PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: https://peerj.com/articles/6947
items: Biochemical changes throughout early- and middle-stages of embryogenesis in lobsters (Homarus americanus) under different thermal regimes
items: Dissection of three quantitative trait loci for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.)
items: Retrospective correlation analysis of plasma Immunoglobulin G and clinical performance in CIDP
items: Fish nursery value of algae habitats in temperate coastal reefs
items: Cosmetic colouring by Bearded Vultures Gypaetus barbatus: still no evidence for an antibacterial function
items: Foot pressure distribution in White Rhinoceroses (Ceratotherium simum) during walking
items: Cells released from S. epidermidis biofilms present increased antibiotic tolerance to multiple antibiotics
items: Retrotransposon-based genetic variation of Poa annua populations from contrasting climate conditions
items: Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae

https://peerj.com/articles/6947
type: item
type: AcademicArticle
title: Comparison of the National Early Warning Score (NEWS) and the Modified Early Warning Score (MEWS) for predicting admission and in-hospital mortality in elderly patients in the pre-hospital setting and in the emergency department
description: The aim of this study is to evaluate the usefulness of the pre-hospital National Early Warning Score (pNEWS) and the pre-hospital Modified Early Warning Score (pMEWS) for predicting admission and in-hospital mortality in elderly patients presenting to the emergency department (ED). We also compare the value of the pNEWS with that of the ED NEWS (eNEWS) and ED MEWS (eMEWS) for predicting admission and in-hospital mortality. This retrospective, single-centre observational study was carried out in the ED of Jikei University Kashiwa Hospital, in Chiba, Japan, from 1st April 2017 to 31st March 2018. All patients aged 65 years or older were included in this study. The pNEWS/eNEWS were derived from seven common physiological vital signs: respiratory rate, peripheral oxygen saturation, the presence of inhaled oxygen parameters, body temperature, systolic blood pressure, pulse rate and Alert, responds to Voice, responds to Pain, Unresponsive (AVPU) score, whereas the pMEWS/eMEWS were derived from six common physiological vital signs: respiratory rate, peripheral oxygen saturation, body temperature, systolic blood pressure, pulse rate and AVPU score. Discrimination was assessed by plotting the receiver operating characteristic (ROC) curve and calculating the area under the ROC curve (AUC). The median pNEWS, pMEWS, eNEWS and eMEWS were significantly higher at admission than at discharge (p < 0.001). The median pNEWS, pMEWS, eNEWS and eMEWS of non-survivors were significantly higher than those of the survivors (p < 0.001). The AUC for predicting admission was 0.559 for the pNEWS and 0.547 for the pMEWS. There was no significant difference between the AUCs of the pNEWS and the pMEWS for predicting admission (p = 0.102). The AUCs for predicting in-hospital mortality were 0.678 for the pNEWS and 0.652 for the pMEWS. There was no significant difference between the AUCs of the pNEWS and the pMEWS for predicting in-hospital mortality (p = 0.081). The AUC for predicting admission was …
format: application/pdf
format: text/html
creator: Toshiya Mitsunaga
creator: Izumu Hasegawa
creator: Masahiko Uzura
creator: Kenji Okuno
creator: Kei Otani
creator: Yuhei Ohtaki
creator: Akihiro Sekine
creator: Satoshi Takeda
subject: Emergency and Critical Care
subject: Geriatrics
subject: Public Health
description: doi:10.7717/peerj.6947
publisher: PeerJ Inc.
rights: © 2019 Mitsunaga et al.
abstract: The aim of this study is to evaluate the usefulness of the pre-hospital National Early Warning Score (pNEWS) and the pre-hospital Modified Early Warning Score (pMEWS) for predicting admission and in-hospital mortality in elderly patients presenting to the emergency department (ED). We also compare the value of the pNEWS with that of the ED NEWS (eNEWS) and ED MEWS (eMEWS) for predicting admission and in-hospital mortality. This retrospective, single-centre observational study was carried out in the ED of Jikei University Kashiwa Hospital, in Chiba, Japan, from 1st April 2017 to 31st March 2018. All patients aged 65 years or older were included in this study. The pNEWS/eNEWS were derived from seven common physiological vital signs: respiratory rate, peripheral oxygen saturation, the presence of inhaled oxygen parameters, body temperature, systolic blood pressure, pulse rate and Alert, responds to Voice, responds to Pain, Unresponsive (AVPU) score, whereas the pMEWS/eMEWS were derived from six common physiological vital signs: respiratory rate, peripheral oxygen saturation, body temperature, systolic blood pressure, pulse rate and AVPU score. Discrimination was assessed by plotting the receiver operating characteristic (ROC) curve and calculating the area under the ROC curve (AUC). The median pNEWS, pMEWS, eNEWS and eMEWS were significantly higher at admission than at discharge (p < 0.001). The median pNEWS, pMEWS, eNEWS and eMEWS of non-survivors were significantly higher than those of the survivors (p < 0.001). The AUC for predicting admission was 0.559 for the pNEWS and 0.547 for the pMEWS. There was no significant difference between the AUCs of the pNEWS and the pMEWS for predicting admission (p = 0.102). The AUCs for predicting in-hospital mortality were 0.678 for the pNEWS and 0.652 for the pMEWS. There was no significant difference between the AUCs of the pNEWS and the pMEWS for predicting in-hospital mortality (p = 0.081). The AUC for predicting admission was …
bibliographic citation: Mitsunaga et al. (2019) Comparison of the National Early Warning Score (NEWS) and the Modified Early Warning Score (MEWS) for predicting admission and in-hospital mortality in elderly patients in the pre-hospital setting and in the emergency department. PeerJ 7:e6947 https://doi.org/10.7717/peerj.6947
date submitted: 2019-01-23
date accepted: 2019-04-09
issued: 2019-05-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mitsunaga
  given name: Toshiya
author list: Agent
  family name: Hasegawa
  given name: Izumu
author list: Agent
  family name: Uzura
  given name: Masahiko
author list: Agent
  family name: Okuno
  given name: Kenji
author list: Agent
  family name: Otani
  given name: Kei
author list: Agent
  family name: Ohtaki
  given name: Yuhei
author list: Agent
  family name: Sekine
  given name: Akihiro
author list: Agent
  family name: Takeda
  given name: Satoshi
doi: 10.7717/peerj.6947
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-16
copyright: © 2019 Mitsunaga et al.
