PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Swabs to genomes: a comprehensive workflow
items: Childhood socioeconomic deprivation, but not current mood, is associated with behavioural disinhibition in adults
items: Individual consistency in the behaviors of newly-settled reef fish
items: Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest
items: Self-generated morphology in lagoon reefs
items: Impacts of sea level rise and climate change on coastal plant species in the central California coast
items: Tactile roughness perception in the presence of olfactory and trigeminal stimulants
items: Comparison of methods used to estimate coral cover in the Hawaiian Islands
items: The unnatural history of Kāne‘ohe Bay: coral reef resilience in the face of centuries of anthropogenic impacts
items: Transgenic LRRK2R1441G rats–a model for Parkinson disease?

Swabs to genomes: a comprehensive workflow
type: item
type: AcademicArticle
description: The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
format: application/pdf
format: text/html
creator: Madison I. Dunitz
creator: Jenna M. Lang
creator: Guillaume Jospin
creator: Aaron E. Darling
creator: Jonathan A. Eisen
creator: David A. Coil
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.960
publisher: PeerJ Inc.
rights: © 2015 Dunitz et al.
abstract: The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
bibliographic citation: Dunitz et al. (2015) Swabs to genomes: a comprehensive workflow. PeerJ 3:e960 https://doi.org/10.7717/peerj.960
date submitted: 2015-01-30
date accepted: 2015-04-24
issued: 2015-05-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dunitz
  given name: Madison I.
author list: Agent
  family name: Lang
  given name: Jenna M.
author list: Agent
  family name: Jospin
  given name: Guillaume
author list: Agent
  family name: Darling
  given name: Aaron E.
author list: Agent
  family name: Eisen
  given name: Jonathan A.
author list: Agent
  family name: Coil
  given name: David A.
doi: 10.7717/peerj.960
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-14
copyright: © 2015 Dunitz et al.
attribution name: Dunitz et al.

Childhood socioeconomic deprivation, but not current mood, is associated with behavioural disinhibition in adults
type: item
type: AcademicArticle
description: There is evidence to suggest that impulsivity is predicted by socioeconomic background, with people from more deprived backgrounds tending to be more impulsive, and by current mood, with poorer mood associated with greater impulsivity. However, impulsivity is not a unitary construct, and previous research in this area has focused on measures of ‘waiting’ impulsivity rather than behavioural disinhibition. We administered a standard measure of behavioural disinhibition, the stop-signal task, to 58 adult participants from a community sample. We had measured socioeconomic background using participant postcode at age 16, and assigned participants to receive either a neutral or a negative mood induction. We found no effects of mood on behavioural disinhibition, but we found a significant effect of socioeconomic background. Participants who had lived in more deprived postcodes at age 16 showed longer stop-signal reaction times, and hence greater behavioural disinhibition. The pattern was independent of participant age and overall reaction time. Though caution is required inferring causality from correlation, it is possible that that experiencing socioeconomic deprivation in childhood and adolescence may lead to greater behavioural disinhibition in adulthood.
format: application/pdf
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creator: Tünde Paál
creator: Thomas Carpenter
creator: Daniel Nettle
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.964
publisher: PeerJ Inc.
rights: © 2015 Paál et al.
abstract: There is evidence to suggest that impulsivity is predicted by socioeconomic background, with people from more deprived backgrounds tending to be more impulsive, and by current mood, with poorer mood associated with greater impulsivity. However, impulsivity is not a unitary construct, and previous research in this area has focused on measures of ‘waiting’ impulsivity rather than behavioural disinhibition. We administered a standard measure of behavioural disinhibition, the stop-signal task, to 58 adult participants from a community sample. We had measured socioeconomic background using participant postcode at age 16, and assigned participants to receive either a neutral or a negative mood induction. We found no effects of mood on behavioural disinhibition, but we found a significant effect of socioeconomic background. Participants who had lived in more deprived postcodes at age 16 showed longer stop-signal reaction times, and hence greater behavioural disinhibition. The pattern was independent of participant age and overall reaction time. Though caution is required inferring causality from correlation, it is possible that that experiencing socioeconomic deprivation in childhood and adolescence may lead to greater behavioural disinhibition in adulthood.
