PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Arrival and diversification of mabuyine skinks (Squamata: Scincidae) in the Neotropics based on a fossil-calibrated timetree
items: Single exponential decay waveform; a synergistic combination of electroporation and electrolysis (E2) for tissue ablation
items: Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)
items: Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing
items: https://peerj.com/articles/3183
items: Quantitative assessment of fibroblast growth factor receptor 1 expression in neurons and glia
items: Pollinator diversity and reproductive success of Epipactis helleborine (L.) Crantz (Orchidaceae) in anthropogenic and natural habitats
items: The evolution of logic circuits for the purpose of protein contact map prediction
items: Automated identification of insect vectors of Chagas disease in Brazil and Mexico: the Virtual Vector Lab
items: Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California

Arrival and diversification of mabuyine skinks (Squamata: Scincidae) in the Neotropics based on a fossil-calibrated timetree
type: item
type: AcademicArticle
description: Background The evolution of South American Mabuyinae skinks holds significant biogeographic interest because its sister lineage is distributed across the African continent and adjacent islands. Moreover, at least one insular species, Trachylepis atlantica, has independently reached the New World through transoceanic dispersal. To clarify the evolutionary history of both Neotropical lineages, this study aimed to infer an updated timescale using the largest species and gene sampling dataset ever assembled for this group. By extending the analysis to the Scincidae family, we could employ fossil information to estimate mabuyinae divergence times and carried out a formal statistical biogeography analysis. To unveil macroevolutionary patterns, we also inferred diversification rates for this lineage and evaluated whether the colonization of South American continent significantly altered the mode of Mabuyinae evolution. Methods A time-calibrated phylogeny was inferred under the Bayesian framework employing fossil information. This timetree was used to (i) evaluate the historical biogeography of mabuiyines using the statistical approach implemented in BioGeoBEARS; (ii) estimate macroevolutionary diversification rates of the South American Mabuyinae lineages and the patterns of evolution of selected traits, namely, the mode of reproduction, body mass and snout–vent length; (iii) test the hypothesis of differential macroevolutionary patterns in South American lineages in BAMM and GeoSSE; and (iv) re-evaluate the ancestral state of the mode of reproduction of mabuyines. Results Our results corroborated the hypothesis that the occupation of the South American continent by Mabuyinae consisted of two independent dispersion events that occurred between the Oligocene and the Miocene. We found significant differences in speciation rates between the New World and the remaining Mabuyinae clades only in GeoSSE. The influence of phenotypic traits on diversification rates was not supporte…
format: application/pdf
format: text/html
creator: Anieli Guirro Pereira
creator: Carlos G. Schrago
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Genetics
description: doi:10.7717/peerj.3194
publisher: PeerJ Inc.
rights: © 2017 Pereira and Schrago
abstract: Background The evolution of South American Mabuyinae skinks holds significant biogeographic interest because its sister lineage is distributed across the African continent and adjacent islands. Moreover, at least one insular species, Trachylepis atlantica, has independently reached the New World through transoceanic dispersal. To clarify the evolutionary history of both Neotropical lineages, this study aimed to infer an updated timescale using the largest species and gene sampling dataset ever assembled for this group. By extending the analysis to the Scincidae family, we could employ fossil information to estimate mabuyinae divergence times and carried out a formal statistical biogeography analysis. To unveil macroevolutionary patterns, we also inferred diversification rates for this lineage and evaluated whether the colonization of South American continent significantly altered the mode of Mabuyinae evolution. Methods A time-calibrated phylogeny was inferred under the Bayesian framework employing fossil information. This timetree was used to (i) evaluate the historical biogeography of mabuiyines using the statistical approach implemented in BioGeoBEARS; (ii) estimate macroevolutionary diversification rates of the South American Mabuyinae lineages and the patterns of evolution of selected traits, namely, the mode of reproduction, body mass and snout–vent length; (iii) test the hypothesis of differential macroevolutionary patterns in South American lineages in BAMM and GeoSSE; and (iv) re-evaluate the ancestral state of the mode of reproduction of mabuyines. Results Our results corroborated the hypothesis that the occupation of the South American continent by Mabuyinae consisted of two independent dispersion events that occurred between the Oligocene and the Miocene. We found significant differences in speciation rates between the New World and the remaining Mabuyinae clades only in GeoSSE. The influence of phenotypic traits on diversification rates was not supporte…
bibliographic citation: Pereira et al. (2017) Arrival and diversification of mabuyine skinks (Squamata: Scincidae) in the Neotropics based on a fossil-calibrated timetree. PeerJ 5:e3194 https://doi.org/10.7717/peerj.3194
date submitted: 2016-11-21
date accepted: 2017-03-16
issued: 2017-04-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pereira
  given name: Anieli Guirro
author list: Agent
  family name: Schrago
  given name: Carlos G.
