PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A randomized control trial feasibility evaluation of an mHealth intervention for wheelchair skill training among middle-aged and older adults
items: Relationship between hemoglobin glycation index and extent of coronary heart disease in individuals with type 2 diabetes mellitus: a cross-sectional study
items: Clone wars: asexual reproduction dominates in the invasive range of Tubastraea spp. (Anthozoa: Scleractinia) in the South-Atlantic Ocean
items: New whaitsioids (Therapsida: Therocephalia) from the Teekloof Formation of South Africa and therocephalian diversity during the end-Guadalupian extinction
items: The Plasmodium berghei RC strain is highly diverged and harbors putatively novel drug resistance variants
items: Assessing the living and dead proportions of cold-water coral colonies: implications for deep-water Marine Protected Area monitoring in a changing ocean
items: Impact of land reclamation and agricultural water regime on the distribution and conservation status of the endangered Dryophytes suweonensis
items: Accuracy of microbial community diversity estimated by closed- and open-reference OTUs
items: Exceptional soft tissues preservation in a mummified frog-eating Eocene salamander
items: Alpha-arylphorin is a mitogen in the Heliothis virescens midgut cell secretome upon Cry1Ac intoxication

A randomized control trial feasibility evaluation of an mHealth intervention for wheelchair skill training among middle-aged and older adults
type: item
type: AcademicArticle
description: Background Providing mobility skills training to manual wheelchair (MWC) users can have a positive impact on community participation, confidence and quality of life. Often such training is restricted or not provided at all because of the expense of, and limited access to, occupational and physical therapists before and after discharge. This is particularly true among middle-aged and older adults, who often have limited access to rehabilitation services and require more time to learn motor skills. A monitored MWC skills training home program, delivered using a computer tablet (mHealth), was developed as an alternative approach to service delivery. The purpose of this study was to evaluate the feasibility of implementing this mHealth MWC skills training program among middle-aged and older adults. Methods A 2 × 2 factorial design randomized controlled trial (RCT) was used to compare the mHealth intervention and control groups, with additional wheeling time as a second factor. Community-dwelling MWC users aged 55 and older, who had used their MWC for less than two years and propelled with two hands, were recruited. Feasibility outcomes related to process, resources, management and treatment criteria were collected. Results Eighteen participants were recruited, with a retention rate of 94%. Mean (±SD) duration for the first and second in-person training sessions were 90.1 ± 20.5 and 62.1 ± 5.5 min, respectively. In the treatment group, 78% achieved the minimum amount of home training (i.e., 300 min) over four weeks and 56% achieved the preferred training threshold (i.e., 600 min). Trainers reported only seven minor protocol deviations. No tablets were lost or damaged and there was one incident of tablet malfunction. No injuries or adverse incidents were reported during data collection or training activities. Participants indicated 98% agreement on the post-treatment benefit questionnaire. Discussion Overall, the study protocol enabled implementation of the intervention i…
format: application/pdf
format: text/html
creator: Edward M. Giesbrecht
creator: William C. Miller
subject: Clinical Trials
subject: Geriatrics
subject: Kinesiology
subject: Public Health
description: doi:10.7717/peerj.3879
publisher: PeerJ Inc.
rights: © 2017 Giesbrecht and Miller
abstract: Background Providing mobility skills training to manual wheelchair (MWC) users can have a positive impact on community participation, confidence and quality of life. Often such training is restricted or not provided at all because of the expense of, and limited access to, occupational and physical therapists before and after discharge. This is particularly true among middle-aged and older adults, who often have limited access to rehabilitation services and require more time to learn motor skills. A monitored MWC skills training home program, delivered using a computer tablet (mHealth), was developed as an alternative approach to service delivery. The purpose of this study was to evaluate the feasibility of implementing this mHealth MWC skills training program among middle-aged and older adults. Methods A 2 × 2 factorial design randomized controlled trial (RCT) was used to compare the mHealth intervention and control groups, with additional wheeling time as a second factor. Community-dwelling MWC users aged 55 and older, who had used their MWC for less than two years and propelled with two hands, were recruited. Feasibility outcomes related to process, resources, management and treatment criteria were collected. Results Eighteen participants were recruited, with a retention rate of 94%. Mean (±SD) duration for the first and second in-person training sessions were 90.1 ± 20.5 and 62.1 ± 5.5 min, respectively. In the treatment group, 78% achieved the minimum amount of home training (i.e., 300 min) over four weeks and 56% achieved the preferred training threshold (i.e., 600 min). Trainers reported only seven minor protocol deviations. No tablets were lost or damaged and there was one incident of tablet malfunction. No injuries or adverse incidents were reported during data collection or training activities. Participants indicated 98% agreement on the post-treatment benefit questionnaire. Discussion Overall, the study protocol enabled implementation of the intervention i…
bibliographic citation: Giesbrecht et al. (2017) A randomized control trial feasibility evaluation of an mHealth intervention for wheelchair skill training among middle-aged and older adults. PeerJ 5:e3879 https://doi.org/10.7717/peerj.3879
date submitted: 2017-07-15
date accepted: 2017-09-12
issued: 2017-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giesbrecht
  given name: Edward M.
