PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bone lesions in Chinese POEMS syndrome patients: imaging characteristics and clinical implications
items: Microbial production and characterization of poly-3-hydroxybutyrate by Neptunomonas antarctica
items: The physiological consequences of varied heat exposure events in adult Myzus persicae: a single prolonged exposure compared to repeated shorter exposures
items: A framework for smartphone-enabled, patient-generated health data analysis
items: Stable isotopes in bivalves as indicators of nutrient source in coastal waters in the Bocas del Toro Archipelago, Panama
items: Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model
items: Decoupling the response of an estuarine shrimp to architectural components of habitat structure
items: Effects of salinity change on two superoxide dismutases (SODs) in juvenile marbled eel Anguilla marmorata
items: The masquerade game: marine mimicry adaptation between egg-cowries and octocorals
items: Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I?

Bone lesions in Chinese POEMS syndrome patients: imaging characteristics and clinical implications
type: item
type: AcademicArticle
description: Objective. Bone lesion is crucial for diagnosing and management of polyneuropathy, organomegaly, endocrinopathy, monoclonal protein, and skin change (POEMS) syndrome, a rare plasma cell disorder. This study is to compare the effectiveness of X-ray skeletal survey (SS) and computed tomography (CT) for detecting bone lesions in Chinese POEMS syndrome patients, and to investigate the relationship between bone lesion features and serum markers. Methods. SS and chest/abdomen/pelvic CT images of 38 Chinese patients (26 males, 12 females, aged 21–70 years) with POEMS syndrome recruited at our medical center between January 2013 and January 2015 were retrospectively analyzed. Bone lesions identified by CT were further categorized according to the size (<5 mm, 5–10 mm, >10 mm) and appearance (osteosclerotic, lytic, mixed). The percentage of plasma cells in bone marrow smears, type of immunoglobulin, platelet (Plt), and levels of serum bone metabolic markers and inflammatory factors including alkaline phosphatase (ALP), calcium, phosphate, parathyroid hormone (PTH), beta-isomerized C-telopeptide (β-CTx), vascular endothelial growth factor (VEGF), and interleukin (IL)-6 levels were also recorded. Results. Of the 38 POEMS syndrome patients, the immunoglobulin heavy chain isotypes were IgA in 25 patients (65.8%; 25/38) and IgG in 13 patients (34.2%; 13/38), and the light chain isotypes were λ in 35 patients (92.1%; 35/38) and κ in 3 patients (7.9%; 3/38). There were 23 patients with thrombocytosis. More patients with bone lesions were detected by CT than by SS (97.4% vs. 86.8%). The most commonly affected location was the pelvis (89.5%), followed by the spine, clavicle/scapula/sternum/ribs, skull, and long bones. Of the 38 POEMS syndrome patients, 35 (94.6%) had osteosclerotic and 32 (86.5%) had mixed lesions. Osteosclerotic lesions were typically scattered, variable in size, and plaque-like, whereas mixed lesions were pouch-shaped or soup bubble-like with a clear sclerotic marg…
format: application/pdf
format: text/html
creator: Fengdan Wang
creator: Xufei Huang
creator: Yan Zhang
creator: Jian Li
creator: Daobin Zhou
creator: Zhengyu Jin
subject: Hematology
subject: Orthopedics
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.2294
publisher: PeerJ Inc.
rights: © 2016 Wang et al.
