PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Pulmonary transcriptomic responses indicate a dual role of inflammation in pneumonia development and viral clearance during 2009 pandemic influenza infection
items: The effects of familiarity on escape responses in the Trinidadian guppy (Poecilia reticulata)
items: Evidence for continual hybridization rather than hybrid speciation between Ligularia duciformis and L. paradoxa (Asteraceae)
items: Light induced intraspecific variability in response to thermal stress in the hard coral Stylophora pistillata
items: Illegal use of natural resources in federal protected areas of the Brazilian Amazon
items: https://peerj.com/articles/3901
items: Infection of army ant pupae by two new parasitoid mites (Mesostigmata: Uropodina)
items: Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences
items: Virulence test using nematodes to prescreen Nocardia species capable of inducing neurodegeneration and behavioral disorders
items: Clinical outcomes of residual or recurrent nasopharyngeal carcinoma treated with endoscopic nasopharyngectomy plus chemoradiotherapy or with chemoradiotherapy alone: a retrospective study

Pulmonary transcriptomic responses indicate a dual role of inflammation in pneumonia development and viral clearance during 2009 pandemic influenza infection
type: item
type: AcademicArticle
description: Background The interaction between influenza virus and the host response to infection clearly plays an important role in determining the outcome of infection. While much is known on the participation of inflammation on the pathogenesis of severe A (H1N1) pandemic 09-influenza virus, its role in the course of non-fatal pneumonia has not been fully addressed. Methods A systems biology approach was used to define gene expression profiles, histology and viral dynamics in the lungs of healthy immune-competent mice with pneumonia caused by a human influenza A (H1N1) pdm09 virus, which successfully resolved the infection. Results Viral infection activated a marked pro-inflammatory response at the lung level paralleling the emergence of histological changes. Cellular immune response and cytokine signaling were the two signaling pathway categories more representative of our analysis. This transcriptome response was associated to viral clearance, and its resolution was accompanied by resolution of histopathology. Discussion These findings suggest a dual role of pulmonary inflammation in viral clearance and development of pneumonia during non-fatal infection caused by the 2009 pandemic influenza virus. Understanding the dynamics of the host’s transcriptomic and virological changes over the course of the infection caused by A (H1N1) pdm09 virus may help identifying the immune response profiles associated with an effective response against influenza virus.
format: application/pdf
format: text/html
creator: Raquel Almansa
creator: Pamela Martínez-Orellana
creator: Lucía Rico
creator: Verónica Iglesias
creator: Alicia Ortega
creator: Beatriz Vidaña
creator: Jorge Martínez
creator: Ana Expósito
creator: María Montoya
creator: Jesús F. Bermejo-Martin
subject: Global Health
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.3915
publisher: PeerJ Inc.
rights: © 2017 Almansa et al.
abstract: Background The interaction between influenza virus and the host response to infection clearly plays an important role in determining the outcome of infection. While much is known on the participation of inflammation on the pathogenesis of severe A (H1N1) pandemic 09-influenza virus, its role in the course of non-fatal pneumonia has not been fully addressed. Methods A systems biology approach was used to define gene expression profiles, histology and viral dynamics in the lungs of healthy immune-competent mice with pneumonia caused by a human influenza A (H1N1) pdm09 virus, which successfully resolved the infection. Results Viral infection activated a marked pro-inflammatory response at the lung level paralleling the emergence of histological changes. Cellular immune response and cytokine signaling were the two signaling pathway categories more representative of our analysis. This transcriptome response was associated to viral clearance, and its resolution was accompanied by resolution of histopathology. Discussion These findings suggest a dual role of pulmonary inflammation in viral clearance and development of pneumonia during non-fatal infection caused by the 2009 pandemic influenza virus. Understanding the dynamics of the host’s transcriptomic and virological changes over the course of the infection caused by A (H1N1) pdm09 virus may help identifying the immune response profiles associated with an effective response against influenza virus.
bibliographic citation: Almansa et al. (2017) Pulmonary transcriptomic responses indicate a dual role of inflammation in pneumonia development and viral clearance during 2009 pandemic influenza infection. PeerJ 5:e3915 https://doi.org/10.7717/peerj.3915
date submitted: 2017-05-23
date accepted: 2017-09-21
issued: 2017-10-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Almansa
  given name: Raquel
author list: Agent
  family name: Martínez-Orellana
  given name: Pamela
author list: Agent
  family name: Rico
  given name: Lucía
author list: Agent
  family name: Iglesias
  given name: Verónica
author list: Agent
  family name: Ortega
  given name: Alicia
author list: Agent
  family name: Vidaña
  given name: Beatriz
author list: Agent
  family name: Martínez
  given name: Jorge
author list: Agent
  family name: Expósito
  given name: Ana
author list: Agent
  family name: Montoya
  given name: María
author list: Agent
  family name: Bermejo-Martin
  given name: Jesús F.
doi: 10.7717/peerj.3915
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-11
copyright: © 2017 Almansa et al.
attribution name: Almansa et al.

