PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Timing and ecological priority shaped the diversification of sedges in the Himalayas
items: A behavioral and genetic study of multiple paternity in a polygamous marine invertebrate, Octopus oliveri
items: The cutting-edge morphology of the mole snake’s dental apparatus
items: Move it or lose it: interspecific variation in risk response of pond-breeding anurans
items: Chronic intake of high-dose of blueberry leaf extract does not augment the harmful effects of ethanol in rats
items: Digital dissection of the pelvis and hindlimb of the red-legged running frog, Phlyctimantis maculatus, using Diffusible Iodine Contrast Enhanced computed microtomography (DICE μCT)
items: Metabolic traits specific for lipid-overproducing strain of Mucor circinelloides WJ11 identified by genome-scale modeling approach
items: Antioxidant enzyme cycling over reproductive lunar cycles in Pocillopora damicornis
items: The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)
items: The influence of pharmacologically-induced affective states on attention bias in sheep

Timing and ecological priority shaped the diversification of sedges in the Himalayas
type: item
type: AcademicArticle
description: Background Diversification patterns in the Himalayas have been important to our understanding of global biodiversity. Despite recent broad-scale studies, the most diverse angiosperm genus of the temperate zone—Carex L. (Cyperaceae), with ca. 2100 species worldwide—has not yet been studied in the Himalayas, which contains 189 Carex species. Here the timing and phylogenetic pattern of lineage and ecological diversification were inferred in this ecologically significant genus. We particularly investigated whether priority, adaptation to ecological conditions, or both explain the highly successful radiation of the Kobresia clade (ca. 60 species, of which around 40 are present in the Himalayas) of Himalayan Carex. Methods Phylogenetic relationships were inferred using maximum likelihood analysis of two nuclear ribosomal DNA (nrDNA) regions (ITS and ETS) and one plastid gene (matK); the resulting tree was time-calibrated using penalized likelihood and a fossil calibration at the root of the tree. Biogeographical reconstruction for estimation of historical events and ancestral ranges was performed using the dispersal-extinction-cladogenesis (DEC) model, and reciprocal effects between biogeography and diversification were inferred using the geographic state speciation and extinction (GeoSSE) model. Climatic envelopes for all species for which mapped specimen data available were estimated using climatic data from WORLDCLIM, and climatic niche evolution was inferred using a combination of Ornstein-Uhlenbeck models of shifting adaptive optima and maximum likelihood inference of ancestral character states under a Brownian motion model. Results The Himalayan Carex flora represents three of the five major Carex clades, each represented by multiple origins within the Himalayas. The oldest Carex radiation in the region, dating to ca. 20 Ma, near the time of Himalayan orogeny, gave rise to the now abundant Kobresia clade via long-distance dispersal from the Nearctic. The Himalayan C…
format: application/pdf
format: text/html
creator: Uzma
creator: Pedro Jiménez-Mejías
creator: Rabia Amir
creator: Muhammad Qasim Hayat
creator: Andrew L. Hipp
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.6792
publisher: PeerJ Inc.
rights: © 2019 Uzma et al.
abstract: Background Diversification patterns in the Himalayas have been important to our understanding of global biodiversity. Despite recent broad-scale studies, the most diverse angiosperm genus of the temperate zone—Carex L. (Cyperaceae), with ca. 2100 species worldwide—has not yet been studied in the Himalayas, which contains 189 Carex species. Here the timing and phylogenetic pattern of lineage and ecological diversification were inferred in this ecologically significant genus. We particularly investigated whether priority, adaptation to ecological conditions, or both explain the highly successful radiation of the Kobresia clade (ca. 60 species, of which around 40 are present in the Himalayas) of Himalayan Carex. Methods Phylogenetic relationships were inferred using maximum likelihood analysis of two nuclear ribosomal DNA (nrDNA) regions (ITS and ETS) and one plastid gene (matK); the resulting tree was time-calibrated using penalized likelihood and a fossil calibration at the root of the tree. Biogeographical reconstruction for estimation of historical events and ancestral ranges was performed using the dispersal-extinction-cladogenesis (DEC) model, and reciprocal effects between biogeography and diversification were inferred using the geographic state speciation and extinction (GeoSSE) model. Climatic envelopes for all species for which mapped specimen data available were estimated using climatic data from WORLDCLIM, and climatic niche evolution was inferred using a combination of Ornstein-Uhlenbeck models of shifting adaptive optima and maximum likelihood inference of ancestral character states under a Brownian motion model. Results The Himalayan Carex flora represents three of the five major Carex clades, each represented by multiple origins within the Himalayas. The oldest Carex radiation in the region, dating to ca. 20 Ma, near the time of Himalayan orogeny, gave rise to the now abundant Kobresia clade via long-distance dispersal from the Nearctic. The Himalayan C…
bibliographic citation: Uzma et al. (2019) Timing and ecological priority shaped the diversification of sedges in the Himalayas. PeerJ 7:e6792 https://doi.org/10.7717/peerj.6792
date submitted: 2018-11-29
date accepted: 2019-03-15
issued: 2019-06-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Uzma
author list: Agent
  family name: Jiménez-Mejías
  given name: Pedro
author list: Agent
  family name: Amir
  given name: Rabia
author list: Agent
  family name: Hayat
  given name: Muhammad Qasim
author list: Agent
  family name: Hipp
  given name: Andrew L.
doi: 10.7717/peerj.6792
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-07
copyright: ©2019 Uzma et al.
attribution name: Uzma et al.

