PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Importance of considering interoceptive abilities in alexithymia assessment
items: Magnetically directed antioxidant and antimicrobial agent: synthesis and surface functionalization of magnetite with quercetin
items: Validating anthropogenic threat maps as a tool for assessing river ecological integrity in Andean–Amazon basins
items: Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey
items: New sources of Sym2A allele in the pea (Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX
items: Transcriptional characterization and response to defense elicitors of mevalonate pathway genes in cotton (Gossypium arboreum L.)
items: Roles of phytohormone changes in the grain yield of rice plants exposed to heat: a review
items: Low expression or hypermethylation of PLK2 might predict favorable prognosis for patients with glioblastoma multiforme
items: Hematological convergence between Mesozoic marine reptiles (Sauropterygia) and extant aquatic amniotes elucidates diving adaptations in plesiosaurs
items: Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum)

Importance of considering interoceptive abilities in alexithymia assessment
type: item
type: AcademicArticle
description: Background Recent studies have shown that people with high alexithymia scores have decreased interoceptive abilities, which can be associated with psychological and physical disorders. Early assessments of the alexithymia trait included the evaluation of these abilities through the dimension measuring the difficulty in identifying and distinguishing between feelings and bodily sensations (the 26-item Toronto Alexithymia Scale; TAS-26). The revised version of the TAS, the TAS-20, contains a three-factor solution that does not involve a dimension assessing interoceptive abilities. However, the three items allowing the evaluation of these abilities are still present in the TAS-20. In this context, we hypothesized that the 3 items which assess interoceptive abilities in the TAS-20 should constitute an independent factor. In addition to exploring the internal structure of the TAS-20, we examined its external validity by assessing the relationships between the new factors and self-reported measures of personality trait and psychological and physical health. Method Two online studies (N = 253 and N = 287) were performed. The participants completed the TAS-20 and a set of psychological questionnaires (e.g., anxiety, depression) and health questions (e.g., “Do you suffer from a somatic disorder?”). The structure of the TAS-20 was examined using exploratory factor analysis (EFA), followed by an investigation of the relationships between the resulting new factors and other psychological and health data using regressions. In both studies, EFA revealed a new structure of the questionnaire consisting of four dimensions: (1) difficulty in the awareness of feelings, (2) externally oriented thinking, (3) difficulty in interoceptive abilities, and (4) poor affective sharing. The first factor was positively associated with all self-reported psychological and personality trait measures while the third factor was associated more with somatic disorders and medication intake. Results Our …
format: application/pdf
format: text/html
creator: Alicia Fournier
creator: Olivier Luminet
creator: Michael Dambrun
creator: Frédéric Dutheil
creator: Sonia Pellissier
creator: Laurie Mondillon
subject: Global Health
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.7615
publisher: PeerJ Inc.
rights: © 2019 Fournier et al.
abstract: Background Recent studies have shown that people with high alexithymia scores have decreased interoceptive abilities, which can be associated with psychological and physical disorders. Early assessments of the alexithymia trait included the evaluation of these abilities through the dimension measuring the difficulty in identifying and distinguishing between feelings and bodily sensations (the 26-item Toronto Alexithymia Scale; TAS-26). The revised version of the TAS, the TAS-20, contains a three-factor solution that does not involve a dimension assessing interoceptive abilities. However, the three items allowing the evaluation of these abilities are still present in the TAS-20. In this context, we hypothesized that the 3 items which assess interoceptive abilities in the TAS-20 should constitute an independent factor. In addition to exploring the internal structure of the TAS-20, we examined its external validity by assessing the relationships between the new factors and self-reported measures of personality trait and psychological and physical health. Method Two online studies (N = 253 and N = 287) were performed. The participants completed the TAS-20 and a set of psychological questionnaires (e.g., anxiety, depression) and health questions (e.g., “Do you suffer from a somatic disorder?”). The structure of the TAS-20 was examined using exploratory factor analysis (EFA), followed by an investigation of the relationships between the resulting new factors and other psychological and health data using regressions. In both studies, EFA revealed a new structure of the questionnaire consisting of four dimensions: (1) difficulty in the awareness of feelings, (2) externally oriented thinking, (3) difficulty in interoceptive abilities, and (4) poor affective sharing. The first factor was positively associated with all self-reported psychological and personality trait measures while the third factor was associated more with somatic disorders and medication intake. Results Our …
bibliographic citation: Fournier et al. (2019) Importance of considering interoceptive abilities in alexithymia assessment. PeerJ 7:e7615 https://doi.org/10.7717/peerj.7615
date submitted: 2019-03-26
date accepted: 2019-08-05
issued: 2019-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fournier
  given name: Alicia
author list: Agent
  family name: Luminet
  given name: Olivier
author list: Agent
  family name: Dambrun
  given name: Michael
author list: Agent
  family name: Dutheil
  given name: Frédéric
author list: Agent
  family name: Pellissier
  given name: Sonia
author list: Agent
  family name: Mondillon
  given name: Laurie
doi: 10.7717/peerj.7615
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-20
copyright: © 2019 Fournier et al.
attribution name: Fournier et al.

