PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Biogeography rather than substrate type determines bacterial colonization dynamics of marine plastics
items: Habitat ephemerality affects the evolution of contrasting growth strategies and cannibalism in anuran larvae
items: Capturing and analyzing pattern diversity: an example using the melanistic spotted patterns of leopard geckos
items: Hepatitis C core antigen test as an alternative for diagnosing HCV infection: mathematical model and cost-effectiveness analysis
items: Synopsis of Habenaria s.l. (Orchidaceae) in New Guinea and adjacent islands
items: A new species of Proceratophrys Miranda-Ribeiro, 1920 (Anura, Odontophrynidae) from Southern Amazonia, Brazil
items: Independent validation of downscaled climate estimates from a coastal Alaska watershed using local historical weather journals
items: Estrogen receptor alpha regulates the expression of adipogenic genes genetically and epigenetically in rat bone marrow-derived mesenchymal stem cells
items: Seagrass contribution to blue carbon in a shallow karstic coastal area of the Gulf of Mexico
items: Carbon and nitrogen metabolism under nitrogen variation affects flavonoid accumulation in the leaves of Coreopsis tinctoria

Biogeography rather than substrate type determines bacterial colonization dynamics of marine plastics
type: item
type: AcademicArticle
description: Since the middle of the 20th century, plastics have been incorporated into our everyday lives at an exponential rate. In recent years, the negative impacts of plastics, especially as environmental pollutants, have become evident. Marine plastic debris represents a relatively new and increasingly abundant substrate for colonization by microbial organisms, although the full functional potential of these organisms is yet to be uncovered. In the present study, we investigated plastic type and incubation location as drivers of marine bacterial community structure development on plastics, i.e., the Plastisphere, via 16S rRNA amplicon analysis. Four distinct plastic types: high-density polyethylene (HDPE), linear low-density polyethylene (LDPE), polyamide (PA), polymethyl methacrylate (PMMA), and glass-slide controls were incubated for five weeks in the coastal waters of four different biogeographic locations (Cape Verde, Chile, Japan, South Africa) during July and August of 2019. The primary driver of the coastal Plastisphere composition was identified as incubation location, i.e., biogeography, while substrate type did not have a significant effect on bacterial community composition. The bacterial communities were consistently dominated by the classes Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia, irrespective of sampling location or substrate type, however a core bacterial Plastisphere community was not observable at lower taxonomic levels. Overall, this study sheds light on the question of whether bacterial communities on plastic debris are shaped by the physicochemical properties of the substrate they grow on or by the marine environment in which the plastics are immersed. This study enhances the current understanding of biogeographic variability in the Plastisphere by including biofilms from plastics incubated in the previously uncharted Southern Hemisphere.
format: application/pdf
format: text/html
creator: Ashley K. Coons
creator: Kathrin Busch
creator: Mark Lenz
creator: Ute Hentschel
creator: Erik Borchert
subject: Biodiversity
subject: Bioinformatics
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.12135
publisher: PeerJ Inc.
rights: © 2021 Coons et al.
abstract: Since the middle of the 20th century, plastics have been incorporated into our everyday lives at an exponential rate. In recent years, the negative impacts of plastics, especially as environmental pollutants, have become evident. Marine plastic debris represents a relatively new and increasingly abundant substrate for colonization by microbial organisms, although the full functional potential of these organisms is yet to be uncovered. In the present study, we investigated plastic type and incubation location as drivers of marine bacterial community structure development on plastics, i.e., the Plastisphere, via 16S rRNA amplicon analysis. Four distinct plastic types: high-density polyethylene (HDPE), linear low-density polyethylene (LDPE), polyamide (PA), polymethyl methacrylate (PMMA), and glass-slide controls were incubated for five weeks in the coastal waters of four different biogeographic locations (Cape Verde, Chile, Japan, South Africa) during July and August of 2019. The primary driver of the coastal Plastisphere composition was identified as incubation location, i.e., biogeography, while substrate type did not have a significant effect on bacterial community composition. The bacterial communities were consistently dominated by the classes Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia, irrespective of sampling location or substrate type, however a core bacterial Plastisphere community was not observable at lower taxonomic levels. Overall, this study sheds light on the question of whether bacterial communities on plastic debris are shaped by the physicochemical properties of the substrate they grow on or by the marine environment in which the plastics are immersed. This study enhances the current understanding of biogeographic variability in the Plastisphere by including biofilms from plastics incubated in the previously uncharted Southern Hemisphere.
bibliographic citation: Coons et al. (2021) Biogeography rather than substrate type determines bacterial colonization dynamics of marine plastics. PeerJ 9:e12135 https://doi.org/10.7717/peerj.12135
date submitted: 2021-04-22
date accepted: 2021-08-18
issued: 2021-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coons
  given name: Ashley K.
author list: Agent
  family name: Busch
  given name: Kathrin
author list: Agent
  family name: Lenz
  given name: Mark
author list: Agent
  family name: Hentschel
  given name: Ute
author list: Agent
  family name: Borchert
  given name: Erik
doi: 10.7717/peerj.12135
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-13
copyright: ©2021 Coons et al.
attribution name: Coons et al.