A behavioral and genetic study of multiple paternity in a polygamous marine invertebrate, Octopus oliveri
type: item
type: AcademicArticle
description: Octopus oliveri is a widespread and common rocky intertidal cephalopod that mates readily in the laboratory, but for which mating behavior has not been reported previously. Four sets of behavioral experiments were recorded wherein three males, small, medium & large in varying order, were introduced to each of six females, for a total of 24 individual females and 12 individual males utilized in the experiments. Video analysis shows that successful mating occurred in each of the mount, reach and beak-to-beak positions. Mating was observed for all males, regardless of size relative to the female, or order of introduction. Females showed preference for the first male to which they were introduced in experimental pairings rather than any specific male trait, and mating time increased significantly with increasing female size. Five novel microsatellite markers were developed and used to test paternity in the eleven broods resulting from these experimental pairings. We found skewed paternity in each brood, with early male precedence and male size being the best predictors of parentage. Multiple paternity was observed in every experimental cross but was estimated to be comparatively low in the field, suggesting that sperm limitation might be common in this species. We saw no evidence of direct sperm competition in Octopus oliveri, but larger males produced significantly more offspring. This study contributes to the growing research on cephalopod mating systems and indicates that octopus mating dynamics might be more variable and complex than thought previously.
format: application/pdf
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creator: Heather Ylitalo
creator: Thomas A. Oliver
creator: Iria Fernandez-Silva
creator: James B. Wood
creator: Robert J. Toonen
subject: Animal Behavior
subject: Ecology
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.6927
publisher: PeerJ Inc.
rights: © 2019 Ylitalo et al.
abstract: Octopus oliveri is a widespread and common rocky intertidal cephalopod that mates readily in the laboratory, but for which mating behavior has not been reported previously. Four sets of behavioral experiments were recorded wherein three males, small, medium & large in varying order, were introduced to each of six females, for a total of 24 individual females and 12 individual males utilized in the experiments. Video analysis shows that successful mating occurred in each of the mount, reach and beak-to-beak positions. Mating was observed for all males, regardless of size relative to the female, or order of introduction. Females showed preference for the first male to which they were introduced in experimental pairings rather than any specific male trait, and mating time increased significantly with increasing female size. Five novel microsatellite markers were developed and used to test paternity in the eleven broods resulting from these experimental pairings. We found skewed paternity in each brood, with early male precedence and male size being the best predictors of parentage. Multiple paternity was observed in every experimental cross but was estimated to be comparatively low in the field, suggesting that sperm limitation might be common in this species. We saw no evidence of direct sperm competition in Octopus oliveri, but larger males produced significantly more offspring. This study contributes to the growing research on cephalopod mating systems and indicates that octopus mating dynamics might be more variable and complex than thought previously.
bibliographic citation: Ylitalo et al. (2019) A behavioral and genetic study of multiple paternity in a polygamous marine invertebrate, Octopus oliveri. PeerJ 7:e6927 https://doi.org/10.7717/peerj.6927
date submitted: 2018-10-30
date accepted: 2019-04-07
issued: 2019-06-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ylitalo
  given name: Heather
author list: Agent
  family name: Oliver
  given name: Thomas A.
author list: Agent
  family name: Fernandez-Silva
  given name: Iria
author list: Agent
  family name: Wood
  given name: James B.
author list: Agent
  family name: Toonen
  given name: Robert J.
doi: 10.7717/peerj.6927
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-07
copyright: ©2019 Ylitalo et al.
attribution name: Ylitalo et al.

The cutting-edge morphology of the mole snake’s dental apparatus
type: item
type: AcademicArticle
description: The mole snake (Pseudaspis cana) is capable of inflicting unusual bites in defence and during male combat that present as two parallel lacerations. We investigated the dental morphology of the mole snake by making SEM images, and by CT-scanning and digitally reconstructing the skulls of 14 specimens comprising both sexes. The lengths, volumes, shapes and positions of maxillary and dentary teeth were compared within individuals, between individuals, and between sexes. CT reconstructions show the occurrence of large, flat triangular teeth at the posterior end of the maxilla that are angled to point towards the posterior of the skull. SEM imagery highlights the presence of sharp ridges (carinae) on the posterior edges of the posterior dentary and maxillary teeth. Males have greater dental specialization, maxillary tooth variation, enlargement of the posterior-most maxillary teeth, and dentary teeth with posterior carinae. We hypothesize that mole snake dental specializations are adaptations for their particular form of male combat and possibly for subduing prey in the confines of underground burrows. Our findings reveal a complex dental morphology in mole snakes and provide impetus for further studies on the functional morphology of snake teeth.
