PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Habitat conditions strongly affect macro- and microelement concentrations in Taraxacum microspecies growing on coastal meadows along a soil salinity gradient
items: Spatially resolved dendritic integration: towards a functional classification of neurons
items: DPM1 expression as a potential prognostic tumor marker in hepatocellular carcinoma
items: HIV-1 promoter is gradually silenced when integrated into BACH2 in Jurkat T-cells
items: Wnt16 signaling promotes osteoblast differentiation of periosteal derived cells in vitro and in vivo
items: Modelling the effects of Spartina alterniflora invasion on the landscape succession of Yancheng coastal natural wetlands, China
items: The paleobiology and paleoecology of South African Lystrosaurus
items: Classification of ovarian cancer associated with BRCA1 mutations, immune checkpoints, and tumor microenvironment based on immunogenomic profiling
items: The pandemic paradox: domestic violence and happiness of women
items: Two new species of Tardigrada from moss cushions (Grimmia sp.) in a xerothermic habitat in northeast Tennessee (USA, North America), with the first identification of males in the genus Viridiscus

Habitat conditions strongly affect macro- and microelement concentrations in Taraxacum microspecies growing on coastal meadows along a soil salinity gradient
type: item
type: AcademicArticle
description: Wild greens can contribute to the human diet as an important source of essential nutrients and drugs. Since environmental factors, including soil properties, may affect the chemical composition of plants, it is necessary among others to assess various habitats in terms of their usefulness for wild plant harvesting and to study impact of environmental factors on the qualitative and quantitative chemical composition of plants. This study was aimed at (1) examining the mineral composition of leaves of three dandelion microspecies, (2) determining the variability of macro- and microelement concentrations in dandelion leaves from populations growing on salty, brackish and non-saline coastal meadows, and (3) assessing the effects of different habitat conditions on the mineral composition of dandelion leaves. It was hypothesized that dandelion microspecies would differ significantly in the mineral composition of leaves. It was also expected that soil conditions would significantly affect nutrient concentrations in dandelion leaves, with soil salinity being the most important factor that differentiated studied populations. Leaves of three dandelion microspecies (Taraxacum balticum, T. nordstedtii, T. haematicum) were harvested in Baltic costal grasslands, along the soil salinity gradient, to determine macro- and microelement concentrations. Soil samples collected in the closest vicinity of the harvested plants showed the study sites to differ significantly in their soil properties. Moderately saline and organic soils, rich in potassium (K), magnesium (Mg), and calcium (Ca), supported T. balticum. Moderately or weakly saline and non-saline, organic or mineral soils, with lower median values of K, Mg, and Ca, were typical of T. nordstedtii sites, while the lowest median values of all the soil properties studied were found for T. haematicum sites. Our results proved that dandelion microspecies differ significantly in the mineral composition of their leaves. The between-microsp…
format: application/pdf
format: text/html
creator: Beata Bosiacka
creator: Monika Myśliwy
creator: Mateusz Bosiacki
subject: Biogeography
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Environmental Impacts
description: doi:10.7717/peerj.10233
publisher: PeerJ Inc.
rights: © 2020 Bosiacka et al.
abstract: Wild greens can contribute to the human diet as an important source of essential nutrients and drugs. Since environmental factors, including soil properties, may affect the chemical composition of plants, it is necessary among others to assess various habitats in terms of their usefulness for wild plant harvesting and to study impact of environmental factors on the qualitative and quantitative chemical composition of plants. This study was aimed at (1) examining the mineral composition of leaves of three dandelion microspecies, (2) determining the variability of macro- and microelement concentrations in dandelion leaves from populations growing on salty, brackish and non-saline coastal meadows, and (3) assessing the effects of different habitat conditions on the mineral composition of dandelion leaves. It was hypothesized that dandelion microspecies would differ significantly in the mineral composition of leaves. It was also expected that soil conditions would significantly affect nutrient concentrations in dandelion leaves, with soil salinity being the most important factor that differentiated studied populations. Leaves of three dandelion microspecies (Taraxacum balticum, T. nordstedtii, T. haematicum) were harvested in Baltic costal grasslands, along the soil salinity gradient, to determine macro- and microelement concentrations. Soil samples collected in the closest vicinity of the harvested plants showed the study sites to differ significantly in their soil properties. Moderately saline and organic soils, rich in potassium (K), magnesium (Mg), and calcium (Ca), supported T. balticum. Moderately or weakly saline and non-saline, organic or mineral soils, with lower median values of K, Mg, and Ca, were typical of T. nordstedtii sites, while the lowest median values of all the soil properties studied were found for T. haematicum sites. Our results proved that dandelion microspecies differ significantly in the mineral composition of their leaves. The between-microsp…
bibliographic citation: Bosiacka et al. (2020) Habitat conditions strongly affect macro- and microelement concentrations in Taraxacum microspecies growing on coastal meadows along a soil salinity gradient. PeerJ 8:e10233 https://doi.org/10.7717/peerj.10233
date submitted: 2020-06-15
date accepted: 2020-10-02
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bosiacka
  given name: Beata
author list: Agent
  family name: Myśliwy
  given name: Monika
author list: Agent
  family name: Bosiacki
  given name: Mateusz
doi: 10.7717/peerj.10233
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: ©2020 Bosiacka et al.
attribution name: Bosiacka et al.

