PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Cross-platform normalization of microarray and RNA-seq data for machine learning applications
items: Microscopical and elemental FESEM and Phenom ProX-SEM-EDS analysis of osteocyte- and blood vessel-like microstructures obtained from fossil vertebrates of the Eocene Messel Pit, Germany
items: The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content
items: Chronic unpredicted mild stress-induced depression alter saxagliptin pharmacokinetics and CYP450 activity in GK rats
items: Molecular diversity of bacteria in commercially available “Spirulina” food supplements
items: Bust economics: foragers choose high quality habitats in lean times
items: Comparative morphology of the mouthparts of the megadiverse South African monkey beetles (Scarabaeidae: Hopliini): feeding adaptations and guild structure
items: Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage
items: Revised phylogenetic analysis of the Aetosauria (Archosauria: Pseudosuchia); assessing the effects of incongruent morphological character sets
items: Rat liver regeneration following ablation with irreversible electroporation

Cross-platform normalization of microarray and RNA-seq data for machine learning applications
type: item
type: AcademicArticle
description: Large, publicly available gene expression datasets are often analyzed with the aid of machine learning algorithms. Although RNA-seq is increasingly the technology of choice, a wealth of expression data already exist in the form of microarray data. If machine learning models built from legacy data can be applied to RNA-seq data, larger, more diverse training datasets can be created and validation can be performed on newly generated data. We developed Training Distribution Matching (TDM), which transforms RNA-seq data for use with models constructed from legacy platforms. We evaluated TDM, as well as quantile normalization, nonparanormal transformation, and a simple log2 transformation, on both simulated and biological datasets of gene expression. Our evaluation included both supervised and unsupervised machine learning approaches. We found that TDM exhibited consistently strong performance across settings and that quantile normalization also performed well in many circumstances. We also provide a TDM package for the R programming language.
format: application/pdf
format: text/html
creator: Jeffrey A. Thompson
creator: Jie Tan
creator: Casey S. Greene
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.1621
publisher: PeerJ Inc.
rights: © 2016 Thompson et al.
abstract: Large, publicly available gene expression datasets are often analyzed with the aid of machine learning algorithms. Although RNA-seq is increasingly the technology of choice, a wealth of expression data already exist in the form of microarray data. If machine learning models built from legacy data can be applied to RNA-seq data, larger, more diverse training datasets can be created and validation can be performed on newly generated data. We developed Training Distribution Matching (TDM), which transforms RNA-seq data for use with models constructed from legacy platforms. We evaluated TDM, as well as quantile normalization, nonparanormal transformation, and a simple log2 transformation, on both simulated and biological datasets of gene expression. Our evaluation included both supervised and unsupervised machine learning approaches. We found that TDM exhibited consistently strong performance across settings and that quantile normalization also performed well in many circumstances. We also provide a TDM package for the R programming language.
bibliographic citation: Thompson et al. (2016) Cross-platform normalization of microarray and RNA-seq data for machine learning applications. PeerJ 4:e1621 https://doi.org/10.7717/peerj.1621
date submitted: 2015-10-30
date accepted: 2016-01-02
issued: 2016-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thompson
  given name: Jeffrey A.
author list: Agent
  family name: Tan
  given name: Jie
author list: Agent
  family name: Greene
  given name: Casey S.
doi: 10.7717/peerj.1621
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-21
copyright: © 2016 Thompson et al.
attribution name: Thompson et al.

