PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Specific and reliable detection of Myosin 1C isoform A by RTqPCR in prostate cancer cells
items: Reassessing public opinion of captive cetacean attractions with a photo elicitation survey
items: De novo annotation of the transcriptome of the Northern Wheatear (Oenanthe oenanthe)
items: Exploratory investigation of region level risk factors of Ebola Virus Disease in West Africa
items: Chondrogenic differentiation of adipose-derived mesenchymal stem cells induced by L-ascorbic acid and platelet rich plasma on silk fibroin scaffold
items: Recommended nitrogen fertilization enhances soil carbon sequestration in China’s monsoonal temperate zone
items: Influencing factors and health risk assessment of microcystins in the Yongjiang river (China) by Monte Carlo simulation
items: An emerging viral pathogen truncates population age structure in a European amphibian and may reduce population viability
items: Soil moisture dynamics under two rainfall frequency treatments drive early spring CO2 gas exchange of lichen-dominated biocrusts in central Spain
items: https://peerj.com/articles/5883

Specific and reliable detection of Myosin 1C isoform A by RTqPCR in prostate cancer cells
type: item
type: AcademicArticle
description: Background Prostate cancer (PC) diagnostics and treatment often present a challenging task due to cancer subtype heterogeneity and differential disease progression in patient subgroups. Hence, the critical issue is finding a reliable and sensitive diagnostic and prognostic PC marker, especially for cases of biopsies with low percentages of cancer cells. Isoform A of myosin 1C was shown to be expressed in PC cells and responsible for their invasive properties, however, its feasibility for diagnostic purposes remains to be elucidated. Methods To verify the role of myosin 1C isoform A mRNA expression as a putative prostate cancer marker we performed RT qPCR normalized by three reference genes (GAPDH, YWHAZ, HPRT1) on PC3, RWPE-1, LNCaP and 22Rv1 cell lines. Myosin 1C isoform A detection specificity was confirmed by immunofluorescence staining, cancer and non-cancer prostate cell lines were immunophenotyped by flow cytometry. Results Median normalized mRNA expression level of myosin 1C isoform A in PC cells (PC3 and 22Rv1) is two orders of magnitude higher compared to RWPE-1 cells, which functionally correspond to benign prostate cells. Myosin 1C isoform A expression allows PC cell detection even at a dilution ratio of 1:1000 cancer to non-cancer cells. At the protein level, the mean fluorescence intensity of myosin 1C isoform A staining in PC3 nuclei was only twice as high as in RWPE-1, while the immunophenotypes of both cell lines were similar (CD44+/CD90-/CD133-/CD57-/CD24+-). Conclusions We report a distinct difference in myosin 1C isoform A mRNA levels in malignant (PC3) and benign (RWPE-1) prostate cell lines and suggest a combination of three reference genes for accurate data normalization. For the first time we provide an immunophenotype comparison of RWPE-1 and PC3 cells and demonstrate that RT qPCR analysis of MYO 1C A using appropriate reference genes is sufficient for PC detection even in low-abundance cancer specimens.
format: application/pdf
format: text/html
creator: Aleena A. Saidova
creator: Daria M. Potashnikova
creator: Anna V. Tvorogova
creator: Ivan V. Maly
creator: Wilma A. Hofmann
creator: Ivan A. Vorobjev
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.5970
publisher: PeerJ Inc.
rights: © 2018 Saidova et al.
abstract: Background Prostate cancer (PC) diagnostics and treatment often present a challenging task due to cancer subtype heterogeneity and differential disease progression in patient subgroups. Hence, the critical issue is finding a reliable and sensitive diagnostic and prognostic PC marker, especially for cases of biopsies with low percentages of cancer cells. Isoform A of myosin 1C was shown to be expressed in PC cells and responsible for their invasive properties, however, its feasibility for diagnostic purposes remains to be elucidated. Methods To verify the role of myosin 1C isoform A mRNA expression as a putative prostate cancer marker we performed RT qPCR normalized by three reference genes (GAPDH, YWHAZ, HPRT1) on PC3, RWPE-1, LNCaP and 22Rv1 cell lines. Myosin 1C isoform A detection specificity was confirmed by immunofluorescence staining, cancer and non-cancer prostate cell lines were immunophenotyped by flow cytometry. Results Median normalized mRNA expression level of myosin 1C isoform A in PC cells (PC3 and 22Rv1) is two orders of magnitude higher compared to RWPE-1 cells, which functionally correspond to benign prostate cells. Myosin 1C isoform A expression allows PC cell detection even at a dilution ratio of 1:1000 cancer to non-cancer cells. At the protein level, the mean fluorescence intensity of myosin 1C isoform A staining in PC3 nuclei was only twice as high as in RWPE-1, while the immunophenotypes of both cell lines were similar (CD44+/CD90-/CD133-/CD57-/CD24+-). Conclusions We report a distinct difference in myosin 1C isoform A mRNA levels in malignant (PC3) and benign (RWPE-1) prostate cell lines and suggest a combination of three reference genes for accurate data normalization. For the first time we provide an immunophenotype comparison of RWPE-1 and PC3 cells and demonstrate that RT qPCR analysis of MYO 1C A using appropriate reference genes is sufficient for PC detection even in low-abundance cancer specimens.
bibliographic citation: Saidova et al. (2018) Specific and reliable detection of Myosin 1C isoform A by RTqPCR in prostate cancer cells. PeerJ 6:e5970 https://doi.org/10.7717/peerj.5970
date submitted: 2018-09-13
date accepted: 2018-10-19
issued: 2018-11-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saidova
  given name: Aleena A.
author list: Agent
  family name: Potashnikova
  given name: Daria M.
author list: Agent
  family name: Tvorogova
  given name: Anna V.
author list: Agent
  family name: Maly
  given name: Ivan V.
author list: Agent
  family name: Hofmann
  given name: Wilma A.
author list: Agent
  family name: Vorobjev
  given name: Ivan A.
doi: 10.7717/peerj.5970
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-20
copyright: ©2018 Saidova et al.
attribution name: Saidova et al.

