PeerJ Preprints
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Articles published in PeerJ Preprints
PeerJ Inc.
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PeerJ Preprints
2167-9843
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https://peerj.com/preprints/28002v3
A simplified correlation between vertebrate evolution and Paleozoic geomagnetism
Background. Despite a fifty-year failure of paleontologists to find a viable connection between geomagnetic polarity reversals and evolutionary patterns, recent paleobiology databases show that the early appearance, radiation, and diversification of Paleozoic vertebrates tends to occur during periods having frequent collapses of the Earth’s geomagnetic field. The transition time during the collapse of the Earth’s protective magnetic shield can last thousands of years, and the effects on biota are unknown. Solar and cosmic radiation, volcanism, climate alteration, low-frequency electromagnetic fields, depletion of ozone, the stripping of atmospheric oxygen, and increasing production of Carbon14 in the stratosphere have been proposed as possible causes, but previous studies have found no effects.
Methods. Using published databases, we compiled a spreadsheet showing the first appearance of 2104 genera with each genus assigned to one of 8 major taxonomic groups. From Gradstein’s Geologic Time Scale 2012, we delineated 17 Paleozoic zones with either high or low levels of polarity reversals.
Results. From our compilation, 727 Paleozoic vertebrates represent the initial radiation and diversification of individual Paleozoic vertebrate clades. After compensating for sample-size and external geologic and sampling biases, the resulting Pearson’s correlation coefficient between the 727 genera and geomagnetic polarity zones equals 0.8, a result that suggests a strong relationship exists between Paleozoic vertebrates and geomagnetism.
Discussion. The question: is this apparent connection between geomagnetism and the evolution of Paleozoic vertebrate due to environmental or biologic factors. If biologic, why are vertebrates the only biota effected? And after an indeterminate period of time, how do vertebrates become immune to the ongoing effects of polarity reversals?
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doi:10.7287/peerj.preprints.28002v3
A simplified correlation between vertebrate evolution and Paleozoic geomagnetism
John P Staub
Evolutionary Studies
Paleontology
doi:10.7287/peerj.preprints.28002v3
PeerJ Inc.
© 2019 Staub
Background. Despite a fifty-year failure of paleontologists to find a viable connection between geomagnetic polarity reversals and evolutionary patterns, recent paleobiology databases show that the early appearance, radiation, and diversification of Paleozoic vertebrates tends to occur during periods having frequent collapses of the Earth’s geomagnetic field. The transition time during the collapse of the Earth’s protective magnetic shield can last thousands of years, and the effects on biota are unknown. Solar and cosmic radiation, volcanism, climate alteration, low-frequency electromagnetic fields, depletion of ozone, the stripping of atmospheric oxygen, and increasing production of Carbon14 in the stratosphere have been proposed as possible causes, but previous studies have found no effects.
Methods. Using published databases, we compiled a spreadsheet showing the first appearance of 2104 genera with each genus assigned to one of 8 major taxonomic groups. From Gradstein’s Geologic Time Scale 2012, we delineated 17 Paleozoic zones with either high or low levels of polarity reversals.
Results. From our compilation, 727 Paleozoic vertebrates represent the initial radiation and diversification of individual Paleozoic vertebrate clades. After compensating for sample-size and external geologic and sampling biases, the resulting Pearson’s correlation coefficient between the 727 genera and geomagnetic polarity zones equals 0.8, a result that suggests a strong relationship exists between Paleozoic vertebrates and geomagnetism.
Discussion. The question: is this apparent connection between geomagnetism and the evolution of Paleozoic vertebrate due to environmental or biologic factors. If biologic, why are vertebrates the only biota effected? And after an indeterminate period of time, how do vertebrates become immune to the ongoing effects of polarity reversals?
Staub (2019) A simplified correlation between vertebrate evolution and Paleozoic geomagnetism. PeerJ Preprints 7:e28002v3 https://doi.org/10.7287/peerj.preprints.28002v3
2019-12-31
2019-12-31
Staub
John P
10.7287/peerj.preprints.28002v3
https://peerj.com/preprints/28002v3
7
https://peerj.com/preprints/28002v3
10.7287/peerj.preprints.28002v3
2167-9843
7
PeerJ Preprints
2019-12-31
© 2019 Staub
Staub
-
https://peerj.com/preprints/28004v3
Development and application of a robotic zebra finch (RoboFinch) to study multimodal cues in vocal communication
Understanding animal behaviour through psychophysical experimentation is often limited by insufficiently realistic stimulus representation. Important physical dimensions of signals and cues, especially those that are outside the spectrum of human perception, can be difficult to standardize and control separately with currently available recording and displaying techniques (e.g. video displays). Accurate stimulus control is in particular important when studying multimodal signals, as spatial and temporal alignment between stimuli is often crucial. Especially for audiovisual presentations, some of these limitations can be circumvented by the employment of animal robots that are superior to video presentations in all situations requiring realistic 3D presentations to animals. Here we report the development of a robotic zebra finch, called RoboFinch, and how it can be used to study vocal learning in a songbird, the zebra finch.
