PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Soil organic carbon estimation using remote sensing data-driven machine learning
items: Creation of complex reef structures through coral restoration does not affect associated fish populations on a remote, well-protected, Caribbean reef
items: Short-term microplastic effects on marine meiofauna abundance, diversity and community composition
items: Genome-wide analysis of cellulose synthase (CesA) and cellulose synthase-like (Csl) proteins in Cannabis sativa L
items: Life history strategy of Tubastraea spp. corals in an upwelling area on the Southwest Atlantic: growth, fecundity, settlement, and recruitment
items: Immune infiltration and prognosis in gastric cancer: role of NAD+ metabolism-related markers
items: Transcription factor NF-E2-related factor 2 plays a critical role in acute lung injury/acute respiratory distress syndrome (ALI/ARDS) by regulating ferroptosis
items: Neighborhood structure-guided brain functional networks estimation for mild cognitive impairment identification
items: Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar
items: Genome-wide identification and evolution of the SAP gene family in sunflower (Helianthus annuus L.) and expression analysis under salt and drought stress

Soil organic carbon estimation using remote sensing data-driven machine learning
type: item
type: AcademicArticle
description: Soil organic carbon (SOC) is a crucial component of the global carbon cycle, playing a significant role in ecosystem health and carbon balance. In this study, we focused on assessing the surface SOC content in Shandong Province based on land use types, and explored its spatial distribution pattern and influencing factors. Machine learning methods including random forest (RF), extreme gradient boosting (XGBoost), and support vector machine (SVM) were employed to estimate the surface SOC content in Shandong Province using diverse data sources like sample data, remote sensing data, socio-economic data, soil texture data, topographic data, and meteorological data. The results revealed that the SOC content in Shandong Province was 8.78 g/kg, exhibiting significant variation across different regions. Comparing the model error and correlation coefficient, the XGBoost model showed the highest prediction accuracy, with a coefficient of determination (R²) of 0.7548, root mean square error (RMSE) of 7.6792, and relative percentage difference (RPD) of 1.1311. Elevation and Clay exhibited the highest explanatory power in clarifying the surface SOC content in Shandong Province, contributing 21.74% and 13.47%, respectively. The spatial distribution analysis revealed that SOC content was higher in forest-covered mountainous regions compared to cropland-covered plains and coastal areas. In conclusion, these findings offer valuable scientific insights for land use planning and SOC conservation.
format: application/pdf
format: text/html
creator: Qi Chen
creator: Yiting Wang
creator: Xicun Zhu
subject: Ecosystem Science
subject: Soil Science
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.17836
publisher: PeerJ Inc.
rights: © 2024 Chen et al.
abstract: Soil organic carbon (SOC) is a crucial component of the global carbon cycle, playing a significant role in ecosystem health and carbon balance. In this study, we focused on assessing the surface SOC content in Shandong Province based on land use types, and explored its spatial distribution pattern and influencing factors. Machine learning methods including random forest (RF), extreme gradient boosting (XGBoost), and support vector machine (SVM) were employed to estimate the surface SOC content in Shandong Province using diverse data sources like sample data, remote sensing data, socio-economic data, soil texture data, topographic data, and meteorological data. The results revealed that the SOC content in Shandong Province was 8.78 g/kg, exhibiting significant variation across different regions. Comparing the model error and correlation coefficient, the XGBoost model showed the highest prediction accuracy, with a coefficient of determination (R²) of 0.7548, root mean square error (RMSE) of 7.6792, and relative percentage difference (RPD) of 1.1311. Elevation and Clay exhibited the highest explanatory power in clarifying the surface SOC content in Shandong Province, contributing 21.74% and 13.47%, respectively. The spatial distribution analysis revealed that SOC content was higher in forest-covered mountainous regions compared to cropland-covered plains and coastal areas. In conclusion, these findings offer valuable scientific insights for land use planning and SOC conservation.
bibliographic citation: Chen et al. (2024) Soil organic carbon estimation using remote sensing data-driven machine learning. PeerJ 12:e17836 https://doi.org/10.7717/peerj.17836
date submitted: 2024-04-04
date accepted: 2024-07-09
issued: 2024-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Qi
author list: Agent
  family name: Wang
  given name: Yiting
author list: Agent
  family name: Zhu
  given name: Xicun
doi: 10.7717/peerj.17836
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-01
copyright: © 2024 Chen et al.
attribution name: Chen et al.

Creation of complex reef structures through coral restoration does not affect associated fish populations on a remote, well-protected, Caribbean reef
type: item
type: AcademicArticle
description: Coral reef ecosystems are facing severe degradation due to anthropogenic activities at both local and global scales. In response, extensive restoration efforts are underway, aiming to bolster coral cover and enhance reef fish communities to foster facilitation between fish and corals. This reciprocal relationship is anticipated to improve overall restoration efficacy and enhance coral reef resilience in the face of global warming. Here, we investigate the impact of coral restoration using out-planted Acropora cervicornis colonies attached to raised domes on the associated fish community on the isolated, well-protected reef of Little Cayman Island in the Central Caribbean. Surveys were conducted immediately preceding out-planting, five days later, and 85 days later to capture temporal changes in the fish community. After 85 days of out-planting, there were no changes in fish biomass, abundance, or species richness for the entire fish community. This pattern was consistent for selected fish functional groups. Additionally, no significant differences were observed in the fish community before outplanting, five days after out-planting, or 85 days after out-planting of restoration domes. Our results underscore the limited impact of coral restoration for influencing fish communities in the isolated and highly protected reef of Little Cayman over an 85-day period. Consequently, our findings have implications for using coral restoration as a mechanism to enhance fish populations, particularly in marginally disturbed regions where structural complexity has not been lost. Future restoration programs should therefore incorporate local knowledge of environmental history and restoration needs along with an increased data-driven understanding of the intricate interaction between fish and coral populations to be successful.
