PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Increased risk of periodontitis in patients with psoriatic disease: a nationwide population-based retrospective cohort study
items: Adult zebra finches rehearse highly variable song patterns during sleep
items: Response to “An exceptionally preserved 110 million years old praying mantis provides new insights into the predatory behaviour of early mantodeans”
items: 5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro
items: Sediment tolerance mechanisms identified in sponges using advanced imaging techniques
items: Activation of Rho-kinase and focal adhesion kinase regulates the organization of stress fibers and focal adhesions in the central part of fibroblasts
items: Lowland extirpation of anuran populations on a tropical mountain
items: Virus like particles as a platform for cancer vaccine development
items: Genome-wide in silico identification of membrane-bound transcription factors in plant species
items: Fitness implications of sex-specific catch-up growth in Nephila senegalensis, a spider with extreme reversed SSD

Increased risk of periodontitis in patients with psoriatic disease: a nationwide population-based retrospective cohort study
type: item
type: AcademicArticle
description: Aims Periodontitis and psoriatic disease, including psoriasis (PS) and psoriatic arthritis (PsA), share the common risk factors and co-morbidities. However, the risk of periodontitis in patients with psoriatic disease still needs further investigation. This study was a nationwide population-based retrospective cohort study assessing the risk of periodontitis from psoriatic disease exposure. Materials and Methods Patients with newly diagnosed psoriatic disease from 2003 to 2012 were identified from the Taiwanese National Health Insurance Research Database. The 1:4 ratio propensity score matched controls were selected from no psoriatic disease participations. The subsequent risk of periodontitis was evaluated in exposure and comparison groups. Multiple Cox proportional hazard models were used for the estimation. Results A total of 3,487 psoriatic disease patients and 13,948 controls were identified. Incidence rate of periodontitis was higher in patients with PsA. The adjusted hazard ratio (aHRs) for moderate/severe periodontitis were 0.85 (95% CI [0.65–1.11]) in PS group and 1.66 (95% CI [0.99–2.78]) in PsA group. The aHRs of PsA were increased over time, aHRs was changed from 0.65 (0–11 months from index date) to 1.34 (≥12 months from index date) in all types of periodontitis and from 1.09 to 1.79 in moderate/severe periodontitis group, respectively. Conclusions The increased risk of periodontitis was observed, especially the association between PsA and moderate/severe periodontitis. The patients with psoriatic disease should receive regular periodontal evaluation.
format: application/pdf
format: text/html
creator: Ni-Yu Su
creator: Jing-Yang Huang
creator: Chien-Jen Hu
creator: Hui-Chieh Yu
creator: Yu-Chao Chang
subject: Dentistry
subject: Dermatology
subject: Epidemiology
subject: Public Health
subject: Rheumatology
description: doi:10.7717/peerj.4064
publisher: PeerJ Inc.
rights: © 2017 Su et al.
abstract: Aims Periodontitis and psoriatic disease, including psoriasis (PS) and psoriatic arthritis (PsA), share the common risk factors and co-morbidities. However, the risk of periodontitis in patients with psoriatic disease still needs further investigation. This study was a nationwide population-based retrospective cohort study assessing the risk of periodontitis from psoriatic disease exposure. Materials and Methods Patients with newly diagnosed psoriatic disease from 2003 to 2012 were identified from the Taiwanese National Health Insurance Research Database. The 1:4 ratio propensity score matched controls were selected from no psoriatic disease participations. The subsequent risk of periodontitis was evaluated in exposure and comparison groups. Multiple Cox proportional hazard models were used for the estimation. Results A total of 3,487 psoriatic disease patients and 13,948 controls were identified. Incidence rate of periodontitis was higher in patients with PsA. The adjusted hazard ratio (aHRs) for moderate/severe periodontitis were 0.85 (95% CI [0.65–1.11]) in PS group and 1.66 (95% CI [0.99–2.78]) in PsA group. The aHRs of PsA were increased over time, aHRs was changed from 0.65 (0–11 months from index date) to 1.34 (≥12 months from index date) in all types of periodontitis and from 1.09 to 1.79 in moderate/severe periodontitis group, respectively. Conclusions The increased risk of periodontitis was observed, especially the association between PsA and moderate/severe periodontitis. The patients with psoriatic disease should receive regular periodontal evaluation.
bibliographic citation: Su et al. (2017) Increased risk of periodontitis in patients with psoriatic disease: a nationwide population-based retrospective cohort study. PeerJ 5:e4064 https://doi.org/10.7717/peerj.4064
date submitted: 2017-08-24
date accepted: 2017-10-29
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Ni-Yu
author list: Agent
  family name: Huang
  given name: Jing-Yang
author list: Agent
  family name: Hu
  given name: Chien-Jen
author list: Agent
  family name: Yu
  given name: Hui-Chieh
author list: Agent
  family name: Chang
  given name: Yu-Chao
doi: 10.7717/peerj.4064
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Su et al.
attribution name: Su et al.

