PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparative analysis of the ribosomal DNA repeat unit (rDNA) of Perna viridis (Linnaeus, 1758) and Perna canaliculus (Gmelin, 1791)
items: Identification of Aloperine as an anti-apoptotic Bcl2 protein inhibitor in glioma cells
items: Effects of mechanical and chemical control on invasive Spartina alterniflora in the Yellow River Delta, China
items: Proteomics and bioinformatics analysis reveal potential roles of cadmium-binding proteins in cadmium tolerance and accumulation of Enterobacter cloacae
items: Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)
items: The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine
items: lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes
items: Type I-like behavior of the type II α7 nicotinic acetylcholine receptor positive allosteric modulator A-867744
items: Revealing biases in the sampling of ecological interaction networks
items: Nutrient availability induces community shifts in seagrass meadows grazed by turtles

Comparative analysis of the ribosomal DNA repeat unit (rDNA) of Perna viridis (Linnaeus, 1758) and Perna canaliculus (Gmelin, 1791)
type: item
type: AcademicArticle
description: Perna viridis and P. canaliculus are economically and ecologically important species of shellfish. In this study, the complete ribosomal DNA (rDNA) unit sequences of these species were determined for the first time. The gene order, 18S rRNA–internal transcribed spacer (ITS) 1–5.8S rRNA–ITS2–28S rRNA–intergenic spacer (IGS), was similar to that observed in other eukaryotes. The lengths of the P. viridis and P. canaliculus rDNA sequences ranged from 8,432 to 8,616 bp and from 7,597 to 7,610 bp, respectively, this variability was mainly attributable to the IGS region. The putative transcription termination site and initiation site were confirmed. Perna viridis and P. canaliculus rDNA contained two (length: 93 and 40 bp) and one (length: 131 bp) repeat motifs, respectively. Individual intra-species differences mainly involved the copy number of repeat units. In P. viridis, three cytosine-guanine (CpG) sites with sizes of 440, 1,075 and 537 bp were found to cover nearly the entire IGS sequence, whereas in P. canaliculus, two CpG islands with sizes of 361 and 484 bp were identified. The phylogenetic trees constructed with maximum likelihood and neighbour-joining methods and based on ITS sequences were identical and included three major clusters. Species of the same genus were easily clustered together.
format: application/pdf
format: text/html
creator: Zhansheng Guo
creator: Leng Han
creator: Zhenlin Liang
creator: Xuguang Hou
subject: Aquaculture, Fisheries and Fish Science
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.7644
publisher: PeerJ Inc.
rights: © 2019 Guo et al.
abstract: Perna viridis and P. canaliculus are economically and ecologically important species of shellfish. In this study, the complete ribosomal DNA (rDNA) unit sequences of these species were determined for the first time. The gene order, 18S rRNA–internal transcribed spacer (ITS) 1–5.8S rRNA–ITS2–28S rRNA–intergenic spacer (IGS), was similar to that observed in other eukaryotes. The lengths of the P. viridis and P. canaliculus rDNA sequences ranged from 8,432 to 8,616 bp and from 7,597 to 7,610 bp, respectively, this variability was mainly attributable to the IGS region. The putative transcription termination site and initiation site were confirmed. Perna viridis and P. canaliculus rDNA contained two (length: 93 and 40 bp) and one (length: 131 bp) repeat motifs, respectively. Individual intra-species differences mainly involved the copy number of repeat units. In P. viridis, three cytosine-guanine (CpG) sites with sizes of 440, 1,075 and 537 bp were found to cover nearly the entire IGS sequence, whereas in P. canaliculus, two CpG islands with sizes of 361 and 484 bp were identified. The phylogenetic trees constructed with maximum likelihood and neighbour-joining methods and based on ITS sequences were identical and included three major clusters. Species of the same genus were easily clustered together.
bibliographic citation: Guo et al. (2019) Comparative analysis of the ribosomal DNA repeat unit (rDNA) of Perna viridis (Linnaeus, 1758) and Perna canaliculus (Gmelin, 1791). PeerJ 7:e7644 https://doi.org/10.7717/peerj.7644
date submitted: 2019-03-27
date accepted: 2019-08-08
issued: 2019-09-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Zhansheng
author list: Agent
  family name: Han
  given name: Leng
author list: Agent
  family name: Liang
  given name: Zhenlin
author list: Agent
  family name: Hou
  given name: Xuguang
doi: 10.7717/peerj.7644
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-03
copyright: © 2019 Guo et al.
attribution name: Guo et al.

