PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Role of microRNA miR171 in plant development
items: Identification of key biomarkers based on the proliferation of secondary hyperparathyroidism by bioinformatics analysis and machine learning
items: Evaluation of sugarcane promising clones based on the morphophysiological traits developed from fuzz
items: Toxic effects of sodium dodecyl sulfate on planarian Dugesia japonica
items: Varying intensities of chronic stress induce inconsistent responses in weight and plasma metabolites in house sparrows (Passer domesticus)
items: Alteration of the oral and gut microbiota in patients with Kawasaki disease
items: Track cycling sprint sex differences using power data
items: Optimization of a tri-drug treatment against lung cancer using orthogonal design in preclinical studies
items: First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome
items: The postcranial anatomy of Gorgonops torvus (Synapsida, Gorgonopsia) from the late Permian of South Africa

Role of microRNA miR171 in plant development
type: item
type: AcademicArticle
description: MicroRNAs (miRNAs) are endogenous non-coding small RNA with 19–24 nucleotides (nts) in length, which play an essential role in regulating gene expression at the post-transcriptional level. As one of the first miRNAs found in plants, miR171 is a typical class of conserved miRNAs. The miR171 sequences among different species are highly similar, and the vast majority of them have both “GAGCCG” and “CAAUAU” fragments. In addition to being involved in plant growth and development, hormone signaling and stress response, miR171 also plays multiple and important roles in plants through interactions with microbe and other small-RNAs. The miRNA functions by regulating the expression of target genes. Most of miR171’s target genes are in the GRAS gene family, but also include some NSP, miRNAs, lncRNAs, and other genes. This review is intended to summarize recent updates on miR171 regarding its function in plant life and hopefully provide new ideas for understanding miR171 function and regulatory mechanisms.
format: application/pdf
format: text/html
creator: Ling Ling Pei
creator: Ling Ling Zhang
creator: Xin Liu
creator: Jing Jiang
subject: Agricultural Science
subject: Developmental Biology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.15632
publisher: PeerJ Inc.
rights: © 2023 Pei et al.
abstract: MicroRNAs (miRNAs) are endogenous non-coding small RNA with 19–24 nucleotides (nts) in length, which play an essential role in regulating gene expression at the post-transcriptional level. As one of the first miRNAs found in plants, miR171 is a typical class of conserved miRNAs. The miR171 sequences among different species are highly similar, and the vast majority of them have both “GAGCCG” and “CAAUAU” fragments. In addition to being involved in plant growth and development, hormone signaling and stress response, miR171 also plays multiple and important roles in plants through interactions with microbe and other small-RNAs. The miRNA functions by regulating the expression of target genes. Most of miR171’s target genes are in the GRAS gene family, but also include some NSP, miRNAs, lncRNAs, and other genes. This review is intended to summarize recent updates on miR171 regarding its function in plant life and hopefully provide new ideas for understanding miR171 function and regulatory mechanisms.
bibliographic citation: Pei et al. (2023) Role of microRNA miR171 in plant development. PeerJ 11:e15632 https://doi.org/10.7717/peerj.15632
date submitted: 2022-12-15
date accepted: 2023-06-02
issued: 2023-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pei
  given name: Ling Ling
author list: Agent
  family name: Zhang
  given name: Ling Ling
author list: Agent
  family name: Liu
  given name: Xin
author list: Agent
  family name: Jiang
  given name: Jing
doi: 10.7717/peerj.15632
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-10
copyright: ©2023 Pei et al.
attribution name: Pei et al.

Identification of key biomarkers based on the proliferation of secondary hyperparathyroidism by bioinformatics analysis and machine learning
type: item
type: AcademicArticle
description: Objective Secondary hyperparathyroidism (SHPT) is a frequent complication of chronic kidney disease (CKD) associated with morbidity and mortality. This study aims to identify potential biomarkers that may be used to predict the progression of SHPT and to elucidate the molecular mechanisms of SHPT pathogenesis at the transcriptome level. Methods We analyzed differentially expressed genes (DEGs) between diffuse and nodular parathyroid hyperplasia of SHPT patients from the GSE75886 dataset, and then verified DEG levels with the GSE83421 data file of primary hyperparathyroidism (PHPT) patients. Candidate gene sets were selected by machine learning screens of differential genes and immune cell infiltration was explored with the CIBERSORT algorithm. RcisTarget was used to predict transcription factors, and Cytoscape was used to construct a lncRNA-miRNA-mRNA network to identify possible molecular mechanisms. Immunohistochemistry (IHC) staining and quantitative real-time polymerase chain reaction (qRT-PCR) were used to verify the expression of screened genes in parathyroid tissues of SHPT patients and animal models. Results A total of 614 DEGs in GSE75886 were obtained as candidate gene sets for further analysis. Five key genes (USP12, CIDEA, PCOLCE2, CAPZA1, and ACCN2) had significant expression differences between groups and were screened with the best ranking in the machine learning process. These genes were shown to be closely related to immune cell infiltration levels and play important roles in the immune microenvironment. Transcription factor ZBTB6 was identified as the master regulator, alongside multiple other transcription factors. Combined with qPCR and IHC assay of hyperplastic parathyroid tissues from SHPT patients and rats confirm differential expression of USP12, CIDEA, PCOLCE2, CAPZA1, and ACCN2, suggesting that they may play important roles in the proliferation and progression of SHPT. Conclusion USP12, CIDEA, PCOLCE2, CAPZA1, and ACCN2 have great potential…
format: application/pdf
format: text/html
creator: Aiwen Shen
creator: Jialin Shi
creator: Yu Wang
creator: Qian Zhang
creator: Jing Chen
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Nephrology
subject: Histology
description: doi:10.7717/peerj.15633
publisher: PeerJ Inc.
