PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effect of iron saturation of bovine lactoferrin on the inhibition of hepatitis B virus in vitro
items: Use of digital strategies in the diagnosis of oral squamous cell carcinoma: a scoping review
items: Combination administration of alprazolam and N-Ethylmaleimide synergistically enhances sleep behaviors in mice with no potential CNS side effects
items: Pathological caudal skeleton of an ichthyodectiform fish from the Upper Cretaceous Niobrara Formation of western Kansas, USA
items: Identification and characterization of the CRK gene family in the wheat genome and analysis of their expression profile in response to high temperature-induced male sterility
items: Caffeoylquinic acid profiling: comparative analysis in yerba mate, Indian camphorweed, and stevia extracts with emphasis on the influence of brewing conditions and cold storage in yerba mate infusion
items: XA21-mediated resistance to Xanthomonas oryzae pv. oryzae is dose dependent
items: Synergistic effect of seaweed extract and boric acid and/or calcium chloride on productivity and physico-chemical properties of Valencia orange
items: Whole-genome analysis of Escherichia coli isolated from wild Amur tiger (Panthera tigris altaica) and North China leopard (Panthera pardus japonensis)
items: A comparison of five methods to maximize RNA and DNA isolation yield from adipose tissue

Effect of iron saturation of bovine lactoferrin on the inhibition of hepatitis B virus in vitro
type: item
type: AcademicArticle
description: Background Hepatitis B virus (HBV) infection poses a major public health problem worldwide. Bovine lactoferrin (bLf) is a natural product that can inhibit HBV, but the effect of iron saturation on its resistance to HBV is unknown. Aims The purpose of this study is to investigate the impact of iron saturation of bLf against HBV. Methods HepG2 cells were cultured in DMEM high glucose containing 10% inactivated fetal calf serum, at 37 °C, in 5% CO2. MTT method was used to detect the cytotoxicity of bLf to HepG2 cells. Apo-bLf and holo-bLf were prepared from bLf. Iron saturation of these proteins was determined by atomic absorption spectrophotometry. Non-cytotoxic concentrations of candidate proteins were used in anti-HBV tests. Fluorescent quantitative polymerase chain reaction was used to detect HBV-DNA. Results The TC50 and TC0of bLf were 54.570 mg/ml and 1.997 mg/ml, respectively. The iron saturation of bLf, apo-bLf and holo-bLf were 10.29%, 8.42% and 85.32%, respectively. In this study, four non-cytotoxic concentrations of candidate proteins (1.5, 1.0, 0.5, and 0.1 mg/ml, respectively) were used to inhibit HBV in HepG2 cells. The results showed that 1.5 mg/ml bLf and 0.1 mg/ml holo-bLf effectively impaired the HBV-DNA amplification in HBV-infected HepG2 cells (P < 0.05). However, apo-bLf, and Fe3+ did not show the anti-HBV effects. Conclusion A total of 1.5 mg/ml bLf and 0.1 mg/ml holo-bLf could inhibit HBV-DNA in HepG2 cells. Complete bLf structure, appropriate concentration and iron saturation of bLf are necessary conditions for anti-HBV effects.
format: application/pdf
format: text/html
creator: Haibo Zhou
creator: Yiwei Zhu
creator: Ning Liu
creator: Wencui Zhang
creator: Jianchun Han
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.17302
publisher: PeerJ Inc.
rights: © 2024 Zhou et al.
abstract: Background Hepatitis B virus (HBV) infection poses a major public health problem worldwide. Bovine lactoferrin (bLf) is a natural product that can inhibit HBV, but the effect of iron saturation on its resistance to HBV is unknown. Aims The purpose of this study is to investigate the impact of iron saturation of bLf against HBV. Methods HepG2 cells were cultured in DMEM high glucose containing 10% inactivated fetal calf serum, at 37 °C, in 5% CO2. MTT method was used to detect the cytotoxicity of bLf to HepG2 cells. Apo-bLf and holo-bLf were prepared from bLf. Iron saturation of these proteins was determined by atomic absorption spectrophotometry. Non-cytotoxic concentrations of candidate proteins were used in anti-HBV tests. Fluorescent quantitative polymerase chain reaction was used to detect HBV-DNA. Results The TC50 and TC0of bLf were 54.570 mg/ml and 1.997 mg/ml, respectively. The iron saturation of bLf, apo-bLf and holo-bLf were 10.29%, 8.42% and 85.32%, respectively. In this study, four non-cytotoxic concentrations of candidate proteins (1.5, 1.0, 0.5, and 0.1 mg/ml, respectively) were used to inhibit HBV in HepG2 cells. The results showed that 1.5 mg/ml bLf and 0.1 mg/ml holo-bLf effectively impaired the HBV-DNA amplification in HBV-infected HepG2 cells (P < 0.05). However, apo-bLf, and Fe3+ did not show the anti-HBV effects. Conclusion A total of 1.5 mg/ml bLf and 0.1 mg/ml holo-bLf could inhibit HBV-DNA in HepG2 cells. Complete bLf structure, appropriate concentration and iron saturation of bLf are necessary conditions for anti-HBV effects.
bibliographic citation: Zhou et al. (2024) Effect of iron saturation of bovine lactoferrin on the inhibition of hepatitis B virus in vitro. PeerJ 12:e17302 https://doi.org/10.7717/peerj.17302
date submitted: 2022-06-27
date accepted: 2024-04-04
issued: 2024-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Haibo
author list: Agent
  family name: Zhu
  given name: Yiwei
author list: Agent
  family name: Liu
  given name: Ning
author list: Agent
  family name: Zhang
  given name: Wencui
author list: Agent
  family name: Han
  given name: Jianchun
doi: 10.7717/peerj.17302
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-07
copyright: ©2024 Zhou et al.
attribution name: Zhou et al.

