PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts
items: Updated advances of linking psychosocial factors and sex hormones with systemic lupus erythematosus susceptibility and development
items: Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend
items: https://peerj.com/articles/7227
items: Expression of osteopontin, matrix metalloproteinase-2 and -9 proteins in vascular instability in brain arteriovenous malformation
items: Do human screams permit individual recognition?
items: Sevoflurane postconditioning alleviates hypoxia-reoxygenation injury of cardiomyocytes by promoting mitochondrial autophagy through the HIF-1/BNIP3 signaling pathway
items: Osteology and phylogeny of Robustichthys luopingensis, the largest holostean fish in the Middle Triassic
items: Isolation and identification of a halophilic and alkaliphilic microalgal strain
items: Decoupled recovery of ecological communities after reclamation

Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts
type: item
type: AcademicArticle
description: Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.
format: application/pdf
format: text/html
creator: Joshua I. Brian
creator: Simon K. Davy
creator: Shaun P. Wilkinson
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.7178
publisher: PeerJ Inc.
rights: © 2019 Brian et al.
abstract: Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.
bibliographic citation: Brian et al. (2019) Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts. PeerJ 7:e7178 https://doi.org/10.7717/peerj.7178
date submitted: 2019-03-24
date accepted: 2019-05-22
issued: 2019-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brian
  given name: Joshua I.
author list: Agent
  family name: Davy
  given name: Simon K.
author list: Agent
  family name: Wilkinson
  given name: Shaun P.
doi: 10.7717/peerj.7178
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-25
copyright: © 2019 Brian et al.
attribution name: Brian et al.

Updated advances of linking psychosocial factors and sex hormones with systemic lupus erythematosus susceptibility and development
type: item
type: AcademicArticle
description: Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that primarily affects women, especially those of reproductive age. Genetics, environment, and gene-environment interactions play key roles in the development of SLE. Despite the numerous susceptibility genes of SLE identified to date, gene therapy is far from a clinical reality. Thus, more attention should be paid to the risk factors and underlying mechanisms of SLE. Currently, it is reported that psychosocial factors and sex hormones play vital roles in patients with SLE, which still need further investigated. The purpose of this review is to update the roles and mechanisms of psychosocial factors and sex hormones in the susceptibility and development of SLE. Based on review articles and reports in reputable peer-reviewed journals and government websites, this paper summarized psychosocial factors (e.g., alexithymia, depression, anxiety, negative emotions, and perceived stress) and sex hormones (e.g., estrogens, progesterone, androgens, and prolactin) involved in SLE. We further explore the mechanisms linking these factors with SLE susceptibility and development, which can guide the establishment of practical measures to benefit SLE patients and offer new ideas for therapeutic strategies.
format: application/pdf
format: text/html
creator: Qingjun Pan
creator: Xiaoqun Chen
creator: Shuzhen Liao
creator: Xiaocui Chen
creator: Chunfei Zhao
creator: Yong-zhi Xu
creator: Hua-feng Liu
subject: Allergy and Clinical Immunology
subject: Immunology
subject: Nephrology
subject: Rheumatology
description: doi:10.7717/peerj.7179
publisher: PeerJ Inc.
rights: © 2019 Pan et al.
abstract: Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that primarily affects women, especially those of reproductive age. Genetics, environment, and gene-environment interactions play key roles in the development of SLE. Despite the numerous susceptibility genes of SLE identified to date, gene therapy is far from a clinical reality. Thus, more attention should be paid to the risk factors and underlying mechanisms of SLE. Currently, it is reported that psychosocial factors and sex hormones play vital roles in patients with SLE, which still need further investigated. The purpose of this review is to update the roles and mechanisms of psychosocial factors and sex hormones in the susceptibility and development of SLE. Based on review articles and reports in reputable peer-reviewed journals and government websites, this paper summarized psychosocial factors (e.g., alexithymia, depression, anxiety, negative emotions, and perceived stress) and sex hormones (e.g., estrogens, progesterone, androgens, and prolactin) involved in SLE. We further explore the mechanisms linking these factors with SLE susceptibility and development, which can guide the establishment of practical measures to benefit SLE patients and offer new ideas for therapeutic strategies.
bibliographic citation: Pan et al. (2019) Updated advances of linking psychosocial factors and sex hormones with systemic lupus erythematosus susceptibility and development. PeerJ 7:e7179 https://doi.org/10.7717/peerj.7179
date submitted: 2019-03-05
date accepted: 2019-05-22
issued: 2019-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Qingjun
author list: Agent
  family name: Chen
  given name: Xiaoqun
author list: Agent
  family name: Liao
  given name: Shuzhen
author list: Agent
  family name: Chen
  given name: Xiaocui
author list: Agent
  family name: Zhao
  given name: Chunfei
author list: Agent
  family name: Xu
  given name: Yong-zhi
author list: Agent
  family name: Liu
  given name: Hua-feng
doi: 10.7717/peerj.7179
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-25
copyright: © 2019 Pan et al.
attribution name: Pan et al.

Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend
type: item
type: AcademicArticle
description: It is vital to understand the conservation and evolution of gene promoter sequences in order to understand environmental adaptation. The level of promoter conservation varies greatly between housekeeping (HK) and tissue-specific (TS) genes, denoting differences in the strength of the evolutionary constraints. Here, we analyzed promoter conservation and evolution to exploit differential regulation between HK and TS genes. The analysis of conserved elements showed CpG islands, short tandem repeats and G-quadruplex sequences are highly enriched in HK promoters relative to TS promoters. In addition, the type and density of regulatory motifs in TS promoters are much higher than HK promoters, indicating that TS genes show more complex regulatory patterns than HK genes. Moreover, the evolutionary dynamics of promoters showed similar evolutionary trend to coding sequences. HK promoters suffer more stringent selective pressure in the long-term evolutionary process. HK genes tend to show increased upstream sequence conservation due to stringent selection pressures acting on the promoter regions. The specificity of TS gene expression may be due to complex regulatory motifs acting in different tissues or conditions. The results from this study can be used to deepen our understanding of adaptive evolution.
format: application/pdf
format: text/html
creator: Kai Wei
creator: Lei Ma
creator: Tingting Zhang
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.7204
publisher: PeerJ Inc.
rights: © 2019 Wei et al.
abstract: It is vital to understand the conservation and evolution of gene promoter sequences in order to understand environmental adaptation. The level of promoter conservation varies greatly between housekeeping (HK) and tissue-specific (TS) genes, denoting differences in the strength of the evolutionary constraints. Here, we analyzed promoter conservation and evolution to exploit differential regulation between HK and TS genes. The analysis of conserved elements showed CpG islands, short tandem repeats and G-quadruplex sequences are highly enriched in HK promoters relative to TS promoters. In addition, the type and density of regulatory motifs in TS promoters are much higher than HK promoters, indicating that TS genes show more complex regulatory patterns than HK genes. Moreover, the evolutionary dynamics of promoters showed similar evolutionary trend to coding sequences. HK promoters suffer more stringent selective pressure in the long-term evolutionary process. HK genes tend to show increased upstream sequence conservation due to stringent selection pressures acting on the promoter regions. The specificity of TS gene expression may be due to complex regulatory motifs acting in different tissues or conditions. The results from this study can be used to deepen our understanding of adaptive evolution.
bibliographic citation: Wei et al. (2019) Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend. PeerJ 7:e7204 https://doi.org/10.7717/peerj.7204
date submitted: 2019-02-18
date accepted: 2019-05-29
issued: 2019-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Kai
author list: Agent
  family name: Ma
  given name: Lei
author list: Agent
  family name: Zhang
  given name: Tingting
doi: 10.7717/peerj.7204
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-25
copyright: © 2019 Wei et al.
attribution name: Wei et al.

