PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genome-wide identification and expression analysis of the Trihelix transcription factor family in potato (Solanum tuberosum L.) during development
items: Losartan and dapagliflozin combination therapy in reducing uric acid level compared to monotherapy in patients with heart failure
items: Effects of a single bout of exercise on human hemocytes and serum interleukin 3, erythropoietin, and soluble transferrin receptor in a hot and humid environment
items: Assessment of genotype by environment and yield performance of tropical maize hybrids using stability statistics and graphical biplots
items: Vascular synovial phenotype indicates poor response to JAK inhibitors in rheumatoid arthritis patients: a pilot study
items: Expression of CK7, CK19 and p16 in HPV-mediated oropharyngeal squamous cell carcinoma
items: Effects of temperature and size class on the gut digesta microbiota of the sea urchin Tripneustes ventricosus
items: Exploration of severe early childhood caries microbiota through a novel developed nutrient enriched microbiological medium, high through-put 16S rRNA sequencing and culturomics
items: Pereskia bleo augments NK cell cytotoxicity against triple-negative breast cancer cells (MDA-MB-231)
items: Analysing the spatial variation of soil respiration during the early growing season of different grasslands in China

Genome-wide identification and expression analysis of the Trihelix transcription factor family in potato (Solanum tuberosum L.) during development
type: item
type: AcademicArticle
description: Trihelix transcription factors (TF) are photoresponsive proteins featuring a characteristic three-helix structure (helix-loop-helix-loop-helix) and contain the Myb/SANT-LIKE (MSL) domain. They perform crucial functions in the development and stress-response of plants. However, the function of the Trihelix TF in potato (Solanum tuberosum L.) remains unknown. In the present study, forty-three StMSLs were characterized in the potato genome and named StMSL1 to StMSL43. Structural domain analysis revealed that motifs 1 and 2 may play a central role in the implementation of trihelix gene functions, and motifs 4 and 9 may be related to specific functions of StMSL. Phylogenetic analysis divided the StMSLs into six groups (SIP1, GT1, GT2, GTγ, SH4 and GT3). The GT3 group, which is rarely identified in the Trihelix TF family, contained three StMSLs. The 43 StMSLs were unevenly distributed on 12 chromosomes in potato and comprised two pairs of tandem duplication and five pairs of segmental duplication genes. Additionally, RNA-Seq analysis found that 36 out of the 43 StMSLs were expressed in at least one of the 12 tissues, with some exhibiting tissue-specific expression patterns. Trihelix transcriptional regulation network analysis identified 387 genes as potential targets of the 36 StMSL genes, and these genes have a wide variety of functions. Furthermore, RNA-Seq analysis revealed that at least 18 StMSLs were upregulated in response to osmotic stress. The induced pattern of eight StMSLs was subsequently validated using qRT-PCR. This study provides a detailed insight into the StMSLs of the potato and lays the foundation for further analysis of the functions of the Trihelix gene in plant development.
format: application/pdf
format: text/html
creator: Chao Mei
creator: Yuwei Liu
creator: Huiyang Song
creator: Jinghao Li
creator: Qianna Song
creator: Yonghong Duan
creator: Ruiyun Feng
subject: Plant Science
description: doi:10.7717/peerj.18578
publisher: PeerJ Inc.
rights: © 2024 Mei et al.
abstract: Trihelix transcription factors (TF) are photoresponsive proteins featuring a characteristic three-helix structure (helix-loop-helix-loop-helix) and contain the Myb/SANT-LIKE (MSL) domain. They perform crucial functions in the development and stress-response of plants. However, the function of the Trihelix TF in potato (Solanum tuberosum L.) remains unknown. In the present study, forty-three StMSLs were characterized in the potato genome and named StMSL1 to StMSL43. Structural domain analysis revealed that motifs 1 and 2 may play a central role in the implementation of trihelix gene functions, and motifs 4 and 9 may be related to specific functions of StMSL. Phylogenetic analysis divided the StMSLs into six groups (SIP1, GT1, GT2, GTγ, SH4 and GT3). The GT3 group, which is rarely identified in the Trihelix TF family, contained three StMSLs. The 43 StMSLs were unevenly distributed on 12 chromosomes in potato and comprised two pairs of tandem duplication and five pairs of segmental duplication genes. Additionally, RNA-Seq analysis found that 36 out of the 43 StMSLs were expressed in at least one of the 12 tissues, with some exhibiting tissue-specific expression patterns. Trihelix transcriptional regulation network analysis identified 387 genes as potential targets of the 36 StMSL genes, and these genes have a wide variety of functions. Furthermore, RNA-Seq analysis revealed that at least 18 StMSLs were upregulated in response to osmotic stress. The induced pattern of eight StMSLs was subsequently validated using qRT-PCR. This study provides a detailed insight into the StMSLs of the potato and lays the foundation for further analysis of the functions of the Trihelix gene in plant development.
bibliographic citation: Mei et al. (2024) Genome-wide identification and expression analysis of the Trihelix transcription factor family in potato (Solanum tuberosum L.) during development. PeerJ 12:e18578 https://doi.org/10.7717/peerj.18578
date submitted: 2024-05-20
date accepted: 2024-11-04
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mei
  given name: Chao
author list: Agent
  family name: Liu
  given name: Yuwei
author list: Agent
  family name: Song
  given name: Huiyang
author list: Agent
  family name: Li
  given name: Jinghao
author list: Agent
  family name: Song
  given name: Qianna
author list: Agent
  family name: Duan
  given name: Yonghong
author list: Agent
  family name: Feng
  given name: Ruiyun
doi: 10.7717/peerj.18578
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Mei et al.
attribution name: Mei et al.