Adult zebra finches rehearse highly variable song patterns during sleep
type: item
type: AcademicArticle
description: Brain activity during sleep is fairly ubiquitous and the best studied possible function is a role in memory consolidation, including motor memory. One suggested mechanism of how neural activity effects these benefits is through reactivation of neurons in patterns resembling those of the preceding experience. The specific patterns of motor activation replayed during sleep are largely unknown for any system. Brain areas devoted to song production in the songbird brain exhibit spontaneous song-like activity during sleep, but single cell neural recordings did not permit detection of the specific song patterns. We have now discovered that this sleep activation can be detected in the muscles of the vocal organ, thus providing a unique window into song-related brain activity at night. We show that male zebra finches (Taeniopygia guttata) frequently exhibit spontaneous song-like activity during the night, but that the fictive song patterns are highly variable and uncoordinated compared to the highly stereotyped day-time song production. This substantial variability is not consistent with the idea that night-time activity replays day-time experiences for consolidation. Although the function of this frequent activation is unknown, it may represent a mechanism for exploring motor space or serve to generate internal error signals that help maintain the high stereotypy of day-time song. In any case, the described activity supports the emerging insight that brain activity during sleep may serve a variety of functions.
format: application/pdf
format: text/html
creator: Brent K. Young
creator: Gabriel B. Mindlin
creator: Ezequiel Arneodo
creator: Franz Goller
subject: Animal Behavior
subject: Neuroscience
subject: Computational Science
description: doi:10.7717/peerj.4052
publisher: PeerJ Inc.
rights: © 2017 Young et al.
abstract: Brain activity during sleep is fairly ubiquitous and the best studied possible function is a role in memory consolidation, including motor memory. One suggested mechanism of how neural activity effects these benefits is through reactivation of neurons in patterns resembling those of the preceding experience. The specific patterns of motor activation replayed during sleep are largely unknown for any system. Brain areas devoted to song production in the songbird brain exhibit spontaneous song-like activity during sleep, but single cell neural recordings did not permit detection of the specific song patterns. We have now discovered that this sleep activation can be detected in the muscles of the vocal organ, thus providing a unique window into song-related brain activity at night. We show that male zebra finches (Taeniopygia guttata) frequently exhibit spontaneous song-like activity during the night, but that the fictive song patterns are highly variable and uncoordinated compared to the highly stereotyped day-time song production. This substantial variability is not consistent with the idea that night-time activity replays day-time experiences for consolidation. Although the function of this frequent activation is unknown, it may represent a mechanism for exploring motor space or serve to generate internal error signals that help maintain the high stereotypy of day-time song. In any case, the described activity supports the emerging insight that brain activity during sleep may serve a variety of functions.
bibliographic citation: Young et al. (2017) Adult zebra finches rehearse highly variable song patterns during sleep. PeerJ 5:e4052 https://doi.org/10.7717/peerj.4052
date submitted: 2017-09-15
date accepted: 2017-10-27
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Young
  given name: Brent K.
author list: Agent
  family name: Mindlin
  given name: Gabriel B.
author list: Agent
  family name: Arneodo
  given name: Ezequiel
author list: Agent
  family name: Goller
  given name: Franz
doi: 10.7717/peerj.4052
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Young et al.
attribution name: Young et al.

Response to “An exceptionally preserved 110 million years old praying mantis provides new insights into the predatory behaviour of early mantodeans”
type: item
type: AcademicArticle
description: Hörnig, Haug & Haug (2017) published a description of a new specimen of Santanmantis axelrodi MB.I.2068, an extinct species of praying mantis from the Crato Formation of Brazil. According to Hörnig, Haug & Haug (2017), the discovery of this new specimen brought with it implications for praying mantis character evolution and predatory behavior; it is with these lines of reasoning that we find fault. More specifically, we point to four flawed assumptions in their study that led to their unsubstantiated conclusion that S. axelrodi employed their mesothoracic legs in prey capture.
format: application/pdf
format: text/html
creator: Sydney K. Brannoch
creator: Gavin J. Svenson
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.4046
publisher: PeerJ Inc.
