PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: TET1 may contribute to hypoxia-induced epithelial to mesenchymal transition of endometrial epithelial cells in endometriosis
items: Prophet forecasting model: a machine learning approach to predict the concentration of air pollutants (PM2.5, PM10, O3, NO2, SO2, CO) in Seoul, South Korea
items: Seasonal and successional dynamics of size-dependent plant demographic rates in a tropical dry forest
items: Rediscovery of Cyperus flavescens (Cyperaceae) on the northeast periphery of its range in Europe
items: Potential role of cellular miRNAs in coronavirus-host interplay
items: Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles
items: The impact of climate change on flow conditions and wetland ecosystems in the Lower Biebrza River (Poland)
items: Methylase-assisted subcloning for high throughput BioBrick assembly
items: ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences
items: Intergenerational implications of alcohol intake: metabolic disorders in alcohol-naïve rat offspring

TET1 may contribute to hypoxia-induced epithelial to mesenchymal transition of endometrial epithelial cells in endometriosis
type: item
type: AcademicArticle
description: Background Endometriosis (EMs) is a non-malignant gynecological disease, whose pathogenesis remains to be clarified. Recent studies have found that hypoxia induces epithelial-mesenchymal transition (EMT) as well as epigenetic modification in EMs. However, the relationship between EMT and demethylation modification under hypoxia status in EMs remains unknown. Methods The expression of N-cadherin, E-cadherin and TET1 in normal endometria, eutopic endometria and ovarian endometriomas was assessed by immunohistochemistry and immunofluorescence double staining. 5-hmC was detected by fluorescence-based ELISA kit using a specific 5-hmC antibody. Overexpression and inhibition of TET1 or hypoxia-inducible factor 2α (HIF-2α) were performed by plasmid and siRNA transfection. The expression of HIF-2α, TET1 and EMT markers in Ishikawa (ISK) cells (widely used as endometrial epithelial cells) was evaluated by western blotting. The interaction of HIF-2α and TET1 was analyzed by chromatin immunoprecipitation. Results Demethylation enzyme TET1 (ten-eleven translocation1) was elevated in glandular epithelium of ovarian endometrioma, along with the activation of EMT (increased expression of N-cadherin, and decreased expression of E-cadherin) and global increase of epigenetic modification marker 5-hmC(5-hydroxymethylcytosine). Besides, endometriosis lesions had more TET1 and N-cadherin co-localized cells. Further study showed that ISK cells exhibited enhanced EMT, and increased expression of TET1 and HIF-2α under hypoxic condition. Hypoxia-induced EMT was partly regulated by TET1 and HIF-2α. HIF-2α inhibition mitigated TET1 expression changes provoked by hypoxia. Conclusions Hypoxia induces the expression of TET1 regulated by HIF-2α, thus may promote EMT in endometriosis.
format: application/pdf
format: text/html
creator: Jingni Wu
creator: Xidie Li
creator: Hongyan Huang
creator: Xiaomeng Xia
creator: Mengmeng Zhang
creator: Xiaoling Fang
subject: Gynecology and Obstetrics
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.9950
publisher: PeerJ Inc.
rights: © 2020 Wu et al.
abstract: Background Endometriosis (EMs) is a non-malignant gynecological disease, whose pathogenesis remains to be clarified. Recent studies have found that hypoxia induces epithelial-mesenchymal transition (EMT) as well as epigenetic modification in EMs. However, the relationship between EMT and demethylation modification under hypoxia status in EMs remains unknown. Methods The expression of N-cadherin, E-cadherin and TET1 in normal endometria, eutopic endometria and ovarian endometriomas was assessed by immunohistochemistry and immunofluorescence double staining. 5-hmC was detected by fluorescence-based ELISA kit using a specific 5-hmC antibody. Overexpression and inhibition of TET1 or hypoxia-inducible factor 2α (HIF-2α) were performed by plasmid and siRNA transfection. The expression of HIF-2α, TET1 and EMT markers in Ishikawa (ISK) cells (widely used as endometrial epithelial cells) was evaluated by western blotting. The interaction of HIF-2α and TET1 was analyzed by chromatin immunoprecipitation. Results Demethylation enzyme TET1 (ten-eleven translocation1) was elevated in glandular epithelium of ovarian endometrioma, along with the activation of EMT (increased expression of N-cadherin, and decreased expression of E-cadherin) and global increase of epigenetic modification marker 5-hmC(5-hydroxymethylcytosine). Besides, endometriosis lesions had more TET1 and N-cadherin co-localized cells. Further study showed that ISK cells exhibited enhanced EMT, and increased expression of TET1 and HIF-2α under hypoxic condition. Hypoxia-induced EMT was partly regulated by TET1 and HIF-2α. HIF-2α inhibition mitigated TET1 expression changes provoked by hypoxia. Conclusions Hypoxia induces the expression of TET1 regulated by HIF-2α, thus may promote EMT in endometriosis.
