PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Soil mineralized carbon drives more carbon stock in coniferous-broadleaf mixed plantations compared to pure plantations
items: A comprehensive drought monitoring method integrating multi-source data
items: Telomere-to-telomere genome assembly of Phaeodactylum tricornutum
items: Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity
items: Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2
items: The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents
items: Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus
items: Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area
items: Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis)
items: Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations

Soil mineralized carbon drives more carbon stock in coniferous-broadleaf mixed plantations compared to pure plantations
type: item
type: AcademicArticle
description: Forest soil carbon (C) sequestration has an important effect on global C dynamics and is regulated by various environmental factors. Mixed and pure plantations are common afforestation choices in north China, but how forest type and environmental factors interact to affect soil C stock remains unclear. We hypothesize that forest type changes soil physicochemical properties and surface biological factors, and further contributes to soil active C components, which together affect soil C sequestration capacity and C dynamic processes. Three 46-year-old 25 m × 25 m pure Pinus tabulaeformis forests (PF) and three 47-year-old 25 m × 25 m mixed coniferous-broadleaf (Pinus tabulaeformis-Quercus liaotungensis) forests (MF) were selected as the two treatments and sampled in August 2016. In 2017, soil temperature (ST) at 10 cm were measured every 30 min for the entire vegetation season. Across 0–50 cm (five soil layers, 10 cm per layer), we also measured C components and environmental factors which may affect soil C sequestration, including soil organic carbon (SOC), soil total nitrogen (STN), dissolved organic carbon (DOC), microbial biomass carbon (MBC), soil moisture (SM) and soil pH. We then incubated samples for 56 days at 25 °C to monitor the C loss through CO2 release, characterized as cumulative mineralization carbon (CMC) and mineralized carbon (MC). Our results indicate that ST, pH, SM and litter thickness were affected by forest type. Average SOC stock in MF was 20% higher than in PF (MF: 11.29 kg m−2; PF: 13.52 kg m−2). Higher CMC under PF caused more soil C lost, and CMC increased 14.5% in PF (4.67 g kg−1 soil) compared to MF (4.04 g kg−1 soil) plots over the two-month incubation period. SOC stock was significantly positively correlated with SM (p < 0.001, R2 = 0.43), DOC (p < 0.001, R2 = 0.47) and CMC (p < 0.001, R2 = 0.33), and significantly negatively correlated with pH (p < 0.001, R2 = −0.37) and MC (p < 0.001, R2 = −0.32). SOC stock and litter thickness may h…
format: application/pdf
format: text/html
creator: Zhenzhen Hao
creator: Zhanjun Quan
creator: Yu Han
creator: Chen Lv
creator: Xiang Zhao
creator: Wenjie Jing
creator: Linghui Zhu
creator: Junyong Ma
subject: Plant Science
subject: Soil Science
subject: Climate Change Biology
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.13542
publisher: PeerJ Inc.
rights: © 2022 Hao et al.
abstract: Forest soil carbon (C) sequestration has an important effect on global C dynamics and is regulated by various environmental factors. Mixed and pure plantations are common afforestation choices in north China, but how forest type and environmental factors interact to affect soil C stock remains unclear. We hypothesize that forest type changes soil physicochemical properties and surface biological factors, and further contributes to soil active C components, which together affect soil C sequestration capacity and C dynamic processes. Three 46-year-old 25 m × 25 m pure Pinus tabulaeformis forests (PF) and three 47-year-old 25 m × 25 m mixed coniferous-broadleaf (Pinus tabulaeformis-Quercus liaotungensis) forests (MF) were selected as the two treatments and sampled in August 2016. In 2017, soil temperature (ST) at 10 cm were measured every 30 min for the entire vegetation season. Across 0–50 cm (five soil layers, 10 cm per layer), we also measured C components and