PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: https://peerj.com/articles/4751
items: Citizen science data suggest that a novel rig improves landing rate and reduces injury and handling time in recreational angling with artificial lures in Baltic pike (Esox lucius)
items: Perinatal specimens of Maiasaura from the Upper Cretaceous of Montana (USA): insights into the early ontogeny of saurolophine hadrosaurid dinosaurs
items: Comparing the catch composition, profitability and discard survival from different trammel net designs targeting common spiny lobster (Palinurus elephas) in a Mediterranean fishery
items: Identification and expression analysis of cytokinin metabolic genes IPTs, CYP735A and CKXs in the biofuel plant Jatropha curcas
items: Geographical variation in colour of female threespine stickleback (Gasterosteus aculeatus)
items: Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines
items: Genetic inactivation of alpha-synuclein affects embryonic development of dopaminergic neurons of the substantia nigra, but not the ventral tegmental area, in mouse brain
items: Novel, non-symbiotic isolates of Neorhizobium from a dryland agricultural soil
items: Pollution of the sediments of the coastal zone of the Sambia Peninsula and the Curonian Spit (Southeastern Baltic Sea)

https://peerj.com/articles/4751
type: item
type: AcademicArticle
title: Greenland shark (Somniosus microcephalus) feeding behavior on static fishing gear, effect of SMART (Selective Magnetic and Repellent-Treated) hook deterrent technology, and factors influencing entanglement in bottom longlines
description: The Greenland Shark (Somniosus microcephalus) is the most common bycatch in the Greenland halibut (Reinhardtius hippoglossoides) bottom longline fishery in Cumberland Sound, Canada. Historically, this inshore fishery has been prosecuted through the ice during winter but winter storms and unpredictable landfast ice conditions since the mid-1990s have led to interest in developing a summer fishery during the ice-free season. However, bycatch of Greenland shark was found to increase substantially with 570 sharks captured during an experimental Greenland halibut summer fishery (i.e., mean of 6.3 sharks per 1,000 hooks set) and mortality was reported to be about 50% due in part to fishers killing sharks that were severely entangled in longline gear. This study investigated whether the SMART (Selective Magnetic and Repellent-Treated) hook technology is a practical deterrent to Greenland shark predation and subsequent bycatch on bottom longlines. Greenland shark feeding behavior, feeding kinematics, and variables affecting entanglement/disentanglement and release are also described. The SMART hook failed to deter Greenland shark predation, i.e., all sharks were captured on SMART hooks, some with more than one SMART hook in their jaw. Moreover, recently captured Greenland sharks did not exhibit a behavioral response to SMART hooks. In situ observations of Greenland shark feeding show that this species uses a powerful inertial suction mode of feeding and was able to draw bait into the mouth from a distance of 25–35 cm. This method of feeding is suggested to negate the potential deterrent effects of electropositive metal and magnetic alloy substitutions to the SMART hook technology. The number of hooks entangled by a Greenland shark and time to disentangle and live-release a shark was found to increase with body length.
format: application/pdf
format: text/html
creator: Scott M. Grant
creator: Rennie Sullivan
creator: Kevin J. Hedges
subject: Animal Behavior
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.4751
publisher: PeerJ Inc.
rights: © 2018 Grant et al.
abstract: The Greenland Shark (Somniosus microcephalus) is the most common bycatch in the Greenland halibut (Reinhardtius hippoglossoides) bottom longline fishery in Cumberland Sound, Canada. Historically, this inshore fishery has been prosecuted through the ice during winter but winter storms and unpredictable landfast ice conditions since the mid-1990s have led to interest in developing a summer fishery during the ice-free season. However, bycatch of Greenland shark was found to increase substantially with 570 sharks captured during an experimental Greenland halibut summer fishery (i.e., mean of 6.3 sharks per 1,000 hooks set) and mortality was reported to be about 50% due in part to fishers killing sharks that were severely entangled in longline gear. This study investigated whether the SMART (Selective Magnetic and Repellent-Treated) hook technology is a practical deterrent to Greenland shark predation and subsequent bycatch on bottom longlines. Greenland shark feeding behavior, feeding kinematics, and variables affecting entanglement/disentanglement and release are also described. The SMART hook failed to deter Greenland shark predation, i.e., all sharks were captured on SMART hooks, some with more than one SMART hook in their jaw. Moreover, recently captured Greenland sharks did not exhibit a behavioral response to SMART hooks. In situ observations of Greenland shark feeding show that this species uses a powerful inertial suction mode of feeding and was able to draw bait into the mouth from a distance of 25–35 cm. This method of feeding is suggested to negate the potential deterrent effects of electropositive metal and magnetic alloy substitutions to the SMART hook technology. The number of hooks entangled by a Greenland shark and time to disentangle and live-release a shark was found to increase with body length.
