PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The association between non-suicidal self-injury and negative life events in children and adolescents in underdeveloped regions of south-western China
items: Three new species of Microlaimus (Nematoda: Microlaimidae) from the South Atlantic
items: Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii
items: Analysis of the role and mechanism of EGCG in septic cardiomyopathy based on network pharmacology
items: Optimizing seawater temperature conditions to increase the productivity of ex situ coral nurseries
items: Perfluoroalkyl acids in sediment and water surrounding historical fire training areas at Barksdale Air Force Base
items: Expression of connexin-43 in surgical resections of primary tumor and lymph node metastases of squamous cell carcinoma and adenocarcinoma of the lung: a retrospective study
items: Environmental enrichment changes rabbits’ behavior, serum hormone level and further affects cecal microbiota
items: Long-term consumption of artificial sweeteners does not affect cardiovascular health and survival in rats
items: Full-length transcriptome analysis of Adiantum flabellulatum gametophyte

The association between non-suicidal self-injury and negative life events in children and adolescents in underdeveloped regions of south-western China
type: item
type: AcademicArticle
description: Background The association between negative life events and Non-suicidal self-injury (NSSI) in children and adolescents has been extensively discussed. Nevertheless, little is known about the relationship between negative life events and repetition and severity of NSSI. This survey aims to understand the association between NSSI prevalence, severity, repetition and the negative life events in children and adolescents in underdeveloped regions in south-western China. Methods In this population-based cross-sectional study, 3,146 children and adolescents were included from underdeveloped regions of south-western China, and each of them requested to complete a self-assessment questionnaire. The Modified Version of Adolescents Self-Harm Scale (MASHS) and the Adolescent Self-rating negative Life Events Check-list were used to evaluate NSSI behaviors and negative life events, respectively. The statistical implementation of this study was carried out in the R statistical software, and the logistic regression analysis method was used to analyze the relationship between negative life events and adolescents’ non-suicidal self-injury behaviors. Results The average age of all included participants was 13.31 years old. The lifetime prevalence of NSSI was 47.0% (95% CI [36.3–58.0%]). Gender, grade level and ASLEC was positively associated with NSSI. Further analysis revealed that, for all five dimensions of ASLEC, only interpersonal relationship factor (IRF) (OR 1.77 (95% CI [1.06–2.97])), health adaptation factor (HAF) (OR 2.08 (95% CI [1.31–3.31])) showed prominent association with NSSI. Multivariate Logistic regression models revealed that, repetitive NSSI (OR 4.54 (95% CI [3.66–5.63])) and NSSI severity (OR 9.01 (95% CI [6.11–13.29])) were positively associated with ASLEC. Conclusion NSSI is very common among children and adolescents in underdeveloped regions of south-western China. Negative life event are positively associated with NSSI, repeated NSSI, and severe NSSI. Negati…
format: application/pdf
format: text/html
creator: Fan Yang
creator: Linling Jiang
creator: Jing Miao
creator: Xiufeng Xu
creator: Hailiang Ran
creator: Yusan Che
creator: Die Fang
creator: TianLan Wang
creator: Yuanyuan Xiao
creator: Jin Lu
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.12665
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Background The association between negative life events and Non-suicidal self-injury (NSSI) in children and adolescents has been extensively discussed. Nevertheless, little is known about the relationship between negative life events and repetition and severity of NSSI. This survey aims to understand the association between NSSI prevalence, severity, repetition and the negative life events in children and adolescents in underdeveloped regions in south-western China. Methods In this population-based cross-sectional study, 3,146 children and adolescents were included from underdeveloped regions of south-western China, and each of them requested to complete a self-assessment questionnaire. The Modified Version of Adolescents Self-Harm Scale (MASHS) and the Adolescent Self-rating negative Life Events Check-list were used to evaluate NSSI behaviors and negative life events, respectively. The statistical implementation of this study was carried out in the R statistical software, and the logistic regression analysis method was used to analyze the relationship between negative life events and adolescents’ non-suicidal self-injury behaviors. Results The average age of all included participants was 13.31 years old. The lifetime prevalence of NSSI was 47.0% (95% CI [36.3–58.0%]). Gender, grade level and ASLEC was positively associated with NSSI. Further analysis revealed that, for all five dimensions of ASLEC, only interpersonal relationship factor (IRF) (OR 1.77 (95% CI [1.06–2.97])), health adaptation factor (HAF) (OR 2.08 (95% CI [1.31–3.31])) showed prominent association with NSSI. Multivariate Logistic regression models revealed that, repetitive NSSI (OR 4.54 (95% CI [3.66–5.63])) and NSSI severity (OR 9.01 (95% CI [6.11–13.29])) were positively associated with ASLEC. Conclusion NSSI is very common among children and adolescents in underdeveloped regions of south-western China. Negative life event are positively associated with NSSI, repeated NSSI, and severe NSSI. Negati…
bibliographic citation: Yang et al. (2022) The association between non-suicidal self-injury and negative life events in children and adolescents in underdeveloped regions of south-western China. PeerJ 10:e12665 https://doi.org/10.7717/peerj.12665
date submitted: 2021-08-02
date accepted: 2021-11-30
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Fan
author list: Agent
  family name: Jiang
  given name: Linling
author list: Agent
  family name: Miao
  given name: Jing
author list: Agent
  family name: Xu
  given name: Xiufeng
author list: Agent
  family name: Ran
  given name: Hailiang
author list: Agent
  family name: Che
  given name: Yusan
author list: Agent
  family name: Fang
  given name: Die
author list: Agent
  family name: Wang
  given name: TianLan
author list: Agent
  family name: Xiao
  given name: Yuanyuan
author list: Agent
  family name: Lu
  given name: Jin
doi: 10.7717/peerj.12665
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: © 2022 Yang et al.
attribution name: Yang et al.

