PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Expanding our understanding of the trade in marine aquarium animals
items: Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy
items: RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing
items: Sequence variability of Chrysanthemum stunt viroid in different chrysanthemum cultivars
items: Causal events enter awareness faster than non-causal events
items: Floral vasculature and its variation for carpellary supply in Anthurium (Araceae, Alismatales)
items: Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants
items: Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola
items: Computer simulation of Cerebral Arteriovenous Malformation—validation analysis of hemodynamics parameters
items: The use of gene interaction networks to improve the identification of cancer driver genes

Expanding our understanding of the trade in marine aquarium animals
type: item
type: AcademicArticle
description: The trade of live marine animals for home and public aquaria has grown into a major global industry. Millions of marine fishes and invertebrates are removed from coral reefs and associated habitats each year. The majority are imported into the United States, with the remainder sent to Europe, Japan, and a handful of other countries. Despite the recent growth and diversification of the aquarium trade, to date, data collection is not mandatory, and hence comprehensive information on species volume and diversity is lacking. This lack of information makes it impossible to study trade pathways. Without species-specific volume and diversity data, it is unclear how importing and exporting governments can oversee this industry effectively or how sustainability should be encouraged. To expand our knowledge and understanding of the trade, and to effectively communicate this new understanding, we introduce the publically-available Marine Aquarium Biodiversity and Trade Flow online database (https://www.aquariumtradedata.org/). This tool was created to communicate the volume and diversity of marine fishes and/or invertebrates imported into the US over three complete years (2008, 2009, and 2011) and three partial years (2000, 2004, 2005). To create this tool, invoices pertaining to shipments of live marine fishes and invertebrates were scanned and analyzed for species name, species quantities, country of origin, port of entry, and city of import destination. Here we focus on the analysis of the later three years of data and also produce an estimate for the entirety of 2000, 2004, and 2005. The three-year aggregate totals (2008, 2009, 2011) indicate that just under 2,300 fish and 725 invertebrate species were imported into the US cumulatively, although just under 1,800 fish and 550 invertebrate species were traded annually. Overall, the total number of live marine animals decreased between 2008 and 2011. In 2008, 2009, and 2011, the total number of individual fish (8.2, 7.3, and …
format: application/pdf
format: text/html
creator: Andrew L. Rhyne
creator: Michael F. Tlusty
creator: Joseph T. Szczebak
creator: Robert J. Holmberg
subject: Marine Biology
subject: Science Policy
description: doi:10.7717/peerj.2949
publisher: PeerJ Inc.
rights: © 2017 Rhyne et al.
abstract: The trade of live marine animals for home and public aquaria has grown into a major global industry. Millions of marine fishes and invertebrates are removed from coral reefs and associated habitats each year. The majority are imported into the United States, with the remainder sent to Europe, Japan, and a handful of other countries. Despite the recent growth and diversification of the aquarium trade, to date, data collection is not mandatory, and hence comprehensive information on species volume and diversity is lacking. This lack of information makes it impossible to study trade pathways. Without species-specific volume and diversity data, it is unclear how importing and exporting governments can oversee this industry effectively or how sustainability should be encouraged. To expand our knowledge and understanding of the trade, and to effectively communicate this new understanding, we introduce the publically-available Marine Aquarium Biodiversity and Trade Flow online database (https://www.aquariumtradedata.org/). This tool was created to communicate the volume and diversity of marine fishes and/or invertebrates imported into the US over three complete years (2008, 2009, and 2011) and three partial years (2000, 2004, 2005). To create this tool, invoices pertaining to shipments of live marine fishes and invertebrates were scanned and analyzed for species name, species quantities, country of origin, port of entry, and city of import destination. Here we focus on the analysis of the later three years of data and also produce an estimate for the entirety of 2000, 2004, and 2005. The three-year aggregate totals (2008, 2009, 2011) indicate that just under 2,300 fish and 725 invertebrate species were imported into the US cumulatively, although just under 1,800 fish and 550 invertebrate species were traded annually. Overall, the total number of live marine animals decreased between 2008 and 2011. In 2008, 2009, and 2011, the total number of individual fish (8.2, 7.3, and …
bibliographic citation: Rhyne et al. (2017) Expanding our understanding of the trade in marine aquarium animals. PeerJ 5:e2949 https://doi.org/10.7717/peerj.2949
date submitted: 2015-06-12
date accepted: 2016-12-30
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rhyne
  given name: Andrew L.
author list: Agent
  family name: Tlusty
  given name: Michael F.
author list: Agent
  family name: Szczebak
  given name: Joseph T.
author list: Agent
  family name: Holmberg
  given name: Robert J.
doi: 10.7717/peerj.2949
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Rhyne et al.
attribution name: Rhyne et al.

