PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Population genetics of the main population of brown bears in southwest Asia
items: A secretory hexokinase plays an active role in the proliferation of Nosema bombycis
items: Does Twitter language reliably predict heart disease? A commentary on Eichstaedt et al. (2015a)
items: How much genetic variation is stored in the endangered and fragmented shrub Tetraena mongolica Maxim?
items: Short-tailed mice with a long fossil record: the genus Leggadina (Rodentia: Muridae) from the Quaternary of Queensland, Australia
items: Interleukin 35 induced Th2 and Tregs bias under normal conditions in mice
items: Plant dominance in a subalpine montane meadow: biotic vs. abiotic controls of subordinate diversity within and across sites
items: Improving remote estimation of winter crops gross ecosystem production by inclusion of leaf area index in a spectral model
items: Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes
items: The genetic status of the Hungarian brown trout populations: exploration of a blind spot on the European map of Salmo trutta studies

Population genetics of the main population of brown bears in southwest Asia
type: item
type: AcademicArticle
description: Genetic studies of the Eurasian brown bear (Ursus arctos) have so far focused on populations from Europe and North America, although the largest distribution area of brown bears is in Asia. In this study, we reveal population genetic parameters for the brown bear population inhabiting the Grand Kaçkar Mountains (GKM) in the north east of Turkey, western Lesser Caucasus. Using both hair (N = 147) and tissue samples (N = 7) collected between 2008 and 2014, we found substantial levels of genetic variation (10 microsatellite loci). Bear samples (hair) taken from rubbing trees worked better for genotyping than those from power poles, regardless of the year collected. Genotyping also revealed that bears moved between habitat patches, despite ongoing massive habitat alterations and the creation of large water reservoirs. This population has the potential to serve as a genetic reserve for future reintroductions in the Middle East. Due to the importance of the GKM population for on-going and future conservation actions, the impacts of habitat alterations in the region ought to be minimized; e.g., by establishing green bridges or corridors over reservoirs and major roads to maintain habitat connectivity and gene flow among populations in the Lesser Caucasus.
format: application/pdf
format: text/html
creator: Hüseyin Ambarlı
creator: Deniz Mengüllüoğlu
creator: Jörns Fickel
creator: Daniel W. Förster
subject: Biogeography
subject: Conservation Biology
subject: Genetics
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.5660
publisher: PeerJ Inc.
rights: © 2018 Ambarlı et al.
abstract: Genetic studies of the Eurasian brown bear (Ursus arctos) have so far focused on populations from Europe and North America, although the largest distribution area of brown bears is in Asia. In this study, we reveal population genetic parameters for the brown bear population inhabiting the Grand Kaçkar Mountains (GKM) in the north east of Turkey, western Lesser Caucasus. Using both hair (N = 147) and tissue samples (N = 7) collected between 2008 and 2014, we found substantial levels of genetic variation (10 microsatellite loci). Bear samples (hair) taken from rubbing trees worked better for genotyping than those from power poles, regardless of the year collected. Genotyping also revealed that bears moved between habitat patches, despite ongoing massive habitat alterations and the creation of large water reservoirs. This population has the potential to serve as a genetic reserve for future reintroductions in the Middle East. Due to the importance of the GKM population for on-going and future conservation actions, the impacts of habitat alterations in the region ought to be minimized; e.g., by establishing green bridges or corridors over reservoirs and major roads to maintain habitat connectivity and gene flow among populations in the Lesser Caucasus.
bibliographic citation: Ambarlı et al. (2018) Population genetics of the main population of brown bears in southwest Asia. PeerJ 6:e5660 https://doi.org/10.7717/peerj.5660
date submitted: 2018-03-08
date accepted: 2018-08-29
issued: 2018-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ambarlı
  given name: Hüseyin
author list: Agent
  family name: Mengüllüoğlu
  given name: Deniz
author list: Agent
  family name: Fickel
  given name: Jörns
author list: Agent
  family name: Förster
  given name: Daniel W.
doi: 10.7717/peerj.5660
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-21
copyright: ©2018 Ambarlı et al.
attribution name: Ambarlı et al.

A secretory hexokinase plays an active role in the proliferation of Nosema bombycis
type: item
type: AcademicArticle
description: The microsporidian Nosema bombycis is an obligate intracellular parasite of Bombyx mori, that lost its intact tricarboxylic acid cycle and mitochondria during evolution but retained its intact glycolysis pathway. N. bombycis hexokinase (NbHK) is not only a rate-limiting enzyme of glycolysis but also a secretory protein. Indirect immunofluorescence assays and recombinant HK overexpressed in BmN cells showed that NbHK localized in the nucleus and cytoplasm of host cell during the meront stage. When N. bombycis matured, NbHK tended to concentrate at the nuclei of host cells. Furthermore, the transcriptional profile of NbHK implied it functioned during N. bombycis’ proliferation stages. A knock-down of NbHK effectively suppressed the proliferation of N. bombycis indicating that NbHK is an important protein for parasite to control its host.
