PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Characterization of a profilin-like protein from Fasciola hepatica
items: Description of a new genus and species for a common and widespread Amazonian satyrine butterfly (Lepidoptera: Nymphalidae: Satyrinae: Satyrini)
items: Comparing multiple comparisons: practical guidance for choosing the best multiple comparisons test
items: The phylogeny and systematics of Xiphosura
items: Identification and characterization of critical genes associated with tamoxifen resistance in breast cancer
items: Patterns of telomere length with age in African mole-rats: New insights from quantitative fluorescence in situ hybridisation (qFISH)
items: Comprehensive analysis of circRNA expression profiles and circRNA-associated competing endogenous RNA networks in IgA nephropathy
items: Effects of monofilament nylon versus braided multifilament nylon gangions on catch rates of Greenland shark (Somniosus microcephalus) in bottom set longlines
items: Bacterial exposure leads to variable mortality but not a measurable increase in surface antimicrobials across ant species
items: Moderately low nitrogen application mitigate the negative effects of salt stress on annual ryegrass seedlings

Characterization of a profilin-like protein from Fasciola hepatica
type: item
type: AcademicArticle
description: Fasciola hepatica is the causative agent of fasciolosis, an important disease of humans and livestock around the world. There is an urgent requirement for novel treatments for F. hepatica due to increasing reports of drug resistance appearing around the world. The outer body covering of F. hepatica is referred to as the tegument membrane which is of crucial importance for the modulation of the host response and parasite survival; therefore, tegument proteins may represent novel drug or vaccine targets. Previous studies have identified a profilin-like protein in the tegument of F. hepatica. Profilin is a regulatory component of the actin cytoskeleton in all eukaryotic cells, and in some protozoan parasites, profilin has been shown to drive a potent IL-12 response. This study characterized the identified profilin form F. hepatica (termed FhProfilin) for the first time. Recombinant expression of FhProfilin resulted in a protein approximately 14 kDa in size which was determined to be dimeric like other profilins isolated from a range of eukaryotic organisms. FhProfilin was shown to bind poly-L-proline (pLp) and sequester actin monomers which is characteristic of the profilin family; however, there was no binding of FhProfilin to phosphatidylinositol lipids. Despite FhProfilin being a component of the tegument, it was shown not to generate an immune response in experimentally infected sheep or cattle.
format: application/pdf
format: text/html
creator: Jessica Wilkie
creator: Timothy C. Cameron
creator: Travis Beddoe
subject: Biochemistry
subject: Molecular Biology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.10503
publisher: PeerJ Inc.
rights: © 2020 Wilkie et al.
abstract: Fasciola hepatica is the causative agent of fasciolosis, an important disease of humans and livestock around the world. There is an urgent requirement for novel treatments for F. hepatica due to increasing reports of drug resistance appearing around the world. The outer body covering of F. hepatica is referred to as the tegument membrane which is of crucial importance for the modulation of the host response and parasite survival; therefore, tegument proteins may represent novel drug or vaccine targets. Previous studies have identified a profilin-like protein in the tegument of F. hepatica. Profilin is a regulatory component of the actin cytoskeleton in all eukaryotic cells, and in some protozoan parasites, profilin has been shown to drive a potent IL-12 response. This study characterized the identified profilin form F. hepatica (termed FhProfilin) for the first time. Recombinant expression of FhProfilin resulted in a protein approximately 14 kDa in size which was determined to be dimeric like other profilins isolated from a range of eukaryotic organisms. FhProfilin was shown to bind poly-L-proline (pLp) and sequester actin monomers which is characteristic of the profilin family; however, there was no binding of FhProfilin to phosphatidylinositol lipids. Despite FhProfilin being a component of the tegument, it was shown not to generate an immune response in experimentally infected sheep or cattle.
bibliographic citation: Wilkie et al. (2020) Characterization of a profilin-like protein from Fasciola hepatica. PeerJ 8:e10503 https://doi.org/10.7717/peerj.10503
date submitted: 2020-06-10
date accepted: 2020-11-15
issued: 2020-12-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilkie
  given name: Jessica
author list: Agent
  family name: Cameron
  given name: Timothy C.
author list: Agent
  family name: Beddoe
  given name: Travis
doi: 10.7717/peerj.10503
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-07
copyright: © 2020 Wilkie et al.
attribution name: Wilkie et al.

Description of a new genus and species for a common and widespread Amazonian satyrine butterfly (Lepidoptera: Nymphalidae: Satyrinae: Satyrini)
type: item
type: AcademicArticle
description: We here propose a new monotypic butterfly genus Scriptor Nakahara & Espeland, n. gen. to accommodate a new species, S. sphenophorus Lamas & Nakahara, n. sp., described and named herein. Scriptor sphenophorus n. gen. and n. sp.is a relatively common and widespread butterfly species which is recovered as a member of the so-called “Splendeuptychia clade” in the nymphalid subtribe Euptychiina, based on our molecular phylogenetic analysis using a maximum likelihood approach. Nevertheless, its sister group is not confidently resolved in any analysis, supporting a relatively distant relationship to any described genus as well as our decision to establish a new monotypic genus. We further discuss the proposed taxonomy in the light of frequent criticism of the description of monotypic taxa, as well as emphasize the importance of incorporating multiple evidence when describing new genera, illustrated by reference to several recent generic descriptions in this subtribe.
