PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comprehensive assessment of the coupling coordination degree between urbanization and ecological environment in the Siberian and Far East Federal Districts, Russia from 2005 to 2017
items: Physiological and anatomical differentiation of two sympatric weed populations
items: Optimizing a reliable ex vivo human blood model to analyze expression of Staphylococcus epidermidis genes
items: Identification of prognostic risk factors for pancreatic cancer using bioinformatics analysis
items: Quantitatively assessing mekosuchine crocodile locomotion by geometric morphometric and finite element analysis of the forelimb
items: A potential role for Galectin-3 inhibitors in the treatment of COVID-19
items: Aggregation pathways of human γ D crystallin induced by metal ions revealed by time dependent methods
items: Historical museum collections and contemporary population studies implicate roads and introduced predatory bullfrogs in the decline of western pond turtles
items: Potential of rice straw biochar, sulfur and ryegrass (Lolium perenne L.) in remediating soil contaminated with nickel through irrigation with untreated wastewater
items: Identifying potential threats to soil biodiversity

Comprehensive assessment of the coupling coordination degree between urbanization and ecological environment in the Siberian and Far East Federal Districts, Russia from 2005 to 2017
type: item
type: AcademicArticle
description: The urbanization growth in the 20th and 21st centuries has led to a series of unprecedented problems in the ecological environment. Based on constructing an integrated urbanization-ecological environment index system, this article conducts a comprehensive evaluation of the coupling coordination degree between urbanization and the ecological environment and uncovers its spatiotemporal variation characteristics in the Siberian and Far East Federal Districts, Russia from 2005 to 2017. The coupling coordination of urbanization and the ecological environment in the Siberian and Far East Federal Districts improve from slightly unbalanced development stage to barely balanced development stage from 2005 to 2017. In 2017, more than half regions achieved the barely balanced development of urbanization and the ecological environment. However, the most desirable development stage, the superior balanced development stage, is never achieved in the Siberian and Far East Federal Districts during the study period. The spatial pattern of the coupling coordination degree of urbanization and the ecological environment in the Siberian and Far East Federal District gradually changes from “dumbbell” to “high-north low-south”. The south part of the Siberian and Far East Federal Districts should be paid more attention in the future urban development process. This research will provide support in the future coordination of urban development in the Siberian and Far East Federal Districts.
format: application/pdf
format: text/html
creator: Ji Zheng
creator: Yingjie Hu
creator: Tamir Boldanov
creator: Tcogto Bazarzhapov
creator: Dan Meng
creator: Yu Li
creator: Suocheng Dong
subject: Biogeography
subject: Ecosystem Science
subject: Environmental Sciences
subject: Coupled Natural and Human Systems
subject: Environmental Impacts
description: doi:10.7717/peerj.9125
publisher: PeerJ Inc.
rights: © 2020 Zheng et al.
abstract: The urbanization growth in the 20th and 21st centuries has led to a series of unprecedented problems in the ecological environment. Based on constructing an integrated urbanization-ecological environment index system, this article conducts a comprehensive evaluation of the coupling coordination degree between urbanization and the ecological environment and uncovers its spatiotemporal variation characteristics in the Siberian and Far East Federal Districts, Russia from 2005 to 2017. The coupling coordination of urbanization and the ecological environment in the Siberian and Far East Federal Districts improve from slightly unbalanced development stage to barely balanced development stage from 2005 to 2017. In 2017, more than half regions achieved the barely balanced development of urbanization and the ecological environment. However, the most desirable development stage, the superior balanced development stage, is never achieved in the Siberian and Far East Federal Districts during the study period. The spatial pattern of the coupling coordination degree of urbanization and the ecological environment in the Siberian and Far East Federal District gradually changes from “dumbbell” to “high-north low-south”. The south part of the Siberian and Far East Federal Districts should be paid more attention in the future urban development process. This research will provide support in the future coordination of urban development in the Siberian and Far East Federal Districts.
bibliographic citation: Zheng et al. (2020) Comprehensive assessment of the coupling coordination degree between urbanization and ecological environment in the Siberian and Far East Federal Districts, Russia from 2005 to 2017. PeerJ 8:e9125 https://doi.org/10.7717/peerj.9125
date submitted: 2019-12-04
date accepted: 2020-04-14
issued: 2020-06-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Ji
author list: Agent
  family name: Hu
  given name: Yingjie
author list: Agent
  family name: Boldanov
  given name: Tamir
author list: Agent
  family name: Bazarzhapov
  given name: Tcogto
author list: Agent
  family name: Meng
  given name: Dan
author list: Agent
  family name: Li
  given name: Yu
author list: Agent
  family name: Dong
  given name: Suocheng
doi: 10.7717/peerj.9125
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-15
copyright: © 2020 Zheng et al.
attribution name: Zheng et al.