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy
type: item
type: AcademicArticle
description: The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.
format: application/pdf
format: text/html
creator: William J. Brazelton
creator: Christopher N. Thornton
creator: Alex Hyer
creator: Katrina I. Twing
creator: August A. Longino
creator: Susan Q. Lang
creator: Marvin D. Lilley
creator: Gretchen L. Früh-Green
creator: Matthew O. Schrenk
subject: Ecology
subject: Environmental Sciences
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.2945
publisher: PeerJ Inc.
rights: © 2017 Brazelton et al.
abstract: The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.
bibliographic citation: Brazelton et al. (2017) Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy. PeerJ 5:e2945 https://doi.org/10.7717/peerj.2945
date submitted: 2016-07-22
date accepted: 2016-12-27
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brazelton
  given name: William J.
author list: Agent
  family name: Thornton
  given name: Christopher N.
author list: Agent
  family name: Hyer
  given name: Alex
author list: Agent
  family name: Twing
  given name: Katrina I.
author list: Agent
  family name: Longino
  given name: August A.
author list: Agent
  family name: Lang
  given name: Susan Q.
author list: Agent
  family name: Lilley
  given name: Marvin D.
author list: Agent
  family name: Früh-Green
  given name: Gretchen L.
author list: Agent
  family name: Schrenk
  given name: Matthew O.
doi: 10.7717/peerj.2945
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Brazelton et al.
attribution name: Brazelton et al.

RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing
type: item
type: AcademicArticle
description: Background Transposable element (TE) polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE polymorphisms, particularly transposition events or non-reference insertion sites can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools. Methods We have developed the tool RelocaTE2 for identification of TE insertion sites at high sensitivity and specificity. RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina. These sequence reads are used as seeds to pinpoint chromosome locations where TEs have transposed. RelocaTE2 detects target site duplication (TSD) of TE insertions allowing it to report TE polymorphism loci with single base pair precision. Results and Discussion The performance of RelocaTE2 is evaluated using both simulated and real sequence data. RelocaTE2 demonstrate high level of sensitivity and specificity, particularly when the sequence coverage is not shallow. In comparison to other tools tested, RelocaTE2 achieves the best balance between sensitivity and specificity. In particular, RelocaTE2 performs best in prediction of TSDs for TE insertions. Even in highly repetitive regions, such as those tested on rice chromosome 4, RelocaTE2 is able to report up to 95% of simulated TE insertions with less than 0.1% false positive rate using 10-fold genome coverage resequencing data. RelocaTE2 provides a robust solution to identify TE insertion sites and can be incorporated into anal…
format: application/pdf
format: text/html
creator: Jinfeng Chen
creator: Travis R. Wrightsman
creator: Susan R. Wessler
creator: Jason E. Stajich
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.2942
publisher: PeerJ Inc.
rights: © 2017 Chen et al.
abstract: Background Transposable element (TE) polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE polymorphisms, particularly transposition events or non-reference insertion sites can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools. Methods We have developed the tool RelocaTE2 for identification of TE insertion sites at high sensitivity and specificity. RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina. These sequence reads are used as seeds to pinpoint chromosome locations where TEs have transposed. RelocaTE2 detects target site duplication (TSD) of TE insertions allowing it to report TE polymorphism loci with single base pair precision. Results and Discussion The performance of RelocaTE2 is evaluated using both simulated and real sequence data. RelocaTE2 demonstrate high level of sensitivity and specificity, particularly when the sequence coverage is not shallow. In comparison to other tools tested, RelocaTE2 achieves the best balance between sensitivity and specificity. In particular, RelocaTE2 performs best in prediction of TSDs for TE insertions. Even in highly repetitive regions, such as those tested on rice chromosome 4, RelocaTE2 is able to report up to 95% of simulated TE insertions with less than 0.1% false positive rate using 10-fold genome coverage resequencing data. RelocaTE2 provides a robust solution to identify TE insertion sites and can be incorporated into anal…
bibliographic citation: Chen et al. (2017) RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing. PeerJ 5:e2942 https://doi.org/10.7717/peerj.2942
date submitted: 2016-09-20
date accepted: 2016-12-26
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jinfeng
author list: Agent
  family name: Wrightsman
  given name: Travis R.
author list: Agent
  family name: Wessler
  given name: Susan R.
author list: Agent
  family name: Stajich
  given name: Jason E.
doi: 10.7717/peerj.2942
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Chen et al.
attribution name: Chen et al.