rights: © 2023 Shen et al.
abstract: Objective Secondary hyperparathyroidism (SHPT) is a frequent complication of chronic kidney disease (CKD) associated with morbidity and mortality. This study aims to identify potential biomarkers that may be used to predict the progression of SHPT and to elucidate the molecular mechanisms of SHPT pathogenesis at the transcriptome level. Methods We analyzed differentially expressed genes (DEGs) between diffuse and nodular parathyroid hyperplasia of SHPT patients from the GSE75886 dataset, and then verified DEG levels with the GSE83421 data file of primary hyperparathyroidism (PHPT) patients. Candidate gene sets were selected by machine learning screens of differential genes and immune cell infiltration was explored with the CIBERSORT algorithm. RcisTarget was used to predict transcription factors, and Cytoscape was used to construct a lncRNA-miRNA-mRNA network to identify possible molecular mechanisms. Immunohistochemistry (IHC) staining and quantitative real-time polymerase chain reaction (qRT-PCR) were used to verify the expression of screened genes in parathyroid tissues of SHPT patients and animal models. Results A total of 614 DEGs in GSE75886 were obtained as candidate gene sets for further analysis. Five key genes (USP12, CIDEA, PCOLCE2, CAPZA1, and ACCN2) had significant expression differences between groups and were screened with the best ranking in the machine learning process. These genes were shown to be closely related to immune cell infiltration levels and play important roles in the immune microenvironment. Transcription factor ZBTB6 was identified as the master regulator, alongside multiple other transcription factors. Combined with qPCR and IHC assay of hyperplastic parathyroid tissues from SHPT patients and rats confirm differential expression of USP12, CIDEA, PCOLCE2, CAPZA1, and ACCN2, suggesting that they may play important roles in the proliferation and progression of SHPT. Conclusion USP12, CIDEA, PCOLCE2, CAPZA1, and ACCN2 have great potential…
bibliographic citation: Shen et al. (2023) Identification of key biomarkers based on the proliferation of secondary hyperparathyroidism by bioinformatics analysis and machine learning. PeerJ 11:e15633 https://doi.org/10.7717/peerj.15633
date submitted: 2023-02-13
date accepted: 2023-06-03
issued: 2023-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shen
  given name: Aiwen
author list: Agent
  family name: Shi
  given name: Jialin
author list: Agent
  family name: Wang
  given name: Yu
author list: Agent
  family name: Zhang
  given name: Qian
author list: Agent
  family name: Chen
  given name: Jing
doi: 10.7717/peerj.15633
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-10
copyright: © 2023 Shen et al.
attribution name: Shen et al.

Evaluation of sugarcane promising clones based on the morphophysiological traits developed from fuzz
type: item
type: AcademicArticle
description: Sugarcane is one of the critical commercial crops and principal sources of ethanol and sugar worldwide. Unfavorable conditions and poor seed setting rates hinder variety development in sugarcane. Countries like Pakistan directly import fuzz (true seed) and other propagation material from the USA, China, Brazil, etc. In this study, we imported fuzz from China, developed 29 genotypes germinating in the glasshouse, and evaluated at field conditions along with two local checks (CPF-251 and HSF-240). Morphophysiological data were recorded, including plant height (PH), cane length (CL), internodal length (IL), tiller number (TN), brix percentage (B), cane diameter (CD), chlorophyll a (Chl. a), chlorophyll b (Chl. b), and total chlorophyll (T. Chl). Results showed highly significant (p < 0.001) differences among the sugarcane accessions for all the studied traits. High broad-sense heritability (81.89% to 99.91%) was recorded for all the studied parameters. Genetic Advance (GA) ranges from 4.6% to 65.32%. The highest GA was observed for PH (65.32%), followed by CL (63.28%). Chlorophyll leaching assay was also performed at different time points (0, 50, 100, 150, and 200 min). All the genotypes showed the same leaching trend at all times, and better performing genotypes showed less leaching compared to poor performing, indicating the high amount of cutin and wax on the leaf surface. Correlation analysis showed that PH, CL, IL, and TN had significant associations. Principal components analysis (PCA) further confirms these results. Based on PCA and correlation results, PH, CL, IL, and TN can be utilized as a selection criterion for sugarcane improvement. Genotypes such as NS-4a, NS-5, NS-6, NS-8, NS-9, and NS-15 are recommended for future breeding programs related to sugarcane variety development.
