PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard (Podarcis lilfordi) gut microbiota
items: Influences of oxygen and temperature interaction on the antibacterial activity, antioxidant activity, serum biochemical indices, blood indices and growth performance of crucian carp
items: Epigenetic regulation of dental-derived stem cells and their application in pulp and periodontal regeneration
items: Agricultural water allocation with climate change based on gray wolf optimization in a semi-arid region of China
items: Two new temporary ectoparasitic isopods (Cymothoida: Cymothooidea) from Korean waters with a note on geographical distributions of Rocinela Leach, 1818 and Gnathia Leach, 1814
items: Integrative genomic and transcriptomic analyses of a bud sport mutant ‘Jinzao Wuhe’ with the phenotype of large berries in grapevines
items: Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes
items: Left ventricle dysfunction in patients with critical neonatal pulmonary stenosis: echocardiographic predictors. A single-center retrospective study
items: Modeling the response of Japanese quail to arginine intake
items: A new Meckel’s cartilage from the Devonian Hangenberg black shale in Morocco and its position in chondrichthyan jaw morphospace

Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard (Podarcis lilfordi) gut microbiota
type: item
type: AcademicArticle
description: Background Integrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Insular vertebrates provide ideal natural systems to understand patterns of host-gut microbiota coevolution, the resilience and plasticity these microbial communities over temporal and spatial scales, and ultimately their role in the host ecological adaptation. Methods Here we used the endemic Balearic wall lizard Podarcis lilfordi to dissect the drivers of the microbial diversity within and across host allopatric populations/islets. By focusing on three extensively studied populations/islets of Mallorca (Spain) and fecal sampling from individually identified lizards along two years (both in spring and autumn), we sorted out the effect of islet, sex, life stage, year and season on the microbiota composition. We further related microbiota diversity to host genetics, trophic ecology and expected annual metabolic changes. Results All the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (based on microsatellites) and trophic niche distances (based on stable isotopes and fecal content). Within populations, a large proportion of ASVs (30–50%) were recurrently found along the four sampling dates. The microbial diversity was strongly marked by seasonality, with no sex effect and a marginal life stage and annual effect. The microbiota showed seasonal fluctuations along the two sampled years, primarily due to changes in the relative abundances of fermentative bacteria (mostly families Lachnospiraceae and Ruminococcaceae), without any major compositional turnover. Conclusions These results support a large resilience of the major compositional aspects of the P. …
format: application/pdf
format: text/html
creator: Laura Baldo
creator: Giacomo Tavecchia
creator: Andreu Rotger
creator: José Manuel Igual
creator: Joan Lluís Riera
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.14511
publisher: PeerJ Inc.
rights: © 2023 Baldo et al.
abstract: Background Integrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Insular vertebrates provide ideal natural systems to understand patterns of host-gut microbiota coevolution, the resilience and plasticity these microbial communities over temporal and spatial scales, and ultimately their role in the host ecological adaptation. Methods Here we used the endemic Balearic wall lizard Podarcis lilfordi to dissect the drivers of the microbial diversity within and across host allopatric populations/islets. By focusing on three extensively studied populations/islets of Mallorca (Spain) and fecal sampling from individually identified lizards along two years (both in spring and autumn), we sorted out the effect of islet, sex, life stage, year and season on the microbiota composition. We further related microbiota diversity to host genetics, trophic ecology and expected annual metabolic changes. Results All the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (based on microsatellites) and trophic niche distances (based on stable isotopes and fecal content). Within populations, a large proportion of ASVs (30–50%) were recurrently found along the four sampling dates. The microbial diversity was strongly marked by seasonality, with no sex effect and a marginal life stage and annual effect. The microbiota showed seasonal fluctuations along the two sampled years, primarily due to changes in the relative abundances of fermentative bacteria (mostly families Lachnospiraceae and Ruminococcaceae), without any major compositional turnover. Conclusions These results support a large resilience of the major compositional aspects of the P. …
bibliographic citation: Baldo et al. (2023) Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard (Podarcis lilfordi) gut microbiota. PeerJ 11:e14511 https://doi.org/10.7717/peerj.14511
date submitted: 2022-09-16
date accepted: 2022-11-14
issued: 2023-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baldo
  given name: Laura
author list: Agent
  family name: Tavecchia
  given name: Giacomo
author list: Agent
  family name: Rotger
  given name: Andreu
author list: Agent
  family name: Igual
  given name: José Manuel
author list: Agent
  family name: Riera
  given name: Joan Lluís
doi: 10.7717/peerj.14511
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-03
copyright: ©2023 Baldo et al.
attribution name: Baldo et al.