attribution name: Mitsunaga et al.

Biochemical changes throughout early- and middle-stages of embryogenesis in lobsters (Homarus americanus) under different thermal regimes
type: item
type: AcademicArticle
description: Most marine crustacean eggs contain the full complement of nutritional resources required to fuel their growth and development. Given the propensity of many ovigerous (egg-bearing) American lobsters (Homarus americanus) to undergo seasonal inshore-to-offshore migrations, thereby potentially exposing their eggs to varying thermal regimes, the goal of this study was to determine the impact of water temperature on egg quality over their course of development. This was accomplished by documenting changes in total lipids, proteins, and size (volume) of eggs subjected to one of three thermal regimes: inshore, offshore, and constant (16 °C) conditions. Total egg lipids showed a marked decrease over time, while protein levels increased over the same period. Although there were no significant differences in total lipids, proteins, or egg sizes between eggs exposed to inshore and offshore temperatures, they differed from values for eggs exposed to a constant temperature, which also hatched almost three months sooner. This is most likely due to the fact that eggs held at a constant temperature did not experience a period of slow development during the colder months from November to March that are important for synchronizing egg hatch and may be compromised by elevated seawater temperatures.
format: application/pdf
format: text/html
creator: Jason S. Goldstein
creator: Winsor H. Watson III
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Developmental Biology
subject: Zoology
description: doi:10.7717/peerj.6952
publisher: PeerJ Inc.
rights: © 2019 Goldstein and Watson III
abstract: Most marine crustacean eggs contain the full complement of nutritional resources required to fuel their growth and development. Given the propensity of many ovigerous (egg-bearing) American lobsters (Homarus americanus) to undergo seasonal inshore-to-offshore migrations, thereby potentially exposing their eggs to varying thermal regimes, the goal of this study was to determine the impact of water temperature on egg quality over their course of development. This was accomplished by documenting changes in total lipids, proteins, and size (volume) of eggs subjected to one of three thermal regimes: inshore, offshore, and constant (16 °C) conditions. Total egg lipids showed a marked decrease over time, while protein levels increased over the same period. Although there were no significant differences in total lipids, proteins, or egg sizes between eggs exposed to inshore and offshore temperatures, they differed from values for eggs exposed to a constant temperature, which also hatched almost three months sooner. This is most likely due to the fact that eggs held at a constant temperature did not experience a period of slow development during the colder months from November to March that are important for synchronizing egg hatch and may be compromised by elevated seawater temperatures.
bibliographic citation: Goldstein et al. (2019) Biochemical changes throughout early- and middle-stages of embryogenesis in lobsters (Homarus americanus) under different thermal regimes. PeerJ 7:e6952 https://doi.org/10.7717/peerj.6952
date submitted: 2018-03-16
date accepted: 2019-04-13
issued: 2019-05-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Goldstein
  given name: Jason S.
author list: Agent
  family name: Watson III
  given name: Winsor H.
doi: 10.7717/peerj.6952
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-16
copyright: ©2019 Goldstein and Watson III
attribution name: Goldstein and Watson III

Dissection of three quantitative trait loci for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.)
type: item
type: AcademicArticle
description: Background Thousand grain weight is a key component of grain yield in rice, and a trait closely related to grain length (GL) and grain width (GW) that are important traits for grain quality. Causal genes for 16 quantitative trait loci (QTL) affecting these traits have been cloned, but more QTL remain to be characterized for establishing a genetic regulating network. A QTL controlling grain size in rice, qGS10, was previously mapped in the interval RM6100–RM228 on chromosome 10. This study aimed to delimitate this QTL to a more precise location. Method A total of 12 populations were used. The ZC9 population comprised 203 S1:2 families derived from a residual heterozygous (RH) plant in the F9 generation of the indica rice cross Teqing (TQ)/IRBB52, segregating the upper region of RM6100–RM228 and three more regions on chromosomes 1, 9, and 11. The Ti52-1 population comprised 171 S1 plants derived from one RH plant in F7 of TQ/IRBB52, segregating a single interval that was in the lower portion of RM6100–RM228. The other ten populations were all derived from Ti52-1, including five S1 populations with sequential segregating regions covering the target region and five near isogenic line (NIL) populations maintaining the same segregating pattern. QTL analysis for 1,000-grain weight, GL, and GW was performed using QTL IciMapping and SAS procedure GLM. Result Three QTL were separated in the original qGS10 region. The qGL10.1 was located in the upper region RM6704–RM3773, shown to affect GL only. The qGS10.1 was located within a 207.1-kb interval flanked by InDel markers Te20811 and Te21018, having a stable and relatively high effect on all the three traits analyzed. The qGS10.2 was located within a 1.2-Mb interval flanked by simple sequence repeat markers RM3123 and RM6673. This QTL also affected all the three traits but the effect was inconsistent across different experiments. QTL for grain size were also detected in all the other three segregating regions. Conclusion Three …
format: application/pdf
format: text/html
creator: Yu-Jun Zhu
creator: Zhi-Chao Sun
creator: Xiao-Jun Niu
creator: Jie-Zheng Ying
creator: Ye-Yang Fan
creator: Tong-Min Mou
creator: Shao-Qing Tang
creator: Jie-Yun Zhuang
subject: Agricultural Science
subject: Genetics
description: doi:10.7717/peerj.6966
publisher: PeerJ Inc.