Losartan and dapagliflozin combination therapy in reducing uric acid level compared to monotherapy in patients with heart failure
type: item
type: AcademicArticle
description: Background Sodium-Glucose Transport Protein 2 (SGLT2) inhibitors, and Angiotensin II Receptor Antagonists (ARBs) also have the effect of reducing serum uric acid but few studies worldwide assessed. Objective Evaluate the effectiveness of serum uric acid lowering treatment of SGLT2 inhibitors, and ARB in heart failure (HF) patients. Methods We conducted a cross-sectional analysis study with 8 weeks of follow-up on 733 heart failure (HF) patients treated at Can Tho Central General Hospital from January 2023 to March 2024. Patients enrolled in the study were examined and received losartan (Group A) or dapagliflozin (Group B) monotherapy or losartan and dapagliflozin combined therapy (Group C). The uric acid concentration group was defined into three subgroups with tertile 1 from smallest to quartile (Q) 1, tertile 2 from Q2 to Q3, and tertile 3 from Q3 to the largest value. Results After 8 weeks of treatment, the uric acid reduction effect between groups A, B, and C showed that the combination group had the optimal reducing effect compared to losartan and dapagliflozin monotherapy with the mean difference being −229.62 ± 76.65 µmol/L, −217.00 ± 146.17 µmol/L, and −284.43 ± 136.32 µmol/L, respectively. In total, combination therapy showed the best reduction outcome in the population of male, female, patients with type 2 diabetes mellitus (T2DM), and dyslipidemia with the mean difference ranging from −226.21 ± 74.65 µmol/L to −231.85 ± 76.28 µmol/L and −209.62 ± 184.94 µmol/L to −225.75 ± 78.53 µmol/L and −273.02 ± 204.54 µmol/L to −308.93 ± 72.97 µmol/L in group A, B, and C, respectively. Conclusion The optimal therapy for reducing uric acid levels in HF patients was the combination of losartan and dapagliflozin, and the effectiveness did not change through sex, T2DM, and dyslipidemia patients.
format: application/pdf
format: text/html
creator: Tuong Le Trong Huynh
creator: Phong Thanh Pham
creator: Hien Dieu Tran
creator: Nhan Dinh Tran
creator: Duong Van Tran
creator: Bao Lam Thai Tran
creator: Khoa Dang Dang Tran
creator: Toan Hoang Ngo
creator: Son Kim Tran
subject: Cardiology
subject: Internal Medicine
description: doi:10.7717/peerj.18595
publisher: PeerJ Inc.
rights: © 2024 Huynh et al.
abstract: Background Sodium-Glucose Transport Protein 2 (SGLT2) inhibitors, and Angiotensin II Receptor Antagonists (ARBs) also have the effect of reducing serum uric acid but few studies worldwide assessed. Objective Evaluate the effectiveness of serum uric acid lowering treatment of SGLT2 inhibitors, and ARB in heart failure (HF) patients. Methods We conducted a cross-sectional analysis study with 8 weeks of follow-up on 733 heart failure (HF) patients treated at Can Tho Central General Hospital from January 2023 to March 2024. Patients enrolled in the study were examined and received losartan (Group A) or dapagliflozin (Group B) monotherapy or losartan and dapagliflozin combined therapy (Group C). The uric acid concentration group was defined into three subgroups with tertile 1 from smallest to quartile (Q) 1, tertile 2 from Q2 to Q3, and tertile 3 from Q3 to the largest value. Results After 8 weeks of treatment, the uric acid reduction effect between groups A, B, and C showed that the combination group had the optimal reducing effect compared to losartan and dapagliflozin monotherapy with the mean difference being −229.62 ± 76.65 µmol/L, −217.00 ± 146.17 µmol/L, and −284.43 ± 136.32 µmol/L, respectively. In total, combination therapy showed the best reduction outcome in the population of male, female, patients with type 2 diabetes mellitus (T2DM), and dyslipidemia with the mean difference ranging from −226.21 ± 74.65 µmol/L to −231.85 ± 76.28 µmol/L and −209.62 ± 184.94 µmol/L to −225.75 ± 78.53 µmol/L and −273.02 ± 204.54 µmol/L to −308.93 ± 72.97 µmol/L in group A, B, and C, respectively. Conclusion The optimal therapy for reducing uric acid levels in HF patients was the combination of losartan and dapagliflozin, and the effectiveness did not change through sex, T2DM, and dyslipidemia patients.
bibliographic citation: Huynh et al. (2024) Losartan and dapagliflozin combination therapy in reducing uric acid level compared to monotherapy in patients with heart failure. PeerJ 12:e18595 https://doi.org/10.7717/peerj.18595
date submitted: 2024-06-10
date accepted: 2024-11-05
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huynh
  given name: Tuong Le Trong
author list: Agent
  family name: Pham
  given name: Phong Thanh
author list: Agent
  family name: Tran
  given name: Hien Dieu
author list: Agent
  family name: Tran
  given name: Nhan Dinh
author list: Agent
  family name: Tran
  given name: Duong Van
author list: Agent
  family name: Tran
  given name: Bao Lam Thai
author list: Agent
  family name: Tran
  given name: Khoa Dang Dang
author list: Agent
  family name: Ngo
  given name: Toan Hoang
author list: Agent
  family name: Tran
  given name: Son Kim
doi: 10.7717/peerj.18595
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Huynh et al.
attribution name: Huynh et al.