Physiological and anatomical differentiation of two sympatric weed populations
type: item
type: AcademicArticle
description: In the vineyards of Rhineland-Palatinate (Germany), two different types of Shepherd’s Purse (Capsella bursa-pastoris) coexist: (1) the common type called ‘wild type’, and (2) the decandric type called Capsella apetala or ‘Spe’ with four stamens in place of the four petals. In this study, we compare the anatomical and physiological characters of rosette leaves of the respective types. Progeny of individual plants was cultivated in growth chambers under low- and high-light conditions. Under low-light conditions, the stomata densities of the adaxial and abaxial epidermis did not differ between the two types. When grown under high-light conditions, wild type and Spe, both exhibited increased stomata densities compared to low-light conditions, but Spe to a lesser extent than the wild type. The maximal photosynthetic capacity of Spe was lower in both, low-light and high-light conditions compared to wild-type plants. Under all CO2 concentrations, Spe seemed to be less productive. The less effective CO2 assimilation of the Spe mutant C. apetala was accompanied by later flowering. This fact prolonged the vegetative phase of Spe by about two weeks and was sufficient for the maintenance of both populations stably over years.
format: application/pdf
format: text/html
creator: Barbara Neuffer
creator: Michael Schorsch
creator: Steffen Hameister
creator: Johannes Knuesting
creator: Jennifer Selinski
creator: Renate Scheibe
subject: Ecology
subject: Evolutionary Studies
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.9226
publisher: PeerJ Inc.
rights: © 2020 Neuffer et al.
abstract: In the vineyards of Rhineland-Palatinate (Germany), two different types of Shepherd’s Purse (Capsella bursa-pastoris) coexist: (1) the common type called ‘wild type’, and (2) the decandric type called Capsella apetala or ‘Spe’ with four stamens in place of the four petals. In this study, we compare the anatomical and physiological characters of rosette leaves of the respective types. Progeny of individual plants was cultivated in growth chambers under low- and high-light conditions. Under low-light conditions, the stomata densities of the adaxial and abaxial epidermis did not differ between the two types. When grown under high-light conditions, wild type and Spe, both exhibited increased stomata densities compared to low-light conditions, but Spe to a lesser extent than the wild type. The maximal photosynthetic capacity of Spe was lower in both, low-light and high-light conditions compared to wild-type plants. Under all CO2 concentrations, Spe seemed to be less productive. The less effective CO2 assimilation of the Spe mutant C. apetala was accompanied by later flowering. This fact prolonged the vegetative phase of Spe by about two weeks and was sufficient for the maintenance of both populations stably over years.
bibliographic citation: Neuffer et al. (2020) Physiological and anatomical differentiation of two sympatric weed populations. PeerJ 8:e9226 https://doi.org/10.7717/peerj.9226
date submitted: 2019-06-07
date accepted: 2020-04-30
issued: 2020-06-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Neuffer
  given name: Barbara
author list: Agent
  family name: Schorsch
  given name: Michael
author list: Agent
  family name: Hameister
  given name: Steffen
author list: Agent
  family name: Knuesting
  given name: Johannes
author list: Agent
  family name: Selinski
  given name: Jennifer
author list: Agent
  family name: Scheibe
  given name: Renate
doi: 10.7717/peerj.9226
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-15
copyright: ©2020 Neuffer et al.
attribution name: Neuffer et al.

Optimizing a reliable ex vivo human blood model to analyze expression of Staphylococcus epidermidis genes
type: item
type: AcademicArticle
description: Human blood is often used as an ex vivo model to mimic the environment encountered by pathogens inside the host. A significant variety of experimental conditions has been reported. However, optimization strategies are often not described. This study aimed to evaluate key parameters that are expected to influence Staphylococcus epidermidis gene expression when using human blood ex vivo models. Our data confirmed that blood antimicrobial activity was dependent on initial bacterial concentration. Furthermore, blood degradation over time resulted in lower antimicrobial activity, with a 2% loss of leukocytes viability correlating with a 5-fold loss of antimicrobial activity against S. epidermidis. We further demonstrated that the volume of human blood could be reduced to as little as 0.18 mL without affecting the stability of gene expression of the tested genes. Overall, the data described herein highlight experimental parameters that should be considered when using a human blood ex vivo model for S. epidermidis gene expression analysis.
format: application/pdf
format: text/html
creator: Susana Brás
creator: Ângela França
creator: Nuno Cerca
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.9295
publisher: PeerJ Inc.
rights: © 2020 Brás et al.
abstract: Human blood is often used as an ex vivo model to mimic the environment encountered by pathogens inside the host. A significant variety of experimental conditions has been reported. However, optimization strategies are often not described. This study aimed to evaluate key parameters that are expected to influence Staphylococcus epidermidis gene expression when using human blood ex vivo models. Our data confirmed that blood antimicrobial activity was dependent on initial bacterial concentration. Furthermore, blood degradation over time resulted in lower antimicrobial activity, with a 2% loss of leukocytes viability correlating with a 5-fold loss of antimicrobial activity against S. epidermidis. We further demonstrated that the volume of human blood could be reduced to as little as 0.18 mL without affecting the stability of gene expression of the tested genes. Overall, the data described herein highlight experimental parameters that should be considered when using a human blood ex vivo model for S. epidermidis gene expression analysis.
bibliographic citation: Brás et al. (2020) Optimizing a reliable ex vivo human blood model to analyze expression of Staphylococcus epidermidis genes. PeerJ 8:e9295 https://doi.org/10.7717/peerj.9295
date submitted: 2020-01-13
date accepted: 2020-05-14
issued: 2020-06-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brás
  given name: Susana
author list: Agent
  family name: França
  given name: Ângela
author list: Agent
  family name: Cerca
  given name: Nuno
doi: 10.7717/peerj.9295
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-15
copyright: ©2020 Brás et al.
attribution name: Brás et al.