https://peerj.com/articles/7227
type: item
type: AcademicArticle
title: Performance of Modified Early Warning Score (MEWS) and Circulation, Respiration, Abdomen, Motor, and Speech (CRAMS) score in trauma severity and in-hospital mortality prediction in multiple trauma patients: a comparison study
description: Background With an increasing number of motor vehicle crashes, there is an urgent need in emergency departments (EDs) to assess patients with multiple trauma quickly, easily, and reliably. Trauma severity can range from a minor to major threats to life or bodily function. In-hospital mortality and trauma severity prediction in such cases is crucial in the ED for the management of multiple trauma and improvement of the outcome of these patients. Previous studies have examined the performance of Modified Early Warning Score (MEWS) or Circulation, Respiration, Abdomen, Motor, and Speech (CRAMS) score based solely on mortality prediction or injury severity prediction. However, to the best of our knowledge, the performances of both scoring systems on in-hospital mortality and trauma severity prediction have not been compared previously. This retrospective study evaluated the value of MEWS and CRAMS score to predict in-hospital mortality and trauma severity in patients presenting to the ED with multiple traumatic injuries. Methods All study subjects were multiple trauma patients. Medical data of 1,127 patients were analyzed between January 2014 and April 2018. The MEWS and CRAMS score were calculated, and logistic regression and receiver operating characteristic curve analysis were conducted to investigate their performances regarding in-hospital mortality and trauma severity prediction. Results For in-hospital mortality prediction, the areas under the receiver operating characteristic curve (AUROCs) for MEWS and CRAMS score were 0.90 and 0.91, respectively, indicating that both of them were good in-hospital mortality predictors. Further, our study indicated that the CRAMS score performed better in trauma severity prediction, with an AUROC value of 0.84, which was higher than that of MEWS (AUROC = 0.77). For trauma severity prediction, the optimal cut-off value for MEWS was 2, while that of the CRAMS score was 8. Conclusions We found that both MEWS and CRAMS score can be …
format: application/pdf
format: text/html
creator: Xiaobin Jiang
creator: Ping Jiang
creator: Yuanshen Mao
subject: Emergency and Critical Care
subject: Evidence Based Medicine
subject: Health Policy
subject: Public Health
description: doi:10.7717/peerj.7227
publisher: PeerJ Inc.
rights: © 2019 Jiang et al.
abstract: Background With an increasing number of motor vehicle crashes, there is an urgent need in emergency departments (EDs) to assess patients with multiple trauma quickly, easily, and reliably. Trauma severity can range from a minor to major threats to life or bodily function. In-hospital mortality and trauma severity prediction in such cases is crucial in the ED for the management of multiple trauma and improvement of the outcome of these patients. Previous studies have examined the performance of Modified Early Warning Score (MEWS) or Circulation, Respiration, Abdomen, Motor, and Speech (CRAMS) score based solely on mortality prediction or injury severity prediction. However, to the best of our knowledge, the performances of both scoring systems on in-hospital mortality and trauma severity prediction have not been compared previously. This retrospective study evaluated the value of MEWS and CRAMS score to predict in-hospital mortality and trauma severity in patients presenting to the ED with multiple traumatic injuries. Methods All study subjects were multiple trauma patients. Medical data of 1,127 patients were analyzed between January 2014 and April 2018. The MEWS and CRAMS score were calculated, and logistic regression and receiver operating characteristic curve analysis were conducted to investigate their performances regarding in-hospital mortality and trauma severity prediction. Results For in-hospital mortality prediction, the areas under the receiver operating characteristic curve (AUROCs) for MEWS and CRAMS score were 0.90 and 0.91, respectively, indicating that both of them were good in-hospital mortality predictors. Further, our study indicated that the CRAMS score performed better in trauma severity prediction, with an AUROC value of 0.84, which was higher than that of MEWS (AUROC = 0.77). For trauma severity prediction, the optimal cut-off value for MEWS was 2, while that of the CRAMS score was 8. Conclusions We found that both MEWS and CRAMS score can be …
bibliographic citation: Jiang et al. (2019) Performance of Modified Early Warning Score (MEWS) and Circulation, Respiration, Abdomen, Motor, and Speech (CRAMS) score in trauma severity and in-hospital mortality prediction in multiple trauma patients: a comparison study. PeerJ 7:e7227 https://doi.org/10.7717/peerj.7227
date submitted: 2018-12-14
date accepted: 2019-05-30
issued: 2019-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Xiaobin
author list: Agent
  family name: Jiang
  given name: Ping
author list: Agent
  family name: Mao
  given name: Yuanshen
doi: 10.7717/peerj.7227
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-25
copyright: © 2019 Jiang et al.
attribution name: Jiang et al.

