PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Dominance of Bacillus species in the wheat (Triticum aestivum L.) rhizosphere and their plant growth promoting potential under salt stress conditions
items: Construction of an anthropometric discriminant model for identification of elite swimmers: an adaptive lasso approach
items: Integrated omics analysis reveals the immunologic characteristics of cystic Peyer’s patches in the cecum of Bactrian camels
items: A more reliable species richness estimator based on the Gamma–Poisson model
items: The biomarkers discovery of hyperuricemia and gout: proteomics and metabolomics
items: On the origin of mitochondria: a multilayer network approach
items: Stem transcriptome screen for selection in wild and cultivated pitahaya (Selenicereus undatus): an epiphytic cactus with edible fruit
items: The role of subjective significance, valence and arousal in the explicit processing of emotion-laden words
items: No effect of attentional modulation by spatial cueing in a masked numerical priming paradigm using continuous flash suppression (CFS)
items: A novel fatty acid metabolism-related gene prognostic signature and candidate drugs for patients with hepatocellular carcinoma

Dominance of Bacillus species in the wheat (Triticum aestivum L.) rhizosphere and their plant growth promoting potential under salt stress conditions
type: item
type: AcademicArticle
description: Wheat (Triticum aestivum L.) is a major source of calorific intake in its various forms and is considered one of the most important staple foods. Improved wheat productivity can contribute substantially to addressing food security in the coming decades. Soil salinity is the most serious limiting factor in crop production and fertilizer use efficiency. In this study, 11 bacteria were isolated from wheat rhizosphere and examined for salt tolerance ability. WGT1, WGT2, WGT3, WGT6, WGT8, and WGT11 were able to tolerate NaCl salinity up to 4%. Bacterial isolates were characterized in vitro for plant growth-promoting properties including indole-3-acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, zinc solubilization, biofilm formation, and cellulase-pectinase production. Six isolates, WGT1, WGT3, WGT4, WGT6, WGT8, and WGT9 showed IAA production ability ranging from 0.7–6 µg m/L. WGT8 displayed the highest IAA production. Five isolates, WGT1, WGT2, WGT5, WGT10, and WGT11, demonstrated phosphate solubilization ranging from 1.4–12.3 µg m/L. WGT2 showed the highest phosphate solubilization. Nitrogen fixation was shown by only two isolates, WGT1 and WGT8. Zinc solubilization was shown by WGT1 and WGT11 on minimal media. All isolates showed biofilm formation ability, where WGT4 exhibited maximum potential. Cellulase production ability was noticed in WGT1, WGT2, WGT4, and WGT5, while pectinase production was observed in WGT2 and WGT3. Phylogenetic identification of potential bacteria isolates confirmed their close relationship with various species of the genus Bacillus. WGT1, WGT2, and WGT3 showed the highest similarity with B. cereus, WGT6 with B. tianshenii, WGT8 with B. subtilis, and WGT11 with B. thuringiensis. Biofertilizer characteristics of salt-tolerant potential rhizospheric bacteria were evaluated by inoculating wheat plants under controlled conditions and field experiments. B. cereus WGT1 and B. thuringiensis WGT11 displayed the maximum potenti…
format: application/pdf
format: text/html
creator: Syeda Tahseen Zahra
creator: Mohsin Tariq
creator: Muhammad Abdullah
creator: Farrukh Azeem
creator: Muhammad Arslan Ashraf
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.14621
publisher: PeerJ Inc.
rights: © 2023 Zahra et al.
abstract: Wheat (Triticum aestivum L.) is a major source of calorific intake in its various forms and is considered one of the most important staple foods. Improved wheat productivity can contribute substantially to addressing food security in the coming decades. Soil salinity is the most serious limiting factor in crop production and fertilizer use efficiency. In this study, 11 bacteria were isolated from wheat rhizosphere and examined for salt tolerance ability. WGT1, WGT2, WGT3, WGT6, WGT8, and WGT11 were able to tolerate NaCl salinity up to 4%. Bacterial isolates were characterized in vitro for plant growth-promoting properties including indole-3-acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, zinc solubilization, biofilm formation, and cellulase-pectinase production. Six isolates, WGT1, WGT3, WGT4, WGT6, WGT8, and WGT9 showed IAA production ability ranging from 0.7–6 µg m/L. WGT8 displayed the highest IAA production. Five isolates, WGT1, WGT2, WGT5, WGT10, and WGT11, demonstrated phosphate solubilization ranging from 1.4–12.3 µg m/L. WGT2 showed the highest phosphate solubilization. Nitrogen fixation was shown by only two isolates, WGT1 and WGT8. Zinc solubilization was shown by WGT1 and WGT11 on minimal media. All isolates showed biofilm formation ability, where WGT4 exhibited maximum potential. Cellulase production ability was noticed in WGT1, WGT2, WGT4, and WGT5, while pectinase production was observed in WGT2 and WGT3. Phylogenetic identification of potential bacteria isolates confirmed their close relationship with various species of the genus Bacillus. WGT1, WGT2, and WGT3 showed the highest similarity with B. cereus, WGT6 with B. tianshenii, WGT8 with B. subtilis, and WGT11 with B. thuringiensis. Biofertilizer characteristics of salt-tolerant potential rhizospheric bacteria were evaluated by inoculating wheat plants under controlled conditions and field experiments. B. cereus WGT1 and B. thuringiensis WGT11 displayed the maximum potenti…
bibliographic citation: Zahra et al. (2023) Dominance of Bacillus species in the wheat (Triticum aestivum L.) rhizosphere and their plant growth promoting potential under salt stress conditions. PeerJ 11:e14621 https://doi.org/10.7717/peerj.14621
date submitted: 2022-09-19
date accepted: 2022-12-01
issued: 2023-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zahra
  given name: Syeda Tahseen
author list: Agent
  family name: Tariq
  given name: Mohsin
author list: Agent
  family name: Abdullah
  given name: Muhammad
author list: Agent
  family name: Azeem
  given name: Farrukh
author list: Agent
  family name: Ashraf
  given name: Muhammad Arslan
doi: 10.7717/peerj.14621
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-09
copyright: © 2023 Zahra et al.