format: application/pdf
format: text/html
creator: Yukang Huang
creator: Shiyi Zheng
creator: Xionge Mei
creator: Bin Yu
creator: Bin Sun
creator: Boning Li
creator: Junhong Wei
creator: Jie Chen
creator: Tian Li
creator: Guoqing Pan
creator: Zeyang Zhou
creator: Chunfeng Li
subject: Microbiology
subject: Molecular Biology
subject: Parasitology
description: doi:10.7717/peerj.5658
publisher: PeerJ Inc.
rights: © 2018 Huang et al.
abstract: The microsporidian Nosema bombycis is an obligate intracellular parasite of Bombyx mori, that lost its intact tricarboxylic acid cycle and mitochondria during evolution but retained its intact glycolysis pathway. N. bombycis hexokinase (NbHK) is not only a rate-limiting enzyme of glycolysis but also a secretory protein. Indirect immunofluorescence assays and recombinant HK overexpressed in BmN cells showed that NbHK localized in the nucleus and cytoplasm of host cell during the meront stage. When N. bombycis matured, NbHK tended to concentrate at the nuclei of host cells. Furthermore, the transcriptional profile of NbHK implied it functioned during N. bombycis’ proliferation stages. A knock-down of NbHK effectively suppressed the proliferation of N. bombycis indicating that NbHK is an important protein for parasite to control its host.
bibliographic citation: Huang et al. (2018) A secretory hexokinase plays an active role in the proliferation of Nosema bombycis. PeerJ 6:e5658 https://doi.org/10.7717/peerj.5658
date submitted: 2018-06-08
date accepted: 2018-08-28
issued: 2018-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Yukang
author list: Agent
  family name: Zheng
  given name: Shiyi
author list: Agent
  family name: Mei
  given name: Xionge
author list: Agent
  family name: Yu
  given name: Bin
author list: Agent
  family name: Sun
  given name: Bin
author list: Agent
  family name: Li
  given name: Boning
author list: Agent
  family name: Wei
  given name: Junhong
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Li
  given name: Tian
author list: Agent
  family name: Pan
  given name: Guoqing
author list: Agent
  family name: Zhou
  given name: Zeyang
author list: Agent
  family name: Li
  given name: Chunfeng
doi: 10.7717/peerj.5658
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-21
copyright: ©2018 Huang et al.
attribution name: Huang et al.

Does Twitter language reliably predict heart disease? A commentary on Eichstaedt et al. (2015a)
type: item
type: AcademicArticle
description: We comment on Eichstaedt et al.’s (2015a) claim to have shown that language patterns among Twitter users, aggregated at the level of US counties, predicted county-level mortality rates from atherosclerotic heart disease (AHD), with “negative” language being associated with higher rates of death from AHD and “positive” language associated with lower rates. First, we examine some of Eichstaedt et al.’s apparent assumptions about the nature of AHD, as well as some issues related to the secondary analysis of online data and to considering counties as communities. Next, using the data files supplied by Eichstaedt et al., we reproduce their regression- and correlation-based models, substituting mortality from an alternative cause of death—namely, suicide—as the outcome variable, and observe that the purported associations between “negative” and “positive” language and mortality are reversed when suicide is used as the outcome variable. We identify numerous other conceptual and methodological limitations that call into question the robustness and generalizability of Eichstaedt et al.’s claims, even when these are based on the results of their ridge regression/machine learning model. We conclude that there is no good evidence that analyzing Twitter data in bulk in this way can add anything useful to our ability to understand geographical variation in AHD mortality rates.
format: application/pdf
format: text/html
creator: Nicholas J.L. Brown
creator: James C. Coyne
subject: Epidemiology
subject: Health Policy
subject: Psychiatry and Psychology
subject: Public Health
subject: Statistics
description: doi:10.7717/peerj.5656
publisher: PeerJ Inc.
rights: © 2018 Brown and Coyne
abstract: We comment on Eichstaedt et al.’s (2015a) claim to have shown that language patterns among Twitter users, aggregated at the level of US counties, predicted county-level mortality rates from atherosclerotic heart disease (AHD), with “negative” language being associated with higher rates of death from AHD and “positive” language associated with lower rates. First, we examine some of Eichstaedt et al.’s apparent assumptions about the nature of AHD, as well as some issues related to the secondary analysis of online data and to considering counties as communities. Next, using the data files supplied by Eichstaedt et al., we reproduce their regression- and correlation-based models, substituting mortality from an alternative cause of death—namely, suicide—as the outcome variable, and observe that the purported associations between “negative” and “positive” language and mortality are reversed when suicide is used as the outcome variable. We identify numerous other conceptual and methodological limitations that call into question the robustness and generalizability of Eichstaedt et al.’s claims, even when these are based on the results of their ridge regression/machine learning model. We conclude that there is no good evidence that analyzing Twitter data in bulk in this way can add anything useful to our ability to understand geographical variation in AHD mortality rates.
