PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes
items: Iberian pig adaptation to acorn consumption: II. Net portal appearance of amino acids
items: ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV
items: Effects of ultraviolet radiation on metabolic rate and fitness of Aedes albopictus and Culex pipiens mosquitoes
items: Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile
items: Elevated CD3low double negative T lymphocyte is associated with pneumonia and its severity in pediatric patients
items: Morphological characterization and staging of bumble bee pupae
items: Nanocontainer designed from an infectious hypodermal and hematopoietic necrosis virus (IHHNV) has excellent physical stability and ability to deliver shrimp tissues
items: Effects of dietary supplementation with Lactobacillus acidophilus on the performance, intestinal physical barrier function, and the expression of NOD-like receptors in weaned piglets
items: Systematic review and meta-analysis of age-related differences in instructed emotion regulation success

First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes
type: item
type: AcademicArticle
description: There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled …
format: application/pdf
format: text/html
creator: Balázs Brankovics
creator: Tomasz Kulik
creator: Jakub Sawicki
creator: Katarzyna Bilska
creator: Hao Zhang
creator: G Sybren de Hoog
creator: Theo AJ van der Lee
creator: Cees Waalwijk
creator: Anne D. van Diepeningen
subject: Bioinformatics
subject: Genomics
subject: Population Biology
description: doi:10.7717/peerj.5963
publisher: PeerJ Inc.
rights: © 2018 Brankovics et al.
abstract: There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled …
bibliographic citation: Brankovics et al. (2018) First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes. PeerJ 6:e5963 https://doi.org/10.7717/peerj.5963
date submitted: 2018-07-02
date accepted: 2018-10-16
issued: 2018-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brankovics
  given name: Balázs
author list: Agent
  family name: Kulik
  given name: Tomasz
author list: Agent
  family name: Sawicki
  given name: Jakub
author list: Agent
  family name: Bilska
  given name: Katarzyna
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: de Hoog
  given name: G Sybren
author list: Agent
  family name: van der Lee
  given name: Theo AJ
author list: Agent
  family name: Waalwijk
  given name: Cees
author list: Agent
  family name: van Diepeningen
  given name: Anne D.
doi: 10.7717/peerj.5963
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-19
copyright: ©2018 Brankovics et al.
attribution name: Brankovics et al.

Iberian pig adaptation to acorn consumption: II. Net portal appearance of amino acids
type: item
type: AcademicArticle
description: In Iberian pig outdoor production, pigs are fed equilibrated diets until the final fattening period when grazing pigs consume mainly acorns from oak trees. Acorns are rich in energy but poor in crude protein where lysine is the first limiting amino acid (AA). Net portal appearance (NPA) is very useful to ascertain AA available for liver and peripheral tissues. The aim of this study was to determine NPA of AA in Iberian gilts fed with acorns and to ascertain if there was an effect of acorn feeding over time. Two sampling periods were carried out (after one day and after one week of acorn feeding) with six gilts (34 kg average BW) set up with three catheters: in carotid artery and portal vein for blood sampling, and ileal vein for a marker infusion to measure portal plasma flow (PPF). Pigs were fed at 2.5 × ME for maintenance a standard diet in two meals, at 09:00 (0.25) and 15:00 h (the remaining 0.75). The day previous to first sampling, pig diet was replaced by 2.4 kg of acorn. A serial blood collection was done at −5 min, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 5 and 6 h after feeding 0.25 of total daily acorn ration. Following identical protocol, one week later the second sampling was done. NPA of sum of essential AA (EAA) was poor. Although increased NPA of histidine (P < 0.001), leucine, phenylalanine and valine (0.05 < P < 0.08) was found after one week of acorn consumption, the sum of EAA did not change. Furthermore, fractional absorption (NPA/AA intake) of EAA, non-essential AA (NEAA) and total AA was 97, 44 and 49% lower, respectively, at the beginning of eating acorn than a week later. Supplementation, with some of the EAA and NEAA to Iberian pigs during the grazing period would be beneficial to overcome the increased portal-drained viscera (PDV) utilization of AA observed in the present study.
format: application/pdf
format: text/html
creator: Manuel Lachica
creator: Jose Miguel Rodríguez-López
creator: Lucrecia González-Valero
creator: Ignacio Fernández-Fígares
subject: Agricultural Science
subject: Nutrition
subject: Natural Resource Management
description: doi:10.7717/peerj.6137
publisher: PeerJ Inc.
rights: © 2018 Lachica et al.
