PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Arabidopsis thaliana exudates induce growth and proteomic changes in Gluconacetobacter diazotrophicus
items: Energy balance of food in a detrito-bryophagous groundhopper (Orthoptera: Tetrigidae)
items: Testing pterosaur ingroup relationships through broader sampling of avemetatarsalian taxa and characters and a range of phylogenetic analysis techniques
items: Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome
items: Ancient globetrotters—connectivity and putative native ranges of two cosmopolitan biofouling amphipods
items: Toxicity thresholds of three insecticides and two fungicides to larvae of the coral Acropora tenuis
items: Identification of 10 Hub genes related to the progression of colorectal cancer by co-expression analysis
items: Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes
items: Change of direction asymmetry across different age categories in youth soccer
items: Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2, the etiologic agent of COVID-19 pandemic: an in silico approach

Arabidopsis thaliana exudates induce growth and proteomic changes in Gluconacetobacter diazotrophicus
type: item
type: AcademicArticle
description: Background Plants interact with a variety of microorganisms during their life cycle, among which beneficial bacteria deserve special attention. Gluconacetobacter diazotrophicus is a beneficial bacterium able to fix nitrogen and promote plant growth. Despite its biotechnological potential, the mechanisms regulating the interaction between G. diazotrophicus and host plants remain unclear. Methods We analyzed the response of G. diazotrophicus to cocultivation with Arabidopsis thaliana seedlings. Bacterial growth in response to cocultivation and plant exudates was analyzed. Through comparative proteomic analysis, G. diazotrophicus proteins regulated during cocultivation were investigated. Finally, the role of some up-accumulated proteins in the response G. diazotrophicus to cocultivation was analyzed by reverse genetics, using insertion mutants. Results Our results revealed the induction of bacterial growth in response to cocultivation. Comparative proteomic analysis identified 450 bacterial proteins, with 39 up-accumulated, and 12 down-accumulated in response to cocultivation. Among the up-accumulated pathways, the metabolism of pentoses and protein synthesis were highlighted. Proteins potentially relevant to bacterial growth response such as ABC-F-Etta, ClpX, Zwf, MetE, AcnA, IlvC, and AccC were also increased. Reverse genetics analysis, using insertion mutants, revealed that the lack of ABC-F-Etta and AccC proteins severely affects G. diazotrophicus response to cocultivation. Our data demonstrated that specific mechanisms are activated in the bacterial response to plant exudates, indicating the essential role of “ribosomal activity” and “fatty acid biosynthesis” in such a process. This is the first study to demonstrate the participation of EttA and AccC proteins in plant-bacteria interactions, and open new perspectives for understanding the initial steps of such associations.
format: application/pdf
format: text/html
creator: Tamires Cruz dos Santos
creator: Mariana Ramos Leandro
creator: Clara Yohana Maia
creator: Patrícia Rangel
creator: Fabiano S. Soares
creator: Ricardo Reis
creator: Lucas Passamani
creator: Vanildo Silveira
creator: Gonçalo Apolinário de Souza Filho
subject: Biotechnology
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9600
publisher: PeerJ Inc.
rights: © 2020 dos Santos et al.
abstract: Background Plants interact with a variety of microorganisms during their life cycle, among which beneficial bacteria deserve special attention. Gluconacetobacter diazotrophicus is a beneficial bacterium able to fix nitrogen and promote plant growth. Despite its biotechnological potential, the mechanisms regulating the interaction between G. diazotrophicus and host plants remain unclear. Methods We analyzed the response of G. diazotrophicus to cocultivation with Arabidopsis thaliana seedlings. Bacterial growth in response to cocultivation and plant exudates was analyzed. Through comparative proteomic analysis, G. diazotrophicus proteins regulated during cocultivation were investigated. Finally, the role of some up-accumulated proteins in the response G. diazotrophicus to cocultivation was analyzed by reverse genetics, using insertion mutants. Results Our results revealed the induction of bacterial growth in response to cocultivation. Comparative proteomic analysis identified 450 bacterial proteins, with 39 up-accumulated, and 12 down-accumulated in response to cocultivation. Among the up-accumulated pathways, the metabolism of pentoses and protein synthesis were highlighted. Proteins potentially relevant to bacterial growth response such as ABC-F-Etta, ClpX, Zwf, MetE, AcnA, IlvC, and AccC were also increased. Reverse genetics analysis, using insertion mutants, revealed that the lack of ABC-F-Etta and AccC proteins severely affects G. diazotrophicus response to cocultivation. Our data demonstrated that specific mechanisms are activated in the bacterial response to plant exudates, indicating the essential role of “ribosomal activity” and “fatty acid biosynthesis” in such a process. This is the first study to demonstrate the participation of EttA and AccC proteins in plant-bacteria interactions, and open new perspectives for understanding the initial steps of such associations.
