PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A multidisciplinary approach to digital mapping of dinosaurian tracksites in the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia
items: The Non-Recurrent Laryngeal Nerve: a meta-analysis and clinical considerations
items: Testing of microsatellite multiplexes for individual identification of Cape Parrots (Poicephalus robustus): paternity testing and monitoring trade
items: Developmental and loco-like effects of a swainsonine-induced inhibition of α-mannosidase in the honey bee, Apis mellifera
items: Plant growth-promoting endophytic bacteria versus pathogenic infections: an example of Bacillus amyloliquefaciens RWL-1 and Fusarium oxysporum f. sp. lycopersici in tomato
items: Evaluation of procedures for typing of group B Streptococcus: a retrospective study
items: Climate-change-induced range shifts of three allergenic ragweeds (Ambrosia L.) in Europe and their potential impact on human health
items: Testing the habituation assumption underlying models of parasitoid foraging behavior
items: Effect of method of deduplication on estimation of differential gene expression using RNA-seq
items: High unexpected genetic diversity of a narrow endemic terrestrial mollusc

A multidisciplinary approach to digital mapping of dinosaurian tracksites in the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia
type: item
type: AcademicArticle
description: The abundant dinosaurian tracksites of the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia, form an important part of the West Kimberley National Heritage Place. Previous attempts to document these tracksites using traditional mapping techniques (e.g., surface overlays, transects and gridlines combined with conventional photography) have been hindered by the non-trivial challenges associated with working in this area, including, but not limited to: (1) the remoteness of many of the tracksites; (2) the occurrence of the majority of the tracksites in the intertidal zone; (3) the size and complexity of many of the tracksites, with some extending over several square kilometres. Using the historically significant and well-known dinosaurian tracksites at Minyirr (Gantheaume Point), we show how these issues can be overcome through the use of an integrated array of remote sensing tools. A combination of high-resolution aerial photography with both manned and unmanned aircraft, airborne and handheld high-resolution lidar imaging and handheld photography enabled the collection of large amounts of digital data from which 3D models of the tracksites at varying resolutions were constructed. The acquired data encompasses a very broad scale, from the sub-millimetre level that details individual tracks, to the multiple-kilometre level, which encompasses discontinuous tracksite exposures and large swathes of coastline. The former are useful for detailed ichnological work, while the latter are being employed to better understand the stratigraphic and temporal relationship between tracksites in a broader geological and palaeoecological context. These approaches and the data they can generate now provide a means through which digital conservation and temporal monitoring of the Dampier Peninsula’s dinosaurian tracksites can occur. As plans for the on-going management of the tracks in this area progress, analysis of the 3D data and 3D…
format: application/pdf
format: text/html
creator: Anthony Romilio
creator: Jorg M. Hacker
creator: Robert Zlot
creator: George Poropat
creator: Michael Bosse
creator: Steven W. Salisbury
subject: Paleontology
subject: Computational Science
description: doi:10.7717/peerj.3013
publisher: PeerJ Inc.
rights: © 2017 Romilio et al.
abstract: The abundant dinosaurian tracksites of the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia, form an important part of the West Kimberley National Heritage Place. Previous attempts to document these tracksites using traditional mapping techniques (e.g., surface overlays, transects and gridlines combined with conventional photography) have been hindered by the non-trivial challenges associated with working in this area, including, but not limited to: (1) the remoteness of many of the tracksites; (2) the occurrence of the majority of the tracksites in the intertidal zone; (3) the size and complexity of many of the tracksites, with some extending over several square kilometres. Using the historically significant and well-known dinosaurian tracksites at Minyirr (Gantheaume Point), we show how these issues can be overcome through the use of an integrated array of remote sensing tools. A combination of high-resolution aerial photography with both manned and unmanned aircraft, airborne and handheld high-resolution lidar imaging and handheld photography enabled the collection of large amounts of digital data from which 3D models of the tracksites at varying resolutions were constructed. The acquired data encompasses a very broad scale, from the sub-millimetre level that details individual tracks, to the multiple-kilometre level, which encompasses discontinuous tracksite exposures and large swathes of coastline. The former are useful for detailed ichnological work, while the latter are being employed to better understand the stratigraphic and temporal relationship between tracksites in a broader geological and palaeoecological context. These approaches and the data they can generate now provide a means through which digital conservation and temporal monitoring of the Dampier Peninsula’s dinosaurian tracksites can occur. As plans for the on-going management of the tracks in this area progress, analysis of the 3D data and 3D…
bibliographic citation: Romilio et al. (2017) A multidisciplinary approach to digital mapping of dinosaurian tracksites in the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia. PeerJ 5:e3013 https://doi.org/10.7717/peerj.3013
date submitted: 2016-12-07
date accepted: 2017-01-23
issued: 2017-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Romilio
  given name: Anthony
author list: Agent
  family name: Hacker
  given name: Jorg M.
author list: Agent
  family name: Zlot
  given name: Robert
author list: Agent
  family name: Poropat
  given name: George
author list: Agent
  family name: Bosse
  given name: Michael
author list: Agent
  family name: Salisbury
  given name: Steven W.
doi: 10.7717/peerj.3013
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-21
copyright: ©2017 Romilio et al.
attribution name: Romilio et al.