format: application/pdf
format: text/html
creator: Bilal Saleem
creator: Muhammad Uzair
creator: Muhammad Noman
creator: Kotb A. Attia
creator: Muqing Zhang
creator: Mona S. Alwahaibi
creator: Nageen Zahra
creator: Muhammad Kashif Naeem
creator: Arif A. Mohammed
creator: Sajid Fiaz
creator: Itoh Kimiko
creator: Muhammad Ramzan Khan
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.15646
publisher: PeerJ Inc.
rights: © 2023 Saleem et al.
abstract: Sugarcane is one of the critical commercial crops and principal sources of ethanol and sugar worldwide. Unfavorable conditions and poor seed setting rates hinder variety development in sugarcane. Countries like Pakistan directly import fuzz (true seed) and other propagation material from the USA, China, Brazil, etc. In this study, we imported fuzz from China, developed 29 genotypes germinating in the glasshouse, and evaluated at field conditions along with two local checks (CPF-251 and HSF-240). Morphophysiological data were recorded, including plant height (PH), cane length (CL), internodal length (IL), tiller number (TN), brix percentage (B), cane diameter (CD), chlorophyll a (Chl. a), chlorophyll b (Chl. b), and total chlorophyll (T. Chl). Results showed highly significant (p < 0.001) differences among the sugarcane accessions for all the studied traits. High broad-sense heritability (81.89% to 99.91%) was recorded for all the studied parameters. Genetic Advance (GA) ranges from 4.6% to 65.32%. The highest GA was observed for PH (65.32%), followed by CL (63.28%). Chlorophyll leaching assay was also performed at different time points (0, 50, 100, 150, and 200 min). All the genotypes showed the same leaching trend at all times, and better performing genotypes showed less leaching compared to poor performing, indicating the high amount of cutin and wax on the leaf surface. Correlation analysis showed that PH, CL, IL, and TN had significant associations. Principal components analysis (PCA) further confirms these results. Based on PCA and correlation results, PH, CL, IL, and TN can be utilized as a selection criterion for sugarcane improvement. Genotypes such as NS-4a, NS-5, NS-6, NS-8, NS-9, and NS-15 are recommended for future breeding programs related to sugarcane variety development.
bibliographic citation: Saleem et al. (2023) Evaluation of sugarcane promising clones based on the morphophysiological traits developed from fuzz. PeerJ 11:e15646 https://doi.org/10.7717/peerj.15646
date submitted: 2023-02-14
date accepted: 2023-06-06
issued: 2023-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saleem
  given name: Bilal
author list: Agent
  family name: Uzair
  given name: Muhammad
author list: Agent
  family name: Noman
  given name: Muhammad
author list: Agent
  family name: Attia
  given name: Kotb A.
author list: Agent
  family name: Zhang
  given name: Muqing
author list: Agent
  family name: Alwahaibi
  given name: Mona S.
author list: Agent
  family name: Zahra
  given name: Nageen
author list: Agent
  family name: Naeem
  given name: Muhammad Kashif
author list: Agent
  family name: Mohammed
  given name: Arif A.
author list: Agent
  family name: Fiaz
  given name: Sajid
author list: Agent
  family name: Kimiko
  given name: Itoh
author list: Agent
  family name: Khan
  given name: Muhammad Ramzan
doi: 10.7717/peerj.15646
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-10
copyright: ©2023 Saleem et al.
attribution name: Saleem et al.

Toxic effects of sodium dodecyl sulfate on planarian Dugesia japonica
type: item
type: AcademicArticle
description: Sodium dodecyl sulfate (SDS) is an anionic surfactant, which is widely used in various fields in human life. However, SDS discharged into the water environment has a certain impact on aquatic organisms. In this study, planarian Dugesia japonica (D. japonica) was used to identify the toxic effects of SDS. A series of SDS solutions with different concentrations were used to treat planarians for the acute toxicity test , and the results showed that the semi-lethal concentration (LC50) of SDS to D. japonica at 24 h, 48 h, 72 h, and 96 h were 4.29 mg/L, 3.76 mg/L, 3.45 mg/L, and 3.20 mg/L respectively. After the planarians were exposed to 0.5 mg/L and 1.0 mg/L SDS solutions for 1, 3, and 5 days, the activities of superoxide dismutase (SOD), catalase (CAT), and malondialdehyde (MDA) content were measured to detect the oxidative stress and lipid peroxidation in planarians. Random amplified polymorphic DNA (RAPD) analysis was performed to detect the genotoxicity caused by SDS to planarians. The results showed that the activities of SOD, CAT, and MDA content increased after the treatment, indicating that SDS induced oxidative stress in planarians. RAPD analysis showed that the genomic template stability (GTS) values of planarians treated by 0.5 mg/L and 1.0 mg/L SDS for 1, 3, and 5 days were 67.86%, 64.29%, 58.93%, and 64.29%, 60.71%, 48.21%, respectively. GTS values decreased with the increasing of SDS concentration and exposure time, indicating that SDS had genotoxicity to planarians in a time and dose-related manner. Fluorescent quantitative PCR (qPCR) was used to investigate the effects of SDS on gene expression of planarians. After the planarians were exposed to 1.0 mg/L SDS solution for 1, 3, and 5 days, the expression of caspase3 was upregulated, and that of piwiA, piwiB, PCNA, cyclinB, and RAD51 were downregulated. These results suggested that SDS might induce apoptosis, affect cell proliferation, differentiation, and DNA repair ability of planarian cells and cause t…
format: application/pdf
format: text/html
creator: Minmin Feng
creator: Zhenbiao Xu
creator: Dandan Yin
creator: Zelong Zhao
creator: Xiuyuan Zhou
creator: Linxia Song
subject: Biochemistry
subject: Toxicology
subject: Zoology
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.15660
publisher: PeerJ Inc.