Influences of oxygen and temperature interaction on the antibacterial activity, antioxidant activity, serum biochemical indices, blood indices and growth performance of crucian carp
type: item
type: AcademicArticle
description: The well-being of fish used in aquaculture is of great interest. Oxygen and temperature are the main factors affecting the welfare of the crucian carp (carassius); however, there are few studies on the combined effects of these on the species. Therefore, this study investigated the impact of different temperatures (18 °C, 24 °C, 30 °C) and oxygen concentrations (2.1 mgL−1, 5.4 mgL−1, 9.3 mgL−1) on serum antibacterial activity, antioxidant activity, hematological parameters and growth performance of the crucian carp. The results showed that there were greater antibacterial properties under conditions of hypoxia at 18 °C (L18) and hyperoxia at 24 °C (H24). The activities of catalase, glutathione peroxidase and total superoxide dismutase were the highest at 24 °C under hypoxia and hyperoxia. In addition, the contents of glucose and total protein first increased and then decreased with the change of temperature; triglycerides were the lowest at 30 °C. The blood parameters of the carp were within a normal range at 24 °C; however, the growth rate was at its lowest under hypoxia treatment at 30 °C (L30). This study showed that high temperature impairs the antibacterial ability, antioxidant capacity and growth performance of the crucian carp, and high oxygen levels can alleviate these adverse reactions. This research provides a theoretical basis for subsequent aquaculture studies.
format: application/pdf
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creator: Bin Wang
creator: Hanping Mao
creator: Jian Zhao
creator: Yong Liu
creator: Yafei Wang
creator: Xiaoxue Du
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
description: doi:10.7717/peerj.14530
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: The well-being of fish used in aquaculture is of great interest. Oxygen and temperature are the main factors affecting the welfare of the crucian carp (carassius); however, there are few studies on the combined effects of these on the species. Therefore, this study investigated the impact of different temperatures (18 °C, 24 °C, 30 °C) and oxygen concentrations (2.1 mgL−1, 5.4 mgL−1, 9.3 mgL−1) on serum antibacterial activity, antioxidant activity, hematological parameters and growth performance of the crucian carp. The results showed that there were greater antibacterial properties under conditions of hypoxia at 18 °C (L18) and hyperoxia at 24 °C (H24). The activities of catalase, glutathione peroxidase and total superoxide dismutase were the highest at 24 °C under hypoxia and hyperoxia. In addition, the contents of glucose and total protein first increased and then decreased with the change of temperature; triglycerides were the lowest at 30 °C. The blood parameters of the carp were within a normal range at 24 °C; however, the growth rate was at its lowest under hypoxia treatment at 30 °C (L30). This study showed that high temperature impairs the antibacterial ability, antioxidant capacity and growth performance of the crucian carp, and high oxygen levels can alleviate these adverse reactions. This research provides a theoretical basis for subsequent aquaculture studies.
bibliographic citation: Wang et al. (2023) Influences of oxygen and temperature interaction on the antibacterial activity, antioxidant activity, serum biochemical indices, blood indices and growth performance of crucian carp. PeerJ 11:e14530 https://doi.org/10.7717/peerj.14530
date submitted: 2022-04-21
date accepted: 2022-11-16
issued: 2023-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Bin
author list: Agent
  family name: Mao
  given name: Hanping
author list: Agent
  family name: Zhao
  given name: Jian
author list: Agent
  family name: Liu
  given name: Yong
author list: Agent
  family name: Wang
  given name: Yafei
author list: Agent
  family name: Du
  given name: Xiaoxue
doi: 10.7717/peerj.14530
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-03
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Epigenetic regulation of dental-derived stem cells and their application in pulp and periodontal regeneration
type: item
type: AcademicArticle
description: Dental-derived stem cells have excellent proliferation ability and multi-directional differentiation potential, making them an important research target in tissue engineering. An increasing number of dental-derived stem cells have been discovered recently, including dental pulp stem cells (DPSCs), stem cells from exfoliated deciduous teeth (SHEDs), stem cells from apical papilla (SCAPs), dental follicle precursor cells (DFPCs), and periodontal ligament stem cells (PDLSCs). These stem cells have significant application prospects in tissue regeneration because they are found in an abundance of sources, and they have good biocompatibility and are highly effective. The biological functions of dental-derived stem cells are regulated in many ways. Epigenetic regulation means changing the expression level and function of a gene without changing its sequence. Epigenetic regulation is involved in many biological processes, such as embryonic development, bone homeostasis, and the fate of stem cells. Existing studies have shown that dental-derived stem cells are also regulated by epigenetic modifications. Pulp and periodontal regeneration refers to the practice of replacing damaged pulp and periodontal tissue and restoring the tissue structure and function under normal physiological conditions. This treatment has better therapeutic effects than traditional treatments. This article reviews the recent research on the mechanism of epigenetic regulation of dental-derived stem cells, and the core issues surrounding the practical application and future use of pulp and periodontal regeneration.