Habitat ephemerality affects the evolution of contrasting growth strategies and cannibalism in anuran larvae
type: item
type: AcademicArticle
description: Ephemeral streams are challenging environments for tadpoles; thus, adaptive features that increase the survival of these larvae should be favored by natural selection. In this study, we compared the adaptive growth strategies of Bombina orientalis (the oriental fire-bellied toad) tadpoles from ephemeral streams with those of such tadpoles from non-ephemeral streams. Using a common garden experiment, we tested the interactive effects of location (ephemeral vs. non-ephemeral), food availability, and growing density on larval period, weight at metamorphosis, and cannibalism. We found that tadpoles from ephemeral streams underwent a shorter larval period compared with those from non-ephemeral streams but that this difference was contingent on food availability. The observed faster growth is likely to be an adaptive response because tadpoles in ephemeral streams experience more biotic/abiotic stressors, such as desiccation risk and limited resources, compared with those in non-ephemeral streams, with their earlier metamorphosis potentially resulting in survival benefits. As a trade-off for their faster growth, tadpoles from ephemeral streams generally had a lower body weight at metamorphosis compared with those from non-ephemeral streams. We also found lower cannibalism rates among tadpoles from ephemeral streams, which can be attributed to the indirect fitness costs of cannibalizing their kin. Our study demonstrates how ephemeral habitats have affected the evolutionary change in cannibalistic behaviors in anurans and provides additional evidence that natural selection has mediated the evolution of growth strategies of tadpoles in ephemeral streams.
format: application/pdf
format: text/html
creator: Dogeun Oh
creator: Yongsu Kim
creator: Sohee Yoo
creator: Changku Kang
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12172
publisher: PeerJ Inc.
rights: © 2021 Oh et al.
abstract: Ephemeral streams are challenging environments for tadpoles; thus, adaptive features that increase the survival of these larvae should be favored by natural selection. In this study, we compared the adaptive growth strategies of Bombina orientalis (the oriental fire-bellied toad) tadpoles from ephemeral streams with those of such tadpoles from non-ephemeral streams. Using a common garden experiment, we tested the interactive effects of location (ephemeral vs. non-ephemeral), food availability, and growing density on larval period, weight at metamorphosis, and cannibalism. We found that tadpoles from ephemeral streams underwent a shorter larval period compared with those from non-ephemeral streams but that this difference was contingent on food availability. The observed faster growth is likely to be an adaptive response because tadpoles in ephemeral streams experience more biotic/abiotic stressors, such as desiccation risk and limited resources, compared with those in non-ephemeral streams, with their earlier metamorphosis potentially resulting in survival benefits. As a trade-off for their faster growth, tadpoles from ephemeral streams generally had a lower body weight at metamorphosis compared with those from non-ephemeral streams. We also found lower cannibalism rates among tadpoles from ephemeral streams, which can be attributed to the indirect fitness costs of cannibalizing their kin. Our study demonstrates how ephemeral habitats have affected the evolutionary change in cannibalistic behaviors in anurans and provides additional evidence that natural selection has mediated the evolution of growth strategies of tadpoles in ephemeral streams.
bibliographic citation: Oh et al. (2021) Habitat ephemerality affects the evolution of contrasting growth strategies and cannibalism in anuran larvae. PeerJ 9:e12172 https://doi.org/10.7717/peerj.12172
date submitted: 2021-06-28
date accepted: 2021-08-27
issued: 2021-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oh
  given name: Dogeun
author list: Agent
  family name: Kim
  given name: Yongsu
author list: Agent
  family name: Yoo
  given name: Sohee
author list: Agent
  family name: Kang
  given name: Changku
doi: 10.7717/peerj.12172
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-13
copyright: ©2021 Oh et al.
attribution name: Oh et al.