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text/html
doi:10.7287/peerj.preprints.28004v3
Development and application of a robotic zebra finch (RoboFinch) to study multimodal cues in vocal communication
Ralph Simon
Judith Varkevisser
Ezequiel Mendoza
Klaus Hochradel
Constance Scharff
Katharina Riebel
Wouter Halfwerk
Animal Behavior
Ecology
Zoology
doi:10.7287/peerj.preprints.28004v3
PeerJ Inc.
© 2019 Simon et al.
Understanding animal behaviour through psychophysical experimentation is often limited by insufficiently realistic stimulus representation. Important physical dimensions of signals and cues, especially those that are outside the spectrum of human perception, can be difficult to standardize and control separately with currently available recording and displaying techniques (e.g. video displays). Accurate stimulus control is in particular important when studying multimodal signals, as spatial and temporal alignment between stimuli is often crucial. Especially for audiovisual presentations, some of these limitations can be circumvented by the employment of animal robots that are superior to video presentations in all situations requiring realistic 3D presentations to animals. Here we report the development of a robotic zebra finch, called RoboFinch, and how it can be used to study vocal learning in a songbird, the zebra finch.
Simon et al. (2019) Development and application of a robotic zebra finch (RoboFinch) to study multimodal cues in vocal communication. PeerJ Preprints 7:e28004v3 https://doi.org/10.7287/peerj.preprints.28004v3
2019-12-30
2019-12-30
Simon
Ralph
Varkevisser
Judith
Mendoza
Ezequiel
Hochradel
Klaus
Scharff
Constance
Riebel
Katharina
Halfwerk
Wouter
10.7287/peerj.preprints.28004v3
https://peerj.com/preprints/28004v3
7
https://peerj.com/preprints/28004v3
10.7287/peerj.preprints.28004v3
2167-9843
7
PeerJ Preprints
2019-12-30
© 2019 Simon et al.
Simon et al.
-
https://peerj.com/preprints/27391
Isolation and characterization of psychrotrophic proteolytic bacteria from landfill site under temperate climatic conditions of Kashmir Himalaya
The temperate climatic regions face the problem of waste accumulation due to lower environmental temperatures. However, these regions harbor cold active microbes viz. psychrotrophic proteolytic bacteria that play an important role in the degradation of protenaceous materials of the waste stream. Hence in the present study psychrotrophic proteolytic bacteria were isolated from waste samples collected from landfill site by using random sampling method under environmental temperature of 10oC. By using serial dilution and spread plate technique a total of 8 morphologically different psychrotrophic proteolytic bacteria were isolated on skim milk agar media at pH of 7.0 and temperature of 10°C after 48hours. Under in-vitro conditions all the isolates produced significant quantities of protease over the control and diameters of hydrolysis zones ranged between 2 to 18 mm at temperature range of 5 to 20oC and after 72 hours. The corresponding quantitative protease activities of the isolates was significant that ranged between 0.5 to 2.25 U/ml and the isolate PB2 was most efficient with highest protease activity of 2.25U/ml at 20oC. Based on 16SrRNA analysis the isolate was identified as Pseudomonas florescence with 96% similarity. It was concluded that the isolates can grow in wide ranges of temperature and could be used for enhanced decomposition of organic wastes during lower temperature conditions in cold regions. Further the isolates could have industrial applications due to the production of cold active proteases that would help economic benefits through energy conservation.
application/pdf
text/html
doi:10.7287/peerj.preprints.27391v2
Isolation and characterization of psychrotrophic proteolytic bacteria from landfill site under temperate climatic conditions of Kashmir Himalaya
Basharat Hamid
Arshid Jehangir
Zahoor Ahmad Baba
Muneer Ahmad Wani
Imran Khan
Agricultural Science
Biotechnology
Ecosystem Science
Microbiology
Environmental Contamination and Remediation
doi:10.7287/peerj.preprints.27391v2
PeerJ Inc.