bibliographic citation: Paál et al. (2015) Childhood socioeconomic deprivation, but not current mood, is associated with behavioural disinhibition in adults. PeerJ 3:e964 https://doi.org/10.7717/peerj.964
date submitted: 2015-03-05
date accepted: 2015-04-27
issued: 2015-05-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paál
  given name: Tünde
author list: Agent
  family name: Carpenter
  given name: Thomas
author list: Agent
  family name: Nettle
  given name: Daniel
doi: 10.7717/peerj.964
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-14
copyright: © 2015 Paál et al.
attribution name: Paál et al.

Individual consistency in the behaviors of newly-settled reef fish
type: item
type: AcademicArticle
description: Flexibility in behavior is advantageous for organisms that transition between stages of a complex life history. However, various constraints can set limits on plasticity, giving rise to the existence of personalities that have associated costs and benefits. Here, we document a field and laboratory experiment that examines the consistency of measures of boldness, activity, and aggressive behavior in the young of a tropical reef fish, Pomacentrus amboinensis (Pomacentridae) immediately following their transition between pelagic larval and benthic juvenile habitats. Newly-settled fish were observed in aquaria and in the field on replicated patches of natural habitat cleared of resident fishes. Seven behavioral traits representing aspects of boldness, activity and aggression were monitored directly and via video camera over short (minutes), medium (hours), and long (3 days) time scales. With the exception of aggression, these behaviors were found to be moderately or highly consistent over all time scales in both laboratory and field settings, implying that these fish show stable personalities within various settings. Our study is the first to examine the temporal constancy of behaviors in both field and laboratory settings in over various time scales at a critically important phase during the life cycle of a reef fish.
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creator: James R. White
creator: Mark G. Meekan
creator: Mark I. McCormick
subject: Animal Behavior
subject: Marine Biology
description: doi:10.7717/peerj.961
publisher: PeerJ Inc.
rights: © 2015 White et al.
abstract: Flexibility in behavior is advantageous for organisms that transition between stages of a complex life history. However, various constraints can set limits on plasticity, giving rise to the existence of personalities that have associated costs and benefits. Here, we document a field and laboratory experiment that examines the consistency of measures of boldness, activity, and aggressive behavior in the young of a tropical reef fish, Pomacentrus amboinensis (Pomacentridae) immediately following their transition between pelagic larval and benthic juvenile habitats. Newly-settled fish were observed in aquaria and in the field on replicated patches of natural habitat cleared of resident fishes. Seven behavioral traits representing aspects of boldness, activity and aggression were monitored directly and via video camera over short (minutes), medium (hours), and long (3 days) time scales. With the exception of aggression, these behaviors were found to be moderately or highly consistent over all time scales in both laboratory and field settings, implying that these fish show stable personalities within various settings. Our study is the first to examine the temporal constancy of behaviors in both field and laboratory settings in over various time scales at a critically important phase during the life cycle of a reef fish.
bibliographic citation: White et al. (2015) Individual consistency in the behaviors of newly-settled reef fish. PeerJ 3:e961 https://doi.org/10.7717/peerj.961
date submitted: 2015-03-28
date accepted: 2015-04-25
issued: 2015-05-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: White
  given name: James R.
author list: Agent
  family name: Meekan
  given name: Mark G.
author list: Agent
  family name: McCormick
  given name: Mark I.
doi: 10.7717/peerj.961
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-14
copyright: © 2015 White et al.
attribution name: White et al.

Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest
type: item
type: AcademicArticle
description: Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m2 and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that could b…
format: application/pdf
format: text/html
creator: Ahmed A. Siddig
creator: Aaron M. Ellison
creator: Scott Jackson
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
description: doi:10.7717/peerj.952
publisher: PeerJ Inc.
rights: © 2015 Siddig et al.
abstract: Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m2 and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that could b…
bibliographic citation: Siddig et al. (2015) Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest. PeerJ 3:e952 https://doi.org/10.7717/peerj.952
date submitted: 2015-02-12
date accepted: 2015-04-21
issued: 2015-05-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Siddig
  given name: Ahmed A.
author list: Agent
  family name: Ellison
  given name: Aaron M.
author list: Agent
  family name: Jackson
  given name: Scott
doi: 10.7717/peerj.952
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-14
copyright: © 2015 Siddig et al.
attribution name: Siddig et al.