rights: © 2019 Zhu et al.
abstract: Background Thousand grain weight is a key component of grain yield in rice, and a trait closely related to grain length (GL) and grain width (GW) that are important traits for grain quality. Causal genes for 16 quantitative trait loci (QTL) affecting these traits have been cloned, but more QTL remain to be characterized for establishing a genetic regulating network. A QTL controlling grain size in rice, qGS10, was previously mapped in the interval RM6100–RM228 on chromosome 10. This study aimed to delimitate this QTL to a more precise location. Method A total of 12 populations were used. The ZC9 population comprised 203 S1:2 families derived from a residual heterozygous (RH) plant in the F9 generation of the indica rice cross Teqing (TQ)/IRBB52, segregating the upper region of RM6100–RM228 and three more regions on chromosomes 1, 9, and 11. The Ti52-1 population comprised 171 S1 plants derived from one RH plant in F7 of TQ/IRBB52, segregating a single interval that was in the lower portion of RM6100–RM228. The other ten populations were all derived from Ti52-1, including five S1 populations with sequential segregating regions covering the target region and five near isogenic line (NIL) populations maintaining the same segregating pattern. QTL analysis for 1,000-grain weight, GL, and GW was performed using QTL IciMapping and SAS procedure GLM. Result Three QTL were separated in the original qGS10 region. The qGL10.1 was located in the upper region RM6704–RM3773, shown to affect GL only. The qGS10.1 was located within a 207.1-kb interval flanked by InDel markers Te20811 and Te21018, having a stable and relatively high effect on all the three traits analyzed. The qGS10.2 was located within a 1.2-Mb interval flanked by simple sequence repeat markers RM3123 and RM6673. This QTL also affected all the three traits but the effect was inconsistent across different experiments. QTL for grain size were also detected in all the other three segregating regions. Conclusion Three …
bibliographic citation: Zhu et al. (2019) Dissection of three quantitative trait loci for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.). PeerJ 7:e6966 https://doi.org/10.7717/peerj.6966
date submitted: 2019-01-08
date accepted: 2019-04-17
issued: 2019-05-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Yu-Jun
author list: Agent
  family name: Sun
  given name: Zhi-Chao
author list: Agent
  family name: Niu
  given name: Xiao-Jun
author list: Agent
  family name: Ying
  given name: Jie-Zheng
author list: Agent
  family name: Fan
  given name: Ye-Yang
author list: Agent
  family name: Mou
  given name: Tong-Min
author list: Agent
  family name: Tang
  given name: Shao-Qing
author list: Agent
  family name: Zhuang
  given name: Jie-Yun
doi: 10.7717/peerj.6966
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-16
copyright: © 2019 Zhu et al.
attribution name: Zhu et al.

Retrospective correlation analysis of plasma Immunoglobulin G and clinical performance in CIDP
type: item
type: AcademicArticle
description: Background Chronic inflammatory demyelinating polyneuropathy (CIDP) can be successfully treated with immunoglobulin either intravenously (IVIG) or subcutaneously (SCIG). Measurement of plasma immunoglobulin G levels (P-IgG) and its correlation to clinical improvement has shown conflicting results. This study aims to clarify whether changes in P-IgG are related to clinical development in patients with CIDP treated with IVIG or SCIG. Methods Patients from five previous studies treated with either IVIG or SCIG with evaluation at baseline and re-evaluation after two or 10/12 weeks, respectively were included. At evaluation and re-evaluation, the following tests were done: combined isokinetic muscle strength (cIKS), grip strength, 9-hole-peg test (9-HPT), 40-meter-walk test (40-MWT), clinical examination of muscle strength score by the Medical Research Council (MRC) and measurement of plasma immunoglobulin G (P-IgG). Results Fifty-five patients were included in the IVIG group and 41 in the SCIG group. There was no correlation between the changes in P-IgG and cIKS in neither the IVIG group (r = 0.137, p = 0.32) nor the SCIG group (r = − 0.048, p = 0.77). Similarly, no correlations could be demonstrated between P-IgG and grip strength, 9-HPT, 40-MWT or MRC. Conclusions In patients with CIDP receiving SCIG or IVIG, changes in P-IgG during treatment did not correlate with changes in muscle strength or other motor performance skills.