doi: 10.7717/peerj.3194
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-04-18
copyright: ©2017 Pereira and Schrago
attribution name: Pereira and Schrago

Single exponential decay waveform; a synergistic combination of electroporation and electrolysis (E2) for tissue ablation
type: item
type: AcademicArticle
description: Background Electrolytic ablation and electroporation based ablation are minimally invasive, non-thermal surgical technologies that employ electrical currents and electric fields to ablate undesirable cells in a volume of tissue. In this study, we explore the attributes of a new tissue ablation technology that simultaneously delivers a synergistic combination of electroporation and electrolysis (E2). Method A new device that delivers a controlled dose of electroporation field and electrolysis currents in the form of a single exponential decay waveform (EDW) was applied to the pig liver, and the effect of various parameters on the extent of tissue ablation was examined with histology. Results Histological analysis shows that E2 delivered as EDW can produce tissue ablation in volumes of clinical significance, using electrical and temporal parameters which, if used in electroporation or electrolysis separately, cannot ablate the tissue. Discussion The E2 combination has advantages over the three basic technologies of non-thermal ablation: electrolytic ablation, electrochemical ablation (reversible electroporation with injection of drugs) and irreversible electroporation. E2 ablates clinically relevant volumes of tissue in a shorter period of time than electrolysis and electroporation, without the need to inject drugs as in reversible electroporation or use paralyzing anesthesia as in irreversible electroporation.
format: application/pdf
format: text/html
creator: Nina Klein
creator: Enric Guenther
creator: Paul Mikus
creator: Michael K. Stehling
creator: Boris Rubinsky
subject: Bioengineering
subject: Biophysics
subject: Oncology
subject: Pathology
subject: Histology
description: doi:10.7717/peerj.3190
publisher: PeerJ Inc.
rights: © 2017 Klein et al.
abstract: Background Electrolytic ablation and electroporation based ablation are minimally invasive, non-thermal surgical technologies that employ electrical currents and electric fields to ablate undesirable cells in a volume of tissue. In this study, we explore the attributes of a new tissue ablation technology that simultaneously delivers a synergistic combination of electroporation and electrolysis (E2). Method A new device that delivers a controlled dose of electroporation field and electrolysis currents in the form of a single exponential decay waveform (EDW) was applied to the pig liver, and the effect of various parameters on the extent of tissue ablation was examined with histology. Results Histological analysis shows that E2 delivered as EDW can produce tissue ablation in volumes of clinical significance, using electrical and temporal parameters which, if used in electroporation or electrolysis separately, cannot ablate the tissue. Discussion The E2 combination has advantages over the three basic technologies of non-thermal ablation: electrolytic ablation, electrochemical ablation (reversible electroporation with injection of drugs) and irreversible electroporation. E2 ablates clinically relevant volumes of tissue in a shorter period of time than electrolysis and electroporation, without the need to inject drugs as in reversible electroporation or use paralyzing anesthesia as in irreversible electroporation.
bibliographic citation: Klein et al. (2017) Single exponential decay waveform; a synergistic combination of electroporation and electrolysis (E2) for tissue ablation. PeerJ 5:e3190 https://doi.org/10.7717/peerj.3190
date submitted: 2016-10-10
date accepted: 2017-03-15
issued: 2017-04-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klein
  given name: Nina
author list: Agent
  family name: Guenther
  given name: Enric
author list: Agent
  family name: Mikus
  given name: Paul
author list: Agent
  family name: Stehling
  given name: Michael K.
author list: Agent
  family name: Rubinsky
  given name: Boris
doi: 10.7717/peerj.3190
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-04-18
copyright: ©2017 Klein et al.
attribution name: Klein et al.

Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)
type: item
type: AcademicArticle
description: Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations.
format: application/pdf
format: text/html
creator: Ciro Rico
creator: Jose Antonio Cuesta
creator: Pilar Drake
creator: Enrique Macpherson
creator: Louis Bernatchez
creator: Amandine D. Marie
subject: Conservation Biology
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.3188
publisher: PeerJ Inc.
rights: © 2017 Rico et al.
abstract: Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations.
bibliographic citation: Rico et al. (2017) Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus). PeerJ 5:e3188 https://doi.org/10.7717/peerj.3188
date submitted: 2016-10-10
date accepted: 2017-03-15
issued: 2017-04-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rico
  given name: Ciro
author list: Agent
  family name: Cuesta
  given name: Jose Antonio
author list: Agent
  family name: Drake
  given name: Pilar
author list: Agent
  family name: Macpherson
  given name: Enrique
author list: Agent
  family name: Bernatchez
  given name: Louis
author list: Agent
  family name: Marie
  given name: Amandine D.
doi: 10.7717/peerj.3188
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-04-18
copyright: ©2017 Rico et al.
attribution name: Rico et al.

Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing
type: item
type: AcademicArticle
description: Prebiotics are selectively fermentable dietary compounds that result in changes in the composition and/or activity of the intestinal microbiota, thus conferring benefits upon host health. In veterinary medicine, commercially available products containing prebiotics have not been well studied with regard to the changes they trigger on the composition of the gut microbiota. This study evaluated the effect of a commercially available nutraceutical containing fructo-oligosaccharides (FOS) and inulin on the fecal microbiota of healthy cats and dogs when administered for 16 days. Fecal samples were collected at two time points before and at two time points during prebiotic administration. Total genomic DNA was obtained from fecal samples and 454-pyrosequencing was used for 16S rRNA gene bacterial profiling. The linear discriminant analysis (LDA) effect size (LEfSe) method was used for detecting bacterial taxa that may respond (i.e., increase or decrease in its relative abundance) to prebiotic administration. Prebiotic administration was associated with a good acceptance and no side effects (e.g., diarrhea) were reported by the owners. A low dose of prebiotics (50 mL total regardless of body weight with the end product containing 0.45% of prebiotics) revealed a lower abundance of Gammaproteobacteria and a higher abundance of Veillonellaceae during prebiotic administration in cats, while Staphylococcaceae showed a higher abundance during prebiotic administration in dogs. These differences were not sufficient to separate bacterial communities as shown by analysis of weighted UniFrac distance metrics. A predictive approach of the fecal bacterial metagenome using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) also did not reveal differences between the period before and during prebiotic administration. A second trial using a higher dose of prebiotics (3.2 mL/kg body weight with the end product containing 3.1% of prebiotics) was teste…
format: application/pdf
format: text/html
creator: Jose F. Garcia-Mazcorro
creator: Jose R. Barcenas-Walls
creator: Jan S. Suchodolski
creator: Jörg M. Steiner
subject: Bioinformatics
subject: Microbiology
subject: Veterinary Medicine
subject: Gastroenterology and Hepatology
subject: Nutrition
description: doi:10.7717/peerj.3184
publisher: PeerJ Inc.
rights: © 2017 Garcia-Mazcorro et al.
abstract: Prebiotics are selectively fermentable dietary compounds that result in changes in the composition and/or activity of the intestinal microbiota, thus conferring benefits upon host health. In veterinary medicine, commercially available products containing prebiotics have not been well studied with regard to the changes they trigger on the composition of the gut microbiota. This study evaluated the effect of a commercially available nutraceutical containing fructo-oligosaccharides (FOS) and inulin on the fecal microbiota of healthy cats and dogs when administered for 16 days. Fecal samples were collected at two time points before and at two time points during prebiotic administration. Total genomic DNA was obtained from fecal samples and 454-pyrosequencing was used for 16S rRNA gene bacterial profiling. The linear discriminant analysis (LDA) effect size (LEfSe) method was used for detecting bacterial taxa that may respond (i.e., increase or decrease in its relative abundance) to prebiotic administration. Prebiotic administration was associated with a good acceptance and no side effects (e.g., diarrhea) were reported by the owners. A low dose of prebiotics (50 mL total regardless of body weight with the end product containing 0.45% of prebiotics) revealed a lower abundance of Gammaproteobacteria and a higher abundance of Veillonellaceae during prebiotic administration in cats, while Staphylococcaceae showed a higher abundance during prebiotic administration in dogs. These differences were not sufficient to separate bacterial communities as shown by analysis of weighted UniFrac distance metrics. A predictive approach of the fecal bacterial metagenome using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) also did not reveal differences between the period before and during prebiotic administration. A second trial using a higher dose of prebiotics (3.2 mL/kg body weight with the end product containing 3.1% of prebiotics) was teste…
bibliographic citation: Garcia-Mazcorro et al. (2017) Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing. PeerJ 5:e3184 https://doi.org/10.7717/peerj.3184
date submitted: 2016-10-17
date accepted: 2017-03-14
issued: 2017-04-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garcia-Mazcorro
  given name: Jose F.
author list: Agent
  family name: Barcenas-Walls
  given name: Jose R.
author list: Agent
  family name: Suchodolski
  given name: Jan S.
author list: Agent
  family name: Steiner
  given name: Jörg M.
doi: 10.7717/peerj.3184
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-04-18
copyright: ©2017 Garcia-Mazcorro et al.
attribution name: Garcia-Mazcorro et al.