Microscopical and elemental FESEM and Phenom ProX-SEM-EDS analysis of osteocyte- and blood vessel-like microstructures obtained from fossil vertebrates of the Eocene Messel Pit, Germany
type: item
type: AcademicArticle
description: The Eocene (∾48 Ma) Messel Pit in Germany is a UNESCO World Heritage Site because of its exceptionally preserved fossils, including vertebrates, invertebrates, and plants. Messel fossil vertebrates are typically characterized by their articulated state, and in some cases the skin, hair, feathers, scales and stomach contents are also preserved. Despite the exceptional macroscopic preservation of Messel fossil vertebrates, the microstructural aspect of these fossils has been poorly explored. In particular, soft tissue structures such as hair or feathers have not been chemically analyzed, nor have bone microstructures. I report here the preservation and recovery of osteocyte-like and blood vessel-like microstructures from the bone of Messel Pit specimens, including the turtles Allaeochelys crassesculpta and Neochelys franzeni, the crocodile Diplocynodon darwini, and the pangolin Eomanis krebsi. I used a Field Emission Scanning Electron Microscope (FESEM) and a Phenom ProX desktop scanning electron microscope (LOT-QuantumDesign) equipped with a thermionic CeB6 source and a high sensitivity multi-mode backscatter electron (BSE) for microscopical and elemental characterization of these bone microstructures. Osteocyte-like and blood vessel-like microstructures are constituted by a thin layer (∾50 nm thickness), external and internal mottled texture with slightly marked striations. Circular to linear marks are common on the external surface of the osteocyte-like microstructures and are interpreted as microbial troughs. Iron (Fe) is the most abundant element found in the osteocyte-like and blood vessel-like microstructures, but not in the bone matrix or collagen fibril-like microstructures. The occurrence of well-preserved soft-tissue elements (at least their physical form) establishes a promising background for future studies on preservation of biomolecules (proteins or DNA) in Messel Pit fossils.
format: application/pdf
format: text/html
creator: Edwin Cadena
subject: Cell Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.1618
publisher: PeerJ Inc.
rights: © 2016 Cadena
abstract: The Eocene (∾48 Ma) Messel Pit in Germany is a UNESCO World Heritage Site because of its exceptionally preserved fossils, including vertebrates, invertebrates, and plants. Messel fossil vertebrates are typically characterized by their articulated state, and in some cases the skin, hair, feathers, scales and stomach contents are also preserved. Despite the exceptional macroscopic preservation of Messel fossil vertebrates, the microstructural aspect of these fossils has been poorly explored. In particular, soft tissue structures such as hair or feathers have not been chemically analyzed, nor have bone microstructures. I report here the preservation and recovery of osteocyte-like and blood vessel-like microstructures from the bone of Messel Pit specimens, including the turtles Allaeochelys crassesculpta and Neochelys franzeni, the crocodile Diplocynodon darwini, and the pangolin Eomanis krebsi. I used a Field Emission Scanning Electron Microscope (FESEM) and a Phenom ProX desktop scanning electron microscope (LOT-QuantumDesign) equipped with a thermionic CeB6 source and a high sensitivity multi-mode backscatter electron (BSE) for microscopical and elemental characterization of these bone microstructures. Osteocyte-like and blood vessel-like microstructures are constituted by a thin layer (∾50 nm thickness), external and internal mottled texture with slightly marked striations. Circular to linear marks are common on the external surface of the osteocyte-like microstructures and are interpreted as microbial troughs. Iron (Fe) is the most abundant element found in the osteocyte-like and blood vessel-like microstructures, but not in the bone matrix or collagen fibril-like microstructures. The occurrence of well-preserved soft-tissue elements (at least their physical form) establishes a promising background for future studies on preservation of biomolecules (proteins or DNA) in Messel Pit fossils.
bibliographic citation: Cadena (2016) Microscopical and elemental FESEM and Phenom ProX-SEM-EDS analysis of osteocyte- and blood vessel-like microstructures obtained from fossil vertebrates of the Eocene Messel Pit, Germany. PeerJ 4:e1618 https://doi.org/10.7717/peerj.1618
date submitted: 2015-09-01
date accepted: 2016-01-02
issued: 2016-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cadena
  given name: Edwin
doi: 10.7717/peerj.1618
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-21
copyright: ©2016 Cadena
attribution name: Cadena

The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content
type: item
type: AcademicArticle
description: Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.
format: application/pdf
format: text/html
creator: Zachery T. Lewis
creator: Jasmine C.C. Davis
creator: Jennifer T. Smilowitz
creator: J. Bruce German
creator: Carlito B. Lebrilla
creator: David A. Mills
subject: Biochemistry
subject: Microbiology
subject: Global Health
description: doi:10.7717/peerj.1612
publisher: PeerJ Inc.
rights: © 2016 Lewis et al.
abstract: Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.
bibliographic citation: Lewis et al. (2016) The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content. PeerJ 4:e1612 https://doi.org/10.7717/peerj.1612
date submitted: 2015-09-11
date accepted: 2015-12-29
issued: 2016-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lewis
  given name: Zachery T.
author list: Agent
  family name: Davis
  given name: Jasmine C.C.
author list: Agent
  family name: Smilowitz
  given name: Jennifer T.
author list: Agent
  family name: German
  given name: J. Bruce
author list: Agent
  family name: Lebrilla
  given name: Carlito B.
author list: Agent
  family name: Mills
  given name: David A.
doi: 10.7717/peerj.1612
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-21
copyright: ©2016 Lewis et al.
attribution name: Lewis et al.

