PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters
items: On the relationship between tumour growth rate and survival in non-small cell lung cancer
items: Transcriptomic profiling of mTOR and ryanodine receptor signaling molecules in developing zebrafish in the absence and presence of PCB 95
items: Age-based and reproductive biology of the Pacific Longnose Parrotfish Hipposcarus longiceps from Guam
items: An exceptionally preserved armored dinosaur reveals the morphology and allometry of osteoderms and their horny epidermal coverings
items: Facilitative and competitive interaction components among New England salt marsh plants
items: DNA barcoding reveals the mislabeling of fish in a popular tourist destination in Brazil
items: Genomic characterization of a new endophytic Streptomyces kebangsaanensis identifies biosynthetic pathway gene clusters for novel phenazine antibiotic production
items: Geological duration of ammonoids controlled their geographical range of fossil distribution
items: Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters
type: item
type: AcademicArticle
description: Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.
format: application/pdf
format: text/html
creator: Gong Cheng
creator: Quan Lu
creator: Ling Ma
creator: Guocai Zhang
creator: Liang Xu
creator: Zongshan Zhou
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.3948
publisher: PeerJ Inc.
rights: © 2017 Cheng et al.
abstract: Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.
bibliographic citation: Cheng et al. (2017) BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters. PeerJ 5:e3948 https://doi.org/10.7717/peerj.3948
date submitted: 2017-06-21
date accepted: 2017-09-30
issued: 2017-11-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Gong
author list: Agent
  family name: Lu
  given name: Quan
author list: Agent
  family name: Ma
  given name: Ling
author list: Agent
  family name: Zhang
  given name: Guocai
author list: Agent
  family name: Xu
  given name: Liang
author list: Agent
  family name: Zhou
  given name: Zongshan
doi: 10.7717/peerj.3948
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-30
copyright: © 2017 Cheng et al.
attribution name: Cheng et al.

On the relationship between tumour growth rate and survival in non-small cell lung cancer
type: item
type: AcademicArticle
description: A recurrent question within oncology drug development is predicting phase III outcome for a new treatment using early clinical data. One approach to tackle this problem has been to derive metrics from mathematical models that describe tumour size dynamics termed re-growth rate and time to tumour re-growth. They have shown to be strong predictors of overall survival in numerous studies but there is debate about how these metrics are derived and if they are more predictive than empirical end-points. This work explores the issues raised in using model-derived metric as predictors for survival analyses. Re-growth rate and time to tumour re-growth were calculated for three large clinical studies by forward and reverse alignment. The latter involves re-aligning patients to their time of progression. Hence, it accounts for the time taken to estimate re-growth rate and time to tumour re-growth but also assesses if these predictors correlate to survival from the time of progression. I found that neither re-growth rate nor time to tumour re-growth correlated to survival using reverse alignment. This suggests that the dynamics of tumours up until disease progression has no relationship to survival post progression. For prediction of a phase III trial I found the metrics performed no better than empirical end-points. These results highlight that care must be taken when relating dynamics of tumour imaging to survival and that bench-marking new approaches to existing ones is essential.
format: application/pdf
format: text/html
creator: Hitesh B. Mistry
subject: Mathematical Biology
subject: Clinical Trials
subject: Oncology
subject: Pharmacology
subject: Statistics
description: doi:10.7717/peerj.4111
publisher: PeerJ Inc.
rights: © 2017 Mistry
abstract: A recurrent question within oncology drug development is predicting phase III outcome for a new treatment using early clinical data. One approach to tackle this problem has been to derive metrics from mathematical models that describe tumour size dynamics termed re-growth rate and time to tumour re-growth. They have shown to be strong predictors of overall survival in numerous studies but there is debate about how these metrics are derived and if they are more predictive than empirical end-points. This work explores the issues raised in using model-derived metric as predictors for survival analyses. Re-growth rate and time to tumour re-growth were calculated for three large clinical studies by forward and reverse alignment. The latter involves re-aligning patients to their time of progression. Hence, it accounts for the time taken to estimate re-growth rate and time to tumour re-growth but also assesses if these predictors correlate to survival from the time of progression. I found that neither re-growth rate nor time to tumour re-growth correlated to survival using reverse alignment. This suggests that the dynamics of tumours up until disease progression has no relationship to survival post progression. For prediction of a phase III trial I found the metrics performed no better than empirical end-points. These results highlight that care must be taken when relating dynamics of tumour imaging to survival and that bench-marking new approaches to existing ones is essential.