format: application/pdf
format: text/html
creator: Lars Kjøbsted Markvardsen
creator: Stine Bruun-Sørensen
creator: Ingelise Christiansen
creator: Henning Andersen
subject: Hematology
subject: Immunology
subject: Neurology
subject: Pharmacology
description: doi:10.7717/peerj.6969
publisher: PeerJ Inc.
rights: © 2019 Markvardsen et al.
abstract: Background Chronic inflammatory demyelinating polyneuropathy (CIDP) can be successfully treated with immunoglobulin either intravenously (IVIG) or subcutaneously (SCIG). Measurement of plasma immunoglobulin G levels (P-IgG) and its correlation to clinical improvement has shown conflicting results. This study aims to clarify whether changes in P-IgG are related to clinical development in patients with CIDP treated with IVIG or SCIG. Methods Patients from five previous studies treated with either IVIG or SCIG with evaluation at baseline and re-evaluation after two or 10/12 weeks, respectively were included. At evaluation and re-evaluation, the following tests were done: combined isokinetic muscle strength (cIKS), grip strength, 9-hole-peg test (9-HPT), 40-meter-walk test (40-MWT), clinical examination of muscle strength score by the Medical Research Council (MRC) and measurement of plasma immunoglobulin G (P-IgG). Results Fifty-five patients were included in the IVIG group and 41 in the SCIG group. There was no correlation between the changes in P-IgG and cIKS in neither the IVIG group (r = 0.137, p = 0.32) nor the SCIG group (r = − 0.048, p = 0.77). Similarly, no correlations could be demonstrated between P-IgG and grip strength, 9-HPT, 40-MWT or MRC. Conclusions In patients with CIDP receiving SCIG or IVIG, changes in P-IgG during treatment did not correlate with changes in muscle strength or other motor performance skills.
bibliographic citation: Markvardsen et al. (2019) Retrospective correlation analysis of plasma Immunoglobulin G and clinical performance in CIDP. PeerJ 7:e6969 https://doi.org/10.7717/peerj.6969
date submitted: 2019-01-21
date accepted: 2019-04-17
issued: 2019-05-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Markvardsen
  given name: Lars Kjøbsted
author list: Agent
  family name: Bruun-Sørensen
  given name: Stine
author list: Agent
  family name: Christiansen
  given name: Ingelise
author list: Agent
  family name: Andersen
  given name: Henning
doi: 10.7717/peerj.6969
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-16
copyright: ©2019 Markvardsen et al.
attribution name: Markvardsen et al.

Fish nursery value of algae habitats in temperate coastal reefs
type: item
type: AcademicArticle
description: The nursery function of coastal habitats is one of the most frequently mentioned and recognized ecosystem services in the valuation of coastal ecosystems. Despite its importance our understanding of the precise habitat parameters and mechanisms that make a habitat important as a nursery area is still limited for many species. The study aimed to establish the importance of different algae morphotypes in providing shelter and food for juvenile coastal fish during the main settlement peaks, in early spring and late summer, in littoral rocky reef systems in the Northwestern Mediterranean. The results of our study showed strong seasonal differences in algae cover, composition and height between the two sampling periods. Overall, during spring the algae were well developed, while in late summer, both density and height, of most algae decreased considerably. Equally, prey biomass, in form of suitable sized invertebrate fauna associated to the algae, decreased. Accordingly, the shelter and food for the fish settling in this habitat during late summer were less abundant, indicating a mismatch between the observed presence of juvenile fish and optimal habitat conditions. Differences in prey densities were detected between algae morphotypes, with structurally more complex algae, such as Cystoseira spp. and Halopteris spp. consistently containing more prey, independent of season, compared to simpler structured morphotypes such as Dictoytales. The study furthermore related juvenile fish density to habitats dominated by different algae morphotypes. Out of the three-study species (Diplodus vulgaris, Symphodus ocellatus, Coris julis) only S. ocellatus showed a significant association with an algae habitat. S. ocellatus related positively to habitats dominated by Dictoytales which provided the highest cover during late summer but had the lowest prey densities. A strong association of this species with Cystoseira, as reported by other studies, could not be confirmed. Cystoseira was a…
format: application/pdf
format: text/html
creator: Hilmar Hinz
creator: Olga Reñones
creator: Adam Gouraguine
creator: Andrew F. Johnson
creator: Joan Moranta
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6797
publisher: PeerJ Inc.
rights: © 2019 Hinz et al.