format: application/pdf
format: text/html
creator: Shinichi Nakahara
creator: Gerardo Lamas
creator: Keith Willmott
creator: Marianne Espeland
subject: Biodiversity
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10324
publisher: PeerJ Inc.
rights: © 2020 Nakahara et al.
abstract: We here propose a new monotypic butterfly genus Scriptor Nakahara & Espeland, n. gen. to accommodate a new species, S. sphenophorus Lamas & Nakahara, n. sp., described and named herein. Scriptor sphenophorus n. gen. and n. sp.is a relatively common and widespread butterfly species which is recovered as a member of the so-called “Splendeuptychia clade” in the nymphalid subtribe Euptychiina, based on our molecular phylogenetic analysis using a maximum likelihood approach. Nevertheless, its sister group is not confidently resolved in any analysis, supporting a relatively distant relationship to any described genus as well as our decision to establish a new monotypic genus. We further discuss the proposed taxonomy in the light of frequent criticism of the description of monotypic taxa, as well as emphasize the importance of incorporating multiple evidence when describing new genera, illustrated by reference to several recent generic descriptions in this subtribe.
bibliographic citation: Nakahara et al. (2020) Description of a new genus and species for a common and widespread Amazonian satyrine butterfly (Lepidoptera: Nymphalidae: Satyrinae: Satyrini). PeerJ 8:e10324 https://doi.org/10.7717/peerj.10324
date submitted: 2020-07-23
date accepted: 2020-10-19
issued: 2020-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nakahara
  given name: Shinichi
author list: Agent
  family name: Lamas
  given name: Gerardo
author list: Agent
  family name: Willmott
  given name: Keith
author list: Agent
  family name: Espeland
  given name: Marianne
doi: 10.7717/peerj.10324
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-04
copyright: ©2020 Nakahara et al.
attribution name: Nakahara et al.

Comparing multiple comparisons: practical guidance for choosing the best multiple comparisons test
type: item
type: AcademicArticle
description: Multiple comparisons tests (MCTs) include the statistical tests used to compare groups (treatments) often following a significant effect reported in one of many types of linear models. Due to a variety of data and statistical considerations, several dozen MCTs have been developed over the decades, with tests ranging from very similar to each other to very different from each other. Many scientific disciplines use MCTs, including >40,000 reports of their use in ecological journals in the last 60 years. Despite the ubiquity and utility of MCTs, several issues remain in terms of their correct use and reporting. In this study, we evaluated 17 different MCTs. We first reviewed the published literature for recommendations on their correct use. Second, we created a simulation that evaluated the performance of nine common MCTs. The tests examined in the simulation were those that often overlapped in usage, meaning the selection of the test based on fit to the data is not unique and that the simulations could inform the selection of one or more tests when a researcher has choices. Based on the literature review and recommendations: planned comparisons are overwhelmingly recommended over unplanned comparisons, for planned non-parametric comparisons the Mann-Whitney-Wilcoxon U test is recommended, Scheffé’s S test is recommended for any linear combination of (unplanned) means, Tukey’s HSD and the Bonferroni or the Dunn-Sidak tests are recommended for pairwise comparisons of groups, and that many other tests exist for particular types of data. All code and data used to generate this paper are available at: https://github.com/stevemidway/MultipleComparisons.
format: application/pdf
format: text/html
creator: Stephen Midway
creator: Matthew Robertson
creator: Shane Flinn
creator: Michael Kaller
subject: Bioinformatics
subject: Ecology
subject: Statistics
subject: Data Science
description: doi:10.7717/peerj.10387
publisher: PeerJ Inc.
rights: © 2020 Midway et al.
abstract: Multiple comparisons tests (MCTs) include the statistical tests used to compare groups (treatments) often following a significant effect reported in one of many types of linear models. Due to a variety of data and statistical considerations, several dozen MCTs have been developed over the decades, with tests ranging from very similar to each other to very different from each other. Many scientific disciplines use MCTs, including >40,000 reports of their use in ecological journals in the last 60 years. Despite the ubiquity and utility of MCTs, several issues remain in terms of their correct use and reporting. In this study, we evaluated 17 different MCTs. We first reviewed the published literature for recommendations on their correct use. Second, we created a simulation that evaluated the performance of nine common MCTs. The tests examined in the simulation were those that often overlapped in usage, meaning the selection of the test based on fit to the data is not unique and that the simulations could inform the selection of one or more tests when a researcher has choices. Based on the literature review and recommendations: planned comparisons are overwhelmingly recommended over unplanned comparisons, for planned non-parametric comparisons the Mann-Whitney-Wilcoxon U test is recommended, Scheffé’s S test is recommended for any linear combination of (unplanned) means, Tukey’s HSD and the Bonferroni or the Dunn-Sidak tests are recommended for pairwise comparisons of groups, and that many other tests exist for particular types of data. All code and data used to generate this paper are available at: https://github.com/stevemidway/MultipleComparisons.
bibliographic citation: Midway et al. (2020) Comparing multiple comparisons: practical guidance for choosing the best multiple comparisons test. PeerJ 8:e10387 https://doi.org/10.7717/peerj.10387
date submitted: 2020-07-20
date accepted: 2020-10-27
issued: 2020-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Midway
  given name: Stephen
author list: Agent
  family name: Robertson
  given name: Matthew
author list: Agent
  family name: Flinn
  given name: Shane
author list: Agent
  family name: Kaller
  given name: Michael
doi: 10.7717/peerj.10387
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-04
copyright: ©2020 Midway et al.
attribution name: Midway et al.

