PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Anthropogenic impacts in protected areas: assessing the efficiency of conservation efforts using Mediterranean ant communities
items: Blood circulation in the ascidian tunicate Corella inflata (Corellidae)
items: Distribution and characteristic of nitrite-dependent anaerobic methane oxidation bacteria by comparative analysis of wastewater treatment plants and agriculture fields in northern China
items: Probabilistic adaptation in changing microbial environments
items: Functional characterisation of phagocytes in the Pacific oyster Crassostrea gigas
items: Age-congruency and contact effects in body expression recognition from point-light displays (PLD)
items: Species interactions in an Andean bird–flowering plant network: phenology is more important than abundance or morphology
items: One-year mortality after severe COPD exacerbation in Bulgaria
items: Diet of the endangered big-headed turtle Platysternon megacephalum
items: Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America

Anthropogenic impacts in protected areas: assessing the efficiency of conservation efforts using Mediterranean ant communities
type: item
type: AcademicArticle
description: In countries with high levels of urbanization, protected areas are often subject to human disturbance. In addition to dealing with fragmentation, land managers also have to confront the loss of characteristic ecosystems due to biotic homogenization, which is the increasing similarity of species assemblages among geographically separate regions. Using ants as a model system, we explored whether anthropogenic factors negatively affect biodiversity of protected areas of a regional network. We first analysed the effect of fragmentation and human activity on ant biodiversity within protected areas. Secondly, we tested whether homogenization could occur among protected areas. We sampled 79 plots in the most common habitats of 32 protected areas in southern Spain and calculated ant community richness and diversity indices, endemic richness, and Bray–Curtis similarity indices (between pairs of plots). We related these indices with patch fragmentation and human disturbance variables, taking into account environmental, spatial and landscape covariates. We used ANOSIM to test for differences between similarity indices, specifically among levels of anthropogenic disturbance. Species richness was positively correlated with the distance from the border of the protected areas and the number of endemic species was negatively correlated with the degree of fragmentation. Ant communities were similar within each protected area but differed across regions. Human disturbance was not correlated with community similarity among sampling points. Our approach suggests how the ability of European protected areas to sustain biodiversity is limited because they remain susceptible to anthropogenic impacts. Although ant communities maintained their biological distinctiveness, we reveal how fragmentation within protected areas is important for community richness and endemism maintenance.
format: application/pdf
format: text/html
creator: Elena Angulo
creator: Raphaël Boulay
creator: Francisca Ruano
creator: Alberto Tinaut
creator: Xim Cerdá
subject: Biodiversity
subject: Biosphere Interactions
subject: Ecology
subject: Environmental Impacts
subject: Natural Resource Management
description: doi:10.7717/peerj.2773
publisher: PeerJ Inc.
rights: © 2016 Angulo et al.
abstract: In countries with high levels of urbanization, protected areas are often subject to human disturbance. In addition to dealing with fragmentation, land managers also have to confront the loss of characteristic ecosystems due to biotic homogenization, which is the increasing similarity of species assemblages among geographically separate regions. Using ants as a model system, we explored whether anthropogenic factors negatively affect biodiversity of protected areas of a regional network. We first analysed the effect of fragmentation and human activity on ant biodiversity within protected areas. Secondly, we tested whether homogenization could occur among protected areas. We sampled 79 plots in the most common habitats of 32 protected areas in southern Spain and calculated ant community richness and diversity indices, endemic richness, and Bray–Curtis similarity indices (between pairs of plots). We related these indices with patch fragmentation and human disturbance variables, taking into account environmental, spatial and landscape covariates. We used ANOSIM to test for differences between similarity indices, specifically among levels of anthropogenic disturbance. Species richness was positively correlated with the distance from the border of the protected areas and the number of endemic species was negatively correlated with the degree of fragmentation. Ant communities were similar within each protected area but differed across regions. Human disturbance was not correlated with community similarity among sampling points. Our approach suggests how the ability of European protected areas to sustain biodiversity is limited because they remain susceptible to anthropogenic impacts. Although ant communities maintained their biological distinctiveness, we reveal how fragmentation within protected areas is important for community richness and endemism maintenance.
bibliographic citation: Angulo et al. (2016) Anthropogenic impacts in protected areas: assessing the efficiency of conservation efforts using Mediterranean ant communities. PeerJ 4:e2773 https://doi.org/10.7717/peerj.2773
date submitted: 2016-05-18
date accepted: 2016-11-08
issued: 2016-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Angulo
  given name: Elena
author list: Agent
  family name: Boulay
  given name: Raphaël
author list: Agent
  family name: Ruano
  given name: Francisca
author list: Agent
  family name: Tinaut
  given name: Alberto
author list: Agent
  family name: Cerdá
  given name: Xim
doi: 10.7717/peerj.2773
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-14
copyright: ©2016 Angulo et al.
attribution name: Angulo et al.