bibliographic citation: Wu et al. (2020) TET1 may contribute to hypoxia-induced epithelial to mesenchymal transition of endometrial epithelial cells in endometriosis. PeerJ 8:e9950 https://doi.org/10.7717/peerj.9950
date submitted: 2020-04-17
date accepted: 2020-08-25
issued: 2020-09-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Jingni
author list: Agent
  family name: Li
  given name: Xidie
author list: Agent
  family name: Huang
  given name: Hongyan
author list: Agent
  family name: Xia
  given name: Xiaomeng
author list: Agent
  family name: Zhang
  given name: Mengmeng
author list: Agent
  family name: Fang
  given name: Xiaoling
doi: 10.7717/peerj.9950
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-15
copyright: ©2020 Wu et al.
attribution name: Wu et al.

Prophet forecasting model: a machine learning approach to predict the concentration of air pollutants (PM2.5, PM10, O3, NO2, SO2, CO) in Seoul, South Korea
type: item
type: AcademicArticle
description: Amidst recent industrialization in South Korea, Seoul has experienced high levels of air pollution, an issue that is magnified due to a lack of effective air pollution prediction techniques. In this study, the Prophet forecasting model (PFM) was used to predict both short-term and long-term air pollution in Seoul. The air pollutants forecasted in this study were PM2.5, PM10, O3, NO2, SO2, and CO, air pollutants responsible for numerous health conditions upon long-term exposure. Current chemical models to predict air pollution require complex source lists making them difficult to use. Machine learning models have also been implemented however their requirement of meteorological parameters render the models ineffective as additional models and infrastructure need to be in place to model meteorology. To address this, a model needs to be created that can accurately predict pollution based on time. A dataset containing three years worth of hourly air quality measurements in Seoul was sourced from the Seoul Open Data Plaza. To optimize the model, PFM has the following parameters: model type, changepoints, seasonality, holidays, and error. Cross validation was performed on the 2017–18 data; then, the model predicted 2019 values. To compare the predicted and actual values and determine the accuracy of the model, the statistical indicators: mean squared error (MSE), mean absolute error (MAE), root mean squared error (RMSE), and coverage were used. PFM predicted PM2.5 and PM10 with a MAE value of 12.6 µg/m3 and 19.6 µg/m3, respectively. PFM also predicted SO2 and CO with a MAE value of 0.00124 ppm and 0.207 ppm, respectively. PFM’s prediction of PM2.5 and PM10 had a MAE approximately 2 times and 4 times less, respectively, than comparable models. PFM’s prediction of SO2and CO had a MAE approximately five times and 50 times less, respectively, than comparable models. In most cases, PFM’s ability to accurately forecast the concentration of air pollutants in Seoul up to one year…
format: application/pdf
format: text/html
creator: Justin Shen
creator: Davesh Valagolam
creator: Serena McCalla
subject: Atmospheric Chemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9961
publisher: PeerJ Inc.
rights: © 2020 Shen et al.
abstract: Amidst recent industrialization in South Korea, Seoul has experienced high levels of air pollution, an issue that is magnified due to a lack of effective air pollution prediction techniques. In this study, the Prophet forecasting model (PFM) was used to predict both short-term and long-term air pollution in Seoul. The air pollutants forecasted in this study were PM2.5, PM10, O3, NO2, SO2, and CO, air pollutants responsible for numerous health conditions upon long-term exposure. Current chemical models to predict air pollution require complex source lists making them difficult to use. Machine learning models have also been implemented however their requirement of meteorological parameters render the models ineffective as additional models and infrastructure need to be in place to model meteorology. To address this, a model needs to be created that can accurately predict pollution based on time. A dataset containing three years worth of hourly air quality measurements in Seoul was sourced from the Seoul Open Data Plaza. To optimize the model, PFM has the following parameters: model type, changepoints, seasonality, holidays, and error. Cross validation was performed on the 2017–18 data; then, the model predicted 2019 values. To compare the predicted and actual values and determine the accuracy of the model, the statistical indicators: mean squared error (MSE), mean absolute error (MAE), root mean squared error (RMSE), and coverage were used. PFM predicted PM2.5 and PM10 with a MAE value of 12.6 µg/m3 and 19.6 µg/m3, respectively. PFM also predicted SO2 and CO with a MAE value of 0.00124 ppm and 0.207 ppm, respectively. PFM’s prediction of PM2.5 and PM10 had a MAE approximately 2 times and 4 times less, respectively, than comparable models. PFM’s prediction of SO2and CO had a MAE approximately five times and 50 times less, respectively, than comparable models. In most cases, PFM’s ability to accurately forecast the concentration of air pollutants in Seoul up to one year…
bibliographic citation: Shen et al. (2020) Prophet forecasting model: a machine learning approach to predict the concentration of air pollutants (PM2.5, PM10, O3, NO2, SO2, CO) in Seoul, South Korea. PeerJ 8:e9961 https://doi.org/10.7717/peerj.9961
date submitted: 2020-07-10
date accepted: 2020-08-25
issued: 2020-09-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shen
  given name: Justin
author list: Agent
  family name: Valagolam
  given name: Davesh
author list: Agent
  family name: McCalla
  given name: Serena
doi: 10.7717/peerj.9961
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-15
copyright: ©2020 Shen et al.
attribution name: Shen et al.

