PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Assessment of the efficacy of using taurine supplements to improve growth and feed utilization of juvenile starry flounder (Platichthys stellatus) given diets based on soy-protein
items: Associations between self-reported and objective face recognition abilities are only evident in above- and below-average recognisers
items: The 2020 elephant die-off in Botswana
items: Silk derived formulations for accelerated wound healing in diabetic mice
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

Assessment of the efficacy of using taurine supplements to improve growth and feed utilization of juvenile starry flounder (Platichthys stellatus) given diets based on soy-protein
type: item
type: AcademicArticle
description: A feeding trial was conducted to assess the feasibility of supplementing taurine in soy-based diets for juvenile starry flounder Platichthys stellatus. The basal diet (Crude protein 66.5%, crude lipid 8.5%) was supplemented with 0 (control), 0.5%, 1.0%, 1.5%, 2.0% and 2.5% taurine to formulate six test diets. Each diet was fed to 40 juvenile fish (22.25 g) in triplicate tanks (120 L) attached to a sea water circulation-system. Fish were fed twice daily by hand to apparent satiation during the 56-d trial. At the end of the trial, fish were counted and weighed for the analyses of growth performance, diet utilization and survival after a 24-h fast. Blood, intestines and muscles were collected for the analyses of serum oxidation resistance, digestive enzymes and body compostion. Livers were collected from the remaining fish at 4 h post-feeding for metabolic enzymes analyses. The results showed that fish fed diets supplemented with 1.0–2.5% taurine grew from 22.25–22.26 g to 47.88–50.40 g with higher average weight gain (25.62–28.12 vs 23.07 g ), specific growth rate (1.37–1.46 vs 1.27%/d ), feed intake (1.04–1.06 vs 1.00%/d), protein efficiency (2.50–2.61 vs 2.44) and lower feed conversion rate (0.84–0.83 vs 0.89) than the control treatment. Diets supplemented with 1.5–2.5% taurine significantly elevated the activities of pepsin (2.47–2.55 vs 2.22, U mg−1 prot), trypsin of distal intestine(14.55–15.24 vs 11.94, U mg−1 prot), hepatic glucokinase (126.62–129.42 vs 105.56, U mg−1 prot) and fatty acid synthetase (125.56-136.89 vs 108.45, U mg−1 prot). All diets supplemented with taurine increased the activities of lipase (32.23–36.67 vs 29.53, U g−1 prot) and trypsin (35.85–37.89 vs 33.54, U mg−1 prot) of proximal intestine, hepatic aspartate transaminase (736.990–832.38 vs 699.24, U mg−1 prot), alanine aminotransferase (477.40–551.86 vs 373.97, U mg−1 prot) and glycogen synthase (2.16–2.59 vs 1.97, U mg−1 prot), as well as serum superoxide dismutase (4.33–4.59 vs 4.07, U m…
format: application/pdf
format: text/html
creator: Peiyu Li
creator: Hongyi Bu
creator: Baoshan Li
creator: Yongzhi Sun
creator: Meiqi Wang
creator: Zhidong Song
subject: Aquaculture, Fisheries and Fish Science
subject: Zoology
description: doi:10.7717/peerj.10597
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: A feeding trial was conducted to assess the feasibility of supplementing taurine in soy-based diets for juvenile starry flounder Platichthys stellatus. The basal diet (Crude protein 66.5%, crude lipid 8.5%) was supplemented with 0 (control), 0.5%, 1.0%, 1.5%, 2.0% and 2.5% taurine to formulate six test diets. Each diet was fed to 40 juvenile fish (22.25 g) in triplicate tanks (120 L) attached to a sea water circulation-system. Fish were fed twice daily by hand to apparent satiation during the 56-d trial. At the end of the trial, fish were counted and weighed for the analyses of growth performance, diet utilization and survival after a 24-h fast. Blood, intestines and muscles were collected for the analyses of serum oxidation resistance, digestive enzymes and body compostion. Livers were collected from the remaining fish at 4 h post-feeding for metabolic enzymes analyses. The results showed that fish fed diets supplemented with 1.0–2.5% taurine grew from 22.25–22.26 g to 47.88–50.40 g with higher average weight gain (25.62–28.12 vs 23.07 g ), specific growth rate (1.37–1.46 vs 1.27%/d ), feed intake (1.04–1.06 vs 1.00%/d), protein efficiency (2.50–2.61 vs 2.44) and lower feed conversion rate (0.84–0.83 vs 0.89) than the control treatment. Diets supplemented with 1.5–2.5% taurine significantly elevated the activities of pepsin (2.47–2.55 vs 2.22, U mg−1 prot), trypsin of distal intestine(14.55–15.24 vs 11.94, U mg−1 prot), hepatic glucokinase (126.62–129.42 vs 105.56, U mg−1 prot) and fatty acid synthetase (125.56-136.89 vs 108.45, U mg−1 prot). All diets supplemented with taurine increased the activities of lipase (32.23–36.67 vs 29.53, U g−1 prot) and trypsin (35.85–37.89 vs 33.54, U mg−1 prot) of proximal intestine, hepatic aspartate transaminase (736.990–832.38 vs 699.24, U mg−1 prot), alanine aminotransferase (477.40–551.86 vs 373.97, U mg−1 prot) and glycogen synthase (2.16–2.59 vs 1.97, U mg−1 prot), as well as serum superoxide dismutase (4.33–4.59 vs 4.07, U m…
bibliographic citation: Li et al. (2021) Assessment of the efficacy of using taurine supplements to improve growth and feed utilization of juvenile starry flounder (Platichthys stellatus) given diets based on soy-protein. PeerJ 9:e10597 https://doi.org/10.7717/peerj.10597
date submitted: 2020-07-24
date accepted: 2020-11-26
issued: 2021-01-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Peiyu
author list: Agent
  family name: Bu
  given name: Hongyi
author list: Agent
  family name: Li
  given name: Baoshan
author list: Agent
  family name: Sun
  given name: Yongzhi
author list: Agent
  family name: Wang
  given name: Meiqi
author list: Agent
  family name: Song
  given name: Zhidong
doi: 10.7717/peerj.10597
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-11
copyright: ©2021 Li et al.
attribution name: Li et al.

Associations between self-reported and objective face recognition abilities are only evident in above- and below-average recognisers
type: item
type: AcademicArticle
description: The 20-Item Prosopagnosia Items (PI-20) was recently introduced as a self-report measure of face recognition abilities and as an instrument to help the diagnosis of prosopagnosia. In general, studies using this questionnaire have shown that observers have moderate to strong insights into their face recognition abilities. However, it remains unknown whether these insights are equivalent for the whole range of face recognition abilities. The present study investigates this issue using the Mandarin version of the PI-20 and the Cambridge Face Memory Test Chinese (CFMT-Chinese). Our results showed a moderate negative association between the PI-20 and the CFMT-Chinese. However, this association was driven by people with low and high face recognition ability, but absent in people within the typical range of face recognition performance. The implications of these results for the study of individual differences and the diagnosis of prosopagnosia are discussed.
format: application/pdf
format: text/html
creator: Alejandro J. Estudillo
creator: Hoo Keat Wong
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.10629
publisher: PeerJ Inc.
rights: © 2021 Estudillo and Wong
abstract: The 20-Item Prosopagnosia Items (PI-20) was recently introduced as a self-report measure of face recognition abilities and as an instrument to help the diagnosis of prosopagnosia. In general, studies using this questionnaire have shown that observers have moderate to strong insights into their face recognition abilities. However, it remains unknown whether these insights are equivalent for the whole range of face recognition abilities. The present study investigates this issue using the Mandarin version of the PI-20 and the Cambridge Face Memory Test Chinese (CFMT-Chinese). Our results showed a moderate negative association between the PI-20 and the CFMT-Chinese. However, this association was driven by people with low and high face recognition ability, but absent in people within the typical range of face recognition performance. The implications of these results for the study of individual differences and the diagnosis of prosopagnosia are discussed.
