PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining
items: A brief introduction to mixed effects modelling and multi-model inference in ecology
items: Evaluation of the glycemic effect of Ceratonia siliqua pods (Carob) on a streptozotocin-nicotinamide induced diabetic rat model
items: The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species
items: Giant worms chez moi! Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipalium spp., Diversibipalium spp.) in metropolitan France and overseas French territories
items: Molecular response of canola to salt stress: insights on tolerance mechanisms
items: Identifying potentially marker symptoms of attention-deficit/hyperactivity disorder
items: Effect of Reactive Black 5 azo dye on soil processes related to C and N cycling
items: Influence of aprepitant on the pharmacodynamics and pharmacokinetics of gliclazide in rats and rabbits
items: Large mammal burrows in late Miocene calcic paleosols from central Argentina: paleoenvironment, taphonomy and producers

Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining
type: item
type: AcademicArticle
description: The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from ‘reading the literature’. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. By merging the text-mining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rule-based algorithm (filter) was constructed in order to automate the search for novel candidate genes with a high degree of likely association to known target genes by (1) ignoring established relationships from the existing literature, as they are already ‘known’, and (2) demanding multiple independent evidences for every novel and potentially relevant relationship. Using selected case studies, we demonstrate the utility of the network resource and filter to (i) discover novel candidate associations between different genes or proteins in the network, and (ii) rapidly evaluate the potential role of any one particular gene or protein. The full network is provided as an open-source resource.
format: application/pdf
format: text/html
creator: Sanna M. Kreula
creator: Suwisa Kaewphan
creator: Filip Ginter
creator: Patrik R. Jones
subject: Computational Biology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.4806
publisher: PeerJ Inc.
rights: © 2018 Kreula et al.
abstract: The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from ‘reading the literature’. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. By merging the text-mining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rule-based algorithm (filter) was constructed in order to automate the search for novel candidate genes with a high degree of likely association to known target genes by (1) ignoring established relationships from the existing literature, as they are already ‘known’, and (2) demanding multiple independent evidences for every novel and potentially relevant relationship. Using selected case studies, we demonstrate the utility of the network resource and filter to (i) discover novel candidate associations between different genes or proteins in the network, and (ii) rapidly evaluate the potential role of any one particular gene or protein. The full network is provided as an open-source resource.
bibliographic citation: Kreula et al. (2018) Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining. PeerJ 6:e4806 https://doi.org/10.7717/peerj.4806
date submitted: 2017-12-15
date accepted: 2018-04-30
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kreula
  given name: Sanna M.
author list: Agent
  family name: Kaewphan
  given name: Suwisa
author list: Agent
  family name: Ginter
  given name: Filip
author list: Agent
  family name: Jones
  given name: Patrik R.
doi: 10.7717/peerj.4806
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: ©2018 Kreula et al.
attribution name: Kreula et al.

A brief introduction to mixed effects modelling and multi-model inference in ecology
type: item
type: AcademicArticle
description: The use of linear mixed effects models (LMMs) is increasingly common in the analysis of biological data. Whilst LMMs offer a flexible approach to modelling a broad range of data types, ecological data are often complex and require complex model structures, and the fitting and interpretation of such models is not always straightforward. The ability to achieve robust biological inference requires that practitioners know how and when to apply these tools. Here, we provide a general overview of current methods for the application of LMMs to biological data, and highlight the typical pitfalls that can be encountered in the statistical modelling process. We tackle several issues regarding methods of model selection, with particular reference to the use of information theory and multi-model inference in ecology. We offer practical solutions and direct the reader to key references that provide further technical detail for those seeking a deeper understanding. This overview should serve as a widely accessible code of best practice for applying LMMs to complex biological problems and model structures, and in doing so improve the robustness of conclusions drawn from studies investigating ecological and evolutionary questions.
format: application/pdf
format: text/html
creator: Xavier A. Harrison
creator: Lynda Donaldson
creator: Maria Eugenia Correa-Cano
creator: Julian Evans
creator: David N. Fisher
creator: Cecily E.D. Goodwin
creator: Beth S. Robinson
creator: David J. Hodgson
creator: Richard Inger
subject: Ecology
subject: Evolutionary Studies
subject: Statistics
description: doi:10.7717/peerj.4794
publisher: PeerJ Inc.
rights: © 2018 Harrison et al.
abstract: The use of linear mixed effects models (LMMs) is increasingly common in the analysis of biological data. Whilst LMMs offer a flexible approach to modelling a broad range of data types, ecological data are often complex and require complex model structures, and the fitting and interpretation of such models is not always straightforward. The ability to achieve robust biological inference requires that practitioners know how and when to apply these tools. Here, we provide a general overview of current methods for the application of LMMs to biological data, and highlight the typical pitfalls that can be encountered in the statistical modelling process. We tackle several issues regarding methods of model selection, with particular reference to the use of information theory and multi-model inference in ecology. We offer practical solutions and direct the reader to key references that provide further technical detail for those seeking a deeper understanding. This overview should serve as a widely accessible code of best practice for applying LMMs to complex biological problems and model structures, and in doing so improve the robustness of conclusions drawn from studies investigating ecological and evolutionary questions.