Identification of prognostic risk factors for pancreatic cancer using bioinformatics analysis
type: item
type: AcademicArticle
description: Background Pancreatic cancer is one of the most common malignant cancers worldwide. Currently, the pathogenesis of pancreatic cancer remains unclear; thus, it is necessary to explore its precise molecular mechanisms. Methods To identify candidate genes involved in the tumorigenesis and proliferation of pancreatic cancer, the microarray datasets GSE32676, GSE15471 and GSE71989 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between Pancreatic ductal adenocarcinoma (PDAC) and nonmalignant samples were screened by GEO2R. The Database for Annotation Visualization and Integrated Discovery (DAVID) online tool was used to obtain a synthetic set of functional annotation information for the DEGs. A PPI network of the DEGs was established using the Search Tool for the Retrieval of Interacting Genes (STRING) database, and a combination of more than 0.4 was considered statistically significant for the PPI. Subsequently, we visualized the PPI network using Cytoscape. Functional module analysis was then performed using Molecular Complex Detection (MCODE). Genes with a degree ≥10 were chosen as hub genes, and pathways of the hub genes were visualized using ClueGO and CluePedia. Additionally, GenCLiP 2.0 was used to explore interactions of hub genes. The Literature Mining Gene Networks module was applied to explore the cocitation of hub genes. The Cytoscape plugin iRegulon was employed to analyze transcription factors regulating the hub genes. Furthermore, the expression levels of the 13 hub genes in pancreatic cancer tissues and normal samples were validated using the Gene Expression Profiling Interactive Analysis (GEPIA) platform. Moreover, overall survival and disease-free survival analyses according to the expression of hub genes were performed using Kaplan-Meier curve analysis in the cBioPortal online platform. The relationship between expression level and tumor grade was analyzed using the online database Oncomine. Lastly…
format: application/pdf
format: text/html
creator: Dandan Jin
creator: Yujie Jiao
creator: Jie Ji
creator: Wei Jiang
creator: Wenkai Ni
creator: Yingcheng Wu
creator: Runzhou Ni
creator: Cuihua Lu
creator: Lishuai Qu
creator: Hongbing Ni
creator: Jinxia Liu
creator: Weisong Xu
creator: MingBing Xiao
subject: Bioinformatics
subject: Oncology
subject: Statistics
description: doi:10.7717/peerj.9301
publisher: PeerJ Inc.
rights: © 2020 Jin et al.
abstract: Background Pancreatic cancer is one of the most common malignant cancers worldwide. Currently, the pathogenesis of pancreatic cancer remains unclear; thus, it is necessary to explore its precise molecular mechanisms. Methods To identify candidate genes involved in the tumorigenesis and proliferation of pancreatic cancer, the microarray datasets GSE32676, GSE15471 and GSE71989 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between Pancreatic ductal adenocarcinoma (PDAC) and nonmalignant samples were screened by GEO2R. The Database for Annotation Visualization and Integrated Discovery (DAVID) online tool was used to obtain a synthetic set of functional annotation information for the DEGs. A PPI network of the DEGs was established using the Search Tool for the Retrieval of Interacting Genes (STRING) database, and a combination of more than 0.4 was considered statistically significant for the PPI. Subsequently, we visualized the PPI network using Cytoscape. Functional module analysis was then performed using Molecular Complex Detection (MCODE). Genes with a degree ≥10 were chosen as hub genes, and pathways of the hub genes were visualized using ClueGO and CluePedia. Additionally, GenCLiP 2.0 was used to explore interactions of hub genes. The Literature Mining Gene Networks module was applied to explore the cocitation of hub genes. The Cytoscape plugin iRegulon was employed to analyze transcription factors regulating the hub genes. Furthermore, the expression levels of the 13 hub genes in pancreatic cancer tissues and normal samples were validated using the Gene Expression Profiling Interactive Analysis (GEPIA) platform. Moreover, overall survival and disease-free survival analyses according to the expression of hub genes were performed using Kaplan-Meier curve analysis in the cBioPortal online platform. The relationship between expression level and tumor grade was analyzed using the online database Oncomine. Lastly…
bibliographic citation: Jin et al. (2020) Identification of prognostic risk factors for pancreatic cancer using bioinformatics analysis. PeerJ 8:e9301 https://doi.org/10.7717/peerj.9301
date submitted: 2019-04-18
date accepted: 2020-05-15
issued: 2020-06-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Dandan
author list: Agent
  family name: Jiao
  given name: Yujie
author list: Agent
  family name: Ji
  given name: Jie
author list: Agent
  family name: Jiang
  given name: Wei
author list: Agent
  family name: Ni
  given name: Wenkai
author list: Agent
  family name: Wu
  given name: Yingcheng
author list: Agent
  family name: Ni
  given name: Runzhou
author list: Agent
  family name: Lu
  given name: Cuihua
author list: Agent
  family name: Qu
  given name: Lishuai
author list: Agent
  family name: Ni
  given name: Hongbing
author list: Agent
  family name: Liu
  given name: Jinxia
author list: Agent
  family name: Xu
  given name: Weisong
author list: Agent
  family name: Xiao
  given name: MingBing
doi: 10.7717/peerj.9301
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-15
copyright: ©2020 Jin et al.
attribution name: Jin et al.

