PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The role of acute stress recovery in emotional resilience
items: Metabolites profiling of Sapota fruit pulp via a multiplex approach of gas and ultra performance liquid chromatography/mass spectroscopy in relation to its lipase inhibition effect
items: The sicariid spiders in the state of Bahia, Brazil (Arachnida: Araneae)
items: The role of NF-kappaB in the inflammatory processes related to dental caries, pulpitis, apical periodontitis, and periodontitis–a narrative review
items: Phenotyping 172 strawberry genotypes for water soaking reveals a close relationship with skin water permeance
items: Comparisons of genome assembly tools for characterization of Mycobacterium tuberculosis genomes using hybrid sequencing technologies
items: A short stature allele enhances tolerance to zinc deficiency and translocation of zinc in barley
items: Genome-wide identification and characterization of the sucrose invertase gene family in Hemerocallis citrina
items: Marine catfishes (Ariidae—Siluriformes) from the Coastal Amazon: mitochondrial DNA barcode for a recent diversification group?
items: Levels of biomarkers associated with subconcussive head hits in mixed martial arts fighters

The role of acute stress recovery in emotional resilience
type: item
type: AcademicArticle
description: Background Resilience refers to the process of demonstrating better outcomes than would be expected based on the adversity one experienced. Resilience is increasingly measured using a residual approach, which typically assesses adversity and mental health outcomes over a longitudinal timeframe. It remains unknown to what extent such a residual-based measurement of resilience is sensitive to variation in acute stress resilience, a candidate resilience factor. Methods Fifty-seven emerging adults enrolled in tertiary education completed measures of adversity and emotional experiences. To assess stress recovery, participants were exposed to a lab-based adverse event from which a Laboratory Stress Resilience Index was derived. Results We derived a residual-based measure of emotional resilience from regressing emotional experience scores onto adversity scores. This residual-based measure of emotional resilience predicted variance in the Laboratory Stress Resilience Index over and above that predicted by both a traditional resilience measure and the emotional experiences measure. These findings suggest that acute stress resilience may be a factor underpinning variation in emotional resilience, and that the residual-based approach to measuring resilience is sensitive to such variation in stress resilience.
format: application/pdf
format: text/html
creator: Lies Notebaert
creator: Roger Harris
creator: Colin MacLeod
creator: Monique Crane
creator: Romola S. Bucks
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.17911
publisher: PeerJ Inc.
rights: © 2024 Notebaert et al.
abstract: Background Resilience refers to the process of demonstrating better outcomes than would be expected based on the adversity one experienced. Resilience is increasingly measured using a residual approach, which typically assesses adversity and mental health outcomes over a longitudinal timeframe. It remains unknown to what extent such a residual-based measurement of resilience is sensitive to variation in acute stress resilience, a candidate resilience factor. Methods Fifty-seven emerging adults enrolled in tertiary education completed measures of adversity and emotional experiences. To assess stress recovery, participants were exposed to a lab-based adverse event from which a Laboratory Stress Resilience Index was derived. Results We derived a residual-based measure of emotional resilience from regressing emotional experience scores onto adversity scores. This residual-based measure of emotional resilience predicted variance in the Laboratory Stress Resilience Index over and above that predicted by both a traditional resilience measure and the emotional experiences measure. These findings suggest that acute stress resilience may be a factor underpinning variation in emotional resilience, and that the residual-based approach to measuring resilience is sensitive to such variation in stress resilience.
bibliographic citation: Notebaert et al. (2024) The role of acute stress recovery in emotional resilience. PeerJ 12:e17911 https://doi.org/10.7717/peerj.17911
date submitted: 2023-09-22
date accepted: 2024-07-23
issued: 2024-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Notebaert
  given name: Lies
author list: Agent
  family name: Harris
  given name: Roger
author list: Agent
  family name: MacLeod
  given name: Colin
author list: Agent
  family name: Crane
  given name: Monique
author list: Agent
  family name: Bucks
  given name: Romola S.
doi: 10.7717/peerj.17911
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-29
copyright: © 2024 Notebaert et al.
attribution name: Notebaert et al.

Metabolites profiling of Sapota fruit pulp via a multiplex approach of gas and ultra performance liquid chromatography/mass spectroscopy in relation to its lipase inhibition effect
type: item
type: AcademicArticle
description: Background Sapota, Manilkara zapota L., are tasty, juicy, and nutrient-rich fruits, and likewise used for several medicinal uses. Methods The current study represents an integrated metabolites profiling of sapota fruits pulp via GC/MS and UPLC/MS, alongside assessment of antioxidant capacity, pancreatic lipase (PL), and α-glucosidase enzymes inhibitory effects. Results GC/MS analysis of silylated primary polar metabolites led to the identification of 68 compounds belonging to sugars (74%), sugar acids (18.27%), and sugar alcohols (7%) mediating the fruit sweetness. Headspace SPME-GC/MS analysis led to the detection of 17 volatile compounds belonging to nitrogenous compounds (72%), ethers (7.8%), terpenes (7.6%), and aldehydes (5.8%). Non-polar metabolites profiling by HR-UPLC/MS/MS-based Global Natural Products Social (GNPS) molecular networking led to the assignment of 31 peaks, with several novel sphingolipids and fatty acyl amides reported for the first time. Total phenolic content was estimated at 6.79 ± 0.12 mg gallic acid equivalent/gram extract (GAE/g extract), but no flavonoids were detected. The antioxidant capacities of fruit were at 1.62 ± 0.2, 1.49 ± 0.11, and 3.58 ± 0.14 mg Trolox equivalent/gram extract (TE/g extract) via DPPH, ABTS, and FRAP assays, respectively. In vitro enzyme inhibition assays revealed a considerable pancreatic lipase inhibition effect (IC50 = 2.2 ± 0.25 mg/mL), whereas no inhibitory effect towards α-glucosidase enzyme was detected. This study provides better insight into sapota fruit’s flavor, nutritional, and secondary metabolites composition mediating for its sensory and health attributes.
