PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China
items: Genetic variation of the Chilean endemic long-haired mouse Abrothrix longipilis (Rodentia, Supramyomorpha, Cricetidae) in a geographical and environmental context
items: Diagnostic and prognostic values of upregulated SPC25 in patients with hepatocellular carcinoma
items: A comparison of lodgepole and spruce needle chemistry impacts on terrestrial biogeochemical processes during isolated decomposition
items: Endophytic Burkholderia sp. SSG as a potential biofertilizer promoting boxwood growth
items: Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey
items: Chlorine-based DUWL disinfectant leads to a different microbial composition of water derived biofilms compared to H2O2-based chemical disinfectants in vitro
items: Decomposition of dinosaurian remains inferred by invertebrate traces on vertebrate bone reveal new insights into Late Jurassic ecology, decay, and climate in western Colorado
items: Canine SOD1 harboring E40K or T18S mutations promotes protein aggregation without reducing the global structural stability
items: Craniofacial characteristics of Syrian adolescents with Class II division 1 malocclusion: a retrospective study

Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China
type: item
type: AcademicArticle
description: Construction of hydropower stations has been an important approach to meet China’s increasing power demand, but the impact of construction of hydropower stations on river microbiota is not fully understood. To evaluate this, the microbial composition from 18 sampling sites in the downstream of Jinsha River of China, upstream and downstream of two completed and two under-construction hydropower stations, were analyzed using high-throughput 16S rRNA gene sequencing. Three independent samples from each site were analyzed. A total of 18,683 OTUs from 1,350 genera were identified at 97% sequence similarity. Our results showed that the completion of hydropower stations would significantly increase the relative abundances of Acidobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Nitrospirae, and Planctomycetes, especially the relative abundance of Synechococcus dOTUs and thus increase the risk of algal blooms. PCA based on all KEGG pathways and the significantly different KEGG pathways showed the predicted metabolic characteristics of the water microbiota by PICRUSt in the activated hydropower station group were significant difference to the other groups. Results from canonical correspondence analysis showed that water temperature and dissolved oxygen had significant effects on microbiota composition. These results are important for assessing the impact of hydropower stations on river microbiota and their potential environmental risks.
format: application/pdf
format: text/html
creator: Xiaojuan Chen
creator: Da He
creator: Lianfeng Zhou
creator: Yankun Cao
creator: Zhanjing Li
subject: Biodiversity
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.9500
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Construction of hydropower stations has been an important approach to meet China’s increasing power demand, but the impact of construction of hydropower stations on river microbiota is not fully understood. To evaluate this, the microbial composition from 18 sampling sites in the downstream of Jinsha River of China, upstream and downstream of two completed and two under-construction hydropower stations, were analyzed using high-throughput 16S rRNA gene sequencing. Three independent samples from each site were analyzed. A total of 18,683 OTUs from 1,350 genera were identified at 97% sequence similarity. Our results showed that the completion of hydropower stations would significantly increase the relative abundances of Acidobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Nitrospirae, and Planctomycetes, especially the relative abundance of Synechococcus dOTUs and thus increase the risk of algal blooms. PCA based on all KEGG pathways and the significantly different KEGG pathways showed the predicted metabolic characteristics of the water microbiota by PICRUSt in the activated hydropower station group were significant difference to the other groups. Results from canonical correspondence analysis showed that water temperature and dissolved oxygen had significant effects on microbiota composition. These results are important for assessing the impact of hydropower stations on river microbiota and their potential environmental risks.
bibliographic citation: Chen et al. (2020) Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China. PeerJ 8:e9500 https://doi.org/10.7717/peerj.9500
date submitted: 2019-11-29
date accepted: 2020-06-17
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xiaojuan
author list: Agent
  family name: He
  given name: Da
author list: Agent
  family name: Zhou
  given name: Lianfeng
author list: Agent
  family name: Cao
  given name: Yankun
author list: Agent
  family name: Li
  given name: Zhanjing
doi: 10.7717/peerj.9500
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: © 2020 Chen et al.
attribution name: Chen et al.

Genetic variation of the Chilean endemic long-haired mouse Abrothrix longipilis (Rodentia, Supramyomorpha, Cricetidae) in a geographical and environmental context
type: item
type: AcademicArticle
description: Quaternary climate and associated vegetational changes affected the fauna of the Chilean Mediterranean ecosystem. Here we studied the genetic variation of the long-haired mouse, Abrothrix longipilis, a sigmodontine rodent endemic to this area. Within an environmentally explicit context, we examined the geographic distribution of the genetic diversity and demographic history of the species based on sequences of the mitochondrial Cytochrome-b gene of 50 individuals from 13 localities and a large panel of single nucleotide polymorphisms of 17 individuals from 6 localities. The gene genealogy of A. longipilis revealed three intraspecific lineages that are allopatric and latitudinally segregated (northern, central, and southern lineages) with an estimated crown age for the whole species clade of 552.3 kyr B.P. A principal component analysis based on 336,596 SNP loci is in line with the information given by the the mitochondrial gene genealogy. Along its complete distributional range, A. longipilis showed patterns of isolation by distance and also isolation by environment. The general pattern of historical demography showed stability for most intraspecific lineages of A. longipilis. Northern and central lineages showed signals of historical demographic stability, while the southern lineage showed contrasting signals. In agreement with this, the niche models performed showed that in the northern range of A. longipilis, areas of high suitability for this species increased towards the present time; areas of central range would have remained relatively stable, while southern areas would have experienced more change through time. In summary, our study shows three distinct allopatric lineages of A. longipilis, each showing slightly different demographic history.
