PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Differential attraction of drosophilids to banana baits inoculated with Saccharomyces cerevisiae and Hanseniaspora uvarum within a Neotropical forest remnant
items: A novel application of mark-recapture to examine behaviour associated with the online trade in elephant ivory
items: Aerodynamic forces and flows of the full and partial clap-fling motions in insects
items: Description of Arundel Clay ornithomimosaur material and a reinterpretation of Nedcolbertia justinhofmanni as an “Ostrich Dinosaur”: biogeographic implications
items: Hard time to be parents? Sea urchin fishery shifts potential reproductive contribution of population onto the shoulders of the young adults
items: The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within genus Morus L
items: BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation
items: Attachment anxiety is associated with a fear of becoming fat, which is mediated by binge eating
items: Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi
items: True’s beaked whale (Mesoplodon mirus) in Macaronesia

Differential attraction of drosophilids to banana baits inoculated with Saccharomyces cerevisiae and Hanseniaspora uvarum within a Neotropical forest remnant
type: item
type: AcademicArticle
description: Background Yeasts are a necessary requisite in the diet of most Drosophila species that, in turn, may vector their dispersal in natural environments. Differential attractiveness experiments and the isolation of yeasts consumed by Drosophila may be informative for characterizing this association. Hanseniaspora uvarum is among the most common yeast species isolated from Drosophila crops, with high attractiveness to drosophilids. Saccharomyces cerevisiae has been widely used to collect flies, and it allows broad sampling of almost all local Drosophila species. Pronounced differences in the field concerning Drosophila attractivity to baits seeded with these yeast species have been previously reported. However, few explicit generalizations have been set. Since late fifties, no field experiments of Drosophila attractivity were carried out in the Neotropical region, which is facing shifts in abiotic and biotic factors. Our objective is to characterize preference behavior that mediates the interaction in the wild among Neotropical Drosophila species and yeasts associated with them. We want to set a broad generalization about drosophilids attracted to these yeasts. Here we present the results of a differential attractiveness experiment we carried out in a natural Atlantic Rainforest fragment to assess the preferences of Drosophila species groups to baits inoculated with H. uvarum and S. cerevisiae. Methods Both yeast species were cultured in GYMP broth and separately poured in autoclaved mashed banana that was left fermenting. In the field, we collected drosophilids over five arrays of three different baits: non-inoculated autoclaved banana and banana inoculated with each yeast. In the laboratory the drosophilids were sorted to five sets according to their external morphology and/or genitalia: tripunctata; guarani; willistoni; exotic; and the remaining flies pooled in others. Results and Conclusions Uninoculated banana baits attracted virtually no flies. We found significant…
format: application/pdf
format: text/html
creator: Marcos R.D. Batista
creator: Fabiana Uno
creator: Rafael D. Chaves
creator: Rosana Tidon
creator: Carlos A. Rosa
creator: Louis B. Klaczko
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Microbiology
subject: Mycology
description: doi:10.7717/peerj.3063
publisher: PeerJ Inc.
rights: © 2017 Batista et al.
abstract: Background Yeasts are a necessary requisite in the diet of most Drosophila species that, in turn, may vector their dispersal in natural environments. Differential attractiveness experiments and the isolation of yeasts consumed by Drosophila may be informative for characterizing this association. Hanseniaspora uvarum is among the most common yeast species isolated from Drosophila crops, with high attractiveness to drosophilids. Saccharomyces cerevisiae has been widely used to collect flies, and it allows broad sampling of almost all local Drosophila species. Pronounced differences in the field concerning Drosophila attractivity to baits seeded with these yeast species have been previously reported. However, few explicit generalizations have been set. Since late fifties, no field experiments of Drosophila attractivity were carried out in the Neotropical region, which is facing shifts in abiotic and biotic factors. Our objective is to characterize preference behavior that mediates the interaction in the wild among Neotropical Drosophila species and yeasts associated with them. We want to set a broad generalization about drosophilids attracted to these yeasts. Here we present the results of a differential attractiveness experiment we carried out in a natural Atlantic Rainforest fragment to assess the preferences of Drosophila species groups to baits inoculated with H. uvarum and S. cerevisiae. Methods Both yeast species were cultured in GYMP broth and separately poured in autoclaved mashed banana that was left fermenting. In the field, we collected drosophilids over five arrays of three different baits: non-inoculated autoclaved banana and banana inoculated with each yeast. In the laboratory the drosophilids were sorted to five sets according to their external morphology and/or genitalia: tripunctata; guarani; willistoni; exotic; and the remaining flies pooled in others. Results and Conclusions Uninoculated banana baits attracted virtually no flies. We found significant…
bibliographic citation: Batista et al. (2017) Differential attraction of drosophilids to banana baits inoculated with Saccharomyces cerevisiae and Hanseniaspora uvarum within a Neotropical forest remnant. PeerJ 5:e3063 https://doi.org/10.7717/peerj.3063
date submitted: 2016-08-25
date accepted: 2017-02-03
issued: 2017-03-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Batista
  given name: Marcos R.D.