rights: © 2023 Feng et al.
abstract: Sodium dodecyl sulfate (SDS) is an anionic surfactant, which is widely used in various fields in human life. However, SDS discharged into the water environment has a certain impact on aquatic organisms. In this study, planarian Dugesia japonica (D. japonica) was used to identify the toxic effects of SDS. A series of SDS solutions with different concentrations were used to treat planarians for the acute toxicity test , and the results showed that the semi-lethal concentration (LC50) of SDS to D. japonica at 24 h, 48 h, 72 h, and 96 h were 4.29 mg/L, 3.76 mg/L, 3.45 mg/L, and 3.20 mg/L respectively. After the planarians were exposed to 0.5 mg/L and 1.0 mg/L SDS solutions for 1, 3, and 5 days, the activities of superoxide dismutase (SOD), catalase (CAT), and malondialdehyde (MDA) content were measured to detect the oxidative stress and lipid peroxidation in planarians. Random amplified polymorphic DNA (RAPD) analysis was performed to detect the genotoxicity caused by SDS to planarians. The results showed that the activities of SOD, CAT, and MDA content increased after the treatment, indicating that SDS induced oxidative stress in planarians. RAPD analysis showed that the genomic template stability (GTS) values of planarians treated by 0.5 mg/L and 1.0 mg/L SDS for 1, 3, and 5 days were 67.86%, 64.29%, 58.93%, and 64.29%, 60.71%, 48.21%, respectively. GTS values decreased with the increasing of SDS concentration and exposure time, indicating that SDS had genotoxicity to planarians in a time and dose-related manner. Fluorescent quantitative PCR (qPCR) was used to investigate the effects of SDS on gene expression of planarians. After the planarians were exposed to 1.0 mg/L SDS solution for 1, 3, and 5 days, the expression of caspase3 was upregulated, and that of piwiA, piwiB, PCNA, cyclinB, and RAD51 were downregulated. These results suggested that SDS might induce apoptosis, affect cell proliferation, differentiation, and DNA repair ability of planarian cells and cause t…
bibliographic citation: Feng et al. (2023) Toxic effects of sodium dodecyl sulfate on planarian Dugesia japonica. PeerJ 11:e15660 https://doi.org/10.7717/peerj.15660
date submitted: 2023-02-14
date accepted: 2023-06-07
issued: 2023-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: Minmin
author list: Agent
  family name: Xu
  given name: Zhenbiao
author list: Agent
  family name: Yin
  given name: Dandan
author list: Agent
  family name: Zhao
  given name: Zelong
author list: Agent
  family name: Zhou
  given name: Xiuyuan
author list: Agent
  family name: Song
  given name: Linxia
doi: 10.7717/peerj.15660
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-10
copyright: ©2023 Feng et al.
attribution name: Feng et al.

Varying intensities of chronic stress induce inconsistent responses in weight and plasma metabolites in house sparrows (Passer domesticus)
type: item
type: AcademicArticle
description: One of the biggest unanswered questions in the field of stress physiology is whether variation in chronic stress intensity will produce proportional (a gradient or graded) physiological response. We were specifically interested in the timing of the entrance into homeostatic overload, or the start of chronic stress symptoms. To attempt to fill this knowledge gap we split 40 captive house sparrows (Passer domesticus) into four groups (high stress, medium stress, low stress, and a captivity-only control) and subjected them to six bouts of chronic stress over a 6-month period. We varied the number of stressors/day and the length of each individual bout with the goal of producing groups that would experience different magnitudes of wear-and-tear. To evaluate the impact of chronic stress, at the start and end of each stress bout we measured body weight and three plasma metabolites (glucose, ketones, and uric acid) in both a fasted and fed state. All metrics showed significant differences across treatment groups, with the high stress group most frequently showing the greatest changes. However, the changes did not produce a consistent profile that matched the different chronic stress intensities. We also took samples after a prolonged recovery period of 6 weeks after the chronic stressors ended. The only group difference that persisted after 6 weeks was weight—all differences across groups in metabolites recovered. The results indicate that common blood metabolites are sensitive to stressors and may show signs of wear-and-tear, but are not reliable indicators of the intensity of long-term chronic stress. Furthermore, regulatory mechanisms are robust enough to recover within 6 weeks post-stress.
