PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Mitochondrial complex I deficiency leads to the retardation of early embryonic development in Ndufs4 knockout mice
items: A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation
items: Ranking of critical species to preserve the functionality of mutualistic networks using the k-core decomposition
items: Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata
items: Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes
items: Body composition estimation from selected slices: equations computed from a new semi-automatic thresholding method developed on whole-body CT scans
items: Toxicity, repellency and flushing out in Triatoma infestans (Hemiptera: Reduviidae) exposed to the repellents DEET and IR3535
items: Face recognition is similarly affected by viewpoint in school-aged children and adults
items: Lygistorrhinidae (Diptera: Bibionomorpha: Sciaroidea) in early Eocene Cambay amber
items: Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

Mitochondrial complex I deficiency leads to the retardation of early embryonic development in Ndufs4 knockout mice
type: item
type: AcademicArticle
description: Background The NDUFS4 gene encodes an 18-kD subunit of mitochondria complex I, and mutations in this gene lead to the development of a severe neurodegenerative disease called Leigh syndrome (LS) in humans. To investigate the disease phenotypes and molecular mechanisms of Leigh syndrome, the Ndufs4 knockout (KO) mouse has been widely used as a novel animal model. Because the homozygotes cannot survive beyond child-bearing age, whether Ndufs4 and mitochondrial complex I influence early embryonic development remains unknown. In our study, we attempted to investigate embryonic development in Ndufs4 KO mice, which can be regarded as a Leigh disease model and were created through the CRISPR (clustered regularly interspaced short palindromic repeat) and Cas9 (CRISPR associated)-mediated genome editing system. Methods We first designed a single guide RNA (sgRNA) targeting exon 2 of Ndufs4 to delete the NDUFS4 protein in mouse embryos to mimic Leigh syndrome. Then, we described the phenotypes of our mouse model by forced swimming and the open-field test as well as by assessing other behavioral characteristics. Intracytoplasmic sperm injection (ICSI) was performed to obtain KO embryos to test the influence of NDUFS4 deletion on early embryonic development. Results In this study, we first generated Ndufs4 KO mice with physical and behavioral phenotypes similar to Leigh syndrome using the CRISPR/Cas9 system. The low developmental rate of KO embryos that were derived from knockout gametes indicated that the absence of NDUFS4 impaired the development of preimplantation embryos. Discussion In this paper, we first obtained Ndufs4 KO mice that could mimic Leigh syndrome using the CRISPR/Cas9 system. Then, we identified the role of NDUFS4 in early embryonic development, shedding light on its roles in the respiratory chain and fertility. Our model provides a useful tool with which to investigate the function of Ndufs4. Although the pathological mechanisms of the disease need to be dis…
format: application/pdf
format: text/html
creator: Mei Wang
creator: Ya-Ping Huang
creator: Han Wu
creator: Ke Song
creator: Cong Wan
creator: A-Ni Chi
creator: Ya-Mei Xiao
creator: Xiao-Yang Zhao
subject: Developmental Biology
subject: Molecular Biology
description: doi:10.7717/peerj.3339
publisher: PeerJ Inc.
rights: © 2017 Wang et al.