The effects of familiarity on escape responses in the Trinidadian guppy (Poecilia reticulata)
type: item
type: AcademicArticle
description: Predation is the main cause of mortality during early life stages. The ability to avoid and evade potential threats is, therefore, favoured to evolve during the early stages of life. It is also during these early stages that the process of familiarization occurs. It has long been recognized that associating with familiar individuals confers antipredator benefits. Yet gaps in our knowledge remain about how predator evasion is affected by social experience during early stages. In this study, we test the hypothesis that familiarization acquired during early life stages improves escape responses. Using the guppy Poecilia reticulata, we examine the effect of different recent social conditions in the three main components of predator evasion. Using high-speed motion analysis, we compared the number of individuals in each test group that responded to a visual stimulus, their reactive distance and magnitude of their response (maximum speed, maximum acceleration and distance) in groups composed either of familiar or non-familiar individuals. Contrary to the prediction, groups composed of familiar individuals were less responsive than groups of unfamiliar individuals. Reactive distance and magnitude of response were more dependent on individual size rather than on familiarity. Larger individuals reached higher maximum speeds and total distances in their escape response. Our result indicates that familiarity is likely to affect behaviour earlier in a predator-prey interaction, which then affects the behavioural component of the response. Taken together, our study contributes to previous ones by distinguishing which components of an escape response are modulated by familiarity.
format: application/pdf
format: text/html
creator: Hayley L. Wolcott
creator: Alfredo F. Ojanguren
creator: Miguel Barbosa
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
description: doi:10.7717/peerj.3899
publisher: PeerJ Inc.
rights: © 2017 Wolcott et al.
abstract: Predation is the main cause of mortality during early life stages. The ability to avoid and evade potential threats is, therefore, favoured to evolve during the early stages of life. It is also during these early stages that the process of familiarization occurs. It has long been recognized that associating with familiar individuals confers antipredator benefits. Yet gaps in our knowledge remain about how predator evasion is affected by social experience during early stages. In this study, we test the hypothesis that familiarization acquired during early life stages improves escape responses. Using the guppy Poecilia reticulata, we examine the effect of different recent social conditions in the three main components of predator evasion. Using high-speed motion analysis, we compared the number of individuals in each test group that responded to a visual stimulus, their reactive distance and magnitude of their response (maximum speed, maximum acceleration and distance) in groups composed either of familiar or non-familiar individuals. Contrary to the prediction, groups composed of familiar individuals were less responsive than groups of unfamiliar individuals. Reactive distance and magnitude of response were more dependent on individual size rather than on familiarity. Larger individuals reached higher maximum speeds and total distances in their escape response. Our result indicates that familiarity is likely to affect behaviour earlier in a predator-prey interaction, which then affects the behavioural component of the response. Taken together, our study contributes to previous ones by distinguishing which components of an escape response are modulated by familiarity.
bibliographic citation: Wolcott et al. (2017) The effects of familiarity on escape responses in the Trinidadian guppy (Poecilia reticulata). PeerJ 5:e3899 https://doi.org/10.7717/peerj.3899
date submitted: 2017-04-19
date accepted: 2017-09-16
issued: 2017-10-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wolcott
  given name: Hayley L.
author list: Agent
  family name: Ojanguren
  given name: Alfredo F.
author list: Agent
  family name: Barbosa
  given name: Miguel
doi: 10.7717/peerj.3899
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-11
copyright: ©2017 Wolcott et al.
attribution name: Wolcott et al.