abstract: In Iberian pig outdoor production, pigs are fed equilibrated diets until the final fattening period when grazing pigs consume mainly acorns from oak trees. Acorns are rich in energy but poor in crude protein where lysine is the first limiting amino acid (AA). Net portal appearance (NPA) is very useful to ascertain AA available for liver and peripheral tissues. The aim of this study was to determine NPA of AA in Iberian gilts fed with acorns and to ascertain if there was an effect of acorn feeding over time. Two sampling periods were carried out (after one day and after one week of acorn feeding) with six gilts (34 kg average BW) set up with three catheters: in carotid artery and portal vein for blood sampling, and ileal vein for a marker infusion to measure portal plasma flow (PPF). Pigs were fed at 2.5 × ME for maintenance a standard diet in two meals, at 09:00 (0.25) and 15:00 h (the remaining 0.75). The day previous to first sampling, pig diet was replaced by 2.4 kg of acorn. A serial blood collection was done at −5 min, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 5 and 6 h after feeding 0.25 of total daily acorn ration. Following identical protocol, one week later the second sampling was done. NPA of sum of essential AA (EAA) was poor. Although increased NPA of histidine (P < 0.001), leucine, phenylalanine and valine (0.05 < P < 0.08) was found after one week of acorn consumption, the sum of EAA did not change. Furthermore, fractional absorption (NPA/AA intake) of EAA, non-essential AA (NEAA) and total AA was 97, 44 and 49% lower, respectively, at the beginning of eating acorn than a week later. Supplementation, with some of the EAA and NEAA to Iberian pigs during the grazing period would be beneficial to overcome the increased portal-drained viscera (PDV) utilization of AA observed in the present study.
bibliographic citation: Lachica et al. (2018) Iberian pig adaptation to acorn consumption: II. Net portal appearance of amino acids. PeerJ 6:e6137 https://doi.org/10.7717/peerj.6137
date submitted: 2018-02-27
date accepted: 2018-11-20
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lachica
  given name: Manuel
author list: Agent
  family name: Rodríguez-López
  given name: Jose Miguel
author list: Agent
  family name: González-Valero
  given name: Lucrecia
author list: Agent
  family name: Fernández-Fígares
  given name: Ignacio
doi: 10.7717/peerj.6137
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: ©2018 Lachica et al.
attribution name: Lachica et al.

ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV
type: item
type: AcademicArticle
description: In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain–Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (www.structurome.bb.iastate.edu), a repository of RNA folding data for humans and their pathogens.
format: application/pdf
format: text/html
creator: Ryan J. Andrews
creator: Julien Roche
creator: Walter N. Moss
subject: Bioinformatics
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.6136
publisher: PeerJ Inc.
rights: © 2018 Andrews et al.
abstract: In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain–Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (www.structurome.bb.iastate.edu), a repository of RNA folding data for humans and their pathogens.
bibliographic citation: Andrews et al. (2018) ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV. PeerJ 6:e6136 https://doi.org/10.7717/peerj.6136
date submitted: 2018-08-08
date accepted: 2018-11-15
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Andrews
  given name: Ryan J.
author list: Agent
  family name: Roche
  given name: Julien
author list: Agent
  family name: Moss
  given name: Walter N.
doi: 10.7717/peerj.6136
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: © 2018 Andrews et al.
attribution name: Andrews et al.

Effects of ultraviolet radiation on metabolic rate and fitness of Aedes albopictus and Culex pipiens mosquitoes
type: item
type: AcademicArticle
description: Natural and anthropogenic changes (e.g., land use change, pollution) will alter many environmental factors in the coming years, including the amount of solar radiation reaching the earth’s surface. Alterations in solar radiation exposure is likely to impact the ecologies of many living organisms, including invertebrates that inhabit aquatic habitats. In this study, we assessed the effect of UV-B radiation on the metabolic rates and fitness (survival, development time, body size) of Aedes albopictus and Culex pipiens mosquitoes and the activity of their microbial food resources in experimental aquatic microcosms. We exposed single-species cohorts of newly hatched Ae. albopictus and Cx. pipiens larvae and a control treatment with no larvae to three UV-B conditions that mimicked those in full-sun and shade in the field and to a control condition with no UV-B radiation. Our results indicated that UV-B radiation affected the metabolic rates of both Ae. albopictus and Cx. pipiens larvae, with significantly higher rates found in full-sun compared to shade and no-UV conditions, 8 and 15 days after exposure began. Ae. albopictus and Cx. pipiens survival was also affected by UV-B radiation condition, with significantly lower survival in full-sun compared to shade and no UV-B conditions. Microbial metabolic rates were consistently significantly lower in full-sun compared to shade and no-UV conditions, especially at 8 days of exposure. These results show that UV-B radiation at levels found in open spaces showed strong and important impacts on the metabolic rates and survival of Ae. albopictus and Cx. pipiens larvae. Decreased survival of Ae. albopictus and Cx. pipiens with higher UV-B radiation levels may be caused by both direct exposure to radiation as well as the indirect effects of reduced microbial food, resulting in greater metabolic demands and stress. Negative impacts of UV-B radiation on the survival of Ae. albopictus and Cx. pipiens are likely to have important implic…
format: application/pdf
format: text/html
creator: Oswaldo C. Villena
creator: Bahram Momen
creator: Joseph Sullivan
creator: Paul T. Leisnham
subject: Ecology
subject: Ecosystem Science
subject: Entomology
description: doi:10.7717/peerj.6133
publisher: PeerJ Inc.