© 2019 Hamid et al.
The temperate climatic regions face the problem of waste accumulation due to lower environmental temperatures. However, these regions harbor cold active microbes viz. psychrotrophic proteolytic bacteria that play an important role in the degradation of protenaceous materials of the waste stream. Hence in the present study psychrotrophic proteolytic bacteria were isolated from waste samples collected from landfill site by using random sampling method under environmental temperature of 10oC. By using serial dilution and spread plate technique a total of 8 morphologically different psychrotrophic proteolytic bacteria were isolated on skim milk agar media at pH of 7.0 and temperature of 10°C after 48hours. Under in-vitro conditions all the isolates produced significant quantities of protease over the control and diameters of hydrolysis zones ranged between 2 to 18 mm at temperature range of 5 to 20oC and after 72 hours. The corresponding quantitative protease activities of the isolates was significant that ranged between 0.5 to 2.25 U/ml and the isolate PB2 was most efficient with highest protease activity of 2.25U/ml at 20oC. Based on 16SrRNA analysis the isolate was identified as Pseudomonas florescence with 96% similarity. It was concluded that the isolates can grow in wide ranges of temperature and could be used for enhanced decomposition of organic wastes during lower temperature conditions in cold regions. Further the isolates could have industrial applications due to the production of cold active proteases that would help economic benefits through energy conservation.
Hamid et al. (2019) Isolation and characterization of psychrotrophic proteolytic bacteria from landfill site under temperate climatic conditions of Kashmir Himalaya. PeerJ Preprints 7:e27391v2 https://doi.org/10.7287/peerj.preprints.27391v2
2019-12-21
2019-12-21
Hamid
Basharat
Jehangir
Arshid
Baba
Zahoor Ahmad
Wani
Muneer Ahmad
Khan
Imran
10.7287/peerj.preprints.27391v2
https://peerj.com/preprints/27391
7
https://peerj.com/preprints/27391
10.7287/peerj.preprints.27391v2
2167-9843
7
PeerJ Preprints
2019-12-21
© 2019 Hamid et al.
Hamid et al.
-
https://peerj.com/preprints/27829
Data-driven classification of the certainty of scholarly assertions
The grammatical structures scholars use to express their assertions are intended to convey various degrees of certainty or speculation. Prior studies have suggested a variety of categorization systems for scholarly certainty; however, these have not been objectively tested for their validity, particularly with respect to representing the interpretation by the reader, rather than the intention of the author. In this study, we use a series of questionnaires to determine how researchers classify various scholarly assertions, using three distinct certainty classification systems. We find that there are three distinct categories of certainty along a spectrum from high to low. We show that these categories can be detected in an automated manner, using a machine learning model, with a cross-validation accuracy of 89.2% relative to an author-annotated corpus, and 82.2% accuracy against a publicly-annotated corpus. This finding provides an opportunity for contextual metadata related to certainty to be captured as a part of text-mining pipelines, which currently miss these subtle linguistic cues. We provide an exemplar machine-accessible representation - a Nanopublication - where certainty category is embedded as metadata in a formal, ontology-based manner within text-mined scholarly assertions.
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text/html
doi:10.7287/peerj.preprints.27829v2
Data-driven classification of the certainty of scholarly assertions
Mario Prieto
Helena Deus
Anita De Waard
Erik Schultes
Beatriz García-Jiménez
Mark D Wilkinson
Bioinformatics
Computational Science
Data Mining and Machine Learning
doi:10.7287/peerj.preprints.27829v2
PeerJ Inc.
© 2019 Prieto et al.
The grammatical structures scholars use to express their assertions are intended to convey various degrees of certainty or speculation. Prior studies have suggested a variety of categorization systems for scholarly certainty; however, these have not been objectively tested for their validity, particularly with respect to representing the interpretation by the reader, rather than the intention of the author. In this study, we use a series of questionnaires to determine how researchers classify various scholarly assertions, using three distinct certainty classification systems. We find that there are three distinct categories of certainty along a spectrum from high to low. We show that these categories can be detected in an automated manner, using a machine learning model, with a cross-validation accuracy of 89.2% relative to an author-annotated corpus, and 82.2% accuracy against a publicly-annotated corpus. This finding provides an opportunity for contextual metadata related to certainty to be captured as a part of text-mining pipelines, which currently miss these subtle linguistic cues. We provide an exemplar machine-accessible representation - a Nanopublication - where certainty category is embedded as metadata in a formal, ontology-based manner within text-mined scholarly assertions.
