PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Retrospective study of prognostic factors in pediatric invasive pneumococcal disease
items: Antibiotic resistance potential of the healthy preterm infant gut microbiome
items: Validation of ultrasonographic muscle thickness measurements as compared to the gold standard of computed tomography in dogs
items: Effects of groundwater abstraction on two keystone tree species in an arid savanna national park
items: Halocarbon emissions by selected tropical seaweeds: species-specific and compound-specific responses under changing pH
items: Polymorphism in the major histocompatibility complex (MHC class II B) genes of the Rufous-backed Bunting (Emberiza jankowskii)
items: Size matters: relationships between body size and body mass of common coastal, aquatic invertebrates in the Baltic Sea
items: Exploration of immunoglobulin transcriptomes from mice immunized with three-finger toxins and phospholipases A2 from the Central American coral snake, Micrurus nigrocinctus
items: No apparent influence of psychometrically-defined schizotypy on orientation-dependent contextual modulation of visual contrast detection
items: Brood size and sex ratio in response to host quality and wasp traits in the gregarious parasitoid Oomyzus sokolowskii (Hymenoptera: Eulophidae)

Retrospective study of prognostic factors in pediatric invasive pneumococcal disease
type: item
type: AcademicArticle
description: Streptococcus pneumoniae remains the leading causative pathogen in pediatric pneumonia and bacteremia throughout the world. The invasive pneumococcal disease (IPD) is known as isolation of S. pneumoniae from a normally sterile site (e.g., blood, cerebrospinal fluid, synovial fluid, pericardial fluid, pleural fluid, or peritoneal fluid). The aim of this study is to survey the clinical manifestations and laboratory results of IPD and identify the prognostic factors of mortality. From January 2001 to December 2006, a retrospective review of chart was performed in a teaching hospital in Taipei. The hospitalized pediatric patients with the diagnosis of pneumonia, arthritis, infectious endocarditis, meningitis or sepsis were recruited. Among them, 50 patients were pneumococcal infections proved by positive culture results or antigen tests. Clinical manifestations, laboratory data and hospitalization courses were analyzed. The median age was 3.5-year-old and there were 30 male patients (60%). Eight patients (16%) had underlying disease such as leukemia or congenital heart disease. Hemolytic uremic syndrome (HUS) was observed in ten patients and extracorporeal membrane oxygenation (ECMO) was performed in three patients. Leukocytosis, elevated C-reactive protein and AST level were noted in most of the patients. The overall mortality rate was 10%. We found that leukopenia, thrombocytopenia and high CRP level were significant predictors for mortality. In conclusion, S. pneumoniae remains an important health threat worldwide and IPD is life-threatening with high mortality rate. We found leukopenia, thrombocytopenia, and high CRP levels to be associated with mortality in pediatric IPD, and these factors are worthy of special attention at admission. Although we failed to identify a statistically significant prognostic factor in multivariate analysis due to relatively small sample size, we suggest an aggressive antibiotic treatment in patients with these factors at admission. Furt…
format: application/pdf
format: text/html
creator: Nan-Chang Chiu
creator: Hsin Chi
creator: Chun-Chih Peng
creator: Hung-Yang Chang
creator: Daniel Tsung-Ning Huang
creator: Lung Chang
creator: Wei-Te Lei
creator: Chien-Yu Lin
subject: Emergency and Critical Care
subject: Epidemiology
subject: Infectious Diseases
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.2941
publisher: PeerJ Inc.
rights: © 2017 Chiu et al.
abstract: Streptococcus pneumoniae remains the leading causative pathogen in pediatric pneumonia and bacteremia throughout the world. The invasive pneumococcal disease (IPD) is known as isolation of S. pneumoniae from a normally sterile site (e.g., blood, cerebrospinal fluid, synovial fluid, pericardial fluid, pleural fluid, or peritoneal fluid). The aim of this study is to survey the clinical manifestations and laboratory results of IPD and identify the prognostic factors of mortality. From January 2001 to December 2006, a retrospective review of chart was performed in a teaching hospital in Taipei. The hospitalized pediatric patients with the diagnosis of pneumonia, arthritis, infectious endocarditis, meningitis or sepsis were recruited. Among them, 50 patients were pneumococcal infections proved by positive culture results or antigen tests. Clinical manifestations, laboratory data and hospitalization courses were analyzed. The median age was 3.5-year-old and there were 30 male patients (60%). Eight patients (16%) had underlying disease such as leukemia or congenital heart disease. Hemolytic uremic syndrome (HUS) was observed in ten patients and extracorporeal membrane oxygenation (ECMO) was performed in three patients. Leukocytosis, elevated C-reactive protein and AST level were noted in most of the patients. The overall mortality rate was 10%. We found that leukopenia, thrombocytopenia and high CRP level were significant predictors for mortality. In conclusion, S. pneumoniae remains an important health threat worldwide and IPD is life-threatening with high mortality rate. We found leukopenia, thrombocytopenia, and high CRP levels to be associated with mortality in pediatric IPD, and these factors are worthy of special attention at admission. Although we failed to identify a statistically significant prognostic factor in multivariate analysis due to relatively small sample size, we suggest an aggressive antibiotic treatment in patients with these factors at admission. Furt…
bibliographic citation: Chiu et al. (2017) Retrospective study of prognostic factors in pediatric invasive pneumococcal disease. PeerJ 5:e2941 https://doi.org/10.7717/peerj.2941
date submitted: 2016-10-02
date accepted: 2016-12-26
issued: 2017-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chiu
  given name: Nan-Chang
author list: Agent
  family name: Chi
  given name: Hsin
author list: Agent
  family name: Peng
  given name: Chun-Chih
author list: Agent
  family name: Chang
  given name: Hung-Yang
author list: Agent
  family name: Huang
  given name: Daniel Tsung-Ning
author list: Agent
  family name: Chang
  given name: Lung
author list: Agent
  family name: Lei
  given name: Wei-Te
author list: Agent
  family name: Lin
  given name: Chien-Yu
doi: 10.7717/peerj.2941
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-25
copyright: ©2017 Chiu et al.