attribution name: Zahra et al.

Construction of an anthropometric discriminant model for identification of elite swimmers: an adaptive lasso approach
type: item
type: AcademicArticle
description: Background Anthropometric characteristics are important factors that affect swimming performance. The aim of this study is to build a discriminant model using anthropometric factors to identify elite short-to-medium-distance freestyle swimmers through an adaptive Lasso approach. Methods The study recruited 254 swimmers (145 males and 109 females) who were divided them into elite (aged 17.9 ± 2.2 years, FINA points 793.8 ± 73.8) and non-elite (aged 17.1 ± 1.3 years, FINA points 560.6 ± 78.7) groups. Data for 73 variables were obtained, including basic information, anthropometric and derivative indicators. After filtering out highly correlated variables, 24 candidate variables were retained to be used in adaptive Lasso to select variables for prediction of elite swimmers. Deviance and area under the curve (AUC) were applied to assess the goodness of fit and prediction accuracy of the model, respectively. Results The adaptive Lasso selected 12 variables using the whole sample, with an AUC being 0.926 (95% CI [0.895–0.956]; P = 2.42 × 10−29). In stratified analysis by gender, nine variables were selected for male swimmers with an AUC of 0.921 (95% CI [0.880–0.963]; P = 8.82 × 10−17), and eight variables were for female swimmers with an AUC of 0.941 (95% CI [0.898–0.984]; P = 7.67 × 10−15). Conclusion The adaptive Lasso showed satisfactory performance in selecting anthropometric characteristics to identify elite swimmers. Additional studies with longitudinal data or data from other ethnicities are needed to validate our findings.
format: application/pdf
format: text/html
creator: Qile Pan
creator: Rongxin Zhu
creator: Jun Qiu
creator: Guang Cai
subject: Anatomy and Physiology
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.14635
publisher: PeerJ Inc.
rights: © 2023 Pan et al.
abstract: Background Anthropometric characteristics are important factors that affect swimming performance. The aim of this study is to build a discriminant model using anthropometric factors to identify elite short-to-medium-distance freestyle swimmers through an adaptive Lasso approach. Methods The study recruited 254 swimmers (145 males and 109 females) who were divided them into elite (aged 17.9 ± 2.2 years, FINA points 793.8 ± 73.8) and non-elite (aged 17.1 ± 1.3 years, FINA points 560.6 ± 78.7) groups. Data for 73 variables were obtained, including basic information, anthropometric and derivative indicators. After filtering out highly correlated variables, 24 candidate variables were retained to be used in adaptive Lasso to select variables for prediction of elite swimmers. Deviance and area under the curve (AUC) were applied to assess the goodness of fit and prediction accuracy of the model, respectively. Results The adaptive Lasso selected 12 variables using the whole sample, with an AUC being 0.926 (95% CI [0.895–0.956]; P = 2.42 × 10−29). In stratified analysis by gender, nine variables were selected for male swimmers with an AUC of 0.921 (95% CI [0.880–0.963]; P = 8.82 × 10−17), and eight variables were for female swimmers with an AUC of 0.941 (95% CI [0.898–0.984]; P = 7.67 × 10−15). Conclusion The adaptive Lasso showed satisfactory performance in selecting anthropometric characteristics to identify elite swimmers. Additional studies with longitudinal data or data from other ethnicities are needed to validate our findings.
bibliographic citation: Pan et al. (2023) Construction of an anthropometric discriminant model for identification of elite swimmers: an adaptive lasso approach. PeerJ 11:e14635 https://doi.org/10.7717/peerj.14635
date submitted: 2022-07-25
date accepted: 2022-12-05
issued: 2023-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Qile
author list: Agent
  family name: Zhu
  given name: Rongxin
author list: Agent
  family name: Qiu
  given name: Jun
author list: Agent
  family name: Cai
  given name: Guang
doi: 10.7717/peerj.14635
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-09
copyright: © 2023 Pan et al.
attribution name: Pan et al.