https://peerj.com/articles/3183
type: item
type: AcademicArticle
title: Microanatomy and paleohistology of the intercentra of North American metoposaurids from the Upper Triassic of Petrified Forest National Park (Arizona, USA) with implications for the taxonomy and ontogeny of the group
description: Metoposaurids are temnospondyl amphibians that are commonly recovered from the Chinle Formation deposits of North America. Two species, Koskinonodon perfectus and Apachesaurus gregorii, are known from Petrified Forest National Park (PEFO), AZ. Small, elongate intercentra are the single diagnostic postcranial characteristic of the smaller A. gregorii. However, a poor understanding of the earliest life stages of Koskinonodon perfectus and other large metoposaurids makes it unclear whether the proportions of the intercentra are a diagnostic feature for species discrimination or whether they are influenced by ontogeny. Previous work on metoposaurid intercentra has shown that ontogenetic information can be extrapolated from histological analyses. Here, we perform an analysis of the microanatomy and the histology of metoposaurid intercentra from PEFO to determine their ontogenetic maturity and in turn whether elongate intercentra are a reliable taxonomic feature for distinguishing North American metoposaurids. Our findings suggest that the elongate intercentra are the result of ontogenetic variation within a single large-bodied metoposaurid taxon rather than interspecific variation between two metoposaurids of vastly different adult sizes. These findings have significant implications for the taxonomy of North American metoposaurids and subsequently for interpretations of the Chinle Basin paleoenvironment. Furthermore, this study provides the first histological characterization of North American metoposaurid intercentra, thereby improving the understanding of vertebral ontogeny within Metoposauridae and offering new insights into the ecology of large metoposaurids.
format: application/pdf
format: text/html
creator: Bryan M. Gee
creator: William G. Parker
creator: Adam D. Marsh
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Histology
description: doi:10.7717/peerj.3183
publisher: PeerJ Inc.
rights: © 2017 Gee et al.
abstract: Metoposaurids are temnospondyl amphibians that are commonly recovered from the Chinle Formation deposits of North America. Two species, Koskinonodon perfectus and Apachesaurus gregorii, are known from Petrified Forest National Park (PEFO), AZ. Small, elongate intercentra are the single diagnostic postcranial characteristic of the smaller A. gregorii. However, a poor understanding of the earliest life stages of Koskinonodon perfectus and other large metoposaurids makes it unclear whether the proportions of the intercentra are a diagnostic feature for species discrimination or whether they are influenced by ontogeny. Previous work on metoposaurid intercentra has shown that ontogenetic information can be extrapolated from histological analyses. Here, we perform an analysis of the microanatomy and the histology of metoposaurid intercentra from PEFO to determine their ontogenetic maturity and in turn whether elongate intercentra are a reliable taxonomic feature for distinguishing North American metoposaurids. Our findings suggest that the elongate intercentra are the result of ontogenetic variation within a single large-bodied metoposaurid taxon rather than interspecific variation between two metoposaurids of vastly different adult sizes. These findings have significant implications for the taxonomy of North American metoposaurids and subsequently for interpretations of the Chinle Basin paleoenvironment. Furthermore, this study provides the first histological characterization of North American metoposaurid intercentra, thereby improving the understanding of vertebral ontogeny within Metoposauridae and offering new insights into the ecology of large metoposaurids.
bibliographic citation: Gee et al. (2017) Microanatomy and paleohistology of the intercentra of North American metoposaurids from the Upper Triassic of Petrified Forest National Park (Arizona, USA) with implications for the taxonomy and ontogeny of the group. PeerJ 5:e3183 https://doi.org/10.7717/peerj.3183
date submitted: 2016-11-20
date accepted: 2017-03-14
issued: 2017-04-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gee
  given name: Bryan M.
author list: Agent
  family name: Parker
  given name: William G.
author list: Agent
  family name: Marsh
  given name: Adam D.
doi: 10.7717/peerj.3183
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-04-18
copyright: © 2017 Gee et al.
attribution name: Gee et al.