The Non-Recurrent Laryngeal Nerve: a meta-analysis and clinical considerations
type: item
type: AcademicArticle
description: Background The Non-Recurrent Laryngeal Nerve (NRLN) is a rare embryologically-derived variant of the Recurrent Laryngeal Nerve (RLN). The presence of an NRLN significantly increases the risk of iatrogenic injury and operative complications. Our aim was to provide a comprehensive meta-analysis of the overall prevalence of the NRLN, its origin, and its association with an aberrant subclavian artery. Methods Through March 2016, a database search was performed of PubMed, CNKI, ScienceDirect, EMBASE, BIOSIS, SciELO, and Web of Science. The references in the included articles were also extensively searched. At least two reviewers judged eligibility and assessed and extracted articles. MetaXL was used for analysis, with all pooled prevalence rates calculated using a random effects model. Heterogeneity among the included studies was assessed using the Chi2 test and the I2 statistic. Results Fifty-three studies (33,571 right RLNs) reported data on the prevalence of a right NRLN. The pooled prevalence estimate was 0.7% (95% CI [0.6–0.9]). The NRLN was found to originate from the vagus nerve at or above the laryngotracheal junction in 58.3% and below it in 41.7%. A right NRLN was associated with an aberrant subclavian artery in 86.7% of cases. Conclusion The NRLN is a rare yet very clinically relevant structure for surgeons and is associated with increased risk of iatrogenic injury, most often leading to temporary or permanent vocal cord paralysis. A thorough understanding of the prevalence, origin, and associated pathologies is vital for preventing injuries and complications.
format: application/pdf
format: text/html
creator: Brandon Michael Henry
creator: Silvia Sanna
creator: Matthew J. Graves
creator: Jens Vikse
creator: Beatrice Sanna
creator: Iwona M. Tomaszewska
creator: R. Shane Tubbs
creator: Jerzy A. Walocha
creator: Krzysztof A. Tomaszewski
subject: Anatomy and Physiology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.3012
publisher: PeerJ Inc.
rights: © 2017 Henry et al.
abstract: Background The Non-Recurrent Laryngeal Nerve (NRLN) is a rare embryologically-derived variant of the Recurrent Laryngeal Nerve (RLN). The presence of an NRLN significantly increases the risk of iatrogenic injury and operative complications. Our aim was to provide a comprehensive meta-analysis of the overall prevalence of the NRLN, its origin, and its association with an aberrant subclavian artery. Methods Through March 2016, a database search was performed of PubMed, CNKI, ScienceDirect, EMBASE, BIOSIS, SciELO, and Web of Science. The references in the included articles were also extensively searched. At least two reviewers judged eligibility and assessed and extracted articles. MetaXL was used for analysis, with all pooled prevalence rates calculated using a random effects model. Heterogeneity among the included studies was assessed using the Chi2 test and the I2 statistic. Results Fifty-three studies (33,571 right RLNs) reported data on the prevalence of a right NRLN. The pooled prevalence estimate was 0.7% (95% CI [0.6–0.9]). The NRLN was found to originate from the vagus nerve at or above the laryngotracheal junction in 58.3% and below it in 41.7%. A right NRLN was associated with an aberrant subclavian artery in 86.7% of cases. Conclusion The NRLN is a rare yet very clinically relevant structure for surgeons and is associated with increased risk of iatrogenic injury, most often leading to temporary or permanent vocal cord paralysis. A thorough understanding of the prevalence, origin, and associated pathologies is vital for preventing injuries and complications.
bibliographic citation: Henry et al. (2017) The Non-Recurrent Laryngeal Nerve: a meta-analysis and clinical considerations. PeerJ 5:e3012 https://doi.org/10.7717/peerj.3012
date submitted: 2016-07-25
date accepted: 2017-01-22
issued: 2017-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Henry
  given name: Brandon Michael
author list: Agent
  family name: Sanna
  given name: Silvia
author list: Agent
  family name: Graves
  given name: Matthew J.
author list: Agent
  family name: Vikse
  given name: Jens
author list: Agent
  family name: Sanna
  given name: Beatrice
author list: Agent
  family name: Tomaszewska
  given name: Iwona M.
author list: Agent
  family name: Tubbs
  given name: R. Shane
author list: Agent
  family name: Walocha
  given name: Jerzy A.
author list: Agent
  family name: Tomaszewski
  given name: Krzysztof A.
doi: 10.7717/peerj.3012
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-21
copyright: ©2017 Henry et al.
attribution name: Henry et al.