format: application/pdf
format: text/html
creator: Ursula K. Beattie
creator: Nina Fefferman
creator: L. Michael Romero
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.15661
publisher: PeerJ Inc.
rights: © 2023 Beattie et al.
abstract: One of the biggest unanswered questions in the field of stress physiology is whether variation in chronic stress intensity will produce proportional (a gradient or graded) physiological response. We were specifically interested in the timing of the entrance into homeostatic overload, or the start of chronic stress symptoms. To attempt to fill this knowledge gap we split 40 captive house sparrows (Passer domesticus) into four groups (high stress, medium stress, low stress, and a captivity-only control) and subjected them to six bouts of chronic stress over a 6-month period. We varied the number of stressors/day and the length of each individual bout with the goal of producing groups that would experience different magnitudes of wear-and-tear. To evaluate the impact of chronic stress, at the start and end of each stress bout we measured body weight and three plasma metabolites (glucose, ketones, and uric acid) in both a fasted and fed state. All metrics showed significant differences across treatment groups, with the high stress group most frequently showing the greatest changes. However, the changes did not produce a consistent profile that matched the different chronic stress intensities. We also took samples after a prolonged recovery period of 6 weeks after the chronic stressors ended. The only group difference that persisted after 6 weeks was weight—all differences across groups in metabolites recovered. The results indicate that common blood metabolites are sensitive to stressors and may show signs of wear-and-tear, but are not reliable indicators of the intensity of long-term chronic stress. Furthermore, regulatory mechanisms are robust enough to recover within 6 weeks post-stress.
bibliographic citation: Beattie et al. (2023) Varying intensities of chronic stress induce inconsistent responses in weight and plasma metabolites in house sparrows (Passer domesticus). PeerJ 11:e15661 https://doi.org/10.7717/peerj.15661
date submitted: 2023-03-02
date accepted: 2023-06-07
issued: 2023-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beattie
  given name: Ursula K.
author list: Agent
  family name: Fefferman
  given name: Nina
author list: Agent
  family name: Romero
  given name: L. Michael
doi: 10.7717/peerj.15661
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-10
copyright: © 2023 Beattie et al.
attribution name: Beattie et al.

Alteration of the oral and gut microbiota in patients with Kawasaki disease
type: item
type: AcademicArticle
description: Background Kawasaki disease (KD) is a multi-systemic vasculitis that primarily affects children and has an unknown cause. Although an increasing number of studies linking the gut microbiota with KD, the unchallengeable etiology of KD is not available. Methods Here, we obtained fecal and oral samples from KD patients and healthy controls, and then we use high-throughput sequencing to examine the diversity and composition of microbiota. Results Results showed that both in the gut and oral microbiota, the diversity of KD patients was significantly lower than that of the healthy controls. In the gut microbiota, a higher abundance of Enterococcus (40.12% vs less than 0.1%), Bifidobacterium (20.71% vs 3.06%), Escherichia-Shigella (17.56% vs 0.61%), Streptococcus (5.97% vs 0.11%) and Blautia (4.69% vs 0.1%) was observed in the KD patients, and enrichment of Enterococcus in the patients was observed. In terms of oral microbiota, the prevalence of Streptococcus (21.99% vs 0.1%), Rothia (3.02% vs 0.1%), and Escherichia-Shigella (0.68% vs 0.0%) were significantly higher in the KD patients, with the enrichment of Streptococcus and Escherichia-Shigella. Additionally, significant differences in microbial community function between KD patients and healthy controls in the fecal samples were also observed, which will affect the colonization and reproduction of gut microbiota. Conclusions These results suggested that the dysbiosis of gut and oral microbiota are both related to KD pathogenesis, of which, the prevalence of Enterococcus in the gut and higher abundance of Streptococcus and Escherichia-Shigella in the oral cavity will be a potential biomarker of the KD. Overall, this study not only confirms that the disturbance of gut microbiota is a causative trigger of KD but also provides new insight into the oral microbiota involved in KD pathogenesis.
format: application/pdf
format: text/html
creator: Qinghuang Zeng
creator: Renhe Zeng
creator: Jianbin Ye
subject: Microbiology
subject: Molecular Biology
subject: Cardiology
subject: Gastroenterology and Hepatology
subject: Pediatrics
description: doi:10.7717/peerj.15662
publisher: PeerJ Inc.
rights: © 2023 Zeng et al.