Sequence variability of Chrysanthemum stunt viroid in different chrysanthemum cultivars
type: item
type: AcademicArticle
description: Viroids are the smallest infectious agents, and their genomes consist of a short single strand of RNA that does not encode any protein. Chrysanthemum stunt viroid (CSVd), a member of the family Pospiviroidae, causes chrysanthemum stunt disease. Here, we report the genomic variations of CSVd to understand the sequence variability of CSVd in different chrysanthemum cultivars. We randomly sampled 36 different chrysanthemum cultivars and examined the infection of CSVd in each cultivar by reverse transcription polymerase chain reaction (RT-PCR). Eleven cultivars were infected by CSVd. Cloning followed by Sanger sequencing successfully identified a total of 271 CSVd genomes derived from 12 plants from 11 cultivars. They were further classified into 105 CSVd variants. Each single chrysanthemum plant had a different set of CSVd variants. Moreover, different single plants from the same cultivar had different sets of CSVd variants but identical consensus genome sequences. A phylogenetic tree using 12 consensus genome sequences revealed three groups of CSVd genomes, while six different groups were defined by the phylogenetic analysis using 105 variants. Based on the consensus CSVd genome, by combining all variant sequences, we identified 99 single-nucleotide variations (SNVs) as well as three nucleotide positions showing high mutation rates. Although 99 SNVs were identified, most CSVd genomes in this study were derived from variant 1, which is identical to known CSVd SK1 showing pathogenicity.
format: application/pdf
format: text/html
creator: Hoseong Choi
creator: Yeonhwa Jo
creator: Ju-Yeon Yoon
creator: Seung-Kook Choi
creator: Won Kyong Cho
subject: Agricultural Science
subject: Biodiversity
subject: Genomics
subject: Plant Science
subject: Virology
description: doi:10.7717/peerj.2933
publisher: PeerJ Inc.
rights: © 2017 Choi et al.
abstract: Viroids are the smallest infectious agents, and their genomes consist of a short single strand of RNA that does not encode any protein. Chrysanthemum stunt viroid (CSVd), a member of the family Pospiviroidae, causes chrysanthemum stunt disease. Here, we report the genomic variations of CSVd to understand the sequence variability of CSVd in different chrysanthemum cultivars. We randomly sampled 36 different chrysanthemum cultivars and examined the infection of CSVd in each cultivar by reverse transcription polymerase chain reaction (RT-PCR). Eleven cultivars were infected by CSVd. Cloning followed by Sanger sequencing successfully identified a total of 271 CSVd genomes derived from 12 plants from 11 cultivars. They were further classified into 105 CSVd variants. Each single chrysanthemum plant had a different set of CSVd variants. Moreover, different single plants from the same cultivar had different sets of CSVd variants but identical consensus genome sequences. A phylogenetic tree using 12 consensus genome sequences revealed three groups of CSVd genomes, while six different groups were defined by the phylogenetic analysis using 105 variants. Based on the consensus CSVd genome, by combining all variant sequences, we identified 99 single-nucleotide variations (SNVs) as well as three nucleotide positions showing high mutation rates. Although 99 SNVs were identified, most CSVd genomes in this study were derived from variant 1, which is identical to known CSVd SK1 showing pathogenicity.
bibliographic citation: Choi et al. (2017) Sequence variability of Chrysanthemum stunt viroid in different chrysanthemum cultivars. PeerJ 5:e2933 https://doi.org/10.7717/peerj.2933
date submitted: 2016-10-05
date accepted: 2016-12-22
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: Hoseong
author list: Agent
  family name: Jo
  given name: Yeonhwa
author list: Agent
  family name: Yoon
  given name: Ju-Yeon
author list: Agent
  family name: Choi
  given name: Seung-Kook
author list: Agent
  family name: Cho
  given name: Won Kyong
doi: 10.7717/peerj.2933
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Choi et al.
attribution name: Choi et al.

