PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Analysis of technical characteristics of typical lower limb balance movements in Tai Chi: a cross-sectional study based on AnyBody bone muscle modeling
items: Development of a novel prediction model based on protein structure for identifying RPE65-associated inherited retinal disease (IRDs) of missense variants
items: Estimating plant biomass in agroecosystems using a drop-plate meter
items: Transcriptomic characterization revealed that METTL7A inhibits melanoma progression via the p53 signaling pathway and immunomodulatory pathway
items: Mutation-derived, genomic instability-associated lncRNAs are prognostic markers in gliomas
items: Extraction and characterisation of pigment from Yanzhiguo [Prunus napaulensis (Ser.) Steud.]
items: The novel role of LDHA/LDHB in the prognostic value and tumor-immune infiltration in clear cell renal cell carcinoma
items: Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest
items: The impact of containment policy and mobility on COVID-19 cases through structural equation model in Chile, Singapore, South Korea and Israel
items: Long-term survival, growth, and reproduction of Acropora palmata sexual recruits outplanted onto Mexican Caribbean reefs

Analysis of technical characteristics of typical lower limb balance movements in Tai Chi: a cross-sectional study based on AnyBody bone muscle modeling
type: item
type: AcademicArticle
description: Background Tai Chi is an excellent traditional Chinese physical fitness exercise, and its unique balancing movements are very important for improving human balance. In this study, the two most representative Tai Chi balance movements, “knee lift balance” and “leg stirrup balance”, were selected to establish the lower limb bone muscle model of Tai Chi balance movements by using computer simulation modeling technology, aiming to analyze the characteristics of the lower limb movement mechanisms of typical balance movements, to provide a quantitative theoretical basis for improving the scientific level of Tai Chi. Method A total of 16 subjects were recruited for this study. the BTS three-dimensional motion capture system and three-dimensional force platform were used for motion data acquisition, the physiological electromyographic signals were collected using BTS surface electromyography, and the lower limb bone muscle model of Tai Chi balance movements was established by AnyBody human simulation. Result In the knee lift balancing movement, the balance leg hip abduction/adduction angle, hip flexion/extension moment, and the strength of the rectus femoris muscle, biceps femoris short capitis, and iliacus muscle of the amateur group was significantly smaller than that of the professional group (P < 0.01). In the leg stirrup balance movement, the knee flexion/extension angle of the balancing leg in the amateur group was significantly greater than that in the professional group (P < 0.01), and the hip flexion/extension angle, hip inversion/abduction angle, knee flexion/extension moment, hip flexion/extension moment, the strength iliacus, gluteus maximus, and obturator internus were significantly smaller than those in the professional group (P < 0.01). The integral EMG of the biceps femoris of the support leg in the amateur group was significantly smaller than that of the professional group (P < 0.01). The integral EMG of the lateral femoral muscle of the balance leg was sig…
format: application/pdf
format: text/html
creator: Haojie Li
creator: Xin Wang
creator: Zhihao Du
creator: Shunze Shen
subject: Kinesiology
subject: Healthcare Services
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.15817
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background Tai Chi is an excellent traditional Chinese physical fitness exercise, and its unique balancing movements are very important for improving human balance. In this study, the two most representative Tai Chi balance movements, “knee lift balance” and “leg stirrup balance”, were selected to establish the lower limb bone muscle model of Tai Chi balance movements by using computer simulation modeling technology, aiming to analyze the characteristics of the lower limb movement mechanisms of typical balance movements, to provide a quantitative theoretical basis for improving the scientific level of Tai Chi. Method A total of 16 subjects were recruited for this study. the BTS three-dimensional motion capture system and three-dimensional force platform were used for motion data acquisition, the physiological electromyographic signals were collected using BTS surface electromyography, and the lower limb bone muscle model of Tai Chi balance movements was established by AnyBody human simulation. Result In the knee lift balancing movement, the balance leg hip abduction/adduction angle, hip flexion/extension moment, and the strength of the rectus femoris muscle, biceps femoris short capitis, and iliacus muscle of the amateur group was significantly smaller than that of the professional group (P < 0.01). In the leg stirrup balance movement, the knee flexion/extension angle of the balancing leg in the amateur group was significantly greater than that in the professional group (P < 0.01), and the hip flexion/extension angle, hip inversion/abduction angle, knee flexion/extension moment, hip flexion/extension moment, the strength iliacus, gluteus maximus, and obturator internus were significantly smaller than those in the professional group (P < 0.01). The integral EMG of the biceps femoris of the support leg in the amateur group was significantly smaller than that of the professional group (P < 0.01). The integral EMG of the lateral femoral muscle of the balance leg was sig…
bibliographic citation: Li et al. (2023) Analysis of technical characteristics of typical lower limb balance movements in Tai Chi: a cross-sectional study based on AnyBody bone muscle modeling. PeerJ 11:e15817 https://doi.org/10.7717/peerj.15817
date submitted: 2023-04-11
date accepted: 2023-07-10
issued: 2023-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Haojie
author list: Agent
  family name: Wang
  given name: Xin
author list: Agent
  family name: Du
  given name: Zhihao
author list: Agent
  family name: Shen
  given name: Shunze
doi: 10.7717/peerj.15817
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-03
copyright: ©2023 Li et al.
attribution name: Li et al.

