PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Leaf arrangements are invalid in the taxonomy of orchid species
items: Using electroretinograms and multi-model inference to identify spectral classes of photoreceptors and relative opsin expression levels
items: A laid-back trip through the Hennigian Forests
items: Long-term resource addition to a detrital food web yields a pattern of responses more complex than pervasive bottom-up control
items: In vitro assessment of anti-proliferative effect induced by α-mangostin from Cratoxylum arborescens on HeLa cells
items: Identifying genes and regulatory pathways associated with the scleractinian coral calcification process
items: A positive readout single transcript reporter for site-specific mRNA cleavage
items: The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs
items: A longitudinal study of the diabetic skin and wound microbiome
items: A highly pathogenic porcine reproductive and respiratory syndrome virus candidate vaccine based on Japanese encephalitis virus replicon system

Leaf arrangements are invalid in the taxonomy of orchid species
type: item
type: AcademicArticle
description: The selection and validation of proper distinguishing characters are of crucial importance in taxonomic revisions. The modern classifications of orchids utilize the molecular tools, but still the selection and identification of the material used in these studies is for the most part related to general species morphology. One of the vegetative characters quoted in orchid manuals is leaf arrangement. However, phyllotactic diversity and ontogenetic changeability have not been analysed in detail in reference to particular taxonomic groups. Therefore, we evaluated the usefulness of leaf arrangements in the taxonomy of the genus Epipactis Zinn, 1757. Typical leaf arrangements in shoots of this genus are described as distichous or spiral. However, in the course of field research and screening of herbarium materials, we indisputably disproved the presence of distichous phyllotaxis in the species Epipactis purpurata Sm. and confirmed the spiral Fibonacci pattern as the dominant leaf arrangement. In addition, detailed analyses revealed the presence of atypical decussate phyllotaxis in this species, as well as demonstrated the ontogenetic formation of pseudowhorls. These findings confirm ontogenetic variability and plasticity in E. purpurata. Our results are discussed in the context of their significance in delimitations of complex taxa within the genus Epipactis.
format: application/pdf
format: text/html
creator: Anna Jakubska-Busse
creator: Elżbieta Żołubak
creator: Zbigniew Łobas
creator: Edyta Magdalena Gola
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.3609
publisher: PeerJ Inc.
rights: © 2017 Jakubska-Busse et al.
abstract: The selection and validation of proper distinguishing characters are of crucial importance in taxonomic revisions. The modern classifications of orchids utilize the molecular tools, but still the selection and identification of the material used in these studies is for the most part related to general species morphology. One of the vegetative characters quoted in orchid manuals is leaf arrangement. However, phyllotactic diversity and ontogenetic changeability have not been analysed in detail in reference to particular taxonomic groups. Therefore, we evaluated the usefulness of leaf arrangements in the taxonomy of the genus Epipactis Zinn, 1757. Typical leaf arrangements in shoots of this genus are described as distichous or spiral. However, in the course of field research and screening of herbarium materials, we indisputably disproved the presence of distichous phyllotaxis in the species Epipactis purpurata Sm. and confirmed the spiral Fibonacci pattern as the dominant leaf arrangement. In addition, detailed analyses revealed the presence of atypical decussate phyllotaxis in this species, as well as demonstrated the ontogenetic formation of pseudowhorls. These findings confirm ontogenetic variability and plasticity in E. purpurata. Our results are discussed in the context of their significance in delimitations of complex taxa within the genus Epipactis.
bibliographic citation: Jakubska-Busse et al. (2017) Leaf arrangements are invalid in the taxonomy of orchid species. PeerJ 5:e3609 https://doi.org/10.7717/peerj.3609
date submitted: 2017-04-29
date accepted: 2017-07-03
issued: 2017-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jakubska-Busse
  given name: Anna
author list: Agent
  family name: Żołubak
  given name: Elżbieta
author list: Agent
  family name: Łobas
  given name: Zbigniew
author list: Agent
  family name: Gola
  given name: Edyta Magdalena
doi: 10.7717/peerj.3609
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-07-21
copyright: ©2017 Jakubska-Busse et al.
attribution name: Jakubska-Busse et al.