bibliographic citation: Harrison et al. (2018) A brief introduction to mixed effects modelling and multi-model inference in ecology. PeerJ 6:e4794 https://doi.org/10.7717/peerj.4794
date submitted: 2017-07-26
date accepted: 2018-04-27
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harrison
  given name: Xavier A.
author list: Agent
  family name: Donaldson
  given name: Lynda
author list: Agent
  family name: Correa-Cano
  given name: Maria Eugenia
author list: Agent
  family name: Evans
  given name: Julian
author list: Agent
  family name: Fisher
  given name: David N.
author list: Agent
  family name: Goodwin
  given name: Cecily E.D.
author list: Agent
  family name: Robinson
  given name: Beth S.
author list: Agent
  family name: Hodgson
  given name: David J.
author list: Agent
  family name: Inger
  given name: Richard
doi: 10.7717/peerj.4794
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: © 2018 Harrison et al.
attribution name: Harrison et al.

Evaluation of the glycemic effect of Ceratonia siliqua pods (Carob) on a streptozotocin-nicotinamide induced diabetic rat model
type: item
type: AcademicArticle
description: Background Ceratonia siliqua pods (carob) have been nominated to control the high blood glucose of diabetics. In Yemen, however, its antihyperglycemic activity has not been yet assessed. Thus, this study evaluated the in vitro inhibitory effect of the methanolic extract of carob pods against α-amylase and α-glucosidase and the in vivo glycemic effect of such extract in streptozotocin-nicotinamide induced diabetic rats. Methods 2,2-diphenyl-1-picrylhydrazyl (DPPH) and Ferric reducing antioxidant power assay (FRAP) were applied to evaluate the antioxidant activity of carob. In vitro cytotoxicity of carob was conducted on human hepatocytes (WRL68) and rat pancreatic β-cells (RIN-5F). Acute oral toxicity of carob was conducted on a total of 18 male and 18 female Sprague-Dawley (SD) rats, which were subdivided into three groups (n = 6), namely: high and low dose carob-treated (CS5000 and CS2000, respectively) as well as the normal control (NC) receiving a single oral dose of 5,000 mg kg−1 carob, 2,000 mg kg−1 carob and 5 mL kg−1 distilled water for 14 days, respectively. Alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, total bilirubin, creatinine and urea were assessed. Livers and kidneys were harvested for histopathology. In vitro inhibitory effect against α-amylase and α-glucosidase was evaluated. In vivo glycemic activity was conducted on 24 male SD rats which were previously intraperitoneally injected with 55 mg kg−1 streptozotocin (STZ) followed by 210 mg kg−1nicotinamide to induce type 2 diabetes mellitus. An extra non-injected group (n = 6) was added as a normal control (NC). The injected-rats were divided into four groups (n = 6), namely: diabetic control (D0), 5 mg kg−1glibenclamide-treated diabetic (GD), 500 mg kg−1 carob-treated diabetic (CS500) and 1,000 mg kg−1 carob-treated diabetic (CS1000). All groups received a single oral daily dose of their treatment for 4 weeks. Body weight, fasting blood glucose (FBG), oral glucose toleranc…
format: application/pdf
format: text/html
creator: Mousa A. Qasem
creator: Mohamed Ibrahim Noordin
creator: Aditya Arya
creator: Abdulsamad Alsalahi
creator: Soher Nagi Jayash
subject: Diabetes and Endocrinology
subject: Pharmacology
description: doi:10.7717/peerj.4788
publisher: PeerJ Inc.
rights: © 2018 Qasem et al.
