PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification and validation of candidate genes dysregulated in alveolar macrophages of acute respiratory distress syndrome
items: Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma
items: Removal or component reversal of local geomagnetic field affects foraging orientation preference in migratory insect brown planthopper Nilaparvata lugens
items: Identification of hub genes and transcription factor-miRNA-mRNA pathways in mice and human renal ischemia-reperfusion injury
items: Identification of genes and gene expression associated with dispersal capacity in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)
items: Assessment of antimycobacterial activities of pure compounds extracted from Thai medicinal plants against clarithromycin-resistant Mycobacterium abscessus
items: Blood cells and hematological parameters of the mountain dragon, Diploderma micangshanensis (Squamata: Lacertilia: Agamidae)
items: Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization
items: Modernising tactile acuity assessment; clinimetrics of semi-automated tests and effects of age, sex and anthropometry on performance
items: Salinity effects on water potential and the normalized difference vegetation index in four species of a saline semi-arid ecosystem

Identification and validation of candidate genes dysregulated in alveolar macrophages of acute respiratory distress syndrome
type: item
type: AcademicArticle
description: Background Acute respiratory distress syndrome (ARDS) is a common cause of death in ICU patients and its underlying mechanism remains unclear, which leads to its high mortality rate. This study aimed to identify candidate genes potentially implicating in the pathogenesis of ARDS and provide novel therapeutic targets. Methods Using bioinformatics tools, we searched for differentially expressed genes (DEGs) in an ARDS microarray dataset downloaded from the Gene Expression Omnibus (GEO) database. Afterwards, functional enrichment analysis of GO, KEGG, GSEA and WGCNA were carried out to investigate the potential involvement of these DEGs. Moreover, the Protein–protein interaction (PPI) network was constructed and molecular complexes and hub genes were identified, followed by prognosis analysis of the hub genes. Further, we performed qRT-PCR, Western Blot and flow cytometry analysis to detect candidate genes of CCR2 and FPR3 in macrophage model of LPS-induced ARDS and primary alveolar macrophages(AMs). Macrophage chemotaxis was evaluated using Transwell assay. Results DEGs mainly involved in myeloid leukocyte activation, cell chemotaxis, adenylate cyclase-modulating G protein-coupled receptor signaling pathway and cytokine-cytokine receptor interaction. Basing on the constructed PPI network, we identified five molecular complexes and 10 hub genes potentially participating in the pathogenesis of ARDS. It was observed that candidate genes of CCR2 and FPR3 were significantly over-expressed in primary alveolar macrophages from ARDS patients and macrophgae model of LPS-induced ARDS. Moreover, in vitro transwell assay demonstrated that CCR2 and FPR3 down-regulation, respectively, inhibited LPS-triggered macrophage chemotaxis toward CCL2. Finally, a positive correlation between FPR3 and CCR2 expression was confirmed using pearson correlation analysis and Western Blot assay. Conclusions Our study identified CCR2 and FPR3 as the candidate genes which can promote macrophage chemot…
format: application/pdf
format: text/html
creator: Yong Mao
creator: Xin Lv
creator: Wei Xu
creator: Youguo Ying
creator: Zonghe Qin
creator: Handi Liao
creator: Li Chen
creator: Ya Liu
subject: Bioinformatics
subject: Cell Biology
subject: Emergency and Critical Care
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.12312
publisher: PeerJ Inc.
rights: © 2021 Mao et al.
abstract: Background Acute respiratory distress syndrome (ARDS) is a common cause of death in ICU patients and its underlying mechanism remains unclear, which leads to its high mortality rate. This study aimed to identify candidate genes potentially implicating in the pathogenesis of ARDS and provide novel therapeutic targets. Methods Using bioinformatics tools, we searched for differentially expressed genes (DEGs) in an ARDS microarray dataset downloaded from the Gene Expression Omnibus (GEO) database. Afterwards, functional enrichment analysis of GO, KEGG, GSEA and WGCNA were carried out to investigate the potential involvement of these DEGs. Moreover, the Protein–protein interaction (PPI) network was constructed and molecular complexes and hub genes were identified, followed by prognosis analysis of the hub genes. Further, we performed qRT-PCR, Western Blot and flow cytometry analysis to detect candidate genes of CCR2 and FPR3 in macrophage model of LPS-induced ARDS and primary alveolar macrophages(AMs). Macrophage chemotaxis was evaluated using Transwell assay. Results DEGs mainly involved in myeloid leukocyte activation, cell chemotaxis, adenylate cyclase-modulating G protein-coupled receptor signaling pathway and cytokine-cytokine receptor interaction. Basing on the constructed PPI network, we identified five molecular complexes and 10 hub genes potentially participating in the pathogenesis of ARDS. It was observed that candidate genes of CCR2 and FPR3 were significantly over-expressed in primary alveolar macrophages from ARDS patients and macrophgae model of LPS-induced ARDS. Moreover, in vitro transwell assay demonstrated that CCR2 and FPR3 down-regulation, respectively, inhibited LPS-triggered macrophage chemotaxis toward CCL2. Finally, a positive correlation between FPR3 and CCR2 expression was confirmed using pearson correlation analysis and Western Blot assay. Conclusions Our study identified CCR2 and FPR3 as the candidate genes which can promote macrophage chemot…
bibliographic citation: Mao et al. (2021) Identification and validation of candidate genes dysregulated in alveolar macrophages of acute respiratory distress syndrome. PeerJ 9:e12312 https://doi.org/10.7717/peerj.12312
date submitted: 2021-05-31
date accepted: 2021-09-24
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mao
  given name: Yong
author list: Agent
  family name: Lv
  given name: Xin
author list: Agent
  family name: Xu
  given name: Wei
author list: Agent
  family name: Ying
  given name: Youguo
author list: Agent
  family name: Qin
  given name: Zonghe
author list: Agent
  family name: Liao
  given name: Handi
author list: Agent
  family name: Chen
  given name: Li
author list: Agent
  family name: Liu
  given name: Ya
doi: 10.7717/peerj.12312
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: ©2021 Mao et al.