author list: Agent
  family name: Miller
  given name: William C.
doi: 10.7717/peerj.3879
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-05
copyright: © 2017 Giesbrecht and Miller
attribution name: Giesbrecht and Miller

Relationship between hemoglobin glycation index and extent of coronary heart disease in individuals with type 2 diabetes mellitus: a cross-sectional study
type: item
type: AcademicArticle
description: Background Individuals with type 2 diabetes (T2D) are at an increased risk of coronary heart disease (CHD). Diabetic complications have recently been associated with a measure of glucose metabolism known as the hemoglobin glycation index (HGI). Currently there is insufficient information regarding a potential link between HGI and cardiovascular disease. This study aimed to investigate the relationship between HGI and extent of CHD in individuals with T2D. Methods This cross-sectional study screened individuals visiting the endocrinology clinic between June 2012 and May 2016 for eligibility. Enrollment criteria included individuals above 21 years of age with T2D diagnosed in the preceding ten years. Candidates with hemoglobin disorders, pregnancy, and existing coronary artery disease were excluded. Fasting plasma glucose (FPG) and glycated hemoglobin A1c (HbA1c) were sampled three months prior to angiography. The regression equation of predicted HbA1c = 0.008 × FPG + 6.28 described the linear relationship between these variables. HGI was calculated as the difference between the measured HbA1c and predicted HbA1c. Participants were classified into two groups according to the presence of supranormal (≥0) or subnormal HGI (<0). Results Among 423 participants, people with supranormal HGI harbored an increased prevalence of multiple vessel disease relative to those with subnormal HGI (Odds ratio (OR): 3.9, 95% CI [2.64–5.98], P < 0.001). Moreover, individuals with supranormal HGI more frequently demonstrated lesions involving the left anterior descending artery (OR: 3.0, 95% CI [1.97–4.66], P < 0.001). The intergroup difference in mean HbA1c was statistically nonsignificant (7.5 ± 1.0% versus 7.4 ± 1.1%, P = 0.80). Discussion This study demonstrated that HGI correlated with the extent of CHD in individuals with T2D. People with supranormal HGI harbored a higher prevalence of extensive cardiovascular disease compared to those with subnormal HGI. The relationship between HG…
format: application/pdf
format: text/html
creator: Po Chung Cheng
creator: Shang Ren Hsu
creator: Yun Chung Cheng
creator: Yu Hsiu Liu
subject: Cardiology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.3875
publisher: PeerJ Inc.
rights: © 2017 Cheng et al.
abstract: Background Individuals with type 2 diabetes (T2D) are at an increased risk of coronary heart disease (CHD). Diabetic complications have recently been associated with a measure of glucose metabolism known as the hemoglobin glycation index (HGI). Currently there is insufficient information regarding a potential link between HGI and cardiovascular disease. This study aimed to investigate the relationship between HGI and extent of CHD in individuals with T2D. Methods This cross-sectional study screened individuals visiting the endocrinology clinic between June 2012 and May 2016 for eligibility. Enrollment criteria included individuals above 21 years of age with T2D diagnosed in the preceding ten years. Candidates with hemoglobin disorders, pregnancy, and existing coronary artery disease were excluded. Fasting plasma glucose (FPG) and glycated hemoglobin A1c (HbA1c) were sampled three months prior to angiography. The regression equation of predicted HbA1c = 0.008 × FPG + 6.28 described the linear relationship between these variables. HGI was calculated as the difference between the measured HbA1c and predicted HbA1c. Participants were classified into two groups according to the presence of supranormal (≥0) or subnormal HGI (<0). Results Among 423 participants, people with supranormal HGI harbored an increased prevalence of multiple vessel disease relative to those with subnormal HGI (Odds ratio (OR): 3.9, 95% CI [2.64–5.98], P < 0.001). Moreover, individuals with supranormal HGI more frequently demonstrated lesions involving the left anterior descending artery (OR: 3.0, 95% CI [1.97–4.66], P < 0.001). The intergroup difference in mean HbA1c was statistically nonsignificant (7.5 ± 1.0% versus 7.4 ± 1.1%, P = 0.80). Discussion This study demonstrated that HGI correlated with the extent of CHD in individuals with T2D. People with supranormal HGI harbored a higher prevalence of extensive cardiovascular disease compared to those with subnormal HGI. The relationship between HG…
bibliographic citation: Cheng et al. (2017) Relationship between hemoglobin glycation index and extent of coronary heart disease in individuals with type 2 diabetes mellitus: a cross-sectional study. PeerJ 5:e3875 https://doi.org/10.7717/peerj.3875
date submitted: 2017-07-14
date accepted: 2017-09-09
issued: 2017-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Po Chung
author list: Agent
  family name: Hsu
  given name: Shang Ren
author list: Agent
  family name: Cheng
  given name: Yun Chung
author list: Agent
  family name: Liu
  given name: Yu Hsiu
doi: 10.7717/peerj.3875
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-05
copyright: ©2017 Cheng et al.
attribution name: Cheng et al.