Testing of microsatellite multiplexes for individual identification of Cape Parrots (Poicephalus robustus): paternity testing and monitoring trade
type: item
type: AcademicArticle
description: Background Illegal trade in rare wildlife species is a major threat to many parrot species around the world. Wildlife forensics plays an important role in the preservation of endangered or threatened wildlife species. Identification of illegally harvested or traded animals through DNA techniques is one of the many methods used during forensic investigations. Natural populations of the South African endemic Cape Parrot (Poicephalus robustus) are negatively affected by the removal of eggs and chicks for the pet trade. Methods In this study, 16 microsatellite markers specifically designed for the South African endemic Cape Parrot (P. robustus) are assessed for their utility in forensic casework. Using these 16 loci, the genetic diversity of a subset of the captive Cape Parrot population was also assessed and compared to three wild Cape Parrot populations. Results It was determined that the full 16 locus panel has sufficient discriminatory power to be used in parentage analyses and can be used to determine if a bird has been bred in captivity and so can be legally traded or if it has been illegally removed from the wild. In cases where birds have been removed from the wild, this study suggests that a reduced 12 locus microsatellite panel has sufficient power to assign confiscated birds to geographic population of origin. Discussion The level of genetic diversity observed within the captive Cape Parrot population was similar to that observed in the wild populations, which suggests that the captive population is not suffering from decreased levels of genetic diversity. The captive Cape Parrots did however have double the number of private alleles compared to that observed in the most genetically diverse wild population. This is probably due to the presence of rare alleles present in the founder population, which has not been lost due to genetic drift, as many of the individuals tested in this study are F1–F3 wild descendants. The results from this study provide a suit of …
format: application/pdf
format: text/html
creator: Willem G. Coetzer
creator: Colleen T. Downs
creator: Mike R. Perrin
creator: Sandi Willows-Munro
subject: Conservation Biology
subject: Genetics
subject: Veterinary Medicine
subject: Zoology
subject: Legal Issues
description: doi:10.7717/peerj.2900
publisher: PeerJ Inc.
rights: © 2017 Coetzer et al.
abstract: Background Illegal trade in rare wildlife species is a major threat to many parrot species around the world. Wildlife forensics plays an important role in the preservation of endangered or threatened wildlife species. Identification of illegally harvested or traded animals through DNA techniques is one of the many methods used during forensic investigations. Natural populations of the South African endemic Cape Parrot (Poicephalus robustus) are negatively affected by the removal of eggs and chicks for the pet trade. Methods In this study, 16 microsatellite markers specifically designed for the South African endemic Cape Parrot (P. robustus) are assessed for their utility in forensic casework. Using these 16 loci, the genetic diversity of a subset of the captive Cape Parrot population was also assessed and compared to three wild Cape Parrot populations. Results It was determined that the full 16 locus panel has sufficient discriminatory power to be used in parentage analyses and can be used to determine if a bird has been bred in captivity and so can be legally traded or if it has been illegally removed from the wild. In cases where birds have been removed from the wild, this study suggests that a reduced 12 locus microsatellite panel has sufficient power to assign confiscated birds to geographic population of origin. Discussion The level of genetic diversity observed within the captive Cape Parrot population was similar to that observed in the wild populations, which suggests that the captive population is not suffering from decreased levels of genetic diversity. The captive Cape Parrots did however have double the number of private alleles compared to that observed in the most genetically diverse wild population. This is probably due to the presence of rare alleles present in the founder population, which has not been lost due to genetic drift, as many of the individuals tested in this study are F1–F3 wild descendants. The results from this study provide a suit of …
bibliographic citation: Coetzer et al. (2017) Testing of microsatellite multiplexes for individual identification of Cape Parrots (Poicephalus robustus): paternity testing and monitoring trade. PeerJ 5:e2900 https://doi.org/10.7717/peerj.2900
date submitted: 2016-07-19
date accepted: 2016-12-12
issued: 2017-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coetzer
  given name: Willem G.
author list: Agent
  family name: Downs
  given name: Colleen T.
author list: Agent
  family name: Perrin
  given name: Mike R.
author list: Agent
  family name: Willows-Munro
  given name: Sandi
doi: 10.7717/peerj.2900
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-21
copyright: © 2017 Coetzer et al.
attribution name: Coetzer et al.

Developmental and loco-like effects of a swainsonine-induced inhibition of α-mannosidase in the honey bee, Apis mellifera
type: item
type: AcademicArticle
description: Background Deficiencies in lysosomal a-mannosidase (LAM) activity in animals, caused either by mutations or by consuming toxic alkaloids, lead to severe phenotypic and behavioural consequences. Yet, epialleles adversely affecting LAM expression exist in the honey bee population suggesting that they might be beneficial in certain contexts and cannot be eliminated by natural selection. Methods We have used a combination of enzymology, molecular biology and metabolomics to characterise the catalytic properties of honey bee LAM (AmLAM) and then used an indolizidine alkaloid swainsonine to inhibit its activity in vitro and in vivo. Results We show that AmLAM is inhibited in vitro by swainsonine albeit at slightly higher concentrations than in other animals. Dietary exposure of growing larvae to swainsonine leads to pronounced metabolic changes affecting not only saccharides, but also amino acids, polyols and polyamines. Interestingly, the abundance of two fatty acids implicated in epigenetic regulation is significantly reduced in treated individuals. Additionally, swainsonie causes loco-like symptoms, increased mortality and a subtle decrease in the rate of larval growth resulting in a subsequent developmental delay in pupal metamorphosis. Discussion We consider our findings in the context of cellular LAM function, larval development, environmental toxicity and colony-level impacts. The observed developmental heterochrony in swainsonine-treated larvae with lower LAM activity offer a plausible explanation for the existence of epialleles with impaired LAM expression. Individuals carrying such epialleles provide an additional level of epigenetic diversity that could be beneficial for the functioning of a colony whereby more flexibility in timing of adult emergence might be useful for task allocation.
