, 90 proteins were differentially expressed (DEPs) with 46 up-regulated and 44 down-regulated (fold change > 1.3 or < 0.77, p < 0.05). Functional enrichment based on GO, KEGG and protein domain revealed that the DEPs were associated with membrane trafficking and transporters, modifying cell wall composition, defense response and signal transduction. In conclusion, our results highlight the involvement of GmMATE13, GmMATE75, GmMATE87 and H+-ATPase in Al-induced citrate secretion in PM of TBS roots, and ABC transporters and Ca2+ have been implicated in internal detoxification and signaling of Al, respectively. Importantly, our data provides six receptor-like protein kinases (RLKs) as candidate proteins for further investigating Al signal transmembrane mechanisms.
bibliographic citation: Wei et al. (2020) Plasma membrane proteomic analysis by TMT-PRM provides insight into mechanisms of aluminum resistance in tamba black soybean roots tips. PeerJ 8:e9312 https://doi.org/10.7717/peerj.9312
date submitted: 2020-02-10
date accepted: 2020-05-17
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Yunmin
author list: Agent
  family name: Jiang
  given name: Caode
author list: Agent
  family name: Han
  given name: Rongrong
author list: Agent
  family name: Xie
  given name: Yonghong
author list: Agent
  family name: Liu
  given name: Lusheng
author list: Agent
  family name: Yu
  given name: Yongxiong
doi: 10.7717/peerj.9312
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: © 2020 Wei et al.
attribution name: Wei et al.

Non-linear responses of net ecosystem productivity to gradient warming in a paddy field in Northeast China
type: item
type: AcademicArticle
description: Global warming has a known impact on ecosystems but there is a lack of understanding about its impact on ecosystem processes. Net ecosystem productivity (NEP) and its components play a key part in the global carbon cycle. Analysing the impact of global warming on NEP will improve our understanding of how warming affects ecosystems. In our study, conducted in 2018, five warming treatments were manipulated (0 W, 500 W, 1000 W, 1500 W, and 3000 W) using three repetitions of far infrared open warming over a paddy field in Northeast China. NEP and its two related components, gross primary productivity (GPP) and ecosystem respiration (ER), were measured using the static chamber-infrared gas analyser method to explore the effects of different warming magnitudes on NEP. Results showed that measurement dates, warming treatments, and their interactions significantly affected NEP, ER, and GPP. Warming significantly increased NEP and its components but they showed a non-linear response to different warming magnitudes. The maximum increases in NEP and its components occurred at 1500 W warming. NEP is closely related to its components and the non-linear response of NEP may have primarily resulted from that of GPP. Gradient warming non-linearly increased GPP in the paddy field studied in Northeast China, resulting in the non-linear response of NEP. This study provides a basis for predicting the responses of carbon cycles in future climate events.
format: application/pdf
format: text/html
creator: Yulu Sun
creator: Fuyao Qu
creator: Xianjin Zhu
creator: Bei Sun
creator: Guojiao Wang
creator: Hong Yin
creator: Tao Wan
creator: Xiaowen Song
creator: Qian Chen
subject: Ecology
subject: Ecosystem Science
subject: Climate Change Biology
description: doi:10.7717/peerj.9327
publisher: PeerJ Inc.
rights: © 2020 Sun et al.
abstract: Global warming has a known impact on ecosystems but there is a lack of understanding about its impact on ecosystem processes. Net ecosystem productivity (NEP) and its components play a key part in the global carbon cycle. Analysing the impact of global warming on NEP will improve our understanding of how warming affects ecosystems. In our study, conducted in 2018, five warming treatments were manipulated (0 W, 500 W, 1000 W, 1500 W, and 3000 W) using three repetitions of far infrared open warming over a paddy field in Northeast China. NEP and its two related components, gross primary productivity (GPP) and ecosystem respiration (ER), were measured using the static chamber-infrared gas analyser method to explore the effects of different warming magnitudes on NEP. Results showed that measurement dates, warming treatments, and their interactions significantly affected NEP, ER, and GPP. Warming significantly increased NEP and its components but they showed a non-linear response to different warming magnitudes. The maximum increases in NEP and its components occurred at 1500 W warming. NEP is closely related to its components and the non-linear response of NEP may have primarily resulted from that of GPP. Gradient warming non-linearly increased GPP in the paddy field studied in Northeast China, resulting in the non-linear response of NEP. This study provides a basis for predicting the responses of carbon cycles in future climate events.
