PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Nonspecific stress response to temperature increase in Gammarus lacustris Sars with respect to oxygen-limited thermal tolerance concept
items: Dramatic decline and limited recovery of a green crab (Carcinus maenas) population in the Minas Basin, Canada after the summer of 2013
items: Exome sequencing study of 20 patients with high myopia
items: Phylogeography of Swertia perennis in Europe based on cpDNA markers
items: Th2 cytokine bias induced by silver nanoparticles in peripheral blood mononuclear cells of common bottlenose dolphins (Tursiops truncatus)
items: https://peerj.com/articles/5558
items: Luciferin production and luciferase transcription in the bioluminescent copepod Metridia lucens
items: Urban waste disposal explains the distribution of Black Vultures (Coragyps atratus) in an Amazonian metropolis: management implications for birdstrikes and urban planning
items: Economic value of trees in the estate of the Harewood House stately home in the United Kingdom
items: Maxent estimation of aquatic Escherichia coli stream impairment

Nonspecific stress response to temperature increase in Gammarus lacustris Sars with respect to oxygen-limited thermal tolerance concept
type: item
type: AcademicArticle
description: The previously undescribed dynamics of the heat shock protein HSP70 and subsequent lipid peroxidation products have been assessed alongside lactate dehydrogenase activity for Gammarus lacustris Sars, an amphipod species from the saltwater Lake Shira (Republic of Khakassia). Individuals were exposed to a gradual temperature increase of 1 °C/hour (total exposure duration of 26 hours) starting from the mean annual temperature of their habitat (7 °C) up to 33 °C. A complex of biochemical reactions occurred when saltwater G. lactustris was exposed to the gradual changes in temperature. This was characterized by a decrease in lactate dehydrogenase activity and the launching of lipid peroxidation. The HSP70 level did not change significantly during the entire experiment. In agreement with the concept of oxygen-limited thermal tolerance, an accumulation of the most toxic lipid peroxides (triene conjugates and Schiff bases) in phospholipids occurred at the same time and temperature as the accumulation of lactate. The main criterion overriding the temperature threshold was, therefore, the transition to anaerobiosis, confirmed by the elevated lactate levels as observed in our previous associated study, and by the development of cellular stress, which was expressed by an accumulation of lipid peroxidation products. An earlier hypothesis, based on freshwater individuals of the same species, has been confirmed whereby the increased thermotolerance of G. lacustris from the saltwater lake was caused by differences in energy metabolism and energy supply of nonspecific cellular stress-response mechanisms. With the development of global climate change, these reactions could be advantageous for saltwater G. lacustris. The studied biochemical reactions can be used as biomarkers for the stress status of aquatic organisms when their habitat temperature changes.
format: application/pdf
format: text/html
creator: Kseniya Vereshchagina
creator: Elizaveta Kondrateva
creator: Denis Axenov-Gribanov
creator: Zhanna Shatilina
creator: Andrey Khomich
creator: Daria Bedulina
creator: Egor Zadereev
creator: Maxim Timofeyev
subject: Ecology
subject: Zoology
subject: Climate Change Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.5571
publisher: PeerJ Inc.
rights: © 2018 Vereshchagina et al.
abstract: The previously undescribed dynamics of the heat shock protein HSP70 and subsequent lipid peroxidation products have been assessed alongside lactate dehydrogenase activity for Gammarus lacustris Sars, an amphipod species from the saltwater Lake Shira (Republic of Khakassia). Individuals were exposed to a gradual temperature increase of 1 °C/hour (total exposure duration of 26 hours) starting from the mean annual temperature of their habitat (7 °C) up to 33 °C. A complex of biochemical reactions occurred when saltwater G. lactustris was exposed to the gradual changes in temperature. This was characterized by a decrease in lactate dehydrogenase activity and the launching of lipid peroxidation. The HSP70 level did not change significantly during the entire experiment. In agreement with the concept of oxygen-limited thermal tolerance, an accumulation of the most toxic lipid peroxides (triene conjugates and Schiff bases) in phospholipids occurred at the same time and temperature as the accumulation of lactate. The main criterion overriding the temperature threshold was, therefore, the transition to anaerobiosis, confirmed by the elevated lactate levels as observed in our previous associated study, and by the development of cellular stress, which was expressed by an accumulation of lipid peroxidation products. An earlier hypothesis, based on freshwater individuals of the same species, has been confirmed whereby the increased thermotolerance of G. lacustris from the saltwater lake was caused by differences in energy metabolism and energy supply of nonspecific cellular stress-response mechanisms. With the development of global climate change, these reactions could be advantageous for saltwater G. lacustris. The studied biochemical reactions can be used as biomarkers for the stress status of aquatic organisms when their habitat temperature changes.
bibliographic citation: Vereshchagina et al. (2018) Nonspecific stress response to temperature increase in Gammarus lacustris Sars with respect to oxygen-limited thermal tolerance concept. PeerJ 6:e5571 https://doi.org/10.7717/peerj.5571
date submitted: 2018-02-22
date accepted: 2018-08-14
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vereshchagina
  given name: Kseniya
author list: Agent
  family name: Kondrateva
  given name: Elizaveta
author list: Agent
  family name: Axenov-Gribanov
  given name: Denis
author list: Agent
  family name: Shatilina
  given name: Zhanna
author list: Agent
  family name: Khomich
  given name: Andrey
author list: Agent
  family name: Bedulina
  given name: Daria
author list: Agent
  family name: Zadereev
  given name: Egor
author list: Agent
  family name: Timofeyev
  given name: Maxim
doi: 10.7717/peerj.5571
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: ©2018 Vereshchagina et al.
attribution name: Vereshchagina et al.