Quantitatively assessing mekosuchine crocodile locomotion by geometric morphometric and finite element analysis of the forelimb
type: item
type: AcademicArticle
description: Morphological shifts observed in the fossil record of a lineage potentially indicate concomitant shifts in ecology of that lineage. Mekosuchine crocodiles of Cenozoic Australia display departures from the typical eusuchian body-plan both in the cranium and postcranium. Previous qualitative studies have suggested that these crocodiles had a more terrestrial habitus than extant crocodylians, yet the capacity of mekosuchine locomotion remains to be tested. Limb bone shape, such as diaphyseal cross-section and curvature, has been related to habitual use and locomotory function across a wide variety of taxa. Available specimens of mekosuchine limbs, primarily humeri, are distinctly columnar compared with those of extant crocodylians. Here we apply a quantitative approach to biomechanics in mekosuchine taxa using both geomorphic morphometric and finite element methods to measure bone shape and estimate locomotory stresses in a comparative context. Our results show mekosuchines appear to diverge from extant semi-aquatic saltwater and freshwater crocodiles in cross-sectional geometry of the diaphysis and generate different structural stresses between models that simulate sprawling and high-walk gaits. The extant crocodylians display generally rounded cross-sectional diaphyseal outlines, which may provide preliminary indication of resistance to torsional loads that predominate during sprawling gait, whereas mekosuchine humeri appear to vary between a series of elliptical outlines. Mekosuchine structural stresses are comparatively lower than those of the extant crocodylians and reduce under high-walk gait in some instances. This appears to be a function of bending moments induced by differing configurations of diaphyseal curvature. Additionally, the neutral axis of structural stresses is differently oriented in mekosuchines. This suggests a shift in the focus of biomechanical optimisation, from torsional to axial loadings. Our results lend quantitative support to the terrestr…
format: application/pdf
format: text/html
creator: Michael D. Stein
creator: Suzanne J. Hand
creator: Michael Archer
creator: Stephen Wroe
creator: Laura A.B. Wilson
subject: Animal Behavior
subject: Biophysics
subject: Ecology
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.9349
publisher: PeerJ Inc.
rights: © 2020 Stein et al.
abstract: Morphological shifts observed in the fossil record of a lineage potentially indicate concomitant shifts in ecology of that lineage. Mekosuchine crocodiles of Cenozoic Australia display departures from the typical eusuchian body-plan both in the cranium and postcranium. Previous qualitative studies have suggested that these crocodiles had a more terrestrial habitus than extant crocodylians, yet the capacity of mekosuchine locomotion remains to be tested. Limb bone shape, such as diaphyseal cross-section and curvature, has been related to habitual use and locomotory function across a wide variety of taxa. Available specimens of mekosuchine limbs, primarily humeri, are distinctly columnar compared with those of extant crocodylians. Here we apply a quantitative approach to biomechanics in mekosuchine taxa using both geomorphic morphometric and finite element methods to measure bone shape and estimate locomotory stresses in a comparative context. Our results show mekosuchines appear to diverge from extant semi-aquatic saltwater and freshwater crocodiles in cross-sectional geometry of the diaphysis and generate different structural stresses between models that simulate sprawling and high-walk gaits. The extant crocodylians display generally rounded cross-sectional diaphyseal outlines, which may provide preliminary indication of resistance to torsional loads that predominate during sprawling gait, whereas mekosuchine humeri appear to vary between a series of elliptical outlines. Mekosuchine structural stresses are comparatively lower than those of the extant crocodylians and reduce under high-walk gait in some instances. This appears to be a function of bending moments induced by differing configurations of diaphyseal curvature. Additionally, the neutral axis of structural stresses is differently oriented in mekosuchines. This suggests a shift in the focus of biomechanical optimisation, from torsional to axial loadings. Our results lend quantitative support to the terrestr…
bibliographic citation: Stein et al. (2020) Quantitatively assessing mekosuchine crocodile locomotion by geometric morphometric and finite element analysis of the forelimb. PeerJ 8:e9349 https://doi.org/10.7717/peerj.9349
date submitted: 2019-12-19
date accepted: 2020-05-22
issued: 2020-06-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stein
  given name: Michael D.
author list: Agent
  family name: Hand
  given name: Suzanne J.
author list: Agent
  family name: Archer
  given name: Michael
author list: Agent
  family name: Wroe
  given name: Stephen
author list: Agent
  family name: Wilson
  given name: Laura A.B.
doi: 10.7717/peerj.9349
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-15
copyright: ©2020 Stein et al.
attribution name: Stein et al.