Three new species of Microlaimus (Nematoda: Microlaimidae) from the South Atlantic
type: item
type: AcademicArticle
description: Three new species of Microlaimus are described from the continental shelf of the Campos Basin, southwest Atlantic, Brazil. Microlaimus campiensis sp. n. differs from all other species in the presence of two anterior testes, slender spicules with enlarged proximal ends, 7–11 pre-cloacal papilliform supplements, and females with a pair of constriction structures, one on each branch of the ovary. Microlaimus alexandri sp. n. shows sexual dimorphism in the size of the amphidial fovea, which occupies 100% of the diameter of the corresponding area in the male; the buccal cavity provided with five teeth and a slightly cuticularized cuticular ring. Microlaimus vitorius sp. n. has four longitudinal-lateral rows of glands associated with small pores, one seta and three pores small pre-cloacal, and the gubernaculum has a triangular base. An amendment to the diagnosis of the genus is proposed, where the number of teeth was modified.
format: application/pdf
format: text/html
creator: Rita C. Lima
creator: Patrícia F. Neres
creator: André M. Esteves
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12734
publisher: PeerJ Inc.
rights: © 2022 Lima et al.
abstract: Three new species of Microlaimus are described from the continental shelf of the Campos Basin, southwest Atlantic, Brazil. Microlaimus campiensis sp. n. differs from all other species in the presence of two anterior testes, slender spicules with enlarged proximal ends, 7–11 pre-cloacal papilliform supplements, and females with a pair of constriction structures, one on each branch of the ovary. Microlaimus alexandri sp. n. shows sexual dimorphism in the size of the amphidial fovea, which occupies 100% of the diameter of the corresponding area in the male; the buccal cavity provided with five teeth and a slightly cuticularized cuticular ring. Microlaimus vitorius sp. n. has four longitudinal-lateral rows of glands associated with small pores, one seta and three pores small pre-cloacal, and the gubernaculum has a triangular base. An amendment to the diagnosis of the genus is proposed, where the number of teeth was modified.
bibliographic citation: Lima et al. (2022) Three new species of Microlaimus (Nematoda: Microlaimidae) from the South Atlantic. PeerJ 10:e12734 https://doi.org/10.7717/peerj.12734
date submitted: 2020-10-19
date accepted: 2021-12-12
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lima
  given name: Rita C.
author list: Agent
  family name: Neres
  given name: Patrícia F.
author list: Agent
  family name: Esteves
  given name: André M.
doi: 10.7717/peerj.12734
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: © 2022 Lima et al.
attribution name: Lima et al.

Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii
type: item
type: AcademicArticle
description: Background Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology. Methods We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore Beroe ovata using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species. Results The protist belongs to the genus Thraustochytrium based on the 18S rRNA sequence analysis. We designated the isolated protist as T. aureum ssp. strugatskii. The closest species with the genome assembly is Schizochytrium aggregatum. Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes. Conclusion Our findings suggest that the T. aureum ssp. strugatskii is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.
format: application/pdf
format: text/html
creator: Dmitrii K. Konstantinov
creator: Aleksei Menzorov
creator: Olga Krivenko
creator: Alexey V. Doroshkov
subject: Bioinformatics
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12737
publisher: PeerJ Inc.
rights: © 2022 Konstantinov et al.
abstract: Background Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology. Methods We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore Beroe ovata using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species. Results The protist belongs to the genus Thraustochytrium based on the 18S rRNA sequence analysis. We designated the isolated protist as T. aureum ssp. strugatskii. The closest species with the genome assembly is Schizochytrium aggregatum. Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes. Conclusion Our findings suggest that the T. aureum ssp. strugatskii is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.
bibliographic citation: Konstantinov et al. (2022) Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii. PeerJ 10:e12737 https://doi.org/10.7717/peerj.12737
date submitted: 2020-12-01
date accepted: 2021-12-13
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Konstantinov
  given name: Dmitrii K.
author list: Agent
  family name: Menzorov
  given name: Aleksei
author list: Agent
  family name: Krivenko
  given name: Olga
author list: Agent
  family name: Doroshkov
  given name: Alexey V.
doi: 10.7717/peerj.12737
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Konstantinov et al.
attribution name: Konstantinov et al.

