PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Which psychological, social and physical environmental characteristics predict changes in physical activity and sedentary behaviors during early retirement? A longitudinal study
items: Psychophysical measurements in children: challenges, pitfalls, and considerations
items: A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations
items: Poly(ADP-ribosylation) is present in murine sciatic nerve fibers and is altered in a Charcot-Marie-Tooth-1E neurodegenerative model
items: A survey of fishes associated with Hawaiian deep-water Halimeda kanaloana (Bryopsidales: Halimedaceae) and Avrainvillea sp. (Bryopsidales: Udoteaceae) meadows
items: Sooty tern (Onychoprion fuscatus) survival, oil spills, shrimp fisheries, and hurricanes
items: Screening of a natural compound library identifies emodin, a natural compound from Rheum palmatum Linn that inhibits DPP4
items: Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex
items: Transcriptome sequencing and SNP detection in Phoebe chekiangensis
items: Cave features, seasonality and subterranean distribution of non-obligate cave dwellers

Which psychological, social and physical environmental characteristics predict changes in physical activity and sedentary behaviors during early retirement? A longitudinal study
type: item
type: AcademicArticle
description: Background In the context of healthy ageing, it is necessary to identify opportunities to implement health interventions in order to develop an active lifestyle with sufficient physical activity and limited sedentary time in middle-aged and older adults. The transition to retirement is such an opportunity, as individuals tend to establish new routines at the start of retirement. Before health interventions can be developed, the psychological, social and physical environmental determinants of physical activity and sedentary behaviors during early retirement should be identified, ideally with longitudinal studies. The aim of this paper was first to examine whether psychological, social and physical environmental factors at the start of retirement predict longitudinal changes in physical activity and sedentary behaviors during the first years of retirement. Second, moderating effects of gender and educational levels were examined. Methods This longitudinal study was conducted in Flanders, Belgium. In total, 180 recently retired (>1 month, <2 years at baseline) adults completed a postal questionnaire twice (in 2012–2013 and two years later in 2014–2015). The validated questionnaire assessed socio-demographic information, physical activity, sedentary behaviors, and psychological, social and physical environmental characteristics. Multiple moderated hierarchic regression analyses were conducted in SPSS 22.0. Results Higher perceived residential density (p < 0.001) and lower aesthetics (p = 0.08) predicted an increase in active transportation (adjusted R2 = 0.18). Higher baseline self-efficacy was associated with an increase in leisure-time physical activity (p = 0.001, adjusted R2 = 0.13). A more positive perception of old age (p = 0.04) and perceiving less street connectivity (p = 0.001) were associated with an increase in screen time (adjusted R2 = 0.06). Finally, higher baseline levels of modeling from friends (p = 0.06) and lower perceived land use mix access (p = 0.0…
format: application/pdf
format: text/html
creator: Delfien Van Dyck
creator: Greet Cardon
creator: Ilse De Bourdeaudhuij
subject: Geriatrics
subject: Global Health
subject: Health Policy
subject: Public Health
description: doi:10.7717/peerj.3242
publisher: PeerJ Inc.
rights: © 2017 Van Dyck et al.
abstract: Background In the context of healthy ageing, it is necessary to identify opportunities to implement health interventions in order to develop an active lifestyle with sufficient physical activity and limited sedentary time in middle-aged and older adults. The transition to retirement is such an opportunity, as individuals tend to establish new routines at the start of retirement. Before health interventions can be developed, the psychological, social and physical environmental determinants of physical activity and sedentary behaviors during early retirement should be identified, ideally with longitudinal studies. The aim of this paper was first to examine whether psychological, social and physical environmental factors at the start of retirement predict longitudinal changes in physical activity and sedentary behaviors during the first years of retirement. Second, moderating effects of gender and educational levels were examined. Methods This longitudinal study was conducted in Flanders, Belgium. In total, 180 recently retired (>1 month, <2 years at baseline) adults completed a postal questionnaire twice (in 2012–2013 and two years later in 2014–2015). The validated questionnaire assessed socio-demographic information, physical activity, sedentary behaviors, and psychological, social and physical environmental characteristics. Multiple moderated hierarchic regression analyses were conducted in SPSS 22.0. Results Higher perceived residential density (p < 0.001) and lower aesthetics (p = 0.08) predicted an increase in active transportation (adjusted R2 = 0.18). Higher baseline self-efficacy was associated with an increase in leisure-time physical activity (p = 0.001, adjusted R2 = 0.13). A more positive perception of old age (p = 0.04) and perceiving less street connectivity (p = 0.001) were associated with an increase in screen time (adjusted R2 = 0.06). Finally, higher baseline levels of modeling from friends (p = 0.06) and lower perceived land use mix access (p = 0.0…
bibliographic citation: Van Dyck et al. (2017) Which psychological, social and physical environmental characteristics predict changes in physical activity and sedentary behaviors during early retirement? A longitudinal study. PeerJ 5:e3242 https://doi.org/10.7717/peerj.3242
date submitted: 2016-09-01
date accepted: 2017-03-28
issued: 2017-05-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Van Dyck
  given name: Delfien
author list: Agent
  family name: Cardon
  given name: Greet
author list: Agent
  family name: De Bourdeaudhuij
  given name: Ilse
doi: 10.7717/peerj.3242
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-11
copyright: ©2017 Van Dyck et al.