Effects of a single bout of exercise on human hemocytes and serum interleukin 3, erythropoietin, and soluble transferrin receptor in a hot and humid environment
type: item
type: AcademicArticle
description: Background Exercise in humid and hot environments (HHEs) may result in decreased perception, motor performance, and memory owing to endogenous heat production and exogenous load. However, whether a single bout of exercise (SBOE) intensity affects the magnitude of changes in the levels of hemocytes remains controversial. In this article, we aimed to investigate the effects of a SBOE of varying intensities on blood cells in HHE. Methods Thirty-two volunteers were randomly divided into a quiet control group (QC), 55% VO2max intensity exercise group (HHE55%), 70% VO2max intensity exercise group (HHE70%), and 85% VO2max intensity exercise group (HHE85%). The participants in the exercise groups were assigned to perform an SBOE on the treadmill under HHE conditions for 30 min, whereas participants in the QC remained still under HHE conditions for 30 min (temperature: 28–32 °C, relative humidity: 85–95%). Results The net body mass (NBM), perfusion index (PI), mean corpuscular volume (MCV), platelet (PLT), and plateletcrit (PCT) values were affected significantly by the exercise intensity (P < 0.01) the hemoglobin (HGB) and neutrophil count (NE) were affected significantly by exercise intensity (P < 0.05). After an SBOE, compared with that before exercise, the sublingual temperature (ST) of all groups, the NBM and MCV of all exercise groups, the PI of the HHE55% and HHE70% groups, the HGB, hematocrit (HCT), and NE of the HHE70% group, the red blood cell count (RBC), PLT, and PCT of the HHE70% and HHE85% groups, and the white blood cell count (WBC) of HHE85% changed very significantly (P < 0.01). The PCT of QC, blood oxygen saturation (SaO2), and soluble transferrin receptor (sTfR) levels in the HHE55% group, the lymphocyte count (LY) in the HHE70% group, and the HGB and HCT in the HHE85% group changed significantly (P < 0.05). Conclusion Low- and moderate-intensity SBOE in HHE could increase the serum EPO and serum sTfR levels and decrease the serum IL-3 levels. Conversely, …
format: application/pdf
format: text/html
creator: Yuhu Lv
creator: Lin Cheng
creator: Xiqian Zhang
creator: Fenglin Peng
creator: Yu Yuan
creator: Xiquan Weng
creator: Wen-Tao Lin
subject: Molecular Biology
subject: Anatomy and Physiology
subject: Hematology
subject: Kinesiology
description: doi:10.7717/peerj.18603
publisher: PeerJ Inc.
rights: © 2024 Lv et al.
abstract: Background Exercise in humid and hot environments (HHEs) may result in decreased perception, motor performance, and memory owing to endogenous heat production and exogenous load. However, whether a single bout of exercise (SBOE) intensity affects the magnitude of changes in the levels of hemocytes remains controversial. In this article, we aimed to investigate the effects of a SBOE of varying intensities on blood cells in HHE. Methods Thirty-two volunteers were randomly divided into a quiet control group (QC), 55% VO2max intensity exercise group (HHE55%), 70% VO2max intensity exercise group (HHE70%), and 85% VO2max intensity exercise group (HHE85%). The participants in the exercise groups were assigned to perform an SBOE on the treadmill under HHE conditions for 30 min, whereas participants in the QC remained still under HHE conditions for 30 min (temperature: 28–32 °C, relative humidity: 85–95%). Results The net body mass (NBM), perfusion index (PI), mean corpuscular volume (MCV), platelet (PLT), and plateletcrit (PCT) values were affected significantly by the exercise intensity (P < 0.01) the hemoglobin (HGB) and neutrophil count (NE) were affected significantly by exercise intensity (P < 0.05). After an SBOE, compared with that before exercise, the sublingual temperature (ST) of all groups, the NBM and MCV of all exercise groups, the PI of the HHE55% and HHE70% groups, the HGB, hematocrit (HCT), and NE of the HHE70% group, the red blood cell count (RBC), PLT, and PCT of the HHE70% and HHE85% groups, and the white blood cell count (WBC) of HHE85% changed very significantly (P < 0.01). The PCT of QC, blood oxygen saturation (SaO2), and soluble transferrin receptor (sTfR) levels in the HHE55% group, the lymphocyte count (LY) in the HHE70% group, and the HGB and HCT in the HHE85% group changed significantly (P < 0.05). Conclusion Low- and moderate-intensity SBOE in HHE could increase the serum EPO and serum sTfR levels and decrease the serum IL-3 levels. Conversely, …
bibliographic citation: Lv et al. (2024) Effects of a single bout of exercise on human hemocytes and serum interleukin 3, erythropoietin, and soluble transferrin receptor in a hot and humid environment. PeerJ 12:e18603 https://doi.org/10.7717/peerj.18603
date submitted: 2021-07-09
date accepted: 2024-11-06
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lv
  given name: Yuhu
author list: Agent
  family name: Cheng
  given name: Lin
author list: Agent
  family name: Zhang
  given name: Xiqian
author list: Agent
  family name: Peng
  given name: Fenglin
author list: Agent
  family name: Yuan
  given name: Yu
author list: Agent
  family name: Weng
  given name: Xiquan
author list: Agent
  family name: Lin
  given name: Wen-Tao
doi: 10.7717/peerj.18603
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Lv et al.
attribution name: Lv et al.

Assessment of genotype by environment and yield performance of tropical maize hybrids using stability statistics and graphical biplots
type: item
type: AcademicArticle
description: Background Enhancing maize grain yield in tropical regions faces significant challenges due to variability in agroclimate, soil conditions, and agroecosystems. Understanding genotype (G) by environment (E) interaction (GEI) in plant breeding is crucial for selecting and developing high-yielding genotypes adapted to diverse environments. Methods Ten maize hybrids, including eight candidates and two commercial varieties, were evaluated across ten environments in Indonesia using a randomized complete block design with three replications. The GEI effect and yield stability were assessed using stability statistics, additive main effects and multiplicative interaction model (AMMI), and genotype + genotype × environment (GGE) biplot methods. Results and Discussion Analysis of variance revealed a significant GEI effect, indicating differences in hybrid responses for grain yield (GY), allowing for stability analysis. G01 showed the highest GY based on the best linear unbiased prediction (BLUP) across environments. Correlation analysis indicated strong associations between stability statistics (YSi and S(6)) and GY, aiding in the selection of high-yielding hybrids. The integration of AMMI with the BLUP method, and weighted average of absolute scores (WAASB), enabled precise measurement of genotype stability. Overall, G01 (R0211), G04 (R0105), G05 (R0118), and G07 (R0641) emerged as high-yielding, stable hybrids based on stability statistics, AMMI, GGE biplot, and WAASB rankings. These hybrids offer promising candidates for maize genetic improvement programs in tropical regions.