Self-generated morphology in lagoon reefs
type: item
type: AcademicArticle
description: The three-dimensional form of a coral reef develops through interactions and feedbacks between its constituent organisms and their environment. Reef morphology therefore contains a potential wealth of ecological information, accessible if the relationships between morphology and ecology can be decoded. Traditionally, reef morphology has been attributed to external controls such as substrate topography or hydrodynamic influences. Little is known about inherent reef morphology in the absence of external control. Here we use reef growth simulations, based on observations in the cellular reefs of Western Australia’s Houtman Abrolhos Islands, to show that reef morphology is fundamentally determined by the mechanical behaviour of the reef-building organisms themselves—specifically their tendency to either remain in place or to collapse. Reef-building organisms that tend to remain in place, such as massive and encrusting corals or coralline algae, produce nodular reefs, whereas those that tend to collapse, such as branching Acropora, produce cellular reefs. The purest reef growth forms arise in sheltered lagoons dominated by a single type of reef builder, as in the branching Acropora-dominated lagoons of the Abrolhos. In these situations reef morphology can be considered a phenotype of the predominant reef building organism. The capacity to infer coral type from reef morphology can potentially be used to identify and map specific coral habitat in remotely sensed images. More generally, identifying ecological mechanisms underlying other examples of self-generated reef morphology can potentially improve our understanding of present-day reef ecology, because any ecological process capable of shaping a reef will almost invariably be an important process in real time on the living reef.
format: application/pdf
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creator: David Blakeway
creator: Michael G. Hamblin
subject: Computational Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.935
publisher: PeerJ Inc.
rights: © 2015 Blakeway and Hamblin
abstract: The three-dimensional form of a coral reef develops through interactions and feedbacks between its constituent organisms and their environment. Reef morphology therefore contains a potential wealth of ecological information, accessible if the relationships between morphology and ecology can be decoded. Traditionally, reef morphology has been attributed to external controls such as substrate topography or hydrodynamic influences. Little is known about inherent reef morphology in the absence of external control. Here we use reef growth simulations, based on observations in the cellular reefs of Western Australia’s Houtman Abrolhos Islands, to show that reef morphology is fundamentally determined by the mechanical behaviour of the reef-building organisms themselves—specifically their tendency to either remain in place or to collapse. Reef-building organisms that tend to remain in place, such as massive and encrusting corals or coralline algae, produce nodular reefs, whereas those that tend to collapse, such as branching Acropora, produce cellular reefs. The purest reef growth forms arise in sheltered lagoons dominated by a single type of reef builder, as in the branching Acropora-dominated lagoons of the Abrolhos. In these situations reef morphology can be considered a phenotype of the predominant reef building organism. The capacity to infer coral type from reef morphology can potentially be used to identify and map specific coral habitat in remotely sensed images. More generally, identifying ecological mechanisms underlying other examples of self-generated reef morphology can potentially improve our understanding of present-day reef ecology, because any ecological process capable of shaping a reef will almost invariably be an important process in real time on the living reef.
bibliographic citation: Blakeway et al. (2015) Self-generated morphology in lagoon reefs. PeerJ 3:e935 https://doi.org/10.7717/peerj.935
date submitted: 2014-11-01
date accepted: 2015-04-15
issued: 2015-05-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Blakeway
  given name: David
author list: Agent
  family name: Hamblin
  given name: Michael G.