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creator: Mohamed A. Farag
creator: Nermin Ahmed Ragab
creator: Maii Abdelnaby Ismail Maamoun
subject: Biochemistry
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.17914
publisher: PeerJ Inc.
rights: © 2024 Farag et al.
abstract: Background Sapota, Manilkara zapota L., are tasty, juicy, and nutrient-rich fruits, and likewise used for several medicinal uses. Methods The current study represents an integrated metabolites profiling of sapota fruits pulp via GC/MS and UPLC/MS, alongside assessment of antioxidant capacity, pancreatic lipase (PL), and α-glucosidase enzymes inhibitory effects. Results GC/MS analysis of silylated primary polar metabolites led to the identification of 68 compounds belonging to sugars (74%), sugar acids (18.27%), and sugar alcohols (7%) mediating the fruit sweetness. Headspace SPME-GC/MS analysis led to the detection of 17 volatile compounds belonging to nitrogenous compounds (72%), ethers (7.8%), terpenes (7.6%), and aldehydes (5.8%). Non-polar metabolites profiling by HR-UPLC/MS/MS-based Global Natural Products Social (GNPS) molecular networking led to the assignment of 31 peaks, with several novel sphingolipids and fatty acyl amides reported for the first time. Total phenolic content was estimated at 6.79 ± 0.12 mg gallic acid equivalent/gram extract (GAE/g extract), but no flavonoids were detected. The antioxidant capacities of fruit were at 1.62 ± 0.2, 1.49 ± 0.11, and 3.58 ± 0.14 mg Trolox equivalent/gram extract (TE/g extract) via DPPH, ABTS, and FRAP assays, respectively. In vitro enzyme inhibition assays revealed a considerable pancreatic lipase inhibition effect (IC50 = 2.2 ± 0.25 mg/mL), whereas no inhibitory effect towards α-glucosidase enzyme was detected. This study provides better insight into sapota fruit’s flavor, nutritional, and secondary metabolites composition mediating for its sensory and health attributes.
bibliographic citation: Farag et al. (2024) Metabolites profiling of Sapota fruit pulp via a multiplex approach of gas and ultra performance liquid chromatography/mass spectroscopy in relation to its lipase inhibition effect. PeerJ 12:e17914 https://doi.org/10.7717/peerj.17914
date submitted: 2024-04-12
date accepted: 2024-07-23
issued: 2024-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Farag
  given name: Mohamed A.
author list: Agent
  family name: Ragab
  given name: Nermin Ahmed
author list: Agent
  family name: Maamoun
  given name: Maii Abdelnaby Ismail
doi: 10.7717/peerj.17914
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-29
copyright: ©2024 Farag et al.
attribution name: Farag et al.

The sicariid spiders in the state of Bahia, Brazil (Arachnida: Araneae)
type: item
type: AcademicArticle
description: Background Sicariidae is a small family of cryptic and recluse spiders, with 178 species grouped into three genera: Hexophtalma, Loxosceles and Sicarius. Only the last two occur in Brazil, where 29 species are recorded, with a greater number of records in the Southeast and South regions. To date, there is no regionalized study of the distribution of these spiders in the Northeast of Brazil. We presented more than four decades of data on the distribution of sicariid spiders in the state of Bahia. Our research aimed to identify and evaluate the distribution of sicariid species in this region, characterizing them in their biomes and phytophysiognomies. Methods Data covers a period from 1983 to 2024, obtained from articles describing species recorded in Bahia and from three scientific collections from Brazilian institutions: Universidade Federal da Bahia (MHNBA); Instituto Butantan (IBSP); Universidade Federal de Minas Gerais (UFMG). Maps were produced using the QGIS 3.34.1 software, based on geographic coordinates obtained from the original literature, when provided. Species without information on geographic coordinates were georeferenced using the SpeciesLink (geoLoc tool) for the municipalities. Biomes were consulted on the georeference Brazilian institute website and the phytophysiognomies were ignored when not specified in the data of collections or original literature. Results We confirmed 14 species of sicariid spiders in the state of Bahia, eight from the genus Loxosceles (i) and six from Sicarius. The species were recorded in 48 municipalities, located mainly in the Caatinga biome. We recorded a distribution expansion of seven species: Loxosceles amazonica, L. chapadensis, L. karstica, L. similis, Sicarius cariri, S. ornatus and S. tropicus. There is a difference in species composition in the two regions separated by the São Francisco River, an important geographic barrier especially for small invertebrates. More than 75% of the species were registered in the e…
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format: text/html
creator: Júlia Andrade-de-Sá
creator: Tania Kobler Brazil
creator: Rejâne Maria Lira-da-Silva
creator: Antonio Domingos Brescovit
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.17942
publisher: PeerJ Inc.
rights: © 2024 Andrade-de-Sá et al.