Prieto et al. (2019) Data-driven classification of the certainty of scholarly assertions. PeerJ Preprints 7:e27829v2 https://doi.org/10.7287/peerj.preprints.27829v2
2019-12-20
2019-12-20
Prieto
Mario
Deus
Helena
De Waard
Anita
Schultes
Erik
García-Jiménez
Beatriz
Wilkinson
Mark D
10.7287/peerj.preprints.27829v2
https://peerj.com/preprints/27829
7
https://peerj.com/preprints/27829
10.7287/peerj.preprints.27829v2
2167-9843
7
PeerJ Preprints
2019-12-20
© 2019 Prieto et al.
Prieto et al.
-
https://peerj.com/preprints/26877
A roadmap for gene functional characterisation in wheat
To adapt to the challenges of climate change and the growing world population, it is vital to increase global crop production. Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite the importance of wheat, which provides 20 % of the calories consumed by humankind, a lack of genomic information and resources has hindered the functional characterisation of genes in this species. The recent release of a high-quality reference sequence for wheat underpins a suite of genetic and genomic resources that support basic research and breeding. These include accurate gene model annotations, gene expression atlases and gene networks that provide background information about putative gene function. In parallel, sequenced mutation populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources to study gene function in wheat and thereby accelerate improvement in this important crop. We hope that this review provides a helpful guide for plant scientists, especially those expanding into wheat research for the first time, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of wheat, a complex polyploid crop, of vital importance for food and nutrition security.
application/pdf
text/html
doi:10.7287/peerj.preprints.26877v2
A roadmap for gene functional characterisation in wheat
Nikolai M Adamski
Philippa Borrill
Jemima Brinton
Sophie Harrington
Clemence Marchal
Alison R Bentley
Wiliam D Bovill
Luigi Cattivelli
James Cockram
Bruno Contreras-Moreira
Brett Ford
Sreya Ghosh
Wendy Harwood
Keywan Hassani-Pak
Sadiye Hayta
Lee T Hickey
Kostya Kanyuka
Julie King
Marco Maccaferri
Guy Naamati
Curtis J Pozniak
Ricardo H Ramirez-Gonzalez
Carolina Sansaloni
Ben Trevaskis
Luzie U Wingen
Brande BH Wulff
Cristobal Uauy
Genomics
Plant Science
doi:10.7287/peerj.preprints.26877v2
PeerJ Inc.
© 2019 Adamski et al.
To adapt to the challenges of climate change and the growing world population, it is vital to increase global crop production. Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite the importance of wheat, which provides 20 % of the calories consumed by humankind, a lack of genomic information and resources has hindered the functional characterisation of genes in this species. The recent release of a high-quality reference sequence for wheat underpins a suite of genetic and genomic resources that support basic research and breeding. These include accurate gene model annotations, gene expression atlases and gene networks that provide background information about putative gene function. In parallel, sequenced mutation populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources to study gene function in wheat and thereby accelerate improvement in this important crop. We hope that this review provides a helpful guide for plant scientists, especially those expanding into wheat research for the first time, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of wheat, a complex polyploid crop, of vital importance for food and nutrition security.
Adamski et al. (2019) A roadmap for gene functional characterisation in wheat. PeerJ Preprints 7:e26877v2 https://doi.org/10.7287/peerj.preprints.26877v2
2019-12-18
2019-12-18
Adamski
Nikolai M
Borrill
Philippa
Brinton
Jemima
Harrington
Sophie
Marchal
Clemence
Bentley
Alison R
Bovill
Wiliam D
Cattivelli
Luigi
Cockram
James
Contreras-Moreira
Bruno
Ford
Brett
Ghosh
Sreya
Harwood
Wendy
Hassani-Pak
Keywan
Hayta
Sadiye
Hickey
Lee T
Kanyuka
Kostya
King
Julie
Maccaferri
Marco
Naamati
Guy
Pozniak
Curtis J
Ramirez-Gonzalez
Ricardo H
Sansaloni
Carolina
Trevaskis
Ben
Wingen
Luzie U
Wulff
Brande BH
Uauy
Cristobal
10.7287/peerj.preprints.26877v2
https://peerj.com/preprints/26877
7
https://peerj.com/preprints/26877
10.7287/peerj.preprints.26877v2
2167-9843
7
PeerJ Preprints
2019-12-18
© 2019 Adamski et al.
