PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics
items: Regulation of endoplasmic reticulum stress on autophagy and apoptosis of nucleus pulposus cells in intervertebral disc degeneration and its related mechanisms
items: SUMOylation of zebrafish transcription factor Zbtb21 affects its transcription activity
items: Kernel density estimation of allele frequency including undetected alleles
items: Fumaric acid production from fermented oil palm empty fruit bunches using fungal isolate K20: a comparison between free and immobilized cells
items: Predicting central cervical lymph node metastasis in papillary thyroid carcinoma with Hashimoto’s thyroiditis: a practical nomogram based on retrospective study
items: Magnification in preclinical procedures: effect on muscle activity and angular deviations of the neck and trunk
items: Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients
items: Exogenous Hemin enhances the antioxidant defense system of rice by regulating the AsA-GSH cycle under NaCl stress
items: Inhibition of SUV39H1 reduces tumor angiogenesis via Notch1 in oral squamous cell carcinoma

Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics
type: item
type: AcademicArticle
description: Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.
format: application/pdf
format: text/html
creator: Kauthar M. Omar
creator: George L. Kitundu
creator: Adijat O. Jimoh
creator: Dorcus N. Namikelwa
creator: Felix M. Lisso
creator: Abiola A. Babajide
creator: Seun E. Olufemi
creator: Olaitan I. Awe
subject: Agricultural Science
subject: Bioinformatics
subject: Computational Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.17181
publisher: PeerJ Inc.
rights: © 2024 Omar et al.
abstract: Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.
bibliographic citation: Omar et al. (2024) Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics. PeerJ 12:e17181 https://doi.org/10.7717/peerj.17181
date submitted: 2022-12-12
date accepted: 2024-03-11
issued: 2024-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Omar
  given name: Kauthar M.
author list: Agent
  family name: Kitundu
  given name: George L.
author list: Agent
  family name: Jimoh
  given name: Adijat O.
author list: Agent
  family name: Namikelwa
  given name: Dorcus N.
author list: Agent
  family name: Lisso
  given name: Felix M.
author list: Agent
  family name: Babajide
  given name: Abiola A.
author list: Agent
  family name: Olufemi
  given name: Seun E.
author list: Agent
  family name: Awe
  given name: Olaitan I.
doi: 10.7717/peerj.17181
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-22
copyright: ©2024 Omar et al.
attribution name: Omar et al.

Regulation of endoplasmic reticulum stress on autophagy and apoptosis of nucleus pulposus cells in intervertebral disc degeneration and its related mechanisms
type: item
type: AcademicArticle
description: Intervertebral disc degeneration (IVDD) is a common and frequent disease in orthopedics, which seriously affects the quality of life of patients. Endoplasmic reticulum stress (ERS)-regulated autophagy and apoptosis play an important role in nucleus pulposus (NP) cells in IVDD. Hypoxia and serum deprivation were used to induce NP cells. Cell counting kit-8 (CCK-8) assay was used to detect cell activity and immunofluorescence (IF) was applied for the appraisement of glucose regulated protein 78 (GRP78) and green fluorescent protein (GFP)-light chain 3 (LC3). Cell apoptosis was detected by flow cytometry and the expression of LC3II/I was detected by western blot. NP cells under hypoxia and serum deprivation were induced by lipopolysaccharide (LPS), and intervened by ERS inhibitor (4-phenylbutyric acid, 4-PBA) and activator (Thapsigargin, TP). Then, above functional experiments were conducted again and western blot was employed for the evaluation of autophagy-, apoptosis and ERS-related proteins. Finally, NP cells under hypoxia and serum deprivation were stimulated by LPS and intervened using apoptosis inhibitor z-Val-Ala-DL-Asp-fluoromethyl ketone (Z-VAD-FMK) and autophagy inhibitor 3-methyladenine (3-MA). CCK-8 assay, IF, flow cytometry and western blot were performed again. Besides, the levels of inflammatory cytokines were measured with enzyme-linked immunosorbent assay (ELISA) and the protein expressions of programmed death markers were estimated with western blot. It showed that serum deprivation induces autophagy and apoptosis. ERS was significantly activated by LPS in hypoxic and serum deprivation environment, and autophagy and apoptosis were significantly promoted. Overall, ERS affects the occurrence and development of IVDD by regulating autophagy, apoptosis and other programmed death.
format: application/pdf
format: text/html
creator: Jiuming Dai
creator: Jin Liu
creator: Yucheng Shen
creator: Bing Zhang
creator: Chaonian Li
creator: Zhidong Liu
subject: Cell Biology
subject: Molecular Biology
subject: Orthopedics
description: doi:10.7717/peerj.17212
publisher: PeerJ Inc.
rights: © 2024 Dai et al.
