PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Construction and validation of a novel prognostic signature of microRNAs in lung adenocarcinoma
items: Perfluorooctane sulfonate exerts inflammatory bowel disease-like intestinal injury in rats
items: Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes
items: DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai
items: Synergism between calcium nitrate applications and fungal endophytes to increase sugar concentration in Festuca sinensis under cold stress
items: Strategies for recovery of imbalanced full-scale biogas reactor feeding with palm oil mill effluent
items: Reversine, a selective MPS1 inhibitor, induced autophagic cell death via diminished glucose uptake and ATP production in cholangiocarcinoma cells
items: Differential relieving effects of shikonin and its derivatives on inflammation and mucosal barrier damage caused by ulcerative colitis
items: Reproducing country-wide COVID-19 dynamics can require the usage of a set of SIR systems
items: Biochemical characterization and inhibition of thermolabile hemolysin from Vibrio parahaemolyticus by phenolic compounds

Construction and validation of a novel prognostic signature of microRNAs in lung adenocarcinoma
type: item
type: AcademicArticle
description: MicroRNA (miRNA, miR) has been reported to be highly implicated in a wide range of biological processes in lung cancer (LC), and identification of differentially expressed miRNAs between normal and LC samples has been widely used in the discovery of prognostic factors for overall survival (OS) and response to therapy. The present study was designed to develop and evaluate a miRNA-based signature with prognostic value for the OS of lung adenocarcinoma (LUAD), a common histologic subtype of LC. In brief, the miRNA expression profiles and clinicopathological factors of 499 LUAD patients were collected from The Cancer Genome Atlas (TCGA) database. Kaplan–Meier (K-M) survival analysis showed significant correlations between differentially expressed miRNAs and LUAD survival outcomes. Afterward, 1,000 resample LUAD training matrices based on the training set was applied to identify the potential prognostic miRNAs. The least absolute shrinkage and selection operator (LASSO) cox regression analysis was used to constructed a six-miRNA based prognostic signature for LUAD patients. Samples with different risk scores displayed distinct OS in K-M analysis, indicating considerable predictive accuracy of this signature in both training and validation sets. Furthermore, time-dependent receiver operating characteristic (ROC) analysis demonstrated the nomogram achieved higher predictive accuracy than any other clinical variables after incorporating the clinical information (age, sex, stage, and recurrence). In the stratification analysis, the prognostic value of this classifier in LUAD patients was validated to be independent of other clinicopathological variables, such as age, gender, tumor recurrence, and early stage. Gene set annotation analyses were also conducted through the Hallmark gene set and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, indicating target genes of the six miRNAs were positively related to various molecular pathways of cancer, such as hallmark UV re…
format: application/pdf
format: text/html
creator: Wanzhen Li
creator: Shiqing Liu
creator: Shihong Su
creator: Yang Chen
creator: Gengyun Sun
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.10470
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: MicroRNA (miRNA, miR) has been reported to be highly implicated in a wide range of biological processes in lung cancer (LC), and identification of differentially expressed miRNAs between normal and LC samples has been widely used in the discovery of prognostic factors for overall survival (OS) and response to therapy. The present study was designed to develop and evaluate a miRNA-based signature with prognostic value for the OS of lung adenocarcinoma (LUAD), a common histologic subtype of LC. In brief, the miRNA expression profiles and clinicopathological factors of 499 LUAD patients were collected from The Cancer Genome Atlas (TCGA) database. Kaplan–Meier (K-M) survival analysis showed significant correlations between differentially expressed miRNAs and LUAD survival outcomes. Afterward, 1,000 resample LUAD training matrices based on the training set was applied to identify the potential prognostic miRNAs. The least absolute shrinkage and selection operator (LASSO) cox regression analysis was used to constructed a six-miRNA based prognostic signature for LUAD patients. Samples with different risk scores displayed distinct OS in K-M analysis, indicating considerable predictive accuracy of this signature in both training and validation sets. Furthermore, time-dependent receiver operating characteristic (ROC) analysis demonstrated the nomogram achieved higher predictive accuracy than any other clinical variables after incorporating the clinical information (age, sex, stage, and recurrence). In the stratification analysis, the prognostic value of this classifier in LUAD patients was validated to be independent of other clinicopathological variables, such as age, gender, tumor recurrence, and early stage. Gene set annotation analyses were also conducted through the Hallmark gene set and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, indicating target genes of the six miRNAs were positively related to various molecular pathways of cancer, such as hallmark UV re…
bibliographic citation: Li et al. (2021) Construction and validation of a novel prognostic signature of microRNAs in lung adenocarcinoma. PeerJ 9:e10470 https://doi.org/10.7717/peerj.10470
date submitted: 2019-10-21
date accepted: 2020-11-11
issued: 2021-01-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Wanzhen
author list: Agent
  family name: Liu
  given name: Shiqing
author list: Agent
  family name: Su
  given name: Shihong
author list: Agent
  family name: Chen
  given name: Yang
author list: Agent
  family name: Sun
  given name: Gengyun
doi: 10.7717/peerj.10470
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-08
copyright: ©2021 Li et al.
attribution name: Li et al.