Blood circulation in the ascidian tunicate Corella inflata (Corellidae)
type: item
type: AcademicArticle
description: The body of the ascidian tunicate Corella inflata is relatively transparent. Thus, the circulatory system can be visualized by injecting high molecular weight fluorescein labeled dextran into the heart or the large vessels at the ends of the heart without surgery to remove the body wall. In addition, after staining with neutral red, the movement of blood cells can be easily followed to further characterize the circulatory system. The heart is two gently curved concentric tubes extending across the width of the animal. The inner myocardial tube has a partial constriction approximately in the middle. As in other tunicates, the heart is peristaltic and periodically reverses direction. During the branchial phase blood leaves the anterior end of the heart by two asymmetric vessels that connect to the two sides of the branchial basket. Blood then flows in both transverse directions through a complex system of ducts in the basket into large ventral and dorsal vessels which carry blood back to the visceral organs in the posterior of the animal. During the visceral phase blood leaves the posterior end of the heart in two vessels that repeatedly bifurcate and fan into the stomach and gonads. Blood velocity, determined by following individual cells in video frames, is high and pulsatory near the heart. A double peak in velocity at the maximum may be due to the constriction in the middle of the heart tube. Blood velocity progressively decreases with distance from the heart. In peripheral regions with vessels of small diameter blood cells frequently collide with vessel walls and cell motion is erratic. The estimated volume of blood flow during each directional phase is greater than the total volume of the animal. Circulating blood cells are confined to vessels or ducts in the visible parts of the animal and retention of high molecular weight dextran in the vessels is comparable to that seen in vertebrates. These are characteristics of a closed circulatory system.
format: application/pdf
format: text/html
creator: Michael W. Konrad
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.2771
publisher: PeerJ Inc.
rights: © 2016 Konrad
abstract: The body of the ascidian tunicate Corella inflata is relatively transparent. Thus, the circulatory system can be visualized by injecting high molecular weight fluorescein labeled dextran into the heart or the large vessels at the ends of the heart without surgery to remove the body wall. In addition, after staining with neutral red, the movement of blood cells can be easily followed to further characterize the circulatory system. The heart is two gently curved concentric tubes extending across the width of the animal. The inner myocardial tube has a partial constriction approximately in the middle. As in other tunicates, the heart is peristaltic and periodically reverses direction. During the branchial phase blood leaves the anterior end of the heart by two asymmetric vessels that connect to the two sides of the branchial basket. Blood then flows in both transverse directions through a complex system of ducts in the basket into large ventral and dorsal vessels which carry blood back to the visceral organs in the posterior of the animal. During the visceral phase blood leaves the posterior end of the heart in two vessels that repeatedly bifurcate and fan into the stomach and gonads. Blood velocity, determined by following individual cells in video frames, is high and pulsatory near the heart. A double peak in velocity at the maximum may be due to the constriction in the middle of the heart tube. Blood velocity progressively decreases with distance from the heart. In peripheral regions with vessels of small diameter blood cells frequently collide with vessel walls and cell motion is erratic. The estimated volume of blood flow during each directional phase is greater than the total volume of the animal. Circulating blood cells are confined to vessels or ducts in the visible parts of the animal and retention of high molecular weight dextran in the vessels is comparable to that seen in vertebrates. These are characteristics of a closed circulatory system.
bibliographic citation: Konrad (2016) Blood circulation in the ascidian tunicate Corella inflata (Corellidae). PeerJ 4:e2771 https://doi.org/10.7717/peerj.2771
date submitted: 2016-06-11
date accepted: 2016-11-08
issued: 2016-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Konrad
  given name: Michael W.