bibliographic citation: Brown et al. (2018) Does Twitter language reliably predict heart disease? A commentary on Eichstaedt et al. (2015a). PeerJ 6:e5656 https://doi.org/10.7717/peerj.5656
date submitted: 2018-03-06
date accepted: 2018-08-28
issued: 2018-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brown
  given name: Nicholas J.L.
author list: Agent
  family name: Coyne
  given name: James C.
doi: 10.7717/peerj.5656
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-21
copyright: ©2018 Brown and Coyne
attribution name: Brown and Coyne

How much genetic variation is stored in the endangered and fragmented shrub Tetraena mongolica Maxim?
type: item
type: AcademicArticle
description: Tetraena mongolica Maxim (Zygophyllaceae) is an endangered species endemic to western Inner Mongolia and China, and is currently threatened by habitat loss and human over-exploitation. We explored the genetic background, its genetic diversity, population structure, and demographic history, based on 12 polymorphic nuclear microsatellite loci. Our results indicated high genetic diversity in extant populations, but no distinguishable gene cluster corresponding with a specific biogeography. Population demography analysis using a MSVAR indicated a strong, recent population decline approximately 5,455 years ago. These results suggest that the Yellow River and Zhuozi Mountain range may not prevent pollination between populations. Finally, we surmised that the population demography of T. mongolica was likely to have been affected by early mankind activities.
format: application/pdf
format: text/html
creator: Yingbiao Zhi
creator: Zhonglou Sun
creator: Ping Sun
creator: Kai Zhao
creator: Yangnan Guo
creator: Dejian Zhang
creator: Baowei Zhang
subject: Conservation Biology
subject: Ecology
subject: Population Biology
description: doi:10.7717/peerj.5645
publisher: PeerJ Inc.
rights: © 2018 Zhi et al.
abstract: Tetraena mongolica Maxim (Zygophyllaceae) is an endangered species endemic to western Inner Mongolia and China, and is currently threatened by habitat loss and human over-exploitation. We explored the genetic background, its genetic diversity, population structure, and demographic history, based on 12 polymorphic nuclear microsatellite loci. Our results indicated high genetic diversity in extant populations, but no distinguishable gene cluster corresponding with a specific biogeography. Population demography analysis using a MSVAR indicated a strong, recent population decline approximately 5,455 years ago. These results suggest that the Yellow River and Zhuozi Mountain range may not prevent pollination between populations. Finally, we surmised that the population demography of T. mongolica was likely to have been affected by early mankind activities.
bibliographic citation: Zhi et al. (2018) How much genetic variation is stored in the endangered and fragmented shrub Tetraena mongolica Maxim?. PeerJ 6:e5645 https://doi.org/10.7717/peerj.5645
date submitted: 2018-04-25
date accepted: 2018-08-27
issued: 2018-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhi
  given name: Yingbiao
author list: Agent
  family name: Sun
  given name: Zhonglou
author list: Agent
  family name: Sun
  given name: Ping
author list: Agent
  family name: Zhao
  given name: Kai
author list: Agent
  family name: Guo
  given name: Yangnan
author list: Agent
  family name: Zhang
  given name: Dejian
author list: Agent
  family name: Zhang
  given name: Baowei
doi: 10.7717/peerj.5645
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-21
copyright: ©2018 Zhi et al.
attribution name: Zhi et al.

Short-tailed mice with a long fossil record: the genus Leggadina (Rodentia: Muridae) from the Quaternary of Queensland, Australia
type: item
type: AcademicArticle
description: The genus Leggadina (colloquially known as ‘short-tailed mice’) is a common component of Quaternary faunas of northeastern Australia. They represent a member of the Australian old endemic murid radiation that arrived on the continent sometime during the late Cenozoic. Here we describe two new species of extinct Leggadina from Quaternary cave deposits as well as additional material of the extinct Leggadina macrodonta. Leggadina irvini sp. nov. recovered from Middle-Upper (late) Pleistocene cave deposits near Chillagoe, northeastern Queensland, is the biggest member of the genus, being substantially larger than any other species so far described. Leggadina webbi sp. nov. from Middle Pleistocene cave deposits at Mount Etna, central eastern Queensland, shares features with the oldest species of the genus, the Early Pleistocene L. gregoriensis. Based on the current palaeoecological interpretation of the type locality, L. webbi, represents the only member of the genus that inhabited rainforest. The succession of Leggadina species through the late Quaternary suggests an ecological replacement of the extinct large-bodied L. irvini with the extant, small-bodied L. lakedownesis at Chillagoe. At Mt. Etna, the extinct rainforest species L. webbi is replaced with the extant xeric-adapted L. forresti during the latest Middle Pleistocene. This replacement is associated with a mid-Pleistocene shift towards progressive intensifying seasonal and arid climates. Our study adds to the growing list of small-bodied faunal extinctions during the late Quaternary of northern Australia.
