PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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?
items: The diversity of membrane transporters encoded in bacterial arsenic-resistance operons
items: New insights into the lifestyle of Allosaurus (Dinosauria: Theropoda) based on another specimen with multiple pathologies
items: Thylacinus (Marsupialia: Thylacinidae) from the Mio-Pliocene boundary and the diversity of Late Neogene thylacinids in Australia
items: Male convict cichlid 11-ketotestosterone levels throughout the reproductive cycle: an exploratory profile study in laboratory and field populations

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
format: text/html
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.

The diversity of membrane transporters encoded in bacterial arsenic-resistance operons
type: item
type: AcademicArticle
description: Transporter-facilitated arsenite extrusion is the major pathway of arsenic resistance within bacteria. So far only two types of membrane-bound transporter proteins, ArsB and ArsY (ACR3), have been well studied, although the arsenic transporters in bacteria display considerable diversity. Utilizing accumulated genome sequence data, we searched arsenic resistance (ars) operons in about 2,500 bacterial strains and located over 700 membrane-bound transporters which are encoded in these operons. Sequence analysis revealed at least five distinct transporter families, with ArsY being the most dominant, followed by ArsB, ArsP (a recently reported permease family), Major Facilitator protein Superfamily (MFS) and Major Intrinsic Protein (MIP). In addition, other types of transporters encoded in the ars operons were found, but in much lower frequencies. The diversity and evolutionary relationships of these transporters with regard to arsenic resistance will be discussed.
format: application/pdf
format: text/html
creator: Yiren Yang
creator: Shiyang Wu
creator: Ross McCausland Lilley
creator: Ren Zhang
subject: Biochemistry
subject: Bioinformatics
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.943
publisher: PeerJ Inc.
rights: © 2015 Yang et al.
abstract: Transporter-facilitated arsenite extrusion is the major pathway of arsenic resistance within bacteria. So far only two types of membrane-bound transporter proteins, ArsB and ArsY (ACR3), have been well studied, although the arsenic transporters in bacteria display considerable diversity. Utilizing accumulated genome sequence data, we searched arsenic resistance (ars) operons in about 2,500 bacterial strains and located over 700 membrane-bound transporters which are encoded in these operons. Sequence analysis revealed at least five distinct transporter families, with ArsY being the most dominant, followed by ArsB, ArsP (a recently reported permease family), Major Facilitator protein Superfamily (MFS) and Major Intrinsic Protein (MIP). In addition, other types of transporters encoded in the ars operons were found, but in much lower frequencies. The diversity and evolutionary relationships of these transporters with regard to arsenic resistance will be discussed.
bibliographic citation: Yang et al. (2015) The diversity of membrane transporters encoded in bacterial arsenic-resistance operons. PeerJ 3:e943 https://doi.org/10.7717/peerj.943
date submitted: 2015-01-27
date accepted: 2015-04-17
issued: 2015-05-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yiren
author list: Agent
  family name: Wu
  given name: Shiyang
author list: Agent
  family name: Lilley
  given name: Ross McCausland
author list: Agent
  family name: Zhang
  given name: Ren
doi: 10.7717/peerj.943
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-12
copyright: © 2015 Yang et al.
attribution name: Yang et al.