rights: © 2018 Villena et al.
abstract: Natural and anthropogenic changes (e.g., land use change, pollution) will alter many environmental factors in the coming years, including the amount of solar radiation reaching the earth’s surface. Alterations in solar radiation exposure is likely to impact the ecologies of many living organisms, including invertebrates that inhabit aquatic habitats. In this study, we assessed the effect of UV-B radiation on the metabolic rates and fitness (survival, development time, body size) of Aedes albopictus and Culex pipiens mosquitoes and the activity of their microbial food resources in experimental aquatic microcosms. We exposed single-species cohorts of newly hatched Ae. albopictus and Cx. pipiens larvae and a control treatment with no larvae to three UV-B conditions that mimicked those in full-sun and shade in the field and to a control condition with no UV-B radiation. Our results indicated that UV-B radiation affected the metabolic rates of both Ae. albopictus and Cx. pipiens larvae, with significantly higher rates found in full-sun compared to shade and no-UV conditions, 8 and 15 days after exposure began. Ae. albopictus and Cx. pipiens survival was also affected by UV-B radiation condition, with significantly lower survival in full-sun compared to shade and no UV-B conditions. Microbial metabolic rates were consistently significantly lower in full-sun compared to shade and no-UV conditions, especially at 8 days of exposure. These results show that UV-B radiation at levels found in open spaces showed strong and important impacts on the metabolic rates and survival of Ae. albopictus and Cx. pipiens larvae. Decreased survival of Ae. albopictus and Cx. pipiens with higher UV-B radiation levels may be caused by both direct exposure to radiation as well as the indirect effects of reduced microbial food, resulting in greater metabolic demands and stress. Negative impacts of UV-B radiation on the survival of Ae. albopictus and Cx. pipiens are likely to have important implic…
bibliographic citation: Villena et al. (2018) Effects of ultraviolet radiation on metabolic rate and fitness of Aedes albopictus and Culex pipiens mosquitoes. PeerJ 6:e6133 https://doi.org/10.7717/peerj.6133
date submitted: 2018-03-16
date accepted: 2018-11-19
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Villena
  given name: Oswaldo C.
author list: Agent
  family name: Momen
  given name: Bahram
author list: Agent
  family name: Sullivan
  given name: Joseph
author list: Agent
  family name: Leisnham
  given name: Paul T.
doi: 10.7717/peerj.6133
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: ©2018 Villena et al.
attribution name: Villena et al.

Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile
type: item
type: AcademicArticle
description: Quaternary climatic oscillations have impacted Patagonian sigmodontine fauna, leaving traceable genetic footprints. In southern Chile, changes in the landscape included transitions to different vegetation formations as well as the extension of ice sheets. In this study, we focus on the Valdivian forest endemic and recently described sigmodontine species Abrothrix manni. We aim to assess the genetic structure of this species, testing for the existence of intraspecific lineages, and inferring the recent demographic history of the species. Analyses were based on the first 801 bp of the mitochondrial gene Cytocrhome-b from 49 individuals of A. manni collected at 10 localities that covers most part of its geographic distribution. Genealogical analyses recovered two main intraspecific lineages that are geographically segregated and present an intermediate site of secondary contact. Historical demography shows signal of recent population decrease. Based on these results, we proposed that current genetic diversity of A. manni differentiated in at least two distinct refugial areas in southern Chile. This scenario, in addition to be unique among those uncovered for the so far studied Valdivian forest rodents, is noteworthy because of the reduced geographic scale inhabited by the species.