Using electroretinograms and multi-model inference to identify spectral classes of photoreceptors and relative opsin expression levels
type: item
type: AcademicArticle
description: Understanding how individual photoreceptor cells factor in the spectral sensitivity of a visual system is essential to explain how they contribute to the visual ecology of the animal in question. Existing methods that model the absorption of visual pigments use templates which correspond closely to data from thin cross-sections of photoreceptor cells. However, few modeling approaches use a single framework to incorporate physical parameters of real photoreceptors, which can be fused, and can form vertical tiers. Akaike’s information criterion (AICc) was used here to select absorptance models of multiple classes of photoreceptor cells that maximize information, given visual system spectral sensitivity data obtained using extracellular electroretinograms and structural parameters obtained by histological methods. This framework was first used to select among alternative hypotheses of photoreceptor number. It identified spectral classes from a range of dark-adapted visual systems which have between one and four spectral photoreceptor classes. These were the velvet worm, Principapillatus hitoyensis, the branchiopod water flea, Daphnia magna, normal humans, and humans with enhanced S-cone syndrome, a condition in which S-cone frequency is increased due to mutations in a transcription factor that controls photoreceptor expression. Data from the Asian swallowtail, Papilio xuthus, which has at least five main spectral photoreceptor classes in its compound eyes, were included to illustrate potential effects of model over-simplification on multi-model inference. The multi-model framework was then used with parameters of spectral photoreceptor classes and the structural photoreceptor array kept constant. The goal was to map relative opsin expression to visual pigment concentration. It identified relative opsin expression differences for two populations of the bluefin killifish, Lucania goodei. The modeling approach presented here will be useful in selecting the most likely alt…
format: application/pdf
format: text/html
creator: Nicolas Lessios
subject: Animal Behavior
subject: Ecology
subject: Neuroscience
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.3595
publisher: PeerJ Inc.
rights: © 2017 Lessios
abstract: Understanding how individual photoreceptor cells factor in the spectral sensitivity of a visual system is essential to explain how they contribute to the visual ecology of the animal in question. Existing methods that model the absorption of visual pigments use templates which correspond closely to data from thin cross-sections of photoreceptor cells. However, few modeling approaches use a single framework to incorporate physical parameters of real photoreceptors, which can be fused, and can form vertical tiers. Akaike’s information criterion (AICc) was used here to select absorptance models of multiple classes of photoreceptor cells that maximize information, given visual system spectral sensitivity data obtained using extracellular electroretinograms and structural parameters obtained by histological methods. This framework was first used to select among alternative hypotheses of photoreceptor number. It identified spectral classes from a range of dark-adapted visual systems which have between one and four spectral photoreceptor classes. These were the velvet worm, Principapillatus hitoyensis, the branchiopod water flea, Daphnia magna, normal humans, and humans with enhanced S-cone syndrome, a condition in which S-cone frequency is increased due to mutations in a transcription factor that controls photoreceptor expression. Data from the Asian swallowtail, Papilio xuthus, which has at least five main spectral photoreceptor classes in its compound eyes, were included to illustrate potential effects of model over-simplification on multi-model inference. The multi-model framework was then used with parameters of spectral photoreceptor classes and the structural photoreceptor array kept constant. The goal was to map relative opsin expression to visual pigment concentration. It identified relative opsin expression differences for two populations of the bluefin killifish, Lucania goodei. The modeling approach presented here will be useful in selecting the most likely alt…
bibliographic citation: Lessios (2017) Using electroretinograms and multi-model inference to identify spectral classes of photoreceptors and relative opsin expression levels. PeerJ 5:e3595 https://doi.org/10.7717/peerj.3595
date submitted: 2017-01-13
date accepted: 2017-06-29
issued: 2017-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lessios
  given name: Nicolas
doi: 10.7717/peerj.3595
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-07-21
copyright: © 2017 Lessios
attribution name: Lessios

A laid-back trip through the Hennigian Forests
type: item
type: AcademicArticle
description: Background This paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea’s efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as “source” of Hennigian trees, not as a primary subject of the analysis. Switching from the matrix-based thinking to the matrix-free Cladistic approach clearly reveals that optimizations of the character-state changes are related not to the real processes, but to the form of the data representation. Methods We focused our study on the binary data. We wrote the simple ruby-based script FORESTER version 1.0 that helps represent a binary matrix as an array of the rooted trees (as a “Hennigian forest”). The binary representations of the genomic (DNA) data have been made by script 1001. The Average Consensus method as well as the standard Maximum Parsimony (MP) approach has been used to analyze the data. Principle findings The binary matrix may be easily re-written as a set of rooted trees (maximal relationships). The latter might be analyzed by the Average Consensus method. Paradoxically, this method, if applied to the Hennigian forests, in principle can help to identify clades despite the absence of the direct evidence from the primary data. Our approach may handle the clock- or non clock-like matrices, as well as the hypothetical, molecular or morphological data. Discussion Our proposal clearly differs from the numerous phenetic alignment-free techniques of the construction of the phylogenetic trees. Dealing with the relations, not with the actual “data” also distinguishes our approach from all optimization-based methods, if the optimization is defined as a way to reconstruct the sequences of the character-state changes on a tree, either the standard alignment-based techniques or the “direct” alignment-free procedure. We are not viewing our recent framework as an alternative to the three-taxon statement analysis (3TA), but there are two major diff…
format: application/pdf
format: text/html
creator: Evgeny V. Mavrodiev
creator: Christopher Dell
creator: Laura Schroder
subject: Bioinformatics
subject: Taxonomy
subject: Computational Science
description: doi:10.7717/peerj.3578
publisher: PeerJ Inc.
rights: © 2017 Mavrodiev et al.