format: application/pdf
format: text/html
creator: Jonathan Cramb
creator: Gilbert J. Price
creator: Scott A. Hocknull
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.5639
publisher: PeerJ Inc.
rights: © 2018 Cramb et al.
abstract: The genus Leggadina (colloquially known as ‘short-tailed mice’) is a common component of Quaternary faunas of northeastern Australia. They represent a member of the Australian old endemic murid radiation that arrived on the continent sometime during the late Cenozoic. Here we describe two new species of extinct Leggadina from Quaternary cave deposits as well as additional material of the extinct Leggadina macrodonta. Leggadina irvini sp. nov. recovered from Middle-Upper (late) Pleistocene cave deposits near Chillagoe, northeastern Queensland, is the biggest member of the genus, being substantially larger than any other species so far described. Leggadina webbi sp. nov. from Middle Pleistocene cave deposits at Mount Etna, central eastern Queensland, shares features with the oldest species of the genus, the Early Pleistocene L. gregoriensis. Based on the current palaeoecological interpretation of the type locality, L. webbi, represents the only member of the genus that inhabited rainforest. The succession of Leggadina species through the late Quaternary suggests an ecological replacement of the extinct large-bodied L. irvini with the extant, small-bodied L. lakedownesis at Chillagoe. At Mt. Etna, the extinct rainforest species L. webbi is replaced with the extant xeric-adapted L. forresti during the latest Middle Pleistocene. This replacement is associated with a mid-Pleistocene shift towards progressive intensifying seasonal and arid climates. Our study adds to the growing list of small-bodied faunal extinctions during the late Quaternary of northern Australia.
bibliographic citation: Cramb et al. (2018) Short-tailed mice with a long fossil record: the genus Leggadina (Rodentia: Muridae) from the Quaternary of Queensland, Australia. PeerJ 6:e5639 https://doi.org/10.7717/peerj.5639
date submitted: 2018-03-09
date accepted: 2018-08-27
issued: 2018-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cramb
  given name: Jonathan
author list: Agent
  family name: Price
  given name: Gilbert J.
author list: Agent
  family name: Hocknull
  given name: Scott A.
doi: 10.7717/peerj.5639
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-21
copyright: ©2018 Cramb et al.
attribution name: Cramb et al.

Interleukin 35 induced Th2 and Tregs bias under normal conditions in mice
type: item
type: AcademicArticle
description: Objective The benefits of IL-35 treatment have been verified in multiple animal models of diseases, while its influence on T cells immunity under normal condition still needs to be elucidated. The present study was designed to investigate the effects modulating IL-35 levels in vivo and in vitro on T cells, response and also the effects on T cells subsets in normal mice. Methods A plasmid pMSCV-IL-35-GFP carrying mouse linear IL-35 fragment with two subunits joint together was constructed and the heterodimer expression was confirmed. Normal mice were randomly divided into three groups and received an intravenous injection of PBS, pMSCV-GFP and pMSCV-IL-35-GFP respectively. After 72 h, spleen tissues and peripheral blood were harvested for following analysis. Meanwhile, splenic T cells were isolated and incubated with 10, 30, or 50 ng/mL recombinant IL-35 factor for 24 h with the addition of anti-CD3/CD28 in vitro. T-cell subsets were assessed by Fluorescence activated cell sorting (FACS) and related cytokines together with effector molecules were determined by real time PCR. Results Western blotting confirmed a 52 kDa band in the cell lysate of HEK 293T transducted with pMSCV-IL-35-GFP plasmid, indicating a successful expression of IL-35. Ebi3 and IL-12A, two subunits of IL-35, could be identified 72 h post DNA injection. IL-35 upregulation in vivo effectively inhibit CD4+ and CD8+ T cell proliferation and Th1 cytokine secretion. Effector molecules of CD8+ T cells were also remarkably suppressed. On the contrary, high level of IL-35 significantly induced CD4+ CD25+ Tregs and Th2 enhancement. The in vitro study provided similar results. Conclusion The results indicated Th1 and CD8+ T cell inhibition and Th2 and Tregs bias in the presence of IL-35 under a normal state which partly contributed to its therapeutic potential.
format: application/pdf
format: text/html
creator: Xiaoning Zhang
creator: Zhiqiang Zhang
creator: Zhiqiang He
creator: Mingyan Ju
creator: Jiaci Li
creator: Jinghua Yuan
creator: Yaqing Jing
creator: Keqiu Li
creator: Yi Liu
creator: Guang Li
subject: Immunology
subject: Translational Medicine
description: doi:10.7717/peerj.5638
publisher: PeerJ Inc.