format: application/pdf
format: text/html
creator: Lourdes Valdez
creator: Guilermo D’Elía
subject: Biogeography
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.6130
publisher: PeerJ Inc.
rights: © 2018 Valdez and D’Elía
abstract: Quaternary climatic oscillations have impacted Patagonian sigmodontine fauna, leaving traceable genetic footprints. In southern Chile, changes in the landscape included transitions to different vegetation formations as well as the extension of ice sheets. In this study, we focus on the Valdivian forest endemic and recently described sigmodontine species Abrothrix manni. We aim to assess the genetic structure of this species, testing for the existence of intraspecific lineages, and inferring the recent demographic history of the species. Analyses were based on the first 801 bp of the mitochondrial gene Cytocrhome-b from 49 individuals of A. manni collected at 10 localities that covers most part of its geographic distribution. Genealogical analyses recovered two main intraspecific lineages that are geographically segregated and present an intermediate site of secondary contact. Historical demography shows signal of recent population decrease. Based on these results, we proposed that current genetic diversity of A. manni differentiated in at least two distinct refugial areas in southern Chile. This scenario, in addition to be unique among those uncovered for the so far studied Valdivian forest rodents, is noteworthy because of the reduced geographic scale inhabited by the species.
bibliographic citation: Valdez et al. (2018) Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile. PeerJ 6:e6130 https://doi.org/10.7717/peerj.6130
date submitted: 2018-09-24
date accepted: 2018-11-17
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valdez
  given name: Lourdes
author list: Agent
  family name: D’Elía
  given name: Guilermo
doi: 10.7717/peerj.6130
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: ©2018 Valdez and D’Elía
attribution name: Valdez and D’Elía

Elevated CD3low double negative T lymphocyte is associated with pneumonia and its severity in pediatric patients
type: item
type: AcademicArticle
description: Background Previous studies have shown that the adaptive immunity function of T cells in disease states correlates with CD3 surface expression closely. During routine assessment of TBNK subsets in peripheral blood of pediatric patients by flow cytometry, we noticed that variable expression levels of CD3 on CD3+CD4−CD8− double-negative T (DNT) lymphocytes in different patients. The objective of this study was to assess the relationship of CD3 expression levels on DNT cells with disease severity. Methods In this prospective study, we investigated the frequencies of circulating CD4−CD8− DNT cell subsets with CD3low or CD3high phenotype by flow cytometry in 76 pediatric patients with pneumonia, 55 patients with severe pneumonia (SP), and 29 healthy controls (Con). Results The numbers of circulating DNT cells were similar in all groups; however, the frequency of CD3low DNT cell subsets was significantly increased in patients with pneumonia (p < 0.001) and SP (p < 0.001). The elevated CD3low DNT cell frequency showed a positive correlation with the clinical severity of pneumonia. On sub-group analysis, the frequency of CD3low DNT cells was only elevated in children with pneumonia aged <5 years, while no association was observed with the causative pathogen of pneumonia. Conclusions These findings suggest that CD3 expression levels on DNT cell subsets of peripheral lymphocytes may be a valuable biomarker for evaluation of immune response in pediatric infectious disease. CD3low DNT cells were elevated in children with pneumonia aged <5 years, which indicates that it may be an important research target in pediatric infectious diseases.
format: application/pdf
format: text/html
creator: Ying Wang
creator: Wenting Lu
creator: Aipeng Li
creator: Zhengyi Sun
creator: Liying Wang
subject: Immunology
subject: Infectious Diseases
subject: Pediatrics
description: doi:10.7717/peerj.6114
publisher: PeerJ Inc.
rights: © 2018 Wang et al.
abstract: Background Previous studies have shown that the adaptive immunity function of T cells in disease states correlates with CD3 surface expression closely. During routine assessment of TBNK subsets in peripheral blood of pediatric patients by flow cytometry, we noticed that variable expression levels of CD3 on CD3+CD4−CD8− double-negative T (DNT) lymphocytes in different patients. The objective of this study was to assess the relationship of CD3 expression levels on DNT cells with disease severity. Methods In this prospective study, we investigated the frequencies of circulating CD4−CD8− DNT cell subsets with CD3low or CD3high phenotype by flow cytometry in 76 pediatric patients with pneumonia, 55 patients with severe pneumonia (SP), and 29 healthy controls (Con). Results The numbers of circulating DNT cells were similar in all groups; however, the frequency of CD3low DNT cell subsets was significantly increased in patients with pneumonia (p < 0.001) and SP (p < 0.001). The elevated CD3low DNT cell frequency showed a positive correlation with the clinical severity of pneumonia. On sub-group analysis, the frequency of CD3low DNT cells was only elevated in children with pneumonia aged <5 years, while no association was observed with the causative pathogen of pneumonia. Conclusions These findings suggest that CD3 expression levels on DNT cell subsets of peripheral lymphocytes may be a valuable biomarker for evaluation of immune response in pediatric infectious disease. CD3low DNT cells were elevated in children with pneumonia aged <5 years, which indicates that it may be an important research target in pediatric infectious diseases.