Magnetically directed antioxidant and antimicrobial agent: synthesis and surface functionalization of magnetite with quercetin
type: item
type: AcademicArticle
description: Oxidative stress can be reduced substantially using nanoantioxidant materials by tuning its surface morphological features up to a greater extent. The physiochemical, biological and optical properties of the nanoantioxidants can be altered by controlling their size and shape. In view of that, an appropriate synthesis technique should be adopted with optimization of the process variables. Properties of magnetite nanoparticles (IONP) can be tailored to upgrade the performance of biomedicine. Present research deals with the functionalization IONP using a hydrophobic agent of quercetin (Q). The application of quercetin will control its size using both the functionalization method including in-situ and post-synthesis technique. In in-situ techniques, the functionalized magnetite nanoparticles (IONP@Q) have average particles size 6 nm which are smaller than the magnetite (IONP) without functionalization. After post functionalization technique, the average particle size of magnetite IONP@Q2 determined was 11 nm. The nanoparticles also showed high saturation magnetization of about 51–59 emu/g. Before starting the experimental lab work, Prediction Activity Spectra of Substances (PASS) software was used to have a preliminary idea about the biological activities of Q. The antioxidant activity was carried out using 2, 2-diphenyl-1-picrylhydrazyl (DPPH) assay. The antibacterial studies were carried out using well diffusion method. The results obtained were well supported by the simulated results. Furthermore, the values of the half maximal inhibitory concentration (IC50) of the DPPH antioxidant assay were decreased using the functionalized one and it exhibited a 2–3 fold decreasing tendency than the unfunctionalized IONP. This exhibited that the functionalization process can easily enhance the free radical scavenging properties of IONPs up to three times. MIC values confirms that functionalized IONP have excellent antibacterial properties against the strains used (Staphylococcus…
format: application/pdf
format: text/html
creator: Syed Tawab Shah
creator: Wageeh A. Yehye
creator: Zaira Zaman Chowdhury
creator: Khanom Simarani
subject: Biochemistry
subject: Ecotoxicology
subject: Green Chemistry
description: doi:10.7717/peerj.7651
publisher: PeerJ Inc.
rights: © 2019 Shah et al.
abstract: Oxidative stress can be reduced substantially using nanoantioxidant materials by tuning its surface morphological features up to a greater extent. The physiochemical, biological and optical properties of the nanoantioxidants can be altered by controlling their size and shape. In view of that, an appropriate synthesis technique should be adopted with optimization of the process variables. Properties of magnetite nanoparticles (IONP) can be tailored to upgrade the performance of biomedicine. Present research deals with the functionalization IONP using a hydrophobic agent of quercetin (Q). The application of quercetin will control its size using both the functionalization method including in-situ and post-synthesis technique. In in-situ techniques, the functionalized magnetite nanoparticles (IONP@Q) have average particles size 6 nm which are smaller than the magnetite (IONP) without functionalization. After post functionalization technique, the average particle size of magnetite IONP@Q2 determined was 11 nm. The nanoparticles also showed high saturation magnetization of about 51–59 emu/g. Before starting the experimental lab work, Prediction Activity Spectra of Substances (PASS) software was used to have a preliminary idea about the biological activities of Q. The antioxidant activity was carried out using 2, 2-diphenyl-1-picrylhydrazyl (DPPH) assay. The antibacterial studies were carried out using well diffusion method. The results obtained were well supported by the simulated results. Furthermore, the values of the half maximal inhibitory concentration (IC50) of the DPPH antioxidant assay were decreased using the functionalized one and it exhibited a 2–3 fold decreasing tendency than the unfunctionalized IONP. This exhibited that the functionalization process can easily enhance the free radical scavenging properties of IONPs up to three times. MIC values confirms that functionalized IONP have excellent antibacterial properties against the strains used (Staphylococcus…
bibliographic citation: Shah et al. (2019) Magnetically directed antioxidant and antimicrobial agent: synthesis and surface functionalization of magnetite with quercetin. PeerJ 7:e7651 https://doi.org/10.7717/peerj.7651
date submitted: 2018-12-17
date accepted: 2019-08-09
issued: 2019-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shah
  given name: Syed Tawab
author list: Agent
  family name: Yehye
  given name: Wageeh A.
author list: Agent
  family name: Chowdhury
  given name: Zaira Zaman
author list: Agent
  family name: Simarani
  given name: Khanom
doi: 10.7717/peerj.7651
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-20
copyright: ©2019 Shah et al.
attribution name: Shah et al.