attribution name: Mao et al.

Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Hepatocellular carcinoma (HCC) is an inflammation-associated tumor involved in immune tolerance and evasion in the immune microenvironment. Heat shock proteins (HSPs) are involved in the occurrence, progression, and immune regulation of tumors. Therefore, HSPs have been considered potential therapeutic targets. Here, we aimed to elucidate the value of HSP family A (Hsp70) member 4 (HSPA4) in the diagnosis and predicting prognosis of HCC, and its relationship with immune cell infiltration, immune cell biomarkers, and immune checkpoints. Gene mutation, DNA methylation, and the pathway involved in HCC were also analyzed. Methods The gene expression omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to compare HSPA4 expression, and the results were confirmed by immunohistochemical staining of clinical samples. R package was used to analyze the correlation between HSPA4 and cancer stage, and to establish receiver operating characteristic (ROC) curve of diagnosis, time-dependent survival ROC curve, and a nomogram model. cBioPortal and MethSurv were used to identify genetic alterations and DNA methylation, and their effect on prognosis. The Tumor Immune Estimation Resource (TIMER) was used to analyze immune cell infiltration, immune cell biomarkers, and immune checkpoints. The STRING database was used to analyze protein–protein interaction network information. Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the functions of HSPA4 and its functional partner genes. Results Overexpression of HSPA4 was identified in 25 cancers. Overexpression of HSPA4 considerably correlated with cancer stage and alpha-fetoprotein (AFP) level in HCC. Patients with higher HSPA4 expression showed poorer prognosis. HSPA4 expression can accurately identify tumor from normal tissue (AUC = 0.957). The area under 1-, 3-, and 5-year survival ROCs were above 0.6. The HSPA4 genetic alteration rate was …
format: application/pdf
format: text/html
creator: Bing-Bing Shang
creator: Jun Chen
creator: Zhi-Guo Wang
creator: Hui Liu
subject: Bioinformatics
subject: Oncology
subject: Histology
description: doi:10.7717/peerj.12315
publisher: PeerJ Inc.
rights: © 2021 Shang et al.
abstract: Background Hepatocellular carcinoma (HCC) is an inflammation-associated tumor involved in immune tolerance and evasion in the immune microenvironment. Heat shock proteins (HSPs) are involved in the occurrence, progression, and immune regulation of tumors. Therefore, HSPs have been considered potential therapeutic targets. Here, we aimed to elucidate the value of HSP family A (Hsp70) member 4 (HSPA4) in the diagnosis and predicting prognosis of HCC, and its relationship with immune cell infiltration, immune cell biomarkers, and immune checkpoints. Gene mutation, DNA methylation, and the pathway involved in HCC were also analyzed. Methods The gene expression omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to compare HSPA4 expression, and the results were confirmed by immunohistochemical staining of clinical samples. R package was used to analyze the correlation between HSPA4 and cancer stage, and to establish receiver operating characteristic (ROC) curve of diagnosis, time-dependent survival ROC curve, and a nomogram model. cBioPortal and MethSurv were used to identify genetic alterations and DNA methylation, and their effect on prognosis. The Tumor Immune Estimation Resource (TIMER) was used to analyze immune cell infiltration, immune cell biomarkers, and immune checkpoints. The STRING database was used to analyze protein–protein interaction network information. Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the functions of HSPA4 and its functional partner genes. Results Overexpression of HSPA4 was identified in 25 cancers. Overexpression of HSPA4 considerably correlated with cancer stage and alpha-fetoprotein (AFP) level in HCC. Patients with higher HSPA4 expression showed poorer prognosis. HSPA4 expression can accurately identify tumor from normal tissue (AUC = 0.957). The area under 1-, 3-, and 5-year survival ROCs were above 0.6. The HSPA4 genetic alteration rate was …
bibliographic citation: Shang et al. (2021) Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma. PeerJ 9:e12315 https://doi.org/10.7717/peerj.12315
date submitted: 2021-06-25
date accepted: 2021-09-24
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shang
  given name: Bing-Bing
author list: Agent
  family name: Chen
  given name: Jun
author list: Agent
  family name: Wang
  given name: Zhi-Guo
author list: Agent
  family name: Liu
  given name: Hui
doi: 10.7717/peerj.12315
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: © 2021 Shang et al.
attribution name: Shang et al.

