PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The use of artificial substrate units to improve inventories of cryptic crustacean species on Caribbean coral reefs
items: Sensation of the tiniest kind: the antennal sensilla of the smallest free-living insect Scydosella musawasensis (Coleoptera: Ptiliidae)
items: Identifying MMP14 and COL12A1 as a potential combination of prognostic biomarkers in pancreatic ductal adenocarcinoma using integrated bioinformatics analysis
items: A meta-analysis contrasting active versus passive restoration practices in dryland agricultural ecosystems
items: Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana
items: Morph-specific seasonal variation of aggressive behaviour in a polymorphic lizard species
items: Identification of hub genes associated with the pathogenesis of diffuse large B-cell lymphoma subtype one characterized by host response via integrated bioinformatic analyses
items: The cranial morphology of Tanystropheus hydroides (Tanystropheidae, Archosauromorpha) as revealed by synchrotron microtomography
items: Translocation of an arctic seashore plant reveals signs of maladaptation to altered climatic conditions
items: Genome-wide identification and analysis of the thiolase family in insects

The use of artificial substrate units to improve inventories of cryptic crustacean species on Caribbean coral reefs
type: item
type: AcademicArticle
description: Motile cryptofauna inhabiting coral reefs are complex assemblages that utilize the space available among dead coral stands and the surrounding coral rubble substrate. They comprise a group of organisms largely overlooked in biodiversity estimates because they are hard to collect and identify, and their collection causes disturbance that is unsustainable in light of widespread reef degradation. Artificial substrate units (ASUs) provide a better sampling alternative and have the potential to enhance biodiversity estimates. The present study examines the effectiveness of ASUs made with defaunated coral rubble to estimate the diversity of motile cryptic crustaceans in the back-reef zone of the Puerto Morelos Reef National Park, Mexico. Species richness, Simpson’s diversity index, Shannon–Wiener index and the composition of assemblages were compared between ASUs and samples from the surrounding coral rubble substrate. A combined total of 2,740 specimens of 178 different species, belonging to five orders of Crustacea (Amphipoda, Cumacea, Isopoda, Tanaidacea and Decapoda) were collected. Species richness was higher in the surrounding coral rubble and Shannon–Wiener and Simpson indexes were higher in ASUs. Species composition differed between methods, with only 71 species being shared among sampling methods. Decapoda was more speciose in ASUs and Peracarids in the surrounding coral rubble. Combining the use of ASUs with surrounding rubble provided a better inventory of motile cryptic crustacean biodiversity, as 65% of the species were represented by one or two specimens.
format: application/pdf
format: text/html
creator: Luz Verónica Monroy-Velázquez
creator: Rosa E. Rodríguez-Martínez
creator: Paul Blanchon
creator: Fernando Alvarez
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.10389
publisher: PeerJ Inc.
rights: © 2020 Monroy-Velázquez et al.
abstract: Motile cryptofauna inhabiting coral reefs are complex assemblages that utilize the space available among dead coral stands and the surrounding coral rubble substrate. They comprise a group of organisms largely overlooked in biodiversity estimates because they are hard to collect and identify, and their collection causes disturbance that is unsustainable in light of widespread reef degradation. Artificial substrate units (ASUs) provide a better sampling alternative and have the potential to enhance biodiversity estimates. The present study examines the effectiveness of ASUs made with defaunated coral rubble to estimate the diversity of motile cryptic crustaceans in the back-reef zone of the Puerto Morelos Reef National Park, Mexico. Species richness, Simpson’s diversity index, Shannon–Wiener index and the composition of assemblages were compared between ASUs and samples from the surrounding coral rubble substrate. A combined total of 2,740 specimens of 178 different species, belonging to five orders of Crustacea (Amphipoda, Cumacea, Isopoda, Tanaidacea and Decapoda) were collected. Species richness was higher in the surrounding coral rubble and Shannon–Wiener and Simpson indexes were higher in ASUs. Species composition differed between methods, with only 71 species being shared among sampling methods. Decapoda was more speciose in ASUs and Peracarids in the surrounding coral rubble. Combining the use of ASUs with surrounding rubble provided a better inventory of motile cryptic crustacean biodiversity, as 65% of the species were represented by one or two specimens.
bibliographic citation: Monroy-Velázquez et al. (2020) The use of artificial substrate units to improve inventories of cryptic crustacean species on Caribbean coral reefs. PeerJ 8:e10389 https://doi.org/10.7717/peerj.10389
date submitted: 2020-06-03
date accepted: 2020-10-27
issued: 2020-11-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Monroy-Velázquez
  given name: Luz Verónica
author list: Agent
  family name: Rodríguez-Martínez
  given name: Rosa E.
author list: Agent
  family name: Blanchon
  given name: Paul
author list: Agent
  family name: Alvarez
  given name: Fernando
doi: 10.7717/peerj.10389
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-23
copyright: © 2020 Monroy-Velázquez et al.
attribution name: Monroy-Velázquez et al.