Reassessing public opinion of captive cetacean attractions with a photo elicitation survey
type: item
type: AcademicArticle
description: Background Captive cetacean attractions are growing in number globally, their operators citing entertainment, education, and conservation as benefits. Those for and against developing such attractions claim public support. Previous public opinion research, however, shows little consensus, partly due to the introduction of biases in study design that influence participants’ responses. Those involved in, or concerned with, developing and licensing these attractions need to better understand what drives the lack of consensus to take socially-acceptable decisions. Methods We reviewed previous research on public opinion of cetacean captivity, noting possible sources of bias. Survey question wording can be a major source of introduced bias, so we used an open-ended photo elicitation approach. We showed tourists in the Turks Caicos Islands (N = 292) images of a marine mammal park (MMP) killer whale show and a swim-with-the-dolphins (SWTD) attraction and asked for their qualitative comments on the potential development of each. They also indicated how likely they would be to visit each on a Likert scale. Results Respondents were generally against visiting MMP killer whale shows, with 60.9% not likely to visit. SWTD attractions were more popular; 60.3% were likely to visit. For SWTD, USA residents were more likely to visit; older respondents and those staying in all-inclusive resorts were less likely. Those staying in all-inclusive resorts were also less likely to visit MMP killer whale shows. The great majority of qualitative comments centred on either entertainment value or animal welfare concerns. There were very few, if any, comments on the education or conservation value of these attractions. Discussion Our findings contradict several previous studies on public opinion of captive cetaceans that did not use photo elicitation. The support shown for MMP killer whale shows in this survey was well below that claimed by studies conducted on behalf of captive cetacean attracti…
format: application/pdf
format: text/html
creator: Sophia N. Wassermann
creator: Edward J. Hind-Ozan
creator: Julia Seaman
subject: Conservation Biology
subject: Ethical Issues
subject: Science Policy
subject: Natural Resource Management
description: doi:10.7717/peerj.5953
publisher: PeerJ Inc.
rights: © 2018 Wassermann et al.
abstract: Background Captive cetacean attractions are growing in number globally, their operators citing entertainment, education, and conservation as benefits. Those for and against developing such attractions claim public support. Previous public opinion research, however, shows little consensus, partly due to the introduction of biases in study design that influence participants’ responses. Those involved in, or concerned with, developing and licensing these attractions need to better understand what drives the lack of consensus to take socially-acceptable decisions. Methods We reviewed previous research on public opinion of cetacean captivity, noting possible sources of bias. Survey question wording can be a major source of introduced bias, so we used an open-ended photo elicitation approach. We showed tourists in the Turks Caicos Islands (N = 292) images of a marine mammal park (MMP) killer whale show and a swim-with-the-dolphins (SWTD) attraction and asked for their qualitative comments on the potential development of each. They also indicated how likely they would be to visit each on a Likert scale. Results Respondents were generally against visiting MMP killer whale shows, with 60.9% not likely to visit. SWTD attractions were more popular; 60.3% were likely to visit. For SWTD, USA residents were more likely to visit; older respondents and those staying in all-inclusive resorts were less likely. Those staying in all-inclusive resorts were also less likely to visit MMP killer whale shows. The great majority of qualitative comments centred on either entertainment value or animal welfare concerns. There were very few, if any, comments on the education or conservation value of these attractions. Discussion Our findings contradict several previous studies on public opinion of captive cetaceans that did not use photo elicitation. The support shown for MMP killer whale shows in this survey was well below that claimed by studies conducted on behalf of captive cetacean attracti…
bibliographic citation: Wassermann et al. (2018) Reassessing public opinion of captive cetacean attractions with a photo elicitation survey. PeerJ 6:e5953 https://doi.org/10.7717/peerj.5953
date submitted: 2018-05-08
date accepted: 2018-10-18
issued: 2018-11-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wassermann
  given name: Sophia N.
author list: Agent
  family name: Hind-Ozan
  given name: Edward J.
author list: Agent
  family name: Seaman
  given name: Julia
doi: 10.7717/peerj.5953
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-20
copyright: ©2018 Wassermann et al.
attribution name: Wassermann et al.