bibliographic citation: Sun et al. (2020) Non-linear responses of net ecosystem productivity to gradient warming in a paddy field in Northeast China. PeerJ 8:e9327 https://doi.org/10.7717/peerj.9327
date submitted: 2019-11-18
date accepted: 2020-05-18
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Yulu
author list: Agent
  family name: Qu
  given name: Fuyao
author list: Agent
  family name: Zhu
  given name: Xianjin
author list: Agent
  family name: Sun
  given name: Bei
author list: Agent
  family name: Wang
  given name: Guojiao
author list: Agent
  family name: Yin
  given name: Hong
author list: Agent
  family name: Wan
  given name: Tao
author list: Agent
  family name: Song
  given name: Xiaowen
author list: Agent
  family name: Chen
  given name: Qian
doi: 10.7717/peerj.9327
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: ©2020 Sun et al.
attribution name: Sun et al.

Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach
type: item
type: AcademicArticle
description: Background Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization, and the identification of effective therapeutic strategy is a need of the hour to combat SARS-CoV-2 infection. In this scenario, the drug repurposing approach is widely used for the rapid identification of potential drugs against SARS-CoV-2, considering viral and host factors. Methods We adopted a host transcriptome-based drug repurposing strategy utilizing the publicly available high throughput gene expression data on SARS-CoV-2 and other respiratory infection viruses. Based on the consistency in expression status of host factors in different cell types and previous evidence reported in the literature, pro-viral factors of SARS-CoV-2 identified and subject to drug repurposing analysis based on DrugBank and Connectivity Map (CMap) using the web tool, CLUE. Results The upregulated pro-viral factors such as TYMP, PTGS2, C1S, CFB, IFI44, XAF1, CXCL2, and CXCL3 were identified in early infection models of SARS-CoV-2. By further analysis of the drug-perturbed expression profiles in the connectivity map, 27 drugs that can reverse the expression of pro-viral factors were identified, and importantly, twelve of them reported to have anti-viral activity. The direct inhibition of the PTGS2 gene product can be considered as another therapeutic strategy for SARS-CoV-2 infection and could suggest six approved PTGS2 inhibitor drugs for the treatment of COVID-19. The computational study could propose candidate repurposable drugs against COVID-19, and further experimental studies are required for validation.
format: application/pdf
format: text/html
creator: Tamizhini Loganathan
creator: Srimathy Ramachandran
creator: Prakash Shankaran
creator: Devipriya Nagarajan
creator: Suma Mohan S
subject: Bioinformatics
subject: Virology
description: doi:10.7717/peerj.9357
publisher: PeerJ Inc.
rights: © 2020 Loganathan et al.
abstract: Background Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization, and the identification of effective therapeutic strategy is a need of the hour to combat SARS-CoV-2 infection. In this scenario, the drug repurposing approach is widely used for the rapid identification of potential drugs against SARS-CoV-2, considering viral and host factors. Methods We adopted a host transcriptome-based drug repurposing strategy utilizing the publicly available high throughput gene expression data on SARS-CoV-2 and other respiratory infection viruses. Based on the consistency in expression status of host factors in different cell types and previous evidence reported in the literature, pro-viral factors of SARS-CoV-2 identified and subject to drug repurposing analysis based on DrugBank and Connectivity Map (CMap) using the web tool, CLUE. Results The upregulated pro-viral factors such as TYMP, PTGS2, C1S, CFB, IFI44, XAF1, CXCL2, and CXCL3 were identified in early infection models of SARS-CoV-2. By further analysis of the drug-perturbed expression profiles in the connectivity map, 27 drugs that can reverse the expression of pro-viral factors were identified, and importantly, twelve of them reported to have anti-viral activity. The direct inhibition of the PTGS2 gene product can be considered as another therapeutic strategy for SARS-CoV-2 infection and could suggest six approved PTGS2 inhibitor drugs for the treatment of COVID-19. The computational study could propose candidate repurposable drugs against COVID-19, and further experimental studies are required for validation.