format: application/pdf
format: text/html
creator: Alexandra M. Evans
creator: Jonah N. Choiniere
creator: Graham J. Alexander
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.6943
publisher: PeerJ Inc.
rights: © 2019 Evans et al.
abstract: The mole snake (Pseudaspis cana) is capable of inflicting unusual bites in defence and during male combat that present as two parallel lacerations. We investigated the dental morphology of the mole snake by making SEM images, and by CT-scanning and digitally reconstructing the skulls of 14 specimens comprising both sexes. The lengths, volumes, shapes and positions of maxillary and dentary teeth were compared within individuals, between individuals, and between sexes. CT reconstructions show the occurrence of large, flat triangular teeth at the posterior end of the maxilla that are angled to point towards the posterior of the skull. SEM imagery highlights the presence of sharp ridges (carinae) on the posterior edges of the posterior dentary and maxillary teeth. Males have greater dental specialization, maxillary tooth variation, enlargement of the posterior-most maxillary teeth, and dentary teeth with posterior carinae. We hypothesize that mole snake dental specializations are adaptations for their particular form of male combat and possibly for subduing prey in the confines of underground burrows. Our findings reveal a complex dental morphology in mole snakes and provide impetus for further studies on the functional morphology of snake teeth.
bibliographic citation: Evans et al. (2019) The cutting-edge morphology of the mole snake’s dental apparatus. PeerJ 7:e6943 https://doi.org/10.7717/peerj.6943
date submitted: 2019-02-11
date accepted: 2019-04-11
issued: 2019-06-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Evans
  given name: Alexandra M.
author list: Agent
  family name: Choiniere
  given name: Jonah N.
author list: Agent
  family name: Alexander
  given name: Graham J.
doi: 10.7717/peerj.6943
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-07
copyright: ©2019 Evans et al.
attribution name: Evans et al.

Move it or lose it: interspecific variation in risk response of pond-breeding anurans
type: item
type: AcademicArticle
description: Changes in behavior are often the proximate response of animals to human disturbance, with variability in tolerance levels leading some species to exhibit striking shifts in life history, fitness, and/or survival. Thus, elucidating the effects of disturbance on animal behavior, and how this varies among taxonomically similar species with inherently different behaviors and life histories is of value for management and conservation. We evaluated the risk response of three anuran species—southern leopard frog (Lithobates sphenocephalus), Blanchard’s cricket frog (Acris blanchardi), and green tree frog (Hyla cinerea)—to determine how differences in microhabitat use (arboreal vs ground-dwelling) and body size (small vs medium) may play a role in response to a potential threat within a human-altered subtropical forest. Each species responded to risk with both flight and freeze behaviors, however, behaviors were species- and context-specific. As distance to cover increased, southern leopard frogs increased freezing behavior, green tree frogs decreased freezing behavior, and Blanchard’s cricket frogs increased flight response. The propensity of green tree frogs to use the canopy of vegetation as refugia, and the small body size of Blanchard’s cricket frogs likely led to greater flight response as distance to cover increased, whereas innate reliance on camouflage among southern leopard frogs may place them at greater risk to landscaping, agricultural, and transportation practices in open terrain. As such, arboreal and small-bodied species may inherently be better suited in human altered-landscapes compared to larger, ground-dwelling species. As land-use change continues to modify habitats, understanding how species respond to changes in their environment continues to be of importance, particularly in ecosystems where human-wildlife interactions are expected to increase in frequency.
format: application/pdf
format: text/html
creator: Philip Matich
creator: Christopher M. Schalk
subject: Animal Behavior
subject: Ecology
subject: Zoology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.6956
publisher: PeerJ Inc.
rights: © 2019 Matich and Schalk
abstract: Changes in behavior are often the proximate response of animals to human disturbance, with variability in tolerance levels leading some species to exhibit striking shifts in life history, fitness, and/or survival. Thus, elucidating the effects of disturbance on animal behavior, and how this varies among taxonomically similar species with inherently different behaviors and life histories is of value for management and conservation. We evaluated the risk response of three anuran species—southern leopard frog (Lithobates sphenocephalus), Blanchard’s cricket frog (Acris blanchardi), and green tree frog (Hyla cinerea)—to determine how differences in microhabitat use (arboreal vs ground-dwelling) and body size (small vs medium) may play a role in response to a potential threat within a human-altered subtropical forest. Each species responded to risk with both flight and freeze behaviors, however, behaviors were species- and context-specific. As distance to cover increased, southern leopard frogs increased freezing behavior, green tree frogs decreased freezing behavior, and Blanchard’s cricket frogs increased flight response. The propensity of green tree frogs to use the canopy of vegetation as refugia, and the small body size of Blanchard’s cricket frogs likely led to greater flight response as distance to cover increased, whereas innate reliance on camouflage among southern leopard frogs may place them at greater risk to landscaping, agricultural, and transportation practices in open terrain. As such, arboreal and small-bodied species may inherently be better suited in human altered-landscapes compared to larger, ground-dwelling species. As land-use change continues to modify habitats, understanding how species respond to changes in their environment continues to be of importance, particularly in ecosystems where human-wildlife interactions are expected to increase in frequency.