Identification of Aloperine as an anti-apoptotic Bcl2 protein inhibitor in glioma cells
type: item
type: AcademicArticle
description: Objective Aloperine (ALO), an alkaloid isolated from the leaves of Sophora alopecuroides, has been suggested to exhibit anti-inflammatory and anti-tumor properties and is traditionally used to treat various human diseases, including cancer. However, limited information is available about the mechanisms that determine the anti-tumor activities of ALO. Methods Herein, through comprehensive bioinformatics methods and in vitro functional analyses, we evaluated the detailed anti-tumor mechanisms of ALO. Results Using the databases Bioinformatics analysis tool for molecular mechanism of traditional Chinese medicine and PubChem Project, we identified the potential targets of ALO. A protein–protein interaction network was constructed to determine the relationship among these probable targets. Functional enrichment analysis revealed that ALO is potentially involved in the induction of apoptosis. In addition, molecular docking demonstrated that ALO expectedly docks into the active pocket of the Bcl2 protein, suggesting Bcl2 as a direct target of ALO. Moreover, western blot and qPCR analysis showed that ALO downregulated Bcl2 expression in human glioma cell lines, SK-N-AS and U118. Using flow cytometry methods, we further confirmed that ALO significantly promotes apoptosis in SK-N-AS and U118 cell lines, similar to the effect induced by ABT-737, a well-known Bcl2 inhibitor. In addition, Bcl-2 overexpression could rescue ALO-induced Bcl-2 inhibition and suppress pro-apoptotic effects in glioma cells. Conclusion Taken together, these findings suggest that the natural agent ALO effectively enhances apoptosis by acting as a potential Bcl2 inhibitor in human glioma cells.
format: application/pdf
format: text/html
creator: Zhijie Xu
creator: Xiang Wang
creator: Xi Chen
creator: Shuangshuang Zeng
creator: Long Qian
creator: Jie Wei
creator: Zhicheng Gong
creator: Yuanliang Yan
subject: Molecular Biology
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.7652
publisher: PeerJ Inc.
rights: © 2019 Xu et al.
abstract: Objective Aloperine (ALO), an alkaloid isolated from the leaves of Sophora alopecuroides, has been suggested to exhibit anti-inflammatory and anti-tumor properties and is traditionally used to treat various human diseases, including cancer. However, limited information is available about the mechanisms that determine the anti-tumor activities of ALO. Methods Herein, through comprehensive bioinformatics methods and in vitro functional analyses, we evaluated the detailed anti-tumor mechanisms of ALO. Results Using the databases Bioinformatics analysis tool for molecular mechanism of traditional Chinese medicine and PubChem Project, we identified the potential targets of ALO. A protein–protein interaction network was constructed to determine the relationship among these probable targets. Functional enrichment analysis revealed that ALO is potentially involved in the induction of apoptosis. In addition, molecular docking demonstrated that ALO expectedly docks into the active pocket of the Bcl2 protein, suggesting Bcl2 as a direct target of ALO. Moreover, western blot and qPCR analysis showed that ALO downregulated Bcl2 expression in human glioma cell lines, SK-N-AS and U118. Using flow cytometry methods, we further confirmed that ALO significantly promotes apoptosis in SK-N-AS and U118 cell lines, similar to the effect induced by ABT-737, a well-known Bcl2 inhibitor. In addition, Bcl-2 overexpression could rescue ALO-induced Bcl-2 inhibition and suppress pro-apoptotic effects in glioma cells. Conclusion Taken together, these findings suggest that the natural agent ALO effectively enhances apoptosis by acting as a potential Bcl2 inhibitor in human glioma cells.
bibliographic citation: Xu et al. (2019) Identification of Aloperine as an anti-apoptotic Bcl2 protein inhibitor in glioma cells. PeerJ 7:e7652 https://doi.org/10.7717/peerj.7652
date submitted: 2019-05-29
date accepted: 2019-08-09
issued: 2019-09-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Zhijie
author list: Agent
  family name: Wang
  given name: Xiang
author list: Agent
  family name: Chen
  given name: Xi
author list: Agent
  family name: Zeng
  given name: Shuangshuang
author list: Agent
  family name: Qian
  given name: Long
author list: Agent
  family name: Wei
  given name: Jie
author list: Agent
  family name: Gong
  given name: Zhicheng
author list: Agent
  family name: Yan
  given name: Yuanliang
doi: 10.7717/peerj.7652
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-03
copyright: © 2019 Xu et al.
attribution name: Xu et al.