Perfluorooctane sulfonate exerts inflammatory bowel disease-like intestinal injury in rats
type: item
type: AcademicArticle
description: Background Perfluorooctane sulfonate (PFOS), a type of perfluorinated compounds (PFCs), can induce various organ toxicity, including hepatomegaly, immunotoxicity, and gut microbiota disorder. PFCs have been associated with inflammatory bowel disease (IBD). Yet, whether PFOS exposure causes IBD-like disorder and the underlying mechanism remains undefined. Here, we investigated the influence of PFOS exposure on the development of IBD-like disorder in rats. Methods Sprague-Dawley rats were intraperitoneally injected with PFOS (1 or 10 mg/kg) or normal saline (NS) every other day for 15 days. Body weight, serum concentrations of serum amyloid A (SAA) and high sensitivity C reactive protein (hsCRP) were measured. Pathological assessments of villi height and crypt depth in the proximal duodenum and jejunum were performed using H&E staining. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining was used to assay cell apoptosis in the jejunum. The infiltration of inflammatory cells and cytokines in the jejunum were detected by immunohistochemistry analysis. Results PFOS (10 mg/kg) significantly increased the body weight, SAA and hsCRP, whereas no significant differences were observed in PFOS 1 mg/kg group of rats. The villi height and crypt depth in the proximal duodenum and jejunum were significantly reduced upon PFOS exposure. PFOS induced higher histopathological score in intestinal tissues compared to NS. Notably, TUNEL-positive cells were significantly higher in the jejunum upon PFOS exposure. Further, neutrophil and macrophage accumulated, and inflammatory cytokines infiltration were also remarkably increased in rats exposed to PFOS. Conclusion PFOS induces IBD-like phenotypes in rats, with associated inflammatory infiltration to intestinal.
format: application/pdf
format: text/html
creator: Hai Liang
creator: Miao Yang
creator: Cheng Zeng
creator: Wei Wu
creator: Liying Zhao
creator: Yu Wang
subject: Biochemistry
subject: Toxicology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.10644
publisher: PeerJ Inc.
rights: © 2021 Liang et al.
abstract: Background Perfluorooctane sulfonate (PFOS), a type of perfluorinated compounds (PFCs), can induce various organ toxicity, including hepatomegaly, immunotoxicity, and gut microbiota disorder. PFCs have been associated with inflammatory bowel disease (IBD). Yet, whether PFOS exposure causes IBD-like disorder and the underlying mechanism remains undefined. Here, we investigated the influence of PFOS exposure on the development of IBD-like disorder in rats. Methods Sprague-Dawley rats were intraperitoneally injected with PFOS (1 or 10 mg/kg) or normal saline (NS) every other day for 15 days. Body weight, serum concentrations of serum amyloid A (SAA) and high sensitivity C reactive protein (hsCRP) were measured. Pathological assessments of villi height and crypt depth in the proximal duodenum and jejunum were performed using H&E staining. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining was used to assay cell apoptosis in the jejunum. The infiltration of inflammatory cells and cytokines in the jejunum were detected by immunohistochemistry analysis. Results PFOS (10 mg/kg) significantly increased the body weight, SAA and hsCRP, whereas no significant differences were observed in PFOS 1 mg/kg group of rats. The villi height and crypt depth in the proximal duodenum and jejunum were significantly reduced upon PFOS exposure. PFOS induced higher histopathological score in intestinal tissues compared to NS. Notably, TUNEL-positive cells were significantly higher in the jejunum upon PFOS exposure. Further, neutrophil and macrophage accumulated, and inflammatory cytokines infiltration were also remarkably increased in rats exposed to PFOS. Conclusion PFOS induces IBD-like phenotypes in rats, with associated inflammatory infiltration to intestinal.
bibliographic citation: Liang et al. (2021) Perfluorooctane sulfonate exerts inflammatory bowel disease-like intestinal injury in rats. PeerJ 9:e10644 https://doi.org/10.7717/peerj.10644
date submitted: 2020-08-04
date accepted: 2020-12-03
issued: 2021-01-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Hai
author list: Agent
  family name: Yang
  given name: Miao
author list: Agent
  family name: Zeng
  given name: Cheng
author list: Agent
  family name: Wu
  given name: Wei
author list: Agent
  family name: Zhao
  given name: Liying
author list: Agent
  family name: Wang
  given name: Yu
doi: 10.7717/peerj.10644
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-08
copyright: ©2021 Liang et al.
attribution name: Liang et al.

Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes
type: item
type: AcademicArticle
description: The microbiomes of deep and shallow aquifers located in an agricultural area, impacted by an old tin mine, were explored to understand spatial variation in microbial community structures and identify environmental factors influencing microbial distribution patterns through the analysis of 16S rRNA and aioA genes. Although Proteobacteria, Cyanobacteria, Actinobacteria, Patescibacteria, Bacteroidetes, and Epsilonbacteraeota were widespread across the analyzed aquifers, the dominant taxa found in each aquifer were unique. The co-dominance of Burkholderiaceae and Gallionellaceae potentially controlled arsenic immobilization in the aquifers. Analysis of the aioA gene suggested that arsenite-oxidizing bacteria phylogenetically associated with Alpha-, Beta-, and Gamma proteobacteria were present at low abundance (0.85 to 37.13%) and were more prevalent in shallow aquifers and surface water. The concentrations of dissolved oxygen and total phosphorus significantly governed the microbiomes analyzed in this study, while the combination of NO3--N concentration and oxidation-reduction potential significantly influenced the diversity and abundance of arsenite-oxidizing bacteria in the aquifers. The knowledge of microbial community structures and functions in relation to deep and shallow aquifers is required for further development of sustainable aquifer management.
format: application/pdf
format: text/html
creator: Prinpida Sonthiphand
creator: Pasunun Rattanaroongrot
creator: Kasarnchon Mek-yong
creator: Kanthida Kusonmano
creator: Chalida Rangsiwutisak
creator: Pichahpuk Uthaipaisanwong
creator: Srilert Chotpantarat
creator: Teerasit Termsaithong
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.10653
publisher: PeerJ Inc.
rights: © 2021 Sonthiphand et al.
abstract: The microbiomes of deep and shallow aquifers located in an agricultural area, impacted by an old tin mine, were explored to understand spatial variation in microbial community structures and identify environmental factors influencing microbial distribution patterns through the analysis of 16S rRNA and aioA genes. Although Proteobacteria, Cyanobacteria, Actinobacteria, Patescibacteria, Bacteroidetes, and Epsilonbacteraeota were widespread across the analyzed aquifers, the dominant taxa found in each aquifer were unique. The co-dominance of Burkholderiaceae and Gallionellaceae potentially controlled arsenic immobilization in the aquifers. Analysis of the aioA gene suggested that arsenite-oxidizing bacteria phylogenetically associated with Alpha-, Beta-, and Gamma proteobacteria were present at low abundance (0.85 to 37.13%) and were more prevalent in shallow aquifers and surface water. The concentrations of dissolved oxygen and total phosphorus significantly governed the microbiomes analyzed in this study, while the combination of NO3--N concentration and oxidation-reduction potential significantly influenced the diversity and abundance of arsenite-oxidizing bacteria in the aquifers. The knowledge of microbial community structures and functions in relation to deep and shallow aquifers is required for further development of sustainable aquifer management.
bibliographic citation: Sonthiphand et al. (2021) Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes. PeerJ 9:e10653 https://doi.org/10.7717/peerj.10653
date submitted: 2020-09-02
date accepted: 2020-12-04
issued: 2021-01-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sonthiphand
  given name: Prinpida
author list: Agent
  family name: Rattanaroongrot
  given name: Pasunun
author list: Agent
  family name: Mek-yong
  given name: Kasarnchon
author list: Agent
  family name: Kusonmano
  given name: Kanthida
author list: Agent
  family name: Rangsiwutisak
  given name: Chalida
author list: Agent
  family name: Uthaipaisanwong
  given name: Pichahpuk
author list: Agent
  family name: Chotpantarat
  given name: Srilert
author list: Agent
  family name: Termsaithong
  given name: Teerasit
doi: 10.7717/peerj.10653
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-08
copyright: ©2021 Sonthiphand et al.
attribution name: Sonthiphand et al.

DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai
type: item
type: AcademicArticle
description: Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan’s Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversi…
format: application/pdf
format: text/html
creator: Oxana Khapilina
creator: Olesya Raiser
creator: Alevtina Danilova
creator: Vladislav Shevtsov
creator: Ainur Turzhanova
creator: Ruslan Kalendar
subject: Biodiversity
subject: Genetics
subject: Molecular Biology
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.10674
publisher: PeerJ Inc.
rights: © 2021 Khapilina et al.
abstract: Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan’s Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversi…
bibliographic citation: Khapilina et al. (2021) DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai. PeerJ 9:e10674 https://doi.org/10.7717/peerj.10674
date submitted: 2020-08-12
date accepted: 2020-12-09
issued: 2021-01-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khapilina
  given name: Oxana
author list: Agent
  family name: Raiser
  given name: Olesya
author list: Agent
  family name: Danilova
  given name: Alevtina
author list: Agent
  family name: Shevtsov
  given name: Vladislav
author list: Agent
  family name: Turzhanova
  given name: Ainur
author list: Agent
  family name: Kalendar
  given name: Ruslan
doi: 10.7717/peerj.10674
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-08
copyright: © 2021 Khapilina et al.
attribution name: Khapilina et al.