format: application/pdf
format: text/html
creator: Yuyang Chen
creator: Xiayi Wang
creator: Zhuoxuan Wu
creator: Shiyu Jia
creator: Mian Wan
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Dentistry
description: doi:10.7717/peerj.14550
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Dental-derived stem cells have excellent proliferation ability and multi-directional differentiation potential, making them an important research target in tissue engineering. An increasing number of dental-derived stem cells have been discovered recently, including dental pulp stem cells (DPSCs), stem cells from exfoliated deciduous teeth (SHEDs), stem cells from apical papilla (SCAPs), dental follicle precursor cells (DFPCs), and periodontal ligament stem cells (PDLSCs). These stem cells have significant application prospects in tissue regeneration because they are found in an abundance of sources, and they have good biocompatibility and are highly effective. The biological functions of dental-derived stem cells are regulated in many ways. Epigenetic regulation means changing the expression level and function of a gene without changing its sequence. Epigenetic regulation is involved in many biological processes, such as embryonic development, bone homeostasis, and the fate of stem cells. Existing studies have shown that dental-derived stem cells are also regulated by epigenetic modifications. Pulp and periodontal regeneration refers to the practice of replacing damaged pulp and periodontal tissue and restoring the tissue structure and function under normal physiological conditions. This treatment has better therapeutic effects than traditional treatments. This article reviews the recent research on the mechanism of epigenetic regulation of dental-derived stem cells, and the core issues surrounding the practical application and future use of pulp and periodontal regeneration.
bibliographic citation: Chen et al. (2023) Epigenetic regulation of dental-derived stem cells and their application in pulp and periodontal regeneration. PeerJ 11:e14550 https://doi.org/10.7717/peerj.14550
date submitted: 2022-07-29
date accepted: 2022-11-20
issued: 2023-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yuyang
author list: Agent
  family name: Wang
  given name: Xiayi
author list: Agent
  family name: Wu
  given name: Zhuoxuan
author list: Agent
  family name: Jia
  given name: Shiyu
author list: Agent
  family name: Wan
  given name: Mian
doi: 10.7717/peerj.14550
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-03
copyright: ©2023 Chen et al.
attribution name: Chen et al.

Agricultural water allocation with climate change based on gray wolf optimization in a semi-arid region of China
type: item
type: AcademicArticle
description: Background We quantified and evaluated the allocation of soil and water resources in the Aksu River Basin to measure the consequences of climate change on an agricultural irrigation system. Methods We first simulated future climate scenarios in the Aksu River Basin by using a statistical downscaling model (SDSM). We then formulated the optimal allocation scheme of agricultural water as a multiobjective optimization problem and obtained the Pareto optimal solution using the multi-objective grey wolf optimizer (MOGWO). Finally, optimal allocations of water and land resources in the basin at different times were obtained using an analytic hierarchy process (AHP). Results (1) The SDSM is able to simulate future climate change scenarios in the Aksu River Basin. Evapotranspiration (ET0) will increase significantly with variation as will the amount of available water albeit slightly. (2) To alleviate water pressure, the area of cropland should be reduced by 127.5 km2 under RCP4.5 and 377.2 km2 under RCP8.5 scenarios. (3) To be sustainable, the allocation ratio of forest land and water body should increase to 39% of the total water resource in the Aksu River Basin by 2050.