rights: © 2017 Brannoch and Svenson
abstract: Hörnig, Haug & Haug (2017) published a description of a new specimen of Santanmantis axelrodi MB.I.2068, an extinct species of praying mantis from the Crato Formation of Brazil. According to Hörnig, Haug & Haug (2017), the discovery of this new specimen brought with it implications for praying mantis character evolution and predatory behavior; it is with these lines of reasoning that we find fault. More specifically, we point to four flawed assumptions in their study that led to their unsubstantiated conclusion that S. axelrodi employed their mesothoracic legs in prey capture.
bibliographic citation: Brannoch et al. (2017) Response to “An exceptionally preserved 110 million years old praying mantis provides new insights into the predatory behaviour of early mantodeans”. PeerJ 5:e4046 https://doi.org/10.7717/peerj.4046
date submitted: 2017-08-21
date accepted: 2017-10-25
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brannoch
  given name: Sydney K.
author list: Agent
  family name: Svenson
  given name: Gavin J.
doi: 10.7717/peerj.4046
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Brannoch and Svenson
attribution name: Brannoch and Svenson

5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro
type: item
type: AcademicArticle
description: Gastrointestinal mucositis is a debilitating side effect of chemotherapy treatment, with currently no treatment available. As changes in microbial composition have been reported upon chemotherapy treatment in vivo, it is thought that gut microbiota dysbiosis contribute to the mucositis etiology. Yet it is not known whether chemotherapeutics directly cause microbial dysbiosis, thereby increasing mucositis risk, or whether the chemotherapeutic subjected host environment disturbs the microbiome thereby aggravating the disease. To address this question, we used the M-SHIME®, an in vitro mucosal simulator of the human intestinal microbial ecosystem, as an experimental setup that excludes the host factor. The direct impact of two chemotherapeutics, 5-fluorouracil (5-FU) and SN-38 (active metabolite of irinotecan), on the luminal and mucosal gut microbiota from several human donors was investigated through monitoring fermentation activity and next generation sequencing. At a dose of 10 µM in the mucosal environment, 5-FU impacted the functionality and composition of the colon microbiota to a minor extent. Similarly, a daily dose of 10 µM SN-38 in the luminal environment did not cause significant changes in the functionality or microbiome composition. As our mucosal model does not include a host-compartment, our findings strongly indicate that a putative microbial contribution to mucositis is initially triggered by an altered host environment upon chemotherapy.
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format: text/html
creator: Eline Vanlancker
creator: Barbara Vanhoecke
creator: Andrea Stringer
creator: Tom Van de Wiele
subject: Microbiology
subject: Oncology
description: doi:10.7717/peerj.4017
publisher: PeerJ Inc.
rights: © 2017 Vanlancker et al.
abstract: Gastrointestinal mucositis is a debilitating side effect of chemotherapy treatment, with currently no treatment available. As changes in microbial composition have been reported upon chemotherapy treatment in vivo, it is thought that gut microbiota dysbiosis contribute to the mucositis etiology. Yet it is not known whether chemotherapeutics directly cause microbial dysbiosis, thereby increasing mucositis risk, or whether the chemotherapeutic subjected host environment disturbs the microbiome thereby aggravating the disease. To address this question, we used the M-SHIME®, an in vitro mucosal simulator of the human intestinal microbial ecosystem, as an experimental setup that excludes the host factor. The direct impact of two chemotherapeutics, 5-fluorouracil (5-FU) and SN-38 (active metabolite of irinotecan), on the luminal and mucosal gut microbiota from several human donors was investigated through monitoring fermentation activity and next generation sequencing. At a dose of 10 µM in the mucosal environment, 5-FU impacted the functionality and composition of the colon microbiota to a minor extent. Similarly, a daily dose of 10 µM SN-38 in the luminal environment did not cause significant changes in the functionality or microbiome composition. As our mucosal model does not include a host-compartment, our findings strongly indicate that a putative microbial contribution to mucositis is initially triggered by an altered host environment upon chemotherapy.
bibliographic citation: Vanlancker et al. (2017) 5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro. PeerJ 5:e4017 https://doi.org/10.7717/peerj.4017
date submitted: 2017-07-13
date accepted: 2017-10-20
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vanlancker
  given name: Eline
author list: Agent
  family name: Vanhoecke
  given name: Barbara
author list: Agent
  family name: Stringer
  given name: Andrea
author list: Agent
  family name: Van de Wiele
  given name: Tom
doi: 10.7717/peerj.4017
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Vanlancker et al.
attribution name: Vanlancker et al.