abstract: Background Sicariidae is a small family of cryptic and recluse spiders, with 178 species grouped into three genera: Hexophtalma, Loxosceles and Sicarius. Only the last two occur in Brazil, where 29 species are recorded, with a greater number of records in the Southeast and South regions. To date, there is no regionalized study of the distribution of these spiders in the Northeast of Brazil. We presented more than four decades of data on the distribution of sicariid spiders in the state of Bahia. Our research aimed to identify and evaluate the distribution of sicariid species in this region, characterizing them in their biomes and phytophysiognomies. Methods Data covers a period from 1983 to 2024, obtained from articles describing species recorded in Bahia and from three scientific collections from Brazilian institutions: Universidade Federal da Bahia (MHNBA); Instituto Butantan (IBSP); Universidade Federal de Minas Gerais (UFMG). Maps were produced using the QGIS 3.34.1 software, based on geographic coordinates obtained from the original literature, when provided. Species without information on geographic coordinates were georeferenced using the SpeciesLink (geoLoc tool) for the municipalities. Biomes were consulted on the georeference Brazilian institute website and the phytophysiognomies were ignored when not specified in the data of collections or original literature. Results We confirmed 14 species of sicariid spiders in the state of Bahia, eight from the genus Loxosceles (i) and six from Sicarius. The species were recorded in 48 municipalities, located mainly in the Caatinga biome. We recorded a distribution expansion of seven species: Loxosceles amazonica, L. chapadensis, L. karstica, L. similis, Sicarius cariri, S. ornatus and S. tropicus. There is a difference in species composition in the two regions separated by the São Francisco River, an important geographic barrier especially for small invertebrates. More than 75% of the species were registered in the e…
bibliographic citation: Andrade-de-Sá et al. (2024) The sicariid spiders in the state of Bahia, Brazil (Arachnida: Araneae). PeerJ 12:e17942 https://doi.org/10.7717/peerj.17942
date submitted: 2024-03-15
date accepted: 2024-07-29
issued: 2024-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Andrade-de-Sá
  given name: Júlia
author list: Agent
  family name: Brazil
  given name: Tania Kobler
author list: Agent
  family name: Lira-da-Silva
  given name: Rejâne Maria
author list: Agent
  family name: Brescovit
  given name: Antonio Domingos
doi: 10.7717/peerj.17942
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-29
copyright: ©2024 Andrade-de-Sá et al.
attribution name: Andrade-de-Sá et al.

The role of NF-kappaB in the inflammatory processes related to dental caries, pulpitis, apical periodontitis, and periodontitis–a narrative review
type: item
type: AcademicArticle
description: Tooth-related inflammatory disorders, including caries, pulpitis, apical periodontitis (AP), and periodontitis (PD), are primarily caused by resident oral microorganisms. Although these dental inflammatory conditions are typically not life-threatening, neglecting them can result in significant complications and greatly reduce an individual’s quality of life. Nuclear factor κB (NF-κB), a family formed by various combinations of Rel proteins, is extensively involved in inflammatory diseases and even cancer. This study reviews recent data on NF-κB signaling and its role in dental pulp stem cells (DPSCs), dental pulp fibroblasts (DPFs), odontoblasts, human periodontal ligament cells (hPDLCs), and various experimental animal models. The findings indicate that NF-κB signaling is abnormally activated in caries, pulpitis, AP, and PD, leading to changes in related cellular differentiation. Under specific conditions, NF-κB signaling occasionally interacts with other signaling pathways, affecting inflammation, bone metabolism, and tissue regeneration processes. In summary, data collected over recent years confirm the central role of NF-κB in dental inflammatory diseases, potentially providing new insights for drug development targeting NF-κB signaling pathways in the treatment of these conditions. Keywords: NF-κB, dental caries, pulpitis, apical periodontitis, periodontitis.
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creator: Zhonglan Chen
creator: Guangping Lang
creator: Xi Xu
creator: Xinghua Liang
creator: Yalin Han
creator: Yingying Han
subject: Cell Biology
subject: Dentistry
description: doi:10.7717/peerj.17953
publisher: PeerJ Inc.
rights: © 2024 Chen et al.
abstract: Tooth-related inflammatory disorders, including caries, pulpitis, apical periodontitis (AP), and periodontitis (PD), are primarily caused by resident oral microorganisms. Although these dental inflammatory conditions are typically not life-threatening, neglecting them can result in significant complications and greatly reduce an individual’s quality of life. Nuclear factor κB (NF-κB), a family formed by various combinations of Rel proteins, is extensively involved in inflammatory diseases and even cancer. This study reviews recent data on NF-κB signaling and its role in dental pulp stem cells (DPSCs), dental pulp fibroblasts (DPFs), odontoblasts, human periodontal ligament cells (hPDLCs), and various experimental animal models. The findings indicate that NF-κB signaling is abnormally activated in caries, pulpitis, AP, and PD, leading to changes in related cellular differentiation. Under specific conditions, NF-κB signaling occasionally interacts with other signaling pathways, affecting inflammation, bone metabolism, and tissue regeneration processes. In summary, data collected over recent years confirm the central role of NF-κB in dental inflammatory diseases, potentially providing new insights for drug development targeting NF-κB signaling pathways in the treatment of these conditions. Keywords: NF-κB, dental caries, pulpitis, apical periodontitis, periodontitis.
bibliographic citation: Chen et al. (2024) The role of NF-kappaB in the inflammatory processes related to dental caries, pulpitis, apical periodontitis, and periodontitis–a narrative review. PeerJ 12:e17953 https://doi.org/10.7717/peerj.17953
date submitted: 2024-04-16
date accepted: 2024-07-31
issued: 2024-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Chen
  given name: Zhonglan
author list: Agent
  family name: Lang
  given name: Guangping
author list: Agent
  family name: Xu
  given name: Xi
author list: Agent
  family name: Liang
  given name: Xinghua
author list: Agent
  family name: Han
  given name: Yalin
author list: Agent
  family name: Han
  given name: Yingying
doi: 10.7717/peerj.17953
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-29
copyright: © 2024 Chen et al.
attribution name: Chen et al.