bibliographic citation: Wang et al. (2018) Elevated CD3low double negative T lymphocyte is associated with pneumonia and its severity in pediatric patients. PeerJ 6:e6114 https://doi.org/10.7717/peerj.6114
date submitted: 2018-06-25
date accepted: 2018-11-15
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Ying
author list: Agent
  family name: Lu
  given name: Wenting
author list: Agent
  family name: Li
  given name: Aipeng
author list: Agent
  family name: Sun
  given name: Zhengyi
author list: Agent
  family name: Wang
  given name: Liying
doi: 10.7717/peerj.6114
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: ©2018 Wang et al.
attribution name: Wang et al.

Morphological characterization and staging of bumble bee pupae
type: item
type: AcademicArticle
description: Bumble bees (Hymenoptera: Apidae, Bombus) are important pollinators and models for studying mechanisms underlying developmental plasticity, such as factors influencing size, immunity, and social behaviors. Research on such processes, as well as expanding use of gene-manipulation and gene expression technologies, requires a detailed understanding of how these bees develop. Developmental research often uses time-staging of pupae, however dramatic size differences in these bees can generate variation in developmental timing. To study developmental mechanisms in bumble bees, appropriate staging of developing bees using morphology is necessary. In this study, we describe morphological changes across development in several bumble bee species and use this to establish morphology-based staging criteria, establishing 20 distinct illustrated stages. These criteria, defined largely by eye and cuticle pigmentation patterns, are generalizable across members of the subgenus Pyrobombus, and can be used as a framework for study of other bumble bee subgenera. We examine the effects of temperature, caste, size, and species on pupal development, revealing that pupal duration shifts with each of these factors, confirming the importance of staging pupae based on morphology rather than age and the need for standardizing sampling.
format: application/pdf
format: text/html
creator: Li Tian
creator: Heather M. Hines
subject: Agricultural Science
subject: Developmental Biology
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.6089
publisher: PeerJ Inc.
rights: © 2018 Tian and Hines
abstract: Bumble bees (Hymenoptera: Apidae, Bombus) are important pollinators and models for studying mechanisms underlying developmental plasticity, such as factors influencing size, immunity, and social behaviors. Research on such processes, as well as expanding use of gene-manipulation and gene expression technologies, requires a detailed understanding of how these bees develop. Developmental research often uses time-staging of pupae, however dramatic size differences in these bees can generate variation in developmental timing. To study developmental mechanisms in bumble bees, appropriate staging of developing bees using morphology is necessary. In this study, we describe morphological changes across development in several bumble bee species and use this to establish morphology-based staging criteria, establishing 20 distinct illustrated stages. These criteria, defined largely by eye and cuticle pigmentation patterns, are generalizable across members of the subgenus Pyrobombus, and can be used as a framework for study of other bumble bee subgenera. We examine the effects of temperature, caste, size, and species on pupal development, revealing that pupal duration shifts with each of these factors, confirming the importance of staging pupae based on morphology rather than age and the need for standardizing sampling.
bibliographic citation: Tian et al. (2018) Morphological characterization and staging of bumble bee pupae. PeerJ 6:e6089 https://doi.org/10.7717/peerj.6089
date submitted: 2018-10-01
date accepted: 2018-11-08
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tian
  given name: Li
author list: Agent
  family name: Hines
  given name: Heather M.