attribution name: Van Dyck et al.

Psychophysical measurements in children: challenges, pitfalls, and considerations
type: item
type: AcademicArticle
description: Measuring sensory sensitivity is important in studying development and developmental disorders. However, with children, there is a need to balance reliable but lengthy sensory tasks with the child’s ability to maintain motivation and vigilance. We used simulations to explore the problems associated with shortening adaptive psychophysical procedures, and suggest how these problems might be addressed. We quantify how adaptive procedures with too few reversals can over-estimate thresholds, introduce substantial measurement error, and make estimates of individual thresholds less reliable. The associated measurement error also obscures group differences. Adaptive procedures with children should therefore use as many reversals as possible, to reduce the effects of both Type 1 and Type 2 errors. Differences in response consistency, resulting from lapses in attention, further increase the over-estimation of threshold. Comparisons between data from individuals who may differ in lapse rate are therefore problematic, but measures to estimate and account for lapse rates in analyses may mitigate this problem.
format: application/pdf
format: text/html
creator: Caroline Witton
creator: Joel B. Talcott
creator: G. Bruce Henning
subject: Developmental Biology
subject: Neuroscience
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3231
publisher: PeerJ Inc.
rights: © 2017 Witton et al.
abstract: Measuring sensory sensitivity is important in studying development and developmental disorders. However, with children, there is a need to balance reliable but lengthy sensory tasks with the child’s ability to maintain motivation and vigilance. We used simulations to explore the problems associated with shortening adaptive psychophysical procedures, and suggest how these problems might be addressed. We quantify how adaptive procedures with too few reversals can over-estimate thresholds, introduce substantial measurement error, and make estimates of individual thresholds less reliable. The associated measurement error also obscures group differences. Adaptive procedures with children should therefore use as many reversals as possible, to reduce the effects of both Type 1 and Type 2 errors. Differences in response consistency, resulting from lapses in attention, further increase the over-estimation of threshold. Comparisons between data from individuals who may differ in lapse rate are therefore problematic, but measures to estimate and account for lapse rates in analyses may mitigate this problem.
bibliographic citation: Witton et al. (2017) Psychophysical measurements in children: challenges, pitfalls, and considerations. PeerJ 5:e3231 https://doi.org/10.7717/peerj.3231
date submitted: 2016-12-07
date accepted: 2017-03-26
issued: 2017-05-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Witton
  given name: Caroline
author list: Agent
  family name: Talcott
  given name: Joel B.
author list: Agent
  family name: Henning
  given name: G. Bruce
doi: 10.7717/peerj.3231
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-11
copyright: ©2017 Witton et al.
attribution name: Witton et al.

A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations
type: item
type: AcademicArticle
description: The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture and increased urbanisation. Despite this, there is a lack of efficient methods for discovering and monitoring populations. Established macroinvertebrate monitoring methods, such as net sampling, are unsuitable given the organism’s life history, that include long lived diapausing eggs, benthic habits and ephemerally active populations. Conventional hatching methods, such as sediment incubation, are both time consuming and potentially confounded by bet-hedging hatching strategies of diapausing eggs. Here we develop a new molecular diagnostic method to detect viable egg banks of T. cancriformis, and compare its performance to two conventional monitoring methods involving diapausing egg hatching. We apply this method to a collection of pond sediments from the Wildfowl & Wetlands Trust Caerlaverock National Nature Reserve, which holds one of the two remaining British populations of T. cancriformis. DNA barcoding of isolated eggs, using newly designed species-specific primers for a large region of mtDNA, was used to estimate egg viability. These estimates were compared to those obtained by the conventional methods of sediment and isolation hatching. Our method outperformed the conventional methods, revealing six ponds holding viable T. cancriformis diapausing egg banks in Caerlaverock. Additionally, designed species-specific primers for a short region of mtDNA identified degraded, inviable eggs and were used to ascertain the levels of recent mortality within an egg bank. Together with efficient sugar flotation techniques to extract eggs from sediment samples, our molecular method proved to be a faster and more powerful alternative for assessing the viability and condition of T. cancriformis diapausing egg banks.