Spatially resolved dendritic integration: towards a functional classification of neurons
type: item
type: AcademicArticle
description: The vast tree-like dendritic structure of neurons allows them to receive and integrate input from many neurons. A wide variety of neuronal morphologies exist, however, their role in dendritic integration, and how it shapes the response of the neuron, is not yet fully understood. Here, we study the evolution and interactions of dendritic spikes in excitable neurons with complex real branch structures. We focus on dozens of digitally reconstructed illustrative neurons from the online repository NeuroMorpho.org, which contains over 130,000 neurons. Yet, our methods can be promptly extended to any other neuron. This approach allows us to estimate and map specific and heterogeneous patterns of activity observed across extensive dendritic trees with thousands of compartments. We propose a classification of neurons based on the location of the soma (centrality) and the number of branches connected to the soma. These are key topological factors in determining the neuron’s energy consumption, firing rate, and the dynamic range, which quantifies the range in synaptic input rate that can be reliably encoded by the neuron’s firing rate. Moreover, we find that bifurcations, the structural building blocks of complex dendrites, play a major role in increasing the dynamic range of neurons. Our results provide a better understanding of the effects of neuronal morphology in the diversity of neuronal dynamics and function.
format: application/pdf
format: text/html
creator: Christoph Kirch
creator: Leonardo L. Gollo
subject: Computational Biology
subject: Mathematical Biology
subject: Neuroscience
subject: Data Science
description: doi:10.7717/peerj.10250
publisher: PeerJ Inc.
rights: © 2020 Kirch and Gollo
abstract: The vast tree-like dendritic structure of neurons allows them to receive and integrate input from many neurons. A wide variety of neuronal morphologies exist, however, their role in dendritic integration, and how it shapes the response of the neuron, is not yet fully understood. Here, we study the evolution and interactions of dendritic spikes in excitable neurons with complex real branch structures. We focus on dozens of digitally reconstructed illustrative neurons from the online repository NeuroMorpho.org, which contains over 130,000 neurons. Yet, our methods can be promptly extended to any other neuron. This approach allows us to estimate and map specific and heterogeneous patterns of activity observed across extensive dendritic trees with thousands of compartments. We propose a classification of neurons based on the location of the soma (centrality) and the number of branches connected to the soma. These are key topological factors in determining the neuron’s energy consumption, firing rate, and the dynamic range, which quantifies the range in synaptic input rate that can be reliably encoded by the neuron’s firing rate. Moreover, we find that bifurcations, the structural building blocks of complex dendrites, play a major role in increasing the dynamic range of neurons. Our results provide a better understanding of the effects of neuronal morphology in the diversity of neuronal dynamics and function.
bibliographic citation: Kirch et al. (2020) Spatially resolved dendritic integration: towards a functional classification of neurons. PeerJ 8:e10250 https://doi.org/10.7717/peerj.10250
date submitted: 2020-04-28
date accepted: 2020-10-06
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kirch
  given name: Christoph
author list: Agent
  family name: Gollo
  given name: Leonardo L.
doi: 10.7717/peerj.10250
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: © 2020 Kirch and Gollo
attribution name: Kirch and Gollo

DPM1 expression as a potential prognostic tumor marker in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Altered glycosylation of proteins contributes to tumor progression. Dolichol phosphate mannose synthase (DPMS), an essential mannosyltransferase, plays a central role in post-translational modification of proteins, including N-linked glycoproteins, O-mannosylation, C-mannosylation and glycosylphosphatidylinositol anchors synthesis. Little is known about the function of DPMS in liver cancer. Methods The study explored the roles of DPMS in the prognosis of hepatocellular carcinoma using UALCAN, Human Protein Atlas, GEPIA, cBioPortal and Metascape databases. The mRNA expressions of DPM1/2/3 also were detected by quantitative real-time PCR experiments in vitro. Results The transcriptional and proteinic expressions of DPM1/2/3 were both over-expressed in patients with hepatocellular carcinoma. Over-expressions of DPMS were discovered to be dramatically associated with clinical cancer stages and pathological tumor grades in hepatocellular carcinoma patients. In addition, higher mRNA expressions of DPM1/2/3 were found to be significantly related to shorter overall survival in liver cancer patients. Futhermore, high genetic alteration rate of DPMS (41%) was also observed in patients with liver cancer, and genetic alteration in DPMS was associated with shorter overall survival in hepatocellular carcinoma patients. We also performed quantitative real-time PCR experiments in human normal hepatocytes and hepatoma cells to verify the expressions of DPM1/2/3 and results showed that the expression of DPM1 was significantly increased in hepatoma cells SMMC-7721 and HepG2. Conclusions Taken together, these results suggested that DPM1 could be a potential prognostic biomarker for survivals of hepatocellular carcinoma patients.