format: application/pdf
format: text/html
creator: Lourdes Valdez
creator: Marcial Quiroga-Carmona
creator: Guillermo D’Elía
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.9517
publisher: PeerJ Inc.
rights: © 2020 Valdez et al.
abstract: Quaternary climate and associated vegetational changes affected the fauna of the Chilean Mediterranean ecosystem. Here we studied the genetic variation of the long-haired mouse, Abrothrix longipilis, a sigmodontine rodent endemic to this area. Within an environmentally explicit context, we examined the geographic distribution of the genetic diversity and demographic history of the species based on sequences of the mitochondrial Cytochrome-b gene of 50 individuals from 13 localities and a large panel of single nucleotide polymorphisms of 17 individuals from 6 localities. The gene genealogy of A. longipilis revealed three intraspecific lineages that are allopatric and latitudinally segregated (northern, central, and southern lineages) with an estimated crown age for the whole species clade of 552.3 kyr B.P. A principal component analysis based on 336,596 SNP loci is in line with the information given by the the mitochondrial gene genealogy. Along its complete distributional range, A. longipilis showed patterns of isolation by distance and also isolation by environment. The general pattern of historical demography showed stability for most intraspecific lineages of A. longipilis. Northern and central lineages showed signals of historical demographic stability, while the southern lineage showed contrasting signals. In agreement with this, the niche models performed showed that in the northern range of A. longipilis, areas of high suitability for this species increased towards the present time; areas of central range would have remained relatively stable, while southern areas would have experienced more change through time. In summary, our study shows three distinct allopatric lineages of A. longipilis, each showing slightly different demographic history.
bibliographic citation: Valdez et al. (2020) Genetic variation of the Chilean endemic long-haired mouse Abrothrix longipilis (Rodentia, Supramyomorpha, Cricetidae) in a geographical and environmental context. PeerJ 8:e9517 https://doi.org/10.7717/peerj.9517
date submitted: 2020-03-31
date accepted: 2020-06-19
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valdez
  given name: Lourdes
author list: Agent
  family name: Quiroga-Carmona
  given name: Marcial
author list: Agent
  family name: D’Elía
  given name: Guillermo
doi: 10.7717/peerj.9517
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: ©2020 Valdez et al.
attribution name: Valdez et al.

Diagnostic and prognostic values of upregulated SPC25 in patients with hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Spindle pole body component 25 (SPC25) plays a vital role in many cellular processes, such as tumorigenesis. However, the clinical significance of SPC25 in hepatocellular carcinoma (HCC) has not been investigated. This study aimed to explore the expression patterns of SPC25 in HCC and non-neoplastic tissues and to investigate the diagnostic and prognostic values of SPC25. Method The expression of SPC25 was examined in 374 HCC issues and 50 non-neoplastic tissues from The Cancer Genome Atlas (TCGA) cohort. The diagnostic and prognostic values of SPC25 were analyzed via receiver operating characteristic (ROC) curve and survival analyses, respectively. Univariate and multivariate Cox regression analyses were used to identify the prognostic factors and to establish a nomogram. The diagnostic and prognostic values were further validated in an external cohort from the International Cancer Genome Consortium (ICGC) database. Results The expression of SPC25 in HCC tissues was significantly higher than that in normal tissues in both cohorts (all P < 0.001). The ROC curve analysis indicated that SPC25 expression has high diagnostic value in HCC with area under the curve (AUC) value of 0.969 (95% confidence interval [CI] [0.948–0.984]) and 0.945 (95% CI [0.920–0.965]) for TCGA and ICGC cohorts, respectively. Patients with HCC exhibiting high SPC25 expression were associated with worse prognosis than those exhibiting low SPC25 expression in both cohorts (all P < 0.001). SPC25 was independently associated with overall survival in both cohorts (all P < 0.001). The concordance indices of the nomogram for predicting overall survival in TCGA and ICGC cohorts were 0.647 and 0.805, respectively, which were higher than those of the American Joint Committee on Cancer (AJCC) staging system. Conclusion SPC25 was upregulated in HCC and independently predicted poor overall survival of patients with HCC. Therefore, SPC25 is an effective diagnostic and prognostic biomarker for HCC. …
format: application/pdf
format: text/html
creator: Xiaolin Yang
creator: Hongzhi Sun
creator: Ying Song
creator: Li Yang
creator: Haibo Liu
subject: Bioinformatics
subject: Computational Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.9535