bibliographic citation: Mistry (2017) On the relationship between tumour growth rate and survival in non-small cell lung cancer. PeerJ 5:e4111 https://doi.org/10.7717/peerj.4111
date submitted: 2017-09-06
date accepted: 2017-11-09
issued: 2017-11-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mistry
  given name: Hitesh B.
doi: 10.7717/peerj.4111
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-29
copyright: ©2017 Mistry
attribution name: Mistry

Transcriptomic profiling of mTOR and ryanodine receptor signaling molecules in developing zebrafish in the absence and presence of PCB 95
type: item
type: AcademicArticle
description: The mechanistic target of rapamycin (mTOR) and ryanodine receptor (RyR) signaling pathways regulate fundamental processes of neurodevelopment, and genetic mutations within these pathways have been linked to neurodevelopmental disorders. While previous studies have established that these signaling molecules are expressed in developing zebrafish, a detailed characterization of the ontogenetic profile of these signaling molecules is lacking. Thus, we evaluated the spatiotemporal expression of key transcripts in mTOR and RyR signaling pathways in wildtype zebrafish at 24, 72 and 120 hours post fertilization (hpf). We further determined whether transcriptional profiles of a subset of genes in both pathways were altered by exposure to PCB 95 (2,2′,3,5′,6-pentachlorobiphenyl), a pervasive environmental contaminant known to cause developmental neurotoxicity in mammalian systems via RyR-dependent mechanisms. Quantitative PCR revealed that transcription generally increased across development. Genes in the signaling pathway upstream of the mTORC1 complex, and the RyR-paralogs, ryr2a and ryr3, were robustly upregulated, and in situ hybridization of ryr3 coincided with a transcriptional shift from muscle to neuronal tissue after 24 hpf. Static waterborne exposure to PCB 95 beginning at 6 hpf significantly altered transcription of genes in both pathways. These changes were concentration- and time-dependent, and included downregulation of rptor, a member of the mTORC1 complex, at both 72 and 120 hpf, and increased transcript levels of the RyR paralog ryr2b and downstream target of RyR signaling, Wingless-type 2ba (wnt2ba) at 72 hpf. The detailed transcriptomic profiling of key genes within these two signaling pathways provides a baseline for identifying other environmental factors that modify normal spatiotemporal expression patterns of mTOR and RyR signaling pathways in the developing zebrafish, as illustrated here for PCB 95.
format: application/pdf
format: text/html
creator: Daniel F. Frank
creator: Galen W. Miller
creator: Richard E. Connon
creator: Juergen Geist
creator: Pamela J. Lein
subject: Developmental Biology
subject: Neuroscience
subject: Toxicology
description: doi:10.7717/peerj.4106
publisher: PeerJ Inc.
rights: © 2017 Frank et al.
abstract: The mechanistic target of rapamycin (mTOR) and ryanodine receptor (RyR) signaling pathways regulate fundamental processes of neurodevelopment, and genetic mutations within these pathways have been linked to neurodevelopmental disorders. While previous studies have established that these signaling molecules are expressed in developing zebrafish, a detailed characterization of the ontogenetic profile of these signaling molecules is lacking. Thus, we evaluated the spatiotemporal expression of key transcripts in mTOR and RyR signaling pathways in wildtype zebrafish at 24, 72 and 120 hours post fertilization (hpf). We further determined whether transcriptional profiles of a subset of genes in both pathways were altered by exposure to PCB 95 (2,2′,3,5′,6-pentachlorobiphenyl), a pervasive environmental contaminant known to cause developmental neurotoxicity in mammalian systems via RyR-dependent mechanisms. Quantitative PCR revealed that transcription generally increased across development. Genes in the signaling pathway upstream of the mTORC1 complex, and the RyR-paralogs, ryr2a and ryr3, were robustly upregulated, and in situ hybridization of ryr3 coincided with a transcriptional shift from muscle to neuronal tissue after 24 hpf. Static waterborne exposure to PCB 95 beginning at 6 hpf significantly altered transcription of genes in both pathways. These changes were concentration- and time-dependent, and included downregulation of rptor, a member of the mTORC1 complex, at both 72 and 120 hpf, and increased transcript levels of the RyR paralog ryr2b and downstream target of RyR signaling, Wingless-type 2ba (wnt2ba) at 72 hpf. The detailed transcriptomic profiling of key genes within these two signaling pathways provides a baseline for identifying other environmental factors that modify normal spatiotemporal expression patterns of mTOR and RyR signaling pathways in the developing zebrafish, as illustrated here for PCB 95.