The phylogeny and systematics of Xiphosura
type: item
type: AcademicArticle
description: Xiphosurans are aquatic chelicerates with a fossil record extending into the Early Ordovician and known from a total of 88 described species, four of which are extant. Known for their apparent morphological conservatism, for which they have gained notoriety as supposed ‘living fossils’, recent analyses have demonstrated xiphosurans to have an ecologically diverse evolutionary history, with several groups moving into non-marine environments and developing morphologies markedly different from those of the modern species. The combination of their long evolutionary and complex ecological history along with their paradoxical patterns of morphological stasis in some clades and experimentation among others has resulted in Xiphosura being of particular interest for macroevolutionary study. Phylogenetic analyses have shown the current taxonomic framework for Xiphosura—set out in the Treatise of Invertebrate Paleontology in 1955—to be outdated and in need of revision, with several common genera such as Paleolimulus Dunbar, 1923 and Limulitella Størmer, 1952 acting as wastebasket taxa. Here, an expanded xiphosuran phylogeny is presented, comprising 58 xiphosuran species as part of a 158 taxon chelicerate matrix coded for 259 characters. Analysing the matrix under both Bayesian inference and parsimony optimisation criteria retrieves a concordant tree topology that forms the basis of a genus-level systematic revision of xiphosuran taxonomy. The genera Euproops Meek, 1867, Belinurus König, 1820, Paleolimulus, Limulitella, and Limulus are demonstrated to be non-monophyletic and the previously synonymized genera Koenigiella Raymond, 1944 and Prestwichianella Cockerell, 1905 are shown to be valid. In addition, nine new genera (Andersoniella gen. nov., Macrobelinurus gen. nov., and Parabelinurus gen. nov. in Belinurina; Norilimulus gen. nov. in Paleolimulidae; Batracholimulus gen. nov. and Boeotiaspis gen. nov. in Austrolimulidae; and Allolimulus gen. nov., Keuperlimulus gen. nov., a…
format: application/pdf
format: text/html
creator: James C. Lamsdell
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10431
publisher: PeerJ Inc.
rights: © 2020 Lamsdell
abstract: Xiphosurans are aquatic chelicerates with a fossil record extending into the Early Ordovician and known from a total of 88 described species, four of which are extant. Known for their apparent morphological conservatism, for which they have gained notoriety as supposed ‘living fossils’, recent analyses have demonstrated xiphosurans to have an ecologically diverse evolutionary history, with several groups moving into non-marine environments and developing morphologies markedly different from those of the modern species. The combination of their long evolutionary and complex ecological history along with their paradoxical patterns of morphological stasis in some clades and experimentation among others has resulted in Xiphosura being of particular interest for macroevolutionary study. Phylogenetic analyses have shown the current taxonomic framework for Xiphosura—set out in the Treatise of Invertebrate Paleontology in 1955—to be outdated and in need of revision, with several common genera such as Paleolimulus Dunbar, 1923 and Limulitella Størmer, 1952 acting as wastebasket taxa. Here, an expanded xiphosuran phylogeny is presented, comprising 58 xiphosuran species as part of a 158 taxon chelicerate matrix coded for 259 characters. Analysing the matrix under both Bayesian inference and parsimony optimisation criteria retrieves a concordant tree topology that forms the basis of a genus-level systematic revision of xiphosuran taxonomy. The genera Euproops Meek, 1867, Belinurus König, 1820, Paleolimulus, Limulitella, and Limulus are demonstrated to be non-monophyletic and the previously synonymized genera Koenigiella Raymond, 1944 and Prestwichianella Cockerell, 1905 are shown to be valid. In addition, nine new genera (Andersoniella gen. nov., Macrobelinurus gen. nov., and Parabelinurus gen. nov. in Belinurina; Norilimulus gen. nov. in Paleolimulidae; Batracholimulus gen. nov. and Boeotiaspis gen. nov. in Austrolimulidae; and Allolimulus gen. nov., Keuperlimulus gen. nov., a…
bibliographic citation: Lamsdell (2020) The phylogeny and systematics of Xiphosura. PeerJ 8:e10431 https://doi.org/10.7717/peerj.10431
date submitted: 2020-09-10
date accepted: 2020-11-04
issued: 2020-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lamsdell
  given name: James C.