abstract: Background Kawasaki disease (KD) is a multi-systemic vasculitis that primarily affects children and has an unknown cause. Although an increasing number of studies linking the gut microbiota with KD, the unchallengeable etiology of KD is not available. Methods Here, we obtained fecal and oral samples from KD patients and healthy controls, and then we use high-throughput sequencing to examine the diversity and composition of microbiota. Results Results showed that both in the gut and oral microbiota, the diversity of KD patients was significantly lower than that of the healthy controls. In the gut microbiota, a higher abundance of Enterococcus (40.12% vs less than 0.1%), Bifidobacterium (20.71% vs 3.06%), Escherichia-Shigella (17.56% vs 0.61%), Streptococcus (5.97% vs 0.11%) and Blautia (4.69% vs 0.1%) was observed in the KD patients, and enrichment of Enterococcus in the patients was observed. In terms of oral microbiota, the prevalence of Streptococcus (21.99% vs 0.1%), Rothia (3.02% vs 0.1%), and Escherichia-Shigella (0.68% vs 0.0%) were significantly higher in the KD patients, with the enrichment of Streptococcus and Escherichia-Shigella. Additionally, significant differences in microbial community function between KD patients and healthy controls in the fecal samples were also observed, which will affect the colonization and reproduction of gut microbiota. Conclusions These results suggested that the dysbiosis of gut and oral microbiota are both related to KD pathogenesis, of which, the prevalence of Enterococcus in the gut and higher abundance of Streptococcus and Escherichia-Shigella in the oral cavity will be a potential biomarker of the KD. Overall, this study not only confirms that the disturbance of gut microbiota is a causative trigger of KD but also provides new insight into the oral microbiota involved in KD pathogenesis.
bibliographic citation: Zeng et al. (2023) Alteration of the oral and gut microbiota in patients with Kawasaki disease. PeerJ 11:e15662 https://doi.org/10.7717/peerj.15662
date submitted: 2023-03-31
date accepted: 2023-06-07
issued: 2023-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeng
  given name: Qinghuang
author list: Agent
  family name: Zeng
  given name: Renhe
author list: Agent
  family name: Ye
  given name: Jianbin
doi: 10.7717/peerj.15662
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-10
copyright: ©2023 Zeng et al.
attribution name: Zeng et al.

Track cycling sprint sex differences using power data
type: item
type: AcademicArticle
description: Objectives Currently, there are no data on sex differences in the power profiles in sprint track cycling. This cross-section study analyses retrospective data of female and male track sprint cyclists for sex differences. We hypothesized that women would exhibit lower peak power to weight than men, as well as demonstrate a different distribution of power durations related to sprint cycling performance. Design We used training, testing, and racing data from a publicly available online depository (www.strava.com), for 29 track sprint cyclists (eight women providing 18 datasets, and 21 men providing 54 datasets) to create sex-specific profiles. R2 was used to describe model quality, and regression indices are used to compare watts per kilogram (W/kg) for each duration for both sexes against a 1:1 relationship expected for 15-s:15-s W/kg. Results We confirmed our sample were sprint cyclists, displaying higher peak and competition power than track endurance cyclists. All power profiles showed a high model quality (R2 ≥ 0.77). Regression indices for both sexes were similar for all durations, suggesting similar peak power and similar relationship between peak power and endurance level for both men and women (rejecting our hypothesis). The value of R2 for the female sprinters showed greater variation suggesting greater differences within female sprint cyclists. Conclusion The main finding shows female sprint cyclists in this study have very similar relationships between peak power and endurance power as men. Higher variation in W/kg for women in this study than men, within these strong relationships, indicates women in this study, had greater inter-athlete variability, and may thus require more personalised training. Future work needs to be performed with larger samples, and at different levels to optimize these recommendations.
format: application/pdf
format: text/html
creator: Hamish Ferguson
creator: Chris Harnish
creator: Sebastian Klich
creator: Kamil Michalik
creator: Anna Katharina Dunst
creator: Tony Zhou
creator: J Geoffrey Chase
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.15671
publisher: PeerJ Inc.
rights: © 2023 Ferguson et al.
abstract: Objectives Currently, there are no data on sex differences in the power profiles in sprint track cycling. This cross-section study analyses retrospective data of female and male track sprint cyclists for sex differences. We hypothesized that women would exhibit lower peak power to weight than men, as well as demonstrate a different distribution of power durations related to sprint cycling performance. Design We used training, testing, and racing data from a publicly available online depository (www.strava.com), for 29 track sprint cyclists (eight women providing 18 datasets, and 21 men providing 54 datasets) to create sex-specific profiles. R2 was used to describe model quality, and regression indices are used to compare watts per kilogram (W/kg) for each duration for both sexes against a 1:1 relationship expected for 15-s:15-s W/kg. Results We confirmed our sample were sprint cyclists, displaying higher peak and competition power than track endurance cyclists. All power profiles showed a high model quality (R2 ≥ 0.77). Regression indices for both sexes were similar for all durations, suggesting similar peak power and similar relationship between peak power and endurance level for both men and women (rejecting our hypothesis). The value of R2 for the female sprinters showed greater variation suggesting greater differences within female sprint cyclists. Conclusion The main finding shows female sprint cyclists in this study have very similar relationships between peak power and endurance power as men. Higher variation in W/kg for women in this study than men, within these strong relationships, indicates women in this study, had greater inter-athlete variability, and may thus require more personalised training. Future work needs to be performed with larger samples, and at different levels to optimize these recommendations.
bibliographic citation: Ferguson et al. (2023) Track cycling sprint sex differences using power data. PeerJ 11:e15671 https://doi.org/10.7717/peerj.15671
date submitted: 2023-01-09
date accepted: 2023-06-09
issued: 2023-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferguson
  given name: Hamish
author list: Agent
  family name: Harnish
  given name: Chris
author list: Agent
  family name: Klich
  given name: Sebastian
author list: Agent
  family name: Michalik
  given name: Kamil
author list: Agent
  family name: Dunst
  given name: Anna Katharina
author list: Agent
  family name: Zhou
  given name: Tony
author list: Agent
  family name: Chase
  given name: J Geoffrey
doi: 10.7717/peerj.15671
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-10
copyright: © 2023 Ferguson et al.
attribution name: Ferguson et al.