Expression of osteopontin, matrix metalloproteinase-2 and -9 proteins in vascular instability in brain arteriovenous malformation
type: item
type: AcademicArticle
description: Background Matrix metalloproteinase (MMP)-2 and -9 are Osteopontin (OPN) dependent molecules implicated in the destabilization of blood vessels. OPN and MMPs have been studied in brain arteriovenous malformation (BAVM) patients’ tissues and blood samples before intervention. In this study, we compared the serum level of these markers before and after treatment, as well as assessed their protein expressions in BAVM tissues to evaluate their roles in this disease. Methodology Serum samples from six BAVM patients and three control subjects were analyzed using enzyme-linked immunoabsorbent assay (ELISA) for OPN. A total of 10 BAVM patients and five control subjects were analyzed using Multiplex ELISA for MMPs. A total of 16 BAVM tissue samples and two normal brain tissue samples were analyzed using immunohistochemistry. Result MMP-2 and -9 were significantly higher in the serum of BAVM patients before and after treatment than in control patients. There were no significant differences of OPN and MMP-9 serum level in BAVM patients before and after treatment. MMP-2 showed a significant elevation after the treatment. Expression of OPN, MMP-2 and -9 proteins were seen in endothelial cells, perivascular cells and brain parenchyma of BAVM tissues. Conclusion Findings revealed that the level of MMP-2 and -9 in the serum correlated well with the expression in BAVM tissues in several cases. Knockdown studies will be required to determine the relationships and mechanisms of action of these markers in the near future. In addition, studies will be required to investigate the expression of these markers’ potential applications as primary medical therapy targets for BAVM patients.
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creator: Lalita Anbarasen
creator: Jasmine Lim
creator: Retnagowri Rajandram
creator: Kein Seong Mun
creator: Sheau Fung Sia
subject: Molecular Biology
subject: Neuroscience
subject: Pathology
subject: Surgery and Surgical Specialties
subject: Histology
description: doi:10.7717/peerj.7058
publisher: PeerJ Inc.
rights: © 2019 Anbarasen et al.
abstract: Background Matrix metalloproteinase (MMP)-2 and -9 are Osteopontin (OPN) dependent molecules implicated in the destabilization of blood vessels. OPN and MMPs have been studied in brain arteriovenous malformation (BAVM) patients’ tissues and blood samples before intervention. In this study, we compared the serum level of these markers before and after treatment, as well as assessed their protein expressions in BAVM tissues to evaluate their roles in this disease. Methodology Serum samples from six BAVM patients and three control subjects were analyzed using enzyme-linked immunoabsorbent assay (ELISA) for OPN. A total of 10 BAVM patients and five control subjects were analyzed using Multiplex ELISA for MMPs. A total of 16 BAVM tissue samples and two normal brain tissue samples were analyzed using immunohistochemistry. Result MMP-2 and -9 were significantly higher in the serum of BAVM patients before and after treatment than in control patients. There were no significant differences of OPN and MMP-9 serum level in BAVM patients before and after treatment. MMP-2 showed a significant elevation after the treatment. Expression of OPN, MMP-2 and -9 proteins were seen in endothelial cells, perivascular cells and brain parenchyma of BAVM tissues. Conclusion Findings revealed that the level of MMP-2 and -9 in the serum correlated well with the expression in BAVM tissues in several cases. Knockdown studies will be required to determine the relationships and mechanisms of action of these markers in the near future. In addition, studies will be required to investigate the expression of these markers’ potential applications as primary medical therapy targets for BAVM patients.
bibliographic citation: Anbarasen et al. (2019) Expression of osteopontin, matrix metalloproteinase-2 and -9 proteins in vascular instability in brain arteriovenous malformation. PeerJ 7:e7058 https://doi.org/10.7717/peerj.7058
date submitted: 2018-12-30
date accepted: 2019-05-02
issued: 2019-06-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Anbarasen
  given name: Lalita
author list: Agent
  family name: Lim
  given name: Jasmine
author list: Agent
  family name: Rajandram
  given name: Retnagowri
author list: Agent
  family name: Mun
  given name: Kein Seong
author list: Agent
  family name: Sia
  given name: Sheau Fung
doi: 10.7717/peerj.7058
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-24
copyright: © 2019 Anbarasen et al.
attribution name: Anbarasen et al.

