PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Pan-cancer analysis identifies olfactory receptor family 7 subfamily A member 5 as a potential biomarker for glioma
items: The potential role of CD8+ cytotoxic T lymphocytes and one branch connected with tissue-resident memory in non-luminal breast cancer
items: The osteology of the wrist of Heyuannia huangi (Oviraptorosauria) and its implications for the wrist folding mechanism
items: Molecular insights into programmed cell death in esophageal squamous cell carcinoma
items: Predator in proximity: how does a large carnivore respond to anthropogenic pressures at fine-scales? Implications for interface area management
items: Unraveling habitat-driven shifts in alpha, beta, and gamma diversity of hummingbirds and their floral resource
items: Comparative analysis of nutrient composition and antioxidant activity in three dragon fruit cultivars
items: Ginkgetin attenuates bone loss in OVX mice by inhibiting the NF-κB/IκBα signaling pathway
items: Endophytic actinomycetes promote growth and fruits quality of tomato (Solanum lycopersicum): an approach for sustainable tomato production
items: Investigating the regulatory role of HvANT2 in anthocyanin biosynthesis through protein–motif interaction in Qingke

Pan-cancer analysis identifies olfactory receptor family 7 subfamily A member 5 as a potential biomarker for glioma
type: item
type: AcademicArticle
description: Background Human olfactory receptors (ORs) account for approximately 60% of all human G protein-coupled receptors. The functions of ORs extend beyond olfactory perception and have garnered significant attention in tumor biology. However, a comprehensive pan-cancer analysis of ORs in human cancers is lacking. Methods Using data from public databases, such as HPA, TCGA, GEO, GTEx, TIMER2, TISDB, UALCAN, GEPIA2, and GSCA, this study investigated the role of olfactory receptor family 7 subfamily A member 5 (OR7A5) in various cancers. Functional analysis of OR7A5 in LGG and GBM was performed using the CGGA database. Molecular and cellular experiments were performed to validate the expression and biological function of OR7A5 in gliomas. Results The results revealed heightened OR7A5 expression in certain tumors, correlating with the expression levels of immune checkpoints and immune infiltration. In patients with gliomas, the expression levels of OR7A5 were closely associated with adverse prognosis, 1p/19p co-deletion status, and wild-type IDH status. Finally, in vitro experiments confirmed the inhibitory effect of OR7A5 knockdown on the proliferative capacity of glioma cells and on the expression levels of proteins related to lipid metabolism. Conclusion This study establishes OR7A5 as a novel biomarker, potentially offering a novel therapeutic target for gliomas.
format: application/pdf
format: text/html
creator: Yanqiu Bao
creator: Ziqi Tang
creator: Renli Chen
creator: Xuebin Yu
creator: Xuchen Qi
subject: Biochemistry
subject: Bioinformatics
subject: Neurology
subject: Oncology
description: doi:10.7717/peerj.17631
publisher: PeerJ Inc.
rights: © 2024 Bao et al.
abstract: Background Human olfactory receptors (ORs) account for approximately 60% of all human G protein-coupled receptors. The functions of ORs extend beyond olfactory perception and have garnered significant attention in tumor biology. However, a comprehensive pan-cancer analysis of ORs in human cancers is lacking. Methods Using data from public databases, such as HPA, TCGA, GEO, GTEx, TIMER2, TISDB, UALCAN, GEPIA2, and GSCA, this study investigated the role of olfactory receptor family 7 subfamily A member 5 (OR7A5) in various cancers. Functional analysis of OR7A5 in LGG and GBM was performed using the CGGA database. Molecular and cellular experiments were performed to validate the expression and biological function of OR7A5 in gliomas. Results The results revealed heightened OR7A5 expression in certain tumors, correlating with the expression levels of immune checkpoints and immune infiltration. In patients with gliomas, the expression levels of OR7A5 were closely associated with adverse prognosis, 1p/19p co-deletion status, and wild-type IDH status. Finally, in vitro experiments confirmed the inhibitory effect of OR7A5 knockdown on the proliferative capacity of glioma cells and on the expression levels of proteins related to lipid metabolism. Conclusion This study establishes OR7A5 as a novel biomarker, potentially offering a novel therapeutic target for gliomas.
bibliographic citation: Bao et al. (2024) Pan-cancer analysis identifies olfactory receptor family 7 subfamily A member 5 as a potential biomarker for glioma. PeerJ 12:e17631 https://doi.org/10.7717/peerj.17631
date submitted: 2024-02-04
date accepted: 2024-06-04
issued: 2024-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Bao
  given name: Yanqiu
author list: Agent
  family name: Tang
  given name: Ziqi
author list: Agent
  family name: Chen
  given name: Renli
author list: Agent
  family name: Yu
  given name: Xuebin
author list: Agent
  family name: Qi
  given name: Xuchen
doi: 10.7717/peerj.17631
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-10
copyright: ©2024 Bao et al.
attribution name: Bao et al.