bibliographic citation: Estudillo et al. (2021) Associations between self-reported and objective face recognition abilities are only evident in above- and below-average recognisers. PeerJ 9:e10629 https://doi.org/10.7717/peerj.10629
date submitted: 2020-06-09
date accepted: 2020-12-01
issued: 2021-01-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Estudillo
  given name: Alejandro J.
author list: Agent
  family name: Wong
  given name: Hoo Keat
doi: 10.7717/peerj.10629
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-11
copyright: © 2021 Estudillo and Wong
attribution name: Estudillo and Wong

The 2020 elephant die-off in Botswana
type: item
type: AcademicArticle
description: The cause of deaths of 350 elephants in 2020 in a relatively small unprotected area of northern Botswana is unknown, and may never be known. Media speculations about it ignore ecological realities. Worse, they make conjectures that can be detrimental to wildlife and sometimes discredit conservation incentives. A broader understanding of the ecological and conservation issues speaks to elephant management across the Kavango–Zambezi Transfrontier Conservation Area that extends across Botswana, Namibia, Angola, Zambia, and Zimbabwe. Our communication addresses these. Malicious poisoning and poaching are unlikely to have played a role. Other species were unaffected, and elephant carcases had their tusks intact. Restriction of freshwater supplies that force elephants to use pans as a water source possibly polluted by blue-green algae blooms is a possible cause, but as yet not supported by evidence. No other species were involved. A contagious disease is the more probable one. Fences and a deep channel of water confine these elephants’ dispersal. These factors explain the elephants’ relatively high population growth rate despite a spell of increased poaching during 2014–2018. While the deaths represent only ~2% of the area’s elephants, the additive effects of poaching and stress induced by people protecting their crops cause alarm. Confinement and relatively high densities probably explain why the die-off occurred only here. It suggests a re-alignment or removal of fences that restrict elephant movements and limits year-round access to freshwater.
format: application/pdf
format: text/html
creator: Rudi J. van Aarde
creator: Stuart L. Pimm
creator: Robert Guldemond
creator: Ryan Huang
creator: Celesté Maré
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.10686
publisher: PeerJ Inc.
rights: © 2021 van Aarde et al.
abstract: The cause of deaths of 350 elephants in 2020 in a relatively small unprotected area of northern Botswana is unknown, and may never be known. Media speculations about it ignore ecological realities. Worse, they make conjectures that can be detrimental to wildlife and sometimes discredit conservation incentives. A broader understanding of the ecological and conservation issues speaks to elephant management across the Kavango–Zambezi Transfrontier Conservation Area that extends across Botswana, Namibia, Angola, Zambia, and Zimbabwe. Our communication addresses these. Malicious poisoning and poaching are unlikely to have played a role. Other species were unaffected, and elephant carcases had their tusks intact. Restriction of freshwater supplies that force elephants to use pans as a water source possibly polluted by blue-green algae blooms is a possible cause, but as yet not supported by evidence. No other species were involved. A contagious disease is the more probable one. Fences and a deep channel of water confine these elephants’ dispersal. These factors explain the elephants’ relatively high population growth rate despite a spell of increased poaching during 2014–2018. While the deaths represent only ~2% of the area’s elephants, the additive effects of poaching and stress induced by people protecting their crops cause alarm. Confinement and relatively high densities probably explain why the die-off occurred only here. It suggests a re-alignment or removal of fences that restrict elephant movements and limits year-round access to freshwater.
bibliographic citation: van Aarde et al. (2021) The 2020 elephant die-off in Botswana. PeerJ 9:e10686 https://doi.org/10.7717/peerj.10686
date submitted: 2020-11-04
date accepted: 2020-12-11
issued: 2021-01-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van Aarde
  given name: Rudi J.
author list: Agent
  family name: Pimm
  given name: Stuart L.
author list: Agent
  family name: Guldemond
  given name: Robert
author list: Agent
  family name: Huang
  given name: Ryan
author list: Agent
  family name: Maré
  given name: Celesté
doi: 10.7717/peerj.10686
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-11
copyright: © 2021 van Aarde et al.
attribution name: van Aarde et al.