Dramatic decline and limited recovery of a green crab (Carcinus maenas) population in the Minas Basin, Canada after the summer of 2013
type: item
type: AcademicArticle
description: This paper reports the results of a ten-year monitoring program of an Atlantic Canadian population of green crabs, Carcinus maenas, in the Minas Basin of the Bay of Fundy. Intertidal densities, sex and reproductive ratios, juvenile recruitment, subtidal catch-per-unit-effort (CPUE), and sizes of crabs in this population were recorded from 2008 to 2017. In 2013 intertidal densities, mean crab sizes, subtidal CPUE, and proportions of crabs mature and reproducing all dramatically decreased to all-time lows, and large crabs virtually disappeared from the population. From 2014 to 2017 the population partially recovered but remained in an altered state. Potential causes of interannual changes to this population were investigated by correlating intertidal densities to 257 monthly environmental variables and performing stepwise multiple regression analyses. Crab densities in a given year were best explained by potential settlement during the summer and the maximum sea-surface temperature during March of the same year. However, potential roles of other factors (e.g., autumn winds, summer temperatures, North Atlantic Oscillation index) could not be ruled out. Changes in abundances of other species in the area, particularly predators and prey of green crabs, have also been observed and present possible alternative causative agents that should be investigated. Populations of other marine species in the Gulf of Maine-Bay of Fundy region within which the Minas Basin is situated have also been reported to have undergone dramatic changes in and after 2013, suggesting the occurrence of some oceanographic event or regime shift in the region. Declines to the monitored crab population in this study may have resulted from this same 2013 event. These observations have implications for recruitment to marine populations in this region.
format: application/pdf
format: text/html
creator: Brady K. Quinn
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.5566
publisher: PeerJ Inc.
rights: © 2018 Quinn
abstract: This paper reports the results of a ten-year monitoring program of an Atlantic Canadian population of green crabs, Carcinus maenas, in the Minas Basin of the Bay of Fundy. Intertidal densities, sex and reproductive ratios, juvenile recruitment, subtidal catch-per-unit-effort (CPUE), and sizes of crabs in this population were recorded from 2008 to 2017. In 2013 intertidal densities, mean crab sizes, subtidal CPUE, and proportions of crabs mature and reproducing all dramatically decreased to all-time lows, and large crabs virtually disappeared from the population. From 2014 to 2017 the population partially recovered but remained in an altered state. Potential causes of interannual changes to this population were investigated by correlating intertidal densities to 257 monthly environmental variables and performing stepwise multiple regression analyses. Crab densities in a given year were best explained by potential settlement during the summer and the maximum sea-surface temperature during March of the same year. However, potential roles of other factors (e.g., autumn winds, summer temperatures, North Atlantic Oscillation index) could not be ruled out. Changes in abundances of other species in the area, particularly predators and prey of green crabs, have also been observed and present possible alternative causative agents that should be investigated. Populations of other marine species in the Gulf of Maine-Bay of Fundy region within which the Minas Basin is situated have also been reported to have undergone dramatic changes in and after 2013, suggesting the occurrence of some oceanographic event or regime shift in the region. Declines to the monitored crab population in this study may have resulted from this same 2013 event. These observations have implications for recruitment to marine populations in this region.
bibliographic citation: Quinn (2018) Dramatic decline and limited recovery of a green crab (Carcinus maenas) population in the Minas Basin, Canada after the summer of 2013. PeerJ 6:e5566 https://doi.org/10.7717/peerj.5566
date submitted: 2018-03-05
date accepted: 2018-08-13
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quinn
  given name: Brady K.
doi: 10.7717/peerj.5566
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: ©2018 Quinn
attribution name: Quinn

Exome sequencing study of 20 patients with high myopia
type: item
type: AcademicArticle
description: Background High myopia is a common ocular disease worldwide. To expand our current understanding of the genetic basis of high myopia, we carried out a whole exome sequencing (WES) study to identify potential causal gene mutations. Methods A total of 20 individuals with high myopia were exome sequenced. A novel filtering strategy combining phenotypes and functional impact of variants was applied to identify candidate genes by multi-step bioinformatics analyses. Network and enrichment analysis were employed to examine the biological pathways involved in the candidate genes. Results In 16 out of 20 patients, we identified 20 potential pathogenic gene variants for high myopia. A total of 18 variants were located in myopia-associated chromosomal regions. In addition to the novel mutations found in five known myopia genes (ADAMTS18, CSMD1, P3H2, RPGR, and SLC39A5), we also identified pathogenic variants in seven ocular disease genes (ABCA4, CEP290, HSPG2, PCDH15, SAG, SEMA4A, and USH2A) as novel candidate genes. The biological processes associated with vision were significantly enriched in our candidate genes, including visual perception, photoreceptor cell maintenance, retinoid metabolic process, and cellular response to zinc ion starvation. Discussion Systematic mutation analysis of candidate genes was performed using WES data, functional interaction (FI) network, Gene Ontology and pathway enrichment. FI network analysis revealed important network modules and regulator linker genes (EP300, CTNNB1) potentially related to high myopia development. Our study expanded the list of candidate genes associated with high myopia, which increased the genetic screening performance and provided implications for future studies on the molecular genetics of myopia.
