PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: Construction and validation of a prognostic model for gastric cancer patients with tumor deposits
items: Effect of warm-up protocols using lower and higher loads on multiple-set back squat volume-load
items: The role of melatonergic system in intervertebral disc degeneration and its association with low back pain: a clinical study
items: Assessing tooth wear progression in non-human primates: a longitudinal study using intraoral scanning technology

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
format: text/html
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.
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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.
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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.

Construction and validation of a prognostic model for gastric cancer patients with tumor deposits
type: item
type: AcademicArticle
description: Background Tumor deposits (TD) was a significant risk factor impacting the prognosis of patients diagnosed with gastric cancer (GC), yet it was not currently incorporated into TNM staging systems. The objective of this research was to develop a predictive model for assessing the prognosis of patients with TD-positive GC. Methods Retrospective analysis was performed on the data of 4,972 patients treated for GC with D2 radical gastrectomy at Wannan Medical College’s Yijishan Hospital between January 2012 and December 2021. The patients were categorized based on the number of TD (L1: 1, L2: 2–3, L3: ≥4) and the anatomical location of TD (Q1: single area, Q2: multiple areas). In a 3:1 ratio, patients were randomly assigned to one of two groups: training or validation. Results The study included a total of 575 patients who were divided into the training group (n = 432) and validation group (n = 143). Survival analysis showed that the number and anatomical location of TD had a significant impact on the prognosis of patients with TD-positive GC. Univariate analysis of the training group data revealed that tumor size, T-stage, N-stage, histological grade, number and distribution of TD, neural invasion, and postoperative chemotherapy were associated with prognosis. Multivariate Cox regression analysis identified poor histological grade, T4 stage, N3 stage, number of TD, neural invasion, and postoperative chemotherapy as independent prognostic factors for GC patients with TD. A nomogram was developed using these variables, demonstrating well predictive ability for 1, 3, and 5-year overall survival (OS) in the validation set. The DCA curve shows that the constructed model shows a large positive net gain compared to the eighth edition Tumour, Node, Metastasis (TNM) staging system. Conclusion The prognostic model developed for patients with TD-positive GC has a higher clinical utility compared to the eighth edition of TNM staging.
format: application/pdf
format: text/html
creator: Ran Xu
creator: Yisheng Zhang
creator: Zhengguang Wang
creator: Ke Chen
creator: Jun Zhao
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Translational Medicine
description: doi:10.7717/peerj.17751
publisher: PeerJ Inc.
rights: © 2024 Xu et al.
abstract: Background Tumor deposits (TD) was a significant risk factor impacting the prognosis of patients diagnosed with gastric cancer (GC), yet it was not currently incorporated into TNM staging systems. The objective of this research was to develop a predictive model for assessing the prognosis of patients with TD-positive GC. Methods Retrospective analysis was performed on the data of 4,972 patients treated for GC with D2 radical gastrectomy at Wannan Medical College’s Yijishan Hospital between January 2012 and December 2021. The patients were categorized based on the number of TD (L1: 1, L2: 2–3, L3: ≥4) and the anatomical location of TD (Q1: single area, Q2: multiple areas). In a 3:1 ratio, patients were randomly assigned to one of two groups: training or validation. Results The study included a total of 575 patients who were divided into the training group (n = 432) and validation group (n = 143). Survival analysis showed that the number and anatomical location of TD had a significant impact on the prognosis of patients with TD-positive GC. Univariate analysis of the training group data revealed that tumor size, T-stage, N-stage, histological grade, number and distribution of TD, neural invasion, and postoperative chemotherapy were associated with prognosis. Multivariate Cox regression analysis identified poor histological grade, T4 stage, N3 stage, number of TD, neural invasion, and postoperative chemotherapy as independent prognostic factors for GC patients with TD. A nomogram was developed using these variables, demonstrating well predictive ability for 1, 3, and 5-year overall survival (OS) in the validation set. The DCA curve shows that the constructed model shows a large positive net gain compared to the eighth edition Tumour, Node, Metastasis (TNM) staging system. Conclusion The prognostic model developed for patients with TD-positive GC has a higher clinical utility compared to the eighth edition of TNM staging.
bibliographic citation: Xu et al. (2024) Construction and validation of a prognostic model for gastric cancer patients with tumor deposits. PeerJ 12:e17751 https://doi.org/10.7717/peerj.17751
date submitted: 2024-04-23
date accepted: 2024-06-25
issued: 2024-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Ran
author list: Agent
  family name: Zhang
  given name: Yisheng
author list: Agent
  family name: Wang
  given name: Zhengguang
author list: Agent
  family name: Chen
  given name: Ke
author list: Agent
  family name: Zhao
  given name: Jun
doi: 10.7717/peerj.17751
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-10
copyright: ©2024 Xu et al.
attribution name: Xu et al.