Validating anthropogenic threat maps as a tool for assessing river ecological integrity in Andean–Amazon basins
type: item
type: AcademicArticle
description: Anthropogenic threat maps are commonly used as a surrogate for the ecological integrity of rivers in freshwater conservation, but a clearer understanding of their relationships is required to develop proper management plans at large scales. Here, we developed and validated empirical models that link the ecological integrity of rivers to threat maps in a large, heterogeneous and biodiverse Andean–Amazon watershed. Through fieldwork, we recorded data on aquatic invertebrate community composition, habitat quality, and physical-chemical parameters to calculate the ecological integrity of 140 streams/rivers across the basin. Simultaneously, we generated maps that describe the location, extent, and magnitude of impact of nine anthropogenic threats to freshwater systems in the basin. Through seven-fold cross-validation procedure, we found that regression models based on anthropogenic threats alone have limited power for predicting the ecological integrity of rivers. However, the prediction accuracy improved when environmental predictors (slope and elevation) were included, and more so when the predictions were carried out at a coarser scale, such as microbasins. Moreover, anthropogenic threats that amplify the incidence of other pressures (roads, human settlements and oil activities) are the most relevant predictors of ecological integrity. We concluded that threat maps can offer an overall picture of the ecological integrity pattern of the basin, becoming a useful tool for broad-scale conservation planning for freshwater ecosystems. While it is always advisable to have finer scale in situ measurements of ecological integrity, our study shows that threat maps provide fast and cost-effective results, which so often are needed for pressing management and conservation actions.
format: application/pdf
format: text/html
creator: Janeth Lessmann
creator: Maria J. Troya
creator: Alexander S. Flecker
creator: W. Chris Funk
creator: Juan M. Guayasamin
creator: Valeria Ochoa-Herrera
creator: N. LeRoy Poff
creator: Esteban Suárez
creator: Andrea C. Encalada
subject: Conservation Biology
subject: Freshwater Biology
subject: Aquatic and Marine Chemistry
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.8060
publisher: PeerJ Inc.
rights: © 2019 Lessmann et al.
abstract: Anthropogenic threat maps are commonly used as a surrogate for the ecological integrity of rivers in freshwater conservation, but a clearer understanding of their relationships is required to develop proper management plans at large scales. Here, we developed and validated empirical models that link the ecological integrity of rivers to threat maps in a large, heterogeneous and biodiverse Andean–Amazon watershed. Through fieldwork, we recorded data on aquatic invertebrate community composition, habitat quality, and physical-chemical parameters to calculate the ecological integrity of 140 streams/rivers across the basin. Simultaneously, we generated maps that describe the location, extent, and magnitude of impact of nine anthropogenic threats to freshwater systems in the basin. Through seven-fold cross-validation procedure, we found that regression models based on anthropogenic threats alone have limited power for predicting the ecological integrity of rivers. However, the prediction accuracy improved when environmental predictors (slope and elevation) were included, and more so when the predictions were carried out at a coarser scale, such as microbasins. Moreover, anthropogenic threats that amplify the incidence of other pressures (roads, human settlements and oil activities) are the most relevant predictors of ecological integrity. We concluded that threat maps can offer an overall picture of the ecological integrity pattern of the basin, becoming a useful tool for broad-scale conservation planning for freshwater ecosystems. While it is always advisable to have finer scale in situ measurements of ecological integrity, our study shows that threat maps provide fast and cost-effective results, which so often are needed for pressing management and conservation actions.
bibliographic citation: Lessmann et al. (2019) Validating anthropogenic threat maps as a tool for assessing river ecological integrity in Andean–Amazon basins. PeerJ 7:e8060 https://doi.org/10.7717/peerj.8060
date submitted: 2019-04-01
date accepted: 2019-10-18
issued: 2019-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lessmann
  given name: Janeth
author list: Agent
  family name: Troya
  given name: Maria J.
author list: Agent
  family name: Flecker
  given name: Alexander S.
author list: Agent
  family name: Funk
  given name: W. Chris
author list: Agent
  family name: Guayasamin
  given name: Juan M.
author list: Agent
  family name: Ochoa-Herrera
  given name: Valeria
author list: Agent
  family name: Poff
  given name: N. LeRoy
author list: Agent
  family name: Suárez
  given name: Esteban
author list: Agent
  family name: Encalada
  given name: Andrea C.
doi: 10.7717/peerj.8060
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-20
copyright: © 2019 Lessmann et al.
attribution name: Lessmann et al.

Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey
type: item
type: AcademicArticle
description: Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children’s health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.
format: application/pdf
format: text/html
creator: Roberto Cabrera-Contreras
creator: Rosa I. Santamaría
creator: Patricia Bustos
creator: Irma Martínez-Flores
creator: Enrique Meléndez-Herrada
creator: Rubén Morelos-Ramírez
creator: Martín Barbosa-Amezcua
creator: Vanessa González-Covarrubias
creator: Eugenia Silva-Herzog
creator: Xavier Soberón
creator: Víctor González
subject: Genomics
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.8068
publisher: PeerJ Inc.
rights: © 2019 Cabrera-Contreras et al.
abstract: Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children’s health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.
bibliographic citation: Cabrera-Contreras et al. (2019) Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey. PeerJ 7:e8068 https://doi.org/10.7717/peerj.8068
date submitted: 2019-04-29
date accepted: 2019-10-20
issued: 2019-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cabrera-Contreras
  given name: Roberto
author list: Agent
  family name: Santamaría
  given name: Rosa I.
author list: Agent
  family name: Bustos
  given name: Patricia
author list: Agent
  family name: Martínez-Flores
  given name: Irma
author list: Agent
  family name: Meléndez-Herrada
  given name: Enrique
author list: Agent
  family name: Morelos-Ramírez
  given name: Rubén
author list: Agent
  family name: Barbosa-Amezcua
  given name: Martín
author list: Agent
  family name: González-Covarrubias
  given name: Vanessa
author list: Agent
  family name: Silva-Herzog
  given name: Eugenia
author list: Agent
  family name: Soberón
  given name: Xavier
author list: Agent
  family name: González
  given name: Víctor
doi: 10.7717/peerj.8068
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-20
copyright: ©2019 Cabrera-Contreras et al.
attribution name: Cabrera-Contreras et al.