Sediment tolerance mechanisms identified in sponges using advanced imaging techniques
type: item
type: AcademicArticle
description: Terrestrial runoff, resuspension events and dredging can affect filter-feeding sponges by elevating the concentration of suspended sediments, reducing light intensity, and smothering sponges with sediments. To investigate how sponges respond to pressures associated with increased sediment loads, the abundant and widely distributed Indo-Pacific species Ianthella basta was exposed to elevated suspended sediment concentrations, sediment deposition, and light attenuation for 48 h (acute exposure) and 4 weeks (chronic exposure). In order to visualise the response mechanisms, sponge tissue was examined by 3D X-ray microscopy and scanning electron microscopy (SEM). Acute exposures resulted in sediment rapidly accumulating in the aquiferous system of I. basta, although this sediment was fully removed within three days. Sediment removal took longer (>2 weeks) following chronic exposures, and I. basta also exhibited tissue regression and a smaller aquiferous system. The application of advanced imaging approaches revealed that I. basta employs a multilevel system for sediment rejection and elimination, containing both active and passive components. Sponges responded to sediment stress through (i) mucus production, (ii) exclusion of particles by incurrent pores, (iii) closure of oscula and pumping cessation, (iv) expulsion of particles from the aquiferous system, and (v) tissue regression to reduce the volume of the aquiferous system, thereby entering a dormant state. These mechanisms would result in tolerance and resilience to exposure to variable and high sediment loads associated with both anthropogenic impacts like dredging programs and natural pressures like flood events.
format: application/pdf
format: text/html
creator: Brian W. Strehlow
creator: Mari-Carmen Pineda
creator: Alan Duckworth
creator: Gary A. Kendrick
creator: Michael Renton
creator: Muhammad Azmi Abdul Wahab
creator: Nicole S. Webster
creator: Peta L. Clode
subject: Ecology
subject: Marine Biology
subject: Biosphere Interactions
description: doi:10.7717/peerj.3904
publisher: PeerJ Inc.
rights: © 2017 Strehlow et al.
abstract: Terrestrial runoff, resuspension events and dredging can affect filter-feeding sponges by elevating the concentration of suspended sediments, reducing light intensity, and smothering sponges with sediments. To investigate how sponges respond to pressures associated with increased sediment loads, the abundant and widely distributed Indo-Pacific species Ianthella basta was exposed to elevated suspended sediment concentrations, sediment deposition, and light attenuation for 48 h (acute exposure) and 4 weeks (chronic exposure). In order to visualise the response mechanisms, sponge tissue was examined by 3D X-ray microscopy and scanning electron microscopy (SEM). Acute exposures resulted in sediment rapidly accumulating in the aquiferous system of I. basta, although this sediment was fully removed within three days. Sediment removal took longer (>2 weeks) following chronic exposures, and I. basta also exhibited tissue regression and a smaller aquiferous system. The application of advanced imaging approaches revealed that I. basta employs a multilevel system for sediment rejection and elimination, containing both active and passive components. Sponges responded to sediment stress through (i) mucus production, (ii) exclusion of particles by incurrent pores, (iii) closure of oscula and pumping cessation, (iv) expulsion of particles from the aquiferous system, and (v) tissue regression to reduce the volume of the aquiferous system, thereby entering a dormant state. These mechanisms would result in tolerance and resilience to exposure to variable and high sediment loads associated with both anthropogenic impacts like dredging programs and natural pressures like flood events.
bibliographic citation: Strehlow et al. (2017) Sediment tolerance mechanisms identified in sponges using advanced imaging techniques. PeerJ 5:e3904 https://doi.org/10.7717/peerj.3904
date submitted: 2017-06-08
date accepted: 2017-09-18
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Strehlow
  given name: Brian W.
author list: Agent
  family name: Pineda
  given name: Mari-Carmen
author list: Agent
  family name: Duckworth
  given name: Alan
author list: Agent
  family name: Kendrick
  given name: Gary A.
author list: Agent
  family name: Renton
  given name: Michael
author list: Agent
  family name: Abdul Wahab
  given name: Muhammad Azmi
author list: Agent
  family name: Webster
  given name: Nicole S.
author list: Agent
  family name: Clode
  given name: Peta L.
doi: 10.7717/peerj.3904
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Strehlow et al.
attribution name: Strehlow et al.