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Background Spindle pole body component 25 (SPC25) plays a vital role in many cellular processes, such as tumorigenesis. However, the clinical significance of SPC25 in hepatocellular carcinoma (HCC) has not been investigated. This study aimed to explore the expression patterns of SPC25 in HCC and non-neoplastic tissues and to investigate the diagnostic and prognostic values of SPC25. Method The expression of SPC25 was examined in 374 HCC issues and 50 non-neoplastic tissues from The Cancer Genome Atlas (TCGA) cohort. The diagnostic and prognostic values of SPC25 were analyzed via receiver operating characteristic (ROC) curve and survival analyses, respectively. Univariate and multivariate Cox regression analyses were used to identify the prognostic factors and to establish a nomogram. The diagnostic and prognostic values were further validated in an external cohort from the International Cancer Genome Consortium (ICGC) database. Results The expression of SPC25 in HCC tissues was significantly higher than that in normal tissues in both cohorts (all P < 0.001). The ROC curve analysis indicated that SPC25 expression has high diagnostic value in HCC with area under the curve (AUC) value of 0.969 (95% confidence interval [CI] [0.948–0.984]) and 0.945 (95% CI [0.920–0.965]) for TCGA and ICGC cohorts, respectively. Patients with HCC exhibiting high SPC25 expression were associated with worse prognosis than those exhibiting low SPC25 expression in both cohorts (all P < 0.001). SPC25 was independently associated with overall survival in both cohorts (all P < 0.001). The concordance indices of the nomogram for predicting overall survival in TCGA and ICGC cohorts were 0.647 and 0.805, respectively, which were higher than those of the American Joint Committee on Cancer (AJCC) staging system. Conclusion SPC25 was upregulated in HCC and independently predicted poor overall survival of patients with HCC. Therefore, SPC25 is an effective diagnostic and prognostic biomarker for HCC. …
bibliographic citation: Yang et al. (2020) Diagnostic and prognostic values of upregulated SPC25 in patients with hepatocellular carcinoma. PeerJ 8:e9535 https://doi.org/10.7717/peerj.9535
date submitted: 2019-12-22
date accepted: 2020-06-23
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Xiaolin
author list: Agent
  family name: Sun
  given name: Hongzhi
author list: Agent
  family name: Song
  given name: Ying
author list: Agent
  family name: Yang
  given name: Li
author list: Agent
  family name: Liu
  given name: Haibo
doi: 10.7717/peerj.9535
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: ©2020 Yang et al.
attribution name: Yang et al.

A comparison of lodgepole and spruce needle chemistry impacts on terrestrial biogeochemical processes during isolated decomposition
type: item
type: AcademicArticle
description: This study investigates the isolated decomposition of spruce and lodgepole conifer needles to enhance our understanding of how needle litter impacts near-surface terrestrial biogeochemical processes. Harvested needles were exported to a subalpine meadow to enable a discrete analysis of the decomposition processes over 2 years. Initial chemistry revealed the lodgepole needles to be less recalcitrant with a lower carbon to nitrogen (C:N) ratio. Total C and N fundamentally shifted within needle species over time with decreased C:N ratios for spruce and increased ratios for lodgepole. Differences in chemistry correlated with CO2 production and soil microbial communities. The most pronounced trends were associated with lodgepole needles in comparison to the spruce and needle-free controls. Increased organic carbon and nitrogen concentrations associated with needle presence in soil extractions further corroborate the results with clear biogeochemical signatures in association with needle chemistry. Interestingly, no clear differentiation was observed as a function of bark beetle impacted spruce needles vs those derived from healthy spruce trees despite initial differences in needle chemistry. These results reveal that the inherent chemistry associated with tree species has a greater impact on soil biogeochemical signatures during isolated needle decomposition. By extension, biogeochemical shifts associated with bark beetle infestation are likely driven more by changes such as the cessation of rhizospheric processes than by needle litter decomposition.
format: application/pdf
format: text/html
creator: Laura T. Leonard
creator: Kristin Mikkelson
creator: Zhao Hao
creator: Eoin L. Brodie
creator: Kenneth H. Williams
creator: Jonathan O. Sharp
subject: Ecosystem Science
subject: Soil Science
subject: Biogeochemistry
subject: Environmental Impacts
description: doi:10.7717/peerj.9538
publisher: PeerJ Inc.
rights: © 2020 Leonard et al.
abstract: This study investigates the isolated decomposition of spruce and lodgepole conifer needles to enhance our understanding of how needle litter impacts near-surface terrestrial biogeochemical processes. Harvested needles were exported to a subalpine meadow to enable a discrete analysis of the decomposition processes over 2 years. Initial chemistry revealed the lodgepole needles to be less recalcitrant with a lower carbon to nitrogen (C:N) ratio. Total C and N fundamentally shifted within needle species over time with decreased C:N ratios for spruce and increased ratios for lodgepole. Differences in chemistry correlated with CO2 production and soil microbial communities. The most pronounced trends were associated with lodgepole needles in comparison to the spruce and needle-free controls. Increased organic carbon and nitrogen concentrations associated with needle presence in soil extractions further corroborate the results with clear biogeochemical signatures in association with needle chemistry. Interestingly, no clear differentiation was observed as a function of bark beetle impacted spruce needles vs those derived from healthy spruce trees despite initial differences in needle chemistry. These results reveal that the inherent chemistry associated with tree species has a greater impact on soil biogeochemical signatures during isolated needle decomposition. By extension, biogeochemical shifts associated with bark beetle infestation are likely driven more by changes such as the cessation of rhizospheric processes than by needle litter decomposition.