bibliographic citation: Matich et al. (2019) Move it or lose it: interspecific variation in risk response of pond-breeding anurans. PeerJ 7:e6956 https://doi.org/10.7717/peerj.6956
date submitted: 2018-11-20
date accepted: 2019-04-13
issued: 2019-06-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matich
  given name: Philip
author list: Agent
  family name: Schalk
  given name: Christopher M.
doi: 10.7717/peerj.6956
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-07
copyright: © 2019 Matich and Schalk
attribution name: Matich and Schalk

Chronic intake of high-dose of blueberry leaf extract does not augment the harmful effects of ethanol in rats
type: item
type: AcademicArticle
description: Excessive alcohol consumption is a risk factor for liver diseases. Enhancement of alcohol metabolism could be an effective strategy to prevent these adverse effects since it promotes the clearance of ethanol and acetaldehyde from the serum. Polyphenol-rich products have shown to protect against alcohol-related liver damage. Blueberry leaves have attracted attention as they are rich polyphenols such as proantocyanidins and chlorogenic acid. In this study, we investigated the effects of a high dose of blueberry leaf extract (BLEx) on alcohol metabolism during chronic intake of ethanol. Seven-week old Sprague-Dawley (SD) rats were divided into four groups: normal liquid diet group (NLD), normal liquid diet + BLEx group (NLD + BLEx), alcohol liquid diet group (ALD), and alcohol liquid diet + BLEx (ALD + BLEx). Then, rats were fed experimental diet for 5 weeks and at the end of feeding period, body weight, food intake, liver weight, indices of liver injury, expression and activity of alcohol metabolism-related and anti-oxidative enzymes, and levels of carbonyl protein, triglyceride (TG), and total cholesterol (T-Chol) were measured. Body weight and food intake decreased, whereas liver aldehyde dehydrogenase (ALDH) activity, liver microsomal cytochrome P450 2E1 (CYP2E1) protein and mRNA expression, and heme oxygenase 1 (HO-1) mRNA expression were upregulated by ethanol intake. Dietary BLEx, however, did not affect any of these ethanol-related changes. Indices of liver injury, expression and activity of other alcohol metabolism-related enzymes, liver carbonyl protein, TG, and T-Chol levels were not altered by ethanol and BLEx. Thus, chronic BLEx intake does not ameliorate the harmful effects of ethanol.
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creator: Kaede Yamasaki
creator: Kazuhiro Sugamoto
creator: Teruaki Arakawa
creator: Kazuo Nishiyama
creator: Masao Yamasaki
subject: Food Science and Technology
subject: Metabolic Sciences
description: doi:10.7717/peerj.6989
publisher: PeerJ Inc.
rights: © 2019 Yamasaki et al.
abstract: Excessive alcohol consumption is a risk factor for liver diseases. Enhancement of alcohol metabolism could be an effective strategy to prevent these adverse effects since it promotes the clearance of ethanol and acetaldehyde from the serum. Polyphenol-rich products have shown to protect against alcohol-related liver damage. Blueberry leaves have attracted attention as they are rich polyphenols such as proantocyanidins and chlorogenic acid. In this study, we investigated the effects of a high dose of blueberry leaf extract (BLEx) on alcohol metabolism during chronic intake of ethanol. Seven-week old Sprague-Dawley (SD) rats were divided into four groups: normal liquid diet group (NLD), normal liquid diet + BLEx group (NLD + BLEx), alcohol liquid diet group (ALD), and alcohol liquid diet + BLEx (ALD + BLEx). Then, rats were fed experimental diet for 5 weeks and at the end of feeding period, body weight, food intake, liver weight, indices of liver injury, expression and activity of alcohol metabolism-related and anti-oxidative enzymes, and levels of carbonyl protein, triglyceride (TG), and total cholesterol (T-Chol) were measured. Body weight and food intake decreased, whereas liver aldehyde dehydrogenase (ALDH) activity, liver microsomal cytochrome P450 2E1 (CYP2E1) protein and mRNA expression, and heme oxygenase 1 (HO-1) mRNA expression were upregulated by ethanol intake. Dietary BLEx, however, did not affect any of these ethanol-related changes. Indices of liver injury, expression and activity of other alcohol metabolism-related enzymes, liver carbonyl protein, TG, and T-Chol levels were not altered by ethanol and BLEx. Thus, chronic BLEx intake does not ameliorate the harmful effects of ethanol.
bibliographic citation: Yamasaki et al. (2019) Chronic intake of high-dose of blueberry leaf extract does not augment the harmful effects of ethanol in rats. PeerJ 7:e6989 https://doi.org/10.7717/peerj.6989
date submitted: 2019-01-25
date accepted: 2019-04-20
issued: 2019-06-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yamasaki
  given name: Kaede
author list: Agent
  family name: Sugamoto
  given name: Kazuhiro
author list: Agent
  family name: Arakawa
  given name: Teruaki
author list: Agent
  family name: Nishiyama
  given name: Kazuo
author list: Agent
  family name: Yamasaki
  given name: Masao
doi: 10.7717/peerj.6989
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-07
copyright: ©2019 Yamasaki et al.
attribution name: Yamasaki et al.