abstract: Background Ceratonia siliqua pods (carob) have been nominated to control the high blood glucose of diabetics. In Yemen, however, its antihyperglycemic activity has not been yet assessed. Thus, this study evaluated the in vitro inhibitory effect of the methanolic extract of carob pods against α-amylase and α-glucosidase and the in vivo glycemic effect of such extract in streptozotocin-nicotinamide induced diabetic rats. Methods 2,2-diphenyl-1-picrylhydrazyl (DPPH) and Ferric reducing antioxidant power assay (FRAP) were applied to evaluate the antioxidant activity of carob. In vitro cytotoxicity of carob was conducted on human hepatocytes (WRL68) and rat pancreatic β-cells (RIN-5F). Acute oral toxicity of carob was conducted on a total of 18 male and 18 female Sprague-Dawley (SD) rats, which were subdivided into three groups (n = 6), namely: high and low dose carob-treated (CS5000 and CS2000, respectively) as well as the normal control (NC) receiving a single oral dose of 5,000 mg kg−1 carob, 2,000 mg kg−1 carob and 5 mL kg−1 distilled water for 14 days, respectively. Alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, total bilirubin, creatinine and urea were assessed. Livers and kidneys were harvested for histopathology. In vitro inhibitory effect against α-amylase and α-glucosidase was evaluated. In vivo glycemic activity was conducted on 24 male SD rats which were previously intraperitoneally injected with 55 mg kg−1 streptozotocin (STZ) followed by 210 mg kg−1nicotinamide to induce type 2 diabetes mellitus. An extra non-injected group (n = 6) was added as a normal control (NC). The injected-rats were divided into four groups (n = 6), namely: diabetic control (D0), 5 mg kg−1glibenclamide-treated diabetic (GD), 500 mg kg−1 carob-treated diabetic (CS500) and 1,000 mg kg−1 carob-treated diabetic (CS1000). All groups received a single oral daily dose of their treatment for 4 weeks. Body weight, fasting blood glucose (FBG), oral glucose toleranc…
bibliographic citation: Qasem et al. (2018) Evaluation of the glycemic effect of Ceratonia siliqua pods (Carob) on a streptozotocin-nicotinamide induced diabetic rat model. PeerJ 6:e4788 https://doi.org/10.7717/peerj.4788
date submitted: 2018-03-07
date accepted: 2018-04-27
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qasem
  given name: Mousa A.
author list: Agent
  family name: Noordin
  given name: Mohamed Ibrahim
author list: Agent
  family name: Arya
  given name: Aditya
author list: Agent
  family name: Alsalahi
  given name: Abdulsamad
author list: Agent
  family name: Jayash
  given name: Soher Nagi
doi: 10.7717/peerj.4788
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: ©2018 Qasem et al.
attribution name: Qasem et al.

The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species
type: item
type: AcademicArticle
description: Colobanthus apetalus is a member of the genus Colobanthus, one of the 86 genera of the large family Caryophyllaceae which groups annual and perennial herbs (rarely shrubs) that are widely distributed around the globe, mainly in the Holarctic. The genus Colobanthus consists of 25 species, including Colobanthus quitensis, an extremophile plant native to the maritime Antarctic. Complete chloroplast (cp) genomes are useful for phylogenetic studies and species identification. In this study, next-generation sequencing (NGS) was used to identify the cp genome of C. apetalus. The complete cp genome of C. apetalus has the length of 151,228 bp, 36.65% GC content, and a quadripartite structure with a large single copy (LSC) of 83,380 bp and a small single copy (SSC) of 17,206 bp separated by inverted repeats (IRs) of 25,321 bp. The cp genome contains 131 genes, including 112 unique genes and 19 genes which are duplicated in the IRs. The group of 112 unique genes features 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames (ORFs). A total of 12 forward repeats, 10 palindromic repeats, five reverse repeats and three complementary repeats were detected. In addition, a simple sequence repeat (SSR) analysis revealed 41 (mono-, di-, tri-, tetra-, penta- and hexanucleotide) SSRs, most of which were AT-rich. A detailed comparison of C. apetalus and C. quitensis cp genomes revealed identical gene content and order. A phylogenetic tree was built based on the sequences of 76 protein-coding genes that are shared by the eleven sequenced representatives of Caryophyllaceae and C. apetalus, and it revealed that C. apetalus and C. quitensis form a clade that is closely related to Silene species and Agrostemma githago. Moreover, the genus Silene appeared as a polymorphic taxon. The results of this study expand our knowledge about the evolution and molecular biology of Caryophyllaceae.
format: application/pdf
format: text/html
creator: Piotr Androsiuk
creator: Jan Paweł Jastrzębski
creator: Łukasz Paukszto
creator: Adam Okorski
creator: Agnieszka Pszczółkowska
creator: Katarzyna Joanna Chwedorzewska
creator: Justyna Koc
creator: Ryszard Górecki
creator: Irena Giełwanowska
subject: Biodiversity
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.4723
publisher: PeerJ Inc.
rights: © 2018 Androsiuk et al.