Analysis of the role and mechanism of EGCG in septic cardiomyopathy based on network pharmacology
type: item
type: AcademicArticle
description: Background Septic cardiomyopathy (SC) is a common complication of sepsis that leads to an increase in mortality. The pathogenesis of septic cardiomyopathy is unclear, and there is currently no effective treatment. EGCG (epigallocatechin gallate) is a polyphenol that has anti-inflammatory, antiapoptotic, and antioxidative stress effects. However, the role of EGCG in septic cardiomyopathy is unknown. Methods Network pharmacology was used to predict the potential targets and molecular mechanisms of EGCG in the treatment of septic cardiomyopathy, including the construction and analysis of protein-protein interaction (PPI) network, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and molecular docking. The mouse model of septic cardiomyopathy was established after intraperitoneal injection of LPS (lipopolysaccharide). The myocardial protective effect of EGCG on septic mice is observed by cardiac ultrasound and HE staining. RT-PCR is used to verify the expression level of the EGCG target in the septic cardiomyopathy mouse model. Results A total of 128 anti-SC potential targets of EGCGareselected for analysis. The GO enrichment analysis and KEGG pathway analysis results indicated that the anti-SC targets of EGCG mainly participate in inflammatory and apoptosis processes. Molecular docking results suggest that EGCG has a high affinity for the crystal structure of six targets (IL-6 (interleukin-6), TNF (tumor necrosis factor), Caspase3, MAPK3 (Mitogen-activated protein kinase 3), AKT1, and VEGFA (vascular endothelial growth factor)), and the experimental verification result showed levated expression of these 6 hub targets in the LPS group, but there is an obvious decrease in expression in the LPS + EGCG group. The functional and morphological changes found by echocardiography and HE staining show that EGCG can effectively improve the cardiac function that is reduced by LPS. Conclusion Our results reveal that EGCG may be a potentially ef…
format: application/pdf
format: text/html
creator: Ji Wu
creator: Zhenhua Wang
creator: Shanling Xu
creator: Yang Fu
creator: Yi Gao
creator: Zuxiang Wu
creator: Yun Yu
creator: Yougen Yuan
creator: Lin Zhou
creator: Ping Li
subject: Bioinformatics
subject: Molecular Biology
subject: Cardiology
subject: Radiology and Medical Imaging
subject: Histology
description: doi:10.7717/peerj.12994
publisher: PeerJ Inc.
rights: © 2022 Wu et al.
abstract: Background Septic cardiomyopathy (SC) is a common complication of sepsis that leads to an increase in mortality. The pathogenesis of septic cardiomyopathy is unclear, and there is currently no effective treatment. EGCG (epigallocatechin gallate) is a polyphenol that has anti-inflammatory, antiapoptotic, and antioxidative stress effects. However, the role of EGCG in septic cardiomyopathy is unknown. Methods Network pharmacology was used to predict the potential targets and molecular mechanisms of EGCG in the treatment of septic cardiomyopathy, including the construction and analysis of protein-protein interaction (PPI) network, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and molecular docking. The mouse model of septic cardiomyopathy was established after intraperitoneal injection of LPS (lipopolysaccharide). The myocardial protective effect of EGCG on septic mice is observed by cardiac ultrasound and HE staining. RT-PCR is used to verify the expression level of the EGCG target in the septic cardiomyopathy mouse model. Results A total of 128 anti-SC potential targets of EGCGareselected for analysis. The GO enrichment analysis and KEGG pathway analysis results indicated that the anti-SC targets of EGCG mainly participate in inflammatory and apoptosis processes. Molecular docking results suggest that EGCG has a high affinity for the crystal structure of six targets (IL-6 (interleukin-6), TNF (tumor necrosis factor), Caspase3, MAPK3 (Mitogen-activated protein kinase 3), AKT1, and VEGFA (vascular endothelial growth factor)), and the experimental verification result showed levated expression of these 6 hub targets in the LPS group, but there is an obvious decrease in expression in the LPS + EGCG group. The functional and morphological changes found by echocardiography and HE staining show that EGCG can effectively improve the cardiac function that is reduced by LPS. Conclusion Our results reveal that EGCG may be a potentially ef…
bibliographic citation: Wu et al. (2022) Analysis of the role and mechanism of EGCG in septic cardiomyopathy based on network pharmacology. PeerJ 10:e12994 https://doi.org/10.7717/peerj.12994
date submitted: 2021-08-04
date accepted: 2022-02-02
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Ji
author list: Agent
  family name: Wang
  given name: Zhenhua
author list: Agent
  family name: Xu
  given name: Shanling
author list: Agent
  family name: Fu
  given name: Yang
author list: Agent
  family name: Gao
  given name: Yi
author list: Agent
  family name: Wu
  given name: Zuxiang
author list: Agent
  family name: Yu
  given name: Yun
author list: Agent
  family name: Yuan
  given name: Yougen
author list: Agent
  family name: Zhou
  given name: Lin
author list: Agent
  family name: Li
  given name: Ping
doi: 10.7717/peerj.12994
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Wu et al.
attribution name: Wu et al.