Adamski et al.
-
https://peerj.com/preprints/27879
An introduction to phylosymbiosis
Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as “microbial community relationships that recapitulate the phylogeny of their host”, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host-microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host-microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modeling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual, and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigations from a diversity of disciplines.
application/pdf
text/html
doi:10.7287/peerj.preprints.27879v2
An introduction to phylosymbiosis
Shen Jean Lim
Seth R Bordenstein
Biodiversity
Bioinformatics
Evolutionary Studies
Microbiology
doi:10.7287/peerj.preprints.27879v2
PeerJ Inc.
© 2019 Lim et al.
Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as “microbial community relationships that recapitulate the phylogeny of their host”, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host-microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host-microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modeling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual, and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigations from a diversity of disciplines.
Lim et al. (2019) An introduction to phylosymbiosis. PeerJ Preprints 7:e27879v2 https://doi.org/10.7287/peerj.preprints.27879v2
2019-12-11
2019-12-11
Lim
Shen Jean
Bordenstein
Seth R
10.7287/peerj.preprints.27879v2
https://peerj.com/preprints/27879
7
https://peerj.com/preprints/27879
10.7287/peerj.preprints.27879v2
2167-9843
7
PeerJ Preprints
2019-12-11
© 2019 Lim et al.
Lim et al.
-
https://peerj.com/preprints/27353
Seven myths on crowding and peripheral vision
Crowding has become a hot topic in vision research and some fundamentals are now widely agreed upon. For the classical crowding task, one would likely agree with the following statements. (1) Bouma’s law can, succinctly and unequivocally, be stated as saying that critical distance for crowding is about half the target’s eccentricity. (2) Crowding is predominantly a peripheral phenomenon. (3) Peripheral vision extends to at most 90° eccentricity. (4) Resolution threshold (the minimal angle of resolution, MAR) increases strongly and linearly with eccentricity. Crowding increases at an even steeper rate. (5) Crowding is asymmetric as Bouma has shown. For that inner-outer asymmetry, the peripheral flanker has more effect. (6) Critical crowding distance corresponds to a constant cortical distance in primary visual areas like V1. (7) Except for Bouma’s seminal paper in 1970, crowding research mostly became prominent starting in the 2000s. I propose the answer is ‘not really’ or ‘not quite’ to these assertions. So should we care? I think we should, before we write the textbook chapters for the next generation.
application/pdf
text/html
doi:10.7287/peerj.preprints.27353v4
Seven myths on crowding and peripheral vision
Hans Strasburger
Computational Biology
Neuroscience
Anatomy and Physiology
Ophthalmology
Psychiatry and Psychology
doi:10.7287/peerj.preprints.27353v4
PeerJ Inc.
© 2019 Strasburger
Crowding has become a hot topic in vision research and some fundamentals are now widely agreed upon. For the classical crowding task, one would likely agree with the following statements. (1) Bouma’s law can, succinctly and unequivocally, be stated as saying that critical distance for crowding is about half the target’s eccentricity. (2) Crowding is predominantly a peripheral phenomenon. (3) Peripheral vision extends to at most 90° eccentricity. (4) Resolution threshold (the minimal angle of resolution, MAR) increases strongly and linearly with eccentricity. Crowding increases at an even steeper rate. (5) Crowding is asymmetric as Bouma has shown. For that inner-outer asymmetry, the peripheral flanker has more effect. (6) Critical crowding distance corresponds to a constant cortical distance in primary visual areas like V1. (7) Except for Bouma’s seminal paper in 1970, crowding research mostly became prominent starting in the 2000s. I propose the answer is ‘not really’ or ‘not quite’ to these assertions. So should we care? I think we should, before we write the textbook chapters for the next generation.