Phenotyping 172 strawberry genotypes for water soaking reveals a close relationship with skin water permeance
type: item
type: AcademicArticle
description: Water soaking is a commercially important disorder of field-grown strawberries that is exacerbated by surface wetness and high humidity. The objective was to establish the effect of genotype on susceptibility to water soaking. Three greenhouse-grown model ‘collections’ were used comprising a total of 172 different genotypes: (1) a segregating F2 population, (2) a collection of strawberry cultivars and breeding clones, and (3) a collection of wild Fragaria species. A standardized immersion assay was used to induce water soaking. Potential relationships between water soaking and water uptake characteristics, depth of the achene depressions, fruit firmness, cuticle mass and strain relaxation and microcracking were investigated. Further, the effect of downregulating the polygalacturonase genes (FaPG1 and FaPG2) on the susceptibility to water soaking was investigated. The collection of wild species was most susceptible to water soaking. This was followed by the collection of cultivars and breeding clones, and by the F2 population. Susceptibility to water soaking was strongly correlated with water uptake rate (mass of water, per fruit, per time). For the pooled dataset of 172 genotypes, 46% of the variability in water soaking was accounted for by the permeance of the skin to osmotic water uptake. Susceptibility to water soaking was not, or was only poorly correlated with measurements of fruit surface area or of the osmotic potential of the expressed fruit juice. The only exceptions were the wild Fragaria species which were highly variable in fruit size and also in fruit osmotic potential. For genotypes from the F2 and the wild species collections, firmer fruit were less susceptible to water soaking than softer fruit. There were no relationships between fruit firmness and susceptibility to water soaking in transgenic plants in which FaPG1 and FaPG2 were down-regulated. Susceptibility to water soaking was not related to cuticle mass per unit fruit surface area, nor to strai…
format: application/pdf
format: text/html
creator: Grecia Hurtado
creator: Klaus Olbricht
creator: Jose A. Mercado
creator: Sara Pose
creator: Moritz Knoche
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.17960
publisher: PeerJ Inc.
rights: © 2024 Hurtado et al.
abstract: Water soaking is a commercially important disorder of field-grown strawberries that is exacerbated by surface wetness and high humidity. The objective was to establish the effect of genotype on susceptibility to water soaking. Three greenhouse-grown model ‘collections’ were used comprising a total of 172 different genotypes: (1) a segregating F2 population, (2) a collection of strawberry cultivars and breeding clones, and (3) a collection of wild Fragaria species. A standardized immersion assay was used to induce water soaking. Potential relationships between water soaking and water uptake characteristics, depth of the achene depressions, fruit firmness, cuticle mass and strain relaxation and microcracking were investigated. Further, the effect of downregulating the polygalacturonase genes (FaPG1 and FaPG2) on the susceptibility to water soaking was investigated. The collection of wild species was most susceptible to water soaking. This was followed by the collection of cultivars and breeding clones, and by the F2 population. Susceptibility to water soaking was strongly correlated with water uptake rate (mass of water, per fruit, per time). For the pooled dataset of 172 genotypes, 46% of the variability in water soaking was accounted for by the permeance of the skin to osmotic water uptake. Susceptibility to water soaking was not, or was only poorly correlated with measurements of fruit surface area or of the osmotic potential of the expressed fruit juice. The only exceptions were the wild Fragaria species which were highly variable in fruit size and also in fruit osmotic potential. For genotypes from the F2 and the wild species collections, firmer fruit were less susceptible to water soaking than softer fruit. There were no relationships between fruit firmness and susceptibility to water soaking in transgenic plants in which FaPG1 and FaPG2 were down-regulated. Susceptibility to water soaking was not related to cuticle mass per unit fruit surface area, nor to strai…
bibliographic citation: Hurtado et al. (2024) Phenotyping 172 strawberry genotypes for water soaking reveals a close relationship with skin water permeance. PeerJ 12:e17960 https://doi.org/10.7717/peerj.17960
date submitted: 2024-06-17
date accepted: 2024-08-01
issued: 2024-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hurtado
  given name: Grecia
author list: Agent
  family name: Olbricht
  given name: Klaus
author list: Agent
  family name: Mercado
  given name: Jose A.
author list: Agent
  family name: Pose
  given name: Sara
author list: Agent
  family name: Knoche
  given name: Moritz
doi: 10.7717/peerj.17960
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-29
copyright: © 2024 Hurtado et al.
attribution name: Hurtado et al.