Clone wars: asexual reproduction dominates in the invasive range of Tubastraea spp. (Anthozoa: Scleractinia) in the South-Atlantic Ocean
type: item
type: AcademicArticle
description: Although the invasive azooxanthellate corals Tubastraea coccinea and T. tagusensis are spreading quickly and outcompeting native species in the Atlantic Ocean, there is little information regarding the genetic structure and path of introduction for these species. Here we present the first data on genetic diversity and clonal structure from these two species using a new set of microsatellite markers. High proportions of clones were observed, indicating that asexual reproduction has a major role in the local population dynamics and, therefore, represents one of the main reasons for the invasion success. Although no significant population structure was found, results suggest the occurrence of multiple invasions for T. coccinea and also that both species are being transported along the coast by vectors such as oil platforms and monobouys, spreading these invasive species. In addition to the description of novel microsatellite markers, this study sheds new light into the invasive process of Tubastraea.
format: application/pdf
format: text/html
creator: Katia Cristina Cruz Capel
creator: Robert J. Toonen
creator: Caio T.C.C. Rachid
creator: Joel C. Creed
creator: Marcelo V. Kitahara
creator: Zac Forsman
creator: Carla Zilberberg
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.3873
publisher: PeerJ Inc.
rights: © 2017 Capel et al.
abstract: Although the invasive azooxanthellate corals Tubastraea coccinea and T. tagusensis are spreading quickly and outcompeting native species in the Atlantic Ocean, there is little information regarding the genetic structure and path of introduction for these species. Here we present the first data on genetic diversity and clonal structure from these two species using a new set of microsatellite markers. High proportions of clones were observed, indicating that asexual reproduction has a major role in the local population dynamics and, therefore, represents one of the main reasons for the invasion success. Although no significant population structure was found, results suggest the occurrence of multiple invasions for T. coccinea and also that both species are being transported along the coast by vectors such as oil platforms and monobouys, spreading these invasive species. In addition to the description of novel microsatellite markers, this study sheds new light into the invasive process of Tubastraea.
bibliographic citation: Capel et al. (2017) Clone wars: asexual reproduction dominates in the invasive range of Tubastraea spp. (Anthozoa: Scleractinia) in the South-Atlantic Ocean. PeerJ 5:e3873 https://doi.org/10.7717/peerj.3873
date submitted: 2017-07-20
date accepted: 2017-09-09
issued: 2017-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Capel
  given name: Katia Cristina Cruz
author list: Agent
  family name: Toonen
  given name: Robert J.
author list: Agent
  family name: Rachid
  given name: Caio T.C.C.
author list: Agent
  family name: Creed
  given name: Joel C.
author list: Agent
  family name: Kitahara
  given name: Marcelo V.
author list: Agent
  family name: Forsman
  given name: Zac
author list: Agent
  family name: Zilberberg
  given name: Carla
doi: 10.7717/peerj.3873
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-05
copyright: ©2017 Capel et al.
attribution name: Capel et al.

New whaitsioids (Therapsida: Therocephalia) from the Teekloof Formation of South Africa and therocephalian diversity during the end-Guadalupian extinction
type: item
type: AcademicArticle
description: Two new species of therocephalian therapsids are described from the upper Permian Teekloof Formation of the Karoo Basin, South Africa. They include two specimens of a whaitsiid, Microwhaitsia mendrezi gen. et sp. nov., and a single, small whaitsioid Ophidostoma tatarinovi gen. et sp. nov., which preserves a combination of primitive and apomorphic features. A phylogenetic analysis of 56 therapsid taxa and 136 craniodental and postcranial characters places the new taxa within the monophyletic sister group of baurioids—Whaitsioidea—with Microwhaitsia as a basal whaitsiid and Ophidostoma as an aberrant whaitsioid just outside the hofmeyriid+whaitsiid subclade. The new records support that whaitsioids were diverse during the early-late Permian (Wuchiapingian) and that the dichotomy between whaitsiid-line and baurioid-line eutherocephalians was established early on. The oldest Gondwanan whaitsiid Microwhaitsia and additional records from the lower strata of the Teekloof Formation suggest that whaitsioids had diversified by the early Wuchiapingian and no later than Pristerognathus Assemblage Zone times. Prior extinction estimates based on species counts are reflected in an analysis of origination/extinction rates, which imply increasing faunal turnover from Guadalupian to Lopingian (late Permian) times. The new records support a growing body of evidence that some key Lopingian synapsid clades originated near or prior to the Guadalupian-Lopingian boundary ca. 260–259 million years ago, but only radiated following the end-Guadalupian extinction of dinocephalians and basal therocephalian predators (long-fuse model). Ongoing collecting in older portions of the Teekloof Formation (e.g., Pristerognathus Assemblage Zone) will shed further light on early eutherocephalians during this murky but critical time in their evolutionary diversification.