attribution name: Chiu et al.

Antibiotic resistance potential of the healthy preterm infant gut microbiome
type: item
type: AcademicArticle
description: Background Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. Results Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. Conclusions We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.
format: application/pdf
format: text/html
creator: Graham Rose
creator: Alexander G. Shaw
creator: Kathleen Sim
creator: David J. Wooldridge
creator: Ming-Shi Li
creator: Saheer Gharbia
creator: Raju Misra
creator: John Simon Kroll
subject: Computational Biology
subject: Genomics
subject: Microbiology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.2928
publisher: PeerJ Inc.
rights: © 2017 Rose et al.
abstract: Background Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. Results Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. Conclusions We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.
bibliographic citation: Rose et al. (2017) Antibiotic resistance potential of the healthy preterm infant gut microbiome. PeerJ 5:e2928 https://doi.org/10.7717/peerj.2928
date submitted: 2016-09-30
date accepted: 2016-12-20
issued: 2017-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rose
  given name: Graham
author list: Agent
  family name: Shaw
  given name: Alexander G.
author list: Agent
  family name: Sim
  given name: Kathleen
author list: Agent
  family name: Wooldridge
  given name: David J.
author list: Agent
  family name: Li
  given name: Ming-Shi
author list: Agent
  family name: Gharbia
  given name: Saheer
author list: Agent
  family name: Misra
  given name: Raju
author list: Agent
  family name: Kroll
  given name: John Simon
doi: 10.7717/peerj.2928
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-25
copyright: ©2017 Rose et al.
attribution name: Rose et al.

Validation of ultrasonographic muscle thickness measurements as compared to the gold standard of computed tomography in dogs
type: item
type: AcademicArticle
description: Objective The objective was to quantitatively evaluate the validity of ultrasonographic (US) muscle measurements as compared to the gold standard of computed tomography (CT) in the canine. Design This was a prospective study. Population Twenty-five, client-owned dogs scheduled for CT as part of a diagnostic work-up for the management of their primary disease process were included. Materials and Methods Specific appendicular (cubital flexors and extensors, coxofemoral flexors and extensors) and axial (temporalis, supraspinatus, infraspinatus, lumbar epaxials) muscle groups were selected for quantitative measure based on CT planning and patient position. Prior to CT scan, the skin over the muscle sites was shaved and marked with a permanent marker. Patient body position was determined based on the patient’s CT plan; positioning was consistent between CT and US imaging. To ensure identical imaging position for both CT and US measurements, radio-opaque fiducial markers were placed directly over the skin marks once the dog was positioned. Quantitative measurements (cm) for both lean muscle mass (LMM) and subcutaneous adipose (SQA) were recorded. Statistical comparisons between CT and US values were done separately for each site and type. Results Muscle groups and associated SQA measured by US and CT were not statistically different based on an adjusted p-value using Bonferroni’s correction (p < 0.0031). In addition, all LMM and SQA sites had good reliability and agreement (Cronbach’s α = 0.8 − 1.0) between the two metrics, excluding the coxofemoral extensor muscle group (Cronbach’s α = 0.73232). Linear regression analysis of muscle measures indicated close agreement (slope range 0.93–1.09) and minimal bias of variation (intercept range 0.05–0.11) between CT versus US modalities, with the exception of the coxofemoral extensor muscle. Similarly, SQA CT and US measures indicated close agreement with the slope range of 0.88–1.02 and minimal bias of variation with an intercep…
format: application/pdf
format: text/html
creator: Lindsey E. Bullen
creator: Maria G. Evola
creator: Emily H. Griffith
creator: Gabriela S. Seiler
creator: Korinn E. Saker
subject: Veterinary Medicine
subject: Nutrition
subject: Radiology and Medical Imaging
subject: Science and Medical Education
description: doi:10.7717/peerj.2926
publisher: PeerJ Inc.
rights: © 2017 Bullen et al.