A potential role for Galectin-3 inhibitors in the treatment of COVID-19
type: item
type: AcademicArticle
description: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19), has been declared a global pandemic by the World Health Organization. With no standard of care for the treatment of COVID-19, there is an urgent need to identify therapies that may be effective in treatment. Recent evidence has implicated the development of cytokine release syndrome as the major cause of fatality in COVID-19 patients, with elevated levels of interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) observed in patients. Galectin-3 (Gal-3) is an animal lectin that has been implicated in the disease process of a variety of inflammatory conditions. Inhibitors of the small molecule Gal-3 have been shown to reduce the levels of both IL-6 and TNF-α in vitro and have shown anti-inflammatory effects in vivo. Additionally, a key domain in the spike protein of β-coronaviridae, a genus which includes SARS-CoV2, is nearly identical in morphology to human Gal-3. These spike proteins are critical for the virus’ entry into host cells. Here we provide a systematic review of the available literature and an impetus for further research on the use of Gal-3 inhibitors in the treatment of COVID-19. Further, we propose a dual mechanism by which Gal-3 inhibition may be beneficial in the treatment of COVID-19, both suppressing the host inflammatory response and impeding viral attachment to host cells.
format: application/pdf
format: text/html
creator: John L. Caniglia
creator: Maheedhara R. Guda
creator: Swapna Asuthkar
creator: Andrew J. Tsung
creator: Kiran K. Velpula
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.9392
publisher: PeerJ Inc.
rights: © 2020 Caniglia et al.
abstract: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19), has been declared a global pandemic by the World Health Organization. With no standard of care for the treatment of COVID-19, there is an urgent need to identify therapies that may be effective in treatment. Recent evidence has implicated the development of cytokine release syndrome as the major cause of fatality in COVID-19 patients, with elevated levels of interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) observed in patients. Galectin-3 (Gal-3) is an animal lectin that has been implicated in the disease process of a variety of inflammatory conditions. Inhibitors of the small molecule Gal-3 have been shown to reduce the levels of both IL-6 and TNF-α in vitro and have shown anti-inflammatory effects in vivo. Additionally, a key domain in the spike protein of β-coronaviridae, a genus which includes SARS-CoV2, is nearly identical in morphology to human Gal-3. These spike proteins are critical for the virus’ entry into host cells. Here we provide a systematic review of the available literature and an impetus for further research on the use of Gal-3 inhibitors in the treatment of COVID-19. Further, we propose a dual mechanism by which Gal-3 inhibition may be beneficial in the treatment of COVID-19, both suppressing the host inflammatory response and impeding viral attachment to host cells.
bibliographic citation: Caniglia et al. (2020) A potential role for Galectin-3 inhibitors in the treatment of COVID-19. PeerJ 8:e9392 https://doi.org/10.7717/peerj.9392
date submitted: 2020-05-14
date accepted: 2020-05-29
issued: 2020-06-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caniglia
  given name: John L.
author list: Agent
  family name: Guda
  given name: Maheedhara R.
author list: Agent
  family name: Asuthkar
  given name: Swapna
author list: Agent
  family name: Tsung
  given name: Andrew J.
author list: Agent
  family name: Velpula
  given name: Kiran K.
doi: 10.7717/peerj.9392
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-15
copyright: © 2020 Caniglia et al.
attribution name: Caniglia et al.

Aggregation pathways of human γ D crystallin induced by metal ions revealed by time dependent methods
type: item
type: AcademicArticle
description: Cataract formation is a slow accumulative process due to protein aggregates promoted by different factors over time. Zinc and copper ions have been reported to induce the formation of aggregates opaque to light in the human gamma D crystallin (HγD) in a concentration and temperature dependent manner. In order to gain insight into the mechanism of metal-induced aggregation of HγD under conditions that mimic more closely the slow, accumulative process of the disease, we have studied the non-equilibrium process with the minimal metal dose that triggers HγD aggregation. Using a wide variety of biophysics techniques such as turbidimetry, dynamic light scattering, fluorescence, nuclear magnetic resonance and computational methods, we obtained information on the molecular mechanisms for the formation of aggregates. Zn(II) ions bind to different regions at the protein, probably with similar affinities. This binding induces a small conformational rearrangement within and between domains and aggregates via the formation of metal bridges without any detectable unfolded intermediates. In contrast, Cu(II)-induced aggregation includes a lag time, in which the N-terminal domain partially unfolds while the C-terminal domain and parts of the N-terminal domain remain in a native-like conformation. This partially unfolded intermediate is prone to form the high-molecular weight aggregates. Our results clearly show that different external factors can promote protein aggregation following different pathways.
format: application/pdf
format: text/html
creator: Arline Fernández-Silva
creator: Leidys French-Pacheco
creator: Lina Rivillas-Acevedo
creator: Carlos Amero
subject: Biochemistry
subject: Biophysics
description: doi:10.7717/peerj.9178
publisher: PeerJ Inc.
rights: © 2020 Fernández-Silva et al.