format: application/pdf
format: text/html
creator: Ling Wan
creator: Boling Deng
creator: Zhengzheng Wu
creator: Xiaoming Chen
subject: Bioinformatics
subject: Computational Biology
subject: Genetics
subject: Genomics
subject: Translational Medicine
description: doi:10.7717/peerj.5552
publisher: PeerJ Inc.
rights: © 2018 Wan et al.
abstract: Background High myopia is a common ocular disease worldwide. To expand our current understanding of the genetic basis of high myopia, we carried out a whole exome sequencing (WES) study to identify potential causal gene mutations. Methods A total of 20 individuals with high myopia were exome sequenced. A novel filtering strategy combining phenotypes and functional impact of variants was applied to identify candidate genes by multi-step bioinformatics analyses. Network and enrichment analysis were employed to examine the biological pathways involved in the candidate genes. Results In 16 out of 20 patients, we identified 20 potential pathogenic gene variants for high myopia. A total of 18 variants were located in myopia-associated chromosomal regions. In addition to the novel mutations found in five known myopia genes (ADAMTS18, CSMD1, P3H2, RPGR, and SLC39A5), we also identified pathogenic variants in seven ocular disease genes (ABCA4, CEP290, HSPG2, PCDH15, SAG, SEMA4A, and USH2A) as novel candidate genes. The biological processes associated with vision were significantly enriched in our candidate genes, including visual perception, photoreceptor cell maintenance, retinoid metabolic process, and cellular response to zinc ion starvation. Discussion Systematic mutation analysis of candidate genes was performed using WES data, functional interaction (FI) network, Gene Ontology and pathway enrichment. FI network analysis revealed important network modules and regulator linker genes (EP300, CTNNB1) potentially related to high myopia development. Our study expanded the list of candidate genes associated with high myopia, which increased the genetic screening performance and provided implications for future studies on the molecular genetics of myopia.
bibliographic citation: Wan et al. (2018) Exome sequencing study of 20 patients with high myopia. PeerJ 6:e5552 https://doi.org/10.7717/peerj.5552
date submitted: 2018-06-17
date accepted: 2018-08-07
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wan
  given name: Ling
author list: Agent
  family name: Deng
  given name: Boling
author list: Agent
  family name: Wu
  given name: Zhengzheng
author list: Agent
  family name: Chen
  given name: Xiaoming
doi: 10.7717/peerj.5552
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: © 2018 Wan et al.
attribution name: Wan et al.

Phylogeography of Swertia perennis in Europe based on cpDNA markers
type: item
type: AcademicArticle
description: Background Swertia perennis(Gentianaceae) is a perennial diploid and clonal plant species that is discontinuously distributed in peat bogs in the mountains of Europe, Asia and North America as well as in the lowlands of Europe. The current geographical dispersion of S. perennis is probably the result of quaternary climatic changes that have played an important role in determining the distribution of Swertia and other plant and animal species. Methods In this study we used molecular techniques and combined data from chloroplast DNA markers (trnLF region and trnH-psbA spacer) to elucidate the phylogeography of S. perennis in Europe. Plants were collected from 28 populations in different locations in the lowlands and mountainous areas of Europe (e.g., the Carpathians, Sudetes, Bohemian Forest and Alps). cDNA was analysed to detect the genetic relationship between specimens from different locations. Results A total of 20 haplotypes were identified across the dataset. They were characterised by a high level of genetic variability but showed a lack of phylogeographical structure. This pattern may be the result of repeated recolonization and expansion from several areas. Such genetic differentiation may also be attributed to the relatively long-term isolation of S. perennis in Pleistocene refugia in Europe, which resulted in independent separation of different cpDNA phylogenetic lineages and variation in the nucleotide composition of cpDNA. Discussion The lack of strong phylogeographical structure makes it impossible to indicate the centre of haplotype diversity; however, refugia located in the Carpathians, Sudetes or Alps are the most probable sites where S. perennis existed in Europe. This lack of structure may also indicate a high level of gene flow in times when the landscape and fen systems were not fragmented in numerous geographically-isolated populations. This makes it difficult to speculate about the relationships between Asiatic and European plant populations and…
format: application/pdf
format: text/html
creator: Jacek Urbaniak
creator: Paweł Kwiatkowski
creator: Paweł Pawlikowski
subject: Biogeography
subject: Conservation Biology
subject: Molecular Biology
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.5512
publisher: PeerJ Inc.
rights: © 2018 Urbaniak et al.