abstract: Objective. Bone lesion is crucial for diagnosing and management of polyneuropathy, organomegaly, endocrinopathy, monoclonal protein, and skin change (POEMS) syndrome, a rare plasma cell disorder. This study is to compare the effectiveness of X-ray skeletal survey (SS) and computed tomography (CT) for detecting bone lesions in Chinese POEMS syndrome patients, and to investigate the relationship between bone lesion features and serum markers. Methods. SS and chest/abdomen/pelvic CT images of 38 Chinese patients (26 males, 12 females, aged 21–70 years) with POEMS syndrome recruited at our medical center between January 2013 and January 2015 were retrospectively analyzed. Bone lesions identified by CT were further categorized according to the size (<5 mm, 5–10 mm, >10 mm) and appearance (osteosclerotic, lytic, mixed). The percentage of plasma cells in bone marrow smears, type of immunoglobulin, platelet (Plt), and levels of serum bone metabolic markers and inflammatory factors including alkaline phosphatase (ALP), calcium, phosphate, parathyroid hormone (PTH), beta-isomerized C-telopeptide (β-CTx), vascular endothelial growth factor (VEGF), and interleukin (IL)-6 levels were also recorded. Results. Of the 38 POEMS syndrome patients, the immunoglobulin heavy chain isotypes were IgA in 25 patients (65.8%; 25/38) and IgG in 13 patients (34.2%; 13/38), and the light chain isotypes were λ in 35 patients (92.1%; 35/38) and κ in 3 patients (7.9%; 3/38). There were 23 patients with thrombocytosis. More patients with bone lesions were detected by CT than by SS (97.4% vs. 86.8%). The most commonly affected location was the pelvis (89.5%), followed by the spine, clavicle/scapula/sternum/ribs, skull, and long bones. Of the 38 POEMS syndrome patients, 35 (94.6%) had osteosclerotic and 32 (86.5%) had mixed lesions. Osteosclerotic lesions were typically scattered, variable in size, and plaque-like, whereas mixed lesions were pouch-shaped or soup bubble-like with a clear sclerotic marg…
bibliographic citation: Wang et al. (2016) Bone lesions in Chinese POEMS syndrome patients: imaging characteristics and clinical implications. PeerJ 4:e2294 https://doi.org/10.7717/peerj.2294
date submitted: 2016-04-02
date accepted: 2016-07-06
issued: 2016-08-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Fengdan
author list: Agent
  family name: Huang
  given name: Xufei
author list: Agent
  family name: Zhang
  given name: Yan
author list: Agent
  family name: Li
  given name: Jian
author list: Agent
  family name: Zhou
  given name: Daobin
author list: Agent
  family name: Jin
  given name: Zhengyu
doi: 10.7717/peerj.2294
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-02
copyright: ©2016 Wang et al.
attribution name: Wang et al.

Microbial production and characterization of poly-3-hydroxybutyrate by Neptunomonas antarctica
type: item
type: AcademicArticle
description: Considering the industrial interest of biodegradable polymer poly-3-hydroxybutyrate (PHB), the marine bacteria Neptunomonas antarctica was studied for its ability to accumulate PHB. The extracted polymer was confirmed to be PHB by nuclear magnetic resonance analysis. In shake flask cultures using natural seawater as medium components, PHB was produced up to 2.12 g/L with a yield of 0.18 g PHB/g fructose. In the presence of artificial seawater, the PHB titer and yield reached 2.13 g/L and 0.13 g PHB/g fructose, respectively. The accumulated polymer gradually decreased when fructose was exhausted, indicating that intracellular PHB was degraded by N. antarctica. The weight-average and number-average molecular weights of PHB produced within natural seawater were 2.4 × 105 g/mol and 1.7 × 105 g/mol, respectively. Our results highlight the potential of N. antarctica for PHB production with seawater as a nutrient source.
format: application/pdf
format: text/html
creator: Xiao-Jie Liu
creator: Jie Zhang
creator: Peng-Hui Hong
creator: Zheng-Jun Li
subject: Biotechnology
subject: Microbiology
description: doi:10.7717/peerj.2291
publisher: PeerJ Inc.
rights: © 2016 Liu et al.
abstract: Considering the industrial interest of biodegradable polymer poly-3-hydroxybutyrate (PHB), the marine bacteria Neptunomonas antarctica was studied for its ability to accumulate PHB. The extracted polymer was confirmed to be PHB by nuclear magnetic resonance analysis. In shake flask cultures using natural seawater as medium components, PHB was produced up to 2.12 g/L with a yield of 0.18 g PHB/g fructose. In the presence of artificial seawater, the PHB titer and yield reached 2.13 g/L and 0.13 g PHB/g fructose, respectively. The accumulated polymer gradually decreased when fructose was exhausted, indicating that intracellular PHB was degraded by N. antarctica. The weight-average and number-average molecular weights of PHB produced within natural seawater were 2.4 × 105 g/mol and 1.7 × 105 g/mol, respectively. Our results highlight the potential of N. antarctica for PHB production with seawater as a nutrient source.
bibliographic citation: Liu et al. (2016) Microbial production and characterization of poly-3-hydroxybutyrate by Neptunomonas antarctica. PeerJ 4:e2291 https://doi.org/10.7717/peerj.2291
date submitted: 2016-03-12
date accepted: 2016-07-01
issued: 2016-08-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiao-Jie
author list: Agent
  family name: Zhang
  given name: Jie
author list: Agent
  family name: Hong
  given name: Peng-Hui
author list: Agent
  family name: Li
  given name: Zheng-Jun
doi: 10.7717/peerj.2291
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-02
copyright: ©2016 Liu et al.
attribution name: Liu et al.