bibliographic citation: dos Santos et al. (2020) Arabidopsis thaliana exudates induce growth and proteomic changes in Gluconacetobacter diazotrophicus. PeerJ 8:e9600 https://doi.org/10.7717/peerj.9600
date submitted: 2020-03-17
date accepted: 2020-07-03
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: dos Santos
  given name: Tamires Cruz
author list: Agent
  family name: Leandro
  given name: Mariana Ramos
author list: Agent
  family name: Maia
  given name: Clara Yohana
author list: Agent
  family name: Rangel
  given name: Patrícia
author list: Agent
  family name: Soares
  given name: Fabiano S.
author list: Agent
  family name: Reis
  given name: Ricardo
author list: Agent
  family name: Passamani
  given name: Lucas
author list: Agent
  family name: Silveira
  given name: Vanildo
author list: Agent
  family name: de Souza Filho
  given name: Gonçalo Apolinário
doi: 10.7717/peerj.9600
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 dos Santos et al.
attribution name: dos Santos et al.

Energy balance of food in a detrito-bryophagous groundhopper (Orthoptera: Tetrigidae)
type: item
type: AcademicArticle
description: Detritus (decaying organic matter) and phyllodes of mosses are two main components in the diet of groundhoppers (Orthoptera: Tetrigidae). We studied the energy balance of consumed food under laboratory conditions in the detrito-bryophagous groundhopper, Tetrix subulata (Linnaeus, 1758). The results indicated that the energy food budget of this detrito-bryophagous groundhopper was comparable to those of small herbivorous grasshoppers (Acrididae: Gomphocerinae, Melanoplinae), which have a similar energy food budget of approximately 800–1,100 J/g. T. subulata consumed four times more detritus than mosses, although both components provided similar amounts of energy (ca. 15–16 kJ/g). However, in contrast with detritus, moss fragments passed through the digestive tract without a distinct change in their mass or a loss in their energy value. We assume that moss may cause the longer retention of semifluid mass of partly digested food in the alimentary tract; hence, the digestion and efficiency of nutrient absorption from detritus could be more effective.
format: application/pdf
format: text/html
creator: Kateřina Kuřavová
creator: Jan Šipoš
creator: Petr Kočárek
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Food Science and Technology
subject: Zoology
description: doi:10.7717/peerj.9603
publisher: PeerJ Inc.
rights: © 2020 Kuřavová et al.
abstract: Detritus (decaying organic matter) and phyllodes of mosses are two main components in the diet of groundhoppers (Orthoptera: Tetrigidae). We studied the energy balance of consumed food under laboratory conditions in the detrito-bryophagous groundhopper, Tetrix subulata (Linnaeus, 1758). The results indicated that the energy food budget of this detrito-bryophagous groundhopper was comparable to those of small herbivorous grasshoppers (Acrididae: Gomphocerinae, Melanoplinae), which have a similar energy food budget of approximately 800–1,100 J/g. T. subulata consumed four times more detritus than mosses, although both components provided similar amounts of energy (ca. 15–16 kJ/g). However, in contrast with detritus, moss fragments passed through the digestive tract without a distinct change in their mass or a loss in their energy value. We assume that moss may cause the longer retention of semifluid mass of partly digested food in the alimentary tract; hence, the digestion and efficiency of nutrient absorption from detritus could be more effective.
bibliographic citation: Kuřavová et al. (2020) Energy balance of food in a detrito-bryophagous groundhopper (Orthoptera: Tetrigidae). PeerJ 8:e9603 https://doi.org/10.7717/peerj.9603
date submitted: 2019-09-24
date accepted: 2020-07-03
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kuřavová
  given name: Kateřina
author list: Agent
  family name: Šipoš
  given name: Jan
author list: Agent
  family name: Kočárek
  given name: Petr
doi: 10.7717/peerj.9603
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: ©2020 Kuřavová et al.
attribution name: Kuřavová et al.

