PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium
items: Eye movements while judging faces for trustworthiness and dominance
items: The antioxidant activities, cytotoxic properties, and identification of water-soluble compounds of Ficus deltoidea leaves
items: Residue management alters microbial diversity and activity without affecting their community composition in black soil, Northeast China
items: Modulating factors of the abundance and distribution of Achelous spinimanus (Latreille, 1819) (Decapoda, Portunoidea), a fishery resource, in Southeastern Brazil
items: Could resistance to lactate accumulation contribute to the better swimming performance of Brycon amazonicus when compared to Colossoma macropomum?
items: Regional differences in an established population of invasive Indo-Pacific lionfish (Pterois volitans and P. miles) in south Florida
items: Distribution of deep-water corals, sponges, and demersal fisheries landings in Southern California, USA: implications for conservation priorities
items: Production of exopolysaccharide by strains of Lactobacillus plantarum YO175 and OF101 isolated from traditional fermented cereal beverage
items: Population structure in the Andaman keelback, Xenochrophis tytleri: geographical distance and oceanic barriers to dispersal influence genetic divergence on the Andaman archipelago

Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium
type: item
type: AcademicArticle
description: Background Osteoclast differentiation in the inflamed synovium of rheumatoid arthritis (RA) affected joints leads to the formation of bone lesions. Reconstruction and analysis of protein interaction networks underlying specific disease phenotypes are essential for designing therapeutic interventions. In this study, we have created a network that captures signal flow leading to osteoclast differentiation. Based on transcriptome analysis, we have indicated the potential mechanisms responsible for the phenotype in the RA affected synovium. Method We collected information on gene expression, pathways and protein interactions related to RA from literature and databases namely Gene Expression Omnibus, Kyoto Encyclopedia of Genes and Genomes pathway and STRING. Based on these information, we created a network for the differentiation of osteoclasts. We identified the differentially regulated network genes and reported the signaling that are responsible for the process in the RA affected synovium. Result Our network reveals the mechanisms underlying the activation of the neutrophil cytosolic factor complex in connection to osteoclastogenesis in RA. Additionally, the study reports the predominance of the canonical pathway of NF-κB activation in the diseased synovium. The network also confirms that the upregulation of T cell receptor signaling and downregulation of transforming growth factor beta signaling pathway favor osteoclastogenesis in RA. To the best of our knowledge, this is the first comprehensive protein–protein interaction network describing RA driven osteoclastogenesis in the synovium. Discussion This study provides information that can be used to build models of the signal flow involved in the process of osteoclast differentiation. The models can further be used to design therapies to ameliorate bone destruction in the RA affected joints.
format: application/pdf
format: text/html
creator: Shilpa Harshan
creator: Poulami Dey
creator: Srivatsan Ragunathan
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Immunology
subject: Rheumatology
description: doi:10.7717/peerj.5743
publisher: PeerJ Inc.
rights: © 2018 Harshan et al.
abstract: Background Osteoclast differentiation in the inflamed synovium of rheumatoid arthritis (RA) affected joints leads to the formation of bone lesions. Reconstruction and analysis of protein interaction networks underlying specific disease phenotypes are essential for designing therapeutic interventions. In this study, we have created a network that captures signal flow leading to osteoclast differentiation. Based on transcriptome analysis, we have indicated the potential mechanisms responsible for the phenotype in the RA affected synovium. Method We collected information on gene expression, pathways and protein interactions related to RA from literature and databases namely Gene Expression Omnibus, Kyoto Encyclopedia of Genes and Genomes pathway and STRING. Based on these information, we created a network for the differentiation of osteoclasts. We identified the differentially regulated network genes and reported the signaling that are responsible for the process in the RA affected synovium. Result Our network reveals the mechanisms underlying the activation of the neutrophil cytosolic factor complex in connection to osteoclastogenesis in RA. Additionally, the study reports the predominance of the canonical pathway of NF-κB activation in the diseased synovium. The network also confirms that the upregulation of T cell receptor signaling and downregulation of transforming growth factor beta signaling pathway favor osteoclastogenesis in RA. To the best of our knowledge, this is the first comprehensive protein–protein interaction network describing RA driven osteoclastogenesis in the synovium. Discussion This study provides information that can be used to build models of the signal flow involved in the process of osteoclast differentiation. The models can further be used to design therapies to ameliorate bone destruction in the RA affected joints.
bibliographic citation: Harshan et al. (2018) Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium. PeerJ 6:e5743 https://doi.org/10.7717/peerj.5743
date submitted: 2018-05-02
date accepted: 2018-09-12
issued: 2018-10-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harshan
  given name: Shilpa
author list: Agent
  family name: Dey
  given name: Poulami
author list: Agent
  family name: Ragunathan
  given name: Srivatsan
doi: 10.7717/peerj.5743
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-11
copyright: © 2018 Harshan et al.
attribution name: Harshan et al.