format: application/pdf
format: text/html
creator: Laura Wedd
creator: Regan Ashby
creator: Sylvain Foret
creator: Ryszard Maleszka
subject: Biochemistry
subject: Developmental Biology
subject: Molecular Biology
subject: Toxicology
description: doi:10.7717/peerj.3109
publisher: PeerJ Inc.
rights: © 2017 Wedd et al.
abstract: Background Deficiencies in lysosomal a-mannosidase (LAM) activity in animals, caused either by mutations or by consuming toxic alkaloids, lead to severe phenotypic and behavioural consequences. Yet, epialleles adversely affecting LAM expression exist in the honey bee population suggesting that they might be beneficial in certain contexts and cannot be eliminated by natural selection. Methods We have used a combination of enzymology, molecular biology and metabolomics to characterise the catalytic properties of honey bee LAM (AmLAM) and then used an indolizidine alkaloid swainsonine to inhibit its activity in vitro and in vivo. Results We show that AmLAM is inhibited in vitro by swainsonine albeit at slightly higher concentrations than in other animals. Dietary exposure of growing larvae to swainsonine leads to pronounced metabolic changes affecting not only saccharides, but also amino acids, polyols and polyamines. Interestingly, the abundance of two fatty acids implicated in epigenetic regulation is significantly reduced in treated individuals. Additionally, swainsonie causes loco-like symptoms, increased mortality and a subtle decrease in the rate of larval growth resulting in a subsequent developmental delay in pupal metamorphosis. Discussion We consider our findings in the context of cellular LAM function, larval development, environmental toxicity and colony-level impacts. The observed developmental heterochrony in swainsonine-treated larvae with lower LAM activity offer a plausible explanation for the existence of epialleles with impaired LAM expression. Individuals carrying such epialleles provide an additional level of epigenetic diversity that could be beneficial for the functioning of a colony whereby more flexibility in timing of adult emergence might be useful for task allocation.
bibliographic citation: Wedd et al. (2017) Developmental and loco-like effects of a swainsonine-induced inhibition of α-mannosidase in the honey bee, Apis mellifera. PeerJ 5:e3109 https://doi.org/10.7717/peerj.3109
date submitted: 2016-11-18
date accepted: 2017-02-20
issued: 2017-03-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wedd
  given name: Laura
author list: Agent
  family name: Ashby
  given name: Regan
author list: Agent
  family name: Foret
  given name: Sylvain
author list: Agent
  family name: Maleszka
  given name: Ryszard
doi: 10.7717/peerj.3109
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-16
copyright: ©2017 Wedd et al.
attribution name: Wedd et al.

Plant growth-promoting endophytic bacteria versus pathogenic infections: an example of Bacillus amyloliquefaciens RWL-1 and Fusarium oxysporum f. sp. lycopersici in tomato
type: item
type: AcademicArticle
description: Fungal pathogenic attacks are one of the major threats to the growth and productivity of crop plants. Currently, instead of synthetic fungicides, the use of plant growth-promoting bacterial endophytes has been considered intriguingly eco-friendly in nature. Here, we aimed to investigate the in vitro and in vivo antagonistic approach by using seed-borne endophytic Bacillus amyloliquefaciens RWL-1 against pathogenic Fusarium oxysporum f. sp. lycopersici. The results revealed significant suppression of pathogenic fungal growth by Bacillus amyloliquefaciens in vitro. Further to this, we inoculated tomato plants with RWL-1 and F. oxysporum f. sp. lycopersici in the root zone. The results showed that the growth attributes and biomass were significantly enhanced by endophytic-inoculation during disease incidence as compared to F. oxysporum f. sp. lycopersici infected plants. Under pathogenic infection, the RWL-1-applied plants showed increased amino acid metabolism of cell wall related (e.g., aspartic acid, glutamic acid, serine (Ser), and proline (Pro)) as compared to diseased plants. In case of endogenous phytohormones, significantly lower amount of jasmonic acid (JA) and higher amount of salicylic acid (SA) contents was recorded in RWL-1-treated diseased plants. The phytohormones regulation in disease incidences might be correlated with the ability of RWL-1 to produce organic acids (e.g., succinic acid, acetic acid, propionic acid, and citric acid) during the inoculation and infection of tomato plants. The current findings suggest that RWL-1 inoculation promoted and rescued plant growth by modulating defense hormones and regulating amino acids. This suggests that bacterial endophytes could be used for possible control of F. oxysporum f. sp. lycopersici in an eco-friendly way.