abstract: Background The NDUFS4 gene encodes an 18-kD subunit of mitochondria complex I, and mutations in this gene lead to the development of a severe neurodegenerative disease called Leigh syndrome (LS) in humans. To investigate the disease phenotypes and molecular mechanisms of Leigh syndrome, the Ndufs4 knockout (KO) mouse has been widely used as a novel animal model. Because the homozygotes cannot survive beyond child-bearing age, whether Ndufs4 and mitochondrial complex I influence early embryonic development remains unknown. In our study, we attempted to investigate embryonic development in Ndufs4 KO mice, which can be regarded as a Leigh disease model and were created through the CRISPR (clustered regularly interspaced short palindromic repeat) and Cas9 (CRISPR associated)-mediated genome editing system. Methods We first designed a single guide RNA (sgRNA) targeting exon 2 of Ndufs4 to delete the NDUFS4 protein in mouse embryos to mimic Leigh syndrome. Then, we described the phenotypes of our mouse model by forced swimming and the open-field test as well as by assessing other behavioral characteristics. Intracytoplasmic sperm injection (ICSI) was performed to obtain KO embryos to test the influence of NDUFS4 deletion on early embryonic development. Results In this study, we first generated Ndufs4 KO mice with physical and behavioral phenotypes similar to Leigh syndrome using the CRISPR/Cas9 system. The low developmental rate of KO embryos that were derived from knockout gametes indicated that the absence of NDUFS4 impaired the development of preimplantation embryos. Discussion In this paper, we first obtained Ndufs4 KO mice that could mimic Leigh syndrome using the CRISPR/Cas9 system. Then, we identified the role of NDUFS4 in early embryonic development, shedding light on its roles in the respiratory chain and fertility. Our model provides a useful tool with which to investigate the function of Ndufs4. Although the pathological mechanisms of the disease need to be dis…
bibliographic citation: Wang et al. (2017) Mitochondrial complex I deficiency leads to the retardation of early embryonic development in Ndufs4 knockout mice. PeerJ 5:e3339 https://doi.org/10.7717/peerj.3339
date submitted: 2017-03-21
date accepted: 2017-04-20
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Mei
author list: Agent
  family name: Huang
  given name: Ya-Ping
author list: Agent
  family name: Wu
  given name: Han
author list: Agent
  family name: Song
  given name: Ke
author list: Agent
  family name: Wan
  given name: Cong
author list: Agent
  family name: Chi
  given name: A-Ni
author list: Agent
  family name: Xiao
  given name: Ya-Mei
author list: Agent
  family name: Zhao
  given name: Xiao-Yang
doi: 10.7717/peerj.3339
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: ©2017 Wang et al.
attribution name: Wang et al.

A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation
type: item
type: AcademicArticle
description: Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric “species-pump” model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by “ecological speciation” along an elevational gradient.
format: application/pdf
format: text/html
creator: Robert G. Moyle
creator: Joseph D. Manthey
creator: Peter A. Hosner
creator: Mustafa Rahman
creator: Maklarin Lakim
creator: Frederick H. Sheldon
subject: Biodiversity
subject: Biogeography
subject: Zoology
description: doi:10.7717/peerj.3335
publisher: PeerJ Inc.
rights: © 2017 Moyle et al.
abstract: Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric “species-pump” model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by “ecological speciation” along an elevational gradient.
bibliographic citation: Moyle et al. (2017) A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation. PeerJ 5:e3335 https://doi.org/10.7717/peerj.3335
date submitted: 2016-06-15
date accepted: 2017-04-19
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moyle
  given name: Robert G.
author list: Agent
  family name: Manthey
  given name: Joseph D.
author list: Agent
  family name: Hosner
  given name: Peter A.
author list: Agent
  family name: Rahman
  given name: Mustafa
author list: Agent
  family name: Lakim
  given name: Maklarin
author list: Agent
  family name: Sheldon
  given name: Frederick H.
doi: 10.7717/peerj.3335
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: © 2017 Moyle et al.
attribution name: Moyle et al.