Quantitative assessment of fibroblast growth factor receptor 1 expression in neurons and glia
type: item
type: AcademicArticle
description: Background Fibroblast growth factors (FGFs) and their receptors (FGFRs) have numerous functions in the developing and adult central nervous system (CNS). For example, the FGFR1 receptor is important for proliferation and fate specification of radial glial cells in the cortex and hippocampus, oligodendrocyte proliferation and regeneration, midline glia morphology and soma translocation, Bergmann glia morphology, and cerebellar morphogenesis. In addition, FGFR1 signaling in astrocytes is required for postnatal maturation of interneurons expressing parvalbumin (PV). FGFR1 is implicated in synapse formation in the hippocampus, and alterations in the expression of Fgfr1 and its ligand, Fgf2 accompany major depression. Understanding which cell types express Fgfr1 during development may elucidate its roles in normal development of the brain as well as illuminate possible causes of certain neuropsychiatric disorders. Methods Here, we used a BAC transgenic reporter line to trace Fgfr1 expression in the developing postnatal murine CNS. The specific transgenic line employed was created by the GENSAT project, tgFGFR1-EGFPGP338Gsat, and includes a gene encoding enhanced green fluorescent protein (EGFP) under the regulation of the Fgfr1 promoter, to trace Fgfr1 expression in the developing CNS. Unbiased stereological counts were performed for several cell types in the cortex and hippocampus. Results This model reveals that Fgfr1 is primarily expressed in glial cells, in both astrocytes and oligodendrocytes, along with some neurons. Dual labeling experiments indicate that the proportion of GFP+ (Fgfr1+) cells that are also GFAP+ increases from postnatal day 7 (P7) to 1 month, illuminating dynamic changes in Fgfr1 expression during postnatal development of the cortex. In postnatal neurogenic areas, GFP expression was also observed in SOX2, doublecortin (DCX), and brain lipid-binding protein (BLBP) expressing cells. Fgfr1 is also highly expressed in DCX positive cells of the dentate…
format: application/pdf
format: text/html
creator: Lisha Choubey
creator: Jantzen C. Collette
creator: Karen Müller Smith
subject: Developmental Biology
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3173
publisher: PeerJ Inc.
rights: © 2017 Choubey et al.
abstract: Background Fibroblast growth factors (FGFs) and their receptors (FGFRs) have numerous functions in the developing and adult central nervous system (CNS). For example, the FGFR1 receptor is important for proliferation and fate specification of radial glial cells in the cortex and hippocampus, oligodendrocyte proliferation and regeneration, midline glia morphology and soma translocation, Bergmann glia morphology, and cerebellar morphogenesis. In addition, FGFR1 signaling in astrocytes is required for postnatal maturation of interneurons expressing parvalbumin (PV). FGFR1 is implicated in synapse formation in the hippocampus, and alterations in the expression of Fgfr1 and its ligand, Fgf2 accompany major depression. Understanding which cell types express Fgfr1 during development may elucidate its roles in normal development of the brain as well as illuminate possible causes of certain neuropsychiatric disorders. Methods Here, we used a BAC transgenic reporter line to trace Fgfr1 expression in the developing postnatal murine CNS. The specific transgenic line employed was created by the GENSAT project, tgFGFR1-EGFPGP338Gsat, and includes a gene encoding enhanced green fluorescent protein (EGFP) under the regulation of the Fgfr1 promoter, to trace Fgfr1 expression in the developing CNS. Unbiased stereological counts were performed for several cell types in the cortex and hippocampus. Results This model reveals that Fgfr1 is primarily expressed in glial cells, in both astrocytes and oligodendrocytes, along with some neurons. Dual labeling experiments indicate that the proportion of GFP+ (Fgfr1+) cells that are also GFAP+ increases from postnatal day 7 (P7) to 1 month, illuminating dynamic changes in Fgfr1 expression during postnatal development of the cortex. In postnatal neurogenic areas, GFP expression was also observed in SOX2, doublecortin (DCX), and brain lipid-binding protein (BLBP) expressing cells. Fgfr1 is also highly expressed in DCX positive cells of the dentate…
bibliographic citation: Choubey et al. (2017) Quantitative assessment of fibroblast growth factor receptor 1 expression in neurons and glia. PeerJ 5:e3173 https://doi.org/10.7717/peerj.3173
date submitted: 2016-08-04
date accepted: 2017-03-13
issued: 2017-04-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choubey
  given name: Lisha
author list: Agent
  family name: Collette
  given name: Jantzen C.
author list: Agent
  family name: Smith
  given name: Karen Müller
doi: 10.7717/peerj.3173
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-04-18
copyright: ©2017 Choubey et al.
attribution name: Choubey et al.