Optimization of a tri-drug treatment against lung cancer using orthogonal design in preclinical studies
type: item
type: AcademicArticle
description: A growing body of evidence suggests that anesthetics impact the outcome of patients with cancer after surgical intervention. However, the optimal dose and underlying mechanisms of co-administered anesthetics in lung tumor therapy have been poorly studied. Here, we aimed to investigate the role of combined anesthetics propofol, sufentanil, and rocuronium in treating lung cancer using an orthogonal experimental design and to explore the optimal combination of anesthetics. First, we evaluated the effects of the three anesthetics on the proliferation and invasion of A-549 cells using Cell Counting Kit 8 and Transwell migration and invasion assays. Subsequently, we applied the orthogonal experimental design (OED) method to screen the appropriate concentrations of the combined anesthetics with the most effective antitumor activity. We found that all three agents inhibited the proliferation of A-549 cells in a dose- and time-dependent manner when applied individually or in combination, with the highest differences in the magnitude of inhibition occurring 24 h after combined drug exposure. The optimal combination of the three anesthetics that achieved the strongest reduction in cell viability was 1.4 µmol/L propofol, 2 nmol/L sufentanil, and 7.83 µmol/L rocuronium. This optimal 3-drug combination produced a more beneficial result at 24 h than either single drug. Our results provide a theoretical basis for improving the efficacy of lung tumor treatment and optimizing anesthetic strategies.
format: application/pdf
format: text/html
creator: Jing Tan
creator: Lijun Wang
creator: Xuming Song
creator: Yijian Zhang
creator: Zhenghuan Song
creator: Manlin Duan
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.15672
publisher: PeerJ Inc.
rights: © 2023 Tan et al.
abstract: A growing body of evidence suggests that anesthetics impact the outcome of patients with cancer after surgical intervention. However, the optimal dose and underlying mechanisms of co-administered anesthetics in lung tumor therapy have been poorly studied. Here, we aimed to investigate the role of combined anesthetics propofol, sufentanil, and rocuronium in treating lung cancer using an orthogonal experimental design and to explore the optimal combination of anesthetics. First, we evaluated the effects of the three anesthetics on the proliferation and invasion of A-549 cells using Cell Counting Kit 8 and Transwell migration and invasion assays. Subsequently, we applied the orthogonal experimental design (OED) method to screen the appropriate concentrations of the combined anesthetics with the most effective antitumor activity. We found that all three agents inhibited the proliferation of A-549 cells in a dose- and time-dependent manner when applied individually or in combination, with the highest differences in the magnitude of inhibition occurring 24 h after combined drug exposure. The optimal combination of the three anesthetics that achieved the strongest reduction in cell viability was 1.4 µmol/L propofol, 2 nmol/L sufentanil, and 7.83 µmol/L rocuronium. This optimal 3-drug combination produced a more beneficial result at 24 h than either single drug. Our results provide a theoretical basis for improving the efficacy of lung tumor treatment and optimizing anesthetic strategies.
bibliographic citation: Tan et al. (2023) Optimization of a tri-drug treatment against lung cancer using orthogonal design in preclinical studies. PeerJ 11:e15672 https://doi.org/10.7717/peerj.15672
date submitted: 2023-04-05
date accepted: 2023-06-11
issued: 2023-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Jing
author list: Agent
  family name: Wang
  given name: Lijun
author list: Agent
  family name: Song
  given name: Xuming
author list: Agent
  family name: Zhang
  given name: Yijian
author list: Agent
  family name: Song
  given name: Zhenghuan
author list: Agent
  family name: Duan
  given name: Manlin
doi: 10.7717/peerj.15672
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-10
copyright: ©2023 Tan et al.
attribution name: Tan et al.