bibliographic citation: Leonard et al. (2020) A comparison of lodgepole and spruce needle chemistry impacts on terrestrial biogeochemical processes during isolated decomposition. PeerJ 8:e9538 https://doi.org/10.7717/peerj.9538
date submitted: 2020-02-17
date accepted: 2020-06-23
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leonard
  given name: Laura T.
author list: Agent
  family name: Mikkelson
  given name: Kristin
author list: Agent
  family name: Hao
  given name: Zhao
author list: Agent
  family name: Brodie
  given name: Eoin L.
author list: Agent
  family name: Williams
  given name: Kenneth H.
author list: Agent
  family name: Sharp
  given name: Jonathan O.
doi: 10.7717/peerj.9538
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: © 2020 Leonard et al.
attribution name: Leonard et al.

Endophytic Burkholderia sp. SSG as a potential biofertilizer promoting boxwood growth
type: item
type: AcademicArticle
description: Background Burkholderia sp. SSG is a bacterial endophyte isolated from boxwood leaves showing a resistant response to infection by the boxwood blight pathogen Calonectria pseudonaviculata. SSG acted as a protective and curative biocontrol agent for boxwood blight and as a bio-sanitizer of disease inoculum in the field. Many gene clusters involved in antibiotic production and plant growth promotion (PGP) were found in the genome, giving this endophyte great application potential as a treatment for plant protection. However, the PGP features have not been documented. This study investigated the plant growth promotion activity of SSG in boxwood. Methods To determine whether SSG is a plant growth promoting bacterium, four PGP traits, auxin and siderophore production, nitrogen fixation and phosphate solubilization, were examined in the laboratory with colorimetric or agar plate assays. The plant growth promoting activity of SSG was tested on three boxwood varieties characterized by slow, intermediate and fast growth rates, namely Justin Brouwers, Buddy and Winter Gem, respectively. These plants were drenched with an SSG cell suspension or water and washed plant weight was compared before and after treatment to determine growth changes after 10 months. Results The SSG culture was sustainable on nitrogen free media, suggesting that SSG may fix atmospheric nitrogen. It was also a strong phosphate solubilizer and a potent siderophore and indole-3-acetic acid (IAA) producer. Significant growth promotion was observed on boxwood cultivars Justin Brouwers, Buddy and Winter Gem 10 months after plant roots were drenched with SSG cells. The growth rate of treated plants was 76.1, 58.3, and 37.3% higher than that of the control, respectively. The degree of growth promotion was significantly different among plant varieties, notably more pronounced with the slow and intermediate growers. This study demonstrates that the SSG bacterium has multiple PGP traits and is a prospective plant …
format: application/pdf
format: text/html
creator: Ping Kong
creator: Chuanxue Hong
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.9547
publisher: PeerJ Inc.
rights: © 2020 Kong and Hong
abstract: Background Burkholderia sp. SSG is a bacterial endophyte isolated from boxwood leaves showing a resistant response to infection by the boxwood blight pathogen Calonectria pseudonaviculata. SSG acted as a protective and curative biocontrol agent for boxwood blight and as a bio-sanitizer of disease inoculum in the field. Many gene clusters involved in antibiotic production and plant growth promotion (PGP) were found in the genome, giving this endophyte great application potential as a treatment for plant protection. However, the PGP features have not been documented. This study investigated the plant growth promotion activity of SSG in boxwood. Methods To determine whether SSG is a plant growth promoting bacterium, four PGP traits, auxin and siderophore production, nitrogen fixation and phosphate solubilization, were examined in the laboratory with colorimetric or agar plate assays. The plant growth promoting activity of SSG was tested on three boxwood varieties characterized by slow, intermediate and fast growth rates, namely Justin Brouwers, Buddy and Winter Gem, respectively. These plants were drenched with an SSG cell suspension or water and washed plant weight was compared before and after treatment to determine growth changes after 10 months. Results The SSG culture was sustainable on nitrogen free media, suggesting that SSG may fix atmospheric nitrogen. It was also a strong phosphate solubilizer and a potent siderophore and indole-3-acetic acid (IAA) producer. Significant growth promotion was observed on boxwood cultivars Justin Brouwers, Buddy and Winter Gem 10 months after plant roots were drenched with SSG cells. The growth rate of treated plants was 76.1, 58.3, and 37.3% higher than that of the control, respectively. The degree of growth promotion was significantly different among plant varieties, notably more pronounced with the slow and intermediate growers. This study demonstrates that the SSG bacterium has multiple PGP traits and is a prospective plant …
bibliographic citation: Kong et al. (2020) Endophytic Burkholderia sp. SSG as a potential biofertilizer promoting boxwood growth. PeerJ 8:e9547 https://doi.org/10.7717/peerj.9547
date submitted: 2020-04-21
date accepted: 2020-06-24
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Ping
author list: Agent
  family name: Hong
  given name: Chuanxue
doi: 10.7717/peerj.9547
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: ©2020 Kong and Hong
attribution name: Kong and Hong

Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey
type: item
type: AcademicArticle
description: Williams’s jerboa (Scarturus williamsi), a medium-sized jerboa distributed in Anatolia and its adjacent regions, is a member of the four- and five-toed jerboas found mostly in Asia. Disagreements about the taxonomy of this taxon at the genus/species level continue to exist. Here, we report the first effort to sequence and assemble the mitochondrial genome of Williams’s jerboa from Turkey. The mitochondrial genome of S. williamsi was 16,653 bp in total length and contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and two non-coding regions (the D-loop and OL region) with intergenic spacer. All of the genes, except ND6 and eight tRNAs, were encoded on the heavy chain strand, similar to the features of mitogenomes of other rodents. When compared with all available rodent mitochondrial genomes, Williams’s jerboa showed (1) a serine deletion at the 3′-end of the ATP8 gene, (2) the ND5 gene terminated with a TAG codon and (3) a tandem repeat cluster (273 bp in length) in the control region. Williams’s jerboa and Siberian jerboa grouped as sister taxa despite the high genetic distance (17.6%) between them, belonging to Allactaginae. This result is consistent with the latest pre-revision, which suggests that Williams’s jerboa and the Siberian jerboa may belong to separate genera, as Scarturus and Orientallactaga, respectively. The present study provides a reference mitochondrial genome for Williams’s jerboa for further molecular studies of other species of Dipodoidea and Rodentia.