abstract: The nursery function of coastal habitats is one of the most frequently mentioned and recognized ecosystem services in the valuation of coastal ecosystems. Despite its importance our understanding of the precise habitat parameters and mechanisms that make a habitat important as a nursery area is still limited for many species. The study aimed to establish the importance of different algae morphotypes in providing shelter and food for juvenile coastal fish during the main settlement peaks, in early spring and late summer, in littoral rocky reef systems in the Northwestern Mediterranean. The results of our study showed strong seasonal differences in algae cover, composition and height between the two sampling periods. Overall, during spring the algae were well developed, while in late summer, both density and height, of most algae decreased considerably. Equally, prey biomass, in form of suitable sized invertebrate fauna associated to the algae, decreased. Accordingly, the shelter and food for the fish settling in this habitat during late summer were less abundant, indicating a mismatch between the observed presence of juvenile fish and optimal habitat conditions. Differences in prey densities were detected between algae morphotypes, with structurally more complex algae, such as Cystoseira spp. and Halopteris spp. consistently containing more prey, independent of season, compared to simpler structured morphotypes such as Dictoytales. The study furthermore related juvenile fish density to habitats dominated by different algae morphotypes. Out of the three-study species (Diplodus vulgaris, Symphodus ocellatus, Coris julis) only S. ocellatus showed a significant association with an algae habitat. S. ocellatus related positively to habitats dominated by Dictoytales which provided the highest cover during late summer but had the lowest prey densities. A strong association of this species with Cystoseira, as reported by other studies, could not be confirmed. Cystoseira was a…
bibliographic citation: Hinz et al. (2019) Fish nursery value of algae habitats in temperate coastal reefs. PeerJ 7:e6797 https://doi.org/10.7717/peerj.6797
date submitted: 2018-11-07
date accepted: 2019-03-17
issued: 2019-05-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hinz
  given name: Hilmar
author list: Agent
  family name: Reñones
  given name: Olga
author list: Agent
  family name: Gouraguine
  given name: Adam
author list: Agent
  family name: Johnson
  given name: Andrew F.
author list: Agent
  family name: Moranta
  given name: Joan
doi: 10.7717/peerj.6797
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-15
copyright: ©2019 Hinz et al.
attribution name: Hinz et al.

Cosmetic colouring by Bearded Vultures Gypaetus barbatus: still no evidence for an antibacterial function
type: item
type: AcademicArticle
description: Bearded Vultures regularly visit ferruginous springs for cosmetic purposes to obtain their reddish plumage colouration. Different hypotheses have been proposed to explain this deliberate application of adventitious colouration: (1) to signal individual dominance status; (2) to exploit an anti-bacterial effect of iron oxides or ochre to reduce feather degradation by bacteria and, in parallel (3) to enable incubating birds to transfer this protection to their developing embryos to increase hatching success. Here, we re-evaluate the antibacterial hypothesis using three experimental approaches: (a) by applying feather-degrading bacteria to stained and unstained bearded vulture feathers; (b) by assessing the antibacterial activity of ochre; and (c) by comparing the breeding success of orange individuals with pale ones. Our findings suggest that the in vitro addition of feather degrading Bacillus licheniformis to naturally stained Bearded Vulture feathers did not retard feather degradation compared to controls. Iron particles from red soil (ochre) or iron salts had no antibacterial effect on the growth of three species of bacteria (Escherichia coli, Kocuria rhizophila and Bacillus licheniformis), incubated either in the dark or under visible light. Finally, breeding success did not differ between territories occupied by pale individuals versus orange ones. These results run counter to the hypothesis that iron oxides have an antibacterial role in Bearded Vultures. The use of red soils by Bearded Vultures may function as a territorial status signal, but may also be involved in other processes, such as pair formation and the long-term maintenance of the pair bond, as suggested for the closely related Egyptian vulture Neophron percnopterus.
format: application/pdf
format: text/html
creator: Antoni Margalida
creator: Markus S. Braun
creator: Juan José Negro
creator: Karl Schulze-Hagen
creator: Michael Wink
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6783
publisher: PeerJ Inc.
rights: © 2019 Margalida et al.
abstract: Bearded Vultures regularly visit ferruginous springs for cosmetic purposes to obtain their reddish plumage colouration. Different hypotheses have been proposed to explain this deliberate application of adventitious colouration: (1) to signal individual dominance status; (2) to exploit an anti-bacterial effect of iron oxides or ochre to reduce feather degradation by bacteria and, in parallel (3) to enable incubating birds to transfer this protection to their developing embryos to increase hatching success. Here, we re-evaluate the antibacterial hypothesis using three experimental approaches: (a) by applying feather-degrading bacteria to stained and unstained bearded vulture feathers; (b) by assessing the antibacterial activity of ochre; and (c) by comparing the breeding success of orange individuals with pale ones. Our findings suggest that the in vitro addition of feather degrading Bacillus licheniformis to naturally stained Bearded Vulture feathers did not retard feather degradation compared to controls. Iron particles from red soil (ochre) or iron salts had no antibacterial effect on the growth of three species of bacteria (Escherichia coli, Kocuria rhizophila and Bacillus licheniformis), incubated either in the dark or under visible light. Finally, breeding success did not differ between territories occupied by pale individuals versus orange ones. These results run counter to the hypothesis that iron oxides have an antibacterial role in Bearded Vultures. The use of red soils by Bearded Vultures may function as a territorial status signal, but may also be involved in other processes, such as pair formation and the long-term maintenance of the pair bond, as suggested for the closely related Egyptian vulture Neophron percnopterus.
bibliographic citation: Margalida et al. (2019) Cosmetic colouring by Bearded Vultures Gypaetus barbatus: still no evidence for an antibacterial function. PeerJ 7:e6783 https://doi.org/10.7717/peerj.6783
date submitted: 2018-12-18
date accepted: 2019-03-14
issued: 2019-05-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Margalida
  given name: Antoni
author list: Agent
  family name: Braun
  given name: Markus S.
author list: Agent
  family name: Negro
  given name: Juan José
author list: Agent
  family name: Schulze-Hagen
  given name: Karl
author list: Agent
  family name: Wink
  given name: Michael
doi: 10.7717/peerj.6783
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-15
copyright: ©2019 Margalida et al.
attribution name: Margalida et al.