De novo annotation of the transcriptome of the Northern Wheatear (Oenanthe oenanthe)
type: item
type: AcademicArticle
description: We have sequenced a partial transcriptome of the Northern Wheatear (Oenanthe oenanthe), a species with one of the longest migrations on Earth. The transcriptome was constructed de novo using RNA-Seq sequence data from the pooled mRNA of six different tissues: brain, muscle, intestine, liver, adipose tissue and skin. The samples came from nine captive-bred wheatears collected at three different stages of the endogenous autumn migratory period: (1) lean birds prior the onset of migration, (2) during the fattening stage and (3) individuals at their migratory body mass plateau, when they have almost doubled their lean body mass. The sample structure used to build up the transcriptome of the Northern Wheatears concerning tissue composition and time guarantees the future survey of the regulatory genes involved in the development of the migratory phenotype. Through the pre-migratory period, birds accomplish outstanding physical and behavioural changes that involve all organ systems. Nevertheless, the molecular mechanisms through which birds synchronize and control hyperphagia, fattening, restlessness increase, immunity boosting and tuning the muscles for such endurance flight are still largely unknown. The use of RNA-Seq has emerged as a powerful tool to analyse complex traits on a broad scale, and we believe it can help to characterize the migratory phenotype of wheatears at an unprecedented level. The primary challenge to conduct quantitative transcriptomic studies in non-model species is the availability of a reference transcriptome, which we have constructed and described in this paper. The cDNA was sequenced by pyrosequencing using the Genome Sequencer Roche GS FLX System; with single paired-end reads of about 400 bp. We estimate the total number of genes at 15,640, of which 67% could be annotated using Turkey and Zebra Finch genomes, or protein sequence information from SwissProt and NCBI databases. With our study, we have made a first step towards understanding the …
format: application/pdf
format: text/html
creator: Roberto Carlos Frias-Soler
creator: Lilian Villarín Pildaín
creator: Agnes Hotz-Wagenblatt
creator: Jonas Kolibius
creator: Franz Bairlein
creator: Michael Wink
subject: Animal Behavior
subject: Bioinformatics
subject: Conservation Biology
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.5860
publisher: PeerJ Inc.
rights: © 2018 Frias-Soler et al.
abstract: We have sequenced a partial transcriptome of the Northern Wheatear (Oenanthe oenanthe), a species with one of the longest migrations on Earth. The transcriptome was constructed de novo using RNA-Seq sequence data from the pooled mRNA of six different tissues: brain, muscle, intestine, liver, adipose tissue and skin. The samples came from nine captive-bred wheatears collected at three different stages of the endogenous autumn migratory period: (1) lean birds prior the onset of migration, (2) during the fattening stage and (3) individuals at their migratory body mass plateau, when they have almost doubled their lean body mass. The sample structure used to build up the transcriptome of the Northern Wheatears concerning tissue composition and time guarantees the future survey of the regulatory genes involved in the development of the migratory phenotype. Through the pre-migratory period, birds accomplish outstanding physical and behavioural changes that involve all organ systems. Nevertheless, the molecular mechanisms through which birds synchronize and control hyperphagia, fattening, restlessness increase, immunity boosting and tuning the muscles for such endurance flight are still largely unknown. The use of RNA-Seq has emerged as a powerful tool to analyse complex traits on a broad scale, and we believe it can help to characterize the migratory phenotype of wheatears at an unprecedented level. The primary challenge to conduct quantitative transcriptomic studies in non-model species is the availability of a reference transcriptome, which we have constructed and described in this paper. The cDNA was sequenced by pyrosequencing using the Genome Sequencer Roche GS FLX System; with single paired-end reads of about 400 bp. We estimate the total number of genes at 15,640, of which 67% could be annotated using Turkey and Zebra Finch genomes, or protein sequence information from SwissProt and NCBI databases. With our study, we have made a first step towards understanding the …
bibliographic citation: Frias-Soler et al. (2018) De novo annotation of the transcriptome of the Northern Wheatear (Oenanthe oenanthe). PeerJ 6:e5860 https://doi.org/10.7717/peerj.5860
date submitted: 2017-06-12
date accepted: 2018-10-02
issued: 2018-11-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frias-Soler
  given name: Roberto Carlos
author list: Agent
  family name: Villarín Pildaín
  given name: Lilian
author list: Agent
  family name: Hotz-Wagenblatt
  given name: Agnes
author list: Agent
  family name: Kolibius
  given name: Jonas
author list: Agent
  family name: Bairlein
  given name: Franz
author list: Agent
  family name: Wink
  given name: Michael
doi: 10.7717/peerj.5860
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-20
copyright: ©2018 Frias-Soler et al.
attribution name: Frias-Soler et al.

Exploratory investigation of region level risk factors of Ebola Virus Disease in West Africa
type: item
type: AcademicArticle
description: Background Ebola Virus Disease (EVD) is a highly infectious disease that has produced over 25,000 cases in the past 50 years. While many past outbreaks resulted in relatively few cases, the 2014 outbreak in West Africa was the most deadly occurrence of EVD to date, producing over 15,000 confirmed cases. Objective In this study, we investigated population level predictors of EVD risk at the regional level in Sierra Leone, Liberia, and Guinea. Methods Spatial and descriptive analyses were conducted to assess distribution of EVD cases. Choropleth maps showing the spatial distribution of EVD risk across the study area were generated in ArcGIS. Poisson and negative binomial models were then used to investigate population and regional predictors of EVD risk. Results Results indicated that the risk of EVD was significantly lower in areas with higher proportions of: (a) the population living in urban areas, (b) households with a low quality or no toilets, and (c) married men working in blue collar jobs. However, risk of EVD was significantly higher in areas with high mean years of education. Conclusions The identified significant predictors of high risk were associated with areas with higher levels of urbanization. This may be due to higher population densities in the more urban centers and hence higher potential of infectious contact. However, there is need to better understand the role of urbanization and individual contact structure in an Ebola outbreak. We discuss shortcomings in available data and emphasize the need to consider spatial scale in future data collection and epidemiological studies.
format: application/pdf
format: text/html
creator: Benjamin Levy
creator: Agricola Odoi
subject: Epidemiology
subject: Infectious Diseases
subject: Statistics
description: doi:10.7717/peerj.5888
publisher: PeerJ Inc.