bibliographic citation: Grant et al. (2018) Greenland shark (Somniosus microcephalus) feeding behavior on static fishing gear, effect of SMART (Selective Magnetic and Repellent-Treated) hook deterrent technology, and factors influencing entanglement in bottom longlines. PeerJ 6:e4751 https://doi.org/10.7717/peerj.4751
date submitted: 2017-12-01
date accepted: 2018-04-22
issued: 2018-05-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grant
  given name: Scott M.
author list: Agent
  family name: Sullivan
  given name: Rennie
author list: Agent
  family name: Hedges
  given name: Kevin J.
doi: 10.7717/peerj.4751
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-17
copyright: © 2018 Grant et al.
attribution name: Grant et al.

Citizen science data suggest that a novel rig improves landing rate and reduces injury and handling time in recreational angling with artificial lures in Baltic pike (Esox lucius)
type: item
type: AcademicArticle
description: The optimal terminal gear in hook-and-line recreational fishing maximizes landing rates and minimizes injury to the fish because some fish will be released after capture. We designed a novel rig configuration in artificial lure fishing for top predators and examined its effectiveness in angling for Baltic northern pike (Esox lucius) using a citizen science approach based on observational data collected from volunteer anglers in the field. The novel rig included two changes to traditional rig designs common to artificial lure angling. First, hooks were mounted in a way giving better hook exposure and eliminating lever-arm effects from the lure to the hooks once a fish is hooked. This construction allowed the second change, being a shift to hooks 4–5 sizes smaller than those used on traditional hook mounts. We analysed observational data collected by volunteer anglers using either the novel rig or a standard rig mount in two types of artificial lures (softbait and hardbait) of the same size (about 17 cm). Using N = 768 pike contacts as input data, we showed the landing rates of pike targeted with artificial lures significantly and substantially increased from 45% with normal-rigs to 85% when the same lure types were fished with the novel rig configuration. Lure type and water temperature had no effects on landing rates. Moreover, hardbaits on normal-rigs produced significantly more injury, bleeding and elevated unhooking time compared to fish captured on hardbaits with release-rigs. We conclude that simple changes to traditional hook sizes and mounts in lure fishing may benefit both anglers and the fishes that are to be released and that citizen science projects with volunteer anglers are able to provide good data in proof-of-concept studies. Further experimental studies are needed to differentiate hook size from hook mount effects because both variables were confounded in the results of the observational data presented here.
format: application/pdf
format: text/html
creator: Jens Jakob Bursell
creator: Robert Arlinghaus
subject: Fisheries and Fish Science
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.4744
publisher: PeerJ Inc.
rights: © 2018 Bursell and Arlinghaus
abstract: The optimal terminal gear in hook-and-line recreational fishing maximizes landing rates and minimizes injury to the fish because some fish will be released after capture. We designed a novel rig configuration in artificial lure fishing for top predators and examined its effectiveness in angling for Baltic northern pike (Esox lucius) using a citizen science approach based on observational data collected from volunteer anglers in the field. The novel rig included two changes to traditional rig designs common to artificial lure angling. First, hooks were mounted in a way giving better hook exposure and eliminating lever-arm effects from the lure to the hooks once a fish is hooked. This construction allowed the second change, being a shift to hooks 4–5 sizes smaller than those used on traditional hook mounts. We analysed observational data collected by volunteer anglers using either the novel rig or a standard rig mount in two types of artificial lures (softbait and hardbait) of the same size (about 17 cm). Using N = 768 pike contacts as input data, we showed the landing rates of pike targeted with artificial lures significantly and substantially increased from 45% with normal-rigs to 85% when the same lure types were fished with the novel rig configuration. Lure type and water temperature had no effects on landing rates. Moreover, hardbaits on normal-rigs produced significantly more injury, bleeding and elevated unhooking time compared to fish captured on hardbaits with release-rigs. We conclude that simple changes to traditional hook sizes and mounts in lure fishing may benefit both anglers and the fishes that are to be released and that citizen science projects with volunteer anglers are able to provide good data in proof-of-concept studies. Further experimental studies are needed to differentiate hook size from hook mount effects because both variables were confounded in the results of the observational data presented here.