format: application/pdf
format: text/html
creator: Adam K. Huttenlocker
creator: Roger M.H. Smith
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
subject: Taxonomy
subject: Anatomy and Physiology
description: doi:10.7717/peerj.3868
publisher: PeerJ Inc.
rights: © 2017 Huttenlocker and Smith
abstract: Two new species of therocephalian therapsids are described from the upper Permian Teekloof Formation of the Karoo Basin, South Africa. They include two specimens of a whaitsiid, Microwhaitsia mendrezi gen. et sp. nov., and a single, small whaitsioid Ophidostoma tatarinovi gen. et sp. nov., which preserves a combination of primitive and apomorphic features. A phylogenetic analysis of 56 therapsid taxa and 136 craniodental and postcranial characters places the new taxa within the monophyletic sister group of baurioids—Whaitsioidea—with Microwhaitsia as a basal whaitsiid and Ophidostoma as an aberrant whaitsioid just outside the hofmeyriid+whaitsiid subclade. The new records support that whaitsioids were diverse during the early-late Permian (Wuchiapingian) and that the dichotomy between whaitsiid-line and baurioid-line eutherocephalians was established early on. The oldest Gondwanan whaitsiid Microwhaitsia and additional records from the lower strata of the Teekloof Formation suggest that whaitsioids had diversified by the early Wuchiapingian and no later than Pristerognathus Assemblage Zone times. Prior extinction estimates based on species counts are reflected in an analysis of origination/extinction rates, which imply increasing faunal turnover from Guadalupian to Lopingian (late Permian) times. The new records support a growing body of evidence that some key Lopingian synapsid clades originated near or prior to the Guadalupian-Lopingian boundary ca. 260–259 million years ago, but only radiated following the end-Guadalupian extinction of dinocephalians and basal therocephalian predators (long-fuse model). Ongoing collecting in older portions of the Teekloof Formation (e.g., Pristerognathus Assemblage Zone) will shed further light on early eutherocephalians during this murky but critical time in their evolutionary diversification.
bibliographic citation: Huttenlocker et al. (2017) New whaitsioids (Therapsida: Therocephalia) from the Teekloof Formation of South Africa and therocephalian diversity during the end-Guadalupian extinction. PeerJ 5:e3868 https://doi.org/10.7717/peerj.3868
date submitted: 2017-07-25
date accepted: 2017-09-08
issued: 2017-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huttenlocker
  given name: Adam K.
author list: Agent
  family name: Smith
  given name: Roger M.H.
doi: 10.7717/peerj.3868
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-05
copyright: ©2017 Huttenlocker and Smith
attribution name: Huttenlocker and Smith

The Plasmodium berghei RC strain is highly diverged and harbors putatively novel drug resistance variants
type: item
type: AcademicArticle
description: Background The current first line drugs for treating uncomplicated malaria are artemisinin (ART) combination therapies. However, Plasmodium falciparum parasites resistant to ART and partner drugs are spreading, which threatens malaria control efforts. Rodent malaria species are useful models for understanding antimalarial resistance, in particular genetic variants responsible for cross resistance to different compounds. Methods The Plasmodium berghei RC strain (PbRC) is described as resistant to different antimalarials, including chloroquine (CQ) and ART. In an attempt to identify the genetic basis for the antimalarial resistance trait in PbRC, its genome was sequenced and compared with five other previously sequenced P. berghei strains. Results We found that PbRC is eight-fold less sensitive to the ART derivative artesunate than the reference strain PbANKA. The genome of PbRC is markedly different from other strains, and 6,974 single nucleotide variants private to PbRC were identified. Among these PbRC private variants, non-synonymous changes were identified in genes known to modulate antimalarial sensitivity in rodent malaria species, including notably the ubiquitin carboxyl-terminal hydrolase 1 gene. However, no variants were found in some genes with strong evidence of association with ART resistance in P. falciparum such as K13 propeller protein. Discussion The variants identified in PbRC provide insight into P. berghei genome diversity and genetic factors that could modulate CQ and ART resistance in Plasmodium spp.