Testing pterosaur ingroup relationships through broader sampling of avemetatarsalian taxa and characters and a range of phylogenetic analysis techniques
type: item
type: AcademicArticle
description: The pterosaurs first appear in the fossil record in the middle of the Late Triassic. Their earliest representatives are known from Northern Hemisphere localities but, by the end of the Jurassic Period, this clade of flying reptiles achieved a global distribution, as well as high levels of diversity and disparity. Our understanding of early pterosaur evolution and the fundamental interrelationships within Pterosauria has improved dramatically in recent decades. However, there is still debate about how the various pterosaur subgroups relate to one another and about which taxa comprise these. Many recent phylogenetic analyses, while sampling well from among the known Triassic and Early Jurassic pterosaurs, have not included many non-pterosaurian ornithodirans or other avemetatarsalians. Given the close relationship between these groups of archosaurs, the omission of other ornithodirans and avemetatarsalians has the potential to adversely affect the results of phylogenetic analyses, in terms of character optimisation and ingroup relationships recovered. This study has addressed this issue and tests the relationships between the early diverging pterosaur taxa following the addition of avemetatarsalian taxa and anatomical characters to an existing early pterosaur dataset. This study has, for the first time, included taxa that represent the aphanosaurs, lagerpetids, silesaurids and dinosaurs, in addition to early pterosaurs. Anatomical characters used in other recent studies of archosaurs and early dinosaurs have also been incorporated. By expanding the outgroup taxa and anatomical character coverage in this pterosaur dataset, better resolution between the taxa within certain early pterosaur subclades has been achieved and stronger support for some existing clades has been found; other purported clades of early pterosaurs have not been found in this analysis—for example there is no support for a monophyletic Eopterosauria or Eudimorphodontidae. Further support has been fou…
format: application/pdf
format: text/html
creator: Matthew G. Baron
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9604
publisher: PeerJ Inc.
rights: © 2020 Baron
abstract: The pterosaurs first appear in the fossil record in the middle of the Late Triassic. Their earliest representatives are known from Northern Hemisphere localities but, by the end of the Jurassic Period, this clade of flying reptiles achieved a global distribution, as well as high levels of diversity and disparity. Our understanding of early pterosaur evolution and the fundamental interrelationships within Pterosauria has improved dramatically in recent decades. However, there is still debate about how the various pterosaur subgroups relate to one another and about which taxa comprise these. Many recent phylogenetic analyses, while sampling well from among the known Triassic and Early Jurassic pterosaurs, have not included many non-pterosaurian ornithodirans or other avemetatarsalians. Given the close relationship between these groups of archosaurs, the omission of other ornithodirans and avemetatarsalians has the potential to adversely affect the results of phylogenetic analyses, in terms of character optimisation and ingroup relationships recovered. This study has addressed this issue and tests the relationships between the early diverging pterosaur taxa following the addition of avemetatarsalian taxa and anatomical characters to an existing early pterosaur dataset. This study has, for the first time, included taxa that represent the aphanosaurs, lagerpetids, silesaurids and dinosaurs, in addition to early pterosaurs. Anatomical characters used in other recent studies of archosaurs and early dinosaurs have also been incorporated. By expanding the outgroup taxa and anatomical character coverage in this pterosaur dataset, better resolution between the taxa within certain early pterosaur subclades has been achieved and stronger support for some existing clades has been found; other purported clades of early pterosaurs have not been found in this analysis—for example there is no support for a monophyletic Eopterosauria or Eudimorphodontidae. Further support has been fou…
bibliographic citation: Baron (2020) Testing pterosaur ingroup relationships through broader sampling of avemetatarsalian taxa and characters and a range of phylogenetic analysis techniques. PeerJ 8:e9604 https://doi.org/10.7717/peerj.9604
date submitted: 2020-04-08
date accepted: 2020-07-03
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baron
  given name: Matthew G.
doi: 10.7717/peerj.9604
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 Baron
attribution name: Baron

Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome
type: item
type: AcademicArticle
description: Sugarcane contributes 80% of global sugar production and to bioethanol generation for the bioenergy industry. Its productivity is threatened by drought that can cause up to 60% yield loss. This study used RNA-Seq to gain a better understanding of the underlying mechanism by which drought-tolerant sugarcane copes with water stress. We compared gene expression in KPS01-12 (drought-tolerant genotype) and UT12 (drought-sensitive genotype) that have significantly different yield loss rates under drought conditions. We treated KPS01-12 and UT12 with mild and moderate water stress and found differentially expressed genes in various biological processes. KPS01-12 had higher expression of genes that were involved in water retention, antioxidant secondary metabolite biosynthesis, and oxidative and osmotic stress response than UT12. In contrast, the sensitive genotype had more down-regulated genes that were involved in photosynthesis, carbon fixation and Calvin cycle than the tolerant genotype. Our obtained expression profiles suggest that the tolerant sugarcane has a more effective genetic response than the sensitive genotype at the initiation of drought stress. The knowledge gained from this study may be applied in breeding programs to improve sugarcane production in drought conditions.