Silk derived formulations for accelerated wound healing in diabetic mice
type: item
type: AcademicArticle
description: Background The present study aimed to prepare effective silk derived formulations in combination with plant extract (Aloe vera gel) to speed up the wound healing process in diabetic mice. Methods Diabetes was induced in albino mice by using alloxan monohydrate. After successful induction of diabetes in mice, excision wounds were created via biopsy puncture (6 mm). Wound healing effect of silk sericin (5%) and silk fibroin (5%) individually and in combination with 5% Aloe vera gel was evaluated by determining the percent wound contraction, healing time and histological analysis. Results The results indicated that the best biocompatible silk combination was of 5% silk fibroin and 5% Aloe vera gel in which wounds were healed in 13 days with wound contraction: 98.33 ± 0.80%. In contrast, the wound of the control group (polyfax) healed in 19 day shaving 98.5 ± 0.67% contraction. Histological analysis revealed that the wounds which were treated with silk formulations exhibited an increased growth of blood vessels, collagen fibers, and much reduced inflammation. Conclusion It can be concluded that a combination of Bombyx mori silk and Aloe vera gel is a natural biomaterial that can be utilized in wound dressings and to prepare more innovative silk based formulations for speedy recovery of chronic wounds.
format: application/pdf
format: text/html
creator: Muniba Tariq
creator: Hafiz Muhammad Tahir
creator: Samima Asad Butt
creator: Shaukat Ali
creator: Asma Bashir Ahmad
creator: Chand Raza
creator: Muhammad Summer
creator: Ali Hassan
creator: Junaid Nadeem
subject: Entomology
subject: Zoology
subject: Dermatology
subject: Diabetes and Endocrinology
subject: Drugs and Devices
description: doi:10.7717/peerj.10232
publisher: PeerJ Inc.
rights: © 2021 Tariq et al.
abstract: Background The present study aimed to prepare effective silk derived formulations in combination with plant extract (Aloe vera gel) to speed up the wound healing process in diabetic mice. Methods Diabetes was induced in albino mice by using alloxan monohydrate. After successful induction of diabetes in mice, excision wounds were created via biopsy puncture (6 mm). Wound healing effect of silk sericin (5%) and silk fibroin (5%) individually and in combination with 5% Aloe vera gel was evaluated by determining the percent wound contraction, healing time and histological analysis. Results The results indicated that the best biocompatible silk combination was of 5% silk fibroin and 5% Aloe vera gel in which wounds were healed in 13 days with wound contraction: 98.33 ± 0.80%. In contrast, the wound of the control group (polyfax) healed in 19 day shaving 98.5 ± 0.67% contraction. Histological analysis revealed that the wounds which were treated with silk formulations exhibited an increased growth of blood vessels, collagen fibers, and much reduced inflammation. Conclusion It can be concluded that a combination of Bombyx mori silk and Aloe vera gel is a natural biomaterial that can be utilized in wound dressings and to prepare more innovative silk based formulations for speedy recovery of chronic wounds.
bibliographic citation: Tariq et al. (2021) Silk derived formulations for accelerated wound healing in diabetic mice. PeerJ 9:e10232 https://doi.org/10.7717/peerj.10232
date submitted: 2020-04-23
date accepted: 2020-10-02
issued: 2021-01-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tariq
  given name: Muniba
author list: Agent
  family name: Tahir
  given name: Hafiz Muhammad
author list: Agent
  family name: Butt
  given name: Samima Asad
author list: Agent
  family name: Ali
  given name: Shaukat
author list: Agent
  family name: Ahmad
  given name: Asma Bashir
author list: Agent
  family name: Raza
  given name: Chand
author list: Agent
  family name: Summer
  given name: Muhammad
author list: Agent
  family name: Hassan
  given name: Ali
author list: Agent
  family name: Nadeem
  given name: Junaid
doi: 10.7717/peerj.10232
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-08
copyright: © 2021 Tariq et al.
attribution name: Tariq et al.

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
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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.

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