abstract: Intervertebral disc degeneration (IVDD) is a common and frequent disease in orthopedics, which seriously affects the quality of life of patients. Endoplasmic reticulum stress (ERS)-regulated autophagy and apoptosis play an important role in nucleus pulposus (NP) cells in IVDD. Hypoxia and serum deprivation were used to induce NP cells. Cell counting kit-8 (CCK-8) assay was used to detect cell activity and immunofluorescence (IF) was applied for the appraisement of glucose regulated protein 78 (GRP78) and green fluorescent protein (GFP)-light chain 3 (LC3). Cell apoptosis was detected by flow cytometry and the expression of LC3II/I was detected by western blot. NP cells under hypoxia and serum deprivation were induced by lipopolysaccharide (LPS), and intervened by ERS inhibitor (4-phenylbutyric acid, 4-PBA) and activator (Thapsigargin, TP). Then, above functional experiments were conducted again and western blot was employed for the evaluation of autophagy-, apoptosis and ERS-related proteins. Finally, NP cells under hypoxia and serum deprivation were stimulated by LPS and intervened using apoptosis inhibitor z-Val-Ala-DL-Asp-fluoromethyl ketone (Z-VAD-FMK) and autophagy inhibitor 3-methyladenine (3-MA). CCK-8 assay, IF, flow cytometry and western blot were performed again. Besides, the levels of inflammatory cytokines were measured with enzyme-linked immunosorbent assay (ELISA) and the protein expressions of programmed death markers were estimated with western blot. It showed that serum deprivation induces autophagy and apoptosis. ERS was significantly activated by LPS in hypoxic and serum deprivation environment, and autophagy and apoptosis were significantly promoted. Overall, ERS affects the occurrence and development of IVDD by regulating autophagy, apoptosis and other programmed death.
bibliographic citation: Dai et al. (2024) Regulation of endoplasmic reticulum stress on autophagy and apoptosis of nucleus pulposus cells in intervertebral disc degeneration and its related mechanisms. PeerJ 12:e17212 https://doi.org/10.7717/peerj.17212
date submitted: 2023-12-07
date accepted: 2024-03-19
issued: 2024-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dai
  given name: Jiuming
author list: Agent
  family name: Liu
  given name: Jin
author list: Agent
  family name: Shen
  given name: Yucheng
author list: Agent
  family name: Zhang
  given name: Bing
author list: Agent
  family name: Li
  given name: Chaonian
author list: Agent
  family name: Liu
  given name: Zhidong
doi: 10.7717/peerj.17212
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-22
copyright: © 2024 Dai et al.
attribution name: Dai et al.

SUMOylation of zebrafish transcription factor Zbtb21 affects its transcription activity
type: item
type: AcademicArticle
description: Background Post-translational modification by Small Ubiquitin-like MOdifier (SUMO) is an important mechanism to regulate protein activity, protein stability, and localization of substrates. Zbtb21 is a zinc finger and BTB (Broad-complex, Tram-track and Bric à brac) domain-containing transcription factor. Bioinformatic prediction suggests several putative SUMOylated sites in Zbtb21 protein. Methods Two evolutionarily conserved lysine residues in Zbtb21 protein were mutated alone or in combination to disrupt the binding with SUMO molecules. Western blot and co-immunoprecipitation analyses were performed to detect the SUMOylation state of wild type and mutant Zbtb21 proteins, respectively. Luciferase reporter assays were conducted to evaluate their transcription activities. Meanwhile, immunofluorescence staining was carried out to show their sub-nuclear localizations. Finally, co-immunoprecipitation was performed to detect the interaction between Zbtb21 and its partners. Results Phylogenetically conserved lysines 419 and 845 of zebrafish Zbtb21 protein can be conjugated with SUMO molecules. SUMOylation does not affect the subcellular localization and protein stability of Zbtb21, as well as the interaction with Zbtb14 or Zbtb21. Nevertheless, luciferase reporter assays revealed that Zbtb21 is a dual-function transcription factor which exerts activation or repression effect on different promoters, and SUMOylation can modulate the transcriptional activity of Zbtb21 in regulating downstream target genes. Hence, Zbtb21 is identified as a novel substrate of SUMOylation, which would be important for its function. Conclusions Zebrafish Zbtb21 protein can be SUMOylated on lysines 419 and 845, which is evolutionary conserved. SUMOylation affects the dual role of Zbtb21 on transcription.
format: application/pdf
format: text/html
creator: Zhou Fang
creator: Yun Deng
creator: Haihong Wang
creator: Jun Zhou
subject: Biochemistry
subject: Developmental Biology
description: doi:10.7717/peerj.17234
publisher: PeerJ Inc.
rights: © 2024 Fang et al.