format: application/pdf
format: text/html
creator: Graham S. Sellers
creator: Larry R. Griffin
creator: Bernd Hänfling
creator: Africa Gómez
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Environmental Sciences
subject: Molecular Biology
description: doi:10.7717/peerj.3228
publisher: PeerJ Inc.
rights: © 2017 Sellers et al.
abstract: The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture and increased urbanisation. Despite this, there is a lack of efficient methods for discovering and monitoring populations. Established macroinvertebrate monitoring methods, such as net sampling, are unsuitable given the organism’s life history, that include long lived diapausing eggs, benthic habits and ephemerally active populations. Conventional hatching methods, such as sediment incubation, are both time consuming and potentially confounded by bet-hedging hatching strategies of diapausing eggs. Here we develop a new molecular diagnostic method to detect viable egg banks of T. cancriformis, and compare its performance to two conventional monitoring methods involving diapausing egg hatching. We apply this method to a collection of pond sediments from the Wildfowl & Wetlands Trust Caerlaverock National Nature Reserve, which holds one of the two remaining British populations of T. cancriformis. DNA barcoding of isolated eggs, using newly designed species-specific primers for a large region of mtDNA, was used to estimate egg viability. These estimates were compared to those obtained by the conventional methods of sediment and isolation hatching. Our method outperformed the conventional methods, revealing six ponds holding viable T. cancriformis diapausing egg banks in Caerlaverock. Additionally, designed species-specific primers for a short region of mtDNA identified degraded, inviable eggs and were used to ascertain the levels of recent mortality within an egg bank. Together with efficient sugar flotation techniques to extract eggs from sediment samples, our molecular method proved to be a faster and more powerful alternative for assessing the viability and condition of T. cancriformis diapausing egg banks.
bibliographic citation: Sellers et al. (2017) A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations. PeerJ 5:e3228 https://doi.org/10.7717/peerj.3228
date submitted: 2016-12-07
date accepted: 2017-03-25
issued: 2017-05-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sellers
  given name: Graham S.
author list: Agent
  family name: Griffin
  given name: Larry R.
author list: Agent
  family name: Hänfling
  given name: Bernd
author list: Agent
  family name: Gómez
  given name: Africa
doi: 10.7717/peerj.3228
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-11
copyright: ©2017 Sellers et al.
attribution name: Sellers et al.

Poly(ADP-ribosylation) is present in murine sciatic nerve fibers and is altered in a Charcot-Marie-Tooth-1E neurodegenerative model
type: item
type: AcademicArticle
description: Background Poly-ADP-ribose (PAR) is a polymer synthesized by poly-ADP-ribose polymerases (PARPs) as a postranslational protein modification and catabolized mainly by poly-ADP-ribose glycohydrolase (PARG). In spite of the existence of cytoplasmic PARPs and PARG, research has been focused on nuclear PARPs and PAR, demonstrating roles in the maintenance of chromatin architecture and the participation in DNA damage responses and transcriptional regulation. We have recently detected non-nuclear PAR structurally and functionally associated to the E-cadherin rich zonula adherens and the actin cytoskeleton of VERO epithelial cells. Myelinating Schwann cells (SC) are stabilized by E-cadherin rich autotypic adherens junctions (AJ). We wondered whether PAR would map to these regions. Besides, we have demonstrated an altered microfilament pattern in peripheral nerves of Trembler-J (Tr-J) model of CMT1-E. We hypothesized that cytoplasmic PAR would accompany such modified F-actin pattern. Methods Wild-type (WT) and Tr-J mice sciatic nerves cryosections were subjected to immunohistofluorescence with anti-PAR antibodies (including antibody validation), F-actin detection with a phalloidin probe and DAPI/DNA counterstaining. Confocal image stacks were subjected to a colocalization highlighter and to semi-quantitative image analysis. Results We have shown for the first time the presence of PAR in sciatic nerves. Cytoplasmic PAR colocalized with F-actin at non-compact myelin regions in WT nerves. Moreover, in Tr-J, cytoplasmic PAR was augmented in close correlation with actin. In addition, nuclear PAR was detected in WT SC and was moderately increased in Tr-J SC. Discussion The presence of PAR associated to non-compact myelin regions (which constitute E-cadherin rich autotypic AJ/actin anchorage regions) and the co-alterations experienced by PAR and the actin cytoskeleton in epithelium and nerves, suggest that PAR may be a constitutive component of AJ/actin anchorage regions. Is PAR st…
format: application/pdf
format: text/html
creator: Laura I. Lafon Hughes
creator: Carlos J. Romeo Cardeillac
creator: Karina B. Cal Castillo
creator: Salomé C. Vilchez Larrea
creator: José R. Sotelo Sosa
creator: Gustavo A. Folle Ungo
creator: Silvia H. Fernández Villamil
creator: Alejandra E. Kun González
subject: Cell Biology
subject: Neuroscience
subject: Histology
description: doi:10.7717/peerj.3318
publisher: PeerJ Inc.