bibliographic citation: Frank et al. (2017) Transcriptomic profiling of mTOR and ryanodine receptor signaling molecules in developing zebrafish in the absence and presence of PCB 95. PeerJ 5:e4106 https://doi.org/10.7717/peerj.4106
date submitted: 2017-05-19
date accepted: 2017-11-08
issued: 2017-11-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frank
  given name: Daniel F.
author list: Agent
  family name: Miller
  given name: Galen W.
author list: Agent
  family name: Connon
  given name: Richard E.
author list: Agent
  family name: Geist
  given name: Juergen
author list: Agent
  family name: Lein
  given name: Pamela J.
doi: 10.7717/peerj.4106
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-29
copyright: © 2017 Frank et al.
attribution name: Frank et al.

Age-based and reproductive biology of the Pacific Longnose Parrotfish Hipposcarus longiceps from Guam
type: item
type: AcademicArticle
description: The Pacific longnose parrotfish Hipposcarus longiceps (Valenciennes 1840) represents a prime fishery resource throughout much of the tropical Pacific. In this study, we sampled the species from the Guam commercial fishery market across five consecutive years to characterize reproductive and age-based demographic information imperative for informed fishery management. Compared with other parrotfishes, this species was found to be large-bodied, but has only a moderate life span of 10 + years. Hipposcarus longiceps was confirmed as a diandric protogynous hermaphrodite with highly sex-specific growth patterns and an overall mean asymptotic length of 434 mm fork length (FL). Females were estimated to reach median maturity at 329 mm FL (2.4 years) and have a median length at female-to-male sex change of 401 mm FL. Life-history trait values derived here were used to update previous models relating life history and vulnerability to overexploitation. We found that enhancement of just one species’ trait values improved model fits considerably, which strengthens the conclusion that life-history traits are a strong determinant of species’ vulnerability in the parrotfishes. This information is an imperative complement to other data sources facilitating formal stock assessment of a key fishery target.
format: application/pdf
format: text/html
creator: Brett M. Taylor
creator: Eric Cruz
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.4079
publisher: PeerJ Inc.
rights: © 2017 Taylor and Cruz
abstract: The Pacific longnose parrotfish Hipposcarus longiceps (Valenciennes 1840) represents a prime fishery resource throughout much of the tropical Pacific. In this study, we sampled the species from the Guam commercial fishery market across five consecutive years to characterize reproductive and age-based demographic information imperative for informed fishery management. Compared with other parrotfishes, this species was found to be large-bodied, but has only a moderate life span of 10 + years. Hipposcarus longiceps was confirmed as a diandric protogynous hermaphrodite with highly sex-specific growth patterns and an overall mean asymptotic length of 434 mm fork length (FL). Females were estimated to reach median maturity at 329 mm FL (2.4 years) and have a median length at female-to-male sex change of 401 mm FL. Life-history trait values derived here were used to update previous models relating life history and vulnerability to overexploitation. We found that enhancement of just one species’ trait values improved model fits considerably, which strengthens the conclusion that life-history traits are a strong determinant of species’ vulnerability in the parrotfishes. This information is an imperative complement to other data sources facilitating formal stock assessment of a key fishery target.
bibliographic citation: Taylor et al. (2017) Age-based and reproductive biology of the Pacific Longnose Parrotfish Hipposcarus longiceps from Guam. PeerJ 5:e4079 https://doi.org/10.7717/peerj.4079
date submitted: 2017-08-22
date accepted: 2017-11-01
issued: 2017-11-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Taylor
  given name: Brett M.