bibliographic citation: Loganathan et al. (2020) Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach. PeerJ 8:e9357 https://doi.org/10.7717/peerj.9357
date submitted: 2020-04-20
date accepted: 2020-05-24
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Loganathan
  given name: Tamizhini
author list: Agent
  family name: Ramachandran
  given name: Srimathy
author list: Agent
  family name: Shankaran
  given name: Prakash
author list: Agent
  family name: Nagarajan
  given name: Devipriya
author list: Agent
  family name: Mohan S
  given name: Suma
doi: 10.7717/peerj.9357
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: © 2020 Loganathan et al.
attribution name: Loganathan et al.

Relationship between the average slope in the active commuting to and from school and fitness in adolescents: the mediator role of fatness
type: item
type: AcademicArticle
description: Active commuting to and from school (ACS) has been recognized as a potential tool to improve physical fitness. Thus, this study aims to test the relationships between the average slope in the ACS and physical fitness, as well as to verify the mediator role of fatness in the relationship between average slope and physical fitness. A total of 257 participants, 137 boys and 120 girls, from 22 schools belonged to first and second High School grades participated in this study. Based on self-reported measure and Google Earth, participants were grouped into the active commuter (number of trips was ≥5, and the time of the trip was ≥15 min), mixed commuter (number of weekly trips was <5, and the time spent on the trip was <15 min) and passive commuter groups (those who reported traveling regularly by car, motorcycle, or bus). Specifically, in the active commuter group, a positive association between the average slope in the ACS with fatness was found, which in turn was positively related to strength lower limbs and cardiorrespiratory fitness. The average slope was not significantly associated with physical fitness indicators. Furtheremore, fatness did not mediate the relathionship between average slope and physical fitness. This research concluded positive associations between average slope and the body fat in the ACS. The tendency of findings signal that the average slope should be taken into account along with the distance, time and frequency of the active commuting.
format: application/pdf
format: text/html
creator: Pedro Antonio Sánchez Miguel
creator: David Sánchez Oliva
creator: Mikel Vaquero Solís
creator: J. J. Pulido
creator: Miguel Angel Tapia Serrano
subject: Evidence Based Medicine
subject: Global Health
subject: Kinesiology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.8824
publisher: PeerJ Inc.
rights: © 2020 Sánchez Miguel et al.
abstract: Active commuting to and from school (ACS) has been recognized as a potential tool to improve physical fitness. Thus, this study aims to test the relationships between the average slope in the ACS and physical fitness, as well as to verify the mediator role of fatness in the relationship between average slope and physical fitness. A total of 257 participants, 137 boys and 120 girls, from 22 schools belonged to first and second High School grades participated in this study. Based on self-reported measure and Google Earth, participants were grouped into the active commuter (number of trips was ≥5, and the time of the trip was ≥15 min), mixed commuter (number of weekly trips was <5, and the time spent on the trip was <15 min) and passive commuter groups (those who reported traveling regularly by car, motorcycle, or bus). Specifically, in the active commuter group, a positive association between the average slope in the ACS with fatness was found, which in turn was positively related to strength lower limbs and cardiorrespiratory fitness. The average slope was not significantly associated with physical fitness indicators. Furtheremore, fatness did not mediate the relathionship between average slope and physical fitness. This research concluded positive associations between average slope and the body fat in the ACS. The tendency of findings signal that the average slope should be taken into account along with the distance, time and frequency of the active commuting.