rights: © 2017 Lafon Hughes et al.
abstract: Background Poly-ADP-ribose (PAR) is a polymer synthesized by poly-ADP-ribose polymerases (PARPs) as a postranslational protein modification and catabolized mainly by poly-ADP-ribose glycohydrolase (PARG). In spite of the existence of cytoplasmic PARPs and PARG, research has been focused on nuclear PARPs and PAR, demonstrating roles in the maintenance of chromatin architecture and the participation in DNA damage responses and transcriptional regulation. We have recently detected non-nuclear PAR structurally and functionally associated to the E-cadherin rich zonula adherens and the actin cytoskeleton of VERO epithelial cells. Myelinating Schwann cells (SC) are stabilized by E-cadherin rich autotypic adherens junctions (AJ). We wondered whether PAR would map to these regions. Besides, we have demonstrated an altered microfilament pattern in peripheral nerves of Trembler-J (Tr-J) model of CMT1-E. We hypothesized that cytoplasmic PAR would accompany such modified F-actin pattern. Methods Wild-type (WT) and Tr-J mice sciatic nerves cryosections were subjected to immunohistofluorescence with anti-PAR antibodies (including antibody validation), F-actin detection with a phalloidin probe and DAPI/DNA counterstaining. Confocal image stacks were subjected to a colocalization highlighter and to semi-quantitative image analysis. Results We have shown for the first time the presence of PAR in sciatic nerves. Cytoplasmic PAR colocalized with F-actin at non-compact myelin regions in WT nerves. Moreover, in Tr-J, cytoplasmic PAR was augmented in close correlation with actin. In addition, nuclear PAR was detected in WT SC and was moderately increased in Tr-J SC. Discussion The presence of PAR associated to non-compact myelin regions (which constitute E-cadherin rich autotypic AJ/actin anchorage regions) and the co-alterations experienced by PAR and the actin cytoskeleton in epithelium and nerves, suggest that PAR may be a constitutive component of AJ/actin anchorage regions. Is PAR st…
bibliographic citation: Lafon Hughes et al. (2017) Poly(ADP-ribosylation) is present in murine sciatic nerve fibers and is altered in a Charcot-Marie-Tooth-1E neurodegenerative model. PeerJ 5:e3318 https://doi.org/10.7717/peerj.3318
date submitted: 2017-02-03
date accepted: 2017-04-15
issued: 2017-05-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lafon Hughes
  given name: Laura I.
author list: Agent
  family name: Romeo Cardeillac
  given name: Carlos J.
author list: Agent
  family name: Cal Castillo
  given name: Karina B.
author list: Agent
  family name: Vilchez Larrea
  given name: Salomé C.
author list: Agent
  family name: Sotelo Sosa
  given name: José R.
author list: Agent
  family name: Folle Ungo
  given name: Gustavo A.
author list: Agent
  family name: Fernández Villamil
  given name: Silvia H.
author list: Agent
  family name: Kun González
  given name: Alejandra E.
doi: 10.7717/peerj.3318
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-10
copyright: ©2017 Lafon Hughes et al.
attribution name: Lafon Hughes et al.

A survey of fishes associated with Hawaiian deep-water Halimeda kanaloana (Bryopsidales: Halimedaceae) and Avrainvillea sp. (Bryopsidales: Udoteaceae) meadows
type: item
type: AcademicArticle
description: The invasive macroalgal species Avrainvillea sp. and native species Halimeda kanaloana form expansive meadows that extend to depths of 80 m or more in the waters off of O‘ahu and Maui, respectively. Despite their wide depth distribution, comparatively little is known about the biota associated with these macroalgal species. Our primary goals were to provide baseline information on the fish fauna associated with these deep-water macroalgal meadows and to compare the abundance and diversity of fishes between the meadow interior and sandy perimeters. Because both species form structurally complex three-dimensional canopies, we hypothesized that they would support a greater abundance and diversity of fishes when compared to surrounding sandy areas. We surveyed the fish fauna associated with these meadows using visual surveys and collections made with clove-oil anesthetic. Using these techniques, we recorded a total of 49 species from 25 families for H. kanaloana meadows and surrounding sandy areas, and 28 species from 19 families for Avrainvillea sp. habitats. Percent endemism was 28.6% and 10.7%, respectively. Wrasses (Family Labridae) were the most speciose taxon in both habitats (11 and six species, respectively), followed by gobies for H. kanaloana (six species). The wrasse Oxycheilinus bimaculatus and cardinalfish Apogonichthys perdix were the most frequently-occurring species within the H. kanaloana and Avrainvillea canopies, respectively. Obligate herbivores and food-fish species were rare in both habitats. Surprisingly, the density and abundance of small epibenthic fishes were greater in open sand than in the meadow canopy. In addition, species richness was also higher in open sand for Avrainvillea sp. We hypothesize that the dense holdfasts and rhizoids present within the meadow canopy may impede benthic-dwelling or bioturbator species, which accounted for 86% and 57% of individuals collected in sand adjacent to H. kanaloana and Avrainvillea sp. habitats, respe…
format: application/pdf
format: text/html
creator: Ross C. Langston
creator: Heather L. Spalding
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.3307
publisher: PeerJ Inc.