Ranking of critical species to preserve the functionality of mutualistic networks using the k-core decomposition
type: item
type: AcademicArticle
description: Background Network analysis has become a relevant approach to analyze cascading species extinctions resulting from perturbations on mutualistic interactions as a result of environmental change. In this context, it is essential to be able to point out key species, whose stability would prevent cascading extinctions, and the consequent loss of ecosystem function. In this study, we aim to explain how the k-core decomposition sheds light on the understanding the robustness of bipartite mutualistic networks. Methods We defined three k-magnitudes based on the k-core decomposition: k-radius, k-degree, and k-risk. The first one, k-radius, quantifies the distance from a node to the innermost shell of the partner guild, while k-degree provides a measure of centrality in the k-shell based decomposition. k-risk is a way to measure the vulnerability of a network to the loss of a particular species. Using these magnitudes we analyzed 89 mutualistic networks involving plant pollinators or seed dispersers. Two static extinction procedures were implemented in which k-degree and k-risk were compared against other commonly used ranking indexes, as for example MusRank, explained in detail in Material and Methods. Results When extinctions take place in both guilds, k-risk is the best ranking index if the goal is to identify the key species to preserve the giant component. When species are removed only in the primary class and cascading extinctions are measured in the secondary class, the most effective ranking index to identify the key species to preserve the giant component is k-degree. However, MusRank index was more effective when the goal is to identify the key species to preserve the greatest species richness in the second class. Discussion The k-core decomposition offers a new topological view of the structure of mutualistic networks. The new k-radius, k-degree and k-risk magnitudes take advantage of its properties and provide new insight into the structure of mutualistic networks…
format: application/pdf
format: text/html
creator: Javier García-Algarra
creator: Juan Manuel Pastor
creator: José María Iriondo
creator: Javier Galeano
subject: Ecology
subject: Ecosystem Science
subject: Natural Resource Management
subject: Statistics
description: doi:10.7717/peerj.3321
publisher: PeerJ Inc.
rights: © 2017 García-Algarra et al.
abstract: Background Network analysis has become a relevant approach to analyze cascading species extinctions resulting from perturbations on mutualistic interactions as a result of environmental change. In this context, it is essential to be able to point out key species, whose stability would prevent cascading extinctions, and the consequent loss of ecosystem function. In this study, we aim to explain how the k-core decomposition sheds light on the understanding the robustness of bipartite mutualistic networks. Methods We defined three k-magnitudes based on the k-core decomposition: k-radius, k-degree, and k-risk. The first one, k-radius, quantifies the distance from a node to the innermost shell of the partner guild, while k-degree provides a measure of centrality in the k-shell based decomposition. k-risk is a way to measure the vulnerability of a network to the loss of a particular species. Using these magnitudes we analyzed 89 mutualistic networks involving plant pollinators or seed dispersers. Two static extinction procedures were implemented in which k-degree and k-risk were compared against other commonly used ranking indexes, as for example MusRank, explained in detail in Material and Methods. Results When extinctions take place in both guilds, k-risk is the best ranking index if the goal is to identify the key species to preserve the giant component. When species are removed only in the primary class and cascading extinctions are measured in the secondary class, the most effective ranking index to identify the key species to preserve the giant component is k-degree. However, MusRank index was more effective when the goal is to identify the key species to preserve the greatest species richness in the second class. Discussion The k-core decomposition offers a new topological view of the structure of mutualistic networks. The new k-radius, k-degree and k-risk magnitudes take advantage of its properties and provide new insight into the structure of mutualistic networks…
bibliographic citation: García-Algarra et al. (2017) Ranking of critical species to preserve the functionality of mutualistic networks using the k-core decomposition. PeerJ 5:e3321 https://doi.org/10.7717/peerj.3321
date submitted: 2017-03-07
date accepted: 2017-04-15
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Algarra
  given name: Javier
author list: Agent
  family name: Pastor
  given name: Juan Manuel
author list: Agent
  family name: Iriondo
  given name: José María
author list: Agent
  family name: Galeano
  given name: Javier
doi: 10.7717/peerj.3321
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: ©2017 García-Algarra et al.
attribution name: García-Algarra et al.

Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata
type: item
type: AcademicArticle
description: We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2–3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata, whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers.
format: application/pdf
format: text/html
creator: Hollie M. Putnam
creator: Diane K. Adams
creator: Ehud Zelzion
creator: Nicole E. Wagner
creator: Huan Qiu
creator: Tali Mass
creator: Paul G. Falkowski
creator: Ruth D. Gates
creator: Debashish Bhattacharya
subject: Ecology
subject: Evolutionary Studies
subject: Marine Biology
description: doi:10.7717/peerj.3319
publisher: PeerJ Inc.
rights: © 2017 Putnam et al.
abstract: We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2–3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata, whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers.