Removal or component reversal of local geomagnetic field affects foraging orientation preference in migratory insect brown planthopper Nilaparvata lugens
type: item
type: AcademicArticle
description: Background Migratory brown planthopper Nilaparvata lugens (N. lugens) annually migrates to Northeast Asia in spring and returns to Southeast Asia in autumn. However, mechanisms for orientation and navigation during their flight remain largely unknown. The geomagnetic field (GMF) is an important source of directional information for animals (including N. lugens), yet the magnetic compass involved has not been fully identified. Methods Here we assessed the influences of GMF on the foraging orientation preference of N. lugens by removing or component reversal of local GMF. At the same time, we examined the role of iron-sulfur cluster assembly1 (IscA1), a putative component of magnetoreceptor, in the foraging orientation preference of N. lugens under the controlled magnetic fields by RNA silencing (RNAi). Results We found that the near-zero magnetic field (NZMF) or vertical reversal of GMF could lead to N. lugens losing the foraging orientation preference, suggesting that a normal level of GMF, in the way of either intensity or inclination, was essential for the foraging orientation of N. lugens. Moreover, the gene knockdown of IscA1, also affected the foraging orientation preference of N. lugens, pointing out a potential role of IscA1 in the insects’ sensing of variation in the GMF. Discussion These results suggested a foraging orientation preference is associated with the GMF and revealed new insights into the relationship between the IscA1 and magnetosensitivity mechanism in N. lugens.
format: application/pdf
format: text/html
creator: Yingchao Zhang
creator: Weidong Pan
subject: Agricultural Science
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.12351
publisher: PeerJ Inc.
rights: © 2021 Zhang and Pan
abstract: Background Migratory brown planthopper Nilaparvata lugens (N. lugens) annually migrates to Northeast Asia in spring and returns to Southeast Asia in autumn. However, mechanisms for orientation and navigation during their flight remain largely unknown. The geomagnetic field (GMF) is an important source of directional information for animals (including N. lugens), yet the magnetic compass involved has not been fully identified. Methods Here we assessed the influences of GMF on the foraging orientation preference of N. lugens by removing or component reversal of local GMF. At the same time, we examined the role of iron-sulfur cluster assembly1 (IscA1), a putative component of magnetoreceptor, in the foraging orientation preference of N. lugens under the controlled magnetic fields by RNA silencing (RNAi). Results We found that the near-zero magnetic field (NZMF) or vertical reversal of GMF could lead to N. lugens losing the foraging orientation preference, suggesting that a normal level of GMF, in the way of either intensity or inclination, was essential for the foraging orientation of N. lugens. Moreover, the gene knockdown of IscA1, also affected the foraging orientation preference of N. lugens, pointing out a potential role of IscA1 in the insects’ sensing of variation in the GMF. Discussion These results suggested a foraging orientation preference is associated with the GMF and revealed new insights into the relationship between the IscA1 and magnetosensitivity mechanism in N. lugens.
bibliographic citation: Zhang et al. (2021) Removal or component reversal of local geomagnetic field affects foraging orientation preference in migratory insect brown planthopper Nilaparvata lugens. PeerJ 9:e12351 https://doi.org/10.7717/peerj.12351
date submitted: 2020-08-18
date accepted: 2021-09-29
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yingchao
author list: Agent
  family name: Pan
  given name: Weidong
doi: 10.7717/peerj.12351
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: © 2021 Zhang and Pan
attribution name: Zhang and Pan

Identification of hub genes and transcription factor-miRNA-mRNA pathways in mice and human renal ischemia-reperfusion injury
type: item
type: AcademicArticle
description: Background Renal ischemia-reperfusion injury (IRI) is a disease with high incidence rate in kidney related surgery. Micro RNA (miRNA) and transcription factors (TFs) are widely involved in the process of renal IRI through regulation of their target genes. However, the regulatory relationships and functional roles of TFs, miRNAs and mRNAs in the progression of renal IRI are insufficiently understood. The present study aimed to clarify the underlying mechanism of regulatory relationships in renal IRI. Methods Six gene expression profiles were downloaded from Gene Expression Omnibus (GEO). Differently expressed genes (DEGs) and differently expressed miRNAs (DEMs) were identified through RRA integrated analysis of mRNA datasets (GSE39548, GSE87025, GSE52004, GSE71647, and GSE131288) and miRNA datasets (GSE29495). miRDB and TransmiR v2.0 database were applied to predict target genes of miRNA and TFs, respectively. DEGs were applied for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, followed with construction of protein-protein interaction (PPI) network. Then, the TF-miRNA-mRNA network was constructed. Correlation coefficient and ROC analysis were used to verify regulatory relationship between genes and their diagnostic value in GSE52004. Furthermore, in independent mouse RNA-seq datasets GSE98622, human RNA-seq GSE134386 and in vitro, the expression of hub genes and genes from the network were observed and correlation coefficient and ROC analysis were validated. Results A total of 21 DEMs and 187 DEGs were identified in renal IRI group compared to control group. The results of PPI analysis showed 15 hub genes. The TF-miRNA-mRNA regulatory network was constructed and several important pathways were identified and further verified, including Junb-miR-223-Ranbp3l, Cebpb-miR-223-Ranbp3l, Cebpb-miR-21-Ranbp3l and Cebpb-miR-181b-Bsnd. Four regulatory loops were identified, including Fosl2-miR-155, Fosl2-miR-146a, Cebpb-miR-155 and Mafk-miR-25. …
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format: text/html
creator: Peng Ke
creator: Lin Qian
creator: Yi Zhou
creator: Liu Feng
creator: Zhentao Zhang
creator: Chengjie Zheng
creator: Mengnan Chen
creator: Xinlei Huang
creator: Xiaodan Wu
subject: Bioinformatics
subject: Nephrology
subject: Urology
subject: Medical Genetics
description: doi:10.7717/peerj.12375
publisher: PeerJ Inc.