doi: 10.7717/peerj.10431
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-04
copyright: ©2020 Lamsdell
attribution name: Lamsdell

Identification and characterization of critical genes associated with tamoxifen resistance in breast cancer
type: item
type: AcademicArticle
description: Background Tamoxifen resistance in breast cancer is an unsolved problem in clinical practice. The aim of this study was to determine the potential mechanisms of tamoxifen resistance through bioinformatics analysis. Methods Gene expression profiles of tamoxifen-resistant MCF-7/TR and MCF-7 cells were acquired from the Gene Expression Omnibus dataset GSE26459, and differentially expressed genes (DEGs) were detected with R software. We conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses using Database for Annotation, Visualization and Integrated Discovery. A protein–protein interaction (PPI) network was generated, and we analyzed hub genes in the network with the Search Tool for the Retrieval of Interacting Genes database. Finally, we used siRNAs to silence the target genes and conducted the MTS assay. Results We identified 865 DEGs, 399 of which were upregulated. GO analysis indicated that most genes are related to telomere organization, extracellular exosomes, and binding-related items for protein heterodimerization. PPI network construction revealed that the top 10 hub genes—ACLY, HSPD1, PFAS, GART, TXN, HSPH1, HSPE1, IRAS, TRAP1, and ATIC—might be associated with tamoxifen resistance. Consistently, RT-qPCR analysis indicated that the expression of these 10 genes was increased in MCF-7/TR cells comparing with MCF-7 cells. Four hub genes (TXN, HSPD1, HSPH1 and ATIC) were related to overall survival in patients who accepted tamoxifen. In addition, knockdown of HSPH1 by siRNA may lead to reduced growth of MCF-7/TR cell with a trend close to significance (P = 0.07), indicating that upregulation of HSPH1 may play a role in tamoxifen resistance. Conclusion This study revealed a number of critical hub genes that might serve as therapeutic targets in breast cancer resistant to tamoxifen and provided potential directions for uncovering the mechanisms of tamoxifen resistance.
format: application/pdf
format: text/html
creator: Kai Zhang
creator: Kuikui Jiang
creator: Ruoxi Hong
creator: Fei Xu
creator: Wen Xia
creator: Ge Qin
creator: Kaping Lee
creator: Qiufan Zheng
creator: Qianyi Lu
creator: Qinglian Zhai
creator: Shusen Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Drugs and Devices
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.10468
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Background Tamoxifen resistance in breast cancer is an unsolved problem in clinical practice. The aim of this study was to determine the potential mechanisms of tamoxifen resistance through bioinformatics analysis. Methods Gene expression profiles of tamoxifen-resistant MCF-7/TR and MCF-7 cells were acquired from the Gene Expression Omnibus dataset GSE26459, and differentially expressed genes (DEGs) were detected with R software. We conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses using Database for Annotation, Visualization and Integrated Discovery. A protein–protein interaction (PPI) network was generated, and we analyzed hub genes in the network with the Search Tool for the Retrieval of Interacting Genes database. Finally, we used siRNAs to silence the target genes and conducted the MTS assay. Results We identified 865 DEGs, 399 of which were upregulated. GO analysis indicated that most genes are related to telomere organization, extracellular exosomes, and binding-related items for protein heterodimerization. PPI network construction revealed that the top 10 hub genes—ACLY, HSPD1, PFAS, GART, TXN, HSPH1, HSPE1, IRAS, TRAP1, and ATIC—might be associated with tamoxifen resistance. Consistently, RT-qPCR analysis indicated that the expression of these 10 genes was increased in MCF-7/TR cells comparing with MCF-7 cells. Four hub genes (TXN, HSPD1, HSPH1 and ATIC) were related to overall survival in patients who accepted tamoxifen. In addition, knockdown of HSPH1 by siRNA may lead to reduced growth of MCF-7/TR cell with a trend close to significance (P = 0.07), indicating that upregulation of HSPH1 may play a role in tamoxifen resistance. Conclusion This study revealed a number of critical hub genes that might serve as therapeutic targets in breast cancer resistant to tamoxifen and provided potential directions for uncovering the mechanisms of tamoxifen resistance.
bibliographic citation: Zhang et al. (2020) Identification and characterization of critical genes associated with tamoxifen resistance in breast cancer. PeerJ 8:e10468 https://doi.org/10.7717/peerj.10468
date submitted: 2020-07-24
date accepted: 2020-11-11
issued: 2020-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhang
  given name: Kai
author list: Agent
  family name: Jiang
  given name: Kuikui
author list: Agent
  family name: Hong
  given name: Ruoxi
author list: Agent
  family name: Xu
  given name: Fei
author list: Agent
  family name: Xia
  given name: Wen
author list: Agent
  family name: Qin
  given name: Ge
author list: Agent
  family name: Lee
  given name: Kaping
author list: Agent
  family name: Zheng
  given name: Qiufan
author list: Agent
  family name: Lu
  given name: Qianyi
author list: Agent
  family name: Zhai
  given name: Qinglian
author list: Agent
  family name: Wang
  given name: Shusen
doi: 10.7717/peerj.10468
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-04
copyright: © 2020 Zhang et al.
attribution name: Zhang et al.