doi: 10.7717/peerj.6089
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: © 2018 Tian and Hines
attribution name: Tian and Hines

Nanocontainer designed from an infectious hypodermal and hematopoietic necrosis virus (IHHNV) has excellent physical stability and ability to deliver shrimp tissues
type: item
type: AcademicArticle
description: Background A virus-like particle (VLP) is an excellent tool for a compound delivery system due to its simple composition, symmetrical structure and self-assembly. Its surface modification both chemically and genetically is established, leading to the target-specific delivery and improved encapsulation efficiency. However, its physical stabilities against many harsh conditions that guarantee long term storage and oral administration have been much less studied. Methods IHHNV-VLPs were reconstructed from recombinant IHHNV capsid protein in E. coli. Their physical properties against three strong physical conditions including long term storage (0–30 days) in 4 °C, physical stabilities against broad ranged pH (4–9) and against three types of digestive enzymes were tested. Disassembly and reassembly of VLPs for encapsidating an enhanced green fluorescent protein tagged plasmid DNA (EGFP-VLPs) were controlled by the use of reducing agent (DTT) and calcium specific chelating agent (EGTA). Lastly, delivering ability of EGFP-VLPs was performed in vivo by intramuscular injection and traced the expression of GFP in the shrimp tissues 24 hr post-injection. Results Upon its purification, IHHNV-VLPs were able to be kept at 4 °C up to 30 days with only slight degradation. They were very stable in basic condition (pH 8–9) and to a lesser extent in acidic condition (pH 4–6) while they could stand digestions of trypsin and chymotrypsin better than pepsin. As similar with many other non-enveloped viruses, the assembly of IHHNV-VLPs was dependent on both disulfide bridging and calcium ions which allowed us to control disassembly and reassembly of these VLPs to pack EGFP plasmid DNA. IHHNV-VLPs could deliver EGFP plasmids into shrimp muscles and gills as evident by RT-PCR and confocal microscopy demonstrating the expression of GFP in the targeted tissues. Discussion There are extensive data in which capsid proteins of the non-enveloped viruses in the form of VLPs are constructed and used…
format: application/pdf
format: text/html
creator: Pauline Kiatmetha
creator: Charoonroj Chotwiwatthanakun
creator: Pitchanee Jariyapong
creator: Wanida Santimanawong
creator: Puey Ounjai
creator: Wattana Weerachatyanukul
subject: Aquaculture, Fisheries and Fish Science
subject: Biotechnology
subject: Cell Biology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.6079
publisher: PeerJ Inc.
rights: © 2018 Kiatmetha et al.
abstract: Background A virus-like particle (VLP) is an excellent tool for a compound delivery system due to its simple composition, symmetrical structure and self-assembly. Its surface modification both chemically and genetically is established, leading to the target-specific delivery and improved encapsulation efficiency. However, its physical stabilities against many harsh conditions that guarantee long term storage and oral administration have been much less studied. Methods IHHNV-VLPs were reconstructed from recombinant IHHNV capsid protein in E. coli. Their physical properties against three strong physical conditions including long term storage (0–30 days) in 4 °C, physical stabilities against broad ranged pH (4–9) and against three types of digestive enzymes were tested. Disassembly and reassembly of VLPs for encapsidating an enhanced green fluorescent protein tagged plasmid DNA (EGFP-VLPs) were controlled by the use of reducing agent (DTT) and calcium specific chelating agent (EGTA). Lastly, delivering ability of EGFP-VLPs was performed in vivo by intramuscular injection and traced the expression of GFP in the shrimp tissues 24 hr post-injection. Results Upon its purification, IHHNV-VLPs were able to be kept at 4 °C up to 30 days with only slight degradation. They were very stable in basic condition (pH 8–9) and to a lesser extent in acidic condition (pH 4–6) while they could stand digestions of trypsin and chymotrypsin better than pepsin. As similar with many other non-enveloped viruses, the assembly of IHHNV-VLPs was dependent on both disulfide bridging and calcium ions which allowed us to control disassembly and reassembly of these VLPs to pack EGFP plasmid DNA. IHHNV-VLPs could deliver EGFP plasmids into shrimp muscles and gills as evident by RT-PCR and confocal microscopy demonstrating the expression of GFP in the targeted tissues. Discussion There are extensive data in which capsid proteins of the non-enveloped viruses in the form of VLPs are constructed and used…
bibliographic citation: Kiatmetha et al. (2018) Nanocontainer designed from an infectious hypodermal and hematopoietic necrosis virus (IHHNV) has excellent physical stability and ability to deliver shrimp tissues. PeerJ 6:e6079 https://doi.org/10.7717/peerj.6079
date submitted: 2018-07-27
date accepted: 2018-11-06
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kiatmetha
  given name: Pauline
author list: Agent
  family name: Chotwiwatthanakun
  given name: Charoonroj
author list: Agent
  family name: Jariyapong
  given name: Pitchanee
author list: Agent
  family name: Santimanawong
  given name: Wanida
author list: Agent
  family name: Ounjai
  given name: Puey
author list: Agent
  family name: Weerachatyanukul
  given name: Wattana
doi: 10.7717/peerj.6079
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: ©2018 Kiatmetha et al.
attribution name: Kiatmetha et al.