author list: Agent
  family name: Cruz
  given name: Eric
doi: 10.7717/peerj.4079
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-29
copyright: ©2017 Taylor and Cruz
attribution name: Taylor and Cruz

An exceptionally preserved armored dinosaur reveals the morphology and allometry of osteoderms and their horny epidermal coverings
type: item
type: AcademicArticle
description: Although the evolution and function of “exaggerated” bony projections in ornithischian dinosaurs has been subject to significant debate recently, our understanding of the structure and morphology of their epidermal keratinized coverings is greatly limited. The holotype of Borealopelta, a new nodosaurid ankylosaur, preserves osteoderms and extensive epidermal structures (dark organic residues), in anatomic position across the entire precaudal length. Contrasting previous specimens, organic epiosteodermal scales, often in the form of horn-like (keratinous) sheaths, cap and exaggerate nearly all osteoderms, allowing for morphometric and allometric analyses of both the bony osteoderms and their horny sheaths. A total of 172 osteoderms were quantified, with osteoderm spine length and height being positively allometric with respect to basal length and width. Despite tight correlations between the different measures amongst all other osteoderms, the large parascapular spines represent consistent outliers. Thickness and relative contribution of the keratinized epiosteodermal scales/sheaths varies greatly by region, ranging from 2% to 6% for posterior thoracics, to ∼25% (1.3×) for the parascapular spines—similar to horn sheaths in some bovid analogues. Relative to the bony cores, the horny portions of the spines are strongly positively allometric (slope = 2.3, CI = 1.8–2.8). Strong allometric scaling, species-specific morphology, and significant keratinous extension of the cervicoscapular spines is consistent with elaboration under socio-sexual selection. This marks the first allometric analysis of ornithischian soft tissues.
format: application/pdf
format: text/html
creator: Caleb M. Brown
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.4066
publisher: PeerJ Inc.
rights: © 2017 Brown
abstract: Although the evolution and function of “exaggerated” bony projections in ornithischian dinosaurs has been subject to significant debate recently, our understanding of the structure and morphology of their epidermal keratinized coverings is greatly limited. The holotype of Borealopelta, a new nodosaurid ankylosaur, preserves osteoderms and extensive epidermal structures (dark organic residues), in anatomic position across the entire precaudal length. Contrasting previous specimens, organic epiosteodermal scales, often in the form of horn-like (keratinous) sheaths, cap and exaggerate nearly all osteoderms, allowing for morphometric and allometric analyses of both the bony osteoderms and their horny sheaths. A total of 172 osteoderms were quantified, with osteoderm spine length and height being positively allometric with respect to basal length and width. Despite tight correlations between the different measures amongst all other osteoderms, the large parascapular spines represent consistent outliers. Thickness and relative contribution of the keratinized epiosteodermal scales/sheaths varies greatly by region, ranging from 2% to 6% for posterior thoracics, to ∼25% (1.3×) for the parascapular spines—similar to horn sheaths in some bovid analogues. Relative to the bony cores, the horny portions of the spines are strongly positively allometric (slope = 2.3, CI = 1.8–2.8). Strong allometric scaling, species-specific morphology, and significant keratinous extension of the cervicoscapular spines is consistent with elaboration under socio-sexual selection. This marks the first allometric analysis of ornithischian soft tissues.
bibliographic citation: Brown (2017) An exceptionally preserved armored dinosaur reveals the morphology and allometry of osteoderms and their horny epidermal coverings. PeerJ 5:e4066 https://doi.org/10.7717/peerj.4066
date submitted: 2017-05-12
date accepted: 2017-10-29
issued: 2017-11-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brown
  given name: Caleb M.
doi: 10.7717/peerj.4066
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-29
copyright: © 2017 Brown
attribution name: Brown

Facilitative and competitive interaction components among New England salt marsh plants
type: item
type: AcademicArticle
description: Intra- and interspecific interactions can be broken down into facilitative and competitive components. The net interaction between two organisms is simply the sum of these counteracting elements. Disentangling the positive and negative components of species interactions is a critical step in advancing our understanding of how the interaction between organisms shift along physical and biotic gradients. We performed a manipulative field experiment to quantify the positive and negative components of the interactions between a perennial forb, Aster tenuifolius, and three dominant, matrix-forming grasses and rushes in a New England salt marsh. Specifically, we asked whether positive and negative interaction components: (1) are unique or redundant across three matrix-forming species (two grasses; Distichlis spicata and Spartina patens, and one rush; Juncus gerardi), and (2) change across Aster life stages (seedling, juvenile, and adult). For adult Aster the strength of the facilitative component of the matrix-forb interaction was stronger than the competitive component for two of the three matrix species, leading to net positive interactions. There was no statistically significant variation among matrix species in their net or component effects. We found little difference in the effects of J. gerardi on Aster at later life-history stages; interaction component strengths did not differ between juveniles and adults. However, mortality of seedlings in neighbor removal plots was 100%, indicating a particularly strong and critical facilitative effect of matrix species on this forb during the earliest life stages. Overall, our results indicate that matrix forming grasses and rushes have important, yet largely redundant, positive net effects on Aster performance across its life cycle. Studies that untangle various components of interactions and their contingencies are critical to both expanding our basic understanding of community organization, and predicting how natural communi…
format: application/pdf
format: text/html
creator: John F. Bruno
creator: Tatyana A. Rand
creator: Nancy C. Emery
creator: Mark D. Bertness
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
subject: Plant Science
description: doi:10.7717/peerj.4049
publisher: PeerJ Inc.