abstract: Objective The objective was to quantitatively evaluate the validity of ultrasonographic (US) muscle measurements as compared to the gold standard of computed tomography (CT) in the canine. Design This was a prospective study. Population Twenty-five, client-owned dogs scheduled for CT as part of a diagnostic work-up for the management of their primary disease process were included. Materials and Methods Specific appendicular (cubital flexors and extensors, coxofemoral flexors and extensors) and axial (temporalis, supraspinatus, infraspinatus, lumbar epaxials) muscle groups were selected for quantitative measure based on CT planning and patient position. Prior to CT scan, the skin over the muscle sites was shaved and marked with a permanent marker. Patient body position was determined based on the patient’s CT plan; positioning was consistent between CT and US imaging. To ensure identical imaging position for both CT and US measurements, radio-opaque fiducial markers were placed directly over the skin marks once the dog was positioned. Quantitative measurements (cm) for both lean muscle mass (LMM) and subcutaneous adipose (SQA) were recorded. Statistical comparisons between CT and US values were done separately for each site and type. Results Muscle groups and associated SQA measured by US and CT were not statistically different based on an adjusted p-value using Bonferroni’s correction (p < 0.0031). In addition, all LMM and SQA sites had good reliability and agreement (Cronbach’s α = 0.8 − 1.0) between the two metrics, excluding the coxofemoral extensor muscle group (Cronbach’s α = 0.73232). Linear regression analysis of muscle measures indicated close agreement (slope range 0.93–1.09) and minimal bias of variation (intercept range 0.05–0.11) between CT versus US modalities, with the exception of the coxofemoral extensor muscle. Similarly, SQA CT and US measures indicated close agreement with the slope range of 0.88–1.02 and minimal bias of variation with an intercep…
bibliographic citation: Bullen et al. (2017) Validation of ultrasonographic muscle thickness measurements as compared to the gold standard of computed tomography in dogs. PeerJ 5:e2926 https://doi.org/10.7717/peerj.2926
date submitted: 2016-10-18
date accepted: 2016-12-19
issued: 2017-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bullen
  given name: Lindsey E.
author list: Agent
  family name: Evola
  given name: Maria G.
author list: Agent
  family name: Griffith
  given name: Emily H.
author list: Agent
  family name: Seiler
  given name: Gabriela S.
author list: Agent
  family name: Saker
  given name: Korinn E.
doi: 10.7717/peerj.2926
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-25
copyright: ©2017 Bullen et al.
attribution name: Bullen et al.

Effects of groundwater abstraction on two keystone tree species in an arid savanna national park
type: item
type: AcademicArticle
description: Background In arid systems with no surface water, deep boreholes in ephemeral river beds provide for humans and animals. With continually increasing infrastructure development for tourism in arid wildlife parks such as the Kgalagadi Transfrontier Park in southern Africa, we ask what effects increased abstraction may have on large trees. Large trees in arid savannas perform essential ecosystem services by providing food, shade, nesting sites and increased nutrients for many other plant and animal species and for this are regarded as keystone species. Methods We determine seasonal fluctuations in the water table while also determining the water source for the dominant large tree species in the Auob and Nossob rivers in the Park. We also determine the extent to which these trees are physiologically stressed using leaf δ13C, xylem pressure potentials, specific leaf area and an estimate of canopy death. We do this both upstream and downstream of a low water use borehole in the Auob River and a high water use borehole in the Nossob River. Results Our results show that the trees are indeed using deep groundwater in the wet season and that this is the same water used by people. In the dry season, trees in the Auob downstream of the active borehole become detached from the aquifer and use more isotopically enriched soil water. In the Nossob in the dry season, all trees use isotopically enriched soil water, and downstream of the active borehole use stomatal regulation to maintain leaf water potentials. These results suggest that trees in the more heavily utilised Nossob are under more water stress than those trees in the Auob but that trees in both rivers demonstrate physiological adaptation to the changes in available water with smaller heavier leaves, no significant canopy dieback and in the dry season in the Nossob stomatal regulation of leaf water potentials. Discussion An increase in abstraction of groundwater particularly at the Nossob borehole may cause an additional d…
format: application/pdf
format: text/html
creator: Eleanor Shadwell
creator: Edmund February
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Soil Science
description: doi:10.7717/peerj.2923
publisher: PeerJ Inc.
rights: © 2017 Shadwell and February
abstract: Background In arid systems with no surface water, deep boreholes in ephemeral river beds provide for humans and animals. With continually increasing infrastructure development for tourism in arid wildlife parks such as the Kgalagadi Transfrontier Park in southern Africa, we ask what effects increased abstraction may have on large trees. Large trees in arid savannas perform essential ecosystem services by providing food, shade, nesting sites and increased nutrients for many other plant and animal species and for this are regarded as keystone species. Methods We determine seasonal fluctuations in the water table while also determining the water source for the dominant large tree species in the Auob and Nossob rivers in the Park. We also determine the extent to which these trees are physiologically stressed using leaf δ13C, xylem pressure potentials, specific leaf area and an estimate of canopy death. We do this both upstream and downstream of a low water use borehole in the Auob River and a high water use borehole in the Nossob River. Results Our results show that the trees are indeed using deep groundwater in the wet season and that this is the same water used by people. In the dry season, trees in the Auob downstream of the active borehole become detached from the aquifer and use more isotopically enriched soil water. In the Nossob in the dry season, all trees use isotopically enriched soil water, and downstream of the active borehole use stomatal regulation to maintain leaf water potentials. These results suggest that trees in the more heavily utilised Nossob are under more water stress than those trees in the Auob but that trees in both rivers demonstrate physiological adaptation to the changes in available water with smaller heavier leaves, no significant canopy dieback and in the dry season in the Nossob stomatal regulation of leaf water potentials. Discussion An increase in abstraction of groundwater particularly at the Nossob borehole may cause an additional d…