Digital dissection of the pelvis and hindlimb of the red-legged running frog, Phlyctimantis maculatus, using Diffusible Iodine Contrast Enhanced computed microtomography (DICE μCT)
type: item
type: AcademicArticle
description: Background The current study applies both traditional and Diffusible Iodine Contrast Enhanced computed microtomography (DICE µCT) techniques to reveal the musculoskeletal anatomy of Phlyctimantis maculatus. DICE µCT has emerged as a powerful tool to visualise intricate musculoskeletal anatomy. By generating 3D digital models, anatomical analyses can be conducted non-destructively, preserving the in situ 3D topography of the system, therefore eliminating some of the drawbacks associated with traditional methods. We aim to describe the musculature of the spine, pelvis, and hindlimb, compare the musculoskeletal anatomy and pelvic morphology of P. maculatus with functionally diverse frogs, and produce 3D digital anatomy reference data. Method An adult frog was stained using an aqueous Lugol’s solution and scanned in a SkyScan1176 in vivo µCT scanner. Scan images were reconstructed, resampled, and digitally segmented to produce a 3D model. A further adult female frog was dissected traditionally for visualisation of tendinous insertions. Results Our work revealed three main findings: (1) P. maculatus has similar gross muscular anatomy to Rana catesbeiana (bullfrog) but is distinct from those species that exhibit ancestral traits (leopelmids) and those that are highly specialised (pipids), (2) P. maculatus’s pelvic anatomy best fits the description of Emerson’s walking/hopping pelvic morphotype IIA, and (3) a split in the semimembranosus and gracilis major muscles is consistent with the reported myology in other anuran species. Discussion While DICE µCT methods were instrumental in characterising the 3D anatomy, traditional dissection was still required to visualise important structures such as the knee aponeurosis, tendinous insertions, and fasciae. Nonetheless, the anatomical data presented here marks the first detailed digital description of an arboreal and terrestrial frog. Further, our digital model presents P. maculatus as a good frog model system and as such has for…
format: application/pdf
format: text/html
creator: Amber J. Collings
creator: Christopher T. Richards
subject: Evolutionary Studies
subject: Zoology
subject: Anatomy and Physiology
description: doi:10.7717/peerj.7003
publisher: PeerJ Inc.
rights: © 2019 Collings and Richards
abstract: Background The current study applies both traditional and Diffusible Iodine Contrast Enhanced computed microtomography (DICE µCT) techniques to reveal the musculoskeletal anatomy of Phlyctimantis maculatus. DICE µCT has emerged as a powerful tool to visualise intricate musculoskeletal anatomy. By generating 3D digital models, anatomical analyses can be conducted non-destructively, preserving the in situ 3D topography of the system, therefore eliminating some of the drawbacks associated with traditional methods. We aim to describe the musculature of the spine, pelvis, and hindlimb, compare the musculoskeletal anatomy and pelvic morphology of P. maculatus with functionally diverse frogs, and produce 3D digital anatomy reference data. Method An adult frog was stained using an aqueous Lugol’s solution and scanned in a SkyScan1176 in vivo µCT scanner. Scan images were reconstructed, resampled, and digitally segmented to produce a 3D model. A further adult female frog was dissected traditionally for visualisation of tendinous insertions. Results Our work revealed three main findings: (1) P. maculatus has similar gross muscular anatomy to Rana catesbeiana (bullfrog) but is distinct from those species that exhibit ancestral traits (leopelmids) and those that are highly specialised (pipids), (2) P. maculatus’s pelvic anatomy best fits the description of Emerson’s walking/hopping pelvic morphotype IIA, and (3) a split in the semimembranosus and gracilis major muscles is consistent with the reported myology in other anuran species. Discussion While DICE µCT methods were instrumental in characterising the 3D anatomy, traditional dissection was still required to visualise important structures such as the knee aponeurosis, tendinous insertions, and fasciae. Nonetheless, the anatomical data presented here marks the first detailed digital description of an arboreal and terrestrial frog. Further, our digital model presents P. maculatus as a good frog model system and as such has for…
bibliographic citation: Collings et al. (2019) Digital dissection of the pelvis and hindlimb of the red-legged running frog, Phlyctimantis maculatus, using Diffusible Iodine Contrast Enhanced computed microtomography (DICE μCT). PeerJ 7:e7003 https://doi.org/10.7717/peerj.7003
date submitted: 2018-12-11
date accepted: 2019-04-23
issued: 2019-06-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Collings
  given name: Amber J.