The physiological consequences of varied heat exposure events in adult Myzus persicae: a single prolonged exposure compared to repeated shorter exposures
type: item
type: AcademicArticle
description: The study of environmental stress tolerance in aphids has primarily been at low temperatures. In these cases, and in the rare cases of high temperature tolerance assessments, all exposures had been during a single stress event. In the present study, we examined the physiological consequences of repeated high temperature exposure with recovery periods between these stress events in Myzus persicae. We subjected individuals to either a single prolonged three hour heating event, or three one hour heating events with a recovery time of 24 h between bouts. Aphids exposed to repeated bouts of high temperatures had more glucose and higher expression of proteins and osmolyte compounds, such as glycerol, compared to the prolonged exposure group. However, aphids exposed to the repeated high temperature treatment had reduced sources of energy such as trehalose and triglyceride compounds than the prolonged exposure group. Recovery time had more physiological costs (based on production of more protein and consumption of more trehalose and triglyceride) and benefits (based on production of more osmolytes) in repeated high temperature treatments. As aphids are known to respond differently to constant versus ‘natural’ fluctuating temperature regimes, conclusions drawn from constant temperature data sets may be problematic. We suggest future experiments assessing insect responses to thermal stress incorporate a repeated stress and recovery pattern into their methodologies.
format: application/pdf
format: text/html
creator: Behnaz Ghaedi
creator: Nigel R. Andrew
subject: Ecosystem Science
subject: Entomology
subject: Environmental Sciences
description: doi:10.7717/peerj.2290
publisher: PeerJ Inc.
rights: © 2016 Ghaedi and Andrew
abstract: The study of environmental stress tolerance in aphids has primarily been at low temperatures. In these cases, and in the rare cases of high temperature tolerance assessments, all exposures had been during a single stress event. In the present study, we examined the physiological consequences of repeated high temperature exposure with recovery periods between these stress events in Myzus persicae. We subjected individuals to either a single prolonged three hour heating event, or three one hour heating events with a recovery time of 24 h between bouts. Aphids exposed to repeated bouts of high temperatures had more glucose and higher expression of proteins and osmolyte compounds, such as glycerol, compared to the prolonged exposure group. However, aphids exposed to the repeated high temperature treatment had reduced sources of energy such as trehalose and triglyceride compounds than the prolonged exposure group. Recovery time had more physiological costs (based on production of more protein and consumption of more trehalose and triglyceride) and benefits (based on production of more osmolytes) in repeated high temperature treatments. As aphids are known to respond differently to constant versus ‘natural’ fluctuating temperature regimes, conclusions drawn from constant temperature data sets may be problematic. We suggest future experiments assessing insect responses to thermal stress incorporate a repeated stress and recovery pattern into their methodologies.
bibliographic citation: Ghaedi et al. (2016) The physiological consequences of varied heat exposure events in adult Myzus persicae: a single prolonged exposure compared to repeated shorter exposures. PeerJ 4:e2290 https://doi.org/10.7717/peerj.2290
date submitted: 2015-12-30
date accepted: 2016-07-05
issued: 2016-08-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ghaedi
  given name: Behnaz
author list: Agent
  family name: Andrew
  given name: Nigel R.
doi: 10.7717/peerj.2290
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-02
copyright: ©2016 Ghaedi and Andrew
attribution name: Ghaedi and Andrew

A framework for smartphone-enabled, patient-generated health data analysis
type: item
type: AcademicArticle
description: Background: Digital medicine and smartphone-enabled health technologies provide a novel source of human health and human biology data. However, in part due to its intricacies, few methods have been established to analyze and interpret data in this domain. We previously conducted a six-month interventional trial examining the efficacy of a comprehensive smartphone-based health monitoring program for individuals with chronic disease. This included 38 individuals with hypertension who recorded 6,290 blood pressure readings over the trial. Methods: In the present study, we provide a hypothesis testing framework for unstructured time series data, typical of patient-generated mobile device data. We used a mixed model approach for unequally spaced repeated measures using autoregressive and generalized autoregressive models, and applied this to the blood pressure data generated in this trial. Results: We were able to detect, roughly, a 2 mmHg decrease in both systolic and diastolic blood pressure over the course of the trial despite considerable intra- and inter-individual variation. Furthermore, by supplementing this finding by using a sequential analysis approach, we observed this result over three months prior to the official study end—highlighting the effectiveness of leveraging the digital nature of this data source to form timely conclusions. Conclusions: Health data generated through the use of smartphones and other mobile devices allow individuals the opportunity to make informed health decisions, and provide researchers the opportunity to address innovative health and biology questions. The hypothesis testing framework we present can be applied in future studies utilizing digital medicine technology or implemented in the technology itself to support the quantified self.