format: application/pdf
format: text/html
creator: Wanapinun Nawae
creator: Jeremy R. Shearman
creator: Sithichoke Tangphatsornruang
creator: Prapat Punpee
creator: Thippawan Yoocha
creator: Duangjai Sangsrakru
creator: Chaiwat Naktang
creator: Chutima Sonthirod
creator: Warodom Wirojsirasak
creator: Kittipat Ukoskit
creator: Klanarong Sriroth
creator: Peeraya Klomsa-ard
creator: Wirulda Pootakham
subject: Bioinformatics
subject: Biotechnology
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.9608
publisher: PeerJ Inc.
rights: © 2020 Nawae et al.
abstract: Sugarcane contributes 80% of global sugar production and to bioethanol generation for the bioenergy industry. Its productivity is threatened by drought that can cause up to 60% yield loss. This study used RNA-Seq to gain a better understanding of the underlying mechanism by which drought-tolerant sugarcane copes with water stress. We compared gene expression in KPS01-12 (drought-tolerant genotype) and UT12 (drought-sensitive genotype) that have significantly different yield loss rates under drought conditions. We treated KPS01-12 and UT12 with mild and moderate water stress and found differentially expressed genes in various biological processes. KPS01-12 had higher expression of genes that were involved in water retention, antioxidant secondary metabolite biosynthesis, and oxidative and osmotic stress response than UT12. In contrast, the sensitive genotype had more down-regulated genes that were involved in photosynthesis, carbon fixation and Calvin cycle than the tolerant genotype. Our obtained expression profiles suggest that the tolerant sugarcane has a more effective genetic response than the sensitive genotype at the initiation of drought stress. The knowledge gained from this study may be applied in breeding programs to improve sugarcane production in drought conditions.
bibliographic citation: Nawae et al. (2020) Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome. PeerJ 8:e9608 https://doi.org/10.7717/peerj.9608
date submitted: 2020-01-17
date accepted: 2020-07-05
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nawae
  given name: Wanapinun
author list: Agent
  family name: Shearman
  given name: Jeremy R.
author list: Agent
  family name: Tangphatsornruang
  given name: Sithichoke
author list: Agent
  family name: Punpee
  given name: Prapat
author list: Agent
  family name: Yoocha
  given name: Thippawan
author list: Agent
  family name: Sangsrakru
  given name: Duangjai
author list: Agent
  family name: Naktang
  given name: Chaiwat
author list: Agent
  family name: Sonthirod
  given name: Chutima
author list: Agent
  family name: Wirojsirasak
  given name: Warodom
author list: Agent
  family name: Ukoskit
  given name: Kittipat
author list: Agent
  family name: Sriroth
  given name: Klanarong
author list: Agent
  family name: Klomsa-ard
  given name: Peeraya
author list: Agent
  family name: Pootakham
  given name: Wirulda
doi: 10.7717/peerj.9608
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 Nawae et al.
attribution name: Nawae et al.

Ancient globetrotters—connectivity and putative native ranges of two cosmopolitan biofouling amphipods
type: item
type: AcademicArticle
description: The geographic distributions of some coastal marine species have appeared as cosmopolitan ever since they were first scientifically documented. In particular, for many benthic species that are associated with anthropogenic substrata, there is much speculation as to whether or not their broad distributions can be explained by natural mechanisms of dispersal. Here, we focused on two congeneric coastal crustaceans with cosmopolitan distributions—the tube-dwelling amphipods Jassa marmorata and Jassa slatteryi. Both species are common elements of marine biofouling on nearly all kinds of artificial hard substrata in temperate to warm seas. We hypothesized that the two species’ modern occurrences across the oceans are the result of human shipping activities that started centuries ago. Mitochondrial DNA sequences of the CO1 fragment of specimens from distinct marine regions around the world were analysed, evaluating genetic structure and migration models and making inferences on putative native ranges of the two Jassa species. Populations of both species exhibited considerable genetic diversity with differing levels of geographic structure. For both species, at least two dominant haplotypes were shared among several geographic populations. Rapid demographic expansion and high migration rates between geographically distant regions support a scenario of ongoing dispersal all over the world. Our findings indicate that the likely former native range of J. marmorata is the Northwest Atlantic, whereas the likely former native range of J. slatteryi is the Northern Pacific region. As corroborated by the genetic connectivity between populations, shipping still appears to be the more successful vector of the two species’ dispersal when compared to natural mechanisms. Historical invasion events that likely started centuries ago, along with current ongoing dispersal, confirm these species’ identities as true “neocosmopolitans”.