author list: Agent
  family name: Richards
  given name: Christopher T.
doi: 10.7717/peerj.7003
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-07
copyright: ©2019 Collings and Richards
attribution name: Collings and Richards

Metabolic traits specific for lipid-overproducing strain of Mucor circinelloides WJ11 identified by genome-scale modeling approach
type: item
type: AcademicArticle
description: The genome-scale metabolic model of a lipid-overproducing strain of Mucor circinelloides WJ11 was developed. The model (iNI1159) contained 1,159 genes, 648 EC numbers, 1,537 metabolites, and 1,355 metabolic reactions, which were localized in different compartments of the cell. Using flux balance analysis (FBA), the iNI1159 model was validated by predicting the specific growth rate. The metabolic traits investigated by phenotypic phase plane analysis (PhPP) showed a relationship between the nutrient uptake rate, cell growth, and the triacylglycerol production rate, demonstrating the strength of the model. A putative set of metabolic reactions affecting the lipid-accumulation process was identified when the metabolic flux distributions under nitrogen-limited conditions were altered by performing fast flux variability analysis (fastFVA) and relative flux change. Comparative analysis of the metabolic models of the lipid-overproducing strain WJ11 (iNI1159) and the reference strain CBS277.49 (iWV1213) using both fastFVA and coordinate hit-and-run with rounding (CHRR) showed that the flux distributions between these two models were significantly different. Notably, a higher flux distribution through lipid metabolisms such as lanosterol, zymosterol, glycerolipid and fatty acids biosynthesis in iNI1159 was observed, leading to an increased lipid production when compared to iWV1213. In contrast, iWV1213 exhibited a higher flux distribution across carbohydrate and amino acid metabolisms and thus generated a high flux for biomass production. This study demonstrated that iNI1159 is an effective predictive tool for the pathway engineering of oleaginous strains for the production of diversified oleochemicals with industrial relevance.
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creator: Nattapat Isarankura Na Ayudhya
creator: Kobkul Laoteng
creator: Yuanda Song
creator: Asawin Meechai
creator: Wanwipa Vongsangnak
subject: Bioinformatics
subject: Genomics
subject: Mycology
description: doi:10.7717/peerj.7015
publisher: PeerJ Inc.
rights: © 2019 Isarankura Na Ayudhya et al.
abstract: The genome-scale metabolic model of a lipid-overproducing strain of Mucor circinelloides WJ11 was developed. The model (iNI1159) contained 1,159 genes, 648 EC numbers, 1,537 metabolites, and 1,355 metabolic reactions, which were localized in different compartments of the cell. Using flux balance analysis (FBA), the iNI1159 model was validated by predicting the specific growth rate. The metabolic traits investigated by phenotypic phase plane analysis (PhPP) showed a relationship between the nutrient uptake rate, cell growth, and the triacylglycerol production rate, demonstrating the strength of the model. A putative set of metabolic reactions affecting the lipid-accumulation process was identified when the metabolic flux distributions under nitrogen-limited conditions were altered by performing fast flux variability analysis (fastFVA) and relative flux change. Comparative analysis of the metabolic models of the lipid-overproducing strain WJ11 (iNI1159) and the reference strain CBS277.49 (iWV1213) using both fastFVA and coordinate hit-and-run with rounding (CHRR) showed that the flux distributions between these two models were significantly different. Notably, a higher flux distribution through lipid metabolisms such as lanosterol, zymosterol, glycerolipid and fatty acids biosynthesis in iNI1159 was observed, leading to an increased lipid production when compared to iWV1213. In contrast, iWV1213 exhibited a higher flux distribution across carbohydrate and amino acid metabolisms and thus generated a high flux for biomass production. This study demonstrated that iNI1159 is an effective predictive tool for the pathway engineering of oleaginous strains for the production of diversified oleochemicals with industrial relevance.
bibliographic citation: Isarankura Na Ayudhya et al. (2019) Metabolic traits specific for lipid-overproducing strain of Mucor circinelloides WJ11 identified by genome-scale modeling approach. PeerJ 7:e7015 https://doi.org/10.7717/peerj.7015
date submitted: 2018-11-22
date accepted: 2019-04-20
issued: 2019-06-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Isarankura Na Ayudhya
  given name: Nattapat
author list: Agent
  family name: Laoteng
  given name: Kobkul
author list: Agent
  family name: Song
  given name: Yuanda
author list: Agent
  family name: Meechai
  given name: Asawin
author list: Agent
  family name: Vongsangnak
  given name: Wanwipa
doi: 10.7717/peerj.7015
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-07
copyright: ©2019 Isarankura Na Ayudhya et al.
attribution name: Isarankura Na Ayudhya et al.