Chronic unpredicted mild stress-induced depression alter saxagliptin pharmacokinetics and CYP450 activity in GK rats
type: item
type: AcademicArticle
description: Background. This study was to explore the pharmacokinetics of saxagliptin (Sax) in Goto–Kakizaki (GK) rats complicated with depression induced by chronic unpredicted mild stress (CUMS). The comorbidity of diabetic patients with depression is becoming more and more epidemic. Whether depression mental disorder alters the pharmacokinetics of hypoglycemic drugs in diabetes patients is not clear. Methods. Five-week-old male GK rats were kept in the cage for 7 weeks in a specific pathogen free (SPF)-grade lab until the emergence of diabetes and were then divided into two groups: control group and depression model group. Rats in the CUMS-induced depression group were exposed to a series of stressors for 8 weeks. Plasma serotonin and dopamine levels and behavior of open-field test were used to confirm the establishment of the depression model. All rats were given 0.5 mg/kg Sax orally after 8 weeks and blood samples were collected at different time points. The Sax concentration was assayed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The CYP450 activity of the liver microsomes was determined by using cocktails of probe drugs in which the activities of CYP enzymes were assessed through the determination of the production of the probe drugs. Results. Statistically significant differences in Sax pharmacokinetics were observed for area under curve, clearance, peak concentration, peak time and mean residence time between the depression rats and the control rats, while no statistical differences were observed for half-time and distribution volume by HPLC-MS/MS analysis. The CYP450 activity had different changes in the depression group. Conclusions. These results indicated that CUMS-induced depression alters the drug metabolic process of Sax and CYP450 activity of the liver microsomal enzymes in GK rats.
format: application/pdf
format: text/html
creator: Zhengchao Xia
creator: Hongyan Wei
creator: Jingjing Duan
creator: Ting Zhou
creator: Zhen Yang
creator: Feng Xu
subject: Pharmacology
description: doi:10.7717/peerj.1611
publisher: PeerJ Inc.
rights: © 2016 Xia et al.
abstract: Background. This study was to explore the pharmacokinetics of saxagliptin (Sax) in Goto–Kakizaki (GK) rats complicated with depression induced by chronic unpredicted mild stress (CUMS). The comorbidity of diabetic patients with depression is becoming more and more epidemic. Whether depression mental disorder alters the pharmacokinetics of hypoglycemic drugs in diabetes patients is not clear. Methods. Five-week-old male GK rats were kept in the cage for 7 weeks in a specific pathogen free (SPF)-grade lab until the emergence of diabetes and were then divided into two groups: control group and depression model group. Rats in the CUMS-induced depression group were exposed to a series of stressors for 8 weeks. Plasma serotonin and dopamine levels and behavior of open-field test were used to confirm the establishment of the depression model. All rats were given 0.5 mg/kg Sax orally after 8 weeks and blood samples were collected at different time points. The Sax concentration was assayed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The CYP450 activity of the liver microsomes was determined by using cocktails of probe drugs in which the activities of CYP enzymes were assessed through the determination of the production of the probe drugs. Results. Statistically significant differences in Sax pharmacokinetics were observed for area under curve, clearance, peak concentration, peak time and mean residence time between the depression rats and the control rats, while no statistical differences were observed for half-time and distribution volume by HPLC-MS/MS analysis. The CYP450 activity had different changes in the depression group. Conclusions. These results indicated that CUMS-induced depression alters the drug metabolic process of Sax and CYP450 activity of the liver microsomal enzymes in GK rats.
bibliographic citation: Xia et al. (2016) Chronic unpredicted mild stress-induced depression alter saxagliptin pharmacokinetics and CYP450 activity in GK rats. PeerJ 4:e1611 https://doi.org/10.7717/peerj.1611
date submitted: 2015-11-10
date accepted: 2015-12-29
issued: 2016-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xia
  given name: Zhengchao
author list: Agent
  family name: Wei
  given name: Hongyan
author list: Agent
  family name: Duan
  given name: Jingjing
author list: Agent
  family name: Zhou
  given name: Ting
author list: Agent
  family name: Yang
  given name: Zhen
author list: Agent
  family name: Xu
  given name: Feng
doi: 10.7717/peerj.1611
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-21
copyright: ©2016 Xia et al.
attribution name: Xia et al.