New sources of Sym2A allele in the pea (Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX
type: item
type: AcademicArticle
description: At the onset of legume-rhizobial symbiosis, the mutual recognition of partners occurs based on a complicated interaction between signal molecules and receptors. Bacterial signal molecules named Nod factors (“nodulation factors”) are perceived by the plant LysM-containing receptor-like kinases (LysM-RLKs) that recognize details of its structure (i.e., unique substitutions), thus providing the conditions particular to symbiosis. In the garden pea (Pisum sativum L.), the allelic state of Sym2 gene has long been reported to regulate the symbiotic specificity: for infection to be successful, plants with the Sym2A allele (for “Sym2 Afghan”, as these genotypes originate mostly from Afghanistan) require an additional acetylation of the Nod factor which is irrelevant for genotypes with the Sym2E allele (for “Sym2 European”). Despite being described about 90 years ago, Sym2 has not yet been cloned, though phenotypic analysis suggests it probably encodes a receptor for the Nod factor. Recently, we described a novel pea gene LykX (PsLykX) from the LysM-RLK gene family that demonstrates a perfect correlation between its allelic state and the symbiotic specificity of the Sym2A-type. Here we report on a series of Middle-Eastern pea genotypes exhibiting the phenotype of narrow symbiotic specificity discovered in the VIR plant genetic resources gene bank (Saint-Petersburg, Russia). These genotypes are new sources of Sym2A, as has been confirmed by an allelism test with Sym2A pea cv. Afghanistan. Within these genotypes, LykX is present either in the allelic state characteristic for cv. Afghanistan, or in another, minor allelic state found in two genotypes from Tajikistan and Turkmenistan. Plants carrying the second allele demonstrate the same block of rhizobial infection as cv. Afghanistan when inoculated with an incompatible strain. Intriguingly, this “Tajik” allele of LykX differs from the “European” one by a single nucleotide polymorphism leading to an R75P change in the receptor …
format: application/pdf
format: text/html
creator: Anton S. Sulima
creator: Vladimir A. Zhukov
creator: Olga A. Kulaeva
creator: Ekaterina N. Vasileva
creator: Alexey Y. Borisov
creator: Igor A. Tikhonovich
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.8070
publisher: PeerJ Inc.
rights: © 2019 Sulima et al.
abstract: At the onset of legume-rhizobial symbiosis, the mutual recognition of partners occurs based on a complicated interaction between signal molecules and receptors. Bacterial signal molecules named Nod factors (“nodulation factors”) are perceived by the plant LysM-containing receptor-like kinases (LysM-RLKs) that recognize details of its structure (i.e., unique substitutions), thus providing the conditions particular to symbiosis. In the garden pea (Pisum sativum L.), the allelic state of Sym2 gene has long been reported to regulate the symbiotic specificity: for infection to be successful, plants with the Sym2A allele (for “Sym2 Afghan”, as these genotypes originate mostly from Afghanistan) require an additional acetylation of the Nod factor which is irrelevant for genotypes with the Sym2E allele (for “Sym2 European”). Despite being described about 90 years ago, Sym2 has not yet been cloned, though phenotypic analysis suggests it probably encodes a receptor for the Nod factor. Recently, we described a novel pea gene LykX (PsLykX) from the LysM-RLK gene family that demonstrates a perfect correlation between its allelic state and the symbiotic specificity of the Sym2A-type. Here we report on a series of Middle-Eastern pea genotypes exhibiting the phenotype of narrow symbiotic specificity discovered in the VIR plant genetic resources gene bank (Saint-Petersburg, Russia). These genotypes are new sources of Sym2A, as has been confirmed by an allelism test with Sym2A pea cv. Afghanistan. Within these genotypes, LykX is present either in the allelic state characteristic for cv. Afghanistan, or in another, minor allelic state found in two genotypes from Tajikistan and Turkmenistan. Plants carrying the second allele demonstrate the same block of rhizobial infection as cv. Afghanistan when inoculated with an incompatible strain. Intriguingly, this “Tajik” allele of LykX differs from the “European” one by a single nucleotide polymorphism leading to an R75P change in the receptor …
bibliographic citation: Sulima et al. (2019) New sources of Sym2A allele in the pea (Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX. PeerJ 7:e8070 https://doi.org/10.7717/peerj.8070
date submitted: 2019-07-31
date accepted: 2019-10-20
issued: 2019-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sulima
  given name: Anton S.
author list: Agent
  family name: Zhukov
  given name: Vladimir A.
author list: Agent
  family name: Kulaeva
  given name: Olga A.
author list: Agent
  family name: Vasileva
  given name: Ekaterina N.
author list: Agent
  family name: Borisov
  given name: Alexey Y.
author list: Agent
  family name: Tikhonovich
  given name: Igor A.
doi: 10.7717/peerj.8070
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-20
copyright: ©2019 Sulima et al.
attribution name: Sulima et al.