abstract: Background This paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea’s efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as “source” of Hennigian trees, not as a primary subject of the analysis. Switching from the matrix-based thinking to the matrix-free Cladistic approach clearly reveals that optimizations of the character-state changes are related not to the real processes, but to the form of the data representation. Methods We focused our study on the binary data. We wrote the simple ruby-based script FORESTER version 1.0 that helps represent a binary matrix as an array of the rooted trees (as a “Hennigian forest”). The binary representations of the genomic (DNA) data have been made by script 1001. The Average Consensus method as well as the standard Maximum Parsimony (MP) approach has been used to analyze the data. Principle findings The binary matrix may be easily re-written as a set of rooted trees (maximal relationships). The latter might be analyzed by the Average Consensus method. Paradoxically, this method, if applied to the Hennigian forests, in principle can help to identify clades despite the absence of the direct evidence from the primary data. Our approach may handle the clock- or non clock-like matrices, as well as the hypothetical, molecular or morphological data. Discussion Our proposal clearly differs from the numerous phenetic alignment-free techniques of the construction of the phylogenetic trees. Dealing with the relations, not with the actual “data” also distinguishes our approach from all optimization-based methods, if the optimization is defined as a way to reconstruct the sequences of the character-state changes on a tree, either the standard alignment-based techniques or the “direct” alignment-free procedure. We are not viewing our recent framework as an alternative to the three-taxon statement analysis (3TA), but there are two major diff…
bibliographic citation: Mavrodiev et al. (2017) A laid-back trip through the Hennigian Forests. PeerJ 5:e3578 https://doi.org/10.7717/peerj.3578
date submitted: 2017-04-13
date accepted: 2017-06-23
issued: 2017-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mavrodiev
  given name: Evgeny V.
author list: Agent
  family name: Dell
  given name: Christopher
author list: Agent
  family name: Schroder
  given name: Laura
doi: 10.7717/peerj.3578
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-07-21
copyright: ©2017 Mavrodiev et al.
attribution name: Mavrodiev et al.

Long-term resource addition to a detrital food web yields a pattern of responses more complex than pervasive bottom-up control
type: item
type: AcademicArticle
description: Background Theory predicts strong bottom-up control in detritus-based food webs, yet field experiments with detritus-based terrestrial systems have uncovered contradictory evidence regarding the strength and pervasiveness of bottom-up control processes. Two factors likely leading to contradictory results are experiment duration, which influences exposure to temporal variation in abiotic factors such as rainfall and affects the likelihood of detecting approach to a new equilibrium; and openness of the experimental units to immigration and emigration. To investigate the contribution of these two factors, we conducted a long-term experiment with open and fenced plots in the forest that was the site of an earlier, short-term experiment (3.5 months) with open plots (Chen & Wise, 1999) that produced evidence of strong bottom-up control for 14 taxonomic groupings of primary consumers of fungi and detritus (microbi-detritivores) and their predators. Methods We added artificial high-quality detritus to ten 2 × 2-m forest-floor plots at bi-weekly intervals from April through September in three consecutive years (Supplemented treatment). Ten comparable Ambient plots were controls. Half of the Supplemented and Ambient plots were enclosed by metal fencing. Results Arthropod community structure (based upon 18 response variables) diverged over time between Supplemented and Ambient treatments, with no effect of Fencing on the multivariate response pattern. Fencing possibly influenced only ca. 30% of the subsequent univariate analyses. Multi- and univariate analyses revealed bottom-up control during Year 1 of some, but not all, microbi-detritivores and predators. During the following two years the pattern of responses became more complex than that observed by Chen & Wise (1999). Some taxa showed consistent bottom-up control whereas others did not. Variation across years could not be explained completely by differences in rainfall because some taxa exhibited negative, not positive, r…
format: application/pdf
format: text/html
creator: Kendra L. Lawrence
creator: David H. Wise
subject: Ecology
subject: Soil Science
subject: Zoology
description: doi:10.7717/peerj.3572
publisher: PeerJ Inc.