Causal events enter awareness faster than non-causal events
type: item
type: AcademicArticle
description: Philosophers have long argued that causality cannot be directly observed but requires a conscious inference (Hume, 1967). Albert Michotte however developed numerous visual phenomena in which people seemed to perceive causality akin to primary visual properties like colour or motion (Michotte, 1946). Michotte claimed that the perception of causality did not require a conscious, deliberate inference but, working over 70 years ago, he did not have access to the experimental methods to test this claim. Here we employ Continuous Flash Suppression (CFS)—an interocular suppression technique to render stimuli invisible (Tsuchiya & Koch, 2005)—to test whether causal events enter awareness faster than non-causal events. We presented observers with ‘causal’ and ‘non-causal’ events, and found consistent evidence that participants become aware of causal events more rapidly than non-causal events. Our results suggest that, whilst causality must be inferred from sensory evidence, this inference might be computed at low levels of perceptual processing, and does not depend on a deliberative conscious evaluation of the stimulus. This work therefore supports Michotte’s contention that, like colour or motion, causality is an immediate property of our perception of the world.
format: application/pdf
format: text/html
creator: Pieter Moors
creator: Johan Wagemans
creator: Lee de-Wit
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2932
publisher: PeerJ Inc.
rights: © 2017 Moors et al.
abstract: Philosophers have long argued that causality cannot be directly observed but requires a conscious inference (Hume, 1967). Albert Michotte however developed numerous visual phenomena in which people seemed to perceive causality akin to primary visual properties like colour or motion (Michotte, 1946). Michotte claimed that the perception of causality did not require a conscious, deliberate inference but, working over 70 years ago, he did not have access to the experimental methods to test this claim. Here we employ Continuous Flash Suppression (CFS)—an interocular suppression technique to render stimuli invisible (Tsuchiya & Koch, 2005)—to test whether causal events enter awareness faster than non-causal events. We presented observers with ‘causal’ and ‘non-causal’ events, and found consistent evidence that participants become aware of causal events more rapidly than non-causal events. Our results suggest that, whilst causality must be inferred from sensory evidence, this inference might be computed at low levels of perceptual processing, and does not depend on a deliberative conscious evaluation of the stimulus. This work therefore supports Michotte’s contention that, like colour or motion, causality is an immediate property of our perception of the world.
bibliographic citation: Moors et al. (2017) Causal events enter awareness faster than non-causal events. PeerJ 5:e2932 https://doi.org/10.7717/peerj.2932
date submitted: 2016-11-19
date accepted: 2016-12-21
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moors
  given name: Pieter
author list: Agent
  family name: Wagemans
  given name: Johan
author list: Agent
  family name: de-Wit
  given name: Lee
doi: 10.7717/peerj.2932
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Moors et al.
attribution name: Moors et al.

Floral vasculature and its variation for carpellary supply in Anthurium (Araceae, Alismatales)
type: item
type: AcademicArticle
description: Introduction and Aims Anthurium is the largest genus of Araceae, with 950 species distributed in the neotropics. Despite the great diversity of the genus, the knowledge of its floral vasculature is based on observations in only two species, viz. A. denudatum and A. lhotzkyanum, with remarkable variation in vascular carpellary supply: carpels are either vascularized by ventral bundles alone or by reduced dorsal bundles in addition to the ventral ones. Our main objective is to test this peculiar variation through a detailed anatomical study of the floral vasculature in taxa belonging to some sections of Anthurium designated as monophyletic groups in recent phylogenies. Methods We compare the floral vasculature of 20 neotropical species belonging to distinct sections of Anthurium, using both light and confocal laser scanning microscopies. Results The number and position of vascular bundles are constant within the tepals and stamens, regardless of the species and sections studied. However, the gynoecium vasculature exhibits variation between species belonging to the same or different sections. Our results reveal two patterns of vasculature: carpels vascularized by synlateral bundles alone (Pattern A) and carpels vascularized by both dorsal and synlateral bundles (Pattern B). Pattern A is shared by the majority of species studied here and corroborates the previous data in the literature. Pattern B occurs in three species: A. affine (Anthurium sect. Pachyneurium series Pachyneurium), A. obtusum and A. scandens (Anthurium sect. Tetraspermium), described here for the first time for the genus. Conclusions The variation in the supply to the carpels in Anthurium is corroborated here. However, our results in addition to those from the available literature suggest the existence of three patterns (A, B and C) of carpellary vasculature. Based on the recent phylogeny of Anthurium it is possible to notice that the three patterns of carpellary vasculature occur in representatives of …
format: application/pdf
format: text/html
creator: Letícia P. Poli
creator: Lívia G. Temponi
creator: Alessandra I. Coan
subject: Biodiversity
subject: Plant Science
description: doi:10.7717/peerj.2929
publisher: PeerJ Inc.