Do human screams permit individual recognition?
type: item
type: AcademicArticle
description: The recognition of individuals through vocalizations is a highly adaptive ability in the social behavior of many species, including humans. However, the extent to which nonlinguistic vocalizations such as screams permit individual recognition in humans remains unclear. Using a same-different vocalizer discrimination task, we investigated participants’ ability to correctly identify whether pairs of screams were produced by the same person or two different people, a critical prerequisite to individual recognition. Despite prior theory-based contentions that screams are not acoustically well-suited to conveying identity cues, listeners discriminated individuals at above-chance levels by their screams, including both acoustically modified and unmodified exemplars. We found that vocalizer gender explained some variation in participants’ discrimination abilities and response times, but participant attributes (gender, experience, empathy) did not. Our findings are consistent with abundant evidence from nonhuman primates, suggesting that both human and nonhuman screams convey cues to caller identity, thus supporting the thesis of evolutionary continuity in at least some aspects of scream function across primate species.
format: application/pdf
format: text/html
creator: Jonathan W. M. Engelberg
creator: Jay W. Schwartz
creator: Harold Gouzoules
subject: Animal Behavior
subject: Evolutionary Studies
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.7087
publisher: PeerJ Inc.
rights: © 2019 Engelberg et al.
abstract: The recognition of individuals through vocalizations is a highly adaptive ability in the social behavior of many species, including humans. However, the extent to which nonlinguistic vocalizations such as screams permit individual recognition in humans remains unclear. Using a same-different vocalizer discrimination task, we investigated participants’ ability to correctly identify whether pairs of screams were produced by the same person or two different people, a critical prerequisite to individual recognition. Despite prior theory-based contentions that screams are not acoustically well-suited to conveying identity cues, listeners discriminated individuals at above-chance levels by their screams, including both acoustically modified and unmodified exemplars. We found that vocalizer gender explained some variation in participants’ discrimination abilities and response times, but participant attributes (gender, experience, empathy) did not. Our findings are consistent with abundant evidence from nonhuman primates, suggesting that both human and nonhuman screams convey cues to caller identity, thus supporting the thesis of evolutionary continuity in at least some aspects of scream function across primate species.
bibliographic citation: Engelberg et al. (2019) Do human screams permit individual recognition?. PeerJ 7:e7087 https://doi.org/10.7717/peerj.7087
date submitted: 2018-11-14
date accepted: 2019-05-07
issued: 2019-06-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Engelberg
  given name: Jonathan W. M.
author list: Agent
  family name: Schwartz
  given name: Jay W.
author list: Agent
  family name: Gouzoules
  given name: Harold
doi: 10.7717/peerj.7087
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-24
copyright: © 2019 Engelberg et al.
attribution name: Engelberg et al.

Sevoflurane postconditioning alleviates hypoxia-reoxygenation injury of cardiomyocytes by promoting mitochondrial autophagy through the HIF-1/BNIP3 signaling pathway
type: item
type: AcademicArticle
description: Background Sevoflurane postconditioning (SpostC) can alleviate hypoxia-reoxygenation injury of cardiomyocytes; however, the specific mechanism remains unclear. This study aimed to investigate whether SpostC promotes mitochondrial autophagy through the hypoxia-inducible factor-1 (HIF-1)/BCL2/adenovirus E1B 19-kDa-interacting protein 3 (BNIP3) signaling pathway to attenuate hypoxia-reoxygenation injury in cardiomyocytes. Methods The H9C2 cardiomyocyte hypoxia/reoxygenation model was established and treated with 2.4% sevoflurane at the beginning of reoxygenation. Cell damage was determined by measuring cell viability, lactate dehydrogenase activity, and apoptosis. Mitochondrial ultrastructural and autophagosomes were observed by transmission electron microscope. Western blotting was used to examine the expression of HIF-1, BNIP3, and Beclin-1 proteins. The effects of BNIP3 on promoting autophagy were determined using interfering RNA technology to silence BNIP3. Results Hypoxia-reoxygenation injury led to accumulation of autophagosomes in cardiomyocytes, and cell viability was significantly reduced, which seriously damaged cells. Sevoflurane postconditioning could upregulate HIF-1α and BNIP3 protein expression, promote autophagosome clearance, and reduce cell damage. However, these protective effects were inhibited by 2-methoxyestradiol or sinBNIP3. Conclusion Sevoflurane postconditioning can alleviate hypoxia-reoxygenation injury in cardiomyocytes, and this effect may be achieved by promoting mitochondrial autophagy through the HIF-1/BNIP3 signaling pathway.