The potential role of CD8+ cytotoxic T lymphocytes and one branch connected with tissue-resident memory in non-luminal breast cancer
type: item
type: AcademicArticle
description: Advances in understanding the pathological mechanisms of breast cancer have resulted in the emergence of novel therapeutic strategies. However, triple-negative breast cancer (TNBC), a molecular subtype of breast cancer with a poor prognosis, lacks classical and general therapeutic targets, hindering the clinical application of several therapies to breast cancer. As insights into the unique immunity and molecular mechanisms of TNBC have become more extensive, immunotherapy has gradually become a valuable complementary approach to classical radiotherapy and chemotherapy. CD8+ cells are significant actors in the tumor immunity cycle; thus, research on TNBC immunotherapy is increasingly focused in this direction. Recently, CD8+ tissue-resident memory (TRM) cells, a subpopulation of CD8+ cells, have been explored in relation to breast cancer and found to seemingly play an undeniably important role in tumor surveillance and lymphocytic infiltration. In this review, we summarize the recent advances in the mechanisms and relative targets of CD8+ T cells, and discuss the features and potential applications of CD8+ TRM cells in non-luminal breast cancer immunotherapy.
format: application/pdf
format: text/html
creator: Ziqi Zhao
creator: Xinyu Ma
creator: Zhengang Cai
subject: Cell Biology
subject: Immunology
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.17667
publisher: PeerJ Inc.
rights: © 2024 Zhao et al.
abstract: Advances in understanding the pathological mechanisms of breast cancer have resulted in the emergence of novel therapeutic strategies. However, triple-negative breast cancer (TNBC), a molecular subtype of breast cancer with a poor prognosis, lacks classical and general therapeutic targets, hindering the clinical application of several therapies to breast cancer. As insights into the unique immunity and molecular mechanisms of TNBC have become more extensive, immunotherapy has gradually become a valuable complementary approach to classical radiotherapy and chemotherapy. CD8+ cells are significant actors in the tumor immunity cycle; thus, research on TNBC immunotherapy is increasingly focused in this direction. Recently, CD8+ tissue-resident memory (TRM) cells, a subpopulation of CD8+ cells, have been explored in relation to breast cancer and found to seemingly play an undeniably important role in tumor surveillance and lymphocytic infiltration. In this review, we summarize the recent advances in the mechanisms and relative targets of CD8+ T cells, and discuss the features and potential applications of CD8+ TRM cells in non-luminal breast cancer immunotherapy.
bibliographic citation: Zhao et al. (2024) The potential role of CD8+ cytotoxic T lymphocytes and one branch connected with tissue-resident memory in non-luminal breast cancer. PeerJ 12:e17667 https://doi.org/10.7717/peerj.17667
date submitted: 2024-03-18
date accepted: 2024-06-11
issued: 2024-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhao
  given name: Ziqi
author list: Agent
  family name: Ma
  given name: Xinyu
author list: Agent
  family name: Cai
  given name: Zhengang
doi: 10.7717/peerj.17667
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-10
copyright: © 2024 Zhao et al.
attribution name: Zhao et al.

The osteology of the wrist of Heyuannia huangi (Oviraptorosauria) and its implications for the wrist folding mechanism
type: item
type: AcademicArticle
description: The wrist of extant birds is highly specialized which permits folding of the forelimb in order to protect the pennaceous feathers when they are relaxed. This mechanism is absent in most non-avian theropods and is unknown in oviraptorosaurs because of the rarity of the specimens with well-preserved wrist. Here we give a detailed description of the wrist of two three-dimensionally preserved oviraptorosaurian Heyuannia huangi specimens from the Upper Cretaceous in Southern China. Heyuannia huangi possesses a highly specialized wrist with a strongly dorsoventrally compressed distal ulna, a larger radiale angle and a strongly convex semilunate carpal. The morphology of its wrist suggests that the distal ulna would not hinder the rotation of the manus, resulting in the smallest angle between the manus and the ulna being less than 90 degrees. The combination of the morphology of the wrist of oviraptorosaurs and the phylogenetic result indicates functional convergence in the wrist of oviraptorids and extant birds.
format: application/pdf
format: text/html
creator: Rui Qiu
creator: Yanli Du
creator: Zhiqing Huang
creator: Xufeng Zhu
creator: Xiaoli Yang
creator: Qiang Wang
creator: Xiaolin Wang
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.17669
publisher: PeerJ Inc.
rights: © 2024 Qiu et al.
abstract: The wrist of extant birds is highly specialized which permits folding of the forelimb in order to protect the pennaceous feathers when they are relaxed. This mechanism is absent in most non-avian theropods and is unknown in oviraptorosaurs because of the rarity of the specimens with well-preserved wrist. Here we give a detailed description of the wrist of two three-dimensionally preserved oviraptorosaurian Heyuannia huangi specimens from the Upper Cretaceous in Southern China. Heyuannia huangi possesses a highly specialized wrist with a strongly dorsoventrally compressed distal ulna, a larger radiale angle and a strongly convex semilunate carpal. The morphology of its wrist suggests that the distal ulna would not hinder the rotation of the manus, resulting in the smallest angle between the manus and the ulna being less than 90 degrees. The combination of the morphology of the wrist of oviraptorosaurs and the phylogenetic result indicates functional convergence in the wrist of oviraptorids and extant birds.
bibliographic citation: Qiu et al. (2024) The osteology of the wrist of Heyuannia huangi (Oviraptorosauria) and its implications for the wrist folding mechanism. PeerJ 12:e17669 https://doi.org/10.7717/peerj.17669
date submitted: 2023-10-19
date accepted: 2024-06-11
issued: 2024-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qiu
  given name: Rui
author list: Agent
  family name: Du
  given name: Yanli
author list: Agent
  family name: Huang
  given name: Zhiqing
author list: Agent
  family name: Zhu
  given name: Xufeng
author list: Agent
  family name: Yang
  given name: Xiaoli
author list: Agent
  family name: Wang
  given name: Qiang
author list: Agent
  family name: Wang
  given name: Xiaolin
doi: 10.7717/peerj.17669
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-10
copyright: ©2024 Qiu et al.
attribution name: Qiu et al.