abstract: Background Swertia perennis(Gentianaceae) is a perennial diploid and clonal plant species that is discontinuously distributed in peat bogs in the mountains of Europe, Asia and North America as well as in the lowlands of Europe. The current geographical dispersion of S. perennis is probably the result of quaternary climatic changes that have played an important role in determining the distribution of Swertia and other plant and animal species. Methods In this study we used molecular techniques and combined data from chloroplast DNA markers (trnLF region and trnH-psbA spacer) to elucidate the phylogeography of S. perennis in Europe. Plants were collected from 28 populations in different locations in the lowlands and mountainous areas of Europe (e.g., the Carpathians, Sudetes, Bohemian Forest and Alps). cDNA was analysed to detect the genetic relationship between specimens from different locations. Results A total of 20 haplotypes were identified across the dataset. They were characterised by a high level of genetic variability but showed a lack of phylogeographical structure. This pattern may be the result of repeated recolonization and expansion from several areas. Such genetic differentiation may also be attributed to the relatively long-term isolation of S. perennis in Pleistocene refugia in Europe, which resulted in independent separation of different cpDNA phylogenetic lineages and variation in the nucleotide composition of cpDNA. Discussion The lack of strong phylogeographical structure makes it impossible to indicate the centre of haplotype diversity; however, refugia located in the Carpathians, Sudetes or Alps are the most probable sites where S. perennis existed in Europe. This lack of structure may also indicate a high level of gene flow in times when the landscape and fen systems were not fragmented in numerous geographically-isolated populations. This makes it difficult to speculate about the relationships between Asiatic and European plant populations and…
bibliographic citation: Urbaniak et al. (2018) Phylogeography of Swertia perennis in Europe based on cpDNA markers. PeerJ 6:e5512 https://doi.org/10.7717/peerj.5512
date submitted: 2018-03-06
date accepted: 2018-08-03
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Urbaniak
  given name: Jacek
author list: Agent
  family name: Kwiatkowski
  given name: Paweł
author list: Agent
  family name: Pawlikowski
  given name: Paweł
doi: 10.7717/peerj.5512
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: ©2018 Urbaniak et al.
attribution name: Urbaniak et al.

Th2 cytokine bias induced by silver nanoparticles in peripheral blood mononuclear cells of common bottlenose dolphins (Tursiops truncatus)
type: item
type: AcademicArticle
description: Background Silver nanoparticles (AgNPs) have been widely used in many commercial products due to their excellent antibacterial ability. The AgNPs are released into the environment, gradually accumulate in the ocean, and may affect animals at high trophic levels, such as cetaceans and humans, via the food chain. Hence, the negative health impacts caused by AgNPs in cetaceans are of concern. Cytokines play a major role in the modulation of immune system and can be classified into two types: Th1 and Th2. Th1/Th2 balance can be evaluated by the ratios of their polarizing cytokines (i.e., interferon [IFN]-γ/Interleukin [IL]-4), and animals with imbalanced Th1/Th2 response may become more susceptible to certain kinds of infection. Therefore, the present study evaluated the in vitro cytokine responses of cetacean peripheral blood mononuclear cells (cPBMCs) to 20 nm citrate-AgNPs (C-AgNP20) by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Methods Blood samples were collected from six captive common bottlenose dolphins (Tursiops truncatus). The cPBMCs were isolated and utilized for evaluating the in vitro cytokine responses. The cytokines evaluated included IL-2, IL-4, IL-10, IL-12, interferon (IFN)-γ, and tumor necrosis factor (TNF)-α. The geometric means of two housekeeping genes (HKGs), glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and β2-microglobulin (B2M), of each sample were determined and used to normalize the mRNA expression levels of target genes. Results The ratio of late apoptotic/necrotic cells of cPBMCs significantly increased with or without concanavalin A (ConA) stimulation after 24 h of 10 µg/ml C-AgNP20 treatment. At 4 h of culture, the mRNA expression level of IL-10 was significantly decreased with 1 µg/ml C-AgNP20 treatment. At 24 h of culture with 1 µg/ml C-AgNP20, the mRNA expression levels of all cytokines were significantly decreased, with the exceptions of IL-4 and IL-10. The IFN-γ/IL-4 ratio was significantly decreased a…
format: application/pdf
format: text/html
creator: Wen-Ta Li
creator: Lei-Ya Wang
creator: Hui-Wen Chang
creator: Wei-Cheng Yang
creator: Chieh Lo
creator: Victor Fei Pang
creator: Meng-Hsien Chen
creator: Chian-Ren Jeng
subject: Toxicology
subject: Veterinary Medicine
subject: Immunology
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.5432
publisher: PeerJ Inc.
rights: © 2018 Li et al.