Development of a novel prediction model based on protein structure for identifying RPE65-associated inherited retinal disease (IRDs) of missense variants
type: item
type: AcademicArticle
description: Purpose This study aimed to develop a prediction model to classify RPE65-mediated inherited retinal disease (IRDs) based on protein secondary structure and to analyze phenotype-protein structure correlations of RPE65 missense variants in a Chinese cohort. Methods Pathogenic or likely pathogenic missense variants of RPE65 were obtained from UniProt, ClinVar, and HGMD databases. The three-dimensional structure of RPE65 was retrieved from the Protein Data Bank (PDB) and modified with Pymol software. A novel prediction model was developed using LASSO regression and multivariate logistic regression to identify RPE65-associated IRDs. A total of 21 Chinese probands with RPE65 variants were collected to analyze phenotype-protein structure correlations of RPE65 missense variants. Results The study found that both pathogenic and population missense variants were associated with structural features of RPE65. Pathogenic variants were linked to sheet, β-sheet, strands, β-hairpins, Fe2+ (iron center), and active site cavity, while population variants were related to helix, loop, helices, and helix–helix interactions. The novel prediction model showed accuracy and confidence in predicting the disease type of RPE65 variants (AUC = 0.7531). The study identified 25 missense variants in Chinese patients, accounting for 72.4% of total mutations. A significant correlation was observed between clinical characteristics of RPE65-associated IRDs and changes in amino acid type, specifically for missense variants of F8 (H68Y, P419S). Conclusion The study developed a novel prediction model based on the protein structure of RPE65 and investigated phenotype-protein structure correlations of RPE65 missense variants in a Chinese cohort. The findings provide insights into the precise diagnosis of RPE65-mutated IRDs.
format: application/pdf
format: text/html
creator: Jiawen Wu
creator: Zhongmou Sun
creator: Dao wei Zhang
creator: Hong-Li Liu
creator: Ting Li
creator: Shenghai Zhang
creator: Jihong Wu
subject: Genetics
subject: Molecular Biology
subject: Ophthalmology
subject: Medical Genetics
description: doi:10.7717/peerj.15702
publisher: PeerJ Inc.
rights: © 2023 Wu et al.
abstract: Purpose This study aimed to develop a prediction model to classify RPE65-mediated inherited retinal disease (IRDs) based on protein secondary structure and to analyze phenotype-protein structure correlations of RPE65 missense variants in a Chinese cohort. Methods Pathogenic or likely pathogenic missense variants of RPE65 were obtained from UniProt, ClinVar, and HGMD databases. The three-dimensional structure of RPE65 was retrieved from the Protein Data Bank (PDB) and modified with Pymol software. A novel prediction model was developed using LASSO regression and multivariate logistic regression to identify RPE65-associated IRDs. A total of 21 Chinese probands with RPE65 variants were collected to analyze phenotype-protein structure correlations of RPE65 missense variants. Results The study found that both pathogenic and population missense variants were associated with structural features of RPE65. Pathogenic variants were linked to sheet, β-sheet, strands, β-hairpins, Fe2+ (iron center), and active site cavity, while population variants were related to helix, loop, helices, and helix–helix interactions. The novel prediction model showed accuracy and confidence in predicting the disease type of RPE65 variants (AUC = 0.7531). The study identified 25 missense variants in Chinese patients, accounting for 72.4% of total mutations. A significant correlation was observed between clinical characteristics of RPE65-associated IRDs and changes in amino acid type, specifically for missense variants of F8 (H68Y, P419S). Conclusion The study developed a novel prediction model based on the protein structure of RPE65 and investigated phenotype-protein structure correlations of RPE65 missense variants in a Chinese cohort. The findings provide insights into the precise diagnosis of RPE65-mutated IRDs.
bibliographic citation: Wu et al. (2023) Development of a novel prediction model based on protein structure for identifying RPE65-associated inherited retinal disease (IRDs) of missense variants. PeerJ 11:e15702 https://doi.org/10.7717/peerj.15702
date submitted: 2022-11-25
date accepted: 2023-06-14
issued: 2023-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Jiawen
author list: Agent
  family name: Sun
  given name: Zhongmou
author list: Agent
  family name: Zhang
  given name: Dao wei
author list: Agent
  family name: Liu
  given name: Hong-Li
author list: Agent
  family name: Li
  given name: Ting
author list: Agent
  family name: Zhang
  given name: Shenghai
author list: Agent
  family name: Wu
  given name: Jihong
doi: 10.7717/peerj.15702
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-02
copyright: ©2023 Wu et al.
attribution name: Wu et al.

Estimating plant biomass in agroecosystems using a drop-plate meter
type: item
type: AcademicArticle
description: Reason for doing the work Plant biomass is a commonly used metric to assess agricultural health and productivity. Removing plant material is the most accurate method to estimate plant biomass, but this approach is time consuming, labor intensive, and destructive. Previous attempts to use indirect methods to estimate plant biomass have been limited in breadth and/or have added complexity in data collection and/or modeling. A cost-effective, quick, accurate, and easy to use and understand approach is desirable for use by scientists and growers. Objectives An indirect method for estimating plant biomass using a drop-plate meter was explored for use in broad array of crop systems. Methods Drop-plate data collected by more than 20 individuals from 16 crop types on 312 farms across 15 states were used to generate models to estimate plant biomass among and within crop types. Results A linear model using data from all crop types explained approximately 67% of the variation in plant biomass overall. This model performed differently among crop types and stand heights, which was owed to differences among sample sizes and farming between annual and perennial systems. Comparatively, the model using the combined dataset explained more variance in biomass than models generated with commodity specific data, with the exception of wheat. Conclusions The drop-plate approach described here was inexpensive, quick, simple, and easy to interpret, and the model generated was robust to error and accurate across multiple crop types. The methods met all expectations for a broad-use approach to estimating plant biomass and are recommended for use across all agroecosystems included in this study. While it may be useful in crops beyond those included, validation is suggested before application.
