PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Metabolic syndrome in hospitalized patients with chronic obstructive pulmonary disease
items: Species-level determination of closely related araucarian resins using FTIR spectroscopy and its implications for the provenance of New Zealand amber
items: Factor structure of the happiness-increasing strategies scales (H-ISS): activities and coping strategies in relation to positive and negative affect
items: Multi-level machine learning prediction of protein–protein interactions in Saccharomyces cerevisiae
items: Divergent thermal specialisation of two South African entomopathogenic nematodes
items: Lack of association of vitamin D receptor BsmI gene polymorphism with bone mineral density in Spanish postmenopausal women
items: Histopathology of crustose coralline algae affected by white band and white patch diseases
items: The destructive effect of botulinum neurotoxins on the SNARE protein: SNAP-25 and synaptic membrane fusion
items: Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae)
items: The last marine pelomedusoids (Testudines: Pleurodira): a new species of Bairdemys and the paleoecology of Stereogenyina

Metabolic syndrome in hospitalized patients with chronic obstructive pulmonary disease
type: item
type: AcademicArticle
description: Introduction. The metabolic syndrome (MS) affects 21–53% of patients with chronic obstructive pulmonary disease (COPD) with a higher prevalence in the early stages of COPD, with results being highly variable between studies. MS may also affect natural course of COPD—number of exacerbations, quality of life and lung function. Aim. To examine the prevalence of MS and its correlation with comorbidities and COPD characteristics in patients with COPD admitted for exacerbation. Material and methods. 152 patients with COPD admitted for exacerbation were studied for presence of MS. All of them were also assessed for vitamin D status and diabetes mellitus type 2 (DM). Data were gathered for smoking status and exacerbations during the last year. All patients completed CAT (COPD assessment test) and mMRC (Modified Medical Research Council Dyspnea scale) questionnaires and underwent spirometry. Duration of current hospital stay was recorded. Results. 25% of patients have MS. 23.1% of the male and 29.5% of the female patients have MS (p > 0.05). The prevalence of MS in this study is significantly lower when compared to a national representative study (44.6% in subjects over 45 years). 69.1% of all patients and 97.4% from MS patients have arterial hypertension. The presence of MS is associated with significantly worse cough and sleep (1st and 7th CAT questions; p = 0.002 and p = 0.001 respectively) and higher total CAT score (p = 0.017). Average BMI is 27.31. None of the patients have MS and BMI <25. There is a correlation between the presence of MS and DM (p = 0.008) and with the number of exacerbations in the last year (p = 0.015). There is no correlation between the presence of MS and the pulmonary function. Conclusion. This study among hospitalized COPD patients finds comparable but relatively low prevalence of MS (25%) compared to previously published data (21–53%) and lower prevalence compared to general population (44.6%). MS may impact quality of life and the number of ex…
format: application/pdf
format: text/html
creator: Evgeni Mekov
creator: Yanina Slavova
creator: Adelina Tsakova
creator: Marianka Genova
creator: Dimitar Kostadinov
creator: Delcho Minchev
creator: Dora Marinova
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Internal Medicine
subject: Respiratory Medicine
description: doi:10.7717/peerj.1068
publisher: PeerJ Inc.
rights: © 2015 Mekov et al.
abstract: Introduction. The metabolic syndrome (MS) affects 21–53% of patients with chronic obstructive pulmonary disease (COPD) with a higher prevalence in the early stages of COPD, with results being highly variable between studies. MS may also affect natural course of COPD—number of exacerbations, quality of life and lung function. Aim. To examine the prevalence of MS and its correlation with comorbidities and COPD characteristics in patients with COPD admitted for exacerbation. Material and methods. 152 patients with COPD admitted for exacerbation were studied for presence of MS. All of them were also assessed for vitamin D status and diabetes mellitus type 2 (DM). Data were gathered for smoking status and exacerbations during the last year. All patients completed CAT (COPD assessment test) and mMRC (Modified Medical Research Council Dyspnea scale) questionnaires and underwent spirometry. Duration of current hospital stay was recorded. Results. 25% of patients have MS. 23.1% of the male and 29.5% of the female patients have MS (p > 0.05). The prevalence of MS in this study is significantly lower when compared to a national representative study (44.6% in subjects over 45 years). 69.1% of all patients and 97.4% from MS patients have arterial hypertension. The presence of MS is associated with significantly worse cough and sleep (1st and 7th CAT questions; p = 0.002 and p = 0.001 respectively) and higher total CAT score (p = 0.017). Average BMI is 27.31. None of the patients have MS and BMI <25. There is a correlation between the presence of MS and DM (p = 0.008) and with the number of exacerbations in the last year (p = 0.015). There is no correlation between the presence of MS and the pulmonary function. Conclusion. This study among hospitalized COPD patients finds comparable but relatively low prevalence of MS (25%) compared to previously published data (21–53%) and lower prevalence compared to general population (44.6%). MS may impact quality of life and the number of ex…
bibliographic citation: Mekov et al. (2015) Metabolic syndrome in hospitalized patients with chronic obstructive pulmonary disease. PeerJ 3:e1068 https://doi.org/10.7717/peerj.1068
date submitted: 2015-05-01
date accepted: 2015-06-10
issued: 2015-07-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mekov
  given name: Evgeni
author list: Agent
  family name: Slavova
  given name: Yanina
author list: Agent
  family name: Tsakova
  given name: Adelina
author list: Agent
  family name: Genova
  given name: Marianka
author list: Agent
  family name: Kostadinov
  given name: Dimitar
author list: Agent
  family name: Minchev
  given name: Delcho
author list: Agent
  family name: Marinova
  given name: Dora
doi: 10.7717/peerj.1068
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-02
copyright: © 2015 Mekov et al.