bibliographic citation: Bursell et al. (2018) Citizen science data suggest that a novel rig improves landing rate and reduces injury and handling time in recreational angling with artificial lures in Baltic pike (Esox lucius). PeerJ 6:e4744 https://doi.org/10.7717/peerj.4744
date submitted: 2018-02-01
date accepted: 2018-04-19
issued: 2018-05-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bursell
  given name: Jens Jakob
author list: Agent
  family name: Arlinghaus
  given name: Robert
doi: 10.7717/peerj.4744
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-17
copyright: ©2018 Bursell and Arlinghaus
attribution name: Bursell and Arlinghaus

Perinatal specimens of Maiasaura from the Upper Cretaceous of Montana (USA): insights into the early ontogeny of saurolophine hadrosaurid dinosaurs
type: item
type: AcademicArticle
description: Perinatal specimens of hadrosaurids discovered in the late 1970’s by field crews from Princeton University were significant in providing evidence of the early ontogenetic stages in North American dinosaurs. These specimens from the Campanian (Upper Cretaceous) Two Medicine Formation of Montana consist of over a dozen skeletons referable to the saurolophine hadrosaurid Maiasaura peeblesorum, but never fully figured or described. Here, we provide a more complete documentation of the morphology of these specimens, along with an examination of variation during a large span of the development of saurolophine hadrosaurids. Many ontogenetic changes in the available facial and mandibular elements are associated with the progressive elongation of the preorbital region of the skull and mandible. In the postcranium, limb bones change nearly isometrically, with exception of certain elements of the forelimb. Some cranial and postcranial characters commonly used for inferring hadrosaurid phylogenetic relationships remain invariable during the ontogeny of M. peeblesorum. This indicates that early ontogenetic stages may still provide a limited amount of character information useful for systematics and phylogenetic inference.
format: application/pdf
format: text/html
creator: Albert Prieto-Marquez
creator: Merrilee F. Guenther
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.4734
publisher: PeerJ Inc.
rights: © 2018 Prieto-Marquez and Guenther
abstract: Perinatal specimens of hadrosaurids discovered in the late 1970’s by field crews from Princeton University were significant in providing evidence of the early ontogenetic stages in North American dinosaurs. These specimens from the Campanian (Upper Cretaceous) Two Medicine Formation of Montana consist of over a dozen skeletons referable to the saurolophine hadrosaurid Maiasaura peeblesorum, but never fully figured or described. Here, we provide a more complete documentation of the morphology of these specimens, along with an examination of variation during a large span of the development of saurolophine hadrosaurids. Many ontogenetic changes in the available facial and mandibular elements are associated with the progressive elongation of the preorbital region of the skull and mandible. In the postcranium, limb bones change nearly isometrically, with exception of certain elements of the forelimb. Some cranial and postcranial characters commonly used for inferring hadrosaurid phylogenetic relationships remain invariable during the ontogeny of M. peeblesorum. This indicates that early ontogenetic stages may still provide a limited amount of character information useful for systematics and phylogenetic inference.
bibliographic citation: Prieto-Marquez et al. (2018) Perinatal specimens of Maiasaura from the Upper Cretaceous of Montana (USA): insights into the early ontogeny of saurolophine hadrosaurid dinosaurs. PeerJ 6:e4734 https://doi.org/10.7717/peerj.4734
date submitted: 2018-03-02
date accepted: 2018-04-18
issued: 2018-05-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prieto-Marquez
  given name: Albert
author list: Agent
  family name: Guenther
  given name: Merrilee F.