Capturing and analyzing pattern diversity: an example using the melanistic spotted patterns of leopard geckos
type: item
type: AcademicArticle
description: Animal color patterns are widely studied in ecology, evolution, and through mathematical modeling. Patterns may vary among distinct body parts such as the head, trunk or tail. As large amounts of photographic data is becoming more easily available, there is a growing need for general quantitative methods for capturing and analyzing the full complexity and details of pattern variation. Detailed information on variation in color pattern elements is necessary to understand how patterns are produced and established during development, and which evolutionary forces may constrain such a variation. Here, we develop an approach to capture and analyze variation in melanistic color pattern elements in leopard geckos. We use this data to study the variation among different body parts of leopard geckos and to draw inferences about their development. We compare patterns using 14 different indices such as the ratio of melanistic versus total area, the ellipticity of spots, and the size of spots and use these to define a composite distance between two patterns. Pattern presence/absence among the different body parts indicates a clear pathway of pattern establishment from the head to the back legs. Together with weak within-individual correlation between leg patterns and main body patterns, this suggests that pattern establishment in the head and tail may be independent from the rest of the body. We found that patterns vary greatest in size and density of the spots among body parts and individuals, but little in their average shapes. We also found a correlation between the melanistic patterns of the two front legs, as well as the two back legs, and also between the head, tail and trunk, especially for the density and size of the spots, but not their shape or inter-spot distance. Our data collection and analysis approach can be applied to other organisms to study variation in color patterns between body parts and to address questions on pattern formation and establishment in animals…
format: application/pdf
format: text/html
creator: Tilmann Glimm
creator: Maria Kiskowski
creator: Nickolas Moreno
creator: Ylenia Chiari
subject: Computational Biology
subject: Developmental Biology
subject: Mathematical Biology
subject: Zoology
description: doi:10.7717/peerj.11829
publisher: PeerJ Inc.
rights: © 2021 Glimm et al.
abstract: Animal color patterns are widely studied in ecology, evolution, and through mathematical modeling. Patterns may vary among distinct body parts such as the head, trunk or tail. As large amounts of photographic data is becoming more easily available, there is a growing need for general quantitative methods for capturing and analyzing the full complexity and details of pattern variation. Detailed information on variation in color pattern elements is necessary to understand how patterns are produced and established during development, and which evolutionary forces may constrain such a variation. Here, we develop an approach to capture and analyze variation in melanistic color pattern elements in leopard geckos. We use this data to study the variation among different body parts of leopard geckos and to draw inferences about their development. We compare patterns using 14 different indices such as the ratio of melanistic versus total area, the ellipticity of spots, and the size of spots and use these to define a composite distance between two patterns. Pattern presence/absence among the different body parts indicates a clear pathway of pattern establishment from the head to the back legs. Together with weak within-individual correlation between leg patterns and main body patterns, this suggests that pattern establishment in the head and tail may be independent from the rest of the body. We found that patterns vary greatest in size and density of the spots among body parts and individuals, but little in their average shapes. We also found a correlation between the melanistic patterns of the two front legs, as well as the two back legs, and also between the head, tail and trunk, especially for the density and size of the spots, but not their shape or inter-spot distance. Our data collection and analysis approach can be applied to other organisms to study variation in color patterns between body parts and to address questions on pattern formation and establishment in animals…
bibliographic citation: Glimm et al. (2021) Capturing and analyzing pattern diversity: an example using the melanistic spotted patterns of leopard geckos. PeerJ 9:e11829 https://doi.org/10.7717/peerj.11829
date submitted: 2021-03-31
date accepted: 2021-06-30
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Glimm
  given name: Tilmann
author list: Agent
  family name: Kiskowski
  given name: Maria
author list: Agent
  family name: Moreno
  given name: Nickolas
author list: Agent
  family name: Chiari
  given name: Ylenia
doi: 10.7717/peerj.11829
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: ©2021 Glimm et al.
attribution name: Glimm et al.

Hepatitis C core antigen test as an alternative for diagnosing HCV infection: mathematical model and cost-effectiveness analysis
type: item
type: AcademicArticle
description: Background The cost and complexity of the polymerase chain reaction (PCR) test are barriers to diagnosis and treatment of hepatitis C virus (HCV) infection. We investigated the cost-effectiveness of testing strategies using antigen instead of PCR testing. Methods We developed a mathematical model for HCV to estimate the number of diagnoses and cases of liver disease. We compared the following testing strategies: antibody test followed by PCR in case of positive antibody (baseline strategy); antibody test followed by HCV-antigen test (antibody-antigen); antigen test alone; PCR test alone. We conducted cost-effectiveness analyses considering either the costs of HCV testing of infected and uninfected individuals alone (A1), HCV testing and liver-related complications (A2), or all costs including HCV treatment (A3). The model was parameterized for the country of Georgia. We conducted several sensitivity analyses. Results The baseline scenario could detect 89% of infected individuals. Antibody-antigen detected 86% and antigen alone 88% of infected individuals. PCR testing alone detected 91% of the infected individuals: the remaining 9% either died or spontaneously recovered before testing. In analysis A1, the baseline strategy was not essentially more expensive than antibody-antigen. In analysis A2, strategies using PCR became cheaper than antigen-based strategies. In analysis A3, antibody-antigen was again the cheapest strategy, followed by the baseline strategy, and PCR testing alone. Conclusions Antigen testing, either following a positive antibody test or alone, performed almost as well as the current practice of HCV testing. The cost-effectiveness of these strategies depends on the inclusion of treatment costs.