bibliographic citation: Sánchez Miguel et al. (2020) Relationship between the average slope in the active commuting to and from school and fitness in adolescents: the mediator role of fatness. PeerJ 8:e8824 https://doi.org/10.7717/peerj.8824
date submitted: 2019-09-12
date accepted: 2020-02-28
issued: 2020-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sánchez Miguel
  given name: Pedro Antonio
author list: Agent
  family name: Sánchez Oliva
  given name: David
author list: Agent
  family name: Vaquero Solís
  given name: Mikel
author list: Agent
  family name: Pulido
  given name: J. J.
author list: Agent
  family name: Tapia Serrano
  given name: Miguel Angel
doi: 10.7717/peerj.8824
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-09
copyright: © 2020 Sánchez Miguel et al.
attribution name: Sánchez Miguel et al.

Plastome of the mycoheterotrophic eudicot Exacum paucisquama (Gentianaceae) exhibits extensive gene loss and a highly expanded inverted repeat region
type: item
type: AcademicArticle
description: Mycoheterotrophic plants are highly specialized species able to acquire organic carbon from symbiotic fungi, with relaxed dependence on photosynthesis for carbon fixation. The relaxation of the functional constraint of photosynthesis and thereby the relaxed selective pressure on functional photosynthetic genes usually lead to substantial gene loss and a highly degraded plastid genome in heterotrophs. In this study, we sequenced and analyzed the plastome of the eudicot Exacum paucisquama, providing the first plastid genome of a mycoheterotroph in the family Gentianaceae to date. The E. paucisquama plastome was 44,028 bp in length, which is much smaller than the plastomes of autotrophic eudicots. Although the E. paucisquama plastome had a quadripartite structure, a distinct boundary shift was observed in comparison with the plastomes of other eudicots. We detected extensive gene loss and only 21 putative functional genes (15 protein-coding genes, four rRNA genes and two tRNA genes). Our results provide valuable information for comparative evolutionary analyses of plastomes of heterotrophic species belonging to different phylogenetic groups.
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creator: Zhanghai Li
creator: Xiao Ma
creator: Yi Wen
creator: Sisi Chen
creator: Yan Jiang
creator: Xiaohua Jin
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.9157
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Mycoheterotrophic plants are highly specialized species able to acquire organic carbon from symbiotic fungi, with relaxed dependence on photosynthesis for carbon fixation. The relaxation of the functional constraint of photosynthesis and thereby the relaxed selective pressure on functional photosynthetic genes usually lead to substantial gene loss and a highly degraded plastid genome in heterotrophs. In this study, we sequenced and analyzed the plastome of the eudicot Exacum paucisquama, providing the first plastid genome of a mycoheterotroph in the family Gentianaceae to date. The E. paucisquama plastome was 44,028 bp in length, which is much smaller than the plastomes of autotrophic eudicots. Although the E. paucisquama plastome had a quadripartite structure, a distinct boundary shift was observed in comparison with the plastomes of other eudicots. We detected extensive gene loss and only 21 putative functional genes (15 protein-coding genes, four rRNA genes and two tRNA genes). Our results provide valuable information for comparative evolutionary analyses of plastomes of heterotrophic species belonging to different phylogenetic groups.
bibliographic citation: Li et al. (2020) Plastome of the mycoheterotrophic eudicot Exacum paucisquama (Gentianaceae) exhibits extensive gene loss and a highly expanded inverted repeat region. PeerJ 8:e9157 https://doi.org/10.7717/peerj.9157
date submitted: 2019-09-23
date accepted: 2020-04-18
issued: 2020-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhanghai
author list: Agent
  family name: Ma
  given name: Xiao
author list: Agent
  family name: Wen
  given name: Yi
author list: Agent
  family name: Chen
  given name: Sisi
author list: Agent
  family name: Jiang
  given name: Yan
author list: Agent
  family name: Jin
  given name: Xiaohua
doi: 10.7717/peerj.9157
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-09
copyright: © 2020 Li et al.
attribution name: Li et al.