Use of digital strategies in the diagnosis of oral squamous cell carcinoma: a scoping review
type: item
type: AcademicArticle
description: Telediagnosis uses information and communication technologies to support diagnosis, shortening geographical distances. It helps make decisions about various oral lesions. The objective of this scoping review was to map the existing literature on digital strategies to assist in the diagnosis of oral squamous cell carcinoma. this review was structured based on the 5-stage methodology proposed by Arksey and O’Malley, the Joanna Briggs Institute Manual for Evidence Synthesis and followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews. The methods were registered on the Open Science Framework. The research question was: What digital strategies have been used to assist in the diagnosis of oral squamous cell carcinoma? The search was conducted on PubMed/MEDLINE, Scopus, Web of Science, Embase, and ScienceDirect. Inclusion criteria comprised studies on telediagnosis, teleconsultation or teleconsultation mediated by a professional and studies in English, without date restrictions. The search conducted in June 2023 yielded 1,798 articles, from which 16 studies were included. Telediagnosis was reported in nine studies, involving data screening through applications, clinical images from digital cameras, mobile phones or artificial intelligence. Histopathological images were reported in four studies. Both, telediagnosis and teleconsultation, were mentioned in seven studies, utilizing images and information submission services to platforms, WhatsApp or applications. One study presented teleconsultations involving slides and another study introduced teleconsultation mediated by a professional. Digital strategies telediagnosis and teleconsultations enable the histopathological diagnosis of oral cancer through clinical or histopathological images. The higher the observed diagnostic agreement, the better the performance of the strategy.
format: application/pdf
format: text/html
creator: Rebeka Thiara Nascimento dos Santos
creator: Caroline Augusta Belo Faria
creator: Nathalya Fedechen Martins
creator: Luiz Gustavo de Sousa Duda Júnior
creator: Ana Beatriz Fernandes Azevêdo
creator: Weslay Rodrigues da Silva
creator: Ana Paula Veras Sobral
subject: Dentistry
subject: Oncology
subject: Otorhinolaryngology
subject: Pathology
subject: Healthcare Services
description: doi:10.7717/peerj.17329
publisher: PeerJ Inc.
rights: © 2024 Santos et al.
abstract: Telediagnosis uses information and communication technologies to support diagnosis, shortening geographical distances. It helps make decisions about various oral lesions. The objective of this scoping review was to map the existing literature on digital strategies to assist in the diagnosis of oral squamous cell carcinoma. this review was structured based on the 5-stage methodology proposed by Arksey and O’Malley, the Joanna Briggs Institute Manual for Evidence Synthesis and followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews. The methods were registered on the Open Science Framework. The research question was: What digital strategies have been used to assist in the diagnosis of oral squamous cell carcinoma? The search was conducted on PubMed/MEDLINE, Scopus, Web of Science, Embase, and ScienceDirect. Inclusion criteria comprised studies on telediagnosis, teleconsultation or teleconsultation mediated by a professional and studies in English, without date restrictions. The search conducted in June 2023 yielded 1,798 articles, from which 16 studies were included. Telediagnosis was reported in nine studies, involving data screening through applications, clinical images from digital cameras, mobile phones or artificial intelligence. Histopathological images were reported in four studies. Both, telediagnosis and teleconsultation, were mentioned in seven studies, utilizing images and information submission services to platforms, WhatsApp or applications. One study presented teleconsultations involving slides and another study introduced teleconsultation mediated by a professional. Digital strategies telediagnosis and teleconsultations enable the histopathological diagnosis of oral cancer through clinical or histopathological images. The higher the observed diagnostic agreement, the better the performance of the strategy.
bibliographic citation: Santos et al. (2024) Use of digital strategies in the diagnosis of oral squamous cell carcinoma: a scoping review. PeerJ 12:e17329 https://doi.org/10.7717/peerj.17329
date submitted: 2024-01-02
date accepted: 2024-04-11
issued: 2024-05-07
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Santos
  given name: Rebeka Thiara Nascimento dos
author list: Agent
  family name: Faria
  given name: Caroline Augusta Belo
author list: Agent
  family name: Martins
  given name: Nathalya Fedechen
author list: Agent
  family name: Duda Júnior
  given name: Luiz Gustavo de Sousa
author list: Agent
  family name: Azevêdo
  given name: Ana Beatriz Fernandes
author list: Agent
  family name: Silva
  given name: Weslay Rodrigues da
author list: Agent
  family name: Sobral
  given name: Ana Paula Veras
doi: 10.7717/peerj.17329
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-07
attribution name: Santos et al.