rights: © 2017 Bruno et al.
abstract: Intra- and interspecific interactions can be broken down into facilitative and competitive components. The net interaction between two organisms is simply the sum of these counteracting elements. Disentangling the positive and negative components of species interactions is a critical step in advancing our understanding of how the interaction between organisms shift along physical and biotic gradients. We performed a manipulative field experiment to quantify the positive and negative components of the interactions between a perennial forb, Aster tenuifolius, and three dominant, matrix-forming grasses and rushes in a New England salt marsh. Specifically, we asked whether positive and negative interaction components: (1) are unique or redundant across three matrix-forming species (two grasses; Distichlis spicata and Spartina patens, and one rush; Juncus gerardi), and (2) change across Aster life stages (seedling, juvenile, and adult). For adult Aster the strength of the facilitative component of the matrix-forb interaction was stronger than the competitive component for two of the three matrix species, leading to net positive interactions. There was no statistically significant variation among matrix species in their net or component effects. We found little difference in the effects of J. gerardi on Aster at later life-history stages; interaction component strengths did not differ between juveniles and adults. However, mortality of seedlings in neighbor removal plots was 100%, indicating a particularly strong and critical facilitative effect of matrix species on this forb during the earliest life stages. Overall, our results indicate that matrix forming grasses and rushes have important, yet largely redundant, positive net effects on Aster performance across its life cycle. Studies that untangle various components of interactions and their contingencies are critical to both expanding our basic understanding of community organization, and predicting how natural communi…
bibliographic citation: Bruno et al. (2017) Facilitative and competitive interaction components among New England salt marsh plants. PeerJ 5:e4049 https://doi.org/10.7717/peerj.4049
date submitted: 2017-08-04
date accepted: 2017-10-26
issued: 2017-11-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bruno
  given name: John F.
author list: Agent
  family name: Rand
  given name: Tatyana A.
author list: Agent
  family name: Emery
  given name: Nancy C.
author list: Agent
  family name: Bertness
  given name: Mark D.
doi: 10.7717/peerj.4049
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-29
copyright: ©2017 Bruno et al.
attribution name: Bruno et al.

DNA barcoding reveals the mislabeling of fish in a popular tourist destination in Brazil
type: item
type: AcademicArticle
description: The consumption of raw fish has increased considerably in the West, since it is said to be potentially healthier than processed fish (for containing omega 3 and 6, essential amino acids and vitamins). However this potential benefit, as well as the taste, value and even the risk of extinction are not the same for all species of fish, constituting grounds for fraud. Using the principles of the DNA barcode we revealed mislabelling of fish in Japanese restaurants and fishmarkets in Florianópolis, a popular tourist capital in Brazil. We sequenced the COI gene of 65 samples from fisheries and 80 from restaurants and diagnosed 30% of mislabeled samples in fisheries and 26% in restaurants. We discussed that frauds may have occurred for different reasons: to circumvent surveillance on threatened species; to sell fish with sizes smaller than allowed or abundant species as being a much rarer species (law of supply); to induce product consumption using species with better taste. It should be noted that some substitutions are derived from incorrect identification and are not a fraud per se; they are due to confusion of popular names or misunderstanding by the sellers. Therefore, we suggest the implementation of a systematic regulatory program conducted by governmental agencies to reduce mislabelling in order to avoid further damage to the community (in health and financial issues) and fish stocks.
format: application/pdf
format: text/html
creator: Clisten Fátima Staffen
creator: Mari Dalva Staffen
creator: Mariana Londero Becker
creator: Sara Emelie Löfgren
creator: Yara Costa Netto Muniz
creator: Renato Hajenius Aché de Freitas
creator: Andrea Rita Marrero
subject: Food Science and Technology
subject: Genomics
description: doi:10.7717/peerj.4006
publisher: PeerJ Inc.