abstract: Background Post-translational modification by Small Ubiquitin-like MOdifier (SUMO) is an important mechanism to regulate protein activity, protein stability, and localization of substrates. Zbtb21 is a zinc finger and BTB (Broad-complex, Tram-track and Bric à brac) domain-containing transcription factor. Bioinformatic prediction suggests several putative SUMOylated sites in Zbtb21 protein. Methods Two evolutionarily conserved lysine residues in Zbtb21 protein were mutated alone or in combination to disrupt the binding with SUMO molecules. Western blot and co-immunoprecipitation analyses were performed to detect the SUMOylation state of wild type and mutant Zbtb21 proteins, respectively. Luciferase reporter assays were conducted to evaluate their transcription activities. Meanwhile, immunofluorescence staining was carried out to show their sub-nuclear localizations. Finally, co-immunoprecipitation was performed to detect the interaction between Zbtb21 and its partners. Results Phylogenetically conserved lysines 419 and 845 of zebrafish Zbtb21 protein can be conjugated with SUMO molecules. SUMOylation does not affect the subcellular localization and protein stability of Zbtb21, as well as the interaction with Zbtb14 or Zbtb21. Nevertheless, luciferase reporter assays revealed that Zbtb21 is a dual-function transcription factor which exerts activation or repression effect on different promoters, and SUMOylation can modulate the transcriptional activity of Zbtb21 in regulating downstream target genes. Hence, Zbtb21 is identified as a novel substrate of SUMOylation, which would be important for its function. Conclusions Zebrafish Zbtb21 protein can be SUMOylated on lysines 419 and 845, which is evolutionary conserved. SUMOylation affects the dual role of Zbtb21 on transcription.
bibliographic citation: Fang et al. (2024) SUMOylation of zebrafish transcription factor Zbtb21 affects its transcription activity. PeerJ 12:e17234 https://doi.org/10.7717/peerj.17234
date submitted: 2023-10-06
date accepted: 2024-03-22
issued: 2024-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fang
  given name: Zhou
author list: Agent
  family name: Deng
  given name: Yun
author list: Agent
  family name: Wang
  given name: Haihong
author list: Agent
  family name: Zhou
  given name: Jun
doi: 10.7717/peerj.17234
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-22
copyright: © 2024 Fang et al.
attribution name: Fang et al.

Kernel density estimation of allele frequency including undetected alleles
type: item
type: AcademicArticle
description: Whereas undetected species contribute to estimation of species diversity, undetected alleles have not been used to estimated genetic diversity. Although random sampling guarantees unbiased estimation of allele frequency and genetic diversity measures, using undetected alleles may provide biased but more precise estimators useful for conservation. We newly devised kernel density estimation (KDE) for allele frequency including undetected alleles and tested it in estimation of allele frequency and nucleotide diversity using population generated by coalescent simulation as well as well as real population data. Contrary to expectations, nucleotide diversity estimated by KDE had worse bias and accuracy. Allele frequency estimated by KDE was also worse except when the sample size was small. These might be due to finity of population and/or the curse of dimensionality. In conclusion, KDE of allele frequency does not contribute to genetic diversity estimation.
format: application/pdf
format: text/html
creator: Satoshi Aoki
creator: Keita Fukasawa
subject: Biodiversity
subject: Bioinformatics
subject: Conservation Biology
subject: Ecology
subject: Statistics
description: doi:10.7717/peerj.17248
publisher: PeerJ Inc.
rights: © 2024 Aoki and Fukasawa
abstract: Whereas undetected species contribute to estimation of species diversity, undetected alleles have not been used to estimated genetic diversity. Although random sampling guarantees unbiased estimation of allele frequency and genetic diversity measures, using undetected alleles may provide biased but more precise estimators useful for conservation. We newly devised kernel density estimation (KDE) for allele frequency including undetected alleles and tested it in estimation of allele frequency and nucleotide diversity using population generated by coalescent simulation as well as well as real population data. Contrary to expectations, nucleotide diversity estimated by KDE had worse bias and accuracy. Allele frequency estimated by KDE was also worse except when the sample size was small. These might be due to finity of population and/or the curse of dimensionality. In conclusion, KDE of allele frequency does not contribute to genetic diversity estimation.
bibliographic citation: Aoki et al. (2024) Kernel density estimation of allele frequency including undetected alleles. PeerJ 12:e17248 https://doi.org/10.7717/peerj.17248
date submitted: 2023-11-24
date accepted: 2024-03-25
issued: 2024-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aoki
  given name: Satoshi
author list: Agent
  family name: Fukasawa
  given name: Keita
doi: 10.7717/peerj.17248
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-22
copyright: © 2024 Aoki and Fukasawa
attribution name: Aoki and Fukasawa

Fumaric acid production from fermented oil palm empty fruit bunches using fungal isolate K20: a comparison between free and immobilized cells
type: item
type: AcademicArticle
description: This study investigated the potential of using steam-exploded oil palm empty fruit bunches (EFB) as a renewable feedstock for producing fumaric acid (FA), a food additive widely used for flavor and preservation, through a separate hydrolysis and fermentation process using the fungal isolate K20. The efficiency of FA production by free and immobilized cells was compared. The maximum FA concentration (3.25 g/L), with 0.034 g/L/h productivity, was observed after incubation with the free cells for 96 h. Furthermore, the production was scaled up in a 3-L air-lift fermenter using oil palm EFB-derived glucose as the substrate. The FA concentration, yield, and productivity from 100 g/L initial oil palm EFB-derived glucose were 44 g/L, 0.39 g/g, and 0.41 g/L/h, respectively. The potential for scaling up the fermentation process indicates favorable results, which could have significant implications for industrial applications.