format: application/pdf
format: text/html
creator: Dedy Supriadi
creator: Yusuf Mufti Bimantara
creator: Yuniel Melvanolo Zendrato
creator: Eko Widaryanto
creator: Kuswanto Kuswanto
creator: Budi Waluyo
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.18624
publisher: PeerJ Inc.
rights: © 2024 Supriadi et al.
abstract: Background Enhancing maize grain yield in tropical regions faces significant challenges due to variability in agroclimate, soil conditions, and agroecosystems. Understanding genotype (G) by environment (E) interaction (GEI) in plant breeding is crucial for selecting and developing high-yielding genotypes adapted to diverse environments. Methods Ten maize hybrids, including eight candidates and two commercial varieties, were evaluated across ten environments in Indonesia using a randomized complete block design with three replications. The GEI effect and yield stability were assessed using stability statistics, additive main effects and multiplicative interaction model (AMMI), and genotype + genotype × environment (GGE) biplot methods. Results and Discussion Analysis of variance revealed a significant GEI effect, indicating differences in hybrid responses for grain yield (GY), allowing for stability analysis. G01 showed the highest GY based on the best linear unbiased prediction (BLUP) across environments. Correlation analysis indicated strong associations between stability statistics (YSi and S(6)) and GY, aiding in the selection of high-yielding hybrids. The integration of AMMI with the BLUP method, and weighted average of absolute scores (WAASB), enabled precise measurement of genotype stability. Overall, G01 (R0211), G04 (R0105), G05 (R0118), and G07 (R0641) emerged as high-yielding, stable hybrids based on stability statistics, AMMI, GGE biplot, and WAASB rankings. These hybrids offer promising candidates for maize genetic improvement programs in tropical regions.
bibliographic citation: Supriadi et al. (2024) Assessment of genotype by environment and yield performance of tropical maize hybrids using stability statistics and graphical biplots. PeerJ 12:e18624 https://doi.org/10.7717/peerj.18624
date submitted: 2024-09-11
date accepted: 2024-11-11
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Supriadi
  given name: Dedy
author list: Agent
  family name: Bimantara
  given name: Yusuf Mufti
author list: Agent
  family name: Zendrato
  given name: Yuniel Melvanolo
author list: Agent
  family name: Widaryanto
  given name: Eko
author list: Agent
  family name: Kuswanto
  given name: Kuswanto
author list: Agent
  family name: Waluyo
  given name: Budi
doi: 10.7717/peerj.18624
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Supriadi et al.
attribution name: Supriadi et al.

Vascular synovial phenotype indicates poor response to JAK inhibitors in rheumatoid arthritis patients: a pilot study
type: item
type: AcademicArticle
description: Objective Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease, characterized by significant individual variations in treatment response. Predicting treatment response remains a formidable challenge. This study aims to identify predictors within the synovium associated with the response to JAK inhibitor therapy in RA patients, employing a retrospective approach. Methods A retrospective analysis was conducted on 27 RA patients who underwent synovial biopsy and received JAK inhibitor therapy for at least three months at our center, from January to November 2023. These patients had comprehensive clinical records. Based on their response to JAK inhibitor therapy, as measured by the ACR20 criteria, they were categorized into non-responder and responder groups. We compared clinical data (including sex, age, disease duration), laboratory findings (RF, ACPA, ESR, CRP, etc.), DAS28-CRP scores, and synovial pathology features—such as synovial lining hyperplasia, neovascularization, stromal activation, inflammatory infiltration, and the expression of CD3, CD20, CD68, and CD138 markers in the synovium—between the two groups. Results The rate of non-responder to JAKi was found to be 33.3% (nine cases out of a total of 27 patients). Non-responders, when compared to responders, exhibited longer disease duration, more pronounced synovial neovascularization alongside reduced infiltration of labeled CD20+ and CD138+ cells in the synovium. Multivariate regression analysis identified synovial neovascularization and disease duration as independent predictors of a poor response to JAK inhibitor treatment. Conclusions The presence of vascular phenotype with low inflammation within the synovium of RA patients is an indicator of poor response to JAK inhibitor therapy, highlighting its potential as a predictive marker for treatment outcomes.
format: application/pdf
format: text/html
creator: Mengxia Liu
creator: Pengcheng Liu
creator: JianBin Li
creator: Yiping Huang
creator: Rui Wu
subject: Allergy and Clinical Immunology
subject: Immunology
subject: Rheumatology
description: doi:10.7717/peerj.18631
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Objective Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease, characterized by significant individual variations in treatment response. Predicting treatment response remains a formidable challenge. This study aims to identify predictors within the synovium associated with the response to JAK inhibitor therapy in RA patients, employing a retrospective approach. Methods A retrospective analysis was conducted on 27 RA patients who underwent synovial biopsy and received JAK inhibitor therapy for at least three months at our center, from January to November 2023. These patients had comprehensive clinical records. Based on their response to JAK inhibitor therapy, as measured by the ACR20 criteria, they were categorized into non-responder and responder groups. We compared clinical data (including sex, age, disease duration), laboratory findings (RF, ACPA, ESR, CRP, etc.), DAS28-CRP scores, and synovial pathology features—such as synovial lining hyperplasia, neovascularization, stromal activation, inflammatory infiltration, and the expression of CD3, CD20, CD68, and CD138 markers in the synovium—between the two groups. Results The rate of non-responder to JAKi was found to be 33.3% (nine cases out of a total of 27 patients). Non-responders, when compared to responders, exhibited longer disease duration, more pronounced synovial neovascularization alongside reduced infiltration of labeled CD20+ and CD138+ cells in the synovium. Multivariate regression analysis identified synovial neovascularization and disease duration as independent predictors of a poor response to JAK inhibitor treatment. Conclusions The presence of vascular phenotype with low inflammation within the synovium of RA patients is an indicator of poor response to JAK inhibitor therapy, highlighting its potential as a predictive marker for treatment outcomes.
bibliographic citation: Liu et al. (2024) Vascular synovial phenotype indicates poor response to JAK inhibitors in rheumatoid arthritis patients: a pilot study. PeerJ 12:e18631 https://doi.org/10.7717/peerj.18631
date submitted: 2024-06-03
date accepted: 2024-11-12
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Mengxia
author list: Agent
  family name: Liu
  given name: Pengcheng
author list: Agent
  family name: Li
  given name: JianBin
author list: Agent
  family name: Huang
  given name: Yiping
author list: Agent
  family name: Wu
  given name: Rui
doi: 10.7717/peerj.18631
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Liu et al.
attribution name: Liu et al.