format: application/pdf
format: text/html
creator: Jack V. Johnson
creator: John F. Bruno
creator: Lucas Le Gall
creator: Matthew Louis Doherty
creator: Alex Chequer
creator: Gretchen Goodbody Gringley
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.17855
publisher: PeerJ Inc.
rights: © 2024 Johnson et al.
abstract: Coral reef ecosystems are facing severe degradation due to anthropogenic activities at both local and global scales. In response, extensive restoration efforts are underway, aiming to bolster coral cover and enhance reef fish communities to foster facilitation between fish and corals. This reciprocal relationship is anticipated to improve overall restoration efficacy and enhance coral reef resilience in the face of global warming. Here, we investigate the impact of coral restoration using out-planted Acropora cervicornis colonies attached to raised domes on the associated fish community on the isolated, well-protected reef of Little Cayman Island in the Central Caribbean. Surveys were conducted immediately preceding out-planting, five days later, and 85 days later to capture temporal changes in the fish community. After 85 days of out-planting, there were no changes in fish biomass, abundance, or species richness for the entire fish community. This pattern was consistent for selected fish functional groups. Additionally, no significant differences were observed in the fish community before outplanting, five days after out-planting, or 85 days after out-planting of restoration domes. Our results underscore the limited impact of coral restoration for influencing fish communities in the isolated and highly protected reef of Little Cayman over an 85-day period. Consequently, our findings have implications for using coral restoration as a mechanism to enhance fish populations, particularly in marginally disturbed regions where structural complexity has not been lost. Future restoration programs should therefore incorporate local knowledge of environmental history and restoration needs along with an increased data-driven understanding of the intricate interaction between fish and coral populations to be successful.
bibliographic citation: Johnson et al. (2024) Creation of complex reef structures through coral restoration does not affect associated fish populations on a remote, well-protected, Caribbean reef. PeerJ 12:e17855 https://doi.org/10.7717/peerj.17855
date submitted: 2024-03-22
date accepted: 2024-07-12
issued: 2024-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johnson
  given name: Jack V.
author list: Agent
  family name: Bruno
  given name: John F.
author list: Agent
  family name: Le Gall
  given name: Lucas
author list: Agent
  family name: Doherty
  given name: Matthew Louis
author list: Agent
  family name: Chequer
  given name: Alex
author list: Agent
  family name: Goodbody Gringley
  given name: Gretchen
doi: 10.7717/peerj.17855
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-01
copyright: ©2024 Johnson et al.
attribution name: Johnson et al.

Short-term microplastic effects on marine meiofauna abundance, diversity and community composition
type: item
type: AcademicArticle
description: Background Due to the copious disposal of plastics, marine ecosystems receive a large part of this waste. Microplastics (MPs) are solid particles smaller than 5 millimeters in size. Among the plastic polymers, polystyrene (PS) is one of the most commonly used and discarded. Due to its density being greater than that of water, it accumulates in marine sediments, potentially affecting benthic communities. This study investigated the ingestion of MP and their effect on the meiofauna community of a sandy beach. Meiofauna are an important trophic link between the basal and higher trophic levels of sedimentary food webs and may therefore be substantially involved in trophic transfer of MP and their associated compounds. Methods We incubated microcosms without addition of MP (controls) and treatments contaminated with PS MP (1-µm) in marine sediments at three nominal concentrations (103, 105, 107particles/mL), for nine days, and sampled for meiofauna with collections every three days. At each sampling time, meiofauna were collected, quantified and identified to higher-taxon level, and ingestion of MP was quantified under an epifluorescence microscope. Results Except for Tardigrada, all meiofauna taxa (Nematoda, turbellarians, Copepoda, Nauplii, Acari and Gastrotricha) ingested MP. Absorption was strongly dose dependent, being highest at 107 particles/mL, very low at 105 particles/mL and non-demonstrable at 103 particles/mL. Nematodes accumulated MP mainly in the intestine; MP abundance in the intestine increased with increasing incubation time. The total meiofauna density and species richness were significantly lower at the lowest MP concentration, while at the highest concentration these parameters were very similar to the control. In contrast, Shannon-Wiener diversity and evenness were greater in treatments with low MP concentration. However, these results should be interpreted with caution because of the low meiofauna abundances at the lower two MP concentrations. Concl…
format: application/pdf
format: text/html
creator: Flávia J.L. de França
creator: Tom Moens
creator: Renan B. da Silva
creator: Giovanna L. Pessoa
creator: Débora A.A. França
creator: Giovanni A.P. Dos Santos
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.17641
publisher: PeerJ Inc.