format: application/pdf
format: text/html
creator: Antika Boondaeng
creator: Jureeporn Keabpimai
creator: Chanaporn Trakunjae
creator: Nanthavut Niyomvong
subject: Biotechnology
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.17282
publisher: PeerJ Inc.
rights: © 2024 Boondaeng et al.
abstract: This study investigated the potential of using steam-exploded oil palm empty fruit bunches (EFB) as a renewable feedstock for producing fumaric acid (FA), a food additive widely used for flavor and preservation, through a separate hydrolysis and fermentation process using the fungal isolate K20. The efficiency of FA production by free and immobilized cells was compared. The maximum FA concentration (3.25 g/L), with 0.034 g/L/h productivity, was observed after incubation with the free cells for 96 h. Furthermore, the production was scaled up in a 3-L air-lift fermenter using oil palm EFB-derived glucose as the substrate. The FA concentration, yield, and productivity from 100 g/L initial oil palm EFB-derived glucose were 44 g/L, 0.39 g/g, and 0.41 g/L/h, respectively. The potential for scaling up the fermentation process indicates favorable results, which could have significant implications for industrial applications.
bibliographic citation: Boondaeng et al. (2024) Fumaric acid production from fermented oil palm empty fruit bunches using fungal isolate K20: a comparison between free and immobilized cells. PeerJ 12:e17282 https://doi.org/10.7717/peerj.17282
date submitted: 2024-01-08
date accepted: 2024-04-01
issued: 2024-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boondaeng
  given name: Antika
author list: Agent
  family name: Keabpimai
  given name: Jureeporn
author list: Agent
  family name: Trakunjae
  given name: Chanaporn
author list: Agent
  family name: Niyomvong
  given name: Nanthavut
doi: 10.7717/peerj.17282
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-22
copyright: © 2024 Boondaeng et al.
attribution name: Boondaeng et al.

Predicting central cervical lymph node metastasis in papillary thyroid carcinoma with Hashimoto’s thyroiditis: a practical nomogram based on retrospective study
type: item
type: AcademicArticle
description: Background In papillary thyroid carcinoma (PTC) patients with Hashimoto’s thyroiditis (HT), preoperative ultrasonography frequently reveals the presence of enlarged lymph nodes in the central neck region. These nodes pose a diagnostic challenge due to their potential resemblance to metastatic lymph nodes, thereby impacting the surgical decision-making process for clinicians in terms of determining the appropriate surgical extent. Methods Logistic regression analysis was conducted to identify independent risk factors associated with central lymph node metastasis (CLNM) in PTC patients with HT. Then a prediction model was developed and visualized using a nomogram. The stability of the model was assessed using ten-fold cross-validation. The performance of the model was further evaluated through the use of ROC curve, calibration curve, and decision curve analysis. Results A total of 376 HT PTC patients were included in this study, comprising 162 patients with CLNM and 214 patients without CLNM. The results of the multivariate logistic regression analysis revealed that age, Tg-Ab level, tumor size, punctate echogenic foci, and blood flow grade were identified as independent risk factors associated with the development of CLNM in HT PTC. The area under the curve (AUC) of this model was 0.76 (95% CI [0.71–0.80]). The sensitivity, specificity, accuracy, and positive predictive value of the model were determined to be 88%, 51%, 67%, and 57%, respectively. Conclusions The proposed clinic-ultrasound-based nomogram in this study demonstrated a favorable performance in predicting CLNM in HT PTCs. This predictive tool has the potential to assist clinicians in making well-informed decisions regarding the appropriate extent of surgical intervention for patients.
format: application/pdf
format: text/html
creator: Lirong Wang
creator: Lin Zhang
creator: Dan Wang
creator: Jiawen Chen
creator: Wenxiu Su
creator: Lei Sun
creator: Jue Jiang
creator: Juan Wang
creator: Qi Zhou
subject: Diabetes and Endocrinology
subject: Oncology
subject: Otorhinolaryngology
subject: Radiology and Medical Imaging
subject: Metabolic Sciences
description: doi:10.7717/peerj.17108
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Background In papillary thyroid carcinoma (PTC) patients with Hashimoto’s thyroiditis (HT), preoperative ultrasonography frequently reveals the presence of enlarged lymph nodes in the central neck region. These nodes pose a diagnostic challenge due to their potential resemblance to metastatic lymph nodes, thereby impacting the surgical decision-making process for clinicians in terms of determining the appropriate surgical extent. Methods Logistic regression analysis was conducted to identify independent risk factors associated with central lymph node metastasis (CLNM) in PTC patients with HT. Then a prediction model was developed and visualized using a nomogram. The stability of the model was assessed using ten-fold cross-validation. The performance of the model was further evaluated through the use of ROC curve, calibration curve, and decision curve analysis. Results A total of 376 HT PTC patients were included in this study, comprising 162 patients with CLNM and 214 patients without CLNM. The results of the multivariate logistic regression analysis revealed that age, Tg-Ab level, tumor size, punctate echogenic foci, and blood flow grade were identified as independent risk factors associated with the development of CLNM in HT PTC. The area under the curve (AUC) of this model was 0.76 (95% CI [0.71–0.80]). The sensitivity, specificity, accuracy, and positive predictive value of the model were determined to be 88%, 51%, 67%, and 57%, respectively. Conclusions The proposed clinic-ultrasound-based nomogram in this study demonstrated a favorable performance in predicting CLNM in HT PTCs. This predictive tool has the potential to assist clinicians in making well-informed decisions regarding the appropriate extent of surgical intervention for patients.