format: application/pdf
format: text/html
creator: Long Yang
creator: Jianjiang Wu
creator: Peng Xie
creator: Jin Yu
creator: Xin Li
creator: Jiang Wang
creator: Hong Zheng
subject: Anesthesiology and Pain Management
subject: Cardiology
description: doi:10.7717/peerj.7165
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Background Sevoflurane postconditioning (SpostC) can alleviate hypoxia-reoxygenation injury of cardiomyocytes; however, the specific mechanism remains unclear. This study aimed to investigate whether SpostC promotes mitochondrial autophagy through the hypoxia-inducible factor-1 (HIF-1)/BCL2/adenovirus E1B 19-kDa-interacting protein 3 (BNIP3) signaling pathway to attenuate hypoxia-reoxygenation injury in cardiomyocytes. Methods The H9C2 cardiomyocyte hypoxia/reoxygenation model was established and treated with 2.4% sevoflurane at the beginning of reoxygenation. Cell damage was determined by measuring cell viability, lactate dehydrogenase activity, and apoptosis. Mitochondrial ultrastructural and autophagosomes were observed by transmission electron microscope. Western blotting was used to examine the expression of HIF-1, BNIP3, and Beclin-1 proteins. The effects of BNIP3 on promoting autophagy were determined using interfering RNA technology to silence BNIP3. Results Hypoxia-reoxygenation injury led to accumulation of autophagosomes in cardiomyocytes, and cell viability was significantly reduced, which seriously damaged cells. Sevoflurane postconditioning could upregulate HIF-1α and BNIP3 protein expression, promote autophagosome clearance, and reduce cell damage. However, these protective effects were inhibited by 2-methoxyestradiol or sinBNIP3. Conclusion Sevoflurane postconditioning can alleviate hypoxia-reoxygenation injury in cardiomyocytes, and this effect may be achieved by promoting mitochondrial autophagy through the HIF-1/BNIP3 signaling pathway.
bibliographic citation: Yang et al. (2019) Sevoflurane postconditioning alleviates hypoxia-reoxygenation injury of cardiomyocytes by promoting mitochondrial autophagy through the HIF-1/BNIP3 signaling pathway. PeerJ 7:e7165 https://doi.org/10.7717/peerj.7165
date submitted: 2019-01-17
date accepted: 2019-05-22
issued: 2019-06-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Long
author list: Agent
  family name: Wu
  given name: Jianjiang
author list: Agent
  family name: Xie
  given name: Peng
author list: Agent
  family name: Yu
  given name: Jin
author list: Agent
  family name: Li
  given name: Xin
author list: Agent
  family name: Wang
  given name: Jiang
author list: Agent
  family name: Zheng
  given name: Hong
doi: 10.7717/peerj.7165
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-24
copyright: © 2019 Yang et al.
attribution name: Yang et al.

Osteology and phylogeny of Robustichthys luopingensis, the largest holostean fish in the Middle Triassic
type: item
type: AcademicArticle
description: The extinct ray-finned fish taxon Robustichthys luopingensis from Luoping, eastern Yunnan, China represents the largest holostean known in the Middle Triassic. Despite its potential significance for investigating the holostean phylogeny and reconstructing the Triassic marine ecosystems, Robustichthys has so far not been described in detail and its phylogenetic position within the Holostei was controversy. This study provides a redescription and revision of Robustichthys based upon a comparative study of eight type specimens and nine new specimens. Newly recognized information includes a toothed parasphenoid, a pair of premaxillae not pierced by the olfactory nerve, a splint-like quadratojugal, a hatchet-shaped hyomandibula, an hourglass-shaped symplectic, anterior and posterior ceratohyals, a complete series of branchiostegal rays, and sclerotic bones. A revised reconstruction of Robustichthys is presented. Results of a cladistic analysis confirmed Robustichthys as an ionoscopiform within the Halecomorphi; the previous placements of Robustichthys as a basal ginglymodian and Ionoscopidae as a basal amiiform clade are not supported. The sister group relationship between Sinamiinae (Sinamia and Ikechaoamia) and Amiinae (Amia and Cyclurus) within the Amiidae is newly recognized. This revised topology provides new insights into the evolution and historical paleoecology of halecomorph fishes.
format: application/pdf
format: text/html
creator: Guang-Hui Xu
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.7184
publisher: PeerJ Inc.