Sensation of the tiniest kind: the antennal sensilla of the smallest free-living insect Scydosella musawasensis (Coleoptera: Ptiliidae)
type: item
type: AcademicArticle
description: Miniaturization is a major evolutionary trend prominent in insects, which has resulted in the existence of insects comparable in size to some unicellular protists. The adaptation of the complex antennal multisensory systems to extreme miniaturization is a fascinating problem, which remains almost unexplored. We studied the antennal sensilla of Scydosella musawasensis Hall, 1999 (Coleoptera: Ptiliidae), the smallest free-living insect, using scanning electron microscopy. The antenna of S. musawasensis bears 131 sensilla; no intraspecific variation in the number or position of the sensilla has been revealed. Nine different morphological types of sensilla are described according to their external morphological features and distribution: four types of sensilla trichodea, one type of sensilla chaetica, two types of sensilla styloconica, and two types of sensilla basiconica. Morphometric analysis of the sensilla of S. musawasensis, based on measurements of the lengths and diameters of sensilla and their location and number, showed the absence of significant differences between females and males. Comparative allometric analysis of S. musawasensis and larger Coleoptera showed that the number of sensilla and the size of sensilla chaetica decrease with decreasing body size. However, the number of the types of sensilla and the length and diameter of the multiporous sensilla basiconica revealed no correlation with the body size. Comparison of the acquired data with the results of our earlier study of the antennal sensilla of some of the smallest parasitic wasps is used to put forward hypotheses on the common principles of miniaturization of the antennal sensory systems of insects.
format: application/pdf
format: text/html
creator: Anna V. Diakova
creator: Alexey A. Polilov
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.10401
publisher: PeerJ Inc.
rights: © 2020 Diakova and Polilov
abstract: Miniaturization is a major evolutionary trend prominent in insects, which has resulted in the existence of insects comparable in size to some unicellular protists. The adaptation of the complex antennal multisensory systems to extreme miniaturization is a fascinating problem, which remains almost unexplored. We studied the antennal sensilla of Scydosella musawasensis Hall, 1999 (Coleoptera: Ptiliidae), the smallest free-living insect, using scanning electron microscopy. The antenna of S. musawasensis bears 131 sensilla; no intraspecific variation in the number or position of the sensilla has been revealed. Nine different morphological types of sensilla are described according to their external morphological features and distribution: four types of sensilla trichodea, one type of sensilla chaetica, two types of sensilla styloconica, and two types of sensilla basiconica. Morphometric analysis of the sensilla of S. musawasensis, based on measurements of the lengths and diameters of sensilla and their location and number, showed the absence of significant differences between females and males. Comparative allometric analysis of S. musawasensis and larger Coleoptera showed that the number of sensilla and the size of sensilla chaetica decrease with decreasing body size. However, the number of the types of sensilla and the length and diameter of the multiporous sensilla basiconica revealed no correlation with the body size. Comparison of the acquired data with the results of our earlier study of the antennal sensilla of some of the smallest parasitic wasps is used to put forward hypotheses on the common principles of miniaturization of the antennal sensory systems of insects.
bibliographic citation: Diakova et al. (2020) Sensation of the tiniest kind: the antennal sensilla of the smallest free-living insect Scydosella musawasensis (Coleoptera: Ptiliidae). PeerJ 8:e10401 https://doi.org/10.7717/peerj.10401
date submitted: 2020-09-02
date accepted: 2020-10-29
issued: 2020-11-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Diakova
  given name: Anna V.
author list: Agent
  family name: Polilov
  given name: Alexey A.
doi: 10.7717/peerj.10401
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-23
copyright: ©2020 Diakova and Polilov
attribution name: Diakova and Polilov

Identifying MMP14 and COL12A1 as a potential combination of prognostic biomarkers in pancreatic ductal adenocarcinoma using integrated bioinformatics analysis
type: item
type: AcademicArticle
description: Background Pancreatic ductal adenocarcinoma (PDAC) is a fatal malignant neoplasm. It is necessary to improve the understanding of the underlying molecular mechanisms and identify the key genes and signaling pathways involved in PDAC. Methods The microarray datasets GSE28735, GSE62165, and GSE91035 were downloaded from the Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified by integrated bioinformatics analysis, including protein–protein interaction (PPI) network, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The PPI network was established using the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. GO functional annotation and KEGG pathway analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. Hub genes were validated via the Gene Expression Profiling Interactive Analysis tool (GEPIA) and the Human Protein Atlas (HPA) website. Results A total of 263 DEGs (167 upregulated and 96 downregulated) were common to the three datasets. We used STRING and Cytoscape software to establish the PPI network and then identified key modules. From the PPI network, 225 nodes and 803 edges were selected. The most significant module, which comprised 11 DEGs, was identified using the Molecular Complex Detection plugin. The top 20 hub genes, which were filtered by the CytoHubba plugin, comprised FN1, COL1A1, COL3A1, BGN, POSTN, FBN1, COL5A2, COL12A1, THBS2, COL6A3, VCAN, CDH11, MMP14, LTBP1, IGFBP5, ALB, CXCL12, FAP, MATN3, and COL8A1. These genes were validated using The Cancer Genome Atlas (TCGA) and Genotype–Tissue Expression (GTEx) databases, and the encoded proteins were subsequently validated using the HPA website. The GO analysis results showed that the most significantly enriched biological process, cellular component, and molecular function terms among the 20 hub genes were cell adhesion, proteinaceous extracell…
format: application/pdf
format: text/html
creator: Jingyi Ding
creator: Yanxi Liu
creator: Yu Lai
subject: Bioinformatics
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.10419
publisher: PeerJ Inc.