rights: © 2017 Lawrence and Wise
abstract: Background Theory predicts strong bottom-up control in detritus-based food webs, yet field experiments with detritus-based terrestrial systems have uncovered contradictory evidence regarding the strength and pervasiveness of bottom-up control processes. Two factors likely leading to contradictory results are experiment duration, which influences exposure to temporal variation in abiotic factors such as rainfall and affects the likelihood of detecting approach to a new equilibrium; and openness of the experimental units to immigration and emigration. To investigate the contribution of these two factors, we conducted a long-term experiment with open and fenced plots in the forest that was the site of an earlier, short-term experiment (3.5 months) with open plots (Chen & Wise, 1999) that produced evidence of strong bottom-up control for 14 taxonomic groupings of primary consumers of fungi and detritus (microbi-detritivores) and their predators. Methods We added artificial high-quality detritus to ten 2 × 2-m forest-floor plots at bi-weekly intervals from April through September in three consecutive years (Supplemented treatment). Ten comparable Ambient plots were controls. Half of the Supplemented and Ambient plots were enclosed by metal fencing. Results Arthropod community structure (based upon 18 response variables) diverged over time between Supplemented and Ambient treatments, with no effect of Fencing on the multivariate response pattern. Fencing possibly influenced only ca. 30% of the subsequent univariate analyses. Multi- and univariate analyses revealed bottom-up control during Year 1 of some, but not all, microbi-detritivores and predators. During the following two years the pattern of responses became more complex than that observed by Chen & Wise (1999). Some taxa showed consistent bottom-up control whereas others did not. Variation across years could not be explained completely by differences in rainfall because some taxa exhibited negative, not positive, r…
bibliographic citation: Lawrence et al. (2017) Long-term resource addition to a detrital food web yields a pattern of responses more complex than pervasive bottom-up control. PeerJ 5:e3572 https://doi.org/10.7717/peerj.3572
date submitted: 2017-01-13
date accepted: 2017-06-22
issued: 2017-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lawrence
  given name: Kendra L.
author list: Agent
  family name: Wise
  given name: David H.
doi: 10.7717/peerj.3572
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-07-21
copyright: ©2017 Lawrence and Wise
attribution name: Lawrence and Wise

In vitro assessment of anti-proliferative effect induced by α-mangostin from Cratoxylum arborescens on HeLa cells
type: item
type: AcademicArticle
description: Natural medicinal products possess diverse chemical structures and have been an essential source for drug discovery. Therefore, in this study, α-mangostin (AM) is a plant-derived compound was investigated for the apoptotic effect on human cervical cancer cells (HeLa). The cytotoxic effects of AM on the viability of HeLa and human normal ovarian cell line (SV40) were evaluated by using MTT assay. Results showed that AM inhibited HeLa cells viability at concentration- and time-dependent manner with IC50 value of 24.53 ± 1.48 µM at 24 h. The apoptogenic effects of AM on HeLa were assessed using fluorescence microscopy analysis. The effect of AM on cell proliferation was also studied through clonogenic assay. ROS production evaluation, flow cytometry (cell cycle) analysis, caspases 3/7, 8, and 9 assessment and multiple cytotoxicity assays were conducted to determine the mechanism of cell apoptosis. This was associated with G2/M phase cell cycle arrest and elevation in ROS production. AM induced mitochondrial apoptosis which was confirmed based on the significant increase in the levels of caspases 3/7 and 9 in a dose-dependent manner. Furthermore, the MMP disruption and increased cell permeability, concurrent with cytochrome c release from the mitochondria to the cytosol provided evidence that AM can induce apoptosis via mitochondrial-dependent pathway. AM exerted a remarkable antitumor effect and induced characteristic apoptogenic morphological changes on HeLa cells, which indicates the occurrence of cell death. This study reveals that AM could be a potential antitumor compound on cervical cancer in vitro and can be considered for further cervical cancer preclinical and in vivo testing.
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format: text/html
creator: Aisha I. El habbash
creator: Najihah Mohd Hashim
creator: Mohamed Yousif Ibrahim
creator: Maizatulakmal Yahayu
creator: Fatima Abd Elmutaal Omer
creator: Mashitoh Abd Rahman
creator: Noraziah Nordin
creator: Gwendoline Ee Cheng Lian
subject: Biochemistry
subject: Cell Biology
description: doi:10.7717/peerj.3460
publisher: PeerJ Inc.
rights: © 2017 El habbash et al.
abstract: Natural medicinal products possess diverse chemical structures and have been an essential source for drug discovery. Therefore, in this study, α-mangostin (AM) is a plant-derived compound was investigated for the apoptotic effect on human cervical cancer cells (HeLa). The cytotoxic effects of AM on the viability of HeLa and human normal ovarian cell line (SV40) were evaluated by using MTT assay. Results showed that AM inhibited HeLa cells viability at concentration- and time-dependent manner with IC50 value of 24.53 ± 1.48 µM at 24 h. The apoptogenic effects of AM on HeLa were assessed using fluorescence microscopy analysis. The effect of AM on cell proliferation was also studied through clonogenic assay. ROS production evaluation, flow cytometry (cell cycle) analysis, caspases 3/7, 8, and 9 assessment and multiple cytotoxicity assays were conducted to determine the mechanism of cell apoptosis. This was associated with G2/M phase cell cycle arrest and elevation in ROS production. AM induced mitochondrial apoptosis which was confirmed based on the significant increase in the levels of caspases 3/7 and 9 in a dose-dependent manner. Furthermore, the MMP disruption and increased cell permeability, concurrent with cytochrome c release from the mitochondria to the cytosol provided evidence that AM can induce apoptosis via mitochondrial-dependent pathway. AM exerted a remarkable antitumor effect and induced characteristic apoptogenic morphological changes on HeLa cells, which indicates the occurrence of cell death. This study reveals that AM could be a potential antitumor compound on cervical cancer in vitro and can be considered for further cervical cancer preclinical and in vivo testing.