doi: 10.7717/peerj.2771
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-14
copyright: ©2016 Konrad
attribution name: Konrad

Distribution and characteristic of nitrite-dependent anaerobic methane oxidation bacteria by comparative analysis of wastewater treatment plants and agriculture fields in northern China
type: item
type: AcademicArticle
description: Nitrite-dependent anaerobic methane oxidation (n-damo) is a recently discovered biological process which has been arousing global attention because of its potential in minimizing greenhouse gases emissions. In this study, molecular biological techniques and potential n-damo activity batch experiments were conducted to investigate the presence and diversity of M. oxyfera bacteria in paddy field, corn field, and wastewater treatment plant (WWTP) sites in northern China, as well as lab-scale n-damo enrichment culture. N-damo enrichment culture showed the highest abundance of M. oxyfera bacteria, and positive correlation was observed between potential n-damo rate and abundance of M. oxyfera bacteria. Both paddy field and corn field sites were believed to be better inoculum than WWTP for the enrichment of M. oxyfera bacteria due to their higher abundance and the diversity of M. oxyfera bacteria. Comparative analysis revealed that long biomass retention time, low NH ${}_{4}^{+}$ 4 + and high NO ${}_{2}^{-}$ 2 − content were suitable for the growth of M. oxyfera bacteria.
format: application/pdf
format: text/html
creator: Zhen Hu
creator: Ru Ma
subject: Agricultural Science
subject: Bioengineering
subject: Climate Change Biology
subject: Environmental Sciences
subject: Soil Science
description: doi:10.7717/peerj.2766
publisher: PeerJ Inc.
rights: © 2016 Hu and Ma
abstract: Nitrite-dependent anaerobic methane oxidation (n-damo) is a recently discovered biological process which has been arousing global attention because of its potential in minimizing greenhouse gases emissions. In this study, molecular biological techniques and potential n-damo activity batch experiments were conducted to investigate the presence and diversity of M. oxyfera bacteria in paddy field, corn field, and wastewater treatment plant (WWTP) sites in northern China, as well as lab-scale n-damo enrichment culture. N-damo enrichment culture showed the highest abundance of M. oxyfera bacteria, and positive correlation was observed between potential n-damo rate and abundance of M. oxyfera bacteria. Both paddy field and corn field sites were believed to be better inoculum than WWTP for the enrichment of M. oxyfera bacteria due to their higher abundance and the diversity of M. oxyfera bacteria. Comparative analysis revealed that long biomass retention time, low NH ${}_{4}^{+}$ 4 + and high NO ${}_{2}^{-}$ 2 − content were suitable for the growth of M. oxyfera bacteria.
bibliographic citation: Hu et al. (2016) Distribution and characteristic of nitrite-dependent anaerobic methane oxidation bacteria by comparative analysis of wastewater treatment plants and agriculture fields in northern China. PeerJ 4:e2766 https://doi.org/10.7717/peerj.2766
date submitted: 2016-06-20
date accepted: 2016-11-07
issued: 2016-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Zhen
author list: Agent
  family name: Ma
  given name: Ru
doi: 10.7717/peerj.2766
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-14
copyright: ©2016 Hu and Ma
attribution name: Hu and Ma

Probabilistic adaptation in changing microbial environments
type: item
type: AcademicArticle
description: Microbes growing in animal host environments face fluctuations that have elements of both randomness and predictability. In the mammalian gut, fluctuations in nutrient levels and other physiological parameters are structured by the host’s behavior, diet, health and microbiota composition. Microbial cells that can anticipate environmental fluctuations by exploiting this structure would likely gain a fitness advantage (by adapting their internal state in advance). We propose that the problem of adaptive growth in structured changing environments, such as the gut, can be viewed as probabilistic inference. We analyze environments that are “meta-changing”: where there are changes in the way the environment fluctuates, governed by a mechanism unobservable to cells. We develop a dynamic Bayesian model of these environments and show that a real-time inference algorithm (particle filtering) for this model can be used as a microbial growth strategy implementable in molecular circuits. The growth strategy suggested by our model outperforms heuristic strategies, and points to a class of algorithms that could support real-time probabilistic inference in natural or synthetic cellular circuits.