rights: © 2020 Ding et al.
abstract: Background Pancreatic ductal adenocarcinoma (PDAC) is a fatal malignant neoplasm. It is necessary to improve the understanding of the underlying molecular mechanisms and identify the key genes and signaling pathways involved in PDAC. Methods The microarray datasets GSE28735, GSE62165, and GSE91035 were downloaded from the Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified by integrated bioinformatics analysis, including protein–protein interaction (PPI) network, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The PPI network was established using the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. GO functional annotation and KEGG pathway analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. Hub genes were validated via the Gene Expression Profiling Interactive Analysis tool (GEPIA) and the Human Protein Atlas (HPA) website. Results A total of 263 DEGs (167 upregulated and 96 downregulated) were common to the three datasets. We used STRING and Cytoscape software to establish the PPI network and then identified key modules. From the PPI network, 225 nodes and 803 edges were selected. The most significant module, which comprised 11 DEGs, was identified using the Molecular Complex Detection plugin. The top 20 hub genes, which were filtered by the CytoHubba plugin, comprised FN1, COL1A1, COL3A1, BGN, POSTN, FBN1, COL5A2, COL12A1, THBS2, COL6A3, VCAN, CDH11, MMP14, LTBP1, IGFBP5, ALB, CXCL12, FAP, MATN3, and COL8A1. These genes were validated using The Cancer Genome Atlas (TCGA) and Genotype–Tissue Expression (GTEx) databases, and the encoded proteins were subsequently validated using the HPA website. The GO analysis results showed that the most significantly enriched biological process, cellular component, and molecular function terms among the 20 hub genes were cell adhesion, proteinaceous extracell…
bibliographic citation: Ding et al. (2020) Identifying MMP14 and COL12A1 as a potential combination of prognostic biomarkers in pancreatic ductal adenocarcinoma using integrated bioinformatics analysis. PeerJ 8:e10419 https://doi.org/10.7717/peerj.10419
date submitted: 2020-08-25
date accepted: 2020-11-02
issued: 2020-11-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ding
  given name: Jingyi
author list: Agent
  family name: Liu
  given name: Yanxi
author list: Agent
  family name: Lai
  given name: Yu
doi: 10.7717/peerj.10419
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-23
copyright: ©2020 Ding et al.
attribution name: Ding et al.

A meta-analysis contrasting active versus passive restoration practices in dryland agricultural ecosystems
type: item
type: AcademicArticle
description: Restoration of agricultural drylands globally, here farmlands and grazing lands, is a priority for ecosystem function and biodiversity preservation. Natural areas in drylands are recognized as biodiversity hotspots and face continued human impacts. Global water shortages are driving increased agricultural land retirement providing the opportunity to reclaim some of these lands for natural habitat. We used meta-analysis to contrast different classes of dryland restoration practices. All interventions were categorized as active and passive for the analyses of efficacy in dryland agricultural ecosystems. We evaluated the impact of 19 specific restoration practices from 42 studies on soil, plant, animal, and general habitat targets across 16 countries, for a total of 1,427 independent observations. Passive vegetation restoration and grazing exclusion led to net positive restoration outcomes. Passive restoration practices were more variable and less effective than active restoration practices. Furthermore, passive soil restoration led to net negative restoration outcomes. Active restoration practices consistently led to positive outcomes for soil, plant, and habitat targets. Water supplementation was the most effective restoration practice. These findings suggest that active interventions are necessary and critical in most instances for dryland agricultural ecosystems likely because of severe anthropogenic pressures and concurrent environmental stressors—both past and present.
format: application/pdf
format: text/html
creator: M. Florencia Miguel
creator: H. Scott Butterfield
creator: Christopher J. Lortie
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Environmental Impacts
description: doi:10.7717/peerj.10428
publisher: PeerJ Inc.