bibliographic citation: Wang et al. (2024) Predicting central cervical lymph node metastasis in papillary thyroid carcinoma with Hashimoto’s thyroiditis: a practical nomogram based on retrospective study. PeerJ 12:e17108 https://doi.org/10.7717/peerj.17108
date submitted: 2023-09-18
date accepted: 2024-02-22
issued: 2024-04-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lirong
author list: Agent
  family name: Zhang
  given name: Lin
author list: Agent
  family name: Wang
  given name: Dan
author list: Agent
  family name: Chen
  given name: Jiawen
author list: Agent
  family name: Su
  given name: Wenxiu
author list: Agent
  family name: Sun
  given name: Lei
author list: Agent
  family name: Jiang
  given name: Jue
author list: Agent
  family name: Wang
  given name: Juan
author list: Agent
  family name: Zhou
  given name: Qi
doi: 10.7717/peerj.17108
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-19
copyright: ©2024 Wang et al.
attribution name: Wang et al.

Magnification in preclinical procedures: effect on muscle activity and angular deviations of the neck and trunk
type: item
type: AcademicArticle
description: Objectives This study aimed to assess the effects of different magnification systems on the angular deviations of the neck and trunk and the muscle activities of the upper back and neck during preclinical cavity preparation. Methods This was an experimental laboratory study, with the angular deviations from the neutral positions of the neck and trunk and the activities of the bilateral upper back (the descending and ascending trapezius) and neck (sternocleidomastoid) muscles as the dependent variables. The independent variables were the different magnification systems used (Simple, Galilean, and Keplerian loupes, with direct vision as the control) and prepared teeth (teeth 16, 26, 36, and 46). A dental mannequin phantom head with artificial resin teeth was used, and Class I cavity preparations for composite resin were performed on teeth 16, 26, 36, and 46 using a 1012 round diamond bur at low speed. To analyze the angular deviations, the postures adopted during the procedure were recorded using a tripod-mounted camera positioned to provide a lateral view of the operator. A trained researcher measured the angular deviations using the software entitled “Software for Postural Assessment”—SAPO (version 0.69). Bilateral muscle activity was assessed using surface electromyography. Descriptive statistical analysis was performed, and after verifying the assumptions of normality and homoscedasticity, two-way analysis of variance and the Tukey and Games-Howell post-hoc tests were used to compare the data (α=0.05). Results The angular deviation from the neutral position of the neck was found to be significantly higher during cavity preparations performed with the naked eye and the Simple loupe, irrespective of the prepared tooth. With regard to tooth location, the angular deviation of the neck was significantly greater during cavity preparation on teeth 16 and 26, and the angular deviation of the trunk was significantly greater during cavity preparation on tooth 26, regardless…
format: application/pdf
format: text/html
creator: Júlia Margato Pazos
creator: Ana Flávia Ribeiro Monteiro Fernandes
creator: Edson Donizetti Verri
creator: Guilherme Gallo Costa Gomes
creator: Simone Cecílio Hallak Regalo
creator: Patricia Petromilli Nordi Sasso Garcia
subject: Dentistry
subject: Science and Medical Education
subject: Environmental Health
subject: Biomechanics
description: doi:10.7717/peerj.17188
publisher: PeerJ Inc.
rights: © 2024 Pazos et al.