format: application/pdf
format: text/html
creator: Zhidong Wang
creator: Xining Zhao
creator: Jinglei Wang
creator: Ni Song
creator: Qisheng Han
subject: Agricultural Science
subject: Climate Change Biology
subject: Natural Resource Management
subject: Ecohydrology
description: doi:10.7717/peerj.14577
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Background We quantified and evaluated the allocation of soil and water resources in the Aksu River Basin to measure the consequences of climate change on an agricultural irrigation system. Methods We first simulated future climate scenarios in the Aksu River Basin by using a statistical downscaling model (SDSM). We then formulated the optimal allocation scheme of agricultural water as a multiobjective optimization problem and obtained the Pareto optimal solution using the multi-objective grey wolf optimizer (MOGWO). Finally, optimal allocations of water and land resources in the basin at different times were obtained using an analytic hierarchy process (AHP). Results (1) The SDSM is able to simulate future climate change scenarios in the Aksu River Basin. Evapotranspiration (ET0) will increase significantly with variation as will the amount of available water albeit slightly. (2) To alleviate water pressure, the area of cropland should be reduced by 127.5 km2 under RCP4.5 and 377.2 km2 under RCP8.5 scenarios. (3) To be sustainable, the allocation ratio of forest land and water body should increase to 39% of the total water resource in the Aksu River Basin by 2050.
bibliographic citation: Wang et al. (2023) Agricultural water allocation with climate change based on gray wolf optimization in a semi-arid region of China. PeerJ 11:e14577 https://doi.org/10.7717/peerj.14577
date submitted: 2022-07-05
date accepted: 2022-11-28
issued: 2023-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhidong
author list: Agent
  family name: Zhao
  given name: Xining
author list: Agent
  family name: Wang
  given name: Jinglei
author list: Agent
  family name: Song
  given name: Ni
author list: Agent
  family name: Han
  given name: Qisheng
doi: 10.7717/peerj.14577
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-03
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Two new temporary ectoparasitic isopods (Cymothoida: Cymothooidea) from Korean waters with a note on geographical distributions of Rocinela Leach, 1818 and Gnathia Leach, 1814
type: item
type: AcademicArticle
description: Two new species of temporary ectoparasitic isopods, Rocinela excavata sp. nov. and Gnathia obtusispina sp. nov., are reported from the southern Islands of the Korean Peninsula. Rocinela excavata sp. nov. is distinguishable from its related species by the following characteristics: (1) laterally stepped rostrum; (2) separated eyes; (3) propodal blade having eight robust setae; and (4) merus having four or five blunt robust setae in pereopods 1–3. Gnathia obtusispina sp. nov. differs from its congeners by the combination of the following characteristics: (1) body covered with numerous tubercles and setae, (2) cephalon having tooth-like paraocular ornamentations; and (3) frontal border having two inferior frontolateral processes. These two new species are the 13th Rocinela species and 19th Gnathia species in the temperate Northern Pacific region, respectively. Discovery of these new species represents high species diversity of the genera Rocinela Leach, 1818 and Gnathia Leach, 1814 worldwide as well as in the Northern Pacific region. In addition, faunal diversity analysis on the members of both genera revealed that Rocinela species show high-latitude diversity whereas Gnathia species have low-latitude diversity.
format: application/pdf
format: text/html
creator: Sung Hoon Kim
creator: Jong Guk Kim
creator: Seong Myeong Yoon
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.14593
publisher: PeerJ Inc.
rights: © 2023 Kim et al.
abstract: Two new species of temporary ectoparasitic isopods, Rocinela excavata sp. nov. and Gnathia obtusispina sp. nov., are reported from the southern Islands of the Korean Peninsula. Rocinela excavata sp. nov. is distinguishable from its related species by the following characteristics: (1) laterally stepped rostrum; (2) separated eyes; (3) propodal blade having eight robust setae; and (4) merus having four or five blunt robust setae in pereopods 1–3. Gnathia obtusispina sp. nov. differs from its congeners by the combination of the following characteristics: (1) body covered with numerous tubercles and setae, (2) cephalon having tooth-like paraocular ornamentations; and (3) frontal border having two inferior frontolateral processes. These two new species are the 13th Rocinela species and 19th Gnathia species in the temperate Northern Pacific region, respectively. Discovery of these new species represents high species diversity of the genera Rocinela Leach, 1818 and Gnathia Leach, 1814 worldwide as well as in the Northern Pacific region. In addition, faunal diversity analysis on the members of both genera revealed that Rocinela species show high-latitude diversity whereas Gnathia species have low-latitude diversity.
bibliographic citation: Kim et al. (2023) Two new temporary ectoparasitic isopods (Cymothoida: Cymothooidea) from Korean waters with a note on geographical distributions of Rocinela Leach, 1818 and Gnathia Leach, 1814. PeerJ 11:e14593 https://doi.org/10.7717/peerj.14593
date submitted: 2022-08-29
date accepted: 2022-11-28
issued: 2023-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Sung Hoon
author list: Agent
  family name: Kim
  given name: Jong Guk
author list: Agent
  family name: Yoon
  given name: Seong Myeong
doi: 10.7717/peerj.14593
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-03
copyright: © 2023 Kim et al.
attribution name: Kim et al.