rights: © 2024 de França et al.
abstract: Background Due to the copious disposal of plastics, marine ecosystems receive a large part of this waste. Microplastics (MPs) are solid particles smaller than 5 millimeters in size. Among the plastic polymers, polystyrene (PS) is one of the most commonly used and discarded. Due to its density being greater than that of water, it accumulates in marine sediments, potentially affecting benthic communities. This study investigated the ingestion of MP and their effect on the meiofauna community of a sandy beach. Meiofauna are an important trophic link between the basal and higher trophic levels of sedimentary food webs and may therefore be substantially involved in trophic transfer of MP and their associated compounds. Methods We incubated microcosms without addition of MP (controls) and treatments contaminated with PS MP (1-µm) in marine sediments at three nominal concentrations (103, 105, 107particles/mL), for nine days, and sampled for meiofauna with collections every three days. At each sampling time, meiofauna were collected, quantified and identified to higher-taxon level, and ingestion of MP was quantified under an epifluorescence microscope. Results Except for Tardigrada, all meiofauna taxa (Nematoda, turbellarians, Copepoda, Nauplii, Acari and Gastrotricha) ingested MP. Absorption was strongly dose dependent, being highest at 107 particles/mL, very low at 105 particles/mL and non-demonstrable at 103 particles/mL. Nematodes accumulated MP mainly in the intestine; MP abundance in the intestine increased with increasing incubation time. The total meiofauna density and species richness were significantly lower at the lowest MP concentration, while at the highest concentration these parameters were very similar to the control. In contrast, Shannon-Wiener diversity and evenness were greater in treatments with low MP concentration. However, these results should be interpreted with caution because of the low meiofauna abundances at the lower two MP concentrations. Concl…
bibliographic citation: de França et al. (2024) Short-term microplastic effects on marine meiofauna abundance, diversity and community composition. PeerJ 12:e17641 https://doi.org/10.7717/peerj.17641
date submitted: 2024-01-19
date accepted: 2024-06-06
issued: 2024-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de França
  given name: Flávia J.L.
author list: Agent
  family name: Moens
  given name: Tom
author list: Agent
  family name: da Silva
  given name: Renan B.
author list: Agent
  family name: Pessoa
  given name: Giovanna L.
author list: Agent
  family name: França
  given name: Débora A.A.
author list: Agent
  family name: Dos Santos
  given name: Giovanni A.P.
doi: 10.7717/peerj.17641
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-31
copyright: ©2024 de França et al.
attribution name: de França et al.

Genome-wide analysis of cellulose synthase (CesA) and cellulose synthase-like (Csl) proteins in Cannabis sativa L
type: item
type: AcademicArticle
description: The cellulose and hemicellulose components of plant cell walls are synthesized by the cellulose synthase (CESA) and cellulose synthase-like (CSL) gene families and regulated in response to growth, development, and environmental stimuli. In this study, a total of 29 CESA/CSL family members were identified in Cannabis sativa and were grouped into seven subfamilies (CESA, CSLA, CSLB, CSLC, CSLD, CSLE and CSLG) according to phylogenetic relationships. The CESA/CESA proteins of C. sativa were closely related phylogenetically to the members of the subfamily of other species. The CESA/CSL subfamily members of C. sativa have unique gene structures. In addition, the expressions of four CESA and 10 CsCSL genes in flower, leaf, root, and stem organs of cannabis were detected using RT-qPCR. The results showed that CESA and CSL genes are expressed at varying levels in several organs. This detailed knowledge of the structural, evolutionary, and functional properties of cannabis CESA/CSL genes will provide a basis for designing advanced experiments for genetic manipulation of cell wall biogenesis to improve bast fibers and biofuel production.
format: application/pdf
format: text/html
creator: Hulya Sipahi
creator: Samuel Haiden
creator: Gerald Berkowitz
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.17821
publisher: PeerJ Inc.
rights: © 2024 Sipahi et al.
abstract: The cellulose and hemicellulose components of plant cell walls are synthesized by the cellulose synthase (CESA) and cellulose synthase-like (CSL) gene families and regulated in response to growth, development, and environmental stimuli. In this study, a total of 29 CESA/CSL family members were identified in Cannabis sativa and were grouped into seven subfamilies (CESA, CSLA, CSLB, CSLC, CSLD, CSLE and CSLG) according to phylogenetic relationships. The CESA/CESA proteins of C. sativa were closely related phylogenetically to the members of the subfamily of other species. The CESA/CSL subfamily members of C. sativa have unique gene structures. In addition, the expressions of four CESA and 10 CsCSL genes in flower, leaf, root, and stem organs of cannabis were detected using RT-qPCR. The results showed that CESA and CSL genes are expressed at varying levels in several organs. This detailed knowledge of the structural, evolutionary, and functional properties of cannabis CESA/CSL genes will provide a basis for designing advanced experiments for genetic manipulation of cell wall biogenesis to improve bast fibers and biofuel production.
bibliographic citation: Sipahi et al. (2024) Genome-wide analysis of cellulose synthase (CesA) and cellulose synthase-like (Csl) proteins in Cannabis sativa L. PeerJ 12:e17821 https://doi.org/10.7717/peerj.17821
date submitted: 2023-11-29
date accepted: 2024-07-06
issued: 2024-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sipahi
  given name: Hulya
author list: Agent
  family name: Haiden
  given name: Samuel
author list: Agent
  family name: Berkowitz
  given name: Gerald
doi: 10.7717/peerj.17821
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-31
copyright: ©2024 Sipahi et al.
attribution name: Sipahi et al.