New insights into the lifestyle of Allosaurus (Dinosauria: Theropoda) based on another specimen with multiple pathologies
type: item
type: AcademicArticle
description: Adult large-bodied theropods are often found with numerous pathologies. A large, almost complete, probably adult Allosaurus specimen from the Howe Stephens Quarry, Morrison Formation (Late Kimmeridgian–Early Tithonian), Wyoming, exhibits multiple pathologies. Pathologic bones include the left dentary, two cervical vertebrae, one cervical and several dorsal ribs, the left scapula, the left humerus, the right ischium, and two left pedal phalanges. These pathologies can be classified as follows: the fifth cervical vertebra, the scapula, several ribs and the ischium are probably traumatic, and a callus on the shaft of the left pedal phalanx II-2 is probably traumatic-infectious. Traumatically fractured elements exposed to frequent movement (e.g., the scapula and the ribs) show a tendency to develop pseudarthroses instead of a callus. The pathologies in the lower jaw and a reduced extensor tubercle of the left pedal phalanx II-2 are most likely traumatic or developmental in origin. The pathologies on the fourth cervical are most likely developmental in origin or idiopathic, that on the left humerus could be traumatic, developmental, infectious or idiopathic, whereas the left pedal phalanx IV-1 is classified as idiopathic. With exception of the ischium, all as traumatic/traumatic-infectious classified pathologic elements show unambiguous evidences of healing, indicating that the respective pathologies did not cause the death of this individual. Alignment of the scapula and rib pathologies from the left side suggests that all may have been caused by a single traumatic event. The ischial fracture may have been fatal. The occurrence of multiple lesions interpreted as traumatic pathologies again underlines that large-bodied theropods experienced frequent injuries during life, indicating an active predatory lifestyle, and their survival perhaps supports a gregarious behavior for Allosaurus. Alternatively, the frequent survival of traumatic events could be also related to the p…
format: application/pdf
format: text/html
creator: Christian Foth
creator: Serjoscha W. Evers
creator: Ben Pabst
creator: Octávio Mateus
creator: Alexander Flisch
creator: Mike Patthey
creator: Oliver W.M. Rauhut
subject: Animal Behavior
subject: Paleontology
subject: Veterinary Medicine
subject: Zoology
subject: Pathology
description: doi:10.7717/peerj.940
publisher: PeerJ Inc.
rights: © 2015 Foth et al.
abstract: Adult large-bodied theropods are often found with numerous pathologies. A large, almost complete, probably adult Allosaurus specimen from the Howe Stephens Quarry, Morrison Formation (Late Kimmeridgian–Early Tithonian), Wyoming, exhibits multiple pathologies. Pathologic bones include the left dentary, two cervical vertebrae, one cervical and several dorsal ribs, the left scapula, the left humerus, the right ischium, and two left pedal phalanges. These pathologies can be classified as follows: the fifth cervical vertebra, the scapula, several ribs and the ischium are probably traumatic, and a callus on the shaft of the left pedal phalanx II-2 is probably traumatic-infectious. Traumatically fractured elements exposed to frequent movement (e.g., the scapula and the ribs) show a tendency to develop pseudarthroses instead of a callus. The pathologies in the lower jaw and a reduced extensor tubercle of the left pedal phalanx II-2 are most likely traumatic or developmental in origin. The pathologies on the fourth cervical are most likely developmental in origin or idiopathic, that on the left humerus could be traumatic, developmental, infectious or idiopathic, whereas the left pedal phalanx IV-1 is classified as idiopathic. With exception of the ischium, all as traumatic/traumatic-infectious classified pathologic elements show unambiguous evidences of healing, indicating that the respective pathologies did not cause the death of this individual. Alignment of the scapula and rib pathologies from the left side suggests that all may have been caused by a single traumatic event. The ischial fracture may have been fatal. The occurrence of multiple lesions interpreted as traumatic pathologies again underlines that large-bodied theropods experienced frequent injuries during life, indicating an active predatory lifestyle, and their survival perhaps supports a gregarious behavior for Allosaurus. Alternatively, the frequent survival of traumatic events could be also related to the p…
bibliographic citation: Foth et al. (2015) New insights into the lifestyle of Allosaurus (Dinosauria: Theropoda) based on another specimen with multiple pathologies. PeerJ 3:e940 https://doi.org/10.7717/peerj.940
date submitted: 2015-02-04
date accepted: 2015-04-16
issued: 2015-05-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Foth
  given name: Christian
author list: Agent
  family name: Evers
  given name: Serjoscha W.
author list: Agent
  family name: Pabst
  given name: Ben
author list: Agent
  family name: Mateus
  given name: Octávio
author list: Agent
  family name: Flisch
  given name: Alexander
author list: Agent
  family name: Patthey
  given name: Mike
author list: Agent
  family name: Rauhut
  given name: Oliver W.M.
doi: 10.7717/peerj.940
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-12
copyright: © 2015 Foth et al.
attribution name: Foth et al.