Expression of CK7, CK19 and p16 in HPV-mediated oropharyngeal squamous cell carcinoma
type: item
type: AcademicArticle
description: Background The incidence of oropharyngeal squamous cell carcinoma (OPSCC) mediated by human papilloma virus (HPV) has been steadily increasing worldwide. The specific pathogenesis of HPV-mediated head and neck squamous cell carcinoma (HNSCC) usually induces carcinogenesis in the oropharynx and the roles of CK7, CK19 and p16 in the carcinogenesis mechanism of HPV-mediated OPSCC still remain uncertain. Methods We collected case data and paraffin samples of 69 cases of OPSCC and 40 cases of OSCC from July 2009 to December 2021. Immunohistochemistry was performed on serial paraffin sections from all cases to analyze the expression patterns of CK7, CK19, and p16. HPV-mediated (p16+) and non-HPV-mediated OPSCC were differentiated based on p16 expression. Three to six fields were selected from each case for observation of the expression intensity, localization, and interrelationship of the three proteins. Results In both cancerous nests and pericancerous normal epithelium of OPSCC, various expression combinations of CK7, CK19 and p16 were observed, including CK7+CK19+p16+, CK7−CK19+p16+, and CK7+CK19+p16−, while no expression of CK7+CK19−p16+ was found. The expression of CK7 with CK19, CK7 with p16, and CK19 with p16 all showed consistency in OPSCC (P < 0.05) while only the expression of CK7 and CK19 demonstrated consistency in OSCC (P < 0.05). The positive rates and H-scores for CK7/CK19 in HPV-mediated (p16+) OPSCC were significantly higher than those in non-HPV-mediated OPSCC and OSCC (P < 0.05). Conclusions These results suggest that CK7, CK19 and p16 may relate to HPV-mediated OPSCC. The interaction of CK7, CK19 and p16 may affect the development of HPV-mediated OPSCC.
format: application/pdf
format: text/html
creator: Qizhang Yan
creator: Pengning Chen
creator: Xinyu Chen
creator: Guanxi Chen
creator: Lin Luo
creator: Ping Ruan
creator: Dahai Yu
creator: Xiaojuan Zeng
creator: Mengyu Zhou
subject: Biochemistry
subject: Cell Biology
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.18286
publisher: PeerJ Inc.
rights: © 2024 Yan et al.
abstract: Background The incidence of oropharyngeal squamous cell carcinoma (OPSCC) mediated by human papilloma virus (HPV) has been steadily increasing worldwide. The specific pathogenesis of HPV-mediated head and neck squamous cell carcinoma (HNSCC) usually induces carcinogenesis in the oropharynx and the roles of CK7, CK19 and p16 in the carcinogenesis mechanism of HPV-mediated OPSCC still remain uncertain. Methods We collected case data and paraffin samples of 69 cases of OPSCC and 40 cases of OSCC from July 2009 to December 2021. Immunohistochemistry was performed on serial paraffin sections from all cases to analyze the expression patterns of CK7, CK19, and p16. HPV-mediated (p16+) and non-HPV-mediated OPSCC were differentiated based on p16 expression. Three to six fields were selected from each case for observation of the expression intensity, localization, and interrelationship of the three proteins. Results In both cancerous nests and pericancerous normal epithelium of OPSCC, various expression combinations of CK7, CK19 and p16 were observed, including CK7+CK19+p16+, CK7−CK19+p16+, and CK7+CK19+p16−, while no expression of CK7+CK19−p16+ was found. The expression of CK7 with CK19, CK7 with p16, and CK19 with p16 all showed consistency in OPSCC (P < 0.05) while only the expression of CK7 and CK19 demonstrated consistency in OSCC (P < 0.05). The positive rates and H-scores for CK7/CK19 in HPV-mediated (p16+) OPSCC were significantly higher than those in non-HPV-mediated OPSCC and OSCC (P < 0.05). Conclusions These results suggest that CK7, CK19 and p16 may relate to HPV-mediated OPSCC. The interaction of CK7, CK19 and p16 may affect the development of HPV-mediated OPSCC.
bibliographic citation: Yan et al. (2024) Expression of CK7, CK19 and p16 in HPV-mediated oropharyngeal squamous cell carcinoma. PeerJ 12:e18286 https://doi.org/10.7717/peerj.18286
date submitted: 2024-02-20
date accepted: 2024-09-19
issued: 2024-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Qizhang
author list: Agent
  family name: Chen
  given name: Pengning
author list: Agent
  family name: Chen
  given name: Xinyu
author list: Agent
  family name: Chen
  given name: Guanxi
author list: Agent
  family name: Luo
  given name: Lin
author list: Agent
  family name: Ruan
  given name: Ping
author list: Agent
  family name: Yu
  given name: Dahai
author list: Agent
  family name: Zeng
  given name: Xiaojuan
author list: Agent
  family name: Zhou
  given name: Mengyu
doi: 10.7717/peerj.18286
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-28
copyright: © 2024 Yan et al.
attribution name: Yan et al.