Life history strategy of Tubastraea spp. corals in an upwelling area on the Southwest Atlantic: growth, fecundity, settlement, and recruitment
type: item
type: AcademicArticle
description: Over the past few decades, corals of the genus Tubastraea have spread globally, revealing themselves to be organisms of great invasive capacity. Their constant expansion on the Brazilian coast highlights the need for studies to monitor the invasion process. The growth, fecundity, settlement, and data on the coverage area of three co-occurring Tubastraea species in the 2015–2016 period were related to temperature variation and light irradiance on the rocky shores of Arraial do Cabo, Rio de Janeiro. Hence, this study sought to understand and compare the current invasion scenario and characteristics of the life history strategy of sun coral species based on environmental variables, considering the uniqueness of this upwelling area in the southwestern Atlantic. For that, we evaluate the fecundity, settlement, and growth rates of corals by carrying out comparative studies between species over time and correlating them with the variables temperature and irradiance, according to seasonality. Field growth of colonies was measured every two months during a sample year. Monthly collections were performed to count reproductive oocytes to assess fecundity. Also, quadrats were scrapped from an area near a large patch of sun coral to count newly attached coral larvae and used years later to assess diversity and percentage coverage. Results showed that corals presented greater growth during periods of high thermal amplitude and in months with below-average temperatures. Only Tubastraea sp. had greater growth and polyp increase in areas with higher light incidence, showing a greater increase in total area compared to all the other species analyzed. Despite the observed affinity with high temperatures, settlement rates were also higher during the same periods. Months with low thermal amplitude and higher temperature averages presented high fecundity. While higher water temperature averages showed an affinity with greater coral reproductive activity, growth has been shown to be inver…
format: application/pdf
format: text/html
creator: Nathália Bastos
creator: Layla Poubel Tunala
creator: Ricardo Coutinho
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.17829
publisher: PeerJ Inc.
rights: © 2024 Bastos et al.
abstract: Over the past few decades, corals of the genus Tubastraea have spread globally, revealing themselves to be organisms of great invasive capacity. Their constant expansion on the Brazilian coast highlights the need for studies to monitor the invasion process. The growth, fecundity, settlement, and data on the coverage area of three co-occurring Tubastraea species in the 2015–2016 period were related to temperature variation and light irradiance on the rocky shores of Arraial do Cabo, Rio de Janeiro. Hence, this study sought to understand and compare the current invasion scenario and characteristics of the life history strategy of sun coral species based on environmental variables, considering the uniqueness of this upwelling area in the southwestern Atlantic. For that, we evaluate the fecundity, settlement, and growth rates of corals by carrying out comparative studies between species over time and correlating them with the variables temperature and irradiance, according to seasonality. Field growth of colonies was measured every two months during a sample year. Monthly collections were performed to count reproductive oocytes to assess fecundity. Also, quadrats were scrapped from an area near a large patch of sun coral to count newly attached coral larvae and used years later to assess diversity and percentage coverage. Results showed that corals presented greater growth during periods of high thermal amplitude and in months with below-average temperatures. Only Tubastraea sp. had greater growth and polyp increase in areas with higher light incidence, showing a greater increase in total area compared to all the other species analyzed. Despite the observed affinity with high temperatures, settlement rates were also higher during the same periods. Months with low thermal amplitude and higher temperature averages presented high fecundity. While higher water temperature averages showed an affinity with greater coral reproductive activity, growth has been shown to be inver…
bibliographic citation: Bastos et al. (2024) Life history strategy of Tubastraea spp. corals in an upwelling area on the Southwest Atlantic: growth, fecundity, settlement, and recruitment. PeerJ 12:e17829 https://doi.org/10.7717/peerj.17829
date submitted: 2023-02-03
date accepted: 2024-07-08
issued: 2024-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bastos
  given name: Nathália
author list: Agent
  family name: Poubel Tunala
  given name: Layla
author list: Agent
  family name: Coutinho
  given name: Ricardo
doi: 10.7717/peerj.17829
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-31
copyright: © 2024 Bastos et al.
attribution name: Bastos et al.