Comparisons of genome assembly tools for characterization of Mycobacterium tuberculosis genomes using hybrid sequencing technologies
type: item
type: AcademicArticle
description: Background Next-generation sequencing of Mycobacterium tuberculosis, the infectious agent causing tuberculosis, is improving the understanding of genomic diversity of circulating lineages and strain-types, and informing knowledge of drug resistance mutations. An increasingly popular approach to characterizing M. tuberculosis genomes (size: 4.4 Mbp) and variants (e.g., single nucleotide polymorphisms (SNPs)) involves the de novo assembly of sequence data. Methods We compared the performance of genome assembly tools (Unicycler, RagOut, and RagTag) on sequence data from nine drug resistant M. tuberculosis isolates (multi-drug (MDR) n = 1; pre-extensively-drug (pre-XDR) n = 8) generated using Illumina HiSeq, Oxford Nanopore Technology (ONT) PromethION, and PacBio platforms. Results Our investigation found that Unicycler-based assemblies had significantly higher genome completeness (~98.7%; p values = 0.01) compared to other assembler tools (RagOut = 98.6%, and RagTag = 98.6%). The genome assembly sizes (bp) across isolates and sequencers based on RagOut was significantly longer (p values < 0.001) (4,418,574 ± 8,824 bp) than Unicycler and RagTag assemblies (Unicycler = 4,377,642 ± 55,257 bp, and RagTag = 4,380,711 ± 51,164 bp). RagOut-based assemblies had the fewest contigs (~32) and the longest genome size (4,418,574 bp; vs. H37Rv reference size 4,411,532 bp) and therefore were chosen for downstream analysis. Pan-genome analysis of Illumina and PacBio hybrid assemblies revealed the greatest number of detected genes (4,639 genes; H37Rv reference contains 3,976 genes), while Illumina and ONT hybrid assemblies produced the highest number of SNPs. The number of genes from hybrid assemblies with ONT and PacBio long-reads (mean: 4,620 genes) was greater than short-read assembly alone (4,478 genes). All nine RagOut hybrid genome assemblies detected known mutations in genes associated with MDR-TB and pre-XDR-TB. Conclusions Unicycler software performed the best in terms of achi…
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creator: Kanwara Trisakul
creator: Yothin Hinwan
creator: Jukgarin Eisiri
creator: Kanin Salao
creator: Angkana Chaiprasert
creator: Phalin Kamolwat
creator: Sissades Tongsima
creator: Susana Campino
creator: Jody Phelan
creator: Taane G. Clark
creator: Kiatichai Faksri
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Tuberculosis
description: doi:10.7717/peerj.17964
publisher: PeerJ Inc.
rights: © 2024 Trisakul et al.
abstract: Background Next-generation sequencing of Mycobacterium tuberculosis, the infectious agent causing tuberculosis, is improving the understanding of genomic diversity of circulating lineages and strain-types, and informing knowledge of drug resistance mutations. An increasingly popular approach to characterizing M. tuberculosis genomes (size: 4.4 Mbp) and variants (e.g., single nucleotide polymorphisms (SNPs)) involves the de novo assembly of sequence data. Methods We compared the performance of genome assembly tools (Unicycler, RagOut, and RagTag) on sequence data from nine drug resistant M. tuberculosis isolates (multi-drug (MDR) n = 1; pre-extensively-drug (pre-XDR) n = 8) generated using Illumina HiSeq, Oxford Nanopore Technology (ONT) PromethION, and PacBio platforms. Results Our investigation found that Unicycler-based assemblies had significantly higher genome completeness (~98.7%; p values = 0.01) compared to other assembler tools (RagOut = 98.6%, and RagTag = 98.6%). The genome assembly sizes (bp) across isolates and sequencers based on RagOut was significantly longer (p values < 0.001) (4,418,574 ± 8,824 bp) than Unicycler and RagTag assemblies (Unicycler = 4,377,642 ± 55,257 bp, and RagTag = 4,380,711 ± 51,164 bp). RagOut-based assemblies had the fewest contigs (~32) and the longest genome size (4,418,574 bp; vs. H37Rv reference size 4,411,532 bp) and therefore were chosen for downstream analysis. Pan-genome analysis of Illumina and PacBio hybrid assemblies revealed the greatest number of detected genes (4,639 genes; H37Rv reference contains 3,976 genes), while Illumina and ONT hybrid assemblies produced the highest number of SNPs. The number of genes from hybrid assemblies with ONT and PacBio long-reads (mean: 4,620 genes) was greater than short-read assembly alone (4,478 genes). All nine RagOut hybrid genome assemblies detected known mutations in genes associated with MDR-TB and pre-XDR-TB. Conclusions Unicycler software performed the best in terms of achi…
bibliographic citation: Trisakul et al. (2024) Comparisons of genome assembly tools for characterization of Mycobacterium tuberculosis genomes using hybrid sequencing technologies. PeerJ 12:e17964 https://doi.org/10.7717/peerj.17964
date submitted: 2024-05-30
date accepted: 2024-08-01
issued: 2024-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Trisakul
  given name: Kanwara
author list: Agent
  family name: Hinwan
  given name: Yothin
author list: Agent
  family name: Eisiri
  given name: Jukgarin
author list: Agent
  family name: Salao
  given name: Kanin
author list: Agent
  family name: Chaiprasert
  given name: Angkana
author list: Agent
  family name: Kamolwat
  given name: Phalin
author list: Agent
  family name: Tongsima
  given name: Sissades
author list: Agent
  family name: Campino
  given name: Susana
author list: Agent
  family name: Phelan
  given name: Jody
author list: Agent
  family name: Clark
  given name: Taane G.
author list: Agent
  family name: Faksri
  given name: Kiatichai
doi: 10.7717/peerj.17964
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-29
copyright: © 2024 Trisakul et al.
attribution name: Trisakul et al.