doi: 10.7717/peerj.935
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-12
copyright: © 2015 Blakeway and Hamblin
attribution name: Blakeway and Hamblin

Impacts of sea level rise and climate change on coastal plant species in the central California coast
type: item
type: AcademicArticle
description: Local increases in sea level caused by global climate change pose a significant threat to the persistence of many coastal plant species through exacerbating inundation, flooding, and erosion. In addition to sea level rise (SLR), climate changes in the form of air temperature and precipitation regimes will also alter habitats of coastal plant species. Although numerous studies have analyzed the effect of climate change on future habitats through species distribution models (SDMs), none have incorporated the threat of exposure to SLR. We developed a model that quantified the effect of both SLR and climate change on habitat for 88 rare coastal plant species in San Luis Obispo, Santa Barbara, and Ventura Counties, California, USA (an area of 23,948 km2). Our SLR model projects that by the year 2100, 60 of the 88 species will be threatened by SLR. We found that the probability of being threatened by SLR strongly correlates with a species’ area, elevation, and distance from the coast, and that 10 species could lose their entire current habitat in the study region. We modeled the habitat suitability of these 10 species under future climate using a species distribution model (SDM). Our SDM projects that 4 of the 10 species will lose all suitable current habitats in the region as a result of climate change. While SLR accounts for up to 9.2 km2 loss in habitat, climate change accounts for habitat suitability changes ranging from a loss of 1,439 km2 for one species to a gain of 9,795 km2 for another species. For three species, SLR is projected to reduce future suitable area by as much as 28% of total area. This suggests that while SLR poses a higher risk, climate changes in precipitation and air temperature represents a lesser known but potentially larger risk and a small cumulative effect from both.
format: application/pdf
format: text/html
creator: Kendra L. Garner
creator: Michelle Y. Chang
creator: Matthew T. Fulda
creator: Jonathan A. Berlin
creator: Rachel E. Freed
creator: Melissa M. Soo-Hoo
creator: Dave L. Revell
creator: Makihiko Ikegami
creator: Lorraine E. Flint
creator: Alan L. Flint
creator: Bruce E. Kendall
subject: Biodiversity
subject: Conservation Biology
description: doi:10.7717/peerj.958
publisher: PeerJ Inc.
rights: © 2015 Garner et al.
abstract: Local increases in sea level caused by global climate change pose a significant threat to the persistence of many coastal plant species through exacerbating inundation, flooding, and erosion. In addition to sea level rise (SLR), climate changes in the form of air temperature and precipitation regimes will also alter habitats of coastal plant species. Although numerous studies have analyzed the effect of climate change on future habitats through species distribution models (SDMs), none have incorporated the threat of exposure to SLR. We developed a model that quantified the effect of both SLR and climate change on habitat for 88 rare coastal plant species in San Luis Obispo, Santa Barbara, and Ventura Counties, California, USA (an area of 23,948 km2). Our SLR model projects that by the year 2100, 60 of the 88 species will be threatened by SLR. We found that the probability of being threatened by SLR strongly correlates with a species’ area, elevation, and distance from the coast, and that 10 species could lose their entire current habitat in the study region. We modeled the habitat suitability of these 10 species under future climate using a species distribution model (SDM). Our SDM projects that 4 of the 10 species will lose all suitable current habitats in the region as a result of climate change. While SLR accounts for up to 9.2 km2 loss in habitat, climate change accounts for habitat suitability changes ranging from a loss of 1,439 km2 for one species to a gain of 9,795 km2 for another species. For three species, SLR is projected to reduce future suitable area by as much as 28% of total area. This suggests that while SLR poses a higher risk, climate changes in precipitation and air temperature represents a lesser known but potentially larger risk and a small cumulative effect from both.
bibliographic citation: Garner et al. (2015) Impacts of sea level rise and climate change on coastal plant species in the central California coast. PeerJ 3:e958 https://doi.org/10.7717/peerj.958
date submitted: 2014-12-19
date accepted: 2015-04-24
issued: 2015-05-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garner
  given name: Kendra L.
author list: Agent
  family name: Chang
  given name: Michelle Y.
author list: Agent
  family name: Fulda
  given name: Matthew T.
author list: Agent
  family name: Berlin
  given name: Jonathan A.
author list: Agent
  family name: Freed
  given name: Rachel E.
author list: Agent
  family name: Soo-Hoo
  given name: Melissa M.
author list: Agent
  family name: Revell
  given name: Dave L.
author list: Agent
  family name: Ikegami
  given name: Makihiko
author list: Agent
  family name: Flint
  given name: Lorraine E.
author list: Agent
  family name: Flint
  given name: Alan L.
author list: Agent
  family name: Kendall
  given name: Bruce E.
doi: 10.7717/peerj.958
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-12
copyright: © 2015 Garner et al.
attribution name: Garner et al.