author list: Agent
  family name: Uno
  given name: Fabiana
author list: Agent
  family name: Chaves
  given name: Rafael D.
author list: Agent
  family name: Tidon
  given name: Rosana
author list: Agent
  family name: Rosa
  given name: Carlos A.
author list: Agent
  family name: Klaczko
  given name: Louis B.
doi: 10.7717/peerj.3063
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-09
copyright: ©2017 Batista et al.
attribution name: Batista et al.

A novel application of mark-recapture to examine behaviour associated with the online trade in elephant ivory
type: item
type: AcademicArticle
description: The illegal trade in elephant ivory is driving the unlawful killing of elephants such that populations are now suffering unsustainable reductions. The internet is increasingly being used as a platform to conduct illegal wildlife trade, including elephant ivory. As a globally accessible medium the internet is as highly attractive to those involved in the illegal trade as it is challenging to regulate. Characterising the online illegal wildlife (ivory) trade is complex, yet key to informing enforcement activities. We applied mark-recapture to investigate behaviour associated with the online trade in elephant ivory on eBay UK as a generalist online marketplace. Our results indicate that trade takes place via eBay UK, despite its policy prohibiting this, and that two distinct trading populations exist, characterised by the pattern of their ivory sales. We suggest these may represent a large number of occasional (or non-commercial) sellers and a smaller number of dedicated (or commercial) sellers. Directing resource towards reducing the volume of occasional sales, such as through education, would enable greater focus to be placed upon characterising the extent and value of the illegal, “commercial” online ivory trade. MRC has the potential to characterise the illegal trade in ivory and diverse wildlife commodities traded using various online platforms.
format: application/pdf
format: text/html
creator: Lydia M. Yeo
creator: Rachel S. McCrea
creator: David L. Roberts
subject: Biodiversity
subject: Conservation Biology
description: doi:10.7717/peerj.3048
publisher: PeerJ Inc.
rights: © 2017 Yeo et al.
abstract: The illegal trade in elephant ivory is driving the unlawful killing of elephants such that populations are now suffering unsustainable reductions. The internet is increasingly being used as a platform to conduct illegal wildlife trade, including elephant ivory. As a globally accessible medium the internet is as highly attractive to those involved in the illegal trade as it is challenging to regulate. Characterising the online illegal wildlife (ivory) trade is complex, yet key to informing enforcement activities. We applied mark-recapture to investigate behaviour associated with the online trade in elephant ivory on eBay UK as a generalist online marketplace. Our results indicate that trade takes place via eBay UK, despite its policy prohibiting this, and that two distinct trading populations exist, characterised by the pattern of their ivory sales. We suggest these may represent a large number of occasional (or non-commercial) sellers and a smaller number of dedicated (or commercial) sellers. Directing resource towards reducing the volume of occasional sales, such as through education, would enable greater focus to be placed upon characterising the extent and value of the illegal, “commercial” online ivory trade. MRC has the potential to characterise the illegal trade in ivory and diverse wildlife commodities traded using various online platforms.
bibliographic citation: Yeo et al. (2017) A novel application of mark-recapture to examine behaviour associated with the online trade in elephant ivory. PeerJ 5:e3048 https://doi.org/10.7717/peerj.3048
date submitted: 2016-10-19
date accepted: 2017-01-30
issued: 2017-03-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yeo
  given name: Lydia M.
author list: Agent
  family name: McCrea
  given name: Rachel S.
author list: Agent
  family name: Roberts
  given name: David L.
doi: 10.7717/peerj.3048
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-09
copyright: ©2017 Yeo et al.
attribution name: Yeo et al.