format: application/pdf
format: text/html
creator: Yarden Katz
creator: Michael Springer
subject: Computational Biology
subject: Ecology
subject: Mathematical Biology
subject: Microbiology
subject: Synthetic Biology
description: doi:10.7717/peerj.2716
publisher: PeerJ Inc.
rights: © 2016 Katz and Springer
abstract: Microbes growing in animal host environments face fluctuations that have elements of both randomness and predictability. In the mammalian gut, fluctuations in nutrient levels and other physiological parameters are structured by the host’s behavior, diet, health and microbiota composition. Microbial cells that can anticipate environmental fluctuations by exploiting this structure would likely gain a fitness advantage (by adapting their internal state in advance). We propose that the problem of adaptive growth in structured changing environments, such as the gut, can be viewed as probabilistic inference. We analyze environments that are “meta-changing”: where there are changes in the way the environment fluctuates, governed by a mechanism unobservable to cells. We develop a dynamic Bayesian model of these environments and show that a real-time inference algorithm (particle filtering) for this model can be used as a microbial growth strategy implementable in molecular circuits. The growth strategy suggested by our model outperforms heuristic strategies, and points to a class of algorithms that could support real-time probabilistic inference in natural or synthetic cellular circuits.
bibliographic citation: Katz et al. (2016) Probabilistic adaptation in changing microbial environments. PeerJ 4:e2716 https://doi.org/10.7717/peerj.2716
date submitted: 2016-08-17
date accepted: 2016-10-25
issued: 2016-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Katz
  given name: Yarden
author list: Agent
  family name: Springer
  given name: Michael
doi: 10.7717/peerj.2716
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-14
copyright: ©2016 Katz and Springer
attribution name: Katz and Springer

Functional characterisation of phagocytes in the Pacific oyster Crassostrea gigas
type: item
type: AcademicArticle
description: Invertebrates lack canonical adaptive immunity and mainly rely on innate immune system to fight against pathogens. The phagocytes, which could engulf and kill microbial pathogens, are likely to be of great importance and have to undertake significant roles in invertebrate immune defense. In the present study, flow cytometry combined with histological and lectin staining was employed to characterise functional features of phagocytes in the Pacific oyster Crassostrea gigas. Based on the cell size and cellular contents, haemocytes were categorised into three cell types, i.e., granulocytes, semigranulocytes and agranulocytes. Agranulocytes with smaller cell volume and lower cytoplasmic-to-nuclear ratio did not show phagocytic activity, while semigranulocytes and agranulocytes exhibited larger cell volume, higher cytoplasmic-to-nuclear ratio and phagocytic activity. In addition, granulocytes with higher side scatter (SSC) exhibited higher phagocytic activity than that of semigranulocytes. When β-integrin and lectin-like receptors were blocked by RGD tripeptide and carbohydrates, respectively, the phagocytic activity of both granulocytes and semigranulocytes was significantly inhibited, indicating that β-integrin and certain lectin-like receptors were involved in phagocytosis towards microbes. Moreover, lipopolysaccharide but not peptidylglycan could enhance phagocytic activity of granulocytes and semigranulocytes towards Vibrio splendidus and Staphylococcus aureus. Lectin staining analysis revealed that Lycopersicon esculentum lectin (LEL), binding the epitope polylactosamine, was highly distributed on the extracellular cell surface of phagocytes, and could be utilized as a potential molecular marker to differentiate phagocytes from non-phagocytic haemocytes. The results, collectively, provide knowledge on the functional characters of oyster phagocytes, which would contribute to deep investigation of cell typing and cellular immunity in bivalves.
format: application/pdf
format: text/html
creator: Shuai Jiang
creator: Zhihao Jia
creator: Tao Zhang
creator: Lingling Wang
creator: Limei Qiu
creator: Jinsheng Sun
creator: Linsheng Song
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.2590
publisher: PeerJ Inc.
rights: © 2016 Jiang et al.