Molecular insights into programmed cell death in esophageal squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Esophageal squamous cell carcinoma (ESCC) is a deadly type of esophageal cancer. Programmed cell death (PCD) is an important pathway of cellular self-extermination and is closely involved in cancer progression. A detailed study of its mechanism may contribute to ESCC treatment. Methods We obtained expression profiling data of ESCC patients from public databases and genes related to 12 types of PCD from previous studies. Hub genes in ESCC were screened from PCD-related genes applying differential expression analysis, machine learning analysis, linear support vector machine (SVM), random forest and Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis. In addition, based on the HTFtarget and TargetScan databases, transcription factors (TFs) and miRNAs interacting with the hub genes were selected. The relationship between hub genes and immune cells were analyzed using the CIBERSORT algorithm. Finally, to verify the potential impact of the screened hub genes on ESCC occurrence and development, a series of in vitro cell experiments were conducted. Results We screened 149 PCD-related DEGs, of which five DEGs (INHBA, LRRK2, HSP90AA1, HSPB8, and EIF2AK2) were identified as the hub genes of ESCC. The area under the curve (AUC) of receiver operating characteristic (ROC) curve of the integrated model developed using the hub genes reached 0.997, showing a noticeably high diagnostic accuracy. The number of TFs and miRNAs regulating hub genes was 105 and 22, respectively. INHBA, HSP90AA1 and EIF2AK2 were overexpressed in cancer tissues and cells of ESCC. Notably, INHBA knockdown suppressed ECSS cell migration and invasion and altered the expression of important apoptotic and survival proteins. Conclusion This study identified significant molecules with promising accuracy for the diagnosis of ESCC, which may provide a new perspective and experimental basis for ESCC research.
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creator: Min Chen
creator: Yijun Qi
creator: Shenghua Zhang
creator: Yubo Du
creator: Haodong Cheng
creator: Shegan Gao
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Otorhinolaryngology
description: doi:10.7717/peerj.17690
publisher: PeerJ Inc.
rights: © 2024 Chen et al.
abstract: Background Esophageal squamous cell carcinoma (ESCC) is a deadly type of esophageal cancer. Programmed cell death (PCD) is an important pathway of cellular self-extermination and is closely involved in cancer progression. A detailed study of its mechanism may contribute to ESCC treatment. Methods We obtained expression profiling data of ESCC patients from public databases and genes related to 12 types of PCD from previous studies. Hub genes in ESCC were screened from PCD-related genes applying differential expression analysis, machine learning analysis, linear support vector machine (SVM), random forest and Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis. In addition, based on the HTFtarget and TargetScan databases, transcription factors (TFs) and miRNAs interacting with the hub genes were selected. The relationship between hub genes and immune cells were analyzed using the CIBERSORT algorithm. Finally, to verify the potential impact of the screened hub genes on ESCC occurrence and development, a series of in vitro cell experiments were conducted. Results We screened 149 PCD-related DEGs, of which five DEGs (INHBA, LRRK2, HSP90AA1, HSPB8, and EIF2AK2) were identified as the hub genes of ESCC. The area under the curve (AUC) of receiver operating characteristic (ROC) curve of the integrated model developed using the hub genes reached 0.997, showing a noticeably high diagnostic accuracy. The number of TFs and miRNAs regulating hub genes was 105 and 22, respectively. INHBA, HSP90AA1 and EIF2AK2 were overexpressed in cancer tissues and cells of ESCC. Notably, INHBA knockdown suppressed ECSS cell migration and invasion and altered the expression of important apoptotic and survival proteins. Conclusion This study identified significant molecules with promising accuracy for the diagnosis of ESCC, which may provide a new perspective and experimental basis for ESCC research.
bibliographic citation: Chen et al. (2024) Molecular insights into programmed cell death in esophageal squamous cell carcinoma. PeerJ 12:e17690 https://doi.org/10.7717/peerj.17690
date submitted: 2024-01-31
date accepted: 2024-06-14
issued: 2024-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Min
author list: Agent
  family name: Qi
  given name: Yijun
author list: Agent
  family name: Zhang
  given name: Shenghua
author list: Agent
  family name: Du
  given name: Yubo
author list: Agent
  family name: Cheng
  given name: Haodong
author list: Agent
  family name: Gao
  given name: Shegan
doi: 10.7717/peerj.17690
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-10
copyright: ©2024 Chen et al.
attribution name: Chen et al.

Predator in proximity: how does a large carnivore respond to anthropogenic pressures at fine-scales? Implications for interface area management
type: item
type: AcademicArticle
description: Background Driven by habitat loss and fragmentation, large carnivores are increasingly navigating human-dominated landscapes, where their activity is restricted and their behaviour altered. This movement, however, raises significant concerns and costs for people living nearby. While intricately linked, studies often isolate human and carnivore impacts, hindering effective management efforts. Hence, in this study, we brought these two into a common framework, focusing on an interface area between the critical tiger habitat and the human-dominated multiple-use buffer area of a central Indian protected area. Methods We employed a fine-scale camera trap survey complemented by GPS-collar movement data to understand spatio-temporal activity patterns and adjustments of tigers in response to anthropogenic pressures. We used an occupancy framework to evaluate space use, Bayesian circular GLMs to model temporal activity, and home range and step length analyses to assess the movement patterns of tigers. Further, we used predation-risk models to understand conflict patterns as a function of tiger presence and other habitat variables. Results Despite disturbance, a high proportion of the sampled area was occupied by 17 unique tigers (ψ = 0.76; CI [0.73–0.92]). The distance to villages (β ± SE = 0.63 ± 0.21) and the relative abundance of large-bodied wild prey (β ± SE = 0.72 ± 0.37) emerged as key predictors of tiger space use probability, indicating a preference for wild prey by tigers, while human influences constrained their habitat utilisation. Distance to villages was also identified as the most significant predictor of the tigers’ temporal activity (μ ± σ = 3.03 ± 0.06 rad) that exhibited higher nocturnality near villages. A total of 11% of tiger home ranges were within village boundaries, accompanied by faster movement in these areas (displacement 40–82% higher). Livestock depredation probability by tigers increased with proximity to villages (P = 0.002) and highway (P = 0…
format: application/pdf
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creator: Manu Mohan
creator: Sambandam Sathyakumar
creator: Ramesh Krishnamurthy
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.17693
publisher: PeerJ Inc.