rights: © 2020 Miguel et al.
abstract: Restoration of agricultural drylands globally, here farmlands and grazing lands, is a priority for ecosystem function and biodiversity preservation. Natural areas in drylands are recognized as biodiversity hotspots and face continued human impacts. Global water shortages are driving increased agricultural land retirement providing the opportunity to reclaim some of these lands for natural habitat. We used meta-analysis to contrast different classes of dryland restoration practices. All interventions were categorized as active and passive for the analyses of efficacy in dryland agricultural ecosystems. We evaluated the impact of 19 specific restoration practices from 42 studies on soil, plant, animal, and general habitat targets across 16 countries, for a total of 1,427 independent observations. Passive vegetation restoration and grazing exclusion led to net positive restoration outcomes. Passive restoration practices were more variable and less effective than active restoration practices. Furthermore, passive soil restoration led to net negative restoration outcomes. Active restoration practices consistently led to positive outcomes for soil, plant, and habitat targets. Water supplementation was the most effective restoration practice. These findings suggest that active interventions are necessary and critical in most instances for dryland agricultural ecosystems likely because of severe anthropogenic pressures and concurrent environmental stressors—both past and present.
bibliographic citation: Miguel et al. (2020) A meta-analysis contrasting active versus passive restoration practices in dryland agricultural ecosystems. PeerJ 8:e10428 https://doi.org/10.7717/peerj.10428
date submitted: 2020-09-14
date accepted: 2020-11-03
issued: 2020-11-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miguel
  given name: M. Florencia
author list: Agent
  family name: Butterfield
  given name: H. Scott
author list: Agent
  family name: Lortie
  given name: Christopher J.
doi: 10.7717/peerj.10428
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-23
copyright: © 2020 Miguel et al.
attribution name: Miguel et al.

Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana
type: item
type: AcademicArticle
description: Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850…
format: application/pdf
format: text/html
creator: Lauren K. Hudson
creator: Lisha Constantine-Renna
creator: Linda Thomas
creator: Christina Moore
creator: Xiaorong Qian
creator: Katie Garman
creator: John R. Dunn
creator: Thomas G. Denes
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.10256
publisher: PeerJ Inc.
rights: © 2020 Hudson et al.
abstract: Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850…
bibliographic citation: Hudson et al. (2020) Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana. PeerJ 8:e10256 https://doi.org/10.7717/peerj.10256
date submitted: 2020-06-09
date accepted: 2020-10-06
issued: 2020-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hudson
  given name: Lauren K.
author list: Agent
  family name: Constantine-Renna
  given name: Lisha
author list: Agent
  family name: Thomas
  given name: Linda
author list: Agent
  family name: Moore
  given name: Christina
author list: Agent
  family name: Qian
  given name: Xiaorong
author list: Agent
  family name: Garman
  given name: Katie
author list: Agent
  family name: Dunn
  given name: John R.
author list: Agent
  family name: Denes
  given name: Thomas G.
doi: 10.7717/peerj.10256
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-20
copyright: ©2020 Hudson et al.
attribution name: Hudson et al.

Morph-specific seasonal variation of aggressive behaviour in a polymorphic lizard species
type: item
type: AcademicArticle
description: The persistence of colour polymorphism (CP) within a given population is generally associated with the coexistence of alternative reproductive strategies, each one involving specific trade-offs among behavioural, morphological, physiological, and other life histories. Common wall lizard (Podarcis muralis), is a medium-sized diurnal lizard, showing CP in three main colours (yellow, white, and red) on throat and belly, and a morph-specific pattern for both immunocompetence and seasonal variation of T levels. Yellow males show low stamina with high plasma T levels at the beginning of the season, while white males show high stamina with a higher plasma T levels at the end of the season. We hypothesised the presence of two strategies: a risky one, characterised by high aggressiveness played by yellow-morph, and a conservative one by white morph with low aggressiveness. Thus, we tested the aggressive response to conspecifics of yellow and white morphs using a mirror inserted into their cage, mimicking an intrusion of a stranger in their territories, throughout the breeding season (from April to July, 117 trials). We considered three types of aggressive response, with different levels of aggressiveness: (i) bite against the image reflected in the mirror, (ii) seconds spent by the individuals into the half mirrored cage, and (iii) number of times the lizard entered the half mirrored cage. We also considered the number of tongue flicking as explorative behaviour variable. All lizards were tested after a period of acclimatisation to the captivity conditions. Results demonstrate that yellow males showed a higher aggressive response in the early season and a decrease aggressive response towards the end, whereas white males showed an opposite pattern.
format: application/pdf
format: text/html
creator: Alan Jioele Coladonato
creator: Marco Mangiacotti
creator: Stefano Scali
creator: Marco A. L. Zuffi
creator: Carlotta Pasquariello
creator: Cristian Matellini
creator: Simone Buratti
creator: Mara Battaiola
creator: Roberto Sacchi
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.10268
publisher: PeerJ Inc.