Transcriptional characterization and response to defense elicitors of mevalonate pathway genes in cotton (Gossypium arboreum L.)
type: item
type: AcademicArticle
description: The mevalonate (MVA) pathway is responsible for the biosynthesis of cytosolic terpenes including gossypol and its derivatives, which play an important role in the cotton plant’s defense against pathogens and herbivores. In this study, we identified and cloned 17 potentially functional genes encoding enzymes that catalyze the six steps of the MVA pathway in Gossypium arboreum. Expression pattern analysis by qRT-PCR demonstrated that these genes had tissue-specific expression profiles and were most prevalently expressed in roots. Moreover, these genes were up-regulated in response to several elicitors, including methyl jasmonate and salicylic acid, as well as Verticillium dahliae infection and Helicoverpa armigera infestation. This indicates that the MVA pathway genes are involved in the signaling pathway regulated by exogenous hormones and the resistance of cotton plants to pathogens and herbivores. Our results improve the understanding of cytosolic terpene biosynthesis in Gossypium species and lay the foundation for further research on gossypol biosynthesis.
format: application/pdf
format: text/html
creator: Zhiqiang Zhang
creator: Wei Liu
creator: Zongbin Ma
creator: Wei Zhu
creator: Lin Jia
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.8123
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: The mevalonate (MVA) pathway is responsible for the biosynthesis of cytosolic terpenes including gossypol and its derivatives, which play an important role in the cotton plant’s defense against pathogens and herbivores. In this study, we identified and cloned 17 potentially functional genes encoding enzymes that catalyze the six steps of the MVA pathway in Gossypium arboreum. Expression pattern analysis by qRT-PCR demonstrated that these genes had tissue-specific expression profiles and were most prevalently expressed in roots. Moreover, these genes were up-regulated in response to several elicitors, including methyl jasmonate and salicylic acid, as well as Verticillium dahliae infection and Helicoverpa armigera infestation. This indicates that the MVA pathway genes are involved in the signaling pathway regulated by exogenous hormones and the resistance of cotton plants to pathogens and herbivores. Our results improve the understanding of cytosolic terpene biosynthesis in Gossypium species and lay the foundation for further research on gossypol biosynthesis.
bibliographic citation: Zhang et al. (2019) Transcriptional characterization and response to defense elicitors of mevalonate pathway genes in cotton (Gossypium arboreum L.). PeerJ 7:e8123 https://doi.org/10.7717/peerj.8123
date submitted: 2019-07-29
date accepted: 2019-10-30
issued: 2019-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Zhiqiang
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Ma
  given name: Zongbin
author list: Agent
  family name: Zhu
  given name: Wei
author list: Agent
  family name: Jia
  given name: Lin
doi: 10.7717/peerj.8123
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-20
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Roles of phytohormone changes in the grain yield of rice plants exposed to heat: a review
type: item
type: AcademicArticle
description: During its reproductive phase, rice is susceptible to heat stress. Heat events will occur at all stages during the reproductive phase of rice as a result of global warming. Moreover, rice yield traits respond differently to heat stress during panicle initiation, flowering and grain filling. The reduction in the number of spikelets per panicle of heat-stressed plants is due to the attenuated differentiation of secondary branches and their attached florets as well as the promotion of their degradation during the panicle-initiation stage but is not affected by heat stress thereafter. Spikelet sterility as a result of heat stress is attributed not only to physiological abnormalities in the reproductive organs during the flowering stage but also to structural and morphological abnormalities in reproductive organs during the panicle-initiation stage. The reduced grain weight of heat-stressed plants is due to a reduction in nonstructural carbohydrates, undeveloped vascular bundles, and a reduction in glume size during the panicle-initiation stage, while a shortened grain-filling duration, reduced grain-filling rate, and decreased grain width contribute to reduced grain weight during the grain-filling stage. Thus, screening and breeding rice varieties that have comprehensive tolerance to heat stress at all time points during their reproductive stage may be possible to withstand unpredictable heat events in the future. The responses of yield traits to heat stress are regulated by phytohormone levels, which are determined by phytohormone homeostasis. Currently, the biosynthesis and transport of phytohormones are the key processes that determine phytohormone levels in and grain yield of rice under heat stress. Studies on phytohormone homeostatic responses are needed to further reveal the key processes that determine phytohormone levels under heat conditions.
format: application/pdf
format: text/html
creator: Chao Wu
creator: She Tang
creator: Ganghua Li
creator: Shaohua Wang
creator: Shah Fahad
creator: Yanfeng Ding
subject: Agricultural Science
subject: Plant Science
subject: Environmental Impacts
description: doi:10.7717/peerj.7792
publisher: PeerJ Inc.