rights: © 2024 Mohan et al.
abstract: Background Driven by habitat loss and fragmentation, large carnivores are increasingly navigating human-dominated landscapes, where their activity is restricted and their behaviour altered. This movement, however, raises significant concerns and costs for people living nearby. While intricately linked, studies often isolate human and carnivore impacts, hindering effective management efforts. Hence, in this study, we brought these two into a common framework, focusing on an interface area between the critical tiger habitat and the human-dominated multiple-use buffer area of a central Indian protected area. Methods We employed a fine-scale camera trap survey complemented by GPS-collar movement data to understand spatio-temporal activity patterns and adjustments of tigers in response to anthropogenic pressures. We used an occupancy framework to evaluate space use, Bayesian circular GLMs to model temporal activity, and home range and step length analyses to assess the movement patterns of tigers. Further, we used predation-risk models to understand conflict patterns as a function of tiger presence and other habitat variables. Results Despite disturbance, a high proportion of the sampled area was occupied by 17 unique tigers (ψ = 0.76; CI [0.73–0.92]). The distance to villages (β ± SE = 0.63 ± 0.21) and the relative abundance of large-bodied wild prey (β ± SE = 0.72 ± 0.37) emerged as key predictors of tiger space use probability, indicating a preference for wild prey by tigers, while human influences constrained their habitat utilisation. Distance to villages was also identified as the most significant predictor of the tigers’ temporal activity (μ ± σ = 3.03 ± 0.06 rad) that exhibited higher nocturnality near villages. A total of 11% of tiger home ranges were within village boundaries, accompanied by faster movement in these areas (displacement 40–82% higher). Livestock depredation probability by tigers increased with proximity to villages (P = 0.002) and highway (P = 0…
bibliographic citation: Mohan et al. (2024) Predator in proximity: how does a large carnivore respond to anthropogenic pressures at fine-scales? Implications for interface area management. PeerJ 12:e17693 https://doi.org/10.7717/peerj.17693
date submitted: 2023-11-10
date accepted: 2024-06-14
issued: 2024-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohan
  given name: Manu
author list: Agent
  family name: Sathyakumar
  given name: Sambandam
author list: Agent
  family name: Krishnamurthy
  given name: Ramesh
doi: 10.7717/peerj.17693
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-10
copyright: © 2024 Mohan et al.
attribution name: Mohan et al.

Unraveling habitat-driven shifts in alpha, beta, and gamma diversity of hummingbirds and their floral resource
type: item
type: AcademicArticle
description: Background Biodiversity, crucial for understanding ecosystems, encompasses species richness, composition, and distribution. Ecological and environmental factors, such as habitat type, resource availability, and climate conditions, play pivotal roles in shaping species diversity within and among communities, categorized into alpha (within habitat), beta (between habitats), and gamma (total regional) diversity. Hummingbird communities are influenced by habitat, elevation, and seasonality, making them an ideal system for studying these diversities, shedding light on mutualistic community dynamics and conservation strategies. Methods Over a year-long period, monthly surveys were conducted to record hummingbird species and their visited flowering plants across four habitat types (oak forest, juniper forest, pine forest, and xerophytic shrubland) in Tlaxcala, Mexico. Three locations per habitat type were selected based on conservation status and distance from urban areas. True diversity measures were used to assess alpha, beta, and gamma diversity of hummingbirds and their floral resources. Environmental factors such as altitude and bioclimatic variables were explored for their influence on beta diversity. Results For flowering plants, gamma diversity encompassed 34 species, with oak forests exhibiting the highest richness, while xerophytic shrublands had the highest alpha diversity. In contrast, for hummingbirds, 11 species comprised the gamma diversity, with xerophytic shrublands having the highest richness and alpha diversity. Our data reveal high heterogeneity in species abundance among habitats. Notably, certain floral resources like Loeselia mexicana and Bouvardia ternifolia emerge as key species in multiple habitats, while hummingbirds such as Basilinna leucotis, Selasphorus platycercus, and Calothorax lucifer exhibit varying levels of abundance and habitat preferences. Beta diversity analyses unveil habitat-specific patterns, with species turnover predominantly dr…
format: application/pdf
format: text/html
creator: Hellen Martínez-Roldán
creator: María José Pérez-Crespo
creator: Carlos Lara
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.17713
publisher: PeerJ Inc.
rights: © 2024 Martínez-Roldán et al.