format: application/pdf
format: text/html
creator: Ming Li
creator: Shengli Xia
creator: Ping Shi
subject: Bioinformatics
description: doi:10.7717/peerj.10307
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Background Altered glycosylation of proteins contributes to tumor progression. Dolichol phosphate mannose synthase (DPMS), an essential mannosyltransferase, plays a central role in post-translational modification of proteins, including N-linked glycoproteins, O-mannosylation, C-mannosylation and glycosylphosphatidylinositol anchors synthesis. Little is known about the function of DPMS in liver cancer. Methods The study explored the roles of DPMS in the prognosis of hepatocellular carcinoma using UALCAN, Human Protein Atlas, GEPIA, cBioPortal and Metascape databases. The mRNA expressions of DPM1/2/3 also were detected by quantitative real-time PCR experiments in vitro. Results The transcriptional and proteinic expressions of DPM1/2/3 were both over-expressed in patients with hepatocellular carcinoma. Over-expressions of DPMS were discovered to be dramatically associated with clinical cancer stages and pathological tumor grades in hepatocellular carcinoma patients. In addition, higher mRNA expressions of DPM1/2/3 were found to be significantly related to shorter overall survival in liver cancer patients. Futhermore, high genetic alteration rate of DPMS (41%) was also observed in patients with liver cancer, and genetic alteration in DPMS was associated with shorter overall survival in hepatocellular carcinoma patients. We also performed quantitative real-time PCR experiments in human normal hepatocytes and hepatoma cells to verify the expressions of DPM1/2/3 and results showed that the expression of DPM1 was significantly increased in hepatoma cells SMMC-7721 and HepG2. Conclusions Taken together, these results suggested that DPM1 could be a potential prognostic biomarker for survivals of hepatocellular carcinoma patients.
bibliographic citation: Li et al. (2020) DPM1 expression as a potential prognostic tumor marker in hepatocellular carcinoma. PeerJ 8:e10307 https://doi.org/10.7717/peerj.10307
date submitted: 2020-07-08
date accepted: 2020-10-15
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Ming
author list: Agent
  family name: Xia
  given name: Shengli
author list: Agent
  family name: Shi
  given name: Ping
doi: 10.7717/peerj.10307
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: ©2020 Li et al.
attribution name: Li et al.

HIV-1 promoter is gradually silenced when integrated into BACH2 in Jurkat T-cells
type: item
type: AcademicArticle
description: Background The persistence of the latent HIV-1 reservoir is a major obstacle to curing HIV-1 infection. HIV-1 integrates into the cellular genome and some targeted genomic loci are frequently detected in clonally expanded latently HIV-1 infected cells, for instance, the gene BTB domain and CNC homology 2 (BACH2). Methods We investigated HIV-1 promoter activity after integration into specific sites in BACH2 in Jurkat T-cells. The HIV-1-based vector LTatCL[M] contains two fluorophores: (1) Cerulean, which reports the activity of the HIV-1 promoter and (2) mCherry driven by a constitutive promotor and flanked by genetic insulators. This vector was inserted into introns 2 and 5 of BACH2 of Jurkat T-cells via CRISPR/Cas9 technology in the same and convergent transcriptional orientation of BACH2, and into the genomic safe harbour AAVS1. Single cell clones representing active (Cerulean+/mCherry+) and inactive (Cerulean–/mCherry+) HIV-1 promoters were characterised. Results Upon targeted integration of the 5.3 kb vector LTatCL[M] into BACH2, the HIV-1 promoter was gradually silenced as reflected by the decrease in Cerulean expression over a period of 162 days. Silenced HIV-1 promoters could be reactivated by TNF-α and Romidepsin. This observation was independent of the targeted intron and the transcriptional orientation. BACH2 mRNA and protein expression was not impaired by mono-allelic integration of LTatCL[M]. Conclusion Successful targeted integration of the HIV-1-based vector LTatCL[M] allows longitudinal analyses of HIV-1 promoter activity.
format: application/pdf
format: text/html
creator: Anne Inderbitzin
creator: Yik Lim Kok
creator: Lisa Jörimann
creator: Audrey Kelley
creator: Kathrin Neumann
creator: Daniel Heinzer
creator: Toni Cathomen
creator: Karin J. Metzner
subject: Cell Biology
subject: Genetics
subject: Microbiology
subject: Virology
subject: HIV
description: doi:10.7717/peerj.10321
publisher: PeerJ Inc.
rights: © 2020 Inderbitzin et al.
abstract: Background The persistence of the latent HIV-1 reservoir is a major obstacle to curing HIV-1 infection. HIV-1 integrates into the cellular genome and some targeted genomic loci are frequently detected in clonally expanded latently HIV-1 infected cells, for instance, the gene BTB domain and CNC homology 2 (BACH2). Methods We investigated HIV-1 promoter activity after integration into specific sites in BACH2 in Jurkat T-cells. The HIV-1-based vector LTatCL[M] contains two fluorophores: (1) Cerulean, which reports the activity of the HIV-1 promoter and (2) mCherry driven by a constitutive promotor and flanked by genetic insulators. This vector was inserted into introns 2 and 5 of BACH2 of Jurkat T-cells via CRISPR/Cas9 technology in the same and convergent transcriptional orientation of BACH2, and into the genomic safe harbour AAVS1. Single cell clones representing active (Cerulean+/mCherry+) and inactive (Cerulean–/mCherry+) HIV-1 promoters were characterised. Results Upon targeted integration of the 5.3 kb vector LTatCL[M] into BACH2, the HIV-1 promoter was gradually silenced as reflected by the decrease in Cerulean expression over a period of 162 days. Silenced HIV-1 promoters could be reactivated by TNF-α and Romidepsin. This observation was independent of the targeted intron and the transcriptional orientation. BACH2 mRNA and protein expression was not impaired by mono-allelic integration of LTatCL[M]. Conclusion Successful targeted integration of the HIV-1-based vector LTatCL[M] allows longitudinal analyses of HIV-1 promoter activity.
bibliographic citation: Inderbitzin et al. (2020) HIV-1 promoter is gradually silenced when integrated into BACH2 in Jurkat T-cells. PeerJ 8:e10321 https://doi.org/10.7717/peerj.10321
date submitted: 2020-08-06
date accepted: 2020-10-17
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Inderbitzin
  given name: Anne
author list: Agent
  family name: Kok
  given name: Yik Lim
author list: Agent
  family name: Jörimann
  given name: Lisa
author list: Agent
  family name: Kelley
  given name: Audrey
author list: Agent
  family name: Neumann
  given name: Kathrin
author list: Agent
  family name: Heinzer
  given name: Daniel
author list: Agent
  family name: Cathomen
  given name: Toni
author list: Agent
  family name: Metzner
  given name: Karin J.
doi: 10.7717/peerj.10321
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: © 2020 Inderbitzin et al.
attribution name: Inderbitzin et al.