Effects of temperature and size class on the gut digesta microbiota of the sea urchin Tripneustes ventricosus
type: item
type: AcademicArticle
description: Background Understanding the dynamics of the gut microbiota in sea urchins is crucial for comprehending the ecological balance in marine ecosystems. The gut microbiota plays a vital role in nutrient metabolism, immune system modulation, and pathogen protection. The microbial composition and dynamics of naturally occurring sea urchin Tripneustes ventricosus have yet to be thoroughly investigated. We hypothesized the gut microbiota of T. ventricosus in the Caribbean, varies across life stages and seasons. Methods Thirty-six naturally occurring large individuals and six small individuals (42 animals) were collected from shallow waters on the northeastern coast of Puerto Rico in February and August of 2019. The fecal pellet’s microbiota was characterized by sequencing V4 region of the 16S rRNA gene. Results We found significant differences in the composition of fecal pellet microbiota between seasons and life stages. Phylum Bacteroidota had greater relative abundance in August, while Firmicutes was more dominant in February. Propionigenium and Roseimarinus had greater relative abundance in August, while Candidatus Hepatoplasma, and Kistimonas had greater relative abundance in February. Differences in the gut digest microbiota were not found between small and large urchins, but small urchins displayed a slightly higher diversity and dominance of Bacteroidota and Proteobacteria, while large urchins exhibited a greater relative abundance of Fusobacteria and Desulfobacterota. However, the genera Ferrominas and Propionigenium counts were significantly lower in small individuals. Discussion This is the first report for this species in the Caribbean region and adds to our comprehension of the microbiota of the white sea urchin across collection periods and size classes, highlighting the dynamic nature of the gut microbiota.
format: application/pdf
format: text/html
creator: Ruber Rodríguez-Barreras
creator: Eduardo L. Tosado-Rodríguez
creator: Anelisse Dominicci-Maura
creator: Filipa Godoy-Vitorino
subject: Biodiversity
subject: Ecosystem Science
subject: Marine Biology
subject: Biosphere Interactions
description: doi:10.7717/peerj.18298
publisher: PeerJ Inc.
rights: © 2024 Rodríguez-Barreras et al.
abstract: Background Understanding the dynamics of the gut microbiota in sea urchins is crucial for comprehending the ecological balance in marine ecosystems. The gut microbiota plays a vital role in nutrient metabolism, immune system modulation, and pathogen protection. The microbial composition and dynamics of naturally occurring sea urchin Tripneustes ventricosus have yet to be thoroughly investigated. We hypothesized the gut microbiota of T. ventricosus in the Caribbean, varies across life stages and seasons. Methods Thirty-six naturally occurring large individuals and six small individuals (42 animals) were collected from shallow waters on the northeastern coast of Puerto Rico in February and August of 2019. The fecal pellet’s microbiota was characterized by sequencing V4 region of the 16S rRNA gene. Results We found significant differences in the composition of fecal pellet microbiota between seasons and life stages. Phylum Bacteroidota had greater relative abundance in August, while Firmicutes was more dominant in February. Propionigenium and Roseimarinus had greater relative abundance in August, while Candidatus Hepatoplasma, and Kistimonas had greater relative abundance in February. Differences in the gut digest microbiota were not found between small and large urchins, but small urchins displayed a slightly higher diversity and dominance of Bacteroidota and Proteobacteria, while large urchins exhibited a greater relative abundance of Fusobacteria and Desulfobacterota. However, the genera Ferrominas and Propionigenium counts were significantly lower in small individuals. Discussion This is the first report for this species in the Caribbean region and adds to our comprehension of the microbiota of the white sea urchin across collection periods and size classes, highlighting the dynamic nature of the gut microbiota.
bibliographic citation: Rodríguez-Barreras et al. (2024) Effects of temperature and size class on the gut digesta microbiota of the sea urchin Tripneustes ventricosus. PeerJ 12:e18298 https://doi.org/10.7717/peerj.18298
date submitted: 2023-11-22
date accepted: 2024-09-23
issued: 2024-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodríguez-Barreras
  given name: Ruber
author list: Agent
  family name: Tosado-Rodríguez
  given name: Eduardo L.
author list: Agent
  family name: Dominicci-Maura
  given name: Anelisse
author list: Agent
  family name: Godoy-Vitorino
  given name: Filipa
doi: 10.7717/peerj.18298
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-28
copyright: © 2024 Rodríguez-Barreras et al.
attribution name: Rodríguez-Barreras et al.

Exploration of severe early childhood caries microbiota through a novel developed nutrient enriched microbiological medium, high through-put 16S rRNA sequencing and culturomics
type: item
type: AcademicArticle
description: Introduction Severe early childhood caries (S-ECC) is a widespread disease that harms children physically and mentally. Microorganisms are regarded as the dominant etiology of caries, however, S-ECC microbiome remains largely unknown, nearly 1/4 of them remained uncultivated. To explore S-ECC microbiota, a new bacterial medium, nutrient-enriched microbiological medium (NEMM) was designed in this study. Methods Eleven fresh S-ECC dental plaque samples were collected and cultivated in both NEMM and SHI medium (reference medium) for 0, 1, 3, 6, 9, 15, 21 and 28 days under aerobic and anaerobic conditions. Thereafter, the cultures were harvested, together with their corresponding clinical S-ECC dental plaque samples, for high through-put 16S rRNA sequencing and culturomics. The single colonies were cultured for further confirmation by sequencing the full length of the 16S rRNA gene after bacterial genomic DNA extraction and PCR amplification. Results Either NEMM or SHI medium showed a significant decrease in bacterial alpha diversity compared to clinical dental plaque samples by high throughput 16S rRNA sequencing analysis, indicating a larger room for the improvement of both media. NEMM displayed more living bacteria, abundant bacteria species, uncultured bacteria and capacities in carbohydrate transport and metabolism than SHI medium. The dynamic changes in bacterial community composition over time indicated that some bacteria tended to be enriched at specific time points. Culturomics and identification of bacterial species results were further confirmed by the high throughput 16S rRNA sequencing results. Conclusion We developed a new medium NEMM that could support S-ECC microbiota growth with a higher yield of living bacteria, higher abundance and capacity, and be suitable for cultivating oral uncultured bacteria via culturomics technology.