format: application/pdf
format: text/html
creator: Jan Beermann
creator: Allison K. Hall-Mullen
creator: Charlotte Havermans
creator: Joop WP Coolen
creator: Richard PMA Crooijmans
creator: Bert Dibbits
creator: Christoph Held
creator: Andrea Desiderato
subject: Biogeography
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.9613
publisher: PeerJ Inc.
rights: © 2020 Beermann et al.
abstract: The geographic distributions of some coastal marine species have appeared as cosmopolitan ever since they were first scientifically documented. In particular, for many benthic species that are associated with anthropogenic substrata, there is much speculation as to whether or not their broad distributions can be explained by natural mechanisms of dispersal. Here, we focused on two congeneric coastal crustaceans with cosmopolitan distributions—the tube-dwelling amphipods Jassa marmorata and Jassa slatteryi. Both species are common elements of marine biofouling on nearly all kinds of artificial hard substrata in temperate to warm seas. We hypothesized that the two species’ modern occurrences across the oceans are the result of human shipping activities that started centuries ago. Mitochondrial DNA sequences of the CO1 fragment of specimens from distinct marine regions around the world were analysed, evaluating genetic structure and migration models and making inferences on putative native ranges of the two Jassa species. Populations of both species exhibited considerable genetic diversity with differing levels of geographic structure. For both species, at least two dominant haplotypes were shared among several geographic populations. Rapid demographic expansion and high migration rates between geographically distant regions support a scenario of ongoing dispersal all over the world. Our findings indicate that the likely former native range of J. marmorata is the Northwest Atlantic, whereas the likely former native range of J. slatteryi is the Northern Pacific region. As corroborated by the genetic connectivity between populations, shipping still appears to be the more successful vector of the two species’ dispersal when compared to natural mechanisms. Historical invasion events that likely started centuries ago, along with current ongoing dispersal, confirm these species’ identities as true “neocosmopolitans”.
bibliographic citation: Beermann et al. (2020) Ancient globetrotters—connectivity and putative native ranges of two cosmopolitan biofouling amphipods. PeerJ 8:e9613 https://doi.org/10.7717/peerj.9613
date submitted: 2020-04-16
date accepted: 2020-07-06
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beermann
  given name: Jan
author list: Agent
  family name: Hall-Mullen
  given name: Allison K.
author list: Agent
  family name: Havermans
  given name: Charlotte
author list: Agent
  family name: Coolen
  given name: Joop WP
author list: Agent
  family name: Crooijmans
  given name: Richard PMA
author list: Agent
  family name: Dibbits
  given name: Bert
author list: Agent
  family name: Held
  given name: Christoph
author list: Agent
  family name: Desiderato
  given name: Andrea
doi: 10.7717/peerj.9613
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 Beermann et al.
attribution name: Beermann et al.

Toxicity thresholds of three insecticides and two fungicides to larvae of the coral Acropora tenuis
type: item
type: AcademicArticle
description: Tropical marine ecosystems, such as coral reefs, face several threats to their health and resilience, including poor water quality. Previous studies on the risks posed by pesticides have focused on five priority herbicides; however, as the number of pesticides applied in coastal agriculture increases, a suite of ‘alternative’ pesticides is being detected in tropical nearshore waters. To improve our understanding of the risks posed by alternative pesticides to tropical marine organisms, the effects of three insecticides (diazinon, fipronil, imidacloprid) and two fungicides (chlorothalonil, propiconazole) were tested on larval metamorphosis of the coral Acropora tenuis. A. tenuis larvae were affected by all five pesticides and the reference toxicant copper. The no effect concentration (NEC) and the 10% and 50% effect concentrations (EC10 and EC50, respectively) for larval metamorphosis were estimated from concentration-response curves after 48 h exposure. The NEC, EC10 and EC50 (in µg L−1), respectively, of each pesticide were as follows: chlorothalonil (2.4, 2.8, 6.0); fipronil (12.3, 13.9, 29.1); diazinon (38.0, 40.8, 54.7); imidacloprid (263, 273, 347); and propiconazole (269, 330, 1008). These toxicity thresholds are higher than reported concentrations in monitoring programs; however, these data will contribute to improving water quality guideline values, which inform the total risk assessments posed by complex contaminant mixtures to which these pesticides contribute.