Integrated omics analysis reveals the immunologic characteristics of cystic Peyer’s patches in the cecum of Bactrian camels
type: item
type: AcademicArticle
description: Bactrian camels have specific mucosa-associated lymphoid tissue (MALT) throughout the large intestine, with species-unique cystic Peyer’s patches (PPS) as the main type of tissue. However, detailed information about the molecular characteristics of PPS remains unclear. This study applied a transcriptomic analysis, untargeted metabolomics, and 16S rDNA sequencing to compare the significant differences between PPS and the adjacent normal intestine tissues (NPPS) during the healthy stage of three young Bactrian camels. The results showed that samples from PPS could be easily differentiated from the NPPS samples based on gene expression profile, metabolites, and microbial composition, separately indicated using dimension reduction methods. A total of 7,568 up-regulated and 1,266 down-regulated differentially expressed genes (DEGs) were detected, and an enrichment analysis found 994 DEGs that participated in immune-related functions, and a co-occurance network analysis identified nine hub genes (BTK, P2RX7, Pax5, DSG1, PTPN2, DOCK11, TBX21, IL10, and HLA-DOB) during multiple immunologic processes. Further, PPS and NPPS both had a similar pattern of most compounds among all profiles of metabolites, and only 113 differentially expressed metabolites (DEMs) were identified, with 101 of these being down-regulated. Deoxycholic acid (DCA; VIP = 37.96, log2FC = −2.97, P = 0), cholic acid (CA; VIP = 13.10, log2FC = −2.10, P = 0.01), and lithocholic acid (LCA; VIP = 12.94, log2FC = −1.63, P = 0.01) were the highest contributors to the significant dissimilarities between groups. PPS had significantly lower species richness (Chao1), while Firmicutes (35.92% ± 19.39%), Bacteroidetes (31.73% ± 6.24%), and Proteobacteria (13.96% ± 16.21%) were the main phyla across all samples. The LEfSe analysis showed that Lysinibacillus, Rikenellaceae_RC9_gut_group, Candidatus_Stoquefichus, Mailhella, Alistipes, and Ruminococcaceae_UCG_005 were biomarkers of the NPPS group, while Escherichia_Shigell…
format: application/pdf
format: text/html
creator: Xiao shan Wang
creator: Pei xuan Li
creator: Bao shan Wang
creator: Wang dong Zhang
creator: Wen hui Wang
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.14647
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Bactrian camels have specific mucosa-associated lymphoid tissue (MALT) throughout the large intestine, with species-unique cystic Peyer’s patches (PPS) as the main type of tissue. However, detailed information about the molecular characteristics of PPS remains unclear. This study applied a transcriptomic analysis, untargeted metabolomics, and 16S rDNA sequencing to compare the significant differences between PPS and the adjacent normal intestine tissues (NPPS) during the healthy stage of three young Bactrian camels. The results showed that samples from PPS could be easily differentiated from the NPPS samples based on gene expression profile, metabolites, and microbial composition, separately indicated using dimension reduction methods. A total of 7,568 up-regulated and 1,266 down-regulated differentially expressed genes (DEGs) were detected, and an enrichment analysis found 994 DEGs that participated in immune-related functions, and a co-occurance network analysis identified nine hub genes (BTK, P2RX7, Pax5, DSG1, PTPN2, DOCK11, TBX21, IL10, and HLA-DOB) during multiple immunologic processes. Further, PPS and NPPS both had a similar pattern of most compounds among all profiles of metabolites, and only 113 differentially expressed metabolites (DEMs) were identified, with 101 of these being down-regulated. Deoxycholic acid (DCA; VIP = 37.96, log2FC = −2.97, P = 0), cholic acid (CA; VIP = 13.10, log2FC = −2.10, P = 0.01), and lithocholic acid (LCA; VIP = 12.94, log2FC = −1.63, P = 0.01) were the highest contributors to the significant dissimilarities between groups. PPS had significantly lower species richness (Chao1), while Firmicutes (35.92% ± 19.39%), Bacteroidetes (31.73% ± 6.24%), and Proteobacteria (13.96% ± 16.21%) were the main phyla across all samples. The LEfSe analysis showed that Lysinibacillus, Rikenellaceae_RC9_gut_group, Candidatus_Stoquefichus, Mailhella, Alistipes, and Ruminococcaceae_UCG_005 were biomarkers of the NPPS group, while Escherichia_Shigell…
bibliographic citation: Wang et al. (2023) Integrated omics analysis reveals the immunologic characteristics of cystic Peyer’s patches in the cecum of Bactrian camels. PeerJ 11:e14647 https://doi.org/10.7717/peerj.14647
date submitted: 2022-08-03
date accepted: 2022-12-06
issued: 2023-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiao shan
author list: Agent
  family name: Li
  given name: Pei xuan
author list: Agent
  family name: Wang
  given name: Bao shan
author list: Agent
  family name: Zhang
  given name: Wang dong
author list: Agent
  family name: Wang
  given name: Wen hui
doi: 10.7717/peerj.14647
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-09
copyright: ©2022 Wang et al.
attribution name: Wang et al.