Effects of mechanical and chemical control on invasive Spartina alterniflora in the Yellow River Delta, China
type: item
type: AcademicArticle
description: Spartina alterniflora is one of the most noxious invasive plants in China and many other regions. Exploring environmentally friendly, economic and effective techniques for controlling Spartina alterniflora is of great significance for the management of coastal wetlands. In the present study, different approaches, including mowing and waterlogging, mowing and tilling and herbicide application, were used to control Spartina alterniflora. The results suggest that the integrated approach of mowing and waterlogging could eradicate Spartina alterniflora, the herbicide haloxyfop-r-methyl could kill almost all the Spartina alterniflora, and the integrated approach of mowing and tilling at the end of the growing season was a perfect way to inhibit the germination of Spartina alterniflora in the following year. However, no matter which control approach is adopted, secondary invasion of Spartina alterniflora must be avoided. Otherwise, all the efforts will be wasted in a few years.
format: application/pdf
format: text/html
creator: Baohua Xie
creator: Guangxuan Han
creator: Peiyang Qiao
creator: Baoling Mei
creator: Qing Wang
creator: Yingfeng Zhou
creator: Anfeng Zhang
creator: Weimin Song
creator: Bo Guan
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Natural Resource Management
description: doi:10.7717/peerj.7655
publisher: PeerJ Inc.
rights: © 2019 Xie et al.
abstract: Spartina alterniflora is one of the most noxious invasive plants in China and many other regions. Exploring environmentally friendly, economic and effective techniques for controlling Spartina alterniflora is of great significance for the management of coastal wetlands. In the present study, different approaches, including mowing and waterlogging, mowing and tilling and herbicide application, were used to control Spartina alterniflora. The results suggest that the integrated approach of mowing and waterlogging could eradicate Spartina alterniflora, the herbicide haloxyfop-r-methyl could kill almost all the Spartina alterniflora, and the integrated approach of mowing and tilling at the end of the growing season was a perfect way to inhibit the germination of Spartina alterniflora in the following year. However, no matter which control approach is adopted, secondary invasion of Spartina alterniflora must be avoided. Otherwise, all the efforts will be wasted in a few years.
bibliographic citation: Xie et al. (2019) Effects of mechanical and chemical control on invasive Spartina alterniflora in the Yellow River Delta, China. PeerJ 7:e7655 https://doi.org/10.7717/peerj.7655
date submitted: 2019-04-21
date accepted: 2019-08-10
issued: 2019-09-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Baohua
author list: Agent
  family name: Han
  given name: Guangxuan
author list: Agent
  family name: Qiao
  given name: Peiyang
author list: Agent
  family name: Mei
  given name: Baoling
author list: Agent
  family name: Wang
  given name: Qing
author list: Agent
  family name: Zhou
  given name: Yingfeng
author list: Agent
  family name: Zhang
  given name: Anfeng
author list: Agent
  family name: Song
  given name: Weimin
author list: Agent
  family name: Guan
  given name: Bo
doi: 10.7717/peerj.7655
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-03
copyright: © 2019 Xie et al.
attribution name: Xie et al.

Proteomics and bioinformatics analysis reveal potential roles of cadmium-binding proteins in cadmium tolerance and accumulation of Enterobacter cloacae
type: item
type: AcademicArticle
description: Background Enterobacter cloacae (EC) is a Gram-negative bacterium that has been utilized extensively in biotechnological and environmental science applications, possibly because of its high capability for adapting itself and surviving in hazardous conditions. A search for the EC from agricultural and industrial areas that possesses high capability to tolerate and/or accumulate cadmium ions has been conducted in this study. Plausible mechanisms of cellular adaptations in the presence of toxic cadmium have also been proposed. Methods Nine strains of EC were isolated and subsequently identified by biochemical characterization and MALDI-Biotyper. Minimum inhibitory concentrations (MICs) against cadmium, zinc and copper ions were determined by agar dilution method. Growth tolerance against cadmium ions was spectrophotometrically monitored at 600 nm. Cadmium accumulation at both cellular and protein levels was investigated using atomic absorption spectrophotometer. Proteomics analysis by 2D-DIGE in conjunction with protein identification by QTOF-LC-MS/MS was used to study differentially expressed proteins between the tolerant and intolerant strains as consequences of cadmium exposure. Expression of such proteins was confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Bioinformatics tools were applied to propose the functional roles of cadmium-binding protein and its association in cadmium tolerance mechanisms. Results The cadmium-tolerant strain (EC01) and intolerant strain (EC07) with the MICs of 1.6 and 0.4 mM, respectively, were isolated. The whole cell lysate of EC01 exhibited approximately two-fold higher in cadmium binding capability than those of the EC07 and ATCC 13047, possibly by the expression of Cd-binding proteins. Our proteomics analysis revealed the higher expression of DUF326-like domain (a high cysteine-rich protein) of up to 220 fold in the EC01 than that of the EC07. Confirmation of the transcription level of this gene b…
format: application/pdf
format: text/html
creator: Kitipong Chuanboon
creator: Piyada Na Nakorn
creator: Supitcha Pannengpetch
creator: Vishuda Laengsri
creator: Pornlada Nuchnoi
creator: Chartchalerm Isarankura-Na-Ayudhya
creator: Patcharee Isarankura-Na-Ayudhya
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6904
publisher: PeerJ Inc.