Pollinator diversity and reproductive success of Epipactis helleborine (L.) Crantz (Orchidaceae) in anthropogenic and natural habitats
type: item
type: AcademicArticle
description: Background Epipactis helleborine is an Eurasian orchid species which prefers woodland environments but it may also spontaneously and successfully colonise human-made artificial and disturbed habitats such as roadsides, town parks and gardens. It is suggested that orchids colonising anthropogenic habitats are characterised by a specific set of features (e.g., large plant size, fast flower production). However, as it is not well known how pollinator diversity and reproductive success of E. helleborine differs in populations in anthropogenic habitats compared to populations from natural habitats, we wanted to compare pollinator diversity and reproductive success of this orchid species between natural and anthropogenic habitat types. Methods Pollination biology, reproductive success and autogamy in populations of E. helleborine from anthropogenic (roadside) and natural (forest) habitats were compared. Eight populations (four natural and four human-disturbed ones) in two seasons were studied according to height of plants, length of inflorescences, as well as numbers of juvenile shoots, flowering shoots, flowers, and fruits. The number and diversity of insect pollinators were studied in one natural and two human-disturbed populations. Results Reproductive success (the ratio of the number of flowers to the number of fruits) in the populations from anthropogenic habitats was significantly higher than in the natural habitats. Moreover, plants from anthropogenic habitats were larger than those from natural ones. In both types of populations, the main insect pollinators were Syrphidae, Culicidae, Vespidae, Apidae and Formicidae. With respect to the type of pollinators’ mouth-parts, chewing (39%), sponging (34%) and chewing-sucking (20%) pollinators prevailed in anthropogenic habitats. In natural habitats, pollinators with sponging (55%) and chewing mouth-parts (32%) dominated, while chewing-sucking and piercing-sucking insects accounted for 9% and 4% respectively. Discussion W…
format: application/pdf
format: text/html
creator: Agnieszka Rewicz
creator: Radomir Jaskuła
creator: Tomasz Rewicz
creator: Grzegorz Tończyk
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.3159
publisher: PeerJ Inc.
rights: © 2017 Rewicz et al.
abstract: Background Epipactis helleborine is an Eurasian orchid species which prefers woodland environments but it may also spontaneously and successfully colonise human-made artificial and disturbed habitats such as roadsides, town parks and gardens. It is suggested that orchids colonising anthropogenic habitats are characterised by a specific set of features (e.g., large plant size, fast flower production). However, as it is not well known how pollinator diversity and reproductive success of E. helleborine differs in populations in anthropogenic habitats compared to populations from natural habitats, we wanted to compare pollinator diversity and reproductive success of this orchid species between natural and anthropogenic habitat types. Methods Pollination biology, reproductive success and autogamy in populations of E. helleborine from anthropogenic (roadside) and natural (forest) habitats were compared. Eight populations (four natural and four human-disturbed ones) in two seasons were studied according to height of plants, length of inflorescences, as well as numbers of juvenile shoots, flowering shoots, flowers, and fruits. The number and diversity of insect pollinators were studied in one natural and two human-disturbed populations. Results Reproductive success (the ratio of the number of flowers to the number of fruits) in the populations from anthropogenic habitats was significantly higher than in the natural habitats. Moreover, plants from anthropogenic habitats were larger than those from natural ones. In both types of populations, the main insect pollinators were Syrphidae, Culicidae, Vespidae, Apidae and Formicidae. With respect to the type of pollinators’ mouth-parts, chewing (39%), sponging (34%) and chewing-sucking (20%) pollinators prevailed in anthropogenic habitats. In natural habitats, pollinators with sponging (55%) and chewing mouth-parts (32%) dominated, while chewing-sucking and piercing-sucking insects accounted for 9% and 4% respectively. Discussion W…
bibliographic citation: Rewicz et al. (2017) Pollinator diversity and reproductive success of Epipactis helleborine (L.) Crantz (Orchidaceae) in anthropogenic and natural habitats. PeerJ 5:e3159 https://doi.org/10.7717/peerj.3159
date submitted: 2016-05-25
date accepted: 2017-03-07
issued: 2017-04-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rewicz
  given name: Agnieszka
author list: Agent
  family name: Jaskuła
  given name: Radomir
author list: Agent
  family name: Rewicz
  given name: Tomasz
author list: Agent
  family name: Tończyk
  given name: Grzegorz
doi: 10.7717/peerj.3159
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-04-18
copyright: ©2017 Rewicz et al.
attribution name: Rewicz et al.