Molecular diversity of bacteria in commercially available “Spirulina” food supplements
type: item
type: AcademicArticle
description: The cyanobacterium Arthrospira is among the most well-known food supplements worldwide known as “Spirulina.” While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of “Spirulina” supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of “Spirulina” dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) of Arthrospira platensis were the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9–157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e., Pseudomonas, Flavobacterium, Vibrio, Aeromonas, Clostridium, Bacillus, Fusobacterium, Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing of Arthrospira biomass for commercial purposes.
format: application/pdf
format: text/html
creator: Elisabeth Vardaka
creator: Konstantinos A. Kormas
creator: Matina Katsiapi
creator: Savvas Genitsaris
creator: Maria Moustaka-Gouni
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.1610
publisher: PeerJ Inc.
rights: © 2016 Vardaka et al.
abstract: The cyanobacterium Arthrospira is among the most well-known food supplements worldwide known as “Spirulina.” While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of “Spirulina” supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of “Spirulina” dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) of Arthrospira platensis were the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9–157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e., Pseudomonas, Flavobacterium, Vibrio, Aeromonas, Clostridium, Bacillus, Fusobacterium, Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing of Arthrospira biomass for commercial purposes.
bibliographic citation: Vardaka et al. (2016) Molecular diversity of bacteria in commercially available “Spirulina” food supplements. PeerJ 4:e1610 https://doi.org/10.7717/peerj.1610
date submitted: 2015-10-20
date accepted: 2015-12-29
issued: 2016-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vardaka
  given name: Elisabeth
author list: Agent
  family name: Kormas
  given name: Konstantinos A.
author list: Agent
  family name: Katsiapi
  given name: Matina
author list: Agent
  family name: Genitsaris
  given name: Savvas
author list: Agent
  family name: Moustaka-Gouni
  given name: Maria
doi: 10.7717/peerj.1610
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-21
copyright: ©2016 Vardaka et al.
attribution name: Vardaka et al.

Bust economics: foragers choose high quality habitats in lean times
type: item
type: AcademicArticle
description: In environments where food resources are spatially variable and temporarily impoverished, consumers that encounter habitat patches with different food density should focus their foraging initially where food density is highest before they move to patches where food density is lower. Increasing missed opportunity costs should drive individuals progressively to patches with lower food density as resources in the initially high food density patches deplete. To test these expectations, we assessed the foraging decisions of two species of dasyurid marsupials (dunnarts: Sminthopsis hirtipes and S. youngsoni) during a deep drought, or bust period, in the Simpson Desert of central Australia. Dunnarts were allowed access to three patches containing different food densities using an interview chamber experiment. Both species exhibited clear preference for the high density over the lower food density patches as measured in total harvested resources. Similarly, when measuring the proportion of resources harvested within the patches, we observed a marginal preference for patches with initially high densities. Models analyzing behavioral choices at the population level found no differences in behavior between the two species, but models analyzing choices at the individual level uncovered some variation. We conclude that dunnarts can distinguish between habitat patches with different densities of food and preferentially exploit the most valuable. As our observations were made during bust conditions, experiments should be repeated during boom times to assess the foraging economics of dunnarts when environmental resources are high.
format: application/pdf
format: text/html
creator: Sonny S. Bleicher
creator: Christopher R. Dickman
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.1609
publisher: PeerJ Inc.
rights: © 2016 Bleicher and Dickman
abstract: In environments where food resources are spatially variable and temporarily impoverished, consumers that encounter habitat patches with different food density should focus their foraging initially where food density is highest before they move to patches where food density is lower. Increasing missed opportunity costs should drive individuals progressively to patches with lower food density as resources in the initially high food density patches deplete. To test these expectations, we assessed the foraging decisions of two species of dasyurid marsupials (dunnarts: Sminthopsis hirtipes and S. youngsoni) during a deep drought, or bust period, in the Simpson Desert of central Australia. Dunnarts were allowed access to three patches containing different food densities using an interview chamber experiment. Both species exhibited clear preference for the high density over the lower food density patches as measured in total harvested resources. Similarly, when measuring the proportion of resources harvested within the patches, we observed a marginal preference for patches with initially high densities. Models analyzing behavioral choices at the population level found no differences in behavior between the two species, but models analyzing choices at the individual level uncovered some variation. We conclude that dunnarts can distinguish between habitat patches with different densities of food and preferentially exploit the most valuable. As our observations were made during bust conditions, experiments should be repeated during boom times to assess the foraging economics of dunnarts when environmental resources are high.