Immune infiltration and prognosis in gastric cancer: role of NAD+ metabolism-related markers
type: item
type: AcademicArticle
description: Background This study endeavored to develop a nicotinamide adenine dinucleotide (NAD+) metabolism-related biomarkers in gastric cancer (GC), which could provide a theoretical foundation for prognosis and therapy of GC patients. Methods In this study, differentially expressed genes (DEGs1) between GC and paraneoplastic tissues were overlapped with NAD+ metabolism-related genes (NMRGs) to identify differentially expressed NMRGs (DE-NMRGs). Then, GC patients were divided into high and low score groups by gene set variation analysis (GSVA) algorithm for differential expression analysis to obtain DEGs2, which was overlapped with DEGs1 for identification of intersection genes. These genes were further analyzed using univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses to obtain prognostic genes for constructing a risk model. Enrichment and immune infiltration analyses further investigated investigate the different risk groups, and qRT-PCR validated the prognostic genes. Results Initially, we identified DE-NMRGs involved in NAD biosynthesis, with seven (DNAJB13, CST2, THPO, CIDEA, ONECUT1, UPK1B and SNCG) showing prognostic significance in GC. Subsequent, a prognostic model was constructed in which the risk score, derived from the expression profiles of these genes, along with gender, emerged as robust independent predictors of patient outcomes in GC. Enrichment analysis linked high-risk patients to synaptic membrane pathways and low-risk to the CMG complex pathway. Tumor immune infiltration analysis revealed correlations between risk scores and immune cell abundance, suggesting a relationship between NAD+ metabolism and immune response in GC. The prognostic significance of our identified genes was validated by qRT-PCR, which confirmed their upregulated expression in GC tissue samples. Conclusion In this study, seven NAD+ metabolism-related markers were established, which is of great significance for the development of prognostic m…
format: application/pdf
format: text/html
creator: Yu Xing
creator: Zili Zhang
creator: Wenqing Gao
creator: Weiliang Song
creator: Tong Li
subject: Genomics
subject: Gastroenterology and Hepatology
subject: Surgery and Surgical Specialties
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17833
publisher: PeerJ Inc.
rights: © 2024 Xing et al.
abstract: Background This study endeavored to develop a nicotinamide adenine dinucleotide (NAD+) metabolism-related biomarkers in gastric cancer (GC), which could provide a theoretical foundation for prognosis and therapy of GC patients. Methods In this study, differentially expressed genes (DEGs1) between GC and paraneoplastic tissues were overlapped with NAD+ metabolism-related genes (NMRGs) to identify differentially expressed NMRGs (DE-NMRGs). Then, GC patients were divided into high and low score groups by gene set variation analysis (GSVA) algorithm for differential expression analysis to obtain DEGs2, which was overlapped with DEGs1 for identification of intersection genes. These genes were further analyzed using univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses to obtain prognostic genes for constructing a risk model. Enrichment and immune infiltration analyses further investigated investigate the different risk groups, and qRT-PCR validated the prognostic genes. Results Initially, we identified DE-NMRGs involved in NAD biosynthesis, with seven (DNAJB13, CST2, THPO, CIDEA, ONECUT1, UPK1B and SNCG) showing prognostic significance in GC. Subsequent, a prognostic model was constructed in which the risk score, derived from the expression profiles of these genes, along with gender, emerged as robust independent predictors of patient outcomes in GC. Enrichment analysis linked high-risk patients to synaptic membrane pathways and low-risk to the CMG complex pathway. Tumor immune infiltration analysis revealed correlations between risk scores and immune cell abundance, suggesting a relationship between NAD+ metabolism and immune response in GC. The prognostic significance of our identified genes was validated by qRT-PCR, which confirmed their upregulated expression in GC tissue samples. Conclusion In this study, seven NAD+ metabolism-related markers were established, which is of great significance for the development of prognostic m…
bibliographic citation: Xing et al. (2024) Immune infiltration and prognosis in gastric cancer: role of NAD+ metabolism-related markers. PeerJ 12:e17833 https://doi.org/10.7717/peerj.17833
date submitted: 2024-04-05
date accepted: 2024-07-09
issued: 2024-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xing
  given name: Yu
author list: Agent
  family name: Zhang
  given name: Zili
author list: Agent
  family name: Gao
  given name: Wenqing
author list: Agent
  family name: Song
  given name: Weiliang
author list: Agent
  family name: Li
  given name: Tong
doi: 10.7717/peerj.17833
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-31
copyright: © 2024 Xing et al.
attribution name: Xing et al.

Transcription factor NF-E2-related factor 2 plays a critical role in acute lung injury/acute respiratory distress syndrome (ALI/ARDS) by regulating ferroptosis
type: item
type: AcademicArticle
description: NRF2 is an important transcription factor that regulates redox homeostasis in vivo and exerts its anti-oxidative stress and anti-inflammatory response by binding to the ARE to activate and regulate the transcription of downstream protective protein genes, reducing the release of reactive oxygen species. Ferroptosis is a novel iron-dependent, lipid peroxidation-driven cell death mode, and recent studies have shown that ferroptosis is closely associated with acute lung injury/acute respiratory distress syndrome (ALI/ARDS). NRF2 is able to regulate ferroptosis through the regulation of the transcription of its target genes to ameliorate ALI/ARDS. Therefore, This article focuses on how NRF2 plays a role in ALI/ARDS by regulating ferroptosis. We further reviewed the literature and deeply analyzed the signaling pathways related to ferroptosis which were regulated by NRF2. Additionally, we sorted out the chemical molecules targeting NRF2 that are effective for ALI/ARDS. This review provides a relevant theoretical basis for further research on this theory and the prevention and treatment of ALI/ARDS. The intended audience is clinicians and researchers in the field of respiratory disease.