rights: © 2019 Chuanboon et al.
abstract: Background Enterobacter cloacae (EC) is a Gram-negative bacterium that has been utilized extensively in biotechnological and environmental science applications, possibly because of its high capability for adapting itself and surviving in hazardous conditions. A search for the EC from agricultural and industrial areas that possesses high capability to tolerate and/or accumulate cadmium ions has been conducted in this study. Plausible mechanisms of cellular adaptations in the presence of toxic cadmium have also been proposed. Methods Nine strains of EC were isolated and subsequently identified by biochemical characterization and MALDI-Biotyper. Minimum inhibitory concentrations (MICs) against cadmium, zinc and copper ions were determined by agar dilution method. Growth tolerance against cadmium ions was spectrophotometrically monitored at 600 nm. Cadmium accumulation at both cellular and protein levels was investigated using atomic absorption spectrophotometer. Proteomics analysis by 2D-DIGE in conjunction with protein identification by QTOF-LC-MS/MS was used to study differentially expressed proteins between the tolerant and intolerant strains as consequences of cadmium exposure. Expression of such proteins was confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Bioinformatics tools were applied to propose the functional roles of cadmium-binding protein and its association in cadmium tolerance mechanisms. Results The cadmium-tolerant strain (EC01) and intolerant strain (EC07) with the MICs of 1.6 and 0.4 mM, respectively, were isolated. The whole cell lysate of EC01 exhibited approximately two-fold higher in cadmium binding capability than those of the EC07 and ATCC 13047, possibly by the expression of Cd-binding proteins. Our proteomics analysis revealed the higher expression of DUF326-like domain (a high cysteine-rich protein) of up to 220 fold in the EC01 than that of the EC07. Confirmation of the transcription level of this gene b…
bibliographic citation: Chuanboon et al. (2019) Proteomics and bioinformatics analysis reveal potential roles of cadmium-binding proteins in cadmium tolerance and accumulation of Enterobacter cloacae. PeerJ 7:e6904 https://doi.org/10.7717/peerj.6904
date submitted: 2019-02-26
date accepted: 2019-04-03
issued: 2019-09-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chuanboon
  given name: Kitipong
author list: Agent
  family name: Na Nakorn
  given name: Piyada
author list: Agent
  family name: Pannengpetch
  given name: Supitcha
author list: Agent
  family name: Laengsri
  given name: Vishuda
author list: Agent
  family name: Nuchnoi
  given name: Pornlada
author list: Agent
  family name: Isarankura-Na-Ayudhya
  given name: Chartchalerm
author list: Agent
  family name: Isarankura-Na-Ayudhya
  given name: Patcharee
doi: 10.7717/peerj.6904
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: ©2019 Chuanboon et al.
attribution name: Chuanboon et al.

Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)
type: item
type: AcademicArticle
description: Background The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India. Results We tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57–88%), polymorphism (3–9 alleles), heterozygosity (0.23–0.63) and produced a cumulative misidentification rate or PID(unbiased) and PID(sibs) value of 4.7 × 10−10 and 1.5 × 10−4, respectively, indicating a high statistical power in individual discrimination from poor quality samples. Conclusion Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive,…
format: application/pdf
format: text/html
creator: Shrushti Modi
creator: Bilal Habib
creator: Pallavi Ghaskadbi
creator: Parag Nigam
creator: Samrat Mondol
subject: Conservation Biology
subject: Genetics
description: doi:10.7717/peerj.7453
publisher: PeerJ Inc.
rights: © 2019 Modi et al.