rights: © 2021 Ke et al.
abstract: Background Renal ischemia-reperfusion injury (IRI) is a disease with high incidence rate in kidney related surgery. Micro RNA (miRNA) and transcription factors (TFs) are widely involved in the process of renal IRI through regulation of their target genes. However, the regulatory relationships and functional roles of TFs, miRNAs and mRNAs in the progression of renal IRI are insufficiently understood. The present study aimed to clarify the underlying mechanism of regulatory relationships in renal IRI. Methods Six gene expression profiles were downloaded from Gene Expression Omnibus (GEO). Differently expressed genes (DEGs) and differently expressed miRNAs (DEMs) were identified through RRA integrated analysis of mRNA datasets (GSE39548, GSE87025, GSE52004, GSE71647, and GSE131288) and miRNA datasets (GSE29495). miRDB and TransmiR v2.0 database were applied to predict target genes of miRNA and TFs, respectively. DEGs were applied for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, followed with construction of protein-protein interaction (PPI) network. Then, the TF-miRNA-mRNA network was constructed. Correlation coefficient and ROC analysis were used to verify regulatory relationship between genes and their diagnostic value in GSE52004. Furthermore, in independent mouse RNA-seq datasets GSE98622, human RNA-seq GSE134386 and in vitro, the expression of hub genes and genes from the network were observed and correlation coefficient and ROC analysis were validated. Results A total of 21 DEMs and 187 DEGs were identified in renal IRI group compared to control group. The results of PPI analysis showed 15 hub genes. The TF-miRNA-mRNA regulatory network was constructed and several important pathways were identified and further verified, including Junb-miR-223-Ranbp3l, Cebpb-miR-223-Ranbp3l, Cebpb-miR-21-Ranbp3l and Cebpb-miR-181b-Bsnd. Four regulatory loops were identified, including Fosl2-miR-155, Fosl2-miR-146a, Cebpb-miR-155 and Mafk-miR-25. …
bibliographic citation: Ke et al. (2021) Identification of hub genes and transcription factor-miRNA-mRNA pathways in mice and human renal ischemia-reperfusion injury. PeerJ 9:e12375 https://doi.org/10.7717/peerj.12375
date submitted: 2021-06-24
date accepted: 2021-10-03
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ke
  given name: Peng
author list: Agent
  family name: Qian
  given name: Lin
author list: Agent
  family name: Zhou
  given name: Yi
author list: Agent
  family name: Feng
  given name: Liu
author list: Agent
  family name: Zhang
  given name: Zhentao
author list: Agent
  family name: Zheng
  given name: Chengjie
author list: Agent
  family name: Chen
  given name: Mengnan
author list: Agent
  family name: Huang
  given name: Xinlei
author list: Agent
  family name: Wu
  given name: Xiaodan
doi: 10.7717/peerj.12375
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: ©2021 Ke et al.
attribution name: Ke et al.

Identification of genes and gene expression associated with dispersal capacity in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)
type: item
type: AcademicArticle
description: Dispersal flights by the mountain pine beetle have allowed range expansion and major damage to pine stands in western Canada. We asked what the genetic and transcriptional basis of mountain pine beetle dispersal capacity is. Using flight mills, RNA-seq and a targeted association study, we compared strong-flying, weak-flying, and non-flying female beetles from the recently colonized northern end of their range. Nearly 3,000 genes were differentially expressed between strong and weak flying beetles, while weak fliers and nonfliers did not significantly differ. The differentially expressed genes were mainly associated with lipid metabolism, muscle maintenance, oxidative stress response, detoxification, endocrine function, and flight behavior. Three variant loci, two in the coding region of genes, were significantly associated with flight capacity but these genes had no known functional link to flight. Several differentially expressed gene systems may be important for sustained flight, while other systems are downregulated during dispersal and likely to conserve energy before host colonization. The candidate genes and SNPs identified here will inform further studies and management of mountain pine beetle, as well as contribute to understanding the mechanisms of insect dispersal flights.