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creator: Warangkhana Songsungthong
creator: Supasak Kulawonganunchai
creator: Alisa Wilantho
creator: Sissades Tongsima
creator: Pongpisid Koonyosying
creator: Chairat Uthaipibull
creator: Sumalee Kamchonwongpaisan
creator: Philip J. Shaw
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Parasitology
description: doi:10.7717/peerj.3766
publisher: PeerJ Inc.
rights: © 2017 Songsungthong et al.
abstract: Background The current first line drugs for treating uncomplicated malaria are artemisinin (ART) combination therapies. However, Plasmodium falciparum parasites resistant to ART and partner drugs are spreading, which threatens malaria control efforts. Rodent malaria species are useful models for understanding antimalarial resistance, in particular genetic variants responsible for cross resistance to different compounds. Methods The Plasmodium berghei RC strain (PbRC) is described as resistant to different antimalarials, including chloroquine (CQ) and ART. In an attempt to identify the genetic basis for the antimalarial resistance trait in PbRC, its genome was sequenced and compared with five other previously sequenced P. berghei strains. Results We found that PbRC is eight-fold less sensitive to the ART derivative artesunate than the reference strain PbANKA. The genome of PbRC is markedly different from other strains, and 6,974 single nucleotide variants private to PbRC were identified. Among these PbRC private variants, non-synonymous changes were identified in genes known to modulate antimalarial sensitivity in rodent malaria species, including notably the ubiquitin carboxyl-terminal hydrolase 1 gene. However, no variants were found in some genes with strong evidence of association with ART resistance in P. falciparum such as K13 propeller protein. Discussion The variants identified in PbRC provide insight into P. berghei genome diversity and genetic factors that could modulate CQ and ART resistance in Plasmodium spp.
bibliographic citation: Songsungthong et al. (2017) The Plasmodium berghei RC strain is highly diverged and harbors putatively novel drug resistance variants. PeerJ 5:e3766 https://doi.org/10.7717/peerj.3766
date submitted: 2017-06-28
date accepted: 2017-08-15
issued: 2017-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Songsungthong
  given name: Warangkhana
author list: Agent
  family name: Kulawonganunchai
  given name: Supasak
author list: Agent
  family name: Wilantho
  given name: Alisa
author list: Agent
  family name: Tongsima
  given name: Sissades
author list: Agent
  family name: Koonyosying
  given name: Pongpisid
author list: Agent
  family name: Uthaipibull
  given name: Chairat
author list: Agent
  family name: Kamchonwongpaisan
  given name: Sumalee
author list: Agent
  family name: Shaw
  given name: Philip J.
doi: 10.7717/peerj.3766
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-05
copyright: © 2017 Songsungthong et al.
attribution name: Songsungthong et al.

Assessing the living and dead proportions of cold-water coral colonies: implications for deep-water Marine Protected Area monitoring in a changing ocean
type: item
type: AcademicArticle
description: Coral growth patterns result from an interplay of coral biology and environmental conditions. In this study colony size and proportion of live and dead skeletons in the cold-water coral (CWC) Lophelia pertusa (Linnaeus, 1758) were measured using video footage from Remotely Operated Vehicle (ROV) transects conducted at the inshore Mingulay Reef Complex (MRC) and at the offshore PISCES site (Rockall Bank) in the NE Atlantic. The main goal of this paper was to explore the development of a simple method to quantify coral growth and its potential application as an assessment tool of the health of these remote habitats. Eighteen colonies were selected and whole colony and dead/living layer size were measured. Live to dead layer ratios for each colony were then determined and analysed. The age of each colony was estimated using previously published data. Our paper shows that: (1) two distinct morphotypes can be described: at the MRC, colonies displayed a ‘cauliflower-shaped’ morphotype whereas at the PISCES site, colonies presented a more flattened ‘bush-shaped’ morphotype; (2) living layer size was positively correlated with whole colony size; (3) live to dead layer ratio was negatively correlated to whole colony size; (4) live to dead layer ratio never exceeded 0.27. These results suggest that as a colony develops and its growth rate slows down, the proportion of living polyps in the colony decreases. Furthermore, at least 73% of L. pertusa colonies are composed of exposed dead coral skeleton, vulnerable to ocean acidification and the associated shallowing of the aragonite saturation horizon, with significant implications for future deep-sea reef framework integrity. The clear visual contrast between white/pale living and grey/dark dead portions of the colonies also gives a new way by which they can be visually monitored over time. The increased use of marine autonomous survey vehicles offers an important new platform from which such a surveying technique could be applie…
format: application/pdf
format: text/html
creator: Johanne Vad
creator: Covadonga Orejas
creator: Juan Moreno-Navas
creator: Helen S. Findlay
creator: J. Murray Roberts
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.3705
publisher: PeerJ Inc.
rights: © 2017 Vad et al.