Validation of a general subjective well-being factor using Classical Test Theory
type: item
type: AcademicArticle
description: Background Subjective Well-Being (SWB) is usually conceptualized in terms of an affective (i.e., judgements of biological emotional reactions and experiences) and a cognitive component (i.e., judgements of life satisfaction in relation to a psychological self-imposed ideal). Recently, researchers have suggested that judgements of harmony in life can replace or at least complement the cognitive component of SWB. Here, however, we go beyond that suggestion and propose that harmony in life should be seen as SWB’s social component since it is the sense of balance between the individual and the world around her—a process that comprises acceptance, adaptation, and balance. By adding judgements of one’s social interactions (i.e., harmony in life) to judgments of one’s life satisfaction (psycho) and judgements of one’s emotional reactions (bio), we propose a tentatively biopsychosocial model of SWB. As a first step, we used different factorial models in order to determine if both a general factor and specific sub-factors contribute to the biopsychosocial model of SWB. Method A total of 527 participants responded to the Positive Affect Negative Affect Schedule (PANAS; 20 items), the Satisfaction with Life Scale (SWLS; five items), and the Harmony in life Scale (HILS; five items). We conducted exploratory and confirmatory factor analyses to validate the biopsychosocial model of subjective well-being and a general factor (SWBS). Results The 20 PANAS items reflected a mixture of general latent structure saturation and specific latent structure saturation, but contributed to their respective specific latent factor (PA: 48%; NA: 49%) more than to the general latent SWBS factor (positive affect: 25%; negative affect: 32%). The five SWLS items contributed to a larger degree to the general SWBS factor (72%) than to life satisfaction itself (22%), while the five HILS items contributed to even a larger degree to the general SWBS factor (98%) than to harmony in life (0%). The bifactor …
format: application/pdf
format: text/html
creator: Ali Al Nima
creator: Kevin M. Cloninger
creator: Franco Lucchese
creator: Sverker Sikström
creator: Danilo Garcia
subject: Global Health
subject: Health Policy
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.9193
publisher: PeerJ Inc.
rights: © 2020 Nima et al.
abstract: Background Subjective Well-Being (SWB) is usually conceptualized in terms of an affective (i.e., judgements of biological emotional reactions and experiences) and a cognitive component (i.e., judgements of life satisfaction in relation to a psychological self-imposed ideal). Recently, researchers have suggested that judgements of harmony in life can replace or at least complement the cognitive component of SWB. Here, however, we go beyond that suggestion and propose that harmony in life should be seen as SWB’s social component since it is the sense of balance between the individual and the world around her—a process that comprises acceptance, adaptation, and balance. By adding judgements of one’s social interactions (i.e., harmony in life) to judgments of one’s life satisfaction (psycho) and judgements of one’s emotional reactions (bio), we propose a tentatively biopsychosocial model of SWB. As a first step, we used different factorial models in order to determine if both a general factor and specific sub-factors contribute to the biopsychosocial model of SWB. Method A total of 527 participants responded to the Positive Affect Negative Affect Schedule (PANAS; 20 items), the Satisfaction with Life Scale (SWLS; five items), and the Harmony in life Scale (HILS; five items). We conducted exploratory and confirmatory factor analyses to validate the biopsychosocial model of subjective well-being and a general factor (SWBS). Results The 20 PANAS items reflected a mixture of general latent structure saturation and specific latent structure saturation, but contributed to their respective specific latent factor (PA: 48%; NA: 49%) more than to the general latent SWBS factor (positive affect: 25%; negative affect: 32%). The five SWLS items contributed to a larger degree to the general SWBS factor (72%) than to life satisfaction itself (22%), while the five HILS items contributed to even a larger degree to the general SWBS factor (98%) than to harmony in life (0%). The bifactor …
bibliographic citation: Nima et al. (2020) Validation of a general subjective well-being factor using Classical Test Theory. PeerJ 8:e9193 https://doi.org/10.7717/peerj.9193
date submitted: 2020-01-22
date accepted: 2020-04-24
issued: 2020-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nima
  given name: Ali Al
author list: Agent
  family name: Cloninger
  given name: Kevin M.
author list: Agent
  family name: Lucchese
  given name: Franco
author list: Agent
  family name: Sikström
  given name: Sverker
author list: Agent
  family name: Garcia
  given name: Danilo
doi: 10.7717/peerj.9193
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-09
copyright: © 2020 Nima et al.
attribution name: Nima et al.