format: application/pdf
format: text/html
creator: JiaLi Deng
creator: Na Li
creator: Liyuan Hao
creator: Shenghao Li
creator: Nie Aiyu
creator: Junli Zhang
creator: XiaoYu Hu
subject: Biochemistry
subject: Cell Biology
subject: Immunology
subject: Infectious Diseases
subject: Respiratory Medicine
description: doi:10.7717/peerj.17692
publisher: PeerJ Inc.
rights: © 2024 Deng et al.
abstract: NRF2 is an important transcription factor that regulates redox homeostasis in vivo and exerts its anti-oxidative stress and anti-inflammatory response by binding to the ARE to activate and regulate the transcription of downstream protective protein genes, reducing the release of reactive oxygen species. Ferroptosis is a novel iron-dependent, lipid peroxidation-driven cell death mode, and recent studies have shown that ferroptosis is closely associated with acute lung injury/acute respiratory distress syndrome (ALI/ARDS). NRF2 is able to regulate ferroptosis through the regulation of the transcription of its target genes to ameliorate ALI/ARDS. Therefore, This article focuses on how NRF2 plays a role in ALI/ARDS by regulating ferroptosis. We further reviewed the literature and deeply analyzed the signaling pathways related to ferroptosis which were regulated by NRF2. Additionally, we sorted out the chemical molecules targeting NRF2 that are effective for ALI/ARDS. This review provides a relevant theoretical basis for further research on this theory and the prevention and treatment of ALI/ARDS. The intended audience is clinicians and researchers in the field of respiratory disease.
bibliographic citation: Deng et al. (2024) Transcription factor NF-E2-related factor 2 plays a critical role in acute lung injury/acute respiratory distress syndrome (ALI/ARDS) by regulating ferroptosis. PeerJ 12:e17692 https://doi.org/10.7717/peerj.17692
date submitted: 2024-03-14
date accepted: 2024-06-14
issued: 2024-07-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: JiaLi
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Hao
  given name: Liyuan
author list: Agent
  family name: Li
  given name: Shenghao
author list: Agent
  family name: Aiyu
  given name: Nie
author list: Agent
  family name: Zhang
  given name: Junli
author list: Agent
  family name: Hu
  given name: XiaoYu
doi: 10.7717/peerj.17692
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-30
copyright: ©2024 Deng et al.
attribution name: Deng et al.

Neighborhood structure-guided brain functional networks estimation for mild cognitive impairment identification
type: item
type: AcademicArticle
description: The adoption and growth of functional magnetic resonance imaging (fMRI) technology, especially through the use of Pearson’s correlation (PC) for constructing brain functional networks (BFN), has significantly advanced brain disease diagnostics by uncovering the brain’s operational mechanisms and offering biomarkers for early detection. However, the PC always tends to make for a dense BFN, which violates the biological prior. Therefore, in practice, researchers use hard-threshold to remove weak connection edges or introduce l1-norm as a regularization term to obtain sparse BFNs. However, these approaches neglect the spatial neighborhood information between regions of interest (ROIs), and ROI with closer distances has higher connectivity prospects than ROI with farther distances due to the principle of simple wiring costs in resent studies. Thus, we propose a neighborhood structure-guided BFN estimation method in this article. In detail, we figure the ROIs’ Euclidean distances and sort them. Then, we apply the K-nearest neighbor (KNN) to find out the top K neighbors closest to the current ROIs, where each ROI’s K neighbors are independent of each other. We establish the connection relationship between the ROIs and these K neighbors and construct the global topology adjacency matrix according to the binary network. Connect ROI nodes with k nearest neighbors using edges to generate an adjacency graph, forming an adjacency matrix. Based on adjacency matrix, PC calculates the correlation coefficient between ROIs connected by edges, and generates the BFN. With the purpose of evaluating the performance of the introduced method, we utilize the estimated BFN for distinguishing individuals with mild cognitive impairment (MCI) from the healthy ones. Experimental outcomes imply this method attains better classification performance than the baselines. Additionally, we compared it with the most commonly used time series methods in deep learning. Results of the performance of K-nea…
format: application/pdf
format: text/html
creator: Lizhong Liang
creator: Zijian Zhu
creator: Hui Su
creator: Tianming Zhao
creator: Yao Lu
subject: Neuroscience
subject: Cognitive Disorders
subject: Neurology
description: doi:10.7717/peerj.17774
publisher: PeerJ Inc.
rights: © 2024 Liang et al.