abstract: Invertebrates lack canonical adaptive immunity and mainly rely on innate immune system to fight against pathogens. The phagocytes, which could engulf and kill microbial pathogens, are likely to be of great importance and have to undertake significant roles in invertebrate immune defense. In the present study, flow cytometry combined with histological and lectin staining was employed to characterise functional features of phagocytes in the Pacific oyster Crassostrea gigas. Based on the cell size and cellular contents, haemocytes were categorised into three cell types, i.e., granulocytes, semigranulocytes and agranulocytes. Agranulocytes with smaller cell volume and lower cytoplasmic-to-nuclear ratio did not show phagocytic activity, while semigranulocytes and agranulocytes exhibited larger cell volume, higher cytoplasmic-to-nuclear ratio and phagocytic activity. In addition, granulocytes with higher side scatter (SSC) exhibited higher phagocytic activity than that of semigranulocytes. When β-integrin and lectin-like receptors were blocked by RGD tripeptide and carbohydrates, respectively, the phagocytic activity of both granulocytes and semigranulocytes was significantly inhibited, indicating that β-integrin and certain lectin-like receptors were involved in phagocytosis towards microbes. Moreover, lipopolysaccharide but not peptidylglycan could enhance phagocytic activity of granulocytes and semigranulocytes towards Vibrio splendidus and Staphylococcus aureus. Lectin staining analysis revealed that Lycopersicon esculentum lectin (LEL), binding the epitope polylactosamine, was highly distributed on the extracellular cell surface of phagocytes, and could be utilized as a potential molecular marker to differentiate phagocytes from non-phagocytic haemocytes. The results, collectively, provide knowledge on the functional characters of oyster phagocytes, which would contribute to deep investigation of cell typing and cellular immunity in bivalves.
bibliographic citation: Jiang et al. (2016) Functional characterisation of phagocytes in the Pacific oyster Crassostrea gigas. PeerJ 4:e2590 https://doi.org/10.7717/peerj.2590
date submitted: 2016-06-29
date accepted: 2016-09-21
issued: 2016-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Shuai
author list: Agent
  family name: Jia
  given name: Zhihao
author list: Agent
  family name: Zhang
  given name: Tao
author list: Agent
  family name: Wang
  given name: Lingling
author list: Agent
  family name: Qiu
  given name: Limei
author list: Agent
  family name: Sun
  given name: Jinsheng
author list: Agent
  family name: Song
  given name: Linsheng
doi: 10.7717/peerj.2590
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-14
copyright: ©2016 Jiang et al.
attribution name: Jiang et al.

Age-congruency and contact effects in body expression recognition from point-light displays (PLD)
type: item
type: AcademicArticle
description: Recognition of older people’s body expressions is a crucial social skill. We here investigate how age, not just of the observer, but also of the observed individual, affects this skill. Age may influence the ability to recognize other people’s body expressions by changes in one’s own ability to perform certain action over the life-span (i.e., an own-age bias may occur, with best recognition for one’s own age). Whole body point light displays of children, young adults and older adults (>70 years) expressing six different emotions were presented to observers of the same three age-groups. Across two variations of the paradigm, no evidence for the predicted own-age bias (a cross-over interaction between one’s own age and the observed person’s age) was found. Instead, experience effects were found with children better recognizing older actors’ expressions of ‘active emotions,’ such as anger and happiness with greater exposure in daily life. Together, the findings suggest that age-related changes in one own’s mobility only influences body expression categorization in young children who interact frequently with older adults.
format: application/pdf
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creator: Petra M.J. Pollux
creator: Frouke Hermens
creator: Alexander P. Willmott
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2796
publisher: PeerJ Inc.
rights: © 2016 Pollux et al.
abstract: Recognition of older people’s body expressions is a crucial social skill. We here investigate how age, not just of the observer, but also of the observed individual, affects this skill. Age may influence the ability to recognize other people’s body expressions by changes in one’s own ability to perform certain action over the life-span (i.e., an own-age bias may occur, with best recognition for one’s own age). Whole body point light displays of children, young adults and older adults (>70 years) expressing six different emotions were presented to observers of the same three age-groups. Across two variations of the paradigm, no evidence for the predicted own-age bias (a cross-over interaction between one’s own age and the observed person’s age) was found. Instead, experience effects were found with children better recognizing older actors’ expressions of ‘active emotions,’ such as anger and happiness with greater exposure in daily life. Together, the findings suggest that age-related changes in one own’s mobility only influences body expression categorization in young children who interact frequently with older adults.
bibliographic citation: Pollux et al. (2016) Age-congruency and contact effects in body expression recognition from point-light displays (PLD). PeerJ 4:e2796 https://doi.org/10.7717/peerj.2796
date submitted: 2016-06-22
date accepted: 2016-11-15
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pollux
  given name: Petra M.J.
author list: Agent
  family name: Hermens
  given name: Frouke
author list: Agent
  family name: Willmott
  given name: Alexander P.
doi: 10.7717/peerj.2796
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Pollux et al.
attribution name: Pollux et al.

