PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: Analysis of 44 Vibrio anguillarum genomes reveals high genetic diversity
items: ARID1A alterations and their clinical significance in cholangiocarcinoma
items: Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs

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shown the current taxonomic framework for Xiphosura—set out in the Treatise of Invertebrate Paleontology in 1955—to be outdated and in need of revision, with several common genera such as Paleolimulus Dunbar, 1923 and Limulitella Størmer, 1952 acting as wastebasket taxa.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.

Analysis of 44 Vibrio anguillarum genomes reveals high genetic diversity
type: item
type: AcademicArticle
description: Vibriosis, a hemorrhagic septicemic disease caused by the bacterium Vibrio anguillarum, is an important bacterial infection in Danish sea-reared rainbow trout. Despite of vaccination, outbreaks still occur, likely because the vaccine is based on V. anguillarum strains from abroad/other hosts than rainbow trout. Information about the genetic diversity of V. anguillarum specifically in Danish rainbow trout, is required to investigate this claim. Consequently, the aim of the present investigation was to sequence and to characterize a collection of 44 V. anguillarum strains obtained primarily from vibriosis outbreaks in Danish rainbow trout. The strains were sequenced, de novo assembled, and the genomes examined for the presence of plasmids, virulence, and acquired antibiotic resistance genes. To investigate the phylogeny, single nucleotide polymorphisms were identified, and the pan-genome was calculated. All strains carried tet(34) encoding tetracycline resistance, and 36 strains also contained qnrVC6 for increased fluoroquinolone/quinolone resistance. But interestingly, all strains were phenotypic sensitive to both oxytetracycline and oxolinic acid. Almost all serotype O1 strains contained a pJM1-like plasmid and nine serotype O2A strains carried the plasmid p15. The distribution of virulence genes was rather similar across the strains, although evident variance among serotypes was observed. Most significant, almost all serotype O2 and O3 strains, as well as the serotype O1 strain without a pJM1-like plasmid, carried genes encoding piscibactin biosynthesis. Hence supporting the hypothesis, that piscibactin plays a crucial role in virulence for pathogenic strains lacking the anguibactin system. The phylogenetic analysis and pan-genome calculations revealed great diversity within V. anguillarum. Serotype O1 strains were in general very similar, whereas considerable variation was found among serotype O2A strains. The great diversity within the V. anguillarum serotype O2A…
format: application/pdf
format: text/html
creator: Mie Johanne Hansen
creator: Egle Kudirkiene
creator: Inger Dalsgaard
subject: Aquaculture, Fisheries and Fish Science
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.10451
publisher: PeerJ Inc.
rights: © 2020 Hansen et al.
abstract: Vibriosis, a hemorrhagic septicemic disease caused by the bacterium Vibrio anguillarum, is an important bacterial infection in Danish sea-reared rainbow trout. Despite of vaccination, outbreaks still occur, likely because the vaccine is based on V. anguillarum strains from abroad/other hosts than rainbow trout. Information about the genetic diversity of V. anguillarum specifically in Danish rainbow trout, is required to investigate this claim. Consequently, the aim of the present investigation was to sequence and to characterize a collection of 44 V. anguillarum strains obtained primarily from vibriosis outbreaks in Danish rainbow trout. The strains were sequenced, de novo assembled, and the genomes examined for the presence of plasmids, virulence, and acquired antibiotic resistance genes. To investigate the phylogeny, single nucleotide polymorphisms were identified, and the pan-genome was calculated. All strains carried tet(34) encoding tetracycline resistance, and 36 strains also contained qnrVC6 for increased fluoroquinolone/quinolone resistance. But interestingly, all strains were phenotypic sensitive to both oxytetracycline and oxolinic acid. Almost all serotype O1 strains contained a pJM1-like plasmid and nine serotype O2A strains carried the plasmid p15. The distribution of virulence genes was rather similar across the strains, although evident variance among serotypes was observed. Most significant, almost all serotype O2 and O3 strains, as well as the serotype O1 strain without a pJM1-like plasmid, carried genes encoding piscibactin biosynthesis. Hence supporting the hypothesis, that piscibactin plays a crucial role in virulence for pathogenic strains lacking the anguibactin system. The phylogenetic analysis and pan-genome calculations revealed great diversity within V. anguillarum. Serotype O1 strains were in general very similar, whereas considerable variation was found among serotype O2A strains. The great diversity within the V. anguillarum serotype O2A…
bibliographic citation: Hansen et al. (2020) Analysis of 44 Vibrio anguillarum genomes reveals high genetic diversity. PeerJ 8:e10451 https://doi.org/10.7717/peerj.10451
date submitted: 2020-06-19
date accepted: 2020-11-09
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hansen
  given name: Mie Johanne
author list: Agent
  family name: Kudirkiene
  given name: Egle
author list: Agent
  family name: Dalsgaard
  given name: Inger
doi: 10.7717/peerj.10451
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: © 2020 Hansen et al.
attribution name: Hansen et al.