abstract: Colobanthus apetalus is a member of the genus Colobanthus, one of the 86 genera of the large family Caryophyllaceae which groups annual and perennial herbs (rarely shrubs) that are widely distributed around the globe, mainly in the Holarctic. The genus Colobanthus consists of 25 species, including Colobanthus quitensis, an extremophile plant native to the maritime Antarctic. Complete chloroplast (cp) genomes are useful for phylogenetic studies and species identification. In this study, next-generation sequencing (NGS) was used to identify the cp genome of C. apetalus. The complete cp genome of C. apetalus has the length of 151,228 bp, 36.65% GC content, and a quadripartite structure with a large single copy (LSC) of 83,380 bp and a small single copy (SSC) of 17,206 bp separated by inverted repeats (IRs) of 25,321 bp. The cp genome contains 131 genes, including 112 unique genes and 19 genes which are duplicated in the IRs. The group of 112 unique genes features 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames (ORFs). A total of 12 forward repeats, 10 palindromic repeats, five reverse repeats and three complementary repeats were detected. In addition, a simple sequence repeat (SSR) analysis revealed 41 (mono-, di-, tri-, tetra-, penta- and hexanucleotide) SSRs, most of which were AT-rich. A detailed comparison of C. apetalus and C. quitensis cp genomes revealed identical gene content and order. A phylogenetic tree was built based on the sequences of 76 protein-coding genes that are shared by the eleven sequenced representatives of Caryophyllaceae and C. apetalus, and it revealed that C. apetalus and C. quitensis form a clade that is closely related to Silene species and Agrostemma githago. Moreover, the genus Silene appeared as a polymorphic taxon. The results of this study expand our knowledge about the evolution and molecular biology of Caryophyllaceae.
bibliographic citation: Androsiuk et al. (2018) The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species. PeerJ 6:e4723 https://doi.org/10.7717/peerj.4723
date submitted: 2018-01-04
date accepted: 2018-04-17
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Androsiuk
  given name: Piotr
author list: Agent
  family name: Jastrzębski
  given name: Jan Paweł
author list: Agent
  family name: Paukszto
  given name: Łukasz
author list: Agent
  family name: Okorski
  given name: Adam
author list: Agent
  family name: Pszczółkowska
  given name: Agnieszka
author list: Agent
  family name: Chwedorzewska
  given name: Katarzyna Joanna
author list: Agent
  family name: Koc
  given name: Justyna
author list: Agent
  family name: Górecki
  given name: Ryszard
author list: Agent
  family name: Giełwanowska
  given name: Irena
doi: 10.7717/peerj.4723
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: ©2018 Androsiuk et al.
attribution name: Androsiuk et al.

Giant worms chez moi! Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipalium spp., Diversibipalium spp.) in metropolitan France and overseas French territories
type: item
type: AcademicArticle
description: Background Species of the genera Bipalium and Diversibipalium, or bipaliines, are giants among land planarians (family Geoplanidae), reaching length of 1 m; they are also easily distinguished from other land flatworms by the characteristic hammer shape of their head. Bipaliines, which have their origin in warm parts of Asia, are invasive species, now widespread worldwide. However, the scientific literature is very scarce about the widespread repartition of these species, and their invasion in European countries has not been studied. Methods In this paper, on the basis of a four year survey based on citizen science, which yielded observations from 1999 to 2017 and a total of 111 records, we provide information about the five species present in Metropolitan France and French overseas territories. We also investigated the molecular variability of cytochrome-oxidase 1 (COI) sequences of specimens. Results Three species are reported from Metropolitan France: Bipalium kewense, Diversibipalium multilineatum, and an unnamed Diversibipalium ‘black’ species. We also report the presence of B. kewense from overseas territories, such as French Polynesia (Oceania), French Guiana (South America), the Caribbean French islands of Martinique, Guadeloupe, Saint Martin and Saint Barthélemy, and Montserrat (Central America), and La Réunion island (off South-East Africa). For B. vagum, observations include French Guiana, Guadeloupe, Martinique, Saint Barthélemy, Saint Martin, Montserrat, La Réunion, and Florida (USA). A probable new species, Diversibipalium sp. ‘blue,’ is reported from Mayotte Island (off South–East Africa). B. kewense, B. vagum and D. multilineatum each showed 0% variability in their COI sequences, whatever their origin, suggesting that the specimens are clonal, and that sexual reproduction is probably absent. COI barcoding was efficient in identifying species, with differences over 10% between species; this suggests that barcoding can be used in the future for identify…
format: application/pdf
format: text/html
creator: Jean-Lou Justine
creator: Leigh Winsor
creator: Delphine Gey
creator: Pierre Gros
creator: Jessica Thévenot
subject: Agricultural Science
subject: Biodiversity
subject: Biogeography
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.4672
publisher: PeerJ Inc.
rights: © 2018 Justine et al.