Effects of dietary supplementation with Lactobacillus acidophilus on the performance, intestinal physical barrier function, and the expression of NOD-like receptors in weaned piglets
type: item
type: AcademicArticle
description: Lactobacillus supplementation is beneficial to the barrier function of the intestinal physical barrier in piglets. However, the mechanisms underlying this beneficial function remain largely unknown. Here, we investigated the effects of dietary supplementation with Lactobacillus acidophilus on the performance, intestinal physical barrier functioning, and NOD-like receptors (NLRs) expression in weaned piglets. Sixteen weaned piglets were randomly allocated to two groups. The control group received a corn-soybean basal diet, while the treatment group received the same diet adding 0.1% L. acidophilus, for 14 days. As a result, dietary L. acidophilus supplementation was found to increase the average daily gain (ADG) (P < 0.05), reduced serum diamine oxidase (DAO) activity (P < 0.05), increased the mRNA expression and protein abundance of occludin in the jejunum and ileum (P < 0.01), reduced the mRNA levels of NOD1 (P < 0.01), receptor interacting serine/threonine kinase 2 (RIPK2) (P < 0.05), nuclear factor κB (NF-κB) (P < 0.01), NLR family pyrin domain containing 3 (NLRP3) (P < 0.01), caspase-1 (P < 0.01), interleukin 1β (IL-1β) (P < 0.05) and IL-18 (P < 0.01) in the jejunum tissues of the weaned pigs. The expression of NLRP3 (P < 0.05), caspase-1 (P < 0.01), IL-1β (P < 0.05) and IL-18 (P < 0.05) was also reduced in the ileum tissues of the weaned pigs. These results showed that L. acidophilus supplementation improves the growth performance, enhances the intestinal physical barrier function, and inhibits the expression of NOD1 and NLRP3 signaling-pathway-related genes in jejunum and ileum tissues. They also suggest that L. acidophilus enhances the intestinal physical barrier functioning by inhibiting IL-1β and IL-18 pro-inflammatory cytokines via the NOD1/NLRP3 signaling pathway in weaned piglets.
format: application/pdf
format: text/html
creator: Shiqiong Wang
creator: Haihua Li
creator: Chenhong Du
creator: Qian Liu
creator: Dongji Yang
creator: Longbin Chen
creator: Qi Zhu
creator: Zhixiang Wang
subject: Agricultural Science
subject: Molecular Biology
subject: Veterinary Medicine
subject: Nutrition
description: doi:10.7717/peerj.6060
publisher: PeerJ Inc.
rights: © 2018 Wang et al.
abstract: Lactobacillus supplementation is beneficial to the barrier function of the intestinal physical barrier in piglets. However, the mechanisms underlying this beneficial function remain largely unknown. Here, we investigated the effects of dietary supplementation with Lactobacillus acidophilus on the performance, intestinal physical barrier functioning, and NOD-like receptors (NLRs) expression in weaned piglets. Sixteen weaned piglets were randomly allocated to two groups. The control group received a corn-soybean basal diet, while the treatment group received the same diet adding 0.1% L. acidophilus, for 14 days. As a result, dietary L. acidophilus supplementation was found to increase the average daily gain (ADG) (P < 0.05), reduced serum diamine oxidase (DAO) activity (P < 0.05), increased the mRNA expression and protein abundance of occludin in the jejunum and ileum (P < 0.01), reduced the mRNA levels of NOD1 (P < 0.01), receptor interacting serine/threonine kinase 2 (RIPK2) (P < 0.05), nuclear factor κB (NF-κB) (P < 0.01), NLR family pyrin domain containing 3 (NLRP3) (P < 0.01), caspase-1 (P < 0.01), interleukin 1β (IL-1β) (P < 0.05) and IL-18 (P < 0.01) in the jejunum tissues of the weaned pigs. The expression of NLRP3 (P < 0.05), caspase-1 (P < 0.01), IL-1β (P < 0.05) and IL-18 (P < 0.05) was also reduced in the ileum tissues of the weaned pigs. These results showed that L. acidophilus supplementation improves the growth performance, enhances the intestinal physical barrier function, and inhibits the expression of NOD1 and NLRP3 signaling-pathway-related genes in jejunum and ileum tissues. They also suggest that L. acidophilus enhances the intestinal physical barrier functioning by inhibiting IL-1β and IL-18 pro-inflammatory cytokines via the NOD1/NLRP3 signaling pathway in weaned piglets.