Species interactions in an Andean bird–flowering plant network: phenology is more important than abundance or morphology
type: item
type: AcademicArticle
description: Biological constraints and neutral processes have been proposed to explain the properties of plant–pollinator networks. Using interactions between nectarivorous birds (hummingbirds and flowerpiercers) and flowering plants in high elevation forests (i.e., “elfin” forests) of the Andes, we explore the importance of biological constraints and neutral processes (random interactions) to explain the observed species interactions and network metrics, such as connectance, specialization, nestedness and asymmetry. In cold environments of elfin forests, which are located at the top of the tropical montane forest zone, many plants are adapted for pollination by birds, making this an ideal system to study plant–pollinator networks. To build the network of interactions between birds and plants, we used direct field observations. We measured abundance of birds using mist-nets and flower abundance using transects, and phenology by scoring presence of birds and flowers over time. We compared the length of birds’ bills to flower length to identify “forbidden interactions”—those interactions that could not result in legitimate floral visits based on mis-match in morphology. Diglossa flowerpiercers, which are characterized as “illegitimate” flower visitors, were relatively abundant. We found that the elfin forest network was nested with phenology being the factor that best explained interaction frequencies and nestedness, providing support for biological constraints hypothesis. We did not find morphological constraints to be important in explaining observed interaction frequencies and network metrics. Other network metrics (connectance, evenness and asymmetry), however, were better predicted by abundance (neutral process) models. Flowerpiercers, which cut holes and access flowers at their base and, consequently, facilitate nectar access for other hummingbirds, explain why morphological mis-matches were relatively unimportant in this system. Future work should focus on how changes in a…
format: application/pdf
format: text/html
creator: Oscar Gonzalez
creator: Bette A. Loiselle
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.2789
publisher: PeerJ Inc.
rights: © 2016 Gonzalez and Loiselle
abstract: Biological constraints and neutral processes have been proposed to explain the properties of plant–pollinator networks. Using interactions between nectarivorous birds (hummingbirds and flowerpiercers) and flowering plants in high elevation forests (i.e., “elfin” forests) of the Andes, we explore the importance of biological constraints and neutral processes (random interactions) to explain the observed species interactions and network metrics, such as connectance, specialization, nestedness and asymmetry. In cold environments of elfin forests, which are located at the top of the tropical montane forest zone, many plants are adapted for pollination by birds, making this an ideal system to study plant–pollinator networks. To build the network of interactions between birds and plants, we used direct field observations. We measured abundance of birds using mist-nets and flower abundance using transects, and phenology by scoring presence of birds and flowers over time. We compared the length of birds’ bills to flower length to identify “forbidden interactions”—those interactions that could not result in legitimate floral visits based on mis-match in morphology. Diglossa flowerpiercers, which are characterized as “illegitimate” flower visitors, were relatively abundant. We found that the elfin forest network was nested with phenology being the factor that best explained interaction frequencies and nestedness, providing support for biological constraints hypothesis. We did not find morphological constraints to be important in explaining observed interaction frequencies and network metrics. Other network metrics (connectance, evenness and asymmetry), however, were better predicted by abundance (neutral process) models. Flowerpiercers, which cut holes and access flowers at their base and, consequently, facilitate nectar access for other hummingbirds, explain why morphological mis-matches were relatively unimportant in this system. Future work should focus on how changes in a…
bibliographic citation: Gonzalez et al. (2016) Species interactions in an Andean bird–flowering plant network: phenology is more important than abundance or morphology. PeerJ 4:e2789 https://doi.org/10.7717/peerj.2789
date submitted: 2016-06-14
date accepted: 2016-11-12
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gonzalez
  given name: Oscar
author list: Agent
  family name: Loiselle
  given name: Bette A.