Seasonal and successional dynamics of size-dependent plant demographic rates in a tropical dry forest
type: item
type: AcademicArticle
description: Tropical forests are globally important for biodiversity conservation and climate change mitigation but are being converted to other land uses. Conversion of seasonally dry tropical forests (SDTF) is particularly high while their protection is low. Secondary succession allows forests to recover their structure, diversity and composition after conversion and subsequent abandonment and is influenced by demographic rates of the constituent species. However, how these rates vary between seasons for different plant sizes at different successional stages in SDTF is not known. The effect of seasonal drought may be more severe early in succession, when temperature and radiation are high, while competition and density-dependent processes may be more important at later stages, when vegetation is tall and dense. Besides, the effects of seasonality and successional stage may vary with plant size. Large plants can better compete with small plants for limiting resources and may also have a greater capacity to withstand stress. We asked how size-dependent density, species density, recruitment and mortality varied between seasons and successional stages in a SDTF. We monitored a chronosequence in Yucatan, Mexico, over six years in three 0.1 ha plots in each of three successional stages: early (3–5 years-old), intermediate (18–20 years-old) and advanced (>50 years-old). Recruitment, mortality and species gain and loss rates were calculated from wet and dry season censuses separately for large (diameter > 5 cm) and small (1–5 cm in diameter) plants. We used linear mixed-effects models to assess the effects of successional stage, seasonality and their changes through time on demographic rates and on plant and species density. Seasonality affected demographic rates and density of large plants, which exhibited high wet-season recruitment and species gain rates at the early stage and high wet-season mortality at the intermediate stage, resulting in an increase in plant and species densit…
format: application/pdf
format: text/html
creator: Irving Saenz-Pedroza
creator: Richard Feldman
creator: Casandra Reyes-García
creator: Jorge A. Meave
creator: Luz Maria Calvo-Irabien
creator: Filogonio May-Pat
creator: Juan M. Dupuy
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.9636
publisher: PeerJ Inc.
rights: © 2020 Saenz-Pedroza et al.
abstract: Tropical forests are globally important for biodiversity conservation and climate change mitigation but are being converted to other land uses. Conversion of seasonally dry tropical forests (SDTF) is particularly high while their protection is low. Secondary succession allows forests to recover their structure, diversity and composition after conversion and subsequent abandonment and is influenced by demographic rates of the constituent species. However, how these rates vary between seasons for different plant sizes at different successional stages in SDTF is not known. The effect of seasonal drought may be more severe early in succession, when temperature and radiation are high, while competition and density-dependent processes may be more important at later stages, when vegetation is tall and dense. Besides, the effects of seasonality and successional stage may vary with plant size. Large plants can better compete with small plants for limiting resources and may also have a greater capacity to withstand stress. We asked how size-dependent density, species density, recruitment and mortality varied between seasons and successional stages in a SDTF. We monitored a chronosequence in Yucatan, Mexico, over six years in three 0.1 ha plots in each of three successional stages: early (3–5 years-old), intermediate (18–20 years-old) and advanced (>50 years-old). Recruitment, mortality and species gain and loss rates were calculated from wet and dry season censuses separately for large (diameter > 5 cm) and small (1–5 cm in diameter) plants. We used linear mixed-effects models to assess the effects of successional stage, seasonality and their changes through time on demographic rates and on plant and species density. Seasonality affected demographic rates and density of large plants, which exhibited high wet-season recruitment and species gain rates at the early stage and high wet-season mortality at the intermediate stage, resulting in an increase in plant and species densit…
bibliographic citation: Saenz-Pedroza et al. (2020) Seasonal and successional dynamics of size-dependent plant demographic rates in a tropical dry forest. PeerJ 8:e9636 https://doi.org/10.7717/peerj.9636
date submitted: 2020-01-10
date accepted: 2020-07-09
issued: 2020-09-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saenz-Pedroza
  given name: Irving
author list: Agent
  family name: Feldman
  given name: Richard
author list: Agent
  family name: Reyes-García
  given name: Casandra
author list: Agent
  family name: Meave
  given name: Jorge A.
author list: Agent
  family name: Calvo-Irabien
  given name: Luz Maria
author list: Agent
  family name: May-Pat
  given name: Filogonio
author list: Agent
  family name: Dupuy
  given name: Juan M.
doi: 10.7717/peerj.9636
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-14
copyright: ©2020 Saenz-Pedroza et al.
attribution name: Saenz-Pedroza et al.