abstract: The adoption and growth of functional magnetic resonance imaging (fMRI) technology, especially through the use of Pearson’s correlation (PC) for constructing brain functional networks (BFN), has significantly advanced brain disease diagnostics by uncovering the brain’s operational mechanisms and offering biomarkers for early detection. However, the PC always tends to make for a dense BFN, which violates the biological prior. Therefore, in practice, researchers use hard-threshold to remove weak connection edges or introduce l1-norm as a regularization term to obtain sparse BFNs. However, these approaches neglect the spatial neighborhood information between regions of interest (ROIs), and ROI with closer distances has higher connectivity prospects than ROI with farther distances due to the principle of simple wiring costs in resent studies. Thus, we propose a neighborhood structure-guided BFN estimation method in this article. In detail, we figure the ROIs’ Euclidean distances and sort them. Then, we apply the K-nearest neighbor (KNN) to find out the top K neighbors closest to the current ROIs, where each ROI’s K neighbors are independent of each other. We establish the connection relationship between the ROIs and these K neighbors and construct the global topology adjacency matrix according to the binary network. Connect ROI nodes with k nearest neighbors using edges to generate an adjacency graph, forming an adjacency matrix. Based on adjacency matrix, PC calculates the correlation coefficient between ROIs connected by edges, and generates the BFN. With the purpose of evaluating the performance of the introduced method, we utilize the estimated BFN for distinguishing individuals with mild cognitive impairment (MCI) from the healthy ones. Experimental outcomes imply this method attains better classification performance than the baselines. Additionally, we compared it with the most commonly used time series methods in deep learning. Results of the performance of K-nea…
bibliographic citation: Liang et al. (2024) Neighborhood structure-guided brain functional networks estimation for mild cognitive impairment identification. PeerJ 12:e17774 https://doi.org/10.7717/peerj.17774
date submitted: 2024-02-02
date accepted: 2024-06-28
issued: 2024-07-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Lizhong
author list: Agent
  family name: Zhu
  given name: Zijian
author list: Agent
  family name: Su
  given name: Hui
author list: Agent
  family name: Zhao
  given name: Tianming
author list: Agent
  family name: Lu
  given name: Yao
doi: 10.7717/peerj.17774
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-30
copyright: ©2024 Liang et al.
attribution name: Liang et al.

Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar
type: item
type: AcademicArticle
description: Background Tracking the spread of antibiotic resistant bacteria is critical to reduce global morbidity and mortality associated with human and animal infections. There is a need to understand the role that wild animals in maintenance and transfer of antibiotic resistance genes (ARGs). Methods This study used metagenomics to identify and compare the abundance of bacterial species and ARGs detected in the gut microbiomes from sympatric humans and wild mouse lemurs in a forest-dominated, roadless region of Madagascar near Ranomafana National Park. We examined the contribution of human geographic location toward differences in ARG abundance and compared the genomic similarity of ARGs between host source microbiomes. Results Alpha and beta diversity of species and ARGs between host sources were distinct but maintained a similar number of detectable ARG alleles. Humans were differentially more abundant for four distinct tetracycline resistance-associated genes compared to lemurs. There was no significant difference in human ARG diversity from different locations. Human and lemur microbiomes shared 14 distinct ARGs with highly conserved in nucleotide identity. Synteny of ARG-associated assemblies revealed a distinct multidrug-resistant gene cassette carrying dfrA1 and aadA1 present in human and lemur microbiomes without evidence of geographic overlap, suggesting that these resistance genes could be widespread in this ecosystem. Further investigation into intermediary processes that maintain drug-resistant bacteria in wildlife settings is needed.
format: application/pdf
format: text/html
creator: Brooke M. Talbot
creator: Julie A. Clennon
creator: Miarintsoa Fara Nantenaina Rakotoarison
creator: Lydia Rautman
creator: Sarah Durry
creator: Leo J. Ragazzo
creator: Patricia C. Wright
creator: Thomas R. Gillespie
creator: Timothy D. Read
subject: Ecology
subject: Genomics
subject: Microbiology
subject: Epidemiology
subject: Environmental Health
description: doi:10.7717/peerj.17805
publisher: PeerJ Inc.
rights: © 2024 Talbot et al.
abstract: Background Tracking the spread of antibiotic resistant bacteria is critical to reduce global morbidity and mortality associated with human and animal infections. There is a need to understand the role that wild animals in maintenance and transfer of antibiotic resistance genes (ARGs). Methods This study used metagenomics to identify and compare the abundance of bacterial species and ARGs detected in the gut microbiomes from sympatric humans and wild mouse lemurs in a forest-dominated, roadless region of Madagascar near Ranomafana National Park. We examined the contribution of human geographic location toward differences in ARG abundance and compared the genomic similarity of ARGs between host source microbiomes. Results Alpha and beta diversity of species and ARGs between host sources were distinct but maintained a similar number of detectable ARG alleles. Humans were differentially more abundant for four distinct tetracycline resistance-associated genes compared to lemurs. There was no significant difference in human ARG diversity from different locations. Human and lemur microbiomes shared 14 distinct ARGs with highly conserved in nucleotide identity. Synteny of ARG-associated assemblies revealed a distinct multidrug-resistant gene cassette carrying dfrA1 and aadA1 present in human and lemur microbiomes without evidence of geographic overlap, suggesting that these resistance genes could be widespread in this ecosystem. Further investigation into intermediary processes that maintain drug-resistant bacteria in wildlife settings is needed.
bibliographic citation: Talbot et al. (2024) Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar. PeerJ 12:e17805 https://doi.org/10.7717/peerj.17805
date submitted: 2024-01-02
date accepted: 2024-07-03
issued: 2024-07-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Talbot
  given name: Brooke M.
author list: Agent
  family name: Clennon
  given name: Julie A.
author list: Agent
  family name: Rakotoarison
  given name: Miarintsoa Fara Nantenaina
author list: Agent
  family name: Rautman
  given name: Lydia
author list: Agent
  family name: Durry
  given name: Sarah
author list: Agent
  family name: Ragazzo
  given name: Leo J.
author list: Agent
  family name: Wright
  given name: Patricia C.
author list: Agent
  family name: Gillespie
  given name: Thomas R.
author list: Agent
  family name: Read
  given name: Timothy D.
doi: 10.7717/peerj.17805
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-30
copyright: ©2024 Talbot et al.
attribution name: Talbot et al.