rights: © 2017 Poli et al.
abstract: Introduction and Aims Anthurium is the largest genus of Araceae, with 950 species distributed in the neotropics. Despite the great diversity of the genus, the knowledge of its floral vasculature is based on observations in only two species, viz. A. denudatum and A. lhotzkyanum, with remarkable variation in vascular carpellary supply: carpels are either vascularized by ventral bundles alone or by reduced dorsal bundles in addition to the ventral ones. Our main objective is to test this peculiar variation through a detailed anatomical study of the floral vasculature in taxa belonging to some sections of Anthurium designated as monophyletic groups in recent phylogenies. Methods We compare the floral vasculature of 20 neotropical species belonging to distinct sections of Anthurium, using both light and confocal laser scanning microscopies. Results The number and position of vascular bundles are constant within the tepals and stamens, regardless of the species and sections studied. However, the gynoecium vasculature exhibits variation between species belonging to the same or different sections. Our results reveal two patterns of vasculature: carpels vascularized by synlateral bundles alone (Pattern A) and carpels vascularized by both dorsal and synlateral bundles (Pattern B). Pattern A is shared by the majority of species studied here and corroborates the previous data in the literature. Pattern B occurs in three species: A. affine (Anthurium sect. Pachyneurium series Pachyneurium), A. obtusum and A. scandens (Anthurium sect. Tetraspermium), described here for the first time for the genus. Conclusions The variation in the supply to the carpels in Anthurium is corroborated here. However, our results in addition to those from the available literature suggest the existence of three patterns (A, B and C) of carpellary vasculature. Based on the recent phylogeny of Anthurium it is possible to notice that the three patterns of carpellary vasculature occur in representatives of …
bibliographic citation: Poli et al. (2017) Floral vasculature and its variation for carpellary supply in Anthurium (Araceae, Alismatales). PeerJ 5:e2929 https://doi.org/10.7717/peerj.2929
date submitted: 2016-09-08
date accepted: 2016-12-20
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Poli
  given name: Letícia P.
author list: Agent
  family name: Temponi
  given name: Lívia G.
author list: Agent
  family name: Coan
  given name: Alessandra I.
doi: 10.7717/peerj.2929
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Poli et al.
attribution name: Poli et al.

Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants
type: item
type: AcademicArticle
description: Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss. Gremlin 2 is a member of the DAN gene family and plays a significant role in tooth development by blocking the ligand-signaling pathway of BMP2 and BMP4. The goal of this study was to investigate the evolutionary history of gremlin 2 in cetartiodactyl mammals, a group that possesses highly divergent teeth morphology. Results from our analyses indicate that gremlin 2 has experienced a mixture of gene loss, gene duplication, and rate acceleration. Although the last common ancestor of cetartiodactyls possessed a single gene copy, pigs and camels are the only cetartiodactyl groups that have retained gremlin 2. According to the phyletic distribution of this gene and synteny analyses, we propose that gremlin 2 was lost in the common ancestor of ruminants and cetaceans between 56.3 and 63.5 million years ago as a product of a chromosomal rearrangement. Our analyses also indicate that the rate of evolution of gremlin 2 has been accelerated in the two groups that have retained this gene. Additionally, the lack of this gene could explain the high diversity of teeth among cetartiodactyl mammals; specifically, the presence of this gene could act as a biological constraint. Thus, our results support the notions that gene loss is a way to increase phenotypic diversity and that gremlin 2 is a dispensable gene, at least in cetartiodactyl mammals.