A more reliable species richness estimator based on the Gamma–Poisson model
type: item
type: AcademicArticle
description: Background Accurately estimating the true richness of a target community is still a statistical challenge, particularly in highly diverse communities. Due to sampling limitations or limited resources, undetected species are present in many surveys and observed richness is an underestimate of true richness. In the literature, methods for estimating the undetected richness of a sample are generally divided into two categories: parametric and nonparametric estimators. Imposing no assumptions on species detection rates, nonparametric methods demonstrate robust statistical performance and are widely used in ecological studies. However, nonparametric estimators may seriously underestimate richness when species composition has a high degree of heterogeneity. Parametric approaches, which reduce the number of parameters by assuming that species-specific detection probabilities follow a given statistical distribution, use traditional statistical inference to calculate species richness estimates. When species detection rates meet the model assumption, the parametric approach could supply a nearly unbiased estimator. However, the infeasibility and inefficiency of solving maximum likelihood functions limit the application of parametric methods in ecological studies when the model assumption is violated, or the collected data is sparse. Method To overcome these estimating challenges associated with parametric methods, an estimator employing the moment estimation method instead of the maximum likelihood estimation method is proposed to estimate parameters based on a Gamma-Poisson mixture model. Drawing on the concept of the Good-Turing frequency formula, the proposed estimator only uses the number of singletons, doubletons, and tripletons in a sample for undetected richness estimation. Results The statistical behavior of the new estimator was evaluated by using real and simulated data sets from various species abundance models. Simulation results indicated that the new estimator r…
format: application/pdf
format: text/html
creator: Chun-Huo Chiu
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Statistics
description: doi:10.7717/peerj.14540
publisher: PeerJ Inc.
rights: © 2023 Chiu
abstract: Background Accurately estimating the true richness of a target community is still a statistical challenge, particularly in highly diverse communities. Due to sampling limitations or limited resources, undetected species are present in many surveys and observed richness is an underestimate of true richness. In the literature, methods for estimating the undetected richness of a sample are generally divided into two categories: parametric and nonparametric estimators. Imposing no assumptions on species detection rates, nonparametric methods demonstrate robust statistical performance and are widely used in ecological studies. However, nonparametric estimators may seriously underestimate richness when species composition has a high degree of heterogeneity. Parametric approaches, which reduce the number of parameters by assuming that species-specific detection probabilities follow a given statistical distribution, use traditional statistical inference to calculate species richness estimates. When species detection rates meet the model assumption, the parametric approach could supply a nearly unbiased estimator. However, the infeasibility and inefficiency of solving maximum likelihood functions limit the application of parametric methods in ecological studies when the model assumption is violated, or the collected data is sparse. Method To overcome these estimating challenges associated with parametric methods, an estimator employing the moment estimation method instead of the maximum likelihood estimation method is proposed to estimate parameters based on a Gamma-Poisson mixture model. Drawing on the concept of the Good-Turing frequency formula, the proposed estimator only uses the number of singletons, doubletons, and tripletons in a sample for undetected richness estimation. Results The statistical behavior of the new estimator was evaluated by using real and simulated data sets from various species abundance models. Simulation results indicated that the new estimator r…
bibliographic citation: Chiu (2023) A more reliable species richness estimator based on the Gamma–Poisson model. PeerJ 11:e14540 https://doi.org/10.7717/peerj.14540
date submitted: 2021-06-22
date accepted: 2022-11-17
issued: 2023-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chiu
  given name: Chun-Huo
doi: 10.7717/peerj.14540
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-06
copyright: ©2023 Chiu
attribution name: Chiu

The biomarkers discovery of hyperuricemia and gout: proteomics and metabolomics
type: item
type: AcademicArticle
description: Background Hyperuricemia and gout are a group of disorders of purine metabolism. In recent years, the incidence of hyperuricemia and gout has been increasing, which is a severe threat to people’s health. Several studies on hyperuricemia and gout in proteomics and metabolomics have been conducted recently. Some literature has identified biomarkers that distinguish asymptomatic hyperuricemia from acute gout or remission of gout. We summarize the physiological processes in which these biomarkers may be involved and their role in disease progression. Methodology We used professional databases including PubMed, Web of Science to conduct the literature review. This review addresses the current landscape of hyperuricemia and gout biomarkers with a focus on proteomics and metabolomics. Results Proteomic methods are used to identify differentially expressed proteins to find specific biomarkers. These findings may be suggestive for the diagnosis and treatment of hyperuricemia and gout to explore the disease pathogenesis. The identified biomarkers may be mediators of the link between hyperuricemia, gout and kidney disease, metabolic syndrome, diabetes and hypertriglyceridemia. Metabolomics reveals the main influential pathways through small molecule metabolites, such as amino acid metabolism, lipid metabolism, or other characteristic metabolic pathways. These studies have contributed to the discovery of Chinese medicine. Some traditional Chinese medicine compounds can improve the metabolic disorders of the disease. Conclusions We suggest some possible relationships of potential biomarkers with inflammatory episodes, complement activation, and metabolic pathways. These biomarkers are able to distinguish between different stages of disease development. However, there are relatively few proteomic as well as metabolomic studies on hyperuricemia and gout, and some experiments are only primary screening tests, which need further in-depth study.
format: application/pdf
format: text/html
creator: Xinghong Wu
creator: Chongge You
subject: Molecular Biology
subject: Rheumatology
description: doi:10.7717/peerj.14554
publisher: PeerJ Inc.