Patterns of telomere length with age in African mole-rats: New insights from quantitative fluorescence in situ hybridisation (qFISH)
type: item
type: AcademicArticle
description: Naked mole-rats Heterocephalus glaber (NMRs) are the longest-lived rodent and also resist the normal signs of senescence. In a number of species, cellular ageing has been correlated with a reduction in telomere length, yet relatively little is known about telomeres and their age-related dynamics in NMRs and other African mole-rats. Here, we apply fluorescence in situ hybridisation (FISH) to quantify telomeric repeat sequences in the NMR, the Damaraland mole-rat, Fukomys damarensis (DMR) and the Mahali mole-rat, Cryptomys hottentotus mahali (MMR). Both terminal and non-terminal telomeric sequences were identified in chromosomes of the NMR and DMR, whilst the MMR displayed only terminal telomeric repeats. Measurements of tooth wear and eruption patterns in wild caught DMRs and MMRs, and known ages in captive bred NMRs, were used to place individuals into relative age classes and compared with a quantitative measure of telomeric fluorescence (as a proxy for telomere size). While NMRs and MMRs failed to show an age-related decline in telomeric fluorescence, the DMR had a significant decrease in fluorescence with age, suggesting a decrease in telomere size in older animals. Our results suggest that among African mole-rats there is variation between species with respect to the role of telomere shortening in ageing, and the replicative theory of cellular senescence.
format: application/pdf
format: text/html
creator: Stephanie R.L. Leonida
creator: Nigel C. Bennett
creator: Andrew R. Leitch
creator: Chris G. Faulkes
subject: Evolutionary Studies
subject: Genetics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.10498
publisher: PeerJ Inc.
rights: © 2020 Leonida et al.
abstract: Naked mole-rats Heterocephalus glaber (NMRs) are the longest-lived rodent and also resist the normal signs of senescence. In a number of species, cellular ageing has been correlated with a reduction in telomere length, yet relatively little is known about telomeres and their age-related dynamics in NMRs and other African mole-rats. Here, we apply fluorescence in situ hybridisation (FISH) to quantify telomeric repeat sequences in the NMR, the Damaraland mole-rat, Fukomys damarensis (DMR) and the Mahali mole-rat, Cryptomys hottentotus mahali (MMR). Both terminal and non-terminal telomeric sequences were identified in chromosomes of the NMR and DMR, whilst the MMR displayed only terminal telomeric repeats. Measurements of tooth wear and eruption patterns in wild caught DMRs and MMRs, and known ages in captive bred NMRs, were used to place individuals into relative age classes and compared with a quantitative measure of telomeric fluorescence (as a proxy for telomere size). While NMRs and MMRs failed to show an age-related decline in telomeric fluorescence, the DMR had a significant decrease in fluorescence with age, suggesting a decrease in telomere size in older animals. Our results suggest that among African mole-rats there is variation between species with respect to the role of telomere shortening in ageing, and the replicative theory of cellular senescence.
bibliographic citation: Leonida et al. (2020) Patterns of telomere length with age in African mole-rats: New insights from quantitative fluorescence in situ hybridisation (qFISH). PeerJ 8:e10498 https://doi.org/10.7717/peerj.10498
date submitted: 2020-07-03
date accepted: 2020-11-15
issued: 2020-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leonida
  given name: Stephanie R.L.
author list: Agent
  family name: Bennett
  given name: Nigel C.
author list: Agent
  family name: Leitch
  given name: Andrew R.
author list: Agent
  family name: Faulkes
  given name: Chris G.
doi: 10.7717/peerj.10498
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-04
copyright: © 2020 Leonida et al.
attribution name: Leonida et al.

Comprehensive analysis of circRNA expression profiles and circRNA-associated competing endogenous RNA networks in IgA nephropathy
type: item
type: AcademicArticle
description: Background Immunoglobulin A nephropathy (IgAN) is immune-mediated primary glomerulonephritis, which is the most common reason leading to renal failure worldwide. The exact pathogenesis of IgAN is not well defined. Accumulating evidence indicates that circular RNAs (circRNAs) play crucial roles in the immune disease by involving in the competing endogenous RNA (ceRNA) network mechanism. At present, the studies of the circRNA profiles and circRNA-associated ceRNA networks in the IgAN are still scarce. This study aimed to elucidate the potential roles of circRNA-associated ceRNA networks of peripheral blood mononuclear cells (PBMCs) in IgAN patients Method CircRNA sequencing was used to identify the differential expressed circRNAs (DEcircRNAs) of PBMCs in IgAN and healthy controls; limma packages from data sets GSE25590 and GSE73953 in the Gene Expression Omnibus (GEO) database, were used to identify differentially expressed micro RNAs (miRNAs) and message RNAs (mRNAs). A circRNA-miRNA-mRNA ceRNA network was constructed to further investigate the mechanisms of IgAN. Then, GO analysis and KEGG enrichment analyses were used to annotate the genes involved in the circRNA-associated ceRNA network. Further, Protein-protein interaction (PPI) networks were established to screen potential hub genes, by using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). Last, a quantitative real-time polymerase chain reaction (qRT-PCR) was applied to verify the hub genes in the ceRNA network. Result A total of 145 circRNAs, 22 miRNAs, and 1,117 mRNAs were differentially expressed in IgAN compared with controls (P < 0.05). A ceRNA network was constructed which contained 16 DEcircRNAs, 72 differential expressed mRNAs (DEmRNAs) and 11 differential expressed miRNAs (DEmiRNAs). KEGG pathway enrichment analysis illustrated the underlying biological functions of the ceRNA-associated genes, such as Nitrogen compound metabolic process, COPII-coated ER to Golgi transport vesicle, …