abstract: Background Silver nanoparticles (AgNPs) have been widely used in many commercial products due to their excellent antibacterial ability. The AgNPs are released into the environment, gradually accumulate in the ocean, and may affect animals at high trophic levels, such as cetaceans and humans, via the food chain. Hence, the negative health impacts caused by AgNPs in cetaceans are of concern. Cytokines play a major role in the modulation of immune system and can be classified into two types: Th1 and Th2. Th1/Th2 balance can be evaluated by the ratios of their polarizing cytokines (i.e., interferon [IFN]-γ/Interleukin [IL]-4), and animals with imbalanced Th1/Th2 response may become more susceptible to certain kinds of infection. Therefore, the present study evaluated the in vitro cytokine responses of cetacean peripheral blood mononuclear cells (cPBMCs) to 20 nm citrate-AgNPs (C-AgNP20) by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Methods Blood samples were collected from six captive common bottlenose dolphins (Tursiops truncatus). The cPBMCs were isolated and utilized for evaluating the in vitro cytokine responses. The cytokines evaluated included IL-2, IL-4, IL-10, IL-12, interferon (IFN)-γ, and tumor necrosis factor (TNF)-α. The geometric means of two housekeeping genes (HKGs), glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and β2-microglobulin (B2M), of each sample were determined and used to normalize the mRNA expression levels of target genes. Results The ratio of late apoptotic/necrotic cells of cPBMCs significantly increased with or without concanavalin A (ConA) stimulation after 24 h of 10 µg/ml C-AgNP20 treatment. At 4 h of culture, the mRNA expression level of IL-10 was significantly decreased with 1 µg/ml C-AgNP20 treatment. At 24 h of culture with 1 µg/ml C-AgNP20, the mRNA expression levels of all cytokines were significantly decreased, with the exceptions of IL-4 and IL-10. The IFN-γ/IL-4 ratio was significantly decreased a…
bibliographic citation: Li et al. (2018) Th2 cytokine bias induced by silver nanoparticles in peripheral blood mononuclear cells of common bottlenose dolphins (Tursiops truncatus). PeerJ 6:e5432 https://doi.org/10.7717/peerj.5432
date submitted: 2018-02-14
date accepted: 2018-07-20
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Wen-Ta
author list: Agent
  family name: Wang
  given name: Lei-Ya
author list: Agent
  family name: Chang
  given name: Hui-Wen
author list: Agent
  family name: Yang
  given name: Wei-Cheng
author list: Agent
  family name: Lo
  given name: Chieh
author list: Agent
  family name: Pang
  given name: Victor Fei
author list: Agent
  family name: Chen
  given name: Meng-Hsien
author list: Agent
  family name: Jeng
  given name: Chian-Ren
doi: 10.7717/peerj.5432
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: ©2018 Li et al.
attribution name: Li et al.

https://peerj.com/articles/5558
type: item
type: AcademicArticle
title: Lessepsian migration and parasitism: richness, prevalence and intensity of parasites in the invasive fish Sphyraena chrysotaenia compared to its native congener Sphyraena sphyraena in Tunisian coastal waters
description: Background Parasites can play various roles in the invasion of non-native species, but these are still understudied in marine ecosystems. This also applies to invasions from the Red Sea to the Mediterranean Sea via the Suez Canal, the so-called Lessepsian migration. In this study, we investigated the role of parasites in the invasion of the Lessepsian migrant Sphyraena chrysotaenia in the Tunisian Mediterranean Sea. Methods We compared metazoan parasite richness, prevalence and intensity of S. chrysotaenia (Perciformes: Sphyraenidae) with infections in its native congener Sphyraena sphyraena by sampling these fish species at seven locations along the Tunisian coast. Additionally, we reviewed the literature to identify native and invasive parasite species recorded in these two hosts. Results Our results suggest the loss of at least two parasite species of the invasive fish. At the same time, the Lessepsian migrant has co-introduced three parasite species during the initial migration to the Mediterranean Sea, that are assumed to originate from the Red Sea of which only one parasite species has been reported during the spread to Tunisian waters. In addition, we found that the invasive fish has acquired six parasite species that are native in the Mediterranean Sea. However, parasite richness, prevalence and intensity were overall much lower in the invasive compared to the native fish host in the Mediterranean Sea. Discussion These results suggest that the Lessepsian migrant may affect native fish hosts by potentially altering the dynamics of native and invasive parasite-host interactions via parasite release, parasite co-introduction and parasite acquisition. They further suggest that the lower infection levels in the invasive fish may result in a competitive advantage over native fish hosts (enemy release hypothesis). This study demonstrates that cross-species comparisons of parasite infection levels are a valuable tool to identify the different roles of parasites in t…
format: application/pdf
format: text/html
creator: Wiem Boussellaa
creator: Lassad Neifar
creator: M. Anouk Goedknegt
creator: David W. Thieltges
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Parasitology
subject: Taxonomy
description: doi:10.7717/peerj.5558
publisher: PeerJ Inc.
rights: © 2018 Boussellaa et al.