rights: © 2018 Levy and Odoi
abstract: Background Ebola Virus Disease (EVD) is a highly infectious disease that has produced over 25,000 cases in the past 50 years. While many past outbreaks resulted in relatively few cases, the 2014 outbreak in West Africa was the most deadly occurrence of EVD to date, producing over 15,000 confirmed cases. Objective In this study, we investigated population level predictors of EVD risk at the regional level in Sierra Leone, Liberia, and Guinea. Methods Spatial and descriptive analyses were conducted to assess distribution of EVD cases. Choropleth maps showing the spatial distribution of EVD risk across the study area were generated in ArcGIS. Poisson and negative binomial models were then used to investigate population and regional predictors of EVD risk. Results Results indicated that the risk of EVD was significantly lower in areas with higher proportions of: (a) the population living in urban areas, (b) households with a low quality or no toilets, and (c) married men working in blue collar jobs. However, risk of EVD was significantly higher in areas with high mean years of education. Conclusions The identified significant predictors of high risk were associated with areas with higher levels of urbanization. This may be due to higher population densities in the more urban centers and hence higher potential of infectious contact. However, there is need to better understand the role of urbanization and individual contact structure in an Ebola outbreak. We discuss shortcomings in available data and emphasize the need to consider spatial scale in future data collection and epidemiological studies.
bibliographic citation: Levy et al. (2018) Exploratory investigation of region level risk factors of Ebola Virus Disease in West Africa. PeerJ 6:e5888 https://doi.org/10.7717/peerj.5888
date submitted: 2017-06-12
date accepted: 2018-10-08
issued: 2018-11-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Levy
  given name: Benjamin
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.5888
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-19
copyright: ©2018 Levy and Odoi
attribution name: Levy and Odoi

Chondrogenic differentiation of adipose-derived mesenchymal stem cells induced by L-ascorbic acid and platelet rich plasma on silk fibroin scaffold
type: item
type: AcademicArticle
description: Articular cartilage is an avascular tissue with limited regenerative property. Therefore, a defect or trauma in articular cartilage due to disease or accident can lead to progressive tissue deterioration. Cartilage tissue engineering, by replacing defective cartilage tissue, is a method for repairing such a problem. In this research, three main aspects—cell, biomaterial scaffold, and bioactive factors—that support tissue engineering study were optimized. Adipose-derived mesenchymal stem cells (ADSC) that become cartilage were grown in an optimized growth medium supplemented with either platelet rich plasma (PRP) or L-ascorbic acid (LAA). As the characterization result, the ADSC used in this experiment could be classified as Mesenchymal Stem Cell (MSC) based on multipotency analysis and cell surface marker analysis. The biomaterial scaffold was fabricated from the Bombyx morii cocoon using silk fibroin by salt leaching method and was engineered to form different sizes of pores to provide optimized support for cell adhesion and growth. Biocompatibility and cytotoxicity evaluation was done using MTT assay to optimize silk fibroin concentration and pore size. Characterized ADSC were grown on the optimized scaffold. LAA and PRP were chosen as bioactive factors to induce ADSC differentiation to become chondrocytes. The concentration optimization of LAA and PRP was analyzed by cell proliferation using MTT assay and chondrogenic differentiation by measuring glycosaminoglycan (GAG) using Alcian Blue at 605 nm wavelength. The optimum silk fibroin concentration, pore size, LAA concentration, and PRP concentration were used to grow and differentiate characterized ADSC for 7, 14, and 21 days. The cell morphology on the scaffold was analyzed using a scanning electron microscope (SEM). The result showed that the ADSC could adhere on plastic, express specific cell surface markers (CD73, CD90, and CD105), and could be differentiated into three types of mature cells. The silk fibroin…
format: application/pdf
format: text/html
creator: Anggraini Barlian
creator: Hermawan Judawisastra
creator: Nayla M. Alfarafisa
creator: Untung A. Wibowo
creator: Imam Rosadi
subject: Bioengineering
subject: Biotechnology
subject: Cell Biology
subject: Developmental Biology
subject: Translational Medicine
description: doi:10.7717/peerj.5809
publisher: PeerJ Inc.
rights: © 2018 Barlian et al.
abstract: Articular cartilage is an avascular tissue with limited regenerative property. Therefore, a defect or trauma in articular cartilage due to disease or accident can lead to progressive tissue deterioration. Cartilage tissue engineering, by replacing defective cartilage tissue, is a method for repairing such a problem. In this research, three main aspects—cell, biomaterial scaffold, and bioactive factors—that support tissue engineering study were optimized. Adipose-derived mesenchymal stem cells (ADSC) that become cartilage were grown in an optimized growth medium supplemented with either platelet rich plasma (PRP) or L-ascorbic acid (LAA). As the characterization result, the ADSC used in this experiment could be classified as Mesenchymal Stem Cell (MSC) based on multipotency analysis and cell surface marker analysis. The biomaterial scaffold was fabricated from the Bombyx morii cocoon using silk fibroin by salt leaching method and was engineered to form different sizes of pores to provide optimized support for cell adhesion and growth. Biocompatibility and cytotoxicity evaluation was done using MTT assay to optimize silk fibroin concentration and pore size. Characterized ADSC were grown on the optimized scaffold. LAA and PRP were chosen as bioactive factors to induce ADSC differentiation to become chondrocytes. The concentration optimization of LAA and PRP was analyzed by cell proliferation using MTT assay and chondrogenic differentiation by measuring glycosaminoglycan (GAG) using Alcian Blue at 605 nm wavelength. The optimum silk fibroin concentration, pore size, LAA concentration, and PRP concentration were used to grow and differentiate characterized ADSC for 7, 14, and 21 days. The cell morphology on the scaffold was analyzed using a scanning electron microscope (SEM). The result showed that the ADSC could adhere on plastic, express specific cell surface markers (CD73, CD90, and CD105), and could be differentiated into three types of mature cells. The silk fibroin…
bibliographic citation: Barlian et al. (2018) Chondrogenic differentiation of adipose-derived mesenchymal stem cells induced by L-ascorbic acid and platelet rich plasma on silk fibroin scaffold. PeerJ 6:e5809 https://doi.org/10.7717/peerj.5809
date submitted: 2018-03-09
date accepted: 2018-09-21
issued: 2018-11-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barlian
  given name: Anggraini
author list: Agent
  family name: Judawisastra
  given name: Hermawan
author list: Agent
  family name: Alfarafisa
  given name: Nayla M.