abstract: Background Species of the genera Bipalium and Diversibipalium, or bipaliines, are giants among land planarians (family Geoplanidae), reaching length of 1 m; they are also easily distinguished from other land flatworms by the characteristic hammer shape of their head. Bipaliines, which have their origin in warm parts of Asia, are invasive species, now widespread worldwide. However, the scientific literature is very scarce about the widespread repartition of these species, and their invasion in European countries has not been studied. Methods In this paper, on the basis of a four year survey based on citizen science, which yielded observations from 1999 to 2017 and a total of 111 records, we provide information about the five species present in Metropolitan France and French overseas territories. We also investigated the molecular variability of cytochrome-oxidase 1 (COI) sequences of specimens. Results Three species are reported from Metropolitan France: Bipalium kewense, Diversibipalium multilineatum, and an unnamed Diversibipalium ‘black’ species. We also report the presence of B. kewense from overseas territories, such as French Polynesia (Oceania), French Guiana (South America), the Caribbean French islands of Martinique, Guadeloupe, Saint Martin and Saint Barthélemy, and Montserrat (Central America), and La Réunion island (off South-East Africa). For B. vagum, observations include French Guiana, Guadeloupe, Martinique, Saint Barthélemy, Saint Martin, Montserrat, La Réunion, and Florida (USA). A probable new species, Diversibipalium sp. ‘blue,’ is reported from Mayotte Island (off South–East Africa). B. kewense, B. vagum and D. multilineatum each showed 0% variability in their COI sequences, whatever their origin, suggesting that the specimens are clonal, and that sexual reproduction is probably absent. COI barcoding was efficient in identifying species, with differences over 10% between species; this suggests that barcoding can be used in the future for identify…
bibliographic citation: Justine et al. (2018) Giant worms chez moi! Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipalium spp., Diversibipalium spp.) in metropolitan France and overseas French territories. PeerJ 6:e4672 https://doi.org/10.7717/peerj.4672
date submitted: 2017-11-16
date accepted: 2018-04-06
issued: 2018-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Justine
  given name: Jean-Lou
author list: Agent
  family name: Winsor
  given name: Leigh
author list: Agent
  family name: Gey
  given name: Delphine
author list: Agent
  family name: Gros
  given name: Pierre
author list: Agent
  family name: Thévenot
  given name: Jessica
doi: 10.7717/peerj.4672
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-22
copyright: © 2018 Justine et al.
attribution name: Justine et al.

Molecular response of canola to salt stress: insights on tolerance mechanisms
type: item
type: AcademicArticle
description: Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests what researchers should focus on in future studies.
format: application/pdf
format: text/html
creator: Reza Shokri-Gharelo
creator: Pouya Motie Noparvar
subject: Agricultural Science
subject: Cell Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.4822
publisher: PeerJ Inc.
rights: © 2018 Shokri-Gharelo and Noparvar
abstract: Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests what researchers should focus on in future studies.
bibliographic citation: Shokri-Gharelo et al. (2018) Molecular response of canola to salt stress: insights on tolerance mechanisms. PeerJ 6:e4822 https://doi.org/10.7717/peerj.4822
date submitted: 2018-03-09
date accepted: 2018-05-02
issued: 2018-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shokri-Gharelo
  given name: Reza
author list: Agent
  family name: Noparvar
  given name: Pouya Motie
doi: 10.7717/peerj.4822
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-22
copyright: ©2018 Shokri-Gharelo and Noparvar
attribution name: Shokri-Gharelo and Noparvar

Identifying potentially marker symptoms of attention-deficit/hyperactivity disorder
type: item
type: AcademicArticle
description: Background For the diagnosis of attention-deficit/hyperactivity disorder (ADHD), the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) proposes that adherence to six symptoms in either group (inattention and hyperactivity/impulsivity) will lead to the diagnosis of one of three presentations of the disorder. Underlying this diagnostic algorithm is the assumption that the 18 symptoms have equal relevance for the diagnosis of ADHD, all are equally severe, and all have the same power to detect the presence of the disorder in all its degrees of severity, without considering the possibility of using marker symptoms. However, several studies have suggested that ADHD symptoms differ in both their power to discriminate the presence of the disorder and the degree of severity they represent. The aim of the present study was to replicate the results of previous research by evaluating the discriminative capacity and relative severity of ADHD symptoms, as well as to extend the investigation of this topic to Spanish-speaking Latin American samples. Methods The properties of ADHD symptoms rated by the parents of 474 Chilean children were analyzed. Symptom parameters were estimated using the graded response model. Results The results suggest that symptoms of ADHD differ substantially in both the accuracy with which they reflect the presence of the disorder, and their relative severity. Symptoms “easily distracted by extraneous stimuli” and “have difficulty sustaining attention in tasks” (inattention) and “is on the go, acting as if driven by motor” (hyperactivity/impulsivity) were the most informative, and those with relatively lower severity thresholds. Discussion The fact that symptoms differ substantially in the probability of being observed conditionally to the trait level suggests the need to refine the diagnostic process by weighting the severity of the symptom, and even to assess the possibility of defining ADHD marker symptoms, as has been done in other disorders…
format: application/pdf
format: text/html
creator: Víctor B. Arias
creator: Igor Esnaola
creator: Jairo Rodríguez-Medina
subject: Psychiatry and Psychology
subject: Statistics
description: doi:10.7717/peerj.4820
publisher: PeerJ Inc.
rights: © 2018 Arias et al.