Optimizing seawater temperature conditions to increase the productivity of ex situ coral nurseries
type: item
type: AcademicArticle
description: Large scale ex situ propagation of coral colonies for reef restoration is a relatively new and developing field. One of the many advantages of utilizing ex situ coral nurseries is the ability to optimize water quality conditions for coral health and survival. Slight alterations in environmental parameters (light, pH, temperature etc.) can affect the health and grow-out time of cultured coral, ultimately influencing production rates. However, corals are also subjected to pests associated with culture facilities such as ciliates, cyanobacterial blooms, and infectious diseases. Therefore, adjusting environmental parameters to optimize coral growth for a shorter ex situ residency time will lead to greater survival and faster restoration. Studies indicate that some coral species demonstrate parabolic tissue growth in response to increasing sea-surface temperatures until the maximum temperature tolerance is reached, whereafter they bleach. To maximize coral growth in Mote Marine Laboratory’s ex situ system, we tested the effect of two water temperature treatments (high temperature: 29.5 ± 0.03 °C; control: 25.2 ± 0.08 °C) on two coral species commonly used in reef restoration. To quantify this, we used four replicates of three genotypes each of Montastraea cavernosa (n = 12) and Acropora palmata (n = 12). Two-dimensional tissue area was recorded monthly using ImageJ and survival rates within each treatment were documented for 7 months. Results found that M. cavernosa had greater growth rates and equal survivorship in the high temperature treatment compared to the control treatment. A. palmata grew faster and had equal survivorship in the control treatment compared with the high temperature treatment. These results suggest that temperature preferences exist among coral species within ex situ systems and restoration practitioners should consider species-specific temperature regimes to maximize ex situ coral growth rates. This information is critical for optimizing productio…
format: application/pdf
format: text/html
creator: Dakotah E. Merck
creator: Chelsea G. Petrik
creator: Alicia A. Manfroy
creator: Erinn M. Muller
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.13017
publisher: PeerJ Inc.
rights: © 2022 Merck et al.
abstract: Large scale ex situ propagation of coral colonies for reef restoration is a relatively new and developing field. One of the many advantages of utilizing ex situ coral nurseries is the ability to optimize water quality conditions for coral health and survival. Slight alterations in environmental parameters (light, pH, temperature etc.) can affect the health and grow-out time of cultured coral, ultimately influencing production rates. However, corals are also subjected to pests associated with culture facilities such as ciliates, cyanobacterial blooms, and infectious diseases. Therefore, adjusting environmental parameters to optimize coral growth for a shorter ex situ residency time will lead to greater survival and faster restoration. Studies indicate that some coral species demonstrate parabolic tissue growth in response to increasing sea-surface temperatures until the maximum temperature tolerance is reached, whereafter they bleach. To maximize coral growth in Mote Marine Laboratory’s ex situ system, we tested the effect of two water temperature treatments (high temperature: 29.5 ± 0.03 °C; control: 25.2 ± 0.08 °C) on two coral species commonly used in reef restoration. To quantify this, we used four replicates of three genotypes each of Montastraea cavernosa (n = 12) and Acropora palmata (n = 12). Two-dimensional tissue area was recorded monthly using ImageJ and survival rates within each treatment were documented for 7 months. Results found that M. cavernosa had greater growth rates and equal survivorship in the high temperature treatment compared to the control treatment. A. palmata grew faster and had equal survivorship in the control treatment compared with the high temperature treatment. These results suggest that temperature preferences exist among coral species within ex situ systems and restoration practitioners should consider species-specific temperature regimes to maximize ex situ coral growth rates. This information is critical for optimizing productio…
bibliographic citation: Merck et al. (2022) Optimizing seawater temperature conditions to increase the productivity of ex situ coral nurseries. PeerJ 10:e13017 https://doi.org/10.7717/peerj.13017
date submitted: 2021-10-04
date accepted: 2022-02-06
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Merck
  given name: Dakotah E.
author list: Agent
  family name: Petrik
  given name: Chelsea G.
author list: Agent
  family name: Manfroy
  given name: Alicia A.
author list: Agent
  family name: Muller
  given name: Erinn M.
doi: 10.7717/peerj.13017
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: © 2022 Merck et al.
attribution name: Merck et al.

Perfluoroalkyl acids in sediment and water surrounding historical fire training areas at Barksdale Air Force Base
type: item
type: AcademicArticle
description: Perfluoroalkyl acids (PFAAs) are environmentally persistent components of surfactants that consist of fully fluorinated carbon chains and a terminal sulfonate or carboxylate polar head moiety. Due to their unique amphiphilic properties, PFAAs are used in the manufacturing of products such as aqueous film forming foams (AFFF). There is cause for concern for PFAA contamination resulting from runoff and groundwater infiltration of AFFF that were used during fire training. This study analyzed water and sediment samples that were collected over a 13-month sampling period from bayous upstream and downstream of two former fire training areas located near Barksdale Air Force Base (BAFB); the occurrence and magnitude of PFAAs supported an aquatic ecological risk assessment of potential impacts of PFAAs at the site. Liquid chromatography coupled with mass spectrometry was used for determination of 6 PFAAs listed under the third Unregulated Contaminant Monitoring Rule (UCMR 3). Total PFAA concentrations in surface water and sediment samples ranged from 0 (ND) −7.1 ng/mL and 0 (ND) −31.4 ng/g, respectively. Perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) were the predominant PFAAs detected. In general, perfluorosulfonates were quantified more frequently and at higher concentrations than perfluorocarboxylates. The perfluoroalkyl chain length of PFAAs also showed significant influence on PFAA concentrations when analyzed by Spearman’s rank correlation analysis. Some contamination we observed in surface water and sediment samples from reference locations could be a result of local runoff from the use of commercial products containing per- and poly-fluoroalkyl substances (PFAS), but AFFF appears to be the primary source given the close proximity of the historical fire training areas.