format: application/pdf
format: text/html
creator: Haiyang Liu
creator: Di Liu
creator: Yexin Liu
creator: Ming Xia
creator: Yan Li
creator: Mei Li
creator: Hong Liu
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Immunology
subject: Nephrology
description: doi:10.7717/peerj.10395
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: Background Immunoglobulin A nephropathy (IgAN) is immune-mediated primary glomerulonephritis, which is the most common reason leading to renal failure worldwide. The exact pathogenesis of IgAN is not well defined. Accumulating evidence indicates that circular RNAs (circRNAs) play crucial roles in the immune disease by involving in the competing endogenous RNA (ceRNA) network mechanism. At present, the studies of the circRNA profiles and circRNA-associated ceRNA networks in the IgAN are still scarce. This study aimed to elucidate the potential roles of circRNA-associated ceRNA networks of peripheral blood mononuclear cells (PBMCs) in IgAN patients Method CircRNA sequencing was used to identify the differential expressed circRNAs (DEcircRNAs) of PBMCs in IgAN and healthy controls; limma packages from data sets GSE25590 and GSE73953 in the Gene Expression Omnibus (GEO) database, were used to identify differentially expressed micro RNAs (miRNAs) and message RNAs (mRNAs). A circRNA-miRNA-mRNA ceRNA network was constructed to further investigate the mechanisms of IgAN. Then, GO analysis and KEGG enrichment analyses were used to annotate the genes involved in the circRNA-associated ceRNA network. Further, Protein-protein interaction (PPI) networks were established to screen potential hub genes, by using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). Last, a quantitative real-time polymerase chain reaction (qRT-PCR) was applied to verify the hub genes in the ceRNA network. Result A total of 145 circRNAs, 22 miRNAs, and 1,117 mRNAs were differentially expressed in IgAN compared with controls (P < 0.05). A ceRNA network was constructed which contained 16 DEcircRNAs, 72 differential expressed mRNAs (DEmRNAs) and 11 differential expressed miRNAs (DEmiRNAs). KEGG pathway enrichment analysis illustrated the underlying biological functions of the ceRNA-associated genes, such as Nitrogen compound metabolic process, COPII-coated ER to Golgi transport vesicle, …
bibliographic citation: Liu et al. (2020) Comprehensive analysis of circRNA expression profiles and circRNA-associated competing endogenous RNA networks in IgA nephropathy. PeerJ 8:e10395 https://doi.org/10.7717/peerj.10395
date submitted: 2020-07-09
date accepted: 2020-10-29
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Haiyang
author list: Agent
  family name: Liu
  given name: Di
author list: Agent
  family name: Liu
  given name: Yexin
author list: Agent
  family name: Xia
  given name: Ming
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: Li
  given name: Mei
author list: Agent
  family name: Liu
  given name: Hong
doi: 10.7717/peerj.10395
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: ©2020 Liu et al.
attribution name: Liu et al.

Effects of monofilament nylon versus braided multifilament nylon gangions on catch rates of Greenland shark (Somniosus microcephalus) in bottom set longlines
type: item
type: AcademicArticle
description: The Greenland shark (Somniosus microcephalus) is the main bycatch species in established and exploratory inshore longline fisheries for Greenland halibut (Reinhardtius hippoglossoides) on the east coast of Baffin Island, Canada. Bycatch and entanglement in longline gear has at times been substantial and post-release survival is questionable when Greenland sharks are released with trailing fishing gear. This study investigated the effect of the type of fishing line used in the gangion and gangion breaking strength on catch rates of Greenland shark and Greenland halibut in bottom set longlines. Circle (size 14/0, 0° offset) hooks were used throughout the study. Behavior of captured sharks, mode of capture (i.e., jaw hook and/or entanglement), level of entanglement in longline gear, time required to disentangle sharks and biological information (sex, body length and health status) were recorded. Catch rates of Greenland shark were independent of monofilament nylon gangion breaking strength and monofilament gangions captured significantly fewer Greenland sharks than the traditional braided multifilament nylon gangion. Catch rates and body size of Greenland halibut did not differ significantly between gangion treatments. Although most (84%) of the Greenland sharks were hooked by the jaw, a high percentage (76%) were entangled in the mainline. The mean length of mainline entangled around the body and/or caudal peduncle and caudal fin was 28.7 m. Greenland sharks exhibited cannibalistic behavior with 15% of captured sharks cannibalized. All remaining sharks were alive and survived the disentanglement process which can be attributed to their lethargic behavior and lack of resistance when hauled to the surface. Thus, as a conservation measure fishers should be encouraged to remove trailing fishing gear prior to release. Our results are used to demonstrate benefits to the fishing industry with regard to an overall reduction in the period of time to disentangle sharks and dama…
format: application/pdf
format: text/html
creator: Scott M. Grant
creator: Jenna G. Munden
creator: Kevin J. Hedges
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.10407
publisher: PeerJ Inc.
rights: © 2020 Grant et al.