bibliographic citation: Shadwell et al. (2017) Effects of groundwater abstraction on two keystone tree species in an arid savanna national park. PeerJ 5:e2923 https://doi.org/10.7717/peerj.2923
date submitted: 2016-09-15
date accepted: 2016-12-19
issued: 2017-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shadwell
  given name: Eleanor
author list: Agent
  family name: February
  given name: Edmund
doi: 10.7717/peerj.2923
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-25
copyright: ©2017 Shadwell and February
attribution name: Shadwell and February

Halocarbon emissions by selected tropical seaweeds: species-specific and compound-specific responses under changing pH
type: item
type: AcademicArticle
description: Five tropical seaweeds, Kappaphycus alvarezii (Doty) Doty ex P.C. Silva, Padina australis Hauck, Sargassum binderi Sonder ex J. Agardh (syn. S. aquifolium (Turner) C. Agardh), Sargassum siliquosum J. Agardh and Turbinaria conoides (J. Agardh) Kützing, were incubated in seawater of pH 8.0, 7.8 (ambient), 7.6, 7.4 and 7.2, to study the effects of changing seawater pH on halocarbon emissions. Eight halocarbon species known to be emitted by seaweeds were investigated: bromoform (CHBr3), dibro­momethane (CH2Br2), iodomethane (CH3I), diiodomethane (CH2I2), bromoiodomethane (CH2BrI), bromochlorometh­ane (CH2BrCl), bromodichloromethane (CHBrCl2), and dibro­mochloromethane (CHBr2Cl). These very short-lived halocarbon gases are believed to contribute to stratospheric halogen concentrations if released in the tropics. It was observed that the seaweeds emit all eight halocarbons assayed, with the exception of K. alvarezii and S. binderi for CH2I2 and CH3I respectively, which were not measurable at the achievable limit of detection. The effect of pH on halocarbon emission by the seaweeds was shown to be species-specific and compound specific. The highest percentage changes in emissions for the halocarbons of interest were observed at the lower pH levels of 7.2 and 7.4 especially in Padina australis and Sargassum spp., showing that lower seawater pH causes elevated emissions of some halocarbon compounds. In general the seaweed least affected by pH change in terms of types of halocarbon emission, was P. australis. The commercially farmed seaweed K. alvarezii was very sensitive to pH change as shown by the high increases in most of the compounds in all pH levels relative to ambient. In terms of percentage decrease in maximum quantum yield of photosynthesis (Fv∕Fm) prior to and after incubation, there were no significant correlations with the various pH levels tested for all seaweeds. The correlation between percentage decrease in the maximum quantum yield of photosynthesis (Fv∕Fm) …
format: application/pdf
format: text/html
creator: Paramjeet Kaur Mithoo-Singh
creator: Fiona S.-L. Keng
creator: Siew-Moi Phang
creator: Emma C. Leedham Elvidge
creator: William T. Sturges
creator: Gill Malin
creator: Noorsaadah Abd Rahman
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Biosphere Interactions
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.2918
publisher: PeerJ Inc.
rights: © 2017 Mithoo-Singh et al.
abstract: Five tropical seaweeds, Kappaphycus alvarezii (Doty) Doty ex P.C. Silva, Padina australis Hauck, Sargassum binderi Sonder ex J. Agardh (syn. S. aquifolium (Turner) C. Agardh), Sargassum siliquosum J. Agardh and Turbinaria conoides (J. Agardh) Kützing, were incubated in seawater of pH 8.0, 7.8 (ambient), 7.6, 7.4 and 7.2, to study the effects of changing seawater pH on halocarbon emissions. Eight halocarbon species known to be emitted by seaweeds were investigated: bromoform (CHBr3), dibro­momethane (CH2Br2), iodomethane (CH3I), diiodomethane (CH2I2), bromoiodomethane (CH2BrI), bromochlorometh­ane (CH2BrCl), bromodichloromethane (CHBrCl2), and dibro­mochloromethane (CHBr2Cl). These very short-lived halocarbon gases are believed to contribute to stratospheric halogen concentrations if released in the tropics. It was observed that the seaweeds emit all eight halocarbons assayed, with the exception of K. alvarezii and S. binderi for CH2I2 and CH3I respectively, which were not measurable at the achievable limit of detection. The effect of pH on halocarbon emission by the seaweeds was shown to be species-specific and compound specific. The highest percentage changes in emissions for the halocarbons of interest were observed at the lower pH levels of 7.2 and 7.4 especially in Padina australis and Sargassum spp., showing that lower seawater pH causes elevated emissions of some halocarbon compounds. In general the seaweed least affected by pH change in terms of types of halocarbon emission, was P. australis. The commercially farmed seaweed K. alvarezii was very sensitive to pH change as shown by the high increases in most of the compounds in all pH levels relative to ambient. In terms of percentage decrease in maximum quantum yield of photosynthesis (Fv∕Fm) prior to and after incubation, there were no significant correlations with the various pH levels tested for all seaweeds. The correlation between percentage decrease in the maximum quantum yield of photosynthesis (Fv∕Fm) …
bibliographic citation: Mithoo-Singh et al. (2017) Halocarbon emissions by selected tropical seaweeds: species-specific and compound-specific responses under changing pH. PeerJ 5:e2918 https://doi.org/10.7717/peerj.2918
date submitted: 2016-08-23
date accepted: 2016-12-17
issued: 2017-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mithoo-Singh
  given name: Paramjeet Kaur
author list: Agent
  family name: Keng
  given name: Fiona S.-L.
author list: Agent
  family name: Phang
  given name: Siew-Moi
author list: Agent
  family name: Leedham Elvidge
  given name: Emma C.
author list: Agent
  family name: Sturges
  given name: William T.
author list: Agent
  family name: Malin
  given name: Gill
author list: Agent
  family name: Abd Rahman
  given name: Noorsaadah
doi: 10.7717/peerj.2918
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-25
copyright: ©2017 Mithoo-Singh et al.
attribution name: Mithoo-Singh et al.