format: application/pdf
format: text/html
creator: Stephen M. Robertson
creator: Ryan B. Schmid
creator: Jonathan G. Lundgren
subject: Agricultural Science
subject: Ecosystem Science
subject: Plant Science
subject: Natural Resource Management
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.15740
publisher: PeerJ Inc.
rights: © 2023 Robertson et al.
abstract: Reason for doing the work Plant biomass is a commonly used metric to assess agricultural health and productivity. Removing plant material is the most accurate method to estimate plant biomass, but this approach is time consuming, labor intensive, and destructive. Previous attempts to use indirect methods to estimate plant biomass have been limited in breadth and/or have added complexity in data collection and/or modeling. A cost-effective, quick, accurate, and easy to use and understand approach is desirable for use by scientists and growers. Objectives An indirect method for estimating plant biomass using a drop-plate meter was explored for use in broad array of crop systems. Methods Drop-plate data collected by more than 20 individuals from 16 crop types on 312 farms across 15 states were used to generate models to estimate plant biomass among and within crop types. Results A linear model using data from all crop types explained approximately 67% of the variation in plant biomass overall. This model performed differently among crop types and stand heights, which was owed to differences among sample sizes and farming between annual and perennial systems. Comparatively, the model using the combined dataset explained more variance in biomass than models generated with commodity specific data, with the exception of wheat. Conclusions The drop-plate approach described here was inexpensive, quick, simple, and easy to interpret, and the model generated was robust to error and accurate across multiple crop types. The methods met all expectations for a broad-use approach to estimating plant biomass and are recommended for use across all agroecosystems included in this study. While it may be useful in crops beyond those included, validation is suggested before application.
bibliographic citation: Robertson et al. (2023) Estimating plant biomass in agroecosystems using a drop-plate meter. PeerJ 11:e15740 https://doi.org/10.7717/peerj.15740
date submitted: 2023-01-11
date accepted: 2023-06-20
issued: 2023-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Robertson
  given name: Stephen M.
author list: Agent
  family name: Schmid
  given name: Ryan B.
author list: Agent
  family name: Lundgren
  given name: Jonathan G.
doi: 10.7717/peerj.15740
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-02
copyright: © 2023 Robertson et al.
attribution name: Robertson et al.

Transcriptomic characterization revealed that METTL7A inhibits melanoma progression via the p53 signaling pathway and immunomodulatory pathway
type: item
type: AcademicArticle
description: METTL7A is a protein-coding gene expected to be associated with methylation, and its expression disorder is associated with a range of diseases. However, few research have been carried out to explore the relationship between METTL7A and tumor malignant phenotype as well as the involvement potential mechanism. We conducted our research via a combination of silico analysis and molecular biology techniques to investigate the biological function of METTL7A in the progression of cancer. Gene expression and clinical information were extracted from the TCGA database to explore expression variation and prognostic value of METTL7A. In vitro, CCK8, transwell, wound healing and colony formation assays were conducted to explore the biological functions of METT7A in cancer cell. GSEA was performed to explore the signaling pathway involved in METTL7A and validated via western blotting. In conclusion, METTL7A was downregulated in most cancer tissues and its low expression was associated with shorter overall survival. In melanoma, METTL7A downregulation was associated with poorer clinical staging, lower levels of TIL infiltration, higher IC50 levels of chemotherapeutic agents, and poorer immunotherapy outcomes. QPCR results confirm that METTL7A is down-regulated in melanoma cells. Cell function assays showed that METTL7A knockdown promoted proliferation, invasion, migration and clone formation of melanoma cells. Mechanistic studies showed that METTL7A inhibits tumorigenicity through the p53 signaling pathway. Meanwhile, METTL7A is also a potential immune regulatory factor.
format: application/pdf
format: text/html
creator: Duoli Zhang
creator: Tao Zou
creator: Qingsong Liu
creator: Jie Chen
creator: Mintao Xiao
creator: Anfu Zheng
creator: Zhuo Zhang
creator: Fukuan Du
creator: Yalan Dai
creator: Shixin Xiang
creator: Xu Wu
creator: Mingxing Li
creator: Yu Chen
creator: Yueshui Zhao
creator: Jing Shen
creator: Guiquan Chen
creator: Zhangang Xiao
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Dermatology
subject: Oncology
description: doi:10.7717/peerj.15799
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: METTL7A is a protein-coding gene expected to be associated with methylation, and its expression disorder is associated with a range of diseases. However, few research have been carried out to explore the relationship between METTL7A and tumor malignant phenotype as well as the involvement potential mechanism. We conducted our research via a combination of silico analysis and molecular biology techniques to investigate the biological function of METTL7A in the progression of cancer. Gene expression and clinical information were extracted from the TCGA database to explore expression variation and prognostic value of METTL7A. In vitro, CCK8, transwell, wound healing and colony formation assays were conducted to explore the biological functions of METT7A in cancer cell. GSEA was performed to explore the signaling pathway involved in METTL7A and validated via western blotting. In conclusion, METTL7A was downregulated in most cancer tissues and its low expression was associated with shorter overall survival. In melanoma, METTL7A downregulation was associated with poorer clinical staging, lower levels of TIL infiltration, higher IC50 levels of chemotherapeutic agents, and poorer immunotherapy outcomes. QPCR results confirm that METTL7A is down-regulated in melanoma cells. Cell function assays showed that METTL7A knockdown promoted proliferation, invasion, migration and clone formation of melanoma cells. Mechanistic studies showed that METTL7A inhibits tumorigenicity through the p53 signaling pathway. Meanwhile, METTL7A is also a potential immune regulatory factor.