Combination administration of alprazolam and N-Ethylmaleimide synergistically enhances sleep behaviors in mice with no potential CNS side effects
type: item
type: AcademicArticle
description: Background N-Ethylmaleimide (NEM), an agonist of the potassium chloride cotransporters 2 (KCC2) receptor, has been correlated with neurosuppressive outcomes, including decreased pain perception and the prevention of epileptic seizures. Nevertheless, its relationship with sleep-inducing effects remains unreported. Objective The present study aimed to investigate the potential enhancement of NEM on the sleep-inducing properties of alprazolam (Alp). Methods The test of the righting reflex was used to identify the appropriate concentrations of Alp and NEM for inducing sleep-promoting effects in mice. Total sleep duration and sleep quality were evaluated through EEG/EMG analysis. The neural mechanism underlying the sleep-promoting effect was examined through c-fos immunoreactivity in the brain using immunofluorescence. Furthermore, potential CNS-side effects of the combination Alp and NEM were assessed using LABORAS automated home-cage behavioral phenotyping. Results Combination administration of Alp (1.84 mg/kg) and NEM (1.0 mg/kg) significantly decreased sleep latency and increased sleep duration in comparison to administering 1.84 mg/kg Alp alone. This effect was characterized by a notable increase in REM duration. The findings from c-fos immunoreactivity indicated that NEM significantly suppressed neuron activation in brain regions associated with wakefulness. Additionally, combination administration of Alp and NEM showed no effects on mouse neural behaviors during automated home cage monitoring. Conclusions This study is the first to propose and demonstrate a combination therapy involving Alp and NEM that not only enhances the hypnotic effect but also mitigates potential CNS side effects, suggesting its potential application in treating insomnia.
format: application/pdf
format: text/html
creator: Siqing Zhu
creator: Jingjing Shi
creator: Yi Zhang
creator: Xuejun Chen
creator: Tong Shi
creator: Liqin Li
subject: Animal Behavior
subject: Biochemistry
subject: Neuroscience
subject: Neurology
description: doi:10.7717/peerj.17342
publisher: PeerJ Inc.
rights: © 2024 Zhu et al.
abstract: Background N-Ethylmaleimide (NEM), an agonist of the potassium chloride cotransporters 2 (KCC2) receptor, has been correlated with neurosuppressive outcomes, including decreased pain perception and the prevention of epileptic seizures. Nevertheless, its relationship with sleep-inducing effects remains unreported. Objective The present study aimed to investigate the potential enhancement of NEM on the sleep-inducing properties of alprazolam (Alp). Methods The test of the righting reflex was used to identify the appropriate concentrations of Alp and NEM for inducing sleep-promoting effects in mice. Total sleep duration and sleep quality were evaluated through EEG/EMG analysis. The neural mechanism underlying the sleep-promoting effect was examined through c-fos immunoreactivity in the brain using immunofluorescence. Furthermore, potential CNS-side effects of the combination Alp and NEM were assessed using LABORAS automated home-cage behavioral phenotyping. Results Combination administration of Alp (1.84 mg/kg) and NEM (1.0 mg/kg) significantly decreased sleep latency and increased sleep duration in comparison to administering 1.84 mg/kg Alp alone. This effect was characterized by a notable increase in REM duration. The findings from c-fos immunoreactivity indicated that NEM significantly suppressed neuron activation in brain regions associated with wakefulness. Additionally, combination administration of Alp and NEM showed no effects on mouse neural behaviors during automated home cage monitoring. Conclusions This study is the first to propose and demonstrate a combination therapy involving Alp and NEM that not only enhances the hypnotic effect but also mitigates potential CNS side effects, suggesting its potential application in treating insomnia.
bibliographic citation: Zhu et al. (2024) Combination administration of alprazolam and N-Ethylmaleimide synergistically enhances sleep behaviors in mice with no potential CNS side effects. PeerJ 12:e17342 https://doi.org/10.7717/peerj.17342
date submitted: 2023-12-08
date accepted: 2024-04-15
issued: 2024-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Siqing
author list: Agent
  family name: Shi
  given name: Jingjing
author list: Agent
  family name: Zhang
  given name: Yi
author list: Agent
  family name: Chen
  given name: Xuejun
author list: Agent
  family name: Shi
  given name: Tong
author list: Agent
  family name: Li
  given name: Liqin
doi: 10.7717/peerj.17342
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-07
copyright: ©2024 Zhu et al.
attribution name: Zhu et al.

Pathological caudal skeleton of an ichthyodectiform fish from the Upper Cretaceous Niobrara Formation of western Kansas, USA
type: item
type: AcademicArticle
description: A series of 12 contiguous caudal vertebrae of an ichthyodectiform fish from the Smoky Hill Chalk Member of the Niobrara Formation is described. The vertebral centra exhibit extensive overgrowth of pathological bone and there is additional pathological bone within the centra and intervertebral spaces, which together resulted in the coossification of most centra. The extent of the pathology is greatest on preural vertebrae 1-3 and decreases anteriorly, which suggests that the pathology began posteriorly and progressed anteriorly. In addition to the pathological overgrowth on bones, the specimen preserves features interpreted as calcified and/or ossified soft tissues associated with the neural and haemal canals. The pathologies are unlike previously described examples of bony pathologies in fish, and it is suggested that they resulted from combined bacterial and fungal infections. As the pathologies developed, they would have adversely impacted the fish’s swimming and feeding abilities, and presumably eventually led to the fish’s death.
format: application/pdf
format: text/html
creator: S Christopher Bennett
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.17353
publisher: PeerJ Inc.