attribution name: Mekov et al.

Species-level determination of closely related araucarian resins using FTIR spectroscopy and its implications for the provenance of New Zealand amber
type: item
type: AcademicArticle
description: Some higher plants, both angiosperms and gymnosperms, can produce resins and some of these resins can polymerize and fossilize to form ambers. Various physical and chemical techniques have been used to identify and profile different plant resins and have then been applied to fossilized resins (ambers), to try to detect their parent plant affinities and understand the process of polymerization, with varying levels of success. Here we focus on resins produced from today’s most resinous conifer family, the Araucariaceae, which are thought to be the parent plants of some of the Southern Hemisphere’s fossil resin deposits. Fourier transform infrared (FTIR) spectra of the resins of closely related Araucariaceae species were examined to test whether they could be distinguished at genus and species level and whether the results could then be used to infer the parent plant of a New Zealand amber. The resin FTIR spectra are distinguishable from each other, and the three Araucaria species sampled produced similar FTIR spectra, to which Wollemia resin is most similar. Interspecific variability of the FTIR spectra is greatest in the three Agathis species tested. The New Zealand amber sample is similar in key shared features with the resin samples, but it does differ from the extant resin samples in key distinguishing features, nonetheless it is most similar to the resin of Agathis australis in this dataset. However on comparison with previously published FTIR spectra of similar aged amber and older (Eocene) resinites both found in coals from New Zealand and fresh Agathis australis resin, our amber has some features that imply a relatively immature resin, which was not expected from an amber of the Miocene age.
format: application/pdf
format: text/html
creator: Leyla J. Seyfullah
creator: Eva-Maria Sadowski
creator: Alexander R. Schmidt
subject: Paleontology
subject: Plant Science
description: doi:10.7717/peerj.1067
publisher: PeerJ Inc.
rights: © 2015 Seyfullah et al.
abstract: Some higher plants, both angiosperms and gymnosperms, can produce resins and some of these resins can polymerize and fossilize to form ambers. Various physical and chemical techniques have been used to identify and profile different plant resins and have then been applied to fossilized resins (ambers), to try to detect their parent plant affinities and understand the process of polymerization, with varying levels of success. Here we focus on resins produced from today’s most resinous conifer family, the Araucariaceae, which are thought to be the parent plants of some of the Southern Hemisphere’s fossil resin deposits. Fourier transform infrared (FTIR) spectra of the resins of closely related Araucariaceae species were examined to test whether they could be distinguished at genus and species level and whether the results could then be used to infer the parent plant of a New Zealand amber. The resin FTIR spectra are distinguishable from each other, and the three Araucaria species sampled produced similar FTIR spectra, to which Wollemia resin is most similar. Interspecific variability of the FTIR spectra is greatest in the three Agathis species tested. The New Zealand amber sample is similar in key shared features with the resin samples, but it does differ from the extant resin samples in key distinguishing features, nonetheless it is most similar to the resin of Agathis australis in this dataset. However on comparison with previously published FTIR spectra of similar aged amber and older (Eocene) resinites both found in coals from New Zealand and fresh Agathis australis resin, our amber has some features that imply a relatively immature resin, which was not expected from an amber of the Miocene age.
bibliographic citation: Seyfullah et al. (2015) Species-level determination of closely related araucarian resins using FTIR spectroscopy and its implications for the provenance of New Zealand amber. PeerJ 3:e1067 https://doi.org/10.7717/peerj.1067
date submitted: 2015-04-17
date accepted: 2015-06-10
issued: 2015-07-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Seyfullah
  given name: Leyla J.
author list: Agent
  family name: Sadowski
  given name: Eva-Maria
author list: Agent
  family name: Schmidt
  given name: Alexander R.
doi: 10.7717/peerj.1067
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-02
copyright: © 2015 Seyfullah et al.
attribution name: Seyfullah et al.