abstract: Objectives This study aimed to assess the effects of different magnification systems on the angular deviations of the neck and trunk and the muscle activities of the upper back and neck during preclinical cavity preparation. Methods This was an experimental laboratory study, with the angular deviations from the neutral positions of the neck and trunk and the activities of the bilateral upper back (the descending and ascending trapezius) and neck (sternocleidomastoid) muscles as the dependent variables. The independent variables were the different magnification systems used (Simple, Galilean, and Keplerian loupes, with direct vision as the control) and prepared teeth (teeth 16, 26, 36, and 46). A dental mannequin phantom head with artificial resin teeth was used, and Class I cavity preparations for composite resin were performed on teeth 16, 26, 36, and 46 using a 1012 round diamond bur at low speed. To analyze the angular deviations, the postures adopted during the procedure were recorded using a tripod-mounted camera positioned to provide a lateral view of the operator. A trained researcher measured the angular deviations using the software entitled “Software for Postural Assessment”—SAPO (version 0.69). Bilateral muscle activity was assessed using surface electromyography. Descriptive statistical analysis was performed, and after verifying the assumptions of normality and homoscedasticity, two-way analysis of variance and the Tukey and Games-Howell post-hoc tests were used to compare the data (α=0.05). Results The angular deviation from the neutral position of the neck was found to be significantly higher during cavity preparations performed with the naked eye and the Simple loupe, irrespective of the prepared tooth. With regard to tooth location, the angular deviation of the neck was significantly greater during cavity preparation on teeth 16 and 26, and the angular deviation of the trunk was significantly greater during cavity preparation on tooth 26, regardless…
bibliographic citation: Pazos et al. (2024) Magnification in preclinical procedures: effect on muscle activity and angular deviations of the neck and trunk. PeerJ 12:e17188 https://doi.org/10.7717/peerj.17188
date submitted: 2023-12-11
date accepted: 2024-03-11
issued: 2024-04-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pazos
  given name: Júlia Margato
author list: Agent
  family name: Fernandes
  given name: Ana Flávia Ribeiro Monteiro
author list: Agent
  family name: Verri
  given name: Edson Donizetti
author list: Agent
  family name: Gomes
  given name: Guilherme Gallo Costa
author list: Agent
  family name: Regalo
  given name: Simone Cecílio Hallak
author list: Agent
  family name: Garcia
  given name: Patricia Petromilli Nordi Sasso
doi: 10.7717/peerj.17188
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-19
copyright: ©2024 Pazos et al.
attribution name: Pazos et al.

Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients
type: item
type: AcademicArticle
description: Background Stroke is a disease with high morbidity, disability, and mortality. Immune factors play a crucial role in the occurrence of ischemic stroke (IS), but their exact mechanism is not clear. This study aims to identify possible immunological mechanisms by recognizing immune-related biomarkers and evaluating the infiltration pattern of immune cells. Methods We downloaded datasets of IS patients from GEO, applied R language to discover differentially expressed genes, and elucidated their biological functions using GO, KEGG analysis, and GSEA analysis. The hub genes were then obtained using two machine learning algorithms (least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE)) and the immune cell infiltration pattern was revealed by CIBERSORT. Gene-drug target networks and mRNA-miRNA-lncRNA regulatory networks were constructed using Cytoscape. Finally, we used RT-qPCR to validate the hub genes and applied logistic regression methods to build diagnostic models validated with ROC curves. Results We screened 188 differentially expressed genes whose functional analysis was enriched to multiple immune-related pathways. Six hub genes (ANTXR2, BAZ2B, C5AR1, PDK4, PPIH, and STK3) were identified using LASSO and SVM-RFE. ANTXR2, BAZ2B, C5AR1, PDK4, and STK3 were positively correlated with neutrophils and gamma delta T cells, and negatively correlated with T follicular helper cells and CD8, while PPIH showed the exact opposite trend. Immune infiltration indicated increased activity of monocytes, macrophages M0, neutrophils, and mast cells, and decreased infiltration of T follicular helper cells and CD8 in the IS group. The ceRNA network consisted of 306 miRNA-mRNA interacting pairs and 285 miRNA-lncRNA interacting pairs. RT-qPCR results indicated that the expression levels of BAZ2B, C5AR1, PDK4, and STK3 were significantly increased in patients with IS. Finally, we developed a diagnostic model based on th…
format: application/pdf
format: text/html
creator: Lin Cong
creator: Yijie He
creator: Yun Wu
creator: Ze Li
creator: Siwen Ding
creator: Weiwei Liang
creator: Xingjun Xiao
creator: Huixue Zhang
creator: Lihua Wang
subject: Bioinformatics
subject: Hematology
subject: Immunology
subject: Neurology
description: doi:10.7717/peerj.17208
publisher: PeerJ Inc.
rights: © 2024 Cong et al.