format: application/pdf
format: text/html
creator: Victor A. Shegelski
creator: Maya L. Evenden
creator: Dezene P.W. Huber
creator: Felix A.H. Sperling
subject: Entomology
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12382
publisher: PeerJ Inc.
rights: © 2021 Shegelski et al.
abstract: Dispersal flights by the mountain pine beetle have allowed range expansion and major damage to pine stands in western Canada. We asked what the genetic and transcriptional basis of mountain pine beetle dispersal capacity is. Using flight mills, RNA-seq and a targeted association study, we compared strong-flying, weak-flying, and non-flying female beetles from the recently colonized northern end of their range. Nearly 3,000 genes were differentially expressed between strong and weak flying beetles, while weak fliers and nonfliers did not significantly differ. The differentially expressed genes were mainly associated with lipid metabolism, muscle maintenance, oxidative stress response, detoxification, endocrine function, and flight behavior. Three variant loci, two in the coding region of genes, were significantly associated with flight capacity but these genes had no known functional link to flight. Several differentially expressed gene systems may be important for sustained flight, while other systems are downregulated during dispersal and likely to conserve energy before host colonization. The candidate genes and SNPs identified here will inform further studies and management of mountain pine beetle, as well as contribute to understanding the mechanisms of insect dispersal flights.
bibliographic citation: Shegelski et al. (2021) Identification of genes and gene expression associated with dispersal capacity in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). PeerJ 9:e12382 https://doi.org/10.7717/peerj.12382
date submitted: 2021-07-15
date accepted: 2021-10-04
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shegelski
  given name: Victor A.
author list: Agent
  family name: Evenden
  given name: Maya L.
author list: Agent
  family name: Huber
  given name: Dezene P.W.
author list: Agent
  family name: Sperling
  given name: Felix A.H.
doi: 10.7717/peerj.12382
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: © 2021 Shegelski et al.
attribution name: Shegelski et al.

Assessment of antimycobacterial activities of pure compounds extracted from Thai medicinal plants against clarithromycin-resistant Mycobacterium abscessus
type: item
type: AcademicArticle
description: Background Infection with Mycobacterium abscessus is usually chronic and is associated with clarithromycin resistance. Increasing drug resistance is a major public-health problem and has led to the search for new antimycobacterial agents. We evaluated the antimycobacterial activity, toxicity, and synergistic effects of several plant secondary metabolites against M. abscessus. Methods Twenty-three compounds were evaluated for antimycobacterial activity against thirty M. abscessus clinical isolates by broth microdilution to determine their minimum inhibitory concentration (MIC) values. Toxicity was evaluated using red and white blood cells (RBCs and WBCs). The compounds were used in combination with clarithromycin to investigate the possibility of synergistic activity. Results Five out of twenty-three compounds (RL008, RL009, RL011, RL012 and RL013) exhibited interesting antimycobacterial activity against M. abscessus, with MIC values ranging from <1 to >128 μg/mL. These extracts did not induce hemolytic effect on RBCs and displayed low toxicity against WBCs. The five least-toxic compounds were tested for synergism with clarithromycin against seven isolates with inducible clarithromycin resistance and seven with acquired clarithromycin resistance. The best synergistic results against these isolates were observed for RL008 and RL009 (8/14 isolates; 57%). Conclusions This study demonstrated antimycobacterial and synergistic activities of pure compounds extracted from medicinal plants against clarithromycin-resistant M. abscessus. This synergistic action, together with clarithromycin, may be effective for treating infections and should be further studied for the development of novel antimicrobial agents.
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format: text/html
creator: Auttawit Sirichoat
creator: Irin Kham-ngam
creator: Orawee Kaewprasert
creator: Pimjai Ananta
creator: Awat Wisetsai
creator: Ratsami Lekphrom
creator: Kiatichai Faksri
subject: Biochemistry
subject: Microbiology
description: doi:10.7717/peerj.12391
publisher: PeerJ Inc.
rights: © 2021 Sirichoat et al.
abstract: Background Infection with Mycobacterium abscessus is usually chronic and is associated with clarithromycin resistance. Increasing drug resistance is a major public-health problem and has led to the search for new antimycobacterial agents. We evaluated the antimycobacterial activity, toxicity, and synergistic effects of several plant secondary metabolites against M. abscessus. Methods Twenty-three compounds were evaluated for antimycobacterial activity against thirty M. abscessus clinical isolates by broth microdilution to determine their minimum inhibitory concentration (MIC) values. Toxicity was evaluated using red and white blood cells (RBCs and WBCs). The compounds were used in combination with clarithromycin to investigate the possibility of synergistic activity. Results Five out of twenty-three compounds (RL008, RL009, RL011, RL012 and RL013) exhibited interesting antimycobacterial activity against M. abscessus, with MIC values ranging from <1 to >128 μg/mL. These extracts did not induce hemolytic effect on RBCs and displayed low toxicity against WBCs. The five least-toxic compounds were tested for synergism with clarithromycin against seven isolates with inducible clarithromycin resistance and seven with acquired clarithromycin resistance. The best synergistic results against these isolates were observed for RL008 and RL009 (8/14 isolates; 57%). Conclusions This study demonstrated antimycobacterial and synergistic activities of pure compounds extracted from medicinal plants against clarithromycin-resistant M. abscessus. This synergistic action, together with clarithromycin, may be effective for treating infections and should be further studied for the development of novel antimicrobial agents.