format: application/pdf
format: text/html
creator: Florita Flores
creator: Sarit Kaserzon
creator: Gabriele Elisei
creator: Gerard Ricardo
creator: Andrew P. Negri
subject: Ecology
subject: Marine Biology
subject: Ecotoxicology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.9615
publisher: PeerJ Inc.
rights: © 2020 Flores et al.
abstract: Tropical marine ecosystems, such as coral reefs, face several threats to their health and resilience, including poor water quality. Previous studies on the risks posed by pesticides have focused on five priority herbicides; however, as the number of pesticides applied in coastal agriculture increases, a suite of ‘alternative’ pesticides is being detected in tropical nearshore waters. To improve our understanding of the risks posed by alternative pesticides to tropical marine organisms, the effects of three insecticides (diazinon, fipronil, imidacloprid) and two fungicides (chlorothalonil, propiconazole) were tested on larval metamorphosis of the coral Acropora tenuis. A. tenuis larvae were affected by all five pesticides and the reference toxicant copper. The no effect concentration (NEC) and the 10% and 50% effect concentrations (EC10 and EC50, respectively) for larval metamorphosis were estimated from concentration-response curves after 48 h exposure. The NEC, EC10 and EC50 (in µg L−1), respectively, of each pesticide were as follows: chlorothalonil (2.4, 2.8, 6.0); fipronil (12.3, 13.9, 29.1); diazinon (38.0, 40.8, 54.7); imidacloprid (263, 273, 347); and propiconazole (269, 330, 1008). These toxicity thresholds are higher than reported concentrations in monitoring programs; however, these data will contribute to improving water quality guideline values, which inform the total risk assessments posed by complex contaminant mixtures to which these pesticides contribute.
bibliographic citation: Flores et al. (2020) Toxicity thresholds of three insecticides and two fungicides to larvae of the coral Acropora tenuis. PeerJ 8:e9615 https://doi.org/10.7717/peerj.9615
date submitted: 2020-05-06
date accepted: 2020-07-06
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Flores
  given name: Florita
author list: Agent
  family name: Kaserzon
  given name: Sarit
author list: Agent
  family name: Elisei
  given name: Gabriele
author list: Agent
  family name: Ricardo
  given name: Gerard
author list: Agent
  family name: Negri
  given name: Andrew P.
doi: 10.7717/peerj.9615
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 Flores et al.
attribution name: Flores et al.

Identification of 10 Hub genes related to the progression of colorectal cancer by co-expression analysis
type: item
type: AcademicArticle
description: Background Colorectal cancer (CRC) is the third most common cancer in the world. The present study is aimed at identifying hub genes associated with the progression of CRC. Method The data of the patients with CRC were obtained from the Gene Expression Omnibus (GEO) database and assessed by weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses performed in R by WGCNA, several hub genes that regulate the mechanism of tumorigenesis in CRC were identified. Differentially expressed genes in the data sets GSE28000 and GSE42284 were used to construct a co-expression network for WGCNA. The yellow, black and blue modules associated with CRC level were filtered. Combining the co-expression network and the PPI network, 15 candidate hub genes were screened. Results After validation using the TCGA-COAD dataset, a total of 10 hub genes (MT1X, MT1G, MT2A, CXCL8, IL1B, CXCL5, CXCL11, IL10RA, GZMB, KIT) closely related to the progression of CRC were identified. The expressions of MT1G, CXCL8, IL1B, CXCL5, CXCL11 and GZMB in CRC tissues were higher than normal tissues (p-value < 0.05). The expressions of MT1X, MT2A, IL10RA and KIT in CRC tissues were lower than normal tissues (p-value < 0.05). Conclusions By combinating with a series of methods including GO enrichment analysis, KEGG pathway analysis, PPI network analysis and gene co-expression network analysis, we identified 10 hub genes that were associated with the progression of CRC.
format: application/pdf
format: text/html
creator: Jie Meng
creator: Rui Su
creator: Yun Liao
creator: Yanyan Li
creator: Ling Li
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.9633
publisher: PeerJ Inc.
rights: © 2020 Meng et al.