bibliographic citation: El habbash et al. (2017) In vitro assessment of anti-proliferative effect induced by α-mangostin from Cratoxylum arborescens on HeLa cells. PeerJ 5:e3460 https://doi.org/10.7717/peerj.3460
date submitted: 2016-08-23
date accepted: 2017-05-24
issued: 2017-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: El habbash
  given name: Aisha I.
author list: Agent
  family name: Mohd Hashim
  given name: Najihah
author list: Agent
  family name: Ibrahim
  given name: Mohamed Yousif
author list: Agent
  family name: Yahayu
  given name: Maizatulakmal
author list: Agent
  family name: Omer
  given name: Fatima Abd Elmutaal
author list: Agent
  family name: Abd Rahman
  given name: Mashitoh
author list: Agent
  family name: Nordin
  given name: Noraziah
author list: Agent
  family name: Lian
  given name: Gwendoline Ee Cheng
doi: 10.7717/peerj.3460
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-07-21
copyright: ©2017 El habbash et al.
attribution name: El habbash et al.

Identifying genes and regulatory pathways associated with the scleractinian coral calcification process
type: item
type: AcademicArticle
description: Reef building corals precipitate calcium carbonate as an exo-skeleton and provide substratum for prosperous marine life. Biomineralization of the coral’s skeleton is a developmental process that occurs concurrently with other proliferation processes that control the animal extension and growth. The development of the animal body is regulated by large gene regulatory networks, which control the expression of gene sets that progressively generate developmental patterns in the animal body. In this study we have explored the gene expression profile and signaling pathways followed by the calcification process of a basal metazoan, the Red Sea scleractinian (stony) coral, Stylophora pistillata. When treated by seawater with high calcium concentrations (addition of 100 gm/L, added as CaCl2.2H2O), the coral increases its calcification rates and associated genes were up-regulated as a result, which were then identified. Gene expression was compared between corals treated with elevated and normal calcium concentrations. Calcification rate measurements and gene expression analysis by microarray RNA transcriptional profiling at two time-points (midday and night-time) revealed several genes common within mammalian gene regulatory networks. This study indicates that core genes of the Wnt and TGF-β/BMP signaling pathways may also play roles in development, growth, and biomineralization in early-diverging organisms such as corals.
format: application/pdf
format: text/html
creator: Eldad Gutner-Hoch
creator: Hiba Waldman Ben-Asher
creator: Ruth Yam
creator: Aldo Shemesh
creator: Oren Levy
subject: Ecology
subject: Environmental Sciences
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.3590
publisher: PeerJ Inc.
rights: © 2017 Gutner-Hoch et al.
abstract: Reef building corals precipitate calcium carbonate as an exo-skeleton and provide substratum for prosperous marine life. Biomineralization of the coral’s skeleton is a developmental process that occurs concurrently with other proliferation processes that control the animal extension and growth. The development of the animal body is regulated by large gene regulatory networks, which control the expression of gene sets that progressively generate developmental patterns in the animal body. In this study we have explored the gene expression profile and signaling pathways followed by the calcification process of a basal metazoan, the Red Sea scleractinian (stony) coral, Stylophora pistillata. When treated by seawater with high calcium concentrations (addition of 100 gm/L, added as CaCl2.2H2O), the coral increases its calcification rates and associated genes were up-regulated as a result, which were then identified. Gene expression was compared between corals treated with elevated and normal calcium concentrations. Calcification rate measurements and gene expression analysis by microarray RNA transcriptional profiling at two time-points (midday and night-time) revealed several genes common within mammalian gene regulatory networks. This study indicates that core genes of the Wnt and TGF-β/BMP signaling pathways may also play roles in development, growth, and biomineralization in early-diverging organisms such as corals.
bibliographic citation: Gutner-Hoch et al. (2017) Identifying genes and regulatory pathways associated with the scleractinian coral calcification process. PeerJ 5:e3590 https://doi.org/10.7717/peerj.3590
date submitted: 2017-01-03
date accepted: 2017-06-27
issued: 2017-07-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gutner-Hoch
  given name: Eldad
author list: Agent
  family name: Waldman Ben-Asher
  given name: Hiba
author list: Agent
  family name: Yam
  given name: Ruth
author list: Agent
  family name: Shemesh
  given name: Aldo
author list: Agent
  family name: Levy
  given name: Oren
doi: 10.7717/peerj.3590
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-07-20
copyright: ©2017 Gutner-Hoch et al.
attribution name: Gutner-Hoch et al.