rights: © 2024 Bennett
abstract: A series of 12 contiguous caudal vertebrae of an ichthyodectiform fish from the Smoky Hill Chalk Member of the Niobrara Formation is described. The vertebral centra exhibit extensive overgrowth of pathological bone and there is additional pathological bone within the centra and intervertebral spaces, which together resulted in the coossification of most centra. The extent of the pathology is greatest on preural vertebrae 1-3 and decreases anteriorly, which suggests that the pathology began posteriorly and progressed anteriorly. In addition to the pathological overgrowth on bones, the specimen preserves features interpreted as calcified and/or ossified soft tissues associated with the neural and haemal canals. The pathologies are unlike previously described examples of bony pathologies in fish, and it is suggested that they resulted from combined bacterial and fungal infections. As the pathologies developed, they would have adversely impacted the fish’s swimming and feeding abilities, and presumably eventually led to the fish’s death.
bibliographic citation: Bennett (2024) Pathological caudal skeleton of an ichthyodectiform fish from the Upper Cretaceous Niobrara Formation of western Kansas, USA. PeerJ 12:e17353 https://doi.org/10.7717/peerj.17353
date submitted: 2024-02-15
date accepted: 2024-04-17
issued: 2024-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bennett
  given name: S Christopher
doi: 10.7717/peerj.17353
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-07
copyright: ©2024 Bennett
attribution name: Bennett

Identification and characterization of the CRK gene family in the wheat genome and analysis of their expression profile in response to high temperature-induced male sterility
type: item
type: AcademicArticle
description: Cysteine-rich receptor-like kinases (CRKs) play many important roles during plant development, including defense responses under both biotic and abiotic stress, reactive oxygen species (ROS) homeostasis, callose deposition and programmed cell death (PCD). However, there are few studies on the involvement of the CRK family in male sterility due to heat stress in wheat (Triticum aestivum L.). In this study, a genome-wide characterization of the CRK family was performed to investigate the structural and functional attributes of the wheat CRKs in anther sterility caused by heat stress. A total of 95 CRK genes were unevenly distributed on 18 chromosomes, with the most genes distributed on chromosome 2B. Paralogous homologous genes with Ka/Ks ratios less than 1 may have undergone strong purifying selection during evolution and are more functionally conserved. The collinearity analysis results of CRK genes showed that wheat and Arabidopsis (A. thaliana), foxtail millet, Brachypodium distachyon (B. distachyon), and rice have three, 12, 15, and 11 pairs of orthologous genes, respectively. In addition, the results of the network interactions of genes and miRNAs showed that five miRNAs were in the hub of the interactions map, namely tae-miR9657b-5p, tae-miR9780, tae-miR9676-5p, tae-miR164, and tae-miR531. Furthermore, qRT-PCR validation of the six TaCRK genes showed that they play key roles in the development of the mononuclear stage anthers, as all six genes were expressed at highly significant levels in heat-stressed male sterile mononuclear stage anthers compared to normal anthers. We hypothesized that the TaCRK gene is significant in the process of high-temperature-induced sterility in wheat based on the combination of anther phenotypes, paraffin sections, and qRT-PCR data. These results improve our understanding of their relationship.
format: application/pdf
format: text/html
creator: Hongzhan Liu
creator: Xiaoyi Li
creator: Zehui Yin
creator: Junmin Hu
creator: Liuyong Xie
creator: Huanhuan Wu
creator: Shuying Han
creator: Bing Li
creator: Huifang Zhang
creator: Chaoqiong Li
creator: Lili Li
creator: Fuli Zhang
creator: Guangxuan Tan
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.17370
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Cysteine-rich receptor-like kinases (CRKs) play many important roles during plant development, including defense responses under both biotic and abiotic stress, reactive oxygen species (ROS) homeostasis, callose deposition and programmed cell death (PCD). However, there are few studies on the involvement of the CRK family in male sterility due to heat stress in wheat (Triticum aestivum L.). In this study, a genome-wide characterization of the CRK family was performed to investigate the structural and functional attributes of the wheat CRKs in anther sterility caused by heat stress. A total of 95 CRK genes were unevenly distributed on 18 chromosomes, with the most genes distributed on chromosome 2B. Paralogous homologous genes with Ka/Ks ratios less than 1 may have undergone strong purifying selection during evolution and are more functionally conserved. The collinearity analysis results of CRK genes showed that wheat and Arabidopsis (A. thaliana), foxtail millet, Brachypodium distachyon (B. distachyon), and rice have three, 12, 15, and 11 pairs of orthologous genes, respectively. In addition, the results of the network interactions of genes and miRNAs showed that five miRNAs were in the hub of the interactions map, namely tae-miR9657b-5p, tae-miR9780, tae-miR9676-5p, tae-miR164, and tae-miR531. Furthermore, qRT-PCR validation of the six TaCRK genes showed that they play key roles in the development of the mononuclear stage anthers, as all six genes were expressed at highly significant levels in heat-stressed male sterile mononuclear stage anthers compared to normal anthers. We hypothesized that the TaCRK gene is significant in the process of high-temperature-induced sterility in wheat based on the combination of anther phenotypes, paraffin sections, and qRT-PCR data. These results improve our understanding of their relationship.
bibliographic citation: Liu et al. (2024) Identification and characterization of the CRK gene family in the wheat genome and analysis of their expression profile in response to high temperature-induced male sterility. PeerJ 12:e17370 https://doi.org/10.7717/peerj.17370
date submitted: 2023-12-29
date accepted: 2024-04-18
issued: 2024-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hongzhan
author list: Agent
  family name: Li
  given name: Xiaoyi
author list: Agent
  family name: Yin
  given name: Zehui
author list: Agent
  family name: Hu
  given name: Junmin
author list: Agent
  family name: Xie
  given name: Liuyong
author list: Agent
  family name: Wu
  given name: Huanhuan
author list: Agent
  family name: Han
  given name: Shuying
author list: Agent
  family name: Li
  given name: Bing
author list: Agent
  family name: Zhang
  given name: Huifang
author list: Agent
  family name: Li
  given name: Chaoqiong
author list: Agent
  family name: Li
  given name: Lili
author list: Agent
  family name: Zhang
  given name: Fuli
author list: Agent
  family name: Tan
  given name: Guangxuan
doi: 10.7717/peerj.17370
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-07
copyright: ©2024 Liu et al.
attribution name: Liu et al.