Integrative genomic and transcriptomic analyses of a bud sport mutant ‘Jinzao Wuhe’ with the phenotype of large berries in grapevines
type: item
type: AcademicArticle
description: Background Bud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. ‘Jinzao Wuhe’ is a bud sport of the elite cultivar ‘Himord Seedless’ with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear. Methods Whole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for ‘Jinzao Wuhe’ and its maternal plant ‘Himord Seedless’ were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation. Results In two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between ‘Himord Seedless’ and ‘Jinzao Wuhe’ harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine. Conclusion Our results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars.
format: application/pdf
format: text/html
creator: Jianquan Huang
creator: Guan Zhang
creator: Yanhao Li
creator: Mingjie Lyu
creator: He Zhang
creator: Na Zhang
creator: Rui Chen
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.14617
publisher: PeerJ Inc.
rights: © 2023 Huang et al.
abstract: Background Bud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. ‘Jinzao Wuhe’ is a bud sport of the elite cultivar ‘Himord Seedless’ with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear. Methods Whole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for ‘Jinzao Wuhe’ and its maternal plant ‘Himord Seedless’ were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation. Results In two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between ‘Himord Seedless’ and ‘Jinzao Wuhe’ harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine. Conclusion Our results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars.
bibliographic citation: Huang et al. (2023) Integrative genomic and transcriptomic analyses of a bud sport mutant ‘Jinzao Wuhe’ with the phenotype of large berries in grapevines. PeerJ 11:e14617 https://doi.org/10.7717/peerj.14617
date submitted: 2022-06-20
date accepted: 2022-12-01
issued: 2023-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Jianquan
author list: Agent
  family name: Zhang
  given name: Guan
author list: Agent
  family name: Li
  given name: Yanhao
author list: Agent
  family name: Lyu
  given name: Mingjie
author list: Agent
  family name: Zhang
  given name: He
author list: Agent
  family name: Zhang
  given name: Na
author list: Agent
  family name: Chen
  given name: Rui
doi: 10.7717/peerj.14617
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-03
copyright: © 2023 Huang et al.
attribution name: Huang et al.

Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes
type: item
type: AcademicArticle
description: Background Endogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes: gag, pol, and env, each of which encodes viral proteins that can be conserved or not. ERVs have been observed in a wide range of vertebrate genomes and their functions are associated with viral silencing and gene regulation. Results In this work, we studied the evolutionary history of endogenous retroviruses associated with five human genes (INPP5B, DET1, PSMA1, USH2A, and MACROD2), which are located within intron sections. To verify the retroviral origin of the candidates, several approaches were used to detect and locate ERV elements. Both orthologous and paralogous genes were identified by Ensembl and then analyzed for ERV presence using RetroTector. A phylogenetic tree was reconstructed to identify the minimum time point of ERV acquisition. From that search, we detected ERVs throughout the primate lineage and in some other groups. Also, we identified the minimum origin of the ERVs from the parvorder Catarrhini to the Homininae subfamily. Conclusions With the data collected, and by observing the transcription factors annotated inside ERVs, we propose that these elements play a relevant role in gene expression regulation and they probably possess important features for tumorigenesis control.
format: application/pdf
format: text/html
creator: Melissa Calero-Layana
creator: Carmen López-Cruz
creator: Agustín Ocaña
creator: Eduardo Tejera
creator: Vinicio Armijos-Jaramillo
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Virology
description: doi:10.7717/peerj.14431
publisher: PeerJ Inc.
rights: © 2022 Calero-Layana et al.