Tactile roughness perception in the presence of olfactory and trigeminal stimulants
type: item
type: AcademicArticle
description: Previous research has shown that odorants consistently evoke associations with textures and their tactile properties like smoothness and roughness. Also, it has been observed that olfaction can modulate tactile perception. We therefore hypothesized that tactile roughness perception may be biased towards the somatosensory connotation of an ambient odorant. We performed two experiments to test this hypothesis. In the first experiment, we investigated the influence of ambient chemosensory stimuli with different roughness connotations on tactile roughness perception. In addition to a pleasant odor with a connotation of softness (PEA), we also included a trigeminal stimulant with a rough, sharp or prickly connotation (Ethanol). We expected that—compared to a No-odorant control condition—tactile texture perception would be biased towards smoothness in the presence of PEA and towards roughness in the presence of Ethanol. However, our results show no significant interaction between chemosensory stimulation and perceived tactile surface roughness. It could be argued that ambient odors may be less effective in stimulating crossmodal associations, since they are by definition extraneous to the tactile stimuli. In an attempt to optimize the conditions for sensory integration, we therefore performed a second experiment in which the olfactory and tactile stimuli were presented in synchrony and in close spatial proximity. In addition, we included pleasant (Lemon) and unpleasant (Indole) odorants that are known to have the ability to affect tactile perception. We expected that tactile stimuli would be perceived as less rough when simultaneously presented with Lemon or PEA (both associated with softness) than when presented with Ethanol or Indole (odors that can be associated with roughness). Again, we found no significant main effect of chemosensory condition on perceived tactile roughness. We discuss the limitations of this study and we present suggestions for future research.
format: application/pdf
format: text/html
creator: Lara A. Koijck
creator: Alexander Toet
creator: Jan B.F. Van Erp
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.955
publisher: PeerJ Inc.
rights: © 2015 Koijck et al.
abstract: Previous research has shown that odorants consistently evoke associations with textures and their tactile properties like smoothness and roughness. Also, it has been observed that olfaction can modulate tactile perception. We therefore hypothesized that tactile roughness perception may be biased towards the somatosensory connotation of an ambient odorant. We performed two experiments to test this hypothesis. In the first experiment, we investigated the influence of ambient chemosensory stimuli with different roughness connotations on tactile roughness perception. In addition to a pleasant odor with a connotation of softness (PEA), we also included a trigeminal stimulant with a rough, sharp or prickly connotation (Ethanol). We expected that—compared to a No-odorant control condition—tactile texture perception would be biased towards smoothness in the presence of PEA and towards roughness in the presence of Ethanol. However, our results show no significant interaction between chemosensory stimulation and perceived tactile surface roughness. It could be argued that ambient odors may be less effective in stimulating crossmodal associations, since they are by definition extraneous to the tactile stimuli. In an attempt to optimize the conditions for sensory integration, we therefore performed a second experiment in which the olfactory and tactile stimuli were presented in synchrony and in close spatial proximity. In addition, we included pleasant (Lemon) and unpleasant (Indole) odorants that are known to have the ability to affect tactile perception. We expected that tactile stimuli would be perceived as less rough when simultaneously presented with Lemon or PEA (both associated with softness) than when presented with Ethanol or Indole (odors that can be associated with roughness). Again, we found no significant main effect of chemosensory condition on perceived tactile roughness. We discuss the limitations of this study and we present suggestions for future research.
bibliographic citation: Koijck et al. (2015) Tactile roughness perception in the presence of olfactory and trigeminal stimulants. PeerJ 3:e955 https://doi.org/10.7717/peerj.955
date submitted: 2014-12-24
date accepted: 2015-04-23
issued: 2015-05-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koijck
  given name: Lara A.
author list: Agent
  family name: Toet
  given name: Alexander
author list: Agent
  family name: Van Erp
  given name: Jan B.F.
doi: 10.7717/peerj.955
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-12
copyright: © 2015 Koijck et al.
attribution name: Koijck et al.