format: application/pdf
format: text/html
creator: Osman İbiş
subject: Biodiversity
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.9569
publisher: PeerJ Inc.
rights: © 2020 İbiş
abstract: Williams’s jerboa (Scarturus williamsi), a medium-sized jerboa distributed in Anatolia and its adjacent regions, is a member of the four- and five-toed jerboas found mostly in Asia. Disagreements about the taxonomy of this taxon at the genus/species level continue to exist. Here, we report the first effort to sequence and assemble the mitochondrial genome of Williams’s jerboa from Turkey. The mitochondrial genome of S. williamsi was 16,653 bp in total length and contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and two non-coding regions (the D-loop and OL region) with intergenic spacer. All of the genes, except ND6 and eight tRNAs, were encoded on the heavy chain strand, similar to the features of mitogenomes of other rodents. When compared with all available rodent mitochondrial genomes, Williams’s jerboa showed (1) a serine deletion at the 3′-end of the ATP8 gene, (2) the ND5 gene terminated with a TAG codon and (3) a tandem repeat cluster (273 bp in length) in the control region. Williams’s jerboa and Siberian jerboa grouped as sister taxa despite the high genetic distance (17.6%) between them, belonging to Allactaginae. This result is consistent with the latest pre-revision, which suggests that Williams’s jerboa and the Siberian jerboa may belong to separate genera, as Scarturus and Orientallactaga, respectively. The present study provides a reference mitochondrial genome for Williams’s jerboa for further molecular studies of other species of Dipodoidea and Rodentia.
bibliographic citation: İbiş (2020) Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey. PeerJ 8:e9569 https://doi.org/10.7717/peerj.9569
date submitted: 2020-02-28
date accepted: 2020-06-29
issued: 2020-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: İbiş
  given name: Osman
doi: 10.7717/peerj.9569
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-16
copyright: © 2020 İbiş
attribution name: İbiş

Chlorine-based DUWL disinfectant leads to a different microbial composition of water derived biofilms compared to H2O2-based chemical disinfectants in vitro
type: item
type: AcademicArticle
description: Background Biofilm formation in dental unit waterlines (DUWL) may lead to health risks for dental staff and patients. Therefore, dental unit waterlines need to be disinfected, for instance by using chemical disinfectants. However, the application of chemical disinfectants may lead to the selection of specific microorganisms. Therefore, the aim of our study was to assess the microbial composition of water-derived biofilms, after a continuous exposure to maintenance doses of commercially available chemical disinfectants, in vitro. Methods The AAA-model was used to grow water derived biofilms. The biofilms were subjected to the maintenance dose of each disinfectant. To determine the microbial composition, the V4 hypervariable region of the 16S rRNA gene was sequenced. The sequences were clustered in operational taxonomic units (OTUs). Results The bacterial composition of biofilms in all treatment groups differed significantly (PERMANOVA F = 4.441, p = 0.001). Pairwise comparisons revealed Anoxyl treated biofilms were significantly different from all groups (p = 0.0001). In the Anoxyl-treated biofilms, the relative abundance of Comamonadaceae and Sphingopyxis was high compared to the Dentosept, Green and Clean and Oxygenal groups. Conclusion We concluded that exposure to low doses of the chlorine-based chemical disinfectant Anoxyl led to a substantially different composition of water derived biofilms compared to biofilms exposed to H2O2-based chemical disinfectants.
format: application/pdf
format: text/html
creator: Charifa Zemouri
creator: Alexa M.G.A. Laheij
creator: Catherine M.C. Volgenant
creator: Bernd W. Brandt
creator: Wim Crielaard
creator: Mark J. Buijs
creator: Egija Zaura
creator: Johannes J. de Soet
subject: Microbiology
subject: Dentistry
subject: Public Health
description: doi:10.7717/peerj.9503
publisher: PeerJ Inc.