Factor structure of the happiness-increasing strategies scales (H-ISS): activities and coping strategies in relation to positive and negative affect
type: item
type: AcademicArticle
description: Background. Previous research (Tkach & Lyubomirsky, 2006) shows that there are eight general happiness-increasing strategies: social affiliation, partying, mental control, goal pursuit, passive leisure, active leisure, religion, and direct attempts. The present study investigates the factor structure of the happiness-increasing strategies scales (H-ISS) and their relationship to positive and negative affect. Method. The present study used participants’ (N = 1,050 and age mean = 34.21 sd = 12.73) responses to the H-ISS in structural equation modeling analyses. Affect was measured using the Positive Affect Negative Affect Schedule. Results. After small modifications we obtained a good model that contains the original eight factors/scales. Moreover, we found that women tend to use social affiliation, mental control, passive leisure, religion, and direct attempts more than men, while men preferred to engage in partying and clubbing more than women. The H-ISS explained significantly the variance of positive affect (R2 = .41) and the variance of negative affect (R2 = .27). Conclusions. Our study is an addition to previous research showing that the factor structure of the happiness-increasing strategies is valid and reliable. However, due to the model fitting issues that arise in the present study, we give some suggestions for improving the instrument.
format: application/pdf
format: text/html
creator: Ali Al Nima
creator: Danilo Garcia
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.1059
publisher: PeerJ Inc.
rights: © 2015 Al Nima and Garcia
abstract: Background. Previous research (Tkach & Lyubomirsky, 2006) shows that there are eight general happiness-increasing strategies: social affiliation, partying, mental control, goal pursuit, passive leisure, active leisure, religion, and direct attempts. The present study investigates the factor structure of the happiness-increasing strategies scales (H-ISS) and their relationship to positive and negative affect. Method. The present study used participants’ (N = 1,050 and age mean = 34.21 sd = 12.73) responses to the H-ISS in structural equation modeling analyses. Affect was measured using the Positive Affect Negative Affect Schedule. Results. After small modifications we obtained a good model that contains the original eight factors/scales. Moreover, we found that women tend to use social affiliation, mental control, passive leisure, religion, and direct attempts more than men, while men preferred to engage in partying and clubbing more than women. The H-ISS explained significantly the variance of positive affect (R2 = .41) and the variance of negative affect (R2 = .27). Conclusions. Our study is an addition to previous research showing that the factor structure of the happiness-increasing strategies is valid and reliable. However, due to the model fitting issues that arise in the present study, we give some suggestions for improving the instrument.
bibliographic citation: Al Nima et al. (2015) Factor structure of the happiness-increasing strategies scales (H-ISS): activities and coping strategies in relation to positive and negative affect. PeerJ 3:e1059 https://doi.org/10.7717/peerj.1059
date submitted: 2015-01-15
date accepted: 2015-06-08
issued: 2015-07-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al Nima
  given name: Ali
author list: Agent
  family name: Garcia
  given name: Danilo
doi: 10.7717/peerj.1059
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-02
copyright: © 2015 Al Nima and Garcia
attribution name: Al Nima and Garcia

Multi-level machine learning prediction of protein–protein interactions in Saccharomyces cerevisiae
type: item
type: AcademicArticle
description: Accurate identification of protein–protein interactions (PPI) is the key step in understanding proteins’ biological functions, which are typically context-dependent. Many existing PPI predictors rely on aggregated features from protein sequences, however only a few methods exploit local information about specific residue contacts. In this work we present a two-stage machine learning approach for prediction of protein–protein interactions. We start with the carefully filtered data on protein complexes available for Saccharomyces cerevisiae in the Protein Data Bank (PDB) database. First, we build linear descriptions of interacting and non-interacting sequence segment pairs based on their inter-residue distances. Secondly, we train machine learning classifiers to predict binary segment interactions for any two short sequence fragments. The final prediction of the protein–protein interaction is done using the 2D matrix representation of all-against-all possible interacting sequence segments of both analysed proteins. The level-I predictor achieves 0.88 AUC for micro-scale, i.e., residue-level prediction. The level-II predictor improves the results further by a more complex learning paradigm. We perform 30-fold macro-scale, i.e., protein-level cross-validation experiment. The level-II predictor using PSIPRED-predicted secondary structure reaches 0.70 precision, 0.68 recall, and 0.70 AUC, whereas other popular methods provide results below 0.6 threshold (recall, precision, AUC). Our results demonstrate that multi-scale sequence features aggregation procedure is able to improve the machine learning results by more than 10% as compared to other sequence representations. Prepared datasets and source code for our experimental pipeline are freely available for download from: http://zubekj.github.io/mlppi/ (open source Python implementation, OS independent).