abstract: Coral growth patterns result from an interplay of coral biology and environmental conditions. In this study colony size and proportion of live and dead skeletons in the cold-water coral (CWC) Lophelia pertusa (Linnaeus, 1758) were measured using video footage from Remotely Operated Vehicle (ROV) transects conducted at the inshore Mingulay Reef Complex (MRC) and at the offshore PISCES site (Rockall Bank) in the NE Atlantic. The main goal of this paper was to explore the development of a simple method to quantify coral growth and its potential application as an assessment tool of the health of these remote habitats. Eighteen colonies were selected and whole colony and dead/living layer size were measured. Live to dead layer ratios for each colony were then determined and analysed. The age of each colony was estimated using previously published data. Our paper shows that: (1) two distinct morphotypes can be described: at the MRC, colonies displayed a ‘cauliflower-shaped’ morphotype whereas at the PISCES site, colonies presented a more flattened ‘bush-shaped’ morphotype; (2) living layer size was positively correlated with whole colony size; (3) live to dead layer ratio was negatively correlated to whole colony size; (4) live to dead layer ratio never exceeded 0.27. These results suggest that as a colony develops and its growth rate slows down, the proportion of living polyps in the colony decreases. Furthermore, at least 73% of L. pertusa colonies are composed of exposed dead coral skeleton, vulnerable to ocean acidification and the associated shallowing of the aragonite saturation horizon, with significant implications for future deep-sea reef framework integrity. The clear visual contrast between white/pale living and grey/dark dead portions of the colonies also gives a new way by which they can be visually monitored over time. The increased use of marine autonomous survey vehicles offers an important new platform from which such a surveying technique could be applie…
bibliographic citation: Vad et al. (2017) Assessing the living and dead proportions of cold-water coral colonies: implications for deep-water Marine Protected Area monitoring in a changing ocean. PeerJ 5:e3705 https://doi.org/10.7717/peerj.3705
date submitted: 2017-03-24
date accepted: 2017-07-27
issued: 2017-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vad
  given name: Johanne
author list: Agent
  family name: Orejas
  given name: Covadonga
author list: Agent
  family name: Moreno-Navas
  given name: Juan
author list: Agent
  family name: Findlay
  given name: Helen S.
author list: Agent
  family name: Roberts
  given name: J. Murray
doi: 10.7717/peerj.3705
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-05
copyright: ©2017 Vad et al.
attribution name: Vad et al.

Impact of land reclamation and agricultural water regime on the distribution and conservation status of the endangered Dryophytes suweonensis
type: item
type: AcademicArticle
description: Knowledge about the distribution and habitat preferences of a species is critical for its conservation. The Suweon Treefrog (Dryophytes suweonensis) is an endangered species endemic to the Republic of Korea. We conducted surveys from 2014 to 2016 at 890 potentially suitable sites across the entire range of the species in South Korea. We then assessed whether D. suweonensis was found in the current and ancestral predicted ranges, reclaimed and protected areas, and how the presence of agricultural floodwater affected its occurrence. Our results describe a 120 km increase in the southernmost known distribution of the species, and the absence of the species at lower latitudes. We then demonstrate a putative constriction on the species ancestral range due to urban encroachment, and provide evidence for a significant increase in its coastal range due to the colonisation of reclaimed land by the species. In addition, we demonstrate that D. suweonensis is present in rice fields that are flooded with water originating from rivers as opposed to being present in rice fields that are irrigated from underground water. Finally, the non-overlap of protected areas and the occurrence of the species shows that only the edge of a single site where D. suweonensis occurs is legally protected. Based on our results and the literature, we suggest the design of a site fitting all the ecological requirements of the species, and suggest the use of such sites to prevent further erosion in the range of D. suweonensis.
format: application/pdf
format: text/html
creator: Amaël Borzée
creator: Kyungmin Kim
creator: Kyongman Heo
creator: Piotr G. Jablonski
creator: Yikweon Jang
subject: Biosphere Interactions
subject: Conservation Biology
subject: Ecology
subject: Environmental Impacts
description: doi:10.7717/peerj.3872
publisher: PeerJ Inc.
rights: © 2017 Borzée et al.
abstract: Knowledge about the distribution and habitat preferences of a species is critical for its conservation. The Suweon Treefrog (Dryophytes suweonensis) is an endangered species endemic to the Republic of Korea. We conducted surveys from 2014 to 2016 at 890 potentially suitable sites across the entire range of the species in South Korea. We then assessed whether D. suweonensis was found in the current and ancestral predicted ranges, reclaimed and protected areas, and how the presence of agricultural floodwater affected its occurrence. Our results describe a 120 km increase in the southernmost known distribution of the species, and the absence of the species at lower latitudes. We then demonstrate a putative constriction on the species ancestral range due to urban encroachment, and provide evidence for a significant increase in its coastal range due to the colonisation of reclaimed land by the species. In addition, we demonstrate that D. suweonensis is present in rice fields that are flooded with water originating from rivers as opposed to being present in rice fields that are irrigated from underground water. Finally, the non-overlap of protected areas and the occurrence of the species shows that only the edge of a single site where D. suweonensis occurs is legally protected. Based on our results and the literature, we suggest the design of a site fitting all the ecological requirements of the species, and suggest the use of such sites to prevent further erosion in the range of D. suweonensis.
bibliographic citation: Borzée et al. (2017) Impact of land reclamation and agricultural water regime on the distribution and conservation status of the endangered Dryophytes suweonensis. PeerJ 5:e3872 https://doi.org/10.7717/peerj.3872
date submitted: 2017-06-13
date accepted: 2017-09-09
issued: 2017-10-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Borzée
  given name: Amaël
author list: Agent
  family name: Kim
  given name: Kyungmin
author list: Agent
  family name: Heo
  given name: Kyongman
author list: Agent
  family name: Jablonski
  given name: Piotr G.
author list: Agent
  family name: Jang
  given name: Yikweon
doi: 10.7717/peerj.3872
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-04
copyright: ©2017 Borzée et al.
attribution name: Borzée et al.