Synergism between calcium nitrate applications and fungal endophytes to increase sugar concentration in Festuca sinensis under cold stress
type: item
type: AcademicArticle
description: Epichloë endophytes have been shown to increase tolerance to biotic and abiotic stresses in many cool-season grasses. We investigated the impact of endophyte infection of Festuca sinensis, on root metabolic activity, photosynthetic pigments, leaf relative water content (RWC) and soluble carbohydrates in a field experiment carried out during chilling and irrigation with Ca(NO3)2. A highly significant (P < 0.001) correlation for Epichloë endophytes was observed for root metabolic activity. Ca(NO3)2 affected very significantly root metabolic activity and total chlorophyll (P < 0.001). Low temperature led to highly significant (P < 0.001) reductions in root metabolic activity, RWC, total chlorophyll, chlorophyll a/b ratio, and carotenoid contents. In addition, the fructose concentrations of shoots were greater on the 14th day than on the 28th day and before treatment, whilst the glucose concentration of roots was much higher on the 28th day than before and after 14 days treatment. Moreover, our results indicated that the addition of calcium nitrate contributed to higher levels of total chlorophylls, soluble sugars, sucrose, fructose or glucose in the shoots and roots in both E+ and E- plants during long periods of chilling. These results suggest that Epichloë endophyte infection and/or exogenous calcium nitrate can confer better tolerance to cold stress.
format: application/pdf
format: text/html
creator: Lianyu Zhou
creator: Chunjie Li
creator: James F. White
creator: Richard D. Johnson
subject: Agricultural Science
subject: Biochemistry
subject: Ecology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.10568
publisher: PeerJ Inc.
rights: © 2021 Zhou et al.
abstract: Epichloë endophytes have been shown to increase tolerance to biotic and abiotic stresses in many cool-season grasses. We investigated the impact of endophyte infection of Festuca sinensis, on root metabolic activity, photosynthetic pigments, leaf relative water content (RWC) and soluble carbohydrates in a field experiment carried out during chilling and irrigation with Ca(NO3)2. A highly significant (P < 0.001) correlation for Epichloë endophytes was observed for root metabolic activity. Ca(NO3)2 affected very significantly root metabolic activity and total chlorophyll (P < 0.001). Low temperature led to highly significant (P < 0.001) reductions in root metabolic activity, RWC, total chlorophyll, chlorophyll a/b ratio, and carotenoid contents. In addition, the fructose concentrations of shoots were greater on the 14th day than on the 28th day and before treatment, whilst the glucose concentration of roots was much higher on the 28th day than before and after 14 days treatment. Moreover, our results indicated that the addition of calcium nitrate contributed to higher levels of total chlorophylls, soluble sugars, sucrose, fructose or glucose in the shoots and roots in both E+ and E- plants during long periods of chilling. These results suggest that Epichloë endophyte infection and/or exogenous calcium nitrate can confer better tolerance to cold stress.
bibliographic citation: Zhou et al. (2021) Synergism between calcium nitrate applications and fungal endophytes to increase sugar concentration in Festuca sinensis under cold stress. PeerJ 9:e10568 https://doi.org/10.7717/peerj.10568
date submitted: 2020-02-20
date accepted: 2020-11-23
issued: 2021-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Lianyu
author list: Agent
  family name: Li
  given name: Chunjie
author list: Agent
  family name: White
  given name: James F.
author list: Agent
  family name: Johnson
  given name: Richard D.
doi: 10.7717/peerj.10568
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-07
copyright: ©2021 Zhou et al.
attribution name: Zhou et al.