Silicon induces hormetic dose-response effects on growth and concentrations of chlorophylls, amino acids and sugars in pepper plants during the early developmental stage
type: item
type: AcademicArticle
description: Background Silicon (Si) is a beneficial element that has been proven to influence plant responses including growth, development and metabolism in a hormetic manner. Methods In the present study, we evaluated the effect of Si on the growth and concentrations of chlorophylls, total amino acids, and total sugars of pepper plants (Capsicum annuum L.) during the early developmental stage in a hydroponic system under conventional (unstressed) conditions. We tested four Si concentrations (applied as calcium silicate): 0, 60, 125 and 250 mg L−1, and growth variables were measured 7, 14, 21 and 28 days after treatment (dat), while biochemical variables were recorded at the end of the experiment, 28 dat. Results The application of 125 mg L−1 Si improved leaf area, fresh and dry biomass weight in leaves and stems, total soluble sugars, and concentrations of chlorophylls a and b in both leaves and stems. The amino acids concentration in leaves and roots, as well as the stem diameter were the highest in plants treated with 60 mg L−1 Si. Nevertheless, Si applications reduced root length, stem diameter and total free amino acids in leaves and stems, especially when applied at the highest concentration (i.e., 250 mg L−1 Si). Conclusion The application of Si has positive effects on pepper plants during the early developmental stage, including stimulation of growth, as well as increased concentrations of chlorophylls, total free amino acids and total soluble sugars. In general, most benefits from Si applications were observed in the range of 60–125 mg L−1 Si, while some negative effects were observed at the highest concentration applied (i.e., 250 mg L−1 Si). Therefore, pepper is a good candidate crop to benefit from Si application during the early developmental stage under unstressed conditions.
format: application/pdf
format: text/html
creator: Libia Iris Trejo-Téllez
creator: Atonaltzin García-Jiménez
creator: Hugo Fernando Escobar-Sepúlveda
creator: Sara Monzerrat Ramírez-Olvera
creator: Jericó Jabín Bello-Bello
creator: Fernando Carlos Gómez-Merino
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.9224
publisher: PeerJ Inc.
rights: © 2020 Trejo-Téllez et al.
abstract: Background Silicon (Si) is a beneficial element that has been proven to influence plant responses including growth, development and metabolism in a hormetic manner. Methods In the present study, we evaluated the effect of Si on the growth and concentrations of chlorophylls, total amino acids, and total sugars of pepper plants (Capsicum annuum L.) during the early developmental stage in a hydroponic system under conventional (unstressed) conditions. We tested four Si concentrations (applied as calcium silicate): 0, 60, 125 and 250 mg L−1, and growth variables were measured 7, 14, 21 and 28 days after treatment (dat), while biochemical variables were recorded at the end of the experiment, 28 dat. Results The application of 125 mg L−1 Si improved leaf area, fresh and dry biomass weight in leaves and stems, total soluble sugars, and concentrations of chlorophylls a and b in both leaves and stems. The amino acids concentration in leaves and roots, as well as the stem diameter were the highest in plants treated with 60 mg L−1 Si. Nevertheless, Si applications reduced root length, stem diameter and total free amino acids in leaves and stems, especially when applied at the highest concentration (i.e., 250 mg L−1 Si). Conclusion The application of Si has positive effects on pepper plants during the early developmental stage, including stimulation of growth, as well as increased concentrations of chlorophylls, total free amino acids and total soluble sugars. In general, most benefits from Si applications were observed in the range of 60–125 mg L−1 Si, while some negative effects were observed at the highest concentration applied (i.e., 250 mg L−1 Si). Therefore, pepper is a good candidate crop to benefit from Si application during the early developmental stage under unstressed conditions.