The evolution of logic circuits for the purpose of protein contact map prediction
type: item
type: AcademicArticle
description: Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset.
format: application/pdf
format: text/html
creator: Samuel D. Chapman
creator: Christoph Adami
creator: Claus O. Wilke
creator: Dukka B KC
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.3139
publisher: PeerJ Inc.
rights: © 2017 Chapman et al.
abstract: Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset.
bibliographic citation: Chapman et al. (2017) The evolution of logic circuits for the purpose of protein contact map prediction. PeerJ 5:e3139 https://doi.org/10.7717/peerj.3139
date submitted: 2016-06-29
date accepted: 2017-03-02
issued: 2017-04-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chapman
  given name: Samuel D.
author list: Agent
  family name: Adami
  given name: Christoph
author list: Agent
  family name: Wilke
  given name: Claus O.
author list: Agent
  family name: B KC
  given name: Dukka
doi: 10.7717/peerj.3139
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-04-18
copyright: ©2017 Chapman et al.
attribution name: Chapman et al.

Automated identification of insect vectors of Chagas disease in Brazil and Mexico: the Virtual Vector Lab
type: item
type: AcademicArticle
description: Identification of arthropods important in disease transmission is a crucial, yet difficult, task that can demand considerable training and experience. An important case in point is that of the 150+ species of Triatominae, vectors of Trypanosoma cruzi, causative agent of Chagas disease across the Americas. We present a fully automated system that is able to identify triatomine bugs from Mexico and Brazil with an accuracy consistently above 80%, and with considerable potential for further improvement. The system processes digital photographs from a photo apparatus into landmarks, and uses ratios of measurements among those landmarks, as well as (in a preliminary exploration) two measurements that approximate aspects of coloration, as the basis for classification. This project has thus produced a working prototype that achieves reasonably robust correct identification rates, although many more developments can and will be added, and—more broadly—the project illustrates the value of multidisciplinary collaborations in resolving difficult and complex challenges.
format: application/pdf
format: text/html
creator: Rodrigo Gurgel-Gonçalves
creator: Ed Komp
creator: Lindsay P. Campbell
creator: Ali Khalighifar
creator: Jarrett Mellenbruch
creator: Vagner José Mendonça
creator: Hannah L. Owens
creator: Keynes de la Cruz Felix
creator: A Townsend Peterson
creator: Janine M. Ramsey
subject: Entomology
subject: Computational Science
description: doi:10.7717/peerj.3040
publisher: PeerJ Inc.
rights: © 2017 Gurgel-Gonçalves et al.
abstract: Identification of arthropods important in disease transmission is a crucial, yet difficult, task that can demand considerable training and experience. An important case in point is that of the 150+ species of Triatominae, vectors of Trypanosoma cruzi, causative agent of Chagas disease across the Americas. We present a fully automated system that is able to identify triatomine bugs from Mexico and Brazil with an accuracy consistently above 80%, and with considerable potential for further improvement. The system processes digital photographs from a photo apparatus into landmarks, and uses ratios of measurements among those landmarks, as well as (in a preliminary exploration) two measurements that approximate aspects of coloration, as the basis for classification. This project has thus produced a working prototype that achieves reasonably robust correct identification rates, although many more developments can and will be added, and—more broadly—the project illustrates the value of multidisciplinary collaborations in resolving difficult and complex challenges.
bibliographic citation: Gurgel-Gonçalves et al. (2017) Automated identification of insect vectors of Chagas disease in Brazil and Mexico: the Virtual Vector Lab. PeerJ 5:e3040 https://doi.org/10.7717/peerj.3040
date submitted: 2016-09-26
date accepted: 2017-01-28
issued: 2017-04-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gurgel-Gonçalves
  given name: Rodrigo
author list: Agent
  family name: Komp
  given name: Ed
author list: Agent
  family name: Campbell
  given name: Lindsay P.
author list: Agent
  family name: Khalighifar
  given name: Ali
author list: Agent
  family name: Mellenbruch
  given name: Jarrett
author list: Agent
  family name: Mendonça
  given name: Vagner José
author list: Agent
  family name: Owens
  given name: Hannah L.
author list: Agent
  family name: de la Cruz Felix
  given name: Keynes
author list: Agent
  family name: Peterson
  given name: A Townsend
author list: Agent
  family name: Ramsey
  given name: Janine M.
doi: 10.7717/peerj.3040
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-04-18
copyright: ©2017 Gurgel-Gonçalves et al.
attribution name: Gurgel-Gonçalves et al.

Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California
type: item
type: AcademicArticle
description: The Pacific coast tick, Dermacentor occidentalis Marx, is found throughout California and can harbor agents that cause human diseases such as anaplasmosis, ehrlichiosis, tularemia, Rocky Mountain spotted fever and rickettsiosis 364D. Previous studies have demonstrated that nonpathogenic endosymbiotic bacteria can interfere with Rickettsia co-infections in other tick species. We hypothesized that within D. occidentalis ticks, interference may exist between different nonpathogenic endosymbiotic or nonendosymbiotic bacteria and Spotted Fever group Rickettsia (SFGR). Using PCR amplification and sequencing of the rompA gene and intergenic region we identified a cohort of SFGR-infected and non-infected D. occidentalis ticks collected from San Diego County. We then amplified a partial segment of the 16S rRNA gene and used next-generation sequencing to elucidate the microbiomes and levels of co-infection in the ticks. The SFGR R. philipii str. 364D and R. rhipicephali were detected in 2.3% and 8.2% of the ticks, respectively, via rompA sequencing. Interestingly, next generation sequencing revealed an inverse relationship between the number of Francisella-like endosymbiont (FLE) 16S rRNA sequences and Rickettsia 16S rRNA sequences within individual ticks that is consistent with partial interference between FLE and SFGR infecting ticks. After excluding the Rickettsia and FLE endosymbionts from the analysis, there was a small but significant difference in microbial community diversity and a pattern of geographic isolation by distance between collection locales. In addition, male ticks had a greater diversity of bacteria than female ticks and ticks that weren’t infected with SFGR had similar microbiomes to canine skin microbiomes. Although experimental studies are required for confirmation, our findings are consistent with the hypothesis that FLEs and, to a lesser extent, other bacteria, interfere with the ability of D. occidentalis to be infected with certain SFGR. The results…
format: application/pdf
format: text/html
creator: Nikos Gurfield
creator: Saran Grewal
creator: Lynnie S. Cua
creator: Pedro J. Torres
creator: Scott T. Kelley
subject: Entomology
subject: Microbiology
description: doi:10.7717/peerj.3202
publisher: PeerJ Inc.
rights: © 2017 Gurfield et al.
abstract: The Pacific coast tick, Dermacentor occidentalis Marx, is found throughout California and can harbor agents that cause human diseases such as anaplasmosis, ehrlichiosis, tularemia, Rocky Mountain spotted fever and rickettsiosis 364D. Previous studies have demonstrated that nonpathogenic endosymbiotic bacteria can interfere with Rickettsia co-infections in other tick species. We hypothesized that within D. occidentalis ticks, interference may exist between different nonpathogenic endosymbiotic or nonendosymbiotic bacteria and Spotted Fever group Rickettsia (SFGR). Using PCR amplification and sequencing of the rompA gene and intergenic region we identified a cohort of SFGR-infected and non-infected D. occidentalis ticks collected from San Diego County. We then amplified a partial segment of the 16S rRNA gene and used next-generation sequencing to elucidate the microbiomes and levels of co-infection in the ticks. The SFGR R. philipii str. 364D and R. rhipicephali were detected in 2.3% and 8.2% of the ticks, respectively, via rompA sequencing. Interestingly, next generation sequencing revealed an inverse relationship between the number of Francisella-like endosymbiont (FLE) 16S rRNA sequences and Rickettsia 16S rRNA sequences within individual ticks that is consistent with partial interference between FLE and SFGR infecting ticks. After excluding the Rickettsia and FLE endosymbionts from the analysis, there was a small but significant difference in microbial community diversity and a pattern of geographic isolation by distance between collection locales. In addition, male ticks had a greater diversity of bacteria than female ticks and ticks that weren’t infected with SFGR had similar microbiomes to canine skin microbiomes. Although experimental studies are required for confirmation, our findings are consistent with the hypothesis that FLEs and, to a lesser extent, other bacteria, interfere with the ability of D. occidentalis to be infected with certain SFGR. The results…
bibliographic citation: Gurfield et al. (2017) Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California. PeerJ 5:e3202 https://doi.org/10.7717/peerj.3202
date submitted: 2016-07-02
date accepted: 2017-03-19
issued: 2017-04-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gurfield
  given name: Nikos
author list: Agent
  family name: Grewal
  given name: Saran
author list: Agent
  family name: Cua
  given name: Lynnie S.
author list: Agent
  family name: Torres
  given name: Pedro J.
author list: Agent
  family name: Kelley
  given name: Scott T.
doi: 10.7717/peerj.3202
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-04-13
copyright: ©2017 Gurfield et al.
attribution name: Gurfield et al.

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