A positive readout single transcript reporter for site-specific mRNA cleavage
type: item
type: AcademicArticle
description: Cleavage of mRNA molecules causes their rapid degradation, thereby playing an important role in regulation of gene expression and host genome defense from viruses and transposons in bacterial and eukaryotic cells. Current negative-readout, and repressor-based positive-readout reporters of mRNA degradation have limitations. Here we report the development of a single transcript that acts as a positive reporter of mRNA cleavage. We show that placement of bacterial CopT and CopA hairpins into the 5′ UTR and 3′ UTR of an mRNA results in inhibition of translation of the intervening coding sequence in Drosophila. An internal poly(A) tract inserted downstream of the coding sequence stabilizes transcripts cut within the 3′ UTR. When these components are combined in a transcript in which targets sites for RNA cleavage are placed between the poly(A) tract and CopA, cleavage results in translational activation, providing a single transcript-based method of sensing mRNA cleavage with a positive readout.
format: application/pdf
format: text/html
creator: Nikolay Kandul
creator: Ming Guo
creator: Bruce A. Hay
subject: Bioengineering
subject: Molecular Biology
subject: Synthetic Biology
description: doi:10.7717/peerj.3602
publisher: PeerJ Inc.
rights: © 2017 Kandul et al.
abstract: Cleavage of mRNA molecules causes their rapid degradation, thereby playing an important role in regulation of gene expression and host genome defense from viruses and transposons in bacterial and eukaryotic cells. Current negative-readout, and repressor-based positive-readout reporters of mRNA degradation have limitations. Here we report the development of a single transcript that acts as a positive reporter of mRNA cleavage. We show that placement of bacterial CopT and CopA hairpins into the 5′ UTR and 3′ UTR of an mRNA results in inhibition of translation of the intervening coding sequence in Drosophila. An internal poly(A) tract inserted downstream of the coding sequence stabilizes transcripts cut within the 3′ UTR. When these components are combined in a transcript in which targets sites for RNA cleavage are placed between the poly(A) tract and CopA, cleavage results in translational activation, providing a single transcript-based method of sensing mRNA cleavage with a positive readout.
bibliographic citation: Kandul et al. (2017) A positive readout single transcript reporter for site-specific mRNA cleavage. PeerJ 5:e3602 https://doi.org/10.7717/peerj.3602
date submitted: 2017-05-04
date accepted: 2017-06-30
issued: 2017-07-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kandul
  given name: Nikolay
author list: Agent
  family name: Guo
  given name: Ming
author list: Agent
  family name: Hay
  given name: Bruce A.
doi: 10.7717/peerj.3602
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-07-20
copyright: ©2017 Kandul et al.
attribution name: Kandul et al.

The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs
type: item
type: AcademicArticle
description: Background The microbial populations that inhabit the gastrointestinal tract (GIT) are known to influence the health and growth performance of the host. Clean hatcheries and machine-based incubation practices in the commercial poultry industry can lead to the acquisition of aberrant microbiota in the GIT of chickens and a very high level of bird-to-bird variation. The lack of microbial profile flock uniformity presents challenges for harnessing and manipulating intestinal bacteria to better serve the host. Methods Cecal contents from high or low performing chickens were used to inoculate the surface of eggs prior to hatching and then the initial gut colonisation was monitored and subsequent changes in gut microbiota composition were followed over time. Two different cecal treatment groups were compared to an untreated control group (n = 32). Bacterial communities were characterised using high-throughput 16S rRNA gene sequencing techniques. Results Cecal microbiota transfer via egg surface application did not transfer the performance profile of the donors to the recipient birds. One of the cecal inoculations provided a more uniform gut microbiota, but this was not reproduced in the second group with a different inoculum. Development of the intestinal community was reproducible in all three groups with some genera like Lactobacillus showing no change, others like Faecalibacterium increased in abundance slowly and steadily over time and others like Enterobacter were abundant only in the first days of life. Discussion The cecal treatment reduced bird-to-bird variation in microbiota composition. Although the high FCR performance of donor birds was not transferred with the cecal microbiota, all three groups, including the control, performed better than standard for the breed. The pattern of microbiota development was similar in all three flocks, indicating that the normal processes of microbiota acquisition largely swamped any effect of the cecal material applied to eggs.
format: application/pdf
format: text/html
creator: Erin E. Donaldson
creator: Dragana Stanley
creator: Robert J. Hughes
creator: Robert J. Moore
subject: Agricultural Science
subject: Microbiology
description: doi:10.7717/peerj.3587
publisher: PeerJ Inc.
rights: © 2017 Donaldson et al.
abstract: Background The microbial populations that inhabit the gastrointestinal tract (GIT) are known to influence the health and growth performance of the host. Clean hatcheries and machine-based incubation practices in the commercial poultry industry can lead to the acquisition of aberrant microbiota in the GIT of chickens and a very high level of bird-to-bird variation. The lack of microbial profile flock uniformity presents challenges for harnessing and manipulating intestinal bacteria to better serve the host. Methods Cecal contents from high or low performing chickens were used to inoculate the surface of eggs prior to hatching and then the initial gut colonisation was monitored and subsequent changes in gut microbiota composition were followed over time. Two different cecal treatment groups were compared to an untreated control group (n = 32). Bacterial communities were characterised using high-throughput 16S rRNA gene sequencing techniques. Results Cecal microbiota transfer via egg surface application did not transfer the performance profile of the donors to the recipient birds. One of the cecal inoculations provided a more uniform gut microbiota, but this was not reproduced in the second group with a different inoculum. Development of the intestinal community was reproducible in all three groups with some genera like Lactobacillus showing no change, others like Faecalibacterium increased in abundance slowly and steadily over time and others like Enterobacter were abundant only in the first days of life. Discussion The cecal treatment reduced bird-to-bird variation in microbiota composition. Although the high FCR performance of donor birds was not transferred with the cecal microbiota, all three groups, including the control, performed better than standard for the breed. The pattern of microbiota development was similar in all three flocks, indicating that the normal processes of microbiota acquisition largely swamped any effect of the cecal material applied to eggs.