Activation of Rho-kinase and focal adhesion kinase regulates the organization of stress fibers and focal adhesions in the central part of fibroblasts
type: item
type: AcademicArticle
description: Specific regulation and activation of focal adhesion kinase (FAK) are thought to be important for focal adhesion formation, and activation of Rho-kinase has been suggested to play a role in determining the effects of FAK on the formation of stress fibers and focal adhesions. To clarify the role of FAK in stress fiber formation and focal adhesion organization, the author examined the formation of new stress fibers and focal adhesions by activation of Rho-kinase in FAK knockout (FAK–/–) fibroblasts. FAK–/– cells were elliptical in shape, and showed reduced numbers of stress fibers and focal adhesions in the central part of the cells along with large focal adhesions in the peripheral regions. Activation of Rho-kinase in FAK–/– cells transiently increased the actin filaments in the cell center, but these did not form typical thick stress fibers. Moreover, only plaque-like structures as the origins of newly formed focal adhesions were observed in the center of the cell. Furthermore, introduction of an exogenous GFP-labeled FAK gene into FAK–/– cells resulted in increased numbers of stress fibers and focal adhesions in the center of the cells, which showed typical fibroblast morphology. These results indicated that FAK plays an important role in the formation of stress fibers and focal adhesions as well as in regulation of cell shape and morphology with the activation of Rho-kinase.
format: application/pdf
format: text/html
creator: Kazuo Katoh
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.4063
publisher: PeerJ Inc.
rights: © 2017 Katoh
abstract: Specific regulation and activation of focal adhesion kinase (FAK) are thought to be important for focal adhesion formation, and activation of Rho-kinase has been suggested to play a role in determining the effects of FAK on the formation of stress fibers and focal adhesions. To clarify the role of FAK in stress fiber formation and focal adhesion organization, the author examined the formation of new stress fibers and focal adhesions by activation of Rho-kinase in FAK knockout (FAK–/–) fibroblasts. FAK–/– cells were elliptical in shape, and showed reduced numbers of stress fibers and focal adhesions in the central part of the cells along with large focal adhesions in the peripheral regions. Activation of Rho-kinase in FAK–/– cells transiently increased the actin filaments in the cell center, but these did not form typical thick stress fibers. Moreover, only plaque-like structures as the origins of newly formed focal adhesions were observed in the center of the cell. Furthermore, introduction of an exogenous GFP-labeled FAK gene into FAK–/– cells resulted in increased numbers of stress fibers and focal adhesions in the center of the cells, which showed typical fibroblast morphology. These results indicated that FAK plays an important role in the formation of stress fibers and focal adhesions as well as in regulation of cell shape and morphology with the activation of Rho-kinase.
bibliographic citation: Katoh (2017) Activation of Rho-kinase and focal adhesion kinase regulates the organization of stress fibers and focal adhesions in the central part of fibroblasts. PeerJ 5:e4063 https://doi.org/10.7717/peerj.4063
date submitted: 2017-09-28
date accepted: 2017-10-29
issued: 2017-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Katoh
  given name: Kazuo
doi: 10.7717/peerj.4063
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-15
copyright: ©2017 Katoh
attribution name: Katoh

Lowland extirpation of anuran populations on a tropical mountain
type: item
type: AcademicArticle
description: Background Climate change and infectious diseases threaten animal and plant species, even in natural and protected areas. To cope with these changes, species may acclimate, adapt, move or decline. Here, we test for shifts in anuran distributions in the Luquillo Mountains (LM), a tropical montane forest in Puerto Rico by comparing species distributions from historical (1931–1989)and current data (2015/2016). Methods Historical data, which included different methodologies, were gathered through the Global Biodiversity Information Facility (GBIF) and published literature, and the current data were collected using acoustic recorders along three elevational transects. Results In the recordings, we detected the 12 native frog species known to occur in LM. Over a span of ∼25 years, two species have become extinct and four species suffered extirpation in lowland areas. As a consequence, low elevation areas in the LM (<300 m) have lost at least six anuran species. Discussion We hypothesize that these extirpations are due to the effects of climate change and infectious diseases, which are restricting many species to higher elevations and a much smaller area. Land use change is not responsible for these changes because LM has been a protected reserve for the past 80 years. However, previous studies indicate that (1) climate change has increased temperatures in Puerto Rico, and (2) Batrachochytrium dendrobatidis (Bd) was found in 10 native species and early detection of Bd coincides with anurans declines in the LM. Our study confirms the general impressions of amphibian population extirpations at low elevations, and corroborates the levels of threat assigned by IUCN.
format: application/pdf
format: text/html
creator: Marconi Campos-Cerqueira
creator: T. Mitchell Aide
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Climate Change Biology
description: doi:10.7717/peerj.4059
publisher: PeerJ Inc.