abstract: Background Colorectal cancer (CRC) is the third most common cancer in the world. The present study is aimed at identifying hub genes associated with the progression of CRC. Method The data of the patients with CRC were obtained from the Gene Expression Omnibus (GEO) database and assessed by weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses performed in R by WGCNA, several hub genes that regulate the mechanism of tumorigenesis in CRC were identified. Differentially expressed genes in the data sets GSE28000 and GSE42284 were used to construct a co-expression network for WGCNA. The yellow, black and blue modules associated with CRC level were filtered. Combining the co-expression network and the PPI network, 15 candidate hub genes were screened. Results After validation using the TCGA-COAD dataset, a total of 10 hub genes (MT1X, MT1G, MT2A, CXCL8, IL1B, CXCL5, CXCL11, IL10RA, GZMB, KIT) closely related to the progression of CRC were identified. The expressions of MT1G, CXCL8, IL1B, CXCL5, CXCL11 and GZMB in CRC tissues were higher than normal tissues (p-value < 0.05). The expressions of MT1X, MT2A, IL10RA and KIT in CRC tissues were lower than normal tissues (p-value < 0.05). Conclusions By combinating with a series of methods including GO enrichment analysis, KEGG pathway analysis, PPI network analysis and gene co-expression network analysis, we identified 10 hub genes that were associated with the progression of CRC.
bibliographic citation: Meng et al. (2020) Identification of 10 Hub genes related to the progression of colorectal cancer by co-expression analysis. PeerJ 8:e9633 https://doi.org/10.7717/peerj.9633
date submitted: 2020-04-27
date accepted: 2020-07-09
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Jie
author list: Agent
  family name: Su
  given name: Rui
author list: Agent
  family name: Liao
  given name: Yun
author list: Agent
  family name: Li
  given name: Yanyan
author list: Agent
  family name: Li
  given name: Ling
doi: 10.7717/peerj.9633
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 Meng et al.
attribution name: Meng et al.

Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes
type: item
type: AcademicArticle
description: Background SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. Methods We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1. Results We found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G–U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C–A mutations in SARS-CoV-2. We discuss possible explanations for these observations.
format: application/pdf
format: text/html
creator: Alexander Y. Panchin
creator: Yuri V. Panchin
subject: Bioinformatics
subject: Computational Biology
subject: Virology
description: doi:10.7717/peerj.9648
publisher: PeerJ Inc.
rights: © 2020 Panchin and Panchin
abstract: Background SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. Methods We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1. Results We found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G–U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C–A mutations in SARS-CoV-2. We discuss possible explanations for these observations.
bibliographic citation: Panchin et al. (2020) Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes. PeerJ 8:e9648 https://doi.org/10.7717/peerj.9648
date submitted: 2020-05-24
date accepted: 2020-07-13
issued: 2020-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Panchin
  given name: Alexander Y.
author list: Agent
  family name: Panchin
  given name: Yuri V.
doi: 10.7717/peerj.9648
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-28
copyright: © 2020 Panchin and Panchin
attribution name: Panchin and Panchin

Change of direction asymmetry across different age categories in youth soccer
type: item
type: AcademicArticle
description: Background In youth, the development of change of direction (COD) and sprint performance is a key component for successfully competing in soccer across age. During a COD, the presence of directional asymmetries may be detrimental due to the unpredictable nature of the sport. Therefore, the aims of the study were to investigate asymmetries in COD ability and to examine the differences in COD and sprint performance across age in young soccer players. Methods Sixty-eight sub-elite soccer players of different age categories (U18, U17, U16, U15) were tested on a 10-m linear sprint test and 90°COD (5-m entry and exit) test in both directions. Asymmetric index (AI) of COD deficit was obtained for dominant (fastest) and non-dominant directions (slowest). Results The results showed that U16 were more asymmetrical than U18, U17, and U15 from large to moderate effects. The sprint time improved linearly across age with U18 and U15 displaying the fastest and slowest 10-m sprint performance (p < 0.01), respectively. Moreover, COD ability measured by COD deficit did not change across age (p > 0.05). Conclusion Given the results of this study, practitioners are encouraged to assess asymmetries between dominant and non-dominant directions rather than solely players’ COD ability in young soccer players.
format: application/pdf
format: text/html
creator: Athos Trecroci
creator: Alessio Rossi
creator: Thomas Dos’Santos
creator: Damiano Formenti
creator: Luca Cavaggioni
creator: Stefano Longo
creator: F. Marcello Iaia
creator: Giampietro Alberti
subject: Kinesiology
subject: Pediatrics
description: doi:10.7717/peerj.9486
publisher: PeerJ Inc.