doi: 10.7717/peerj.4734
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-17
copyright: ©2018 Prieto-Marquez and Guenther
attribution name: Prieto-Marquez and Guenther

Comparing the catch composition, profitability and discard survival from different trammel net designs targeting common spiny lobster (Palinurus elephas) in a Mediterranean fishery
type: item
type: AcademicArticle
description: In the Balearic Islands, different trammel net designs have been adopted to promote fisheries sustainability and reduce discards. Here, we compare the catch performance of three trammel net designs targeting the spiny lobster Palinurus elephas in terms of biomass, species composition and revenue from commercial catches and discards. Designs differ in the netting fiber type (standard polyfilament, PMF, or a new polyethylene multi-monofilament, MMF) and the use of a guarding net or greca, a mesh piece intended to reduce discards. Catches were surveyed by an on-board observer from 1,550 netting walls corresponding to 70 nets. The number of marketable species captured indicated that the lobster trammel net fishery has multiple targets, which contribute significantly to the total revenue. The discarded species ranged from habitat-forming species to elasmobranches, but the magnitude of gear-habitat interactions on the long term dynamics of benthos remains unclear. No relevant differences in revenue and weight of discards were detected after Bayesian analyses. However, the species composition of discards was different when using greca. Interestingly, high immediate survival was found for discarded undersized lobsters, while a seven day survival assessment, using captive observation, gave an asymptotic estimate of survival probability as 0.64 (95% CI [0.54–0.76]). Therefore, it is recommended that it would be beneficial for this stock if an exemption from the EU landing obligation regulation was sought for undersized lobsters in the Balearic trammel net fishery.
format: application/pdf
format: text/html
creator: Gaetano Catanese
creator: Hilmar Hinz
creator: Maria del Mar Gil
creator: Miquel Palmer
creator: Michael Breen
creator: Antoni Mira
creator: Elena Pastor
creator: Amalia Grau
creator: Andrea Campos-Candela
creator: Elka Koleva
creator: Antoni Maria Grau
creator: Beatriz Morales-Nin
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.4707
publisher: PeerJ Inc.
rights: © 2018 Catanese et al.
abstract: In the Balearic Islands, different trammel net designs have been adopted to promote fisheries sustainability and reduce discards. Here, we compare the catch performance of three trammel net designs targeting the spiny lobster Palinurus elephas in terms of biomass, species composition and revenue from commercial catches and discards. Designs differ in the netting fiber type (standard polyfilament, PMF, or a new polyethylene multi-monofilament, MMF) and the use of a guarding net or greca, a mesh piece intended to reduce discards. Catches were surveyed by an on-board observer from 1,550 netting walls corresponding to 70 nets. The number of marketable species captured indicated that the lobster trammel net fishery has multiple targets, which contribute significantly to the total revenue. The discarded species ranged from habitat-forming species to elasmobranches, but the magnitude of gear-habitat interactions on the long term dynamics of benthos remains unclear. No relevant differences in revenue and weight of discards were detected after Bayesian analyses. However, the species composition of discards was different when using greca. Interestingly, high immediate survival was found for discarded undersized lobsters, while a seven day survival assessment, using captive observation, gave an asymptotic estimate of survival probability as 0.64 (95% CI [0.54–0.76]). Therefore, it is recommended that it would be beneficial for this stock if an exemption from the EU landing obligation regulation was sought for undersized lobsters in the Balearic trammel net fishery.
bibliographic citation: Catanese et al. (2018) Comparing the catch composition, profitability and discard survival from different trammel net designs targeting common spiny lobster (Palinurus elephas) in a Mediterranean fishery. PeerJ 6:e4707 https://doi.org/10.7717/peerj.4707
date submitted: 2018-01-16
date accepted: 2018-04-15
issued: 2018-05-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Catanese
  given name: Gaetano
author list: Agent
  family name: Hinz
  given name: Hilmar
author list: Agent
  family name: Gil
  given name: Maria del Mar
author list: Agent
  family name: Palmer
  given name: Miquel
author list: Agent
  family name: Breen
  given name: Michael
author list: Agent
  family name: Mira
  given name: Antoni
author list: Agent
  family name: Pastor
  given name: Elena
author list: Agent
  family name: Grau
  given name: Amalia
author list: Agent
  family name: Campos-Candela
  given name: Andrea
author list: Agent
  family name: Koleva
  given name: Elka
author list: Agent
  family name: Grau
  given name: Antoni Maria
author list: Agent
  family name: Morales-Nin
  given name: Beatriz
doi: 10.7717/peerj.4707
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-17
copyright: © 2018 Catanese et al.
attribution name: Catanese et al.