Thylacinus (Marsupialia: Thylacinidae) from the Mio-Pliocene boundary and the diversity of Late Neogene thylacinids in Australia
type: item
type: AcademicArticle
description: Thylacinus yorkellus is described as a new, moderately small-bodied species of thylacinid from the latest Miocene or, more likely, earliest Pliocene of South Australia. The new species can be diagnosed by the autapomorphic presence a strongly developed precingulid that terminates in a cuspidule on the anterobuccal face of the paraconid of the lower molars and a tiny basal anterior cuspidule on P2, P3 and the lower molars. It is found by cladistic analysis to be the sister species of the recently extinct Th. cynocephalus and distinct from the approximately coeval Th. megiriani from the Northern Territory. New dentary material is described and referred to Th. megiriani. These add character data and allow this species to be re-diagnosed based on autapomorphic character traits. Each of the three known late Miocene to early Pliocene Thylacinus species (Th. potens, Th. megiriani and Th. yorkellus) suggest that, instead of declining, there was a modest radiation of Thylacinus in the late Miocene.
format: application/pdf
format: text/html
creator: Adam M. Yates
subject: Biodiversity
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.931
publisher: PeerJ Inc.
rights: © 2015 Yates
abstract: Thylacinus yorkellus is described as a new, moderately small-bodied species of thylacinid from the latest Miocene or, more likely, earliest Pliocene of South Australia. The new species can be diagnosed by the autapomorphic presence a strongly developed precingulid that terminates in a cuspidule on the anterobuccal face of the paraconid of the lower molars and a tiny basal anterior cuspidule on P2, P3 and the lower molars. It is found by cladistic analysis to be the sister species of the recently extinct Th. cynocephalus and distinct from the approximately coeval Th. megiriani from the Northern Territory. New dentary material is described and referred to Th. megiriani. These add character data and allow this species to be re-diagnosed based on autapomorphic character traits. Each of the three known late Miocene to early Pliocene Thylacinus species (Th. potens, Th. megiriani and Th. yorkellus) suggest that, instead of declining, there was a modest radiation of Thylacinus in the late Miocene.
bibliographic citation: Yates (2015) Thylacinus (Marsupialia: Thylacinidae) from the Mio-Pliocene boundary and the diversity of Late Neogene thylacinids in Australia. PeerJ 3:e931 https://doi.org/10.7717/peerj.931
date submitted: 2015-03-18
date accepted: 2015-04-13
issued: 2015-05-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yates
  given name: Adam M.
doi: 10.7717/peerj.931
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-12
copyright: © 2015 Yates
attribution name: Yates

Male convict cichlid 11-ketotestosterone levels throughout the reproductive cycle: an exploratory profile study in laboratory and field populations
type: item
type: AcademicArticle
description: The convict cichlid (Amatitlania nigrofasciata) has been extensively examined in relation to many behavioral topics, such as courtship, pair-bonding, bi-parental care, and territoriality. Recently, this model species has been utilized in studies on genetics, endocrinology, and neuroanatomy, with an ultimate goal of connecting behavior with its underlying mechanisms. The goal of this study was two-fold: (1) profile the circulating levels of plasma 11KT in the male convict cichlid at multiple points during the reproductive cycle and (2) generally compare the hormonal profiles of the widely used laboratory populations and those of a free-living population in the streams of Costa Rica. The results of the field experiment showed that male convict cichlids had higher levels of circulating 11KT during courtship and lower during the parental care and non-breeding phases. The profile of the laboratory population was similar to the profile of the free-living individuals, with significantly higher levels of 11KT occurring during courtship than during parental care, though the level of 11KT during non-breeding phase was elevated in the laboratory. The high levels of 11KT during courtship and low levels of 11KT during parental care found in both the field and the laboratory is similar to what has been reported in other species of teleosts, and may suggest an important function of 11KT in the expression of courtship behavior and the subsequent onset of parental behaviors in this model species.
format: application/pdf
format: text/html
creator: Natalie April van Breukelen
creator: Jennifer L. Snekser
creator: Murray Itzkowitz
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.949
publisher: PeerJ Inc.
rights: © 2015 van Breukelen et al.
abstract: The convict cichlid (Amatitlania nigrofasciata) has been extensively examined in relation to many behavioral topics, such as courtship, pair-bonding, bi-parental care, and territoriality. Recently, this model species has been utilized in studies on genetics, endocrinology, and neuroanatomy, with an ultimate goal of connecting behavior with its underlying mechanisms. The goal of this study was two-fold: (1) profile the circulating levels of plasma 11KT in the male convict cichlid at multiple points during the reproductive cycle and (2) generally compare the hormonal profiles of the widely used laboratory populations and those of a free-living population in the streams of Costa Rica. The results of the field experiment showed that male convict cichlids had higher levels of circulating 11KT during courtship and lower during the parental care and non-breeding phases. The profile of the laboratory population was similar to the profile of the free-living individuals, with significantly higher levels of 11KT occurring during courtship than during parental care, though the level of 11KT during non-breeding phase was elevated in the laboratory. The high levels of 11KT during courtship and low levels of 11KT during parental care found in both the field and the laboratory is similar to what has been reported in other species of teleosts, and may suggest an important function of 11KT in the expression of courtship behavior and the subsequent onset of parental behaviors in this model species.
bibliographic citation: van Breukelen et al. (2015) Male convict cichlid 11-ketotestosterone levels throughout the reproductive cycle: an exploratory profile study in laboratory and field populations. PeerJ 3:e949 https://doi.org/10.7717/peerj.949
date submitted: 2014-09-18
date accepted: 2015-04-20
issued: 2015-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van Breukelen
  given name: Natalie April
author list: Agent
  family name: Snekser
  given name: Jennifer L.
author list: Agent
  family name: Itzkowitz
  given name: Murray
doi: 10.7717/peerj.949
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-07
copyright: © 2015 van Breukelen et al.
attribution name: van Breukelen et al.

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