rights: © 2023 Wu and You
abstract: Background Hyperuricemia and gout are a group of disorders of purine metabolism. In recent years, the incidence of hyperuricemia and gout has been increasing, which is a severe threat to people’s health. Several studies on hyperuricemia and gout in proteomics and metabolomics have been conducted recently. Some literature has identified biomarkers that distinguish asymptomatic hyperuricemia from acute gout or remission of gout. We summarize the physiological processes in which these biomarkers may be involved and their role in disease progression. Methodology We used professional databases including PubMed, Web of Science to conduct the literature review. This review addresses the current landscape of hyperuricemia and gout biomarkers with a focus on proteomics and metabolomics. Results Proteomic methods are used to identify differentially expressed proteins to find specific biomarkers. These findings may be suggestive for the diagnosis and treatment of hyperuricemia and gout to explore the disease pathogenesis. The identified biomarkers may be mediators of the link between hyperuricemia, gout and kidney disease, metabolic syndrome, diabetes and hypertriglyceridemia. Metabolomics reveals the main influential pathways through small molecule metabolites, such as amino acid metabolism, lipid metabolism, or other characteristic metabolic pathways. These studies have contributed to the discovery of Chinese medicine. Some traditional Chinese medicine compounds can improve the metabolic disorders of the disease. Conclusions We suggest some possible relationships of potential biomarkers with inflammatory episodes, complement activation, and metabolic pathways. These biomarkers are able to distinguish between different stages of disease development. However, there are relatively few proteomic as well as metabolomic studies on hyperuricemia and gout, and some experiments are only primary screening tests, which need further in-depth study.
bibliographic citation: Wu et al. (2023) The biomarkers discovery of hyperuricemia and gout: proteomics and metabolomics. PeerJ 11:e14554 https://doi.org/10.7717/peerj.14554
date submitted: 2022-08-15
date accepted: 2022-11-21
issued: 2023-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Xinghong
author list: Agent
  family name: You
  given name: Chongge
doi: 10.7717/peerj.14554
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-06
copyright: ©2023 Wu and You
attribution name: Wu and You

On the origin of mitochondria: a multilayer network approach
type: item
type: AcademicArticle
description: Backgound The endosymbiotic theory is widely accepted to explain the origin of mitochondria from a bacterial ancestor. While ample evidence supports the intimate connection of Alphaproteobacteria to the mitochondrial ancestor, pinpointing its closest relative within sampled Alphaproteobacteria is still an open evolutionary debate. Many different phylogenetic methods and approaches have been used to answer this challenging question, further compounded by the heterogeneity of sampled taxa, varying evolutionary rates of mitochondrial proteins, and the inherent biases in each method, all factors that can produce phylogenetic artifacts. By harnessing the simplicity and interpretability of protein similarity networks, herein we re-evaluated the origin of mitochondria within an enhanced multilayer framework, which is an extension and improvement of a previously developed method. Methods We used a dataset of eight proteins found in mitochondria (N = 6 organisms) and bacteria (N = 80 organisms). The sequences were aligned and resulting identity matrices were combined to generate an eight-layer multiplex network. Each layer corresponded to a protein network, where nodes represented organisms and edges were placed following mutual sequence identity. The Multi-Newman-Girvan algorithm was applied to evaluate community structure, and bifurcation events linked to network partition allowed to trace patterns of divergence between studied taxa. Results In our network-based analysis, we first examined the topology of the 8-layer multiplex when mitochondrial sequences disconnected from the main alphaproteobacterial cluster. The resulting topology lent firm support toward an Alphaproteobacteria-sister placement for mitochondria, reinforcing the hypothesis that mitochondria diverged from the common ancestor of all Alphaproteobacteria. Additionally, we observed that the divergence of Rickettsiales was an early event in the evolutionary history of alphaproteobacterial clades. Conclusion By…
format: application/pdf
format: text/html
creator: Dérick Gabriel F. Borges
creator: Daniel S. Carvalho
creator: Gilberto C. Bomfim
creator: Pablo Ivan P. Ramos
creator: Jerzy Brzozowski
creator: Aristóteles Góes-Neto
creator: Roberto F. S. Andrade
creator: Charbel El-Hani
subject: Bioinformatics
subject: Evolutionary Studies
description: doi:10.7717/peerj.14571
publisher: PeerJ Inc.
rights: © 2023 Borges et al.
abstract: Backgound The endosymbiotic theory is widely accepted to explain the origin of mitochondria from a bacterial ancestor. While ample evidence supports the intimate connection of Alphaproteobacteria to the mitochondrial ancestor, pinpointing its closest relative within sampled Alphaproteobacteria is still an open evolutionary debate. Many different phylogenetic methods and approaches have been used to answer this challenging question, further compounded by the heterogeneity of sampled taxa, varying evolutionary rates of mitochondrial proteins, and the inherent biases in each method, all factors that can produce phylogenetic artifacts. By harnessing the simplicity and interpretability of protein similarity networks, herein we re-evaluated the origin of mitochondria within an enhanced multilayer framework, which is an extension and improvement of a previously developed method. Methods We used a dataset of eight proteins found in mitochondria (N = 6 organisms) and bacteria (N = 80 organisms). The sequences were aligned and resulting identity matrices were combined to generate an eight-layer multiplex network. Each layer corresponded to a protein network, where nodes represented organisms and edges were placed following mutual sequence identity. The Multi-Newman-Girvan algorithm was applied to evaluate community structure, and bifurcation events linked to network partition allowed to trace patterns of divergence between studied taxa. Results In our network-based analysis, we first examined the topology of the 8-layer multiplex when mitochondrial sequences disconnected from the main alphaproteobacterial cluster. The resulting topology lent firm support toward an Alphaproteobacteria-sister placement for mitochondria, reinforcing the hypothesis that mitochondria diverged from the common ancestor of all Alphaproteobacteria. Additionally, we observed that the divergence of Rickettsiales was an early event in the evolutionary history of alphaproteobacterial clades. Conclusion By…
bibliographic citation: Borges et al. (2023) On the origin of mitochondria: a multilayer network approach. PeerJ 11:e14571 https://doi.org/10.7717/peerj.14571
date submitted: 2021-12-21
date accepted: 2022-11-28
issued: 2023-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Borges
  given name: Dérick Gabriel F.