abstract: The Greenland shark (Somniosus microcephalus) is the main bycatch species in established and exploratory inshore longline fisheries for Greenland halibut (Reinhardtius hippoglossoides) on the east coast of Baffin Island, Canada. Bycatch and entanglement in longline gear has at times been substantial and post-release survival is questionable when Greenland sharks are released with trailing fishing gear. This study investigated the effect of the type of fishing line used in the gangion and gangion breaking strength on catch rates of Greenland shark and Greenland halibut in bottom set longlines. Circle (size 14/0, 0° offset) hooks were used throughout the study. Behavior of captured sharks, mode of capture (i.e., jaw hook and/or entanglement), level of entanglement in longline gear, time required to disentangle sharks and biological information (sex, body length and health status) were recorded. Catch rates of Greenland shark were independent of monofilament nylon gangion breaking strength and monofilament gangions captured significantly fewer Greenland sharks than the traditional braided multifilament nylon gangion. Catch rates and body size of Greenland halibut did not differ significantly between gangion treatments. Although most (84%) of the Greenland sharks were hooked by the jaw, a high percentage (76%) were entangled in the mainline. The mean length of mainline entangled around the body and/or caudal peduncle and caudal fin was 28.7 m. Greenland sharks exhibited cannibalistic behavior with 15% of captured sharks cannibalized. All remaining sharks were alive and survived the disentanglement process which can be attributed to their lethargic behavior and lack of resistance when hauled to the surface. Thus, as a conservation measure fishers should be encouraged to remove trailing fishing gear prior to release. Our results are used to demonstrate benefits to the fishing industry with regard to an overall reduction in the period of time to disentangle sharks and dama…
bibliographic citation: Grant et al. (2020) Effects of monofilament nylon versus braided multifilament nylon gangions on catch rates of Greenland shark (Somniosus microcephalus) in bottom set longlines. PeerJ 8:e10407 https://doi.org/10.7717/peerj.10407
date submitted: 2019-01-05
date accepted: 2020-11-02
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grant
  given name: Scott M.
author list: Agent
  family name: Munden
  given name: Jenna G.
author list: Agent
  family name: Hedges
  given name: Kevin J.
doi: 10.7717/peerj.10407
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: © 2020 Grant et al.
attribution name: Grant et al.

Bacterial exposure leads to variable mortality but not a measurable increase in surface antimicrobials across ant species
type: item
type: AcademicArticle
description: Social insects have co-existed with microbial species for millions of years and have evolved a diversity of collective defenses, including the use of antimicrobials. While many studies have revealed strategies that ants use against microbial entomopathogens, and several have shown ant-produced compounds inhibit environmental bacterial growth, few studies have tested whether exposure to environmental bacteria represents a health threat to ants. We compare four ant species’ responses to exposure to Escherichia coli and Staphylococcus epidermidis bacteria in order to broaden our understanding of microbial health-threats to ants and their ability to defend against them. In a first experiment, we measure worker mortality of Solenopsis invicta, Brachymyrmex chinensis, Aphaenogaster rudis, and Dorymyrmex bureni in response to exposure to E. coli and S. epidermidis. We found that exposure to E. coli was lethal for S. invicta and D. bureni, while all other effects of exposure were not different from experimental controls. In a second experiment, we compared the antimicrobial ability of surface extracts from bacteria-exposed and non-exposed S. invicta and B. chinensis worker ants, to see if exposure to E. coli or S. epidermidis led to an increase in antimicrobial compounds. We found no difference in the inhibitory effects from either treatment group in either species. Our results demonstrate the susceptibility to bacteria is varied across ant species. This variation may correlate with an ant species’ use of surface antimicrobials, as we found significant mortality effects in species which also were producing antimicrobials. Further exploration of a wide range of both bacteria and ant species is likely to reveal unique and nuanced antimicrobial strategies and deepen our understanding of how ant societies respond to microbial health threats.
format: application/pdf
format: text/html
creator: Omar Halawani
creator: Robert R. Dunn
creator: Amy M. Grunden
creator: Adrian A. Smith
subject: Ecology
subject: Entomology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.10412
publisher: PeerJ Inc.
rights: © 2020 Halawani et al.
abstract: Social insects have co-existed with microbial species for millions of years and have evolved a diversity of collective defenses, including the use of antimicrobials. While many studies have revealed strategies that ants use against microbial entomopathogens, and several have shown ant-produced compounds inhibit environmental bacterial growth, few studies have tested whether exposure to environmental bacteria represents a health threat to ants. We compare four ant species’ responses to exposure to Escherichia coli and Staphylococcus epidermidis bacteria in order to broaden our understanding of microbial health-threats to ants and their ability to defend against them. In a first experiment, we measure worker mortality of Solenopsis invicta, Brachymyrmex chinensis, Aphaenogaster rudis, and Dorymyrmex bureni in response to exposure to E. coli and S. epidermidis. We found that exposure to E. coli was lethal for S. invicta and D. bureni, while all other effects of exposure were not different from experimental controls. In a second experiment, we compared the antimicrobial ability of surface extracts from bacteria-exposed and non-exposed S. invicta and B. chinensis worker ants, to see if exposure to E. coli or S. epidermidis led to an increase in antimicrobial compounds. We found no difference in the inhibitory effects from either treatment group in either species. Our results demonstrate the susceptibility to bacteria is varied across ant species. This variation may correlate with an ant species’ use of surface antimicrobials, as we found significant mortality effects in species which also were producing antimicrobials. Further exploration of a wide range of both bacteria and ant species is likely to reveal unique and nuanced antimicrobial strategies and deepen our understanding of how ant societies respond to microbial health threats.
bibliographic citation: Halawani et al. (2020) Bacterial exposure leads to variable mortality but not a measurable increase in surface antimicrobials across ant species. PeerJ 8:e10412 https://doi.org/10.7717/peerj.10412
date submitted: 2020-06-05
date accepted: 2020-11-02
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Halawani
  given name: Omar
author list: Agent
  family name: Dunn
  given name: Robert R.
author list: Agent
  family name: Grunden
  given name: Amy M.
author list: Agent
  family name: Smith
  given name: Adrian A.
doi: 10.7717/peerj.10412
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: © 2020 Halawani et al.
attribution name: Halawani et al.