Effect of warm-up protocols using lower and higher loads on multiple-set back squat volume-load
type: item
type: AcademicArticle
description: Background The present study aimed to investigate the effects of post-activation performance enhancement (PAPE) after three warm-up protocols on back squat performance in trained men. Methods Fourteen resistance-trained men performed conditioning activity (CA) with high-load (HL-CA), low-load (LL-CA), or usual specific warm-up as a control (CON). HL-CA consisted of one set of three repetitions with 90% of one repetition maximum (RM); LL-CA consisted of one set of six repetitions with 45% of 1 RM performed at maximal velocity; CON involved eight repetitions with 45% of 1 RM at controlled velocity. The participant’s performance was measured using the total number of repetitions and volume load (reps × load × sets). Results There were no significant differences between warm-up for the total number of repetitions (p = 0.17) or total volume load (p = 0.15). There was no difference between conditions for the number of repetitions (main condition effect; p = 0.17); however, participants achieved a significantly higher volume load after HL-PAPE than after CON for the first set (p = 0.04). Conclusion High or low equated-load CA used as warm-up strategies did not potentiate subsequent performance enhancement in multiple-set back squat exercise performed until muscle failure in comparison with usual warm-up.
format: application/pdf
format: text/html
creator: Daniel Souza
creator: Anderson Garcia Silva
creator: Arthur Vale
creator: Alana Pessoni
creator: Luan Galvão
creator: Murilo Augusto Araújo
creator: Célio de Paula Júnior
creator: Carlos Vieira
creator: Amilton Vieira
creator: Paulo Gentil
subject: Kinesiology
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.17347
publisher: PeerJ Inc.
rights: © 2024 Souza et al.
abstract: Background The present study aimed to investigate the effects of post-activation performance enhancement (PAPE) after three warm-up protocols on back squat performance in trained men. Methods Fourteen resistance-trained men performed conditioning activity (CA) with high-load (HL-CA), low-load (LL-CA), or usual specific warm-up as a control (CON). HL-CA consisted of one set of three repetitions with 90% of one repetition maximum (RM); LL-CA consisted of one set of six repetitions with 45% of 1 RM performed at maximal velocity; CON involved eight repetitions with 45% of 1 RM at controlled velocity. The participant’s performance was measured using the total number of repetitions and volume load (reps × load × sets). Results There were no significant differences between warm-up for the total number of repetitions (p = 0.17) or total volume load (p = 0.15). There was no difference between conditions for the number of repetitions (main condition effect; p = 0.17); however, participants achieved a significantly higher volume load after HL-PAPE than after CON for the first set (p = 0.04). Conclusion High or low equated-load CA used as warm-up strategies did not potentiate subsequent performance enhancement in multiple-set back squat exercise performed until muscle failure in comparison with usual warm-up.
bibliographic citation: Souza et al. (2024) Effect of warm-up protocols using lower and higher loads on multiple-set back squat volume-load. PeerJ 12:e17347 https://doi.org/10.7717/peerj.17347
date submitted: 2023-10-17
date accepted: 2024-04-17
issued: 2024-07-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Souza
  given name: Daniel
author list: Agent
  family name: Silva
  given name: Anderson Garcia
author list: Agent
  family name: Vale
  given name: Arthur
author list: Agent
  family name: Pessoni
  given name: Alana
author list: Agent
  family name: Galvão
  given name: Luan
author list: Agent
  family name: Araújo
  given name: Murilo Augusto
author list: Agent
  family name: de Paula Júnior
  given name: Célio
author list: Agent
  family name: Vieira
  given name: Carlos
author list: Agent
  family name: Vieira
  given name: Amilton
author list: Agent
  family name: Gentil
  given name: Paulo
doi: 10.7717/peerj.17347
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-09
copyright: © 2024 Souza et al.
attribution name: Souza et al.