format: application/pdf
format: text/html
creator: Rebecca S. Wilkinson
creator: Heather A. Lanza
creator: Adric D. Olson
creator: Joseph F. Mudge
creator: Christopher J. Salice
creator: Todd A. Anderson
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.13054
publisher: PeerJ Inc.
rights: © 2022 Wilkinson et al.
abstract: Perfluoroalkyl acids (PFAAs) are environmentally persistent components of surfactants that consist of fully fluorinated carbon chains and a terminal sulfonate or carboxylate polar head moiety. Due to their unique amphiphilic properties, PFAAs are used in the manufacturing of products such as aqueous film forming foams (AFFF). There is cause for concern for PFAA contamination resulting from runoff and groundwater infiltration of AFFF that were used during fire training. This study analyzed water and sediment samples that were collected over a 13-month sampling period from bayous upstream and downstream of two former fire training areas located near Barksdale Air Force Base (BAFB); the occurrence and magnitude of PFAAs supported an aquatic ecological risk assessment of potential impacts of PFAAs at the site. Liquid chromatography coupled with mass spectrometry was used for determination of 6 PFAAs listed under the third Unregulated Contaminant Monitoring Rule (UCMR 3). Total PFAA concentrations in surface water and sediment samples ranged from 0 (ND) −7.1 ng/mL and 0 (ND) −31.4 ng/g, respectively. Perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) were the predominant PFAAs detected. In general, perfluorosulfonates were quantified more frequently and at higher concentrations than perfluorocarboxylates. The perfluoroalkyl chain length of PFAAs also showed significant influence on PFAA concentrations when analyzed by Spearman’s rank correlation analysis. Some contamination we observed in surface water and sediment samples from reference locations could be a result of local runoff from the use of commercial products containing per- and poly-fluoroalkyl substances (PFAS), but AFFF appears to be the primary source given the close proximity of the historical fire training areas.
bibliographic citation: Wilkinson et al. (2022) Perfluoroalkyl acids in sediment and water surrounding historical fire training areas at Barksdale Air Force Base. PeerJ 10:e13054 https://doi.org/10.7717/peerj.13054
date submitted: 2020-08-17
date accepted: 2022-02-12
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilkinson
  given name: Rebecca S.
author list: Agent
  family name: Lanza
  given name: Heather A.
author list: Agent
  family name: Olson
  given name: Adric D.
author list: Agent
  family name: Mudge
  given name: Joseph F.
author list: Agent
  family name: Salice
  given name: Christopher J.
author list: Agent
  family name: Anderson
  given name: Todd A.
doi: 10.7717/peerj.13054
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Wilkinson et al.
attribution name: Wilkinson et al.

Expression of connexin-43 in surgical resections of primary tumor and lymph node metastases of squamous cell carcinoma and adenocarcinoma of the lung: a retrospective study
type: item
type: AcademicArticle
description: Background Connexins are transmembrane proteins forming gap junctions between the cells, which allow intercellular communication. Significance of gap junctions and connexins in lung carcinoma is not yet understood. The objective of the study was to investigate immunohistochemical expression and the localization of connexin-43 (Cx43) in primary lung carcinoma and its lymphatic metastases. Methods Surgical specimens of excised tumors from 88 patients (45 men and 43 women, 61.9 ± 7.4 years) with lung carcinoma (52 adenocarcinoma (AC), 36 squamous cell carcinoma (SqCC)) who were operated on at the University Hospital “Bezanijska Kosa” in a five-year period (2012–2016) were used. We conducted immunohistochemical staining for Cx43 and measured the degree of expression (percentage of positive cells and staining intensity) as well as localization of Cx43 in primary tumor and in lymphatic metastases. Results Immunohistochemical analysis of the primary tumors revealed that SqCC showed significantly higher percentage of tumor cells expressing Cx43 as well as higher staining intensity than AC (p < 0.001). Almost 70% of samples with SqCC showed high Cx43 expression, whereas AC showed no expression in more than 50% of cases. Localization of Cx43 expression was most often cytoplasmic (AC and SqCC) and combined membranous and cytoplasmic (SqCC) with very rare instances of nuclear localization (AC). Almost the same pattern in distribution, intensity, and localization of Cx43 expression was observed in the lymph node metastases; however, almost a third of AC cases changed the pattern of Cx43 expression in the metastasis compared to primary tumor. Conclusion The results of this study showed that lung carcinomas express Cx43 in more than 65% of cases and that it was aberrantly localized (not membranous localization). We highlighted that SqCC expressed Cx43 more than did AC, both in primary tumor and lymphatic metastases. Further research is needed to establish whether Cx43 could be use…
format: application/pdf
format: text/html
creator: Ivana Savic
creator: Petar Milovanovic
creator: Svetlana Opric
creator: Nebojsa Ivanovic
creator: Dejan Oprić
subject: Oncology
subject: Pathology
subject: Respiratory Medicine
subject: Histology
description: doi:10.7717/peerj.13055
publisher: PeerJ Inc.