rights: © 2019 Wu et al.
abstract: During its reproductive phase, rice is susceptible to heat stress. Heat events will occur at all stages during the reproductive phase of rice as a result of global warming. Moreover, rice yield traits respond differently to heat stress during panicle initiation, flowering and grain filling. The reduction in the number of spikelets per panicle of heat-stressed plants is due to the attenuated differentiation of secondary branches and their attached florets as well as the promotion of their degradation during the panicle-initiation stage but is not affected by heat stress thereafter. Spikelet sterility as a result of heat stress is attributed not only to physiological abnormalities in the reproductive organs during the flowering stage but also to structural and morphological abnormalities in reproductive organs during the panicle-initiation stage. The reduced grain weight of heat-stressed plants is due to a reduction in nonstructural carbohydrates, undeveloped vascular bundles, and a reduction in glume size during the panicle-initiation stage, while a shortened grain-filling duration, reduced grain-filling rate, and decreased grain width contribute to reduced grain weight during the grain-filling stage. Thus, screening and breeding rice varieties that have comprehensive tolerance to heat stress at all time points during their reproductive stage may be possible to withstand unpredictable heat events in the future. The responses of yield traits to heat stress are regulated by phytohormone levels, which are determined by phytohormone homeostasis. Currently, the biosynthesis and transport of phytohormones are the key processes that determine phytohormone levels in and grain yield of rice under heat stress. Studies on phytohormone homeostatic responses are needed to further reveal the key processes that determine phytohormone levels under heat conditions.
bibliographic citation: Wu et al. (2019) Roles of phytohormone changes in the grain yield of rice plants exposed to heat: a review. PeerJ 7:e7792 https://doi.org/10.7717/peerj.7792
date submitted: 2018-07-24
date accepted: 2019-08-29
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Chao
author list: Agent
  family name: Tang
  given name: She
author list: Agent
  family name: Li
  given name: Ganghua
author list: Agent
  family name: Wang
  given name: Shaohua
author list: Agent
  family name: Fahad
  given name: Shah
author list: Agent
  family name: Ding
  given name: Yanfeng
doi: 10.7717/peerj.7792
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: © 2019 Wu et al.
attribution name: Wu et al.

Low expression or hypermethylation of PLK2 might predict favorable prognosis for patients with glioblastoma multiforme
type: item
type: AcademicArticle
description: Background As the most aggressive brain tumor, patients with glioblastoma multiforme (GBM) have a poor prognosis. Our purpose was to explore prognostic value of Polo-like kinase 2 (PLK2) in GBM, a member of the PLKs family. Methods The expression profile of PLK2 in GBM was obtained from The Cancer Genome Atlas database. The PLK2 expression in GBM was tested. Kaplan–Meier curves were generated to assess the association between PLK2 expression and overall survival (OS) in patients with GBM. Furthermore, to assess its prognostic significance in patients with primary GBM, we constructed univariate and multivariate Cox regression models. The association between PLK2 expression and its methylation was then performed. Differentially expressed genes correlated with PLK2 were identified by Pearson test and functional enrichment analysis was performed. Results Overall survival results showed that low PLK2 expression had a favorable prognosis of patients with GBM (P-value = 0.0022). Furthermore, PLK2 (HR = 0.449, 95% CI [0.243–0.830], P-value = 0.011) was positively associated with OS by multivariate Cox regression analysis. In cluster 5, DNA methylated PLK2 had the lowest expression, which implied that PLK2 expression might be affected by its DNA methylation status in GBM. PLK2 in CpG island methylation phenotype (G-CIMP) had lower expression than non G-CIMP group (P = 0.0077). Regression analysis showed that PLK2 expression was negatively correlated with its DNA methylation (P = 0.0062, Pearson r = −0.3855). Among all differentially expressed genes of GBM, CYGB (r = 0.5551; P < 0.0001), ISLR2 (r = 0.5126; P < 0.0001), RPP25 (r = 0.5333; P < 0.0001) and SOX2 (r = −0.4838; P < 0.0001) were strongly correlated with PLK2. Functional enrichment analysis results showed that these genes were enriched several biological processes or pathways that were associated with GBM. Conclusion Polo-like kinase 2 expression is regulated by DNA methylation in GBM, and its low expression or hyper…
format: application/pdf
format: text/html
creator: Xiangping Xia
creator: Fang Cao
creator: Xiaolu Yuan
creator: Qiang Zhang
creator: Wei Chen
creator: Yunhu Yu
creator: Hua Xiao
creator: Chong Han
creator: Shengtao Yao
subject: Bioinformatics
subject: Neurology
subject: Surgery and Surgical Specialties
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.7974
publisher: PeerJ Inc.
rights: © 2019 Xia et al.