bibliographic citation: Zhang et al. (2023) Transcriptomic characterization revealed that METTL7A inhibits melanoma progression via the p53 signaling pathway and immunomodulatory pathway. PeerJ 11:e15799 https://doi.org/10.7717/peerj.15799
date submitted: 2023-03-07
date accepted: 2023-07-05
issued: 2023-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Duoli
author list: Agent
  family name: Zou
  given name: Tao
author list: Agent
  family name: Liu
  given name: Qingsong
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Xiao
  given name: Mintao
author list: Agent
  family name: Zheng
  given name: Anfu
author list: Agent
  family name: Zhang
  given name: Zhuo
author list: Agent
  family name: Du
  given name: Fukuan
author list: Agent
  family name: Dai
  given name: Yalan
author list: Agent
  family name: Xiang
  given name: Shixin
author list: Agent
  family name: Wu
  given name: Xu
author list: Agent
  family name: Li
  given name: Mingxing
author list: Agent
  family name: Chen
  given name: Yu
author list: Agent
  family name: Zhao
  given name: Yueshui
author list: Agent
  family name: Shen
  given name: Jing
author list: Agent
  family name: Chen
  given name: Guiquan
author list: Agent
  family name: Xiao
  given name: Zhangang
doi: 10.7717/peerj.15799
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-02
copyright: ©2023 Zhang et al.
attribution name: Zhang et al.

Mutation-derived, genomic instability-associated lncRNAs are prognostic markers in gliomas
type: item
type: AcademicArticle
description: Background Gliomas are the most commonly-detected malignant tumors of the brain. They contain abundant long non-coding RNAs (lncRNAs), which are valuable cancer biomarkers. LncRNAs may be involved in genomic instability; however, their specific role and mechanism in gliomas remains unclear. LncRNAs that are related to genomic instability have not been reported in gliomas. Methods The transcriptome data from The Cancer Genome Atlas (TCGA) database were analyzed. The co-expression network of genomic instability-related lncRNAs and mRNA was established, and the model of genomic instability-related lncRNA was identified by univariate Cox regression and LASSO analyses. Based on the median risk score obtained in the training set, we divided the samples into high-risk and low-risk groups and proved the survival prediction ability of genomic instability-related lncRNA signatures. The results were verified in the external data set. Finally, a real-time quantitative polymerase chain reaction assay was performed to validate the signature. Results The signatures of 17 lncRNAs (LINC01579, AL022344.1, AC025171.5, LINC01116, MIR155HG, AC131097.3, LINC00906, CYTOR, AC015540.1, SLC25A21.AS1, H19, AL133415.1, SNHG18, FOXD3.AS1, LINC02593, AL354919.2 and CRNDE) related to genomic instability were identified. In the internal data set and Gene Expression Omnibus (GEO) external data set, the low-risk group showed better survival than the high-risk group (P < 0.001). In addition, this feature was identified as an independent risk factor, showing its independent prognostic value with different clinical stratifications. The majority of patients in the low-risk group had isocitrate dehydrogenase 1 (IDH1) mutations. The expression levels of these lncRNAs were significantly higher in glioblastoma cell lines than in normal cells. Conclusions Our study shows that the signature of 17 lncRNAs related to genomic instability has prognostic value for gliomas and could provide a potential therapeutic …
format: application/pdf
format: text/html
creator: Shenglun Li
creator: Yujia Chen
creator: Yuduo Guo
creator: Jiacheng Xu
creator: Xiang Wang
creator: Weihai Ning
creator: Lixin Ma
creator: Yanming Qu
creator: Mingshan Zhang
creator: Hongwei Zhang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Neurology
subject: Oncology
description: doi:10.7717/peerj.15810
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background Gliomas are the most commonly-detected malignant tumors of the brain. They contain abundant long non-coding RNAs (lncRNAs), which are valuable cancer biomarkers. LncRNAs may be involved in genomic instability; however, their specific role and mechanism in gliomas remains unclear. LncRNAs that are related to genomic instability have not been reported in gliomas. Methods The transcriptome data from The Cancer Genome Atlas (TCGA) database were analyzed. The co-expression network of genomic instability-related lncRNAs and mRNA was established, and the model of genomic instability-related lncRNA was identified by univariate Cox regression and LASSO analyses. Based on the median risk score obtained in the training set, we divided the samples into high-risk and low-risk groups and proved the survival prediction ability of genomic instability-related lncRNA signatures. The results were verified in the external data set. Finally, a real-time quantitative polymerase chain reaction assay was performed to validate the signature. Results The signatures of 17 lncRNAs (LINC01579, AL022344.1, AC025171.5, LINC01116, MIR155HG, AC131097.3, LINC00906, CYTOR, AC015540.1, SLC25A21.AS1, H19, AL133415.1, SNHG18, FOXD3.AS1, LINC02593, AL354919.2 and CRNDE) related to genomic instability were identified. In the internal data set and Gene Expression Omnibus (GEO) external data set, the low-risk group showed better survival than the high-risk group (P < 0.001). In addition, this feature was identified as an independent risk factor, showing its independent prognostic value with different clinical stratifications. The majority of patients in the low-risk group had isocitrate dehydrogenase 1 (IDH1) mutations. The expression levels of these lncRNAs were significantly higher in glioblastoma cell lines than in normal cells. Conclusions Our study shows that the signature of 17 lncRNAs related to genomic instability has prognostic value for gliomas and could provide a potential therapeutic …
bibliographic citation: Li et al. (2023) Mutation-derived, genomic instability-associated lncRNAs are prognostic markers in gliomas. PeerJ 11:e15810 https://doi.org/10.7717/peerj.15810
date submitted: 2022-12-08
date accepted: 2023-07-07
issued: 2023-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Shenglun
author list: Agent
  family name: Chen
  given name: Yujia
author list: Agent
  family name: Guo
  given name: Yuduo
author list: Agent
  family name: Xu
  given name: Jiacheng
author list: Agent
  family name: Wang
  given name: Xiang
author list: Agent
  family name: Ning
  given name: Weihai
author list: Agent
  family name: Ma
  given name: Lixin
author list: Agent
  family name: Qu
  given name: Yanming
author list: Agent
  family name: Zhang
  given name: Mingshan
author list: Agent
  family name: Zhang
  given name: Hongwei
doi: 10.7717/peerj.15810
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-02
copyright: © 2023 Li et al.