Aerodynamic forces and flows of the full and partial clap-fling motions in insects
type: item
type: AcademicArticle
description: Most of the previous studies on Weis-Fogh clap-fling mechanism have focused on the vortex structures and velocity fields. Detailed pressure distribution results are provided for the first time in this study to reveal the differences between the full and the partial clap-fling motions. The two motions are studied by numerically solving the Navier–Stokes equations in moving overset grids. The Reynolds number is set to 20, relevant to the tiny flying insects. The following has been shown: (1) During the clap phase, the wings clap together and create a high pressure region in the closing gap between wings, greatly increasing the positive pressure on the lower surface of wing, while pressure on the upper surface is almost unchanged by the interaction; during the fling phase, the wings fling apart and create a low pressure region in the opening gap between wings, greatly increasing the suction pressure on the upper surface of wing, while pressure on the lower surface is almost unchanged by the interaction; (2) The interference effect between wings is most severe at the end of clap phase and the start of the fling phase: two sharp force peaks (8–9 times larger than that of the one-winged case) are generated. But the total force peaks are manifested mostly as drag and barely as lift of the wing, owing to the vertical orientation of the wing section; (3) The wing–wing interaction effect in the partial clap-fling case is much weaker than that in the full clap-fling case, avoiding the generation of huge drag. Compared with a single wing flapping with the same motion, mean lift in the partial case is enhanced by 12% without suffering any efficiency degradation, indicating that partial clap-fling is a more practical choice for tiny insects to employ.
format: application/pdf
format: text/html
creator: Xin Cheng
creator: Mao Sun
subject: Biophysics
subject: Computational Biology
subject: Entomology
subject: Mathematical Biology
subject: Computational Science
description: doi:10.7717/peerj.3002
publisher: PeerJ Inc.
rights: © 2017 Cheng and Sun
abstract: Most of the previous studies on Weis-Fogh clap-fling mechanism have focused on the vortex structures and velocity fields. Detailed pressure distribution results are provided for the first time in this study to reveal the differences between the full and the partial clap-fling motions. The two motions are studied by numerically solving the Navier–Stokes equations in moving overset grids. The Reynolds number is set to 20, relevant to the tiny flying insects. The following has been shown: (1) During the clap phase, the wings clap together and create a high pressure region in the closing gap between wings, greatly increasing the positive pressure on the lower surface of wing, while pressure on the upper surface is almost unchanged by the interaction; during the fling phase, the wings fling apart and create a low pressure region in the opening gap between wings, greatly increasing the suction pressure on the upper surface of wing, while pressure on the lower surface is almost unchanged by the interaction; (2) The interference effect between wings is most severe at the end of clap phase and the start of the fling phase: two sharp force peaks (8–9 times larger than that of the one-winged case) are generated. But the total force peaks are manifested mostly as drag and barely as lift of the wing, owing to the vertical orientation of the wing section; (3) The wing–wing interaction effect in the partial clap-fling case is much weaker than that in the full clap-fling case, avoiding the generation of huge drag. Compared with a single wing flapping with the same motion, mean lift in the partial case is enhanced by 12% without suffering any efficiency degradation, indicating that partial clap-fling is a more practical choice for tiny insects to employ.
bibliographic citation: Cheng et al. (2017) Aerodynamic forces and flows of the full and partial clap-fling motions in insects. PeerJ 5:e3002 https://doi.org/10.7717/peerj.3002
date submitted: 2016-10-01
date accepted: 2017-01-19
issued: 2017-03-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Xin
author list: Agent
  family name: Sun
  given name: Mao
doi: 10.7717/peerj.3002
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-09
copyright: ©2017 Cheng and Sun
attribution name: Cheng and Sun

Description of Arundel Clay ornithomimosaur material and a reinterpretation of Nedcolbertia justinhofmanni as an “Ostrich Dinosaur”: biogeographic implications
type: item
type: AcademicArticle
description: The fossil record of dinosaurs from the Early Cretaceous of Eastern North America is scant, especially since a few stratigraphic units from the east are fossiliferous. Among these stratigraphic units, the Arundel Clay of the eastern seaboard has produced the best-characterized dinosaur faunas known from the Early Cretaceous of Eastern North America. The diverse dinosaur fauna of the Arundel Clay has been thoroughly discussed previously, but a few of the dinosaur species originally described from the Arundel Clay are still regarded as valid genera. Much of the Arundel material is in need of review and redescription. Among the fossils of dinosaurs from this stratigraphic unit are those referred to ornithomimosaurs. Here, the researcher describes ornithomimosaur remains from the Arundel Clay of Prince George’s County, Maryland which may be from two distinct ornithomimosaur taxa. These remains provide key information on the theropods of the Early Cretaceous of Eastern North America. Recent discoveries of small theropod material from the Arundel Clay possibly belonging to ornithomimosaurs are also reviewed and described for the first time. The description of the Arundel material herein along with recent discoveries of basal ornithomimosaurs in the past 15 years has allowed for comparisons with the coelurosaur Nedcolbertia justinhofmanni, suggesting the latter animal was a basal ornithomimosaur rather than a “generalized” coelurosaur as it was originally described. Comparisons between the Arundel ornithomimosaur material and similar Asian and European specimens suggest that both extremely basal ornithomimosaurs and more intermediate or derived forms may have coexisted throughout the northern hemisphere during the Early Cretaceous.