abstract: Background The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India. Results We tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57–88%), polymorphism (3–9 alleles), heterozygosity (0.23–0.63) and produced a cumulative misidentification rate or PID(unbiased) and PID(sibs) value of 4.7 × 10−10 and 1.5 × 10−4, respectively, indicating a high statistical power in individual discrimination from poor quality samples. Conclusion Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive,…
bibliographic citation: Modi et al. (2019) Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus). PeerJ 7:e7453 https://doi.org/10.7717/peerj.7453
date submitted: 2018-10-29
date accepted: 2019-07-10
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Modi
  given name: Shrushti
author list: Agent
  family name: Habib
  given name: Bilal
author list: Agent
  family name: Ghaskadbi
  given name: Pallavi
author list: Agent
  family name: Nigam
  given name: Parag
author list: Agent
  family name: Mondol
  given name: Samrat
doi: 10.7717/peerj.7453
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: © 2019 Modi et al.
attribution name: Modi et al.

The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine
type: item
type: AcademicArticle
description: The thylacine is popularly used as a classic example of convergent evolution between placental and marsupial mammals. Despite having a fossil history spanning over 20 million years and known since the 1960s, the thylacine is often presented in both scientific literature and popular culture as an evolutionary singleton unique in its morphological and ecological adaptations within the Australian ecosystem. Here, we synthesise and critically evaluate the current state of published knowledge regarding the known fossil record of Thylacinidae prior to the appearance of the modern species. We also present phylogenetic analyses and body mass estimates of the thylacinids to reveal trends in the evolution of hypercarnivory and ecological shifts within the family. We find support that Mutpuracinus archibaldi occupies an uncertain position outside of Thylacinidae, and consider Nimbacinus richi to likely be synonymous with N. dicksoni. The Thylacinidae were small-bodied (< ~8 kg) unspecialised faunivores until after the ~15–14 Ma middle Miocene climatic transition (MMCT). After the MMCT they dramatically increase in size and develop adaptations to a hypercarnivorous diet, potentially in response to the aridification of the Australian environment and the concomitant radiation of dasyurids. This fossil history of the thylacinids provides a foundation for understanding the ecology of the modern thylacine. It provides a framework for future studies of the evolution of hypercarnivory, cursoriality, morphological and ecological disparity, and convergence within mammalian carnivores.
format: application/pdf
format: text/html
creator: Douglass S. Rovinsky
creator: Alistair R. Evans
creator: Justin W. Adams
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.7457
publisher: PeerJ Inc.
rights: © 2019 Rovinsky et al.
abstract: The thylacine is popularly used as a classic example of convergent evolution between placental and marsupial mammals. Despite having a fossil history spanning over 20 million years and known since the 1960s, the thylacine is often presented in both scientific literature and popular culture as an evolutionary singleton unique in its morphological and ecological adaptations within the Australian ecosystem. Here, we synthesise and critically evaluate the current state of published knowledge regarding the known fossil record of Thylacinidae prior to the appearance of the modern species. We also present phylogenetic analyses and body mass estimates of the thylacinids to reveal trends in the evolution of hypercarnivory and ecological shifts within the family. We find support that Mutpuracinus archibaldi occupies an uncertain position outside of Thylacinidae, and consider Nimbacinus richi to likely be synonymous with N. dicksoni. The Thylacinidae were small-bodied (< ~8 kg) unspecialised faunivores until after the ~15–14 Ma middle Miocene climatic transition (MMCT). After the MMCT they dramatically increase in size and develop adaptations to a hypercarnivorous diet, potentially in response to the aridification of the Australian environment and the concomitant radiation of dasyurids. This fossil history of the thylacinids provides a foundation for understanding the ecology of the modern thylacine. It provides a framework for future studies of the evolution of hypercarnivory, cursoriality, morphological and ecological disparity, and convergence within mammalian carnivores.
bibliographic citation: Rovinsky et al. (2019) The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine. PeerJ 7:e7457 https://doi.org/10.7717/peerj.7457
date submitted: 2019-03-27
date accepted: 2019-07-10
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rovinsky
  given name: Douglass S.
author list: Agent
  family name: Evans
  given name: Alistair R.
author list: Agent
  family name: Adams
  given name: Justin W.
doi: 10.7717/peerj.7457
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: © 2019 Rovinsky et al.
attribution name: Rovinsky et al.

lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes
type: item
type: AcademicArticle
description: Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or < − 2.0-fold change; p < 0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. QPCR was used to validate chip results. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, the gain/loss of function experiments of lnc-SAMD14-4 was implemented in IL-1β-treated human chondrocytes. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA.
format: application/pdf
format: text/html
creator: Haibin Zhang
creator: Cheng Chen
creator: Yinghong Cui
creator: Yuqing Li
creator: Zhaojun Wang
creator: Xinzhan Mao
creator: Pengcheng Dou
creator: Yihan Li
creator: Chi Ma
subject: Genetics
subject: Genomics
subject: Orthopedics
subject: Ethical Issues
description: doi:10.7717/peerj.7491
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or < − 2.0-fold change; p < 0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. QPCR was used to validate chip results. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, the gain/loss of function experiments of lnc-SAMD14-4 was implemented in IL-1β-treated human chondrocytes. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA.
bibliographic citation: Zhang et al. (2019) lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes. PeerJ 7:e7491 https://doi.org/10.7717/peerj.7491
date submitted: 2018-05-28
date accepted: 2019-07-16
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Haibin
author list: Agent
  family name: Chen
  given name: Cheng
author list: Agent
  family name: Cui
  given name: Yinghong
author list: Agent
  family name: Li
  given name: Yuqing
author list: Agent
  family name: Wang
  given name: Zhaojun
author list: Agent
  family name: Mao
  given name: Xinzhan
author list: Agent
  family name: Dou
  given name: Pengcheng
author list: Agent
  family name: Li
  given name: Yihan
author list: Agent
  family name: Ma
  given name: Chi
doi: 10.7717/peerj.7491
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Type I-like behavior of the type II α7 nicotinic acetylcholine receptor positive allosteric modulator A-867744
type: item
type: AcademicArticle
description: Cognitive impairment often involves the decreased expression or hypofunction of alpha 7-type nicotinic acetylcholine receptors (α7 nAChRs). Agonists or positive allosteric modulators (PAMs) of α7 nAChRs are known to be potential treatments for dementias, different neurodegenerative disorders, pain syndromes and conditions involving inflammation. In some of these conditions, it is desirable to maintain the temporal precision of fast cholinergic events, while in others, this temporal precision is unnecessary. For this reason, the optimal therapeutic effect for distinct indications may require PAMs with different mechanisms of action. The two major mechanisms are called “type I”, which are compounds that augment α7 nAChR-mediated currents but maintain their characteristic fast kinetics; and “type II”, which are compounds that produce augmented and prolonged currents. In this study, we performed a kinetic analysis of two type II PAMs of the α7 nAChR: PNU-120596 and A-867744, using a fast perfusion method that allowed high temporal resolution. We characterized the type of modulation produced by the two compounds, the state-dependence of the modulatory action, and the interaction between the two compounds. We found fundamental differences between the modulation mechanisms by PNU-120596 and A-867744. Most importantly, during brief agonist pulses, A-867744 caused a strikingly type I-like modulation, while PNU-120596 caused a type II-like prolonged activation. Our results demonstrate that specific compounds, even though all labeled as type II PAMs, can behave in completely different ways, including their onset and offset kinetics, state preference, and single channel open time. Our results emphasize that subtle details of the mechanism of action may be significant in assessing the therapeutic applicability of α7 nAChR PAM compounds.
format: application/pdf
format: text/html
creator: Krisztina Pesti
creator: Peter Lukacs
creator: Arpad Mike
subject: Biophysics
subject: Neuroscience
subject: Pharmacology
description: doi:10.7717/peerj.7542
publisher: PeerJ Inc.
rights: © 2019 Pesti et al.
abstract: Cognitive impairment often involves the decreased expression or hypofunction of alpha 7-type nicotinic acetylcholine receptors (α7 nAChRs). Agonists or positive allosteric modulators (PAMs) of α7 nAChRs are known to be potential treatments for dementias, different neurodegenerative disorders, pain syndromes and conditions involving inflammation. In some of these conditions, it is desirable to maintain the temporal precision of fast cholinergic events, while in others, this temporal precision is unnecessary. For this reason, the optimal therapeutic effect for distinct indications may require PAMs with different mechanisms of action. The two major mechanisms are called “type I”, which are compounds that augment α7 nAChR-mediated currents but maintain their characteristic fast kinetics; and “type II”, which are compounds that produce augmented and prolonged currents. In this study, we performed a kinetic analysis of two type II PAMs of the α7 nAChR: PNU-120596 and A-867744, using a fast perfusion method that allowed high temporal resolution. We characterized the type of modulation produced by the two compounds, the state-dependence of the modulatory action, and the interaction between the two compounds. We found fundamental differences between the modulation mechanisms by PNU-120596 and A-867744. Most importantly, during brief agonist pulses, A-867744 caused a strikingly type I-like modulation, while PNU-120596 caused a type II-like prolonged activation. Our results demonstrate that specific compounds, even though all labeled as type II PAMs, can behave in completely different ways, including their onset and offset kinetics, state preference, and single channel open time. Our results emphasize that subtle details of the mechanism of action may be significant in assessing the therapeutic applicability of α7 nAChR PAM compounds.