rights: © 2017 Langston and Spalding
abstract: The invasive macroalgal species Avrainvillea sp. and native species Halimeda kanaloana form expansive meadows that extend to depths of 80 m or more in the waters off of O‘ahu and Maui, respectively. Despite their wide depth distribution, comparatively little is known about the biota associated with these macroalgal species. Our primary goals were to provide baseline information on the fish fauna associated with these deep-water macroalgal meadows and to compare the abundance and diversity of fishes between the meadow interior and sandy perimeters. Because both species form structurally complex three-dimensional canopies, we hypothesized that they would support a greater abundance and diversity of fishes when compared to surrounding sandy areas. We surveyed the fish fauna associated with these meadows using visual surveys and collections made with clove-oil anesthetic. Using these techniques, we recorded a total of 49 species from 25 families for H. kanaloana meadows and surrounding sandy areas, and 28 species from 19 families for Avrainvillea sp. habitats. Percent endemism was 28.6% and 10.7%, respectively. Wrasses (Family Labridae) were the most speciose taxon in both habitats (11 and six species, respectively), followed by gobies for H. kanaloana (six species). The wrasse Oxycheilinus bimaculatus and cardinalfish Apogonichthys perdix were the most frequently-occurring species within the H. kanaloana and Avrainvillea canopies, respectively. Obligate herbivores and food-fish species were rare in both habitats. Surprisingly, the density and abundance of small epibenthic fishes were greater in open sand than in the meadow canopy. In addition, species richness was also higher in open sand for Avrainvillea sp. We hypothesize that the dense holdfasts and rhizoids present within the meadow canopy may impede benthic-dwelling or bioturbator species, which accounted for 86% and 57% of individuals collected in sand adjacent to H. kanaloana and Avrainvillea sp. habitats, respe…
bibliographic citation: Langston et al. (2017) A survey of fishes associated with Hawaiian deep-water Halimeda kanaloana (Bryopsidales: Halimedaceae) and Avrainvillea sp. (Bryopsidales: Udoteaceae) meadows. PeerJ 5:e3307 https://doi.org/10.7717/peerj.3307
date submitted: 2016-11-18
date accepted: 2017-04-13
issued: 2017-05-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Langston
  given name: Ross C.
author list: Agent
  family name: Spalding
  given name: Heather L.
doi: 10.7717/peerj.3307
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-10
copyright: ©2017 Langston and Spalding
attribution name: Langston and Spalding

Sooty tern (Onychoprion fuscatus) survival, oil spills, shrimp fisheries, and hurricanes
type: item
type: AcademicArticle
description: Migratory seabirds face threats from climate change and a variety of anthropogenic disturbances. Although most seabird research has focused on the ecology of individuals at the colony, technological advances now allow researchers to track seabird movements at sea and during migration. We combined telemetry data on Onychoprion fuscatus (sooty terns) with a long-term capture-mark-recapture dataset from the Dry Tortugas National Park to map the movements at sea for this species, calculate estimates of mortality, and investigate the impact of hurricanes on a migratory seabird. Included in the latter analysis is information on the locations of recovered bands from deceased individuals wrecked by tropical storms. We present the first known map of sooty tern migration in the Atlantic Ocean. Our results indicate that the birds had minor overlaps with areas affected by the major 2010 oil spill and a major shrimp fishery. Indices of hurricane strength and occurrence are positively correlated with annual mortality and indices of numbers of wrecked birds. As climate change may lead to an increase in severity and frequency of major hurricanes, this may pose a long-term problem for this colony.
format: application/pdf
format: text/html
creator: Ryan M. Huang
creator: Oron L. Bass Jr
creator: Stuart L. Pimm
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.3287
publisher: PeerJ Inc.