format: application/pdf
format: text/html
creator: Juan C. Opazo
creator: Kattina Zavala
creator: Paola Krall
creator: Rodrigo A. Arias
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.2901
publisher: PeerJ Inc.
rights: © 2017 Opazo et al.
abstract: Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss. Gremlin 2 is a member of the DAN gene family and plays a significant role in tooth development by blocking the ligand-signaling pathway of BMP2 and BMP4. The goal of this study was to investigate the evolutionary history of gremlin 2 in cetartiodactyl mammals, a group that possesses highly divergent teeth morphology. Results from our analyses indicate that gremlin 2 has experienced a mixture of gene loss, gene duplication, and rate acceleration. Although the last common ancestor of cetartiodactyls possessed a single gene copy, pigs and camels are the only cetartiodactyl groups that have retained gremlin 2. According to the phyletic distribution of this gene and synteny analyses, we propose that gremlin 2 was lost in the common ancestor of ruminants and cetaceans between 56.3 and 63.5 million years ago as a product of a chromosomal rearrangement. Our analyses also indicate that the rate of evolution of gremlin 2 has been accelerated in the two groups that have retained this gene. Additionally, the lack of this gene could explain the high diversity of teeth among cetartiodactyl mammals; specifically, the presence of this gene could act as a biological constraint. Thus, our results support the notions that gene loss is a way to increase phenotypic diversity and that gremlin 2 is a dispensable gene, at least in cetartiodactyl mammals.
bibliographic citation: Opazo et al. (2017) Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants. PeerJ 5:e2901 https://doi.org/10.7717/peerj.2901
date submitted: 2016-10-09
date accepted: 2016-12-12
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Opazo
  given name: Juan C.
author list: Agent
  family name: Zavala
  given name: Kattina
author list: Agent
  family name: Krall
  given name: Paola
author list: Agent
  family name: Arias
  given name: Rodrigo A.
doi: 10.7717/peerj.2901
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Opazo et al.
attribution name: Opazo et al.

Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola
type: item
type: AcademicArticle
description: Corynespora cassiicola is a common plant pathogen that causes leaf spot disease in a broad range of crop, and it heavily affect rubber trees in Malaysia (Hsueh, 2011; Nghia et al., 2008). The isolation of UM 591 from a patient’s contact lens indicates the pathogenic potential of this dematiaceous fungus in human. However, the underlying factors that contribute to the opportunistic cross-infection have not been fully studied. We employed genome sequencing and gene homology annotations in attempt to identify these factors in UM 591 using data obtained from publicly available bioinformatics databases. The assembly size of UM 591 genome is 41.8 Mbp, and a total of 13,531 (≥99 bp) genes have been predicted. UM 591 is enriched with genes that encode for glycoside hydrolases, carbohydrate esterases, auxiliary activity enzymes and cell wall degrading enzymes. Virulent genes comprising of CAZymes, peptidases, and hypervirulence-associated cutinases were found to be present in the fungal genome. Comparative analysis result shows that UM 591 possesses higher number of carbohydrate esterases family 10 (CE10) CAZymes compared to other species of fungi in this study, and these enzymes hydrolyses wide range of carbohydrate and non-carbohydrate substrates. Putative melanin, siderophore, ent-kaurene, and lycopene biosynthesis gene clusters are predicted, and these gene clusters denote that UM 591 are capable of protecting itself from the UV and chemical stresses, allowing it to adapt to different environment. Putative sterigmatocystin, HC-toxin, cercosporin, and gliotoxin biosynthesis gene cluster are predicted. This finding have highlighted the necrotrophic and invasive nature of UM 591.
format: application/pdf
format: text/html
creator: Hong Keat Looi
creator: Yue Fen Toh
creator: Su Mei Yew
creator: Shiang Ling Na
creator: Yung-Chie Tan
creator: Pei-Sin Chong
creator: Jia-Shiun Khoo
creator: Wai-Yan Yee
creator: Kee Peng Ng
creator: Chee Sian Kuan
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.2841
publisher: PeerJ Inc.
rights: © 2017 Looi et al.