bibliographic citation: Sirichoat et al. (2021) Assessment of antimycobacterial activities of pure compounds extracted from Thai medicinal plants against clarithromycin-resistant Mycobacterium abscessus. PeerJ 9:e12391 https://doi.org/10.7717/peerj.12391
date submitted: 2021-07-19
date accepted: 2021-10-05
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sirichoat
  given name: Auttawit
author list: Agent
  family name: Kham-ngam
  given name: Irin
author list: Agent
  family name: Kaewprasert
  given name: Orawee
author list: Agent
  family name: Ananta
  given name: Pimjai
author list: Agent
  family name: Wisetsai
  given name: Awat
author list: Agent
  family name: Lekphrom
  given name: Ratsami
author list: Agent
  family name: Faksri
  given name: Kiatichai
doi: 10.7717/peerj.12391
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: © 2021 Sirichoat et al.
attribution name: Sirichoat et al.

Blood cells and hematological parameters of the mountain dragon, Diploderma micangshanensis (Squamata: Lacertilia: Agamidae)
type: item
type: AcademicArticle
description: Hematological characteristics reflect the health status of animals and their physiological adaptation to the environment. However, few studies focused on the species of Diploderma. In this study, the blood cells and the hematological parameters of Diploderma micangshanensis, a species endemic to China, were examined based on 48 healthy adult (32 males and 16 females). The blood cells and hematological parameters of D. micangshanensis were similar to those of other lizard species. Although the values of erythrocyte morphometric characters and hematological parameters varied between males and females, the differences were only significant in the case of the hematocrit and erythrocyte size, which may allow for higher oxygen availability in males. Hemoglobin, mean corpuscular hemoglobin concentration, and mean corpuscle volume were strongly affected by the snout-vent length and/or body mass, which reflect the physiological adaptation to the oxygen requirement of different individuals. This is the first report of hematological data from a species of Diploderma, and the results will provide data for research on the adaptive evolution and health assessment in this species and other congeners.
format: application/pdf
format: text/html
creator: Yinlong Bai
creator: Guanglu Li
creator: Shuaichao Lin
creator: Jianli Xiong
subject: Biochemistry
subject: Veterinary Medicine
subject: Zoology
subject: Hematology
description: doi:10.7717/peerj.12397
publisher: PeerJ Inc.
rights: © 2021 Bai et al.
abstract: Hematological characteristics reflect the health status of animals and their physiological adaptation to the environment. However, few studies focused on the species of Diploderma. In this study, the blood cells and the hematological parameters of Diploderma micangshanensis, a species endemic to China, were examined based on 48 healthy adult (32 males and 16 females). The blood cells and hematological parameters of D. micangshanensis were similar to those of other lizard species. Although the values of erythrocyte morphometric characters and hematological parameters varied between males and females, the differences were only significant in the case of the hematocrit and erythrocyte size, which may allow for higher oxygen availability in males. Hemoglobin, mean corpuscular hemoglobin concentration, and mean corpuscle volume were strongly affected by the snout-vent length and/or body mass, which reflect the physiological adaptation to the oxygen requirement of different individuals. This is the first report of hematological data from a species of Diploderma, and the results will provide data for research on the adaptive evolution and health assessment in this species and other congeners.
bibliographic citation: Bai et al. (2021) Blood cells and hematological parameters of the mountain dragon, Diploderma micangshanensis (Squamata: Lacertilia: Agamidae). PeerJ 9:e12397 https://doi.org/10.7717/peerj.12397
date submitted: 2021-06-14
date accepted: 2021-10-06
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Yinlong
author list: Agent
  family name: Li
  given name: Guanglu
author list: Agent
  family name: Lin
  given name: Shuaichao
author list: Agent
  family name: Xiong
  given name: Jianli
doi: 10.7717/peerj.12397
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: ©2021 Bai et al.
attribution name: Bai et al.

Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization
type: item
type: AcademicArticle
description: Background Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups. Methods We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies. Results We obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridiz…
format: application/pdf
format: text/html
creator: Aaron Liston
creator: Kevin A. Weitemier
creator: Lucas Letelier
creator: János Podani
creator: Yu Zong
creator: Lang Liu
creator: Timothy A. Dickinson
subject: Genomics
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.12418
publisher: PeerJ Inc.
rights: © 2021 Liston et al.
abstract: Background Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups. Methods We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies. Results We obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridiz…
bibliographic citation: Liston et al. (2021) Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization. PeerJ 9:e12418 https://doi.org/10.7717/peerj.12418
date submitted: 2021-01-04
date accepted: 2021-10-10
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liston
  given name: Aaron
author list: Agent
  family name: Weitemier
  given name: Kevin A.
author list: Agent
  family name: Letelier
  given name: Lucas
author list: Agent
  family name: Podani
  given name: János
author list: Agent
  family name: Zong
  given name: Yu
author list: Agent
  family name: Liu
  given name: Lang
author list: Agent
  family name: Dickinson
  given name: Timothy A.
doi: 10.7717/peerj.12418
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: ©2021 Liston et al.
attribution name: Liston et al.