Evidence for continual hybridization rather than hybrid speciation between Ligularia duciformis and L. paradoxa (Asteraceae)
type: item
type: AcademicArticle
description: Background Hybrids possess phenotypic traits that are often intermediate between their parental taxa, which commonly serves as evidence of hybridization in morphological analyses. Natural hybridization has been shown to occur frequently in Ligularia (Asteraceae). In a previous study, Ligularia ×maoniushanensis was demonstrated as a natural hybrid species between L. duciformis and L. paradoxa based on morphological and reproductive traits. Methods We used three chloroplast (cpDNA) fragments (psbA-trnH, trnL-rpl32 and trnQ-5′rps16), the nuclear ribosomal internal transcribed spacer (nrITS), and co-dominant SSR and dominant ISSR markers to study natural hybridization between L. duciformis and L. paradoxa growing sympatrically in two locations. Parental taxa were inferred using network analyses of cpDNA and nrITS haplotypes. Admixture among individuals was examined using the Bayesian clustering programs STRUCTURE and NewHybrids based on the SSR and ISSR data; and potential introgression in the SSR loci was assessed using the INTROGRESS package. Results The putative parental species were clearly distinguished from other sympatric Ligularia species by nrITS data, and L. ×maoniushanensis individuals were confirmed to be the hybrid offspring of L. duciformis and L. paradoxa. Moreover, introgression was detected among several individuals morphologically identified as L. duciformis or L. paradoxa. Analyses of the cpDNA data revealed primarily unidirectional hybridization between L. duciformis and L. paradoxa, with L. paradoxa as the maternal parent in Mt. Maoniu, whereas bidirectional but asymmetrical hybridization was inferred to occur in Heihai Lake. The STRUCTURE analyses based on the SSR data detected two distinct clusters among the three taxa. The NewHybrids analyses showed that individuals circumscribed as L. ×maoniushanensis were dominated by early- and later-generation and backcrossing hybrids. The NewHybrids results based on the ISSR data were congruent with SSR resu…
format: application/pdf
format: text/html
creator: Rong Zhang
creator: Xun Gong
creator: Ryan Folk
subject: Evolutionary Studies
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.3884
publisher: PeerJ Inc.
rights: © 2017 Zhang et al.
abstract: Background Hybrids possess phenotypic traits that are often intermediate between their parental taxa, which commonly serves as evidence of hybridization in morphological analyses. Natural hybridization has been shown to occur frequently in Ligularia (Asteraceae). In a previous study, Ligularia ×maoniushanensis was demonstrated as a natural hybrid species between L. duciformis and L. paradoxa based on morphological and reproductive traits. Methods We used three chloroplast (cpDNA) fragments (psbA-trnH, trnL-rpl32 and trnQ-5′rps16), the nuclear ribosomal internal transcribed spacer (nrITS), and co-dominant SSR and dominant ISSR markers to study natural hybridization between L. duciformis and L. paradoxa growing sympatrically in two locations. Parental taxa were inferred using network analyses of cpDNA and nrITS haplotypes. Admixture among individuals was examined using the Bayesian clustering programs STRUCTURE and NewHybrids based on the SSR and ISSR data; and potential introgression in the SSR loci was assessed using the INTROGRESS package. Results The putative parental species were clearly distinguished from other sympatric Ligularia species by nrITS data, and L. ×maoniushanensis individuals were confirmed to be the hybrid offspring of L. duciformis and L. paradoxa. Moreover, introgression was detected among several individuals morphologically identified as L. duciformis or L. paradoxa. Analyses of the cpDNA data revealed primarily unidirectional hybridization between L. duciformis and L. paradoxa, with L. paradoxa as the maternal parent in Mt. Maoniu, whereas bidirectional but asymmetrical hybridization was inferred to occur in Heihai Lake. The STRUCTURE analyses based on the SSR data detected two distinct clusters among the three taxa. The NewHybrids analyses showed that individuals circumscribed as L. ×maoniushanensis were dominated by early- and later-generation and backcrossing hybrids. The NewHybrids results based on the ISSR data were congruent with SSR resu…
bibliographic citation: Zhang et al. (2017) Evidence for continual hybridization rather than hybrid speciation between Ligularia duciformis and L. paradoxa (Asteraceae). PeerJ 5:e3884 https://doi.org/10.7717/peerj.3884
date submitted: 2016-12-12
date accepted: 2017-09-13
issued: 2017-10-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Rong
author list: Agent
  family name: Gong
  given name: Xun
author list: Agent
  family name: Folk
  given name: Ryan
doi: 10.7717/peerj.3884
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-11
copyright: ©2017 Zhang et al.
attribution name: Zhang et al.

Light induced intraspecific variability in response to thermal stress in the hard coral Stylophora pistillata
type: item
type: AcademicArticle
description: Recent research suggests that prior exposure of several months to elevated irradiance induces enhanced thermal tolerance in scleractinian corals. While this tolerance has been reported at the species level, individual coral colonies may react differently due to individual variability in thermal tolerance. As thermal anomalies are predicted to become common in the upcoming future, intraspecific variation may be key to the survival of coral populations. In order to study light-history based thermal stress responses on individual colonies, we developed a preliminary microcosm experiment where three randomly chosen, aquacultured colonies of the model coral Stylophora pistillata were exposed to two irradiance treatments (200 and 400 μmol photons m−2 s−1) for 31 days, followed by artificially induced heat stress (∼33.4 °C). We found different responses to occur at both the intraspecific and the intracolonial levels, as indicated by either equal, less severe, delayed, and/or even non-necrotic responses of corals previously exposed to the irradiance of 400 compared to 200 μmol photons m−2 s−1. In addition, all individual colonies revealed light-enhanced calcification. Finally, elevated irradiance resulted in a lower chlorophyll a concentration in one colony compared to the control treatment, and the same colony displayed more rapid bleaching compared to the other ones. Taken together, this study highlights the potential importance of intra-individual variability in physiological responses of scleractinian corals and provides recommendations for improving methodological designs for future studies.