format: application/pdf
format: text/html
creator: Maryam Sadeghimehr
creator: Barbara Bertisch
creator: Francesco Negro
creator: Maia Butsashvili
creator: Sonjelle Shilton
creator: Irina Tskhomelidze
creator: Maia Tsereteli
creator: Olivia Keiser
creator: Janne Estill
subject: Epidemiology
subject: Global Health
subject: Health Policy
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.11895
publisher: PeerJ Inc.
rights: © 2021 Sadeghimehr et al.
abstract: Background The cost and complexity of the polymerase chain reaction (PCR) test are barriers to diagnosis and treatment of hepatitis C virus (HCV) infection. We investigated the cost-effectiveness of testing strategies using antigen instead of PCR testing. Methods We developed a mathematical model for HCV to estimate the number of diagnoses and cases of liver disease. We compared the following testing strategies: antibody test followed by PCR in case of positive antibody (baseline strategy); antibody test followed by HCV-antigen test (antibody-antigen); antigen test alone; PCR test alone. We conducted cost-effectiveness analyses considering either the costs of HCV testing of infected and uninfected individuals alone (A1), HCV testing and liver-related complications (A2), or all costs including HCV treatment (A3). The model was parameterized for the country of Georgia. We conducted several sensitivity analyses. Results The baseline scenario could detect 89% of infected individuals. Antibody-antigen detected 86% and antigen alone 88% of infected individuals. PCR testing alone detected 91% of the infected individuals: the remaining 9% either died or spontaneously recovered before testing. In analysis A1, the baseline strategy was not essentially more expensive than antibody-antigen. In analysis A2, strategies using PCR became cheaper than antigen-based strategies. In analysis A3, antibody-antigen was again the cheapest strategy, followed by the baseline strategy, and PCR testing alone. Conclusions Antigen testing, either following a positive antibody test or alone, performed almost as well as the current practice of HCV testing. The cost-effectiveness of these strategies depends on the inclusion of treatment costs.
bibliographic citation: Sadeghimehr et al. (2021) Hepatitis C core antigen test as an alternative for diagnosing HCV infection: mathematical model and cost-effectiveness analysis. PeerJ 9:e11895 https://doi.org/10.7717/peerj.11895
date submitted: 2020-12-23
date accepted: 2021-07-12
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sadeghimehr
  given name: Maryam
author list: Agent
  family name: Bertisch
  given name: Barbara
author list: Agent
  family name: Negro
  given name: Francesco
author list: Agent
  family name: Butsashvili
  given name: Maia
author list: Agent
  family name: Shilton
  given name: Sonjelle
author list: Agent
  family name: Tskhomelidze
  given name: Irina
author list: Agent
  family name: Tsereteli
  given name: Maia
author list: Agent
  family name: Keiser
  given name: Olivia
author list: Agent
  family name: Estill
  given name: Janne
doi: 10.7717/peerj.11895
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: ©2021 Sadeghimehr et al.
attribution name: Sadeghimehr et al.

Synopsis of Habenaria s.l. (Orchidaceae) in New Guinea and adjacent islands
type: item
type: AcademicArticle
description: A taxonomic synopsis of the orchid genus Habenaria in New Guinea and adjacent islands is presented. We confirmed the occurrence of 27 Habenaria species in study area. Sixteen of these are endemic and were not so far found outside New Guinea. Morphological characteristics and illustrations of floral segments of taxa are presented. One new species of Habenaria is described. Four neotypes are selected. An updated key to species groups and species occurring in the study area is provided. The importance of diagnostic floral characters in Habenaria is discussed.
format: application/pdf
format: text/html
creator: Marta Kolanowska
creator: Marta Kras
creator: Sławomir Nowak
creator: Dariusz L. Szlachetko
subject: Biodiversity
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.12011
publisher: PeerJ Inc.
rights: © 2021 Kolanowska et al.
abstract: A taxonomic synopsis of the orchid genus Habenaria in New Guinea and adjacent islands is presented. We confirmed the occurrence of 27 Habenaria species in study area. Sixteen of these are endemic and were not so far found outside New Guinea. Morphological characteristics and illustrations of floral segments of taxa are presented. One new species of Habenaria is described. Four neotypes are selected. An updated key to species groups and species occurring in the study area is provided. The importance of diagnostic floral characters in Habenaria is discussed.
bibliographic citation: Kolanowska et al. (2021) Synopsis of Habenaria s.l. (Orchidaceae) in New Guinea and adjacent islands. PeerJ 9:e12011 https://doi.org/10.7717/peerj.12011
date submitted: 2021-02-25
date accepted: 2021-07-28
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kolanowska
  given name: Marta
author list: Agent
  family name: Kras
  given name: Marta
author list: Agent
  family name: Nowak
  given name: Sławomir
author list: Agent
  family name: Szlachetko
  given name: Dariusz L.
doi: 10.7717/peerj.12011
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: © 2021 Kolanowska et al.
attribution name: Kolanowska et al.