abstract: Background Stroke is a disease with high morbidity, disability, and mortality. Immune factors play a crucial role in the occurrence of ischemic stroke (IS), but their exact mechanism is not clear. This study aims to identify possible immunological mechanisms by recognizing immune-related biomarkers and evaluating the infiltration pattern of immune cells. Methods We downloaded datasets of IS patients from GEO, applied R language to discover differentially expressed genes, and elucidated their biological functions using GO, KEGG analysis, and GSEA analysis. The hub genes were then obtained using two machine learning algorithms (least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE)) and the immune cell infiltration pattern was revealed by CIBERSORT. Gene-drug target networks and mRNA-miRNA-lncRNA regulatory networks were constructed using Cytoscape. Finally, we used RT-qPCR to validate the hub genes and applied logistic regression methods to build diagnostic models validated with ROC curves. Results We screened 188 differentially expressed genes whose functional analysis was enriched to multiple immune-related pathways. Six hub genes (ANTXR2, BAZ2B, C5AR1, PDK4, PPIH, and STK3) were identified using LASSO and SVM-RFE. ANTXR2, BAZ2B, C5AR1, PDK4, and STK3 were positively correlated with neutrophils and gamma delta T cells, and negatively correlated with T follicular helper cells and CD8, while PPIH showed the exact opposite trend. Immune infiltration indicated increased activity of monocytes, macrophages M0, neutrophils, and mast cells, and decreased infiltration of T follicular helper cells and CD8 in the IS group. The ceRNA network consisted of 306 miRNA-mRNA interacting pairs and 285 miRNA-lncRNA interacting pairs. RT-qPCR results indicated that the expression levels of BAZ2B, C5AR1, PDK4, and STK3 were significantly increased in patients with IS. Finally, we developed a diagnostic model based on th…
bibliographic citation: Cong et al. (2024) Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients. PeerJ 12:e17208 https://doi.org/10.7717/peerj.17208
date submitted: 2023-03-16
date accepted: 2024-03-18
issued: 2024-04-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cong
  given name: Lin
author list: Agent
  family name: He
  given name: Yijie
author list: Agent
  family name: Wu
  given name: Yun
author list: Agent
  family name: Li
  given name: Ze
author list: Agent
  family name: Ding
  given name: Siwen
author list: Agent
  family name: Liang
  given name: Weiwei
author list: Agent
  family name: Xiao
  given name: Xingjun
author list: Agent
  family name: Zhang
  given name: Huixue
author list: Agent
  family name: Wang
  given name: Lihua
doi: 10.7717/peerj.17208
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-19
copyright: ©2024 Cong et al.
attribution name: Cong et al.

Exogenous Hemin enhances the antioxidant defense system of rice by regulating the AsA-GSH cycle under NaCl stress
type: item
type: AcademicArticle
description: Abiotic stress caused by soil salinization remains a major global challenge that threatens and severely impacts crop growth, causing yield reduction worldwide. In this study, we aim to investigate the damage of salt stress on the leaf physiology of two varieties of rice (Huanghuazhan, HHZ, and Xiangliangyou900, XLY900) and the regulatory mechanism of Hemin to maintain seedling growth under the imposed stress. Rice leaves were sprayed with 5.0 μmol·L−1 Hemin or 25.0 μmol·L−1 ZnPP (Zinc protoporphyrin IX) at the three leaf and one heart stage, followed by an imposed salt stress treatment regime (50.0 mmol·L−1 sodium chloride (NaCl)). The findings revealed that NaCl stress increased antioxidant enzymes activities and decreased the content of nonenzymatic antioxidants such as ascorbate (AsA) and glutathione (GSH). Furthermore, the content of osmoregulatory substances like soluble proteins and proline was raised. Moreover, salt stress increased reactive oxygen species (ROS) content in the leaves of the two varieties. However, spraying with Hemin increased the activities of antioxidants such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) and accelerated AsA-GSH cycling to remove excess ROS. In summary, Hemin reduced the effect of salt stress on the physiological characteristics of rice leaves due to improved antioxidant defense mechanisms that impeded lipid peroxidation. Thus, Hemin was demonstrated to lessen the damage caused by salt stress.
format: application/pdf
format: text/html
creator: Fengyan Meng
creator: Naijie Feng
creator: Dianfeng Zheng
creator: Meiling Liu
creator: Hang Zhou
creator: Rongjun Zhang
creator: XiXin Huang
creator: Anqi Huang
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.17219
publisher: PeerJ Inc.
rights: © 2024 Meng et al.
abstract: Abiotic stress caused by soil salinization remains a major global challenge that threatens and severely impacts crop growth, causing yield reduction worldwide. In this study, we aim to investigate the damage of salt stress on the leaf physiology of two varieties of rice (Huanghuazhan, HHZ, and Xiangliangyou900, XLY900) and the regulatory mechanism of Hemin to maintain seedling growth under the imposed stress. Rice leaves were sprayed with 5.0 μmol·L−1 Hemin or 25.0 μmol·L−1 ZnPP (Zinc protoporphyrin IX) at the three leaf and one heart stage, followed by an imposed salt stress treatment regime (50.0 mmol·L−1 sodium chloride (NaCl)). The findings revealed that NaCl stress increased antioxidant enzymes activities and decreased the content of nonenzymatic antioxidants such as ascorbate (AsA) and glutathione (GSH). Furthermore, the content of osmoregulatory substances like soluble proteins and proline was raised. Moreover, salt stress increased reactive oxygen species (ROS) content in the leaves of the two varieties. However, spraying with Hemin increased the activities of antioxidants such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) and accelerated AsA-GSH cycling to remove excess ROS. In summary, Hemin reduced the effect of salt stress on the physiological characteristics of rice leaves due to improved antioxidant defense mechanisms that impeded lipid peroxidation. Thus, Hemin was demonstrated to lessen the damage caused by salt stress.
bibliographic citation: Meng et al. (2024) Exogenous Hemin enhances the antioxidant defense system of rice by regulating the AsA-GSH cycle under NaCl stress. PeerJ 12:e17219 https://doi.org/10.7717/peerj.17219
date submitted: 2023-08-29
date accepted: 2024-03-20
issued: 2024-04-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Fengyan
author list: Agent
  family name: Feng
  given name: Naijie
author list: Agent
  family name: Zheng
  given name: Dianfeng
author list: Agent
  family name: Liu
  given name: Meiling
author list: Agent
  family name: Zhou
  given name: Hang
author list: Agent
  family name: Zhang
  given name: Rongjun
author list: Agent
  family name: Huang
  given name: XiXin
author list: Agent
  family name: Huang
  given name: Anqi
doi: 10.7717/peerj.17219
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-19
copyright: © 2024 Meng et al.
attribution name: Meng et al.