Rediscovery of Cyperus flavescens (Cyperaceae) on the northeast periphery of its range in Europe
type: item
type: AcademicArticle
description: In recent years, three large populations of Cyperus flavescens were found in Poland, the richest occurrence of this species in over 30 years. The goal of this research is to determine the habitat factors lead to the mass occurrence of C. flavescens and the present situation of that species and its habitat in Central Europe. Soil conditions of the three populations were studied. To determine the correlation between the occurrence and abundance of species and the chemical parameters of the soil, the DCA and CCA methods were used. The DCA of environmental Ellenberg values was made for all relevés known from Poland. The occurrence of C. flavescens in plant communities in Central Europe was studied. The maximum entropy method was used for potential distribution analysis of C. flavescens. All analyzed traits are important for this species and none has an advantage over another, so the environmental factor affecting the occurrence of C. flavescens is different from the tested. Analysis on Ellenberg values indicate that the longest gradients are temperature, moisture and nutrients. The analysis of vegetation data involving Cyperus flavescens available from Central Europe indicates that this species occurs mainly in the company of Juncus bufonius and Plantago intermedia, whereas other species of the Isoëto-Nanojuncetea class appear rarely. In MaxEnt analysis based on bioclimatic variables, the most important variable is BIO1 (Annual Mean Temperature). The results of our observation indicate that anthropogenic factors such as grazing livestock have a positive effect on the occurrence of the species. It is also very likely that the species is promoted by very warm summers with only short periods of heavy rains. A map of the potential distribution of C. flavescens in Central Europe created according historical and future data show an extension of the range of potential habitats to the north and east.
format: application/pdf
format: text/html
creator: Paweł Marciniuk
creator: Jolanta Marciniuk
creator: Andrzej Łysko
creator: Łukasz Krajewski
creator: Justyna Chudecka
creator: Janina Skrzyczyńska
creator: Agnieszka Anna Popiela
subject: Biodiversity
subject: Biogeography
subject: Bioinformatics
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.9837
publisher: PeerJ Inc.
rights: © 2020 Marciniuk et al.
abstract: In recent years, three large populations of Cyperus flavescens were found in Poland, the richest occurrence of this species in over 30 years. The goal of this research is to determine the habitat factors lead to the mass occurrence of C. flavescens and the present situation of that species and its habitat in Central Europe. Soil conditions of the three populations were studied. To determine the correlation between the occurrence and abundance of species and the chemical parameters of the soil, the DCA and CCA methods were used. The DCA of environmental Ellenberg values was made for all relevés known from Poland. The occurrence of C. flavescens in plant communities in Central Europe was studied. The maximum entropy method was used for potential distribution analysis of C. flavescens. All analyzed traits are important for this species and none has an advantage over another, so the environmental factor affecting the occurrence of C. flavescens is different from the tested. Analysis on Ellenberg values indicate that the longest gradients are temperature, moisture and nutrients. The analysis of vegetation data involving Cyperus flavescens available from Central Europe indicates that this species occurs mainly in the company of Juncus bufonius and Plantago intermedia, whereas other species of the Isoëto-Nanojuncetea class appear rarely. In MaxEnt analysis based on bioclimatic variables, the most important variable is BIO1 (Annual Mean Temperature). The results of our observation indicate that anthropogenic factors such as grazing livestock have a positive effect on the occurrence of the species. It is also very likely that the species is promoted by very warm summers with only short periods of heavy rains. A map of the potential distribution of C. flavescens in Central Europe created according historical and future data show an extension of the range of potential habitats to the north and east.
bibliographic citation: Marciniuk et al. (2020) Rediscovery of Cyperus flavescens (Cyperaceae) on the northeast periphery of its range in Europe. PeerJ 8:e9837 https://doi.org/10.7717/peerj.9837
date submitted: 2020-03-19
date accepted: 2020-08-07
issued: 2020-09-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marciniuk
  given name: Paweł
author list: Agent
  family name: Marciniuk
  given name: Jolanta
author list: Agent
  family name: Łysko
  given name: Andrzej
author list: Agent
  family name: Krajewski
  given name: Łukasz
author list: Agent
  family name: Chudecka
  given name: Justyna
author list: Agent
  family name: Skrzyczyńska
  given name: Janina
author list: Agent
  family name: Popiela
  given name: Agnieszka Anna
doi: 10.7717/peerj.9837
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-14
copyright: ©2020 Marciniuk et al.
attribution name: Marciniuk et al.