Wnt16 signaling promotes osteoblast differentiation of periosteal derived cells in vitro and in vivo
type: item
type: AcademicArticle
description: Background Periosteum plays critical roles in de novo bone formation and fracture repair. Wnt16 has been regarded as a key regulator in periosteum bone formation. However, the role of Wnt16 in periosteum derived cells (PDCs) osteogenic differentiation remains unclear. The study goal is to uncover whether and how Wnt16 acts on the osteogenesis of PDCs. Methods We detected the variation of Wnt16 mRNA expression in PDCs, which were isolated from mouse femur and identified by flow cytometry, cultured in osteogenic medium for 14 days, then knocked down and over-expressed Wnt16 in PDCs to analysis its effects in osteogenesis. Further, we seeded PDCs (Wnt16 over-expressed/vector) in β-tricalcium phosphate cubes, and transplanted this complex into a critical size calvarial defect. Lastly, we used immunofluorescence, Topflash and NFAT luciferase reporter assay to study the possible downstream signaling pathway of Wnt16. Results Wnt16 mRNA expression showed an increasing trend in PDCs under osteogenic induction for 14 days. Wnt16 shRNA reduced mRNA expression of Runx2, collage type I (Col-1) and osteocalcin (OCN) after 7 days of osteogenic induction, as well as alizarin red staining intensity after 21days. Wnt16 also increased the mRNA expression of Runx2 and OCN and the protein production of Runx2 and Col-1 after 2 days of osteogenic stimulation. In the orthotopic transplantation assay, more bone volume, trabecula number and less trabecula space were found in Wnt16 over-expressed group. Besides, in the newly formed tissue Brdu positive area was smaller and Col-1 was larger in Wnt16 over-expressed group compared to the control group. Finally, Wnt16 upregulated CTNNB1/β-catenin expression and its nuclear translocation in PDCs, also increased Topflash reporter luciferase activity. By contrast, Wnt16 failed to increase NFAT reporter luciferase activity. Conclusion Together, Wnt16 plays a positive role in regulating PDCs osteogenesis, and Wnt16 may have a potential use in improvi…
format: application/pdf
format: text/html
creator: Ying Jin
creator: Xiaoyan Sun
creator: Fang Pei
creator: Zhihe Zhao
creator: Jeremy Mao
subject: Biochemistry
subject: Bioengineering
subject: Cell Biology
subject: Dentistry
subject: Orthopedics
description: doi:10.7717/peerj.10374
publisher: PeerJ Inc.
rights: © 2020 Jin et al.
abstract: Background Periosteum plays critical roles in de novo bone formation and fracture repair. Wnt16 has been regarded as a key regulator in periosteum bone formation. However, the role of Wnt16 in periosteum derived cells (PDCs) osteogenic differentiation remains unclear. The study goal is to uncover whether and how Wnt16 acts on the osteogenesis of PDCs. Methods We detected the variation of Wnt16 mRNA expression in PDCs, which were isolated from mouse femur and identified by flow cytometry, cultured in osteogenic medium for 14 days, then knocked down and over-expressed Wnt16 in PDCs to analysis its effects in osteogenesis. Further, we seeded PDCs (Wnt16 over-expressed/vector) in β-tricalcium phosphate cubes, and transplanted this complex into a critical size calvarial defect. Lastly, we used immunofluorescence, Topflash and NFAT luciferase reporter assay to study the possible downstream signaling pathway of Wnt16. Results Wnt16 mRNA expression showed an increasing trend in PDCs under osteogenic induction for 14 days. Wnt16 shRNA reduced mRNA expression of Runx2, collage type I (Col-1) and osteocalcin (OCN) after 7 days of osteogenic induction, as well as alizarin red staining intensity after 21days. Wnt16 also increased the mRNA expression of Runx2 and OCN and the protein production of Runx2 and Col-1 after 2 days of osteogenic stimulation. In the orthotopic transplantation assay, more bone volume, trabecula number and less trabecula space were found in Wnt16 over-expressed group. Besides, in the newly formed tissue Brdu positive area was smaller and Col-1 was larger in Wnt16 over-expressed group compared to the control group. Finally, Wnt16 upregulated CTNNB1/β-catenin expression and its nuclear translocation in PDCs, also increased Topflash reporter luciferase activity. By contrast, Wnt16 failed to increase NFAT reporter luciferase activity. Conclusion Together, Wnt16 plays a positive role in regulating PDCs osteogenesis, and Wnt16 may have a potential use in improvi…
bibliographic citation: Jin et al. (2020) Wnt16 signaling promotes osteoblast differentiation of periosteal derived cells in vitro and in vivo. PeerJ 8:e10374 https://doi.org/10.7717/peerj.10374
date submitted: 2020-06-29
date accepted: 2020-10-26
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Ying
author list: Agent
  family name: Sun
  given name: Xiaoyan
author list: Agent
  family name: Pei
  given name: Fang
author list: Agent
  family name: Zhao
  given name: Zhihe
author list: Agent
  family name: Mao
  given name: Jeremy
doi: 10.7717/peerj.10374
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: ©2020 Jin et al.
attribution name: Jin et al.