abstract: Background For the diagnosis of attention-deficit/hyperactivity disorder (ADHD), the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) proposes that adherence to six symptoms in either group (inattention and hyperactivity/impulsivity) will lead to the diagnosis of one of three presentations of the disorder. Underlying this diagnostic algorithm is the assumption that the 18 symptoms have equal relevance for the diagnosis of ADHD, all are equally severe, and all have the same power to detect the presence of the disorder in all its degrees of severity, without considering the possibility of using marker symptoms. However, several studies have suggested that ADHD symptoms differ in both their power to discriminate the presence of the disorder and the degree of severity they represent. The aim of the present study was to replicate the results of previous research by evaluating the discriminative capacity and relative severity of ADHD symptoms, as well as to extend the investigation of this topic to Spanish-speaking Latin American samples. Methods The properties of ADHD symptoms rated by the parents of 474 Chilean children were analyzed. Symptom parameters were estimated using the graded response model. Results The results suggest that symptoms of ADHD differ substantially in both the accuracy with which they reflect the presence of the disorder, and their relative severity. Symptoms “easily distracted by extraneous stimuli” and “have difficulty sustaining attention in tasks” (inattention) and “is on the go, acting as if driven by motor” (hyperactivity/impulsivity) were the most informative, and those with relatively lower severity thresholds. Discussion The fact that symptoms differ substantially in the probability of being observed conditionally to the trait level suggests the need to refine the diagnostic process by weighting the severity of the symptom, and even to assess the possibility of defining ADHD marker symptoms, as has been done in other disorders…
bibliographic citation: Arias et al. (2018) Identifying potentially marker symptoms of attention-deficit/hyperactivity disorder. PeerJ 6:e4820 https://doi.org/10.7717/peerj.4820
date submitted: 2018-03-10
date accepted: 2018-05-02
issued: 2018-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arias
  given name: Víctor B.
author list: Agent
  family name: Esnaola
  given name: Igor
author list: Agent
  family name: Rodríguez-Medina
  given name: Jairo
doi: 10.7717/peerj.4820
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-22
copyright: ©2018 Arias et al.
attribution name: Arias et al.

Effect of Reactive Black 5 azo dye on soil processes related to C and N cycling
type: item
type: AcademicArticle
description: Azo dyes are one of the largest classes of synthetic dyes being used in textile industries. It has been reported that 15–50% of these dyes find their way into wastewater that is often used for irrigation purpose in developing countries. The effect of azo dyes contamination on soil nitrogen (N) has been studied previously. However, how does the azo dye contamination affect soil carbon (C) cycling is unknown. Therefore, we assessed the effect of azo dye contamination (Reactive Black 5, 30 mg kg−1 dry soil), bacteria that decolorize this dye and dye + bacteria in the presence or absence of maize leaf litter on soil respiration, soil inorganic N and microbial biomass. We found that dye contamination did not induce any change in soil respiration, soil microbial biomass or soil inorganic N availability (P > 0.05). Litter evidently increased soil respiration. Our study concludes that the Reactive Black 5 azo dye (applied in low amount, i.e., 30 mg kg−1 dry soil) contamination did not modify organic matter decomposition, N mineralization and microbial biomass in a silty loam soil.
format: application/pdf
format: text/html
creator: Khadeeja Rehman
creator: Tanvir Shahzad
creator: Amna Sahar
creator: Sabir Hussain
creator: Faisal Mahmood
creator: Muhammad H. Siddique
creator: Muhammad A. Siddique
creator: Muhammad I. Rashid
subject: Soil Science
subject: Environmental Impacts
description: doi:10.7717/peerj.4802
publisher: PeerJ Inc.
rights: © 2018 Rehman et al.
abstract: Azo dyes are one of the largest classes of synthetic dyes being used in textile industries. It has been reported that 15–50% of these dyes find their way into wastewater that is often used for irrigation purpose in developing countries. The effect of azo dyes contamination on soil nitrogen (N) has been studied previously. However, how does the azo dye contamination affect soil carbon (C) cycling is unknown. Therefore, we assessed the effect of azo dye contamination (Reactive Black 5, 30 mg kg−1 dry soil), bacteria that decolorize this dye and dye + bacteria in the presence or absence of maize leaf litter on soil respiration, soil inorganic N and microbial biomass. We found that dye contamination did not induce any change in soil respiration, soil microbial biomass or soil inorganic N availability (P > 0.05). Litter evidently increased soil respiration. Our study concludes that the Reactive Black 5 azo dye (applied in low amount, i.e., 30 mg kg−1 dry soil) contamination did not modify organic matter decomposition, N mineralization and microbial biomass in a silty loam soil.
bibliographic citation: Rehman et al. (2018) Effect of Reactive Black 5 azo dye on soil processes related to C and N cycling. PeerJ 6:e4802 https://doi.org/10.7717/peerj.4802
date submitted: 2018-02-21
date accepted: 2018-04-30
issued: 2018-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rehman
  given name: Khadeeja
author list: Agent
  family name: Shahzad
  given name: Tanvir
author list: Agent
  family name: Sahar
  given name: Amna
author list: Agent
  family name: Hussain
  given name: Sabir
author list: Agent
  family name: Mahmood
  given name: Faisal
author list: Agent
  family name: Siddique
  given name: Muhammad H.
author list: Agent
  family name: Siddique
  given name: Muhammad A.
author list: Agent
  family name: Rashid
  given name: Muhammad I.
doi: 10.7717/peerj.4802
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-22
copyright: ©2018 Rehman et al.
attribution name: Rehman et al.