environmental factors which may affect soil C sequestration, including soil organic carbon (SOC), soil total nitrogen (STN), dissolved organic carbon (DOC), microbial biomass carbon (MBC), soil moisture (SM) and soil pH. We then incubated samples for 56 days at 25 °C to monitor the C loss through CO2 release, characterized as cumulative mineralization carbon (CMC) and mineralized carbon (MC). Our results indicate that ST, pH, SM and litter thickness were affected by forest type. Average SOC stock in MF was 20% higher than in PF (MF: 11.29 kg m−2; PF: 13.52 kg m−2). Higher CMC under PF caused more soil C lost, and CMC increased 14.5% in PF (4.67 g kg−1 soil) compared to MF (4.04 g kg−1 soil) plots over the two-month incubation period. SOC stock was significantly positively correlated with SM (p < 0.001, R2 = 0.43), DOC (p < 0.001, R2 = 0.47) and CMC (p < 0.001, R2 = 0.33), and significantly negatively correlated with pH (p < 0.001, R2 = −0.37) and MC (p < 0.001, R2 = −0.32). SOC stock and litter thickness may h…
bibliographic citation: Hao et al. (2022) Soil mineralized carbon drives more carbon stock in coniferous-broadleaf mixed plantations compared to pure plantations. PeerJ 10:e13542 https://doi.org/10.7717/peerj.13542
date submitted: 2021-03-19
date accepted: 2022-05-15
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Zhenzhen
author list: Agent
  family name: Quan
  given name: Zhanjun
author list: Agent
  family name: Han
  given name: Yu
author list: Agent
  family name: Lv
  given name: Chen
author list: Agent
  family name: Zhao
  given name: Xiang
author list: Agent
  family name: Jing
  given name: Wenjie
author list: Agent
  family name: Zhu
  given name: Linghui
author list: Agent
  family name: Ma
  given name: Junyong
doi: 10.7717/peerj.13542
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Hao et al.
attribution name: Hao et al.

A comprehensive drought monitoring method integrating multi-source data
type: item
type: AcademicArticle
description: Droughts are the most expensive natural disasters on the planet. As a result of climate change and human activities, the incidence and impact of drought have grown in China. Timely and effective monitoring of drought is crucial for water resource management, drought mitigation, and national food security. In this study, we constructed a comprehensive drought index (YCDI) suitable for the Yellow River Basin using principal component analysis and the entropy weight-AHP method, which integrated a standardized precipitation evapotranspiration index (SPEI), self-calibrating Palmer drought severity index (scPDSI), vegetation condition index (VCI), and standardized water storage index (SWSI). SWSI is calculated by the terrestrial water storage anomaly (TWSA), which can more comprehensively reflect the impact of surface water resources on drought (as compared with soil moisture-based indexes). The study results showed that: (1) compared with single drought index, YCDI has stronger ability to monitor drought process. In terms of time scale and drought degree, the monitoring results based on YCDI were similar with data presented in the China Flood and Drought Bulletin and Meteorological Drought Yearbook, reaching ~87% and ~69%, respectively. The correlation between drought intensity and crop harvest area was 0.56. (2) By the combined analysis of the Mann-Kendall test and Moving T test, it was found that the abrupt change of YCDI index at the time of 2009, mainly due to the precipitation in 2009 reached the lowest value in the past 30 years in northern China and extreme high temperature weather. (3) The YCDI of Henan and Shandong provinces in the middle and lower reaches of the basin decreased more significantly, with the maximum value reaching 0.097/yr, while the index in the upper reaches showed an increasing trend with the maximum rate of 0.096/yr. (4) The frequency of mild drought, moderate drought, severe drought and extreme drought in the Yellow River basin during the st…
format: application/pdf
format: text/html
creator: Xiaoliang Shi
creator: Hao Ding
creator: Mengyue Wu
creator: Mengqi Shi
creator: Fei Chen
creator: Yi Li
creator: Yuanqi Yang
subject: Ecohydrology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13560
publisher: PeerJ Inc.
rights: © 2022 Shi et al.