bibliographic citation: Donaldson et al. (2017) The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs. PeerJ 5:e3587 https://doi.org/10.7717/peerj.3587
date submitted: 2017-02-23
date accepted: 2017-06-27
issued: 2017-07-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Donaldson
  given name: Erin E.
author list: Agent
  family name: Stanley
  given name: Dragana
author list: Agent
  family name: Hughes
  given name: Robert J.
author list: Agent
  family name: Moore
  given name: Robert J.
doi: 10.7717/peerj.3587
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-07-20
copyright: ©2017 Donaldson et al.
attribution name: Donaldson et al.

A longitudinal study of the diabetic skin and wound microbiome
type: item
type: AcademicArticle
description: Background Type II diabetes is a chronic health condition which is associated with skin conditions including chronic foot ulcers and an increased incidence of skin infections. The skin microbiome is thought to play important roles in skin defence and immune functioning. Diabetes affects the skin environment, and this may perturb skin microbiome with possible implications for skin infections and wound healing. This study examines the skin and wound microbiome in type II diabetes. Methods Eight type II diabetic subjects with chronic foot ulcers were followed over a time course of 10 weeks, sampling from both foot skin (swabs) and wounds (swabs and debrided tissue) every two weeks. A control group of eight control subjects was also followed over 10 weeks, and skin swabs collected from the foot skin every two weeks. Samples were processed for DNA and subject to 16S rRNA gene PCR and sequencing of the V4 region. Results The diabetic skin microbiome was significantly less diverse than control skin. Community composition was also significantly different between diabetic and control skin, however the most abundant taxa were similar between groups, with differences driven by very low abundant members of the skin communities. Chronic wounds tended to be dominated by the most abundant skin Staphylococcus, while other abundant wound taxa differed by patient. No significant correlations were found between wound duration or healing status and the abundance of any particular taxa. Discussion The major difference observed in this study of the skin microbiome associated with diabetes was a significant reduction in diversity. The long-term effects of reduced diversity are not yet well understood, but are often associated with disease conditions.
format: application/pdf
format: text/html
creator: Melissa Gardiner
creator: Mauro Vicaretti
creator: Jill Sparks
creator: Sunaina Bansal
creator: Stephen Bush
creator: Michael Liu
creator: Aaron Darling
creator: Elizabeth Harry
creator: Catherine M. Burke
subject: Microbiology
subject: Molecular Biology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.3543
publisher: PeerJ Inc.
rights: © 2017 Gardiner et al.
abstract: Background Type II diabetes is a chronic health condition which is associated with skin conditions including chronic foot ulcers and an increased incidence of skin infections. The skin microbiome is thought to play important roles in skin defence and immune functioning. Diabetes affects the skin environment, and this may perturb skin microbiome with possible implications for skin infections and wound healing. This study examines the skin and wound microbiome in type II diabetes. Methods Eight type II diabetic subjects with chronic foot ulcers were followed over a time course of 10 weeks, sampling from both foot skin (swabs) and wounds (swabs and debrided tissue) every two weeks. A control group of eight control subjects was also followed over 10 weeks, and skin swabs collected from the foot skin every two weeks. Samples were processed for DNA and subject to 16S rRNA gene PCR and sequencing of the V4 region. Results The diabetic skin microbiome was significantly less diverse than control skin. Community composition was also significantly different between diabetic and control skin, however the most abundant taxa were similar between groups, with differences driven by very low abundant members of the skin communities. Chronic wounds tended to be dominated by the most abundant skin Staphylococcus, while other abundant wound taxa differed by patient. No significant correlations were found between wound duration or healing status and the abundance of any particular taxa. Discussion The major difference observed in this study of the skin microbiome associated with diabetes was a significant reduction in diversity. The long-term effects of reduced diversity are not yet well understood, but are often associated with disease conditions.
bibliographic citation: Gardiner et al. (2017) A longitudinal study of the diabetic skin and wound microbiome. PeerJ 5:e3543 https://doi.org/10.7717/peerj.3543
date submitted: 2017-04-03
date accepted: 2017-06-14
issued: 2017-07-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gardiner
  given name: Melissa
author list: Agent
  family name: Vicaretti
  given name: Mauro
author list: Agent
  family name: Sparks
  given name: Jill
author list: Agent
  family name: Bansal
  given name: Sunaina
author list: Agent
  family name: Bush
  given name: Stephen
author list: Agent
  family name: Liu
  given name: Michael
author list: Agent
  family name: Darling
  given name: Aaron
author list: Agent
  family name: Harry
  given name: Elizabeth
author list: Agent
  family name: Burke
  given name: Catherine M.
doi: 10.7717/peerj.3543
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-07-20
copyright: ©2017 Gardiner et al.
attribution name: Gardiner et al.