abstract: Cataract formation is a slow accumulative process due to protein aggregates promoted by different factors over time. Zinc and copper ions have been reported to induce the formation of aggregates opaque to light in the human gamma D crystallin (HγD) in a concentration and temperature dependent manner. In order to gain insight into the mechanism of metal-induced aggregation of HγD under conditions that mimic more closely the slow, accumulative process of the disease, we have studied the non-equilibrium process with the minimal metal dose that triggers HγD aggregation. Using a wide variety of biophysics techniques such as turbidimetry, dynamic light scattering, fluorescence, nuclear magnetic resonance and computational methods, we obtained information on the molecular mechanisms for the formation of aggregates. Zn(II) ions bind to different regions at the protein, probably with similar affinities. This binding induces a small conformational rearrangement within and between domains and aggregates via the formation of metal bridges without any detectable unfolded intermediates. In contrast, Cu(II)-induced aggregation includes a lag time, in which the N-terminal domain partially unfolds while the C-terminal domain and parts of the N-terminal domain remain in a native-like conformation. This partially unfolded intermediate is prone to form the high-molecular weight aggregates. Our results clearly show that different external factors can promote protein aggregation following different pathways.
bibliographic citation: Fernández-Silva et al. (2020) Aggregation pathways of human γ D crystallin induced by metal ions revealed by time dependent methods. PeerJ 8:e9178 https://doi.org/10.7717/peerj.9178
date submitted: 2020-02-12
date accepted: 2020-04-22
issued: 2020-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fernández-Silva
  given name: Arline
author list: Agent
  family name: French-Pacheco
  given name: Leidys
author list: Agent
  family name: Rivillas-Acevedo
  given name: Lina
author list: Agent
  family name: Amero
  given name: Carlos
doi: 10.7717/peerj.9178
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-12
copyright: ©2020 Fernández-Silva et al.
attribution name: Fernández-Silva et al.

Historical museum collections and contemporary population studies implicate roads and introduced predatory bullfrogs in the decline of western pond turtles
type: item
type: AcademicArticle
description: The western pond turtle (WPT), recently separated into two paripatrically distributed species (Emys pallida and Emys marmorata), is experiencing significant reductions in its range and population size. In addition to habitat loss, two potential causes of decline are female-biased road mortality and high juvenile mortality from non-native predatory bullfrogs (Rana catesbeiana). However, quantitative analyses of these threats have never been conducted for either species of WPT. We used a combination of historical museum samples and published and unpublished field studies shared with us through personal communications with WPT field researchers (B. Shaffer, P. Scott, R. Fisher, C. Brown, R. Dagit, L. Patterson, T. Engstrom, 2019, personal communications) to quantify the effect of roads and bullfrogs on WPT populations along the west coast of the United States. Both species of WPT shift toward increasingly male biased museum collections over the last century, a trend consistent with increasing, female-biased road mortality. Recent WPT population studies revealed that road density and proximity were significantly associated with increasingly male-biased sex ratios, further suggesting female-biased road mortality. The mean body size of museum collections of E. marmorata, but not E. pallida, has increased over the last 100 years, consistent with reduced recruitment and aging populations that could be driven by invasive predators. Contemporary WPT population sites that co-occur with bullfrogs had significantly greater average body sizes than population sites without bullfrogs, suggesting strong bullfrog predation on small WPT hatchlings and juveniles. Overall, our findings indicate that both species of WPT face demographic challenges which would have been difficult to document without the use of both historical data from natural history collections and contemporary demographic field data. Although correlational, our analyses suggest that female-biased road mortality and pre…
format: application/pdf
format: text/html
creator: E. Griffin Nicholson
creator: Stephanie Manzo
creator: Zachary Devereux
creator: Thomas Paul Morgan
creator: Robert N. Fisher
creator: Christopher Brown
creator: Rosi Dagit
creator: Peter A. Scott
creator: H. Bradley Shaffer
subject: Conservation Biology
subject: Ecology
subject: Environmental Impacts
subject: Population Biology
description: doi:10.7717/peerj.9248
publisher: PeerJ Inc.
rights: © 2020 Nicholson et al.
abstract: The western pond turtle (WPT), recently separated into two paripatrically distributed species (Emys pallida and Emys marmorata), is experiencing significant reductions in its range and population size. In addition to habitat loss, two potential causes of decline are female-biased road mortality and high juvenile mortality from non-native predatory bullfrogs (Rana catesbeiana). However, quantitative analyses of these threats have never been conducted for either species of WPT. We used a combination of historical museum samples and published and unpublished field studies shared with us through personal communications with WPT field researchers (B. Shaffer, P. Scott, R. Fisher, C. Brown, R. Dagit, L. Patterson, T. Engstrom, 2019, personal communications) to quantify the effect of roads and bullfrogs on WPT populations along the west coast of the United States. Both species of WPT shift toward increasingly male biased museum collections over the last century, a trend consistent with increasing, female-biased road mortality. Recent WPT population studies revealed that road density and proximity were significantly associated with increasingly male-biased sex ratios, further suggesting female-biased road mortality. The mean body size of museum collections of E. marmorata, but not E. pallida, has increased over the last 100 years, consistent with reduced recruitment and aging populations that could be driven by invasive predators. Contemporary WPT population sites that co-occur with bullfrogs had significantly greater average body sizes than population sites without bullfrogs, suggesting strong bullfrog predation on small WPT hatchlings and juveniles. Overall, our findings indicate that both species of WPT face demographic challenges which would have been difficult to document without the use of both historical data from natural history collections and contemporary demographic field data. Although correlational, our analyses suggest that female-biased road mortality and pre…
bibliographic citation: Nicholson et al. (2020) Historical museum collections and contemporary population studies implicate roads and introduced predatory bullfrogs in the decline of western pond turtles. PeerJ 8:e9248 https://doi.org/10.7717/peerj.9248
date submitted: 2020-02-04
date accepted: 2020-05-07
issued: 2020-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nicholson
  given name: E. Griffin
author list: Agent
  family name: Manzo
  given name: Stephanie
author list: Agent
  family name: Devereux
  given name: Zachary
author list: Agent
  family name: Morgan
  given name: Thomas Paul
author list: Agent
  family name: Fisher
  given name: Robert N.