rights: © 2018 Zhang et al.
abstract: Objective The benefits of IL-35 treatment have been verified in multiple animal models of diseases, while its influence on T cells immunity under normal condition still needs to be elucidated. The present study was designed to investigate the effects modulating IL-35 levels in vivo and in vitro on T cells, response and also the effects on T cells subsets in normal mice. Methods A plasmid pMSCV-IL-35-GFP carrying mouse linear IL-35 fragment with two subunits joint together was constructed and the heterodimer expression was confirmed. Normal mice were randomly divided into three groups and received an intravenous injection of PBS, pMSCV-GFP and pMSCV-IL-35-GFP respectively. After 72 h, spleen tissues and peripheral blood were harvested for following analysis. Meanwhile, splenic T cells were isolated and incubated with 10, 30, or 50 ng/mL recombinant IL-35 factor for 24 h with the addition of anti-CD3/CD28 in vitro. T-cell subsets were assessed by Fluorescence activated cell sorting (FACS) and related cytokines together with effector molecules were determined by real time PCR. Results Western blotting confirmed a 52 kDa band in the cell lysate of HEK 293T transducted with pMSCV-IL-35-GFP plasmid, indicating a successful expression of IL-35. Ebi3 and IL-12A, two subunits of IL-35, could be identified 72 h post DNA injection. IL-35 upregulation in vivo effectively inhibit CD4+ and CD8+ T cell proliferation and Th1 cytokine secretion. Effector molecules of CD8+ T cells were also remarkably suppressed. On the contrary, high level of IL-35 significantly induced CD4+ CD25+ Tregs and Th2 enhancement. The in vitro study provided similar results. Conclusion The results indicated Th1 and CD8+ T cell inhibition and Th2 and Tregs bias in the presence of IL-35 under a normal state which partly contributed to its therapeutic potential.
bibliographic citation: Zhang et al. (2018) Interleukin 35 induced Th2 and Tregs bias under normal conditions in mice. PeerJ 6:e5638 https://doi.org/10.7717/peerj.5638
date submitted: 2018-05-01
date accepted: 2018-08-24
issued: 2018-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiaoning
author list: Agent
  family name: Zhang
  given name: Zhiqiang
author list: Agent
  family name: He
  given name: Zhiqiang
author list: Agent
  family name: Ju
  given name: Mingyan
author list: Agent
  family name: Li
  given name: Jiaci
author list: Agent
  family name: Yuan
  given name: Jinghua
author list: Agent
  family name: Jing
  given name: Yaqing
author list: Agent
  family name: Li
  given name: Keqiu
author list: Agent
  family name: Liu
  given name: Yi
author list: Agent
  family name: Li
  given name: Guang
doi: 10.7717/peerj.5638
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-21
copyright: ©2018 Zhang et al.
attribution name: Zhang et al.

Plant dominance in a subalpine montane meadow: biotic vs. abiotic controls of subordinate diversity within and across sites
type: item
type: AcademicArticle
description: Background Understanding the underlying factors that determine the relative abundance of plant species is critical to predict both biodiversity and ecosystem function. Biotic and abiotic factors can shape the distribution and the relative abundance of species across natural communities, greatly influencing local biodiversity. Methods Using a combination of an observational study and a five-year plant removal experiment we: (1) documented how plant diversity and composition of montane meadow assemblages vary along a plant dominance gradient using an observational study; (2) tracked above- and belowground functional traits of co-dominant plant species Potentilla and Festuca along a plant dominance gradient in an observational study; (3) determined whether plant species diversity and composition was directly influenced by commonly occurring species Potentilla and Festuca with the use of a randomized plot design, 5-year plant removal experiment (no removal control, Potentilla removed, Festuca removed, n = 10). Results We found that subordinate species diversity and compositional dissimilarity were greatest in Potentilla and Festuca co-dominated sites, where neither Potentilla nor Festuca dominated, rather than at sites where either species became dominant. Further, while above- and belowground plant functional traits varied along a dominance gradient, they did so in a way that inconsistently predicted plant species relative abundance. Also, neither variation in plant functional traits of Festuca and Potentilla nor variation in resources and conditions (such as soil nitrogen and temperature) explained our subordinate diversity patterns. Finally, neither Potentilla nor Festuca influenced subordinate diversity or composition when we directly tested for their impacts in a plant removal experiment. Discussion Taken together, patterns of subordinate diversity and composition were likely driven by abiotic factors rather than biotic interactions. As a result, the role of abioti…
format: application/pdf
format: text/html
creator: Erika LaPlante
creator: Lara Souza
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.5619
publisher: PeerJ Inc.