format: application/pdf
format: text/html
creator: Chase Doran Brownstein
subject: Biogeography
subject: Paleontology
description: doi:10.7717/peerj.3110
publisher: PeerJ Inc.
rights: © 2017 Brownstein
abstract: The fossil record of dinosaurs from the Early Cretaceous of Eastern North America is scant, especially since a few stratigraphic units from the east are fossiliferous. Among these stratigraphic units, the Arundel Clay of the eastern seaboard has produced the best-characterized dinosaur faunas known from the Early Cretaceous of Eastern North America. The diverse dinosaur fauna of the Arundel Clay has been thoroughly discussed previously, but a few of the dinosaur species originally described from the Arundel Clay are still regarded as valid genera. Much of the Arundel material is in need of review and redescription. Among the fossils of dinosaurs from this stratigraphic unit are those referred to ornithomimosaurs. Here, the researcher describes ornithomimosaur remains from the Arundel Clay of Prince George’s County, Maryland which may be from two distinct ornithomimosaur taxa. These remains provide key information on the theropods of the Early Cretaceous of Eastern North America. Recent discoveries of small theropod material from the Arundel Clay possibly belonging to ornithomimosaurs are also reviewed and described for the first time. The description of the Arundel material herein along with recent discoveries of basal ornithomimosaurs in the past 15 years has allowed for comparisons with the coelurosaur Nedcolbertia justinhofmanni, suggesting the latter animal was a basal ornithomimosaur rather than a “generalized” coelurosaur as it was originally described. Comparisons between the Arundel ornithomimosaur material and similar Asian and European specimens suggest that both extremely basal ornithomimosaurs and more intermediate or derived forms may have coexisted throughout the northern hemisphere during the Early Cretaceous.
bibliographic citation: Brownstein (2017) Description of Arundel Clay ornithomimosaur material and a reinterpretation of Nedcolbertia justinhofmanni as an “Ostrich Dinosaur”: biogeographic implications. PeerJ 5:e3110 https://doi.org/10.7717/peerj.3110
date submitted: 2016-07-21
date accepted: 2017-02-20
issued: 2017-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brownstein
  given name: Chase Doran
doi: 10.7717/peerj.3110
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-08
copyright: © 2017 Brownstein
attribution name: Brownstein

Hard time to be parents? Sea urchin fishery shifts potential reproductive contribution of population onto the shoulders of the young adults
type: item
type: AcademicArticle
description: Background In Sardinia, as in other regions of the Mediterranean Sea, sustainable fisheries of the sea urchin Paracentrotus lividus have become a necessity. At harvesting sites, the systematic removal of large individuals (diameter ≥ 50 mm) seriously compromises the biological and ecological functions of sea urchin populations. Specifically, in this study, we compared the reproductive potential of the populations from Mediterranean coastal areas which have different levels of sea urchin fishing pressure. The areas were located at Su Pallosu Bay, where pressure is high and Tavolara-Punta Coda Cavallo, a marine protected area where sea urchin harvesting is low. Methods Reproductive potential was estimated by calculating the gonadosomatic index (GSI) from June 2013 to May 2014 both for individuals of commercial size (diameter without spines, TD ≥ 50 mm) and the undersized ones with gonads (30 ≤ TD < 40 mm and 40 ≤ TD < 50 mm). Gamete output was calculated for the commercial-size class and the undersized individuals with fertile gonads (40 ≤ TD < 50 mm) in relation to their natural density (gamete output per m2). Results The reproductive potential of populations was slightly different at the beginning of the sampling period but it progressed at different rates with an early spring spawning event in the high-pressure zone and two gamete depositions in early and late spring in the low-pressure zone. For each fertile size class, GSI values changed significantly during the year of our study and between the two zones. Although the multiple spawning events determined a two-fold higher total gamete output of population (popTGO) in the low-pressure zone, the population mean gamete output (popMGO) was similar in the two zones. In the high-pressure zone, the commercial-sized individuals represented approximatively 5% of the population, with almost all the individuals smaller than 60 mm producing an amount of gametes nearly three times lower than the undersized ones. Conversely, t…
format: application/pdf
format: text/html
creator: Barbara Loi
creator: Ivan Guala
creator: Rodrigo Pires da Silva
creator: Gianni Brundu
creator: Maura Baroli
creator: Simone Farina
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.3067
publisher: PeerJ Inc.