The role of melatonergic system in intervertebral disc degeneration and its association with low back pain: a clinical study
type: item
type: AcademicArticle
description: Objective The mechanisms of intervertebral disc degeneration (IVDD) in low back pain (LBP) patients are multiples. In this study, we attempt to investigate whether melatonergic system plays a potential role in IVDD patients with LBP by analyzing their clinical specimens. The fucus will be given to the correlation between the melatonin receptor expression and intervertebral disc tissue apoptosis. Methods In this clinical study, 107 lumbar intervertebral disc nucleus pulposus (NP) specimens from patients with LBP were collected with patients’ consents. The disc height (DH) discrepancy ratio, range of motion and sagittal parameters of the pathological plane were measured and Pfirrmann grade was used to classified the grades of IVDD level. Discs at grades 1–3 were served as normal control and grades 4–5 were considered as IVDD. The expression levels of melatonin receptor 1A (MT1) and 1B (MT2) were measured by immunohistochemistry. The apoptosis of NP was assessed using TUNEL staining. Their potential associations among MT1/2, DH, apoptosis, sagittal parameters with IVDD and LBP were evaluated with statistical analysis. Results The incidence of IVDD was positively associated with age and negatively related to VAS scores for LBP (p < 0.001). Patients with higher degree of IVDD also have higher DH discrepancy ratio (p < 0.001), higher prevalence of lumbar instability (p = 0.003) and higher cell apoptosis compared to the control. Nevertheless, no statistically significant correlation was identified between Pfirrmann grade and lumbar sagittal parameters. MT1 and MT2 both were highly expressed in the NP tissues. Importantly, MT1 expression but not MT2 was significantly increased in the intervertebral disc tissue of patients with IVDD and its level correlated well with cell apoptosis level and the severity of IVDD as well as lower VAS scores for LBP. Conclusion The highly elevated MT1 expression was found in NP tissues of patients with IVDD and LBP compared to the control. Thi…
format: application/pdf
format: text/html
creator: Chong Chen
creator: Zongyuan Deng
creator: Zhengran Yu
creator: Yifan Chen
creator: Tao Yu
creator: Changxiang Liang
creator: Yongyu Ye
creator: Yongxiong Huang
creator: Feng-Juan Lyu
creator: Guoyan Liang
creator: Yunbing Chang
subject: Anesthesiology and Pain Management
subject: Neurology
subject: Orthopedics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.17464
publisher: PeerJ Inc.
rights: © 2024 Chen et al.
abstract: Objective The mechanisms of intervertebral disc degeneration (IVDD) in low back pain (LBP) patients are multiples. In this study, we attempt to investigate whether melatonergic system plays a potential role in IVDD patients with LBP by analyzing their clinical specimens. The fucus will be given to the correlation between the melatonin receptor expression and intervertebral disc tissue apoptosis. Methods In this clinical study, 107 lumbar intervertebral disc nucleus pulposus (NP) specimens from patients with LBP were collected with patients’ consents. The disc height (DH) discrepancy ratio, range of motion and sagittal parameters of the pathological plane were measured and Pfirrmann grade was used to classified the grades of IVDD level. Discs at grades 1–3 were served as normal control and grades 4–5 were considered as IVDD. The expression levels of melatonin receptor 1A (MT1) and 1B (MT2) were measured by immunohistochemistry. The apoptosis of NP was assessed using TUNEL staining. Their potential associations among MT1/2, DH, apoptosis, sagittal parameters with IVDD and LBP were evaluated with statistical analysis. Results The incidence of IVDD was positively associated with age and negatively related to VAS scores for LBP (p < 0.001). Patients with higher degree of IVDD also have higher DH discrepancy ratio (p < 0.001), higher prevalence of lumbar instability (p = 0.003) and higher cell apoptosis compared to the control. Nevertheless, no statistically significant correlation was identified between Pfirrmann grade and lumbar sagittal parameters. MT1 and MT2 both were highly expressed in the NP tissues. Importantly, MT1 expression but not MT2 was significantly increased in the intervertebral disc tissue of patients with IVDD and its level correlated well with cell apoptosis level and the severity of IVDD as well as lower VAS scores for LBP. Conclusion The highly elevated MT1 expression was found in NP tissues of patients with IVDD and LBP compared to the control. Thi…
bibliographic citation: Chen et al. (2024) The role of melatonergic system in intervertebral disc degeneration and its association with low back pain: a clinical study. PeerJ 12:e17464 https://doi.org/10.7717/peerj.17464
date submitted: 2024-01-19
date accepted: 2024-05-05
issued: 2024-07-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Chong
author list: Agent
  family name: Deng
  given name: Zongyuan
author list: Agent
  family name: Yu
  given name: Zhengran
author list: Agent
  family name: Chen
  given name: Yifan
author list: Agent
  family name: Yu
  given name: Tao
author list: Agent
  family name: Liang
  given name: Changxiang
author list: Agent
  family name: Ye
  given name: Yongyu
author list: Agent
  family name: Huang
  given name: Yongxiong
author list: Agent
  family name: Lyu
  given name: Feng-Juan
author list: Agent
  family name: Liang
  given name: Guoyan
author list: Agent
  family name: Chang
  given name: Yunbing
doi: 10.7717/peerj.17464
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-09
copyright: ©2024 Chen et al.
attribution name: Chen et al.