attribution name: Li et al.

Extraction and characterisation of pigment from Yanzhiguo [Prunus napaulensis (Ser.) Steud.]
type: item
type: AcademicArticle
description: Yanzhiguo [Prunus napaulensis (Ser.) Steud] belongs to Rosaceae family and is consumed as wild fruit, pulp and juice. However, its potential for extracting natural pigment has not yet been explored. Herein, the components in the fresh Yanzhiguo pulp were preliminarily analyzed by liquid chromatography coupled to mass spectrometry. And, the optimal pre-treatment conditions were established for further extraction of Yanzhiguo pigment based on the a* value. Then, by combining the data from single-factor experiments and response surface methodology, the optimal extraction process was established as: 35% EtOH, a liquid-solid ratio of 200:1 mL g−1, an extraction time of 65 min, and an extraction temperature of 100 °C. Moreover, it was found that the a* value and yield had high fitness except when extracted into ethanol (EtOH) with different concentrations. Meanwhile, our result demonstrated Yanzhiguo pigment had high stability in general environments with carmine (a synthetic pigment) as control, except for extreme environments such as direct (hot) sunlight, high temperature (75 °C) and strong alkaline (pH $\geq$≥ 11). Also, Yanzhiguo pigment exhibited good antioxidant activity. Our results contribute to more information on Yanzhiguo pigment and promote its application by providing efficient extraction technology.
format: application/pdf
format: text/html
creator: Pingping Shi
creator: Haibo Luo
creator: Qiuqiu Huang
creator: Changliang Xu
creator: Xiuzi Tong
creator: Hui Shen
creator: Huosheng Su
creator: Hongmei Pu
creator: Haidan Wang
creator: Lijuan Yu
creator: Hong Li
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.15517
publisher: PeerJ Inc.
rights: © 2023 Shi et al.
abstract: Yanzhiguo [Prunus napaulensis (Ser.) Steud] belongs to Rosaceae family and is consumed as wild fruit, pulp and juice. However, its potential for extracting natural pigment has not yet been explored. Herein, the components in the fresh Yanzhiguo pulp were preliminarily analyzed by liquid chromatography coupled to mass spectrometry. And, the optimal pre-treatment conditions were established for further extraction of Yanzhiguo pigment based on the a* value. Then, by combining the data from single-factor experiments and response surface methodology, the optimal extraction process was established as: 35% EtOH, a liquid-solid ratio of 200:1 mL g−1, an extraction time of 65 min, and an extraction temperature of 100 °C. Moreover, it was found that the a* value and yield had high fitness except when extracted into ethanol (EtOH) with different concentrations. Meanwhile, our result demonstrated Yanzhiguo pigment had high stability in general environments with carmine (a synthetic pigment) as control, except for extreme environments such as direct (hot) sunlight, high temperature (75 °C) and strong alkaline (pH $\geq$≥ 11). Also, Yanzhiguo pigment exhibited good antioxidant activity. Our results contribute to more information on Yanzhiguo pigment and promote its application by providing efficient extraction technology.
bibliographic citation: Shi et al. (2023) Extraction and characterisation of pigment from Yanzhiguo [Prunus napaulensis (Ser.) Steud.]. PeerJ 11:e15517 https://doi.org/10.7717/peerj.15517
date submitted: 2023-02-02
date accepted: 2023-05-15
issued: 2023-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Shi
  given name: Pingping
author list: Agent
  family name: Luo
  given name: Haibo
author list: Agent
  family name: Huang
  given name: Qiuqiu
author list: Agent
  family name: Xu
  given name: Changliang
author list: Agent
  family name: Tong
  given name: Xiuzi
author list: Agent
  family name: Shen
  given name: Hui
author list: Agent
  family name: Su
  given name: Huosheng
author list: Agent
  family name: Pu
  given name: Hongmei
author list: Agent
  family name: Wang
  given name: Haidan
author list: Agent
  family name: Yu
  given name: Lijuan
author list: Agent
  family name: Li
  given name: Hong
doi: 10.7717/peerj.15517
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-01
copyright: © 2023 Shi et al.
attribution name: Shi et al.