Genome-wide identification and evolution of the SAP gene family in sunflower (Helianthus annuus L.) and expression analysis under salt and drought stress
type: item
type: AcademicArticle
description: Stress-associated proteins (SAPs) are known to play an important role in plant responses to abiotic stresses. This study systematically identified members of the sunflower SAP gene family using sunflower genome data. The genes of the sunflower SAP gene family were analyzed using bioinformatic methods, and gene expression was assessed through fluorescence quantification (qRT-PCR) under salt and drought stress. A comprehensive analysis was also performed on the number, structure, collinearity, and phylogeny of seven Compositae species and eight other plant SAP gene families. The sunflower genome was found to have 27 SAP genes, distributed across 14 chromosomes. The evolutionary analysis revealed that the SAP family genes could be divided into three subgroups. Notably, the annuus variety exhibited amplification of the SAP gene for Group 3. Among the Compositae species, C. morifolium demonstrated the highest number of collinearity gene pairs and the closest distance on the phylogenetic tree, suggesting relative conservation in the evolutionary process. An analysis of gene structure revealed that Group 1 exhibited the most complex gene structure, while the majority of HaSAP genes in Group 2 and Group 3 lacked introns. The promoter analysis revealed the presence of cis-acting elements related to ABA, indicating their involvement in stress responses. The expression analysis indicated the potential involvement of 10 genes (HaSAP1, HaSAP3, HaSAP8, HaSAP10, HaSAP15, HaSAP16, HaSAP21, HaSAP22, HaSAP23, and HaSAP26) in sunflower salt tolerance. The expression of these 10 genes were then examined under salt and drought stress using qRT-PCR, and the tissue-specific expression patterns of these 10 genes were also analyzed. HaSAP1, HaSAP21, and HaSAP23 exhibited consistent expression patterns under both salt and drought stress, indicating these genes play a role in both salt tolerance and drought resistance in sunflower. The findings of this study highlight the significant contribu…
format: application/pdf
format: text/html
creator: Chun Zhang
creator: Xiaohong Zhang
creator: Yue Wu
creator: Xiang Li
creator: Chao Du
creator: Na Di
creator: Yang Chen
subject: Agricultural Science
subject: Genomics
subject: Plant Science
subject: Soil Science
subject: Biomechanics
description: doi:10.7717/peerj.17808
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Stress-associated proteins (SAPs) are known to play an important role in plant responses to abiotic stresses. This study systematically identified members of the sunflower SAP gene family using sunflower genome data. The genes of the sunflower SAP gene family were analyzed using bioinformatic methods, and gene expression was assessed through fluorescence quantification (qRT-PCR) under salt and drought stress. A comprehensive analysis was also performed on the number, structure, collinearity, and phylogeny of seven Compositae species and eight other plant SAP gene families. The sunflower genome was found to have 27 SAP genes, distributed across 14 chromosomes. The evolutionary analysis revealed that the SAP family genes could be divided into three subgroups. Notably, the annuus variety exhibited amplification of the SAP gene for Group 3. Among the Compositae species, C. morifolium demonstrated the highest number of collinearity gene pairs and the closest distance on the phylogenetic tree, suggesting relative conservation in the evolutionary process. An analysis of gene structure revealed that Group 1 exhibited the most complex gene structure, while the majority of HaSAP genes in Group 2 and Group 3 lacked introns. The promoter analysis revealed the presence of cis-acting elements related to ABA, indicating their involvement in stress responses. The expression analysis indicated the potential involvement of 10 genes (HaSAP1, HaSAP3, HaSAP8, HaSAP10, HaSAP15, HaSAP16, HaSAP21, HaSAP22, HaSAP23, and HaSAP26) in sunflower salt tolerance. The expression of these 10 genes were then examined under salt and drought stress using qRT-PCR, and the tissue-specific expression patterns of these 10 genes were also analyzed. HaSAP1, HaSAP21, and HaSAP23 exhibited consistent expression patterns under both salt and drought stress, indicating these genes play a role in both salt tolerance and drought resistance in sunflower. The findings of this study highlight the significant contribu…
bibliographic citation: Zhang et al. (2024) Genome-wide identification and evolution of the SAP gene family in sunflower (Helianthus annuus L.) and expression analysis under salt and drought stress. PeerJ 12:e17808 https://doi.org/10.7717/peerj.17808
date submitted: 2024-03-12
date accepted: 2024-07-03
issued: 2024-07-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Chun
author list: Agent
  family name: Zhang
  given name: Xiaohong
author list: Agent
  family name: Wu
  given name: Yue
author list: Agent
  family name: Li
  given name: Xiang
author list: Agent
  family name: Du
  given name: Chao
author list: Agent
  family name: Di
  given name: Na
author list: Agent
  family name: Chen
  given name: Yang
doi: 10.7717/peerj.17808
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-30
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

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