abstract: Background Endogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes: gag, pol, and env, each of which encodes viral proteins that can be conserved or not. ERVs have been observed in a wide range of vertebrate genomes and their functions are associated with viral silencing and gene regulation. Results In this work, we studied the evolutionary history of endogenous retroviruses associated with five human genes (INPP5B, DET1, PSMA1, USH2A, and MACROD2), which are located within intron sections. To verify the retroviral origin of the candidates, several approaches were used to detect and locate ERV elements. Both orthologous and paralogous genes were identified by Ensembl and then analyzed for ERV presence using RetroTector. A phylogenetic tree was reconstructed to identify the minimum time point of ERV acquisition. From that search, we detected ERVs throughout the primate lineage and in some other groups. Also, we identified the minimum origin of the ERVs from the parvorder Catarrhini to the Homininae subfamily. Conclusions With the data collected, and by observing the transcription factors annotated inside ERVs, we propose that these elements play a relevant role in gene expression regulation and they probably possess important features for tumorigenesis control.
bibliographic citation: Calero-Layana et al. (2022) Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes. PeerJ 10:e14431 https://doi.org/10.7717/peerj.14431
date submitted: 2022-08-22
date accepted: 2022-10-31
issued: 2022-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Calero-Layana
  given name: Melissa
author list: Agent
  family name: López-Cruz
  given name: Carmen
author list: Agent
  family name: Ocaña
  given name: Agustín
author list: Agent
  family name: Tejera
  given name: Eduardo
author list: Agent
  family name: Armijos-Jaramillo
  given name: Vinicio
doi: 10.7717/peerj.14431
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-22
copyright: ©2022 Calero-Layana et al.
attribution name: Calero-Layana et al.

Left ventricle dysfunction in patients with critical neonatal pulmonary stenosis: echocardiographic predictors. A single-center retrospective study
type: item
type: AcademicArticle
description: Background The aim of this study is to identify echocardiographic predictors of transient left ventricle dysfunction after pulmonary valve balloon dilatation (PVBD), in neonates with pulmonary valve stenosis (PVS) and atresia with intact septum (PAIVS) at birth. Methods The study includes patients admitted at the Bambino Gesù Children Hospital from January 2012 to January 2017. Clinical, echocardiographic and cardiac catheterization data before and after PVBD were retrospectively analyzed. Results Twenty-nine infants were included in the study (21 male and eight female). The median age was 5.8 ± 7.1 days. Eight patients developed transient LV dysfunction (three PAIVS and five PVS) and comparing data before and after the procedure, there was no difference in right ventricle geometrical and functional parameters except for evidence of at least moderate pulmonary valve regurgitation after PVBD. Conclusion Moderate to severe degree pulmonary valve regurgitation was significant associated to LV dysfunction (p < 0.05) in PVS and PAIVS patients.
format: application/pdf
format: text/html
creator: Carolina D’Anna
creator: Alessio Franceschini
creator: Micol Rebonato
creator: Paolo Ciliberti
creator: Claudia Esposito
creator: Roberto Formigari
creator: Maria Giulia Gagliardi
creator: Paolo Guccione
creator: Gianfranco Butera
creator: Lorenzo Galletti
creator: Marcello Chinali
subject: Cardiology
subject: Pediatrics
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.14056
publisher: PeerJ Inc.
rights: © 2022 D’Anna et al.
abstract: Background The aim of this study is to identify echocardiographic predictors of transient left ventricle dysfunction after pulmonary valve balloon dilatation (PVBD), in neonates with pulmonary valve stenosis (PVS) and atresia with intact septum (PAIVS) at birth. Methods The study includes patients admitted at the Bambino Gesù Children Hospital from January 2012 to January 2017. Clinical, echocardiographic and cardiac catheterization data before and after PVBD were retrospectively analyzed. Results Twenty-nine infants were included in the study (21 male and eight female). The median age was 5.8 ± 7.1 days. Eight patients developed transient LV dysfunction (three PAIVS and five PVS) and comparing data before and after the procedure, there was no difference in right ventricle geometrical and functional parameters except for evidence of at least moderate pulmonary valve regurgitation after PVBD. Conclusion Moderate to severe degree pulmonary valve regurgitation was significant associated to LV dysfunction (p < 0.05) in PVS and PAIVS patients.
bibliographic citation: D’Anna et al. (2022) Left ventricle dysfunction in patients with critical neonatal pulmonary stenosis: echocardiographic predictors. A single-center retrospective study. PeerJ 10:e14056 https://doi.org/10.7717/peerj.14056
date submitted: 2021-03-10
date accepted: 2022-08-24
issued: 2022-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: D’Anna
  given name: Carolina
author list: Agent
  family name: Franceschini
  given name: Alessio
author list: Agent
  family name: Rebonato
  given name: Micol
author list: Agent
  family name: Ciliberti
  given name: Paolo
author list: Agent
  family name: Esposito
  given name: Claudia
author list: Agent
  family name: Formigari
  given name: Roberto
author list: Agent
  family name: Gagliardi
  given name: Maria Giulia
author list: Agent
  family name: Guccione
  given name: Paolo
author list: Agent
  family name: Butera
  given name: Gianfranco
author list: Agent
  family name: Galletti
  given name: Lorenzo
author list: Agent
  family name: Chinali
  given name: Marcello
doi: 10.7717/peerj.14056
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-21
copyright: © 2022 D’Anna et al.
attribution name: D’Anna et al.