rights: © 2017 Staffen et al.
abstract: The consumption of raw fish has increased considerably in the West, since it is said to be potentially healthier than processed fish (for containing omega 3 and 6, essential amino acids and vitamins). However this potential benefit, as well as the taste, value and even the risk of extinction are not the same for all species of fish, constituting grounds for fraud. Using the principles of the DNA barcode we revealed mislabelling of fish in Japanese restaurants and fishmarkets in Florianópolis, a popular tourist capital in Brazil. We sequenced the COI gene of 65 samples from fisheries and 80 from restaurants and diagnosed 30% of mislabeled samples in fisheries and 26% in restaurants. We discussed that frauds may have occurred for different reasons: to circumvent surveillance on threatened species; to sell fish with sizes smaller than allowed or abundant species as being a much rarer species (law of supply); to induce product consumption using species with better taste. It should be noted that some substitutions are derived from incorrect identification and are not a fraud per se; they are due to confusion of popular names or misunderstanding by the sellers. Therefore, we suggest the implementation of a systematic regulatory program conducted by governmental agencies to reduce mislabelling in order to avoid further damage to the community (in health and financial issues) and fish stocks.
bibliographic citation: Staffen et al. (2017) DNA barcoding reveals the mislabeling of fish in a popular tourist destination in Brazil. PeerJ 5:e4006 https://doi.org/10.7717/peerj.4006
date submitted: 2017-07-05
date accepted: 2017-10-18
issued: 2017-11-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Staffen
  given name: Clisten Fátima
author list: Agent
  family name: Staffen
  given name: Mari Dalva
author list: Agent
  family name: Becker
  given name: Mariana Londero
author list: Agent
  family name: Löfgren
  given name: Sara Emelie
author list: Agent
  family name: Muniz
  given name: Yara Costa Netto
author list: Agent
  family name: de Freitas
  given name: Renato Hajenius Aché
author list: Agent
  family name: Marrero
  given name: Andrea Rita
doi: 10.7717/peerj.4006
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-29
copyright: ©2017 Staffen et al.
attribution name: Staffen et al.

Genomic characterization of a new endophytic Streptomyces kebangsaanensis identifies biosynthetic pathway gene clusters for novel phenazine antibiotic production
type: item
type: AcademicArticle
description: Background Streptomyces are well known for their capability to produce many bioactive secondary metabolites with medical and industrial importance. Here we report a novel bioactive phenazine compound, 6-((2-hydroxy-4-methoxyphenoxy) carbonyl) phenazine-1-carboxylic acid (HCPCA) extracted from Streptomyces kebangsaanensis, an endophyte isolated from the ethnomedicinal Portulaca oleracea. Methods The HCPCA chemical structure was determined using nuclear magnetic resonance spectroscopy. We conducted whole genome sequencing for the identification of the gene cluster(s) believed to be responsible for phenazine biosynthesis in order to map its corresponding pathway, in addition to bioinformatics analysis to assess the potential of S. kebangsaanensis in producing other useful secondary metabolites. Results The S. kebangsaanensis genome comprises an 8,328,719 bp linear chromosome with high GC content (71.35%) consisting of 12 rRNA operons, 81 tRNA, and 7,558 protein coding genes. We identified 24 gene clusters involved in polyketide, nonribosomal peptide, terpene, bacteriocin, and siderophore biosynthesis, as well as a gene cluster predicted to be responsible for phenazine biosynthesis. Discussion The HCPCA phenazine structure was hypothesized to derive from the combination of two biosynthetic pathways, phenazine-1,6-dicarboxylic acid and 4-methoxybenzene-1,2-diol, originated from the shikimic acid pathway. The identification of a biosynthesis pathway gene cluster for phenazine antibiotics might facilitate future genetic engineering design of new synthetic phenazine antibiotics. Additionally, these findings confirm the potential of S. kebangsaanensis for producing various antibiotics and secondary metabolites.
format: application/pdf
format: text/html
creator: Juwairiah Remali
creator: Nurul ‘Izzah Mohd Sarmin
creator: Chyan Leong Ng
creator: John J.L. Tiong
creator: Wan M. Aizat
creator: Loke Kok Keong
creator: Noraziah Mohamad Zin
subject: Bioinformatics
subject: Biotechnology
subject: Genomics
subject: Drugs and Devices
description: doi:10.7717/peerj.3738
publisher: PeerJ Inc.