Moderately low nitrogen application mitigate the negative effects of salt stress on annual ryegrass seedlings
type: item
type: AcademicArticle
description: Appropriate application of nitrogen (N) can alleviate the salt stress-induced damage on plants. This study explores the changes of nitrogen requirement in feeding annual ryegrass seedlings under mild salt concentrations (50 mM, 100 mM) plus its underlying mitigation mechanism. Results showed that low salt concentration decreased N requirement as observed from the increment in plant height and biomass at a relative low N level (2.0 mM not 5.0 mM). Under salt treatment, especially at 50 mM NaCl, the OJIP (Chl a fluorescence induction transient) curve and a series of performance indexes (PIABS, RC/CS0, ET0/CS0, ϕE0, ϕ0) peaked whereas DI0/RC, Vj and M0 were the lowest under moderately low N level (2.0 mM). In addition, under salt stress, moderately low N application could maintain the expression of NR (nitrate reductase) and GS (glutamine synthetase) encoding genes at a relatively stable level but had no effect on the expression of detected NRT (nitrate transporter) gene. The seedlings cultured at 2.0 mM N also exhibited the highest activity of CAT and POD antioxidant enzymes and the lowest MDA content and EL under relative low level of salt treatment. These results indicated that mild salt treatment of annual ryegrass seedlings might reduce N requirement while moderately low N application could promote their growth via regulating photosynthesis, alleviating ROS-induced (reactive oxygen species) damage and maintenance of N metabolism. These results also can provide useful reference for nitrogen application in moderation rather than in excess on annual ryegrass in mild or medium salinity areas through understanding the underlying response mechanisms.
format: application/pdf
format: text/html
creator: An Shao
creator: Zhichao Sun
creator: Shugao Fan
creator: Xiao Xu
creator: Wei Wang
creator: Erick Amombo
creator: Yanling Yin
creator: Xiaoning Li
creator: Guangyang Wang
creator: Hongli Wang
creator: Jinmin Fu
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.10427
publisher: PeerJ Inc.
rights: © 2020 Shao et al.
abstract: Appropriate application of nitrogen (N) can alleviate the salt stress-induced damage on plants. This study explores the changes of nitrogen requirement in feeding annual ryegrass seedlings under mild salt concentrations (50 mM, 100 mM) plus its underlying mitigation mechanism. Results showed that low salt concentration decreased N requirement as observed from the increment in plant height and biomass at a relative low N level (2.0 mM not 5.0 mM). Under salt treatment, especially at 50 mM NaCl, the OJIP (Chl a fluorescence induction transient) curve and a series of performance indexes (PIABS, RC/CS0, ET0/CS0, ϕE0, ϕ0) peaked whereas DI0/RC, Vj and M0 were the lowest under moderately low N level (2.0 mM). In addition, under salt stress, moderately low N application could maintain the expression of NR (nitrate reductase) and GS (glutamine synthetase) encoding genes at a relatively stable level but had no effect on the expression of detected NRT (nitrate transporter) gene. The seedlings cultured at 2.0 mM N also exhibited the highest activity of CAT and POD antioxidant enzymes and the lowest MDA content and EL under relative low level of salt treatment. These results indicated that mild salt treatment of annual ryegrass seedlings might reduce N requirement while moderately low N application could promote their growth via regulating photosynthesis, alleviating ROS-induced (reactive oxygen species) damage and maintenance of N metabolism. These results also can provide useful reference for nitrogen application in moderation rather than in excess on annual ryegrass in mild or medium salinity areas through understanding the underlying response mechanisms.
bibliographic citation: Shao et al. (2020) Moderately low nitrogen application mitigate the negative effects of salt stress on annual ryegrass seedlings. PeerJ 8:e10427 https://doi.org/10.7717/peerj.10427
date submitted: 2020-07-29
date accepted: 2020-11-03
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shao
  given name: An
author list: Agent
  family name: Sun
  given name: Zhichao
author list: Agent
  family name: Fan
  given name: Shugao
author list: Agent
  family name: Xu
  given name: Xiao
author list: Agent
  family name: Wang
  given name: Wei
author list: Agent
  family name: Amombo
  given name: Erick
author list: Agent
  family name: Yin
  given name: Yanling
author list: Agent
  family name: Li
  given name: Xiaoning
author list: Agent
  family name: Wang
  given name: Guangyang
author list: Agent
  family name: Wang
  given name: Hongli
author list: Agent
  family name: Fu
  given name: Jinmin
doi: 10.7717/peerj.10427
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: ©2020 Shao et al.
attribution name: Shao et al.

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