A short stature allele enhances tolerance to zinc deficiency and translocation of zinc in barley
type: item
type: AcademicArticle
description: Background Zinc (Zn) content is of great importance in healthy human diet, crop productivity and stress tolerance in soils with zinc deficiency. The genes used to increase yield per unit area such as semi-dwarf 1 (sdw1) is commonly considered to reduce mineral content of grain. Methods In the present study, influence of sdw1.d, a widely used allele for short plant height in barley breeding, on zinc accumulation and tolerance to zinc deficiency were investigated. A near isogenic line of sdw1.d allele, its recurrent parent Tokak 157/37 and donor parent Triumph were grown in zinc-deficient and-sufficient hydroponic cultures. Two experiments were conducted until heading stage and physiological maturity. Results In zinc-deficient conditions, sdw1.d allele increased shoot dry weight by 112.4 mg plant−1, shoot Zn concentration by 0.9 ppm, but decreased root Zn concentration by 6.6 ppm. It did not affect grain characteristics, but increased grain Zn content. In zinc-sufficient conditions, sdw1.d allele increased shoot Zn content, and decreased root Zn content. sdw1.d did not affect grain weight but increased grain Zn concentration by about 30% under zinc-sufficient conditions. The results showed that sdw1.d allele has no negative effect on tolerance to zinc deficiency, and even promotes tolerance to zinc deficiency by more Zn translocation. It was revealed that sdw1.d allele improves Zn accumulation under both zinc-deficient and zinc-sufficient condition. The sdw1.d allele could contribute to solving the problems in plant growth and development caused by zinc-deficiency via improving tolerance to zinc-deficiency. It could also provide a better Zn biofortification.
format: application/pdf
format: text/html
creator: Ibrahim Saygili
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.17994
publisher: PeerJ Inc.
rights: © 2024 Saygili
abstract: Background Zinc (Zn) content is of great importance in healthy human diet, crop productivity and stress tolerance in soils with zinc deficiency. The genes used to increase yield per unit area such as semi-dwarf 1 (sdw1) is commonly considered to reduce mineral content of grain. Methods In the present study, influence of sdw1.d, a widely used allele for short plant height in barley breeding, on zinc accumulation and tolerance to zinc deficiency were investigated. A near isogenic line of sdw1.d allele, its recurrent parent Tokak 157/37 and donor parent Triumph were grown in zinc-deficient and-sufficient hydroponic cultures. Two experiments were conducted until heading stage and physiological maturity. Results In zinc-deficient conditions, sdw1.d allele increased shoot dry weight by 112.4 mg plant−1, shoot Zn concentration by 0.9 ppm, but decreased root Zn concentration by 6.6 ppm. It did not affect grain characteristics, but increased grain Zn content. In zinc-sufficient conditions, sdw1.d allele increased shoot Zn content, and decreased root Zn content. sdw1.d did not affect grain weight but increased grain Zn concentration by about 30% under zinc-sufficient conditions. The results showed that sdw1.d allele has no negative effect on tolerance to zinc deficiency, and even promotes tolerance to zinc deficiency by more Zn translocation. It was revealed that sdw1.d allele improves Zn accumulation under both zinc-deficient and zinc-sufficient condition. The sdw1.d allele could contribute to solving the problems in plant growth and development caused by zinc-deficiency via improving tolerance to zinc-deficiency. It could also provide a better Zn biofortification.
bibliographic citation: Saygili (2024) A short stature allele enhances tolerance to zinc deficiency and translocation of zinc in barley. PeerJ 12:e17994 https://doi.org/10.7717/peerj.17994
date submitted: 2024-06-06
date accepted: 2024-08-07
issued: 2024-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saygili
  given name: Ibrahim
doi: 10.7717/peerj.17994
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-29
copyright: © 2024 Saygili
attribution name: Saygili

Genome-wide identification and characterization of the sucrose invertase gene family in Hemerocallis citrina
type: item
type: AcademicArticle
description: Background Sucrose invertase is an important catalytic enzyme that is widely distributed in plants and can irreversibly hydrolyze sucrose into fructose and glucose. Daylily is an important perennial flower worldwide and a traditional vegetable in East Asia. Previous studies have suggested that sucrose invertase is involved in the aging of daylily flowers. However, knowledge about the number, physicochemical properties, and expression patterns of daylily sucrose invertases is still lacking. Identifying the daylily sucrose invertase family genes in the genome is highly important for understanding phylogenetic evolution and determining the genetic function of sucrose invertase. Methods To obtain basic knowledge about the number, classification, sequence composition, and physicochemical properties of sucrose invertases in daylily, bioinformatics software was used to analyze the genome of Hemerocallis citrina (H. citrina), and the basic properties of sucrose invertase genes and proteins were obtained. Then, combined with transcriptome data from flower organs at different developmental stages, the expression patterns of each gene were clarified. Finally, the reliability of the transcriptome data was verified by quantitative real-time polymerase chain reaction (PCR). Results Through software analysis, 35 sucrose invertases were identified from the H. citrina genome and named HcINV1-HcINV35; these enzymes belong to three subfamilies: cell wall invertases, vacuolar invertases, and chloroplast invertases. The amino acid composition, motif types, promoter composition, gene structure, protein physicochemical properties, gene chromosomal localization, and evolutionary adaptability of daylily invertases were determined; these results provided a comprehensive understanding of daylily invertases. The transcriptome expression profile combined with fluorescence quantitative reverse transcription-polymerase chain reaction (RT‒PCR) analysis suggested that almost all daylily invertase g…
format: application/pdf
format: text/html
creator: Guangying Ma
creator: Ziwei Zuo
creator: Lupeng Xie
creator: Jiao Han
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.17999
publisher: PeerJ Inc.