Caffeoylquinic acid profiling: comparative analysis in yerba mate, Indian camphorweed, and stevia extracts with emphasis on the influence of brewing conditions and cold storage in yerba mate infusion
type: item
type: AcademicArticle
description: Herbal infusions exhibit diverse pharmacological effects, such as antioxidant, anti-inflammatory, anticancer, antihypertensive, and antineurodegenerative activities, which can be attributed to the high content of phenolic compounds (e.g., caffeoylquinic acids (CQAs)). In this study, we used ultraperformance liquid chromatography to determine the content of CQAs in the methanolic extracts of model herbs, namely, yerba mate (Ilex paraguariensis), stevia (Stevia rebaudiana), and Indian camphorweed (Pluchea indica (L.) Less.). The results revealed that yerba mate had the highest total CQA content (108.05 ± 1.12 mg/g of dry weight). Furthermore, we evaluated the effect of brewing conditions and storage at 4 °C under dark and light conditions on the antioxidant property and total phenolic and CQA contents of a yerba mate infusion. The analysis of the yerba mate infusions prepared with different steeping times, dried leaf weights, and water temperatures revealed that the amount of extracted CQAs was maximized (∼175 mg/150 mL) when 6 g of dried leaves were steeped in hot water for 10 min. A total of 10-day refrigerated storage resulted in no significant changes in the antioxidant activity and total phenolic and CQA contents of an infusion kept in a brown container (dark). However, the antioxidant properties and total phenolic and CQA contents were negatively affected when kept in a clear container, suggesting the detrimental effect of light exposure. Our study provides practical recommendations for improving the preparation and storage of herbal infusions, thus catering to the needs of consumers, food scientists, and commercial producers. Moreover, it is the first study of the influence of light exposure on the content of crucial quality attributes within plant-based beverages.
format: application/pdf
format: text/html
creator: Gholamreza Khaksar
creator: Nantachaporn Chaichana
creator: Kitipong Assatarakul
creator: Supaart Sirikantaramas
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.17250
publisher: PeerJ Inc.
rights: © 2024 Khaksar et al.
abstract: Herbal infusions exhibit diverse pharmacological effects, such as antioxidant, anti-inflammatory, anticancer, antihypertensive, and antineurodegenerative activities, which can be attributed to the high content of phenolic compounds (e.g., caffeoylquinic acids (CQAs)). In this study, we used ultraperformance liquid chromatography to determine the content of CQAs in the methanolic extracts of model herbs, namely, yerba mate (Ilex paraguariensis), stevia (Stevia rebaudiana), and Indian camphorweed (Pluchea indica (L.) Less.). The results revealed that yerba mate had the highest total CQA content (108.05 ± 1.12 mg/g of dry weight). Furthermore, we evaluated the effect of brewing conditions and storage at 4 °C under dark and light conditions on the antioxidant property and total phenolic and CQA contents of a yerba mate infusion. The analysis of the yerba mate infusions prepared with different steeping times, dried leaf weights, and water temperatures revealed that the amount of extracted CQAs was maximized (∼175 mg/150 mL) when 6 g of dried leaves were steeped in hot water for 10 min. A total of 10-day refrigerated storage resulted in no significant changes in the antioxidant activity and total phenolic and CQA contents of an infusion kept in a brown container (dark). However, the antioxidant properties and total phenolic and CQA contents were negatively affected when kept in a clear container, suggesting the detrimental effect of light exposure. Our study provides practical recommendations for improving the preparation and storage of herbal infusions, thus catering to the needs of consumers, food scientists, and commercial producers. Moreover, it is the first study of the influence of light exposure on the content of crucial quality attributes within plant-based beverages.
bibliographic citation: Khaksar et al. (2024) Caffeoylquinic acid profiling: comparative analysis in yerba mate, Indian camphorweed, and stevia extracts with emphasis on the influence of brewing conditions and cold storage in yerba mate infusion. PeerJ 12:e17250 https://doi.org/10.7717/peerj.17250
date submitted: 2023-11-24
date accepted: 2024-03-25
issued: 2024-05-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khaksar
  given name: Gholamreza
author list: Agent
  family name: Chaichana
  given name: Nantachaporn
author list: Agent
  family name: Assatarakul
  given name: Kitipong
author list: Agent
  family name: Sirikantaramas
  given name: Supaart
doi: 10.7717/peerj.17250
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-06
copyright: © 2024 Khaksar et al.
attribution name: Khaksar et al.