Strategies for recovery of imbalanced full-scale biogas reactor feeding with palm oil mill effluent
type: item
type: AcademicArticle
description: Background Full-scale biogas production from palm oil mill effluent (POME) was inhibited by low pH and highly volatile fatty acid (VFA) accumulation. Three strategies were investigated for recovering the anaerobic digestion (AD) imbalance on biogas production, namely the dilution method (tap water vs. biogas effluent), pH adjustment method (NaOH, NaHCO3, Ca(OH)2, oil palm ash), and bioaugmentation (active methane-producing sludge) method. The highly economical and feasible method was selected and validated in a full-scale application. Results The inhibited sludge from a full-scale biogas reactor could be recovered within 30–36 days by employing various strategies. Dilution of the inhibited sludge with biogas effluent at a ratio of 8:2, pH adjustment with 0.14% w/v NaOH, and 8.0% w/v oil palm ash were considered to be more economically feasible than other strategies tested (dilution with tap water, or pH adjustment with 0.50% w/v Ca(OH)2, or 1.25% NaHCO3 and bioaugmentation) with a recovery time of 30–36 days. The recovered biogas reactor exhibited a 35–83% higher methane yield than self-recovery, with a significantly increased hydrolysis constant (kH) and specific methanogenic activity (SMA). The population of Clostridium sp., Bacillus sp., and Methanosarcina sp. increased in the recovered sludge. The imbalanced full-scale hybrid cover lagoon reactor was recovered within 15 days by dilution with biogas effluent at a ratio of 8:2 and a better result than the lab-scale test (36 days). Conclusion Dilution of the inhibited sludge with biogas effluent could recover the imbalance of the full-scale POME-biogas reactor with economically feasible and high biogas production performance.
format: application/pdf
format: text/html
creator: Nantharat Wongfaed
creator: Prawit Kongjan
creator: Wantanasak Suksong
creator: Poonsuk Prasertsan
creator: Sompong O-Thong
subject: Biotechnology
subject: Microbiology
subject: Freshwater Biology
subject: Natural Resource Management
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.10592
publisher: PeerJ Inc.
rights: © 2021 Wongfaed et al.
abstract: Background Full-scale biogas production from palm oil mill effluent (POME) was inhibited by low pH and highly volatile fatty acid (VFA) accumulation. Three strategies were investigated for recovering the anaerobic digestion (AD) imbalance on biogas production, namely the dilution method (tap water vs. biogas effluent), pH adjustment method (NaOH, NaHCO3, Ca(OH)2, oil palm ash), and bioaugmentation (active methane-producing sludge) method. The highly economical and feasible method was selected and validated in a full-scale application. Results The inhibited sludge from a full-scale biogas reactor could be recovered within 30–36 days by employing various strategies. Dilution of the inhibited sludge with biogas effluent at a ratio of 8:2, pH adjustment with 0.14% w/v NaOH, and 8.0% w/v oil palm ash were considered to be more economically feasible than other strategies tested (dilution with tap water, or pH adjustment with 0.50% w/v Ca(OH)2, or 1.25% NaHCO3 and bioaugmentation) with a recovery time of 30–36 days. The recovered biogas reactor exhibited a 35–83% higher methane yield than self-recovery, with a significantly increased hydrolysis constant (kH) and specific methanogenic activity (SMA). The population of Clostridium sp., Bacillus sp., and Methanosarcina sp. increased in the recovered sludge. The imbalanced full-scale hybrid cover lagoon reactor was recovered within 15 days by dilution with biogas effluent at a ratio of 8:2 and a better result than the lab-scale test (36 days). Conclusion Dilution of the inhibited sludge with biogas effluent could recover the imbalance of the full-scale POME-biogas reactor with economically feasible and high biogas production performance.
bibliographic citation: Wongfaed et al. (2021) Strategies for recovery of imbalanced full-scale biogas reactor feeding with palm oil mill effluent. PeerJ 9:e10592 https://doi.org/10.7717/peerj.10592
date submitted: 2019-10-29
date accepted: 2020-11-26
issued: 2021-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wongfaed
  given name: Nantharat
author list: Agent
  family name: Kongjan
  given name: Prawit
author list: Agent
  family name: Suksong
  given name: Wantanasak
author list: Agent
  family name: Prasertsan
  given name: Poonsuk
author list: Agent
  family name: O-Thong
  given name: Sompong
doi: 10.7717/peerj.10592
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-07
copyright: ©2021 Wongfaed et al.
attribution name: Wongfaed et al.

Reversine, a selective MPS1 inhibitor, induced autophagic cell death via diminished glucose uptake and ATP production in cholangiocarcinoma cells
type: item
type: AcademicArticle
description: Reversine is a selective inhibitor of mitotic kinase monopolar spindle 1 (MPS1) and has been reported as an anticancer agent in various cancers. The effects of reversine on bile duct cancer, cholangiocarcinoma (CCA), a lethal cancer in Northeastern Thailand, were investigated. This study reports that reversine inhibited cell proliferation of CCA cell lines in dose- and time-dependent manners but had less inhibitory effect on an immortalized cholangiocyte cell line. Reversine also triggered apoptotic cell death by decreasing anti-apoptotic proteins, Bcl-XL and Mcl-1, increasing Bax pro-apoptotic protein and activating caspase-3 activity. Moreover, reversine induced autophagic cell death by increasing LC3-II and Beclin 1 while decreasing p62. Reversine activated autophagy via the AKT signaling pathway. Additionally, this study demonstrated for the first time that reversine could diminish the expression of Hypoxia-Inducible Factor 1- alpha (HIF-1α) and glucose transporter 1 (GLUT1), resulting in a reduction of glucose uptake and energy production in CCA cell lines. These findings suggest that reversine could be a good candidate as an alternative or supplementary drug for CCA treatment.