Eye movements while judging faces for trustworthiness and dominance
type: item
type: AcademicArticle
description: Past studies examining how people judge faces for trustworthiness and dominance have suggested that they use particular facial features (e.g. mouth features for trustworthiness, eyebrow and cheek features for dominance ratings) to complete the task. Here, we examine whether eye movements during the task reflect the importance of these features. We here compared eye movements for trustworthiness and dominance ratings of face images under three stimulus configurations: Small images (mimicking large viewing distances), large images (mimicking face to face viewing), and a moving window condition (removing extrafoveal information). Whereas first area fixated, dwell times, and number of fixations depended on the size of the stimuli and the availability of extrafoveal vision, and varied substantially across participants, no clear task differences were found. These results indicate that gaze patterns for face stimuli are highly individual, do not vary between trustworthiness and dominance ratings, but are influenced by the size of the stimuli and the availability of extrafoveal vision.
format: application/pdf
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creator: Frouke Hermens
creator: Marius Golubickis
creator: C. Neil Macrae
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.5702
publisher: PeerJ Inc.
rights: © 2018 Hermens et al.
abstract: Past studies examining how people judge faces for trustworthiness and dominance have suggested that they use particular facial features (e.g. mouth features for trustworthiness, eyebrow and cheek features for dominance ratings) to complete the task. Here, we examine whether eye movements during the task reflect the importance of these features. We here compared eye movements for trustworthiness and dominance ratings of face images under three stimulus configurations: Small images (mimicking large viewing distances), large images (mimicking face to face viewing), and a moving window condition (removing extrafoveal information). Whereas first area fixated, dwell times, and number of fixations depended on the size of the stimuli and the availability of extrafoveal vision, and varied substantially across participants, no clear task differences were found. These results indicate that gaze patterns for face stimuli are highly individual, do not vary between trustworthiness and dominance ratings, but are influenced by the size of the stimuli and the availability of extrafoveal vision.
bibliographic citation: Hermens et al. (2018) Eye movements while judging faces for trustworthiness and dominance. PeerJ 6:e5702 https://doi.org/10.7717/peerj.5702
date submitted: 2018-03-23
date accepted: 2018-09-06
issued: 2018-10-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hermens
  given name: Frouke
author list: Agent
  family name: Golubickis
  given name: Marius
author list: Agent
  family name: Macrae
  given name: C. Neil
doi: 10.7717/peerj.5702
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-11
copyright: © 2018 Hermens et al.
attribution name: Hermens et al.

The antioxidant activities, cytotoxic properties, and identification of water-soluble compounds of Ficus deltoidea leaves
type: item
type: AcademicArticle
description: Leaves from three varieties of Ficus deltoidea, colloquially termed small- (FDS), medium- (FDM), and big-type leaf (FDB), were subjected to water extraction. The crude extracts were fractionated using water (WF) and ethyl acetate (EAF). The phenolic and flavonoid content, antioxidant activity, and cytotoxicity of the fractions were investigated. The EAF had the highest phenolic and flavonoid content compared to the other FDS fractions. Conversely, the FDM crude extract had the highest phenolic and flavonoid content compared to the other FDM samples. Antioxidant activity was highest in the FDB crude extract. Ultra-high–performance liquid chromatography showed that two compounds, vitexin and coumaric acid, were present in the FDB crude extract. Additionally, the F. deltoidea leaves caused no signs of toxicity in a normal liver cell line. Our findings show that F. deltoidea varieties have excellent antioxidant activity with no cytotoxic effects on normal liver cells.
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creator: Noor Nazirahanie Abrahim
creator: Puteri Shafinaz Abdul-Rahman
creator: Norhaniza Aminudin
subject: Biochemistry
subject: Cell Biology
subject: Food Science and Technology
subject: Plant Science
subject: Translational Medicine
description: doi:10.7717/peerj.5694
publisher: PeerJ Inc.
rights: © 2018 Abrahim et al.
abstract: Leaves from three varieties of Ficus deltoidea, colloquially termed small- (FDS), medium- (FDM), and big-type leaf (FDB), were subjected to water extraction. The crude extracts were fractionated using water (WF) and ethyl acetate (EAF). The phenolic and flavonoid content, antioxidant activity, and cytotoxicity of the fractions were investigated. The EAF had the highest phenolic and flavonoid content compared to the other FDS fractions. Conversely, the FDM crude extract had the highest phenolic and flavonoid content compared to the other FDM samples. Antioxidant activity was highest in the FDB crude extract. Ultra-high–performance liquid chromatography showed that two compounds, vitexin and coumaric acid, were present in the FDB crude extract. Additionally, the F. deltoidea leaves caused no signs of toxicity in a normal liver cell line. Our findings show that F. deltoidea varieties have excellent antioxidant activity with no cytotoxic effects on normal liver cells.
bibliographic citation: Abrahim et al. (2018) The antioxidant activities, cytotoxic properties, and identification of water-soluble compounds of Ficus deltoidea leaves. PeerJ 6:e5694 https://doi.org/10.7717/peerj.5694
date submitted: 2018-03-07
date accepted: 2018-09-05
issued: 2018-10-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abrahim
  given name: Noor Nazirahanie
author list: Agent
  family name: Abdul-Rahman
  given name: Puteri Shafinaz
author list: Agent
  family name: Aminudin
  given name: Norhaniza
doi: 10.7717/peerj.5694
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-11
copyright: ©2018 Abrahim et al.
attribution name: Abrahim et al.