rights: © 2020 Zemouri et al.
abstract: Background Biofilm formation in dental unit waterlines (DUWL) may lead to health risks for dental staff and patients. Therefore, dental unit waterlines need to be disinfected, for instance by using chemical disinfectants. However, the application of chemical disinfectants may lead to the selection of specific microorganisms. Therefore, the aim of our study was to assess the microbial composition of water-derived biofilms, after a continuous exposure to maintenance doses of commercially available chemical disinfectants, in vitro. Methods The AAA-model was used to grow water derived biofilms. The biofilms were subjected to the maintenance dose of each disinfectant. To determine the microbial composition, the V4 hypervariable region of the 16S rRNA gene was sequenced. The sequences were clustered in operational taxonomic units (OTUs). Results The bacterial composition of biofilms in all treatment groups differed significantly (PERMANOVA F = 4.441, p = 0.001). Pairwise comparisons revealed Anoxyl treated biofilms were significantly different from all groups (p = 0.0001). In the Anoxyl-treated biofilms, the relative abundance of Comamonadaceae and Sphingopyxis was high compared to the Dentosept, Green and Clean and Oxygenal groups. Conclusion We concluded that exposure to low doses of the chlorine-based chemical disinfectant Anoxyl led to a substantially different composition of water derived biofilms compared to biofilms exposed to H2O2-based chemical disinfectants.
bibliographic citation: Zemouri et al. (2020) Chlorine-based DUWL disinfectant leads to a different microbial composition of water derived biofilms compared to H2O2-based chemical disinfectants in vitro. PeerJ 8:e9503 https://doi.org/10.7717/peerj.9503
date submitted: 2020-03-27
date accepted: 2020-06-17
issued: 2020-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zemouri
  given name: Charifa
author list: Agent
  family name: Laheij
  given name: Alexa M.G.A.
author list: Agent
  family name: Volgenant
  given name: Catherine M.C.
author list: Agent
  family name: Brandt
  given name: Bernd W.
author list: Agent
  family name: Crielaard
  given name: Wim
author list: Agent
  family name: Buijs
  given name: Mark J.
author list: Agent
  family name: Zaura
  given name: Egija
author list: Agent
  family name: de Soet
  given name: Johannes J.
doi: 10.7717/peerj.9503
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-15
copyright: ©2020 Zemouri et al.
attribution name: Zemouri et al.

Decomposition of dinosaurian remains inferred by invertebrate traces on vertebrate bone reveal new insights into Late Jurassic ecology, decay, and climate in western Colorado
type: item
type: AcademicArticle
description: A survey of 2,368 vertebrate fossils from the Upper Jurassic Mygatt-Moore Quarry (MMQ) (Morrison Formation, Brushy Basin Member) in western Colorado revealed 2,161 bone surface modifications on 884 specimens. This is the largest, site-wide bone surface modification survey of any Jurassic locality. Traces made by invertebrate actors were common in the assemblage, second in observed frequency after vertebrate bite marks. Invertebrate traces are found on 16.174% of the total surveyed material and comprise 20.148% of all identified traces. Six distinct invertebrate trace types were identified, including pits and furrows, rosettes, two types of bioglyph scrapes, bore holes and chambers. A minimum of four trace makers are indicated by the types, sizes and morphologies of the traces. Potential trace makers are inferred to be dermestid or clerid beetles, gastropods, an unknown necrophagous insect, and an unknown osteophagus insect. Of these, only gastropods are preserved at the site as body fossils. The remaining potential trace makers are part of the hidden paleodiversity from the North American Late Jurassic Period, revealed only through this ichnologic and taphonomic analysis. Site taphonomy suggests variable, but generally slow burial rates that range from months up to 6 years, while invertebrate traces on exposed elements indicate a minimum residence time of five months for carcasses with even few preserved invertebrate traces. These traces provide insight into the paleoecology, paleoclimate, and site formation of the MMQ, especially with regards to residence times of the skeletal remains on the paleolandscape. Comprehensive taphonomic studies, like this survey, are useful in exploring patterns of paleoecology and site formation, but they are also rare in Mesozoic assemblages. Additional work is required to determine if 16.174% is typical of bulk-collected fossils from Jurassic ecosystems in North America, or if the MMQ represents an unusual locality.
format: application/pdf
format: text/html
creator: Julia B. McHugh
creator: Stephanie K. Drumheller
creator: Anja Riedel
creator: Miriam Kane
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Paleontology
description: doi:10.7717/peerj.9510
publisher: PeerJ Inc.
rights: © 2020 McHugh et al.