format: application/pdf
format: text/html
creator: Shreya S. Gollamudi
creator: Eric J. Topol
creator: Nathan E. Wineinger
subject: Cardiology
subject: Evidence Based Medicine
subject: Translational Medicine
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.2284
publisher: PeerJ Inc.
rights: © 2016 Gollamudi et al.
abstract: Background: Digital medicine and smartphone-enabled health technologies provide a novel source of human health and human biology data. However, in part due to its intricacies, few methods have been established to analyze and interpret data in this domain. We previously conducted a six-month interventional trial examining the efficacy of a comprehensive smartphone-based health monitoring program for individuals with chronic disease. This included 38 individuals with hypertension who recorded 6,290 blood pressure readings over the trial. Methods: In the present study, we provide a hypothesis testing framework for unstructured time series data, typical of patient-generated mobile device data. We used a mixed model approach for unequally spaced repeated measures using autoregressive and generalized autoregressive models, and applied this to the blood pressure data generated in this trial. Results: We were able to detect, roughly, a 2 mmHg decrease in both systolic and diastolic blood pressure over the course of the trial despite considerable intra- and inter-individual variation. Furthermore, by supplementing this finding by using a sequential analysis approach, we observed this result over three months prior to the official study end—highlighting the effectiveness of leveraging the digital nature of this data source to form timely conclusions. Conclusions: Health data generated through the use of smartphones and other mobile devices allow individuals the opportunity to make informed health decisions, and provide researchers the opportunity to address innovative health and biology questions. The hypothesis testing framework we present can be applied in future studies utilizing digital medicine technology or implemented in the technology itself to support the quantified self.
bibliographic citation: Gollamudi et al. (2016) A framework for smartphone-enabled, patient-generated health data analysis. PeerJ 4:e2284 https://doi.org/10.7717/peerj.2284
date submitted: 2016-03-22
date accepted: 2016-07-03
issued: 2016-08-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gollamudi
  given name: Shreya S.
author list: Agent
  family name: Topol
  given name: Eric J.
author list: Agent
  family name: Wineinger
  given name: Nathan E.
doi: 10.7717/peerj.2284
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-02
copyright: © 2016 Gollamudi et al.
attribution name: Gollamudi et al.

Stable isotopes in bivalves as indicators of nutrient source in coastal waters in the Bocas del Toro Archipelago, Panama
type: item
type: AcademicArticle
description: To examine N-isotope ratios (15N/14N) in tissues and shell organic matrix of bivalves as a proxy for natural and anthropogenic nutrient fluxes in coastal environments, Pinctada imbricata, Isognomon alatus, and Brachidontes exustusbivalves were live-collected and analyzed from eight sites in Bocas del Toro, Panama. Sites represent a variety of coastal environments, including more urbanized, uninhabited, riverine, and oceanic sites. Growth under differing environmental conditions is confirmed by δ18O values, with open ocean Escudo de Veraguas shells yielding the highest average δ18O (−1.0‰) value and freshwater endmember Rio Guarumo the lowest (−1.7‰). At all sites there is no single dominant source of organic matter contributing to bivalve δ15N and δ13C values. Bivalve δ15N and δ13C values likely represent a mixture of mangrove and seagrass N and C, although terrestrial sources cannot be ruled out. Despite hydrographic differences between end-members, we see minimal δ15N and δ13C difference between bivalves from the river-influenced Rio Guarumo site and those from the oceanic Escudo de Veraguas site, with no evidence for N from open-ocean phytoplankton in the latter. Populated sites yield relative 15N enrichments suggestive of anthropogenic nutrient input, but low δ15N values overall make this interpretation equivocal. Lastly, δ15N values of tissue and shell organic matrix correlate significantly for pterioideans P. imbricata and I. alatus. Thus for these species, N isotope studies of historical and fossil shells should provide records of ecology of past environments.