A new species of Proceratophrys Miranda-Ribeiro, 1920 (Anura, Odontophrynidae) from Southern Amazonia, Brazil
type: item
type: AcademicArticle
description: Based on concordant differences in morphology, male advertisement call, and 16S mtDNA barcode distance, we describe a new species of Proceratophrys from southern Amazonia, in the states of Mato Grosso and Pará, Brazil. The new species is most similar to P. concavitympanum and P. ararype but differs from these species by its proportionally larger eyes and features of the advertisement call. Additionally, genetic distance between the new species and its congeners is 3.0–10.4% based on a fragment of the 16S rRNA gene, which is greater than the threshold typically characterizing distinct species of anurans. Using an integrative approach (molecular, bioacoustics, and adult morphology), we were able to distinguish the new species from other congeneric species. The new species is known only from the type locality where it is threatened by illegal logging and gold mining as well as hydroelectric dams.
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creator: Diego J. Santana
creator: Leandro Alves da Silva
creator: Anathielle Caroline Sant’Anna
creator: Donald B. Shepard
creator: Sarah Mângia
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12012
publisher: PeerJ Inc.
rights: © 2021 Santana et al.
abstract: Based on concordant differences in morphology, male advertisement call, and 16S mtDNA barcode distance, we describe a new species of Proceratophrys from southern Amazonia, in the states of Mato Grosso and Pará, Brazil. The new species is most similar to P. concavitympanum and P. ararype but differs from these species by its proportionally larger eyes and features of the advertisement call. Additionally, genetic distance between the new species and its congeners is 3.0–10.4% based on a fragment of the 16S rRNA gene, which is greater than the threshold typically characterizing distinct species of anurans. Using an integrative approach (molecular, bioacoustics, and adult morphology), we were able to distinguish the new species from other congeneric species. The new species is known only from the type locality where it is threatened by illegal logging and gold mining as well as hydroelectric dams.
bibliographic citation: Santana et al. (2021) A new species of Proceratophrys Miranda-Ribeiro, 1920 (Anura, Odontophrynidae) from Southern Amazonia, Brazil. PeerJ 9:e12012 https://doi.org/10.7717/peerj.12012
date submitted: 2021-04-09
date accepted: 2021-07-28
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santana
  given name: Diego J.
author list: Agent
  family name: Silva
  given name: Leandro Alves da
author list: Agent
  family name: Sant’Anna
  given name: Anathielle Caroline
author list: Agent
  family name: Shepard
  given name: Donald B.
author list: Agent
  family name: Mângia
  given name: Sarah
doi: 10.7717/peerj.12012
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: © 2021 Santana et al.
attribution name: Santana et al.

Independent validation of downscaled climate estimates from a coastal Alaska watershed using local historical weather journals
type: item
type: AcademicArticle
description: Downscaling coarse global and regional climate models allows researchers to access weather and climate data at finer temporal and spatial resolution, but there remains a need to compare these models with empirical data sources to assess model accuracy. Here, we validate a widely used software for generating North American downscaled climate data, ClimateNA, with a novel empirical data source, 20th century weather journals kept by Admiralty Island, Alaska homesteader, Allen Hasselborg. Using Hasselborg’s journals, we calculated monthly precipitation and monthly mean of the maximum daily air temperature across the years 1926 to 1954 and compared these to ClimateNA data generated from the Hasselborg homestead location and adjacent areas. To demonstrate the utility and potential implications of this validation for other disciplines such as hydrology, we used an established regression equation to generate time series of 95% low duration flow estimates for the month of August using mean annual precipitation from ClimateNA predictions and Hasselborg data. Across 279 months, we found strong correlation between modeled and observed measurements of monthly precipitation (ρ = 0.74) and monthly mean of the maximum daily air temperature (ρ = 0.98). Monthly precipitation residuals (calculated as ClimateNA data - Hasselborg data) generally demonstrated heteroscedasticity around zero, but a negative trend in residual values starting during the last decade of observations may have been due to a shift to the cold-phase Pacific Decadal Oscillation. Air temperature residuals demonstrated a consistent but small positive bias, with ClimateNA tending to overestimate air temperature relative to Hasselborg’s journals. The degree of correlation between weather patterns observed at the Hasselborg homestead site and ClimateNA data extracted from spatial grid cells across the region varied by wet and dry climate years. Monthly precipitation from both data sources tended to be more similar acros…
format: application/pdf
format: text/html
creator: Emily R. Williamson
creator: Christopher J. Sergeant
subject: Ecosystem Science
subject: Climate Change Biology
subject: Atmospheric Chemistry
subject: Ecohydrology
description: doi:10.7717/peerj.12055
publisher: PeerJ Inc.