format: application/pdf
format: text/html
creator: Arjen Tilstra
creator: Tim Wijgerde
creator: Francisco Dini-Andreote
creator: Britas Klemens Eriksson
creator: Joana Falcão Salles
creator: Ido Pen
creator: Ronald Osinga
creator: Christian Wild
subject: Ecology
subject: Marine Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.3802
publisher: PeerJ Inc.
rights: © 2017 Tilstra et al.
abstract: Recent research suggests that prior exposure of several months to elevated irradiance induces enhanced thermal tolerance in scleractinian corals. While this tolerance has been reported at the species level, individual coral colonies may react differently due to individual variability in thermal tolerance. As thermal anomalies are predicted to become common in the upcoming future, intraspecific variation may be key to the survival of coral populations. In order to study light-history based thermal stress responses on individual colonies, we developed a preliminary microcosm experiment where three randomly chosen, aquacultured colonies of the model coral Stylophora pistillata were exposed to two irradiance treatments (200 and 400 μmol photons m−2 s−1) for 31 days, followed by artificially induced heat stress (∼33.4 °C). We found different responses to occur at both the intraspecific and the intracolonial levels, as indicated by either equal, less severe, delayed, and/or even non-necrotic responses of corals previously exposed to the irradiance of 400 compared to 200 μmol photons m−2 s−1. In addition, all individual colonies revealed light-enhanced calcification. Finally, elevated irradiance resulted in a lower chlorophyll a concentration in one colony compared to the control treatment, and the same colony displayed more rapid bleaching compared to the other ones. Taken together, this study highlights the potential importance of intra-individual variability in physiological responses of scleractinian corals and provides recommendations for improving methodological designs for future studies.
bibliographic citation: Tilstra et al. (2017) Light induced intraspecific variability in response to thermal stress in the hard coral Stylophora pistillata. PeerJ 5:e3802 https://doi.org/10.7717/peerj.3802
date submitted: 2017-02-16
date accepted: 2017-08-23
issued: 2017-10-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tilstra
  given name: Arjen
author list: Agent
  family name: Wijgerde
  given name: Tim
author list: Agent
  family name: Dini-Andreote
  given name: Francisco
author list: Agent
  family name: Eriksson
  given name: Britas Klemens
author list: Agent
  family name: Salles
  given name: Joana Falcão
author list: Agent
  family name: Pen
  given name: Ido
author list: Agent
  family name: Osinga
  given name: Ronald
author list: Agent
  family name: Wild
  given name: Christian
doi: 10.7717/peerj.3802
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-11
copyright: © 2017 Tilstra et al.
attribution name: Tilstra et al.

Illegal use of natural resources in federal protected areas of the Brazilian Amazon
type: item
type: AcademicArticle
description: Background The Brazilian Amazon is the world’s largest rainforest regions and plays a key role in biodiversity conservation as well as climate adaptation and mitigation. The government has created a network of protected areas (PAs) to ensure long-term conservation of the region. However, despite the importance of and positive advances in the establishment of PAs, natural resource depletion in the Brazilian Amazon is pervasive. Methods We evaluated a total of 4,243 official law enforcement records generated between 2010 and 2015 to understand the geographical distribution of the illegal use of resources in federal PAs in the Brazilian Amazon. We classified illegal activities into ten categories and used generalized additive models (GAMs) to evaluate the relationship between illegal use of natural resources inside PAs with management type, age of PAs, population density, and accessibility. Results We found 27 types of illegal use of natural resources that were grouped into 10 categories of illegal activities. Most infractions were related to suppression and degradation of vegetation (37.40%), followed by illegal fishing (27.30%) and hunting activities (18.20%). The explanatory power of the GAMs was low for all categories of illegal activity, with a maximum explained variation of 41.2% for illegal activities as a whole, and a minimum of 14.6% for hunting activities. Discussion These findings demonstrate that even though PAs are fundamental for nature conservation in the Brazilian Amazon, the pressures and threats posed by human activities include a broad range of illegal uses of natural resources. Population density up to 50 km from a PA is a key variable, influencing illegal activities. These threats endanger long-term conservation and many efforts are still needed to maintain PAs that are large enough and sufficiently intact to maintain ecosystem functions and protect biodiversity.
format: application/pdf
format: text/html
creator: Érico E. Kauano
creator: Jose M.C. Silva
creator: Fernanda Michalski
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Environmental Sciences
subject: Legal Issues
description: doi:10.7717/peerj.3902
publisher: PeerJ Inc.
rights: © 2017 Kauano et al.