bibliographic citation: Putnam et al. (2017) Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata. PeerJ 5:e3319 https://doi.org/10.7717/peerj.3319
date submitted: 2016-12-17
date accepted: 2017-04-15
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Putnam
  given name: Hollie M.
author list: Agent
  family name: Adams
  given name: Diane K.
author list: Agent
  family name: Zelzion
  given name: Ehud
author list: Agent
  family name: Wagner
  given name: Nicole E.
author list: Agent
  family name: Qiu
  given name: Huan
author list: Agent
  family name: Mass
  given name: Tali
author list: Agent
  family name: Falkowski
  given name: Paul G.
author list: Agent
  family name: Gates
  given name: Ruth D.
author list: Agent
  family name: Bhattacharya
  given name: Debashish
doi: 10.7717/peerj.3319
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: ©2017 Putnam et al.
attribution name: Putnam et al.

Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes
type: item
type: AcademicArticle
description: Coptis chinensis Franch., the Chinese goldthread (‘Weilian’ in Chinese), one of the most important medicinal plants from the family Ranunculaceae, and its rhizome has been widely used in Traditional Chinese Medicine for centuries. Here, we analyzed the chemical components and the transcriptome of the Chinese goldthread from three biotopes, including Zhenping, Zunyi and Shizhu. We built comprehensive, high-quality de novo transcriptome assemblies of the Chinese goldthread from short-read RNA-Sequencing data, obtaining 155,710 transcripts and 56,071 unigenes. More than 98.39% and 95.97% of core eukaryotic genes were found in the transcripts and unigenes respectively, indicating that this unigene set capture the majority of the coding genes. A total of 520,462, 493,718, and 507,247 heterozygous SNPs were identified in the three accessions from Zhenping, Zunyi, and Shizhu respectively, indicating high polymorphism in coding regions of the Chinese goldthread (∼1%). Chemical analyses of the rhizome identified six major components, including berberine, palmatine, coptisine, epiberberine, columbamine, and jatrorrhizine. Berberine has the highest concentrations, followed by coptisine, palmatine, and epiberberine sequentially for all the three accessions. The drug quality of the accession from Shizhu may be the highest among these accessions. Differential analyses of the transcriptome identified four pivotal candidate enzymes, including aspartate aminotransferaseprotein, polyphenol oxidase, primary-amine oxidase, and tyrosine decarboxylase, were significantly differentially expressed and may be responsible for the difference of alkaloids contents in the accessions from different biotopes.
format: application/pdf
format: text/html
creator: Hanting Chen
creator: Cao Deng
creator: Hu Nie
creator: Gang Fan
creator: Yang He
subject: Biochemistry
subject: Bioinformatics
subject: Computational Biology
subject: Plant Science
description: doi:10.7717/peerj.3303
publisher: PeerJ Inc.
rights: © 2017 Chen et al.
abstract: Coptis chinensis Franch., the Chinese goldthread (‘Weilian’ in Chinese), one of the most important medicinal plants from the family Ranunculaceae, and its rhizome has been widely used in Traditional Chinese Medicine for centuries. Here, we analyzed the chemical components and the transcriptome of the Chinese goldthread from three biotopes, including Zhenping, Zunyi and Shizhu. We built comprehensive, high-quality de novo transcriptome assemblies of the Chinese goldthread from short-read RNA-Sequencing data, obtaining 155,710 transcripts and 56,071 unigenes. More than 98.39% and 95.97% of core eukaryotic genes were found in the transcripts and unigenes respectively, indicating that this unigene set capture the majority of the coding genes. A total of 520,462, 493,718, and 507,247 heterozygous SNPs were identified in the three accessions from Zhenping, Zunyi, and Shizhu respectively, indicating high polymorphism in coding regions of the Chinese goldthread (∼1%). Chemical analyses of the rhizome identified six major components, including berberine, palmatine, coptisine, epiberberine, columbamine, and jatrorrhizine. Berberine has the highest concentrations, followed by coptisine, palmatine, and epiberberine sequentially for all the three accessions. The drug quality of the accession from Shizhu may be the highest among these accessions. Differential analyses of the transcriptome identified four pivotal candidate enzymes, including aspartate aminotransferaseprotein, polyphenol oxidase, primary-amine oxidase, and tyrosine decarboxylase, were significantly differentially expressed and may be responsible for the difference of alkaloids contents in the accessions from different biotopes.