rights: © 2020 Coladonato et al.
abstract: The persistence of colour polymorphism (CP) within a given population is generally associated with the coexistence of alternative reproductive strategies, each one involving specific trade-offs among behavioural, morphological, physiological, and other life histories. Common wall lizard (Podarcis muralis), is a medium-sized diurnal lizard, showing CP in three main colours (yellow, white, and red) on throat and belly, and a morph-specific pattern for both immunocompetence and seasonal variation of T levels. Yellow males show low stamina with high plasma T levels at the beginning of the season, while white males show high stamina with a higher plasma T levels at the end of the season. We hypothesised the presence of two strategies: a risky one, characterised by high aggressiveness played by yellow-morph, and a conservative one by white morph with low aggressiveness. Thus, we tested the aggressive response to conspecifics of yellow and white morphs using a mirror inserted into their cage, mimicking an intrusion of a stranger in their territories, throughout the breeding season (from April to July, 117 trials). We considered three types of aggressive response, with different levels of aggressiveness: (i) bite against the image reflected in the mirror, (ii) seconds spent by the individuals into the half mirrored cage, and (iii) number of times the lizard entered the half mirrored cage. We also considered the number of tongue flicking as explorative behaviour variable. All lizards were tested after a period of acclimatisation to the captivity conditions. Results demonstrate that yellow males showed a higher aggressive response in the early season and a decrease aggressive response towards the end, whereas white males showed an opposite pattern.
bibliographic citation: Coladonato et al. (2020) Morph-specific seasonal variation of aggressive behaviour in a polymorphic lizard species. PeerJ 8:e10268 https://doi.org/10.7717/peerj.10268
date submitted: 2020-07-21
date accepted: 2020-10-07
issued: 2020-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coladonato
  given name: Alan Jioele
author list: Agent
  family name: Mangiacotti
  given name: Marco
author list: Agent
  family name: Scali
  given name: Stefano
author list: Agent
  family name: Zuffi
  given name: Marco A. L.
author list: Agent
  family name: Pasquariello
  given name: Carlotta
author list: Agent
  family name: Matellini
  given name: Cristian
author list: Agent
  family name: Buratti
  given name: Simone
author list: Agent
  family name: Battaiola
  given name: Mara
author list: Agent
  family name: Sacchi
  given name: Roberto
doi: 10.7717/peerj.10268
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-20
copyright: © 2020 Coladonato et al.
attribution name: Coladonato et al.

Identification of hub genes associated with the pathogenesis of diffuse large B-cell lymphoma subtype one characterized by host response via integrated bioinformatic analyses
type: item
type: AcademicArticle
description: Background Host response diffuse large B-cell lymphoma (HR DLBCL) shares features of histologically defined T-cell/histiocyte-rich B-cell lymphoma, including fewer genetic abnormalities, frequent splenic and bone marrow involvement, and younger age at presentation. HR DLBCL is inherently less responsive to the standard treatment for DLBCL. Moreover, the mechanism of infiltration of HR DLBCL with preexisting abundant T-cells and dendritic cells is unknown, and their associated underlying immune responses incompletely defined. Here, hub genes and pathogenesis associated with HR DLBCL were explored to reveal molecular mechanisms and treatment targets. Methods Differentially expressed genes were identified in three datasets (GSE25638, GSE44337, GSE56315). The expression profile of the genes in the GSE53786 dataset was used to constructed a co-expression network. Protein-protein interactions analysis in the modules of interest identified candidate hub genes. Then screening of real hub genes was carried out by survival analysis within the GSE53786 and GSE10846 datasets. Expression of hub genes was validated in the Gene expression profiling interactive analysis, Oncomine databases and human tissue specimens. Functional enrichment analysis and Gene set enrichment analysis were utilized to investigate the potential mechanisms. Tumor Immune Estimation Resource and The Cancer Genome Atlas were used to mine the association of the hub gene with tumor immunity, potential upstream regulators were predicted using bioinformatics tools. Results A total of 274 common differentially expressed genes were identified. Within the key module, we identified CXCL10 as a real hub gene. The validation of upregulated expression level of CXCL10 was consistent with our study. CXCL10 might have a regulatory effect on tumor immunity. The predicted miRNA (hsa-mir-6849-3p) and transcription factor (IRF9) might regulate gene expression in the hub module.
format: application/pdf
format: text/html
creator: Lingna Zhou
creator: Liya Ding
creator: Yuqi Gong
creator: Jing Zhao
creator: Gong Xin
creator: Ren Zhou
creator: Wei Zhang
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.10269
publisher: PeerJ Inc.
rights: © 2020 Zhou et al.