format: application/pdf
format: text/html
creator: Raheem Shahzad
creator: Abdul Latif Khan
creator: Saqib Bilal
creator: Sajjad Asaf
creator: In-Jung Lee
subject: Agricultural Science
subject: Biotechnology
subject: Plant Science
description: doi:10.7717/peerj.3107
publisher: PeerJ Inc.
rights: © 2017 Shahzad et al.
abstract: Fungal pathogenic attacks are one of the major threats to the growth and productivity of crop plants. Currently, instead of synthetic fungicides, the use of plant growth-promoting bacterial endophytes has been considered intriguingly eco-friendly in nature. Here, we aimed to investigate the in vitro and in vivo antagonistic approach by using seed-borne endophytic Bacillus amyloliquefaciens RWL-1 against pathogenic Fusarium oxysporum f. sp. lycopersici. The results revealed significant suppression of pathogenic fungal growth by Bacillus amyloliquefaciens in vitro. Further to this, we inoculated tomato plants with RWL-1 and F. oxysporum f. sp. lycopersici in the root zone. The results showed that the growth attributes and biomass were significantly enhanced by endophytic-inoculation during disease incidence as compared to F. oxysporum f. sp. lycopersici infected plants. Under pathogenic infection, the RWL-1-applied plants showed increased amino acid metabolism of cell wall related (e.g., aspartic acid, glutamic acid, serine (Ser), and proline (Pro)) as compared to diseased plants. In case of endogenous phytohormones, significantly lower amount of jasmonic acid (JA) and higher amount of salicylic acid (SA) contents was recorded in RWL-1-treated diseased plants. The phytohormones regulation in disease incidences might be correlated with the ability of RWL-1 to produce organic acids (e.g., succinic acid, acetic acid, propionic acid, and citric acid) during the inoculation and infection of tomato plants. The current findings suggest that RWL-1 inoculation promoted and rescued plant growth by modulating defense hormones and regulating amino acids. This suggests that bacterial endophytes could be used for possible control of F. oxysporum f. sp. lycopersici in an eco-friendly way.
bibliographic citation: Shahzad et al. (2017) Plant growth-promoting endophytic bacteria versus pathogenic infections: an example of Bacillus amyloliquefaciens RWL-1 and Fusarium oxysporum f. sp. lycopersici in tomato. PeerJ 5:e3107 https://doi.org/10.7717/peerj.3107
date submitted: 2016-10-26
date accepted: 2017-02-20
issued: 2017-03-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shahzad
  given name: Raheem
author list: Agent
  family name: Khan
  given name: Abdul Latif
author list: Agent
  family name: Bilal
  given name: Saqib
author list: Agent
  family name: Asaf
  given name: Sajjad
author list: Agent
  family name: Lee
  given name: In-Jung
doi: 10.7717/peerj.3107
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-16
copyright: © 2017 Shahzad et al.
attribution name: Shahzad et al.

Evaluation of procedures for typing of group B Streptococcus: a retrospective study
type: item
type: AcademicArticle
description: Background This study evaluates two procedures for typing of Streptococcus agalactiae (group B streptococci; GBS) isolates, using retrospective typing data from the period 2010 to 2014 with a commercial latex agglutination test (latex test) and the Lancefield precipitation test (LP test). Furthermore, the genotype distribution of phenotypically non-typable (NT) GBS isolates is presented. We also raise the awareness, that the difference in typing results obtained by phenotypical methods and genotype based methods may have implications on vaccine surveillance in case a GBS vaccine is introduced. Methods A total of 616 clinical GBS isolates from 2010 to 2014 were tested with both a latex test and the LP test. Among these, 66 isolates were genotyped by PCR, including 41 isolates that were phenotypically NT. Results The latex test provided a serotype for 83.8% of the isolates (95% CI [80.7–86.6]) compared to 87.5% (95% CI [84.6–90.0]) obtained by the LP method. The two assays provided identical capsular identification for all sero-typeable isolates (excluding NT isolates). The PCR assay provided a genotype designation to the 41 isolates defined as phenotypically NT isolates. Discussion We found that the latex test showed a slightly lower identification percentage than the LP test. Our recommendation is to use the latex agglutination as the routine primary assay for GBS surveillance, and then use the more labour intensive precipitation test on the NT isolates to increase the serotyping rate. A genotype could be assigned to all the phenotypically NT isolates, however, as a consequence genotyping will overestimate the coverage from possible future capsular polysaccharide based GBS vaccines.
format: application/pdf
format: text/html
creator: Hans-Christian Slotved
creator: Steen Hoffmann
subject: Microbiology
subject: Epidemiology
subject: Infectious Diseases
subject: Internal Medicine
subject: Pediatrics
description: doi:10.7717/peerj.3105
publisher: PeerJ Inc.