abstract: Droughts are the most expensive natural disasters on the planet. As a result of climate change and human activities, the incidence and impact of drought have grown in China. Timely and effective monitoring of drought is crucial for water resource management, drought mitigation, and national food security. In this study, we constructed a comprehensive drought index (YCDI) suitable for the Yellow River Basin using principal component analysis and the entropy weight-AHP method, which integrated a standardized precipitation evapotranspiration index (SPEI), self-calibrating Palmer drought severity index (scPDSI), vegetation condition index (VCI), and standardized water storage index (SWSI). SWSI is calculated by the terrestrial water storage anomaly (TWSA), which can more comprehensively reflect the impact of surface water resources on drought (as compared with soil moisture-based indexes). The study results showed that: (1) compared with single drought index, YCDI has stronger ability to monitor drought process. In terms of time scale and drought degree, the monitoring results based on YCDI were similar with data presented in the China Flood and Drought Bulletin and Meteorological Drought Yearbook, reaching ~87% and ~69%, respectively. The correlation between drought intensity and crop harvest area was 0.56. (2) By the combined analysis of the Mann-Kendall test and Moving T test, it was found that the abrupt change of YCDI index at the time of 2009, mainly due to the precipitation in 2009 reached the lowest value in the past 30 years in northern China and extreme high temperature weather. (3) The YCDI of Henan and Shandong provinces in the middle and lower reaches of the basin decreased more significantly, with the maximum value reaching 0.097/yr, while the index in the upper reaches showed an increasing trend with the maximum rate of 0.096/yr. (4) The frequency of mild drought, moderate drought, severe drought and extreme drought in the Yellow River basin during the st…
bibliographic citation: Shi et al. (2022) A comprehensive drought monitoring method integrating multi-source data. PeerJ 10:e13560 https://doi.org/10.7717/peerj.13560
date submitted: 2022-03-10
date accepted: 2022-05-19
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Xiaoliang
author list: Agent
  family name: Ding
  given name: Hao
author list: Agent
  family name: Wu
  given name: Mengyue
author list: Agent
  family name: Shi
  given name: Mengqi
author list: Agent
  family name: Chen
  given name: Fei
author list: Agent
  family name: Li
  given name: Yi
author list: Agent
  family name: Yang
  given name: Yuanqi
doi: 10.7717/peerj.13560
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Shi et al.
attribution name: Shi et al.

Telomere-to-telomere genome assembly of Phaeodactylum tricornutum
type: item
type: AcademicArticle
description: Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomere genome for Phaeodactylum tricornutum. We developed a graph-based approach to extract all unique telomeres, and used this information to manually correct assembly errors. In total, we found 25 nuclear chromosomes that comprise all previously assembled fragments, in addition to the chloroplast and mitochondrial genomes. We found that chromosome 19 has filtered long-read coverage and a quality estimate that suggests significantly less haplotype sequence variation than the other chromosomes. This work improves upon the previous genome assembly and provides new opportunities for genetic engineering of this species, including creating designer synthetic chromosomes.
format: application/pdf
format: text/html
creator: Daniel J. Giguere
creator: Alexander T. Bahcheli
creator: Samuel S. Slattery
creator: Rushali R. Patel
creator: Tyler S. Browne
creator: Martin Flatley
creator: Bogumil J. Karas
creator: David R. Edgell
creator: Gregory B. Gloor
subject: Bioinformatics
subject: Genomics
subject: Marine Biology
subject: Plant Science
subject: Synthetic Biology
description: doi:10.7717/peerj.13607
publisher: PeerJ Inc.
rights: © 2022 Giguere et al.
abstract: Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomere genome for Phaeodactylum tricornutum. We developed a graph-based approach to extract all unique telomeres, and used this information to manually correct assembly errors. In total, we found 25 nuclear chromosomes that comprise all previously assembled fragments, in addition to the chloroplast and mitochondrial genomes. We found that chromosome 19 has filtered long-read coverage and a quality estimate that suggests significantly less haplotype sequence variation than the other chromosomes. This work improves upon the previous genome assembly and provides new opportunities for genetic engineering of this species, including creating designer synthetic chromosomes.
bibliographic citation: Giguere et al. (2022) Telomere-to-telomere genome assembly of Phaeodactylum tricornutum. PeerJ 10:e13607 https://doi.org/10.7717/peerj.13607
date submitted: 2021-05-11
date accepted: 2022-05-27
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giguere
  given name: Daniel J.
author list: Agent
  family name: Bahcheli
  given name: Alexander T.
author list: Agent
  family name: Slattery
  given name: Samuel S.
author list: Agent
  family name: Patel
  given name: Rushali R.
author list: Agent
  family name: Browne
  given name: Tyler S.
author list: Agent
  family name: Flatley
  given name: Martin
author list: Agent
  family name: Karas
  given name: Bogumil J.
author list: Agent
  family name: Edgell
  given name: David R.
author list: Agent
  family name: Gloor
  given name: Gregory B.
doi: 10.7717/peerj.13607
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: ©2022 Giguere et al.
attribution name: Giguere et al.

Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity
type: item
type: AcademicArticle
description: Background Interleukin-18 (IL-18) is prone to form multimers resulting in inactive aggregates, making this cytokine unstable for clinical use. Therefore, mutations have been introduced into recombinant IL-18 to overcome this issue. Methods To prevent the formation of disulfide bonds between the IL-18 molecules, multiple mutations targeting surface cysteines (C38, C68, C76, and C127) were introduced into our previously modified human IL-18 double mutant E6K+T63A (IL-18 DM) by direct gene synthesis. The open reading frames of IL-18 wild-type (WT), IL-18 DM, and IL-18 multiple mutant E6K+T63A+C38S+C68S+C76S+C127S (IL-18 DM1234) were inserted in the pET28a expression vector and transformed into Escherichia coli Rosetta2 (DE3) pLysS cells for protein production. The inclusion bodies of WT and mutated IL-18 were extracted by sonication and refolded by stepwise dialysis using 8 M urea as the starting concentration. The refolded IL-18 proteins were tested for aggregation using the ProteoStat protein aggregation assay. Their activity was also investigated by treating NK-92MI cells with each IL-18 at concentrations of 75, 150, and 300 ng/ml with 0.5 ng/ml of human IL-12 and interferon-gamma (IFN-γ) levels in the supernatant were evaluated using ELISA. The structure of modified IL-18 was visualized using molecular dynamics (MD) simulations. Results IL-18 DM1234 exhibited the lowest aggregation signal, approximately 1.79- and 1.63-fold less than that of the WT and IL-18 DM proteins. Additionally, the IFN-γ inducing activity of IL-18 DM1234 was about 10 and 2.8 times higher than that of the WT and IL-18 DM, respectively. MD simulations revealed that binding site I of IL-18 DM1234 was altered mainly due to surface cysteine replacement with serine (C-to-S substitution). This is the first report showing that C-to-S substitutions in IL-18 improved its activity and stability, suggesting the use of this modified IL-18 for medical purposes in the future.
format: application/pdf
format: text/html
creator: Jirakrit Saetang
creator: Niran Roongsawang
creator: Surasak Sangkhathat
creator: Supayang Piyawan Voravuthikunchai
creator: Natnaree Sangkaew
creator: Napat Prompat
creator: Teerapol Srichana
creator: Varomyalin Tipmanee
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Translational Medicine
description: doi:10.7717/peerj.13626
publisher: PeerJ Inc.
rights: © 2022 Saetang et al.
abstract: Background Interleukin-18 (IL-18) is prone to form multimers resulting in inactive aggregates, making this cytokine unstable for clinical use. Therefore, mutations have been introduced into recombinant IL-18 to overcome this issue. Methods To prevent the formation of disulfide bonds between the IL-18 molecules, multiple mutations targeting surface cysteines (C38, C68, C76, and C127) were introduced into our previously modified human IL-18 double mutant E6K+T63A (IL-18 DM) by direct gene synthesis. The open reading frames of IL-18 wild-type (WT), IL-18 DM, and IL-18 multiple mutant E6K+T63A+C38S+C68S+C76S+C127S (IL-18 DM1234) were inserted in the pET28a expression vector and transformed into Escherichia coli Rosetta2 (DE3) pLysS cells for protein production. The inclusion bodies of WT and mutated IL-18 were extracted by sonication and refolded by stepwise dialysis using 8 M urea as the starting concentration. The refolded IL-18 proteins were tested for aggregation using the ProteoStat protein aggregation assay. Their activity was also investigated by treating NK-92MI cells with each IL-18 at concentrations of 75, 150, and 300 ng/ml with 0.5 ng/ml of human IL-12 and interferon-gamma (IFN-γ) levels in the supernatant were evaluated using ELISA. The structure of modified IL-18 was visualized using molecular dynamics (MD) simulations. Results IL-18 DM1234 exhibited the lowest aggregation signal, approximately 1.79- and 1.63-fold less than that of the WT and IL-18 DM proteins. Additionally, the IFN-γ inducing activity of IL-18 DM1234 was about 10 and 2.8 times higher than that of the WT and IL-18 DM, respectively. MD simulations revealed that binding site I of IL-18 DM1234 was altered mainly due to surface cysteine replacement with serine (C-to-S substitution). This is the first report showing that C-to-S substitutions in IL-18 improved its activity and stability, suggesting the use of this modified IL-18 for medical purposes in the future.