rights: © 2024 Ma et al.
abstract: Background Sucrose invertase is an important catalytic enzyme that is widely distributed in plants and can irreversibly hydrolyze sucrose into fructose and glucose. Daylily is an important perennial flower worldwide and a traditional vegetable in East Asia. Previous studies have suggested that sucrose invertase is involved in the aging of daylily flowers. However, knowledge about the number, physicochemical properties, and expression patterns of daylily sucrose invertases is still lacking. Identifying the daylily sucrose invertase family genes in the genome is highly important for understanding phylogenetic evolution and determining the genetic function of sucrose invertase. Methods To obtain basic knowledge about the number, classification, sequence composition, and physicochemical properties of sucrose invertases in daylily, bioinformatics software was used to analyze the genome of Hemerocallis citrina (H. citrina), and the basic properties of sucrose invertase genes and proteins were obtained. Then, combined with transcriptome data from flower organs at different developmental stages, the expression patterns of each gene were clarified. Finally, the reliability of the transcriptome data was verified by quantitative real-time polymerase chain reaction (PCR). Results Through software analysis, 35 sucrose invertases were identified from the H. citrina genome and named HcINV1-HcINV35; these enzymes belong to three subfamilies: cell wall invertases, vacuolar invertases, and chloroplast invertases. The amino acid composition, motif types, promoter composition, gene structure, protein physicochemical properties, gene chromosomal localization, and evolutionary adaptability of daylily invertases were determined; these results provided a comprehensive understanding of daylily invertases. The transcriptome expression profile combined with fluorescence quantitative reverse transcription-polymerase chain reaction (RT‒PCR) analysis suggested that almost all daylily invertase g…
bibliographic citation: Ma et al. (2024) Genome-wide identification and characterization of the sucrose invertase gene family in Hemerocallis citrina. PeerJ 12:e17999 https://doi.org/10.7717/peerj.17999
date submitted: 2024-05-17
date accepted: 2024-08-07
issued: 2024-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Guangying
author list: Agent
  family name: Zuo
  given name: Ziwei
author list: Agent
  family name: Xie
  given name: Lupeng
author list: Agent
  family name: Han
  given name: Jiao
doi: 10.7717/peerj.17999
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-29
copyright: © 2024 Ma et al.
attribution name: Ma et al.

Marine catfishes (Ariidae—Siluriformes) from the Coastal Amazon: mitochondrial DNA barcode for a recent diversification group?
type: item
type: AcademicArticle
description: Background Ariidae species play a significant role as fishing resources in the Amazon region. However, the family’s systematic classification is notably challenging, particularly regarding species delimitation within certain genera. This difficulty arises from pronounced morphological similarities among species, posing obstacles to accurate species recognition. Methods Following morphological identification, mitochondrial markers (COI and Cytb) were employed to assess the diversity of Ariidae species in the Amazon. Results Our sampling efforts yielded 12 species, representing 92% of the coastal Amazon region’s diversity. Morphological identification findings were largely corroborated by molecular data, particularly for species within the Sciades and Bagre genera. Nonetheless, despite morphological support, Cathorops agassizii and Cathorops spixii displayed minimal genetic divergence (0.010). Similarly, Notarius quadriscutis and Notarius phrygiatus formed a single clade with no genetic divergence, indicating mitochondrial introgression. For the majority of taxa examined, both COI and Cytb demonstrated efficacy as DNA barcodes, with Cytb exhibiting greater polymorphism and resolution. Consequently, the molecular tools utilized proved highly effective for species discrimination and identification.
format: application/pdf
format: text/html
creator: Ítalo Lutz
creator: Thais Martins
creator: Paula Santana
creator: Charles Ferreira
creator: Josy Miranda
creator: Suane Matos
creator: Valdemiro Muhala
creator: Iracilda Sampaio
creator: Marcelo Vallinoto
creator: Grazielle Evangelista-Gomes
subject: Aquaculture, Fisheries and Fish Science
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.17581
publisher: PeerJ Inc.
rights: © 2024 Lutz et al.
abstract: Background Ariidae species play a significant role as fishing resources in the Amazon region. However, the family’s systematic classification is notably challenging, particularly regarding species delimitation within certain genera. This difficulty arises from pronounced morphological similarities among species, posing obstacles to accurate species recognition. Methods Following morphological identification, mitochondrial markers (COI and Cytb) were employed to assess the diversity of Ariidae species in the Amazon. Results Our sampling efforts yielded 12 species, representing 92% of the coastal Amazon region’s diversity. Morphological identification findings were largely corroborated by molecular data, particularly for species within the Sciades and Bagre genera. Nonetheless, despite morphological support, Cathorops agassizii and Cathorops spixii displayed minimal genetic divergence (0.010). Similarly, Notarius quadriscutis and Notarius phrygiatus formed a single clade with no genetic divergence, indicating mitochondrial introgression. For the majority of taxa examined, both COI and Cytb demonstrated efficacy as DNA barcodes, with Cytb exhibiting greater polymorphism and resolution. Consequently, the molecular tools utilized proved highly effective for species discrimination and identification.