rights: © 2017 Campos-Cerqueira and Aide
abstract: Background Climate change and infectious diseases threaten animal and plant species, even in natural and protected areas. To cope with these changes, species may acclimate, adapt, move or decline. Here, we test for shifts in anuran distributions in the Luquillo Mountains (LM), a tropical montane forest in Puerto Rico by comparing species distributions from historical (1931–1989)and current data (2015/2016). Methods Historical data, which included different methodologies, were gathered through the Global Biodiversity Information Facility (GBIF) and published literature, and the current data were collected using acoustic recorders along three elevational transects. Results In the recordings, we detected the 12 native frog species known to occur in LM. Over a span of ∼25 years, two species have become extinct and four species suffered extirpation in lowland areas. As a consequence, low elevation areas in the LM (<300 m) have lost at least six anuran species. Discussion We hypothesize that these extirpations are due to the effects of climate change and infectious diseases, which are restricting many species to higher elevations and a much smaller area. Land use change is not responsible for these changes because LM has been a protected reserve for the past 80 years. However, previous studies indicate that (1) climate change has increased temperatures in Puerto Rico, and (2) Batrachochytrium dendrobatidis (Bd) was found in 10 native species and early detection of Bd coincides with anurans declines in the LM. Our study confirms the general impressions of amphibian population extirpations at low elevations, and corroborates the levels of threat assigned by IUCN.
bibliographic citation: Campos-Cerqueira et al. (2017) Lowland extirpation of anuran populations on a tropical mountain. PeerJ 5:e4059 https://doi.org/10.7717/peerj.4059
date submitted: 2017-08-04
date accepted: 2017-10-28
issued: 2017-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Campos-Cerqueira
  given name: Marconi
author list: Agent
  family name: Aide
  given name: T. Mitchell
doi: 10.7717/peerj.4059
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-15
copyright: ©2017 Campos-Cerqueira and Aide
attribution name: Campos-Cerqueira and Aide

Virus like particles as a platform for cancer vaccine development
type: item
type: AcademicArticle
description: Cancers have killed millions of people in human history and are still posing a serious health problem worldwide. Therefore, there is an urgent need for developing preventive and therapeutic cancer vaccines. Among various cancer vaccine development platforms, virus-like particles (VLPs) offer several advantages. VLPs are multimeric nanostructures with morphology resembling that of native viruses and are mainly composed of surface structural proteins of viruses but are devoid of viral genetic materials rendering them neither infective nor replicative. In addition, they can be engineered to display multiple, highly ordered heterologous epitopes or peptides in order to optimize the antigenicity and immunogenicity of the displayed entities. Like native viruses, specific epitopes displayed on VLPs can be taken up, processed, and presented by antigen-presenting cells to elicit potent specific humoral and cell-mediated immune responses. Several studies also indicated that VLPs could overcome the immunosuppressive state of the tumor microenvironment and break self-tolerance to elicit strong cytotoxic lymphocyte activity, which is crucial for both virus clearance and destruction of cancerous cells. Collectively, these unique characteristics of VLPs make them optimal cancer vaccine candidates. This review discusses current progress in the development of VLP-based cancer vaccines and some potential drawbacks of VLPs in cancer vaccine development. Extracellular vesicles with close resembling to viral particles are also discussed and compared with VLPs as a platform in cancer vaccine developments.
format: application/pdf
format: text/html
creator: Hui Kian Ong
creator: Wen Siang Tan
creator: Kok Lian Ho
subject: Immunology
subject: Pharmacology
description: doi:10.7717/peerj.4053
publisher: PeerJ Inc.
rights: © 2017 Ong et al.
abstract: Cancers have killed millions of people in human history and are still posing a serious health problem worldwide. Therefore, there is an urgent need for developing preventive and therapeutic cancer vaccines. Among various cancer vaccine development platforms, virus-like particles (VLPs) offer several advantages. VLPs are multimeric nanostructures with morphology resembling that of native viruses and are mainly composed of surface structural proteins of viruses but are devoid of viral genetic materials rendering them neither infective nor replicative. In addition, they can be engineered to display multiple, highly ordered heterologous epitopes or peptides in order to optimize the antigenicity and immunogenicity of the displayed entities. Like native viruses, specific epitopes displayed on VLPs can be taken up, processed, and presented by antigen-presenting cells to elicit potent specific humoral and cell-mediated immune responses. Several studies also indicated that VLPs could overcome the immunosuppressive state of the tumor microenvironment and break self-tolerance to elicit strong cytotoxic lymphocyte activity, which is crucial for both virus clearance and destruction of cancerous cells. Collectively, these unique characteristics of VLPs make them optimal cancer vaccine candidates. This review discusses current progress in the development of VLP-based cancer vaccines and some potential drawbacks of VLPs in cancer vaccine development. Extracellular vesicles with close resembling to viral particles are also discussed and compared with VLPs as a platform in cancer vaccine developments.