Potential role of cellular miRNAs in coronavirus-host interplay
type: item
type: AcademicArticle
description: Host miRNAs are known as important regulators of virus replication and pathogenesis. They can interact with various viruses through several possible mechanisms including direct binding of viral RNA. Identification of human miRNAs involved in coronavirus-host interplay becomes important due to the ongoing COVID-19 pandemic. In this article we performed computational prediction of high-confidence direct interactions between miRNAs and seven human coronavirus RNAs. As a result, we identified six miRNAs (miR-21-3p, miR-195-5p, miR-16-5p, miR-3065-5p, miR-424-5p and miR-421) with high binding probability across all analyzed viruses. Further bioinformatic analysis of binding sites revealed high conservativity of miRNA binding regions within RNAs of human coronaviruses and their strains. In order to discover the entire miRNA-virus interplay we further analyzed lungs miRNome of SARS-CoV infected mice using publicly available miRNA sequencing data. We found that miRNA miR-21-3p has the largest probability of binding the human coronavirus RNAs and being dramatically up-regulated in mouse lungs during infection induced by SARS-CoV.
format: application/pdf
format: text/html
creator: Stepan Nersisyan
creator: Narek Engibaryan
creator: Aleksandra Gorbonos
creator: Ksenia Kirdey
creator: Alexey Makhonin
creator: Alexander Tonevitsky
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Virology
subject: Medical Genetics
description: doi:10.7717/peerj.9994
publisher: PeerJ Inc.
rights: © 2020 Nersisyan et al.
abstract: Host miRNAs are known as important regulators of virus replication and pathogenesis. They can interact with various viruses through several possible mechanisms including direct binding of viral RNA. Identification of human miRNAs involved in coronavirus-host interplay becomes important due to the ongoing COVID-19 pandemic. In this article we performed computational prediction of high-confidence direct interactions between miRNAs and seven human coronavirus RNAs. As a result, we identified six miRNAs (miR-21-3p, miR-195-5p, miR-16-5p, miR-3065-5p, miR-424-5p and miR-421) with high binding probability across all analyzed viruses. Further bioinformatic analysis of binding sites revealed high conservativity of miRNA binding regions within RNAs of human coronaviruses and their strains. In order to discover the entire miRNA-virus interplay we further analyzed lungs miRNome of SARS-CoV infected mice using publicly available miRNA sequencing data. We found that miRNA miR-21-3p has the largest probability of binding the human coronavirus RNAs and being dramatically up-regulated in mouse lungs during infection induced by SARS-CoV.
bibliographic citation: Nersisyan et al. (2020) Potential role of cellular miRNAs in coronavirus-host interplay. PeerJ 8:e9994 https://doi.org/10.7717/peerj.9994
date submitted: 2020-07-08
date accepted: 2020-08-28
issued: 2020-09-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nersisyan
  given name: Stepan
author list: Agent
  family name: Engibaryan
  given name: Narek
author list: Agent
  family name: Gorbonos
  given name: Aleksandra
author list: Agent
  family name: Kirdey
  given name: Ksenia
author list: Agent
  family name: Makhonin
  given name: Alexey
author list: Agent
  family name: Tonevitsky
  given name: Alexander
doi: 10.7717/peerj.9994
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-14
copyright: © 2020 Nersisyan et al.
attribution name: Nersisyan et al.

Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles
type: item
type: AcademicArticle
description: Bark beetles are feared as pests in forestry but they also support a large number of other taxa that exploit the beetles and their galleries. Among arthropods, mites are the largest taxon associated with bark beetles. Many of these mites are phoretic and often involved in complex interactions with the beetles and other organisms. Within the oribatid mite family Scheloribatidae, only two of the three nominal species of Paraleius have been frequently found in galleries of bark beetles and on the beetles themselves. One of the species, P. leontonychus, has a wide distribution range spanning over three ecozones of the world and is believed to be a host generalist, reported from numerous bark beetle and tree species. In the present study, phylogenetic analyses of one mitochondrial and two nuclear genes identified six well supported, fairly divergent clades within P. leontonychus which we consider to represent distinct species based on molecular species delimitation methods and largely congruent clustering in mitochondrial and nuclear gene trees. These species do not tend to be strictly host specific and might occur syntopically. Moreover, mito-nuclear discordance indicates a case of past hybridization/introgression among distinct Paraleius species, the first case of interspecific hybridization reported in mites other than ticks.
format: application/pdf
format: text/html
creator: Sylvia Schäffer
creator: Stephan Koblmüller
subject: Biodiversity
subject: Entomology
subject: Evolutionary Studies
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.9710
publisher: PeerJ Inc.
rights: © 2020 Schäffer and Koblmüller
abstract: Bark beetles are feared as pests in forestry but they also support a large number of other taxa that exploit the beetles and their galleries. Among arthropods, mites are the largest taxon associated with bark beetles. Many of these mites are phoretic and often involved in complex interactions with the beetles and other organisms. Within the oribatid mite family Scheloribatidae, only two of the three nominal species of Paraleius have been frequently found in galleries of bark beetles and on the beetles themselves. One of the species, P. leontonychus, has a wide distribution range spanning over three ecozones of the world and is believed to be a host generalist, reported from numerous bark beetle and tree species. In the present study, phylogenetic analyses of one mitochondrial and two nuclear genes identified six well supported, fairly divergent clades within P. leontonychus which we consider to represent distinct species based on molecular species delimitation methods and largely congruent clustering in mitochondrial and nuclear gene trees. These species do not tend to be strictly host specific and might occur syntopically. Moreover, mito-nuclear discordance indicates a case of past hybridization/introgression among distinct Paraleius species, the first case of interspecific hybridization reported in mites other than ticks.