abstract: Background Host response diffuse large B-cell lymphoma (HR DLBCL) shares features of histologically defined T-cell/histiocyte-rich B-cell lymphoma, including fewer genetic abnormalities, frequent splenic and bone marrow involvement, and younger age at presentation. HR DLBCL is inherently less responsive to the standard treatment for DLBCL. Moreover, the mechanism of infiltration of HR DLBCL with preexisting abundant T-cells and dendritic cells is unknown, and their associated underlying immune responses incompletely defined. Here, hub genes and pathogenesis associated with HR DLBCL were explored to reveal molecular mechanisms and treatment targets. Methods Differentially expressed genes were identified in three datasets (GSE25638, GSE44337, GSE56315). The expression profile of the genes in the GSE53786 dataset was used to constructed a co-expression network. Protein-protein interactions analysis in the modules of interest identified candidate hub genes. Then screening of real hub genes was carried out by survival analysis within the GSE53786 and GSE10846 datasets. Expression of hub genes was validated in the Gene expression profiling interactive analysis, Oncomine databases and human tissue specimens. Functional enrichment analysis and Gene set enrichment analysis were utilized to investigate the potential mechanisms. Tumor Immune Estimation Resource and The Cancer Genome Atlas were used to mine the association of the hub gene with tumor immunity, potential upstream regulators were predicted using bioinformatics tools. Results A total of 274 common differentially expressed genes were identified. Within the key module, we identified CXCL10 as a real hub gene. The validation of upregulated expression level of CXCL10 was consistent with our study. CXCL10 might have a regulatory effect on tumor immunity. The predicted miRNA (hsa-mir-6849-3p) and transcription factor (IRF9) might regulate gene expression in the hub module.
bibliographic citation: Zhou et al. (2020) Identification of hub genes associated with the pathogenesis of diffuse large B-cell lymphoma subtype one characterized by host response via integrated bioinformatic analyses. PeerJ 8:e10269 https://doi.org/10.7717/peerj.10269
date submitted: 2020-07-22
date accepted: 2020-10-07
issued: 2020-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Lingna
author list: Agent
  family name: Ding
  given name: Liya
author list: Agent
  family name: Gong
  given name: Yuqi
author list: Agent
  family name: Zhao
  given name: Jing
author list: Agent
  family name: Xin
  given name: Gong
author list: Agent
  family name: Zhou
  given name: Ren
author list: Agent
  family name: Zhang
  given name: Wei
doi: 10.7717/peerj.10269
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-20
copyright: ©2020 Zhou et al.
attribution name: Zhou et al.

The cranial morphology of Tanystropheus hydroides (Tanystropheidae, Archosauromorpha) as revealed by synchrotron microtomography
type: item
type: AcademicArticle
description: The postcranial morphology of the extremely long-necked Tanystropheus hydroides is well-known, but observations of skull morphology were previously limited due to compression of the known specimens. Here we provide a detailed description of the skull of PIMUZ T 2790, including a partial endocast and endosseous labyrinth, based on synchrotron microtomographic data, and compare its morphology to that of other early Archosauromorpha. In many features, such as the wide and flattened snout and the configuration of the temporal and palatal regions, Tanystropheus hydroides differs strongly from other early archosauromorphs. The braincase possesses a combination of derived archosaur traits, such as the presence of a laterosphenoid and the ossification of the lateral wall of the braincase, but also differs from archosauriforms in the morphology of the ventral ramus of the opisthotic, the horizontal orientation of the parabasisphenoid, and the absence of a clearly defined crista prootica. Tanystropheus hydroides was a ram-feeder that likely caught its prey through a laterally directed snapping bite. Although the cranial morphology of other archosauromorph lineages is relatively well-represented, the skulls of most tanystropheid taxa remain poorly understood due to compressed and often fragmentary specimens. The recent descriptions of the skulls of Macrocnemus bassanii and now Tanystropheus hydroides reveal a large cranial disparity in the clade, reflecting wide ecological diversity, and highlighting the importance of non-archosauriform Archosauromorpha to both terrestrial and aquatic ecosystems during the Triassic.
format: application/pdf
format: text/html
creator: Stephan N.F. Spiekman
creator: James M. Neenan
creator: Nicholas C. Fraser
creator: Vincent Fernandez
creator: Olivier Rieppel
creator: Stefania Nosotti
creator: Torsten M. Scheyer
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.10299
publisher: PeerJ Inc.
rights: © 2020 Spiekman et al.