bibliographic citation: Pesti et al. (2019) Type I-like behavior of the type II α7 nicotinic acetylcholine receptor positive allosteric modulator A-867744. PeerJ 7:e7542 https://doi.org/10.7717/peerj.7542
date submitted: 2019-03-05
date accepted: 2019-07-24
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pesti
  given name: Krisztina
author list: Agent
  family name: Lukacs
  given name: Peter
author list: Agent
  family name: Mike
  given name: Arpad
doi: 10.7717/peerj.7542
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: ©2019 Pesti et al.
attribution name: Pesti et al.

Revealing biases in the sampling of ecological interaction networks
type: item
type: AcademicArticle
description: The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases with respect to both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly heterogeneous. These ecological and statistical issues directly affect ecologists’ abilities to accurately construct ecological networks. However, statistical biases introduced by sampling are difficult to quantify in the absence of full knowledge of the underlying ecological network’s structure. To explore properties of large-scale ecological networks, we developed the software EcoNetGen, which constructs and samples networks with predetermined topologies. These networks may represent a wide variety of communities that vary in size and types of ecological interactions. We sampled these networks with different mathematical sampling designs that correspond to methods used in field observations. The observed networks generated by each sampling process were then analyzed with respect to the number of components, size of components and other network metrics. We show that the sampling effort needed to estimate underlying network properties depends strongly both on the sampling design and on the underlying network topology. In particular, networks with random or scale-free modules require more complete sampling to reveal their structure, compared to networks whose modules are nested or bipartite. Overall, modules with nested structure were the easiest to detect, regardless of the sampling design used. Sampling a network starting with any species that had a high degree (e.g., abundant generalist species) was consistently found to be the most accurate strategy to estimate network structure. Because high-degree species tend to be generalists, abundant in natural communities relative to specialists, and connected to each other, sampling b…
format: application/pdf
format: text/html
creator: Marcus A.M. de Aguiar
creator: Erica A. Newman
creator: Mathias M. Pires
creator: Justin D. Yeakel
creator: Carl Boettiger
creator: Laura A. Burkle
creator: Dominique Gravel
creator: Paulo R. Guimarães
creator: James L. O’Donnell
creator: Timothée Poisot
creator: Marie-Josée Fortin
creator: David H. Hembry
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Mathematical Biology
subject: Data Science
description: doi:10.7717/peerj.7566
publisher: PeerJ Inc.
rights: © 2019 de Aguiar et al.
abstract: The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases with respect to both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly heterogeneous. These ecological and statistical issues directly affect ecologists’ abilities to accurately construct ecological networks. However, statistical biases introduced by sampling are difficult to quantify in the absence of full knowledge of the underlying ecological network’s structure. To explore properties of large-scale ecological networks, we developed the software EcoNetGen, which constructs and samples networks with predetermined topologies. These networks may represent a wide variety of communities that vary in size and types of ecological interactions. We sampled these networks with different mathematical sampling designs that correspond to methods used in field observations. The observed networks generated by each sampling process were then analyzed with respect to the number of components, size of components and other network metrics. We show that the sampling effort needed to estimate underlying network properties depends strongly both on the sampling design and on the underlying network topology. In particular, networks with random or scale-free modules require more complete sampling to reveal their structure, compared to networks whose modules are nested or bipartite. Overall, modules with nested structure were the easiest to detect, regardless of the sampling design used. Sampling a network starting with any species that had a high degree (e.g., abundant generalist species) was consistently found to be the most accurate strategy to estimate network structure. Because high-degree species tend to be generalists, abundant in natural communities relative to specialists, and connected to each other, sampling b…
bibliographic citation: de Aguiar et al. (2019) Revealing biases in the sampling of ecological interaction networks. PeerJ 7:e7566 https://doi.org/10.7717/peerj.7566
date submitted: 2019-04-23
date accepted: 2019-07-29
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Aguiar
  given name: Marcus A.M.
author list: Agent
  family name: Newman
  given name: Erica A.
author list: Agent
  family name: Pires
  given name: Mathias M.
author list: Agent
  family name: Yeakel
  given name: Justin D.
author list: Agent
  family name: Boettiger
  given name: Carl
author list: Agent
  family name: Burkle
  given name: Laura A.
author list: Agent
  family name: Gravel
  given name: Dominique
author list: Agent
  family name: Guimarães
  given name: Paulo R.
author list: Agent
  family name: O’Donnell
  given name: James L.
author list: Agent
  family name: Poisot
  given name: Timothée
author list: Agent
  family name: Fortin
  given name: Marie-Josée
author list: Agent
  family name: Hembry
  given name: David H.
doi: 10.7717/peerj.7566
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: © 2019 de Aguiar et al.
attribution name: de Aguiar et al.