bibliographic citation: Chen et al. (2017) Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes. PeerJ 5:e3303 https://doi.org/10.7717/peerj.3303
date submitted: 2017-01-18
date accepted: 2017-04-12
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Hanting
author list: Agent
  family name: Deng
  given name: Cao
author list: Agent
  family name: Nie
  given name: Hu
author list: Agent
  family name: Fan
  given name: Gang
author list: Agent
  family name: He
  given name: Yang
doi: 10.7717/peerj.3303
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: ©2017 Chen et al.
attribution name: Chen et al.

Body composition estimation from selected slices: equations computed from a new semi-automatic thresholding method developed on whole-body CT scans
type: item
type: AcademicArticle
description: Background Estimating volumes and masses of total body components is important for the study and treatment monitoring of nutrition and nutrition-related disorders, cancer, joint replacement, energy-expenditure and exercise physiology. While several equations have been offered for estimating total body components from MRI slices, no reliable and tested method exists for CT scans. For the first time, body composition data was derived from 41 high-resolution whole-body CT scans. From these data, we defined equations for estimating volumes and masses of total body AT and LT from corresponding tissue areas measured in selected CT scan slices. Methods We present a new semi-automatic approach to defining the density cutoff between adipose tissue (AT) and lean tissue (LT) in such material. An intra-class correlation coefficient (ICC) was used to validate the method. The equations for estimating the whole-body composition volume and mass from areas measured in selected slices were modeled with ordinary least squares (OLS) linear regressions and support vector machine regression (SVMR). Results and Discussion The best predictive equation for total body AT volume was based on the AT area of a single slice located between the 4th and 5th lumbar vertebrae (L4-L5) and produced lower prediction errors (|PE| = 1.86 liters, %PE = 8.77) than previous equations also based on CT scans. The LT area of the mid-thigh provided the lowest prediction errors (|PE| = 2.52 liters, %PE = 7.08) for estimating whole-body LT volume. We also present equations to predict total body AT and LT masses from a slice located at L4-L5 that resulted in reduced error compared with the previously published equations based on CT scans. The multislice SVMR predictor gave the theoretical upper limit for prediction precision of volumes and cross-validated the results.
format: application/pdf
format: text/html
creator: Alizé Lacoste Jeanson
creator: Ján Dupej
creator: Chiara Villa
creator: Jaroslav Brůžek
subject: Nutrition
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.3302
publisher: PeerJ Inc.
rights: © 2017 Lacoste Jeanson et al.
abstract: Background Estimating volumes and masses of total body components is important for the study and treatment monitoring of nutrition and nutrition-related disorders, cancer, joint replacement, energy-expenditure and exercise physiology. While several equations have been offered for estimating total body components from MRI slices, no reliable and tested method exists for CT scans. For the first time, body composition data was derived from 41 high-resolution whole-body CT scans. From these data, we defined equations for estimating volumes and masses of total body AT and LT from corresponding tissue areas measured in selected CT scan slices. Methods We present a new semi-automatic approach to defining the density cutoff between adipose tissue (AT) and lean tissue (LT) in such material. An intra-class correlation coefficient (ICC) was used to validate the method. The equations for estimating the whole-body composition volume and mass from areas measured in selected slices were modeled with ordinary least squares (OLS) linear regressions and support vector machine regression (SVMR). Results and Discussion The best predictive equation for total body AT volume was based on the AT area of a single slice located between the 4th and 5th lumbar vertebrae (L4-L5) and produced lower prediction errors (|PE| = 1.86 liters, %PE = 8.77) than previous equations also based on CT scans. The LT area of the mid-thigh provided the lowest prediction errors (|PE| = 2.52 liters, %PE = 7.08) for estimating whole-body LT volume. We also present equations to predict total body AT and LT masses from a slice located at L4-L5 that resulted in reduced error compared with the previously published equations based on CT scans. The multislice SVMR predictor gave the theoretical upper limit for prediction precision of volumes and cross-validated the results.