author list: Agent
  family name: Wibowo
  given name: Untung A.
author list: Agent
  family name: Rosadi
  given name: Imam
doi: 10.7717/peerj.5809
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-19
copyright: ©2018 Barlian et al.
attribution name: Barlian et al.

Recommended nitrogen fertilization enhances soil carbon sequestration in China’s monsoonal temperate zone
type: item
type: AcademicArticle
description: China consumes more than one-third of the world’s nitrogen (N) fertilizer, and an increasing amount of N fertilizer has been applied over the past decades. Although N fertilization can increase the carbon sequestration potentials of cropland in China, the quantitative effects of different N fertilizer application levels on soil carbon changes have not been evaluated. Therefore, a 12-year cultivation experiment was conducted under three N fertilizer application levels (no N fertilizer input, the recommended N fertilizer input after soil testing, and the estimated additional fertilizer input) to estimate the effect of N addition on soil carbon changes in the root layer (0–80 cm) and non-root layer (80–200 cm) using a within-study meta-analysis method. The results showed significant declines in the soil inorganic carbon (SIC) in the root layers and significant growth in the SIC in the non-root layers under N fertilizer input. The soil organic carbon (SOC) in the root layers and the non-root layer significantly decreased under all the treatments. In addition, the recommended N fertilizer application level significantly increased the SOC and soil total carbon stocks compared with the future N fertilizer application level and no N input, while the future N fertilization significantly decreased the SIC and soil total carbon compared with no N input. The results suggest that N fertilization can rearrange the soil carbon distribution over the entire soil profile, and the recommended N fertilization rather than excess N input can increase the soil carbon stock, which suggests that the national soil testing program in China can improve the soil carbon sequestration potential.
format: application/pdf
format: text/html
creator: Shaofei Jin
subject: Agricultural Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.5983
publisher: PeerJ Inc.
rights: © 2018 Jin
abstract: China consumes more than one-third of the world’s nitrogen (N) fertilizer, and an increasing amount of N fertilizer has been applied over the past decades. Although N fertilization can increase the carbon sequestration potentials of cropland in China, the quantitative effects of different N fertilizer application levels on soil carbon changes have not been evaluated. Therefore, a 12-year cultivation experiment was conducted under three N fertilizer application levels (no N fertilizer input, the recommended N fertilizer input after soil testing, and the estimated additional fertilizer input) to estimate the effect of N addition on soil carbon changes in the root layer (0–80 cm) and non-root layer (80–200 cm) using a within-study meta-analysis method. The results showed significant declines in the soil inorganic carbon (SIC) in the root layers and significant growth in the SIC in the non-root layers under N fertilizer input. The soil organic carbon (SOC) in the root layers and the non-root layer significantly decreased under all the treatments. In addition, the recommended N fertilizer application level significantly increased the SOC and soil total carbon stocks compared with the future N fertilizer application level and no N input, while the future N fertilization significantly decreased the SIC and soil total carbon compared with no N input. The results suggest that N fertilization can rearrange the soil carbon distribution over the entire soil profile, and the recommended N fertilization rather than excess N input can increase the soil carbon stock, which suggests that the national soil testing program in China can improve the soil carbon sequestration potential.
bibliographic citation: Jin (2018) Recommended nitrogen fertilization enhances soil carbon sequestration in China’s monsoonal temperate zone. PeerJ 6:e5983 https://doi.org/10.7717/peerj.5983
date submitted: 2018-07-04
date accepted: 2018-10-22
issued: 2018-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Shaofei
doi: 10.7717/peerj.5983
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-16
copyright: ©2018 Jin
attribution name: Jin

Influencing factors and health risk assessment of microcystins in the Yongjiang river (China) by Monte Carlo simulation
type: item
type: AcademicArticle
description: The Yongjiang river is a large, shallow, hyper-trophic, freshwater river in Guangxi, China. To investigate the presence of microcystin-RR, microcystin-LR, and microcystin-YR (MC-RR, MC-LR, and MC-YR) in the Yongjiang river and describe their correlation with environmental factors, as well as, assess health risk using Monte Carlo simulation, 90 water samples were collected at three sample points from March to December 2017. Results showed that during the monitoring period, total concentrations of MC-RR (TMC-RR), MC-YR (TMC-YR), and MC-LR (TMC-LR) varied from 0.0224 to 0.3783 μg/L, 0.0329 to 0.1433 μg/L, and 0.0341 to 0.2663 μg/L, respectively. Total phosphorus (TP) content appeared to be related to TMC-LR and the total concentrations of microcystins (TMCs), while pH and total nitrogen (TN)/TP ratio appeared to be related to TMC-RR and TMC-YR, respectively. Using the professional health risk assessment software @Risk7.5, the risks of dietary intake of microcystins (MCs), including the carcinogenic risk and non-carcinogenic risk, were evaluated. It was found that the carcinogenic risk of MC-RR from drinking water was higher than MC-LR and MC-YR, and the presence of MCs would lead to high potential health risks, especially in children. The carcinogenic risk of MC-RR to children was >1 × 10−4, the maximum allowance level recommended by the US Environmental Protection Agency; as for adults, it was >5 × 10−5, the maximum allowance level recommended by the International Commission on Radiological Protection. The non-carcinogenic hazard index (HI) of MC-RR, MC-YR, and MC-LR increased successively, indicating that MC-LR was more hazardous to human health than MC-YR and MC-RR, but its HI was <1. This suggests that MCs pose less risk to health. However, it is necessary to strengthen the protection and monitoring of drinking water source for effective control of water pollution and safeguarding of human health.