author list: Agent
  family name: Brown
  given name: Christopher
author list: Agent
  family name: Dagit
  given name: Rosi
author list: Agent
  family name: Scott
  given name: Peter A.
author list: Agent
  family name: Shaffer
  given name: H. Bradley
doi: 10.7717/peerj.9248
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-12
copyright: © 2020 Nicholson et al.
attribution name: Nicholson et al.

Potential of rice straw biochar, sulfur and ryegrass (Lolium perenne L.) in remediating soil contaminated with nickel through irrigation with untreated wastewater
type: item
type: AcademicArticle
description: Background Untreated wastewater carries substantial amount of heavy metals and causes potential ecological risks to the environment, food quality, soil health and sustainable agriculture. Methodology In order to reduce the incidence of nickel (Ni2+) contamination in soils, two separate experiments (incubation and greenhouse) were conducted to investigate the potentials of rice straw biochar and elemental sulfur in remediating Ni2+ polluted soil due to the irrigation with wastewater. Five incubation periods (1, 7, 14, 28 and 56 days), three biochar doses (0, 10 and 20 g kg−1 of soil) and two doses of sulfur (0 and 5 g kg−1 of soil) were used in the incubation experiment then the Ni2+ was extracted from the soil and analyzed, while ryegrass seeds Lolium perenne L. (Poales: Poaceae) and the same doses of biochar and sulfur were used in the greenhouse experiment then the plants Ni2+-uptake was determined. Results The results of the incubation experiment revealed a dose-dependent reduction of DTPA-extractable Ni2+ in soils treated with biochar. Increasing the biochar dose from 0 g kg−1 (control) to 10 or 20 g kg−1 (treatments) decreased the DTPA-extractable Ni2+ from the soil by 24.6% and 39.4%, respectively. The application of sulfur increased the Ni2+-uptake by ryegrass plant which was used as hyper-accumulator of heavy metals in the green house experiment. However, the biochar decreased the Ni2+-uptake by the plant therefore it can be used as animal feed. Conclusions These results indicate that the biochar and sulfur could be applied separately to remediate the Ni2+-contaminated soils either through adsorbing the Ni2+ by biochar or increasing the Ni2+ availability by sulfur to be easily uptaken by the hyper-accumulator plant, and hence promote a sustainable agriculture.
format: application/pdf
format: text/html
creator: Inas A. Hashem
creator: Aonalah Y. Abbas
creator: Abo El-Nasr H. Abd El-Hamed
creator: Haythum M.S. Salem
creator: Omr E.M. El-hosseiny
creator: Mohamed A. Abdel-Salam
creator: Muhammad Hamzah Saleem
creator: Wenbing Zhou
creator: Ronggui Hu
subject: Agricultural Science
subject: Ecology
subject: Soil Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.9267
publisher: PeerJ Inc.
rights: © 2020 Hashem et al.
abstract: Background Untreated wastewater carries substantial amount of heavy metals and causes potential ecological risks to the environment, food quality, soil health and sustainable agriculture. Methodology In order to reduce the incidence of nickel (Ni2+) contamination in soils, two separate experiments (incubation and greenhouse) were conducted to investigate the potentials of rice straw biochar and elemental sulfur in remediating Ni2+ polluted soil due to the irrigation with wastewater. Five incubation periods (1, 7, 14, 28 and 56 days), three biochar doses (0, 10 and 20 g kg−1 of soil) and two doses of sulfur (0 and 5 g kg−1 of soil) were used in the incubation experiment then the Ni2+ was extracted from the soil and analyzed, while ryegrass seeds Lolium perenne L. (Poales: Poaceae) and the same doses of biochar and sulfur were used in the greenhouse experiment then the plants Ni2+-uptake was determined. Results The results of the incubation experiment revealed a dose-dependent reduction of DTPA-extractable Ni2+ in soils treated with biochar. Increasing the biochar dose from 0 g kg−1 (control) to 10 or 20 g kg−1 (treatments) decreased the DTPA-extractable Ni2+ from the soil by 24.6% and 39.4%, respectively. The application of sulfur increased the Ni2+-uptake by ryegrass plant which was used as hyper-accumulator of heavy metals in the green house experiment. However, the biochar decreased the Ni2+-uptake by the plant therefore it can be used as animal feed. Conclusions These results indicate that the biochar and sulfur could be applied separately to remediate the Ni2+-contaminated soils either through adsorbing the Ni2+ by biochar or increasing the Ni2+ availability by sulfur to be easily uptaken by the hyper-accumulator plant, and hence promote a sustainable agriculture.