Comparison of methods used to estimate coral cover in the Hawaiian Islands
type: item
type: AcademicArticle
description: Nine coral survey methods were compared at ten sites in various reef habitats with different levels of coral cover in Kāne‘ohe Bay, O’ahu, Hawaiʻi. Mean estimated coverage at the different sites ranged from less than 10% cover to greater than 90% cover. The methods evaluated include line transects, various visual and photographic belt transects, video transects and visual estimates. At each site 25 m transect lines were laid out and secured. Observers skilled in each method measured coral cover at each site. The time required to run each transect, time required to process data and time to record the results were documented. Cost of hardware and software for each method was also tabulated. Results of this investigation indicate that all of the methods used provide a good first estimate of coral cover on a reef. However, there were differences between the methods in detecting the number of coral species. For example, the classic “quadrat” method allows close examination of small and cryptic coral species that are not detected by other methods such as the “towboard” surveys. The time, effort and cost involved with each method varied widely, and the suitability of each method for answering particular research questions in various environments was evaluated. Results of this study support the finding of three other comparison method studies conducted at various geographic locations throughout the world. Thus, coral cover measured by different methods can be legitimately combined or compared in many situations. The success of a recent modeling effort based on coral cover data consisting of observations taken in Hawai‘i using the different methods supports this conclusion.
format: application/pdf
format: text/html
creator: Paul L. Jokiel
creator: Kuʻulei S. Rodgers
creator: Eric K. Brown
creator: Jean C. Kenyon
creator: Greta Aeby
creator: William R. Smith
creator: Fred Farrell
subject: Marine Biology
description: doi:10.7717/peerj.954
publisher: PeerJ Inc.
rights: © 2015 Jokiel et al.
abstract: Nine coral survey methods were compared at ten sites in various reef habitats with different levels of coral cover in Kāne‘ohe Bay, O’ahu, Hawaiʻi. Mean estimated coverage at the different sites ranged from less than 10% cover to greater than 90% cover. The methods evaluated include line transects, various visual and photographic belt transects, video transects and visual estimates. At each site 25 m transect lines were laid out and secured. Observers skilled in each method measured coral cover at each site. The time required to run each transect, time required to process data and time to record the results were documented. Cost of hardware and software for each method was also tabulated. Results of this investigation indicate that all of the methods used provide a good first estimate of coral cover on a reef. However, there were differences between the methods in detecting the number of coral species. For example, the classic “quadrat” method allows close examination of small and cryptic coral species that are not detected by other methods such as the “towboard” surveys. The time, effort and cost involved with each method varied widely, and the suitability of each method for answering particular research questions in various environments was evaluated. Results of this study support the finding of three other comparison method studies conducted at various geographic locations throughout the world. Thus, coral cover measured by different methods can be legitimately combined or compared in many situations. The success of a recent modeling effort based on coral cover data consisting of observations taken in Hawai‘i using the different methods supports this conclusion.
bibliographic citation: Jokiel et al. (2015) Comparison of methods used to estimate coral cover in the Hawaiian Islands. PeerJ 3:e954 https://doi.org/10.7717/peerj.954
date submitted: 2015-01-03
date accepted: 2015-04-22
issued: 2015-05-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jokiel
  given name: Paul L.
author list: Agent
  family name: Rodgers
  given name: Kuʻulei S.
author list: Agent
  family name: Brown
  given name: Eric K.
author list: Agent
  family name: Kenyon
  given name: Jean C.
author list: Agent
  family name: Aeby
  given name: Greta
author list: Agent
  family name: Smith
  given name: William R.
author list: Agent
  family name: Farrell
  given name: Fred
doi: 10.7717/peerj.954
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-12
copyright: © 2015 Jokiel et al.
attribution name: Jokiel et al.