Residue management alters microbial diversity and activity without affecting their community composition in black soil, Northeast China
type: item
type: AcademicArticle
description: Residue management is an important agricultural practice for improving soil fertility. To reveal the impact of residue management on soil microbial community, we conducted a field experiment with three treatments: no straw returning (control, CK), straw returning (SR), and straw returning combined with cow manure (SM). Our results indicated that soil organic matter content was significantly higher in SR treatment than CK in both seedling and jointing stages. In seedling stage, the lowest total nitrogen content was observed in CK treatment, and significantly lower than that in SM and SR treatment. Furthermore, soil available phosphorus content was significantly higher in SM and SR treatment than CK in jointing stage. In the seedling stage, the soil microbial average wellcolor development (AWCD) value, microbial McIntosh index, and Shannon index of CK and SM treatments were significantly higher than those in SR treatment. The AWCD value and McIntosh index in the jointing stage showed similar patterns: SM > CK > SR. Permutational multivariate analysis of variance indicated that soil microbial community was significantly affected by growth stage, but unaffected by residue management. The partial Mantel test revealed that the available potassium and the C/N ratio had independent effects on soil microbial community. Overall, our results indicated that straw returning combined with cow manure had a beneficial effect on soil fertility, microbial activity and diversity.
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format: text/html
creator: Siyu Gu
creator: Xingjun Guo
creator: Yuetong Cai
creator: Zehui Zhang
creator: Shuai Wu
creator: Xin Li
creator: Huihui Zhang
creator: Wei Yang
subject: Agricultural Science
subject: Biodiversity
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.5754
publisher: PeerJ Inc.
rights: © 2018 Gu et al.
abstract: Residue management is an important agricultural practice for improving soil fertility. To reveal the impact of residue management on soil microbial community, we conducted a field experiment with three treatments: no straw returning (control, CK), straw returning (SR), and straw returning combined with cow manure (SM). Our results indicated that soil organic matter content was significantly higher in SR treatment than CK in both seedling and jointing stages. In seedling stage, the lowest total nitrogen content was observed in CK treatment, and significantly lower than that in SM and SR treatment. Furthermore, soil available phosphorus content was significantly higher in SM and SR treatment than CK in jointing stage. In the seedling stage, the soil microbial average wellcolor development (AWCD) value, microbial McIntosh index, and Shannon index of CK and SM treatments were significantly higher than those in SR treatment. The AWCD value and McIntosh index in the jointing stage showed similar patterns: SM > CK > SR. Permutational multivariate analysis of variance indicated that soil microbial community was significantly affected by growth stage, but unaffected by residue management. The partial Mantel test revealed that the available potassium and the C/N ratio had independent effects on soil microbial community. Overall, our results indicated that straw returning combined with cow manure had a beneficial effect on soil fertility, microbial activity and diversity.
bibliographic citation: Gu et al. (2018) Residue management alters microbial diversity and activity without affecting their community composition in black soil, Northeast China. PeerJ 6:e5754 https://doi.org/10.7717/peerj.5754
date submitted: 2018-07-11
date accepted: 2018-09-14
issued: 2018-10-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gu
  given name: Siyu
author list: Agent
  family name: Guo
  given name: Xingjun
author list: Agent
  family name: Cai
  given name: Yuetong
author list: Agent
  family name: Zhang
  given name: Zehui
author list: Agent
  family name: Wu
  given name: Shuai
author list: Agent
  family name: Li
  given name: Xin
author list: Agent
  family name: Zhang
  given name: Huihui
author list: Agent
  family name: Yang
  given name: Wei
doi: 10.7717/peerj.5754
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-10
copyright: ©2018 Gu et al.
attribution name: Gu et al.