Antioxidant enzyme cycling over reproductive lunar cycles in Pocillopora damicornis
type: item
type: AcademicArticle
description: The impacts of continued degradation of watersheds on coastal coral reefs world-wide is alarming, and action addressing anthropogenic stressors and subsequent rehabilitation of watersheds and adjacent reefs is an urgent priority. The aim of this study is to develop and improve the use of antioxidant enzymes as bioindicators of stress in coral species. In order to fully develop such tools, it is necessary to first understand baseline cycling of these enzymes within coral tissues. Due to inherent links between reproduction and oxidative stress, these aims may be facilitated by sampling coral tissues over reproductively-linked lunar cycles to determine variations from baseline. By developing a greater understanding of biochemical markers of stress in corals, specifically antioxidant defense enzymes catalase (CAT), glutathione reductase (GR), glutathione peroxidase (GPx), and superoxide dismutase (SOD) in Hawaiian Pocillopora damicornis, we have provided molecular tools that identify thresholds of stress on coral reefs. Our results suggest that the coral reproductive state is a significant factor affecting the activity of antioxidant enzymes. Specifically, CAT and GR display maximum activity during peak reproductive state. Whereas significant maximal Se-independent GPx and SOD activity was measured during off-peak reproductive cycles. Such insight into the cyclical variation of the activity of these enzymes should be applied towards differentiating the influence of natural biological activity cycling in diagnostic tests identifying the effects of different physical environmental factors and chemical pollutants on coral health. Through the development and application of these molecular biomarkers of stress, we look to improve our ability to identify problems at the sub-lethal level, when action can be taken to mitigate a/biotic impacts.
format: application/pdf
format: text/html
creator: James W.A. Murphy
creator: Abby C. Collier
creator: Robert H. Richmond
subject: Biochemistry
subject: Conservation Biology
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.7020
publisher: PeerJ Inc.
rights: © 2019 Murphy et al.
abstract: The impacts of continued degradation of watersheds on coastal coral reefs world-wide is alarming, and action addressing anthropogenic stressors and subsequent rehabilitation of watersheds and adjacent reefs is an urgent priority. The aim of this study is to develop and improve the use of antioxidant enzymes as bioindicators of stress in coral species. In order to fully develop such tools, it is necessary to first understand baseline cycling of these enzymes within coral tissues. Due to inherent links between reproduction and oxidative stress, these aims may be facilitated by sampling coral tissues over reproductively-linked lunar cycles to determine variations from baseline. By developing a greater understanding of biochemical markers of stress in corals, specifically antioxidant defense enzymes catalase (CAT), glutathione reductase (GR), glutathione peroxidase (GPx), and superoxide dismutase (SOD) in Hawaiian Pocillopora damicornis, we have provided molecular tools that identify thresholds of stress on coral reefs. Our results suggest that the coral reproductive state is a significant factor affecting the activity of antioxidant enzymes. Specifically, CAT and GR display maximum activity during peak reproductive state. Whereas significant maximal Se-independent GPx and SOD activity was measured during off-peak reproductive cycles. Such insight into the cyclical variation of the activity of these enzymes should be applied towards differentiating the influence of natural biological activity cycling in diagnostic tests identifying the effects of different physical environmental factors and chemical pollutants on coral health. Through the development and application of these molecular biomarkers of stress, we look to improve our ability to identify problems at the sub-lethal level, when action can be taken to mitigate a/biotic impacts.
bibliographic citation: Murphy et al. (2019) Antioxidant enzyme cycling over reproductive lunar cycles in Pocillopora damicornis. PeerJ 7:e7020 https://doi.org/10.7717/peerj.7020
date submitted: 2018-03-21
date accepted: 2019-04-25
issued: 2019-06-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Murphy
  given name: James W.A.
author list: Agent
  family name: Collier
  given name: Abby C.
author list: Agent
  family name: Richmond
  given name: Robert H.
doi: 10.7717/peerj.7020
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-07
copyright: ©2019 Murphy et al.
attribution name: Murphy et al.

The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)
type: item
type: AcademicArticle
description: This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome has a total of 158,227 bp containing 111 genes, including 76 protein-coding genes, 31 tRNA genes and 4 ribosomal RNA genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed while the proportion of nucleotide sites differing between the two species was equal to 0.0018. The six most variable regions were, in increasing order of variability, psbK-psbI, trnG-psbfM, rpl32, trnV, ndhI-ndh and ndhD-psaC. These highly variable chloroplast regions in addition to 160 chloroplast microsatellites identified (of which 46 were variable between the two species) will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.
format: application/pdf
format: text/html
creator: James R. P. Worth
creator: Luxian Liu
creator: Fu-Jin Wei
creator: Nobuhiro Tomaru
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.7026
publisher: PeerJ Inc.
rights: © 2019 Worth et al.
abstract: This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome has a total of 158,227 bp containing 111 genes, including 76 protein-coding genes, 31 tRNA genes and 4 ribosomal RNA genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed while the proportion of nucleotide sites differing between the two species was equal to 0.0018. The six most variable regions were, in increasing order of variability, psbK-psbI, trnG-psbfM, rpl32, trnV, ndhI-ndh and ndhD-psaC. These highly variable chloroplast regions in addition to 160 chloroplast microsatellites identified (of which 46 were variable between the two species) will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.
bibliographic citation: Worth et al. (2019) The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana). PeerJ 7:e7026 https://doi.org/10.7717/peerj.7026
date submitted: 2019-01-09
date accepted: 2019-04-24
issued: 2019-06-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Worth
  given name: James R. P.
author list: Agent
  family name: Liu
  given name: Luxian
author list: Agent
  family name: Wei
  given name: Fu-Jin
author list: Agent
  family name: Tomaru
  given name: Nobuhiro
doi: 10.7717/peerj.7026
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-07
copyright: © 2019 Worth et al.
attribution name: Worth et al.