author list: Agent
  family name: Carvalho
  given name: Daniel S.
author list: Agent
  family name: Bomfim
  given name: Gilberto C.
author list: Agent
  family name: Ramos
  given name: Pablo Ivan P.
author list: Agent
  family name: Brzozowski
  given name: Jerzy
author list: Agent
  family name: Góes-Neto
  given name: Aristóteles
author list: Agent
  family name: F. S. Andrade
  given name: Roberto
author list: Agent
  family name: El-Hani
  given name: Charbel
doi: 10.7717/peerj.14571
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-06
copyright: © 2023 Borges et al.
attribution name: Borges et al.

Stem transcriptome screen for selection in wild and cultivated pitahaya (Selenicereus undatus): an epiphytic cactus with edible fruit
type: item
type: AcademicArticle
description: Dragon fruit, pitahaya or pitaya are common names for the species in the Hylocereus group of Selenicereus that produce edible fruit. These Neotropical epiphytic cacti are considered promising underutilized crops and are currently cultivated around the world. The most important species, S. undatus, has been managed in the Maya domain for centuries and is the focus of this article. Transcriptome profiles from stems of wild and cultivated plants of this species were compared. We hypothesized that differences in transcriptomic signatures could be associated with genes related to drought stress. De novo transcriptome assembly and the analysis of differentially expressed genes (DEGs) allowed us to identify a total of 9,203 DEGs in the Hunucmá cultivar relative of wild Mozomboa plants. Of these, 4,883 represent up-regulated genes and 4,320, down-regulated genes. Additionally, 6,568 DEGs were identified from a comparison between the Umán cultivar and wild plants, revealing 3,286 up-regulated and 3,282 down-regulated genes. Approximately half of the DEGs are shared by the two cultivated plants. Differences between the two cultivars that were collected in the same region could be the result of differences in management. Metabolism was the most representative functional category in both cultivars. The up-regulated genes of both cultivars formed a network related to the hormone-mediated signaling pathway that includes cellular responses to auxin stimulus and to hormone stimulus. These cellular reactions have been documented in several cultivated plants in which drought-tolerant cultivars modify auxin transport and ethylene signaling, resulting in a better redistribution of assimilates.
format: application/pdf
format: text/html
creator: Omar Oltehua-López
creator: Mario A. Arteaga-Vázquez
creator: Victoria Sosa
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14581
publisher: PeerJ Inc.
rights: © 2023 Oltehua-López et al.
abstract: Dragon fruit, pitahaya or pitaya are common names for the species in the Hylocereus group of Selenicereus that produce edible fruit. These Neotropical epiphytic cacti are considered promising underutilized crops and are currently cultivated around the world. The most important species, S. undatus, has been managed in the Maya domain for centuries and is the focus of this article. Transcriptome profiles from stems of wild and cultivated plants of this species were compared. We hypothesized that differences in transcriptomic signatures could be associated with genes related to drought stress. De novo transcriptome assembly and the analysis of differentially expressed genes (DEGs) allowed us to identify a total of 9,203 DEGs in the Hunucmá cultivar relative of wild Mozomboa plants. Of these, 4,883 represent up-regulated genes and 4,320, down-regulated genes. Additionally, 6,568 DEGs were identified from a comparison between the Umán cultivar and wild plants, revealing 3,286 up-regulated and 3,282 down-regulated genes. Approximately half of the DEGs are shared by the two cultivated plants. Differences between the two cultivars that were collected in the same region could be the result of differences in management. Metabolism was the most representative functional category in both cultivars. The up-regulated genes of both cultivars formed a network related to the hormone-mediated signaling pathway that includes cellular responses to auxin stimulus and to hormone stimulus. These cellular reactions have been documented in several cultivated plants in which drought-tolerant cultivars modify auxin transport and ethylene signaling, resulting in a better redistribution of assimilates.
bibliographic citation: Oltehua-López et al. (2023) Stem transcriptome screen for selection in wild and cultivated pitahaya (Selenicereus undatus): an epiphytic cactus with edible fruit. PeerJ 11:e14581 https://doi.org/10.7717/peerj.14581
date submitted: 2022-07-01
date accepted: 2022-11-28
issued: 2023-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oltehua-López
  given name: Omar
author list: Agent
  family name: Arteaga-Vázquez
  given name: Mario A.
author list: Agent
  family name: Sosa
  given name: Victoria
doi: 10.7717/peerj.14581
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-06
copyright: © 2023 Oltehua-López et al.
attribution name: Oltehua-López et al.