bibliographic citation: Saetang et al. (2022) Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity. PeerJ 10:e13626 https://doi.org/10.7717/peerj.13626
date submitted: 2022-03-15
date accepted: 2022-06-02
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saetang
  given name: Jirakrit
author list: Agent
  family name: Roongsawang
  given name: Niran
author list: Agent
  family name: Sangkhathat
  given name: Surasak
author list: Agent
  family name: Voravuthikunchai
  given name: Supayang Piyawan
author list: Agent
  family name: Sangkaew
  given name: Natnaree
author list: Agent
  family name: Prompat
  given name: Napat
author list: Agent
  family name: Srichana
  given name: Teerapol
author list: Agent
  family name: Tipmanee
  given name: Varomyalin
doi: 10.7717/peerj.13626
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: ©2022 Saetang et al.
attribution name: Saetang et al.

Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2
type: item
type: AcademicArticle
description: Background The COVID-19 pandemic is still a global public health issue. Omicron, a SARS-CoV-2 B.1.1.529 variant, has raised concerns about transmission and vaccine effectiveness. Omicron currently has the greatest number of variantions. Methods To gain a better understanding of the significance of these variations and the dynamics of the interaction between the Omicron spike (S) protein and its human host factor angiotensin-converting enzyme 2 (ACE2), triplicate 500 ns molecular dynamics simulations were run using the structure of the S protein’s receptor-binding domain (RBD) in complex with ACE2. The interaction and binding energy, determined using the molecular mechanics—generalized Born surface area approach, were compared to the original SARS-CoV-2 and the B.1.617 variant. Results Though mutations K417N and G496S in the S protein RBD disrupt interactions found in the original SARS-CoV-2 complex, mutations Q493R and N501Y introduce interactions not found in the original complex. Interaction at a key viral hotspot and hydrophobic contacts at ACE2’s N-terminus were preserved, but intermolecular hydrogen bonds and polar contacts in the S-ACE2 interface were lower than in the original SARS-CoV-2 interface.
format: application/pdf
format: text/html
creator: Priya Antony
creator: Amie Jobe
creator: Ranjit Vijayan
subject: Bioinformatics
subject: Computational Biology
subject: COVID-19
description: doi:10.7717/peerj.13680
publisher: PeerJ Inc.
rights: © 2022 Antony et al.
abstract: Background The COVID-19 pandemic is still a global public health issue. Omicron, a SARS-CoV-2 B.1.1.529 variant, has raised concerns about transmission and vaccine effectiveness. Omicron currently has the greatest number of variantions. Methods To gain a better understanding of the significance of these variations and the dynamics of the interaction between the Omicron spike (S) protein and its human host factor angiotensin-converting enzyme 2 (ACE2), triplicate 500 ns molecular dynamics simulations were run using the structure of the S protein’s receptor-binding domain (RBD) in complex with ACE2. The interaction and binding energy, determined using the molecular mechanics—generalized Born surface area approach, were compared to the original SARS-CoV-2 and the B.1.617 variant. Results Though mutations K417N and G496S in the S protein RBD disrupt interactions found in the original SARS-CoV-2 complex, mutations Q493R and N501Y introduce interactions not found in the original complex. Interaction at a key viral hotspot and hydrophobic contacts at ACE2’s N-terminus were preserved, but intermolecular hydrogen bonds and polar contacts in the S-ACE2 interface were lower than in the original SARS-CoV-2 interface.
bibliographic citation: Antony et al. (2022) Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2. PeerJ 10:e13680 https://doi.org/10.7717/peerj.13680
date submitted: 2022-03-28
date accepted: 2022-06-14
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Antony
  given name: Priya
author list: Agent
  family name: Jobe
  given name: Amie
author list: Agent
  family name: Vijayan
  given name: Ranjit
doi: 10.7717/peerj.13680
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Antony et al.
attribution name: Antony et al.