format: application/pdf
format: text/html
creator: Chan-Chan Xiao
creator: Mao-Jian Chen
creator: Fan-Biao Mei
creator: Xiang Fang
creator: Tian-Ren Huang
creator: Ji-Lin Li
creator: Wei Deng
creator: Yuan-Dong Li
subject: Ecotoxicology
subject: Environmental Impacts
description: doi:10.7717/peerj.5955
publisher: PeerJ Inc.
rights: © 2018 Xiao et al.
abstract: The Yongjiang river is a large, shallow, hyper-trophic, freshwater river in Guangxi, China. To investigate the presence of microcystin-RR, microcystin-LR, and microcystin-YR (MC-RR, MC-LR, and MC-YR) in the Yongjiang river and describe their correlation with environmental factors, as well as, assess health risk using Monte Carlo simulation, 90 water samples were collected at three sample points from March to December 2017. Results showed that during the monitoring period, total concentrations of MC-RR (TMC-RR), MC-YR (TMC-YR), and MC-LR (TMC-LR) varied from 0.0224 to 0.3783 μg/L, 0.0329 to 0.1433 μg/L, and 0.0341 to 0.2663 μg/L, respectively. Total phosphorus (TP) content appeared to be related to TMC-LR and the total concentrations of microcystins (TMCs), while pH and total nitrogen (TN)/TP ratio appeared to be related to TMC-RR and TMC-YR, respectively. Using the professional health risk assessment software @Risk7.5, the risks of dietary intake of microcystins (MCs), including the carcinogenic risk and non-carcinogenic risk, were evaluated. It was found that the carcinogenic risk of MC-RR from drinking water was higher than MC-LR and MC-YR, and the presence of MCs would lead to high potential health risks, especially in children. The carcinogenic risk of MC-RR to children was >1 × 10−4, the maximum allowance level recommended by the US Environmental Protection Agency; as for adults, it was >5 × 10−5, the maximum allowance level recommended by the International Commission on Radiological Protection. The non-carcinogenic hazard index (HI) of MC-RR, MC-YR, and MC-LR increased successively, indicating that MC-LR was more hazardous to human health than MC-YR and MC-RR, but its HI was <1. This suggests that MCs pose less risk to health. However, it is necessary to strengthen the protection and monitoring of drinking water source for effective control of water pollution and safeguarding of human health.
bibliographic citation: Xiao et al. (2018) Influencing factors and health risk assessment of microcystins in the Yongjiang river (China) by Monte Carlo simulation. PeerJ 6:e5955 https://doi.org/10.7717/peerj.5955
date submitted: 2018-06-06
date accepted: 2018-10-16
issued: 2018-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Chan-Chan
author list: Agent
  family name: Chen
  given name: Mao-Jian
author list: Agent
  family name: Mei
  given name: Fan-Biao
author list: Agent
  family name: Fang
  given name: Xiang
author list: Agent
  family name: Huang
  given name: Tian-Ren
author list: Agent
  family name: Li
  given name: Ji-Lin
author list: Agent
  family name: Deng
  given name: Wei
author list: Agent
  family name: Li
  given name: Yuan-Dong
doi: 10.7717/peerj.5955
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-16
copyright: © 2018 Xiao et al.
attribution name: Xiao et al.

An emerging viral pathogen truncates population age structure in a European amphibian and may reduce population viability
type: item
type: AcademicArticle
description: Infectious diseases can alter the demography of their host populations, reducing their viability even in the absence of mass mortality. Amphibians are the most threatened group of vertebrates globally, and emerging infectious diseases play a large role in their continued population declines. Viruses belonging to the genus Ranavirus are responsible for one of the deadliest and most widespread of these diseases. To date, no work has used individual level data to investigate how ranaviruses affect population demographic structure. We used skeletochronology and morphology to evaluate the impact of ranaviruses on the age structure of populations of the European common frog (Rana temporaria) in the UK. We compared ecologically similar populations that differed most notably in their historical presence or absence of ranavirosis (the acute syndrome caused by ranavirus infection). Our results suggest that ranavirosis may truncate the age structure of R. temporaria populations. One potential explanation for such a shift might be increased adult mortality and subsequent shifts in the life history of younger age classes that increase reproductive output earlier in life. Additionally, we constructed population projection models which indicated that such increased adult mortality could heighten the vulnerability of frog populations to stochastic environmental challenges.
format: application/pdf
format: text/html
creator: Lewis J. Campbell
creator: Trenton W.J. Garner
creator: Giulia Tessa
creator: Benjamin C. Scheele
creator: Amber G.F. Griffiths
creator: Lena Wilfert
creator: Xavier A. Harrison
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Freshwater Biology
subject: Population Biology
description: doi:10.7717/peerj.5949
publisher: PeerJ Inc.