bibliographic citation: Ong et al. (2017) Virus like particles as a platform for cancer vaccine development. PeerJ 5:e4053 https://doi.org/10.7717/peerj.4053
date submitted: 2017-07-14
date accepted: 2017-10-27
issued: 2017-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ong
  given name: Hui Kian
author list: Agent
  family name: Tan
  given name: Wen Siang
author list: Agent
  family name: Ho
  given name: Kok Lian
doi: 10.7717/peerj.4053
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-15
copyright: ©2017 Ong et al.
attribution name: Ong et al.

Genome-wide in silico identification of membrane-bound transcription factors in plant species
type: item
type: AcademicArticle
description: Membrane-bound transcription factors (MTFs) are located in cellular membranes due to their transmembrane domains. In plants, proteolytic processing is considered to be the main mechanism for MTF activation, which ensures the liberation of MTFs from membranes and further their translocation into the nucleus to regulate gene expression; this process skips both the transcriptional and translational stages, and thus it guarantees the prompt responses of plants to various stimuli. Currently, information concerning plant MTFs is limited to model organisms, including Arabidopsis thaliana and Oryza sativa, and little is known in other plant species at the genome level. In the present study, seven membrane topology predictors widely used by the research community were employed to establish a reliable workflow for MTF identification. Genome-wide in silico analysis of MTFs was then performed in 14 plant species spanning the chlorophytes, bryophytes, gymnosperms, monocots and eudicots. A total of 1,089 MTFs have been identified from a total of 25,850 transcription factors in these 14 plant species. These MTFs belong to 52 gene family, and the top six most abundant families are the NAC (128), SBP (77), C2H2 (70), bZIP (67), MYB-related (65) and bHLH (63) families. The MTFs have transmembrane spans ranging from one to thirteen, and 71.5% and 21.1% of the MTFs have one and two transmembrane motifs, respectively. Most of the MTFs in this study have transmembrane motifs located in either N- or C-terminal regions, indicating that proteolytic cleavage could be a conserved mechanism for MTF activation. Additionally, approximately half of the MTFs in the genome of either Arabidopsis thaliana or Gossypium raimondii could be potentially regulated by alternative splicing, indicating that alternative splicing is another conserved activation mechanism for MTFs. The present study performed systematic analyses of MTFs in plant lineages at the genome level, and provides invaluable information f…
format: application/pdf
format: text/html
creator: Shixiang Yao
creator: Lili Deng
creator: Kaifang Zeng
subject: Plant Science
description: doi:10.7717/peerj.4051
publisher: PeerJ Inc.
rights: © 2017 Yao et al.
abstract: Membrane-bound transcription factors (MTFs) are located in cellular membranes due to their transmembrane domains. In plants, proteolytic processing is considered to be the main mechanism for MTF activation, which ensures the liberation of MTFs from membranes and further their translocation into the nucleus to regulate gene expression; this process skips both the transcriptional and translational stages, and thus it guarantees the prompt responses of plants to various stimuli. Currently, information concerning plant MTFs is limited to model organisms, including Arabidopsis thaliana and Oryza sativa, and little is known in other plant species at the genome level. In the present study, seven membrane topology predictors widely used by the research community were employed to establish a reliable workflow for MTF identification. Genome-wide in silico analysis of MTFs was then performed in 14 plant species spanning the chlorophytes, bryophytes, gymnosperms, monocots and eudicots. A total of 1,089 MTFs have been identified from a total of 25,850 transcription factors in these 14 plant species. These MTFs belong to 52 gene family, and the top six most abundant families are the NAC (128), SBP (77), C2H2 (70), bZIP (67), MYB-related (65) and bHLH (63) families. The MTFs have transmembrane spans ranging from one to thirteen, and 71.5% and 21.1% of the MTFs have one and two transmembrane motifs, respectively. Most of the MTFs in this study have transmembrane motifs located in either N- or C-terminal regions, indicating that proteolytic cleavage could be a conserved mechanism for MTF activation. Additionally, approximately half of the MTFs in the genome of either Arabidopsis thaliana or Gossypium raimondii could be potentially regulated by alternative splicing, indicating that alternative splicing is another conserved activation mechanism for MTFs. The present study performed systematic analyses of MTFs in plant lineages at the genome level, and provides invaluable information f…
bibliographic citation: Yao et al. (2017) Genome-wide in silico identification of membrane-bound transcription factors in plant species. PeerJ 5:e4051 https://doi.org/10.7717/peerj.4051
date submitted: 2017-06-06
date accepted: 2017-10-27
issued: 2017-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Shixiang
author list: Agent
  family name: Deng
  given name: Lili
author list: Agent
  family name: Zeng
  given name: Kaifang
doi: 10.7717/peerj.4051
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-15
copyright: ©2017 Yao et al.
attribution name: Yao et al.