Identification and expression analysis of cytokinin metabolic genes IPTs, CYP735A and CKXs in the biofuel plant Jatropha curcas
type: item
type: AcademicArticle
description: The seed oil of Jatropha curcas is considered a potential bioenergy source that could replace fossil fuels. However, the seed yield of Jatropha is low and has yet to be improved. We previously reported that exogenous cytokinin treatment increased the seed yield of Jatropha. Cytokinin levels are directly regulated by isopentenyl transferase (IPT), cytochrome P450 monooxygenase, family 735, subfamily A (CYP735A), and cytokinin oxidase/dehydrogenase (CKX). In this study, we cloned six IPT genes, one JcCYP735A gene, and seven JcCKX genes. The expression patterns of these 14 genes in various organs were determined using real-time quantitative PCR. JcIPT1 was primarily expressed in roots and seeds, JcIPT2 was expressed in roots, apical meristems, and mature leaves, JcIPT3 was expressed in stems and mature leaves, JcIPT5 was expressed in roots and mature leaves, JcIPT6 was expressed in seeds at 10 days after pollination, and JcIPT9 was expressed in mature leaves. JcCYP735A was mainly expressed in roots, flower buds, and seeds. The seven JcCKX genes also showed different expression patterns in different organs of Jatropha. In addition, CK levels were detected in flower buds and seeds at different stages of development. The concentration of N6-(Δ2-isopentenyl)-adenine (iP), iP-riboside, and trans-zeatin (tZ) increased with flower development, and the concentration of iP decreased with seed development, while that of tZ increased. We further analyzed the function of JcCYP735A using the CRISPR-Cas9 system, and found that the concentrations of tZ and tZ-riboside decreased significantly in the Jccyp735a mutants, which showed severely retarded growth. These findings will be helpful for further studies of the functions of cytokinin metabolic genes and understanding the roles of cytokinins in Jatropha growth and development.
format: application/pdf
format: text/html
creator: Li Cai
creator: Lu Zhang
creator: Qiantang Fu
creator: Zeng-Fu Xu
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.4812
publisher: PeerJ Inc.
rights: © 2018 Cai et al.
abstract: The seed oil of Jatropha curcas is considered a potential bioenergy source that could replace fossil fuels. However, the seed yield of Jatropha is low and has yet to be improved. We previously reported that exogenous cytokinin treatment increased the seed yield of Jatropha. Cytokinin levels are directly regulated by isopentenyl transferase (IPT), cytochrome P450 monooxygenase, family 735, subfamily A (CYP735A), and cytokinin oxidase/dehydrogenase (CKX). In this study, we cloned six IPT genes, one JcCYP735A gene, and seven JcCKX genes. The expression patterns of these 14 genes in various organs were determined using real-time quantitative PCR. JcIPT1 was primarily expressed in roots and seeds, JcIPT2 was expressed in roots, apical meristems, and mature leaves, JcIPT3 was expressed in stems and mature leaves, JcIPT5 was expressed in roots and mature leaves, JcIPT6 was expressed in seeds at 10 days after pollination, and JcIPT9 was expressed in mature leaves. JcCYP735A was mainly expressed in roots, flower buds, and seeds. The seven JcCKX genes also showed different expression patterns in different organs of Jatropha. In addition, CK levels were detected in flower buds and seeds at different stages of development. The concentration of N6-(Δ2-isopentenyl)-adenine (iP), iP-riboside, and trans-zeatin (tZ) increased with flower development, and the concentration of iP decreased with seed development, while that of tZ increased. We further analyzed the function of JcCYP735A using the CRISPR-Cas9 system, and found that the concentrations of tZ and tZ-riboside decreased significantly in the Jccyp735a mutants, which showed severely retarded growth. These findings will be helpful for further studies of the functions of cytokinin metabolic genes and understanding the roles of cytokinins in Jatropha growth and development.
bibliographic citation: Cai et al. (2018) Identification and expression analysis of cytokinin metabolic genes IPTs, CYP735A and CKXs in the biofuel plant Jatropha curcas. PeerJ 6:e4812 https://doi.org/10.7717/peerj.4812
date submitted: 2018-03-15
date accepted: 2018-04-30
issued: 2018-05-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Li
author list: Agent
  family name: Zhang
  given name: Lu
author list: Agent
  family name: Fu
  given name: Qiantang
author list: Agent
  family name: Xu
  given name: Zeng-Fu
doi: 10.7717/peerj.4812
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-16
copyright: © 2018 Cai et al.
attribution name: Cai et al.