bibliographic citation: Lacoste Jeanson et al. (2017) Body composition estimation from selected slices: equations computed from a new semi-automatic thresholding method developed on whole-body CT scans. PeerJ 5:e3302 https://doi.org/10.7717/peerj.3302
date submitted: 2016-12-16
date accepted: 2017-04-12
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lacoste Jeanson
  given name: Alizé
author list: Agent
  family name: Dupej
  given name: Ján
author list: Agent
  family name: Villa
  given name: Chiara
author list: Agent
  family name: Brůžek
  given name: Jaroslav
doi: 10.7717/peerj.3302
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: ©2017 Lacoste Jeanson et al.
attribution name: Lacoste Jeanson et al.

Toxicity, repellency and flushing out in Triatoma infestans (Hemiptera: Reduviidae) exposed to the repellents DEET and IR3535
type: item
type: AcademicArticle
description: DEET and IR3535 are insect repellents present worldwide in commercial products; their efficacy has been mainly evaluated in mosquitoes. This study compares the toxicological effects and the behavioral responses induced by both repellents on the blood-sucking bug Triatoma infestans Klug (Hemiptera: Reduviidae), one of the main vectors of Chagas disease. When applied topically, the Median Lethal Dose (72 h) for DEET was 220.8 µg/insect. Using IR3535, topical application of 500 µg/insect killed no nymphs. The minimum concentration that produced repellency was the same for both compounds: 1,15 µg/cm2. The effect of a mixture DEET:IR3535 1:1 was similar to that of their pure components. Flushing out was assessed in a chamber with a shelter containing groups of ten nymphs. The repellents were aerosolized on the shelter and the number of insects leaving it was recorded for 60 min. During that time, 0.006 g/m3 of the positive control tetramethrin flushed out 76.7% of the nymphs, while 1.76 g/m3 of DEET or IR3535 flushed out 30 and 0%, respectively. The concentrations required for both compounds to produce toxicity or flushing out are too high to have any practical applications. However, they showed a promising repellency. Additional research should be done to evaluate their possible use for personal protection against T. infestans bites.
format: application/pdf
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creator: Mercedes M.N. Reynoso
creator: Emilia A. Seccacini
creator: Javier A. Calcagno
creator: Eduardo N. Zerba
creator: Raúl A. Alzogaray
subject: Biosphere Interactions
subject: Ecotoxicology
subject: Entomology
subject: Toxicology
description: doi:10.7717/peerj.3292
publisher: PeerJ Inc.
rights: © 2017 Reynoso et al.
abstract: DEET and IR3535 are insect repellents present worldwide in commercial products; their efficacy has been mainly evaluated in mosquitoes. This study compares the toxicological effects and the behavioral responses induced by both repellents on the blood-sucking bug Triatoma infestans Klug (Hemiptera: Reduviidae), one of the main vectors of Chagas disease. When applied topically, the Median Lethal Dose (72 h) for DEET was 220.8 µg/insect. Using IR3535, topical application of 500 µg/insect killed no nymphs. The minimum concentration that produced repellency was the same for both compounds: 1,15 µg/cm2. The effect of a mixture DEET:IR3535 1:1 was similar to that of their pure components. Flushing out was assessed in a chamber with a shelter containing groups of ten nymphs. The repellents were aerosolized on the shelter and the number of insects leaving it was recorded for 60 min. During that time, 0.006 g/m3 of the positive control tetramethrin flushed out 76.7% of the nymphs, while 1.76 g/m3 of DEET or IR3535 flushed out 30 and 0%, respectively. The concentrations required for both compounds to produce toxicity or flushing out are too high to have any practical applications. However, they showed a promising repellency. Additional research should be done to evaluate their possible use for personal protection against T. infestans bites.