format: application/pdf
format: text/html
creator: Lauren E. Graniero
creator: Ethan L. Grossman
creator: Aaron O’Dea
subject: Aquaculture, Fisheries and Fish Science
subject: Ecosystem Science
subject: Marine Biology
description: doi:10.7717/peerj.2278
publisher: PeerJ Inc.
rights: © 2016 Graniero et al.
abstract: To examine N-isotope ratios (15N/14N) in tissues and shell organic matrix of bivalves as a proxy for natural and anthropogenic nutrient fluxes in coastal environments, Pinctada imbricata, Isognomon alatus, and Brachidontes exustusbivalves were live-collected and analyzed from eight sites in Bocas del Toro, Panama. Sites represent a variety of coastal environments, including more urbanized, uninhabited, riverine, and oceanic sites. Growth under differing environmental conditions is confirmed by δ18O values, with open ocean Escudo de Veraguas shells yielding the highest average δ18O (−1.0‰) value and freshwater endmember Rio Guarumo the lowest (−1.7‰). At all sites there is no single dominant source of organic matter contributing to bivalve δ15N and δ13C values. Bivalve δ15N and δ13C values likely represent a mixture of mangrove and seagrass N and C, although terrestrial sources cannot be ruled out. Despite hydrographic differences between end-members, we see minimal δ15N and δ13C difference between bivalves from the river-influenced Rio Guarumo site and those from the oceanic Escudo de Veraguas site, with no evidence for N from open-ocean phytoplankton in the latter. Populated sites yield relative 15N enrichments suggestive of anthropogenic nutrient input, but low δ15N values overall make this interpretation equivocal. Lastly, δ15N values of tissue and shell organic matrix correlate significantly for pterioideans P. imbricata and I. alatus. Thus for these species, N isotope studies of historical and fossil shells should provide records of ecology of past environments.
bibliographic citation: Graniero et al. (2016) Stable isotopes in bivalves as indicators of nutrient source in coastal waters in the Bocas del Toro Archipelago, Panama. PeerJ 4:e2278 https://doi.org/10.7717/peerj.2278
date submitted: 2015-06-20
date accepted: 2016-07-01
issued: 2016-08-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Graniero
  given name: Lauren E.
author list: Agent
  family name: Grossman
  given name: Ethan L.
author list: Agent
  family name: O’Dea
  given name: Aaron
doi: 10.7717/peerj.2278
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-02
copyright: ©2016 Graniero et al.
attribution name: Graniero et al.

Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model
type: item
type: AcademicArticle
description: One of the simplest models of adaptation to a new environment is Fisher’s Geometric Model (FGM), in which populations move on a multidimensional landscape defined by the traits under selection. The predictions of this model have been found to be consistent with current observations of patterns of fitness increase in experimentally evolved populations. Recent studies investigated the dynamics of allele frequency change along adaptation of microbes to simple laboratory conditions and unveiled a dramatic pattern of competition between cohorts of mutations, i.e., multiple mutations simultaneously segregating and ultimately reaching fixation. Here, using simulations, we study the dynamics of phenotypic and genetic change as asexual populations under clonal interference climb a Fisherian landscape, and ask about the conditions under which FGM can display the simultaneous increase and fixation of multiple mutations—mutation cohorts—along the adaptive walk. We find that FGM under clonal interference, and with varying levels of pleiotropy, can reproduce the experimentally observed competition between different cohorts of mutations, some of which have a high probability of fixation along the adaptive walk. Overall, our results show that the surprising dynamics of mutation cohorts recently observed during experimental adaptation of microbial populations can be expected under one of the oldest and simplest theoretical models of adaptation—FGM.
format: application/pdf
format: text/html
creator: Jorge A. Moura de Sousa
creator: João Alpedrinha
creator: Paulo R.A. Campos
creator: Isabel Gordo
subject: Evolutionary Studies
subject: Genetics
subject: Mathematical Biology
description: doi:10.7717/peerj.2256
publisher: PeerJ Inc.
rights: © 2016 Moura de Sousa et al.
abstract: One of the simplest models of adaptation to a new environment is Fisher’s Geometric Model (FGM), in which populations move on a multidimensional landscape defined by the traits under selection. The predictions of this model have been found to be consistent with current observations of patterns of fitness increase in experimentally evolved populations. Recent studies investigated the dynamics of allele frequency change along adaptation of microbes to simple laboratory conditions and unveiled a dramatic pattern of competition between cohorts of mutations, i.e., multiple mutations simultaneously segregating and ultimately reaching fixation. Here, using simulations, we study the dynamics of phenotypic and genetic change as asexual populations under clonal interference climb a Fisherian landscape, and ask about the conditions under which FGM can display the simultaneous increase and fixation of multiple mutations—mutation cohorts—along the adaptive walk. We find that FGM under clonal interference, and with varying levels of pleiotropy, can reproduce the experimentally observed competition between different cohorts of mutations, some of which have a high probability of fixation along the adaptive walk. Overall, our results show that the surprising dynamics of mutation cohorts recently observed during experimental adaptation of microbial populations can be expected under one of the oldest and simplest theoretical models of adaptation—FGM.