rights: © 2022 Savic et al.
abstract: Background Connexins are transmembrane proteins forming gap junctions between the cells, which allow intercellular communication. Significance of gap junctions and connexins in lung carcinoma is not yet understood. The objective of the study was to investigate immunohistochemical expression and the localization of connexin-43 (Cx43) in primary lung carcinoma and its lymphatic metastases. Methods Surgical specimens of excised tumors from 88 patients (45 men and 43 women, 61.9 ± 7.4 years) with lung carcinoma (52 adenocarcinoma (AC), 36 squamous cell carcinoma (SqCC)) who were operated on at the University Hospital “Bezanijska Kosa” in a five-year period (2012–2016) were used. We conducted immunohistochemical staining for Cx43 and measured the degree of expression (percentage of positive cells and staining intensity) as well as localization of Cx43 in primary tumor and in lymphatic metastases. Results Immunohistochemical analysis of the primary tumors revealed that SqCC showed significantly higher percentage of tumor cells expressing Cx43 as well as higher staining intensity than AC (p < 0.001). Almost 70% of samples with SqCC showed high Cx43 expression, whereas AC showed no expression in more than 50% of cases. Localization of Cx43 expression was most often cytoplasmic (AC and SqCC) and combined membranous and cytoplasmic (SqCC) with very rare instances of nuclear localization (AC). Almost the same pattern in distribution, intensity, and localization of Cx43 expression was observed in the lymph node metastases; however, almost a third of AC cases changed the pattern of Cx43 expression in the metastasis compared to primary tumor. Conclusion The results of this study showed that lung carcinomas express Cx43 in more than 65% of cases and that it was aberrantly localized (not membranous localization). We highlighted that SqCC expressed Cx43 more than did AC, both in primary tumor and lymphatic metastases. Further research is needed to establish whether Cx43 could be use…
bibliographic citation: Savic et al. (2022) Expression of connexin-43 in surgical resections of primary tumor and lymph node metastases of squamous cell carcinoma and adenocarcinoma of the lung: a retrospective study. PeerJ 10:e13055 https://doi.org/10.7717/peerj.13055
date submitted: 2020-07-22
date accepted: 2022-02-12
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Savic
  given name: Ivana
author list: Agent
  family name: Milovanovic
  given name: Petar
author list: Agent
  family name: Opric
  given name: Svetlana
author list: Agent
  family name: Ivanovic
  given name: Nebojsa
author list: Agent
  family name: Oprić
  given name: Dejan
doi: 10.7717/peerj.13055
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Savic et al.
attribution name: Savic et al.

Environmental enrichment changes rabbits’ behavior, serum hormone level and further affects cecal microbiota
type: item
type: AcademicArticle
description: Many studies have shown that stress is associated with gut microbiota. Environmental enrichment (EE) could reduce stress in farm animals; however, limited information is available on the microbial community composition in rabbits raised with or without EE. This study aimed to identify EE influences on the behavior, serum hormonal levels, and cecal microbiota of rabbits. Two hundred Rex rabbits were segregated randomly within four cohorts (n = 50); reared for 76 d within standardized enclosures (non-enriched) or within cages containing a willow-stick (WS), rubber-duck (RD), or a can of beans (CB). The rabbits’ ingestive, rest, locomotion, exploratory, grooming, and abnormal behavior were observed. The serum hormone levels for rabbits were measured, and cecal specimens were sequencedfrom the V3–V4 region using 16S rRNA amplicons. Environmental enrichment increased feeding and drinking time, promoted exploratory behavior, and reduced abnormal behavior in rabbits. Insulin-like growth factor 1(IGF-1) levels of the enriched cohorts were elevated in comparison to the control cohort. Serum cortisol level for CB cohort was markedly reduced in comparison to the control cohort (p < 0.05), while dopamine levels for CB cohort peaked. Further, we found that EE mainly affected the dominant microbiota. Several families, such as Erysipelotrichaceae, Tannerellaceae, Enterobacteriaceae, Burkholderiaceae, and Prevotellaceae were markedly reduced within the CB cohort. Bacteria such as Alloprevotella, Bifidobacterium, Enterobacteriaceae, Parabacteroides, and Erysipelatoclostridium were identified as having negative associations with the presence of serum cortisol. EE influenced rabbit behavior and serum hormonal levels, and CB enrichment was the most suitable for rabbits. Further, cecal microbiota composition and diversity were affected by CB enrichment. These findings suggested that CB could be considered for use in rabbit husbandry.
format: application/pdf
format: text/html
creator: Yang Feng
creator: Huimei Fan
creator: Xue Liang
creator: Xiaofeng Wang
creator: Guoyan Gao
creator: Shuangbao Gun
subject: Animal Behavior
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.13068
publisher: PeerJ Inc.
rights: © 2022 Feng et al.