bibliographic citation: Reynoso et al. (2017) Toxicity, repellency and flushing out in Triatoma infestans (Hemiptera: Reduviidae) exposed to the repellents DEET and IR3535. PeerJ 5:e3292 https://doi.org/10.7717/peerj.3292
date submitted: 2017-02-01
date accepted: 2017-04-10
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reynoso
  given name: Mercedes M.N.
author list: Agent
  family name: Seccacini
  given name: Emilia A.
author list: Agent
  family name: Calcagno
  given name: Javier A.
author list: Agent
  family name: Zerba
  given name: Eduardo N.
author list: Agent
  family name: Alzogaray
  given name: Raúl A.
doi: 10.7717/peerj.3292
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: ©2017 Reynoso et al.
attribution name: Reynoso et al.

Face recognition is similarly affected by viewpoint in school-aged children and adults
type: item
type: AcademicArticle
description: There is an ongoing debate on the question when face processing abilities mature. One aspect that has been part of this debate is the ability to recognize faces in and across different viewpoints. Here, we tested 128 participants consisting of school-age children (ages, 5–10 years) and adults (ages, 19–37 years) in two experiments to investigate the effects of different viewpoints (including front, three-quarter, profile view) on face recognition during development. Furthermore, we compared recognition performance for faces to that of another object category (cars). In the first experiment (n = 88) we tested if the pattern of performance for faces presented in different viewpoints is similar in school-aged children and adults. Participants completed a two-alternative-forced-choice (2AFC) memory task comprising images of both faces and cars in front, three-quarter and profile view, which were presented in the same viewpoint during learning and testing. In the second experiment (n = 40) we tested if face recognition is similarly affected by viewpoint changes in children and adults. In this experiment the 2AFC memory task included a change of viewpoint between learning and testing. While in both experiments we found higher recognition performance for faces with increasing age, the overall pattern of both viewpoint and viewpoint-change-effects and also the difference between view-change- and no-change-conditions was similar across age groups. In contrast to faces, no viewpoint effects were observed in cars (experiment 1), viewpoint change effects, however, were similar for cars and faces (experiment 2). In sum, our results suggest early maturity of the ability to recognize faces in and across different viewpoints.
format: application/pdf
format: text/html
creator: Marisa Nordt
creator: Sarah Weigelt
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3253
publisher: PeerJ Inc.
rights: © 2017 Nordt and Weigelt
abstract: There is an ongoing debate on the question when face processing abilities mature. One aspect that has been part of this debate is the ability to recognize faces in and across different viewpoints. Here, we tested 128 participants consisting of school-age children (ages, 5–10 years) and adults (ages, 19–37 years) in two experiments to investigate the effects of different viewpoints (including front, three-quarter, profile view) on face recognition during development. Furthermore, we compared recognition performance for faces to that of another object category (cars). In the first experiment (n = 88) we tested if the pattern of performance for faces presented in different viewpoints is similar in school-aged children and adults. Participants completed a two-alternative-forced-choice (2AFC) memory task comprising images of both faces and cars in front, three-quarter and profile view, which were presented in the same viewpoint during learning and testing. In the second experiment (n = 40) we tested if face recognition is similarly affected by viewpoint changes in children and adults. In this experiment the 2AFC memory task included a change of viewpoint between learning and testing. While in both experiments we found higher recognition performance for faces with increasing age, the overall pattern of both viewpoint and viewpoint-change-effects and also the difference between view-change- and no-change-conditions was similar across age groups. In contrast to faces, no viewpoint effects were observed in cars (experiment 1), viewpoint change effects, however, were similar for cars and faces (experiment 2). In sum, our results suggest early maturity of the ability to recognize faces in and across different viewpoints.