abstract: The postcranial morphology of the extremely long-necked Tanystropheus hydroides is well-known, but observations of skull morphology were previously limited due to compression of the known specimens. Here we provide a detailed description of the skull of PIMUZ T 2790, including a partial endocast and endosseous labyrinth, based on synchrotron microtomographic data, and compare its morphology to that of other early Archosauromorpha. In many features, such as the wide and flattened snout and the configuration of the temporal and palatal regions, Tanystropheus hydroides differs strongly from other early archosauromorphs. The braincase possesses a combination of derived archosaur traits, such as the presence of a laterosphenoid and the ossification of the lateral wall of the braincase, but also differs from archosauriforms in the morphology of the ventral ramus of the opisthotic, the horizontal orientation of the parabasisphenoid, and the absence of a clearly defined crista prootica. Tanystropheus hydroides was a ram-feeder that likely caught its prey through a laterally directed snapping bite. Although the cranial morphology of other archosauromorph lineages is relatively well-represented, the skulls of most tanystropheid taxa remain poorly understood due to compressed and often fragmentary specimens. The recent descriptions of the skulls of Macrocnemus bassanii and now Tanystropheus hydroides reveal a large cranial disparity in the clade, reflecting wide ecological diversity, and highlighting the importance of non-archosauriform Archosauromorpha to both terrestrial and aquatic ecosystems during the Triassic.
bibliographic citation: Spiekman et al. (2020) The cranial morphology of Tanystropheus hydroides (Tanystropheidae, Archosauromorpha) as revealed by synchrotron microtomography. PeerJ 8:e10299 https://doi.org/10.7717/peerj.10299
date submitted: 2020-08-06
date accepted: 2020-10-14
issued: 2020-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Spiekman
  given name: Stephan N.F.
author list: Agent
  family name: Neenan
  given name: James M.
author list: Agent
  family name: Fraser
  given name: Nicholas C.
author list: Agent
  family name: Fernandez
  given name: Vincent
author list: Agent
  family name: Rieppel
  given name: Olivier
author list: Agent
  family name: Nosotti
  given name: Stefania
author list: Agent
  family name: Scheyer
  given name: Torsten M.
doi: 10.7717/peerj.10299
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-20
copyright: © 2020 Spiekman et al.
attribution name: Spiekman et al.

Translocation of an arctic seashore plant reveals signs of maladaptation to altered climatic conditions
type: item
type: AcademicArticle
description: Ongoing anthropogenic climate change alters the local climatic conditions to which species may be adapted. Information on species’ climatic requirements and their intraspecific variation is necessary for predicting the effects of climate change on biodiversity. We used a climatic gradient to test whether populations of two allopatric varieties of an arctic seashore herb (Primula nutans ssp. finmarchica) show adaptation to their local climates and how a future warmer climate may affect them. Our experimental set-up combined a reciprocal translocation within the distribution range of the species with an experiment testing the performance of the sampled populations in warmer climatic conditions south of their range. We monitored survival, size, and flowering over four growing seasons as measures of performance and, thus, proxies of fitness. We found that both varieties performed better in experimental gardens towards the north. Interestingly, highest up in the north, the southern variety outperformed the northern one. Supported by weather data, this suggests that the climatic optima of both varieties have moved at least partly outside their current range. Further warming would make the current environments of both varieties even less suitable. We conclude that Primula nutans ssp. finmarchica is already suffering from adaptational lag due to climate change, and that further warming may increase this maladaptation, especially for the northern variety. The study also highlights that it is not sufficient to run only reciprocal translocation experiments. Climate change is already shifting the optimum conditions for many species and adaptation needs also to be tested outside the current range of the focal taxon in order to include both historic conditions and future conditions.
format: application/pdf
format: text/html
creator: Maria Hällfors
creator: Susanna Lehvävirta
creator: Tone Aandahl
creator: Iida-Maria Lehtimäki
creator: Lars Ola Nilsson
creator: Anna Ruotsalainen
creator: Leif E. Schulman
creator: Marko T. Hyvärinen
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.10357
publisher: PeerJ Inc.
rights: © 2020 Hällfors et al.
abstract: Ongoing anthropogenic climate change alters the local climatic conditions to which species may be adapted. Information on species’ climatic requirements and their intraspecific variation is necessary for predicting the effects of climate change on biodiversity. We used a climatic gradient to test whether populations of two allopatric varieties of an arctic seashore herb (Primula nutans ssp. finmarchica) show adaptation to their local climates and how a future warmer climate may affect them. Our experimental set-up combined a reciprocal translocation within the distribution range of the species with an experiment testing the performance of the sampled populations in warmer climatic conditions south of their range. We monitored survival, size, and flowering over four growing seasons as measures of performance and, thus, proxies of fitness. We found that both varieties performed better in experimental gardens towards the north. Interestingly, highest up in the north, the southern variety outperformed the northern one. Supported by weather data, this suggests that the climatic optima of both varieties have moved at least partly outside their current range. Further warming would make the current environments of both varieties even less suitable. We conclude that Primula nutans ssp. finmarchica is already suffering from adaptational lag due to climate change, and that further warming may increase this maladaptation, especially for the northern variety. The study also highlights that it is not sufficient to run only reciprocal translocation experiments. Climate change is already shifting the optimum conditions for many species and adaptation needs also to be tested outside the current range of the focal taxon in order to include both historic conditions and future conditions.