Modernising tactile acuity assessment; clinimetrics of semi-automated tests and effects of age, sex and anthropometry on performance
type: item
type: AcademicArticle
description: Background Reduced tactile acuity has been observed in several chronic pain conditions and has been proposed as a clinical indicator of somatosensory impairments related to the condition. As some interventions targeting these impairments have resulted in pain reduction, assessing tactile acuity may have significant clinical potential. While two-point discrimination threshold (TPDT) is a popular method of assessing tactile acuity, large measurement error has been observed (impeding responsiveness) and its validity has been questioned. The recently developed semi-automated ‘imprint Tactile Acuity Device’ (iTAD) may improve tactile acuity assessment, but clinimetric properties of its scores (accuracy score, response time and rate correct score) need further examination. Aims Experiment 1: To determine inter-rater reliability and measurement error of TPDT and iTAD assessments. Experiment 2: To determine internal consistencies and floor or ceiling effects of iTAD scores, and investigate effects of age, sex, and anthropometry on performance. Methods Experiment 1: To assess inter-rater reliability (ICC(2,1)) and measurement error (coefficient of variation (CoV)), three assessors each performed TPDT and iTAD assessments at the neck in forty healthy participants. Experiment 2: To assess internal consistency (ICC(2,k)) and floor or ceiling effects (skewness z-scores), one hundred healthy participants performed the iTAD’s localisation and orientation tests. Balanced for sex, participants were equally divided over five age brackets (18–30, 31–40, 41–50, 51–60 and 61–70). Age, sex, body mass index (BMI) and neck surface area were assessed to examine their direct (using multiple linear regression analysis) and indirect (using sequential mediation analysis) relationship with iTAD scores. Results Mean ICC(2,1) was moderate for TPDT (0.70) and moderate-to-good for the various iTAD scores (0.65–0.86). The CoV was 25.3% for TPDT and ranged from 6.1% to 16.5% for iTAD scores. Internal …
format: application/pdf
format: text/html
creator: Nick A. Olthof
creator: Michel W. Coppieters
creator: G Lorimer Moseley
creator: Michele Sterling
creator: Dylan J. Chippindall
creator: Daniel S. Harvie
subject: Anesthesiology and Pain Management
subject: Drugs and Devices
subject: Neurology
description: doi:10.7717/peerj.12192
publisher: PeerJ Inc.
rights: © 2021 Olthof et al.
abstract: Background Reduced tactile acuity has been observed in several chronic pain conditions and has been proposed as a clinical indicator of somatosensory impairments related to the condition. As some interventions targeting these impairments have resulted in pain reduction, assessing tactile acuity may have significant clinical potential. While two-point discrimination threshold (TPDT) is a popular method of assessing tactile acuity, large measurement error has been observed (impeding responsiveness) and its validity has been questioned. The recently developed semi-automated ‘imprint Tactile Acuity Device’ (iTAD) may improve tactile acuity assessment, but clinimetric properties of its scores (accuracy score, response time and rate correct score) need further examination. Aims Experiment 1: To determine inter-rater reliability and measurement error of TPDT and iTAD assessments. Experiment 2: To determine internal consistencies and floor or ceiling effects of iTAD scores, and investigate effects of age, sex, and anthropometry on performance. Methods Experiment 1: To assess inter-rater reliability (ICC(2,1)) and measurement error (coefficient of variation (CoV)), three assessors each performed TPDT and iTAD assessments at the neck in forty healthy participants. Experiment 2: To assess internal consistency (ICC(2,k)) and floor or ceiling effects (skewness z-scores), one hundred healthy participants performed the iTAD’s localisation and orientation tests. Balanced for sex, participants were equally divided over five age brackets (18–30, 31–40, 41–50, 51–60 and 61–70). Age, sex, body mass index (BMI) and neck surface area were assessed to examine their direct (using multiple linear regression analysis) and indirect (using sequential mediation analysis) relationship with iTAD scores. Results Mean ICC(2,1) was moderate for TPDT (0.70) and moderate-to-good for the various iTAD scores (0.65–0.86). The CoV was 25.3% for TPDT and ranged from 6.1% to 16.5% for iTAD scores. Internal …
bibliographic citation: Olthof et al. (2021) Modernising tactile acuity assessment; clinimetrics of semi-automated tests and effects of age, sex and anthropometry on performance. PeerJ 9:e12192 https://doi.org/10.7717/peerj.12192
date submitted: 2021-05-06
date accepted: 2021-08-31
issued: 2021-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olthof
  given name: Nick A.
author list: Agent
  family name: Coppieters
  given name: Michel W.
author list: Agent
  family name: Moseley
  given name: G Lorimer
author list: Agent
  family name: Sterling
  given name: Michele
author list: Agent
  family name: Chippindall
  given name: Dylan J.
author list: Agent
  family name: Harvie
  given name: Daniel S.
doi: 10.7717/peerj.12192
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-25
copyright: ©2021 Olthof et al.
attribution name: Olthof et al.