The role of subjective significance, valence and arousal in the explicit processing of emotion-laden words
type: item
type: AcademicArticle
description: Emotional categorisation (deciding whether a word is emotional or not) is a task that employs the explicit analysis of the emotional meaning of words. Therefore, it allows for assessing the role of emotional factors, i.e., valence, arousal, and subjective significance, in emotional word processing. The aim of the current experiment was to investigate the role of subjective significance, a reflective form of activation that is similar to arousal (the automatic form), in the processing of emotional meaning. We applied the orthogonal manipulation of three emotional factors. Thus, we were able to precisely differentiate the effects of each factor and search for interactions between them. We expected valence to shape the late positive complex LPC component, while subjective significance and arousal were expected to shape the P300 and N400 components. We observed the effects of subjective significance throughout the whole span of processing, while the arousal effect was present only in the LPC component. We also observed that amplitudes for N400 and LPC discriminated negative from positive valence. The results showed that all factors included in the analysis should be taken into account while explaining the processing of emotion-laden words; especially interesting is the subjective significance, which was shown to shape processing individually, as well as to come into interaction with valence and arousal.
format: application/pdf
format: text/html
creator: Kamil K. Imbir
creator: Joanna Duda-Goławska
creator: Adrianna Wielgopolan
creator: Adam Sobieszek
creator: Maciej Pastwa
creator: Jaroslaw Zygierewicz
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.14583
publisher: PeerJ Inc.
rights: © 2023 Imbir et al.
abstract: Emotional categorisation (deciding whether a word is emotional or not) is a task that employs the explicit analysis of the emotional meaning of words. Therefore, it allows for assessing the role of emotional factors, i.e., valence, arousal, and subjective significance, in emotional word processing. The aim of the current experiment was to investigate the role of subjective significance, a reflective form of activation that is similar to arousal (the automatic form), in the processing of emotional meaning. We applied the orthogonal manipulation of three emotional factors. Thus, we were able to precisely differentiate the effects of each factor and search for interactions between them. We expected valence to shape the late positive complex LPC component, while subjective significance and arousal were expected to shape the P300 and N400 components. We observed the effects of subjective significance throughout the whole span of processing, while the arousal effect was present only in the LPC component. We also observed that amplitudes for N400 and LPC discriminated negative from positive valence. The results showed that all factors included in the analysis should be taken into account while explaining the processing of emotion-laden words; especially interesting is the subjective significance, which was shown to shape processing individually, as well as to come into interaction with valence and arousal.
bibliographic citation: Imbir et al. (2023) The role of subjective significance, valence and arousal in the explicit processing of emotion-laden words. PeerJ 11:e14583 https://doi.org/10.7717/peerj.14583
date submitted: 2021-06-28
date accepted: 2022-11-28
issued: 2023-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Imbir
  given name: Kamil K.
author list: Agent
  family name: Duda-Goławska
  given name: Joanna
author list: Agent
  family name: Wielgopolan
  given name: Adrianna
author list: Agent
  family name: Sobieszek
  given name: Adam
author list: Agent
  family name: Pastwa
  given name: Maciej
author list: Agent
  family name: Zygierewicz
  given name: Jaroslaw
doi: 10.7717/peerj.14583
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-06
copyright: © 2023 Imbir et al.
attribution name: Imbir et al.

No effect of attentional modulation by spatial cueing in a masked numerical priming paradigm using continuous flash suppression (CFS)
type: item
type: AcademicArticle
description: One notion emerging from studies on unconscious visual processing is that different “blinding techniques” seem to suppress the conscious perception of stimuli at different levels of the neurocognitive architecture. However, even when only the results from a single suppression method are compared, the picture of the scope and limits of unconscious visual processing remains strikingly heterogeneous, as in the case of continuous flash suppression (CFS). To resolve this issue, it has been suggested that high-level semantic processing under CFS is facilitated whenever interocular suppression is attenuated by the removal of visuospatial attention. In this behavioral study, we aimed to further investigate this “CFS-attenuation-by-inattention” hypothesis in a numerical priming study using spatial cueing. Participants performed a number comparison task on a visible target number (“compare number to five”). Prime-target pairs were either congruent (both numbers smaller, or both larger than five) or incongruent. Based on the “CFS-attenuation-by-inattention” hypothesis, we predicted that reaction times (RTs) for congruent prime-target pairs should be faster than for incongruent ones, but only when the prime was presented at the uncued location. In the invisible condition, we observed no priming effects and thus no evidence in support of the “CFS-attenuation-by-inattention” hypothesis. In the visible condition, we found an inverse effect of prime-target congruency. Our results agree with the notion that the representation of CF-suppressed stimuli is fractionated, and limited to their basic, elemental features, thus precluding semantic processing.
format: application/pdf
format: text/html
creator: Juliane Handschack
creator: Marcus Rothkirch
creator: Philipp Sterzer
creator: Guido Hesselmann
subject: Neuroscience
subject: Ophthalmology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.14607
publisher: PeerJ Inc.
rights: © 2022 Handschack et al.