Polymorphism in the major histocompatibility complex (MHC class II B) genes of the Rufous-backed Bunting (Emberiza jankowskii)
type: item
type: AcademicArticle
description: Genetic diversity is one of the pillars of conservation biology research. High genetic diversity and abundant genetic variation in an organism may be suggestive of capacity to adapt to various environmental changes. The major histocompatibility complex (MHC) is known to be highly polymorphic and plays an important role in immune function. It is also considered an ideal model system to investigate genetic diversity in wildlife populations. The Rufous-backed Bunting (Emberiza jankowskii) is an endangered species that has experienced a sharp decline in both population and habitat size. Many historically significant populations are no longer present in previously populated regions, with only three breeding populations present in Inner Mongolia (i.e., the Aolunhua, Gahaitu and Lubei557 populations). Efforts focused on facilitating the conservation of the Rufous-backed Bunting (Emberiza jankowskii) are becoming increasingly important. However, the genetic diversity of E. jankowskii has not been investigated. In the present study, polymorphism in exon 2 of the MHCIIB of E. jankowskii was investigated. This polymorphism was subsequently compared with a related species, the Meadow Bunting (Emberiza cioides). A total of 1.59 alleles/individual were detected in E. jankowskii and 1.73 alleles/individual were identified in E. cioides. The maximum number of alleles per individual from the three E. jankowskii populations suggest the existence of at least three functional loci, while the maximum number of alleles per individual from the three E. cioides populations suggest the presence of at least four functional loci. Two of the alleles were shared between the E. jankowskii and E. cioides. Among the 12 unique alleles identified in E. jankowskii, 10.17 segregating sites per allele were detected, and the nucleotide diversity was 0.1865. Among the 17 unique alleles identified in E. cioides, eight segregating sites per allele were detected, and the nucleotide diversity was 0.1667. Ove…
format: application/pdf
format: text/html
creator: Dan Li
creator: Keping Sun
creator: Yunjiao Zhao
creator: Aiqing Lin
creator: Shi Li
creator: Yunlei Jiang
creator: Jiang Feng
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Zoology
subject: Immunology
description: doi:10.7717/peerj.2917
publisher: PeerJ Inc.
rights: © 2017 Li et al.
abstract: Genetic diversity is one of the pillars of conservation biology research. High genetic diversity and abundant genetic variation in an organism may be suggestive of capacity to adapt to various environmental changes. The major histocompatibility complex (MHC) is known to be highly polymorphic and plays an important role in immune function. It is also considered an ideal model system to investigate genetic diversity in wildlife populations. The Rufous-backed Bunting (Emberiza jankowskii) is an endangered species that has experienced a sharp decline in both population and habitat size. Many historically significant populations are no longer present in previously populated regions, with only three breeding populations present in Inner Mongolia (i.e., the Aolunhua, Gahaitu and Lubei557 populations). Efforts focused on facilitating the conservation of the Rufous-backed Bunting (Emberiza jankowskii) are becoming increasingly important. However, the genetic diversity of E. jankowskii has not been investigated. In the present study, polymorphism in exon 2 of the MHCIIB of E. jankowskii was investigated. This polymorphism was subsequently compared with a related species, the Meadow Bunting (Emberiza cioides). A total of 1.59 alleles/individual were detected in E. jankowskii and 1.73 alleles/individual were identified in E. cioides. The maximum number of alleles per individual from the three E. jankowskii populations suggest the existence of at least three functional loci, while the maximum number of alleles per individual from the three E. cioides populations suggest the presence of at least four functional loci. Two of the alleles were shared between the E. jankowskii and E. cioides. Among the 12 unique alleles identified in E. jankowskii, 10.17 segregating sites per allele were detected, and the nucleotide diversity was 0.1865. Among the 17 unique alleles identified in E. cioides, eight segregating sites per allele were detected, and the nucleotide diversity was 0.1667. Ove…
bibliographic citation: Li et al. (2017) Polymorphism in the major histocompatibility complex (MHC class II B) genes of the Rufous-backed Bunting (Emberiza jankowskii). PeerJ 5:e2917 https://doi.org/10.7717/peerj.2917
date submitted: 2016-04-23
date accepted: 2016-12-16
issued: 2017-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Dan
author list: Agent
  family name: Sun
  given name: Keping
author list: Agent
  family name: Zhao
  given name: Yunjiao
author list: Agent
  family name: Lin
  given name: Aiqing
author list: Agent
  family name: Li
  given name: Shi
author list: Agent
  family name: Jiang
  given name: Yunlei
author list: Agent
  family name: Feng
  given name: Jiang
doi: 10.7717/peerj.2917
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-25
copyright: ©2017 Li et al.
attribution name: Li et al.