format: application/pdf
format: text/html
creator: Piya Prajumwongs
creator: Orawan Waenphimai
creator: Kulthida Vaeteewoottacharn
creator: Sopit Wongkham
creator: Kanlayanee Sawanyawisuth
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.10637
publisher: PeerJ Inc.
rights: © 2021 Prajumwongs et al.
abstract: Reversine is a selective inhibitor of mitotic kinase monopolar spindle 1 (MPS1) and has been reported as an anticancer agent in various cancers. The effects of reversine on bile duct cancer, cholangiocarcinoma (CCA), a lethal cancer in Northeastern Thailand, were investigated. This study reports that reversine inhibited cell proliferation of CCA cell lines in dose- and time-dependent manners but had less inhibitory effect on an immortalized cholangiocyte cell line. Reversine also triggered apoptotic cell death by decreasing anti-apoptotic proteins, Bcl-XL and Mcl-1, increasing Bax pro-apoptotic protein and activating caspase-3 activity. Moreover, reversine induced autophagic cell death by increasing LC3-II and Beclin 1 while decreasing p62. Reversine activated autophagy via the AKT signaling pathway. Additionally, this study demonstrated for the first time that reversine could diminish the expression of Hypoxia-Inducible Factor 1- alpha (HIF-1α) and glucose transporter 1 (GLUT1), resulting in a reduction of glucose uptake and energy production in CCA cell lines. These findings suggest that reversine could be a good candidate as an alternative or supplementary drug for CCA treatment.
bibliographic citation: Prajumwongs et al. (2021) Reversine, a selective MPS1 inhibitor, induced autophagic cell death via diminished glucose uptake and ATP production in cholangiocarcinoma cells. PeerJ 9:e10637 https://doi.org/10.7717/peerj.10637
date submitted: 2020-06-08
date accepted: 2020-12-02
issued: 2021-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prajumwongs
  given name: Piya
author list: Agent
  family name: Waenphimai
  given name: Orawan
author list: Agent
  family name: Vaeteewoottacharn
  given name: Kulthida
author list: Agent
  family name: Wongkham
  given name: Sopit
author list: Agent
  family name: Sawanyawisuth
  given name: Kanlayanee
doi: 10.7717/peerj.10637
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-07
copyright: ©2021 Prajumwongs et al.
attribution name: Prajumwongs et al.

Differential relieving effects of shikonin and its derivatives on inflammation and mucosal barrier damage caused by ulcerative colitis
type: item
type: AcademicArticle
description: Background Ulcerative colitis (UC) is one of the most challenging human diseases. Natural shikonin (SK) and its derivatives (with have higher accumulation) isolated from the root of Lithospermum erythrorhizon have numerous beneficial effects, such as wound healing and anti-inflammatory activities. Some researchers have reported that hydroxynaphthoquinone mixture (HM) and SK attenuate the acute UC induced by dextran sulfate sodium (DSS). However, no existing study has systemically investigated the effectiveness of SK and other hydroxynaphthoquinone natural derivative monomers on UC. Methods In this study, mice were treated with SK and its derivatives (25 mg/kg) and mesalazine (200 mg/kg) after DSS administration daily for one week. Disease progression was monitored daily by observing the changes in clinical signs and body weight. Results Intragastric administration natural single naphthoquinone attenuated the malignant symptoms induced by DSS. SK or its derivatives remarkably suppressed the serum levels of pro-inflammatory cytokines while increasing the inflammatory cytokine interleukin (IL)-10 . Additionally, both SK and alkanin restrained the activities of cyclooxygenase-2 (COX-2), myeloperoxidase (MPO) and inducible nitric oxide synthase (iNOS) in serum and colonic tissues. SK and its derivatives inhibited the activation of nucleotide binding oligomerization domain-like receptors (NLRP3) inflammasome and NF-κB signaling pathway, thereby relieving the DSS-induced disruption of epithelial tight junction (TJ) in colonic tissues. Conclusions Our findings shed more lights on the pharmacological efficacy of SK and its derivatives in UC against inflammation and mucosal barrier damage.