Modulating factors of the abundance and distribution of Achelous spinimanus (Latreille, 1819) (Decapoda, Portunoidea), a fishery resource, in Southeastern Brazil
type: item
type: AcademicArticle
description: This is the first study to examine how different environmental factors may influence the distribution of swimming crab Achelous spinimanus across geographically distant and distinct habitats. We analyzed the influence of bottom water temperature and salinity, sediment texture and organic matter content on the spatiotemporal distribution of A. spinimanus. The crabs were collected from January 1998 until December 1999 by trawling with a shrimp fishing boat outfitted with double-rig nets. The sampling took place in Ubatumirim (UBM), Ubatuba (UBA) and Mar Virado (MV) bays, located in the northern coast of São Paulo State (Brazil). These three bays were chosen as they differed in many physiographic features. We captured 1,911 crabs (UBM = 351; UBA = 1,509; MV = 51), and there were significant differences in abundance between bays and between stations. The distribution of A. spinimanus was primarily associated with sediment features: abundance was higher in stations with sandy sediments classified as gravel, very coarse sand, and intermediate sand. Portunoidea usually burrow in the sediment for protection against predators and to facilitate the capture of fast prey. In addition, the station with the highest abundance of A. spinimanus was also naturally protected from fishing activities, and composed of heterogeneous sediment, in terms of grain size. Hence, the combination of a favorable sediment heterogeneity and protection from fishery activities seemed to be effective modulators of the abundance and distribution of A. spinimanus in these bays.
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creator: Aline Nonato de Sousa
creator: Giovana Bertini
creator: Fabiano Gazzi Taddei
creator: Rogério Caetano da Costa
creator: Thiago Elias da Silva
creator: Adilson Fransozo
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.5720
publisher: PeerJ Inc.
rights: © 2018 Sousa et al.
abstract: This is the first study to examine how different environmental factors may influence the distribution of swimming crab Achelous spinimanus across geographically distant and distinct habitats. We analyzed the influence of bottom water temperature and salinity, sediment texture and organic matter content on the spatiotemporal distribution of A. spinimanus. The crabs were collected from January 1998 until December 1999 by trawling with a shrimp fishing boat outfitted with double-rig nets. The sampling took place in Ubatumirim (UBM), Ubatuba (UBA) and Mar Virado (MV) bays, located in the northern coast of São Paulo State (Brazil). These three bays were chosen as they differed in many physiographic features. We captured 1,911 crabs (UBM = 351; UBA = 1,509; MV = 51), and there were significant differences in abundance between bays and between stations. The distribution of A. spinimanus was primarily associated with sediment features: abundance was higher in stations with sandy sediments classified as gravel, very coarse sand, and intermediate sand. Portunoidea usually burrow in the sediment for protection against predators and to facilitate the capture of fast prey. In addition, the station with the highest abundance of A. spinimanus was also naturally protected from fishing activities, and composed of heterogeneous sediment, in terms of grain size. Hence, the combination of a favorable sediment heterogeneity and protection from fishery activities seemed to be effective modulators of the abundance and distribution of A. spinimanus in these bays.
bibliographic citation: Sousa et al. (2018) Modulating factors of the abundance and distribution of Achelous spinimanus (Latreille, 1819) (Decapoda, Portunoidea), a fishery resource, in Southeastern Brazil. PeerJ 6:e5720 https://doi.org/10.7717/peerj.5720
date submitted: 2018-03-10
date accepted: 2018-09-11
issued: 2018-10-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sousa
  given name: Aline Nonato de
author list: Agent
  family name: Bertini
  given name: Giovana
author list: Agent
  family name: Taddei
  given name: Fabiano Gazzi
author list: Agent
  family name: da Costa
  given name: Rogério Caetano
author list: Agent
  family name: Silva
  given name: Thiago Elias da
author list: Agent
  family name: Fransozo
  given name: Adilson
doi: 10.7717/peerj.5720
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-10
copyright: ©2018 Sousa et al.
attribution name: Sousa et al.

Could resistance to lactate accumulation contribute to the better swimming performance of Brycon amazonicus when compared to Colossoma macropomum?
type: item
type: AcademicArticle
description: Background In the wild, matrinchã (Brycon amazonicus) and tambaqui (Colossoma macropomum) rely strongly on their swimming capacity to perform feeding, migration and reproductive activities. Sustained swimming speed in fishes is performed almost exclusively by aerobic red muscles. The white muscle has high contraction power, but fatigue quickly, being used mainly in sprints and bursts, with a maximum duration of few seconds. The Ucrit test, an incremental velocity procedure, is mainly a measure of the aerobic capacity of a fish, but with a high participation of anaerobic metabolism close to the velocity of fatigue. Our previous study has indicated a high swimming performance of matrinchã (Ucrit) after hypoxia exposure, despite increased levels of lactate in plasma. In contrast, tambaqui with high lactate levels in plasma presented very low swimming performance. Therefore, we aimed to study the resistance of matrinchã and tambaqui to the increased lactate levels in muscle over an incremental velocity test (Ucrit). As a secondary aim, we analyzed the differences in anaerobic metabolism in response to environmental hypoxia, which could also support the better swimming performance of matrinchã, compared to tambaqui. Methods We measured, over incremented velocities in both species, the metabolic rate (the oxygen consumption by the fish; MO2), and the concentrations of lactate and nitrites and nitrates (NOx) in muscles. NOx was measured as an indicator of nitric oxide and its possible role in improving cardiorespiratory capacity in these fishes, which could postpone the use of anaerobic metabolism and lactate production during the swimming test. Also, we submitted fishes until fatigue and hypoxia (0.5 mg L−1) and measured, in addition to the previous parameters, lactate dehydrogenase activity (LDH; the enzyme responsible for lactate production), since that swimming performance could also be explained by the anaerobic capacity of producing ATP. Results Matrinchã exhibited a…
format: application/pdf
format: text/html
creator: Marcio S. Ferreira
creator: Paulo H.R. Aride
creator: Adalberto L. Val
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Freshwater Biology
description: doi:10.7717/peerj.5719
publisher: PeerJ Inc.