Geographical variation in colour of female threespine stickleback (Gasterosteus aculeatus)
type: item
type: AcademicArticle
description: The ecological multifunctionality of colour often results in multiple selective pressures operating on a single trait. Most research on colour evolution focuses on males because they are the most conspicuous sex in most species. This bias can limit inferences about the ecological drivers of colour evolution. For example, little is known about population divergence in colour of female threespine stickleback (Gasterosteus aculeatus), which is among the most intensively-studied model vertebrates in evolution, ecology, and behaviour. In contrast, the evolution and ecology of colour in male stickleback has received considerable attention. One aspect of female colouration that is lacking previous research is non-ornamental body colour. Non-ornamental colour can play defensive and social roles, and indicate other aspects of female stickleback ecology. To remedy this knowledge gap, we measured the colour and brightness of one dorsal and one ventral lateral area on female stickleback from nine lake populations on Vancouver Island. We found that lake populations varied in overall colour brightness and dorso-ventral contrast. In addition, we found that female brightness increased with lake size, indicating potential ecological drivers of these colour differences. Our results demonstrate that there is substantial scope for future research on female colour diversification, which has been overlooked because past researchers focused on dramatic male nuptial colours.
format: application/pdf
format: text/html
creator: Connor M. French
creator: Travis Ingram
creator: Daniel I. Bolnick
subject: Biodiversity
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.4807
publisher: PeerJ Inc.
rights: © 2018 French et al.
abstract: The ecological multifunctionality of colour often results in multiple selective pressures operating on a single trait. Most research on colour evolution focuses on males because they are the most conspicuous sex in most species. This bias can limit inferences about the ecological drivers of colour evolution. For example, little is known about population divergence in colour of female threespine stickleback (Gasterosteus aculeatus), which is among the most intensively-studied model vertebrates in evolution, ecology, and behaviour. In contrast, the evolution and ecology of colour in male stickleback has received considerable attention. One aspect of female colouration that is lacking previous research is non-ornamental body colour. Non-ornamental colour can play defensive and social roles, and indicate other aspects of female stickleback ecology. To remedy this knowledge gap, we measured the colour and brightness of one dorsal and one ventral lateral area on female stickleback from nine lake populations on Vancouver Island. We found that lake populations varied in overall colour brightness and dorso-ventral contrast. In addition, we found that female brightness increased with lake size, indicating potential ecological drivers of these colour differences. Our results demonstrate that there is substantial scope for future research on female colour diversification, which has been overlooked because past researchers focused on dramatic male nuptial colours.
bibliographic citation: French et al. (2018) Geographical variation in colour of female threespine stickleback (Gasterosteus aculeatus). PeerJ 6:e4807 https://doi.org/10.7717/peerj.4807
date submitted: 2018-03-10
date accepted: 2018-04-30
issued: 2018-05-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: French
  given name: Connor M.
author list: Agent
  family name: Ingram
  given name: Travis
author list: Agent
  family name: Bolnick
  given name: Daniel I.
doi: 10.7717/peerj.4807
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-16
copyright: © 2018 French et al.
attribution name: French et al.

Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines
type: item
type: AcademicArticle
description: Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region.
format: application/pdf
format: text/html
creator: Andrian P. Gajigan
creator: Aletta T. Yñiguez
creator: Cesar L. Villanoy
creator: Maria Lourdes San Diego-McGlone
creator: Gil S. Jacinto
creator: Cecilia Conaco
subject: Biodiversity
subject: Microbiology
subject: Biological Oceanography
description: doi:10.7717/peerj.4781
publisher: PeerJ Inc.
rights: © 2018 Gajigan et al.
abstract: Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region.
bibliographic citation: Gajigan et al. (2018) Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines. PeerJ 6:e4781 https://doi.org/10.7717/peerj.4781
date submitted: 2018-01-08
date accepted: 2018-04-26
issued: 2018-05-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gajigan
  given name: Andrian P.
author list: Agent
  family name: Yñiguez
  given name: Aletta T.
author list: Agent
  family name: Villanoy
  given name: Cesar L.
author list: Agent
  family name: San Diego-McGlone
  given name: Maria Lourdes
author list: Agent
  family name: Jacinto
  given name: Gil S.
author list: Agent
  family name: Conaco
  given name: Cecilia
doi: 10.7717/peerj.4781
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-16
copyright: ©2018 Gajigan et al.
attribution name: Gajigan et al.