rights: © 2017 Loi et al.
abstract: Background In Sardinia, as in other regions of the Mediterranean Sea, sustainable fisheries of the sea urchin Paracentrotus lividus have become a necessity. At harvesting sites, the systematic removal of large individuals (diameter ≥ 50 mm) seriously compromises the biological and ecological functions of sea urchin populations. Specifically, in this study, we compared the reproductive potential of the populations from Mediterranean coastal areas which have different levels of sea urchin fishing pressure. The areas were located at Su Pallosu Bay, where pressure is high and Tavolara-Punta Coda Cavallo, a marine protected area where sea urchin harvesting is low. Methods Reproductive potential was estimated by calculating the gonadosomatic index (GSI) from June 2013 to May 2014 both for individuals of commercial size (diameter without spines, TD ≥ 50 mm) and the undersized ones with gonads (30 ≤ TD < 40 mm and 40 ≤ TD < 50 mm). Gamete output was calculated for the commercial-size class and the undersized individuals with fertile gonads (40 ≤ TD < 50 mm) in relation to their natural density (gamete output per m2). Results The reproductive potential of populations was slightly different at the beginning of the sampling period but it progressed at different rates with an early spring spawning event in the high-pressure zone and two gamete depositions in early and late spring in the low-pressure zone. For each fertile size class, GSI values changed significantly during the year of our study and between the two zones. Although the multiple spawning events determined a two-fold higher total gamete output of population (popTGO) in the low-pressure zone, the population mean gamete output (popMGO) was similar in the two zones. In the high-pressure zone, the commercial-sized individuals represented approximatively 5% of the population, with almost all the individuals smaller than 60 mm producing an amount of gametes nearly three times lower than the undersized ones. Conversely, t…
bibliographic citation: Loi et al. (2017) Hard time to be parents? Sea urchin fishery shifts potential reproductive contribution of population onto the shoulders of the young adults. PeerJ 5:e3067 https://doi.org/10.7717/peerj.3067
date submitted: 2016-11-04
date accepted: 2017-02-05
issued: 2017-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Loi
  given name: Barbara
author list: Agent
  family name: Guala
  given name: Ivan
author list: Agent
  family name: Pires da Silva
  given name: Rodrigo
author list: Agent
  family name: Brundu
  given name: Gianni
author list: Agent
  family name: Baroli
  given name: Maura
author list: Agent
  family name: Farina
  given name: Simone
doi: 10.7717/peerj.3067
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-08
copyright: ©2017 Loi et al.
attribution name: Loi et al.

The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within genus Morus L
type: item
type: AcademicArticle
description: Trees in the Morus genera belong to the Moraceae family. To better understand the species status of genus Morus and to provide information for studies on evolutionary biology within the genus, the complete chloroplast (cp) genomes of M. cathayana and M. multicaulis were sequenced. The plastomes of the two species are 159,265 bp and 159,103 bp, respectively, with corresponding 83 and 82 simple sequence repeats (SSRs). Similar to the SSRs of M. mongolica and M. indica cp genomes, more than 70% are mononucleotides, ten are in coding regions, and one exhibits nucleotide content polymorphism. Results for codon usage and relative synonymous codon usage show a strong bias towards NNA and NNT codons in the two cp genomes. Analysis of a plot of the effective number of codons (ENc) for five Morus spp. cp genomes showed that most genes follow the standard curve, but several genes have ENc values below the expected curve. The results indicate that both natural selection and mutational bias have contributed to the codon bias. Ten highly variable regions were identified among the five Morus spp. cp genomes, and 154 single-nucleotide polymorphism mutation events were accurately located in the gene coding region.
format: application/pdf
format: text/html
creator: Wei Qing Kong
creator: Jin Hong Yang
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.3037
publisher: PeerJ Inc.
rights: © 2017 Kong and Yang
abstract: Trees in the Morus genera belong to the Moraceae family. To better understand the species status of genus Morus and to provide information for studies on evolutionary biology within the genus, the complete chloroplast (cp) genomes of M. cathayana and M. multicaulis were sequenced. The plastomes of the two species are 159,265 bp and 159,103 bp, respectively, with corresponding 83 and 82 simple sequence repeats (SSRs). Similar to the SSRs of M. mongolica and M. indica cp genomes, more than 70% are mononucleotides, ten are in coding regions, and one exhibits nucleotide content polymorphism. Results for codon usage and relative synonymous codon usage show a strong bias towards NNA and NNT codons in the two cp genomes. Analysis of a plot of the effective number of codons (ENc) for five Morus spp. cp genomes showed that most genes follow the standard curve, but several genes have ENc values below the expected curve. The results indicate that both natural selection and mutational bias have contributed to the codon bias. Ten highly variable regions were identified among the five Morus spp. cp genomes, and 154 single-nucleotide polymorphism mutation events were accurately located in the gene coding region.