rights: © 2018 Campbell et al.
abstract: Infectious diseases can alter the demography of their host populations, reducing their viability even in the absence of mass mortality. Amphibians are the most threatened group of vertebrates globally, and emerging infectious diseases play a large role in their continued population declines. Viruses belonging to the genus Ranavirus are responsible for one of the deadliest and most widespread of these diseases. To date, no work has used individual level data to investigate how ranaviruses affect population demographic structure. We used skeletochronology and morphology to evaluate the impact of ranaviruses on the age structure of populations of the European common frog (Rana temporaria) in the UK. We compared ecologically similar populations that differed most notably in their historical presence or absence of ranavirosis (the acute syndrome caused by ranavirus infection). Our results suggest that ranavirosis may truncate the age structure of R. temporaria populations. One potential explanation for such a shift might be increased adult mortality and subsequent shifts in the life history of younger age classes that increase reproductive output earlier in life. Additionally, we constructed population projection models which indicated that such increased adult mortality could heighten the vulnerability of frog populations to stochastic environmental challenges.
bibliographic citation: Campbell et al. (2018) An emerging viral pathogen truncates population age structure in a European amphibian and may reduce population viability. PeerJ 6:e5949 https://doi.org/10.7717/peerj.5949
date submitted: 2018-07-19
date accepted: 2018-10-17
issued: 2018-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Campbell
  given name: Lewis J.
author list: Agent
  family name: Garner
  given name: Trenton W.J.
author list: Agent
  family name: Tessa
  given name: Giulia
author list: Agent
  family name: Scheele
  given name: Benjamin C.
author list: Agent
  family name: Griffiths
  given name: Amber G.F.
author list: Agent
  family name: Wilfert
  given name: Lena
author list: Agent
  family name: Harrison
  given name: Xavier A.
doi: 10.7717/peerj.5949
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-16
copyright: © 2018 Campbell et al.
attribution name: Campbell et al.

Soil moisture dynamics under two rainfall frequency treatments drive early spring CO2 gas exchange of lichen-dominated biocrusts in central Spain
type: item
type: AcademicArticle
description: Background Biocrusts, communities dominated by mosses, lichens, cyanobacteria, and other microorganisms, largely affect the carbon cycle of drylands. As poikilohydric organisms, their activity time is often limited to short hydration events. The photosynthetic and respiratory response of biocrusts to hydration events is not only determined by the overall amount of available water, but also by the frequency and size of individual rainfall pulses. Methods We experimentally assessed the carbon exchange of a biocrust community dominated by the lichen Diploschistes diacapsis in central Spain. We compared the effect of two simulated precipitation patterns providing the same overall amount of water, but with different pulse sizes and frequency (high frequency: five mm/day vs. low frequency: 15 mm/3 days), on net/gross photosynthesis and dark respiration. Results Radiation and soil temperature, together with the watering treatment, affected the rates of net and gross photosynthesis, as well as dark respiration. On average, the low frequency treatment showed a 46% ± 3% (mean ± 1 SE) lower rate of net photosynthesis, a 13% ± 7% lower rate of dark respiration, and a 24% ± 8% lower rate of gross photosynthesis. However, on the days when samples of both treatments were watered, no differences between their carbon fluxes were observed. The carbon flux response of D. diacapsis was modulated by the environmental conditions and was particularly dependent on the antecedent soil moisture. Discussion In line with other studies, we found a synergetic effect of individual pulse size, frequency, environmental conditions, and antecedent moisture on the carbon exchange fluxes of biocrusts. However, most studies on this subject were conducted in summer and they obtained results different from ours, so we conclude that there is a need for long-term experiments of manipulated precipitation impacts on the carbon exchange of biocrusts. This will enable a more complete assessment of the impacts o…
format: application/pdf
format: text/html
creator: Selina Baldauf
creator: Mónica Ladrón de Guevara
creator: Fernando T. Maestre
creator: Britta Tietjen
subject: Ecology
subject: Soil Science
subject: Climate Change Biology
description: doi:10.7717/peerj.5904
publisher: PeerJ Inc.
rights: © 2018 Baldauf et al.
abstract: Background Biocrusts, communities dominated by mosses, lichens, cyanobacteria, and other microorganisms, largely affect the carbon cycle of drylands. As poikilohydric organisms, their activity time is often limited to short hydration events. The photosynthetic and respiratory response of biocrusts to hydration events is not only determined by the overall amount of available water, but also by the frequency and size of individual rainfall pulses. Methods We experimentally assessed the carbon exchange of a biocrust community dominated by the lichen Diploschistes diacapsis in central Spain. We compared the effect of two simulated precipitation patterns providing the same overall amount of water, but with different pulse sizes and frequency (high frequency: five mm/day vs. low frequency: 15 mm/3 days), on net/gross photosynthesis and dark respiration. Results Radiation and soil temperature, together with the watering treatment, affected the rates of net and gross photosynthesis, as well as dark respiration. On average, the low frequency treatment showed a 46% ± 3% (mean ± 1 SE) lower rate of net photosynthesis, a 13% ± 7% lower rate of dark respiration, and a 24% ± 8% lower rate of gross photosynthesis. However, on the days when samples of both treatments were watered, no differences between their carbon fluxes were observed. The carbon flux response of D. diacapsis was modulated by the environmental conditions and was particularly dependent on the antecedent soil moisture. Discussion In line with other studies, we found a synergetic effect of individual pulse size, frequency, environmental conditions, and antecedent moisture on the carbon exchange fluxes of biocrusts. However, most studies on this subject were conducted in summer and they obtained results different from ours, so we conclude that there is a need for long-term experiments of manipulated precipitation impacts on the carbon exchange of biocrusts. This will enable a more complete assessment of the impacts o…
bibliographic citation: Baldauf et al. (2018) Soil moisture dynamics under two rainfall frequency treatments drive early spring CO2 gas exchange of lichen-dominated biocrusts in central Spain. PeerJ 6:e5904 https://doi.org/10.7717/peerj.5904
date submitted: 2018-05-02
date accepted: 2018-10-09
issued: 2018-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baldauf
  given name: Selina
author list: Agent
  family name: Ladrón de Guevara
  given name: Mónica
author list: Agent
  family name: Maestre
  given name: Fernando T.