The influence of pharmacologically-induced affective states on attention bias in sheep
type: item
type: AcademicArticle
description: When an individual attends to certain types of information more than others, the behavior is termed an attention bias. The occurrence of attention biases in humans and animals can depend on their affective states. Based on evidence from the human literature and prior studies in sheep, we hypothesized that an attention bias test could discriminate between pharmacologically-induced positive and negative affective states in sheep. The test measured allocation of attention between a threat and a positive stimulus using key measures of looking time and vigilance. Eighty 7-year-old Merino ewes were allocated to one of four treatment groups; Anxious (m-chlorophenylpiperazine), Calm (diazepam), Happy (morphine) and Control (saline). Drugs were administered 30 min prior to attention bias testing. The test was conducted in a 4 × 4.2 m arena with high opaque walls. An approximately life-size photograph of a sheep was positioned on one wall of the arena (positive stimulus). A small window with a retractable opaque cover was positioned on the opposite wall, behind which a dog was standing quietly (threat). The dog was visible for 3 s after a single sheep entered the arena, then the window was covered and the dog was removed. Sheep then remained in the arena for 3 min while behaviors were recorded. Key behaviors included time looking toward the dog wall or photo wall, duration of vigilance behavior and latency to become non-vigilant. In contrast with our hypothesis, no significant differences were found between treatment groups for duration of vigilance or looking behaviors, although Anxious sheep tended to be more vigilant than Control animals (P < 0.1) and had a longer latency to become non-vigilant (P < 0.001). A total of 24 of 80 animals were vigilant for the entire test duration. This censoring of data may explain why no differences were detected between groups for vigilance duration. Overall, a lack of difference between groups may suggest the test cannot discriminate posit…
format: application/pdf
format: text/html
creator: Jessica E. Monk
creator: Caroline Lee
creator: Sue Belson
creator: Ian G. Colditz
creator: Dana L.M. Campbell
subject: Agricultural Science
subject: Animal Behavior
description: doi:10.7717/peerj.7033
publisher: PeerJ Inc.
rights: © 2019 Monk et al.
abstract: When an individual attends to certain types of information more than others, the behavior is termed an attention bias. The occurrence of attention biases in humans and animals can depend on their affective states. Based on evidence from the human literature and prior studies in sheep, we hypothesized that an attention bias test could discriminate between pharmacologically-induced positive and negative affective states in sheep. The test measured allocation of attention between a threat and a positive stimulus using key measures of looking time and vigilance. Eighty 7-year-old Merino ewes were allocated to one of four treatment groups; Anxious (m-chlorophenylpiperazine), Calm (diazepam), Happy (morphine) and Control (saline). Drugs were administered 30 min prior to attention bias testing. The test was conducted in a 4 × 4.2 m arena with high opaque walls. An approximately life-size photograph of a sheep was positioned on one wall of the arena (positive stimulus). A small window with a retractable opaque cover was positioned on the opposite wall, behind which a dog was standing quietly (threat). The dog was visible for 3 s after a single sheep entered the arena, then the window was covered and the dog was removed. Sheep then remained in the arena for 3 min while behaviors were recorded. Key behaviors included time looking toward the dog wall or photo wall, duration of vigilance behavior and latency to become non-vigilant. In contrast with our hypothesis, no significant differences were found between treatment groups for duration of vigilance or looking behaviors, although Anxious sheep tended to be more vigilant than Control animals (P < 0.1) and had a longer latency to become non-vigilant (P < 0.001). A total of 24 of 80 animals were vigilant for the entire test duration. This censoring of data may explain why no differences were detected between groups for vigilance duration. Overall, a lack of difference between groups may suggest the test cannot discriminate posit…
bibliographic citation: Monk et al. (2019) The influence of pharmacologically-induced affective states on attention bias in sheep. PeerJ 7:e7033 https://doi.org/10.7717/peerj.7033
date submitted: 2019-02-15
date accepted: 2019-04-27
issued: 2019-06-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Monk
  given name: Jessica E.
author list: Agent
  family name: Lee
  given name: Caroline
author list: Agent
  family name: Belson
  given name: Sue
author list: Agent
  family name: Colditz
  given name: Ian G.
author list: Agent
  family name: Campbell
  given name: Dana L.M.
doi: 10.7717/peerj.7033
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-06-07
copyright: © 2019 Monk et al.
attribution name: Monk et al.

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