rights: © 2018 Ferreira et al.
abstract: Background In the wild, matrinchã (Brycon amazonicus) and tambaqui (Colossoma macropomum) rely strongly on their swimming capacity to perform feeding, migration and reproductive activities. Sustained swimming speed in fishes is performed almost exclusively by aerobic red muscles. The white muscle has high contraction power, but fatigue quickly, being used mainly in sprints and bursts, with a maximum duration of few seconds. The Ucrit test, an incremental velocity procedure, is mainly a measure of the aerobic capacity of a fish, but with a high participation of anaerobic metabolism close to the velocity of fatigue. Our previous study has indicated a high swimming performance of matrinchã (Ucrit) after hypoxia exposure, despite increased levels of lactate in plasma. In contrast, tambaqui with high lactate levels in plasma presented very low swimming performance. Therefore, we aimed to study the resistance of matrinchã and tambaqui to the increased lactate levels in muscle over an incremental velocity test (Ucrit). As a secondary aim, we analyzed the differences in anaerobic metabolism in response to environmental hypoxia, which could also support the better swimming performance of matrinchã, compared to tambaqui. Methods We measured, over incremented velocities in both species, the metabolic rate (the oxygen consumption by the fish; MO2), and the concentrations of lactate and nitrites and nitrates (NOx) in muscles. NOx was measured as an indicator of nitric oxide and its possible role in improving cardiorespiratory capacity in these fishes, which could postpone the use of anaerobic metabolism and lactate production during the swimming test. Also, we submitted fishes until fatigue and hypoxia (0.5 mg L−1) and measured, in addition to the previous parameters, lactate dehydrogenase activity (LDH; the enzyme responsible for lactate production), since that swimming performance could also be explained by the anaerobic capacity of producing ATP. Results Matrinchã exhibited a…
bibliographic citation: Ferreira et al. (2018) Could resistance to lactate accumulation contribute to the better swimming performance of Brycon amazonicus when compared to Colossoma macropomum?. PeerJ 6:e5719 https://doi.org/10.7717/peerj.5719
date submitted: 2018-03-09
date accepted: 2018-09-11
issued: 2018-10-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferreira
  given name: Marcio S.
author list: Agent
  family name: Aride
  given name: Paulo H.R.
author list: Agent
  family name: Val
  given name: Adalberto L.
doi: 10.7717/peerj.5719
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-10
copyright: ©2018 Ferreira et al.
attribution name: Ferreira et al.

Regional differences in an established population of invasive Indo-Pacific lionfish (Pterois volitans and P. miles) in south Florida
type: item
type: AcademicArticle
description: About nine years ago (circa 2009), Indo-Pacific lionfishes (Pterois volitans and P. miles) invaded the south Florida coral reef ecosystem. During the intervening period of time, there has been substantial research on their biology, life history, demography, and habitat preferences; however, little is known concerning their regional population status and trends in the region. Here, we use a large-scale fisheries independent reef fish visual survey to investigate lionfish population status among three south Florida regions: Dry Tortugas, Florida Keys, and southeast Florida. Density estimates (ind ha−1) have been relatively stable since 2012, and are lower than other areas reported in the western Atlantic and Caribbean Sea. Low, stable population densities in south Florida suggest there may be a natural mechanism for lionfish population control. In the Dry Tortugas, lionfish density in 2016 was significantly lower (0.6 ind ha−1 ± 0.15 SE) than the two other south Florida regions. The Dry Tortugas region has the highest percentage of marine protected areas, the lowest level of exploitation, and thus the highest densities of potential lionfish predators and competitors. In the Florida Keys and southeast Florida in 2016, lionfish densities were greater (5.4 ind ha−1 ± 1.0 SE and 9.0 ± 2.7 SE, respectively) than the Dry Tortugas. Fishing pressure on lionfish was higher in these two regions, but densities of several potential predators and competitors were substantially lower. Despite relatively low regional lionfish densities that can be attributed to some combination of fishing mortality and natural biocontrol, lionfish are still well established in the south Florida coral reef ecosystem, warranting continued concern.