rights: © 2018 LaPlante and Souza
abstract: Background Understanding the underlying factors that determine the relative abundance of plant species is critical to predict both biodiversity and ecosystem function. Biotic and abiotic factors can shape the distribution and the relative abundance of species across natural communities, greatly influencing local biodiversity. Methods Using a combination of an observational study and a five-year plant removal experiment we: (1) documented how plant diversity and composition of montane meadow assemblages vary along a plant dominance gradient using an observational study; (2) tracked above- and belowground functional traits of co-dominant plant species Potentilla and Festuca along a plant dominance gradient in an observational study; (3) determined whether plant species diversity and composition was directly influenced by commonly occurring species Potentilla and Festuca with the use of a randomized plot design, 5-year plant removal experiment (no removal control, Potentilla removed, Festuca removed, n = 10). Results We found that subordinate species diversity and compositional dissimilarity were greatest in Potentilla and Festuca co-dominated sites, where neither Potentilla nor Festuca dominated, rather than at sites where either species became dominant. Further, while above- and belowground plant functional traits varied along a dominance gradient, they did so in a way that inconsistently predicted plant species relative abundance. Also, neither variation in plant functional traits of Festuca and Potentilla nor variation in resources and conditions (such as soil nitrogen and temperature) explained our subordinate diversity patterns. Finally, neither Potentilla nor Festuca influenced subordinate diversity or composition when we directly tested for their impacts in a plant removal experiment. Discussion Taken together, patterns of subordinate diversity and composition were likely driven by abiotic factors rather than biotic interactions. As a result, the role of abioti…
bibliographic citation: LaPlante et al. (2018) Plant dominance in a subalpine montane meadow: biotic vs. abiotic controls of subordinate diversity within and across sites. PeerJ 6:e5619 https://doi.org/10.7717/peerj.5619
date submitted: 2018-03-07
date accepted: 2018-08-18
issued: 2018-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: LaPlante
  given name: Erika
author list: Agent
  family name: Souza
  given name: Lara
doi: 10.7717/peerj.5619
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-21
copyright: ©2018 LaPlante and Souza
attribution name: LaPlante and Souza

Improving remote estimation of winter crops gross ecosystem production by inclusion of leaf area index in a spectral model
type: item
type: AcademicArticle
description: The hysteresis of the seasonal relationships between vegetation indices (VIs) and gross ecosystem production (GEP) results in differences between these relationships during vegetative and reproductive phases of plant development cycle and may limit their applicability for estimation of croplands productivity over the entire season. To mitigate this problem and to increase the accuracy of remote sensing-based models for GEP estimation we developed a simple empirical model where greenness-related VIs are multiplied by the leaf area index (LAI). The product of this multiplication has the same seasonality as GEP, and specifically for vegetative periods of winter crops, it allowed the accuracy of GEP estimations to increase and resulted in a significant reduction of the hysteresis of VIs vs. GEP. Our objective was to test the multiyear relationships between VIs and daily GEP in order to develop more general models maintaining reliable performance when applied to years characterized by different climatic conditions. The general model parametrized with NDVI and LAI product allowed to estimate daily GEP of winter and spring crops with an error smaller than 14%, and the rate of GEP over- (for spring barley) or underestimation (for winter crops and potato) was smaller than 25%. The proposed approach may increase the accuracy of crop productivity estimation when greenness VIs are saturating early in the growing season.
format: application/pdf
format: text/html
creator: Radosław Juszczak
creator: Bogna Uździcka
creator: Marcin Stróżecki
creator: Karolina Sakowska
subject: Agricultural Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.5613
publisher: PeerJ Inc.
rights: © 2018 Juszczak et al.
abstract: The hysteresis of the seasonal relationships between vegetation indices (VIs) and gross ecosystem production (GEP) results in differences between these relationships during vegetative and reproductive phases of plant development cycle and may limit their applicability for estimation of croplands productivity over the entire season. To mitigate this problem and to increase the accuracy of remote sensing-based models for GEP estimation we developed a simple empirical model where greenness-related VIs are multiplied by the leaf area index (LAI). The product of this multiplication has the same seasonality as GEP, and specifically for vegetative periods of winter crops, it allowed the accuracy of GEP estimations to increase and resulted in a significant reduction of the hysteresis of VIs vs. GEP. Our objective was to test the multiyear relationships between VIs and daily GEP in order to develop more general models maintaining reliable performance when applied to years characterized by different climatic conditions. The general model parametrized with NDVI and LAI product allowed to estimate daily GEP of winter and spring crops with an error smaller than 14%, and the rate of GEP over- (for spring barley) or underestimation (for winter crops and potato) was smaller than 25%. The proposed approach may increase the accuracy of crop productivity estimation when greenness VIs are saturating early in the growing season.
bibliographic citation: Juszczak et al. (2018) Improving remote estimation of winter crops gross ecosystem production by inclusion of leaf area index in a spectral model. PeerJ 6:e5613 https://doi.org/10.7717/peerj.5613
date submitted: 2018-06-15
date accepted: 2018-08-21
issued: 2018-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Juszczak
  given name: Radosław
author list: Agent
  family name: Uździcka
  given name: Bogna
author list: Agent
  family name: Stróżecki
  given name: Marcin
author list: Agent
  family name: Sakowska
  given name: Karolina
doi: 10.7717/peerj.5613
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-21
copyright: ©2018 Juszczak et al.
attribution name: Juszczak et al.

Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes
type: item
type: AcademicArticle
description: Background Denitrification is one of the main pathways of the N-cycle, during which nitrate is converted to dinitrogen gas, in four consecutive reactions that are each catalyzed by a different metalloenzyme. One of the intermediate metabolites is nitrous oxide, which has a global warming impact greater then carbon dioxide and which atmospheric concentration has been increasing in the last years. The four denitrification enzymes have been isolated and biochemically characterized from Marinobacter hydrocarbonoclasticus in our lab. Methods Bioinformatic analysis of the M. hydrocarbonoclasticus genome to identify the genes involved in the denitrification pathway. The relative gene expression of the gene encoding the catalytic subunits of those enzymes was analyzed during the growth under microoxic conditions. The consumption of nitrate and nitrite, and the reduction of nitric oxide and nitrous oxide by whole-cells was monitored during anoxic and microoxic growth in the presence of 10 mM sodium nitrate at pH 7.5. Results The bioinformatic analysis shows that genes encoding the enzymes and accessory factors required for each step of the denitrification pathway are clustered together. An unusual feature is the co-existence of genes encoding a q- and a c-type nitric oxide reductase, with only the latter being transcribed at similar levels as the ones encoding the catalytic subunits of the other denitrifying enzymes, when cells are grown in the presence of nitrate under microoxic conditions. Using either a batch- or a closed system, nitrate is completely consumed in the beginning of the growth, with transient formation of nitrite, and whole-cells can reduce nitric oxide and nitrous oxide from mid-exponential phase until being collected (time-point 50 h). Discussion M. hydrocarbonoclasticus cells can reduce nitric and nitrous oxide in vivo, indicating that the four denitrification steps are active. Gene expression profile together with promoter regions analysis indicates the …
format: application/pdf
format: text/html
creator: Cíntia Carreira
creator: Olga Mestre
creator: Rute F. Nunes
creator: Isabel Moura
creator: Sofia R. Pauleta
subject: Biochemistry
subject: Marine Biology
subject: Microbiology
subject: Aquatic and Marine Chemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.5603
publisher: PeerJ Inc.
rights: © 2018 Carreira et al.
abstract: Background Denitrification is one of the main pathways of the N-cycle, during which nitrate is converted to dinitrogen gas, in four consecutive reactions that are each catalyzed by a different metalloenzyme. One of the intermediate metabolites is nitrous oxide, which has a global warming impact greater then carbon dioxide and which atmospheric concentration has been increasing in the last years. The four denitrification enzymes have been isolated and biochemically characterized from Marinobacter hydrocarbonoclasticus in our lab. Methods Bioinformatic analysis of the M. hydrocarbonoclasticus genome to identify the genes involved in the denitrification pathway. The relative gene expression of the gene encoding the catalytic subunits of those enzymes was analyzed during the growth under microoxic conditions. The consumption of nitrate and nitrite, and the reduction of nitric oxide and nitrous oxide by whole-cells was monitored during anoxic and microoxic growth in the presence of 10 mM sodium nitrate at pH 7.5. Results The bioinformatic analysis shows that genes encoding the enzymes and accessory factors required for each step of the denitrification pathway are clustered together. An unusual feature is the co-existence of genes encoding a q- and a c-type nitric oxide reductase, with only the latter being transcribed at similar levels as the ones encoding the catalytic subunits of the other denitrifying enzymes, when cells are grown in the presence of nitrate under microoxic conditions. Using either a batch- or a closed system, nitrate is completely consumed in the beginning of the growth, with transient formation of nitrite, and whole-cells can reduce nitric oxide and nitrous oxide from mid-exponential phase until being collected (time-point 50 h). Discussion M. hydrocarbonoclasticus cells can reduce nitric and nitrous oxide in vivo, indicating that the four denitrification steps are active. Gene expression profile together with promoter regions analysis indicates the …
bibliographic citation: Carreira et al. (2018) Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes. PeerJ 6:e5603 https://doi.org/10.7717/peerj.5603
date submitted: 2018-03-07
date accepted: 2018-08-18
issued: 2018-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carreira
  given name: Cíntia
author list: Agent
  family name: Mestre
  given name: Olga
author list: Agent
  family name: Nunes
  given name: Rute F.
author list: Agent
  family name: Moura
  given name: Isabel
author list: Agent
  family name: Pauleta
  given name: Sofia R.
doi: 10.7717/peerj.5603
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-21
copyright: ©2018 Carreira et al.
attribution name: Carreira et al.