The novel role of LDHA/LDHB in the prognostic value and tumor-immune infiltration in clear cell renal cell carcinoma
type: item
type: AcademicArticle
description: Lactate dehydrogenase (LDH) is a crucial glycolytic enzyme which mediates the metabolic plasticity of cancer cells, however its clinical significance in renal cell carcinoma (RCC) is poorly understood. Herein, we examined the prognostic significance of the two primary components of LDH, i.e., LDHA and LDHB, in clear cell RCC (ccRCC) patients and further explored their association with immune infiltration in ccRCC. In this study, the expression levels of LDHA and LDHB were examined in ccRCC and adjacent normal tissues by Gene Expression Profiling Interactive Analysis 2 (GEPIA2), UALCAN, and western blotting (WB) analyses, and their prognostic values were estimated in 150 ccRCC and 30 adjacent normal tissues by immunohistochemistry (IHC) analysis. The relationship to immune infiltration of LDHA and LDHB genes was further investigated using tumor immune estimation resource 2 (TIMER2) and Tumor-Immune System Interactions and DrugBank (TISIDB) databases, respectively. Public databases and WB analyses demonstrated higher LDHA and lower LDHB in ccRCC than in non-tumor tissues. IHC analysis revealed that LDHA and LDHB expression profiles were significantly associated with tumor grade, stage, size, and overall survival (OS). Univariate survival analysis displayed that high grade, advanced stage, large tumor, metastasis, high LDHA, and low LDHB expression were significantly associated with a poorer OS, and multivariate analysis revealed tumor stage and LDHB were identified as independent predictors for OS in patients with ccRCC. Further TIMER2 and TISIDB analyses demonstrated that LDHA and LDHB expression was significantly related to multiple immune cells and immune inhibitors in over 500 ccRCC patients. These findings revealed that LDHB was an independent favorable predictor, and LDHA and LDHB correlated with tumor immune infiltrates in ccRCC patients, which indicated LDHA/LDHB could be implicated in the tumorigenesis of ccRCC and might be potential therapeutic targets for p…
format: application/pdf
format: text/html
creator: Jie Chen
creator: Fei Wu
creator: Yehua Cao
creator: Yuanxin Xing
creator: Qingyong Liu
creator: Zuohui Zhao
subject: Genomics
subject: Nephrology
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.15749
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Lactate dehydrogenase (LDH) is a crucial glycolytic enzyme which mediates the metabolic plasticity of cancer cells, however its clinical significance in renal cell carcinoma (RCC) is poorly understood. Herein, we examined the prognostic significance of the two primary components of LDH, i.e., LDHA and LDHB, in clear cell RCC (ccRCC) patients and further explored their association with immune infiltration in ccRCC. In this study, the expression levels of LDHA and LDHB were examined in ccRCC and adjacent normal tissues by Gene Expression Profiling Interactive Analysis 2 (GEPIA2), UALCAN, and western blotting (WB) analyses, and their prognostic values were estimated in 150 ccRCC and 30 adjacent normal tissues by immunohistochemistry (IHC) analysis. The relationship to immune infiltration of LDHA and LDHB genes was further investigated using tumor immune estimation resource 2 (TIMER2) and Tumor-Immune System Interactions and DrugBank (TISIDB) databases, respectively. Public databases and WB analyses demonstrated higher LDHA and lower LDHB in ccRCC than in non-tumor tissues. IHC analysis revealed that LDHA and LDHB expression profiles were significantly associated with tumor grade, stage, size, and overall survival (OS). Univariate survival analysis displayed that high grade, advanced stage, large tumor, metastasis, high LDHA, and low LDHB expression were significantly associated with a poorer OS, and multivariate analysis revealed tumor stage and LDHB were identified as independent predictors for OS in patients with ccRCC. Further TIMER2 and TISIDB analyses demonstrated that LDHA and LDHB expression was significantly related to multiple immune cells and immune inhibitors in over 500 ccRCC patients. These findings revealed that LDHB was an independent favorable predictor, and LDHA and LDHB correlated with tumor immune infiltrates in ccRCC patients, which indicated LDHA/LDHB could be implicated in the tumorigenesis of ccRCC and might be potential therapeutic targets for p…
bibliographic citation: Chen et al. (2023) The novel role of LDHA/LDHB in the prognostic value and tumor-immune infiltration in clear cell renal cell carcinoma. PeerJ 11:e15749 https://doi.org/10.7717/peerj.15749
date submitted: 2023-04-05
date accepted: 2023-06-22
issued: 2023-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Wu
  given name: Fei
author list: Agent
  family name: Cao
  given name: Yehua
author list: Agent
  family name: Xing
  given name: Yuanxin
author list: Agent
  family name: Liu
  given name: Qingyong
author list: Agent
  family name: Zhao
  given name: Zuohui
doi: 10.7717/peerj.15749
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-01
copyright: ©2023 Chen et al.
attribution name: Chen et al.

Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest
type: item
type: AcademicArticle
description: The Brazilian Atlantic Forest and its associated ecosystems are highly biodiverse but still understudied, especially with respect to eukaryotic microbes. Protists represent the largest proportion of eukaryotic diversity and play important roles in nutrient cycling and maintenance of the ecosystems in which they occur. However, much of protist diversity remains unknown, particularly in the Neotropics. Understanding the taxonomic and functional diversity of these organisms is urgently needed, not only to fill this gap in our knowledge, but also to enable the development of public policies for biological conservation. This is the first study to investigate the taxonomic and trophic diversity of the major protist groups in freshwater systems and brackish coastal lagoons located in fragments of the Brazilian Atlantic Forest by DNA metabarcoding, using high-throughput sequencing of the gene coding for the V4 region of the 18S rRNA gene. We compared α and β diversity for all protist communities and assessed the relative abundance of phototrophic, consumer, and parasitic taxa. We found that the protist communities of coastal lagoons are as diverse as the freshwater systems studied in terms of α diversity, although differed significantly in terms of taxonomic composition. Our results still showed a notable functional homogeneity between the trophic groups in freshwater environments. Beta diversity was higher among freshwater samples, suggesting a greater level of heterogeneity within this group of samples concerning the composition and abundance of OTUs.Ciliophora was the most represented group in freshwater, while Diatomea dominated diversity in coastal lagoons.
format: application/pdf
format: text/html
creator: Vanessa Carvalho da Silva
creator: Noemi Fernandes
subject: Biodiversity
subject: Microbiology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.15762
publisher: PeerJ Inc.
rights: © 2023
abstract: The Brazilian Atlantic Forest and its associated ecosystems are highly biodiverse but still understudied, especially with respect to eukaryotic microbes. Protists represent the largest proportion of eukaryotic diversity and play important roles in nutrient cycling and maintenance of the ecosystems in which they occur. However, much of protist diversity remains unknown, particularly in the Neotropics. Understanding the taxonomic and functional diversity of these organisms is urgently needed, not only to fill this gap in our knowledge, but also to enable the development of public policies for biological conservation. This is the first study to investigate the taxonomic and trophic diversity of the major protist groups in freshwater systems and brackish coastal lagoons located in fragments of the Brazilian Atlantic Forest by DNA metabarcoding, using high-throughput sequencing of the gene coding for the V4 region of the 18S rRNA gene. We compared α and β diversity for all protist communities and assessed the relative abundance of phototrophic, consumer, and parasitic taxa. We found that the protist communities of coastal lagoons are as diverse as the freshwater systems studied in terms of α diversity, although differed significantly in terms of taxonomic composition. Our results still showed a notable functional homogeneity between the trophic groups in freshwater environments. Beta diversity was higher among freshwater samples, suggesting a greater level of heterogeneity within this group of samples concerning the composition and abundance of OTUs.Ciliophora was the most represented group in freshwater, while Diatomea dominated diversity in coastal lagoons.
bibliographic citation: Carvalho da Silva et al. (2023) Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest. PeerJ 11:e15762 https://doi.org/10.7717/peerj.15762
date submitted: 2023-04-17
date accepted: 2023-06-27
issued: 2023-08-01
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Carvalho da Silva
  given name: Vanessa
author list: Agent
  family name: Fernandes
  given name: Noemi
doi: 10.7717/peerj.15762
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-01

The impact of containment policy and mobility on COVID-19 cases through structural equation model in Chile, Singapore, South Korea and Israel
type: item
type: AcademicArticle
description: Objectives The study aims to understand the impact of containment policy and mobility on COVID-19 cases in Chile, Singapore, South Korea and Israel. To provide experience in epidemic prevention and control. Methods Structural equation modeling (SEM) of containment policies, mobility, and COVID-19 cases were used to test and analyze the proposed hypotheses. Results Chile, Israel and Singapore adopted containment strategies, focusing on closure measures. South Korea adopted a mitigation strategy with fewer closure measures, focusing on vaccination and severe case management. There was a significant negative relationship among containment policies, mobility, and COVID-19 cases. Conclusion To control the COVID-19 and slow down the increase of COVID-19 cases, countries can increase the stringency of containment policies when COVID-19 epidemic is more severe. Thus, countries can take measures from the following three aspects: strengthen the risk monitoring, and keep abreast of the COVID-19 risk; adjust closure measures in time and reduce mobility; and strengthen public education on COVID-19 prevention to motivate citizen to consciously adhere to preventive measures.
format: application/pdf
format: text/html
creator: Jun Jiao
creator: Leiyu Shi
creator: Manfei Yang
creator: Junyan Yang
creator: Meiheng Liu
creator: Gang Sun
subject: Global Health
subject: Health Policy
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.15769
publisher: PeerJ Inc.
rights: © 2023 Jiao et al.
abstract: Objectives The study aims to understand the impact of containment policy and mobility on COVID-19 cases in Chile, Singapore, South Korea and Israel. To provide experience in epidemic prevention and control. Methods Structural equation modeling (SEM) of containment policies, mobility, and COVID-19 cases were used to test and analyze the proposed hypotheses. Results Chile, Israel and Singapore adopted containment strategies, focusing on closure measures. South Korea adopted a mitigation strategy with fewer closure measures, focusing on vaccination and severe case management. There was a significant negative relationship among containment policies, mobility, and COVID-19 cases. Conclusion To control the COVID-19 and slow down the increase of COVID-19 cases, countries can increase the stringency of containment policies when COVID-19 epidemic is more severe. Thus, countries can take measures from the following three aspects: strengthen the risk monitoring, and keep abreast of the COVID-19 risk; adjust closure measures in time and reduce mobility; and strengthen public education on COVID-19 prevention to motivate citizen to consciously adhere to preventive measures.
bibliographic citation: Jiao et al. (2023) The impact of containment policy and mobility on COVID-19 cases through structural equation model in Chile, Singapore, South Korea and Israel. PeerJ 11:e15769 https://doi.org/10.7717/peerj.15769
date submitted: 2023-02-16
date accepted: 2023-06-28
issued: 2023-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiao
  given name: Jun
author list: Agent
  family name: Shi
  given name: Leiyu
author list: Agent
  family name: Yang
  given name: Manfei
author list: Agent
  family name: Yang
  given name: Junyan
author list: Agent
  family name: Liu
  given name: Meiheng
author list: Agent
  family name: Sun
  given name: Gang
doi: 10.7717/peerj.15769
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-01
copyright: ©2023 Jiao et al.
attribution name: Jiao et al.