abstract: One notion emerging from studies on unconscious visual processing is that different “blinding techniques” seem to suppress the conscious perception of stimuli at different levels of the neurocognitive architecture. However, even when only the results from a single suppression method are compared, the picture of the scope and limits of unconscious visual processing remains strikingly heterogeneous, as in the case of continuous flash suppression (CFS). To resolve this issue, it has been suggested that high-level semantic processing under CFS is facilitated whenever interocular suppression is attenuated by the removal of visuospatial attention. In this behavioral study, we aimed to further investigate this “CFS-attenuation-by-inattention” hypothesis in a numerical priming study using spatial cueing. Participants performed a number comparison task on a visible target number (“compare number to five”). Prime-target pairs were either congruent (both numbers smaller, or both larger than five) or incongruent. Based on the “CFS-attenuation-by-inattention” hypothesis, we predicted that reaction times (RTs) for congruent prime-target pairs should be faster than for incongruent ones, but only when the prime was presented at the uncued location. In the invisible condition, we observed no priming effects and thus no evidence in support of the “CFS-attenuation-by-inattention” hypothesis. In the visible condition, we found an inverse effect of prime-target congruency. Our results agree with the notion that the representation of CF-suppressed stimuli is fractionated, and limited to their basic, elemental features, thus precluding semantic processing.
bibliographic citation: Handschack et al. (2023) No effect of attentional modulation by spatial cueing in a masked numerical priming paradigm using continuous flash suppression (CFS). PeerJ 11:e14607 https://doi.org/10.7717/peerj.14607
date submitted: 2022-09-01
date accepted: 2022-11-30
issued: 2023-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Handschack
  given name: Juliane
author list: Agent
  family name: Rothkirch
  given name: Marcus
author list: Agent
  family name: Sterzer
  given name: Philipp
author list: Agent
  family name: Hesselmann
  given name: Guido
doi: 10.7717/peerj.14607
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-06
copyright: ©2022 Handschack et al.
attribution name: Handschack et al.

A novel fatty acid metabolism-related gene prognostic signature and candidate drugs for patients with hepatocellular carcinoma
type: item
type: AcademicArticle
description: Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Fatty acid metabolism (FAM) is associated with the development and treatment of HCC. This study aimed to build a FAM-related gene model to assess the prognosis of HCC and provide guidance for individual treatment. RNA-sequencing data of patients with HCC from The Cancer Genome Atlas and Gene Expression Omnibus database (GSE14520) were extracted as the training and validation sets, respectively. A FAM-related gene predictive signature was built, and the performance of prognostic model was assessed. The immune infiltration and drug sensitivity were also evaluated. Quantitative real-time polymerase chain reaction and western blot were performed to evaluate the levels of the model genes. A 12-gene FAM-related risk signature was constructed; patients with a higher risk score had poorer prognosis than those with a lower risk score. Risk score was shown as an independent risk factor for overall survival of HCC, and the signature was further confirmed as an effective and accurate model. A nomogram was constructed, and it exhibited the good performance in the prognostic prediction. In addition, the immune cell infiltration and sensitivity to chemotherapy drugs were correlated with different risk levels. Finally, quantitative real-time polymerase chain reaction and western blot proved the changes of above genes. Differential expression of FAM-related genes can be used to predict response to immunotherapy and chemotherapy, and improve the clinical prognosis evaluation of patients with HCC, which provides new clues for further experimental exploration and verification on FAM-related genes in HCC.
format: application/pdf
format: text/html
creator: Jingze Yang
creator: Xin Yang
creator: Jinlu Guo
creator: Shi Liu
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Immunology
description: doi:10.7717/peerj.14622
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Fatty acid metabolism (FAM) is associated with the development and treatment of HCC. This study aimed to build a FAM-related gene model to assess the prognosis of HCC and provide guidance for individual treatment. RNA-sequencing data of patients with HCC from The Cancer Genome Atlas and Gene Expression Omnibus database (GSE14520) were extracted as the training and validation sets, respectively. A FAM-related gene predictive signature was built, and the performance of prognostic model was assessed. The immune infiltration and drug sensitivity were also evaluated. Quantitative real-time polymerase chain reaction and western blot were performed to evaluate the levels of the model genes. A 12-gene FAM-related risk signature was constructed; patients with a higher risk score had poorer prognosis than those with a lower risk score. Risk score was shown as an independent risk factor for overall survival of HCC, and the signature was further confirmed as an effective and accurate model. A nomogram was constructed, and it exhibited the good performance in the prognostic prediction. In addition, the immune cell infiltration and sensitivity to chemotherapy drugs were correlated with different risk levels. Finally, quantitative real-time polymerase chain reaction and western blot proved the changes of above genes. Differential expression of FAM-related genes can be used to predict response to immunotherapy and chemotherapy, and improve the clinical prognosis evaluation of patients with HCC, which provides new clues for further experimental exploration and verification on FAM-related genes in HCC.
bibliographic citation: Yang et al. (2023) A novel fatty acid metabolism-related gene prognostic signature and candidate drugs for patients with hepatocellular carcinoma. PeerJ 11:e14622 https://doi.org/10.7717/peerj.14622
date submitted: 2022-10-05
date accepted: 2022-12-02
issued: 2023-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Jingze
author list: Agent
  family name: Yang
  given name: Xin
author list: Agent
  family name: Guo
  given name: Jinlu
author list: Agent
  family name: Liu
  given name: Shi
doi: 10.7717/peerj.14622
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-06
copyright: ©2022 Yang et al.
attribution name: Yang et al.

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