bibliographic citation: Kong et al. (2017) The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within genus Morus L. PeerJ 5:e3037 https://doi.org/10.7717/peerj.3037
date submitted: 2016-07-08
date accepted: 2017-01-27
issued: 2017-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Wei Qing
author list: Agent
  family name: Yang
  given name: Jin Hong
doi: 10.7717/peerj.3037
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-08
copyright: ©2017 Kong and Yang
attribution name: Kong and Yang

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation
type: item
type: AcademicArticle
description: Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes.
format: application/pdf
format: text/html
creator: Elaina D. Graham
creator: John F. Heidelberg
creator: Benjamin J. Tully
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.3035
publisher: PeerJ Inc.
rights: © 2017 Graham et al.
abstract: Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes.
bibliographic citation: Graham et al. (2017) BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PeerJ 5:e3035 https://doi.org/10.7717/peerj.3035
date submitted: 2016-09-26
date accepted: 2017-01-26
issued: 2017-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Graham
  given name: Elaina D.
author list: Agent
  family name: Heidelberg
  given name: John F.
author list: Agent
  family name: Tully
  given name: Benjamin J.
doi: 10.7717/peerj.3035
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-08
copyright: ©2017 Graham et al.
attribution name: Graham et al.

Attachment anxiety is associated with a fear of becoming fat, which is mediated by binge eating
type: item
type: AcademicArticle
description: Background Previous work demonstrated that individuals with higher levels of attachment anxiety are prone to increased binge eating (Alexander & Siegel, 2013). Given that our society rejects obese individuals and individuals with higher levels of attachment anxiety tend to be highly sensitive to rejection (Downey & Feldman, 1996), it follows that those with increased attachment anxiety may be especially fearful of becoming fat. Methods Undergraduate psychology students (n = 148) completed surveys measuring attachment, binge eating, and fear of becoming fat. Results The data demonstrate that attachment anxiety is positively associated with a fear of becoming fat (β = .30, p < .001) and binge eating mediates this relationship. In other words, binge eating underlies the fear of becoming fat. Discussion These findings contribute to a more refined understanding of binge eating which may create pathways for professionals to develop targeted interventions.
format: application/pdf
format: text/html
creator: Katherine E. Alexander
subject: Nutrition
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.3034
publisher: PeerJ Inc.
rights: © 2017 Alexander
abstract: Background Previous work demonstrated that individuals with higher levels of attachment anxiety are prone to increased binge eating (Alexander & Siegel, 2013). Given that our society rejects obese individuals and individuals with higher levels of attachment anxiety tend to be highly sensitive to rejection (Downey & Feldman, 1996), it follows that those with increased attachment anxiety may be especially fearful of becoming fat. Methods Undergraduate psychology students (n = 148) completed surveys measuring attachment, binge eating, and fear of becoming fat. Results The data demonstrate that attachment anxiety is positively associated with a fear of becoming fat (β = .30, p < .001) and binge eating mediates this relationship. In other words, binge eating underlies the fear of becoming fat. Discussion These findings contribute to a more refined understanding of binge eating which may create pathways for professionals to develop targeted interventions.
bibliographic citation: Alexander (2017) Attachment anxiety is associated with a fear of becoming fat, which is mediated by binge eating. PeerJ 5:e3034 https://doi.org/10.7717/peerj.3034
date submitted: 2016-08-25
date accepted: 2017-01-26
issued: 2017-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alexander
  given name: Katherine E.
doi: 10.7717/peerj.3034
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-08
copyright: ©2017 Alexander
attribution name: Alexander

Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi
type: item
type: AcademicArticle
description: American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi: amastigotes, epimastigotes and trypomastigotes. This analysis allowed us to delineate specific transcriptomic profiling for each stage, and also to identify those biological processes of major relevance in each state. Stage specific expression profiling evidenced the plasticity of T. cruzi to adapt quickly to different conditions, with particular focus on membrane remodeling and metabolic shifts along the life cycle. Epimastigotes, which replicate in the gut of insect vectors, showed higher expression of genes related to energy metabolism, mainly Krebs cycle, respiratory chain and oxidative phosphorylation related genes, and anabolism related genes associated to nucleotide and steroid biosynthesis; also, a general down-regulation of surface glycoprotein coding genes was seen at this stage. Trypomastigotes, living extracellularly in the bloodstream of mammals, express a plethora of surface proteins and signaling genes involved in invasion and evasion of immune response. Amastigotes mostly express membrane transporters and genes involved in regulation of cell cycle, and also express a specific subset of surface glycoprotein coding genes. In addition, these results allowed us to improve the annotation of the Dm28c genome, identifying new ORFs and set the stage for construction of networks of co-expression, which can give clues about coded proteins of unknown functions.