format: application/pdf
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creator: David R. Bryan
creator: Jeremiah Blondeau
creator: Ashley Siana
creator: Jerald S. Ault
subject: Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.5700
publisher: PeerJ Inc.
rights: © 2018 Bryan et al.
abstract: About nine years ago (circa 2009), Indo-Pacific lionfishes (Pterois volitans and P. miles) invaded the south Florida coral reef ecosystem. During the intervening period of time, there has been substantial research on their biology, life history, demography, and habitat preferences; however, little is known concerning their regional population status and trends in the region. Here, we use a large-scale fisheries independent reef fish visual survey to investigate lionfish population status among three south Florida regions: Dry Tortugas, Florida Keys, and southeast Florida. Density estimates (ind ha−1) have been relatively stable since 2012, and are lower than other areas reported in the western Atlantic and Caribbean Sea. Low, stable population densities in south Florida suggest there may be a natural mechanism for lionfish population control. In the Dry Tortugas, lionfish density in 2016 was significantly lower (0.6 ind ha−1 ± 0.15 SE) than the two other south Florida regions. The Dry Tortugas region has the highest percentage of marine protected areas, the lowest level of exploitation, and thus the highest densities of potential lionfish predators and competitors. In the Florida Keys and southeast Florida in 2016, lionfish densities were greater (5.4 ind ha−1 ± 1.0 SE and 9.0 ± 2.7 SE, respectively) than the Dry Tortugas. Fishing pressure on lionfish was higher in these two regions, but densities of several potential predators and competitors were substantially lower. Despite relatively low regional lionfish densities that can be attributed to some combination of fishing mortality and natural biocontrol, lionfish are still well established in the south Florida coral reef ecosystem, warranting continued concern.
bibliographic citation: Bryan et al. (2018) Regional differences in an established population of invasive Indo-Pacific lionfish (Pterois volitans and P. miles) in south Florida. PeerJ 6:e5700 https://doi.org/10.7717/peerj.5700
date submitted: 2018-05-25
date accepted: 2018-09-06
issued: 2018-10-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bryan
  given name: David R.
author list: Agent
  family name: Blondeau
  given name: Jeremiah
author list: Agent
  family name: Siana
  given name: Ashley
author list: Agent
  family name: Ault
  given name: Jerald S.
doi: 10.7717/peerj.5700
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-10
copyright: ©2018 Bryan et al.
attribution name: Bryan et al.

Distribution of deep-water corals, sponges, and demersal fisheries landings in Southern California, USA: implications for conservation priorities
type: item
type: AcademicArticle
description: Deep-sea corals in Southern California are diverse and abundant but subject to multiple stressors, including bottom-contact fisheries using mobile and fixed gear. There is a need for more information on the distribution of these taxa in relation to the distribution of demersal fishing effort, and the distribution of marine protected areas, in order to improve spatial planning. There are many marine managed areas in Southern California, including essential fish habitat (EFH) areas, conservation areas, and a national marine sanctuary, but specific areas of overlap between bottom fishing and benthic epifauna are poorly known. Groundfish surveys were conducted by the National Marine Fisheries Service using a remotely operated vehicle throughout Southern California between 2003 and 2011 to document abundance and distribution of deep-water rockfish and flatfish to a depth of 500 m. Corals and sponges were also common in these images, providing an opportunity to examine these communities. Analyses of 34,792 still images revealed abundance and diversity of coral and sponge taxa, as well as frequency of fishing debris. The occurrence data were overlaid in a geographic information system with landings data for deep-water (>50 m) demersal fisheries to identify areas of spatial overlap. Corals or sponges were observed in 23% of images. A total of 15 coral genera and six sponge morphotypes were identified. A total of 70 species codes were targeted by deep-water demersal fisheries operating below 50 m for years 2007–2011. A novel priority-setting algorithm was developed to identify areas of high richness, abundance, and fishing intensity (RAFi). Several highly-ranked areas were already protected as EFH (Footprint, Piggy Bank). Other highly-ranked sites (West Catalina Island, San Clemente Island, 9-Mile Bank, Santa Rosa Flats) were encompassed by transient gear restrictions, such as Rockfish conservation areas, but are now recommended for permanent protection by the Pacific Fisher…
format: application/pdf
format: text/html
creator: Enrique J. Salgado
creator: Stephanie E. Nehasil
creator: Peter J. Etnoyer
subject: Conservation Biology
subject: Marine Biology
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.5697
publisher: PeerJ Inc.