XA21-mediated resistance to Xanthomonas oryzae pv. oryzae is dose dependent
type: item
type: AcademicArticle
description: The rice receptor kinase XA21 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight disease. To investigate the relationship between the expression level of XA21 and resulting resistance, we generated independent HA-XA21 transgenic rice lines accumulating the XA21 immune receptor fused with an HA epitope tag. Whole-genome sequence analysis identified the T-DNA insertion sites in sixteen independent T0 events. Through quantification of the HA-XA21 protein and assessment of the resistance to Xoo strain PXO99 in six independent transgenic lines, we observed that XA21-mediated resistance is dose dependent. In contrast, based on the four agronomic traits quantified in these experiments, yield is unlikely to be affected by the expression level of HA-XA21. These findings extend our knowledge of XA21-mediated defense and contribute to the growing number of well-defined genomic landing pads in the rice genome that can be targeted for gene insertion without compromising yield.
format: application/pdf
format: text/html
creator: Nan Zhang
creator: Xiaoou Dong
creator: Rashmi Jain
creator: Deling Ruan
creator: Artur Teixeira de Araujo Junior
creator: Yan Li
creator: Anna Lipzen
creator: Joel Martin
creator: Kerrie Barry
creator: Pamela C. Ronald
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.17323
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: The rice receptor kinase XA21 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight disease. To investigate the relationship between the expression level of XA21 and resulting resistance, we generated independent HA-XA21 transgenic rice lines accumulating the XA21 immune receptor fused with an HA epitope tag. Whole-genome sequence analysis identified the T-DNA insertion sites in sixteen independent T0 events. Through quantification of the HA-XA21 protein and assessment of the resistance to Xoo strain PXO99 in six independent transgenic lines, we observed that XA21-mediated resistance is dose dependent. In contrast, based on the four agronomic traits quantified in these experiments, yield is unlikely to be affected by the expression level of HA-XA21. These findings extend our knowledge of XA21-mediated defense and contribute to the growing number of well-defined genomic landing pads in the rice genome that can be targeted for gene insertion without compromising yield.
bibliographic citation: Zhang et al. (2024) XA21-mediated resistance to Xanthomonas oryzae pv. oryzae is dose dependent. PeerJ 12:e17323 https://doi.org/10.7717/peerj.17323
date submitted: 2023-09-28
date accepted: 2024-04-10
issued: 2024-05-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Nan
author list: Agent
  family name: Dong
  given name: Xiaoou
author list: Agent
  family name: Jain
  given name: Rashmi
author list: Agent
  family name: Ruan
  given name: Deling
author list: Agent
  family name: de Araujo Junior
  given name: Artur Teixeira
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: Lipzen
  given name: Anna
author list: Agent
  family name: Martin
  given name: Joel
author list: Agent
  family name: Barry
  given name: Kerrie
author list: Agent
  family name: Ronald
  given name: Pamela C.
doi: 10.7717/peerj.17323
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-06
copyright: ©2024 Zhang et al.
attribution name: Zhang et al.

Synergistic effect of seaweed extract and boric acid and/or calcium chloride on productivity and physico-chemical properties of Valencia orange
type: item
type: AcademicArticle
description: Many citrus species and cultivars are grown successfully in tropical and subtropical countries, as well as in arid and semi-arid regions with low levels of organic matter and low cation exchange, resulting in lower nutrient uptake by the plant. The essential nutrients needed for citrus flowering and fruit set are limited in winter due to a reduction in transpiration rate, negatively effecting vegetative growth, flowering, yield, and fruit quality. The present investigation was carried out to assess the nutritional status, fruit yield parameters, and fruit quality of Valencia orange trees after foliar spraying of seaweed extract (SW) combined with calcium chloride and boric acid and their combinations in the 2020/2021 and 2021/2022 seasons. The treatments were arranged in a split-plot design (three levels spraying seaweed extract × four levels spraying calcium chloride and boric acid and their combinations × four replicates × one tree/replicate). The results indicated that all of the characteristics measured, including leaf chlorophyll, leaf mineral contents, fruit yield parameters, fruit physical properties, and fruit chemical properties, were significantly affected by the foliar spraying of seaweed extract (SW) combined with calcium chloride and boric acid and their combinations. Although all treatments increased the productivity and the physical and chemical properties of Valencia orange fruits compared to the control, a treatment of 10 g/L SW combined with 0.5 g/L boric acid and 1 g/L calcium chloride produced superior results. This ratio of SW, boric acid, and calcium chloride is therefore recommended to enhance productivity and improve the physico-chemical properties of Valencia orange for greater fruit yield.
format: application/pdf
format: text/html
creator: Abdullah Alebidi
creator: Mahmoud Abdel-Sattar
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.17378
publisher: PeerJ Inc.
rights: © 2024 Alebidi and Abdel-Sattar
abstract: Many citrus species and cultivars are grown successfully in tropical and subtropical countries, as well as in arid and semi-arid regions with low levels of organic matter and low cation exchange, resulting in lower nutrient uptake by the plant. The essential nutrients needed for citrus flowering and fruit set are limited in winter due to a reduction in transpiration rate, negatively effecting vegetative growth, flowering, yield, and fruit quality. The present investigation was carried out to assess the nutritional status, fruit yield parameters, and fruit quality of Valencia orange trees after foliar spraying of seaweed extract (SW) combined with calcium chloride and boric acid and their combinations in the 2020/2021 and 2021/2022 seasons. The treatments were arranged in a split-plot design (three levels spraying seaweed extract × four levels spraying calcium chloride and boric acid and their combinations × four replicates × one tree/replicate). The results indicated that all of the characteristics measured, including leaf chlorophyll, leaf mineral contents, fruit yield parameters, fruit physical properties, and fruit chemical properties, were significantly affected by the foliar spraying of seaweed extract (SW) combined with calcium chloride and boric acid and their combinations. Although all treatments increased the productivity and the physical and chemical properties of Valencia orange fruits compared to the control, a treatment of 10 g/L SW combined with 0.5 g/L boric acid and 1 g/L calcium chloride produced superior results. This ratio of SW, boric acid, and calcium chloride is therefore recommended to enhance productivity and improve the physico-chemical properties of Valencia orange for greater fruit yield.