bibliographic citation: Schäffer et al. (2020) Unexpected diversity in the host-generalist oribatid mite Paraleius leontonychus (Oribatida, Scheloribatidae) phoretic on Palearctic bark beetles. PeerJ 8:e9710 https://doi.org/10.7717/peerj.9710
date submitted: 2020-05-20
date accepted: 2020-07-23
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schäffer
  given name: Sylvia
author list: Agent
  family name: Koblmüller
  given name: Stephan
doi: 10.7717/peerj.9710
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: © 2020 Schäffer and Koblmüller
attribution name: Schäffer and Koblmüller

The impact of climate change on flow conditions and wetland ecosystems in the Lower Biebrza River (Poland)
type: item
type: AcademicArticle
description: Water plays a key role in the functioning of wetlands and a shortage or contamination of it leads to changes in habitat conditions and degradation of ecosystems. This article scrutinizes the impact of climate change on the hydrological characteristics of floods (maximum flow, duration, volume) in the River Biebrza wetlands (North-East Poland). We analysed the trends in duration and volume of flood and maximum discharges in the historical period 1970–2000 and predicted these for the future periods 2020–2050 and 2070–2100, respectively. Next we assessed the impact on the wetland ecosystems. The basis of our assessments consists of statistical analyses of hydrographs and calculations by the Soil and Water Assessment Tool hydrological model and considering nine bias-corrected climate models. The results indicate that both volume and duration of winter floods will keep increasing continuously under Representative Concentration Pathways 4.5 and 8.5. The reduction in peak annual floods is expected to decline slightly in both scenarios. On the other hand, the analysis of trends in mean and standard deviation revealed negligible tendencies in the datasets for summer and winter hydrological seasons within the three time frames analysed (1970–2000; 2020–2050; 2070–2100). We foresee several future implications for the floodplain ecosystems. Shifts in transversal ecosystem zonation parallel to the river will likely take place with more highly productive flood tolerant vegetation types. Nutrient availability and algal blooms during spring inundations will likely increase. Slowdown of organic matter turnover later in summer will lead to a higher peat accumulation rate. Logistical problems with summer mowing and removal of bushes in winter may enhance shrub encroachment.
format: application/pdf
format: text/html
creator: Dorota Mirosław-Świątek
creator: Paweł Marcinkowski
creator: Krzysztof Kochanek
creator: Martin J. Wassen
subject: Ecosystem Science
subject: Climate Change Biology
subject: Ecohydrology
subject: Environmental Impacts
description: doi:10.7717/peerj.9778
publisher: PeerJ Inc.
rights: © 2020 Mirosław-Świątek et al.
abstract: Water plays a key role in the functioning of wetlands and a shortage or contamination of it leads to changes in habitat conditions and degradation of ecosystems. This article scrutinizes the impact of climate change on the hydrological characteristics of floods (maximum flow, duration, volume) in the River Biebrza wetlands (North-East Poland). We analysed the trends in duration and volume of flood and maximum discharges in the historical period 1970–2000 and predicted these for the future periods 2020–2050 and 2070–2100, respectively. Next we assessed the impact on the wetland ecosystems. The basis of our assessments consists of statistical analyses of hydrographs and calculations by the Soil and Water Assessment Tool hydrological model and considering nine bias-corrected climate models. The results indicate that both volume and duration of winter floods will keep increasing continuously under Representative Concentration Pathways 4.5 and 8.5. The reduction in peak annual floods is expected to decline slightly in both scenarios. On the other hand, the analysis of trends in mean and standard deviation revealed negligible tendencies in the datasets for summer and winter hydrological seasons within the three time frames analysed (1970–2000; 2020–2050; 2070–2100). We foresee several future implications for the floodplain ecosystems. Shifts in transversal ecosystem zonation parallel to the river will likely take place with more highly productive flood tolerant vegetation types. Nutrient availability and algal blooms during spring inundations will likely increase. Slowdown of organic matter turnover later in summer will lead to a higher peat accumulation rate. Logistical problems with summer mowing and removal of bushes in winter may enhance shrub encroachment.
bibliographic citation: Mirosław-Świątek et al. (2020) The impact of climate change on flow conditions and wetland ecosystems in the Lower Biebrza River (Poland). PeerJ 8:e9778 https://doi.org/10.7717/peerj.9778
date submitted: 2020-03-03
date accepted: 2020-07-30
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mirosław-Świątek
  given name: Dorota
author list: Agent
  family name: Marcinkowski
  given name: Paweł
author list: Agent
  family name: Kochanek
  given name: Krzysztof
author list: Agent
  family name: Wassen
  given name: Martin J.
doi: 10.7717/peerj.9778
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: © 2020 Mirosław-Świątek et al.
attribution name: Mirosław-Świątek et al.