bibliographic citation: Wang et al. (2018) Effects of dietary supplementation with Lactobacillus acidophilus on the performance, intestinal physical barrier function, and the expression of NOD-like receptors in weaned piglets. PeerJ 6:e6060 https://doi.org/10.7717/peerj.6060
date submitted: 2018-07-17
date accepted: 2018-11-04
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Shiqiong
author list: Agent
  family name: Li
  given name: Haihua
author list: Agent
  family name: Du
  given name: Chenhong
author list: Agent
  family name: Liu
  given name: Qian
author list: Agent
  family name: Yang
  given name: Dongji
author list: Agent
  family name: Chen
  given name: Longbin
author list: Agent
  family name: Zhu
  given name: Qi
author list: Agent
  family name: Wang
  given name: Zhixiang
doi: 10.7717/peerj.6060
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: ©2018 Wang et al.
attribution name: Wang et al.

Systematic review and meta-analysis of age-related differences in instructed emotion regulation success
type: item
type: AcademicArticle
description: The process model of emotion regulation (ER) is based on stages in the emotion generative process at which regulation may occur. This meta-analysis examines age-related differences in the subjective, behavioral, and physiological outcomes of instructed ER strategies that may be initiated after an emotional event has occurred; attentional deployment, cognitive change, and response modulation. Within-process strategy, stimulus type, and valence were also tested as potential moderators of the effect of age on ER. A systematic search of the literature identified 156 relevant comparisons from 11 studies. Few age-related differences were found. In our analysis of the subjective outcome of response modulation strategies, young adults used expressive enhancement successfully (g = 0.48), but not expressive suppression (g = 0.04). Response modulation strategies had a small positive effect among older adults, and enhancement vs suppression did not moderate this success (g = 0.31 and g = 0.10, respectively). Young adults effectively used response modulation to regulate subjective emotion in response to pictures (g = 0.41) but not films (g = 0.01). Older adults were able to regulate in response to both pictures (g = 0.26) and films (g = 0.11). Interestingly, both age groups effectively used detached reappraisal, but not positive reappraisal to regulate emotional behavior. We conclude that, in line with well-established theories of socioemotional aging, there is a lack of evidence for age differences in the effects of instructed ER strategies, with some moderators suggesting more consistent effectiveness for older compared to younger adults.
format: application/pdf
format: text/html
creator: Brooke Brady
creator: Ian I. Kneebone
creator: Nida Denson
creator: Phoebe E. Bailey
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6051
publisher: PeerJ Inc.
rights: © 2018 Brady et al.
abstract: The process model of emotion regulation (ER) is based on stages in the emotion generative process at which regulation may occur. This meta-analysis examines age-related differences in the subjective, behavioral, and physiological outcomes of instructed ER strategies that may be initiated after an emotional event has occurred; attentional deployment, cognitive change, and response modulation. Within-process strategy, stimulus type, and valence were also tested as potential moderators of the effect of age on ER. A systematic search of the literature identified 156 relevant comparisons from 11 studies. Few age-related differences were found. In our analysis of the subjective outcome of response modulation strategies, young adults used expressive enhancement successfully (g = 0.48), but not expressive suppression (g = 0.04). Response modulation strategies had a small positive effect among older adults, and enhancement vs suppression did not moderate this success (g = 0.31 and g = 0.10, respectively). Young adults effectively used response modulation to regulate subjective emotion in response to pictures (g = 0.41) but not films (g = 0.01). Older adults were able to regulate in response to both pictures (g = 0.26) and films (g = 0.11). Interestingly, both age groups effectively used detached reappraisal, but not positive reappraisal to regulate emotional behavior. We conclude that, in line with well-established theories of socioemotional aging, there is a lack of evidence for age differences in the effects of instructed ER strategies, with some moderators suggesting more consistent effectiveness for older compared to younger adults.
bibliographic citation: Brady et al. (2018) Systematic review and meta-analysis of age-related differences in instructed emotion regulation success. PeerJ 6:e6051 https://doi.org/10.7717/peerj.6051
date submitted: 2018-08-22
date accepted: 2018-10-31
issued: 2018-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brady
  given name: Brooke
author list: Agent
  family name: Kneebone
  given name: Ian I.
author list: Agent
  family name: Denson
  given name: Nida
author list: Agent
  family name: Bailey
  given name: Phoebe E.
doi: 10.7717/peerj.6051
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-18
copyright: © 2018 Brady et al.
attribution name: Brady et al.

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