rights: © 2019 Xu
abstract: The extinct ray-finned fish taxon Robustichthys luopingensis from Luoping, eastern Yunnan, China represents the largest holostean known in the Middle Triassic. Despite its potential significance for investigating the holostean phylogeny and reconstructing the Triassic marine ecosystems, Robustichthys has so far not been described in detail and its phylogenetic position within the Holostei was controversy. This study provides a redescription and revision of Robustichthys based upon a comparative study of eight type specimens and nine new specimens. Newly recognized information includes a toothed parasphenoid, a pair of premaxillae not pierced by the olfactory nerve, a splint-like quadratojugal, a hatchet-shaped hyomandibula, an hourglass-shaped symplectic, anterior and posterior ceratohyals, a complete series of branchiostegal rays, and sclerotic bones. A revised reconstruction of Robustichthys is presented. Results of a cladistic analysis confirmed Robustichthys as an ionoscopiform within the Halecomorphi; the previous placements of Robustichthys as a basal ginglymodian and Ionoscopidae as a basal amiiform clade are not supported. The sister group relationship between Sinamiinae (Sinamia and Ikechaoamia) and Amiinae (Amia and Cyclurus) within the Amiidae is newly recognized. This revised topology provides new insights into the evolution and historical paleoecology of halecomorph fishes.
bibliographic citation: Xu (2019) Osteology and phylogeny of Robustichthys luopingensis, the largest holostean fish in the Middle Triassic. PeerJ 7:e7184 https://doi.org/10.7717/peerj.7184
date submitted: 2019-04-19
date accepted: 2019-05-24
issued: 2019-06-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Guang-Hui
doi: 10.7717/peerj.7184
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-24
copyright: © 2019 Xu
attribution name: Xu

Isolation and identification of a halophilic and alkaliphilic microalgal strain
type: item
type: AcademicArticle
description: Halophilic and alkaliphilic microalgal strain SAE1 was isolated from the saline–alkaline soil of Songnen Plain of Northeast China. Morphological observation revealed that SAE1 has a simple cellular structure, single cell, spherical, diameter of four to six μm, cell wall of about 0.22 μm thick, two chloroplasts and one nucleus. Analysis of the phylogenetic tree constructed by 18S sequence homology suggests that SAE1 is highly homologous to Nannochloris sp. BLD-15, with only four base substitutions in the homologous region. SAE1 was initially considered as Nannochloris sp. Analysis of the halophilic and alkaliphilic characteristics of SAE1 indicates that it can grow under one M NaHCO3 and NaCl concentrations, with optimal growth under 400 mM NaHCO3 and 200 mM NaCl. The intracellular ultrastructure of SAE1 significantly changed after NaCl and NaHCO3 treatments. A large number of starch grains accumulated after treatment with 400 mM NaHCO3 in cells, but few were found after treatment with 200 mM NaCl and none in the living condition without treatment. We conjectured that one of the metabolic characteristics of alkaliphilic (NaHCO3) microalga SAE1 is the formation of massive starch grains, which induce glycerol anabolism and increase osmotic pressure, thereby enhancing its ability to resist saline–sodic conditions. This feature of alkaliphilic (NaHCO3) microalga SAE1 contributes to its growth in the carbonate soil of Songnen Plain.
format: application/pdf
format: text/html
creator: Chenxi Liu
creator: Jiali Liu
creator: Songmiao Hu
creator: Xin Wang
creator: Xuhui Wang
creator: Qingjie Guan
subject: Cell Biology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.7189
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Halophilic and alkaliphilic microalgal strain SAE1 was isolated from the saline–alkaline soil of Songnen Plain of Northeast China. Morphological observation revealed that SAE1 has a simple cellular structure, single cell, spherical, diameter of four to six μm, cell wall of about 0.22 μm thick, two chloroplasts and one nucleus. Analysis of the phylogenetic tree constructed by 18S sequence homology suggests that SAE1 is highly homologous to Nannochloris sp. BLD-15, with only four base substitutions in the homologous region. SAE1 was initially considered as Nannochloris sp. Analysis of the halophilic and alkaliphilic characteristics of SAE1 indicates that it can grow under one M NaHCO3 and NaCl concentrations, with optimal growth under 400 mM NaHCO3 and 200 mM NaCl. The intracellular ultrastructure of SAE1 significantly changed after NaCl and NaHCO3 treatments. A large number of starch grains accumulated after treatment with 400 mM NaHCO3 in cells, but few were found after treatment with 200 mM NaCl and none in the living condition without treatment. We conjectured that one of the metabolic characteristics of alkaliphilic (NaHCO3) microalga SAE1 is the formation of massive starch grains, which induce glycerol anabolism and increase osmotic pressure, thereby enhancing its ability to resist saline–sodic conditions. This feature of alkaliphilic (NaHCO3) microalga SAE1 contributes to its growth in the carbonate soil of Songnen Plain.