bibliographic citation: Trejo-Téllez et al. (2020) Silicon induces hormetic dose-response effects on growth and concentrations of chlorophylls, amino acids and sugars in pepper plants during the early developmental stage. PeerJ 8:e9224 https://doi.org/10.7717/peerj.9224
date submitted: 2020-01-06
date accepted: 2020-04-30
issued: 2020-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Trejo-Téllez
  given name: Libia Iris
author list: Agent
  family name: García-Jiménez
  given name: Atonaltzin
author list: Agent
  family name: Escobar-Sepúlveda
  given name: Hugo Fernando
author list: Agent
  family name: Ramírez-Olvera
  given name: Sara Monzerrat
author list: Agent
  family name: Bello-Bello
  given name: Jericó Jabín
author list: Agent
  family name: Gómez-Merino
  given name: Fernando Carlos
doi: 10.7717/peerj.9224
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-09
copyright: © 2020 Trejo-Téllez et al.
attribution name: Trejo-Téllez et al.

Bacterial communities associated with cell phones and shoes
type: item
type: AcademicArticle
description: Background Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively. Findings We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States. Conclusions We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of “environmental” taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.
format: application/pdf
format: text/html
creator: David A. Coil
creator: Russell Y. Neches
creator: Jenna M. Lang
creator: Guillaume Jospin
creator: Wendy E. Brown
creator: Darlene Cavalier
creator: Jarrad Hampton-Marcell
creator: Jack A. Gilbert
creator: Jonathan A. Eisen
subject: Biogeography
subject: Bioinformatics
subject: Microbiology
description: doi:10.7717/peerj.9235
publisher: PeerJ Inc.
rights: © 2020 Coil et al.
abstract: Background Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively. Findings We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States. Conclusions We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of “environmental” taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.
bibliographic citation: Coil et al. (2020) Bacterial communities associated with cell phones and shoes. PeerJ 8:e9235 https://doi.org/10.7717/peerj.9235
date submitted: 2019-02-01
date accepted: 2020-05-05
issued: 2020-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coil
  given name: David A.
author list: Agent
  family name: Neches
  given name: Russell Y.
author list: Agent
  family name: Lang
  given name: Jenna M.
author list: Agent
  family name: Jospin
  given name: Guillaume
author list: Agent
  family name: Brown
  given name: Wendy E.
author list: Agent
  family name: Cavalier
  given name: Darlene
author list: Agent
  family name: Hampton-Marcell
  given name: Jarrad
author list: Agent
  family name: Gilbert
  given name: Jack A.
author list: Agent
  family name: Eisen
  given name: Jonathan A.
doi: 10.7717/peerj.9235
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-09
copyright: ©2020 Coil et al.
attribution name: Coil et al.

Effectiveness of topical antibiotics in treating corals affected by Stony Coral Tissue Loss Disease
type: item
type: AcademicArticle
description: Since 2014, Stony Coral Tissue Loss Disease (SCTLD) has led to mass mortality of the majority of hard coral species on the Florida Reef Tract. Following the successful treatment of SCTLD lesions on laboratory corals using water dosed with antibiotics, two topical pastes were developed as vehicles to directly apply antibiotic treatments to wild corals. These pastes were tested as placebos and with additions of amoxicillin on active SCTLD lesions on multiple coral species. The effectiveness of the pastes without antibiotics (placebo treatments) was 4% and 9%, no different from untreated controls. Adding amoxicillin to both pastes significantly increased effectiveness to 70% and 84%. Effectiveness with this method was seen across five different coral species, with success rates of the more effective paste ranging from 67% (Colpophyllia natans) to 90% (Orbicella faveolata and Montastraea cavernosa). Topical antibiotic application is a viable and effective tool for halting disease lesions on corals affected by SCTLD.
format: application/pdf
format: text/html
creator: Karen L. Neely
creator: Kevin A. Macaulay
creator: Emily K. Hower
creator: Michelle A. Dobler
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.9289
publisher: PeerJ Inc.
rights: © 2020 Neely et al.