rights: © 2017 Slotved and Hoffmann
abstract: Background This study evaluates two procedures for typing of Streptococcus agalactiae (group B streptococci; GBS) isolates, using retrospective typing data from the period 2010 to 2014 with a commercial latex agglutination test (latex test) and the Lancefield precipitation test (LP test). Furthermore, the genotype distribution of phenotypically non-typable (NT) GBS isolates is presented. We also raise the awareness, that the difference in typing results obtained by phenotypical methods and genotype based methods may have implications on vaccine surveillance in case a GBS vaccine is introduced. Methods A total of 616 clinical GBS isolates from 2010 to 2014 were tested with both a latex test and the LP test. Among these, 66 isolates were genotyped by PCR, including 41 isolates that were phenotypically NT. Results The latex test provided a serotype for 83.8% of the isolates (95% CI [80.7–86.6]) compared to 87.5% (95% CI [84.6–90.0]) obtained by the LP method. The two assays provided identical capsular identification for all sero-typeable isolates (excluding NT isolates). The PCR assay provided a genotype designation to the 41 isolates defined as phenotypically NT isolates. Discussion We found that the latex test showed a slightly lower identification percentage than the LP test. Our recommendation is to use the latex agglutination as the routine primary assay for GBS surveillance, and then use the more labour intensive precipitation test on the NT isolates to increase the serotyping rate. A genotype could be assigned to all the phenotypically NT isolates, however, as a consequence genotyping will overestimate the coverage from possible future capsular polysaccharide based GBS vaccines.
bibliographic citation: Slotved et al. (2017) Evaluation of procedures for typing of group B Streptococcus: a retrospective study. PeerJ 5:e3105 https://doi.org/10.7717/peerj.3105
date submitted: 2016-12-23
date accepted: 2017-02-18
issued: 2017-03-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Slotved
  given name: Hans-Christian
author list: Agent
  family name: Hoffmann
  given name: Steen
doi: 10.7717/peerj.3105
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-16
copyright: ©2017 Slotved and Hoffmann
attribution name: Slotved and Hoffmann

Climate-change-induced range shifts of three allergenic ragweeds (Ambrosia L.) in Europe and their potential impact on human health
type: item
type: AcademicArticle
description: Invasive allergenic plant species may have severe health-related impacts. In this study we aim to predict the effects of climate change on the distribution of three allergenic ragweed species (Ambrosia spp.) in Europe and discuss the potential associated health impact. We built species distribution models based on presence-only data for three ragweed species, using MAXENT software. Future climatic habitat suitability was modeled under two IPCC climate change scenarios (RCP 6.0 and RCP 8.5). We quantify the extent of the increase in ‘high allergy risk’ (HAR) areas, i.e., parts of Europe with climatic conditions corresponding to the highest quartile (25%) of present day habitat suitability for each of the three species. We estimate that by year 2100, the distribution range of all three ragweed species increases towards Northern and Eastern Europe under all climate scenarios. HAR areas will expand in Europe by 27–100%, depending on species and climate scenario. Novel HAR areas will occur mostly in Denmark, France, Germany, Russia and the Baltic countries, and overlap with densely populated cities such as Paris and St. Petersburg. We conclude that areas in Europe affected by severe ragweed associated allergy problems are likely to increase substantially by year 2100, affecting millions of people. To avoid this, management strategies must be developed that restrict ragweed dispersal and establishment of new populations. Precautionary efforts should limit the spread of ragweed seeds and reduce existing populations. Only by applying cross-countries management plans can managers mitigate future health risks and economical consequences of a ragweed expansion in Europe.
format: application/pdf
format: text/html
creator: Karen Rasmussen
creator: Jakob Thyrring
creator: Robert Muscarella
creator: Finn Borchsenius
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Environmental Sciences
subject: Plant Science
description: doi:10.7717/peerj.3104
publisher: PeerJ Inc.
rights: © 2017 Rasmussen et al.
abstract: Invasive allergenic plant species may have severe health-related impacts. In this study we aim to predict the effects of climate change on the distribution of three allergenic ragweed species (Ambrosia spp.) in Europe and discuss the potential associated health impact. We built species distribution models based on presence-only data for three ragweed species, using MAXENT software. Future climatic habitat suitability was modeled under two IPCC climate change scenarios (RCP 6.0 and RCP 8.5). We quantify the extent of the increase in ‘high allergy risk’ (HAR) areas, i.e., parts of Europe with climatic conditions corresponding to the highest quartile (25%) of present day habitat suitability for each of the three species. We estimate that by year 2100, the distribution range of all three ragweed species increases towards Northern and Eastern Europe under all climate scenarios. HAR areas will expand in Europe by 27–100%, depending on species and climate scenario. Novel HAR areas will occur mostly in Denmark, France, Germany, Russia and the Baltic countries, and overlap with densely populated cities such as Paris and St. Petersburg. We conclude that areas in Europe affected by severe ragweed associated allergy problems are likely to increase substantially by year 2100, affecting millions of people. To avoid this, management strategies must be developed that restrict ragweed dispersal and establishment of new populations. Precautionary efforts should limit the spread of ragweed seeds and reduce existing populations. Only by applying cross-countries management plans can managers mitigate future health risks and economical consequences of a ragweed expansion in Europe.
bibliographic citation: Rasmussen et al. (2017) Climate-change-induced range shifts of three allergenic ragweeds (Ambrosia L.) in Europe and their potential impact on human health. PeerJ 5:e3104 https://doi.org/10.7717/peerj.3104
date submitted: 2016-08-22
date accepted: 2017-02-18
issued: 2017-03-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rasmussen
  given name: Karen
author list: Agent
  family name: Thyrring
  given name: Jakob
author list: Agent
  family name: Muscarella
  given name: Robert
author list: Agent
  family name: Borchsenius
  given name: Finn
doi: 10.7717/peerj.3104
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-16
copyright: ©2017 Rasmussen et al.
attribution name: Rasmussen et al.