abstract: Background Biodiversity, crucial for understanding ecosystems, encompasses species richness, composition, and distribution. Ecological and environmental factors, such as habitat type, resource availability, and climate conditions, play pivotal roles in shaping species diversity within and among communities, categorized into alpha (within habitat), beta (between habitats), and gamma (total regional) diversity. Hummingbird communities are influenced by habitat, elevation, and seasonality, making them an ideal system for studying these diversities, shedding light on mutualistic community dynamics and conservation strategies. Methods Over a year-long period, monthly surveys were conducted to record hummingbird species and their visited flowering plants across four habitat types (oak forest, juniper forest, pine forest, and xerophytic shrubland) in Tlaxcala, Mexico. Three locations per habitat type were selected based on conservation status and distance from urban areas. True diversity measures were used to assess alpha, beta, and gamma diversity of hummingbirds and their floral resources. Environmental factors such as altitude and bioclimatic variables were explored for their influence on beta diversity. Results For flowering plants, gamma diversity encompassed 34 species, with oak forests exhibiting the highest richness, while xerophytic shrublands had the highest alpha diversity. In contrast, for hummingbirds, 11 species comprised the gamma diversity, with xerophytic shrublands having the highest richness and alpha diversity. Our data reveal high heterogeneity in species abundance among habitats. Notably, certain floral resources like Loeselia mexicana and Bouvardia ternifolia emerge as key species in multiple habitats, while hummingbirds such as Basilinna leucotis, Selasphorus platycercus, and Calothorax lucifer exhibit varying levels of abundance and habitat preferences. Beta diversity analyses unveil habitat-specific patterns, with species turnover predominantly dr…
bibliographic citation: Martínez-Roldán et al. (2024) Unraveling habitat-driven shifts in alpha, beta, and gamma diversity of hummingbirds and their floral resource. PeerJ 12:e17713 https://doi.org/10.7717/peerj.17713
date submitted: 2024-01-19
date accepted: 2024-06-18
issued: 2024-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Martínez-Roldán
  given name: Hellen
author list: Agent
  family name: Pérez-Crespo
  given name: María José
author list: Agent
  family name: Lara
  given name: Carlos
doi: 10.7717/peerj.17713
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-10
copyright: © 2024 Martínez-Roldán et al.
attribution name: Martínez-Roldán et al.

Comparative analysis of nutrient composition and antioxidant activity in three dragon fruit cultivars
type: item
type: AcademicArticle
description: Dragon fruit has significant economic value in many countries due to has excellent nutritional content, health advantages, and adaptability to different climates, making it an important crop in the global fruit industry. This study aimed to gather comprehensive nutritional data on three dragon fruit cultivars by analysing the levels of micronutrients, fibre, carbohydrates, antioxidants, vitamins, and minerals in their pulps. Uniform dragon fruit samples underwent thorough analysis for proximate composition, mineral content, pigments, antioxidants, and vitamin C, with statistical methods used to assess significant differences among the parameters studied. The proximate composition analysis revealed significant differences among the three dragon fruit cultivars. Among the proximate components, protein (0.40 ± 0.02 g/100 g), moisture (91.33 ± 0.88%), crude fibre (0.32 ± 0.07 g/100 g), and ash (1.27 ± 0.09 g/100 g) were more abundant in Hylocereus costaricensis than in Hylocereus undatus and Hylocereus megalanthus. On the other hand, Hylocereus undatus had higher carbohydrate (17.02 ± 0.63 g/100 g) and energy (69.74 ± 2.44 kcal/100 g) contents. K (7.23 ± 0.35 mg/100 g), Ca (1.61 ± 0.13 mg/100 g), Fe (1.84 ± 0.05 mg/100 g), and Zn (0.37 ± 0.034 mg/100 g) are highly abundant in H. costaricensis. Additionally, Hylocereus costaricensis had the highest anthocyanin content (120.15 ± 3.29 mg/g FW) and total carotenoid content (72.51 ± 1.62 mg/g FW), along with the highest vitamin C content (8.92 ± 0.13 mg/g FW) and total soluble phenolic content (572.48 ± 20.77 mg/100 g). Its remarkable antioxidant activity was further highlighted by the lowest SC50 value (13.50 ± 0.4 mg/mL) for its DPPH radical scavenging capacity. The total soluble sugar content was highest in Hylocereus megalanthus (8.72 ± 0.30 g/100 g FW). Hierarchical clustering analysis revealed distinct trait and genotype associations; among the studied cultivars, Hylocereus costaricensis demonstrated superior performan…
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creator: Afsana Yasmin
creator: Mousumi Jahan Sumi
creator: Keya Akter
creator: Rakibul Hasan Md. Rabbi
creator: Hesham S. Almoallim
creator: Mohammad Javed Ansari
creator: Akbar Hossain
creator: Shahin Imran
subject: Agricultural Science
subject: Biochemistry
description: doi:10.7717/peerj.17719
publisher: PeerJ Inc.
rights: © 2024 Yasmin et al.