format: application/pdf
format: text/html
creator: Hongwei Han
creator: Wenxue Sun
creator: Lu Feng
creator: Zhongling Wen
creator: Minkai Yang
creator: Yingying Ma
creator: Jiangyan Fu
creator: Xiaopeng Ma
creator: Xinhong Xu
creator: Zhaoyue Wang
creator: Tongming Yin
creator: Xiao-Ming Wang
creator: Gui-Hua Lu
creator: Jin-Liang Qi
creator: Hongyan Lin
creator: Yonghua Yang
subject: Drugs and Devices
subject: Gastroenterology and Hepatology
subject: Immunology
description: doi:10.7717/peerj.10675
publisher: PeerJ Inc.
rights: © 2021 Han et al.
abstract: Background Ulcerative colitis (UC) is one of the most challenging human diseases. Natural shikonin (SK) and its derivatives (with have higher accumulation) isolated from the root of Lithospermum erythrorhizon have numerous beneficial effects, such as wound healing and anti-inflammatory activities. Some researchers have reported that hydroxynaphthoquinone mixture (HM) and SK attenuate the acute UC induced by dextran sulfate sodium (DSS). However, no existing study has systemically investigated the effectiveness of SK and other hydroxynaphthoquinone natural derivative monomers on UC. Methods In this study, mice were treated with SK and its derivatives (25 mg/kg) and mesalazine (200 mg/kg) after DSS administration daily for one week. Disease progression was monitored daily by observing the changes in clinical signs and body weight. Results Intragastric administration natural single naphthoquinone attenuated the malignant symptoms induced by DSS. SK or its derivatives remarkably suppressed the serum levels of pro-inflammatory cytokines while increasing the inflammatory cytokine interleukin (IL)-10 . Additionally, both SK and alkanin restrained the activities of cyclooxygenase-2 (COX-2), myeloperoxidase (MPO) and inducible nitric oxide synthase (iNOS) in serum and colonic tissues. SK and its derivatives inhibited the activation of nucleotide binding oligomerization domain-like receptors (NLRP3) inflammasome and NF-κB signaling pathway, thereby relieving the DSS-induced disruption of epithelial tight junction (TJ) in colonic tissues. Conclusions Our findings shed more lights on the pharmacological efficacy of SK and its derivatives in UC against inflammation and mucosal barrier damage.
bibliographic citation: Han et al. (2021) Differential relieving effects of shikonin and its derivatives on inflammation and mucosal barrier damage caused by ulcerative colitis. PeerJ 9:e10675 https://doi.org/10.7717/peerj.10675
date submitted: 2020-08-13
date accepted: 2020-12-09
issued: 2021-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Hongwei
author list: Agent
  family name: Sun
  given name: Wenxue
author list: Agent
  family name: Feng
  given name: Lu
author list: Agent
  family name: Wen
  given name: Zhongling
author list: Agent
  family name: Yang
  given name: Minkai
author list: Agent
  family name: Ma
  given name: Yingying
author list: Agent
  family name: Fu
  given name: Jiangyan
author list: Agent
  family name: Ma
  given name: Xiaopeng
author list: Agent
  family name: Xu
  given name: Xinhong
author list: Agent
  family name: Wang
  given name: Zhaoyue
author list: Agent
  family name: Yin
  given name: Tongming
author list: Agent
  family name: Wang
  given name: Xiao-Ming
author list: Agent
  family name: Lu
  given name: Gui-Hua
author list: Agent
  family name: Qi
  given name: Jin-Liang
author list: Agent
  family name: Lin
  given name: Hongyan
author list: Agent
  family name: Yang
  given name: Yonghua
doi: 10.7717/peerj.10675
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-07
copyright: ©2021 Han et al.
attribution name: Han et al.

Reproducing country-wide COVID-19 dynamics can require the usage of a set of SIR systems
type: item
type: AcademicArticle
description: This work shows that simple compartmental epidemiological models may not reproduce actually reported country-wide statistics since the latter reflects the cumulative amount of infected persons, which in fact is a sum of outbreaks within different patched. It the same time, the multilogistic decomposition of such epidemiological curves reveals components, which are quite close to the solutions of the SIR model in logistic approximations characterised by different sets of parameters including time shifts. This line of reasoning is confirmed by processing data for Spain and Russia in details and, additionally, is illustrated for several other countries.
format: application/pdf
format: text/html
creator: Eugene B. Postnikov
subject: Mathematical Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.10679
publisher: PeerJ Inc.
rights: © 2021 Postnikov
abstract: This work shows that simple compartmental epidemiological models may not reproduce actually reported country-wide statistics since the latter reflects the cumulative amount of infected persons, which in fact is a sum of outbreaks within different patched. It the same time, the multilogistic decomposition of such epidemiological curves reveals components, which are quite close to the solutions of the SIR model in logistic approximations characterised by different sets of parameters including time shifts. This line of reasoning is confirmed by processing data for Spain and Russia in details and, additionally, is illustrated for several other countries.