Methylase-assisted subcloning for high throughput BioBrick assembly
type: item
type: AcademicArticle
description: The BioBrick standard makes possible iterated pairwise assembly of cloned parts without any depletion of unique restriction sites. Every part that conforms to the standard is compatible with every other part, thereby fostering a worldwide user community. The assembly methods, however, are labor intensive or inefficient compared to some newer ones so the standard may be falling out of favor. An easier way to assemble BioBricks is described herein. Plasmids encoding BioBrick parts are purified from Escherichia coli cells that express a foreign site-specific DNA methyltransferase, so that each is subsequently protected in vitro from the activity of a particular restriction endonuclease. Each plasmid is double-digested and all resulting restriction fragments are ligated together without gel purification. The ligation products are subsequently double-digested with another pair of restriction endonucleases so only the desired insert-recipient vector construct retains the capacity to transform E. coli. This 4R/2M BioBrick assembly protocol is more efficient and accurate than established workflows including 3A assembly. It is also much easier than gel purification to miniaturize, automate and perform more assembly reactions in parallel. As such, it should streamline DNA assembly for the existing community of BioBrick users, and possibly encourage others to join.
format: application/pdf
format: text/html
creator: Ichiro Matsumura
subject: Bioengineering
subject: Molecular Biology
subject: Synthetic Biology
description: doi:10.7717/peerj.9841
publisher: PeerJ Inc.
rights: © 2020 Matsumura
abstract: The BioBrick standard makes possible iterated pairwise assembly of cloned parts without any depletion of unique restriction sites. Every part that conforms to the standard is compatible with every other part, thereby fostering a worldwide user community. The assembly methods, however, are labor intensive or inefficient compared to some newer ones so the standard may be falling out of favor. An easier way to assemble BioBricks is described herein. Plasmids encoding BioBrick parts are purified from Escherichia coli cells that express a foreign site-specific DNA methyltransferase, so that each is subsequently protected in vitro from the activity of a particular restriction endonuclease. Each plasmid is double-digested and all resulting restriction fragments are ligated together without gel purification. The ligation products are subsequently double-digested with another pair of restriction endonucleases so only the desired insert-recipient vector construct retains the capacity to transform E. coli. This 4R/2M BioBrick assembly protocol is more efficient and accurate than established workflows including 3A assembly. It is also much easier than gel purification to miniaturize, automate and perform more assembly reactions in parallel. As such, it should streamline DNA assembly for the existing community of BioBrick users, and possibly encourage others to join.
bibliographic citation: Matsumura (2020) Methylase-assisted subcloning for high throughput BioBrick assembly. PeerJ 8:e9841 https://doi.org/10.7717/peerj.9841
date submitted: 2020-04-27
date accepted: 2020-08-10
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matsumura
  given name: Ichiro
doi: 10.7717/peerj.9841
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: ©2020 Matsumura
attribution name: Matsumura

ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences
type: item
type: AcademicArticle
description: Biominerals are crucial to the fitness of many organism and studies of the mechanisms of biomineralization are driving research into novel materials. Biomineralization is generally controlled by a matrix of organic molecules including proteins, so proteomic studies of biominerals are important for understanding biomineralization mechanisms. Many such studies identify large numbers of proteins of unknown function, which are often of low sequence complexity and biased in their amino acid composition. A lack of user-friendly tools to find patterns in such sequences and robustly analyse their statistical properties relative to the background proteome means that they are often neglected in follow-up studies. Here we present ProminTools, a user-friendly package for comparison of two sets of protein sequences in terms of their global properties and motif content. Outputs include data tables, graphical summaries in an html file and an R-script as a starting point for data-set specific visualizations. We demonstrate the utility of ProminTools using a previously published shell matrix proteome of the giant limpet Lottia gigantea.
format: application/pdf
format: text/html
creator: Alastair W. Skeffington
creator: Andreas Donath
subject: Biochemistry
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.9852
publisher: PeerJ Inc.
rights: © 2020 Skeffington and Donath
abstract: Biominerals are crucial to the fitness of many organism and studies of the mechanisms of biomineralization are driving research into novel materials. Biomineralization is generally controlled by a matrix of organic molecules including proteins, so proteomic studies of biominerals are important for understanding biomineralization mechanisms. Many such studies identify large numbers of proteins of unknown function, which are often of low sequence complexity and biased in their amino acid composition. A lack of user-friendly tools to find patterns in such sequences and robustly analyse their statistical properties relative to the background proteome means that they are often neglected in follow-up studies. Here we present ProminTools, a user-friendly package for comparison of two sets of protein sequences in terms of their global properties and motif content. Outputs include data tables, graphical summaries in an html file and an R-script as a starting point for data-set specific visualizations. We demonstrate the utility of ProminTools using a previously published shell matrix proteome of the giant limpet Lottia gigantea.