bibliographic citation: Alebidi et al. (2024) Synergistic effect of seaweed extract and boric acid and/or calcium chloride on productivity and physico-chemical properties of Valencia orange. PeerJ 12:e17378 https://doi.org/10.7717/peerj.17378
date submitted: 2024-02-05
date accepted: 2024-04-20
issued: 2024-05-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alebidi
  given name: Abdullah
author list: Agent
  family name: Abdel-Sattar
  given name: Mahmoud
doi: 10.7717/peerj.17378
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-06
copyright: © 2024 Alebidi and Abdel-Sattar
attribution name: Alebidi and Abdel-Sattar

Whole-genome analysis of Escherichia coli isolated from wild Amur tiger (Panthera tigris altaica) and North China leopard (Panthera pardus japonensis)
type: item
type: AcademicArticle
description: Background Escherichia coli is an important intestinal flora, of which pathogenic E. coli is capable of causing many enteric and extra-intestinal diseases. Antibiotics are essential for the treatment of bacterial infections caused by pathogenic E. coli; however, with the widespread use of antibiotics, drug resistance in E. coli has become particularly serious, posing a global threat to human, animal, and environmental health. While the drug resistance and pathogenicity of E. coli carried by tigers and leopards in captivity have been studied intensively in recent years, there is an extreme lack of information on E. coli in these top predators in the wild environment. Methods Whole genome sequencing data of 32 E. coli strains collected from the feces of wild Amur tiger (Panthera tigris altaica, n = 24) and North China leopard (Panthera pardus japonensis, n = 8) were analyzed in this article. The multi-locus sequence types, serotypes, virulence and resistance genotypes, plasmid replicon types, and core genomic SNPs phylogeny of these isolates were studied. Additionally, antimicrobial susceptibility testing (AST) was performed on these E. coli isolates. Results Among the E. coli isolates studied, 18 different sequence types were identified, with ST939 (21.9%), ST10 (15.6%), and ST3246 (9.4%) being the most prevalent. A total of 111 virulence genes were detected, averaging about 54 virulence genes per sample. They contribute to invasion, adherence, immune evasion, efflux pump, toxin, motility, stress adaption, and other virulence-related functions of E. coli. Sixty-eight AMR genes and point mutations were identified. Among the detected resistance genes, those belonging to the efflux pump family were the most abundant. Thirty-two E. coli isolates showed the highest rate of resistance to tetracycline (14/32; 43.8%), followed by imipenem (4/32; 12.5%), ciprofloxacin (3/32; 9.4%), doxycycline (2/32; 6.3%), and norfloxacin (1/32; 3.1%). Conclusions Our results suggest that E.…
format: application/pdf
format: text/html
creator: Hongjia Li
creator: Tianming Lan
creator: Hao Zhai
creator: Mengchao Zhou
creator: Denghui Chen
creator: Yaxian Lu
creator: Lei Han
creator: Jinpu Wei
creator: Shaochun Zhou
creator: Haitao Xu
creator: Lihong Tian
creator: Guangshun Jiang
creator: Zhijun Hou
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.17381
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background Escherichia coli is an important intestinal flora, of which pathogenic E. coli is capable of causing many enteric and extra-intestinal diseases. Antibiotics are essential for the treatment of bacterial infections caused by pathogenic E. coli; however, with the widespread use of antibiotics, drug resistance in E. coli has become particularly serious, posing a global threat to human, animal, and environmental health. While the drug resistance and pathogenicity of E. coli carried by tigers and leopards in captivity have been studied intensively in recent years, there is an extreme lack of information on E. coli in these top predators in the wild environment. Methods Whole genome sequencing data of 32 E. coli strains collected from the feces of wild Amur tiger (Panthera tigris altaica, n = 24) and North China leopard (Panthera pardus japonensis, n = 8) were analyzed in this article. The multi-locus sequence types, serotypes, virulence and resistance genotypes, plasmid replicon types, and core genomic SNPs phylogeny of these isolates were studied. Additionally, antimicrobial susceptibility testing (AST) was performed on these E. coli isolates. Results Among the E. coli isolates studied, 18 different sequence types were identified, with ST939 (21.9%), ST10 (15.6%), and ST3246 (9.4%) being the most prevalent. A total of 111 virulence genes were detected, averaging about 54 virulence genes per sample. They contribute to invasion, adherence, immune evasion, efflux pump, toxin, motility, stress adaption, and other virulence-related functions of E. coli. Sixty-eight AMR genes and point mutations were identified. Among the detected resistance genes, those belonging to the efflux pump family were the most abundant. Thirty-two E. coli isolates showed the highest rate of resistance to tetracycline (14/32; 43.8%), followed by imipenem (4/32; 12.5%), ciprofloxacin (3/32; 9.4%), doxycycline (2/32; 6.3%), and norfloxacin (1/32; 3.1%). Conclusions Our results suggest that E.…
bibliographic citation: Li et al. (2024) Whole-genome analysis of Escherichia coli isolated from wild Amur tiger (Panthera tigris altaica) and North China leopard (Panthera pardus japonensis). PeerJ 12:e17381 https://doi.org/10.7717/peerj.17381
date submitted: 2024-01-26
date accepted: 2024-04-21
issued: 2024-05-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Hongjia
author list: Agent
  family name: Lan
  given name: Tianming
author list: Agent
  family name: Zhai
  given name: Hao
author list: Agent
  family name: Zhou
  given name: Mengchao
author list: Agent
  family name: Chen
  given name: Denghui
author list: Agent
  family name: Lu
  given name: Yaxian
author list: Agent
  family name: Han
  given name: Lei
author list: Agent
  family name: Wei
  given name: Jinpu
author list: Agent
  family name: Zhou
  given name: Shaochun
author list: Agent
  family name: Xu
  given name: Haitao
author list: Agent
  family name: Tian
  given name: Lihong
author list: Agent
  family name: Jiang
  given name: Guangshun
author list: Agent
  family name: Hou
  given name: Zhijun
doi: 10.7717/peerj.17381
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-06
copyright: © 2024 Li et al.