bibliographic citation: Bleicher et al. (2016) Bust economics: foragers choose high quality habitats in lean times. PeerJ 4:e1609 https://doi.org/10.7717/peerj.1609
date submitted: 2015-11-25
date accepted: 2015-12-29
issued: 2016-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bleicher
  given name: Sonny S.
author list: Agent
  family name: Dickman
  given name: Christopher R.
doi: 10.7717/peerj.1609
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-21
copyright: ©2016 Bleicher and Dickman
attribution name: Bleicher and Dickman

Comparative morphology of the mouthparts of the megadiverse South African monkey beetles (Scarabaeidae: Hopliini): feeding adaptations and guild structure
type: item
type: AcademicArticle
description: Although anthophilous Coleoptera are regarded to be unspecialised flower-visiting insects, monkey beetles (Scarabaeidae: Hopliini) represent one of the most important groups of pollinating insects in South Africa’s floristic hotspot of the Greater Cape Region. South African monkey beetles are known to feed on floral tissue; however, some species seem to specialise on pollen and/or nectar. The present study examined the mouthpart morphology and gut content of various hopliine species to draw conclusions on their feeding preferences. According to the specialisations of their mouthparts, the investigated species were classified into different feeding groups. Adaptations to pollen-feeding included a well-developed, toothed molar and a lobe-like, setose lacinia mobilis on the mandible as well as curled hairs or sclerotized teeth on the galea of the maxillae. Furthermore, elongated mouthparts were interpreted as adaptations for nectar feeding. Floral- and folial-tissue feeding species showed sclerotized teeth on the maxilla, but the lacinia was mostly found to be reduced to a sclerotized ledge. While species could clearly be identified as floral or folial tissue feeding, several species showed intermediate traits suggesting both pollen and nectar feeding adaptations. Mismatches found between mouthpart morphology and previously reported flower visiting behaviours across different genera and species requires alternative explanations, not necessarily associated with feeding preferences. Although detailed examinations of the mouthparts allowed conclusions about the feeding preference and flower-visiting behaviour, additional morphological and behavioural investigations, combined with greater taxon sampling and phylogenetic data, are still necessary to fully understand hopliine host plant relationships, related to monkey beetle diversity.
format: application/pdf
format: text/html
creator: Florian Karolyi
creator: Teresa Hansal
creator: Harald W. Krenn
creator: Jonathan F. Colville
subject: Animal Behavior
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.1597
publisher: PeerJ Inc.
rights: © 2016 Karolyi et al.
abstract: Although anthophilous Coleoptera are regarded to be unspecialised flower-visiting insects, monkey beetles (Scarabaeidae: Hopliini) represent one of the most important groups of pollinating insects in South Africa’s floristic hotspot of the Greater Cape Region. South African monkey beetles are known to feed on floral tissue; however, some species seem to specialise on pollen and/or nectar. The present study examined the mouthpart morphology and gut content of various hopliine species to draw conclusions on their feeding preferences. According to the specialisations of their mouthparts, the investigated species were classified into different feeding groups. Adaptations to pollen-feeding included a well-developed, toothed molar and a lobe-like, setose lacinia mobilis on the mandible as well as curled hairs or sclerotized teeth on the galea of the maxillae. Furthermore, elongated mouthparts were interpreted as adaptations for nectar feeding. Floral- and folial-tissue feeding species showed sclerotized teeth on the maxilla, but the lacinia was mostly found to be reduced to a sclerotized ledge. While species could clearly be identified as floral or folial tissue feeding, several species showed intermediate traits suggesting both pollen and nectar feeding adaptations. Mismatches found between mouthpart morphology and previously reported flower visiting behaviours across different genera and species requires alternative explanations, not necessarily associated with feeding preferences. Although detailed examinations of the mouthparts allowed conclusions about the feeding preference and flower-visiting behaviour, additional morphological and behavioural investigations, combined with greater taxon sampling and phylogenetic data, are still necessary to fully understand hopliine host plant relationships, related to monkey beetle diversity.