abstract: Background The Brazilian Amazon is the world’s largest rainforest regions and plays a key role in biodiversity conservation as well as climate adaptation and mitigation. The government has created a network of protected areas (PAs) to ensure long-term conservation of the region. However, despite the importance of and positive advances in the establishment of PAs, natural resource depletion in the Brazilian Amazon is pervasive. Methods We evaluated a total of 4,243 official law enforcement records generated between 2010 and 2015 to understand the geographical distribution of the illegal use of resources in federal PAs in the Brazilian Amazon. We classified illegal activities into ten categories and used generalized additive models (GAMs) to evaluate the relationship between illegal use of natural resources inside PAs with management type, age of PAs, population density, and accessibility. Results We found 27 types of illegal use of natural resources that were grouped into 10 categories of illegal activities. Most infractions were related to suppression and degradation of vegetation (37.40%), followed by illegal fishing (27.30%) and hunting activities (18.20%). The explanatory power of the GAMs was low for all categories of illegal activity, with a maximum explained variation of 41.2% for illegal activities as a whole, and a minimum of 14.6% for hunting activities. Discussion These findings demonstrate that even though PAs are fundamental for nature conservation in the Brazilian Amazon, the pressures and threats posed by human activities include a broad range of illegal uses of natural resources. Population density up to 50 km from a PA is a key variable, influencing illegal activities. These threats endanger long-term conservation and many efforts are still needed to maintain PAs that are large enough and sufficiently intact to maintain ecosystem functions and protect biodiversity.
bibliographic citation: Kauano et al. (2017) Illegal use of natural resources in federal protected areas of the Brazilian Amazon. PeerJ 5:e3902 https://doi.org/10.7717/peerj.3902
date submitted: 2017-06-19
date accepted: 2017-09-18
issued: 2017-10-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kauano
  given name: Érico E.
author list: Agent
  family name: Silva
  given name: Jose M.C.
author list: Agent
  family name: Michalski
  given name: Fernanda
doi: 10.7717/peerj.3902
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-10
copyright: ©2017 Kauano et al.
attribution name: Kauano et al.

https://peerj.com/articles/3901
type: item
type: AcademicArticle
title: Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region
description: We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100–375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). The Numts ranged from 226–19,522 nt in length and included copies of all mitochondrial genes except tRNAPro, ND6, and tRNAGlu. Strix occidentalis caurina and S. varia exhibited an average of 10.74% (8.68% uncorrected p-distance) divergence across the non-tRNA mitochondrial genes.
format: application/pdf
format: text/html
creator: Zachary R. Hanna
creator: James B. Henderson
creator: Anna B. Sellas
creator: Jérôme Fuchs
creator: Rauri C.K. Bowie
creator: John P. Dumbacher
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.3901
publisher: PeerJ Inc.
rights: © 2017 Hanna et al.
abstract: We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100–375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). The Numts ranged from 226–19,522 nt in length and included copies of all mitochondrial genes except tRNAPro, ND6, and tRNAGlu. Strix occidentalis caurina and S. varia exhibited an average of 10.74% (8.68% uncorrected p-distance) divergence across the non-tRNA mitochondrial genes.
bibliographic citation: Hanna et al. (2017) Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region. PeerJ 5:e3901 https://doi.org/10.7717/peerj.3901
date submitted: 2017-07-31
date accepted: 2017-09-18
issued: 2017-10-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hanna
  given name: Zachary R.
author list: Agent
  family name: Henderson
  given name: James B.
author list: Agent
  family name: Sellas
  given name: Anna B.
author list: Agent
  family name: Fuchs
  given name: Jérôme
author list: Agent
  family name: Bowie
  given name: Rauri C.K.
author list: Agent
  family name: Dumbacher
  given name: John P.
doi: 10.7717/peerj.3901
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-10
copyright: ©2017 Hanna et al.
attribution name: Hanna et al.

Infection of army ant pupae by two new parasitoid mites (Mesostigmata: Uropodina)
type: item
type: AcademicArticle
description: A great variety of parasites and parasitoids exploit ant societies. Among them are the Mesostigmata mites, a particularly common and diverse group of ant-associated arthropods. While parasitism is ubiquitous in Mesostigmata, parasitoidism has only been described in the genus Macrodinychus. Yet information about the basic biology of most Macrodinychus species is lacking. Out of 24 formally described species, information about basic life-history traits is only available for three species. Here we formally describe two new Macrodinychus species, i.e. Macrodinychus hilpertae and Macrodinychus derbyensis. In both species, immature stages developed as ecto-parasitoids on ant pupae of the South-East Asian army ant Leptogenys distinguenda. By piercing the developing ant with their chelicera, the mites apparently suck ant hemolymph, ultimately killing host individuals. We compare infection rates among all studied Macrodinychus species and discuss possible host countermeasures against parasitoidism. The cryptic lifestyle of living inside ant nests has certainly hampered the scientific discovery of Macrodinychus mites and we expect that many more macrodinychid species await scientific discovery and description.