format: application/pdf
format: text/html
creator: Julian Zubek
creator: Marcin Tatjewski
creator: Adam Boniecki
creator: Maciej Mnich
creator: Subhadip Basu
creator: Dariusz Plewczynski
subject: Bioinformatics
description: doi:10.7717/peerj.1041
publisher: PeerJ Inc.
rights: © 2015 Zubek et al.
abstract: Accurate identification of protein–protein interactions (PPI) is the key step in understanding proteins’ biological functions, which are typically context-dependent. Many existing PPI predictors rely on aggregated features from protein sequences, however only a few methods exploit local information about specific residue contacts. In this work we present a two-stage machine learning approach for prediction of protein–protein interactions. We start with the carefully filtered data on protein complexes available for Saccharomyces cerevisiae in the Protein Data Bank (PDB) database. First, we build linear descriptions of interacting and non-interacting sequence segment pairs based on their inter-residue distances. Secondly, we train machine learning classifiers to predict binary segment interactions for any two short sequence fragments. The final prediction of the protein–protein interaction is done using the 2D matrix representation of all-against-all possible interacting sequence segments of both analysed proteins. The level-I predictor achieves 0.88 AUC for micro-scale, i.e., residue-level prediction. The level-II predictor improves the results further by a more complex learning paradigm. We perform 30-fold macro-scale, i.e., protein-level cross-validation experiment. The level-II predictor using PSIPRED-predicted secondary structure reaches 0.70 precision, 0.68 recall, and 0.70 AUC, whereas other popular methods provide results below 0.6 threshold (recall, precision, AUC). Our results demonstrate that multi-scale sequence features aggregation procedure is able to improve the machine learning results by more than 10% as compared to other sequence representations. Prepared datasets and source code for our experimental pipeline are freely available for download from: http://zubekj.github.io/mlppi/ (open source Python implementation, OS independent).
bibliographic citation: Zubek et al. (2015) Multi-level machine learning prediction of protein–protein interactions in Saccharomyces cerevisiae. PeerJ 3:e1041 https://doi.org/10.7717/peerj.1041
date submitted: 2015-03-27
date accepted: 2015-05-31
issued: 2015-07-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zubek
  given name: Julian
author list: Agent
  family name: Tatjewski
  given name: Marcin
author list: Agent
  family name: Boniecki
  given name: Adam
author list: Agent
  family name: Mnich
  given name: Maciej
author list: Agent
  family name: Basu
  given name: Subhadip
author list: Agent
  family name: Plewczynski
  given name: Dariusz
doi: 10.7717/peerj.1041
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-02
copyright: © 2015 Zubek et al.
attribution name: Zubek et al.

Divergent thermal specialisation of two South African entomopathogenic nematodes
type: item
type: AcademicArticle
description: Thermal physiology of entomopathogenic nematodes (EPN) is a critical aspect of field performance and fitness. Thermal limits for survival and activity, and the ability of these limits to adjust (i.e., show phenotypic flexibility) depending on recent thermal history, are generally poorly established, especially for non-model nematode species. Here we report the acute thermal limits for survival, and the thermal acclimation-related plasticity thereof for two key endemic South African EPN species, Steinernema yirgalemense and Heterorhabditis zealandica. Results including LT50 indicate S. yirgalemense (LT50 = 40.8 ± 0.3 °C) has greater high temperature tolerance than H. zealandica (LT50 = 36.7 ± 0.2 °C), but S. yirgalemense (LT50 = −2.4 ± 0 °C) has poorer low temperature tolerance in comparison to H. zealandica (LT50 = −9.7 ± 0.3 °C), suggesting these two EPN species occupy divergent thermal niches to one another. Acclimation had both negative and positive effects on temperature stress survival of both species, although the overall variation meant that many of these effects were non-significant. There was no indication of a consistent loss of plasticity with improved basal thermal tolerance for either species at upper lethal temperatures. At lower temperatures measured for H. zealandica, the 5 °C acclimation lowered survival until below −12.5 °C, where after it increased survival. Such results indicate that the thermal niche breadth of EPN species can differ significantly depending on recent thermal conditions, and should be characterized across a broad range of species to understand the evolution of thermal limits to performance and survival in this group.
format: application/pdf
format: text/html
creator: Matthew P. Hill
creator: Antoinette P. Malan
creator: John S. Terblanche
subject: Agricultural Science
subject: Entomology
subject: Parasitology
description: doi:10.7717/peerj.1023
publisher: PeerJ Inc.
rights: © 2015 Hill et al.