Nutrient availability induces community shifts in seagrass meadows grazed by turtles
type: item
type: AcademicArticle
description: In the Caribbean, green turtles graze seagrass meadows dominated by Thalassia testudinum through rotational grazing, resulting in the creation of grazed and recovering (abandoned) patches surrounded by ungrazed seagrasses. We evaluated the seagrass community and its environment along a turtle grazing gradient; with the duration of (simulated) grazing as a proxy for the level of grazing pressure. The grazing levels consisted of Short-term (4 months clipping), Medium-term (8 months clipping), Long-term grazing (8 months of clipping in previously grazed areas), 8-months recovery of previously grazed patches, and ungrazed or unclipped patches as controls. We measured biomass and density of the seagrasses and rhizophytic algae, and changes in sediment parameters. Medium- and Long-term grazing promoted a shift in community species composition. At increasing grazing pressure, the total biomass of T. testudinum declined, whereas that of early-successional increased. Ammonium concentrations were highest in the patches of Medium-term (9.2 + 0.8 μM) and Long-term grazing levels (11.0 + 2.2 μM) and were lowest in the control areas (4.6 + 1.5 μM). T. testudinum is a late-successional species that maintains sediment nutrient concentrations at levels below the requirements of early-successional species when dominant. When the abundance of this species declines due to grazing, these resources become available, likely driving a shift in community composition toward a higher abundance of early-successional species.
format: application/pdf
format: text/html
creator: Isis Gabriela Martínez López
creator: Marloes van Den Akker
creator: Liene Walk
creator: Marieke M. van Katwijk
creator: Tjisse van Der Heide
creator: Brigitta I. van Tussenbroek
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.7570
publisher: PeerJ Inc.
rights: © 2019 Martínez López et al.
abstract: In the Caribbean, green turtles graze seagrass meadows dominated by Thalassia testudinum through rotational grazing, resulting in the creation of grazed and recovering (abandoned) patches surrounded by ungrazed seagrasses. We evaluated the seagrass community and its environment along a turtle grazing gradient; with the duration of (simulated) grazing as a proxy for the level of grazing pressure. The grazing levels consisted of Short-term (4 months clipping), Medium-term (8 months clipping), Long-term grazing (8 months of clipping in previously grazed areas), 8-months recovery of previously grazed patches, and ungrazed or unclipped patches as controls. We measured biomass and density of the seagrasses and rhizophytic algae, and changes in sediment parameters. Medium- and Long-term grazing promoted a shift in community species composition. At increasing grazing pressure, the total biomass of T. testudinum declined, whereas that of early-successional increased. Ammonium concentrations were highest in the patches of Medium-term (9.2 + 0.8 μM) and Long-term grazing levels (11.0 + 2.2 μM) and were lowest in the control areas (4.6 + 1.5 μM). T. testudinum is a late-successional species that maintains sediment nutrient concentrations at levels below the requirements of early-successional species when dominant. When the abundance of this species declines due to grazing, these resources become available, likely driving a shift in community composition toward a higher abundance of early-successional species.
bibliographic citation: Martínez López et al. (2019) Nutrient availability induces community shifts in seagrass meadows grazed by turtles. PeerJ 7:e7570 https://doi.org/10.7717/peerj.7570
date submitted: 2019-04-04
date accepted: 2019-07-29
issued: 2019-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez López
  given name: Isis Gabriela
author list: Agent
  family name: van Den Akker
  given name: Marloes
author list: Agent
  family name: Walk
  given name: Liene
author list: Agent
  family name: van Katwijk
  given name: Marieke M.
author list: Agent
  family name: van Der Heide
  given name: Tjisse
author list: Agent
  family name: van Tussenbroek
  given name: Brigitta I.
doi: 10.7717/peerj.7570
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-02
copyright: © 2019 Martínez López et al.
attribution name: Martínez López et al.

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