bibliographic citation: Karolyi et al. (2016) Comparative morphology of the mouthparts of the megadiverse South African monkey beetles (Scarabaeidae: Hopliini): feeding adaptations and guild structure. PeerJ 4:e1597 https://doi.org/10.7717/peerj.1597
date submitted: 2015-09-30
date accepted: 2015-12-23
issued: 2016-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karolyi
  given name: Florian
author list: Agent
  family name: Hansal
  given name: Teresa
author list: Agent
  family name: Krenn
  given name: Harald W.
author list: Agent
  family name: Colville
  given name: Jonathan F.
doi: 10.7717/peerj.1597
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-21
copyright: © 2016 Karolyi et al.
attribution name: Karolyi et al.

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage
type: item
type: AcademicArticle
description: The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.
format: application/pdf
format: text/html
creator: Chodon Sass
creator: William J.D. Iles
creator: Craig F. Barrett
creator: Selena Y. Smith
creator: Chelsea D. Specht
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.1584
publisher: PeerJ Inc.
rights: © 2016 Sass et al.
abstract: The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.
bibliographic citation: Sass et al. (2016) Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage. PeerJ 4:e1584 https://doi.org/10.7717/peerj.1584
date submitted: 2015-09-07
date accepted: 2016-12-18
issued: 2016-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sass
  given name: Chodon
author list: Agent
  family name: Iles
  given name: William J.D.
author list: Agent
  family name: Barrett
  given name: Craig F.
author list: Agent
  family name: Smith
  given name: Selena Y.
author list: Agent
  family name: Specht
  given name: Chelsea D.
doi: 10.7717/peerj.1584
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-21
copyright: © 2016 Sass et al.
attribution name: Sass et al.

Revised phylogenetic analysis of the Aetosauria (Archosauria: Pseudosuchia); assessing the effects of incongruent morphological character sets
type: item
type: AcademicArticle
description: Aetosauria is an early-diverging clade of pseudosuchians (crocodile-line archosaurs) that had a global distribution and high species diversity as a key component of various Late Triassic terrestrial faunas. It is one of only two Late Triassic clades of large herbivorous archosaurs, and thus served a critical ecological role. Nonetheless, aetosaur phylogenetic relationships are still poorly understood, owing to an overreliance on osteoderm characters, which are often poorly constructed and suspected to be highly homoplastic. A new phylogenetic analysis of the Aetosauria, comprising 27 taxa and 83 characters, includes more than 40 new characters that focus on better sampling the cranial and endoskeletal regions, and represents the most comprenhensive phylogeny of the clade to date. Parsimony analysis recovered three most parsimonious trees; the strict consensus of these trees finds an Aetosauria that is divided into two main clades: Desmatosuchia, which includes the Desmatosuchinae and the Stagonolepidinae, and Aetosaurinae, which includes the Typothoracinae. As defined Desmatosuchinae now contains Neoaetosauroides engaeus and several taxa that were previously referred to the genus Stagonolepis, and a new clade, Desmatosuchini, is erected for taxa more closely related to Desmatosuchus. Overall support for some clades is still weak, and Partitioned Bremer Support (PBS) is applied for the first time to a strictly morphological dataset demonstrating that this weak support is in part because of conflict in the phylogenetic signals of cranial versus postcranial characters. PBS helps identify homoplasy among characters from various body regions, presumably the result of convergent evolution within discrete anatomical modules. It is likely that at least some of this character conflict results from different body regions evolving at different rates, which may have been under different selective pressures.
format: application/pdf
format: text/html
creator: William G. Parker
subject: Evolutionary studies
subject: Paleontology
description: doi:10.7717/peerj.1583
publisher: PeerJ Inc.