abstract: Background Parasites can play various roles in the invasion of non-native species, but these are still understudied in marine ecosystems. This also applies to invasions from the Red Sea to the Mediterranean Sea via the Suez Canal, the so-called Lessepsian migration. In this study, we investigated the role of parasites in the invasion of the Lessepsian migrant Sphyraena chrysotaenia in the Tunisian Mediterranean Sea. Methods We compared metazoan parasite richness, prevalence and intensity of S. chrysotaenia (Perciformes: Sphyraenidae) with infections in its native congener Sphyraena sphyraena by sampling these fish species at seven locations along the Tunisian coast. Additionally, we reviewed the literature to identify native and invasive parasite species recorded in these two hosts. Results Our results suggest the loss of at least two parasite species of the invasive fish. At the same time, the Lessepsian migrant has co-introduced three parasite species during the initial migration to the Mediterranean Sea, that are assumed to originate from the Red Sea of which only one parasite species has been reported during the spread to Tunisian waters. In addition, we found that the invasive fish has acquired six parasite species that are native in the Mediterranean Sea. However, parasite richness, prevalence and intensity were overall much lower in the invasive compared to the native fish host in the Mediterranean Sea. Discussion These results suggest that the Lessepsian migrant may affect native fish hosts by potentially altering the dynamics of native and invasive parasite-host interactions via parasite release, parasite co-introduction and parasite acquisition. They further suggest that the lower infection levels in the invasive fish may result in a competitive advantage over native fish hosts (enemy release hypothesis). This study demonstrates that cross-species comparisons of parasite infection levels are a valuable tool to identify the different roles of parasites in t…
bibliographic citation: Boussellaa et al. (2018) Lessepsian migration and parasitism: richness, prevalence and intensity of parasites in the invasive fish Sphyraena chrysotaenia compared to its native congener Sphyraena sphyraena in Tunisian coastal waters. PeerJ 6:e5558 https://doi.org/10.7717/peerj.5558
date submitted: 2018-03-13
date accepted: 2018-08-07
issued: 2018-09-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boussellaa
  given name: Wiem
author list: Agent
  family name: Neifar
  given name: Lassad
author list: Agent
  family name: Goedknegt
  given name: M. Anouk
author list: Agent
  family name: Thieltges
  given name: David W.
doi: 10.7717/peerj.5558
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-14
copyright: ©2018 Boussellaa et al.
attribution name: Boussellaa et al.

Luciferin production and luciferase transcription in the bioluminescent copepod Metridia lucens
type: item
type: AcademicArticle
description: Bioluminescent copepods are often the most abundant marine zooplankton and play critical roles in oceanic food webs. Metridia copepods exhibit particularly bright bioluminescence, and the molecular basis of their light production has just recently begun to be explored. Here we add to this body of work by transcriptomically profiling Metridia lucens, a common species found in temperate, northern, and southern latitudes. In this previously molecularly-uncharacterized species, we find the typical luciferase paralog gene set found in Metridia. More surprisingly, we recover noteworthy putative luciferase sequences that had not been described from Metridia species, indicating that bioluminescence produced by these copepods may be more complex than previously known. This includes another copepod luciferase, as well as one from a shrimp. Furthermore, feeding experiments using mass spectrometry and 13C labelled L-tyrosine and L-phenylalanine firmly establish that M. lucens produces its own coelenterazine luciferin rather than acquiring it through diet. This coelenterazine synthesis has only been directly confirmed in one other copepod species.
format: application/pdf
format: text/html
creator: Michael Tessler
creator: Jean P. Gaffney
creator: Jason M. Crawford
creator: Eric Trautman
creator: Nehaben A. Gujarati
creator: Philip Alatalo
creator: Vincent A. Pieribone
creator: David F. Gruber
subject: Biochemistry
subject: Evolutionary Studies
subject: Genomics
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.5506
publisher: PeerJ Inc.
rights: © 2018 Tessler et al.
abstract: Bioluminescent copepods are often the most abundant marine zooplankton and play critical roles in oceanic food webs. Metridia copepods exhibit particularly bright bioluminescence, and the molecular basis of their light production has just recently begun to be explored. Here we add to this body of work by transcriptomically profiling Metridia lucens, a common species found in temperate, northern, and southern latitudes. In this previously molecularly-uncharacterized species, we find the typical luciferase paralog gene set found in Metridia. More surprisingly, we recover noteworthy putative luciferase sequences that had not been described from Metridia species, indicating that bioluminescence produced by these copepods may be more complex than previously known. This includes another copepod luciferase, as well as one from a shrimp. Furthermore, feeding experiments using mass spectrometry and 13C labelled L-tyrosine and L-phenylalanine firmly establish that M. lucens produces its own coelenterazine luciferin rather than acquiring it through diet. This coelenterazine synthesis has only been directly confirmed in one other copepod species.
bibliographic citation: Tessler et al. (2018) Luciferin production and luciferase transcription in the bioluminescent copepod Metridia lucens. PeerJ 6:e5506 https://doi.org/10.7717/peerj.5506
date submitted: 2018-05-01
date accepted: 2018-07-29
issued: 2018-09-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tessler
  given name: Michael
author list: Agent
  family name: Gaffney
  given name: Jean P.
author list: Agent
  family name: Crawford
  given name: Jason M.
author list: Agent
  family name: Trautman
  given name: Eric
author list: Agent
  family name: Gujarati
  given name: Nehaben A.
author list: Agent
  family name: Alatalo
  given name: Philip
author list: Agent
  family name: Pieribone
  given name: Vincent A.
author list: Agent
  family name: Gruber
  given name: David F.
doi: 10.7717/peerj.5506
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-14
copyright: ©2018 Tessler et al.
attribution name: Tessler et al.