First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome
type: item
type: AcademicArticle
description: Background The Andean condor (Vultur gryphus) is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome. Methods This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways. Results Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with Clostridium perfringens, a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for Clostridium perfringens and Plesiomonas shigelloides, respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.
format: application/pdf
format: text/html
creator: J. Eduardo Martinez-Hernandez
creator: Pablo Berrios
creator: Rodrigo Santibáñez
creator: Yesid Cuesta Astroz
creator: Carolina Sanchez
creator: Alberto J. M. Martin
creator: Annette N. Trombert
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Virology
subject: Zoology
description: doi:10.7717/peerj.15235
publisher: PeerJ Inc.
rights: © 2023 Martinez-Hernandez et al.
abstract: Background The Andean condor (Vultur gryphus) is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome. Methods This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways. Results Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with Clostridium perfringens, a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for Clostridium perfringens and Plesiomonas shigelloides, respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.
bibliographic citation: Martinez-Hernandez et al. (2023) First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome. PeerJ 11:e15235 https://doi.org/10.7717/peerj.15235
date submitted: 2022-08-23
date accepted: 2023-03-28
issued: 2023-07-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martinez-Hernandez
  given name: J. Eduardo
author list: Agent
  family name: Berrios
  given name: Pablo
author list: Agent
  family name: Santibáñez
  given name: Rodrigo
author list: Agent
  family name: Cuesta Astroz
  given name: Yesid
author list: Agent
  family name: Sanchez
  given name: Carolina
author list: Agent
  family name: Martin
  given name: Alberto J. M.
author list: Agent
  family name: Trombert
  given name: Annette N.
doi: 10.7717/peerj.15235
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-07
copyright: © 2023 Martinez-Hernandez et al.
attribution name: Martinez-Hernandez et al.

The postcranial anatomy of Gorgonops torvus (Synapsida, Gorgonopsia) from the late Permian of South Africa
type: item
type: AcademicArticle
description: Gorgonopsians are among the most recognizable groups of synapsids from the Permian period and have an extensive but mostly cranial fossil record. By contrast, relatively little is known about their postcranial anatomy. Here, we describe a nearly complete, semi-articulated skeleton of a gorgonopsian (identified as Gorgonops torvus) from the late Permian Endothiodon Assemblage Zone of the South African Karoo Basin and discuss its paleobiological implications. Known gorgonopsian postcrania indicate morphological conservatism in the group, but the skeletal anatomy of Gorgonops does differ from that of other gorgonopsians in some respects, such as in the triangular radiale and short terminal phalanges in the manus, and a weakly developed distinction between pubis and ischium in ventral aspect of the pelvic girdle. Similarities between the specimen described herein and a historically problematic specimen originally referred to “Scymnognathus cf. whaitsi” confirm referral of the latter specimen to Gorgonops. Since descriptions of gorgonopsian postcrania are rare, new interpretations of the lifestyle and ecology of Gorgonopsia can be drawn from our contribution. We conclude that gorgonopsians were likely ambush predators, able to chase their prey over short distances and pin them down with strong forelimbs before using their canines for the kill. This is evidenced by their different fore- and hindlimb morphology; the former stouter and more robust in comparison to the longer, more gracile, back legs. Furthermore, the completeness of the study specimen facilitates calculation of an estimated body mass of approximately 98 kg, similar to that of a modern lioness.
format: application/pdf
format: text/html
creator: Eva-Maria Bendel
creator: Christian F. Kammerer
creator: Roger M. H. Smith
creator: Jörg Fröbisch
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15378
publisher: PeerJ Inc.
rights: © 2023 Bendel et al.
abstract: Gorgonopsians are among the most recognizable groups of synapsids from the Permian period and have an extensive but mostly cranial fossil record. By contrast, relatively little is known about their postcranial anatomy. Here, we describe a nearly complete, semi-articulated skeleton of a gorgonopsian (identified as Gorgonops torvus) from the late Permian Endothiodon Assemblage Zone of the South African Karoo Basin and discuss its paleobiological implications. Known gorgonopsian postcrania indicate morphological conservatism in the group, but the skeletal anatomy of Gorgonops does differ from that of other gorgonopsians in some respects, such as in the triangular radiale and short terminal phalanges in the manus, and a weakly developed distinction between pubis and ischium in ventral aspect of the pelvic girdle. Similarities between the specimen described herein and a historically problematic specimen originally referred to “Scymnognathus cf. whaitsi” confirm referral of the latter specimen to Gorgonops. Since descriptions of gorgonopsian postcrania are rare, new interpretations of the lifestyle and ecology of Gorgonopsia can be drawn from our contribution. We conclude that gorgonopsians were likely ambush predators, able to chase their prey over short distances and pin them down with strong forelimbs before using their canines for the kill. This is evidenced by their different fore- and hindlimb morphology; the former stouter and more robust in comparison to the longer, more gracile, back legs. Furthermore, the completeness of the study specimen facilitates calculation of an estimated body mass of approximately 98 kg, similar to that of a modern lioness.
bibliographic citation: Bendel et al. (2023) The postcranial anatomy of Gorgonops torvus (Synapsida, Gorgonopsia) from the late Permian of South Africa. PeerJ 11:e15378 https://doi.org/10.7717/peerj.15378
date submitted: 2022-11-23
date accepted: 2023-04-18
issued: 2023-07-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bendel
  given name: Eva-Maria
author list: Agent
  family name: Kammerer
  given name: Christian F.
author list: Agent
  family name: Smith
  given name: Roger M. H.
author list: Agent
  family name: Fröbisch
  given name: Jörg
doi: 10.7717/peerj.15378
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-07
copyright: © 2023 Bendel et al.
attribution name: Bendel et al.

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