Accuracy of microbial community diversity estimated by closed- and open-reference OTUs
type: item
type: AcademicArticle
description: Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity (closed), then clusters unmatched reads using a de novo method (open). Implementations of these methods in the QIIME package were tested on several mock community datasets with 20 strains using different sequencing technologies and primers. Richness (number of reported OTUs) was often greatly exaggerated, with hundreds or thousands of OTUs generated on Illumina datasets. Between-sample diversity was also found to be highly exaggerated in many cases, with weighted Jaccard distances between identical mock samples often close to one, indicating very low similarity. Non-overlapping hyper-variable regions in 70% of species were assigned to different OTUs. On mock communities with Illumina V4 reads, 56% to 88% of predicted genus names were false positives. Biological inferences obtained using these methods are therefore not reliable.
format: application/pdf
format: text/html
creator: Robert C. Edgar
subject: Bioinformatics
subject: Computational Biology
subject: Microbiology
description: doi:10.7717/peerj.3889
publisher: PeerJ Inc.
rights: © 2017 Edgar
abstract: Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity (closed), then clusters unmatched reads using a de novo method (open). Implementations of these methods in the QIIME package were tested on several mock community datasets with 20 strains using different sequencing technologies and primers. Richness (number of reported OTUs) was often greatly exaggerated, with hundreds or thousands of OTUs generated on Illumina datasets. Between-sample diversity was also found to be highly exaggerated in many cases, with weighted Jaccard distances between identical mock samples often close to one, indicating very low similarity. Non-overlapping hyper-variable regions in 70% of species were assigned to different OTUs. On mock communities with Illumina V4 reads, 56% to 88% of predicted genus names were false positives. Biological inferences obtained using these methods are therefore not reliable.
bibliographic citation: Edgar (2017) Accuracy of microbial community diversity estimated by closed- and open-reference OTUs. PeerJ 5:e3889 https://doi.org/10.7717/peerj.3889
date submitted: 2017-06-30
date accepted: 2017-09-13
issued: 2017-10-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Edgar
  given name: Robert C.
doi: 10.7717/peerj.3889
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-04
copyright: ©2017 Edgar
attribution name: Edgar

Exceptional soft tissues preservation in a mummified frog-eating Eocene salamander
type: item
type: AcademicArticle
description: Fossils are almost always represented by hard tissues but we present here the exceptional case of a three-dimensionally preserved specimen that was ‘mummified’ (likely between 40 and 34 million years ago) in a terrestrial karstic environment. This fossil is the incomplete body of a salamander, Phosphotriton sigei, whose skeleton and external morphology are well preserved, as revealed by phase-contrast synchrotron X-ray microtomography. In addition, internal structures composed of soft tissues preserved in three dimensions are now identified: a lung, the spinal cord, a lumbosacral plexus, the digestive tract, muscles and urogenital organs that may be cloacal glands. These are among the oldest known cases of three-dimensional preservation of these organs in vertebrates and shed light on the ecology of this salamander. Indeed, the digestive tract contains remains of a frog, which represents the only known case of an extinct salamander that fed on a frog, an extremely rare type of predation in extant salamanders. These new data improve our scarce knowledge on soft tissue anatomy of early urodeles and should prove useful for future biologists and palaeontologists working on urodele evolutionary biology. We also suggest that the presence of bat guano and carcasses represented a close source of phosphorus, favouring preservation of soft tissues. Bone microanatomy indicates that P. sigei was likely amphibious or terrestrial, and was probably not neotenic.
format: application/pdf
format: text/html
creator: Jérémy Tissier
creator: Jean-Claude Rage
creator: Michel Laurin
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.3861
publisher: PeerJ Inc.
rights: © 2017 Tissier et al.
abstract: Fossils are almost always represented by hard tissues but we present here the exceptional case of a three-dimensionally preserved specimen that was ‘mummified’ (likely between 40 and 34 million years ago) in a terrestrial karstic environment. This fossil is the incomplete body of a salamander, Phosphotriton sigei, whose skeleton and external morphology are well preserved, as revealed by phase-contrast synchrotron X-ray microtomography. In addition, internal structures composed of soft tissues preserved in three dimensions are now identified: a lung, the spinal cord, a lumbosacral plexus, the digestive tract, muscles and urogenital organs that may be cloacal glands. These are among the oldest known cases of three-dimensional preservation of these organs in vertebrates and shed light on the ecology of this salamander. Indeed, the digestive tract contains remains of a frog, which represents the only known case of an extinct salamander that fed on a frog, an extremely rare type of predation in extant salamanders. These new data improve our scarce knowledge on soft tissue anatomy of early urodeles and should prove useful for future biologists and palaeontologists working on urodele evolutionary biology. We also suggest that the presence of bat guano and carcasses represented a close source of phosphorus, favouring preservation of soft tissues. Bone microanatomy indicates that P. sigei was likely amphibious or terrestrial, and was probably not neotenic.