Size matters: relationships between body size and body mass of common coastal, aquatic invertebrates in the Baltic Sea
type: item
type: AcademicArticle
description: Background Organism biomass is one of the most important variables in ecological studies, making biomass estimations one of the most common laboratory tasks. Biomass of small macroinvertebrates is usually estimated as dry mass or ash-free dry mass (hereafter ‘DM’ vs. ‘AFDM’) per sample; a laborious and time consuming process, that often can be speeded up using easily measured and reliable proxy variables like body size or wet (fresh) mass. Another common way of estimating AFDM (one of the most accurate but also time-consuming estimates of biologically active tissue mass) is the use of AFDM/DM ratios as conversion factors. So far, however, these ratios typically ignore the possibility that the relative mass of biologically active vs. non-active support tissue (e.g., protective exoskeleton or shell)—and therefore, also AFDM/DM ratios—may change with body size, as previously shown for taxa like spiders, vertebrates and trees. Methods We collected aquatic, epibenthic macroinvertebrates (>1 mm) in 32 shallow bays along a 360 km stretch of the Swedish coast along the Baltic Sea; one of the largest brackish water bodies on Earth. We then estimated statistical relationships between the body size (length or height in mm), body dry mass and ash-free dry mass for 14 of the most common taxa; five gastropods, three bivalves, three crustaceans and three insect larvae. Finally, we statistically estimated the potential influence of body size on the AFDM/DM ratio per taxon. Results For most taxa, non-linear regression models describing the power relationship between body size and (i) DM and (ii) AFDM fit the data well (as indicated by low SE and high R2). Moreover, for more than half of the taxa studied (including the vast majority of the shelled molluscs), body size had a negative influence on organism AFDM/DM ratios. Discussion The good fit of the modelled power relationships suggests that the constants reported here can be used to quickly estimate organism dry- and ash-free dry m…
format: application/pdf
format: text/html
creator: Johan Eklöf
creator: Åsa Austin
creator: Ulf Bergström
creator: Serena Donadi
creator: Britas D.H.K. Eriksson
creator: Joakim Hansen
creator: Göran Sundblad
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.2906
publisher: PeerJ Inc.
rights: © 2017 Eklöf et al.
abstract: Background Organism biomass is one of the most important variables in ecological studies, making biomass estimations one of the most common laboratory tasks. Biomass of small macroinvertebrates is usually estimated as dry mass or ash-free dry mass (hereafter ‘DM’ vs. ‘AFDM’) per sample; a laborious and time consuming process, that often can be speeded up using easily measured and reliable proxy variables like body size or wet (fresh) mass. Another common way of estimating AFDM (one of the most accurate but also time-consuming estimates of biologically active tissue mass) is the use of AFDM/DM ratios as conversion factors. So far, however, these ratios typically ignore the possibility that the relative mass of biologically active vs. non-active support tissue (e.g., protective exoskeleton or shell)—and therefore, also AFDM/DM ratios—may change with body size, as previously shown for taxa like spiders, vertebrates and trees. Methods We collected aquatic, epibenthic macroinvertebrates (>1 mm) in 32 shallow bays along a 360 km stretch of the Swedish coast along the Baltic Sea; one of the largest brackish water bodies on Earth. We then estimated statistical relationships between the body size (length or height in mm), body dry mass and ash-free dry mass for 14 of the most common taxa; five gastropods, three bivalves, three crustaceans and three insect larvae. Finally, we statistically estimated the potential influence of body size on the AFDM/DM ratio per taxon. Results For most taxa, non-linear regression models describing the power relationship between body size and (i) DM and (ii) AFDM fit the data well (as indicated by low SE and high R2). Moreover, for more than half of the taxa studied (including the vast majority of the shelled molluscs), body size had a negative influence on organism AFDM/DM ratios. Discussion The good fit of the modelled power relationships suggests that the constants reported here can be used to quickly estimate organism dry- and ash-free dry m…
bibliographic citation: Eklöf et al. (2017) Size matters: relationships between body size and body mass of common coastal, aquatic invertebrates in the Baltic Sea. PeerJ 5:e2906 https://doi.org/10.7717/peerj.2906
date submitted: 2016-08-25
date accepted: 2016-12-12
issued: 2017-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eklöf
  given name: Johan
author list: Agent
  family name: Austin
  given name: Åsa
author list: Agent
  family name: Bergström
  given name: Ulf
author list: Agent
  family name: Donadi
  given name: Serena
author list: Agent
  family name: Eriksson
  given name: Britas D.H.K.
author list: Agent
  family name: Hansen
  given name: Joakim
author list: Agent
  family name: Sundblad
  given name: Göran
doi: 10.7717/peerj.2906
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-25
copyright: ©2017 Eklöf et al.
attribution name: Eklöf et al.