ARID1A alterations and their clinical significance in cholangiocarcinoma
type: item
type: AcademicArticle
description: Background ARID1A is a member of the SWI/SNF chromatin remodeling complex. It functions as a tumor suppressor and several therapeutic targets in ARID1A-mutated cancers are currently under development, including EZH2. A synthetic lethal relationship between ARID1A and EZH2 has been revealed in several tumor entities. Although genomic alterations of ARID1A have been described in various cancers, no study has examined correlations between ARID1A gene mutation and protein expression with clinicopathologic parameters and prognosis, particularly in liver fluke-related cholangiocarcinoma (Ov-CCA). Here, we investigated the clinical significance of ARID1A mutations and protein expression in CCA tissues and determined whether there is a correlation with EZH2 protein expression. Methods We evaluated ARID1A and EZH2 immunoreactivity using immunohistochemistry in 98 Ov-CCA with a wide range of clinicopathological features. Somatic mutations of ARID1A were analyzed using the ICGC sequencing data in 489 of Ov and non Ov-CCA and assessed prognostic values. Results While detecting a loss or reduction of ARID1A expression in 54 cases (55%) in Ov-CCA, ARID1A expression was associated with ARID1A mutations (p < 0.001, adjusted p-value < 0.001). We observed that 12 of 13 tumors (92%) with loss of ARID1A expression had truncating mutations. There were nine of 13 tumors (69%) with loss of ARID1A expression and 25 of 41 tumors (61%) with low ARID1A expression exhibited distant metastasis (p = 0.028, adjusted p-value = 0.168). ARID1A was predominantly mutated in Ov-CCA compared to non Ov-CCA (24% and 14% in Ov-CCA and non Ov-CCA, respectively, p = 0.027). There were 36 of 72 (50%) and 52 of 79 (66%) tumors with ARID1A mutation showed tumor stage IV and T3/T4, respectively. The significant mutual exclusivity and co-occurrence between ARID1A and TP53/KRAS mutations were not found in ICGC cohort. In addition, high EZH2 expression, a potential synthetic lethal target in ARID1A-mutated tumors, …
format: application/pdf
format: text/html
creator: Achira Namjan
creator: Anchalee Techasen
creator: Watcharin Loilome
creator: Prakasit Sa-ngaimwibool
creator: Apinya Jusakul
subject: Genetics
subject: Gastroenterology and Hepatology
subject: Pathology
subject: Histology
description: doi:10.7717/peerj.10464
publisher: PeerJ Inc.
rights: © 2020 Namjan et al.
abstract: Background ARID1A is a member of the SWI/SNF chromatin remodeling complex. It functions as a tumor suppressor and several therapeutic targets in ARID1A-mutated cancers are currently under development, including EZH2. A synthetic lethal relationship between ARID1A and EZH2 has been revealed in several tumor entities. Although genomic alterations of ARID1A have been described in various cancers, no study has examined correlations between ARID1A gene mutation and protein expression with clinicopathologic parameters and prognosis, particularly in liver fluke-related cholangiocarcinoma (Ov-CCA). Here, we investigated the clinical significance of ARID1A mutations and protein expression in CCA tissues and determined whether there is a correlation with EZH2 protein expression. Methods We evaluated ARID1A and EZH2 immunoreactivity using immunohistochemistry in 98 Ov-CCA with a wide range of clinicopathological features. Somatic mutations of ARID1A were analyzed using the ICGC sequencing data in 489 of Ov and non Ov-CCA and assessed prognostic values. Results While detecting a loss or reduction of ARID1A expression in 54 cases (55%) in Ov-CCA, ARID1A expression was associated with ARID1A mutations (p < 0.001, adjusted p-value < 0.001). We observed that 12 of 13 tumors (92%) with loss of ARID1A expression had truncating mutations. There were nine of 13 tumors (69%) with loss of ARID1A expression and 25 of 41 tumors (61%) with low ARID1A expression exhibited distant metastasis (p = 0.028, adjusted p-value = 0.168). ARID1A was predominantly mutated in Ov-CCA compared to non Ov-CCA (24% and 14% in Ov-CCA and non Ov-CCA, respectively, p = 0.027). There were 36 of 72 (50%) and 52 of 79 (66%) tumors with ARID1A mutation showed tumor stage IV and T3/T4, respectively. The significant mutual exclusivity and co-occurrence between ARID1A and TP53/KRAS mutations were not found in ICGC cohort. In addition, high EZH2 expression, a potential synthetic lethal target in ARID1A-mutated tumors, …
bibliographic citation: Namjan et al. (2020) ARID1A alterations and their clinical significance in cholangiocarcinoma. PeerJ 8:e10464 https://doi.org/10.7717/peerj.10464
date submitted: 2020-07-28
date accepted: 2020-11-10
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Namjan
  given name: Achira
author list: Agent
  family name: Techasen
  given name: Anchalee
author list: Agent
  family name: Loilome
  given name: Watcharin
author list: Agent
  family name: Sa-ngaimwibool
  given name: Prakasit
author list: Agent
  family name: Jusakul
  given name: Apinya
doi: 10.7717/peerj.10464
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: ©2020 Namjan et al.
attribution name: Namjan et al.

Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs
type: item
type: AcademicArticle
description: The true myrtle, Myrtus communis, is a small perennial evergreen tree that occurs in Europe, Africa, and Asia with a circum-Mediterranean geographic distribution. Unfortunately, the Mediterranean Forests, where M. communis occurs, are critically endangered and are currently restricted to small fragmented areas in protected conservation units. In the present work, we performed, for the first time, a metabarcoding study on the spatial variation of fungal community structure in the foliar endophytome of this endemic plant of the Mediterranean biome, using bipartite network analysis as a model. The local bipartite network of Myrtus communis individuals and their foliar endophytic fungi is very low connected, with low nestedness, and moderately high specialization and modularity. Similar network patterns were also retrieved in both culture-dependent and amplicon metagenomics of foliar endophytes in distinct arboreal hosts in varied biomes. Furthermore, the majority of putative fungal endophytes species were basidiomycete woody saprotrophs of the orders Polyporales, Agaricales, and Hymenochaetales. Altogether, these findings suggest a possible adaptation of these wood-decaying fungi to cope with moisture limitation and spatial scarcity of their primary substrate (dead wood), which are totally consistent with the predictions of the viaphytism hypothesis that wood-decomposing fungi inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia, during periods of environmental stress.
format: application/pdf
format: text/html
creator: Aline Bruna M. Vaz
creator: Paula Luize C. Fonseca
creator: Felipe F. Silva
creator: Gabriel Quintanilha-Peixoto
creator: Inmaculada Sampedro
creator: Jose A. Siles
creator: Anderson Carmo
creator: Rodrigo B. Kato
creator: Vasco Azevedo
creator: Fernanda Badotti
creator: Juan A. Ocampo
creator: Carlos A. Rosa
creator: Aristóteles Góes-Neto
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.10487
publisher: PeerJ Inc.
rights: © 2020 Vaz et al.
abstract: The true myrtle, Myrtus communis, is a small perennial evergreen tree that occurs in Europe, Africa, and Asia with a circum-Mediterranean geographic distribution. Unfortunately, the Mediterranean Forests, where M. communis occurs, are critically endangered and are currently restricted to small fragmented areas in protected conservation units. In the present work, we performed, for the first time, a metabarcoding study on the spatial variation of fungal community structure in the foliar endophytome of this endemic plant of the Mediterranean biome, using bipartite network analysis as a model. The local bipartite network of Myrtus communis individuals and their foliar endophytic fungi is very low connected, with low nestedness, and moderately high specialization and modularity. Similar network patterns were also retrieved in both culture-dependent and amplicon metagenomics of foliar endophytes in distinct arboreal hosts in varied biomes. Furthermore, the majority of putative fungal endophytes species were basidiomycete woody saprotrophs of the orders Polyporales, Agaricales, and Hymenochaetales. Altogether, these findings suggest a possible adaptation of these wood-decaying fungi to cope with moisture limitation and spatial scarcity of their primary substrate (dead wood), which are totally consistent with the predictions of the viaphytism hypothesis that wood-decomposing fungi inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia, during periods of environmental stress.
bibliographic citation: Vaz et al. (2020) Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs. PeerJ 8:e10487 https://doi.org/10.7717/peerj.10487
date submitted: 2020-01-29
date accepted: 2020-11-12
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vaz
  given name: Aline Bruna M.
author list: Agent
  family name: Fonseca
  given name: Paula Luize C.
author list: Agent
  family name: Silva
  given name: Felipe F.
author list: Agent
  family name: Quintanilha-Peixoto
  given name: Gabriel
author list: Agent
  family name: Sampedro
  given name: Inmaculada
author list: Agent
  family name: Siles
  given name: Jose A.
author list: Agent
  family name: Carmo
  given name: Anderson
author list: Agent
  family name: Kato
  given name: Rodrigo B.
author list: Agent
  family name: Azevedo
  given name: Vasco
author list: Agent
  family name: Badotti
  given name: Fernanda
author list: Agent
  family name: Ocampo
  given name: Juan A.
author list: Agent
  family name: Rosa
  given name: Carlos A.
author list: Agent
  family name: Góes-Neto
  given name: Aristóteles
doi: 10.7717/peerj.10487
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: © 2020 Vaz et al.
attribution name: Vaz et al.

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