The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents
type: item
type: AcademicArticle
description: Background Extensive literature revealed the relations of depression with behavioral inhibition system (BIS) and behavioral activation system (BAS) as vulnerability and with resilience separately. Besides, the concept of resilience is still broad and ambiguous. Thus, this study aimed to reveal the mediation of two aspects of resilience: trait and process, in the relations of BIS and BAS to depression among adolescents. Methods The data set used in this study was a cross-sectional survey among 965 adolescents. The obtained data from the self-reported questionnaires used in this study were as below: Depression Serf-Rating Scale for Children (DSRS-C), Behavioral Inhibition and Behavioral Activation System Scale (BIS/BASS), and Bidimensional Resilience Scale (BRS). Structural equation modeling (SEM) was conducted to verify the hypothesized relations among BIS/BAS, trait and behavior resilience, and depressive symptoms. Results The obtained indices of fit from SEM were good or sufficient (χ2 = 562.911, df = 96, p < 0.001; CFI = 0.925; NFI = 0.913; RMSEA = 0.073, 90% CI [0.067, 0.079]; SRMR = 0.066). And the modeling showed that both BIS/BAS directly and indirectly influenced to depression. The indirect effects of BIS/BAS were mediated only trait resilience except the indirect effect of BIS via behavioral resilience. Discussion Our results suggested that trait resilience played a significant mediation role in the relationships between BIS/BAS and depression. Trait but not process resilience could be considered suitable as an intervention target in line with decreasing depression.
format: application/pdf
format: text/html
creator: Akihiro Masuyama
creator: Takahiro Kubo
creator: Hiroki Shinkawa
creator: Daichi Sugawara
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.13687
publisher: PeerJ Inc.
rights: © 2022 Masuyama et al.
abstract: Background Extensive literature revealed the relations of depression with behavioral inhibition system (BIS) and behavioral activation system (BAS) as vulnerability and with resilience separately. Besides, the concept of resilience is still broad and ambiguous. Thus, this study aimed to reveal the mediation of two aspects of resilience: trait and process, in the relations of BIS and BAS to depression among adolescents. Methods The data set used in this study was a cross-sectional survey among 965 adolescents. The obtained data from the self-reported questionnaires used in this study were as below: Depression Serf-Rating Scale for Children (DSRS-C), Behavioral Inhibition and Behavioral Activation System Scale (BIS/BASS), and Bidimensional Resilience Scale (BRS). Structural equation modeling (SEM) was conducted to verify the hypothesized relations among BIS/BAS, trait and behavior resilience, and depressive symptoms. Results The obtained indices of fit from SEM were good or sufficient (χ2 = 562.911, df = 96, p < 0.001; CFI = 0.925; NFI = 0.913; RMSEA = 0.073, 90% CI [0.067, 0.079]; SRMR = 0.066). And the modeling showed that both BIS/BAS directly and indirectly influenced to depression. The indirect effects of BIS/BAS were mediated only trait resilience except the indirect effect of BIS via behavioral resilience. Discussion Our results suggested that trait resilience played a significant mediation role in the relationships between BIS/BAS and depression. Trait but not process resilience could be considered suitable as an intervention target in line with decreasing depression.
bibliographic citation: Masuyama et al. (2022) The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents. PeerJ 10:e13687 https://doi.org/10.7717/peerj.13687
date submitted: 2022-03-25
date accepted: 2022-06-15
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Masuyama
  given name: Akihiro
author list: Agent
  family name: Kubo
  given name: Takahiro
author list: Agent
  family name: Shinkawa
  given name: Hiroki
author list: Agent
  family name: Sugawara
  given name: Daichi
doi: 10.7717/peerj.13687
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Masuyama et al.
attribution name: Masuyama et al.

Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus
type: item
type: AcademicArticle
description: Background Cyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages. Methods A combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated. Results The results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus. Conclusions Leaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan).
format: application/pdf
format: text/html
creator: Zhaokui Du
creator: Weida Lin
creator: Jinxing Zhu
creator: Junmin Li
subject: Agricultural Science
subject: Biochemistry
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.13689
publisher: PeerJ Inc.
rights: © 2022 Du et al.
abstract: Background Cyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages. Methods A combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated. Results The results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus. Conclusions Leaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan).
bibliographic citation: Du et al. (2022) Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus. PeerJ 10:e13689 https://doi.org/10.7717/peerj.13689
date submitted: 2021-08-31
date accepted: 2022-06-16
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Du
  given name: Zhaokui
author list: Agent
  family name: Lin
  given name: Weida
author list: Agent
  family name: Zhu
  given name: Jinxing
author list: Agent
  family name: Li
  given name: Junmin
doi: 10.7717/peerj.13689
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Du et al.
attribution name: Du et al.

Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area
type: item
type: AcademicArticle
description: We evaluated the role of gene flow and wild-crop introgression on the structure and genetic diversity of Lima bean (Phaseolus lunatus) in the Yucatan Peninsula, an important Mesoamerican diversity area for this crop, using a genotyping-by-sequencing approach (15,168 SNP markers) and two scales. At the local scale, STRUCTURE and NGSEP analyses showed predominantly crop-to-wild introgression, but also evidence of a bidirectional gene flow in the two wild-weedy-crop complexes studied (Itzinté and Dzitnup). The ABBA-BABA tests showed a higher introgression in Itzinté (the older complex) than in Dzitnup (the younger one); at the allelic level, the wild-crop introgression in Itzinté was similar in both directions, in Dzitnup it was higher from crop-to-wild; and at the chromosomal level, introgression in Itzinté was from wild-to-crop, whereas in Dzitnup it occured in the opposite direction. Also, we found HE values slightly higher in the domesticated accessions than in the wild ones, in both complexes (Itzinté: wild = 0.31, domesticated = 0.34; Dzinup: wild = 0.27, domesticated = 0.36), but %P and π estimators were higher in the wild accessions than in the domesticated ones. At a regional scale, STRUCTURE and MIGRATE showed a low gene flow, predominantly from crop-to-wild; and STRUCTURE, Neighbor-Joining and PCoA analyses indicated the existence of two wild groups and one domesticated group, with a marked genetic structure based in the existence of domesticated MI and wild MII gene pools. Also, at the regional scale, we found a higher genetic diversity in the wild accessions than in the domesticated ones, in all estimators used (e.g., HE = 0.27 and HE = 0.17, respectively). Our results indicate that gene flow and introgression are playing an important role at the local scale, but its consequences on the structure and genetic diversity of the Lima bean are not clearly reflected at the regional scale, where diversity patterns between wild and domesticated populations could b…
format: application/pdf
format: text/html
creator: Mauricio Heredia-Pech
creator: Mariana Chávez-Pesqueira
creator: Matilde M. Ortiz-García
creator: Rubén Humberto Andueza-Noh
creator: María Isabel Chacón-Sánchez
creator: Jaime Martínez-Castillo
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13690
publisher: PeerJ Inc.
rights: © 2022 Heredia-Pech et al.
abstract: We evaluated the role of gene flow and wild-crop introgression on the structure and genetic diversity of Lima bean (Phaseolus lunatus) in the Yucatan Peninsula, an important Mesoamerican diversity area for this crop, using a genotyping-by-sequencing approach (15,168 SNP markers) and two scales. At the local scale, STRUCTURE and NGSEP analyses showed predominantly crop-to-wild introgression, but also evidence of a bidirectional gene flow in the two wild-weedy-crop complexes studied (Itzinté and Dzitnup). The ABBA-BABA tests showed a higher introgression in Itzinté (the older complex) than in Dzitnup (the younger one); at the allelic level, the wild-crop introgression in Itzinté was similar in both directions, in Dzitnup it was higher from crop-to-wild; and at the chromosomal level, introgression in Itzinté was from wild-to-crop, whereas in Dzitnup it occured in the opposite direction. Also, we found HE values slightly higher in the domesticated accessions than in the wild ones, in both complexes (Itzinté: wild = 0.31, domesticated = 0.34; Dzinup: wild = 0.27, domesticated = 0.36), but %P and π estimators were higher in the wild accessions than in the domesticated ones. At a regional scale, STRUCTURE and MIGRATE showed a low gene flow, predominantly from crop-to-wild; and STRUCTURE, Neighbor-Joining and PCoA analyses indicated the existence of two wild groups and one domesticated group, with a marked genetic structure based in the existence of domesticated MI and wild MII gene pools. Also, at the regional scale, we found a higher genetic diversity in the wild accessions than in the domesticated ones, in all estimators used (e.g., HE = 0.27 and HE = 0.17, respectively). Our results indicate that gene flow and introgression are playing an important role at the local scale, but its consequences on the structure and genetic diversity of the Lima bean are not clearly reflected at the regional scale, where diversity patterns between wild and domesticated populations could b…
bibliographic citation: Heredia-Pech et al. (2022) Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area. PeerJ 10:e13690 https://doi.org/10.7717/peerj.13690
date submitted: 2022-01-28
date accepted: 2022-06-16
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heredia-Pech
  given name: Mauricio
author list: Agent
  family name: Chávez-Pesqueira
  given name: Mariana
author list: Agent
  family name: Ortiz-García
  given name: Matilde M.