bibliographic citation: Nordt et al. (2017) Face recognition is similarly affected by viewpoint in school-aged children and adults. PeerJ 5:e3253 https://doi.org/10.7717/peerj.3253
date submitted: 2016-11-21
date accepted: 2017-03-31
issued: 2017-05-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nordt
  given name: Marisa
author list: Agent
  family name: Weigelt
  given name: Sarah
doi: 10.7717/peerj.3253
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-18
copyright: ©2017 Nordt and Weigelt
attribution name: Nordt and Weigelt

Lygistorrhinidae (Diptera: Bibionomorpha: Sciaroidea) in early Eocene Cambay amber
type: item
type: AcademicArticle
description: One new genus and three new species of Lygistorrhinidae in early Eocene Cambay amber from India are described, which significantly increases our knowledge about this group in the Eocene. Lygistorrhina indica n. sp. is the oldest fossil known from this extant genus. Indorrhina sahnii n. gen. et sp. shows morphological similarities to each of the two extant genera Lygistorrhina and Asiorrhina. Palaeognoriste orientale is the third species known from a group that has only been recorded from Eocene Baltic amber before. The latter finding reveals faunal links between Cambay amber and the probably slightly younger Baltic amber, adding further evidence that faunal exchange between Europe/Asia and India took place before the formation of Cambay amber.
format: application/pdf
format: text/html
creator: Frauke Stebner
creator: Hukam Singh
creator: Jes Rust
creator: David A. Grimaldi
subject: Entomology
subject: Paleontology
description: doi:10.7717/peerj.3313
publisher: PeerJ Inc.
rights: © 2017 Stebner et al.
abstract: One new genus and three new species of Lygistorrhinidae in early Eocene Cambay amber from India are described, which significantly increases our knowledge about this group in the Eocene. Lygistorrhina indica n. sp. is the oldest fossil known from this extant genus. Indorrhina sahnii n. gen. et sp. shows morphological similarities to each of the two extant genera Lygistorrhina and Asiorrhina. Palaeognoriste orientale is the third species known from a group that has only been recorded from Eocene Baltic amber before. The latter finding reveals faunal links between Cambay amber and the probably slightly younger Baltic amber, adding further evidence that faunal exchange between Europe/Asia and India took place before the formation of Cambay amber.
bibliographic citation: Stebner et al. (2017) Lygistorrhinidae (Diptera: Bibionomorpha: Sciaroidea) in early Eocene Cambay amber. PeerJ 5:e3313 https://doi.org/10.7717/peerj.3313
date submitted: 2017-01-18
date accepted: 2017-04-13
issued: 2017-05-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stebner
  given name: Frauke
author list: Agent
  family name: Singh
  given name: Hukam
author list: Agent
  family name: Rust
  given name: Jes
author list: Agent
  family name: Grimaldi
  given name: David A.
doi: 10.7717/peerj.3313
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-17
copyright: ©2017 Stebner et al.
attribution name: Stebner et al.

Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities
type: item
type: AcademicArticle
description: Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil produ…
format: application/pdf
format: text/html
creator: Olivier Laroche
creator: Susanna A. Wood
creator: Louis A. Tremblay
creator: Gavin Lear
creator: Joanne I. Ellis
creator: Xavier Pochon
subject: Bioinformatics
subject: Environmental Impacts
subject: Environmental Sciences
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.3347
publisher: PeerJ Inc.
rights: © 2017 Laroche et al.
abstract: Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil produ…
bibliographic citation: Laroche et al. (2017) Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. PeerJ 5:e3347 https://doi.org/10.7717/peerj.3347
date submitted: 2017-02-01
date accepted: 2017-04-22
issued: 2017-05-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Laroche
  given name: Olivier
author list: Agent
  family name: Wood
  given name: Susanna A.
author list: Agent
  family name: Tremblay
  given name: Louis A.
author list: Agent
  family name: Lear
  given name: Gavin
author list: Agent
  family name: Ellis
  given name: Joanne I.
author list: Agent
  family name: Pochon
  given name: Xavier
doi: 10.7717/peerj.3347
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-17
copyright: ©2017 Laroche et al.
attribution name: Laroche et al.

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