author list: Agent
  family name: Tietjen
  given name: Britta
doi: 10.7717/peerj.5904
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-16
copyright: © 2018 Baldauf et al.
attribution name: Baldauf et al.

https://peerj.com/articles/5883
type: item
type: AcademicArticle
title: A new microvertebrate assemblage from the Mussentuchit Member, Cedar Mountain Formation: insights into the paleobiodiversity and paleobiogeography of early Late Cretaceous ecosystems in western North America
description: The vertebrate fauna of the Late Cretaceous Mussentuchit Member of the Cedar Mountain Formation has been studied for nearly three decades, yet the fossil-rich unit continues to produce new information about life in western North America approximately 97 million years ago. Here we report on the composition of the Cliffs of Insanity (COI) microvertebrate locality, a newly sampled site containing perhaps one of the densest concentrations of microvertebrate fossils yet discovered in the Mussentuchit Member. The COI locality preserves osteichthyan, lissamphibian, testudinatan, mesoeucrocodylian, dinosaurian, metatherian, and trace fossil remains and is among the most taxonomically rich microvertebrate localities in the Mussentuchit Member. To better refine taxonomic identifications of isolated theropod dinosaur teeth, we used quantitative analyses of taxonomically comprehensive databases of theropod tooth measurements, adding new data on theropod tooth morphodiversity in this poorly understood interval. We further provide the first descriptions of tyrannosauroid premaxillary teeth and document the earliest North American record of adocid remains, extending the appearance of this ancestrally Asian clade by 5 million years in western North America and supporting studies of pre-Cenomaninan Laurasian faunal exchange across Beringia. The overabundance of mesoeucrocodylian remains at the COI locality produces a comparatively low measure of relative biodiversity when compared to other microvertebrate sites in the Mussentuchit Member using both raw and subsampling methods. Much more microvertebrate research is necessary to understand the roles of changing ecology and taphonomy that may be linked to transgression of the Western Interior Seaway or microhabitat variation.
format: application/pdf
format: text/html
creator: Haviv M. Avrahami
creator: Terry A. Gates
creator: Andrew B. Heckert
creator: Peter J. Makovicky
creator: Lindsay E. Zanno
subject: Biodiversity
subject: Biogeography
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.5883
publisher: PeerJ Inc.
rights: © 2018 Avrahami et al.
abstract: The vertebrate fauna of the Late Cretaceous Mussentuchit Member of the Cedar Mountain Formation has been studied for nearly three decades, yet the fossil-rich unit continues to produce new information about life in western North America approximately 97 million years ago. Here we report on the composition of the Cliffs of Insanity (COI) microvertebrate locality, a newly sampled site containing perhaps one of the densest concentrations of microvertebrate fossils yet discovered in the Mussentuchit Member. The COI locality preserves osteichthyan, lissamphibian, testudinatan, mesoeucrocodylian, dinosaurian, metatherian, and trace fossil remains and is among the most taxonomically rich microvertebrate localities in the Mussentuchit Member. To better refine taxonomic identifications of isolated theropod dinosaur teeth, we used quantitative analyses of taxonomically comprehensive databases of theropod tooth measurements, adding new data on theropod tooth morphodiversity in this poorly understood interval. We further provide the first descriptions of tyrannosauroid premaxillary teeth and document the earliest North American record of adocid remains, extending the appearance of this ancestrally Asian clade by 5 million years in western North America and supporting studies of pre-Cenomaninan Laurasian faunal exchange across Beringia. The overabundance of mesoeucrocodylian remains at the COI locality produces a comparatively low measure of relative biodiversity when compared to other microvertebrate sites in the Mussentuchit Member using both raw and subsampling methods. Much more microvertebrate research is necessary to understand the roles of changing ecology and taphonomy that may be linked to transgression of the Western Interior Seaway or microhabitat variation.
bibliographic citation: Avrahami et al. (2018) A new microvertebrate assemblage from the Mussentuchit Member, Cedar Mountain Formation: insights into the paleobiodiversity and paleobiogeography of early Late Cretaceous ecosystems in western North America. PeerJ 6:e5883 https://doi.org/10.7717/peerj.5883
date submitted: 2018-05-30
date accepted: 2018-10-08
issued: 2018-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Avrahami
  given name: Haviv M.
author list: Agent
  family name: Gates
  given name: Terry A.
author list: Agent
  family name: Heckert
  given name: Andrew B.
author list: Agent
  family name: Makovicky
  given name: Peter J.
author list: Agent
  family name: Zanno
  given name: Lindsay E.
doi: 10.7717/peerj.5883
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-16
copyright: © 2018 Avrahami et al.
attribution name: Avrahami et al.

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