Influence of aprepitant on the pharmacodynamics and pharmacokinetics of gliclazide in rats and rabbits
type: item
type: AcademicArticle
description: Background Concomitant drug administration is a general phenomenon in patients with chronic diseases such as diabetes mellitus. Among the currently available oral antidiabetic drugs, gliclazide is a commonly prescribed drug considering its multiple benefits in diabetic patients. Aprepitant is a commonly prescribed antiemetic drug which is mainly metabolized by CYP3A4, reported to have modest inductive and inhibitory effects on CYP2C9 and CYP3A4, respectively. Since gliclazide is metabolized by CYP2C9 (major) and CYP3A4 (minor), it is very difficult to predict the influence of aprepitant and its metabolic interaction with gliclazide. Considering the complexity associated with the combination of aprepitant and gliclazide, this study was designed to evaluate the influence of aprepitant on the pharmacodynamics (PD) and pharmacokinetics (PK) of gliclazide in animal models. Methods The PD interaction studies were conducted in both rodent (normal and alloxan-induced diabetic rats) and non-rodent (rabbits) animal models (n = 6) while the PK interaction study was conducted in normal rabbits (n = 6). An extrapolated human therapeutic oral dose of gliclazide, aprepitant and their combination were administered to rats and rabbits with 7 days washout between each treatment. For the multiple-dose interaction study, the same groups were administered with an interacting drug (aprepitant) for 7 days and then the combination of aprepitant and gliclazide on the 8th day. From the collected animal blood samples, blood glucose (by Glucose-Oxidase/Peroxidase method), insulin (by ELISA method) and gliclazide concentration levels (by HPLC method) were determined. Non-compartmental PK analysis was conducted by Phoenix WinNonlin software to determine the PK parameters of gliclazide. Statistical analysis was performed by student’s paired t-test. Results The pharmacodynamic activity (blood glucose reduction and insulin levels) of gliclazide was significantly (p < 0.05) influenced by aprepitant …
format: application/pdf
format: text/html
creator: Raghunandan Reddy Kura
creator: Eswar Kumar Kilari
creator: Mastan Shaik
subject: Diabetes and Endocrinology
subject: Pharmacology
description: doi:10.7717/peerj.4798
publisher: PeerJ Inc.
rights: © 2018 Kura et al.
abstract: Background Concomitant drug administration is a general phenomenon in patients with chronic diseases such as diabetes mellitus. Among the currently available oral antidiabetic drugs, gliclazide is a commonly prescribed drug considering its multiple benefits in diabetic patients. Aprepitant is a commonly prescribed antiemetic drug which is mainly metabolized by CYP3A4, reported to have modest inductive and inhibitory effects on CYP2C9 and CYP3A4, respectively. Since gliclazide is metabolized by CYP2C9 (major) and CYP3A4 (minor), it is very difficult to predict the influence of aprepitant and its metabolic interaction with gliclazide. Considering the complexity associated with the combination of aprepitant and gliclazide, this study was designed to evaluate the influence of aprepitant on the pharmacodynamics (PD) and pharmacokinetics (PK) of gliclazide in animal models. Methods The PD interaction studies were conducted in both rodent (normal and alloxan-induced diabetic rats) and non-rodent (rabbits) animal models (n = 6) while the PK interaction study was conducted in normal rabbits (n = 6). An extrapolated human therapeutic oral dose of gliclazide, aprepitant and their combination were administered to rats and rabbits with 7 days washout between each treatment. For the multiple-dose interaction study, the same groups were administered with an interacting drug (aprepitant) for 7 days and then the combination of aprepitant and gliclazide on the 8th day. From the collected animal blood samples, blood glucose (by Glucose-Oxidase/Peroxidase method), insulin (by ELISA method) and gliclazide concentration levels (by HPLC method) were determined. Non-compartmental PK analysis was conducted by Phoenix WinNonlin software to determine the PK parameters of gliclazide. Statistical analysis was performed by student’s paired t-test. Results The pharmacodynamic activity (blood glucose reduction and insulin levels) of gliclazide was significantly (p < 0.05) influenced by aprepitant …
bibliographic citation: Kura et al. (2018) Influence of aprepitant on the pharmacodynamics and pharmacokinetics of gliclazide in rats and rabbits. PeerJ 6:e4798 https://doi.org/10.7717/peerj.4798
date submitted: 2018-02-23
date accepted: 2018-04-30
issued: 2018-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kura
  given name: Raghunandan Reddy
author list: Agent
  family name: Kilari
  given name: Eswar Kumar
author list: Agent
  family name: Shaik
  given name: Mastan
doi: 10.7717/peerj.4798
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-22
copyright: ©2018 Kura et al.
attribution name: Kura et al.