abstract: Since 2014, Stony Coral Tissue Loss Disease (SCTLD) has led to mass mortality of the majority of hard coral species on the Florida Reef Tract. Following the successful treatment of SCTLD lesions on laboratory corals using water dosed with antibiotics, two topical pastes were developed as vehicles to directly apply antibiotic treatments to wild corals. These pastes were tested as placebos and with additions of amoxicillin on active SCTLD lesions on multiple coral species. The effectiveness of the pastes without antibiotics (placebo treatments) was 4% and 9%, no different from untreated controls. Adding amoxicillin to both pastes significantly increased effectiveness to 70% and 84%. Effectiveness with this method was seen across five different coral species, with success rates of the more effective paste ranging from 67% (Colpophyllia natans) to 90% (Orbicella faveolata and Montastraea cavernosa). Topical antibiotic application is a viable and effective tool for halting disease lesions on corals affected by SCTLD.
bibliographic citation: Neely et al. (2020) Effectiveness of topical antibiotics in treating corals affected by Stony Coral Tissue Loss Disease. PeerJ 8:e9289 https://doi.org/10.7717/peerj.9289
date submitted: 2020-01-10
date accepted: 2020-05-13
issued: 2020-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Neely
  given name: Karen L.
author list: Agent
  family name: Macaulay
  given name: Kevin A.
author list: Agent
  family name: Hower
  given name: Emily K.
author list: Agent
  family name: Dobler
  given name: Michelle A.
doi: 10.7717/peerj.9289
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-09
copyright: © 2020 Neely et al.
attribution name: Neely et al.

Within-person structures of daily cognitive performance differ from between-person structures of cognitive abilities
type: item
type: AcademicArticle
description: Over a century of research on between-person differences has resulted in the consensus that human cognitive abilities are hierarchically organized, with a general factor, termed general intelligence or “g,” uppermost. Surprisingly, it is unknown whether this body of evidence is informative about how cognition is structured within individuals. Using data from 101 young adults performing nine cognitive tasks on 100 occasions distributed over six months, we find that the structures of individuals’ cognitive abilities vary among each other, and deviate greatly from the modal between-person structure. Working memory contributes the largest share of common variance to both between- and within-person structures, but the g factor is much less prominent within than between persons. We conclude that between-person structures of cognitive abilities cannot serve as a surrogate for within-person structures. To reveal the development and organization of human intelligence, individuals need to be studied over time.
format: application/pdf
format: text/html
creator: Florian Schmiedek
creator: Martin Lövdén
creator: Timo von Oertzen
creator: Ulman Lindenberger
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.9290
publisher: PeerJ Inc.
rights: © 2020 Schmiedek et al.
abstract: Over a century of research on between-person differences has resulted in the consensus that human cognitive abilities are hierarchically organized, with a general factor, termed general intelligence or “g,” uppermost. Surprisingly, it is unknown whether this body of evidence is informative about how cognition is structured within individuals. Using data from 101 young adults performing nine cognitive tasks on 100 occasions distributed over six months, we find that the structures of individuals’ cognitive abilities vary among each other, and deviate greatly from the modal between-person structure. Working memory contributes the largest share of common variance to both between- and within-person structures, but the g factor is much less prominent within than between persons. We conclude that between-person structures of cognitive abilities cannot serve as a surrogate for within-person structures. To reveal the development and organization of human intelligence, individuals need to be studied over time.
bibliographic citation: Schmiedek et al. (2020) Within-person structures of daily cognitive performance differ from between-person structures of cognitive abilities. PeerJ 8:e9290 https://doi.org/10.7717/peerj.9290
date submitted: 2019-10-14
date accepted: 2020-05-13
issued: 2020-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schmiedek
  given name: Florian
author list: Agent
  family name: Lövdén
  given name: Martin
author list: Agent
  family name: von Oertzen
  given name: Timo
author list: Agent
  family name: Lindenberger
  given name: Ulman
doi: 10.7717/peerj.9290
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-09
copyright: ©2020 Schmiedek et al.
attribution name: Schmiedek et al.

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