abstract: A survey of 2,368 vertebrate fossils from the Upper Jurassic Mygatt-Moore Quarry (MMQ) (Morrison Formation, Brushy Basin Member) in western Colorado revealed 2,161 bone surface modifications on 884 specimens. This is the largest, site-wide bone surface modification survey of any Jurassic locality. Traces made by invertebrate actors were common in the assemblage, second in observed frequency after vertebrate bite marks. Invertebrate traces are found on 16.174% of the total surveyed material and comprise 20.148% of all identified traces. Six distinct invertebrate trace types were identified, including pits and furrows, rosettes, two types of bioglyph scrapes, bore holes and chambers. A minimum of four trace makers are indicated by the types, sizes and morphologies of the traces. Potential trace makers are inferred to be dermestid or clerid beetles, gastropods, an unknown necrophagous insect, and an unknown osteophagus insect. Of these, only gastropods are preserved at the site as body fossils. The remaining potential trace makers are part of the hidden paleodiversity from the North American Late Jurassic Period, revealed only through this ichnologic and taphonomic analysis. Site taphonomy suggests variable, but generally slow burial rates that range from months up to 6 years, while invertebrate traces on exposed elements indicate a minimum residence time of five months for carcasses with even few preserved invertebrate traces. These traces provide insight into the paleoecology, paleoclimate, and site formation of the MMQ, especially with regards to residence times of the skeletal remains on the paleolandscape. Comprehensive taphonomic studies, like this survey, are useful in exploring patterns of paleoecology and site formation, but they are also rare in Mesozoic assemblages. Additional work is required to determine if 16.174% is typical of bulk-collected fossils from Jurassic ecosystems in North America, or if the MMQ represents an unusual locality.
bibliographic citation: McHugh et al. (2020) Decomposition of dinosaurian remains inferred by invertebrate traces on vertebrate bone reveal new insights into Late Jurassic ecology, decay, and climate in western Colorado. PeerJ 8:e9510 https://doi.org/10.7717/peerj.9510
date submitted: 2020-03-16
date accepted: 2020-06-18
issued: 2020-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McHugh
  given name: Julia B.
author list: Agent
  family name: Drumheller
  given name: Stephanie K.
author list: Agent
  family name: Riedel
  given name: Anja
author list: Agent
  family name: Kane
  given name: Miriam
doi: 10.7717/peerj.9510
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-15
copyright: © 2020 McHugh et al.
attribution name: McHugh et al.

Canine SOD1 harboring E40K or T18S mutations promotes protein aggregation without reducing the global structural stability
type: item
type: AcademicArticle
description: Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease associated with aggregation of superoxide dismutase 1 (SOD1) protein. More than 160 mutations in human SOD1 have been identified in familial ALS and extensively characterized in previous studies. Here, we investigated the effects of T18S and E40K mutations on protein aggregation of canine SOD1. These two mutations are exclusively found in canine degenerative myelopathy (an ALS-like neurodegenerative disease in dogs), whose phenotype is unknown at the level of protein folding. Interestingly, the T18S and E40K mutations did not alter far-UV CD spectrum, enzymatic activity, or global structural stability of canine SOD1. However, thioflavin-T assay and transmission electron microscopy analysis revealed that these mutations promote formation of fibrous aggregates, in particular in the Cu2+/Zn2+-unbound state. These evidence suggested that the T18S and E40K mutations promote protein aggregation through a unique mechanism, possibly involving destabilization of the local structure, reduction of net negative charge, or production of disulfide-linked oligomers.
format: application/pdf
format: text/html
creator: Shintaro Kimura
creator: Yuji O. Kamatari
creator: Yukina Kuwahara
creator: Hideaki Hara
creator: Osamu Yamato
creator: Sadatoshi Maeda
creator: Hiroaki Kamishina
creator: Ryo Honda
subject: Biochemistry
subject: Molecular Biology
subject: Neuroscience
subject: Veterinary Medicine
description: doi:10.7717/peerj.9512
publisher: PeerJ Inc.
rights: © 2020 Kimura et al.
abstract: Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease associated with aggregation of superoxide dismutase 1 (SOD1) protein. More than 160 mutations in human SOD1 have been identified in familial ALS and extensively characterized in previous studies. Here, we investigated the effects of T18S and E40K mutations on protein aggregation of canine SOD1. These two mutations are exclusively found in canine degenerative myelopathy (an ALS-like neurodegenerative disease in dogs), whose phenotype is unknown at the level of protein folding. Interestingly, the T18S and E40K mutations did not alter far-UV CD spectrum, enzymatic activity, or global structural stability of canine SOD1. However, thioflavin-T assay and transmission electron microscopy analysis revealed that these mutations promote formation of fibrous aggregates, in particular in the Cu2+/Zn2+-unbound state. These evidence suggested that the T18S and E40K mutations promote protein aggregation through a unique mechanism, possibly involving destabilization of the local structure, reduction of net negative charge, or production of disulfide-linked oligomers.
bibliographic citation: Kimura et al. (2020) Canine SOD1 harboring E40K or T18S mutations promotes protein aggregation without reducing the global structural stability. PeerJ 8:e9512 https://doi.org/10.7717/peerj.9512
date submitted: 2020-01-31
date accepted: 2020-06-18
issued: 2020-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kimura
  given name: Shintaro
author list: Agent
  family name: Kamatari
  given name: Yuji O.
author list: Agent
  family name: Kuwahara
  given name: Yukina
author list: Agent
  family name: Hara
  given name: Hideaki
author list: Agent
  family name: Yamato
  given name: Osamu
author list: Agent
  family name: Maeda
  given name: Sadatoshi
author list: Agent
  family name: Kamishina
  given name: Hiroaki
author list: Agent
  family name: Honda
  given name: Ryo
doi: 10.7717/peerj.9512
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-15
copyright: ©2020 Kimura et al.
attribution name: Kimura et al.