Urban waste disposal explains the distribution of Black Vultures (Coragyps atratus) in an Amazonian metropolis: management implications for birdstrikes and urban planning
type: item
type: AcademicArticle
description: Collision rates between aircraft and birds have been rising worldwide. The increases in both air traffic and population sizes of large-bodied birds in cities lacking urban planning result in human-wildlife conflicts, economic loss and even lethal casualties. Black Vultures (Coragyps atratus) represent the most hazardous bird to Brazilian civil and military aviation on the basis of their flight behavior, body mass and consequently physical damage to aircraft following collisions. This study investigated how storage apparatus and type of organic residue discarded in public street markets modulate the spatial distribution and abundance of urban Black Vultures in the largest city in the Amazon (Manaus, Brazil). We estimated Black Vulture abundance in relation to the type of solid human waste (animal or plant), the type of waste storage containers and market sizes in terms of the number of vendor stalls at 20 public markets. We also visually quantified the abundance of Black Vultures in urban markets in relation to air traffic. Our results suggest that urban solid waste storage procedures currently used (or the lack thereof) are related to the occurrence and abundance of Black Vultures. Moreover, storage type and the proportion of animal protein (red meat and fish) within rubbish bins directly affects foraging aggregations in vultures. We recommend that policymakers should invest more efforts in building larger and more resistant closable waste containers to avoid organic solid waste exposure. We also identified five outdoor markets as urgent priorities to improve waste disposal. Finally, our waste management guidelines would not only reduce aviation collision risks but also benefit human health and well-being in most cities.
format: application/pdf
format: text/html
creator: Giase M. de Araujo
creator: Carlos A. Peres
creator: Fabricio B. Baccaro
creator: Rafael S. Guerta
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Coupled Natural and Human Systems
subject: Population Biology
description: doi:10.7717/peerj.5491
publisher: PeerJ Inc.
rights: © 2018 Araujo et al.
abstract: Collision rates between aircraft and birds have been rising worldwide. The increases in both air traffic and population sizes of large-bodied birds in cities lacking urban planning result in human-wildlife conflicts, economic loss and even lethal casualties. Black Vultures (Coragyps atratus) represent the most hazardous bird to Brazilian civil and military aviation on the basis of their flight behavior, body mass and consequently physical damage to aircraft following collisions. This study investigated how storage apparatus and type of organic residue discarded in public street markets modulate the spatial distribution and abundance of urban Black Vultures in the largest city in the Amazon (Manaus, Brazil). We estimated Black Vulture abundance in relation to the type of solid human waste (animal or plant), the type of waste storage containers and market sizes in terms of the number of vendor stalls at 20 public markets. We also visually quantified the abundance of Black Vultures in urban markets in relation to air traffic. Our results suggest that urban solid waste storage procedures currently used (or the lack thereof) are related to the occurrence and abundance of Black Vultures. Moreover, storage type and the proportion of animal protein (red meat and fish) within rubbish bins directly affects foraging aggregations in vultures. We recommend that policymakers should invest more efforts in building larger and more resistant closable waste containers to avoid organic solid waste exposure. We also identified five outdoor markets as urgent priorities to improve waste disposal. Finally, our waste management guidelines would not only reduce aviation collision risks but also benefit human health and well-being in most cities.
bibliographic citation: Araujo et al. (2018) Urban waste disposal explains the distribution of Black Vultures (Coragyps atratus) in an Amazonian metropolis: management implications for birdstrikes and urban planning. PeerJ 6:e5491 https://doi.org/10.7717/peerj.5491
date submitted: 2018-03-13
date accepted: 2018-07-30
issued: 2018-09-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Araujo
  given name: Giase M. de
author list: Agent
  family name: Peres
  given name: Carlos A.
author list: Agent
  family name: Baccaro
  given name: Fabricio B.
author list: Agent
  family name: Guerta
  given name: Rafael S.
doi: 10.7717/peerj.5491
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-14
copyright: ©2018 Araujo et al.
attribution name: Araujo et al.

Economic value of trees in the estate of the Harewood House stately home in the United Kingdom
type: item
type: AcademicArticle
description: The estates of stately homes or manor houses are an untapped resource for assessing the ecosystem services provided by trees. Many of these estates have large collections of trees with clear value in terms of carbon storage, runoff prevention, and pollution removal along with additional benefits to biodiversity and human health. The estate of Harewood House in North Yorkshire represents an ideal example of such a stately home with a mixture of parkland and more formally planted gardens. The trees in each type of garden were analysed for height, diameter at breast height and light exposure. The data were then processed in iTrees software to generate economic benefits for each tree in both gardens. The analysis found that the larger North Front parkland garden had greater total benefits but the more densely planted formal West Garden had the greater per hectare value. In total, the trees on Harewood House estate are estimated to provide approximately £29 million in ecosystem service benefits. This study is the first to analyse the trees of stately homes for economic benefits and highlights that the trees are a valuable commodity for the estates. This should be considered in future planning and management of such estates.
format: application/pdf
format: text/html
creator: Julie Peacock
creator: Joey Ting
creator: Karen L. Bacon
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.5411
publisher: PeerJ Inc.
rights: © 2018 Peacock et al.