bibliographic citation: Skeffington et al. (2020) ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences. PeerJ 8:e9852 https://doi.org/10.7717/peerj.9852
date submitted: 2020-04-14
date accepted: 2020-08-11
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Skeffington
  given name: Alastair W.
author list: Agent
  family name: Donath
  given name: Andreas
doi: 10.7717/peerj.9852
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: ©2020 Skeffington and Donath
attribution name: Skeffington and Donath

Intergenerational implications of alcohol intake: metabolic disorders in alcohol-naïve rat offspring
type: item
type: AcademicArticle
description: Alcohol drinking may be associated with an increased risk of various metabolic diseases. Rat lines selectively bred for alcohol preference and alcohol avoidance constitute an interesting model to study inherited factors related to alcohol drinking and metabolic disorders. The aim of the present study was to compare the levels of selected laboratory biomarkers of metabolic disorders in blood samples from naïve offspring of Warsaw alcohol high-preferring (WHP), Warsaw alcohol low-preferring (WLP), and wild Wistar rats. Blood samples were collected from 3-month old (300–350 g) alcohol-naïve, male offspring of WHP (n = 8) and WLP rats (n = 8), as well as alcohol-naïve, male, wild Wistar rats. Markers of metabolic, hepatic, and pancreatic disorders were analysed (levels of homocysteine, glucose, total cholesterol, triglycerides and γ-glutamyl transferase (GGT), aspartate (AST), alanine aminotransferase (ALT), and amylase serum activities). Alcohol-naïve offspring of WHP, WLP, and wild Wistar rats differed significantly in the levels of triglycerides, total cholesterol, homocysteine, as well as in the activity of GGT, ALT, AST, and amylase enzymes. Most markers in the alcohol-naïve offspring of WHP rats were altered even thought they were never exposed to alcohol pre- or postnatally. This may suggest that parental alcohol abuse can have a detrimental influence on offspring vulnerability to metabolic disorders.
format: application/pdf
format: text/html
creator: Pawel Mierzejewski
creator: Alicja Zakrzewska
creator: Julita Kuczyńska
creator: Edyta Wyszogrodzka
creator: Monika Dominiak
subject: Biochemistry
subject: Genetics
subject: Psychiatry and Psychology
subject: Metabolic Sciences
description: doi:10.7717/peerj.9886
publisher: PeerJ Inc.
rights: © 2020 Mierzejewski et al.
abstract: Alcohol drinking may be associated with an increased risk of various metabolic diseases. Rat lines selectively bred for alcohol preference and alcohol avoidance constitute an interesting model to study inherited factors related to alcohol drinking and metabolic disorders. The aim of the present study was to compare the levels of selected laboratory biomarkers of metabolic disorders in blood samples from naïve offspring of Warsaw alcohol high-preferring (WHP), Warsaw alcohol low-preferring (WLP), and wild Wistar rats. Blood samples were collected from 3-month old (300–350 g) alcohol-naïve, male offspring of WHP (n = 8) and WLP rats (n = 8), as well as alcohol-naïve, male, wild Wistar rats. Markers of metabolic, hepatic, and pancreatic disorders were analysed (levels of homocysteine, glucose, total cholesterol, triglycerides and γ-glutamyl transferase (GGT), aspartate (AST), alanine aminotransferase (ALT), and amylase serum activities). Alcohol-naïve offspring of WHP, WLP, and wild Wistar rats differed significantly in the levels of triglycerides, total cholesterol, homocysteine, as well as in the activity of GGT, ALT, AST, and amylase enzymes. Most markers in the alcohol-naïve offspring of WHP rats were altered even thought they were never exposed to alcohol pre- or postnatally. This may suggest that parental alcohol abuse can have a detrimental influence on offspring vulnerability to metabolic disorders.
bibliographic citation: Mierzejewski et al. (2020) Intergenerational implications of alcohol intake: metabolic disorders in alcohol-naïve rat offspring. PeerJ 8:e9886 https://doi.org/10.7717/peerj.9886
date submitted: 2020-03-13
date accepted: 2020-08-16
issued: 2020-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mierzejewski
  given name: Pawel
author list: Agent
  family name: Zakrzewska
  given name: Alicja
author list: Agent
  family name: Kuczyńska
  given name: Julita
author list: Agent
  family name: Wyszogrodzka
  given name: Edyta
author list: Agent
  family name: Dominiak
  given name: Monika
doi: 10.7717/peerj.9886
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-11
copyright: ©2020 Mierzejewski et al.
attribution name: Mierzejewski et al.

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