Testing the habituation assumption underlying models of parasitoid foraging behavior
type: item
type: AcademicArticle
description: Background Habituation, a form of non-associative learning, has several well-defined characteristics that apply to a wide range of physiological and behavioral responses in many organisms. In classic patch time allocation models, habituation is considered to be a major mechanistic component of parasitoid behavioral strategies. However, parasitoid behavioral responses to host cues have not previously been tested for the known, specific characteristics of habituation. Methods In the laboratory, we tested whether the foraging behavior of the egg parasitoid Trissolcus basalis shows specific characteristics of habituation in response to consecutive encounters with patches of host (Nezara viridula) chemical contact cues (footprints), in particular: (i) a training interval-dependent decline in response intensity, and (ii) a training interval-dependent recovery of the response. Results As would be expected of a habituated response, wasps trained at higher frequencies decreased their behavioral response to host footprints more quickly and to a greater degree than those trained at low frequencies, and subsequently showed a more rapid, although partial, recovery of their behavioral response to host footprints. This putative habituation learning could not be blocked by cold anesthesia, ingestion of an ATPase inhibitor, or ingestion of a protein synthesis inhibitor. Discussion Our study provides support for the assumption that diminishing responses of parasitoids to chemical indicators of host presence constitutes habituation as opposed to sensory fatigue, and provides a preliminary basis for exploring the underlying mechanisms.
format: application/pdf
format: text/html
creator: Paul K. Abram
creator: Antonino Cusumano
creator: Katrina Abram
creator: Stefano Colazza
creator: Ezio Peri
subject: Animal Behavior
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.3097
publisher: PeerJ Inc.
rights: © 2017 Abram et al.
abstract: Background Habituation, a form of non-associative learning, has several well-defined characteristics that apply to a wide range of physiological and behavioral responses in many organisms. In classic patch time allocation models, habituation is considered to be a major mechanistic component of parasitoid behavioral strategies. However, parasitoid behavioral responses to host cues have not previously been tested for the known, specific characteristics of habituation. Methods In the laboratory, we tested whether the foraging behavior of the egg parasitoid Trissolcus basalis shows specific characteristics of habituation in response to consecutive encounters with patches of host (Nezara viridula) chemical contact cues (footprints), in particular: (i) a training interval-dependent decline in response intensity, and (ii) a training interval-dependent recovery of the response. Results As would be expected of a habituated response, wasps trained at higher frequencies decreased their behavioral response to host footprints more quickly and to a greater degree than those trained at low frequencies, and subsequently showed a more rapid, although partial, recovery of their behavioral response to host footprints. This putative habituation learning could not be blocked by cold anesthesia, ingestion of an ATPase inhibitor, or ingestion of a protein synthesis inhibitor. Discussion Our study provides support for the assumption that diminishing responses of parasitoids to chemical indicators of host presence constitutes habituation as opposed to sensory fatigue, and provides a preliminary basis for exploring the underlying mechanisms.
bibliographic citation: Abram et al. (2017) Testing the habituation assumption underlying models of parasitoid foraging behavior. PeerJ 5:e3097 https://doi.org/10.7717/peerj.3097
date submitted: 2016-10-21
date accepted: 2017-02-15
issued: 2017-03-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abram
  given name: Paul K.
author list: Agent
  family name: Cusumano
  given name: Antonino
author list: Agent
  family name: Abram
  given name: Katrina
author list: Agent
  family name: Colazza
  given name: Stefano
author list: Agent
  family name: Peri
  given name: Ezio
doi: 10.7717/peerj.3097
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-16
copyright: ©2017 Abram et al.
attribution name: Abram et al.