abstract: Dragon fruit has significant economic value in many countries due to has excellent nutritional content, health advantages, and adaptability to different climates, making it an important crop in the global fruit industry. This study aimed to gather comprehensive nutritional data on three dragon fruit cultivars by analysing the levels of micronutrients, fibre, carbohydrates, antioxidants, vitamins, and minerals in their pulps. Uniform dragon fruit samples underwent thorough analysis for proximate composition, mineral content, pigments, antioxidants, and vitamin C, with statistical methods used to assess significant differences among the parameters studied. The proximate composition analysis revealed significant differences among the three dragon fruit cultivars. Among the proximate components, protein (0.40 ± 0.02 g/100 g), moisture (91.33 ± 0.88%), crude fibre (0.32 ± 0.07 g/100 g), and ash (1.27 ± 0.09 g/100 g) were more abundant in Hylocereus costaricensis than in Hylocereus undatus and Hylocereus megalanthus. On the other hand, Hylocereus undatus had higher carbohydrate (17.02 ± 0.63 g/100 g) and energy (69.74 ± 2.44 kcal/100 g) contents. K (7.23 ± 0.35 mg/100 g), Ca (1.61 ± 0.13 mg/100 g), Fe (1.84 ± 0.05 mg/100 g), and Zn (0.37 ± 0.034 mg/100 g) are highly abundant in H. costaricensis. Additionally, Hylocereus costaricensis had the highest anthocyanin content (120.15 ± 3.29 mg/g FW) and total carotenoid content (72.51 ± 1.62 mg/g FW), along with the highest vitamin C content (8.92 ± 0.13 mg/g FW) and total soluble phenolic content (572.48 ± 20.77 mg/100 g). Its remarkable antioxidant activity was further highlighted by the lowest SC50 value (13.50 ± 0.4 mg/mL) for its DPPH radical scavenging capacity. The total soluble sugar content was highest in Hylocereus megalanthus (8.72 ± 0.30 g/100 g FW). Hierarchical clustering analysis revealed distinct trait and genotype associations; among the studied cultivars, Hylocereus costaricensis demonstrated superior performan…
bibliographic citation: Yasmin et al. (2024) Comparative analysis of nutrient composition and antioxidant activity in three dragon fruit cultivars. PeerJ 12:e17719 https://doi.org/10.7717/peerj.17719
date submitted: 2024-04-23
date accepted: 2024-06-18
issued: 2024-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yasmin
  given name: Afsana
author list: Agent
  family name: Sumi
  given name: Mousumi Jahan
author list: Agent
  family name: Akter
  given name: Keya
author list: Agent
  family name: Rabbi
  given name: Rakibul Hasan Md.
author list: Agent
  family name: Almoallim
  given name: Hesham S.
author list: Agent
  family name: Ansari
  given name: Mohammad Javed
author list: Agent
  family name: Hossain
  given name: Akbar
author list: Agent
  family name: Imran
  given name: Shahin
doi: 10.7717/peerj.17719
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-10
copyright: ©2024 Yasmin et al.
attribution name: Yasmin et al.

Ginkgetin attenuates bone loss in OVX mice by inhibiting the NF-κB/IκBα signaling pathway
type: item
type: AcademicArticle
description: Background Osteoporosis is a disease associated with bone resorption, characterized primarily by the excessive activation of osteoclasts. Ginkgetin is a compound purified from natural ginkgo leaves which has various biological properties, including anti-inflammation, antioxidant, and anti-tumor effects. This study investigated the bone-protective effects of ginkgetin in ovariectomized (OVX) mice and explored their potential signaling pathway in inhibiting osteoclastogenesis in a mouse model of osteoporosis. Methods Biochemical assays were performed to assess the levels of Ca, ALP, and P in the blood. Micro CT scanning was used to evaluate the impact of ginkgetin on bone loss in mice. RT-PCR was employed to detect the expression of osteoclast-related genes (ctsk, c-fos, trap) in their femoral tissue. Hematoxylin and eosin (H&E) staining was utilized to assess the histopathological changes in femoral tissue due to ginkgetin. The TRAP staining was used to evaluate the impact of ginkgetin osteoclast generation in vivo. Western blot analysis was conducted to investigate the effect of ginkgetin on the expression of p-NF-κB p65 and IκBα proteins in mice. Results Our findings indicate that ginkgetin may increase the serum levels of ALP and P, while decreasing the serum level of Ca in OVX mice. H&E staining and micro CT scanning results suggest that ginkgetin can inhibit bone loss in OVX mice. The TRAP staining results showed ginkgetin suppresses the generation of osteoclasts in OVX mice. RT-PCR results demonstrate that ginkgetin downregulate the expression of osteoclast-related genes (ctsk, c-fos, trap) in the femoral tissue of mice, and this effect is dose-dependent. Western blot analysis results reveal that ginkgetin can inhibit the expression of p-NF-κB p65 and IκBα proteins in mice. Conclusion Ginkgetin can impact osteoclast formation and activation in OVX mice by inhibiting the NF-κB/IκBα signaling pathway, thereby attenuating bone loss in mice.
format: application/pdf
format: text/html
creator: GeJin Wei
creator: Xiongbo Liang
creator: Feng Wu
creator: Changzhi Cheng
creator: Shasha Huang
creator: Yanping Zeng
subject: Biochemistry
description: doi:10.7717/peerj.17722
publisher: PeerJ Inc.
rights: © 2024 Wei et al.
abstract: Background Osteoporosis is a disease associated with bone resorption, characterized primarily by the excessive activation of osteoclasts. Ginkgetin is a compound purified from natural ginkgo leaves which has various biological properties, including anti-inflammation, antioxidant, and anti-tumor effects. This study investigated the bone-protective effects of ginkgetin in ovariectomized (OVX) mice and explored their potential signaling pathway in inhibiting osteoclastogenesis in a mouse model of osteoporosis. Methods Biochemical assays were performed to assess the levels of Ca, ALP, and P in the blood. Micro CT scanning was used to evaluate the impact of ginkgetin on bone loss in mice. RT-PCR was employed to detect the expression of osteoclast-related genes (ctsk, c-fos, trap) in their femoral tissue. Hematoxylin and eosin (H&E) staining was utilized to assess the histopathological changes in femoral tissue due to ginkgetin. The TRAP staining was used to evaluate the impact of ginkgetin osteoclast generation in vivo. Western blot analysis was conducted to investigate the effect of ginkgetin on the expression of p-NF-κB p65 and IκBα proteins in mice. Results Our findings indicate that ginkgetin may increase the serum levels of ALP and P, while decreasing the serum level of Ca in OVX mice. H&E staining and micro CT scanning results suggest that ginkgetin can inhibit bone loss in OVX mice. The TRAP staining results showed ginkgetin suppresses the generation of osteoclasts in OVX mice. RT-PCR results demonstrate that ginkgetin downregulate the expression of osteoclast-related genes (ctsk, c-fos, trap) in the femoral tissue of mice, and this effect is dose-dependent. Western blot analysis results reveal that ginkgetin can inhibit the expression of p-NF-κB p65 and IκBα proteins in mice. Conclusion Ginkgetin can impact osteoclast formation and activation in OVX mice by inhibiting the NF-κB/IκBα signaling pathway, thereby attenuating bone loss in mice.