Long-term survival, growth, and reproduction of Acropora palmata sexual recruits outplanted onto Mexican Caribbean reefs
type: item
type: AcademicArticle
description: Acropora palmata is a foundational yet endangered Caribbean reef-building coral species. The lack of recovery after a disease outbreak and low recruitment has led to widespread use of fragmentation to restore populations. Another option is the production of sexual recruits (settlers) via assisted reproduction to improve the genetic diversity of depleted populations; however, the viability of this approach has not been tested over the long term. In 2011 and 2012, A. palmata larvae were cultured, settled, and the sexual recruits raised in an ex-situ nursery. Survival and growth were monitored over time. In 2014, these two F1 cohorts were moved to an in-situ nursery and after one year, a subset (29 colonies) was outplanted onto Cuevones Reef in the Mexican Caribbean. Growth and survival of these colonies were monitored periodically and compared to colonies that remained in the in-situ nursery. In 2019, samples were collected and analyzed for fertility and fecundity. 53% of the colonies were gravid and fecundity was 5.61 ± 1.91 oocytes and 3.04 ± 0.26 spermaries per polyp. A further 14 colonies from these two cohorts were outplanted in 2020 onto Picudas Reef and monitored during the subsequent spawning seasons. Two years after outplanting onto Picudas Reef, all colonies were alive and spawning of three of these colonies was recorded in 2022 in synchrony with the wild population. Gametes were collected from two colonies and crossed, with 15% fertilization success. Spermatozoa from wild colonies were then added and fertilization success increased to 95%. The resultant larvae followed normal development and symbiont uptake was visible within two weeks. The F2 generation was settled, maintained in an ex-situ nursery, and monitored for survival and growth. Both F1 and F2 generations followed a Type III survival curve with high initial mortality while in the ex-situ nursery and low later-stage mortality. The growth rates of these colonies increased three-fold after outplantin…
format: application/pdf
format: text/html
creator: Sandra Mendoza Quiroz
creator: Aurora Urania Beltrán-Torres
creator: Maria Victoria Grosso-Becerra
creator: Daniela Muñoz Villareal
creator: Raúl Tecalco Rentería
creator: Anastazia T. Banaszak
subject: Developmental Biology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.15813
publisher: PeerJ Inc.
rights: © 2023 Mendoza Quiroz et al.
abstract: Acropora palmata is a foundational yet endangered Caribbean reef-building coral species. The lack of recovery after a disease outbreak and low recruitment has led to widespread use of fragmentation to restore populations. Another option is the production of sexual recruits (settlers) via assisted reproduction to improve the genetic diversity of depleted populations; however, the viability of this approach has not been tested over the long term. In 2011 and 2012, A. palmata larvae were cultured, settled, and the sexual recruits raised in an ex-situ nursery. Survival and growth were monitored over time. In 2014, these two F1 cohorts were moved to an in-situ nursery and after one year, a subset (29 colonies) was outplanted onto Cuevones Reef in the Mexican Caribbean. Growth and survival of these colonies were monitored periodically and compared to colonies that remained in the in-situ nursery. In 2019, samples were collected and analyzed for fertility and fecundity. 53% of the colonies were gravid and fecundity was 5.61 ± 1.91 oocytes and 3.04 ± 0.26 spermaries per polyp. A further 14 colonies from these two cohorts were outplanted in 2020 onto Picudas Reef and monitored during the subsequent spawning seasons. Two years after outplanting onto Picudas Reef, all colonies were alive and spawning of three of these colonies was recorded in 2022 in synchrony with the wild population. Gametes were collected from two colonies and crossed, with 15% fertilization success. Spermatozoa from wild colonies were then added and fertilization success increased to 95%. The resultant larvae followed normal development and symbiont uptake was visible within two weeks. The F2 generation was settled, maintained in an ex-situ nursery, and monitored for survival and growth. Both F1 and F2 generations followed a Type III survival curve with high initial mortality while in the ex-situ nursery and low later-stage mortality. The growth rates of these colonies increased three-fold after outplantin…
bibliographic citation: Mendoza Quiroz et al. (2023) Long-term survival, growth, and reproduction of Acropora palmata sexual recruits outplanted onto Mexican Caribbean reefs. PeerJ 11:e15813 https://doi.org/10.7717/peerj.15813
date submitted: 2023-01-18
date accepted: 2023-07-07
issued: 2023-08-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mendoza Quiroz
  given name: Sandra
author list: Agent
  family name: Beltrán-Torres
  given name: Aurora Urania
author list: Agent
  family name: Grosso-Becerra
  given name: Maria Victoria
author list: Agent
  family name: Muñoz Villareal
  given name: Daniela
author list: Agent
  family name: Tecalco Rentería
  given name: Raúl
author list: Agent
  family name: Banaszak
  given name: Anastazia T.
doi: 10.7717/peerj.15813
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-01
copyright: ©2023 Mendoza Quiroz et al.
attribution name: Mendoza Quiroz et al.

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