Exploration of immunoglobulin transcriptomes from mice immunized with three-finger toxins and phospholipases A2 from the Central American coral snake, Micrurus nigrocinctus
type: item
type: AcademicArticle
description: Snakebite envenomings represent a neglected public health issue in many parts of the rural tropical world. Animal-derived antivenoms have existed for more than a hundred years and are effective in neutralizing snake venom toxins when timely administered. However, the low immunogenicity of many small but potent snake venom toxins represents a challenge for obtaining a balanced immune response against the medically relevant components of the venom. Here, we employ high-throughput sequencing of the immunoglobulin (Ig) transcriptome of mice immunized with a three-finger toxin and a phospholipase A2 from the venom of the Central American coral snake, Micrurus nigrocinctus. Although exploratory in nature, our indicate results showed that only low frequencies of mRNA encoding IgG isotypes, the most relevant isotype for therapeutic purposes, were present in splenocytes of five mice immunized with 6 doses of the two types of toxins over 90 days. Furthermore, analysis of Ig heavy chain transcripts showed that no particular combination of variable (V) and joining (J) gene segments had been selected in the immunization process, as would be expected after a strong humoral immune response to a single antigen. Combined with the titration of toxin-specific antibodies in the sera of immunized mice, these data support the low immunogenicity of three-finger toxins and phospholipases A2found in M. nigrocinctusvenoms, and highlight the need for future studies analyzing the complexity of antibody responses to toxins at the molecular level.
format: application/pdf
format: text/html
creator: Andreas H. Laustsen
creator: Mikael Engmark
creator: Christopher Clouser
creator: Sonia Timberlake
creator: Francois Vigneault
creator: José María Gutiérrez
creator: Bruno Lomonte
subject: Bioinformatics
subject: Biotechnology
subject: Toxicology
subject: Immunology
subject: Synthetic Biology
description: doi:10.7717/peerj.2924
publisher: PeerJ Inc.
rights: © 2017 Laustsen et al.
abstract: Snakebite envenomings represent a neglected public health issue in many parts of the rural tropical world. Animal-derived antivenoms have existed for more than a hundred years and are effective in neutralizing snake venom toxins when timely administered. However, the low immunogenicity of many small but potent snake venom toxins represents a challenge for obtaining a balanced immune response against the medically relevant components of the venom. Here, we employ high-throughput sequencing of the immunoglobulin (Ig) transcriptome of mice immunized with a three-finger toxin and a phospholipase A2 from the venom of the Central American coral snake, Micrurus nigrocinctus. Although exploratory in nature, our indicate results showed that only low frequencies of mRNA encoding IgG isotypes, the most relevant isotype for therapeutic purposes, were present in splenocytes of five mice immunized with 6 doses of the two types of toxins over 90 days. Furthermore, analysis of Ig heavy chain transcripts showed that no particular combination of variable (V) and joining (J) gene segments had been selected in the immunization process, as would be expected after a strong humoral immune response to a single antigen. Combined with the titration of toxin-specific antibodies in the sera of immunized mice, these data support the low immunogenicity of three-finger toxins and phospholipases A2found in M. nigrocinctusvenoms, and highlight the need for future studies analyzing the complexity of antibody responses to toxins at the molecular level.
bibliographic citation: Laustsen et al. (2017) Exploration of immunoglobulin transcriptomes from mice immunized with three-finger toxins and phospholipases A2 from the Central American coral snake, Micrurus nigrocinctus. PeerJ 5:e2924 https://doi.org/10.7717/peerj.2924
date submitted: 2016-08-15
date accepted: 2016-12-19
issued: 2017-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Laustsen
  given name: Andreas H.
author list: Agent
  family name: Engmark
  given name: Mikael
author list: Agent
  family name: Clouser
  given name: Christopher
author list: Agent
  family name: Timberlake
  given name: Sonia
author list: Agent
  family name: Vigneault
  given name: Francois
author list: Agent
  family name: Gutiérrez
  given name: José María
author list: Agent
  family name: Lomonte
  given name: Bruno
doi: 10.7717/peerj.2924
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-24
copyright: ©2017 Laustsen et al.
attribution name: Laustsen et al.

No apparent influence of psychometrically-defined schizotypy on orientation-dependent contextual modulation of visual contrast detection
type: item
type: AcademicArticle
description: We investigated the relationship between psychometrically-defined schizotypy and the ability to detect a visual target pattern. Target detection is typically impaired by a surrounding pattern (context) with an orientation that is parallel to the target, relative to a surrounding pattern with an orientation that is orthogonal to the target (orientation-dependent contextual modulation). Based on reports that this effect is reduced in those with schizophrenia, we hypothesised that there would be a negative relationship between the relative score on psychometrically-defined schizotypy and the relative effect of orientation-dependent contextual modulation. We measured visual contrast detection thresholds and scores on the Oxford-Liverpool Inventory of Feelings and Experiences (O-LIFE) from a non-clinical sample (N = 100). Contrary to our hypothesis, we find an absence of a monotonic relationship between the relative magnitude of orientation-dependent contextual modulation of visual contrast detection and the relative score on any of the subscales of the O-LIFE. The apparent difference of this result with previous reports on those with schizophrenia suggests that orientation-dependent contextual modulation may be an informative condition in which schizophrenia and psychometrically-defined schizotypy are dissociated. However, further research is also required to clarify the strength of orientation-dependent contextual modulation in those with schizophrenia.
format: application/pdf
format: text/html
creator: Damien J. Mannion
creator: Chris Donkin
creator: Thomas J. Whitford
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2921
publisher: PeerJ Inc.
rights: © 2017 Mannion et al.