Strasburger (2019) Seven myths on crowding and peripheral vision. PeerJ Preprints 7:e27353v4 https://doi.org/10.7287/peerj.preprints.27353v4
2019-12-06
2019-12-06
Strasburger
Hans
10.7287/peerj.preprints.27353v4
https://peerj.com/preprints/27353
7
https://peerj.com/preprints/27353
10.7287/peerj.preprints.27353v4
2167-9843
7
PeerJ Preprints
2019-12-06
© 2019 Strasburger
Strasburger
-
https://peerj.com/preprints/27989
A simple method for the selective quantification of polyethylene, polypropylene, and polystyrene plastic debris in soil by pyrolysis-gas chromatography/mass spectrometry
The lack of adequate analytical methods for the quantification of plastic debris in soil challenges a better understanding of their occurrence and fate in the terrestrial environment. With this proof-of-principle study, we developed a simple and fast method for the selective quantification of the three most environmentally relevant polymers polyethylene (PE), polypropylene (PP), and polystyrene (PS) in soil using pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). In order to facilitate the preparation of calibration series and to better account for the heterogeneity of soil matrix, polymers were dissolved in 1,2,4-trichlorobenzene (TCB) at 120 °C. Thereby, liquid sample aliquots from up to 4 g of solid sample became amenable to pyrolysis without further preparation. To evaluate the performance of this approach, three reference soils with 1.73–5.16 % organic carbon (Corg) were spiked at 50 and 250 μg g−1 of each polymer and extracted with TCB. A prior cleanup step with methanol, flocculation with KAl(SO4)2, and Fenton digestion were tested for their suitability to reduce potentially interfering Corg. Calibration curves responded linearly (adj. R2 > 0.996) with instrumental detection limits of 1–86 ng corresponding to method detection limits of 1–86 μg g−1. The measurement repeatability was 3.2–7.2 % relative standard deviation. Recoveries of 70–128 % were achieved for plastic contents of 250 μg g−1 extracted with TCB without prior cleanup from soils with less than 2.5 % Corg. A higher Corg particularly interfered with the quantification of PE. The addition of non-target polymers (polyethylene terephthalate, polyvinyl chloride, poly(methyl methacrylate), and tire wear particles) did not interfere with the quantification of the analytes highlighting the selectivity of the method. Further research is needed to determine low plastic contents in soils exceeding 2.5 % Corg. With 1–3 h processing time per sample, our method has the potential for routine analyses and screening studies of agricultural systems to be complemented with microspectroscopic techniques for additional information on particle shapes and sizes.
application/pdf
text/html
doi:10.7287/peerj.preprints.27989v2
A simple method for the selective quantification of polyethylene, polypropylene, and polystyrene plastic debris in soil by pyrolysis-gas chromatography/mass spectrometry
Zacharias Steinmetz
Aaron Kintzi
Katherine Muñoz
Gabriele E. Schaumann
Soil Science
Environmental Contamination and Remediation
doi:10.7287/peerj.preprints.27989v2
PeerJ Inc.
© 2019 Steinmetz et al.
The lack of adequate analytical methods for the quantification of plastic debris in soil challenges a better understanding of their occurrence and fate in the terrestrial environment. With this proof-of-principle study, we developed a simple and fast method for the selective quantification of the three most environmentally relevant polymers polyethylene (PE), polypropylene (PP), and polystyrene (PS) in soil using pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). In order to facilitate the preparation of calibration series and to better account for the heterogeneity of soil matrix, polymers were dissolved in 1,2,4-trichlorobenzene (TCB) at 120 °C. Thereby, liquid sample aliquots from up to 4 g of solid sample became amenable to pyrolysis without further preparation. To evaluate the performance of this approach, three reference soils with 1.73–5.16 % organic carbon (Corg) were spiked at 50 and 250 μg g−1 of each polymer and extracted with TCB. A prior cleanup step with methanol, flocculation with KAl(SO4)2, and Fenton digestion were tested for their suitability to reduce potentially interfering Corg. Calibration curves responded linearly (adj. R2 > 0.996) with instrumental detection limits of 1–86 ng corresponding to method detection limits of 1–86 μg g−1. The measurement repeatability was 3.2–7.2 % relative standard deviation. Recoveries of 70–128 % were achieved for plastic contents of 250 μg g−1 extracted with TCB without prior cleanup from soils with less than 2.5 % Corg. A higher Corg particularly interfered with the quantification of PE. The addition of non-target polymers (polyethylene terephthalate, polyvinyl chloride, poly(methyl methacrylate), and tire wear particles) did not interfere with the quantification of the analytes highlighting the selectivity of the method. Further research is needed to determine low plastic contents in soils exceeding 2.5 % Corg. With 1–3 h processing time per sample, our method has the potential for routine analyses and screening studies of agricultural systems to be complemented with microspectroscopic techniques for additional information on particle shapes and sizes.