format: application/pdf
format: text/html
creator: Luisa Berná
creator: Maria Laura Chiribao
creator: Gonzalo Greif
creator: Matias Rodriguez
creator: Fernando Alvarez-Valin
creator: Carlos Robello
subject: Biochemistry
subject: Genomics
subject: Molecular Biology
subject: Parasitology
subject: Infectious Diseases
description: doi:10.7717/peerj.3017
publisher: PeerJ Inc.
rights: © 2017 Berná et al.
abstract: American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi: amastigotes, epimastigotes and trypomastigotes. This analysis allowed us to delineate specific transcriptomic profiling for each stage, and also to identify those biological processes of major relevance in each state. Stage specific expression profiling evidenced the plasticity of T. cruzi to adapt quickly to different conditions, with particular focus on membrane remodeling and metabolic shifts along the life cycle. Epimastigotes, which replicate in the gut of insect vectors, showed higher expression of genes related to energy metabolism, mainly Krebs cycle, respiratory chain and oxidative phosphorylation related genes, and anabolism related genes associated to nucleotide and steroid biosynthesis; also, a general down-regulation of surface glycoprotein coding genes was seen at this stage. Trypomastigotes, living extracellularly in the bloodstream of mammals, express a plethora of surface proteins and signaling genes involved in invasion and evasion of immune response. Amastigotes mostly express membrane transporters and genes involved in regulation of cell cycle, and also express a specific subset of surface glycoprotein coding genes. In addition, these results allowed us to improve the annotation of the Dm28c genome, identifying new ORFs and set the stage for construction of networks of co-expression, which can give clues about coded proteins of unknown functions.
bibliographic citation: Berná et al. (2017) Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi. PeerJ 5:e3017 https://doi.org/10.7717/peerj.3017
date submitted: 2016-12-07
date accepted: 2017-01-23
issued: 2017-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Berná
  given name: Luisa
author list: Agent
  family name: Chiribao
  given name: Maria Laura
author list: Agent
  family name: Greif
  given name: Gonzalo
author list: Agent
  family name: Rodriguez
  given name: Matias
author list: Agent
  family name: Alvarez-Valin
  given name: Fernando
author list: Agent
  family name: Robello
  given name: Carlos
doi: 10.7717/peerj.3017
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-08
copyright: ©2017 Berná et al.
attribution name: Berná et al.

True’s beaked whale (Mesoplodon mirus) in Macaronesia
type: item
type: AcademicArticle
description: The True’s beaked whale (Mesoplodon mirus, True 1913) is a poorly known member of the Ziphiidae family. Its distribution in the northern hemisphere is thought to be restricted to the temperate or warm temperate waters of the North Atlantic, while a few stranding records from the southern hemisphere suggest a wider and antitropical distribution, extending to waters from the Atlantic coast of Brazil to South Africa, Mozambique, Australia and the Tasman Sea coast of New Zealand. This paper (i) reports the first molecular confirmation of the occurrence of the True’s beaked whale at the southern limit of its distribution recorded in the northeast Atlantic: the Azores and Canary Islands (macaronesian ecoregion); (ii) describes a new colouration for this species using evidence from a whale with molecular species confirmation; and (iii) contributes to the sparse worldwide database of live sightings, including the first underwater video recording of this species and close images of a calf. Species identification was confirmed in two cases using mitochondrial DNA control region and cytochrome b gene markers: a subadult male True’s beaked whale that stranded in El Hierro, Canary Islands, in November 2012, and a subadult male found floating dead near Faial, the Azores, in July 2004. The whale that stranded in the Canary Islands had a clearly delimited white area on its head, extending posteriorly from the tip of the beak to cover the blowhole dorsally and the gular grooves ventrally. This colouration contrasts with previous descriptions for the species and it may be rare, but it exemplifies the variability of the colouration of True’s beaked whales in the North Atlantic, further confirmed here by live sightings data. The recording of several observations of this species in deep but relatively coastal waters off the Azores and the Canary Islands suggests that these archipelagos may be unique locations to study the behaviour of the enigmatic True’s beaked whale.