A highly pathogenic porcine reproductive and respiratory syndrome virus candidate vaccine based on Japanese encephalitis virus replicon system
type: item
type: AcademicArticle
description: In the swine industry, porcine reproductive and respiratory syndrome (PRRS) is a highly contagious disease which causes heavy economic losses worldwide. Effective prevention and disease control is an important issue. In this study, we described the construction of a Japanese encephalitis virus (JEV) DNA-based replicon with a cytomegalovirus (CMV) promoter based on the genome of Japanese encephalitis live vaccine virus SA14-14-2, which is capable of offering a potentially novel way to develop and produce vaccines against a major pathogen of global health. This JEV DNA-based replicon contains a large deletion in the structural genes (C-prM-E). A PRRSV GP5/M was inserted into the deletion position of JEV DNA-based replicons to develop a chimeric replicon vaccine candidate for PRRSV. The results showed that BALB/c mice models with the replicon vaccines pJEV-REP-G-2A-M-IRES and pJEV-REP-G-2A-M stimulated antibody responses and induced a cellular immune response. Analysis of ELSA data showed that vaccination with the replicon vaccine expressing GP5/M induced a better antibodies response than traditional DNA vaccines. Therefore, the results suggested that this ectopic expression system based on JEV DNA-based replicons may represent a useful molecular platform for various biological applications, and the JEV DNA-based replicons expressing GP5/M can be further developed into a novel, safe vaccine candidate for PRRS.
format: application/pdf
format: text/html
creator: Pingsheng Hu
creator: Xiaoming Chen
creator: Lihong Huang
creator: Shukai Liu
creator: Fuyu Zang
creator: Jinchao Xing
creator: Youyue Zhang
creator: Jiaqi Liang
creator: Guihong Zhang
creator: Ming Liao
creator: Wenbao Qi
subject: Veterinary Medicine
subject: Virology
subject: Infectious Diseases
description: doi:10.7717/peerj.3514
publisher: PeerJ Inc.
rights: © 2017 Hu et al.
abstract: In the swine industry, porcine reproductive and respiratory syndrome (PRRS) is a highly contagious disease which causes heavy economic losses worldwide. Effective prevention and disease control is an important issue. In this study, we described the construction of a Japanese encephalitis virus (JEV) DNA-based replicon with a cytomegalovirus (CMV) promoter based on the genome of Japanese encephalitis live vaccine virus SA14-14-2, which is capable of offering a potentially novel way to develop and produce vaccines against a major pathogen of global health. This JEV DNA-based replicon contains a large deletion in the structural genes (C-prM-E). A PRRSV GP5/M was inserted into the deletion position of JEV DNA-based replicons to develop a chimeric replicon vaccine candidate for PRRSV. The results showed that BALB/c mice models with the replicon vaccines pJEV-REP-G-2A-M-IRES and pJEV-REP-G-2A-M stimulated antibody responses and induced a cellular immune response. Analysis of ELSA data showed that vaccination with the replicon vaccine expressing GP5/M induced a better antibodies response than traditional DNA vaccines. Therefore, the results suggested that this ectopic expression system based on JEV DNA-based replicons may represent a useful molecular platform for various biological applications, and the JEV DNA-based replicons expressing GP5/M can be further developed into a novel, safe vaccine candidate for PRRS.
bibliographic citation: Hu et al. (2017) A highly pathogenic porcine reproductive and respiratory syndrome virus candidate vaccine based on Japanese encephalitis virus replicon system. PeerJ 5:e3514 https://doi.org/10.7717/peerj.3514
date submitted: 2017-05-06
date accepted: 2017-06-07
issued: 2017-07-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Pingsheng
author list: Agent
  family name: Chen
  given name: Xiaoming
author list: Agent
  family name: Huang
  given name: Lihong
author list: Agent
  family name: Liu
  given name: Shukai
author list: Agent
  family name: Zang
  given name: Fuyu
author list: Agent
  family name: Xing
  given name: Jinchao
author list: Agent
  family name: Zhang
  given name: Youyue
author list: Agent
  family name: Liang
  given name: Jiaqi
author list: Agent
  family name: Zhang
  given name: Guihong
author list: Agent
  family name: Liao
  given name: Ming
author list: Agent
  family name: Qi
  given name: Wenbao
doi: 10.7717/peerj.3514
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-07-20
copyright: ©2017 Hu et al.
attribution name: Hu et al.

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