rights: © 2017 Huang et al.
abstract: Migratory seabirds face threats from climate change and a variety of anthropogenic disturbances. Although most seabird research has focused on the ecology of individuals at the colony, technological advances now allow researchers to track seabird movements at sea and during migration. We combined telemetry data on Onychoprion fuscatus (sooty terns) with a long-term capture-mark-recapture dataset from the Dry Tortugas National Park to map the movements at sea for this species, calculate estimates of mortality, and investigate the impact of hurricanes on a migratory seabird. Included in the latter analysis is information on the locations of recovered bands from deceased individuals wrecked by tropical storms. We present the first known map of sooty tern migration in the Atlantic Ocean. Our results indicate that the birds had minor overlaps with areas affected by the major 2010 oil spill and a major shrimp fishery. Indices of hurricane strength and occurrence are positively correlated with annual mortality and indices of numbers of wrecked birds. As climate change may lead to an increase in severity and frequency of major hurricanes, this may pose a long-term problem for this colony.
bibliographic citation: Huang et al. (2017) Sooty tern (Onychoprion fuscatus) survival, oil spills, shrimp fisheries, and hurricanes. PeerJ 5:e3287 https://doi.org/10.7717/peerj.3287
date submitted: 2016-09-05
date accepted: 2017-04-08
issued: 2017-05-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Ryan M.
author list: Agent
  family name: Bass Jr
  given name: Oron L.
author list: Agent
  family name: Pimm
  given name: Stuart L.
doi: 10.7717/peerj.3287
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-10
copyright: ©2017 Huang et al.
attribution name: Huang et al.

Screening of a natural compound library identifies emodin, a natural compound from Rheum palmatum Linn that inhibits DPP4
type: item
type: AcademicArticle
description: Historically, Chinese herbal medicines have been widely used in the treatment of hyperglycemia, but the mechanisms underlying their effectiveness remain largely unknown. Here, we screened a compound library primarily comprised of natural compounds extracted from herbs and marine organisms. The results showed that emodin, a natural compound from Rheum palmatum Linn, inhibited DPP4 activity with an in vitro IC50 of 5.76 µM without inhibiting either DPP8 or DPP9. A docking model revealed that emodin binds to DPP4 protein through Glu205 and Glu206, although with low affinity. Moreover, emodin treatment (3, 10 and 30 mg/kg, P.O.) in mice decreased plasma DPP4 activity in a dose-dependent manner. Our study suggests that emodin inhibits DPP4 activity and may represent a novel therapeutic for the treatment of type 2 diabetes.
format: application/pdf
format: text/html
creator: Zhaokai Wang
creator: Longhe Yang
creator: Hu Fan
creator: Peng Wu
creator: Fang Zhang
creator: Chao Zhang
creator: Wenjie Liu
creator: Min Li
subject: Cell Biology
subject: Diabetes and Endocrinology
subject: Drugs and Devices
description: doi:10.7717/peerj.3283
publisher: PeerJ Inc.
rights: © 2017 Wang et al.
abstract: Historically, Chinese herbal medicines have been widely used in the treatment of hyperglycemia, but the mechanisms underlying their effectiveness remain largely unknown. Here, we screened a compound library primarily comprised of natural compounds extracted from herbs and marine organisms. The results showed that emodin, a natural compound from Rheum palmatum Linn, inhibited DPP4 activity with an in vitro IC50 of 5.76 µM without inhibiting either DPP8 or DPP9. A docking model revealed that emodin binds to DPP4 protein through Glu205 and Glu206, although with low affinity. Moreover, emodin treatment (3, 10 and 30 mg/kg, P.O.) in mice decreased plasma DPP4 activity in a dose-dependent manner. Our study suggests that emodin inhibits DPP4 activity and may represent a novel therapeutic for the treatment of type 2 diabetes.
bibliographic citation: Wang et al. (2017) Screening of a natural compound library identifies emodin, a natural compound from Rheum palmatum Linn that inhibits DPP4. PeerJ 5:e3283 https://doi.org/10.7717/peerj.3283
date submitted: 2016-12-21
date accepted: 2017-04-07
issued: 2017-05-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhaokai
author list: Agent
  family name: Yang
  given name: Longhe
author list: Agent
  family name: Fan
  given name: Hu
author list: Agent
  family name: Wu
  given name: Peng
author list: Agent
  family name: Zhang
  given name: Fang
author list: Agent
  family name: Zhang
  given name: Chao
author list: Agent
  family name: Liu
  given name: Wenjie
author list: Agent
  family name: Li
  given name: Min
doi: 10.7717/peerj.3283
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-10
copyright: ©2017 Wang et al.
attribution name: Wang et al.