bibliographic citation: Liu et al. (2019) Isolation and identification of a halophilic and alkaliphilic microalgal strain. PeerJ 7:e7189 https://doi.org/10.7717/peerj.7189
date submitted: 2018-11-07
date accepted: 2019-05-25
issued: 2019-06-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Chenxi
author list: Agent
  family name: Liu
  given name: Jiali
author list: Agent
  family name: Hu
  given name: Songmiao
author list: Agent
  family name: Wang
  given name: Xin
author list: Agent
  family name: Wang
  given name: Xuhui
author list: Agent
  family name: Guan
  given name: Qingjie
doi: 10.7717/peerj.7189
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-24
copyright: © 2019 Liu et al.
attribution name: Liu et al.

Decoupled recovery of ecological communities after reclamation
type: item
type: AcademicArticle
description: Grassland restoration is largely focused on creating plant communities that match reference conditions. However, these communities reflect only a subset of the biodiversity of grassland systems. We conducted a multi-trophic study to assess ecosystem recovery following energy development for oil and gas extraction in northern US Great Plains rangelands. We compared soil factors, plant species composition and cover, and nematode trophic structuring between reclaimed oil and gas well sites (“reclaims”) that comprise a chronosequence of two—33 years since reclamation and adjacent, undeveloped rangeland at distances of 50 m and 150 m from reclaim edges. Soils and plant communities in reclaims did not match those on undeveloped rangeland even after 33 years. Reclaimed soils had higher salt concentrations and pH than undeveloped soils. Reclaims had lower overall plant cover, a greater proportion of exotic and ruderal plant cover and lower native plant species richness than undeveloped rangeland. However, nematode communities appear to have recovered following reclamation. Although total and omni-carnivorous nematode abundances differed between reclaimed well sites and undeveloped rangeland, community composition and structure did not. These findings suggest that current reclamation practices recover the functional composition of nematode communities, but not soil conditions or plant communities. Our results show that plant communities have failed to recover through reclamation: high soil salinity may create a persistent impediment to native plant growth and ecosystem recovery.
format: application/pdf
format: text/html
creator: Zachary A. Sylvain
creator: David H. Branson
creator: Tatyana A. Rand
creator: Natalie M. West
creator: Erin K. Espeland
subject: Biodiversity
subject: Ecology
subject: Environmental Impacts
description: doi:10.7717/peerj.7038
publisher: PeerJ Inc.
rights: © 2019
abstract: Grassland restoration is largely focused on creating plant communities that match reference conditions. However, these communities reflect only a subset of the biodiversity of grassland systems. We conducted a multi-trophic study to assess ecosystem recovery following energy development for oil and gas extraction in northern US Great Plains rangelands. We compared soil factors, plant species composition and cover, and nematode trophic structuring between reclaimed oil and gas well sites (“reclaims”) that comprise a chronosequence of two—33 years since reclamation and adjacent, undeveloped rangeland at distances of 50 m and 150 m from reclaim edges. Soils and plant communities in reclaims did not match those on undeveloped rangeland even after 33 years. Reclaimed soils had higher salt concentrations and pH than undeveloped soils. Reclaims had lower overall plant cover, a greater proportion of exotic and ruderal plant cover and lower native plant species richness than undeveloped rangeland. However, nematode communities appear to have recovered following reclamation. Although total and omni-carnivorous nematode abundances differed between reclaimed well sites and undeveloped rangeland, community composition and structure did not. These findings suggest that current reclamation practices recover the functional composition of nematode communities, but not soil conditions or plant communities. Our results show that plant communities have failed to recover through reclamation: high soil salinity may create a persistent impediment to native plant growth and ecosystem recovery.
bibliographic citation: Sylvain et al. (2019) Decoupled recovery of ecological communities after reclamation. PeerJ 7:e7038 https://doi.org/10.7717/peerj.7038
date submitted: 2018-09-13
date accepted: 2019-04-29
issued: 2019-06-21
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Sylvain
  given name: Zachary A.
author list: Agent
  family name: Branson
  given name: David H.
author list: Agent
  family name: Rand
  given name: Tatyana A.
author list: Agent
  family name: West
  given name: Natalie M.
author list: Agent
  family name: Espeland
  given name: Erin K.
doi: 10.7717/peerj.7038
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-21

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