Modeling the response of Japanese quail to arginine intake
type: item
type: AcademicArticle
description: Background Understanding how Japanese quails respond to arginine intake has been an objective that previous studies have not fulfilled. The main responses to be quantified include the arginine requirement for maintenance (mg/kg0.67) and egg mass production (mg/g). Quantifying maintenance and production relationships are essential steps for predicting animal response. The current study aimed to describe how quails respond to arginine intake and determine arginine requirements for maintenance and egg production in Japanese quails. Methods The experiment was carried out in a completely randomized design, with seven treatments and seven replicates with individual birds as experimental units. The arginine levels were: 2.43, 3.64, 4.85, 6.07, 9.07, 12.13, and 14.56 g/kg. The experiment lasted for eight weeks. The variables analyzed were daily arginine intake, daily arginine deposition in eggs, and body weight. The data were analyzed using a mixed model, with the experimental unit being the random effect and the experimental levels of arginine as a fixed effect. When the effect of arginine levels was detected (P ≤ 0.05), saturation kinetics and an exponential model with four parameters (monomolecular) were adopted. ANOVA results indicated that dietary arginine levels significantly affected (P < 0.01) the analyzed variables. The formulation strategy of the experimental diets allowed amplitude in the dietary arginine levels, and according to bird responses, arginine was the limiting nutrient. Results The arginine requirement for body weight maintenance (BW0.67) was estimated to be 90 mg/kg BW0.67 by the monomolecular function. The requirement for egg mass (EM) production was estimated to be 25 mg/g per egg. A factorial model was parameterized as follows: daily arginine intake mg/bird = 90 × BW0.67 + 25 × EM ± 12 mg. The model was applied to data obtained from literature, and the resultant error was within the expected limit of 12 mg. The recommended daily arginine intake for…
format: application/pdf
format: text/html
creator: Manoela Sousa
creator: Michele Lima
creator: Rita Brito Vieira
creator: Jaqueline Pavanini
creator: Nelson José Peruzzi
creator: Erikson Raimundo
creator: Daniel Santos
creator: Edney Silva
subject: Agricultural Science
subject: Zoology
description: doi:10.7717/peerj.14337
publisher: PeerJ Inc.
rights: © 2022 Sousa et al.
abstract: Background Understanding how Japanese quails respond to arginine intake has been an objective that previous studies have not fulfilled. The main responses to be quantified include the arginine requirement for maintenance (mg/kg0.67) and egg mass production (mg/g). Quantifying maintenance and production relationships are essential steps for predicting animal response. The current study aimed to describe how quails respond to arginine intake and determine arginine requirements for maintenance and egg production in Japanese quails. Methods The experiment was carried out in a completely randomized design, with seven treatments and seven replicates with individual birds as experimental units. The arginine levels were: 2.43, 3.64, 4.85, 6.07, 9.07, 12.13, and 14.56 g/kg. The experiment lasted for eight weeks. The variables analyzed were daily arginine intake, daily arginine deposition in eggs, and body weight. The data were analyzed using a mixed model, with the experimental unit being the random effect and the experimental levels of arginine as a fixed effect. When the effect of arginine levels was detected (P ≤ 0.05), saturation kinetics and an exponential model with four parameters (monomolecular) were adopted. ANOVA results indicated that dietary arginine levels significantly affected (P < 0.01) the analyzed variables. The formulation strategy of the experimental diets allowed amplitude in the dietary arginine levels, and according to bird responses, arginine was the limiting nutrient. Results The arginine requirement for body weight maintenance (BW0.67) was estimated to be 90 mg/kg BW0.67 by the monomolecular function. The requirement for egg mass (EM) production was estimated to be 25 mg/g per egg. A factorial model was parameterized as follows: daily arginine intake mg/bird = 90 × BW0.67 + 25 × EM ± 12 mg. The model was applied to data obtained from literature, and the resultant error was within the expected limit of 12 mg. The recommended daily arginine intake for…
bibliographic citation: Sousa et al. (2022) Modeling the response of Japanese quail to arginine intake. PeerJ 10:e14337 https://doi.org/10.7717/peerj.14337
date submitted: 2022-06-23
date accepted: 2022-10-13
issued: 2022-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sousa
  given name: Manoela
author list: Agent
  family name: Lima
  given name: Michele
author list: Agent
  family name: Vieira
  given name: Rita Brito
author list: Agent
  family name: Pavanini
  given name: Jaqueline
author list: Agent
  family name: Peruzzi
  given name: Nelson José
author list: Agent
  family name: Raimundo
  given name: Erikson
author list: Agent
  family name: Santos
  given name: Daniel
author list: Agent
  family name: Silva
  given name: Edney
doi: 10.7717/peerj.14337
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-21
copyright: ©2022 Sousa et al.