abstract: Background As the most aggressive brain tumor, patients with glioblastoma multiforme (GBM) have a poor prognosis. Our purpose was to explore prognostic value of Polo-like kinase 2 (PLK2) in GBM, a member of the PLKs family. Methods The expression profile of PLK2 in GBM was obtained from The Cancer Genome Atlas database. The PLK2 expression in GBM was tested. Kaplan–Meier curves were generated to assess the association between PLK2 expression and overall survival (OS) in patients with GBM. Furthermore, to assess its prognostic significance in patients with primary GBM, we constructed univariate and multivariate Cox regression models. The association between PLK2 expression and its methylation was then performed. Differentially expressed genes correlated with PLK2 were identified by Pearson test and functional enrichment analysis was performed. Results Overall survival results showed that low PLK2 expression had a favorable prognosis of patients with GBM (P-value = 0.0022). Furthermore, PLK2 (HR = 0.449, 95% CI [0.243–0.830], P-value = 0.011) was positively associated with OS by multivariate Cox regression analysis. In cluster 5, DNA methylated PLK2 had the lowest expression, which implied that PLK2 expression might be affected by its DNA methylation status in GBM. PLK2 in CpG island methylation phenotype (G-CIMP) had lower expression than non G-CIMP group (P = 0.0077). Regression analysis showed that PLK2 expression was negatively correlated with its DNA methylation (P = 0.0062, Pearson r = −0.3855). Among all differentially expressed genes of GBM, CYGB (r = 0.5551; P < 0.0001), ISLR2 (r = 0.5126; P < 0.0001), RPP25 (r = 0.5333; P < 0.0001) and SOX2 (r = −0.4838; P < 0.0001) were strongly correlated with PLK2. Functional enrichment analysis results showed that these genes were enriched several biological processes or pathways that were associated with GBM. Conclusion Polo-like kinase 2 expression is regulated by DNA methylation in GBM, and its low expression or hyper…
bibliographic citation: Xia et al. (2019) Low expression or hypermethylation of PLK2 might predict favorable prognosis for patients with glioblastoma multiforme. PeerJ 7:e7974 https://doi.org/10.7717/peerj.7974
date submitted: 2019-01-25
date accepted: 2019-10-02
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xia
  given name: Xiangping
author list: Agent
  family name: Cao
  given name: Fang
author list: Agent
  family name: Yuan
  given name: Xiaolu
author list: Agent
  family name: Zhang
  given name: Qiang
author list: Agent
  family name: Chen
  given name: Wei
author list: Agent
  family name: Yu
  given name: Yunhu
author list: Agent
  family name: Xiao
  given name: Hua
author list: Agent
  family name: Han
  given name: Chong
author list: Agent
  family name: Yao
  given name: Shengtao
doi: 10.7717/peerj.7974
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: © 2019 Xia et al.
attribution name: Xia et al.

Hematological convergence between Mesozoic marine reptiles (Sauropterygia) and extant aquatic amniotes elucidates diving adaptations in plesiosaurs
type: item
type: AcademicArticle
description: Plesiosaurs are a prominent group of Mesozoic marine reptiles, belonging to the more inclusive clades Pistosauroidea and Sauropterygia. In the Middle Triassic, the early pistosauroid ancestors of plesiosaurs left their ancestral coastal habitats and increasingly adapted to a life in the open ocean. This ecological shift was accompanied by profound changes in locomotion, sensory ecology and metabolism. However, investigations of physiological adaptations on the cellular level related to the pelagic lifestyle are lacking so far. Using vascular canal diameter, derived from osteohistological thin-sections, we show that inferred red blood cell size significantly increases in pistosauroids compared to more basal sauropterygians. This change appears to have occurred in conjunction with the dispersal to open marine environments, with cell size remaining consistently large in plesiosaurs. Enlarged red blood cells likely represent an adaptation of plesiosaurs repeated deep dives in the pelagic habitat and mirror conditions found in extant marine mammals and birds. Our results emphasize physiological aspects of adaptive convergence among fossil and extant marine amniotes and add to our current understanding of plesiosaur evolution.
format: application/pdf
format: text/html
creator: Corinna V. Fleischle
creator: P. Martin Sander
creator: Tanja Wintrich
creator: Kai R. Caspar
subject: Evolutionary Studies
subject: Paleontology
subject: Histology
description: doi:10.7717/peerj.8022
publisher: PeerJ Inc.
rights: © 2019 Fleischle et al.
abstract: Plesiosaurs are a prominent group of Mesozoic marine reptiles, belonging to the more inclusive clades Pistosauroidea and Sauropterygia. In the Middle Triassic, the early pistosauroid ancestors of plesiosaurs left their ancestral coastal habitats and increasingly adapted to a life in the open ocean. This ecological shift was accompanied by profound changes in locomotion, sensory ecology and metabolism. However, investigations of physiological adaptations on the cellular level related to the pelagic lifestyle are lacking so far. Using vascular canal diameter, derived from osteohistological thin-sections, we show that inferred red blood cell size significantly increases in pistosauroids compared to more basal sauropterygians. This change appears to have occurred in conjunction with the dispersal to open marine environments, with cell size remaining consistently large in plesiosaurs. Enlarged red blood cells likely represent an adaptation of plesiosaurs repeated deep dives in the pelagic habitat and mirror conditions found in extant marine mammals and birds. Our results emphasize physiological aspects of adaptive convergence among fossil and extant marine amniotes and add to our current understanding of plesiosaur evolution.