rights: © 2017 Remali et al.
abstract: Background Streptomyces are well known for their capability to produce many bioactive secondary metabolites with medical and industrial importance. Here we report a novel bioactive phenazine compound, 6-((2-hydroxy-4-methoxyphenoxy) carbonyl) phenazine-1-carboxylic acid (HCPCA) extracted from Streptomyces kebangsaanensis, an endophyte isolated from the ethnomedicinal Portulaca oleracea. Methods The HCPCA chemical structure was determined using nuclear magnetic resonance spectroscopy. We conducted whole genome sequencing for the identification of the gene cluster(s) believed to be responsible for phenazine biosynthesis in order to map its corresponding pathway, in addition to bioinformatics analysis to assess the potential of S. kebangsaanensis in producing other useful secondary metabolites. Results The S. kebangsaanensis genome comprises an 8,328,719 bp linear chromosome with high GC content (71.35%) consisting of 12 rRNA operons, 81 tRNA, and 7,558 protein coding genes. We identified 24 gene clusters involved in polyketide, nonribosomal peptide, terpene, bacteriocin, and siderophore biosynthesis, as well as a gene cluster predicted to be responsible for phenazine biosynthesis. Discussion The HCPCA phenazine structure was hypothesized to derive from the combination of two biosynthetic pathways, phenazine-1,6-dicarboxylic acid and 4-methoxybenzene-1,2-diol, originated from the shikimic acid pathway. The identification of a biosynthesis pathway gene cluster for phenazine antibiotics might facilitate future genetic engineering design of new synthetic phenazine antibiotics. Additionally, these findings confirm the potential of S. kebangsaanensis for producing various antibiotics and secondary metabolites.
bibliographic citation: Remali et al. (2017) Genomic characterization of a new endophytic Streptomyces kebangsaanensis identifies biosynthetic pathway gene clusters for novel phenazine antibiotic production. PeerJ 5:e3738 https://doi.org/10.7717/peerj.3738
date submitted: 2017-05-08
date accepted: 2017-08-04
issued: 2017-11-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Remali
  given name: Juwairiah
author list: Agent
  family name: Sarmin
  given name: Nurul ‘Izzah Mohd
author list: Agent
  family name: Ng
  given name: Chyan Leong
author list: Agent
  family name: Tiong
  given name: John J.L.
author list: Agent
  family name: Aizat
  given name: Wan M.
author list: Agent
  family name: Keong
  given name: Loke Kok
author list: Agent
  family name: Zin
  given name: Noraziah Mohamad
doi: 10.7717/peerj.3738
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-29
copyright: ©2017 Remali et al.
attribution name: Remali et al.

Geological duration of ammonoids controlled their geographical range of fossil distribution
type: item
type: AcademicArticle
description: The latitudinal distributions in Devonian–Cretaceous ammonoids were analyzed at the genus level, and were compared with the hatchling sizes (i.e., ammonitella diameters) and the geological durations. The results show that (1) length of temporal ranges of ammonoids effected broader ranges of fossil distribution and paleobiogeography of ammonoids, and (2) the hatchling size was not related to the geographical range of fossil distribution of ammonoids. Reducing the influence of geological duration in this analysis implies that hatchling size was one of the controlling factors that determined the distribution of ammonoid habitats at any given period in time: ammonoids with smaller hatchling sizes tended to have broader ammonoid habitat ranges. These relationships were somewhat blurred in the Devonian, Carboniferous, Triassic, and Jurassic, which is possibly due to (1) the course of development of a reproductive strategy with smaller hatchling sizes in the Devonian and (2) the high origination rates after the mass extinction events.
format: application/pdf
format: text/html
creator: Ryoji Wani
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.4108
publisher: PeerJ Inc.
rights: © 2017 Wani
abstract: The latitudinal distributions in Devonian–Cretaceous ammonoids were analyzed at the genus level, and were compared with the hatchling sizes (i.e., ammonitella diameters) and the geological durations. The results show that (1) length of temporal ranges of ammonoids effected broader ranges of fossil distribution and paleobiogeography of ammonoids, and (2) the hatchling size was not related to the geographical range of fossil distribution of ammonoids. Reducing the influence of geological duration in this analysis implies that hatchling size was one of the controlling factors that determined the distribution of ammonoid habitats at any given period in time: ammonoids with smaller hatchling sizes tended to have broader ammonoid habitat ranges. These relationships were somewhat blurred in the Devonian, Carboniferous, Triassic, and Jurassic, which is possibly due to (1) the course of development of a reproductive strategy with smaller hatchling sizes in the Devonian and (2) the high origination rates after the mass extinction events.