bibliographic citation: Postnikov (2021) Reproducing country-wide COVID-19 dynamics can require the usage of a set of SIR systems. PeerJ 9:e10679 https://doi.org/10.7717/peerj.10679
date submitted: 2020-05-30
date accepted: 2020-12-09
issued: 2021-01-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Postnikov
  given name: Eugene B.
doi: 10.7717/peerj.10679
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-07
copyright: © 2021 Postnikov
attribution name: Postnikov

Biochemical characterization and inhibition of thermolabile hemolysin from Vibrio parahaemolyticus by phenolic compounds
type: item
type: AcademicArticle
description: Vibrio parahaemolyticus (Vp), a typical microorganism inhabiting marine ecosystems, uses pathogenic virulence molecules such as hemolysins to cause bacterial infections of both human and marine animals. The thermolabile hemolysin VpTLH lyses human erythrocytes by a phospholipase B/A2 enzymatic activity in egg-yolk lecithin. However, few studies have been characterized the biochemical properties and the use of VpTLH as a molecular target for natural compounds as an alternative to control Vp infection. Here, we evaluated the biochemical and inhibition parameters of the recombinant VpTLH using enzymatic and hemolytic assays and determined the molecular interactions by in silico docking analysis. The highest enzymatic activity was at pH 8 and 50 °C, and it was inactivated by 20 min at 60 °C with Tm = 50.9 °C. Additionally, the flavonoids quercetin, epigallocatechin gallate, and morin inhibited the VpTLH activity with IC50 values of 4.5 µM, 6.3 µM, and 9.9 µM, respectively; while phenolics acids were not effective inhibitors for this enzyme. Boltzmann and Arrhenius equation analysis indicate that VpTLH is a thermolabile enzyme. The inhibition of both enzymatic and hemolytic activities by flavonoids agrees with molecular docking, suggesting that flavonoids could interact with the active site’s amino acids. Future research is necessary to evaluate the antibacterial activity of flavonoids against Vp in vivo.
format: application/pdf
format: text/html
creator: Luis E. Vazquez-Morado
creator: Ramon E. Robles-Zepeda
creator: Adrian Ochoa-Leyva
creator: Aldo A. Arvizu-Flores
creator: Adriana Garibay-Escobar
creator: Francisco Castillo-Yañez
creator: Alonso A. Lopez-zavala
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Bioinformatics
subject: Biotechnology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.10506
publisher: PeerJ Inc.
rights: © 2021 Vazquez-Morado et al.
abstract: Vibrio parahaemolyticus (Vp), a typical microorganism inhabiting marine ecosystems, uses pathogenic virulence molecules such as hemolysins to cause bacterial infections of both human and marine animals. The thermolabile hemolysin VpTLH lyses human erythrocytes by a phospholipase B/A2 enzymatic activity in egg-yolk lecithin. However, few studies have been characterized the biochemical properties and the use of VpTLH as a molecular target for natural compounds as an alternative to control Vp infection. Here, we evaluated the biochemical and inhibition parameters of the recombinant VpTLH using enzymatic and hemolytic assays and determined the molecular interactions by in silico docking analysis. The highest enzymatic activity was at pH 8 and 50 °C, and it was inactivated by 20 min at 60 °C with Tm = 50.9 °C. Additionally, the flavonoids quercetin, epigallocatechin gallate, and morin inhibited the VpTLH activity with IC50 values of 4.5 µM, 6.3 µM, and 9.9 µM, respectively; while phenolics acids were not effective inhibitors for this enzyme. Boltzmann and Arrhenius equation analysis indicate that VpTLH is a thermolabile enzyme. The inhibition of both enzymatic and hemolytic activities by flavonoids agrees with molecular docking, suggesting that flavonoids could interact with the active site’s amino acids. Future research is necessary to evaluate the antibacterial activity of flavonoids against Vp in vivo.
bibliographic citation: Vazquez-Morado et al. (2021) Biochemical characterization and inhibition of thermolabile hemolysin from Vibrio parahaemolyticus by phenolic compounds. PeerJ 9:e10506 https://doi.org/10.7717/peerj.10506
date submitted: 2020-09-21
date accepted: 2020-11-16
issued: 2021-01-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vazquez-Morado
  given name: Luis E.
author list: Agent
  family name: Robles-Zepeda
  given name: Ramon E.
author list: Agent
  family name: Ochoa-Leyva
  given name: Adrian
author list: Agent
  family name: Arvizu-Flores
  given name: Aldo A.
author list: Agent
  family name: Garibay-Escobar
  given name: Adriana
author list: Agent
  family name: Castillo-Yañez
  given name: Francisco
author list: Agent
  family name: Lopez-zavala
  given name: Alonso A.
doi: 10.7717/peerj.10506
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-06
copyright: ©2021 Vazquez-Morado et al.
attribution name: Vazquez-Morado et al.

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