abstract: Corynespora cassiicola is a common plant pathogen that causes leaf spot disease in a broad range of crop, and it heavily affect rubber trees in Malaysia (Hsueh, 2011; Nghia et al., 2008). The isolation of UM 591 from a patient’s contact lens indicates the pathogenic potential of this dematiaceous fungus in human. However, the underlying factors that contribute to the opportunistic cross-infection have not been fully studied. We employed genome sequencing and gene homology annotations in attempt to identify these factors in UM 591 using data obtained from publicly available bioinformatics databases. The assembly size of UM 591 genome is 41.8 Mbp, and a total of 13,531 (≥99 bp) genes have been predicted. UM 591 is enriched with genes that encode for glycoside hydrolases, carbohydrate esterases, auxiliary activity enzymes and cell wall degrading enzymes. Virulent genes comprising of CAZymes, peptidases, and hypervirulence-associated cutinases were found to be present in the fungal genome. Comparative analysis result shows that UM 591 possesses higher number of carbohydrate esterases family 10 (CE10) CAZymes compared to other species of fungi in this study, and these enzymes hydrolyses wide range of carbohydrate and non-carbohydrate substrates. Putative melanin, siderophore, ent-kaurene, and lycopene biosynthesis gene clusters are predicted, and these gene clusters denote that UM 591 are capable of protecting itself from the UV and chemical stresses, allowing it to adapt to different environment. Putative sterigmatocystin, HC-toxin, cercosporin, and gliotoxin biosynthesis gene cluster are predicted. This finding have highlighted the necrotrophic and invasive nature of UM 591.
bibliographic citation: Looi et al. (2017) Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola. PeerJ 5:e2841 https://doi.org/10.7717/peerj.2841
date submitted: 2016-06-07
date accepted: 2016-11-29
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Looi
  given name: Hong Keat
author list: Agent
  family name: Toh
  given name: Yue Fen
author list: Agent
  family name: Yew
  given name: Su Mei
author list: Agent
  family name: Na
  given name: Shiang Ling
author list: Agent
  family name: Tan
  given name: Yung-Chie
author list: Agent
  family name: Chong
  given name: Pei-Sin
author list: Agent
  family name: Khoo
  given name: Jia-Shiun
author list: Agent
  family name: Yee
  given name: Wai-Yan
author list: Agent
  family name: Ng
  given name: Kee Peng
author list: Agent
  family name: Kuan
  given name: Chee Sian
doi: 10.7717/peerj.2841
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Looi et al.
attribution name: Looi et al.

Computer simulation of Cerebral Arteriovenous Malformation—validation analysis of hemodynamics parameters
type: item
type: AcademicArticle
description: Problem The purpose of this work is to provide some validation methods for evaluating the hemodynamic assessment of Cerebral Arteriovenous Malformation (CAVM). This article emphasizes the importance of validating noninvasive measurements for CAVM patients, which are designed using lumped models for complex vessel structure. Methods The validation of the hemodynamics assessment is based on invasive clinical measurements and cross-validation techniques with the Philips proprietary validated software’s Qflow and 2D Perfursion. Results The modeling results are validated for 30 CAVM patients for 150 vessel locations. Mean flow, diameter, and pressure were compared between modeling results and with clinical/cross validation measurements, using an independent two-tailed Student t test. Exponential regression analysis was used to assess the relationship between blood flow, vessel diameter, and pressure between them. Univariate analysis is used to assess the relationship between vessel diameter, vessel cross-sectional area, AVM volume, AVM pressure, and AVM flow results were performed with linear or exponential regression. Discussion Modeling results were compared with clinical measurements from vessel locations of cerebral regions. Also, the model is cross validated with Philips proprietary validated software’s Qflow and 2D Perfursion. Our results shows that modeling results and clinical results are nearly matching with a small deviation. Conclusion In this article, we have validated our modeling results with clinical measurements. The new approach for cross-validation is proposed by demonstrating the accuracy of our results with a validated product in a clinical environment.
format: application/pdf
format: text/html
creator: Y. Kiran Kumar
creator: Shashi Bhushan Mehta
creator: Manjunath Ramachandra
subject: Neurology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.2724
publisher: PeerJ Inc.
rights: © 2017 Kumar et al.