Salinity effects on water potential and the normalized difference vegetation index in four species of a saline semi-arid ecosystem
type: item
type: AcademicArticle
description: This study was carried out during January 2020–December 2020 in a semi-desert ecosystem in southern Sonora, Mexico, to determine the annual and daily variations in water potential and the normalized difference vegetation index (NDVI) of Bursera fagaroides Engl., Monogr. Phan., Parkinsonia aculeata L., Sp. Pl.; Prosopis laevigata (Humb. & Bonpl. ex Willd.), and Atriplex canescens (Pursh) Nutt. Soil electrical conductivity, cation content, and physical characteristics were determined at two depths, and water potential (ψ) was measured in roots, stems, and leaves. The daily leaf ψ was measured every 15 days each month to determine the duration of stress (hours) and the stress intensity (SI). The electrical conductivity determinations classified the soil in the experimental area as strongly saline. A significant difference was noted in electrical conductivity between soil depths. The four studied species showed significant gradients of ψ in their organs. In this soil, all four species remained in a stressed condition for approximately 11 h per day. The mean SI was 27%, and B. fagaroides Engl., Monogr. Phan. showed the lowest value. The four species showed increased NDVI values during the rainy months, with P. laevigata (Humb. & Bonpl. ex Willd.) and Parkinsonia aculeata L., Sp. Pl. showing the highest values. The capacity for ψ decrease under saline conditions identified A. canescens (Pursh) Nutt., B. fagaroides Engl., Monogr. Phan. and P. aculeata L., Sp. Pl. as practical and feasible alternatives for establishment in saline soils in southern Sonora for purposes of soil recovery and reforestation.
format: application/pdf
format: text/html
creator: Hebert Hernán Soto Gonzáles
creator: Ofelda Peñuelas-Rubio
creator: Leandris Argentel-Martínez
creator: Aurelio Leyva Ponce
creator: María Hermelinda Herrera Andrade
creator: Mirza Hasanuzzaman
creator: Jorge González Aguilera
creator: Paulo Eduardo Teodoro
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.12297
publisher: PeerJ Inc.
rights: © 2021 Soto Gonzáles et al.
abstract: This study was carried out during January 2020–December 2020 in a semi-desert ecosystem in southern Sonora, Mexico, to determine the annual and daily variations in water potential and the normalized difference vegetation index (NDVI) of Bursera fagaroides Engl., Monogr. Phan., Parkinsonia aculeata L., Sp. Pl.; Prosopis laevigata (Humb. & Bonpl. ex Willd.), and Atriplex canescens (Pursh) Nutt. Soil electrical conductivity, cation content, and physical characteristics were determined at two depths, and water potential (ψ) was measured in roots, stems, and leaves. The daily leaf ψ was measured every 15 days each month to determine the duration of stress (hours) and the stress intensity (SI). The electrical conductivity determinations classified the soil in the experimental area as strongly saline. A significant difference was noted in electrical conductivity between soil depths. The four studied species showed significant gradients of ψ in their organs. In this soil, all four species remained in a stressed condition for approximately 11 h per day. The mean SI was 27%, and B. fagaroides Engl., Monogr. Phan. showed the lowest value. The four species showed increased NDVI values during the rainy months, with P. laevigata (Humb. & Bonpl. ex Willd.) and Parkinsonia aculeata L., Sp. Pl. showing the highest values. The capacity for ψ decrease under saline conditions identified A. canescens (Pursh) Nutt., B. fagaroides Engl., Monogr. Phan. and P. aculeata L., Sp. Pl. as practical and feasible alternatives for establishment in saline soils in southern Sonora for purposes of soil recovery and reforestation.
bibliographic citation: Soto Gonzáles et al. (2021) Salinity effects on water potential and the normalized difference vegetation index in four species of a saline semi-arid ecosystem. PeerJ 9:e12297 https://doi.org/10.7717/peerj.12297
date submitted: 2021-04-09
date accepted: 2021-09-21
issued: 2021-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soto Gonzáles
  given name: Hebert Hernán
author list: Agent
  family name: Peñuelas-Rubio
  given name: Ofelda
author list: Agent
  family name: Argentel-Martínez
  given name: Leandris
author list: Agent
  family name: Leyva Ponce
  given name: Aurelio
author list: Agent
  family name: Herrera Andrade
  given name: María Hermelinda
author list: Agent
  family name: Hasanuzzaman
  given name: Mirza
author list: Agent
  family name: González Aguilera
  given name: Jorge
author list: Agent
  family name: Eduardo Teodoro
  given name: Paulo
doi: 10.7717/peerj.12297
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-25
copyright: © 2021 Soto Gonzáles et al.
attribution name: Soto Gonzáles et al.

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