bibliographic citation: Hashem et al. (2020) Potential of rice straw biochar, sulfur and ryegrass (Lolium perenne L.) in remediating soil contaminated with nickel through irrigation with untreated wastewater. PeerJ 8:e9267 https://doi.org/10.7717/peerj.9267
date submitted: 2019-11-18
date accepted: 2020-05-10
issued: 2020-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hashem
  given name: Inas A.
author list: Agent
  family name: Abbas
  given name: Aonalah Y.
author list: Agent
  family name: Abd El-Hamed
  given name: Abo El-Nasr H.
author list: Agent
  family name: Salem
  given name: Haythum M.S.
author list: Agent
  family name: El-hosseiny
  given name: Omr E.M.
author list: Agent
  family name: Abdel-Salam
  given name: Mohamed A.
author list: Agent
  family name: Saleem
  given name: Muhammad Hamzah
author list: Agent
  family name: Zhou
  given name: Wenbing
author list: Agent
  family name: Hu
  given name: Ronggui
doi: 10.7717/peerj.9267
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-12
copyright: ©2020 Hashem et al.
attribution name: Hashem et al.

Identifying potential threats to soil biodiversity
type: item
type: AcademicArticle
description: A decline in soil biodiversity is generally considered to be the reduction of forms of life living in soils, both in terms of quantity and variety. Where soil biodiversity decline occurs, it can significantly affect the soils’ ability to function, respond to perturbations and recover from a disturbance. Several soil threats have been identified as having negative effects on soil biodiversity, including human intensive exploitation, land-use change and soil organic matter decline. In this review we consider what we mean by soil biodiversity, and why it is important to monitor. After a thorough review of the literature identified on a Web of Science search concerning threats to soil biodiversity (topic search: threat* “soil biodiversity”), we compiled a table of biodiversity threats considered in each paper including climate change, land use change, intensive human exploitation, decline in soil health or plastic; followed by detailed listings of threats studied. This we compared to a previously published expert assessment of threats to soil biodiversity. In addition, we identified emerging threats, particularly microplastics, in the 10 years following these knowledge based rankings. We found that many soil biodiversity studies do not focus on biodiversity sensu stricto, rather these studies examined either changes in abundance and/or diversity of individual groups of soil biota, instead of soil biodiversity as a whole, encompassing all levels of the soil food web. This highlights the complexity of soil biodiversity which is often impractical to assess in all but the largest studies. Published global scientific activity was only partially related to the threats identified by the expert panel assessment. The number of threats and the priority given to the threats (by number of publications) were quite different, indicating a disparity between research actions versus perceived threats. The lack of research effort in key areas of high priority in the threats to soil biodi…
format: application/pdf
format: text/html
creator: Mark Tibbett
creator: Tandra D. Fraser
creator: Sarah Duddigan
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Soil Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.9271
publisher: PeerJ Inc.
rights: © 2020 Tibbett et al.
abstract: A decline in soil biodiversity is generally considered to be the reduction of forms of life living in soils, both in terms of quantity and variety. Where soil biodiversity decline occurs, it can significantly affect the soils’ ability to function, respond to perturbations and recover from a disturbance. Several soil threats have been identified as having negative effects on soil biodiversity, including human intensive exploitation, land-use change and soil organic matter decline. In this review we consider what we mean by soil biodiversity, and why it is important to monitor. After a thorough review of the literature identified on a Web of Science search concerning threats to soil biodiversity (topic search: threat* “soil biodiversity”), we compiled a table of biodiversity threats considered in each paper including climate change, land use change, intensive human exploitation, decline in soil health or plastic; followed by detailed listings of threats studied. This we compared to a previously published expert assessment of threats to soil biodiversity. In addition, we identified emerging threats, particularly microplastics, in the 10 years following these knowledge based rankings. We found that many soil biodiversity studies do not focus on biodiversity sensu stricto, rather these studies examined either changes in abundance and/or diversity of individual groups of soil biota, instead of soil biodiversity as a whole, encompassing all levels of the soil food web. This highlights the complexity of soil biodiversity which is often impractical to assess in all but the largest studies. Published global scientific activity was only partially related to the threats identified by the expert panel assessment. The number of threats and the priority given to the threats (by number of publications) were quite different, indicating a disparity between research actions versus perceived threats. The lack of research effort in key areas of high priority in the threats to soil biodi…
bibliographic citation: Tibbett et al. (2020) Identifying potential threats to soil biodiversity. PeerJ 8:e9271 https://doi.org/10.7717/peerj.9271
date submitted: 2019-10-16
date accepted: 2020-05-11
issued: 2020-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tibbett
  given name: Mark
author list: Agent
  family name: Fraser
  given name: Tandra D.
author list: Agent
  family name: Duddigan
  given name: Sarah
doi: 10.7717/peerj.9271
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-12
copyright: ©2020 Tibbett et al.
attribution name: Tibbett et al.

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