abstract: The estates of stately homes or manor houses are an untapped resource for assessing the ecosystem services provided by trees. Many of these estates have large collections of trees with clear value in terms of carbon storage, runoff prevention, and pollution removal along with additional benefits to biodiversity and human health. The estate of Harewood House in North Yorkshire represents an ideal example of such a stately home with a mixture of parkland and more formally planted gardens. The trees in each type of garden were analysed for height, diameter at breast height and light exposure. The data were then processed in iTrees software to generate economic benefits for each tree in both gardens. The analysis found that the larger North Front parkland garden had greater total benefits but the more densely planted formal West Garden had the greater per hectare value. In total, the trees on Harewood House estate are estimated to provide approximately £29 million in ecosystem service benefits. This study is the first to analyse the trees of stately homes for economic benefits and highlights that the trees are a valuable commodity for the estates. This should be considered in future planning and management of such estates.
bibliographic citation: Peacock et al. (2018) Economic value of trees in the estate of the Harewood House stately home in the United Kingdom. PeerJ 6:e5411 https://doi.org/10.7717/peerj.5411
date submitted: 2018-04-06
date accepted: 2018-07-30
issued: 2018-09-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peacock
  given name: Julie
author list: Agent
  family name: Ting
  given name: Joey
author list: Agent
  family name: Bacon
  given name: Karen L.
doi: 10.7717/peerj.5411
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-14
copyright: ©2018 Peacock et al.
attribution name: Peacock et al.

Maxent estimation of aquatic Escherichia coli stream impairment
type: item
type: AcademicArticle
description: Background The leading cause of surface water impairment in United States’ rivers and streams is pathogen contamination. Although use of fecal indicators has reduced human health risk, current approaches to identify and reduce exposure can be improved. One important knowledge gap within exposure assessment is characterization of complex fate and transport processes of fecal pollution. Novel modeling processes can inform watershed decision-making to improve exposure assessment. Methods We used the ecological model, Maxent, and the fecal indicator bacterium Escherichia coli to identify environmental factors associated with surface water impairment. Samples were collected August, November, February, and May for 8 years on Sinking Creek in Northeast Tennessee and analyzed for 10 water quality parameters and E. coli concentrations. Univariate and multivariate models estimated probability of impairment given the water quality parameters. Model performance was assessed using area under the receiving operating characteristic (AUC) and prediction accuracy, defined as the model’s ability to predict both true positives (impairment) and true negatives (compliance). Univariate models generated action values, or environmental thresholds, to indicate potential E. coli impairment based on a single parameter. Multivariate models predicted probability of impairment given a suite of environmental variables, and jack-knife sensitivity analysis removed unresponsive variables to elicit a set of the most responsive parameters. Results Water temperature univariate models performed best as indicated by AUC, but alkalinity models were the most accurate at correctly classifying impairment. Sensitivity analysis revealed that models were most sensitive to removal of specific conductance. Other sensitive variables included water temperature, dissolved oxygen, discharge, and NO3. The removal of dissolved oxygen improved model performance based on testing AUC, justifying development of two optimiz…
format: application/pdf
format: text/html
creator: Dennis Gilfillan
creator: Timothy A. Joyner
creator: Phillip Scheuerman
subject: Microbiology
subject: Public Health
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.5610
publisher: PeerJ Inc.
rights: © 2018 Gilfillan et al.
abstract: Background The leading cause of surface water impairment in United States’ rivers and streams is pathogen contamination. Although use of fecal indicators has reduced human health risk, current approaches to identify and reduce exposure can be improved. One important knowledge gap within exposure assessment is characterization of complex fate and transport processes of fecal pollution. Novel modeling processes can inform watershed decision-making to improve exposure assessment. Methods We used the ecological model, Maxent, and the fecal indicator bacterium Escherichia coli to identify environmental factors associated with surface water impairment. Samples were collected August, November, February, and May for 8 years on Sinking Creek in Northeast Tennessee and analyzed for 10 water quality parameters and E. coli concentrations. Univariate and multivariate models estimated probability of impairment given the water quality parameters. Model performance was assessed using area under the receiving operating characteristic (AUC) and prediction accuracy, defined as the model’s ability to predict both true positives (impairment) and true negatives (compliance). Univariate models generated action values, or environmental thresholds, to indicate potential E. coli impairment based on a single parameter. Multivariate models predicted probability of impairment given a suite of environmental variables, and jack-knife sensitivity analysis removed unresponsive variables to elicit a set of the most responsive parameters. Results Water temperature univariate models performed best as indicated by AUC, but alkalinity models were the most accurate at correctly classifying impairment. Sensitivity analysis revealed that models were most sensitive to removal of specific conductance. Other sensitive variables included water temperature, dissolved oxygen, discharge, and NO3. The removal of dissolved oxygen improved model performance based on testing AUC, justifying development of two optimiz…
bibliographic citation: Gilfillan et al. (2018) Maxent estimation of aquatic Escherichia coli stream impairment. PeerJ 6:e5610 https://doi.org/10.7717/peerj.5610
date submitted: 2018-03-08
date accepted: 2018-08-20
issued: 2018-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gilfillan
  given name: Dennis
author list: Agent
  family name: Joyner
  given name: Timothy A.
author list: Agent
  family name: Scheuerman
  given name: Phillip
doi: 10.7717/peerj.5610
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-13
copyright: ©2018 Gilfillan et al.
attribution name: Gilfillan et al.

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