Modelling the effects of Spartina alterniflora invasion on the landscape succession of Yancheng coastal natural wetlands, China
type: item
type: AcademicArticle
description: Background The Yancheng coastal natural wetlands (YCNR) are well-preserved silty tidal flat wetlands in China. Due to the severe invasion of Spartina alterniflora, the native ecosystem has undergone great changes. The successful invasion of S. alterniflora reduced the biodiversity of the YCNR, changed the structure and function of the local ecosystem, and eventually led to the degradation of the ecosystem and the loss of ecosystem function and service. Fully understanding the impact of an alien species invasion on YCNR succession is an important prerequisite for protecting and restoring the wetlands. Methods In this study, remote sensing, GIS technology, and a cellular-automaton Markov model were used to simulate the natural succession process of native ecosystems without being affected by alien species. By comparing the landscape of the YCNR with the model simulation results, we gained a better understanding of how alien species affect native landscape-scale ecosystems. Results During the natural succession of the coastal native wetland ecosystem in the YCNR, the pioneer species S. alterniflora occupied the mudflats and expanded seaward. The whole area expanded and moved seaward with an average annual movement of 58.23 m. Phragmites australis seemed to dominate the competition with S. salsa communities, and the area gradually expanded with an average annual movement of 39.89 m. The invasion of S. alterniflora changed the native ecosystem’s spatial succession process, causing the S. salsa ecosystem to be stressed by ecosystems on the side of the sea (S. alterniflora) and that of land (P. australis). The area of the seaward-expanding P. australis ecosystem has been declining. Under a reasonable protected area policy, human activities have enhanced the succession rate of the P. australis ecosystem and have had a small impact on the ecological spatial succession of S. salsa and S. alterniflora.
format: application/pdf
format: text/html
creator: Lingjun Dai
creator: Hongyu Liu
creator: Gang Wang
creator: Cheng Wang
creator: Ziru Guo
creator: Yi Zhou
creator: Yufeng Li
subject: Biogeography
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10400
publisher: PeerJ Inc.
rights: © 2020 Dai et al.
abstract: Background The Yancheng coastal natural wetlands (YCNR) are well-preserved silty tidal flat wetlands in China. Due to the severe invasion of Spartina alterniflora, the native ecosystem has undergone great changes. The successful invasion of S. alterniflora reduced the biodiversity of the YCNR, changed the structure and function of the local ecosystem, and eventually led to the degradation of the ecosystem and the loss of ecosystem function and service. Fully understanding the impact of an alien species invasion on YCNR succession is an important prerequisite for protecting and restoring the wetlands. Methods In this study, remote sensing, GIS technology, and a cellular-automaton Markov model were used to simulate the natural succession process of native ecosystems without being affected by alien species. By comparing the landscape of the YCNR with the model simulation results, we gained a better understanding of how alien species affect native landscape-scale ecosystems. Results During the natural succession of the coastal native wetland ecosystem in the YCNR, the pioneer species S. alterniflora occupied the mudflats and expanded seaward. The whole area expanded and moved seaward with an average annual movement of 58.23 m. Phragmites australis seemed to dominate the competition with S. salsa communities, and the area gradually expanded with an average annual movement of 39.89 m. The invasion of S. alterniflora changed the native ecosystem’s spatial succession process, causing the S. salsa ecosystem to be stressed by ecosystems on the side of the sea (S. alterniflora) and that of land (P. australis). The area of the seaward-expanding P. australis ecosystem has been declining. Under a reasonable protected area policy, human activities have enhanced the succession rate of the P. australis ecosystem and have had a small impact on the ecological spatial succession of S. salsa and S. alterniflora.
bibliographic citation: Dai et al. (2020) Modelling the effects of Spartina alterniflora invasion on the landscape succession of Yancheng coastal natural wetlands, China. PeerJ 8:e10400 https://doi.org/10.7717/peerj.10400
date submitted: 2020-05-14
date accepted: 2020-10-29
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dai
  given name: Lingjun
author list: Agent
  family name: Liu
  given name: Hongyu
author list: Agent
  family name: Wang
  given name: Gang
author list: Agent
  family name: Wang
  given name: Cheng
author list: Agent
  family name: Guo
  given name: Ziru
author list: Agent
  family name: Zhou
  given name: Yi
author list: Agent
  family name: Li
  given name: Yufeng
doi: 10.7717/peerj.10400
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: ©2020 Dai et al.
attribution name: Dai et al.