attribution name: Sousa et al.

A new Meckel’s cartilage from the Devonian Hangenberg black shale in Morocco and its position in chondrichthyan jaw morphospace
type: item
type: AcademicArticle
description: Fossil chondrichthyan remains are mostly known from their teeth, scales or fin spines only, whereas their cartilaginous endoskeletons require exceptional preservational conditions to become fossilized. While most cartilaginous remains of Famennian (Late Devonian) chondrichthyans were found in older layers of the eastern Anti-Atlas, such fossils were unknown from the Hangenberg black shale (HBS) and only a few chondrichthyan teeth had been found therein previously. Here, we describe a Meckel’s cartilage from the Hangenberg black shale in Morocco, which is the first fossil cartilage from these strata. Since no teeth or other skeletal elements have been found in articulation, we used elliptical Fourier (EFA), principal component (PCA), and hierarchical cluster (HCA) analyses to morphologically compare it with 41 chondrichthyan taxa of different size and age and to evaluate its possible systematic affiliation. PCA and HCA position the new specimen closest to some acanthodian and elasmobranch jaws. Accordingly, a holocephalan origin was excluded. The jaw shape as well as the presence of a polygonal pattern, typical for tessellated calcified cartilage, suggest a ctenacanth origin and we assigned the new HBS Meckel’s cartilage to the order Ctenacanthiformes with reservations.
format: application/pdf
format: text/html
creator: Merle Greif
creator: Humberto G. Ferrón
creator: Christian Klug
subject: Evolutionary Studies
subject: Paleontology
subject: Histology
description: doi:10.7717/peerj.14418
publisher: PeerJ Inc.
rights: © 2022 Greif et al.
abstract: Fossil chondrichthyan remains are mostly known from their teeth, scales or fin spines only, whereas their cartilaginous endoskeletons require exceptional preservational conditions to become fossilized. While most cartilaginous remains of Famennian (Late Devonian) chondrichthyans were found in older layers of the eastern Anti-Atlas, such fossils were unknown from the Hangenberg black shale (HBS) and only a few chondrichthyan teeth had been found therein previously. Here, we describe a Meckel’s cartilage from the Hangenberg black shale in Morocco, which is the first fossil cartilage from these strata. Since no teeth or other skeletal elements have been found in articulation, we used elliptical Fourier (EFA), principal component (PCA), and hierarchical cluster (HCA) analyses to morphologically compare it with 41 chondrichthyan taxa of different size and age and to evaluate its possible systematic affiliation. PCA and HCA position the new specimen closest to some acanthodian and elasmobranch jaws. Accordingly, a holocephalan origin was excluded. The jaw shape as well as the presence of a polygonal pattern, typical for tessellated calcified cartilage, suggest a ctenacanth origin and we assigned the new HBS Meckel’s cartilage to the order Ctenacanthiformes with reservations.
bibliographic citation: Greif et al. (2022) A new Meckel’s cartilage from the Devonian Hangenberg black shale in Morocco and its position in chondrichthyan jaw morphospace. PeerJ 10:e14418 https://doi.org/10.7717/peerj.14418
date submitted: 2022-08-09
date accepted: 2022-10-28
issued: 2022-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Greif
  given name: Merle
author list: Agent
  family name: Ferrón
  given name: Humberto G.
author list: Agent
  family name: Klug
  given name: Christian
doi: 10.7717/peerj.14418
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-21
copyright: ©2022 Greif et al.
attribution name: Greif et al.

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