doi: 10.7717/peerj.2789
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Gonzalez and Loiselle
attribution name: Gonzalez and Loiselle

One-year mortality after severe COPD exacerbation in Bulgaria
type: item
type: AcademicArticle
description: Introduction One-year mortality in COPD patients is reported to be between 4% and 43%, depending on the group examined. Aim To examine the one-year mortality in COPD patients after severe exacerbation and the correlation between mortality and patients’ characteristics and comorbidities. Methods A total of 152 COPD patients hospitalized for severe exacerbation were assessed for vitamin D status, diabetes mellitus (DM), arterial hypertension (AH), and metabolic syndrome (MS). Data were gathered about smoking status and number of exacerbations in previous year. CAT and mMRC questionnaires were completed by all patients. Pre- and post-bronchodilatory spirometry was performed. One-year mortality was established from national death register. Results One-year mortality is 7.2%. DM, MS, and VD are not predictors for one-year mortality. However there is a trend for increased mortality in patients with AH (9.5% vs. 2.1%, p = 0.107). There is increased mortality in patients with mMRC > 2 (11.1 vs. 0%, p = 0.013). The presence of severe exacerbation in the previous year is a risk factor for mortality (12.5% vs. 1.4%, p = 0.009). There is a trend for increased mortality in the group with FEV1 < 50% (11.5 vs. 4.4%, p = 0.094). Cox regression shows 3.7% increase in mortality rate for 1% decrease in FEV1, 5.2% for 1% decrease in PEF, 7.8% for one year age increase and 8.1% for 1 CAT point increase (all p < 0.05). Conclusions This study finds relatively low one-year mortality in COPD patients after surviving severe exacerbation. Grade C and FEV1 > 80% may be factors for good prognosis. Risk factors for increased mortality are age, FEV1 value, severe exacerbation in previous year and reduced quality of life.
format: application/pdf
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creator: Evgeni Mekov
creator: Yanina Slavova
creator: Adelina Tsakova
creator: Marianka P. Genova
creator: Dimitar T. Kostadinov
creator: Delcho Minchev
creator: Dora Marinova
creator: Mihail A. Boyanov
subject: Epidemiology
subject: Internal Medicine
subject: Respiratory Medicine
description: doi:10.7717/peerj.2788
publisher: PeerJ Inc.
rights: © 2016 Mekov et al.
abstract: Introduction One-year mortality in COPD patients is reported to be between 4% and 43%, depending on the group examined. Aim To examine the one-year mortality in COPD patients after severe exacerbation and the correlation between mortality and patients’ characteristics and comorbidities. Methods A total of 152 COPD patients hospitalized for severe exacerbation were assessed for vitamin D status, diabetes mellitus (DM), arterial hypertension (AH), and metabolic syndrome (MS). Data were gathered about smoking status and number of exacerbations in previous year. CAT and mMRC questionnaires were completed by all patients. Pre- and post-bronchodilatory spirometry was performed. One-year mortality was established from national death register. Results One-year mortality is 7.2%. DM, MS, and VD are not predictors for one-year mortality. However there is a trend for increased mortality in patients with AH (9.5% vs. 2.1%, p = 0.107). There is increased mortality in patients with mMRC > 2 (11.1 vs. 0%, p = 0.013). The presence of severe exacerbation in the previous year is a risk factor for mortality (12.5% vs. 1.4%, p = 0.009). There is a trend for increased mortality in the group with FEV1 < 50% (11.5 vs. 4.4%, p = 0.094). Cox regression shows 3.7% increase in mortality rate for 1% decrease in FEV1, 5.2% for 1% decrease in PEF, 7.8% for one year age increase and 8.1% for 1 CAT point increase (all p < 0.05). Conclusions This study finds relatively low one-year mortality in COPD patients after surviving severe exacerbation. Grade C and FEV1 > 80% may be factors for good prognosis. Risk factors for increased mortality are age, FEV1 value, severe exacerbation in previous year and reduced quality of life.
bibliographic citation: Mekov et al. (2016) One-year mortality after severe COPD exacerbation in Bulgaria. PeerJ 4:e2788 https://doi.org/10.7717/peerj.2788
date submitted: 2016-08-01
date accepted: 2016-11-11
issued: 2016-12-13
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 P.
author list: Agent
  family name: Kostadinov
  given name: Dimitar T.
author list: Agent
  family name: Minchev
  given name: Delcho
author list: Agent
  family name: Marinova
  given name: Dora
author list: Agent
  family name: Boyanov
  given name: Mihail A.
doi: 10.7717/peerj.2788
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Mekov et al.
attribution name: Mekov et al.