abstract: Many studies have shown that stress is associated with gut microbiota. Environmental enrichment (EE) could reduce stress in farm animals; however, limited information is available on the microbial community composition in rabbits raised with or without EE. This study aimed to identify EE influences on the behavior, serum hormonal levels, and cecal microbiota of rabbits. Two hundred Rex rabbits were segregated randomly within four cohorts (n = 50); reared for 76 d within standardized enclosures (non-enriched) or within cages containing a willow-stick (WS), rubber-duck (RD), or a can of beans (CB). The rabbits’ ingestive, rest, locomotion, exploratory, grooming, and abnormal behavior were observed. The serum hormone levels for rabbits were measured, and cecal specimens were sequencedfrom the V3–V4 region using 16S rRNA amplicons. Environmental enrichment increased feeding and drinking time, promoted exploratory behavior, and reduced abnormal behavior in rabbits. Insulin-like growth factor 1(IGF-1) levels of the enriched cohorts were elevated in comparison to the control cohort. Serum cortisol level for CB cohort was markedly reduced in comparison to the control cohort (p < 0.05), while dopamine levels for CB cohort peaked. Further, we found that EE mainly affected the dominant microbiota. Several families, such as Erysipelotrichaceae, Tannerellaceae, Enterobacteriaceae, Burkholderiaceae, and Prevotellaceae were markedly reduced within the CB cohort. Bacteria such as Alloprevotella, Bifidobacterium, Enterobacteriaceae, Parabacteroides, and Erysipelatoclostridium were identified as having negative associations with the presence of serum cortisol. EE influenced rabbit behavior and serum hormonal levels, and CB enrichment was the most suitable for rabbits. Further, cecal microbiota composition and diversity were affected by CB enrichment. These findings suggested that CB could be considered for use in rabbit husbandry.
bibliographic citation: Feng et al. (2022) Environmental enrichment changes rabbits’ behavior, serum hormone level and further affects cecal microbiota. PeerJ 10:e13068 https://doi.org/10.7717/peerj.13068
date submitted: 2020-12-15
date accepted: 2022-02-15
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: Yang
author list: Agent
  family name: Fan
  given name: Huimei
author list: Agent
  family name: Liang
  given name: Xue
author list: Agent
  family name: Wang
  given name: Xiaofeng
author list: Agent
  family name: Gao
  given name: Guoyan
author list: Agent
  family name: Gun
  given name: Shuangbao
doi: 10.7717/peerj.13068
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Feng et al.
attribution name: Feng et al.

Long-term consumption of artificial sweeteners does not affect cardiovascular health and survival in rats
type: item
type: AcademicArticle
description: Background Recent epidemiological cohort studies have suggested that consumption of artificial sweeteners (AS) is associated with adverse cardiovascular events and mortality. However, these population association studies cannot establish a causal relationship. In this study we investigated the effect of long-term (1-year) consumption of AS (Equal and Splenda, two commonly used AS) on cardiovascular health and survival in rats. Methods Adult Sprague-Dawley rats (both sexes, 4–5 months old) were randomized into the following 3 groups: control (n = 21), AS Equal (n = 21) and Splenda (n = 18). In the AS groups, Equal or Splenda was added to the drinking water (2-packets/250 ml), while drinking water alone was used in the control rats. The treatment was administered for 12 months. Cardiovascular function and survival were monitored in all animals. Results It was found that rats in the AS groups consistently consumed more sweetened water than those in the control group. AS did not affect body weight, non-fasting blood cholesterol, triglycerides, blood pressure or pulse wave velocity. There were no significant differences in left ventricular wall thicknesses, chamber dimension, cardiac function or survival. AS did not affect heart rate or atrial effective refractory period. However, rats in both Equal and Splenda groups had prolonged PR intervals (63 ± 5ms in Equal, 68 ± 6 ms in Splenda, vs 56 ± 8 ms in control, p < 0.05) and a tendency of increased atrial fibrillation inducibility. Conclusion Long-term consumption of AS does not affect cardiovascular structure, function or survival but may cause some electrophysiological abnormalities with prolonged PR intervals and a tendency of increased atrial fibrillation inducibility in rats.
format: application/pdf
format: text/html
creator: Satvinder K. Guru
creator: Ying Li
creator: Olga V. Savinova
creator: Youhua Zhang
subject: Cardiology
subject: Nutrition
subject: Translational Medicine
description: doi:10.7717/peerj.13071
publisher: PeerJ Inc.
rights: © 2022 Guru et al.
abstract: Background Recent epidemiological cohort studies have suggested that consumption of artificial sweeteners (AS) is associated with adverse cardiovascular events and mortality. However, these population association studies cannot establish a causal relationship. In this study we investigated the effect of long-term (1-year) consumption of AS (Equal and Splenda, two commonly used AS) on cardiovascular health and survival in rats. Methods Adult Sprague-Dawley rats (both sexes, 4–5 months old) were randomized into the following 3 groups: control (n = 21), AS Equal (n = 21) and Splenda (n = 18). In the AS groups, Equal or Splenda was added to the drinking water (2-packets/250 ml), while drinking water alone was used in the control rats. The treatment was administered for 12 months. Cardiovascular function and survival were monitored in all animals. Results It was found that rats in the AS groups consistently consumed more sweetened water than those in the control group. AS did not affect body weight, non-fasting blood cholesterol, triglycerides, blood pressure or pulse wave velocity. There were no significant differences in left ventricular wall thicknesses, chamber dimension, cardiac function or survival. AS did not affect heart rate or atrial effective refractory period. However, rats in both Equal and Splenda groups had prolonged PR intervals (63 ± 5ms in Equal, 68 ± 6 ms in Splenda, vs 56 ± 8 ms in control, p < 0.05) and a tendency of increased atrial fibrillation inducibility. Conclusion Long-term consumption of AS does not affect cardiovascular structure, function or survival but may cause some electrophysiological abnormalities with prolonged PR intervals and a tendency of increased atrial fibrillation inducibility in rats.
bibliographic citation: Guru et al. (2022) Long-term consumption of artificial sweeteners does not affect cardiovascular health and survival in rats. PeerJ 10:e13071 https://doi.org/10.7717/peerj.13071
date submitted: 2021-12-09
date accepted: 2022-02-15
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guru
  given name: Satvinder K.