Foot pressure distribution in White Rhinoceroses (Ceratotherium simum) during walking
type: item
type: AcademicArticle
description: White rhinoceroses (Ceratotherium simum) are odd-toed ungulates that belong to the group Perissodactyla. Being second only to elephants in terms of large body mass amongst extant tetrapods, rhinoceroses make fascinating subjects for the study of how large land animals support and move themselves. Rhinoceroses often are kept in captivity for protection from ivory poachers and for educational/touristic purposes, yet a detrimental side effect of captivity can be foot disease (i.e., enthesopathies and osteoarthritis around the phalanges). Foot diseases in large mammals are multifactorial, but locomotor biomechanics (e.g., pressures routinely experienced by the feet) surely can be a contributing factor. However, due to a lack of in vivo experimental data on rhinoceros foot pressures, our knowledge of locomotor performance and its links to foot disease is limited. The overall aim of this study was to characterize peak pressures and center of pressure trajectories in white rhinoceroses during walking. We asked two major questions. First, are peak locomotor pressures the lowest around the fat pad and its lobes (as in the case of elephants)? Second, are peak locomotor pressures concentrated around the areas with the highest reported incidence of pathologies? Our results show a reduction of pressures around the fat pad and its lobes, which is potentially due to the material properties of the fat pad or a tendency to avoid or limit “heel” contact at impact. We also found an even and gradual concentration of foot pressures across all digits, which may be a by-product of the more horizontal foot roll-off during the stance phase. While our exploratory, descriptive sample precluded hypothesis testing, our study provides important new data on rhinoceros locomotion for future studies to build on, and thus impetus for improved implementation in the care of captive/managed rhinoceroses.
format: application/pdf
format: text/html
creator: Olga Panagiotopoulou
creator: Todd C. Pataky
creator: John R. Hutchinson
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.6881
publisher: PeerJ Inc.
rights: © 2019 Panagiotopoulou et al.
abstract: White rhinoceroses (Ceratotherium simum) are odd-toed ungulates that belong to the group Perissodactyla. Being second only to elephants in terms of large body mass amongst extant tetrapods, rhinoceroses make fascinating subjects for the study of how large land animals support and move themselves. Rhinoceroses often are kept in captivity for protection from ivory poachers and for educational/touristic purposes, yet a detrimental side effect of captivity can be foot disease (i.e., enthesopathies and osteoarthritis around the phalanges). Foot diseases in large mammals are multifactorial, but locomotor biomechanics (e.g., pressures routinely experienced by the feet) surely can be a contributing factor. However, due to a lack of in vivo experimental data on rhinoceros foot pressures, our knowledge of locomotor performance and its links to foot disease is limited. The overall aim of this study was to characterize peak pressures and center of pressure trajectories in white rhinoceroses during walking. We asked two major questions. First, are peak locomotor pressures the lowest around the fat pad and its lobes (as in the case of elephants)? Second, are peak locomotor pressures concentrated around the areas with the highest reported incidence of pathologies? Our results show a reduction of pressures around the fat pad and its lobes, which is potentially due to the material properties of the fat pad or a tendency to avoid or limit “heel” contact at impact. We also found an even and gradual concentration of foot pressures across all digits, which may be a by-product of the more horizontal foot roll-off during the stance phase. While our exploratory, descriptive sample precluded hypothesis testing, our study provides important new data on rhinoceros locomotion for future studies to build on, and thus impetus for improved implementation in the care of captive/managed rhinoceroses.
bibliographic citation: Panagiotopoulou et al. (2019) Foot pressure distribution in White Rhinoceroses (Ceratotherium simum) during walking. PeerJ 7:e6881 https://doi.org/10.7717/peerj.6881
date submitted: 2018-11-08
date accepted: 2019-04-01
issued: 2019-05-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Panagiotopoulou
  given name: Olga
author list: Agent
  family name: Pataky
  given name: Todd C.
author list: Agent
  family name: Hutchinson
  given name: John R.
doi: 10.7717/peerj.6881
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-15
copyright: © 2019 Panagiotopoulou et al.
attribution name: Panagiotopoulou et al.

Cells released from S. epidermidis biofilms present increased antibiotic tolerance to multiple antibiotics
type: item
type: AcademicArticle
description: Biofilm released cells (Brc) are thought to present an intermediary phenotype between biofilm and planktonic cells and this has the potential of affecting their antimicrobial tolerance. Aim Compare the antimicrobial tolerance profiles of Brc, planktonic or biofilm cultures of S. epidermidis. Methodology Planktonic, biofilm cultures or Brc from 11 isolates were exposed to peak serum concentrations (PSC) of antibiotics. The antimicrobial killing effect in the three populations was determined by CFU. Results Increased Brc tolerance to vancomycin, teicoplanin, rifampicin, erythromycin, and tetracycline was confirmed in model strain 9142. Furthermore, significant differences in the susceptibility of Brc to vancomycin were further found in 10 other clinical isolates. Conclusions Brc from distinct clinical isolates presented a decreased susceptibility to most antibiotics tested and maintained that enhanced tolerance despite growing planktonically for up to 6 h. Our data suggest that Brc maintain the typical enhanced antibiotic tolerance of biofilm populations, further suggesting that addressing antimicrobial susceptibility in planktonic cultures might not reflect the full potential of biofilm-associated bacteria to survive therapy.