abstract: Thermal physiology of entomopathogenic nematodes (EPN) is a critical aspect of field performance and fitness. Thermal limits for survival and activity, and the ability of these limits to adjust (i.e., show phenotypic flexibility) depending on recent thermal history, are generally poorly established, especially for non-model nematode species. Here we report the acute thermal limits for survival, and the thermal acclimation-related plasticity thereof for two key endemic South African EPN species, Steinernema yirgalemense and Heterorhabditis zealandica. Results including LT50 indicate S. yirgalemense (LT50 = 40.8 ± 0.3 °C) has greater high temperature tolerance than H. zealandica (LT50 = 36.7 ± 0.2 °C), but S. yirgalemense (LT50 = −2.4 ± 0 °C) has poorer low temperature tolerance in comparison to H. zealandica (LT50 = −9.7 ± 0.3 °C), suggesting these two EPN species occupy divergent thermal niches to one another. Acclimation had both negative and positive effects on temperature stress survival of both species, although the overall variation meant that many of these effects were non-significant. There was no indication of a consistent loss of plasticity with improved basal thermal tolerance for either species at upper lethal temperatures. At lower temperatures measured for H. zealandica, the 5 °C acclimation lowered survival until below −12.5 °C, where after it increased survival. Such results indicate that the thermal niche breadth of EPN species can differ significantly depending on recent thermal conditions, and should be characterized across a broad range of species to understand the evolution of thermal limits to performance and survival in this group.
bibliographic citation: Hill et al. (2015) Divergent thermal specialisation of two South African entomopathogenic nematodes. PeerJ 3:e1023 https://doi.org/10.7717/peerj.1023
date submitted: 2015-03-30
date accepted: 2015-05-26
issued: 2015-07-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hill
  given name: Matthew P.
author list: Agent
  family name: Malan
  given name: Antoinette P.
author list: Agent
  family name: Terblanche
  given name: John S.
doi: 10.7717/peerj.1023
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-02
copyright: © 2015 Hill et al.
attribution name: Hill et al.

Lack of association of vitamin D receptor BsmI gene polymorphism with bone mineral density in Spanish postmenopausal women
type: item
type: AcademicArticle
description: Osteoporosis is a polygenic disorder that is determined by the effects of several genes, each with relatively modest effects on bone mass. The aim of this study was to determine whether the vitamin D receptor single nucleotide polymorphism BsmI is associated with bone mineral density (BMD) in Spanish postmenopausal women. A total of 210 unrelated healthy postmenopausal women aged 60 ± 8 years were genotyped using TaqMan® SNP Genotyping Assays. Lumbar and femoral BMD were determined by dual-energy X-ray absorptiometry (DEXA). Daily calcium and vitamin D intake were determined by a food questionnaire. No differences were found in the femoral neck, trochanter, Ward’s Triangle, L2, L3, L4, L2-L4, or between the femoral neck and total hip BMD after further adjustment for potential confounding factors (P > 0.05) (age, BMI, years since menopause and daily calcium intake). The BsmI polymorphism in the VDR gene was not associated with BMD in Spanish postmenopausal women.
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format: text/html
creator: Jose M. Moran
creator: Maria Pedrera-Canal
creator: Francisco J. Rodriguez-Velasco
creator: Vicente Vera
creator: Jesus M. Lavado-Garcia
creator: Pilar Fernandez
creator: Juan D. Pedrera-Zamorano
subject: Diabetes and Endocrinology
subject: Medical Genetics
subject: Women's Health
description: doi:10.7717/peerj.953
publisher: PeerJ Inc.
rights: © 2015 Moran et al.
abstract: Osteoporosis is a polygenic disorder that is determined by the effects of several genes, each with relatively modest effects on bone mass. The aim of this study was to determine whether the vitamin D receptor single nucleotide polymorphism BsmI is associated with bone mineral density (BMD) in Spanish postmenopausal women. A total of 210 unrelated healthy postmenopausal women aged 60 ± 8 years were genotyped using TaqMan® SNP Genotyping Assays. Lumbar and femoral BMD were determined by dual-energy X-ray absorptiometry (DEXA). Daily calcium and vitamin D intake were determined by a food questionnaire. No differences were found in the femoral neck, trochanter, Ward’s Triangle, L2, L3, L4, L2-L4, or between the femoral neck and total hip BMD after further adjustment for potential confounding factors (P > 0.05) (age, BMI, years since menopause and daily calcium intake). The BsmI polymorphism in the VDR gene was not associated with BMD in Spanish postmenopausal women.
bibliographic citation: Moran et al. (2015) Lack of association of vitamin D receptor BsmI gene polymorphism with bone mineral density in Spanish postmenopausal women. PeerJ 3:e953 https://doi.org/10.7717/peerj.953
date submitted: 2015-03-23
date accepted: 2015-04-22
issued: 2015-07-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moran
  given name: Jose M.
author list: Agent
  family name: Pedrera-Canal
  given name: Maria
author list: Agent
  family name: Rodriguez-Velasco
  given name: Francisco J.
author list: Agent
  family name: Vera
  given name: Vicente
author list: Agent
  family name: Lavado-Garcia
  given name: Jesus M.
author list: Agent
  family name: Fernandez
  given name: Pilar
author list: Agent
  family name: Pedrera-Zamorano
  given name: Juan D.
doi: 10.7717/peerj.953
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-07-02
copyright: © 2015 Moran et al.
attribution name: Moran et al.