format: application/pdf
format: text/html
creator: Adrian Brückner
creator: Hans Klompen
creator: Andrew Iain Bruce
creator: Rosli Hashim
creator: Christoph von Beeren
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.3870
publisher: PeerJ Inc.
rights: © 2017 Brückner et al.
abstract: A great variety of parasites and parasitoids exploit ant societies. Among them are the Mesostigmata mites, a particularly common and diverse group of ant-associated arthropods. While parasitism is ubiquitous in Mesostigmata, parasitoidism has only been described in the genus Macrodinychus. Yet information about the basic biology of most Macrodinychus species is lacking. Out of 24 formally described species, information about basic life-history traits is only available for three species. Here we formally describe two new Macrodinychus species, i.e. Macrodinychus hilpertae and Macrodinychus derbyensis. In both species, immature stages developed as ecto-parasitoids on ant pupae of the South-East Asian army ant Leptogenys distinguenda. By piercing the developing ant with their chelicera, the mites apparently suck ant hemolymph, ultimately killing host individuals. We compare infection rates among all studied Macrodinychus species and discuss possible host countermeasures against parasitoidism. The cryptic lifestyle of living inside ant nests has certainly hampered the scientific discovery of Macrodinychus mites and we expect that many more macrodinychid species await scientific discovery and description.
bibliographic citation: Brückner et al. (2017) Infection of army ant pupae by two new parasitoid mites (Mesostigmata: Uropodina). PeerJ 5:e3870 https://doi.org/10.7717/peerj.3870
date submitted: 2017-08-01
date accepted: 2017-09-08
issued: 2017-10-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brückner
  given name: Adrian
author list: Agent
  family name: Klompen
  given name: Hans
author list: Agent
  family name: Bruce
  given name: Andrew Iain
author list: Agent
  family name: Hashim
  given name: Rosli
author list: Agent
  family name: von Beeren
  given name: Christoph
doi: 10.7717/peerj.3870
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-10
copyright: ©2017 Brückner et al.
attribution name: Brückner et al.

Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences
type: item
type: AcademicArticle
description: Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients.
format: application/pdf
format: text/html
creator: Ali Z. Ijaz
creator: Thomas C. Jeffries
creator: Umer Z. Ijaz
creator: Kelly Hamonts
creator: Brajesh K. Singh
subject: Biodiversity
subject: Biogeography
subject: Bioinformatics
subject: Microbiology
description: doi:10.7717/peerj.3827
publisher: PeerJ Inc.
rights: © 2017 Ijaz et al.
abstract: Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients.
bibliographic citation: Ijaz et al. (2017) Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences. PeerJ 5:e3827 https://doi.org/10.7717/peerj.3827
date submitted: 2017-05-18
date accepted: 2017-08-29
issued: 2017-10-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ijaz
  given name: Ali Z.
author list: Agent
  family name: Jeffries
  given name: Thomas C.
author list: Agent
  family name: Ijaz
  given name: Umer Z.
author list: Agent
  family name: Hamonts
  given name: Kelly
author list: Agent
  family name: Singh
  given name: Brajesh K.
doi: 10.7717/peerj.3827
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-10
copyright: ©2017 Ijaz et al.
attribution name: Ijaz et al.

Virulence test using nematodes to prescreen Nocardia species capable of inducing neurodegeneration and behavioral disorders
type: item
type: AcademicArticle
description: Background Parkinson’s disease (PD) is a disorder characterized by dopaminergic neuron programmed cell death. The etiology of PD remains uncertain—some cases are due to selected genes associated with familial heredity, others are due to environmental exposure to toxic components, but over 90% of cases have a sporadic origin. Nocardia are Actinobacteria that can cause human diseases like nocardiosis. This illness can lead to lung infection or central nervous system (CNS) invasion in both immunocompromised and immunocompetent individuals. The main species involved in CNS are N. farcinica, N. nova, N. brasiliensis and N. cyriacigeorgica. Some studies have highlighted the ability of N. cyriacigeorgica to induce Parkinson’s disease-like symptoms in animals. Actinobacteria are known to produce a large variety of secondary metabolites, some of which can be neurotoxic. We hypothesized that neurotoxic secondary metabolite production and the onset of PD-like symptoms in animals could be linked. Methods Here we used a method to screen bacteria that could induce dopaminergic neurodegeneration before performing mouse experiments. Results The nematode Caenorhabditis elegans allowed us to demonstrate that Nocardia strains belonging to N. cyriacigeorgica and N. farcinica species can induce dopaminergic neurodegeneration. Strains of interest involved with the nematodes in neurodegenerative disorders were then injected in mice. Infected mice had behavioral disorders that may be related to neuronal damage, thus confirming the ability of Nocardia strains to induce neurodegeneration. These behavioral disorders were induced by N. cyriacigeorgica species (N. cyriacigeorgica GUH-2 and N. cyriacigeorgica 44484) and N. farcinica 10152. Discussion We conclude that C. elegans is a good model for detecting Nocardia strains involved in neurodegeneration. This model allowed us to detect bacteria with high neurodegenerative effects and which should be studied in mice to characterize the induced be…
format: application/pdf
format: text/html
creator: Claire Bernardin Souibgui
creator: Anthony Zoropogui
creator: Jeremy Voisin
creator: Sebastien Ribun
creator: Valentin Vasselon
creator: Petar Pujic
creator: Veronica Rodriguez-Nava
creator: Patrick Belly
creator: Benoit Cournoyer
creator: Didier Blaha
subject: Microbiology
subject: Neuroscience
subject: Infectious Diseases
description: doi:10.7717/peerj.3823
publisher: PeerJ Inc.