format: application/pdf
format: text/html
creator: Vânia Gaio
creator: Nuno Cerca
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.6884
publisher: PeerJ Inc.
rights: © 2019 Gaio and Cerca
abstract: Biofilm released cells (Brc) are thought to present an intermediary phenotype between biofilm and planktonic cells and this has the potential of affecting their antimicrobial tolerance. Aim Compare the antimicrobial tolerance profiles of Brc, planktonic or biofilm cultures of S. epidermidis. Methodology Planktonic, biofilm cultures or Brc from 11 isolates were exposed to peak serum concentrations (PSC) of antibiotics. The antimicrobial killing effect in the three populations was determined by CFU. Results Increased Brc tolerance to vancomycin, teicoplanin, rifampicin, erythromycin, and tetracycline was confirmed in model strain 9142. Furthermore, significant differences in the susceptibility of Brc to vancomycin were further found in 10 other clinical isolates. Conclusions Brc from distinct clinical isolates presented a decreased susceptibility to most antibiotics tested and maintained that enhanced tolerance despite growing planktonically for up to 6 h. Our data suggest that Brc maintain the typical enhanced antibiotic tolerance of biofilm populations, further suggesting that addressing antimicrobial susceptibility in planktonic cultures might not reflect the full potential of biofilm-associated bacteria to survive therapy.
bibliographic citation: Gaio et al. (2019) Cells released from S. epidermidis biofilms present increased antibiotic tolerance to multiple antibiotics. PeerJ 7:e6884 https://doi.org/10.7717/peerj.6884
date submitted: 2019-02-11
date accepted: 2019-04-01
issued: 2019-05-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gaio
  given name: Vânia
author list: Agent
  family name: Cerca
  given name: Nuno
doi: 10.7717/peerj.6884
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-15
copyright: ©2019 Gaio and Cerca
attribution name: Gaio and Cerca

Retrotransposon-based genetic variation of Poa annua populations from contrasting climate conditions
type: item
type: AcademicArticle
description: Background Poa annua L. is an example of a plant characterized by abundant, worldwide distribution from polar to equatorial regions. Due to its high plasticity and extraordinary expansiveness, P. annua is considered an invasive species capable of occupying and surviving in a wide range of habitats including pioneer zones, areas intensively transformed by human activities, remote subarctic meadows and even the Antarctic Peninsula region. Methods In the present study, we evaluated the utility of inter-primer binding site (iPBS) markers for assessing the genetic variation of P. annua populations representing contrasting environments from the worldwide range of this species. The electrophoretic patterns of polymerase chain reaction products obtained for each individual were used to estimate the genetic diversity and differentiation between populations. Results iPBS genotyping revealed a pattern of genetic variation differentiating the six studied P. annua populations characterized by their different climatic conditions. According to the analysis of molecular variance, the greatest genetic variation was recorded among populations, whereas 41.75% was observed between individuals within populations. The results of principal coordinates analysis (PCoA) and model-based clustering analysis showed a clear subdivision of analyzed populations. According to PCoA, populations from Siberia and the Kola Peninsula were the most different from each other and showed the lowest genetic variability. The application of STRUCTURE software confirmed the unique character of the population from the Kola Peninsula. Discussion The lowest variability of the Siberia population suggested that it was subjected to genetic drift. However, although demographic expansion was indicated by negative values of Fu’s FS statistic and analysis of mismatch distribution, it was not followed by significant traces of a bottleneck or a founder effect. For the Antarctic population, the observed level of genetic var…
format: application/pdf
format: text/html
creator: Piotr Androsiuk
creator: Justyna Koc
creator: Katarzyna Joanna Chwedorzewska
creator: Ryszard Górecki
creator: Irena Giełwanowska
subject: Biodiversity
subject: Biogeography
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.6888
publisher: PeerJ Inc.
rights: © 2019 Androsiuk et al.
abstract: Background Poa annua L. is an example of a plant characterized by abundant, worldwide distribution from polar to equatorial regions. Due to its high plasticity and extraordinary expansiveness, P. annua is considered an invasive species capable of occupying and surviving in a wide range of habitats including pioneer zones, areas intensively transformed by human activities, remote subarctic meadows and even the Antarctic Peninsula region. Methods In the present study, we evaluated the utility of inter-primer binding site (iPBS) markers for assessing the genetic variation of P. annua populations representing contrasting environments from the worldwide range of this species. The electrophoretic patterns of polymerase chain reaction products obtained for each individual were used to estimate the genetic diversity and differentiation between populations. Results iPBS genotyping revealed a pattern of genetic variation differentiating the six studied P. annua populations characterized by their different climatic conditions. According to the analysis of molecular variance, the greatest genetic variation was recorded among populations, whereas 41.75% was observed between individuals within populations. The results of principal coordinates analysis (PCoA) and model-based clustering analysis showed a clear subdivision of analyzed populations. According to PCoA, populations from Siberia and the Kola Peninsula were the most different from each other and showed the lowest genetic variability. The application of STRUCTURE software confirmed the unique character of the population from the Kola Peninsula. Discussion The lowest variability of the Siberia population suggested that it was subjected to genetic drift. However, although demographic expansion was indicated by negative values of Fu’s FS statistic and analysis of mismatch distribution, it was not followed by significant traces of a bottleneck or a founder effect. For the Antarctic population, the observed level of genetic var…
bibliographic citation: Androsiuk et al. (2019) Retrotransposon-based genetic variation of Poa annua populations from contrasting climate conditions. PeerJ 7:e6888 https://doi.org/10.7717/peerj.6888
date submitted: 2018-10-16
date accepted: 2019-04-02
issued: 2019-05-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Androsiuk
  given name: Piotr
author list: Agent
  family name: Koc
  given name: Justyna
author list: Agent
  family name: Chwedorzewska
  given name: Katarzyna Joanna
author list: Agent
  family name: Górecki
  given name: Ryszard
author list: Agent
  family name: Giełwanowska
  given name: Irena
doi: 10.7717/peerj.6888
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-15
copyright: © 2019 Androsiuk et al.