bibliographic citation: Wei et al. (2024) Ginkgetin attenuates bone loss in OVX mice by inhibiting the NF-κB/IκBα signaling pathway. PeerJ 12:e17722 https://doi.org/10.7717/peerj.17722
date submitted: 2023-12-05
date accepted: 2024-06-19
issued: 2024-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: GeJin
author list: Agent
  family name: Liang
  given name: Xiongbo
author list: Agent
  family name: Wu
  given name: Feng
author list: Agent
  family name: Cheng
  given name: Changzhi
author list: Agent
  family name: Huang
  given name: Shasha
author list: Agent
  family name: Zeng
  given name: Yanping
doi: 10.7717/peerj.17722
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-10
copyright: © 2024 Wei et al.
attribution name: Wei et al.

Endophytic actinomycetes promote growth and fruits quality of tomato (Solanum lycopersicum): an approach for sustainable tomato production
type: item
type: AcademicArticle
description: Background Tomato, a fruit with a high vitamin content, is popular for consumption and economically important in Thailand. However, in the past year, the extensive usage of chemicals has significantly decreased tomato yields. Plant Growth-Promoting Rhizobacteria (PGPR) is an alternative that can help improve tomato production system growth and yield quality while using fewer chemicals. The present study aimed to determine whether endophytic actinomycetes promote growth and fruit quality of tomato (Solanum lycopersicum). Methods The experiment was conducted in a net-houses at the Center for Agricultural Resource System Research, Faculty of Agriculture, Chiang Mai University, Chiang Mai province, Thailand. The randomized completely block design (RCBD) was carried out for four treatments with three replications, which was control, inoculation with TGsR-03-04, TGsL-02-05 and TGsR-03-04 with TGsL-02-05 in tomato plant. Isolated Actinomycetes spp. of each treatment was then inoculated into the root zone of tomato seedlings and analyzed by Scanning Electron Microscopy (SEM). The height of tomato plants was measured at 14, 28, 56, and 112 days after transplanting. Final yield and yield quality of tomato was assessed at the maturity phase. Results The SEM result illustrated that the roots of tomato seedlings from all treatments were colonized by endophytic actinomycetes species. This contributed to a significant increase in plant height at 14 days after transplanting (DAT), as found in the TGsR-03-04 treatment (19.40 cm) compared to the control. Besides, all inoculated treatments enhanced tomato yield and yield quality. The highest weight per fruit (47.38 g), fruit length (52.37 mm), vitamin C content (23.30 mg 100 g−1), and lycopene content (145.92 µg g−1) were obtained by inoculation with TGsR-03-04. Moreover, the highest yield (1.47 kg plant−1) was obtained by inoculation with TGsL-02-05. There was no statistically significant difference in the number of fruits per plant,…
format: application/pdf
format: text/html
creator: Jeeranan Khomampai
creator: Nakarin Jeeatid
creator: Thewin Kaeomuangmoon
creator: Wasu Pathom-aree
creator: Pharada Rangseekaew
creator: Thanchanok Yosen
creator: Nuttapon Khongdee
creator: Yupa Chromkaew
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.17725
publisher: PeerJ Inc.
rights: © 2024 Khomampai et al.
abstract: Background Tomato, a fruit with a high vitamin content, is popular for consumption and economically important in Thailand. However, in the past year, the extensive usage of chemicals has significantly decreased tomato yields. Plant Growth-Promoting Rhizobacteria (PGPR) is an alternative that can help improve tomato production system growth and yield quality while using fewer chemicals. The present study aimed to determine whether endophytic actinomycetes promote growth and fruit quality of tomato (Solanum lycopersicum). Methods The experiment was conducted in a net-houses at the Center for Agricultural Resource System Research, Faculty of Agriculture, Chiang Mai University, Chiang Mai province, Thailand. The randomized completely block design (RCBD) was carried out for four treatments with three replications, which was control, inoculation with TGsR-03-04, TGsL-02-05 and TGsR-03-04 with TGsL-02-05 in tomato plant. Isolated Actinomycetes spp. of each treatment was then inoculated into the root zone of tomato seedlings and analyzed by Scanning Electron Microscopy (SEM). The height of tomato plants was measured at 14, 28, 56, and 112 days after transplanting. Final yield and yield quality of tomato was assessed at the maturity phase. Results The SEM result illustrated that the roots of tomato seedlings from all treatments were colonized by endophytic actinomycetes species. This contributed to a significant increase in plant height at 14 days after transplanting (DAT), as found in the TGsR-03-04 treatment (19.40 cm) compared to the control. Besides, all inoculated treatments enhanced tomato yield and yield quality. The highest weight per fruit (47.38 g), fruit length (52.37 mm), vitamin C content (23.30 mg 100 g−1), and lycopene content (145.92 µg g−1) were obtained by inoculation with TGsR-03-04. Moreover, the highest yield (1.47 kg plant−1) was obtained by inoculation with TGsL-02-05. There was no statistically significant difference in the number of fruits per plant,…
bibliographic citation: Khomampai et al. (2024) Endophytic actinomycetes promote growth and fruits quality of tomato (Solanum lycopersicum): an approach for sustainable tomato production. PeerJ 12:e17725 https://doi.org/10.7717/peerj.17725
date submitted: 2024-03-18
date accepted: 2024-06-20
issued: 2024-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khomampai
  given name: Jeeranan
author list: Agent
  family name: Jeeatid
  given name: Nakarin
author list: Agent
  family name: Kaeomuangmoon
  given name: Thewin
author list: Agent
  family name: Pathom-aree
  given name: Wasu
author list: Agent
  family name: Rangseekaew
  given name: Pharada
author list: Agent
  family name: Yosen
  given name: Thanchanok
author list: Agent
  family name: Khongdee
  given name: Nuttapon
author list: Agent
  family name: Chromkaew
  given name: Yupa
doi: 10.7717/peerj.17725
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-10
copyright: ©2024 Khomampai et al.