rights: © 2020 Trecroci et al.
abstract: Background In youth, the development of change of direction (COD) and sprint performance is a key component for successfully competing in soccer across age. During a COD, the presence of directional asymmetries may be detrimental due to the unpredictable nature of the sport. Therefore, the aims of the study were to investigate asymmetries in COD ability and to examine the differences in COD and sprint performance across age in young soccer players. Methods Sixty-eight sub-elite soccer players of different age categories (U18, U17, U16, U15) were tested on a 10-m linear sprint test and 90°COD (5-m entry and exit) test in both directions. Asymmetric index (AI) of COD deficit was obtained for dominant (fastest) and non-dominant directions (slowest). Results The results showed that U16 were more asymmetrical than U18, U17, and U15 from large to moderate effects. The sprint time improved linearly across age with U18 and U15 displaying the fastest and slowest 10-m sprint performance (p < 0.01), respectively. Moreover, COD ability measured by COD deficit did not change across age (p > 0.05). Conclusion Given the results of this study, practitioners are encouraged to assess asymmetries between dominant and non-dominant directions rather than solely players’ COD ability in young soccer players.
bibliographic citation: Trecroci et al. (2020) Change of direction asymmetry across different age categories in youth soccer. PeerJ 8:e9486 https://doi.org/10.7717/peerj.9486
date submitted: 2020-02-18
date accepted: 2020-06-15
issued: 2020-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Trecroci
  given name: Athos
author list: Agent
  family name: Rossi
  given name: Alessio
author list: Agent
  family name: Dos’Santos
  given name: Thomas
author list: Agent
  family name: Formenti
  given name: Damiano
author list: Agent
  family name: Cavaggioni
  given name: Luca
author list: Agent
  family name: Longo
  given name: Stefano
author list: Agent
  family name: Iaia
  given name: F. Marcello
author list: Agent
  family name: Alberti
  given name: Giampietro
doi: 10.7717/peerj.9486
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-27
copyright: ©2020 Trecroci et al.
attribution name: Trecroci et al.

Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2, the etiologic agent of COVID-19 pandemic: an in silico approach
type: item
type: AcademicArticle
description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥90.0% world population coverage for different ethnic groups. Molecular docking and dynamics simulation of the chimeric vaccine with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased IFN-γ and IL-2 cytokines. The codon optimization and mRNA secondary structure prediction revealed that the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19.
format: application/pdf
format: text/html
creator: M. Shaminur Rahman
creator: M. Nazmul Hoque
creator: M. Rafiul Islam
creator: Salma Akter
creator: A. S. M. Rubayet Ul Alam
creator: Mohammad Anwar Siddique
creator: Otun Saha
creator: Md. Mizanur Rahaman
creator: Munawar Sultana
creator: Keith A. Crandall
creator: M. Anwar Hossain
subject: Bioinformatics
subject: Computational Biology
subject: Virology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.9572
publisher: PeerJ Inc.
rights: © 2020 Rahman et al.
abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥90.0% world population coverage for different ethnic groups. Molecular docking and dynamics simulation of the chimeric vaccine with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased IFN-γ and IL-2 cytokines. The codon optimization and mRNA secondary structure prediction revealed that the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19.
bibliographic citation: Rahman et al. (2020) Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2, the etiologic agent of COVID-19 pandemic: an in silico approach. PeerJ 8:e9572 https://doi.org/10.7717/peerj.9572
date submitted: 2020-04-16
date accepted: 2020-06-29
issued: 2020-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rahman
  given name: M. Shaminur
author list: Agent
  family name: Hoque
  given name: M. Nazmul
author list: Agent
  family name: Islam
  given name: M. Rafiul
author list: Agent
  family name: Akter
  given name: Salma
author list: Agent
  family name: Rubayet Ul Alam
  given name: A. S. M.
author list: Agent
  family name: Siddique
  given name: Mohammad Anwar
author list: Agent
  family name: Saha
  given name: Otun
author list: Agent
  family name: Rahaman
  given name: Md. Mizanur
author list: Agent
  family name: Sultana
  given name: Munawar
author list: Agent
  family name: Crandall
  given name: Keith A.
author list: Agent
  family name: Hossain
  given name: M. Anwar
doi: 10.7717/peerj.9572
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-27
copyright: ©2020 Rahman et al.
attribution name: Rahman et al.

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