format: application/pdf
format: text/html
creator: Natacha Aguilar de Soto
creator: Vidal Martín
creator: Monica Silva
creator: Roland Edler
creator: Cristel Reyes
creator: Manuel Carrillo
creator: Agustina Schiavi
creator: Talia Morales
creator: Belen García-Ovide
creator: Anna Sanchez-Mora
creator: Nerea Garcia-Tavero
creator: Lisa Steiner
creator: Michael Scheer
creator: Roland Gockel
creator: Dylan Walker
creator: Enrico Villa
creator: Petra Szlama
creator: Ida K. Eriksson
creator: Marisa Tejedor
creator: Monica Perez-Gil
creator: João Quaresma
creator: Wojtek Bachara
creator: Emma Carroll
subject: Biodiversity
subject: Genetics
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.3059
publisher: PeerJ Inc.
rights: © 2017 Aguilar de Soto et al.
abstract: The True’s beaked whale (Mesoplodon mirus, True 1913) is a poorly known member of the Ziphiidae family. Its distribution in the northern hemisphere is thought to be restricted to the temperate or warm temperate waters of the North Atlantic, while a few stranding records from the southern hemisphere suggest a wider and antitropical distribution, extending to waters from the Atlantic coast of Brazil to South Africa, Mozambique, Australia and the Tasman Sea coast of New Zealand. This paper (i) reports the first molecular confirmation of the occurrence of the True’s beaked whale at the southern limit of its distribution recorded in the northeast Atlantic: the Azores and Canary Islands (macaronesian ecoregion); (ii) describes a new colouration for this species using evidence from a whale with molecular species confirmation; and (iii) contributes to the sparse worldwide database of live sightings, including the first underwater video recording of this species and close images of a calf. Species identification was confirmed in two cases using mitochondrial DNA control region and cytochrome b gene markers: a subadult male True’s beaked whale that stranded in El Hierro, Canary Islands, in November 2012, and a subadult male found floating dead near Faial, the Azores, in July 2004. The whale that stranded in the Canary Islands had a clearly delimited white area on its head, extending posteriorly from the tip of the beak to cover the blowhole dorsally and the gular grooves ventrally. This colouration contrasts with previous descriptions for the species and it may be rare, but it exemplifies the variability of the colouration of True’s beaked whales in the North Atlantic, further confirmed here by live sightings data. The recording of several observations of this species in deep but relatively coastal waters off the Azores and the Canary Islands suggests that these archipelagos may be unique locations to study the behaviour of the enigmatic True’s beaked whale.
bibliographic citation: Aguilar de Soto et al. (2017) True’s beaked whale (Mesoplodon mirus) in Macaronesia. PeerJ 5:e3059 https://doi.org/10.7717/peerj.3059
date submitted: 2016-02-25
date accepted: 2017-02-03
issued: 2017-03-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aguilar de Soto
  given name: Natacha
author list: Agent
  family name: Martín
  given name: Vidal
author list: Agent
  family name: Silva
  given name: Monica
author list: Agent
  family name: Edler
  given name: Roland
author list: Agent
  family name: Reyes
  given name: Cristel
author list: Agent
  family name: Carrillo
  given name: Manuel
author list: Agent
  family name: Schiavi
  given name: Agustina
author list: Agent
  family name: Morales
  given name: Talia
author list: Agent
  family name: García-Ovide
  given name: Belen
author list: Agent
  family name: Sanchez-Mora
  given name: Anna
author list: Agent
  family name: Garcia-Tavero
  given name: Nerea
author list: Agent
  family name: Steiner
  given name: Lisa
author list: Agent
  family name: Scheer
  given name: Michael
author list: Agent
  family name: Gockel
  given name: Roland
author list: Agent
  family name: Walker
  given name: Dylan
author list: Agent
  family name: Villa
  given name: Enrico
author list: Agent
  family name: Szlama
  given name: Petra
author list: Agent
  family name: Eriksson
  given name: Ida K.
author list: Agent
  family name: Tejedor
  given name: Marisa
author list: Agent
  family name: Perez-Gil
  given name: Monica
author list: Agent
  family name: Quaresma
  given name: João
author list: Agent
  family name: Bachara
  given name: Wojtek
author list: Agent
  family name: Carroll
  given name: Emma
doi: 10.7717/peerj.3059
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-07
copyright: ©2017 Aguilar de Soto et al.
attribution name: Aguilar de Soto et al.

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