rights: © 2021 Williamson and Sergeant
abstract: Downscaling coarse global and regional climate models allows researchers to access weather and climate data at finer temporal and spatial resolution, but there remains a need to compare these models with empirical data sources to assess model accuracy. Here, we validate a widely used software for generating North American downscaled climate data, ClimateNA, with a novel empirical data source, 20th century weather journals kept by Admiralty Island, Alaska homesteader, Allen Hasselborg. Using Hasselborg’s journals, we calculated monthly precipitation and monthly mean of the maximum daily air temperature across the years 1926 to 1954 and compared these to ClimateNA data generated from the Hasselborg homestead location and adjacent areas. To demonstrate the utility and potential implications of this validation for other disciplines such as hydrology, we used an established regression equation to generate time series of 95% low duration flow estimates for the month of August using mean annual precipitation from ClimateNA predictions and Hasselborg data. Across 279 months, we found strong correlation between modeled and observed measurements of monthly precipitation (ρ = 0.74) and monthly mean of the maximum daily air temperature (ρ = 0.98). Monthly precipitation residuals (calculated as ClimateNA data - Hasselborg data) generally demonstrated heteroscedasticity around zero, but a negative trend in residual values starting during the last decade of observations may have been due to a shift to the cold-phase Pacific Decadal Oscillation. Air temperature residuals demonstrated a consistent but small positive bias, with ClimateNA tending to overestimate air temperature relative to Hasselborg’s journals. The degree of correlation between weather patterns observed at the Hasselborg homestead site and ClimateNA data extracted from spatial grid cells across the region varied by wet and dry climate years. Monthly precipitation from both data sources tended to be more similar acros…
bibliographic citation: Williamson et al. (2021) Independent validation of downscaled climate estimates from a coastal Alaska watershed using local historical weather journals. PeerJ 9:e12055 https://doi.org/10.7717/peerj.12055
date submitted: 2021-04-01
date accepted: 2021-08-04
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Williamson
  given name: Emily R.
author list: Agent
  family name: Sergeant
  given name: Christopher J.
doi: 10.7717/peerj.12055
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: ©2021 Williamson and Sergeant
attribution name: Williamson and Sergeant

Estrogen receptor alpha regulates the expression of adipogenic genes genetically and epigenetically in rat bone marrow-derived mesenchymal stem cells
type: item
type: AcademicArticle
description: Regulation of the efficacy of epigenetic modifiers is regarded as an important control mechanism in the determination and differentiation of stem cell fate. Studies are showing that the effect of estrogen is important in the differentiation of mesenchymal stem cells (MSCs) into adipocytes, osteocytes, and chondrocytes. Activation of certain transcription factors and epigenetic modifications in related genes play an active role in the initiation and completion of adipogenic differentiation. Understanding the role of estrogen in diseases such as obesity, which increases with the onset of menopause, will pave the way for more effective use of estrogen as a therapeutic option. Demonstration of the differentiation tendencies of MSCs change in the presence/absence of estrogen, especially the evaluation of reversible epigenetic changes, will provide valuable information for clinical applications. In this study, the effect of estrogen on the expression of genes involved in adipogenic differentiation of MSCs and accompanying epigenetic modifications was investigated. Our results showed that estrogen affects the expression of adipogenesis-related transcription factors such as PPARy, C/EBPα and Adipsin. In addition, after estrogen treatment, increased accumulation of estrogen receptor alpha (ERα) and repressive epigenetic markers such as H3K27me2 and H3K27me3 were observed on the promoter of given transcription factors. By using co-immunoprecipitation experiments we were also able to show that ERα physically interacts with the zeste homolog 2 (EZH2) H3K27 methyltransferase in MSCs. We propose that the increase of H3K27me2 and H3K27me3 markers on adipogenic genes upon estrogen treatment may be mediated by the direct interaction of ERα and EZH2. Taken together, these findings suggest that estrogen has a role as an epigenetic switcher in the regulation of H3K27 methylation leading to suppression of adipogenic differentiation of MSC.
format: application/pdf
format: text/html
creator: Ceylan V. Bitirim
creator: Zeynep B. Ozer
creator: Kamil C. Akcali
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.12071
publisher: PeerJ Inc.
rights: © 2021 Bitirim et al.