Steinmetz et al. (2019) A simple method for the selective quantification of polyethylene, polypropylene, and polystyrene plastic debris in soil by pyrolysis-gas chromatography/mass spectrometry. PeerJ Preprints 7:e27989v2 https://doi.org/10.7287/peerj.preprints.27989v2
2019-12-05
2019-12-05
Steinmetz
Zacharias
Kintzi
Aaron
Muñoz
Katherine
Schaumann
Gabriele E.
10.7287/peerj.preprints.27989v2
https://peerj.com/preprints/27989
7
https://peerj.com/preprints/27989
10.7287/peerj.preprints.27989v2
2167-9843
7
PeerJ Preprints
2019-12-05
© 2019 Steinmetz et al.
Steinmetz et al.
-
https://peerj.com/preprints/27355
Preferences and constraints: The value of economic games for studying human behavior
As economic games have spread from experimental economics to other social sciences, so too have critiques of their usefulness for drawing inferences about the “real world.” What these criticisms often miss is that games can be used to reveal individuals’ private preferences in ways that observational and interview data cannot; further, economic games can be designed such that they do provide insights into real-world behavior. Here, we draw on our collective experience using economic games in field contexts to illustrate how researchers can strategically alter the framing or design of economic games to draw inferences about private-world or real-world preferences. A detailed case study from coastal Colombia provides an example of the subtleties of game design and how games can be combined fruitfully with self-report data. We close with a list of concrete recommendations for how to modify economic games to better match particular research questions and research contexts.
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doi:10.7287/peerj.preprints.27355v2
Preferences and constraints: The value of economic games for studying human behavior
Anne C Pisor
Matthew M Gervais
Benjamin G Purzycki
Cody T Ross
Anthropology
Evolutionary Studies
Psychiatry and Psychology
doi:10.7287/peerj.preprints.27355v2
PeerJ Inc.
© 2019 Pisor et al.
As economic games have spread from experimental economics to other social sciences, so too have critiques of their usefulness for drawing inferences about the “real world.” What these criticisms often miss is that games can be used to reveal individuals’ private preferences in ways that observational and interview data cannot; further, economic games can be designed such that they do provide insights into real-world behavior. Here, we draw on our collective experience using economic games in field contexts to illustrate how researchers can strategically alter the framing or design of economic games to draw inferences about private-world or real-world preferences. A detailed case study from coastal Colombia provides an example of the subtleties of game design and how games can be combined fruitfully with self-report data. We close with a list of concrete recommendations for how to modify economic games to better match particular research questions and research contexts.
Pisor et al. (2019) Preferences and constraints: The value of economic games for studying human behavior. PeerJ Preprints 7:e27355v2 https://doi.org/10.7287/peerj.preprints.27355v2
2019-12-04
2019-12-04
Pisor
Anne C
Gervais
Matthew M
Purzycki
Benjamin G
Ross
Cody T
10.7287/peerj.preprints.27355v2
https://peerj.com/preprints/27355
7
https://peerj.com/preprints/27355
10.7287/peerj.preprints.27355v2
2167-9843
7
PeerJ Preprints
2019-12-04
© 2019 Pisor et al.
Pisor et al.
-
https://peerj.com/preprints/27992
Knockdown of AMP-activated protein kinase α2 impairs epithelial-mesenchymal transition in rat renal tubular epithelial cells by downregulating v-ets erythroblastosis virus E26 oncogene homolog-1 and ribosomal protein S6 kinase A1
Background. Epithelial mesenchymal transition (EMT) plays an important regulatory role in obstructive nephropathy and renal fibrosis. As an intracellular energy sensor, AMP-activated protein kinase (AMPK) is essential in the process of EMT. The aim of this study was to reveal changes in the expression of AMPKα2 and to elucidate which AMPKα2 genes play a role during EMT. Methods. In this study, TGF-β1 was used to induce EMT in normal rat renal tubular epithelial (NRK-52E) cells. The shAMPKα2 lentivirus was used to interfere with AMPKα2 expression in EMT-derived NRK-52E cells, where AMPKα2 expression and EMT were detected. Differential gene expression after the AMPKα2 knockdown in EMT-derived NRK-52E cells was examined using a gene microarray. Possible regulatory pathways were analyzed using ingenuity pathway analysis (IPA) and differentially expressed genes were partially verified by quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting. Results. It was found that AMPKα2 was upregulated in TGF-β1-induced EMT-derived NRK-52E cells. EMT progression was significantly inhibited after the expression of AMPKα2 was downregulated by the shAMPKα2 lentivirus. A total of 1,588 differentially expressed genes were detected after the AMPKα2 knockdown in NRK-52E cells in which EMT occurred. The ERK/MAPK pathway was significantly impaired after the AMPKα2 knockdown, as indicated by the IPA analysis. Furthermore, qRT-PCR and western blot results revealed that the expression of AMPKα2, v-ets erythroblastosis virus E26 oncogene homolog-1 (ETS1), and ribosomal protein S6 kinase A1 (RPS6KA1) was upregulated after EMT in NRK-52E cells, while expression of ETS1 and RPS6KA1 was downregulated after the AMPKα2 knockdown. Conclusions. AMPKα2 plays an important role in the regulation of rat renal tubular EMT, which may be achieved by modulating ETS1 and RPS6KA1 in the ERK/MAPK pathway.
