title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1951
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Impacts of sea level rise and climate change on coastal plant species in the central California coast
link: https://peerj.com/articles/958
last-modified: 2015-05-12
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.
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
uri: https://doi.org/10.7717/peerj.958
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Garner et al.

title: Tactile roughness perception in the presence of olfactory and trigeminal stimulants
link: https://peerj.com/articles/955
last-modified: 2015-05-12
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.
creator: Lara A. Koijck
creator: Alexander Toet
creator: Jan B.F. Van Erp
uri: https://doi.org/10.7717/peerj.955
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Koijck et al.

title: Comparison of methods used to estimate coral cover in the Hawaiian Islands
link: https://peerj.com/articles/954
last-modified: 2015-05-12
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.
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
uri: https://doi.org/10.7717/peerj.954
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Jokiel et al.

title: The unnatural history of Kāne‘ohe Bay: coral reef resilience in the face of centuries of anthropogenic impacts
link: https://peerj.com/articles/950
last-modified: 2015-05-12
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 Kāneʻohe Bay developed under estuarine conditions and thus have been subjected to multiple natural stresses. These include storm floods, a more extreme temperature range than more oceanic reefs, high rates of sedimentation, and exposure at extreme low tides. Deposition and degradation of organic materials carried into the bay from the watershed results in low pH conditions such that according to some ocean acidification projections the rich coral reefs in the bay should not exist. Increased global temperature due to anthropogenic fossil fuel emmisions is now impacting these reefs with the first “bleaching event” in 1996 and a second more severe event in 2014. The reefs of Kāneʻohe Bay have developed and persist under rather severe natural and anthropogenic perturbations. To date, these reefs have proved to be very resilient once the stressor has been removed. A major question remains to be answered concerning the limits of Kāneʻohe Bay reef resilience in the face of global climate change.
creator: Keisha D. Bahr
creator: Paul L. Jokiel
creator: Robert J. Toonen
uri: https://doi.org/10.7717/peerj.950
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Bahr et al.

title: Transgenic LRRK2R1441G rats–a model for Parkinson disease?
link: https://peerj.com/articles/945
last-modified: 2015-05-12
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.
creator: Komal T. Shaikh
creator: Alvin Yang
creator: Ekaterina Youshin
creator: Susanne Schmid
uri: https://doi.org/10.7717/peerj.945
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Shaikh et al.

title: The diversity of membrane transporters encoded in bacterial arsenic-resistance operons
link: https://peerj.com/articles/943
last-modified: 2015-05-12
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.
creator: Yiren Yang
creator: Shiyang Wu
creator: Ross McCausland Lilley
creator: Ren Zhang
uri: https://doi.org/10.7717/peerj.943
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Yang et al.

title: New insights into the lifestyle of Allosaurus (Dinosauria: Theropoda) based on another specimen with multiple pathologies
link: https://peerj.com/articles/940
last-modified: 2015-05-12
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 presence of non-endothermic metabolic rates that allow survival based on sporadic food consumption or scavenging behavior. Signs of pathologies consistent with infections are scarce and locally restricted, indicating a successful prevention of the spread of pathogens, as it is the case in extant reptiles (including birds).
creator: Christian Foth
creator: Serjoscha W. Evers
creator: Ben Pabst
creator: Octávio Mateus
creator: Alexander Flisch
creator: Mike Patthey
creator: Oliver W.M. Rauhut
uri: https://doi.org/10.7717/peerj.940
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Foth et al.

title: Thylacinus (Marsupialia: Thylacinidae) from the Mio-Pliocene boundary and the diversity of Late Neogene thylacinids in Australia
link: https://peerj.com/articles/931
last-modified: 2015-05-12
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.
creator: Adam M. Yates
uri: https://doi.org/10.7717/peerj.931
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Yates

title: Male convict cichlid 11-ketotestosterone levels throughout the reproductive cycle: an exploratory profile study in laboratory and field populations
link: https://peerj.com/articles/949
last-modified: 2015-05-07
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.
creator: Natalie April van Breukelen
creator: Jennifer L. Snekser
creator: Murray Itzkowitz
uri: https://doi.org/10.7717/peerj.949
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 van Breukelen et al.

title: Calcium affinity of human α-actinin 1
link: https://peerj.com/articles/944
last-modified: 2015-05-07
description: Due to alternative splicing, the human ACTN1 gene codes for three different transcripts of α-actinin; one isoform that is expressed only in the brain and two with a more general expression pattern. The sequence difference is located to the C-terminal domains and the EF-hand motifs. Therefore, any functional or structural distinction should involve this part of the protein. To investigate this further, the calcium affinities of these three isoforms of α-actinin 1 have been determined by isothermal calorimetry.
creator: Lars Backman
uri: https://doi.org/10.7717/peerj.944
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Backman