abstract: Regulation of the efficacy of epigenetic modifiers is regarded as an important control mechanism in the determination and differentiation of stem cell fate. Studies are showing that the effect of estrogen is important in the differentiation of mesenchymal stem cells (MSCs) into adipocytes, osteocytes, and chondrocytes. Activation of certain transcription factors and epigenetic modifications in related genes play an active role in the initiation and completion of adipogenic differentiation. Understanding the role of estrogen in diseases such as obesity, which increases with the onset of menopause, will pave the way for more effective use of estrogen as a therapeutic option. Demonstration of the differentiation tendencies of MSCs change in the presence/absence of estrogen, especially the evaluation of reversible epigenetic changes, will provide valuable information for clinical applications. In this study, the effect of estrogen on the expression of genes involved in adipogenic differentiation of MSCs and accompanying epigenetic modifications was investigated. Our results showed that estrogen affects the expression of adipogenesis-related transcription factors such as PPARy, C/EBPα and Adipsin. In addition, after estrogen treatment, increased accumulation of estrogen receptor alpha (ERα) and repressive epigenetic markers such as H3K27me2 and H3K27me3 were observed on the promoter of given transcription factors. By using co-immunoprecipitation experiments we were also able to show that ERα physically interacts with the zeste homolog 2 (EZH2) H3K27 methyltransferase in MSCs. We propose that the increase of H3K27me2 and H3K27me3 markers on adipogenic genes upon estrogen treatment may be mediated by the direct interaction of ERα and EZH2. Taken together, these findings suggest that estrogen has a role as an epigenetic switcher in the regulation of H3K27 methylation leading to suppression of adipogenic differentiation of MSC.
bibliographic citation: Bitirim et al. (2021) Estrogen receptor alpha regulates the expression of adipogenic genes genetically and epigenetically in rat bone marrow-derived mesenchymal stem cells. PeerJ 9:e12071 https://doi.org/10.7717/peerj.12071
date submitted: 2021-03-03
date accepted: 2021-08-05
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bitirim
  given name: Ceylan V.
author list: Agent
  family name: Ozer
  given name: Zeynep B.
author list: Agent
  family name: Akcali
  given name: Kamil C.
doi: 10.7717/peerj.12071
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: © 2021 Bitirim et al.
attribution name: Bitirim et al.

Seagrass contribution to blue carbon in a shallow karstic coastal area of the Gulf of Mexico
type: item
type: AcademicArticle
description: Seagrass meadows provide multiple ecosystem services, including carbon sequestration. However, seagrass meadows are among the most threatened ecosystems worldwide. Determining the magnitude of the carbon stocks in seagrass meadows at the regional scale allows for the estimation of their global magnitude and identification of their importance in regional environmental mitigation strategies. The objective of the present study was to determine the structure of seagrass meadows in the Los Petenes Biosfera Reserve (LPBR) and evaluate their contributions to sinks of carbon in this system, located in Yucatan, which is considered the region with the largest seagrass extension in Mexico. Analyses of the seagrass meadows were executed following standardized protocols (spectral analysis, and isotope and carbon stock analyses). The LPBR stores an average of 2.2 ± 1.7 Mg C ha−1 in living biomass and 318 ± 215 Mg C ha−1 in sediment (top 1 m), and this carbon stock decreases with water depth. The seagrass community extends 149,613 ha, which represents the largest organic carbon stock (47 Tg C) documented in seagrass meadows in Mexico. Macroalgae and seagrass represent 76% of the organic carbon stored in sediment. If LPBR seagrass meadows are lost due to natural or anthropogenic impacts, 173 Tg CO2eqemissions could be released, which corresponds to the emissions generated by fossil fuel combustion of 27% of the current Mexican population. This information emphasizes the importance of seagrass meadows as a carbon sink in the region and their contribution to climate change mitigation, thus allowing for the implementation of necessary conservation strategies.
format: application/pdf
format: text/html
creator: Tania C. Cota Lucero
creator: Jorge A. Herrera-Silveira
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Climate Change Biology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.12109
publisher: PeerJ Inc.
rights: © 2021 Cota Lucero and Herrera-Silveira
abstract: Seagrass meadows provide multiple ecosystem services, including carbon sequestration. However, seagrass meadows are among the most threatened ecosystems worldwide. Determining the magnitude of the carbon stocks in seagrass meadows at the regional scale allows for the estimation of their global magnitude and identification of their importance in regional environmental mitigation strategies. The objective of the present study was to determine the structure of seagrass meadows in the Los Petenes Biosfera Reserve (LPBR) and evaluate their contributions to sinks of carbon in this system, located in Yucatan, which is considered the region with the largest seagrass extension in Mexico. Analyses of the seagrass meadows were executed following standardized protocols (spectral analysis, and isotope and carbon stock analyses). The LPBR stores an average of 2.2 ± 1.7 Mg C ha−1 in living biomass and 318 ± 215 Mg C ha−1 in sediment (top 1 m), and this carbon stock decreases with water depth. The seagrass community extends 149,613 ha, which represents the largest organic carbon stock (47 Tg C) documented in seagrass meadows in Mexico. Macroalgae and seagrass represent 76% of the organic carbon stored in sediment. If LPBR seagrass meadows are lost due to natural or anthropogenic impacts, 173 Tg CO2eqemissions could be released, which corresponds to the emissions generated by fossil fuel combustion of 27% of the current Mexican population. This information emphasizes the importance of seagrass meadows as a carbon sink in the region and their contribution to climate change mitigation, thus allowing for the implementation of necessary conservation strategies.