The unnatural history of Kāne‘ohe Bay: coral reef resilience in the face of centuries of anthropogenic impacts
type: item
type: AcademicArticle
description: Kāneʻohe Bay, which is located on the on the NE coast of Oʻahu, Hawaiʻi, represents one of the most intensively studied estuarine coral reef ecosystems in the world. Despite a long history of anthropogenic disturbance, from early settlement to post European contact, the coral reef ecosystem of Kāneʻohe Bay appears to be in better condition in comparison to other reefs around the world. The island of Moku o Loʻe (Coconut Island) in the southern region of the bay became home to the Hawaiʻi Institute of Marine Biology in 1947, where researchers have since documented the various aspects of the unique physical, chemical, and biological features of this coral reef ecosystem. The first human contact by voyaging Polynesians occurred at least 700 years ago. By A.D. 1250 Polynesians voyagers had settled inhabitable islands in the region which led to development of an intensive agricultural, fish pond and ocean resource system that supported a large human population. Anthropogenic disturbance initially involved clearing of land for agriculture, intentional or accidental introduction of alien species, modification of streams to supply water for taro culture, and construction of massive shoreline fish pond enclosures and extensive terraces in the valleys that were used for taro culture. The arrival by the first Europeans in 1778 led to further introductions of plants and animals that radically changed the landscape. Subsequent development of a plantation agricultural system led to increased human immigration, population growth and an end to traditional land and water management practices. The reefs were devastated by extensive dredge and fill operations as well as rapid growth of human population, which led to extensive urbanization of the watershed. By the 1960’s the bay was severely impacted by increased sewage discharge along with increased sedimentation due to improper grading practices and stream channelization, resulting in extensive loss of coral cover. The reefs of Kāneʻ…
format: application/pdf
format: text/html
creator: Keisha D. Bahr
creator: Paul L. Jokiel
creator: Robert J. Toonen
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.950
publisher: PeerJ Inc.
rights: © 2015 Bahr et al.
abstract: Kāneʻohe Bay, which is located on the on the NE coast of Oʻahu, Hawaiʻi, represents one of the most intensively studied estuarine coral reef ecosystems in the world. Despite a long history of anthropogenic disturbance, from early settlement to post European contact, the coral reef ecosystem of Kāneʻohe Bay appears to be in better condition in comparison to other reefs around the world. The island of Moku o Loʻe (Coconut Island) in the southern region of the bay became home to the Hawaiʻi Institute of Marine Biology in 1947, where researchers have since documented the various aspects of the unique physical, chemical, and biological features of this coral reef ecosystem. The first human contact by voyaging Polynesians occurred at least 700 years ago. By A.D. 1250 Polynesians voyagers had settled inhabitable islands in the region which led to development of an intensive agricultural, fish pond and ocean resource system that supported a large human population. Anthropogenic disturbance initially involved clearing of land for agriculture, intentional or accidental introduction of alien species, modification of streams to supply water for taro culture, and construction of massive shoreline fish pond enclosures and extensive terraces in the valleys that were used for taro culture. The arrival by the first Europeans in 1778 led to further introductions of plants and animals that radically changed the landscape. Subsequent development of a plantation agricultural system led to increased human immigration, population growth and an end to traditional land and water management practices. The reefs were devastated by extensive dredge and fill operations as well as rapid growth of human population, which led to extensive urbanization of the watershed. By the 1960’s the bay was severely impacted by increased sewage discharge along with increased sedimentation due to improper grading practices and stream channelization, resulting in extensive loss of coral cover. The reefs of Kāneʻ…
bibliographic citation: Bahr et al. (2015) The unnatural history of Kāne‘ohe Bay: coral reef resilience in the face of centuries of anthropogenic impacts. PeerJ 3:e950 https://doi.org/10.7717/peerj.950
date submitted: 2015-01-04
date accepted: 2015-04-20
issued: 2015-05-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bahr
  given name: Keisha D.
author list: Agent
  family name: Jokiel
  given name: Paul L.
author list: Agent
  family name: Toonen
  given name: Robert J.
doi: 10.7717/peerj.950
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-12
copyright: © 2015 Bahr et al.
attribution name: Bahr et al.