The paleobiology and paleoecology of South African Lystrosaurus
type: item
type: AcademicArticle
description: Lystrosaurus was one of the few tetrapods to survive the end-Permian mass extinction (EPME), the most catastrophic biotic crisis in Phanerozoic history. The significant increased abundance of this genus during the post-extinction Early Triassic recovery period has made Lystrosaurus an iconic survivor taxon globally and ideal for studying changes in growth dynamics during a mass extinction. There is potential evidence of a Lilliput effect in Lystrosaurus in South Africa as the two Triassic species that became highly abundant after the EPME are relatively smaller than the two Permian species. In order to test this hypothesis a detailed examination of the body size and life history of Permo-Triassic Lystrosaurus is required. In this study, the basal skull length and growth patterns of the four South African Lystrosaurus species from the Karoo Basin, L. maccaigi, L. curvatus, L. murrayi and L. declivis, were examined using cranial measurements and bone histology. The basal skull length measurements show that the Triassic species are smaller than the Permian species and supports previous studies. The osteohistology examination of all four species reveal rapidly forming fibrolamellar bone tissues during early to mid-ontogeny. Growth marks are common in L. maccaigi and L. curvatus, but rare and inconsistent in the purely Triassic L. murrayi and L. declivis. The inconsistency of the growth marks in these latter two taxa suggests the presence of developmental plasticity. This feature may have been advantageous in allowing these species to alter their growth patterns in response to environmental cues in the post-extinction Early Triassic climate. An overall transition to slower forming parallel-fibered bone is observed in the largest individuals of L. maccaigi, but absent from the limb bones of the other species. The absence of such bone tissue or outer circumferential lamellae in L. curvatus, L. murrayi and L. declivis indicates that even the largest collected specimens do n…
format: application/pdf
format: text/html
creator: Jennifer Botha
subject: Paleontology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.10408
publisher: PeerJ Inc.
rights: © 2020 Botha
abstract: Lystrosaurus was one of the few tetrapods to survive the end-Permian mass extinction (EPME), the most catastrophic biotic crisis in Phanerozoic history. The significant increased abundance of this genus during the post-extinction Early Triassic recovery period has made Lystrosaurus an iconic survivor taxon globally and ideal for studying changes in growth dynamics during a mass extinction. There is potential evidence of a Lilliput effect in Lystrosaurus in South Africa as the two Triassic species that became highly abundant after the EPME are relatively smaller than the two Permian species. In order to test this hypothesis a detailed examination of the body size and life history of Permo-Triassic Lystrosaurus is required. In this study, the basal skull length and growth patterns of the four South African Lystrosaurus species from the Karoo Basin, L. maccaigi, L. curvatus, L. murrayi and L. declivis, were examined using cranial measurements and bone histology. The basal skull length measurements show that the Triassic species are smaller than the Permian species and supports previous studies. The osteohistology examination of all four species reveal rapidly forming fibrolamellar bone tissues during early to mid-ontogeny. Growth marks are common in L. maccaigi and L. curvatus, but rare and inconsistent in the purely Triassic L. murrayi and L. declivis. The inconsistency of the growth marks in these latter two taxa suggests the presence of developmental plasticity. This feature may have been advantageous in allowing these species to alter their growth patterns in response to environmental cues in the post-extinction Early Triassic climate. An overall transition to slower forming parallel-fibered bone is observed in the largest individuals of L. maccaigi, but absent from the limb bones of the other species. The absence of such bone tissue or outer circumferential lamellae in L. curvatus, L. murrayi and L. declivis indicates that even the largest collected specimens do n…
bibliographic citation: Botha (2020) The paleobiology and paleoecology of South African Lystrosaurus. PeerJ 8:e10408 https://doi.org/10.7717/peerj.10408
date submitted: 2020-07-08
date accepted: 2020-11-02
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Botha
  given name: Jennifer
doi: 10.7717/peerj.10408
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: ©2020 Botha
attribution name: Botha

Classification of ovarian cancer associated with BRCA1 mutations, immune checkpoints, and tumor microenvironment based on immunogenomic profiling
type: item
type: AcademicArticle
description: Background Ovarian cancer is a highly fatal gynecological malignancy and new, more effective treatments are needed. Immunotherapy is gaining attention from researchers worldwide, although it has not proven to be consistently effective in the treatment of ovarian cancer. We studied the immune landscape of ovarian cancer patients to improve the efficacy of immunotherapy as a treatment option. Methods We obtained expression profiles, somatic mutation data, and clinical information from The Cancer Genome Atlas. Ovarian cancer was classified based on 29 immune-associated gene sets, which represented different immune cell types, functions, and pathways. Single-sample gene set enrichment (ssGSEA) was used to quantify the activity or enrichment levels of the gene sets in ovarian cancer, and the unsupervised machine learning method was used sort the classifications. Our classifications were validated using Gene Expression Omnibus datasets. Results We divided ovarian cancer into three subtypes according to the ssGSEA score: subtype 1 (low immunity), subtype 2 (median immunity), and subtype 3 (high immunity). Most tumor-infiltrating immune cells and immune checkpoint molecules were upgraded in subtype 3 compared with those in the other subtypes. The tumor mutation burden (TMB) was not significantly different among the three subtypes. However, patients with BRCA1 mutations were consistently detected in subtype 3. Furthermore, most immune signature pathways were hyperactivated in subtype 3, including T and B cell receptor signaling pathways, PD-L1 expression and PD-1 checkpoint pathway the NF-κB signaling pathway, Th17 cell differentiation and interleukin-17 signaling pathways, and the TNF signaling pathway. Conclusion Ovarian cancer subtypes that are based on immune biosignatures may contribute to the development of novel therapeutic treatment strategies for ovarian cancer.
format: application/pdf
format: text/html
creator: Yousheng Wei
creator: Tingyu Ou
creator: Yan Lu
creator: Guangteng Wu
creator: Ying Long
creator: Xinbin Pan
creator: Desheng Yao
subject: Bioinformatics
subject: Gynecology and Obstetrics
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.10414
publisher: PeerJ Inc.
rights: © 2020 Wei et al.