bibliographic citation: Cota Lucero et al. (2021) Seagrass contribution to blue carbon in a shallow karstic coastal area of the Gulf of Mexico. PeerJ 9:e12109 https://doi.org/10.7717/peerj.12109
date submitted: 2021-01-05
date accepted: 2021-08-14
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cota Lucero
  given name: Tania C.
author list: Agent
  family name: Herrera-Silveira
  given name: Jorge A.
doi: 10.7717/peerj.12109
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: ©2021 Cota Lucero and Herrera-Silveira
attribution name: Cota Lucero and Herrera-Silveira

Carbon and nitrogen metabolism under nitrogen variation affects flavonoid accumulation in the leaves of Coreopsis tinctoria
type: item
type: AcademicArticle
description: Flavonoids are phytochemicals present in medicinal plants and contribute to human health. Coreopsis tinctoria, a species rich in flavonoids, has long been used in traditional medicine and as a food resource. N (nitrogen) fertilization can reduce flavonoid accumulation in C. tinctoria. However, there is limited knowledge regarding N regulatory mechanisms. The aim of this study was to determine the effect of N availability on flavonoid biosynthesis in C. tinctoria and to investigate the relationship between C (carbon) and N metabolism coupled with flavonoid synthesis under controlled conditions. C. tinctoria seedlings were grown hydroponically under five different N levels (0, 0.625, 1.250, 2.500 and 5.000 mM). The related indexes of C, N and flavonoid metabolism of C. tinctoria under N variation were measured and analysed. N availability (low and moderate N levels) regulates enzyme activities related to C and N metabolism, promotes the accumulation of carbohydrates, reduces N metabolite levels, and enhances the internal C/N balance. The flavonoid content in roots and stalks remained relatively stable, while that in leaves peaked at low or intermediate N levels. Flavonoids are closely related to phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate: coenzyme A ligase (4CL), and chalcone-thioase (CHS) activity, significantly positively correlated with carbohydrates and negatively correlated with N metabolites. Thus, C and N metabolism can not only control the distribution of C in amino acid and carbohydrate biosynthesis pathways but also change the distribution in flavonoid biosynthesis pathways, which also provides meaningful information for maintaining high yields while ensuring the nutritional value of crop plants.
format: application/pdf
format: text/html
creator: Zhiyuan Li
creator: Hong Jiang
creator: Huizhuan Yan
creator: Xiumei Jiang
creator: Yan Ma
creator: Yong Qin
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.12152
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Flavonoids are phytochemicals present in medicinal plants and contribute to human health. Coreopsis tinctoria, a species rich in flavonoids, has long been used in traditional medicine and as a food resource. N (nitrogen) fertilization can reduce flavonoid accumulation in C. tinctoria. However, there is limited knowledge regarding N regulatory mechanisms. The aim of this study was to determine the effect of N availability on flavonoid biosynthesis in C. tinctoria and to investigate the relationship between C (carbon) and N metabolism coupled with flavonoid synthesis under controlled conditions. C. tinctoria seedlings were grown hydroponically under five different N levels (0, 0.625, 1.250, 2.500 and 5.000 mM). The related indexes of C, N and flavonoid metabolism of C. tinctoria under N variation were measured and analysed. N availability (low and moderate N levels) regulates enzyme activities related to C and N metabolism, promotes the accumulation of carbohydrates, reduces N metabolite levels, and enhances the internal C/N balance. The flavonoid content in roots and stalks remained relatively stable, while that in leaves peaked at low or intermediate N levels. Flavonoids are closely related to phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate: coenzyme A ligase (4CL), and chalcone-thioase (CHS) activity, significantly positively correlated with carbohydrates and negatively correlated with N metabolites. Thus, C and N metabolism can not only control the distribution of C in amino acid and carbohydrate biosynthesis pathways but also change the distribution in flavonoid biosynthesis pathways, which also provides meaningful information for maintaining high yields while ensuring the nutritional value of crop plants.
bibliographic citation: Li et al. (2021) Carbon and nitrogen metabolism under nitrogen variation affects flavonoid accumulation in the leaves of Coreopsis tinctoria. PeerJ 9:e12152 https://doi.org/10.7717/peerj.12152
date submitted: 2021-05-11
date accepted: 2021-08-22
issued: 2021-09-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhiyuan
author list: Agent
  family name: Jiang
  given name: Hong
author list: Agent
  family name: Yan
  given name: Huizhuan
author list: Agent
  family name: Jiang
  given name: Xiumei
author list: Agent
  family name: Ma
  given name: Yan
author list: Agent
  family name: Qin
  given name: Yong
doi: 10.7717/peerj.12152
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-10
copyright: © 2021 Li et al.
attribution name: Li et al.

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