abstract: Problem The purpose of this work is to provide some validation methods for evaluating the hemodynamic assessment of Cerebral Arteriovenous Malformation (CAVM). This article emphasizes the importance of validating noninvasive measurements for CAVM patients, which are designed using lumped models for complex vessel structure. Methods The validation of the hemodynamics assessment is based on invasive clinical measurements and cross-validation techniques with the Philips proprietary validated software’s Qflow and 2D Perfursion. Results The modeling results are validated for 30 CAVM patients for 150 vessel locations. Mean flow, diameter, and pressure were compared between modeling results and with clinical/cross validation measurements, using an independent two-tailed Student t test. Exponential regression analysis was used to assess the relationship between blood flow, vessel diameter, and pressure between them. Univariate analysis is used to assess the relationship between vessel diameter, vessel cross-sectional area, AVM volume, AVM pressure, and AVM flow results were performed with linear or exponential regression. Discussion Modeling results were compared with clinical measurements from vessel locations of cerebral regions. Also, the model is cross validated with Philips proprietary validated software’s Qflow and 2D Perfursion. Our results shows that modeling results and clinical results are nearly matching with a small deviation. Conclusion In this article, we have validated our modeling results with clinical measurements. The new approach for cross-validation is proposed by demonstrating the accuracy of our results with a validated product in a clinical environment.
bibliographic citation: Kumar et al. (2017) Computer simulation of Cerebral Arteriovenous Malformation—validation analysis of hemodynamics parameters. PeerJ 5:e2724 https://doi.org/10.7717/peerj.2724
date submitted: 2016-02-05
date accepted: 2016-10-25
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kumar
  given name: Y. Kiran
author list: Agent
  family name: Mehta
  given name: Shashi Bhushan
author list: Agent
  family name: Ramachandra
  given name: Manjunath
doi: 10.7717/peerj.2724
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Kumar et al.
attribution name: Kumar et al.

The use of gene interaction networks to improve the identification of cancer driver genes
type: item
type: AcademicArticle
description: Bioinformaticians have implemented different strategies to distinguish cancer driver genes from passenger genes. One of the more recent advances uses a pathway-oriented approach. Methods that employ this strategy are highly dependent on the quality and size of the pathway interaction network employed, and require a powerful statistical environment for analyses. A number of genomic libraries are available in R. DriverNet and DawnRank employ pathway-based methods that use gene interaction graphs in matrix form. We investigated the benefit of combining data from 3 different sources on the prediction outcome of cancer driver genes by DriverNet and DawnRank. An enriched dataset was derived comprising 13,862 genes with 372,250 interactions, which increased its accuracy by 17% and 28%, respectively, compared to their original networks. The study identified 33 new candidate driver genes. Our study highlights the potential of combining networks and weighting edges to provide greater accuracy in the identification of cancer driver genes.
format: application/pdf
format: text/html
creator: Emilie Ramsahai
creator: Kheston Walkins
creator: Vrijesh Tripathi
creator: Melford John
subject: Bioinformatics
subject: Computational Biology
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.2568
publisher: PeerJ Inc.
rights: © 2017 Ramsahai et al.
abstract: Bioinformaticians have implemented different strategies to distinguish cancer driver genes from passenger genes. One of the more recent advances uses a pathway-oriented approach. Methods that employ this strategy are highly dependent on the quality and size of the pathway interaction network employed, and require a powerful statistical environment for analyses. A number of genomic libraries are available in R. DriverNet and DawnRank employ pathway-based methods that use gene interaction graphs in matrix form. We investigated the benefit of combining data from 3 different sources on the prediction outcome of cancer driver genes by DriverNet and DawnRank. An enriched dataset was derived comprising 13,862 genes with 372,250 interactions, which increased its accuracy by 17% and 28%, respectively, compared to their original networks. The study identified 33 new candidate driver genes. Our study highlights the potential of combining networks and weighting edges to provide greater accuracy in the identification of cancer driver genes.
bibliographic citation: Ramsahai et al. (2017) The use of gene interaction networks to improve the identification of cancer driver genes. PeerJ 5:e2568 https://doi.org/10.7717/peerj.2568
date submitted: 2016-02-02
date accepted: 2016-09-14
issued: 2017-01-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramsahai
  given name: Emilie
author list: Agent
  family name: Walkins
  given name: Kheston
author list: Agent
  family name: Tripathi
  given name: Vrijesh
author list: Agent
  family name: John
  given name: Melford
doi: 10.7717/peerj.2568
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-26
copyright: ©2017 Ramsahai et al.
attribution name: Ramsahai et al.

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