rights: © 2018
abstract: Deep-sea corals in Southern California are diverse and abundant but subject to multiple stressors, including bottom-contact fisheries using mobile and fixed gear. There is a need for more information on the distribution of these taxa in relation to the distribution of demersal fishing effort, and the distribution of marine protected areas, in order to improve spatial planning. There are many marine managed areas in Southern California, including essential fish habitat (EFH) areas, conservation areas, and a national marine sanctuary, but specific areas of overlap between bottom fishing and benthic epifauna are poorly known. Groundfish surveys were conducted by the National Marine Fisheries Service using a remotely operated vehicle throughout Southern California between 2003 and 2011 to document abundance and distribution of deep-water rockfish and flatfish to a depth of 500 m. Corals and sponges were also common in these images, providing an opportunity to examine these communities. Analyses of 34,792 still images revealed abundance and diversity of coral and sponge taxa, as well as frequency of fishing debris. The occurrence data were overlaid in a geographic information system with landings data for deep-water (>50 m) demersal fisheries to identify areas of spatial overlap. Corals or sponges were observed in 23% of images. A total of 15 coral genera and six sponge morphotypes were identified. A total of 70 species codes were targeted by deep-water demersal fisheries operating below 50 m for years 2007–2011. A novel priority-setting algorithm was developed to identify areas of high richness, abundance, and fishing intensity (RAFi). Several highly-ranked areas were already protected as EFH (Footprint, Piggy Bank). Other highly-ranked sites (West Catalina Island, San Clemente Island, 9-Mile Bank, Santa Rosa Flats) were encompassed by transient gear restrictions, such as Rockfish conservation areas, but are now recommended for permanent protection by the Pacific Fisher…
bibliographic citation: Salgado et al. (2018) Distribution of deep-water corals, sponges, and demersal fisheries landings in Southern California, USA: implications for conservation priorities. PeerJ 6:e5697 https://doi.org/10.7717/peerj.5697
date submitted: 2018-03-22
date accepted: 2018-09-05
issued: 2018-10-10
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Salgado
  given name: Enrique J.
author list: Agent
  family name: Nehasil
  given name: Stephanie E.
author list: Agent
  family name: Etnoyer
  given name: Peter J.
doi: 10.7717/peerj.5697
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-10

Production of exopolysaccharide by strains of Lactobacillus plantarum YO175 and OF101 isolated from traditional fermented cereal beverage
type: item
type: AcademicArticle
description: Lactobacillus plantarum YO175 and OF101 isolates from Nigerian traditional fermented cereal gruel ‘ogi’, were investigated on the basis of their capability to produce exopolysaccharide (EPS) on sucrose modified deMan Rogosa Sharpe medium (mMRS). Functional groups analysis of the EPSs produced (EPS-YO175 and EPS-OF101) by Fourier-transform infrared (FT-IR) spectroscopy revealed the presence of –OH, C=O and C–H groups. The chemical composition of EPS-YO175 and EPS-OF101 showed the presence of 87.1% and 80.62% carbohydrates and 1.21% and 1.47% protein. For maximum EPS yield, three significant factors were optimized using central composite design and response surface methodology, the predicted maximum EPS produced was 1.38 g/L and 2.19 g/L, while the experimental values were 1.36 g/L and 2.18 g/L for EPS-YO175 and EPS-OF101. The EPS samples showed strong antioxidant activities in-vitro. The scale-up of the production process of the EPS will find its potential application in food industries.
format: application/pdf
format: text/html
creator: Adekemi Titilayo Adesulu-Dahunsi
creator: Kumaraswamy Jeyaram
creator: Abiodun Isiaka Sanni
creator: Kolawole Banwo
subject: Biotechnology
subject: Food Science and Technology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.5326
publisher: PeerJ Inc.
rights: © 2018 Adesulu-Dahunsi et al.
abstract: Lactobacillus plantarum YO175 and OF101 isolates from Nigerian traditional fermented cereal gruel ‘ogi’, were investigated on the basis of their capability to produce exopolysaccharide (EPS) on sucrose modified deMan Rogosa Sharpe medium (mMRS). Functional groups analysis of the EPSs produced (EPS-YO175 and EPS-OF101) by Fourier-transform infrared (FT-IR) spectroscopy revealed the presence of –OH, C=O and C–H groups. The chemical composition of EPS-YO175 and EPS-OF101 showed the presence of 87.1% and 80.62% carbohydrates and 1.21% and 1.47% protein. For maximum EPS yield, three significant factors were optimized using central composite design and response surface methodology, the predicted maximum EPS produced was 1.38 g/L and 2.19 g/L, while the experimental values were 1.36 g/L and 2.18 g/L for EPS-YO175 and EPS-OF101. The EPS samples showed strong antioxidant activities in-vitro. The scale-up of the production process of the EPS will find its potential application in food industries.
bibliographic citation: Adesulu-Dahunsi et al. (2018) Production of exopolysaccharide by strains of Lactobacillus plantarum YO175 and OF101 isolated from traditional fermented cereal beverage. PeerJ 6:e5326 https://doi.org/10.7717/peerj.5326
date submitted: 2018-02-27
date accepted: 2018-07-03
issued: 2018-10-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adesulu-Dahunsi
  given name: Adekemi Titilayo
author list: Agent
  family name: Jeyaram
  given name: Kumaraswamy
author list: Agent
  family name: Sanni
  given name: Abiodun Isiaka
author list: Agent
  family name: Banwo
  given name: Kolawole
doi: 10.7717/peerj.5326
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-10
copyright: ©2018 Adesulu-Dahunsi et al.
attribution name: Adesulu-Dahunsi et al.