bibliographic citation: Tissier et al. (2017) Exceptional soft tissues preservation in a mummified frog-eating Eocene salamander. PeerJ 5:e3861 https://doi.org/10.7717/peerj.3861
date submitted: 2017-08-22
date accepted: 2017-09-07
issued: 2017-10-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tissier
  given name: Jérémy
author list: Agent
  family name: Rage
  given name: Jean-Claude
author list: Agent
  family name: Laurin
  given name: Michel
doi: 10.7717/peerj.3861
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-03
copyright: ©2017 Tissier et al.
attribution name: Tissier et al.

Alpha-arylphorin is a mitogen in the Heliothis virescens midgut cell secretome upon Cry1Ac intoxication
type: item
type: AcademicArticle
description: Insecticidal crystal (Cry) proteins produced by the bacterium Bacillus thuringiensis (Bt) target cells in the midgut epithelium of susceptible larvae. While the mode of action of Cry toxins has been extensively investigated, the midgut response to Cry intoxication and its regulation are not well characterized. In this work, we describe the secreted proteome (secretome) of primary mature midgut cell cultures from Heliothis virescens larvae after exposure to Cry1Ac toxin compared to control buffer treatment. The Cry1Ac-induced secretome caused higher proliferation and differentiation and an overall reduction in total cell mortality over time in primary H. virescens midgut stem cell cultures when compared to treatment with control buffer secretome. Differential proteomics identified four proteins with significant differences in abundance comparing Cry1Ac-treated and control secretomes. The most significant difference detected in the Cry1Ac secretome was an arylphorin subunit alpha protein not detected in the control secretome. Feeding of purified alpha-arylphorin to H. virescens larvae resulted in midgut hyperplasia and significantly reduced susceptibility to Cry1Ac toxin compared to controls. These data identify alpha-arylphorin as a protein with a new putative role in the midgut regeneration process in response to Cry1Ac intoxication and possibly pathogen/abiotic stress, identifying alpha-arylphorin as a potential gene to target with insecticidal gene silencing for pest control.
format: application/pdf
format: text/html
creator: Anais Castagnola
creator: Jerreme Jackson
creator: Omaththage P. Perera
creator: Cris Oppert
creator: Shigetoshi Eda
creator: Juan Luis Jurat-Fuentes
subject: Entomology
subject: Microbiology
subject: Histology
description: doi:10.7717/peerj.3886
publisher: PeerJ Inc.
rights: © 2017 Castagnola et al.
abstract: Insecticidal crystal (Cry) proteins produced by the bacterium Bacillus thuringiensis (Bt) target cells in the midgut epithelium of susceptible larvae. While the mode of action of Cry toxins has been extensively investigated, the midgut response to Cry intoxication and its regulation are not well characterized. In this work, we describe the secreted proteome (secretome) of primary mature midgut cell cultures from Heliothis virescens larvae after exposure to Cry1Ac toxin compared to control buffer treatment. The Cry1Ac-induced secretome caused higher proliferation and differentiation and an overall reduction in total cell mortality over time in primary H. virescens midgut stem cell cultures when compared to treatment with control buffer secretome. Differential proteomics identified four proteins with significant differences in abundance comparing Cry1Ac-treated and control secretomes. The most significant difference detected in the Cry1Ac secretome was an arylphorin subunit alpha protein not detected in the control secretome. Feeding of purified alpha-arylphorin to H. virescens larvae resulted in midgut hyperplasia and significantly reduced susceptibility to Cry1Ac toxin compared to controls. These data identify alpha-arylphorin as a protein with a new putative role in the midgut regeneration process in response to Cry1Ac intoxication and possibly pathogen/abiotic stress, identifying alpha-arylphorin as a potential gene to target with insecticidal gene silencing for pest control.
bibliographic citation: Castagnola et al. (2017) Alpha-arylphorin is a mitogen in the Heliothis virescens midgut cell secretome upon Cry1Ac intoxication. PeerJ 5:e3886 https://doi.org/10.7717/peerj.3886
date submitted: 2017-03-13
date accepted: 2017-09-13
issued: 2017-10-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Castagnola
  given name: Anais
author list: Agent
  family name: Jackson
  given name: Jerreme
author list: Agent
  family name: Perera
  given name: Omaththage P.
author list: Agent
  family name: Oppert
  given name: Cris
author list: Agent
  family name: Eda
  given name: Shigetoshi
author list: Agent
  family name: Jurat-Fuentes
  given name: Juan Luis
doi: 10.7717/peerj.3886
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-03
copyright: ©2017 Castagnola et al.
attribution name: Castagnola et al.

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