abstract: Background Ovarian cancer is a highly fatal gynecological malignancy and new, more effective treatments are needed. Immunotherapy is gaining attention from researchers worldwide, although it has not proven to be consistently effective in the treatment of ovarian cancer. We studied the immune landscape of ovarian cancer patients to improve the efficacy of immunotherapy as a treatment option. Methods We obtained expression profiles, somatic mutation data, and clinical information from The Cancer Genome Atlas. Ovarian cancer was classified based on 29 immune-associated gene sets, which represented different immune cell types, functions, and pathways. Single-sample gene set enrichment (ssGSEA) was used to quantify the activity or enrichment levels of the gene sets in ovarian cancer, and the unsupervised machine learning method was used sort the classifications. Our classifications were validated using Gene Expression Omnibus datasets. Results We divided ovarian cancer into three subtypes according to the ssGSEA score: subtype 1 (low immunity), subtype 2 (median immunity), and subtype 3 (high immunity). Most tumor-infiltrating immune cells and immune checkpoint molecules were upgraded in subtype 3 compared with those in the other subtypes. The tumor mutation burden (TMB) was not significantly different among the three subtypes. However, patients with BRCA1 mutations were consistently detected in subtype 3. Furthermore, most immune signature pathways were hyperactivated in subtype 3, including T and B cell receptor signaling pathways, PD-L1 expression and PD-1 checkpoint pathway the NF-κB signaling pathway, Th17 cell differentiation and interleukin-17 signaling pathways, and the TNF signaling pathway. Conclusion Ovarian cancer subtypes that are based on immune biosignatures may contribute to the development of novel therapeutic treatment strategies for ovarian cancer.
bibliographic citation: Wei et al. (2020) Classification of ovarian cancer associated with BRCA1 mutations, immune checkpoints, and tumor microenvironment based on immunogenomic profiling. PeerJ 8:e10414 https://doi.org/10.7717/peerj.10414
date submitted: 2020-05-27
date accepted: 2020-11-02
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Yousheng
author list: Agent
  family name: Ou
  given name: Tingyu
author list: Agent
  family name: Lu
  given name: Yan
author list: Agent
  family name: Wu
  given name: Guangteng
author list: Agent
  family name: Long
  given name: Ying
author list: Agent
  family name: Pan
  given name: Xinbin
author list: Agent
  family name: Yao
  given name: Desheng
doi: 10.7717/peerj.10414
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: ©2020 Wei et al.
attribution name: Wei et al.

The pandemic paradox: domestic violence and happiness of women
type: item
type: AcademicArticle
description: Background Across the globe, lockdowns have been enforced as a pandemic response to COVID-19. Such lockdown coupled with school closures and stay-at-home orders made women more vulnerable in terms of higher responsibility and spending more time with an abusive partner, if any. Methods This study investigates the situation of women during COVID-19 induced lockdown by focusing on their happiness and inquiring about the incidence of violence. Using the zero-inflated negative binomial model, our findings ascertained that family settings, type of relationship with a spouse, and age significantly affects the positive count of violence during the lockdown. We further estimated the determinants of happiness and found that years of schooling, the role of women in household decision making, and feeling empowered is affecting their happiness. Results Women having higher education have more odds of zero violence. Unemployed women and women who are not working have higher odds of zero violence as compared to women who are working. During this lockdown after the COVID-19 pandemic, women living in urban areas, having higher education, having an adequate household income to meet the expenditures, having lesser anxiety, not facing violence, feeling empowered when their husband is around, and have higher decision-making power are happier. Discussion and conclusion The study is important in the context of happiness and violence inflicted on women during the lockdown and provides the basis to improve the pandemic response policy. The inclusion of women’s safety and happiness in pandemic response policy is important to ensure the well-being of women and to devise better health and economic policy. Our estimates suggest higher education results in less incidence of violence which could be argued as desirable outcomes for building healthy, productive, and happy communities. In addition to this, as pandemic induced lock-down is likely to result in higher unemployment across the globe inclu…
format: application/pdf
format: text/html
creator: Wajiha Haq
creator: Syed Hassan Raza
creator: Tahir Mahmood
subject: Global Health
subject: Infectious Diseases
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.10472
publisher: PeerJ Inc.
rights: © 2020 Haq et al.
abstract: Background Across the globe, lockdowns have been enforced as a pandemic response to COVID-19. Such lockdown coupled with school closures and stay-at-home orders made women more vulnerable in terms of higher responsibility and spending more time with an abusive partner, if any. Methods This study investigates the situation of women during COVID-19 induced lockdown by focusing on their happiness and inquiring about the incidence of violence. Using the zero-inflated negative binomial model, our findings ascertained that family settings, type of relationship with a spouse, and age significantly affects the positive count of violence during the lockdown. We further estimated the determinants of happiness and found that years of schooling, the role of women in household decision making, and feeling empowered is affecting their happiness. Results Women having higher education have more odds of zero violence. Unemployed women and women who are not working have higher odds of zero violence as compared to women who are working. During this lockdown after the COVID-19 pandemic, women living in urban areas, having higher education, having an adequate household income to meet the expenditures, having lesser anxiety, not facing violence, feeling empowered when their husband is around, and have higher decision-making power are happier. Discussion and conclusion The study is important in the context of happiness and violence inflicted on women during the lockdown and provides the basis to improve the pandemic response policy. The inclusion of women’s safety and happiness in pandemic response policy is important to ensure the well-being of women and to devise better health and economic policy. Our estimates suggest higher education results in less incidence of violence which could be argued as desirable outcomes for building healthy, productive, and happy communities. In addition to this, as pandemic induced lock-down is likely to result in higher unemployment across the globe inclu…
bibliographic citation: Haq et al. (2020) The pandemic paradox: domestic violence and happiness of women. PeerJ 8:e10472 https://doi.org/10.7717/peerj.10472
date submitted: 2020-09-04
date accepted: 2020-11-11
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Haq
  given name: Wajiha
author list: Agent
  family name: Raza
  given name: Syed Hassan
author list: Agent
  family name: Mahmood
  given name: Tahir
doi: 10.7717/peerj.10472
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: © 2020 Haq et al.
attribution name: Haq et al.