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex
type: item
type: AcademicArticle
description: Background Molecularly targeted therapies improved survival status of some patients with lung adenocarcinoma, which accounts for 40% of all lung cancers, and in-depth study of gene alterations is important for the personalized treatment. Methods The legacy archive data of clinical information and genomic variations under the project TCGA Lung Adenocarcinoma were downloaded from the GDC Data Portal using R package TCGAbiolinks. The significantly aberrant copy number variants segments were figured out using GAIA. After annotation, the genes involving CNV were used to get enriched pathways. Recurrent amplifications and deletions were identified and visualized by OncoPrint. Genomic alterations in cancer, including CNV and mutations, were represented in Circos. Results The significantly aberrant CNV segments were found, and the genes involved were associated with the immune system. In an analysis of 517 mutation annotated files, we highlighted 63 highly recurrent mutated genes which were associated with lung cancer signaling. These genes involved in important pathways related to cancer progression. The intersections between the genes involving in the significantly aberrant CNV and the genes harboring recurrent somatic SNP were extracted. The PI3K protein family acted as critical roles in the lung adenocarcinoma, since the components of the PI3K protein family include PIK3C2B, PIK3CA, PIK3R1 and so forth were presented in the intersections. Conclusion We represented a comprehensive annotation of genomic alterations in lung adenocarcinoma and proposed that PI3K signaling proteins were critical for it.
format: application/pdf
format: text/html
creator: Zhao min Deng
creator: Lin Liu
creator: Wen hai Qiu
creator: Yong qun Zhang
creator: Hong yan Zhong
creator: Ping Liao
creator: Yun hong Wu
subject: Genetics
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.3216
publisher: PeerJ Inc.
rights: © 2017 Deng et al.
abstract: Background Molecularly targeted therapies improved survival status of some patients with lung adenocarcinoma, which accounts for 40% of all lung cancers, and in-depth study of gene alterations is important for the personalized treatment. Methods The legacy archive data of clinical information and genomic variations under the project TCGA Lung Adenocarcinoma were downloaded from the GDC Data Portal using R package TCGAbiolinks. The significantly aberrant copy number variants segments were figured out using GAIA. After annotation, the genes involving CNV were used to get enriched pathways. Recurrent amplifications and deletions were identified and visualized by OncoPrint. Genomic alterations in cancer, including CNV and mutations, were represented in Circos. Results The significantly aberrant CNV segments were found, and the genes involved were associated with the immune system. In an analysis of 517 mutation annotated files, we highlighted 63 highly recurrent mutated genes which were associated with lung cancer signaling. These genes involved in important pathways related to cancer progression. The intersections between the genes involving in the significantly aberrant CNV and the genes harboring recurrent somatic SNP were extracted. The PI3K protein family acted as critical roles in the lung adenocarcinoma, since the components of the PI3K protein family include PIK3C2B, PIK3CA, PIK3R1 and so forth were presented in the intersections. Conclusion We represented a comprehensive annotation of genomic alterations in lung adenocarcinoma and proposed that PI3K signaling proteins were critical for it.
bibliographic citation: Deng et al. (2017) Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex. PeerJ 5:e3216 https://doi.org/10.7717/peerj.3216
date submitted: 2016-10-28
date accepted: 2017-03-23
issued: 2017-05-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Zhao min
author list: Agent
  family name: Liu
  given name: Lin
author list: Agent
  family name: Qiu
  given name: Wen hai
author list: Agent
  family name: Zhang
  given name: Yong qun
author list: Agent
  family name: Zhong
  given name: Hong yan
author list: Agent
  family name: Liao
  given name: Ping
author list: Agent
  family name: Wu
  given name: Yun hong
doi: 10.7717/peerj.3216
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-10
copyright: ©2017 Deng et al.
attribution name: Deng et al.

Transcriptome sequencing and SNP detection in Phoebe chekiangensis
type: item
type: AcademicArticle
description: Background Phoebe chekiangensis is a rare tree species that is only distributed in south-eastern China. Although this species is famous for its excellent wood properties, it has not been extensively studied at the molecular level. Results Here, the transcriptome of P. chekiangensis was sequenced using next-generation sequencing technology, and 75,647 transcripts with 48,011 unigenes were assembled and annotated. In addition, 162,938 putative single nucleotide polymorphisms (SNPs) were predicted and 25 were further validated using the Sanger method. Conclusion The currently available SNP prediction software packages showed low levels of correspondence when compared. The transcriptome and SNPs will contribute to the exploration of P. chekiangensis genetic resources and the understanding of its molecular mechanisms.