Histopathology of crustose coralline algae affected by white band and white patch diseases
type: item
type: AcademicArticle
description: Crustose coralline algae (CCA) are major benthic calcifiers that play crucial roles in marine ecosystems, particularly coral reefs. Over the past two decades, epizootics have been reported for several CCA species on coral reefs worldwide. However, their causes remain often unknown in part because few studies have investigated CCA pathologies at a microscopic scale. We studied the cellular changes associated with two syndromes: Coralline White Band Syndrome (CWBS) and Coralline White Patch Disease (CWPD) from samples collected in Curaçao, southern Caribbean. Healthy-looking tissue of diseased CCA did not differ from healthy tissue of healthy CCA. In diseased tissues of both pathologies, the three characteristic cell layers of CCA revealed cells completely depleted of protoplasmic content, but presenting an intact cell wall. In addition, CWBS showed a transition area between healthy and diseased tissues consisting of cells partially deprived of protoplasmic material, most likely corresponding to the white band characterizing the disease at the macroscopic level. This transition area was absent in CWPD. Regrowth at the lesion boundary were sometimes observed in both syndromes. Tissues of both healthy and diseased CCA were colonised by diverse boring organisms. Fungal infections associated with the diseased cells were not seen. However, other bioeroders were more abundant in diseased vs healthy CCA and in diseased vs healthy-looking tissues of diseased CCA. Although their role in the pathogenesis is unclear, this suggests that disease increases CCA susceptibility to bioerosion. Further investigations using an integrated approach are needed to carry out the complete diagnosis of these diseases.
format: application/pdf
format: text/html
creator: Gaëlle Quéré
creator: Anne-Leila Meistertzheim
creator: Robert S. Steneck
creator: Maggy M. Nugues
subject: Ecology
subject: Marine Biology
subject: Histology
description: doi:10.7717/peerj.1034
publisher: PeerJ Inc.
rights: © 2015 Quéré et al.
abstract: Crustose coralline algae (CCA) are major benthic calcifiers that play crucial roles in marine ecosystems, particularly coral reefs. Over the past two decades, epizootics have been reported for several CCA species on coral reefs worldwide. However, their causes remain often unknown in part because few studies have investigated CCA pathologies at a microscopic scale. We studied the cellular changes associated with two syndromes: Coralline White Band Syndrome (CWBS) and Coralline White Patch Disease (CWPD) from samples collected in Curaçao, southern Caribbean. Healthy-looking tissue of diseased CCA did not differ from healthy tissue of healthy CCA. In diseased tissues of both pathologies, the three characteristic cell layers of CCA revealed cells completely depleted of protoplasmic content, but presenting an intact cell wall. In addition, CWBS showed a transition area between healthy and diseased tissues consisting of cells partially deprived of protoplasmic material, most likely corresponding to the white band characterizing the disease at the macroscopic level. This transition area was absent in CWPD. Regrowth at the lesion boundary were sometimes observed in both syndromes. Tissues of both healthy and diseased CCA were colonised by diverse boring organisms. Fungal infections associated with the diseased cells were not seen. However, other bioeroders were more abundant in diseased vs healthy CCA and in diseased vs healthy-looking tissues of diseased CCA. Although their role in the pathogenesis is unclear, this suggests that disease increases CCA susceptibility to bioerosion. Further investigations using an integrated approach are needed to carry out the complete diagnosis of these diseases.
bibliographic citation: Quéré et al. (2015) Histopathology of crustose coralline algae affected by white band and white patch diseases. PeerJ 3:e1034 https://doi.org/10.7717/peerj.1034
date submitted: 2015-03-22
date accepted: 2015-05-28
issued: 2015-06-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quéré
  given name: Gaëlle
author list: Agent
  family name: Meistertzheim
  given name: Anne-Leila
author list: Agent
  family name: Steneck
  given name: Robert S.
author list: Agent
  family name: Nugues
  given name: Maggy M.
doi: 10.7717/peerj.1034
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-30
copyright: © 2015 Quéré et al.
attribution name: Quéré et al.