Effect of method of deduplication on estimation of differential gene expression using RNA-seq
type: item
type: AcademicArticle
description: Background RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. Results To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in SAMtools, and deduplication based on one or two molecular indices (MI). We also analyzed the influence of sequencing layout (single read or paired end) and read length. We found that deduplication without MI greatly affects estimated expression values; this effect is the most pronounced for highly expressed genes. Conclusion The use of unique molecular identifiers greatly improves accuracy of RNA-seq analysis, especially for highly expressed genes. We developed a set of scripts that enable handling of MI and their incorporation into RNA-seq analysis pipelines. Deduplication without MI affects results of differential gene expression analysis, producing a high proportion of false negative results. The absence of duplicate read removal is biased towards false positives. In those cases where using MI is not possible, we recommend using paired-end sequencing layout.
format: application/pdf
format: text/html
creator: Anna V. Klepikova
creator: Artem S. Kasianov
creator: Mikhail S. Chesnokov
creator: Natalia L. Lazarevich
creator: Aleksey A. Penin
creator: Maria Logacheva
subject: Genomics
description: doi:10.7717/peerj.3091
publisher: PeerJ Inc.
rights: © 2017 Klepikova et al.
abstract: Background RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. Results To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in SAMtools, and deduplication based on one or two molecular indices (MI). We also analyzed the influence of sequencing layout (single read or paired end) and read length. We found that deduplication without MI greatly affects estimated expression values; this effect is the most pronounced for highly expressed genes. Conclusion The use of unique molecular identifiers greatly improves accuracy of RNA-seq analysis, especially for highly expressed genes. We developed a set of scripts that enable handling of MI and their incorporation into RNA-seq analysis pipelines. Deduplication without MI affects results of differential gene expression analysis, producing a high proportion of false negative results. The absence of duplicate read removal is biased towards false positives. In those cases where using MI is not possible, we recommend using paired-end sequencing layout.
bibliographic citation: Klepikova et al. (2017) Effect of method of deduplication on estimation of differential gene expression using RNA-seq. PeerJ 5:e3091 https://doi.org/10.7717/peerj.3091
date submitted: 2016-11-29
date accepted: 2017-02-14
issued: 2017-03-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klepikova
  given name: Anna V.
author list: Agent
  family name: Kasianov
  given name: Artem S.
author list: Agent
  family name: Chesnokov
  given name: Mikhail S.
author list: Agent
  family name: Lazarevich
  given name: Natalia L.
author list: Agent
  family name: Penin
  given name: Aleksey A.
author list: Agent
  family name: Logacheva
  given name: Maria
doi: 10.7717/peerj.3091
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-16
copyright: ©2017 Klepikova et al.
attribution name: Klepikova et al.

High unexpected genetic diversity of a narrow endemic terrestrial mollusc
type: item
type: AcademicArticle
description: The Iberian Peninsula has an extensive record of species displaying strong genetic structure as a result of their survival in isolated pockets throughout the Pleistocene ice ages. We used mitochondrial and nuclear sequence data to analyze phylogeographic patterns in endemic land snails from a valley of central Portugal (Vale da Couda), putatively assigned to Candidula coudensis, that show an exceptionally narrow distributional range. The genetic survey presented here shows the existence of five main mitochondrial lineages in Vale da Couda that do not cluster together suggesting independent evolutionary histories. Our results also indicate a departure from the expectation that species with restricted distributions have low genetic variability. The putative past and contemporary models of geographic distribution of Vale da Couda lineages are compatible with a scenario of species co-existence in more southern locations during the last glacial maximum (LGM) followed by a post-LGM northern dispersal tracking the species optimal thermal, humidity and soil physical conditions.
format: application/pdf
format: text/html
creator: Pedro M. Madeira
creator: Rosa M. Chefaoui
creator: Regina L. Cunha
creator: Francisco Moreira
creator: Susana Dias
creator: Gonçalo Calado
creator: Rita Castilho
subject: Conservation Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.3069
publisher: PeerJ Inc.
rights: © 2017 Madeira et al.
abstract: The Iberian Peninsula has an extensive record of species displaying strong genetic structure as a result of their survival in isolated pockets throughout the Pleistocene ice ages. We used mitochondrial and nuclear sequence data to analyze phylogeographic patterns in endemic land snails from a valley of central Portugal (Vale da Couda), putatively assigned to Candidula coudensis, that show an exceptionally narrow distributional range. The genetic survey presented here shows the existence of five main mitochondrial lineages in Vale da Couda that do not cluster together suggesting independent evolutionary histories. Our results also indicate a departure from the expectation that species with restricted distributions have low genetic variability. The putative past and contemporary models of geographic distribution of Vale da Couda lineages are compatible with a scenario of species co-existence in more southern locations during the last glacial maximum (LGM) followed by a post-LGM northern dispersal tracking the species optimal thermal, humidity and soil physical conditions.
bibliographic citation: Madeira et al. (2017) High unexpected genetic diversity of a narrow endemic terrestrial mollusc. PeerJ 5:e3069 https://doi.org/10.7717/peerj.3069
date submitted: 2016-08-29
date accepted: 2017-02-06
issued: 2017-03-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Madeira
  given name: Pedro M.
author list: Agent
  family name: Chefaoui
  given name: Rosa M.
author list: Agent
  family name: Cunha
  given name: Regina L.
author list: Agent
  family name: Moreira
  given name: Francisco
author list: Agent
  family name: Dias
  given name: Susana
author list: Agent
  family name: Calado
  given name: Gonçalo
author list: Agent
  family name: Castilho
  given name: Rita
doi: 10.7717/peerj.3069
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-16
copyright: ©2017 Madeira et al.
attribution name: Madeira et al.

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