bibliographic citation: Moura de Sousa et al. (2016) Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model. PeerJ 4:e2256 https://doi.org/10.7717/peerj.2256
date submitted: 2016-02-24
date accepted: 2016-06-23
issued: 2016-08-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moura de Sousa
  given name: Jorge A.
author list: Agent
  family name: Alpedrinha
  given name: João
author list: Agent
  family name: Campos
  given name: Paulo R.A.
author list: Agent
  family name: Gordo
  given name: Isabel
doi: 10.7717/peerj.2256
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-02
copyright: ©2016 Moura de Sousa et al.
attribution name: Moura de Sousa et al.

Decoupling the response of an estuarine shrimp to architectural components of habitat structure
type: item
type: AcademicArticle
description: In order to explore biotic attraction to structure, we examined how the amount and arrangement of artificial biotic stalks affected responses of a shrimp, Palaemon macrodactylus, absent other proximate factors such as predation or interspecific competition. In aquaria, we tested the effect of differing densities of both un-branched and branched stalks, where the amount of material in the branched stalk equaled four-times that of the un-branched. The results clearly showed that it was the amount of material, not how it was arranged, that elicited responses from shrimp. Also, although stalks were not purposefully designed to mimic structural elements found in nature, they did resemble biogenic structure such as hydroids, algae, or plants. In order to test shrimp attraction to a different, perhaps more unfamiliar habitat type, we examined responses to plastic “army men.” These structural elements elicited similar attraction of shrimp, and, in general, shrimp response correlated well with the fractal dimension of both stalks and army men. Overall, these results indicate that attraction to physical structure, regardless of its nature, may be an important driver of high abundances often associated with complex habitats.
format: application/pdf
format: text/html
creator: Jeffrey A. Crooks
creator: Andrew L. Chang
creator: Gregory M. Ruiz
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.2244
publisher: PeerJ Inc.
rights: © 2016 Crooks et al.
abstract: In order to explore biotic attraction to structure, we examined how the amount and arrangement of artificial biotic stalks affected responses of a shrimp, Palaemon macrodactylus, absent other proximate factors such as predation or interspecific competition. In aquaria, we tested the effect of differing densities of both un-branched and branched stalks, where the amount of material in the branched stalk equaled four-times that of the un-branched. The results clearly showed that it was the amount of material, not how it was arranged, that elicited responses from shrimp. Also, although stalks were not purposefully designed to mimic structural elements found in nature, they did resemble biogenic structure such as hydroids, algae, or plants. In order to test shrimp attraction to a different, perhaps more unfamiliar habitat type, we examined responses to plastic “army men.” These structural elements elicited similar attraction of shrimp, and, in general, shrimp response correlated well with the fractal dimension of both stalks and army men. Overall, these results indicate that attraction to physical structure, regardless of its nature, may be an important driver of high abundances often associated with complex habitats.
bibliographic citation: Crooks et al. (2016) Decoupling the response of an estuarine shrimp to architectural components of habitat structure. PeerJ 4:e2244 https://doi.org/10.7717/peerj.2244
date submitted: 2015-12-15
date accepted: 2016-06-22
issued: 2016-08-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Crooks
  given name: Jeffrey A.
author list: Agent
  family name: Chang
  given name: Andrew L.
author list: Agent
  family name: Ruiz
  given name: Gregory M.
doi: 10.7717/peerj.2244
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-02
copyright: © 2016 Crooks et al.
attribution name: Crooks et al.