format: application/pdf
format: text/html
creator: Bing He
creator: Yingang Li
creator: Zhouxian Ni
creator: Li-an Xu
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.3193
publisher: PeerJ Inc.
rights: © 2017 He et al.
abstract: Background Phoebe chekiangensis is a rare tree species that is only distributed in south-eastern China. Although this species is famous for its excellent wood properties, it has not been extensively studied at the molecular level. Results Here, the transcriptome of P. chekiangensis was sequenced using next-generation sequencing technology, and 75,647 transcripts with 48,011 unigenes were assembled and annotated. In addition, 162,938 putative single nucleotide polymorphisms (SNPs) were predicted and 25 were further validated using the Sanger method. Conclusion The currently available SNP prediction software packages showed low levels of correspondence when compared. The transcriptome and SNPs will contribute to the exploration of P. chekiangensis genetic resources and the understanding of its molecular mechanisms.
bibliographic citation: He et al. (2017) Transcriptome sequencing and SNP detection in Phoebe chekiangensis. PeerJ 5:e3193 https://doi.org/10.7717/peerj.3193
date submitted: 2016-11-07
date accepted: 2017-03-16
issued: 2017-05-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Bing
author list: Agent
  family name: Li
  given name: Yingang
author list: Agent
  family name: Ni
  given name: Zhouxian
author list: Agent
  family name: Xu
  given name: Li-an
doi: 10.7717/peerj.3193
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-10
copyright: ©2017 He et al.
attribution name: He et al.

Cave features, seasonality and subterranean distribution of non-obligate cave dwellers
type: item
type: AcademicArticle
description: Seasonality impacts species distributions through changes of the environmental conditions that affect the presence of individuals at a given place. Although the dynamics of cave microclimates are well known, only a few studies have evaluated the effects of such dynamics on non-strictly cave species. Here we assessed if species exploiting subterranean environments show changes in habitat occupation related to seasonal variation of cave microclimates. We surveyed 16 caves in central Italy every month for one year. Caves were subdivided into longitudinal sectors of three meters. In each sector we measured cave morphology and microclimatic features, assessed the occurrence of eight non-troglobitic taxa (orthopterans, spiders, gastropods and amphibians), and related species distribution to environmental features and sampling periods. The occurrence of most species was related to both cave morphology and microclimatic features. The survey month was the major factor determining the presence of species in cave sectors, indicating that cave-dwelling taxa show strong seasonality in activity and distribution. For multiple species, we detected interactions between sampling period and microclimatic features, suggesting that species may associate with different microhabitats throughout the year. The richest communities were found in sites with specific microclimates (i.e., high humidity, warm temperature and low light) but seasonality for species richness was strong as well, stressing the complexity of interactions between outdoor and subterranean environments.
format: application/pdf
format: text/html
creator: Enrico Lunghi
creator: Raoul Manenti
creator: Gentile Francesco Ficetola
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.3169
publisher: PeerJ Inc.
rights: © 2017 Lunghi et al.
abstract: Seasonality impacts species distributions through changes of the environmental conditions that affect the presence of individuals at a given place. Although the dynamics of cave microclimates are well known, only a few studies have evaluated the effects of such dynamics on non-strictly cave species. Here we assessed if species exploiting subterranean environments show changes in habitat occupation related to seasonal variation of cave microclimates. We surveyed 16 caves in central Italy every month for one year. Caves were subdivided into longitudinal sectors of three meters. In each sector we measured cave morphology and microclimatic features, assessed the occurrence of eight non-troglobitic taxa (orthopterans, spiders, gastropods and amphibians), and related species distribution to environmental features and sampling periods. The occurrence of most species was related to both cave morphology and microclimatic features. The survey month was the major factor determining the presence of species in cave sectors, indicating that cave-dwelling taxa show strong seasonality in activity and distribution. For multiple species, we detected interactions between sampling period and microclimatic features, suggesting that species may associate with different microhabitats throughout the year. The richest communities were found in sites with specific microclimates (i.e., high humidity, warm temperature and low light) but seasonality for species richness was strong as well, stressing the complexity of interactions between outdoor and subterranean environments.
bibliographic citation: Lunghi et al. (2017) Cave features, seasonality and subterranean distribution of non-obligate cave dwellers. PeerJ 5:e3169 https://doi.org/10.7717/peerj.3169
date submitted: 2016-11-10
date accepted: 2017-03-11
issued: 2017-05-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lunghi
  given name: Enrico
author list: Agent
  family name: Manenti
  given name: Raoul
author list: Agent
  family name: Ficetola
  given name: Gentile Francesco
doi: 10.7717/peerj.3169
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-05-10
copyright: ©2017 Lunghi et al.
attribution name: Lunghi et al.

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