rights: © 2016 Parker
abstract: Aetosauria is an early-diverging clade of pseudosuchians (crocodile-line archosaurs) that had a global distribution and high species diversity as a key component of various Late Triassic terrestrial faunas. It is one of only two Late Triassic clades of large herbivorous archosaurs, and thus served a critical ecological role. Nonetheless, aetosaur phylogenetic relationships are still poorly understood, owing to an overreliance on osteoderm characters, which are often poorly constructed and suspected to be highly homoplastic. A new phylogenetic analysis of the Aetosauria, comprising 27 taxa and 83 characters, includes more than 40 new characters that focus on better sampling the cranial and endoskeletal regions, and represents the most comprenhensive phylogeny of the clade to date. Parsimony analysis recovered three most parsimonious trees; the strict consensus of these trees finds an Aetosauria that is divided into two main clades: Desmatosuchia, which includes the Desmatosuchinae and the Stagonolepidinae, and Aetosaurinae, which includes the Typothoracinae. As defined Desmatosuchinae now contains Neoaetosauroides engaeus and several taxa that were previously referred to the genus Stagonolepis, and a new clade, Desmatosuchini, is erected for taxa more closely related to Desmatosuchus. Overall support for some clades is still weak, and Partitioned Bremer Support (PBS) is applied for the first time to a strictly morphological dataset demonstrating that this weak support is in part because of conflict in the phylogenetic signals of cranial versus postcranial characters. PBS helps identify homoplasy among characters from various body regions, presumably the result of convergent evolution within discrete anatomical modules. It is likely that at least some of this character conflict results from different body regions evolving at different rates, which may have been under different selective pressures.
bibliographic citation: Parker (2016) Revised phylogenetic analysis of the Aetosauria (Archosauria: Pseudosuchia); assessing the effects of incongruent morphological character sets. PeerJ 4:e1583 https://doi.org/10.7717/peerj.1583
date submitted: 2015-10-07
date accepted: 2015-12-18
issued: 2016-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Parker
  given name: William G.
doi: 10.7717/peerj.1583
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-21
copyright: © 2016 Parker
attribution name: Parker

Rat liver regeneration following ablation with irreversible electroporation
type: item
type: AcademicArticle
description: During the past decade, irreversible electroporation (IRE) ablation has emerged as a promising tool for the treatment of multiple diseases including hepatic cancer. However, the mechanisms behind the tissue regeneration following IRE ablation have not been investigated. Our results indicate that IRE treatment immediately kills the cells at the treatment site preserving the extracellular architecture, in effect causing in vivo decellularization. Over the course of 4 weeks, progenitor cell differentiation, through YAP and notch pathways, together with hepatocyte expansion led to almost complete regeneration of the ablated liver leading to the formation of hepatocyte like cells at the ablated zone. We did not observe significant scarring or tumor formation at the regenerated areas 6 months post IRE. Our study suggests a new model to study the regeneration of liver when the naïve extracellular matrix is decellularized in vivo with completely preserved extracellular architecture.
format: application/pdf
format: text/html
creator: Alexander Golberg
creator: Bote G. Bruinsma
creator: Maria Jaramillo
creator: Martin L. Yarmush
creator: Basak E. Uygun
subject: Bioengineering
subject: Developmental Biology
subject: Gastroenterology and Hepatology
subject: Histology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.1571
publisher: PeerJ Inc.
rights: © 2016 Golberg et al.
abstract: During the past decade, irreversible electroporation (IRE) ablation has emerged as a promising tool for the treatment of multiple diseases including hepatic cancer. However, the mechanisms behind the tissue regeneration following IRE ablation have not been investigated. Our results indicate that IRE treatment immediately kills the cells at the treatment site preserving the extracellular architecture, in effect causing in vivo decellularization. Over the course of 4 weeks, progenitor cell differentiation, through YAP and notch pathways, together with hepatocyte expansion led to almost complete regeneration of the ablated liver leading to the formation of hepatocyte like cells at the ablated zone. We did not observe significant scarring or tumor formation at the regenerated areas 6 months post IRE. Our study suggests a new model to study the regeneration of liver when the naïve extracellular matrix is decellularized in vivo with completely preserved extracellular architecture.
bibliographic citation: Golberg et al. (2016) Rat liver regeneration following ablation with irreversible electroporation. PeerJ 4:e1571 https://doi.org/10.7717/peerj.1571
date submitted: 2015-09-17
date accepted: 2015-12-14
issued: 2016-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Golberg
  given name: Alexander
author list: Agent
  family name: Bruinsma
  given name: Bote G.
author list: Agent
  family name: Jaramillo
  given name: Maria
author list: Agent
  family name: Yarmush
  given name: Martin L.
author list: Agent
  family name: Uygun
  given name: Basak E.
doi: 10.7717/peerj.1571
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-01-21
copyright: © 2016 Golberg et al.
attribution name: Golberg et al.

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