Effects of salinity change on two superoxide dismutases (SODs) in juvenile marbled eel Anguilla marmorata
type: item
type: AcademicArticle
description: Salinity is one of the most important factors that affect the fish growth and survival. Superoxide dismutases (SODs), as the primary antioxidant enzymes, play a first role in the process of preventing oxidative stress caused by excessive superoxide anion (O ${}_{2}^{-}$ 2 − ) in living organisms. In the present study, we investigated the effects of salinity on the gene expressions as well as enzymatic activities of MnSOD and Cu/ZnSOD in gill, intestine, kidney, liver and muscle tissues of the marbled eel Anguilla marmorata. We found that the liver might possess stronger redox capacity compared with other tissues. Furthermore, the gene expressions and enzymatic activities of SODs in juvenile marbled eels could be effectively enhanced by low salinity but inhibited when the salinity was higher than the body tolerance. Our findings indicated that MnSOD and Cu/ZnSOD played vital roles in the adaptation of marbled eels to salinity variation, which contributed to the elucidation of physiological adaptation and regulatory mechanism of SODs in eels.
format: application/pdf
format: text/html
creator: Li Wang
creator: Xiaolu Wang
creator: Shaowu Yin
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Biological Oceanography
subject: Environmental Sciences
subject: Molecular Biology
description: doi:10.7717/peerj.2149
publisher: PeerJ Inc.
rights: © 2016 Wang et al.
abstract: Salinity is one of the most important factors that affect the fish growth and survival. Superoxide dismutases (SODs), as the primary antioxidant enzymes, play a first role in the process of preventing oxidative stress caused by excessive superoxide anion (O ${}_{2}^{-}$ 2 − ) in living organisms. In the present study, we investigated the effects of salinity on the gene expressions as well as enzymatic activities of MnSOD and Cu/ZnSOD in gill, intestine, kidney, liver and muscle tissues of the marbled eel Anguilla marmorata. We found that the liver might possess stronger redox capacity compared with other tissues. Furthermore, the gene expressions and enzymatic activities of SODs in juvenile marbled eels could be effectively enhanced by low salinity but inhibited when the salinity was higher than the body tolerance. Our findings indicated that MnSOD and Cu/ZnSOD played vital roles in the adaptation of marbled eels to salinity variation, which contributed to the elucidation of physiological adaptation and regulatory mechanism of SODs in eels.
bibliographic citation: Wang et al. (2016) Effects of salinity change on two superoxide dismutases (SODs) in juvenile marbled eel Anguilla marmorata. PeerJ 4:e2149 https://doi.org/10.7717/peerj.2149
date submitted: 2016-02-03
date accepted: 2016-05-27
issued: 2016-08-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Li
author list: Agent
  family name: Wang
  given name: Xiaolu
author list: Agent
  family name: Yin
  given name: Shaowu
doi: 10.7717/peerj.2149
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-02
copyright: ©2016 Wang et al.
attribution name: Wang et al.

The masquerade game: marine mimicry adaptation between egg-cowries and octocorals
type: item
type: AcademicArticle
description: Background. Background matching, as a camouflage strategy, is one of the most outstanding examples of adaptation, where little error or mismatch means high vulnerability to predation. It is assumed that the interplay of natural selection and adaptation are the main evolutionary forces shaping the great diversity of phenotypes observed in mimicry; however, there may be other significant processes that intervene in the development of mimicry such as phenotypic plasticity. Based on observations of background mismatching during reproduction events of egg-cowries, sea snails of the family Ovulidae that mimic the octocoral where they inhabit, we wondered if they match the host species diversity. Using observations in the field and molecular systematics, we set out to establish whether the different egg-cowrie color/shape polymorphisms correspond to distinct lineages restricted to specific octocoral species. Methods. Collection and observations of egg-cowries and their octocoral hosts were done using SCUBA diving between 2009 and 2012 at two localities in the Tropical Eastern Pacific (TEP), Malpelo Island and Cabo Corrientes (Colombia). Detailed host preference observations were done bi-annually at Malpelo Island. We analyzed the DNA sequence of the mitochondrial genes COIand 16S rDNA, extensively used in phylogenetic and DNA barcoding studies, to assess the evolutionary relationship among different egg-cowrie colorations and morphologies. Results. No genetic divergence among egg-cowries associated to different species of the same octocoral genus was observed based on the two mitochondrial genes analyzed. For instance, all egg-cowrie individuals from the two sampled localities observed on 8 different Pacifigorgia-Eugorgia species showed negligible mitochondrial divergence yet large morphologic divergence, which suggests that morphologies belonging to at least two sea snail species, Simnia avena(=S. aequalis) and Simnialena rufa, can cross-fertilize. Discussion. Our study s…
format: application/pdf
format: text/html
creator: Juan A. Sánchez
creator: Angela P. Fuentes-Pardo
creator: Íde Ní Almhain
creator: Néstor E. Ardila-Espitia
creator: Jaime Cantera-Kintz
creator: Manu Forero-Shelton
subject: Biodiversity
subject: Evolutionary Studies
subject: Marine Biology
subject: Zoology
subject: Science and Medical Education
description: doi:10.7717/peerj.2051
publisher: PeerJ Inc.