attribution name: Khomampai et al.

Investigating the regulatory role of HvANT2 in anthocyanin biosynthesis through protein–motif interaction in Qingke
type: item
type: AcademicArticle
description: Background Currently, there are no reports on the HvbHLH gene family in the recent barley genome (Morex_V3). Furthermore, the structural genes related to anthocyanin synthesis that interact with HvANT2 have yet to be fully identified. Methods In this study, a bioinformatics approach was used to systematically analyze the HvbHLH gene family. The expression of this gene family was analyzed through RNA sequencing (RNA-seq), and the gene with the most significant expression level, HvANT2, was analyzed using quantitative reverse transcription polymerase chain reaction (qRT-PCR) in different tissues of two differently colored varieties. Finally, structural genes related to anthocyanin synthesis and their interactions with HvANT2 were verified using a yeast one-hybrid (Y1H) assay. Results The study identified 161 bHLH genes, designated as HvbHLH1 to HvbHLH161, from the most recent barley genome available. Evolutionary tree analysis categorized barley bHLH TFs into 21 subfamilies, demonstrating a pronounced similarity to rice and maize. Through RNA-Seq analysis of purple and white grain Qingke, we discovered a significant transcription factor (TF), HvANT2 (HvbHLH78), associated with anthocyanin biosynthesis. Subsequently, HvANT2 protein-motifs interaction assays revealed 41 interacting motifs, three of which were validated through Y1H experiments. These validated motifs were found in the promoter regions of key structural genes (CHI, F3’H, and GT) integral to the anthocyanin synthesis pathway. These findings provide substantial evidence for the pivotal role of HvANT2 TF in anthocyanin biosynthesis.
format: application/pdf
format: text/html
creator: Yan Wang
creator: Lin Chen
creator: Youhua Yao
creator: Lupeng Chen
creator: Yongmei Cui
creator: Likun An
creator: Xin Li
creator: Yixiong Bai
creator: Xiaohua Yao
creator: Kunlun Wu
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.17736
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Background Currently, there are no reports on the HvbHLH gene family in the recent barley genome (Morex_V3). Furthermore, the structural genes related to anthocyanin synthesis that interact with HvANT2 have yet to be fully identified. Methods In this study, a bioinformatics approach was used to systematically analyze the HvbHLH gene family. The expression of this gene family was analyzed through RNA sequencing (RNA-seq), and the gene with the most significant expression level, HvANT2, was analyzed using quantitative reverse transcription polymerase chain reaction (qRT-PCR) in different tissues of two differently colored varieties. Finally, structural genes related to anthocyanin synthesis and their interactions with HvANT2 were verified using a yeast one-hybrid (Y1H) assay. Results The study identified 161 bHLH genes, designated as HvbHLH1 to HvbHLH161, from the most recent barley genome available. Evolutionary tree analysis categorized barley bHLH TFs into 21 subfamilies, demonstrating a pronounced similarity to rice and maize. Through RNA-Seq analysis of purple and white grain Qingke, we discovered a significant transcription factor (TF), HvANT2 (HvbHLH78), associated with anthocyanin biosynthesis. Subsequently, HvANT2 protein-motifs interaction assays revealed 41 interacting motifs, three of which were validated through Y1H experiments. These validated motifs were found in the promoter regions of key structural genes (CHI, F3’H, and GT) integral to the anthocyanin synthesis pathway. These findings provide substantial evidence for the pivotal role of HvANT2 TF in anthocyanin biosynthesis.
bibliographic citation: Wang et al. (2024) Investigating the regulatory role of HvANT2 in anthocyanin biosynthesis through protein–motif interaction in Qingke. PeerJ 12:e17736 https://doi.org/10.7717/peerj.17736
date submitted: 2024-02-12
date accepted: 2024-06-23
issued: 2024-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Chen
  given name: Lin
author list: Agent
  family name: Yao
  given name: Youhua
author list: Agent
  family name: Chen
  given name: Lupeng
author list: Agent
  family name: Cui
  given name: Yongmei
author list: Agent
  family name: An
  given name: Likun
author list: Agent
  family name: Li
  given name: Xin
author list: Agent
  family name: Bai
  given name: Yixiong
author list: Agent
  family name: Yao
  given name: Xiaohua
author list: Agent
  family name: Wu
  given name: Kunlun
doi: 10.7717/peerj.17736
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-10
copyright: ©2024 Wang et al.
attribution name: Wang et al.

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