Craniofacial characteristics of Syrian adolescents with Class II division 1 malocclusion: a retrospective study
type: item
type: AcademicArticle
description: Background Malocclusion characteristics vary across different ethnic groups and populations. Limited data are available regarding the characteristics of Syrian adolescents with Class II division 1 (Class II-1) malocclusion, and the recent inflow of Syrian refugees and immigrants into Europe and many areas worldwide demonstrate the need for updated studies to discover the craniofacial characteristics of these new immigrants. Objectives The present compound cephalometric and tooth-size study sought to assess the dentofacial morphology, upper-airway dimensions, and tooth-size characteristics of Syrian adolescents with Class II-1 malocclusion and compare the results with established Syrian population norms. Materials and Methods The study sample consisted of 43 Syrian patients including 24 females and 19 males with Class II-1 malocclusion (age: 14.3 (±1.5) years, mean (±SD)). Cephalometric radiographs and orthodontic casts were analyzed using special orthodontic software (OnyxCeph3™) and a universal digital caliper, respectively. Statistics were calculated using the SPSS software. Results In Syrian adolescents with Class II-1 malocclusion, the position of the mandible relative to the nasion perpendicular (mean (95% confidence interval)) was −11.01 (−12.45, −9.57) mm. Facial axis angle showed a negative value: −6.25 (−7.65, −4.85) degrees. An obtuse nasolabial angle was observed: 104.05 (101.77, 106.33) degrees. The average width of the upper pharynx was 11.50 (10.53, 12.47) mm; however, there was no prevalence of an upper-pharyngeal width of 5 mm or less. The average value of the anterior tooth-size ratio was 80.69 (79.85, 81.53) percent. In total, 39.5% of the investigated subjects had anterior ratios outside two standard deviations from Bolton’s norm, while 25.6% of the investigated subjects had anterior ratios outside two standard deviations from Syrian population norm. Conclusions In this study, the inter-maxillary discrepancy of Class II-1 Syrian adolescents was a …
format: application/pdf
format: text/html
creator: Alaa Al Ayoubi
creator: Daniel Dalla Torre
creator: Melinda Madléna
subject: Anatomy and Physiology
subject: Dentistry
subject: Evidence Based Medicine
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.9545
publisher: PeerJ Inc.
rights: © 2020 Al Ayoubi et al.
abstract: Background Malocclusion characteristics vary across different ethnic groups and populations. Limited data are available regarding the characteristics of Syrian adolescents with Class II division 1 (Class II-1) malocclusion, and the recent inflow of Syrian refugees and immigrants into Europe and many areas worldwide demonstrate the need for updated studies to discover the craniofacial characteristics of these new immigrants. Objectives The present compound cephalometric and tooth-size study sought to assess the dentofacial morphology, upper-airway dimensions, and tooth-size characteristics of Syrian adolescents with Class II-1 malocclusion and compare the results with established Syrian population norms. Materials and Methods The study sample consisted of 43 Syrian patients including 24 females and 19 males with Class II-1 malocclusion (age: 14.3 (±1.5) years, mean (±SD)). Cephalometric radiographs and orthodontic casts were analyzed using special orthodontic software (OnyxCeph3™) and a universal digital caliper, respectively. Statistics were calculated using the SPSS software. Results In Syrian adolescents with Class II-1 malocclusion, the position of the mandible relative to the nasion perpendicular (mean (95% confidence interval)) was −11.01 (−12.45, −9.57) mm. Facial axis angle showed a negative value: −6.25 (−7.65, −4.85) degrees. An obtuse nasolabial angle was observed: 104.05 (101.77, 106.33) degrees. The average width of the upper pharynx was 11.50 (10.53, 12.47) mm; however, there was no prevalence of an upper-pharyngeal width of 5 mm or less. The average value of the anterior tooth-size ratio was 80.69 (79.85, 81.53) percent. In total, 39.5% of the investigated subjects had anterior ratios outside two standard deviations from Bolton’s norm, while 25.6% of the investigated subjects had anterior ratios outside two standard deviations from Syrian population norm. Conclusions In this study, the inter-maxillary discrepancy of Class II-1 Syrian adolescents was a …
bibliographic citation: Al Ayoubi et al. (2020) Craniofacial characteristics of Syrian adolescents with Class II division 1 malocclusion: a retrospective study. PeerJ 8:e9545 https://doi.org/10.7717/peerj.9545
date submitted: 2020-01-22
date accepted: 2020-06-24
issued: 2020-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al Ayoubi
  given name: Alaa
author list: Agent
  family name: Dalla Torre
  given name: Daniel
author list: Agent
  family name: Madléna
  given name: Melinda
doi: 10.7717/peerj.9545
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-15
copyright: © 2020 Al Ayoubi et al.
attribution name: Al Ayoubi et al.

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