Two new species of Tardigrada from moss cushions (Grimmia sp.) in a xerothermic habitat in northeast Tennessee (USA, North America), with the first identification of males in the genus Viridiscus
type: item
type: AcademicArticle
description: Background The phylum Tardigrada consists of over 1,300 species that inhabit terrestrial, freshwater and marine environments throughout the world. In terrestrial habitats they live primarily in mosses, lichens, leaf litter and soil, whereas tardigrades in freshwater and marine environments are mainly found in sediments and on aquatic plants. More than 65 species have been previously reported in the state of Tennessee, USA. Methods Tardigrades present in moss cushions (Grimmia sp.) collected from a xerothermic habitat on the East Tennessee State University campus, Johnson City, TN, USA, were extracted, mounted on slides, identified, and counted. Additional samples of fresh dried moss were used for integrative analyses, including morphological analysis with phase contrast (PCM) and scanning electron microscopy (SEM), as well as molecular analyses of COI, 18S rRNA, 28S rRNA, and ITS-2 of the Macrobiotus and Milnesium species. Results Five species were found, including two species new to science: Viridiscus miraviridis sp. nov. and Macrobiotus basiatus sp. nov. Viridiscus miraviridis sp. nov. differs from other members of the genus mainly by having a different type of dorsal cuticle and some other, more subtle, morphometric characters. In addition to the two new species, Viridiscus perviridis and Viridiscus viridissimus were present, and males of Vir. viridissimus were found for the first time, the first record of males in the genus Viridiscus. Macrobiotus basiatus sp. nov. is most similar to Macrobiotus nelsonae, but it differs from Mac. nelsonae mainly by the stylet supports being situated in a more anterior position, shorter and narrower egg processes, and a smaller number of areoles around the egg processes. Moreover, the identification of Milnesium inceptum was confirmed as the first record for the USA by analysis of COI.
format: application/pdf
format: text/html
creator: Diane R. Nelson
creator: Rebecca Adkins Fletcher
creator: Roberto Guidetti
creator: Milena Roszkowska
creator: Daria Grobys
creator: Łukasz Kaczmarek
subject: Biodiversity
subject: Ecology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10251
publisher: PeerJ Inc.
rights: © 2020 Nelson et al.
abstract: Background The phylum Tardigrada consists of over 1,300 species that inhabit terrestrial, freshwater and marine environments throughout the world. In terrestrial habitats they live primarily in mosses, lichens, leaf litter and soil, whereas tardigrades in freshwater and marine environments are mainly found in sediments and on aquatic plants. More than 65 species have been previously reported in the state of Tennessee, USA. Methods Tardigrades present in moss cushions (Grimmia sp.) collected from a xerothermic habitat on the East Tennessee State University campus, Johnson City, TN, USA, were extracted, mounted on slides, identified, and counted. Additional samples of fresh dried moss were used for integrative analyses, including morphological analysis with phase contrast (PCM) and scanning electron microscopy (SEM), as well as molecular analyses of COI, 18S rRNA, 28S rRNA, and ITS-2 of the Macrobiotus and Milnesium species. Results Five species were found, including two species new to science: Viridiscus miraviridis sp. nov. and Macrobiotus basiatus sp. nov. Viridiscus miraviridis sp. nov. differs from other members of the genus mainly by having a different type of dorsal cuticle and some other, more subtle, morphometric characters. In addition to the two new species, Viridiscus perviridis and Viridiscus viridissimus were present, and males of Vir. viridissimus were found for the first time, the first record of males in the genus Viridiscus. Macrobiotus basiatus sp. nov. is most similar to Macrobiotus nelsonae, but it differs from Mac. nelsonae mainly by the stylet supports being situated in a more anterior position, shorter and narrower egg processes, and a smaller number of areoles around the egg processes. Moreover, the identification of Milnesium inceptum was confirmed as the first record for the USA by analysis of COI.
bibliographic citation: Nelson et al. (2020) Two new species of Tardigrada from moss cushions (Grimmia sp.) in a xerothermic habitat in northeast Tennessee (USA, North America), with the first identification of males in the genus Viridiscus. PeerJ 8:e10251 https://doi.org/10.7717/peerj.10251
date submitted: 2020-06-29
date accepted: 2020-10-06
issued: 2020-11-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nelson
  given name: Diane R.
author list: Agent
  family name: Adkins Fletcher
  given name: Rebecca
author list: Agent
  family name: Guidetti
  given name: Roberto
author list: Agent
  family name: Roszkowska
  given name: Milena
author list: Agent
  family name: Grobys
  given name: Daria
author list: Agent
  family name: Kaczmarek
  given name: Łukasz
doi: 10.7717/peerj.10251
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-23
copyright: ©2020 Nelson et al.
attribution name: Nelson et al.

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