bibliographic citation: Fleischle et al. (2019) Hematological convergence between Mesozoic marine reptiles (Sauropterygia) and extant aquatic amniotes elucidates diving adaptations in plesiosaurs. PeerJ 7:e8022 https://doi.org/10.7717/peerj.8022
date submitted: 2019-07-23
date accepted: 2019-10-10
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fleischle
  given name: Corinna V.
author list: Agent
  family name: Sander
  given name: P. Martin
author list: Agent
  family name: Wintrich
  given name: Tanja
author list: Agent
  family name: Caspar
  given name: Kai R.
doi: 10.7717/peerj.8022
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: © 2019 Fleischle et al.
attribution name: Fleischle et al.

Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum)
type: item
type: AcademicArticle
description: Superoxide dismutases (SODs) are a family of key antioxidant enzymes that play a crucial role in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, a genome-wide analysis of the SOD gene family in wheat were performed. Twenty-six SOD genes were identified from the whole genome of wheat, including 17 Cu/Zn-SODs, six Fe-SODs, and three Mn-SODs. The chromosomal location mapping analysis indicated that these three types of SOD genes were only distributed on 2, 4, and 7 chromosomes, respectively. Phylogenetic analyses of wheat SODs and several other species revealed that these SOD proteins can be assigned to two major categories. SOD1 mainly comprises of Cu/Zn-SODs, and SOD2 mainly comprises of Fe-SODs and Mn-SODs. Gene structure and motif analyses indicated that most of the SOD genes showed a relatively conserved exon/intron arrangement and motif composition. Analyses of transcriptional data indicated that most of the wheat SOD genes were expressed in almost all of the examined tissues and had important functions in abiotic stress resistance. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to reveal the regulating roles of wheat SOD gene family in response to NaCl, mannitol, and polyethylene glycol stresses. qRT-PCR showed that eight randomly selected genes with relatively high expression levels responded to all three stresses based on released transcriptome data. However, their degree of response and response patterns were different. Interestingly, among these genes, TaSOD1.7, TaSOD1.9, TaSOD2.1, and TaSOD2.3 feature research value owing to their remarkable expression-fold change in leaves or roots under different stresses. Overall, our results provide a basis of further functional research on the SOD gene family in wheat and facilitate their potential use for applications in the genetic improvement on wheat in drought and salt stress environments.
format: application/pdf
format: text/html
creator: Wenqiang Jiang
creator: Lei Yang
creator: Yiqin He
creator: Haotian Zhang
creator: Wei Li
creator: Huaigu Chen
creator: Dongfang Ma
creator: Junliang Yin
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.8062
publisher: PeerJ Inc.
rights: © 2019 Jiang et al.
abstract: Superoxide dismutases (SODs) are a family of key antioxidant enzymes that play a crucial role in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, a genome-wide analysis of the SOD gene family in wheat were performed. Twenty-six SOD genes were identified from the whole genome of wheat, including 17 Cu/Zn-SODs, six Fe-SODs, and three Mn-SODs. The chromosomal location mapping analysis indicated that these three types of SOD genes were only distributed on 2, 4, and 7 chromosomes, respectively. Phylogenetic analyses of wheat SODs and several other species revealed that these SOD proteins can be assigned to two major categories. SOD1 mainly comprises of Cu/Zn-SODs, and SOD2 mainly comprises of Fe-SODs and Mn-SODs. Gene structure and motif analyses indicated that most of the SOD genes showed a relatively conserved exon/intron arrangement and motif composition. Analyses of transcriptional data indicated that most of the wheat SOD genes were expressed in almost all of the examined tissues and had important functions in abiotic stress resistance. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to reveal the regulating roles of wheat SOD gene family in response to NaCl, mannitol, and polyethylene glycol stresses. qRT-PCR showed that eight randomly selected genes with relatively high expression levels responded to all three stresses based on released transcriptome data. However, their degree of response and response patterns were different. Interestingly, among these genes, TaSOD1.7, TaSOD1.9, TaSOD2.1, and TaSOD2.3 feature research value owing to their remarkable expression-fold change in leaves or roots under different stresses. Overall, our results provide a basis of further functional research on the SOD gene family in wheat and facilitate their potential use for applications in the genetic improvement on wheat in drought and salt stress environments.
bibliographic citation: Jiang et al. (2019) Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum). PeerJ 7:e8062 https://doi.org/10.7717/peerj.8062
date submitted: 2018-11-29
date accepted: 2019-10-20
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Wenqiang
author list: Agent
  family name: Yang
  given name: Lei
author list: Agent
  family name: He
  given name: Yiqin
author list: Agent
  family name: Zhang
  given name: Haotian
author list: Agent
  family name: Li
  given name: Wei
author list: Agent
  family name: Chen
  given name: Huaigu
author list: Agent
  family name: Ma
  given name: Dongfang
author list: Agent
  family name: Yin
  given name: Junliang
doi: 10.7717/peerj.8062
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: ©2019 Jiang et al.
attribution name: Jiang et al.

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