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text/html
doi:10.7287/peerj.preprints.27992v2
Knockdown of AMP-activated protein kinase α2 impairs epithelial-mesenchymal transition in rat renal tubular epithelial cells by downregulating v-ets erythroblastosis virus E26 oncogene homolog-1 and ribosomal protein S6 kinase A1
Xiaoming Yin
Fujiang Ma
Xu Fan
Qi Zhao
Xin Liu
Yi Yang
Cell Biology
Urology
doi:10.7287/peerj.preprints.27992v2
PeerJ Inc.
© 2019 Yin et al.
Background. Epithelial mesenchymal transition (EMT) plays an important regulatory role in obstructive nephropathy and renal fibrosis. As an intracellular energy sensor, AMP-activated protein kinase (AMPK) is essential in the process of EMT. The aim of this study was to reveal changes in the expression of AMPKα2 and to elucidate which AMPKα2 genes play a role during EMT. Methods. In this study, TGF-β1 was used to induce EMT in normal rat renal tubular epithelial (NRK-52E) cells. The shAMPKα2 lentivirus was used to interfere with AMPKα2 expression in EMT-derived NRK-52E cells, where AMPKα2 expression and EMT were detected. Differential gene expression after the AMPKα2 knockdown in EMT-derived NRK-52E cells was examined using a gene microarray. Possible regulatory pathways were analyzed using ingenuity pathway analysis (IPA) and differentially expressed genes were partially verified by quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting. Results. It was found that AMPKα2 was upregulated in TGF-β1-induced EMT-derived NRK-52E cells. EMT progression was significantly inhibited after the expression of AMPKα2 was downregulated by the shAMPKα2 lentivirus. A total of 1,588 differentially expressed genes were detected after the AMPKα2 knockdown in NRK-52E cells in which EMT occurred. The ERK/MAPK pathway was significantly impaired after the AMPKα2 knockdown, as indicated by the IPA analysis. Furthermore, qRT-PCR and western blot results revealed that the expression of AMPKα2, v-ets erythroblastosis virus E26 oncogene homolog-1 (ETS1), and ribosomal protein S6 kinase A1 (RPS6KA1) was upregulated after EMT in NRK-52E cells, while expression of ETS1 and RPS6KA1 was downregulated after the AMPKα2 knockdown. Conclusions. AMPKα2 plays an important role in the regulation of rat renal tubular EMT, which may be achieved by modulating ETS1 and RPS6KA1 in the ERK/MAPK pathway.
Yin et al. (2019) Knockdown of AMP-activated protein kinase α2 impairs epithelial-mesenchymal transition in rat renal tubular epithelial cells by downregulating v-ets erythroblastosis virus E26 oncogene homolog-1 and ribosomal protein S6 kinase A1. PeerJ Preprints 7:e27992v2 https://doi.org/10.7287/peerj.preprints.27992v2
2019-12-02
2019-12-02
Yin
Xiaoming
Ma
Fujiang
Fan
Xu
Zhao
Qi
Liu
Xin
Yang
Yi
10.7287/peerj.preprints.27992v2
https://peerj.com/preprints/27992
7
https://peerj.com/preprints/27992
10.7287/peerj.preprints.27992v2
2167-9843
7
PeerJ Preprints
2019-12-02
© 2019 Yin et al.
Yin et al.
PeerJ Preprints
https://peerj.com/preprints/index.rss1?journal=peerj
2167-9843