The destructive effect of botulinum neurotoxins on the SNARE protein: SNAP-25 and synaptic membrane fusion
type: item
type: AcademicArticle
description: Synaptic exocytosis requires the assembly of syntaxin 1A and SNAP-25 on the plasma membrane and synaptobrevin 2 (VAMP2) on the vesicular membrane to bridge the two opposite membranes. It is believed that the three SNARE proteins assemble in steps along the dynamic assembly pathway. The C-terminus of SNAP-25 is known to be the target of botulinum neurotoxins (BoNT/A and BoNT/E) that block neurotransmitters release in vivo. In this study, we employed electron paramagnetic resonance (EPR) spectroscopy to investigate the conformation of the SNAP-25 C-terminus in binary and ternary SNARE complexes. The fluorescence lipid mixing assay shows that the C-terminal of SNAP-25 is essential for membrane fusion, and that the truncated SNAP-25 mutants cleaved by BoNT/A and BoNT/E display different inhibition effects on membrane fusion: SNAP-25E (Δ26) abolishes the fusion activity of the SNARE complex, while SNAP-25A (Δ9) loses most of its function, although it can still form a SDS-resistant SNARE complex as the wild-type SNAP-25. CW-EPR spectra validate the unstable structures of the SNARE complex formed by SNAP-25 mutants. We propose that the truncated SNAP-25 mutants will disrupt the assembly of the SNARE core complex, and then inhibit the synaptic membrane fusion accordingly.
format: application/pdf
format: text/html
creator: Bin Lu
subject: Biochemistry
subject: Biophysics
subject: Microbiology
subject: Neuroscience
description: doi:10.7717/peerj.1065
publisher: PeerJ Inc.
rights: © 2015 Lu
abstract: Synaptic exocytosis requires the assembly of syntaxin 1A and SNAP-25 on the plasma membrane and synaptobrevin 2 (VAMP2) on the vesicular membrane to bridge the two opposite membranes. It is believed that the three SNARE proteins assemble in steps along the dynamic assembly pathway. The C-terminus of SNAP-25 is known to be the target of botulinum neurotoxins (BoNT/A and BoNT/E) that block neurotransmitters release in vivo. In this study, we employed electron paramagnetic resonance (EPR) spectroscopy to investigate the conformation of the SNAP-25 C-terminus in binary and ternary SNARE complexes. The fluorescence lipid mixing assay shows that the C-terminal of SNAP-25 is essential for membrane fusion, and that the truncated SNAP-25 mutants cleaved by BoNT/A and BoNT/E display different inhibition effects on membrane fusion: SNAP-25E (Δ26) abolishes the fusion activity of the SNARE complex, while SNAP-25A (Δ9) loses most of its function, although it can still form a SDS-resistant SNARE complex as the wild-type SNAP-25. CW-EPR spectra validate the unstable structures of the SNARE complex formed by SNAP-25 mutants. We propose that the truncated SNAP-25 mutants will disrupt the assembly of the SNARE core complex, and then inhibit the synaptic membrane fusion accordingly.
bibliographic citation: Lu (2015) The destructive effect of botulinum neurotoxins on the SNARE protein: SNAP-25 and synaptic membrane fusion. PeerJ 3:e1065 https://doi.org/10.7717/peerj.1065
date submitted: 2015-04-21
date accepted: 2015-06-09
issued: 2015-06-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Bin
doi: 10.7717/peerj.1065
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-30
copyright: © 2015 Lu
attribution name: Lu

Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae)
type: item
type: AcademicArticle
description: The funnel-web spider Macrothele calpeiana is a charismatic Mygalomorph with a great interest in basic, applied and translational research. Nevertheless, current scarcity of genomic and transcriptomic data of this species clearly limits the research in this non-model organism. To overcome this limitation, we launched the first tissue-specific enriched RNA-seq analysis in this species using a subtractive hybridization approach, with two main objectives, to characterize the specific transcriptome of the putative chemosensory appendages (palps and first pair of legs), and to provide a new set of DNA markers for further phylogenetic studies. We have characterized the set of transcripts specifically expressed in putative chemosensory tissues of this species, much of them showing features shared by chemosensory system genes. Among specific candidates, we have identified some members of the iGluR and NPC2 families. Moreover, we have demonstrated the utility of these newly generated data as molecular markers by inferring the phylogenetic position M. calpeina in the phylogenetic tree of Mygalomorphs. Our results provide novel resources for researchers interested in spider molecular biology and systematics, which can help to expand our knowledge on the evolutionary processes underlying fundamental biological questions, as species invasion or biodiversity origin and maintenance.
format: application/pdf
format: text/html
creator: Cristina Frías-López
creator: Francisca C. Almeida
creator: Sara Guirao-Rico
creator: Joel Vizueta
creator: Alejandro Sánchez-Gracia
creator: Miquel A. Arnedo
creator: Julio Rozas
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.1064
publisher: PeerJ Inc.