attribution name: Androsiuk et al.

Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae
type: item
type: AcademicArticle
description: Background Chlorophyceae is one of three most species-rich green algal classes and also the only class in core Chlorophyta whose monophyly remains uncontested as gene and taxon sampling improves. However, some key relationships within Chlorophyceae are less clear-cut and warrant further investigation. The present study combined genome-scale chloroplast data and rich sampling in an attempt to resolve the ordinal classification in Chlorophyceae. The traditional division into Sphaeropleales and Volvocales (SV), and a clade containing Oedogoniales, Chaetopeltidales, and Chaetophorales (OCC) was of particular interest with the addition of deeply branching members of these groups, as well as the placement of several incertae sedis taxa. Methods We sequenced 18 chloroplast genomes across Chlorophyceae to compile a data set of 58 protein-coding genes of a total of 68 chlorophycean taxa. We analyzed the concatenated nucleotide and amino acid datasets in the Bayesian and Maximum Likelihood frameworks, supplemented by analyses to examine potential discordant signal among genes. We also examined gene presence and absence data across Chlorophyceae. Results Concatenated analyses yielded at least two well-supported phylogenies: nucleotide data supported the traditional classification with the inclusion of the enigmatic Treubarinia into Sphaeropleales sensu lato. However, amino acid data yielded equally strong support for Sphaeropleaceae as sister to Volvocales, with the rest of the taxa traditionally classified in Sphaeropleales in a separate clade, and Treubarinia as sister to all of the above. Single-gene and other supplementary analyses indicated that the data have low phylogenetic signal at these critical nodes. Major clades were supported by genomic structural features such as gene losses and trans-spliced intron insertions in the plastome. Discussion While the sequence and gene order data support the deep split between the SV and OCC lineages, multiple phylogenetic hypothese…
format: application/pdf
format: text/html
creator: Karolina Fučíková
creator: Paul O. Lewis
creator: Suman Neupane
creator: Kenneth G. Karol
creator: Louise A. Lewis
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.6899
publisher: PeerJ Inc.
rights: © 2019 Fučíková et al.
abstract: Background Chlorophyceae is one of three most species-rich green algal classes and also the only class in core Chlorophyta whose monophyly remains uncontested as gene and taxon sampling improves. However, some key relationships within Chlorophyceae are less clear-cut and warrant further investigation. The present study combined genome-scale chloroplast data and rich sampling in an attempt to resolve the ordinal classification in Chlorophyceae. The traditional division into Sphaeropleales and Volvocales (SV), and a clade containing Oedogoniales, Chaetopeltidales, and Chaetophorales (OCC) was of particular interest with the addition of deeply branching members of these groups, as well as the placement of several incertae sedis taxa. Methods We sequenced 18 chloroplast genomes across Chlorophyceae to compile a data set of 58 protein-coding genes of a total of 68 chlorophycean taxa. We analyzed the concatenated nucleotide and amino acid datasets in the Bayesian and Maximum Likelihood frameworks, supplemented by analyses to examine potential discordant signal among genes. We also examined gene presence and absence data across Chlorophyceae. Results Concatenated analyses yielded at least two well-supported phylogenies: nucleotide data supported the traditional classification with the inclusion of the enigmatic Treubarinia into Sphaeropleales sensu lato. However, amino acid data yielded equally strong support for Sphaeropleaceae as sister to Volvocales, with the rest of the taxa traditionally classified in Sphaeropleales in a separate clade, and Treubarinia as sister to all of the above. Single-gene and other supplementary analyses indicated that the data have low phylogenetic signal at these critical nodes. Major clades were supported by genomic structural features such as gene losses and trans-spliced intron insertions in the plastome. Discussion While the sequence and gene order data support the deep split between the SV and OCC lineages, multiple phylogenetic hypothese…
bibliographic citation: Fučíková et al. (2019) Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae. PeerJ 7:e6899 https://doi.org/10.7717/peerj.6899
date submitted: 2018-08-27
date accepted: 2019-04-02
issued: 2019-05-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fučíková
  given name: Karolina
author list: Agent
  family name: Lewis
  given name: Paul O.
author list: Agent
  family name: Neupane
  given name: Suman
author list: Agent
  family name: Karol
  given name: Kenneth G.
author list: Agent
  family name: Lewis
  given name: Louise A.
doi: 10.7717/peerj.6899
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-15
copyright: ©2019 Fučíková et al.
attribution name: Fučíková et al.

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