rights: © 2017 Bernardin Souibgui et al.
abstract: Background Parkinson’s disease (PD) is a disorder characterized by dopaminergic neuron programmed cell death. The etiology of PD remains uncertain—some cases are due to selected genes associated with familial heredity, others are due to environmental exposure to toxic components, but over 90% of cases have a sporadic origin. Nocardia are Actinobacteria that can cause human diseases like nocardiosis. This illness can lead to lung infection or central nervous system (CNS) invasion in both immunocompromised and immunocompetent individuals. The main species involved in CNS are N. farcinica, N. nova, N. brasiliensis and N. cyriacigeorgica. Some studies have highlighted the ability of N. cyriacigeorgica to induce Parkinson’s disease-like symptoms in animals. Actinobacteria are known to produce a large variety of secondary metabolites, some of which can be neurotoxic. We hypothesized that neurotoxic secondary metabolite production and the onset of PD-like symptoms in animals could be linked. Methods Here we used a method to screen bacteria that could induce dopaminergic neurodegeneration before performing mouse experiments. Results The nematode Caenorhabditis elegans allowed us to demonstrate that Nocardia strains belonging to N. cyriacigeorgica and N. farcinica species can induce dopaminergic neurodegeneration. Strains of interest involved with the nematodes in neurodegenerative disorders were then injected in mice. Infected mice had behavioral disorders that may be related to neuronal damage, thus confirming the ability of Nocardia strains to induce neurodegeneration. These behavioral disorders were induced by N. cyriacigeorgica species (N. cyriacigeorgica GUH-2 and N. cyriacigeorgica 44484) and N. farcinica 10152. Discussion We conclude that C. elegans is a good model for detecting Nocardia strains involved in neurodegeneration. This model allowed us to detect bacteria with high neurodegenerative effects and which should be studied in mice to characterize the induced be…
bibliographic citation: Bernardin Souibgui et al. (2017) Virulence test using nematodes to prescreen Nocardia species capable of inducing neurodegeneration and behavioral disorders. PeerJ 5:e3823 https://doi.org/10.7717/peerj.3823
date submitted: 2017-06-13
date accepted: 2017-08-28
issued: 2017-10-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bernardin Souibgui
  given name: Claire
author list: Agent
  family name: Zoropogui
  given name: Anthony
author list: Agent
  family name: Voisin
  given name: Jeremy
author list: Agent
  family name: Ribun
  given name: Sebastien
author list: Agent
  family name: Vasselon
  given name: Valentin
author list: Agent
  family name: Pujic
  given name: Petar
author list: Agent
  family name: Rodriguez-Nava
  given name: Veronica
author list: Agent
  family name: Belly
  given name: Patrick
author list: Agent
  family name: Cournoyer
  given name: Benoit
author list: Agent
  family name: Blaha
  given name: Didier
doi: 10.7717/peerj.3823
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-10
copyright: ©2017 Bernardin Souibgui et al.
attribution name: Bernardin Souibgui et al.