rights: © 2015 Frías-López et al
abstract: The funnel-web spider Macrothele calpeiana is a charismatic Mygalomorph with a great interest in basic, applied and translational research. Nevertheless, current scarcity of genomic and transcriptomic data of this species clearly limits the research in this non-model organism. To overcome this limitation, we launched the first tissue-specific enriched RNA-seq analysis in this species using a subtractive hybridization approach, with two main objectives, to characterize the specific transcriptome of the putative chemosensory appendages (palps and first pair of legs), and to provide a new set of DNA markers for further phylogenetic studies. We have characterized the set of transcripts specifically expressed in putative chemosensory tissues of this species, much of them showing features shared by chemosensory system genes. Among specific candidates, we have identified some members of the iGluR and NPC2 families. Moreover, we have demonstrated the utility of these newly generated data as molecular markers by inferring the phylogenetic position M. calpeina in the phylogenetic tree of Mygalomorphs. Our results provide novel resources for researchers interested in spider molecular biology and systematics, which can help to expand our knowledge on the evolutionary processes underlying fundamental biological questions, as species invasion or biodiversity origin and maintenance.
bibliographic citation: Frías-López et al. (2015) Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae). PeerJ 3:e1064 https://doi.org/10.7717/peerj.1064
date submitted: 2015-05-19
date accepted: 2015-06-09
issued: 2015-06-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frías-López
  given name: Cristina
author list: Agent
  family name: Almeida
  given name: Francisca C.
author list: Agent
  family name: Guirao-Rico
  given name: Sara
author list: Agent
  family name: Vizueta
  given name: Joel
author list: Agent
  family name: Sánchez-Gracia
  given name: Alejandro
author list: Agent
  family name: Arnedo
  given name: Miquel A.
author list: Agent
  family name: Rozas
  given name: Julio
doi: 10.7717/peerj.1064
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-30
copyright: © 2015 Frías-López et al
attribution name: Frías-López et al

The last marine pelomedusoids (Testudines: Pleurodira): a new species of Bairdemys and the paleoecology of Stereogenyina
type: item
type: AcademicArticle
description: The extinct Stereogenyina turtles form a relatively diverse Podocnemididae lineage, with twelve described and phylogenetically positioned species. They are characterized by a wide geographic and temporal range, from the Eocene of Africa to the Pleistocene of Southeast Asia, and a peculiar palate morphology, with a secondary palate that is unique among side-necked turtles. Here, we describe a new Stereogenyina species, based on an almost complete skull from the middle Miocene Capadare Formation, of Venezuela. A new phylogenetic analysis supports the assignment of the new species to the genus Bairdemys. Based on geometric morphometrics analyses, we related the development of the stereogenyin secondary palate with the acquisition of a durophagous diet. Based on a review of the sedimentary environments where their fossils are found, we also propose that stereogenyins were a marine radiation of podocnemidid turtles, as corroborated by previous studies of fossil eggs and limb morphology. These two inferences allowed us to hypothesize that stereogenyins occupied an ecological niche similar to that of the extant Carettini sea turtles, and that the rise of the latter group may be related to the Stereogenyina diversity fall in the end of the Miocene.
format: application/pdf
format: text/html
creator: Gabriel S. Ferreira
creator: Ascanio D. Rincón
creator: Andrés Solórzano
creator: Max C. Langer
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.1063
publisher: PeerJ Inc.
rights: © 2015 Ferreira et al.
abstract: The extinct Stereogenyina turtles form a relatively diverse Podocnemididae lineage, with twelve described and phylogenetically positioned species. They are characterized by a wide geographic and temporal range, from the Eocene of Africa to the Pleistocene of Southeast Asia, and a peculiar palate morphology, with a secondary palate that is unique among side-necked turtles. Here, we describe a new Stereogenyina species, based on an almost complete skull from the middle Miocene Capadare Formation, of Venezuela. A new phylogenetic analysis supports the assignment of the new species to the genus Bairdemys. Based on geometric morphometrics analyses, we related the development of the stereogenyin secondary palate with the acquisition of a durophagous diet. Based on a review of the sedimentary environments where their fossils are found, we also propose that stereogenyins were a marine radiation of podocnemidid turtles, as corroborated by previous studies of fossil eggs and limb morphology. These two inferences allowed us to hypothesize that stereogenyins occupied an ecological niche similar to that of the extant Carettini sea turtles, and that the rise of the latter group may be related to the Stereogenyina diversity fall in the end of the Miocene.
bibliographic citation: Ferreira et al. (2015) The last marine pelomedusoids (Testudines: Pleurodira): a new species of Bairdemys and the paleoecology of Stereogenyina. PeerJ 3:e1063 https://doi.org/10.7717/peerj.1063
date submitted: 2015-04-02
date accepted: 2015-06-09
issued: 2015-06-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferreira
  given name: Gabriel S.
author list: Agent
  family name: Rincón
  given name: Ascanio D.
author list: Agent
  family name: Solórzano
  given name: Andrés
author list: Agent
  family name: Langer
  given name: Max C.
doi: 10.7717/peerj.1063
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-30
copyright: © 2015 Ferreira et al.
attribution name: Ferreira et al.

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