attribution name: Li et al.

A comparison of five methods to maximize RNA and DNA isolation yield from adipose tissue
type: item
type: AcademicArticle
description: Adipose tissue in the human body occurs in various forms with different functions. It is an energy store, a complex endocrine organ, and a source of cells used in medicine. Many molecular analyses require the isolation of nucleic acids, which can cause some difficulties connected with the large amount of lipids in adipocytes. Ribonucleic acid isolation is particularly challenging due to its low stability and easy degradation by ribonucleases. The study aimed to compare and evaluate five RNA and DNA isolation methods from adipose tissue. The tested material was subcutaneous porcine adipose tissue subjected to different homogenization methods and RNA or DNA purification. A mortar and liquid nitrogen or ceramic beads were used for homogenization. The organic extraction (TriPure Reagent), spin columns with silica-membrane (RNeasy Mini Kit or High Pure PCR Template Preparation Kit), and the automatic MagNA Pure system were used for the purification. Five combinations were compared for RNA and DNA isolation. Obtained samples were evaluated for quantity and quality. The methods were compared in terms of yield (according to tissue mass), purity (A260/280 and A260/230), and nucleic acid degradation (RNA Integrity Number, RIN; DNA Integrity Number, DIN). The results were analyzed statistically. The average RNA yield was highest in method I, which used homogenization with ceramic beads and organic extraction. Low RNA concentration didn’t allow us to measure degradation for all samples in method III (homogenization with ceramic beads and spin-column purification). The highest RNA quality was achieved with method IV using homogenization in liquid nitrogen and spin column purification, which makes it the most effective for RNA isolation from adipose tissue. Required values of DNA yield, purity, and integrity were achieved only with spin column-based methods (III and IV). The most effective method for DNA isolation from adipose tissue is method III, using spin-columns without addi…
format: application/pdf
format: text/html
creator: Pawel Dabrowski
creator: Marta Rasmus
creator: Arkadiusz Jundzill
creator: Tomasz Drewa
creator: Marta Pokrywczynska
subject: Biochemistry
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.17071
publisher: PeerJ Inc.
rights: © 2024 Dabrowski et al.
abstract: Adipose tissue in the human body occurs in various forms with different functions. It is an energy store, a complex endocrine organ, and a source of cells used in medicine. Many molecular analyses require the isolation of nucleic acids, which can cause some difficulties connected with the large amount of lipids in adipocytes. Ribonucleic acid isolation is particularly challenging due to its low stability and easy degradation by ribonucleases. The study aimed to compare and evaluate five RNA and DNA isolation methods from adipose tissue. The tested material was subcutaneous porcine adipose tissue subjected to different homogenization methods and RNA or DNA purification. A mortar and liquid nitrogen or ceramic beads were used for homogenization. The organic extraction (TriPure Reagent), spin columns with silica-membrane (RNeasy Mini Kit or High Pure PCR Template Preparation Kit), and the automatic MagNA Pure system were used for the purification. Five combinations were compared for RNA and DNA isolation. Obtained samples were evaluated for quantity and quality. The methods were compared in terms of yield (according to tissue mass), purity (A260/280 and A260/230), and nucleic acid degradation (RNA Integrity Number, RIN; DNA Integrity Number, DIN). The results were analyzed statistically. The average RNA yield was highest in method I, which used homogenization with ceramic beads and organic extraction. Low RNA concentration didn’t allow us to measure degradation for all samples in method III (homogenization with ceramic beads and spin-column purification). The highest RNA quality was achieved with method IV using homogenization in liquid nitrogen and spin column purification, which makes it the most effective for RNA isolation from adipose tissue. Required values of DNA yield, purity, and integrity were achieved only with spin column-based methods (III and IV). The most effective method for DNA isolation from adipose tissue is method III, using spin-columns without addi…
bibliographic citation: Dabrowski et al. (2024) A comparison of five methods to maximize RNA and DNA isolation yield from adipose tissue. PeerJ 12:e17071 https://doi.org/10.7717/peerj.17071
date submitted: 2022-08-02
date accepted: 2024-02-18
issued: 2024-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dabrowski
  given name: Pawel
author list: Agent
  family name: Rasmus
  given name: Marta
author list: Agent
  family name: Jundzill
  given name: Arkadiusz
author list: Agent
  family name: Drewa
  given name: Tomasz
author list: Agent
  family name: Pokrywczynska
  given name: Marta
doi: 10.7717/peerj.17071
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-03
copyright: © 2024 Dabrowski et al.
attribution name: Dabrowski et al.

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