author list: Agent
  family name: Andueza-Noh
  given name: Rubén Humberto
author list: Agent
  family name: Chacón-Sánchez
  given name: María Isabel
author list: Agent
  family name: Martínez-Castillo
  given name: Jaime
doi: 10.7717/peerj.13690
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: ©2022 Heredia-Pech et al.
attribution name: Heredia-Pech et al.

Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis)
type: item
type: AcademicArticle
description: Background WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses. Results A total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT–PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways. Conclusions We conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding.
format: application/pdf
format: text/html
creator: Zhenfan Yu
creator: Dongdong Zhang
creator: Bin Zeng
creator: Xingyue Liu
creator: Jiahui Yang
creator: Wenwen Gao
creator: Xintong Ma
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13491
publisher: PeerJ Inc.
rights: © 2022 Yu et al.
abstract: Background WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses. Results A total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT–PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways. Conclusions We conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding.
bibliographic citation: Yu et al. (2022) Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis). PeerJ 10:e13491 https://doi.org/10.7717/peerj.13491
date submitted: 2022-01-31
date accepted: 2022-05-03
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Zhenfan
author list: Agent
  family name: Zhang
  given name: Dongdong
author list: Agent
  family name: Zeng
  given name: Bin
author list: Agent
  family name: Liu
  given name: Xingyue
author list: Agent
  family name: Yang
  given name: Jiahui
author list: Agent
  family name: Gao
  given name: Wenwen
author list: Agent
  family name: Ma
  given name: Xintong
doi: 10.7717/peerj.13491
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Yu et al.
attribution name: Yu et al.

Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations
type: item
type: AcademicArticle
description: Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula populations differ between the northeastern Atlantic Ocean and the Mediterranean Sea based on biological features and genetic analysis. In this study, we sample more than 3,000 teeth from 56 S. canicula specimens caught incidentally off Roscoff and Banyuls-sur-Mer. We investigate population differences based on tooth shape and form by using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils.
format: application/pdf
format: text/html
creator: Fidji Berio
creator: Yann Bayle
creator: Daniel Baum
creator: Nicolas Goudemand
creator: Mélanie Debiais-Thibaud
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.13575
publisher: PeerJ Inc.
rights: © 2022 Berio et al.
abstract: Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula populations differ between the northeastern Atlantic Ocean and the Mediterranean Sea based on biological features and genetic analysis. In this study, we sample more than 3,000 teeth from 56 S. canicula specimens caught incidentally off Roscoff and Banyuls-sur-Mer. We investigate population differences based on tooth shape and form by using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils.
bibliographic citation: Berio et al. (2022) Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations. PeerJ 10:e13575 https://doi.org/10.7717/peerj.13575
date submitted: 2022-01-18
date accepted: 2022-05-22
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Berio
  given name: Fidji
author list: Agent
  family name: Bayle
  given name: Yann
author list: Agent
  family name: Baum
  given name: Daniel
author list: Agent
  family name: Goudemand
  given name: Nicolas
author list: Agent
  family name: Debiais-Thibaud
  given name: Mélanie
doi: 10.7717/peerj.13575
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Berio et al.
attribution name: Berio et al.

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