format: application/pdf
format: text/html
creator: Yixin Zhang
creator: Yang Chen
creator: Chang Diao
creator: Haojie Lin
creator: Jingqi Zhu
creator: Ruiqing Sun
creator: Meng Wang
creator: Yuke Chen
creator: Hanzhang Zhou
creator: Zixi Dong
creator: Bin Xia
creator: Yixiang Wang
subject: Genomics
subject: Microbiology
subject: Dentistry
description: doi:10.7717/peerj.18312
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Introduction Severe early childhood caries (S-ECC) is a widespread disease that harms children physically and mentally. Microorganisms are regarded as the dominant etiology of caries, however, S-ECC microbiome remains largely unknown, nearly 1/4 of them remained uncultivated. To explore S-ECC microbiota, a new bacterial medium, nutrient-enriched microbiological medium (NEMM) was designed in this study. Methods Eleven fresh S-ECC dental plaque samples were collected and cultivated in both NEMM and SHI medium (reference medium) for 0, 1, 3, 6, 9, 15, 21 and 28 days under aerobic and anaerobic conditions. Thereafter, the cultures were harvested, together with their corresponding clinical S-ECC dental plaque samples, for high through-put 16S rRNA sequencing and culturomics. The single colonies were cultured for further confirmation by sequencing the full length of the 16S rRNA gene after bacterial genomic DNA extraction and PCR amplification. Results Either NEMM or SHI medium showed a significant decrease in bacterial alpha diversity compared to clinical dental plaque samples by high throughput 16S rRNA sequencing analysis, indicating a larger room for the improvement of both media. NEMM displayed more living bacteria, abundant bacteria species, uncultured bacteria and capacities in carbohydrate transport and metabolism than SHI medium. The dynamic changes in bacterial community composition over time indicated that some bacteria tended to be enriched at specific time points. Culturomics and identification of bacterial species results were further confirmed by the high throughput 16S rRNA sequencing results. Conclusion We developed a new medium NEMM that could support S-ECC microbiota growth with a higher yield of living bacteria, higher abundance and capacity, and be suitable for cultivating oral uncultured bacteria via culturomics technology.
bibliographic citation: Zhang et al. (2024) Exploration of severe early childhood caries microbiota through a novel developed nutrient enriched microbiological medium, high through-put 16S rRNA sequencing and culturomics. PeerJ 12:e18312 https://doi.org/10.7717/peerj.18312
date submitted: 2024-01-19
date accepted: 2024-09-24
issued: 2024-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yixin
author list: Agent
  family name: Chen
  given name: Yang
author list: Agent
  family name: Diao
  given name: Chang
author list: Agent
  family name: Lin
  given name: Haojie
author list: Agent
  family name: Zhu
  given name: Jingqi
author list: Agent
  family name: Sun
  given name: Ruiqing
author list: Agent
  family name: Wang
  given name: Meng
author list: Agent
  family name: Chen
  given name: Yuke
author list: Agent
  family name: Zhou
  given name: Hanzhang
author list: Agent
  family name: Dong
  given name: Zixi
author list: Agent
  family name: Xia
  given name: Bin
author list: Agent
  family name: Wang
  given name: Yixiang
doi: 10.7717/peerj.18312
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-28
copyright: ©2024 Zhang et al.
attribution name: Zhang et al.

Pereskia bleo augments NK cell cytotoxicity against triple-negative breast cancer cells (MDA-MB-231)
type: item
type: AcademicArticle
description: Background Natural killer cells (NK cells) are essential in cancer immunosurveillance in the body as they can recognize cancer cells that lacking MHC class 1 on their surface. Regulatory cytokines, including interleukin (IL)-18, IL-12, IL-10, IL-8, interferon-γ (IFN-γ), and secretory granules like perforin and granzyme are involved in NK cell-mediated cytotoxicity. Stimulating NK cells cytotoxicity towards cancer cells is an ideal strategy to combat cancer naturally. Medicinal plants have been reported to enhance immunity, with Pereskia bleo (P. bleo) particularly noteworthy due to its abundant bioactive compounds and ability to activate immune cells. This study aimed to evaluate the potential of methanol extract of P. bleo leaves (MEPB) for enhancing NK cell cytotoxicity against triple-negative human breast cancer cells (MDA-MB-231). Methods The optimal concentration of MEPB to activate NK cells was determined using healthy blood samples, assessing the expression of IL-12, IL-18, IL-10, IL-8, IFN-γ, perforin, and granzyme B via an enzyme-linked immunosorbent assay (ELISA). NK cell purity from healthy donors and breast cancer patients was determined using specific antibodies, and the number of NK cells was assessed using flow cytometry and a hemocytometer. A co-culture experiment, ELISA, and apoptosis assay were used to evaluate NK-mediated cytotoxicity pathways. Results ELISA data indicated that MEPB at 7.5 µg/ml significantly increased the expression of IFN-γ, IL-12, IL-18, perforin, and granzyme B while decreasing IL-8 and IL-10 expression after 20 hrs of incubation. The average NK cell purity was 87.09 ± 0.043%. Breast cancer patients exhibited lower NK cell counts than healthy donors. Co-culture experiments demonstrated that NK cells induced apoptosis in MDA-MB-231 breast cancer cells in the presence of MEPB by increasing perforin, granzyme B, and IFN-γ expression in both healthy donors and breast cancer patients-experimental groups. P. bleo enhances NK cell ac…
format: application/pdf
format: text/html
creator: Taif Kareem Khalaf
creator: Norzila Ismail
creator: Nor Amalia Nazri
creator: Naveed Ahmed
creator: Aidy Irman Yajid
creator: Rohimah Mohamud
creator: Ramlah Kadir
subject: Cell Biology
subject: Plant Science
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.18420
publisher: PeerJ Inc.