bibliographic citation: Lutz et al. (2024) Marine catfishes (Ariidae—Siluriformes) from the Coastal Amazon: mitochondrial DNA barcode for a recent diversification group?. PeerJ 12:e17581 https://doi.org/10.7717/peerj.17581
date submitted: 2024-02-09
date accepted: 2024-05-25
issued: 2024-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lutz
  given name: Ítalo
author list: Agent
  family name: Martins
  given name: Thais
author list: Agent
  family name: Santana
  given name: Paula
author list: Agent
  family name: Ferreira
  given name: Charles
author list: Agent
  family name: Miranda
  given name: Josy
author list: Agent
  family name: Matos
  given name: Suane
author list: Agent
  family name: Muhala
  given name: Valdemiro
author list: Agent
  family name: Sampaio
  given name: Iracilda
author list: Agent
  family name: Vallinoto
  given name: Marcelo
author list: Agent
  family name: Evangelista-Gomes
  given name: Grazielle
doi: 10.7717/peerj.17581
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-28
copyright: © 2024 Lutz et al.
attribution name: Lutz et al.

Levels of biomarkers associated with subconcussive head hits in mixed martial arts fighters
type: item
type: AcademicArticle
description: Background Concussion and the damage resulting from this event related to brain function have been widely studied; however, little is known about subconcussive impacts, especially in Mixed Martial Arts (MMA) fighters, which is a combat and full contact sport in which most blows are aimed at the head. Objective This study aims to evaluate the biomarker levels associated with subconcussive hits to the head in MMA fighters. Methods This is an exploratory study in which 30 male subjects (10 MMA fighters, 10 healthy individuals who practice muscle training, and 10 healthy sedentary individuals) aged between 18 and 32 years (25.4 ± 3.8) were evaluated. These individuals underwent blood collection to assess their Ubiquitin C-terminal hydrolase (UCH-L1), Glial Fibrillary Acidic Protein (GFAP) and Brain Derived Neurotrophic Factor (BDNF) levels before, immediately after and 72 hours after the sparring session (for the fighters) and were compared between groups. Results Significant differences were found at baseline between active and healthy fighters in BDNF levels (p = 0.03). A significant reduction of BDNF levels were also observed between the post-immediate and 72h after the sparring session (p = 0.03). No differences were observed in the number or severity of symptoms reported by the fighters. Conclusion Despite the exploratory approach, the findings of this study may help to understand the influence of repeated subconcussive hits to the head in MMA fighters, as well as to propose preventive interventions which can minimize the effects of the impact of hits, preserving fighters’ neuronal integrity and function.
format: application/pdf
format: text/html
creator: Nelson Marinho de Lima Filho
creator: Sabrina Gabrielle Gomes Fernandes
creator: Valeria Costa
creator: Daline Araujo
creator: Clecio Godeiro Jr
creator: Gerlane Guerra
creator: Ricardo Oliveira Guerra
creator: Karyna Figueiredo Ribeiro
subject: Biochemistry
subject: Neurology
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.17752
publisher: PeerJ Inc.
rights: © 2024 de Lima Filho et al.
abstract: Background Concussion and the damage resulting from this event related to brain function have been widely studied; however, little is known about subconcussive impacts, especially in Mixed Martial Arts (MMA) fighters, which is a combat and full contact sport in which most blows are aimed at the head. Objective This study aims to evaluate the biomarker levels associated with subconcussive hits to the head in MMA fighters. Methods This is an exploratory study in which 30 male subjects (10 MMA fighters, 10 healthy individuals who practice muscle training, and 10 healthy sedentary individuals) aged between 18 and 32 years (25.4 ± 3.8) were evaluated. These individuals underwent blood collection to assess their Ubiquitin C-terminal hydrolase (UCH-L1), Glial Fibrillary Acidic Protein (GFAP) and Brain Derived Neurotrophic Factor (BDNF) levels before, immediately after and 72 hours after the sparring session (for the fighters) and were compared between groups. Results Significant differences were found at baseline between active and healthy fighters in BDNF levels (p = 0.03). A significant reduction of BDNF levels were also observed between the post-immediate and 72h after the sparring session (p = 0.03). No differences were observed in the number or severity of symptoms reported by the fighters. Conclusion Despite the exploratory approach, the findings of this study may help to understand the influence of repeated subconcussive hits to the head in MMA fighters, as well as to propose preventive interventions which can minimize the effects of the impact of hits, preserving fighters’ neuronal integrity and function.
bibliographic citation: de Lima Filho et al. (2024) Levels of biomarkers associated with subconcussive head hits in mixed martial arts fighters. PeerJ 12:e17752 https://doi.org/10.7717/peerj.17752
date submitted: 2024-01-03
date accepted: 2024-06-25
issued: 2024-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Lima Filho
  given name: Nelson Marinho
author list: Agent
  family name: Fernandes
  given name: Sabrina Gabrielle Gomes
author list: Agent
  family name: Costa
  given name: Valeria
author list: Agent
  family name: Araujo
  given name: Daline
author list: Agent
  family name: Godeiro Jr
  given name: Clecio
author list: Agent
  family name: Guerra
  given name: Gerlane
author list: Agent
  family name: Guerra
  given name: Ricardo Oliveira
author list: Agent
  family name: Ribeiro
  given name: Karyna Figueiredo
doi: 10.7717/peerj.17752
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-28
copyright: ©2024 de Lima Filho et al.
attribution name: de Lima Filho et al.

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