Genetic inactivation of alpha-synuclein affects embryonic development of dopaminergic neurons of the substantia nigra, but not the ventral tegmental area, in mouse brain
type: item
type: AcademicArticle
description: Lesion of the dopaminergic neurons of the nigrostriatal system is a key feature of Parkinson’s disease (PD). Alpha-synuclein is a protein that is a major component of Lewy bodies, histopathological hallmarks of PD, and is involved in regulation of dopamine (DA) neurotransmission. Previous studies of knockout mice have shown that inactivation of alpha-synuclein gene can lead to the reduction in number of DA neurons in the substantia nigra (SN). DA neurons of the SN are known to be the most affected in PD patients whereas DA neurons of neighboring ventral tegmental area (VTA) are much less susceptible to degeneration. Here we have studied the dynamics of changes in TH-positive cell numbers in the SN and VTA during a critical period of their embryonic development in alpha-synuclein knockout mice. This precise study of DA neurons during development of the SN revealed that not only is the number of DA neurons reduced by the end of the period of ontogenic selection, but that the way these neurons are formed is altered in alpha-synuclein knockout mice. At the same time, DA neurons in the VTA are not affected. Alpha-synuclein exerts a modulating effect on the formation of DA neurons in the SN and has no effect on the formation of DA neurons in VTA, the structure that is much less susceptible to degeneration in a brain with PD, suggesting a potential role of alpha-synuclein in the development of the population of DA neurons in substantia nigra.
format: application/pdf
format: text/html
creator: Tatiana V. Tarasova
creator: Olga A. Lytkina
creator: Valeria V. Goloborshcheva
creator: Larisa N. Skuratovskaya
creator: Alexandr I. Antohin
creator: Ruslan K. Ovchinnikov
creator: Michail S. Kukharsky
subject: Developmental Biology
subject: Neuroscience
subject: Neurology
subject: Pathology
description: doi:10.7717/peerj.4779
publisher: PeerJ Inc.
rights: © 2018 Tarasova et al.
abstract: Lesion of the dopaminergic neurons of the nigrostriatal system is a key feature of Parkinson’s disease (PD). Alpha-synuclein is a protein that is a major component of Lewy bodies, histopathological hallmarks of PD, and is involved in regulation of dopamine (DA) neurotransmission. Previous studies of knockout mice have shown that inactivation of alpha-synuclein gene can lead to the reduction in number of DA neurons in the substantia nigra (SN). DA neurons of the SN are known to be the most affected in PD patients whereas DA neurons of neighboring ventral tegmental area (VTA) are much less susceptible to degeneration. Here we have studied the dynamics of changes in TH-positive cell numbers in the SN and VTA during a critical period of their embryonic development in alpha-synuclein knockout mice. This precise study of DA neurons during development of the SN revealed that not only is the number of DA neurons reduced by the end of the period of ontogenic selection, but that the way these neurons are formed is altered in alpha-synuclein knockout mice. At the same time, DA neurons in the VTA are not affected. Alpha-synuclein exerts a modulating effect on the formation of DA neurons in the SN and has no effect on the formation of DA neurons in VTA, the structure that is much less susceptible to degeneration in a brain with PD, suggesting a potential role of alpha-synuclein in the development of the population of DA neurons in substantia nigra.
bibliographic citation: Tarasova et al. (2018) Genetic inactivation of alpha-synuclein affects embryonic development of dopaminergic neurons of the substantia nigra, but not the ventral tegmental area, in mouse brain. PeerJ 6:e4779 https://doi.org/10.7717/peerj.4779
date submitted: 2018-02-20
date accepted: 2018-04-26
issued: 2018-05-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tarasova
  given name: Tatiana V.
author list: Agent
  family name: Lytkina
  given name: Olga A.
author list: Agent
  family name: Goloborshcheva
  given name: Valeria V.
author list: Agent
  family name: Skuratovskaya
  given name: Larisa N.
author list: Agent
  family name: Antohin
  given name: Alexandr I.
author list: Agent
  family name: Ovchinnikov
  given name: Ruslan K.
author list: Agent
  family name: Kukharsky
  given name: Michail S.
doi: 10.7717/peerj.4779
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-16
copyright: ©2018 Tarasova et al.
attribution name: Tarasova et al.