rights: © 2024 Khalaf et al.
abstract: Background Natural killer cells (NK cells) are essential in cancer immunosurveillance in the body as they can recognize cancer cells that lacking MHC class 1 on their surface. Regulatory cytokines, including interleukin (IL)-18, IL-12, IL-10, IL-8, interferon-γ (IFN-γ), and secretory granules like perforin and granzyme are involved in NK cell-mediated cytotoxicity. Stimulating NK cells cytotoxicity towards cancer cells is an ideal strategy to combat cancer naturally. Medicinal plants have been reported to enhance immunity, with Pereskia bleo (P. bleo) particularly noteworthy due to its abundant bioactive compounds and ability to activate immune cells. This study aimed to evaluate the potential of methanol extract of P. bleo leaves (MEPB) for enhancing NK cell cytotoxicity against triple-negative human breast cancer cells (MDA-MB-231). Methods The optimal concentration of MEPB to activate NK cells was determined using healthy blood samples, assessing the expression of IL-12, IL-18, IL-10, IL-8, IFN-γ, perforin, and granzyme B via an enzyme-linked immunosorbent assay (ELISA). NK cell purity from healthy donors and breast cancer patients was determined using specific antibodies, and the number of NK cells was assessed using flow cytometry and a hemocytometer. A co-culture experiment, ELISA, and apoptosis assay were used to evaluate NK-mediated cytotoxicity pathways. Results ELISA data indicated that MEPB at 7.5 µg/ml significantly increased the expression of IFN-γ, IL-12, IL-18, perforin, and granzyme B while decreasing IL-8 and IL-10 expression after 20 hrs of incubation. The average NK cell purity was 87.09 ± 0.043%. Breast cancer patients exhibited lower NK cell counts than healthy donors. Co-culture experiments demonstrated that NK cells induced apoptosis in MDA-MB-231 breast cancer cells in the presence of MEPB by increasing perforin, granzyme B, and IFN-γ expression in both healthy donors and breast cancer patients-experimental groups. P. bleo enhances NK cell ac…
bibliographic citation: Khalaf et al. (2024) Pereskia bleo augments NK cell cytotoxicity against triple-negative breast cancer cells (MDA-MB-231). PeerJ 12:e18420 https://doi.org/10.7717/peerj.18420
date submitted: 2024-07-08
date accepted: 2024-10-08
issued: 2024-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khalaf
  given name: Taif Kareem
author list: Agent
  family name: Ismail
  given name: Norzila
author list: Agent
  family name: Nazri
  given name: Nor Amalia
author list: Agent
  family name: Ahmed
  given name: Naveed
author list: Agent
  family name: Yajid
  given name: Aidy Irman
author list: Agent
  family name: Mohamud
  given name: Rohimah
author list: Agent
  family name: Kadir
  given name: Ramlah
doi: 10.7717/peerj.18420
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-28
copyright: ©2024 Khalaf et al.
attribution name: Khalaf et al.

Analysing the spatial variation of soil respiration during the early growing season of different grasslands in China
type: item
type: AcademicArticle
description: Background As one of the most essential vegetation types, grasslands play a vital role in the global carbon cycle. However, current researches on the spatial variation (SV) of soil respiration (Rs) in grasslands faces great uncertainties. Methods The SV of Rs was analysed by obtaining Rs during the early growing season of three types of grasslands (i.e., alpine meadow, desert steppe, and typical steppe) and related impact factors at 19 sites. Results The results demonstrated that during the early growing season, the Rs of the alpine meadow was the highest, followed by the typical steppe and desert steppe. Moreover, soil temperature was the primary factor affecting the SV of Rs in desert steppe. In contrast, soil water content influenced the SV of Rs in typical steppe. This study increases our understanding of the SV of Rs during the early growing season of different grasslands. It provides an important reference for accurately estimating the SV of Rs in grasslands at various time scales.
format: application/pdf
format: text/html
creator: Jie Liu
creator: Ni Huang
creator: Li Wang
creator: Xiaoyu Lin
creator: Luying Zhu
creator: Zheng Niu
creator: Yuelin Zhang
creator: Wensheng Duan
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.18480
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Background As one of the most essential vegetation types, grasslands play a vital role in the global carbon cycle. However, current researches on the spatial variation (SV) of soil respiration (Rs) in grasslands faces great uncertainties. Methods The SV of Rs was analysed by obtaining Rs during the early growing season of three types of grasslands (i.e., alpine meadow, desert steppe, and typical steppe) and related impact factors at 19 sites. Results The results demonstrated that during the early growing season, the Rs of the alpine meadow was the highest, followed by the typical steppe and desert steppe. Moreover, soil temperature was the primary factor affecting the SV of Rs in desert steppe. In contrast, soil water content influenced the SV of Rs in typical steppe. This study increases our understanding of the SV of Rs during the early growing season of different grasslands. It provides an important reference for accurately estimating the SV of Rs in grasslands at various time scales.
bibliographic citation: Liu et al. (2024) Analysing the spatial variation of soil respiration during the early growing season of different grasslands in China. PeerJ 12:e18480 https://doi.org/10.7717/peerj.18480
date submitted: 2024-01-25
date accepted: 2024-10-16
issued: 2024-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Jie
author list: Agent
  family name: Huang
  given name: Ni
author list: Agent
  family name: Wang
  given name: Li
author list: Agent
  family name: Lin
  given name: Xiaoyu
author list: Agent
  family name: Zhu
  given name: Luying
author list: Agent
  family name: Niu
  given name: Zheng
author list: Agent
  family name: Zhang
  given name: Yuelin
author list: Agent
  family name: Duan
  given name: Wensheng
doi: 10.7717/peerj.18480
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-28
copyright: ©2024 Liu et al.
attribution name: Liu et al.

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