Assessing tooth wear progression in non-human primates: a longitudinal study using intraoral scanning technology
type: item
type: AcademicArticle
description: Intraoral scanners are widely used in a clinical setting for orthodontic treatments and tooth restorations, and are also useful for assessing dental wear and pathology progression. In this study, we assess the utility of using an intraoral scanner and associated software for quantifying dental tissue loss in non-human primates. An upper and lower second molar for 31 captive hamadryas baboons (Papio hamadryas) were assessed for dental tissue loss progression, giving a total sample of 62 teeth. The animals are part of the Southwest National Primate Research Center and were all fed the same monkey-chow diet over their lifetimes. Two molds of each dentition were taken at either two- or three-year intervals, and the associated casts scanned using an intraoral scanner (Medit i700). Tissue loss was calculated in WearCompare by superimposition of the two scans followed by subtraction analysis. Four individuals had dental caries, and were assessed separately. The results demonstrate the reliability of these techniques in capturing tissue loss data, evidenced by the alignment consistency between scans, lack of erroneous tissue gain between scans, and uniformity of tissue loss patterns among individuals (e.g., functional cusps showing the highest degree of wear). The average loss per mm2 per year for all samples combined was 0.05 mm3 (0.04 mm3 for females and 0.08 mm3 for males). There was no significant difference in wear progression between upper and lower molars. Substantial variation in the amount of tissue loss among individuals was found, despite their uniform diet. These findings foster multiple avenues for future research, including the exploration of wear progression across dental crowns and arcades, correlation between different types of tissue loss (e.g., attrition, erosion, fractures, caries), interplay between tissue loss and microwear/topographic analysis, and the genetic underpinnings of tissue loss variation.
format: application/pdf
format: text/html
creator: Ian Towle
creator: Kristin L. Krueger
creator: Raquel Hernando
creator: Leslea J. Hlusko
subject: Animal Behavior
subject: Anthropology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.17614
publisher: PeerJ Inc.
rights: © 2024 Towle et al.
abstract: Intraoral scanners are widely used in a clinical setting for orthodontic treatments and tooth restorations, and are also useful for assessing dental wear and pathology progression. In this study, we assess the utility of using an intraoral scanner and associated software for quantifying dental tissue loss in non-human primates. An upper and lower second molar for 31 captive hamadryas baboons (Papio hamadryas) were assessed for dental tissue loss progression, giving a total sample of 62 teeth. The animals are part of the Southwest National Primate Research Center and were all fed the same monkey-chow diet over their lifetimes. Two molds of each dentition were taken at either two- or three-year intervals, and the associated casts scanned using an intraoral scanner (Medit i700). Tissue loss was calculated in WearCompare by superimposition of the two scans followed by subtraction analysis. Four individuals had dental caries, and were assessed separately. The results demonstrate the reliability of these techniques in capturing tissue loss data, evidenced by the alignment consistency between scans, lack of erroneous tissue gain between scans, and uniformity of tissue loss patterns among individuals (e.g., functional cusps showing the highest degree of wear). The average loss per mm2 per year for all samples combined was 0.05 mm3 (0.04 mm3 for females and 0.08 mm3 for males). There was no significant difference in wear progression between upper and lower molars. Substantial variation in the amount of tissue loss among individuals was found, despite their uniform diet. These findings foster multiple avenues for future research, including the exploration of wear progression across dental crowns and arcades, correlation between different types of tissue loss (e.g., attrition, erosion, fractures, caries), interplay between tissue loss and microwear/topographic analysis, and the genetic underpinnings of tissue loss variation.
bibliographic citation: Towle et al. (2024) Assessing tooth wear progression in non-human primates: a longitudinal study using intraoral scanning technology. PeerJ 12:e17614 https://doi.org/10.7717/peerj.17614
date submitted: 2024-03-20
date accepted: 2024-05-31
issued: 2024-07-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Towle
  given name: Ian
author list: Agent
  family name: Krueger
  given name: Kristin L.
author list: Agent
  family name: Hernando
  given name: Raquel
author list: Agent
  family name: Hlusko
  given name: Leslea J.
doi: 10.7717/peerj.17614
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-09
copyright: ©2024 Towle et al.
attribution name: Towle et al.

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