The genetic status of the Hungarian brown trout populations: exploration of a blind spot on the European map of Salmo trutta studies
type: item
type: AcademicArticle
description: Background Analyses of the control region sequences of European brown trout populations’ mitrochondrial DNA have revealed five main evolutionary lineages (Atlantic, Danubian, Mediterranean, Adriatic, Marble) mostly relating to the main water basins; however, the hybridization between lineages were increasingly reported. Due to the hydrogeography of Hungary, wild populations should theoretically belong to the Danubian lineage, however, this has not been verified by genetic studies. Methods In our study multiple molecular marker sets (mitochondrial sequence, microsatellites, PCR-RFLP of nuclear markers and sex marker) were used to investigate the genetic composition and population genetics of the brown trout populations in two broodstocks, six wild streams in Hungary and one Serbian population. Results The admixture of Atlantic and Danubian lineages in these populations, except the Serbian population with pure Danubian origin, was observed by control region sequences of mitochondrial DNA and PCR-RFLP markers in the nuclear genome, and one unpublished Danubian haplotype was found in Hungarian populations. A sex-specific marker revealed equal gender ratio in broodstocks and Kemence stream, whereas in other wild streams the proportion of female individuals were less than 50%. Structure and principal component analyses based on the alleles of microsatellite loci also revealed overlapping populations, however the populations were still significantly different from each other and were mostly in Hardy-Weinberg equilibrium. Discussion Stocking and migration can have a significant genetic impact on trout populations of wild streams, however there are no guidelines or common practices for stocking of small streams in Hungary, thus the genetic background of these populations should be considered when developing conservation actions.
format: application/pdf
format: text/html
creator: Ágnes Ősz
creator: Ákos Horváth
creator: György Hoitsy
creator: Dóra Kánainé Sipos
creator: Szilvia Keszte
creator: Anna Júlia Sáfrány
creator: Saša Marić
creator: Csaba Palkó
creator: Balázs Tóth
creator: Béla Urbányi
creator: Balázs Kovács
subject: Aquaculture, Fisheries and Fish Science
subject: Genetics
subject: Population Biology
description: doi:10.7717/peerj.5152
publisher: PeerJ Inc.
rights: © 2018 Ősz et al.
abstract: Background Analyses of the control region sequences of European brown trout populations’ mitrochondrial DNA have revealed five main evolutionary lineages (Atlantic, Danubian, Mediterranean, Adriatic, Marble) mostly relating to the main water basins; however, the hybridization between lineages were increasingly reported. Due to the hydrogeography of Hungary, wild populations should theoretically belong to the Danubian lineage, however, this has not been verified by genetic studies. Methods In our study multiple molecular marker sets (mitochondrial sequence, microsatellites, PCR-RFLP of nuclear markers and sex marker) were used to investigate the genetic composition and population genetics of the brown trout populations in two broodstocks, six wild streams in Hungary and one Serbian population. Results The admixture of Atlantic and Danubian lineages in these populations, except the Serbian population with pure Danubian origin, was observed by control region sequences of mitochondrial DNA and PCR-RFLP markers in the nuclear genome, and one unpublished Danubian haplotype was found in Hungarian populations. A sex-specific marker revealed equal gender ratio in broodstocks and Kemence stream, whereas in other wild streams the proportion of female individuals were less than 50%. Structure and principal component analyses based on the alleles of microsatellite loci also revealed overlapping populations, however the populations were still significantly different from each other and were mostly in Hardy-Weinberg equilibrium. Discussion Stocking and migration can have a significant genetic impact on trout populations of wild streams, however there are no guidelines or common practices for stocking of small streams in Hungary, thus the genetic background of these populations should be considered when developing conservation actions.
bibliographic citation: Ősz et al. (2018) The genetic status of the Hungarian brown trout populations: exploration of a blind spot on the European map of Salmo trutta studies. PeerJ 6:e5152 https://doi.org/10.7717/peerj.5152
date submitted: 2018-01-23
date accepted: 2018-06-11
issued: 2018-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ősz
  given name: Ágnes
author list: Agent
  family name: Horváth
  given name: Ákos
author list: Agent
  family name: Hoitsy
  given name: György
author list: Agent
  family name: Kánainé Sipos
  given name: Dóra
author list: Agent
  family name: Keszte
  given name: Szilvia
author list: Agent
  family name: Sáfrány
  given name: Anna Júlia
author list: Agent
  family name: Marić
  given name: Saša
author list: Agent
  family name: Palkó
  given name: Csaba
author list: Agent
  family name: Tóth
  given name: Balázs
author list: Agent
  family name: Urbányi
  given name: Béla
author list: Agent
  family name: Kovács
  given name: Balázs
doi: 10.7717/peerj.5152
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-21
copyright: ©2018 Ősz et al.
attribution name: Ősz et al.

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