bibliographic citation: Wani (2017) Geological duration of ammonoids controlled their geographical range of fossil distribution. PeerJ 5:e4108 https://doi.org/10.7717/peerj.4108
date submitted: 2017-08-22
date accepted: 2017-11-08
issued: 2017-11-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wani
  given name: Ryoji
doi: 10.7717/peerj.4108
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-28
copyright: ©2017 Wani
attribution name: Wani

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1
type: item
type: AcademicArticle
description: Background Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ) to nitrite ( ${\mathrm{NO}}_{2}^{-}$ NO 2 − ). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (N2O) reductase, suggesting that NO and N2O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. Methods Series of oxic and anoxic cultures of strain JAM1 were performed with N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − or sodium nitroprusside, and growth and N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − , ${\mathrm{NO}}_{2}^{-}$ NO 2 − and N2 concentrations were measured. Ammonium ( ${\mathrm{NH}}_{4}^{+}$ NH 4 + )-free cultures were also tested to assess the dynamics of N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − and ${\mathrm{NO}}_{2}^{-}$ NO 2 − . Isotopic labeling of N2O was performed in 15NH4+-amended cultures. Cultures with the JAM1ΔnarG1narG2 double mutant were performed to assess the involvement of the Nar systems on N2O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc-type nitric oxide reductase (cnorB1 and cnorB2) and nitrous oxide reductase (nosZ), and also nnrS and norR that encode NO-sensitive regulators. Results Strain JAM1 can reduce NO to N2O and N2O to N2 and can sustain growth under anoxic conditions by reducing N2O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase, ${\mathrm{NO}}_{3}^{-}$ NO 3 − -amended cultures produce N2O, representing up to 6% of the N-input. ${\mathrm{NO}}_{2}^{-}$ NO 2 − was shown …
format: application/pdf
format: text/html
creator: Florian Mauffrey
creator: Alexandra Cucaita
creator: Philippe Constant
creator: Richard Villemur
subject: Environmental Sciences
subject: Microbiology
subject: Molecular Biology
subject: Biogeochemistry
description: doi:10.7717/peerj.4098
publisher: PeerJ Inc.
rights: © 2017 Mauffrey et al.
abstract: Background Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ) to nitrite ( ${\mathrm{NO}}_{2}^{-}$ NO 2 − ). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (N2O) reductase, suggesting that NO and N2O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. Methods Series of oxic and anoxic cultures of strain JAM1 were performed with N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − or sodium nitroprusside, and growth and N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − , ${\mathrm{NO}}_{2}^{-}$ NO 2 − and N2 concentrations were measured. Ammonium ( ${\mathrm{NH}}_{4}^{+}$ NH 4 + )-free cultures were also tested to assess the dynamics of N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − and ${\mathrm{NO}}_{2}^{-}$ NO 2 − . Isotopic labeling of N2O was performed in 15NH4+-amended cultures. Cultures with the JAM1ΔnarG1narG2 double mutant were performed to assess the involvement of the Nar systems on N2O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc-type nitric oxide reductase (cnorB1 and cnorB2) and nitrous oxide reductase (nosZ), and also nnrS and norR that encode NO-sensitive regulators. Results Strain JAM1 can reduce NO to N2O and N2O to N2 and can sustain growth under anoxic conditions by reducing N2O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase, ${\mathrm{NO}}_{3}^{-}$ NO 3 − -amended cultures produce N2O, representing up to 6% of the N-input. ${\mathrm{NO}}_{2}^{-}$ NO 2 − was shown …
bibliographic citation: Mauffrey et al. (2017) Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1. PeerJ 5:e4098 https://doi.org/10.7717/peerj.4098
date submitted: 2017-09-15
date accepted: 2017-11-06
issued: 2017-11-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mauffrey
  given name: Florian
author list: Agent
  family name: Cucaita
  given name: Alexandra
author list: Agent
  family name: Constant
  given name: Philippe
author list: Agent
  family name: Villemur
  given name: Richard
doi: 10.7717/peerj.4098
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-28
copyright: ©2017 Mauffrey et al.
attribution name: Mauffrey et al.

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