Fitness implications of sex-specific catch-up growth in Nephila senegalensis, a spider with extreme reversed SSD
type: item
type: AcademicArticle
description: Background Animal growth is often constrained by unfavourable conditions and divergences from optimal body size can be detrimental to an individual’s fitness, particularly in species with determinate growth and a narrow time-frame for life-time reproduction. Growth restriction in early juvenile stages can later be compensated by means of plastic developmental responses, such as adaptive catch-up growth (the compensation of growth deficits through delayed development). Although sex differences regarding the mode and degree of growth compensation have been coherently predicted from sex-specific fitness payoffs, inconsistent results imply a need for further research. We used the African Nephila senegalensis, representing an extreme case of female-biased sexual size dimorphism (SSD), to study fitness implications of sex-specific growth compensation. We predicted effective catch-up growth in early food-restricted females to result in full compensation of growth deficits and a life-time fecundity (LTF) equivalent to unrestricted females. Based on a stronger trade-off between size-related benefits and costs of a delayed maturation, we expected less effective catch-up growth in males. Methods We tracked the development of over one thousand spiders in different feeding treatments, e.g., comprising a fixed period of early low feeding conditions followed by unrestricted feeding conditions, permanent unrestricted feeding conditions, or permanent low feeding conditions as a control. In a second experimental section, we assessed female fitness by measuring LTF in a subset of females. In addition, we tested whether compensatory development affected the reproductive lifespan in both sexes and analysed genotype-by-treatment interactions as a potential cause of variation in life-history traits. Results Both sexes delayed maturation to counteract early growth restriction, but only females achieved full compensation of adult body size. Female catch-up growth resulted in equivalent LTF …
format: application/pdf
format: text/html
creator: Rainer Neumann
creator: Nicole Ruppel
creator: Jutta M. Schneider
subject: Animal Behavior
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.4050
publisher: PeerJ Inc.
rights: © 2017 Neumann et al.
abstract: Background Animal growth is often constrained by unfavourable conditions and divergences from optimal body size can be detrimental to an individual’s fitness, particularly in species with determinate growth and a narrow time-frame for life-time reproduction. Growth restriction in early juvenile stages can later be compensated by means of plastic developmental responses, such as adaptive catch-up growth (the compensation of growth deficits through delayed development). Although sex differences regarding the mode and degree of growth compensation have been coherently predicted from sex-specific fitness payoffs, inconsistent results imply a need for further research. We used the African Nephila senegalensis, representing an extreme case of female-biased sexual size dimorphism (SSD), to study fitness implications of sex-specific growth compensation. We predicted effective catch-up growth in early food-restricted females to result in full compensation of growth deficits and a life-time fecundity (LTF) equivalent to unrestricted females. Based on a stronger trade-off between size-related benefits and costs of a delayed maturation, we expected less effective catch-up growth in males. Methods We tracked the development of over one thousand spiders in different feeding treatments, e.g., comprising a fixed period of early low feeding conditions followed by unrestricted feeding conditions, permanent unrestricted feeding conditions, or permanent low feeding conditions as a control. In a second experimental section, we assessed female fitness by measuring LTF in a subset of females. In addition, we tested whether compensatory development affected the reproductive lifespan in both sexes and analysed genotype-by-treatment interactions as a potential cause of variation in life-history traits. Results Both sexes delayed maturation to counteract early growth restriction, but only females achieved full compensation of adult body size. Female catch-up growth resulted in equivalent LTF …
bibliographic citation: Neumann et al. (2017) Fitness implications of sex-specific catch-up growth in Nephila senegalensis, a spider with extreme reversed SSD. PeerJ 5:e4050 https://doi.org/10.7717/peerj.4050
date submitted: 2017-07-21
date accepted: 2017-10-26
issued: 2017-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Neumann
  given name: Rainer
author list: Agent
  family name: Ruppel
  given name: Nicole
author list: Agent
  family name: Schneider
  given name: Jutta M.
doi: 10.7717/peerj.4050
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-15
copyright: ©2017 Neumann et al.
attribution name: Neumann et al.

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