Diet of the endangered big-headed turtle Platysternon megacephalum
type: item
type: AcademicArticle
description: Populations of the big-headed turtle Platysternon megacephalum are declining at unprecedented rates across most of its distribution in Southeast Asia owing to unsustainable harvest for pet, food, and Chinese medicine markets. Research on Asian freshwater turtles becomes more challenging as populations decline and basic ecological information is needed to inform conservation efforts. We examined fecal samples collected from P. megacephalum in five streams in Hong Kong to quantify the diet, and we compared the germination success of ingested and uningested seeds. Fruits, primarily of Machilus spp., were most frequently consumed, followed by insects, plant matter, crabs and mollusks. The niche breadth of adults was wider than that of juveniles. Diet composition differed between sites, which may be attributable to the history of illegal trapping at some sites, which reduced the proportion of larger and older individuals. Digestion of Machilus spp. fruits by P. megacephalum enhanced germination success of seeds by about 30%. However, most digested seeds are likely defecated in water in this highly aquatic species, which limits the potential benefit to dispersal. The results of our study can be used by conservation-related captive breeding programs to ensure a more optimal diet is provided to captive P. megacephalum.
format: application/pdf
format: text/html
creator: Yik-Hei Sung
creator: Billy C.H. Hau
creator: Nancy E. Karraker
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.2784
publisher: PeerJ Inc.
rights: © 2016 Sung et al.
abstract: Populations of the big-headed turtle Platysternon megacephalum are declining at unprecedented rates across most of its distribution in Southeast Asia owing to unsustainable harvest for pet, food, and Chinese medicine markets. Research on Asian freshwater turtles becomes more challenging as populations decline and basic ecological information is needed to inform conservation efforts. We examined fecal samples collected from P. megacephalum in five streams in Hong Kong to quantify the diet, and we compared the germination success of ingested and uningested seeds. Fruits, primarily of Machilus spp., were most frequently consumed, followed by insects, plant matter, crabs and mollusks. The niche breadth of adults was wider than that of juveniles. Diet composition differed between sites, which may be attributable to the history of illegal trapping at some sites, which reduced the proportion of larger and older individuals. Digestion of Machilus spp. fruits by P. megacephalum enhanced germination success of seeds by about 30%. However, most digested seeds are likely defecated in water in this highly aquatic species, which limits the potential benefit to dispersal. The results of our study can be used by conservation-related captive breeding programs to ensure a more optimal diet is provided to captive P. megacephalum.
bibliographic citation: Sung et al. (2016) Diet of the endangered big-headed turtle Platysternon megacephalum. PeerJ 4:e2784 https://doi.org/10.7717/peerj.2784
date submitted: 2016-08-05
date accepted: 2016-11-11
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sung
  given name: Yik-Hei
author list: Agent
  family name: Hau
  given name: Billy C.H.
author list: Agent
  family name: Karraker
  given name: Nancy E.
doi: 10.7717/peerj.2784
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 Sung et al.
attribution name: Sung et al.

Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America
type: item
type: AcademicArticle
description: Background Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth’s most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte–saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest. Methods We cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3–4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolated only from non-living leaves. Results Across the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activity in vitro. Cellulolytic activity differed…
format: application/pdf
format: text/html
creator: Jana M. U’Ren
creator: A. Elizabeth Arnold
subject: Ecology
subject: Microbiology
subject: Mycology
description: doi:10.7717/peerj.2768
publisher: PeerJ Inc.
rights: © 2016 U’Ren and Arnold
abstract: Background Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth’s most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte–saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest. Methods We cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3–4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolated only from non-living leaves. Results Across the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activity in vitro. Cellulolytic activity differed…
bibliographic citation: U’Ren et al. (2016) Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America. PeerJ 4:e2768 https://doi.org/10.7717/peerj.2768
date submitted: 2016-04-17
date accepted: 2016-11-07
issued: 2016-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: U’Ren
  given name: Jana M.
author list: Agent
  family name: Arnold
  given name: A. Elizabeth
doi: 10.7717/peerj.2768
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-12-13
copyright: ©2016 U’Ren and Arnold
attribution name: U’Ren and Arnold

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