Clinical outcomes of residual or recurrent nasopharyngeal carcinoma treated with endoscopic nasopharyngectomy plus chemoradiotherapy or with chemoradiotherapy alone: a retrospective study
type: item
type: AcademicArticle
description: Background Local residual and recurrent nasopharyngeal carcinoma (NPC) generally shows treatment failure after standard radiotherapy with or without concurrent chemotherapy. Whether endoscopic nasopharyngectomy might provide an additional therapeutic advantage remains controversial. Therefore, we retrospectively compared the clinical prognoses of patients with residual or recurrent NPC treated with endoscopic nasopharyngectomy combined with chemoradiotherapy (CRT) with those of patients treated with CRT alone. Methods and Materials A total of sixty-two patients with local residual or recurrent NPC were studied retrospectively: 36 patients received endoscopic nasopharyngectomy combined with CRT, whereas 26 patients who refused the surgery or had surgical contraindications received CRT alone. Serum Epstein-Barr virus (EBV) DNA levels were measured pre- and post-treatment. The differences in prognosis between the two treatment regimens and the pre- and post-treatment changes in EBV-DNA levels were analyzed. Results The median follow-up time was 31 months, with a 3-year overall survival (OS) of 51.40% and a 3-year disease-free survival (DFS) of 46.86%. The surgery + CRT group had a better OS than the CRT alone group did (χ2 = 4.054, P = 0.044). The pretreatment EBV-DNA levels showed a positive correlation with the clinical staging of recurrent NPC (χ2 = 11.674, P = 0.009). Patients with negative pretreatment serum EBV-DNA levels showed a superior OS to those of patients who tested positive for EBV-DNA (>0 copy/mL) (χ2 = 9.833, P = 0.002). The post-treatment EBV-DNA levels, compared with the pretreatment levels, decreased significantly in the surgery + CRT group (Z = − 3.484, P = 0.000). In contrast, the EBV-DNA levels after CRT alone did not decrease significantly (Z = − 1.956, P = 0.051). Multivariate analysis indicated that local staging, pretreatment EBV-DNA load, and the treatment method were independent risk factors for OS. Subgroup analysis indicated that the pati…
format: application/pdf
format: text/html
creator: Jingjin Weng
creator: Jiazhang Wei
creator: Jinyuan Si
creator: Yangda Qin
creator: Min Li
creator: Fei Liu
creator: Yongfeng Si
creator: Jiping Su
subject: Oncology
subject: Otorhinolaryngology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.3912
publisher: PeerJ Inc.
rights: © 2017 Weng et al.
abstract: Background Local residual and recurrent nasopharyngeal carcinoma (NPC) generally shows treatment failure after standard radiotherapy with or without concurrent chemotherapy. Whether endoscopic nasopharyngectomy might provide an additional therapeutic advantage remains controversial. Therefore, we retrospectively compared the clinical prognoses of patients with residual or recurrent NPC treated with endoscopic nasopharyngectomy combined with chemoradiotherapy (CRT) with those of patients treated with CRT alone. Methods and Materials A total of sixty-two patients with local residual or recurrent NPC were studied retrospectively: 36 patients received endoscopic nasopharyngectomy combined with CRT, whereas 26 patients who refused the surgery or had surgical contraindications received CRT alone. Serum Epstein-Barr virus (EBV) DNA levels were measured pre- and post-treatment. The differences in prognosis between the two treatment regimens and the pre- and post-treatment changes in EBV-DNA levels were analyzed. Results The median follow-up time was 31 months, with a 3-year overall survival (OS) of 51.40% and a 3-year disease-free survival (DFS) of 46.86%. The surgery + CRT group had a better OS than the CRT alone group did (χ2 = 4.054, P = 0.044). The pretreatment EBV-DNA levels showed a positive correlation with the clinical staging of recurrent NPC (χ2 = 11.674, P = 0.009). Patients with negative pretreatment serum EBV-DNA levels showed a superior OS to those of patients who tested positive for EBV-DNA (>0 copy/mL) (χ2 = 9.833, P = 0.002). The post-treatment EBV-DNA levels, compared with the pretreatment levels, decreased significantly in the surgery + CRT group (Z = − 3.484, P = 0.000). In contrast, the EBV-DNA levels after CRT alone did not decrease significantly (Z = − 1.956, P = 0.051). Multivariate analysis indicated that local staging, pretreatment EBV-DNA load, and the treatment method were independent risk factors for OS. Subgroup analysis indicated that the pati…
bibliographic citation: Weng et al. (2017) Clinical outcomes of residual or recurrent nasopharyngeal carcinoma treated with endoscopic nasopharyngectomy plus chemoradiotherapy or with chemoradiotherapy alone: a retrospective study. PeerJ 5:e3912 https://doi.org/10.7717/peerj.3912
date submitted: 2017-06-21
date accepted: 2017-09-19
issued: 2017-10-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weng
  given name: Jingjin
author list: Agent
  family name: Wei
  given name: Jiazhang
author list: Agent
  family name: Si
  given name: Jinyuan
author list: Agent
  family name: Qin
  given name: Yangda
author list: Agent
  family name: Li
  given name: Min
author list: Agent
  family name: Liu
  given name: Fei
author list: Agent
  family name: Si
  given name: Yongfeng
author list: Agent
  family name: Su
  given name: Jiping
doi: 10.7717/peerj.3912
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-09
copyright: ©2017 Weng et al.
attribution name: Weng et al.

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