rights: © 2016 Sánchez et al.
abstract: Background. Background matching, as a camouflage strategy, is one of the most outstanding examples of adaptation, where little error or mismatch means high vulnerability to predation. It is assumed that the interplay of natural selection and adaptation are the main evolutionary forces shaping the great diversity of phenotypes observed in mimicry; however, there may be other significant processes that intervene in the development of mimicry such as phenotypic plasticity. Based on observations of background mismatching during reproduction events of egg-cowries, sea snails of the family Ovulidae that mimic the octocoral where they inhabit, we wondered if they match the host species diversity. Using observations in the field and molecular systematics, we set out to establish whether the different egg-cowrie color/shape polymorphisms correspond to distinct lineages restricted to specific octocoral species. Methods. Collection and observations of egg-cowries and their octocoral hosts were done using SCUBA diving between 2009 and 2012 at two localities in the Tropical Eastern Pacific (TEP), Malpelo Island and Cabo Corrientes (Colombia). Detailed host preference observations were done bi-annually at Malpelo Island. We analyzed the DNA sequence of the mitochondrial genes COIand 16S rDNA, extensively used in phylogenetic and DNA barcoding studies, to assess the evolutionary relationship among different egg-cowrie colorations and morphologies. Results. No genetic divergence among egg-cowries associated to different species of the same octocoral genus was observed based on the two mitochondrial genes analyzed. For instance, all egg-cowrie individuals from the two sampled localities observed on 8 different Pacifigorgia-Eugorgia species showed negligible mitochondrial divergence yet large morphologic divergence, which suggests that morphologies belonging to at least two sea snail species, Simnia avena(=S. aequalis) and Simnialena rufa, can cross-fertilize. Discussion. Our study s…
bibliographic citation: Sánchez et al. (2016) The masquerade game: marine mimicry adaptation between egg-cowries and octocorals. PeerJ 4:e2051 https://doi.org/10.7717/peerj.2051
date submitted: 2016-01-23
date accepted: 2016-04-28
issued: 2016-08-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sánchez
  given name: Juan A.
author list: Agent
  family name: Fuentes-Pardo
  given name: Angela P.
author list: Agent
  family name: Ní Almhain
  given name: Íde
author list: Agent
  family name: Ardila-Espitia
  given name: Néstor E.
author list: Agent
  family name: Cantera-Kintz
  given name: Jaime
author list: Agent
  family name: Forero-Shelton
  given name: Manu
doi: 10.7717/peerj.2051
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-02
copyright: ©2016 Sánchez et al.
attribution name: Sánchez et al.

Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I?
type: item
type: AcademicArticle
description: 1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozyme and has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability in a biological context requires it to be able to resist modification by xenobiotic-degrading enzymes like the P450 cytochromes. Quantum chemical computations described in this work show that 1,2-dihydro-1,2-azaborine is much more prone to modification by these enzymes than benzene, unless steric crowding of the ring prevents it from reaching the active site, or otherwise only allows reaction at the less reactive C4-position. This novel heterocyclic compound is therefore expected to be of limited usefulness as an aryl bioisostere.
format: application/pdf
format: text/html
creator: Pedro J. Silva
subject: Biochemistry
subject: Biophysics
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.2299
publisher: PeerJ Inc.
rights: © 2016 Silva
abstract: 1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozyme and has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability in a biological context requires it to be able to resist modification by xenobiotic-degrading enzymes like the P450 cytochromes. Quantum chemical computations described in this work show that 1,2-dihydro-1,2-azaborine is much more prone to modification by these enzymes than benzene, unless steric crowding of the ring prevents it from reaching the active site, or otherwise only allows reaction at the less reactive C4-position. This novel heterocyclic compound is therefore expected to be of limited usefulness as an aryl bioisostere.
bibliographic citation: Silva (2016) Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I?. PeerJ 4:e2299 https://doi.org/10.7717/peerj.2299
date submitted: 2016-05-18
date accepted: 2016-07-06
issued: 2016-07-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Pedro J.
doi: 10.7717/peerj.2299
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-28
copyright: ©2016 Silva
attribution name: Silva

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