abstract: We investigated the relationship between psychometrically-defined schizotypy and the ability to detect a visual target pattern. Target detection is typically impaired by a surrounding pattern (context) with an orientation that is parallel to the target, relative to a surrounding pattern with an orientation that is orthogonal to the target (orientation-dependent contextual modulation). Based on reports that this effect is reduced in those with schizophrenia, we hypothesised that there would be a negative relationship between the relative score on psychometrically-defined schizotypy and the relative effect of orientation-dependent contextual modulation. We measured visual contrast detection thresholds and scores on the Oxford-Liverpool Inventory of Feelings and Experiences (O-LIFE) from a non-clinical sample (N = 100). Contrary to our hypothesis, we find an absence of a monotonic relationship between the relative magnitude of orientation-dependent contextual modulation of visual contrast detection and the relative score on any of the subscales of the O-LIFE. The apparent difference of this result with previous reports on those with schizophrenia suggests that orientation-dependent contextual modulation may be an informative condition in which schizophrenia and psychometrically-defined schizotypy are dissociated. However, further research is also required to clarify the strength of orientation-dependent contextual modulation in those with schizophrenia.
bibliographic citation: Mannion et al. (2017) No apparent influence of psychometrically-defined schizotypy on orientation-dependent contextual modulation of visual contrast detection. PeerJ 5:e2921 https://doi.org/10.7717/peerj.2921
date submitted: 2016-09-28
date accepted: 2016-12-18
issued: 2017-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mannion
  given name: Damien J.
author list: Agent
  family name: Donkin
  given name: Chris
author list: Agent
  family name: Whitford
  given name: Thomas J.
doi: 10.7717/peerj.2921
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-24
copyright: ©2017 Mannion et al.
attribution name: Mannion et al.

Brood size and sex ratio in response to host quality and wasp traits in the gregarious parasitoid Oomyzus sokolowskii (Hymenoptera: Eulophidae)
type: item
type: AcademicArticle
description: This laboratory study investigated whether the larval-pupal parasitoid Oomyzus sokolowskii females adjust their brood size and sex ratio in response to body size and stage of Plutella xylostella larval hosts, as well as to their own body size and the order of oviposition. These factors were analyzed using multiple regression with simultaneous entry of them and their two-way interactions. Parasitoids brood size tended to increase with host body size at parasitism when the 4th instar larval host was attacked, but did not change when the 2nd and 3rd instar larvae were attacked. Parasitoids did not vary in brood size according to their body size, but decreased with their bouts of oviposition on a linear trend from 10 offspring adults emerged per host in the first bout of oviposition down to eight in the third. Parasitoid offspring sex ratio did not change with host instar, host body weight, wasp body size, and oviposition bout. Proportions of male offspring per brood were from 11% to 13% from attacking the 2nd to 4th instar larvae and from 13% to 16% across three successive bouts of oviposition, with a large variation for smaller host larvae and wasps. When fewer than 12 offspring were emerged from a host, one male was most frequently produced; when more than 12 offspring were emerged, two or more males were produced. Our study suggests that O. sokolowskii females may optimize their clutch size in response to body size of mature P. xylostella larvae, and their sex allocation in response to clutch size.
format: application/pdf
format: text/html
creator: Xianwei Li
creator: Liangting Zhu
creator: Ling Meng
creator: Baoping Li
subject: Animal Behavior
subject: Entomology
description: doi:10.7717/peerj.2919
publisher: PeerJ Inc.
rights: © 2017 Li et al.
abstract: This laboratory study investigated whether the larval-pupal parasitoid Oomyzus sokolowskii females adjust their brood size and sex ratio in response to body size and stage of Plutella xylostella larval hosts, as well as to their own body size and the order of oviposition. These factors were analyzed using multiple regression with simultaneous entry of them and their two-way interactions. Parasitoids brood size tended to increase with host body size at parasitism when the 4th instar larval host was attacked, but did not change when the 2nd and 3rd instar larvae were attacked. Parasitoids did not vary in brood size according to their body size, but decreased with their bouts of oviposition on a linear trend from 10 offspring adults emerged per host in the first bout of oviposition down to eight in the third. Parasitoid offspring sex ratio did not change with host instar, host body weight, wasp body size, and oviposition bout. Proportions of male offspring per brood were from 11% to 13% from attacking the 2nd to 4th instar larvae and from 13% to 16% across three successive bouts of oviposition, with a large variation for smaller host larvae and wasps. When fewer than 12 offspring were emerged from a host, one male was most frequently produced; when more than 12 offspring were emerged, two or more males were produced. Our study suggests that O. sokolowskii females may optimize their clutch size in response to body size of mature P. xylostella larvae, and their sex allocation in response to clutch size.
bibliographic citation: Li et al. (2017) Brood size and sex ratio in response to host quality and wasp traits in the gregarious parasitoid Oomyzus sokolowskii (Hymenoptera: Eulophidae). PeerJ 5:e2919 https://doi.org/10.7717/peerj.2919
date submitted: 2016-08-03
date accepted: 2016-12-17
issued: 2017-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xianwei
author list: Agent
  family name: Zhu
  given name: Liangting
author list: Agent
  family name: Meng
  given name: Ling
author list: Agent
  family name: Li
  given name: Baoping
doi: 10.7717/peerj.2919
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-24
copyright: ©2017 Li et al.
attribution name: Li et al.

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