Transgenic LRRK2R1441G rats–a model for Parkinson disease?
type: item
type: AcademicArticle
description: Parkinson disease (PD) is the most common movement disorder, characterized by the progressive degeneration of dopaminergic neurons in the substantia nigra. While the cause of this disease is largely unknown, a rare autosomal dominant familial form of PD is caused by a genetic mutation in the leucine-rich repeat kinase 2 (LRRK2) gene that presumably leads to a gain-of-function of LRRK2 kinase activity. Here, we explored the potential of over expression of this human gene in a new transgenic rat model to serve as an animal model for PD. Commercially available BAC transgenic rats expressing human LRRK2 with the familial PD mutation, R1441G, and their wild-type siblings were tested for deficits in motor function, sensorimotor gating, and higher cognitive function reminiscent of PD through the ages of 3, 6, 9 and 12 months. At 12 months of age, rats were exposed to intraperitoneal injections of the environmental toxin Paraquat or saline. Our results indicate that LRRK2R1441G transgenic rats do not show signs of neurodegeneration and do not develop significant motor or cognitive deficits until the age of 16 months. In addition, LRRK2R1441G transgenic rats did not show increased vulnerability to sub-toxic doses of Paraquat. Gene expression studies indicate that despite genomic presence and initial expression of the transgene, its expression was greatly reduced in our aged rats. We conclude that the transgenic LRRK2R1441G rat is not a valid model for studying the pathology of PD and discuss this in relation to other transgenic rat models.
format: application/pdf
format: text/html
creator: Komal T. Shaikh
creator: Alvin Yang
creator: Ekaterina Youshin
creator: Susanne Schmid
subject: Neuroscience
subject: Neurology
description: doi:10.7717/peerj.945
publisher: PeerJ Inc.
rights: © 2015 Shaikh et al.
abstract: Parkinson disease (PD) is the most common movement disorder, characterized by the progressive degeneration of dopaminergic neurons in the substantia nigra. While the cause of this disease is largely unknown, a rare autosomal dominant familial form of PD is caused by a genetic mutation in the leucine-rich repeat kinase 2 (LRRK2) gene that presumably leads to a gain-of-function of LRRK2 kinase activity. Here, we explored the potential of over expression of this human gene in a new transgenic rat model to serve as an animal model for PD. Commercially available BAC transgenic rats expressing human LRRK2 with the familial PD mutation, R1441G, and their wild-type siblings were tested for deficits in motor function, sensorimotor gating, and higher cognitive function reminiscent of PD through the ages of 3, 6, 9 and 12 months. At 12 months of age, rats were exposed to intraperitoneal injections of the environmental toxin Paraquat or saline. Our results indicate that LRRK2R1441G transgenic rats do not show signs of neurodegeneration and do not develop significant motor or cognitive deficits until the age of 16 months. In addition, LRRK2R1441G transgenic rats did not show increased vulnerability to sub-toxic doses of Paraquat. Gene expression studies indicate that despite genomic presence and initial expression of the transgene, its expression was greatly reduced in our aged rats. We conclude that the transgenic LRRK2R1441G rat is not a valid model for studying the pathology of PD and discuss this in relation to other transgenic rat models.
bibliographic citation: Shaikh et al. (2015) Transgenic LRRK2R1441G rats–a model for Parkinson disease?. PeerJ 3:e945 https://doi.org/10.7717/peerj.945
date submitted: 2015-01-21
date accepted: 2015-04-18
issued: 2015-05-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shaikh
  given name: Komal T.
author list: Agent
  family name: Yang
  given name: Alvin
author list: Agent
  family name: Youshin
  given name: Ekaterina
author list: Agent
  family name: Schmid
  given name: Susanne
doi: 10.7717/peerj.945
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-12
copyright: © 2015 Shaikh et al.
attribution name: Shaikh et al.

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