Population structure in the Andaman keelback, Xenochrophis tytleri: geographical distance and oceanic barriers to dispersal influence genetic divergence on the Andaman archipelago
type: item
type: AcademicArticle
description: Limited gene flow between populations due to geographic distance, presence of barriers or inherent low dispersal ability leads to the formation of genetically structured populations. Strong population structure indicates lowered levels or absence of gene flow which might lead to inbreeding and loss of genetic capacity to recuperate from anthropogenic stress and natural calamities. Terrestrial reptiles are generally known to have low dispersal abilities and few studies have explored drivers of their population structure on continental islands, where both anthropogenic stress and natural calamities are relatively common. We investigated the population structure and drivers of diversification of the Andaman keelback (Xenochrophis tytleri), an endemic, terrestrial and freshwater snake species in the Andaman archipelago, a continental group of islands in the Bay of Bengal. Data was collected from 86 individuals from seven islands and 78 individuals were sequenced for the gene Nuclear Dehydrogenase subunit 4 to identify the number of populations and distribution of genetic diversity across populations. We found 11 haplotypes on seven islands and observed high genetic differentiation between seven populations defined island-wise (FST = 0.82). We further tested the number of populations by incorporating spatial data into Bayesian Clustering Analysis (GENELAND) and identified six populations of the Andaman keelback. We tested for the influence of Isolation-by-distance on these populations. While the overall trend showed a positive correlation between geographic and genetic distance, a correlogram revealed that the positive correlation disappears beyond ∼20–40 km. We also tested for the presence of geographical barriers to gene flow using Monmonier’s algorithm (SPADS), which identified five barriers to dispersal confirming that there are oceanic barriers to dispersal for some island populations of the Andaman keelback. As the Andaman Islands are arranged almost in a straight …
format: application/pdf
format: text/html
creator: Ashwini Venkatanarayana Mohan
creator: Priyanka Swamy
creator: Kartik Shanker
subject: Biogeography
subject: Ecology
subject: Evolutionary Studies
subject: Genetics
subject: Population Biology
description: doi:10.7717/peerj.5752
publisher: PeerJ Inc.
rights: © 2018 Mohan et al.
abstract: Limited gene flow between populations due to geographic distance, presence of barriers or inherent low dispersal ability leads to the formation of genetically structured populations. Strong population structure indicates lowered levels or absence of gene flow which might lead to inbreeding and loss of genetic capacity to recuperate from anthropogenic stress and natural calamities. Terrestrial reptiles are generally known to have low dispersal abilities and few studies have explored drivers of their population structure on continental islands, where both anthropogenic stress and natural calamities are relatively common. We investigated the population structure and drivers of diversification of the Andaman keelback (Xenochrophis tytleri), an endemic, terrestrial and freshwater snake species in the Andaman archipelago, a continental group of islands in the Bay of Bengal. Data was collected from 86 individuals from seven islands and 78 individuals were sequenced for the gene Nuclear Dehydrogenase subunit 4 to identify the number of populations and distribution of genetic diversity across populations. We found 11 haplotypes on seven islands and observed high genetic differentiation between seven populations defined island-wise (FST = 0.82). We further tested the number of populations by incorporating spatial data into Bayesian Clustering Analysis (GENELAND) and identified six populations of the Andaman keelback. We tested for the influence of Isolation-by-distance on these populations. While the overall trend showed a positive correlation between geographic and genetic distance, a correlogram revealed that the positive correlation disappears beyond ∼20–40 km. We also tested for the presence of geographical barriers to gene flow using Monmonier’s algorithm (SPADS), which identified five barriers to dispersal confirming that there are oceanic barriers to dispersal for some island populations of the Andaman keelback. As the Andaman Islands are arranged almost in a straight …
bibliographic citation: Mohan et al. (2018) Population structure in the Andaman keelback, Xenochrophis tytleri: geographical distance and oceanic barriers to dispersal influence genetic divergence on the Andaman archipelago. PeerJ 6:e5752 https://doi.org/10.7717/peerj.5752
date submitted: 2018-03-12
date accepted: 2018-09-13
issued: 2018-10-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohan
  given name: Ashwini Venkatanarayana
author list: Agent
  family name: Swamy
  given name: Priyanka
author list: Agent
  family name: Shanker
  given name: Kartik
doi: 10.7717/peerj.5752
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-09
copyright: © 2018 Mohan et al.
attribution name: Mohan et al.

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