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Savinova
  given name: Olga V.
author list: Agent
  family name: Zhang
  given name: Youhua
doi: 10.7717/peerj.13071
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Guru et al.
attribution name: Guru et al.

Full-length transcriptome analysis of Adiantum flabellulatum gametophyte
type: item
type: AcademicArticle
description: Ferns are important components of plant communities on earth, but their genomes are generally very large, with many redundant genes, making whole genome sequencing of ferns prohibitively expensive and time-consuming. This means there is a significant lack of fern reference genomes, making molecular biology research difficult. The gametophytes of ferns can survive independently, are responsible for sexual reproduction and the feeding of young sporophytes, and play an important role in the alternation of generations. For this study, we selected Adiantum flabellulatum as it has both ornamental and medicinal value and is also an indicator plant of acidic soil. The full-length transcriptome sequencing of its gametophytes was carried out using PacBio three-generation sequencing technology. A total of 354,228 transcripts were obtained, and 231,705 coding sequences (CDSs) were predicted, including 5,749 transcription factors (TFs), 2,214 transcription regulators (TRs) and 4,950 protein kinases (PKs). The transcripts annotated by non-redundant protein sequence database (NR), Kyoto encyclopedia of genes and genomes (KEGG), eukaryotic ortholog groups (KOG), Swissprot, protein family (Pfma), nucleotide sequence database (NT) and gene ontology (GO) were 251,501, 197,474, 193,630, 194,639, 195,956, 113,069 and 197,883, respectively. In addition, 138,995 simple sequence repeats (SSRs) and 111,793 long non-coding RNAs (lncRNAs) were obtained. We selected nine chlorophyll synthase genes for qRT-PCR, and the results showed that the full-length transcript sequences and the annotation information were reliable. This study can provide a reference gene set for subsequent gene expression quantification.
format: application/pdf
format: text/html
creator: Zeping Cai
creator: Zhenyu Xie
creator: Luyao Huang
creator: Zixuan Wang
creator: Min Pan
creator: Xudong Yu
creator: Shitao Xu
creator: Jiajia Luo
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13079
publisher: PeerJ Inc.
rights: © 2022 Cai et al.
abstract: Ferns are important components of plant communities on earth, but their genomes are generally very large, with many redundant genes, making whole genome sequencing of ferns prohibitively expensive and time-consuming. This means there is a significant lack of fern reference genomes, making molecular biology research difficult. The gametophytes of ferns can survive independently, are responsible for sexual reproduction and the feeding of young sporophytes, and play an important role in the alternation of generations. For this study, we selected Adiantum flabellulatum as it has both ornamental and medicinal value and is also an indicator plant of acidic soil. The full-length transcriptome sequencing of its gametophytes was carried out using PacBio three-generation sequencing technology. A total of 354,228 transcripts were obtained, and 231,705 coding sequences (CDSs) were predicted, including 5,749 transcription factors (TFs), 2,214 transcription regulators (TRs) and 4,950 protein kinases (PKs). The transcripts annotated by non-redundant protein sequence database (NR), Kyoto encyclopedia of genes and genomes (KEGG), eukaryotic ortholog groups (KOG), Swissprot, protein family (Pfma), nucleotide sequence database (NT) and gene ontology (GO) were 251,501, 197,474, 193,630, 194,639, 195,956, 113,069 and 197,883, respectively. In addition, 138,995 simple sequence repeats (SSRs) and 111,793 long non-coding RNAs (lncRNAs) were obtained. We selected nine chlorophyll synthase genes for qRT-PCR, and the results showed that the full-length transcript sequences and the annotation information were reliable. This study can provide a reference gene set for subsequent gene expression quantification.
bibliographic citation: Cai et al. (2022) Full-length transcriptome analysis of Adiantum flabellulatum gametophyte. PeerJ 10:e13079 https://doi.org/10.7717/peerj.13079
date submitted: 2021-09-24
date accepted: 2022-02-16
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Zeping
author list: Agent
  family name: Xie
  given name: Zhenyu
author list: Agent
  family name: Huang
  given name: Luyao
author list: Agent
  family name: Wang
  given name: Zixuan
author list: Agent
  family name: Pan
  given name: Min
author list: Agent
  family name: Yu
  given name: Xudong
author list: Agent
  family name: Xu
  given name: Shitao
author list: Agent
  family name: Luo
  given name: Jiajia
doi: 10.7717/peerj.13079
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Cai et al.
attribution name: Cai et al.

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