bibliographic citation: Hällfors et al. (2020) Translocation of an arctic seashore plant reveals signs of maladaptation to altered climatic conditions. PeerJ 8:e10357 https://doi.org/10.7717/peerj.10357
date submitted: 2020-06-04
date accepted: 2020-10-23
issued: 2020-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Hällfors
  given name: Maria
author list: Agent
  family name: Lehvävirta
  given name: Susanna
author list: Agent
  family name: Aandahl
  given name: Tone
author list: Agent
  family name: Lehtimäki
  given name: Iida-Maria
author list: Agent
  family name: Nilsson
  given name: Lars Ola
author list: Agent
  family name: Ruotsalainen
  given name: Anna
author list: Agent
  family name: Schulman
  given name: Leif E.
author list: Agent
  family name: Hyvärinen
  given name: Marko T.
doi: 10.7717/peerj.10357
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-20
copyright: ©2020 Hällfors et al.
attribution name: Hällfors et al.

Genome-wide identification and analysis of the thiolase family in insects
type: item
type: AcademicArticle
description: Thiolases are important enzymes involved in lipid metabolism in both prokaryotes and eukaryotes, and are essential for a range of metabolic pathways, while, little is known for this important family in insects. To shed light on the evolutionary models and functional diversities of the thiolase family, 137 thiolase genes were identified in 20 representative insect genomes. They were mainly classified into five classes, namely cytosolic thiolase (CT-thiolase), T1-thiolase, T2-thiolase, trifunctional enzyme thiolase (TFE-thiolase), and sterol carrier protein 2 thiolase (SCP2-thiolase). The intron number and exon/intron structures of the thiolase genes reserve large diversification. Subcellular localization prediction indicated that all the thiolase proteins were mitochondrial, cytosolic, or peroxisomal enzymes. Four highly conserved sequence fingerprints were found in the insect thiolase proteins, including CxS-, NEAF-, GHP-, and CxGGGxG-motifs. Homology modeling indicated that insect thiolases share similar 3D structures with mammals, fishes, and microorganisms. In Bombyx mori, microarray data and reverse transcription-polymerase chain reaction (RT-PCR) analysis suggested that some thiolases might be involved in steroid metabolism, juvenile hormone (JH), and sex pheromone biosynthesis pathways. In general, sequence and structural characteristics were relatively conserved among insects, bacteria and vertebrates, while different classes of thiolases might have differentiation in specific functions and physiological processes. These results will provide an important foundation for future functional validation of insect thiolases.
format: application/pdf
format: text/html
creator: Shou-Min Fang
subject: Bioinformatics
subject: Entomology
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.10393
publisher: PeerJ Inc.
rights: © 2020 Fang
abstract: Thiolases are important enzymes involved in lipid metabolism in both prokaryotes and eukaryotes, and are essential for a range of metabolic pathways, while, little is known for this important family in insects. To shed light on the evolutionary models and functional diversities of the thiolase family, 137 thiolase genes were identified in 20 representative insect genomes. They were mainly classified into five classes, namely cytosolic thiolase (CT-thiolase), T1-thiolase, T2-thiolase, trifunctional enzyme thiolase (TFE-thiolase), and sterol carrier protein 2 thiolase (SCP2-thiolase). The intron number and exon/intron structures of the thiolase genes reserve large diversification. Subcellular localization prediction indicated that all the thiolase proteins were mitochondrial, cytosolic, or peroxisomal enzymes. Four highly conserved sequence fingerprints were found in the insect thiolase proteins, including CxS-, NEAF-, GHP-, and CxGGGxG-motifs. Homology modeling indicated that insect thiolases share similar 3D structures with mammals, fishes, and microorganisms. In Bombyx mori, microarray data and reverse transcription-polymerase chain reaction (RT-PCR) analysis suggested that some thiolases might be involved in steroid metabolism, juvenile hormone (JH), and sex pheromone biosynthesis pathways. In general, sequence and structural characteristics were relatively conserved among insects, bacteria and vertebrates, while different classes of thiolases might have differentiation in specific functions and physiological processes. These results will provide an important foundation for future functional validation of insect thiolases.
bibliographic citation: Fang (2020) Genome-wide identification and analysis of the thiolase family in insects. PeerJ 8:e10393 https://doi.org/10.7717/peerj.10393
date submitted: 2020-08-26
date accepted: 2020-10-29
issued: 2020-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fang
  given name: Shou-Min
doi: 10.7717/peerj.10393
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-20
copyright: ©2020 Fang
attribution name: Fang

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