Novel, non-symbiotic isolates of Neorhizobium from a dryland agricultural soil
type: item
type: AcademicArticle
description: Semi-selective enrichment, followed by PCR screening, resulted in the successful direct isolation of fast-growing Rhizobia from a dryland agricultural soil. Over 50% of these isolates belong to the genus Neorhizobium, as concluded from partial rpoB and near-complete 16S rDNA sequence analysis. Further genotypic and genomic analysis of five representative isolates confirmed that they form a coherent group within Neorhizobium, closer to N. galegae than to the remaining Neorhizobium species, but clearly differentiated from the former, and constituting at least one new genomospecies within Neorhizobium. All the isolates lacked nod and nif symbiotic genes but contained a repABC replication/maintenance region, characteristic of rhizobial plasmids, within large contigs from their draft genome sequences. These repABC sequences were related, but not identical, to repABC sequences found in symbiotic plasmids from N. galegae, suggesting that the non-symbiotic isolates have the potential to harbor symbiotic plasmids. This is the first report of non-symbiotic members of Neorhizobium from soil.
format: application/pdf
format: text/html
creator: Amalia Soenens
creator: Juan Imperial
subject: Agricultural Science
subject: Biodiversity
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.4776
publisher: PeerJ Inc.
rights: © 2018 Soenens and Imperial
abstract: Semi-selective enrichment, followed by PCR screening, resulted in the successful direct isolation of fast-growing Rhizobia from a dryland agricultural soil. Over 50% of these isolates belong to the genus Neorhizobium, as concluded from partial rpoB and near-complete 16S rDNA sequence analysis. Further genotypic and genomic analysis of five representative isolates confirmed that they form a coherent group within Neorhizobium, closer to N. galegae than to the remaining Neorhizobium species, but clearly differentiated from the former, and constituting at least one new genomospecies within Neorhizobium. All the isolates lacked nod and nif symbiotic genes but contained a repABC replication/maintenance region, characteristic of rhizobial plasmids, within large contigs from their draft genome sequences. These repABC sequences were related, but not identical, to repABC sequences found in symbiotic plasmids from N. galegae, suggesting that the non-symbiotic isolates have the potential to harbor symbiotic plasmids. This is the first report of non-symbiotic members of Neorhizobium from soil.
bibliographic citation: Soenens et al. (2018) Novel, non-symbiotic isolates of Neorhizobium from a dryland agricultural soil. PeerJ 6:e4776 https://doi.org/10.7717/peerj.4776
date submitted: 2018-03-09
date accepted: 2018-04-25
issued: 2018-05-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soenens
  given name: Amalia
author list: Agent
  family name: Imperial
  given name: Juan
doi: 10.7717/peerj.4776
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-16
copyright: ©2018 Soenens and Imperial
attribution name: Soenens and Imperial

Pollution of the sediments of the coastal zone of the Sambia Peninsula and the Curonian Spit (Southeastern Baltic Sea)
type: item
type: AcademicArticle
description: The detailed environmental survey of the coastal zone of the Kaliningrad Region northern coast was carried out. The pollutants distribution in the silty clay fraction and calculation of ecological indexes allowed the evaluation of distribution of potentially harmful elements (PHEs). The sources of pollution in the most intensively used areas were identified, and transit and accumulation zones were allocated. A large area of anomalous content of PHEs was revealed on the underwater coastal slope of the Curonian Spit National Park, which is situated far from the sources of pollution. The alongshore bed load transport provides the contamination of the underwater slope whereas the beaches are less exposed to pollution.
format: application/pdf
format: text/html
creator: Alexander Krek
creator: Viktor Krechik
creator: Aleksandr Danchenkov
creator: Elena Krek
subject: Aquatic and Marine Chemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.4770
publisher: PeerJ Inc.
rights: © 2018 Krek et al.
abstract: The detailed environmental survey of the coastal zone of the Kaliningrad Region northern coast was carried out. The pollutants distribution in the silty clay fraction and calculation of ecological indexes allowed the evaluation of distribution of potentially harmful elements (PHEs). The sources of pollution in the most intensively used areas were identified, and transit and accumulation zones were allocated. A large area of anomalous content of PHEs was revealed on the underwater coastal slope of the Curonian Spit National Park, which is situated far from the sources of pollution. The alongshore bed load transport provides the contamination of the underwater slope whereas the beaches are less exposed to pollution.
bibliographic citation: Krek et al. (2018) Pollution of the sediments of the coastal zone of the Sambia Peninsula and the Curonian Spit (Southeastern Baltic Sea). PeerJ 6:e4770 https://doi.org/10.7717/peerj.4770
date submitted: 2018-02-01
date accepted: 2018-04-24
issued: 2018-05-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Krek
  given name: Alexander
author list: Agent
  family name: Krechik
  given name: Viktor
author list: Agent
  family name: Danchenkov
  given name: Aleksandr
author list: Agent
  family name: Krek
  given name: Elena
doi: 10.7717/peerj.4770
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-16
copyright: ©2018 Krek et al.
attribution name: Krek et al.

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