Large mammal burrows in late Miocene calcic paleosols from central Argentina: paleoenvironment, taphonomy and producers
type: item
type: AcademicArticle
description: Large cylindrical sediment-filled structures interpreted as mammal burrows occur within the loess-paleosol sequence of the late Miocene Cerro Azul Formation of central Argentina. A total of 115 burrow fills from three localities were measured. They are typically shallowly dipping, subcylindrical, unbranched structures with rounded ends and lacking enlargements. The horizontal diameter of the burrows range between 0.15 and 1.50 m, with most of the burrows in the interval of 0.39 to 0.98 m. Geometric morphometric analysis of transverse cross-sections support their distinct subcircular and elliptical (horizontally flattened) shapes. Burrow fills are typically laminated in the lower part and massive in the upper part. The laminated intervals reflect pulses of flowing water entering the abandoned burrow during moderate rains, whereas massive intervals reflect mass flow input of dense sediment-water mixtures during heavy rains that produced sheet floods. Approximately 1% of the burrows contained fragmentary, disarticulated and weathered mammal bones that were introduced in the open burrow by currents along with other sedimentary particles. Analysis of the tetrapod burrow fossil record suggests that Miocene burrows, including those studied herein, reflect a remarkable increase in the average size of the fossorial fauna. We conclude that large late Miocene mammals dug burrows essentially as a shelter against environmental extremes and to escape predation. The simple architecture of the burrows suggests that the producers essentially foraged aboveground. Several mammal groups acquired fossorial habits in response to cold and seasonally dry climatic conditions that prevailed during the late Miocene in southern South America. The considerable range of horizontal diameters of the studied burrows can be attributed to a variety of producers, including dasypodids, the notoungulate Paedotherium minor, Glyptodontidae and Proscelidodon sp.
format: application/pdf
format: text/html
creator: María Cristina Cardonatto
creator: Ricardo Néstor Melchor
subject: Animal Behavior
subject: Paleontology
description: doi:10.7717/peerj.4787
publisher: PeerJ Inc.
rights: © 2018 Cardonatto and Melchor
abstract: Large cylindrical sediment-filled structures interpreted as mammal burrows occur within the loess-paleosol sequence of the late Miocene Cerro Azul Formation of central Argentina. A total of 115 burrow fills from three localities were measured. They are typically shallowly dipping, subcylindrical, unbranched structures with rounded ends and lacking enlargements. The horizontal diameter of the burrows range between 0.15 and 1.50 m, with most of the burrows in the interval of 0.39 to 0.98 m. Geometric morphometric analysis of transverse cross-sections support their distinct subcircular and elliptical (horizontally flattened) shapes. Burrow fills are typically laminated in the lower part and massive in the upper part. The laminated intervals reflect pulses of flowing water entering the abandoned burrow during moderate rains, whereas massive intervals reflect mass flow input of dense sediment-water mixtures during heavy rains that produced sheet floods. Approximately 1% of the burrows contained fragmentary, disarticulated and weathered mammal bones that were introduced in the open burrow by currents along with other sedimentary particles. Analysis of the tetrapod burrow fossil record suggests that Miocene burrows, including those studied herein, reflect a remarkable increase in the average size of the fossorial fauna. We conclude that large late Miocene mammals dug burrows essentially as a shelter against environmental extremes and to escape predation. The simple architecture of the burrows suggests that the producers essentially foraged aboveground. Several mammal groups acquired fossorial habits in response to cold and seasonally dry climatic conditions that prevailed during the late Miocene in southern South America. The considerable range of horizontal diameters of the studied burrows can be attributed to a variety of producers, including dasypodids, the notoungulate Paedotherium minor, Glyptodontidae and Proscelidodon sp.
bibliographic citation: Cardonatto et al. (2018) Large mammal burrows in late Miocene calcic paleosols from central Argentina: paleoenvironment, taphonomy and producers. PeerJ 6:e4787 https://doi.org/10.7717/peerj.4787
date submitted: 2018-03-05
date accepted: 2018-04-27
issued: 2018-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cardonatto
  given name: María Cristina
author list: Agent
  family name: Melchor
  given name: Ricardo Néstor
doi: 10.7717/peerj.4787
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-22
copyright: ©2018 Cardonatto and Melchor
attribution name: Cardonatto and Melchor

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