Inhibition of SUV39H1 reduces tumor angiogenesis via Notch1 in oral squamous cell carcinoma
type: item
type: AcademicArticle
description: Targeting tumor angiogenesis is an important approach in advanced tumor therapy. Here we investigated the effect of the suppressor of variegation 3–9 homolog 1 (SUV39H1) on tumor angiogenesis in oral squamous cell carcinoma (OSCC). The GEPIA database was used to analyze the expression of SUV39H1 in various cancer tissues. The expression of SUV39H1 in OSCC was detected by immunohistochemistry, and the correlation between SUV39H1 and Notch1 and microvascular density (MVD) was analyzed. The effect of SUV39H1 inhibition on OSCC was investigated in vivo by chaetocin treatment. The migration and tube formation of vascular endothelial cells by conditioned culture-medium of different treatments of oral squamous cell cells were measured. The transcriptional level of SUV39H1 is elevated in various cancer tissues. The transcription level of SUV39H1 in head and neck squamous cell carcinoma was significantly higher than that in control. Immunohistochemistry result showed increased SUV39H1 expression in OSCC, which was significantly correlated with T staging. The expression of SUV39H1 was significantly correlated with Notch1 and CD31. In vivo experiment chaetocin treatment significantly inhibit the growth of tumor, and reduce SUV39H1, Notch1, CD31 expression. The decreased expression of SUV39H1 in OSCC cells lead to the decreased expression of Notch1 and VEGF proteins, as well as the decreased migration and tube formation ability of vascular endothelial cells. Inhibition of Notch1 further enhance this effect. Our results suggest inhibition of SUV39H1 may affect angiogenesis by regulating Notch1 expression. This study provides a foundation for SUV39H1 as a potential therapeutic target for OSCC.
format: application/pdf
format: text/html
creator: Yan Chen
creator: Xiuhong Weng
creator: Chuanjie Zhang
creator: Simin Wang
creator: Xuechen Wu
creator: Bo Cheng
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.17222
publisher: PeerJ Inc.
rights: © 2024 Chen et al.
abstract: Targeting tumor angiogenesis is an important approach in advanced tumor therapy. Here we investigated the effect of the suppressor of variegation 3–9 homolog 1 (SUV39H1) on tumor angiogenesis in oral squamous cell carcinoma (OSCC). The GEPIA database was used to analyze the expression of SUV39H1 in various cancer tissues. The expression of SUV39H1 in OSCC was detected by immunohistochemistry, and the correlation between SUV39H1 and Notch1 and microvascular density (MVD) was analyzed. The effect of SUV39H1 inhibition on OSCC was investigated in vivo by chaetocin treatment. The migration and tube formation of vascular endothelial cells by conditioned culture-medium of different treatments of oral squamous cell cells were measured. The transcriptional level of SUV39H1 is elevated in various cancer tissues. The transcription level of SUV39H1 in head and neck squamous cell carcinoma was significantly higher than that in control. Immunohistochemistry result showed increased SUV39H1 expression in OSCC, which was significantly correlated with T staging. The expression of SUV39H1 was significantly correlated with Notch1 and CD31. In vivo experiment chaetocin treatment significantly inhibit the growth of tumor, and reduce SUV39H1, Notch1, CD31 expression. The decreased expression of SUV39H1 in OSCC cells lead to the decreased expression of Notch1 and VEGF proteins, as well as the decreased migration and tube formation ability of vascular endothelial cells. Inhibition of Notch1 further enhance this effect. Our results suggest inhibition of SUV39H1 may affect angiogenesis by regulating Notch1 expression. This study provides a foundation for SUV39H1 as a potential therapeutic target for OSCC.
bibliographic citation: Chen et al. (2024) Inhibition of SUV39H1 reduces tumor angiogenesis via Notch1 in oral squamous cell carcinoma. PeerJ 12:e17222 https://doi.org/10.7717/peerj.17222
date submitted: 2023-04-28
date accepted: 2024-03-20
issued: 2024-04-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yan
author list: Agent
  family name: Weng
  given name: Xiuhong
author list: Agent
  family name: Zhang
  given name: Chuanjie
author list: Agent
  family name: Wang
  given name: Simin
author list: Agent
  family name: Wu
  given name: Xuechen
author list: Agent
  family name: Cheng
  given name: Bo
doi: 10.7717/peerj.17222
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-19
copyright: © 2024 Chen et al.
attribution name: Chen et al.

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