PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effect of strip shelterwood-cuts on the crown morphology plasticity of natural regenerated Pinus tabuliformis saplings in northeastern China
items: On the cognitive bases of illusionism
items: Reviews on common objectives and evaluation indicators for risk communication activities from 2011 to 2017
items: Reproductive pattern in the solanum mealybug, Phenacoccus solani: A new perspective
items: Mitochondrial destiny in type 2 diabetes: the effects of oxidative stress on the dynamics and biogenesis of mitochondria
items: The role of textiles as fomites in the healthcare environment: a review of the infection control risk
items: CircHIPK3 regulates cardiac fibroblast proliferation, migration and phenotypic switching through the miR-152-3p/TGF-β2 axis under hypoxia
items: On the spillover effect and optimal size of marine reserves for sustainable fishing yields
items: Distribution characteristics of serum β2-microglobulin between viral and bacterial lower respiratory tract infections: a retrospective study
items: Engaging inexpensive hands-on activities using Chlamydomonas reinhardtii (a green micro-alga) beads to teach the interplay of photosynthesis and cellular respiration to K4–K16 Biology students

Effect of strip shelterwood-cuts on the crown morphology plasticity of natural regenerated Pinus tabuliformis saplings in northeastern China
type: item
type: AcademicArticle
description: The study analysed the effect of shelterwood-cut strips on the outermost crown profiles and crown characteristics of naturally regenerated Pinus tabuliformis saplings in northeastern China. A total of 49 regenerated saplings from shelterwood-cut strips and 30 from uncut strips were collected. Nonlinear quantile regression was used to develop the outermost crown profile model for the saplings from the shelterwood-cut and uncut strips. The quantile value suitable for describing the outermost crown profiles of the two types of strips was selected using nonparametric boundary regression. The difference in crown morphologies between the shelterwood-cut strips and uncut strips was compared. The results showed that with the same diameter at breast height, the crown radii of the uncut strip saplings were larger than those of the shelterwood-cut strip saplings within the range of 0.2–1.0 for the relative depth into the crown. The largest crown radius of the saplings from the uncut strips was larger than that of the saplings from the shelterwood-cut strips. The inflection points of the shelterwood-cut strip sapling crowns were larger than those of the uncut strip sapling crowns. The crown volume of the small uncut strip saplings was larger than that of the shelterwood-cut strip saplings, and the difference in crown volume decreased with increasing sapling size. The saplings in the early stage of the uncut strips showed a greater growth rate than those of the shelterwood-cut strips, but their growth rate slowed over the long term according to branch-length annual growth. The present study provides a reference for forest management strategy decision making in promoting natural regeneration.
format: application/pdf
format: text/html
creator: Huilin Gao
creator: Jian Feng
creator: You Yin
creator: Wanjin Hu
creator: Yang Qu
creator: Mingguo Liu
subject: Agricultural Science
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.9826
publisher: PeerJ Inc.
rights: © 2020 Gao et al.
abstract: The study analysed the effect of shelterwood-cut strips on the outermost crown profiles and crown characteristics of naturally regenerated Pinus tabuliformis saplings in northeastern China. A total of 49 regenerated saplings from shelterwood-cut strips and 30 from uncut strips were collected. Nonlinear quantile regression was used to develop the outermost crown profile model for the saplings from the shelterwood-cut and uncut strips. The quantile value suitable for describing the outermost crown profiles of the two types of strips was selected using nonparametric boundary regression. The difference in crown morphologies between the shelterwood-cut strips and uncut strips was compared. The results showed that with the same diameter at breast height, the crown radii of the uncut strip saplings were larger than those of the shelterwood-cut strip saplings within the range of 0.2–1.0 for the relative depth into the crown. The largest crown radius of the saplings from the uncut strips was larger than that of the saplings from the shelterwood-cut strips. The inflection points of the shelterwood-cut strip sapling crowns were larger than those of the uncut strip sapling crowns. The crown volume of the small uncut strip saplings was larger than that of the shelterwood-cut strip saplings, and the difference in crown volume decreased with increasing sapling size. The saplings in the early stage of the uncut strips showed a greater growth rate than those of the shelterwood-cut strips, but their growth rate slowed over the long term according to branch-length annual growth. The present study provides a reference for forest management strategy decision making in promoting natural regeneration.
bibliographic citation: Gao et al. (2020) Effect of strip shelterwood-cuts on the crown morphology plasticity of natural regenerated Pinus tabuliformis saplings in northeastern China. PeerJ 8:e9826 https://doi.org/10.7717/peerj.9826
date submitted: 2020-05-14
date accepted: 2020-08-05
issued: 2020-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Huilin
author list: Agent
  family name: Feng
  given name: Jian
author list: Agent
  family name: Yin
  given name: You
author list: Agent
  family name: Hu
  given name: Wanjin
author list: Agent
  family name: Qu
  given name: Yang
author list: Agent
  family name: Liu
  given name: Mingguo
doi: 10.7717/peerj.9826
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-26
copyright: © 2020 Gao et al.
attribution name: Gao et al.

On the cognitive bases of illusionism
type: item
type: AcademicArticle
description: Cognitive scientists have paid very little attention to magic as a distinctly human activity capable of creating situations that are considered impossible because they violate expectations and conclude with the apparent transgression of well-established cognitive and natural laws. This illusory experience of the “impossible” entails a very particular cognitive dissonance that is followed by a subjective and complex “magical experience”. Here, from a perspective inspired by visual neuroscience and ecological cognition, we propose a set of seven fundamental cognitive phenomena (from attention and perception to memory and decision-making) plus a previous pre-sensory stage that magicians interfere with during the presentation of their effects. By doing so, and using as an example the deconstruction of a classic trick, we show how magic offers novel and powerful insights to study human cognition. Furthermore, live magic performances afford to do so in tasks that are more ecological and context-dependent than those usually exploited in artificial laboratory settings. We thus believe that some of the mysteries of how the brain works may be trapped in the split realities present in every magic effect.
format: application/pdf
format: text/html
creator: Jordi Camí
creator: Alex Gomez-Marin
creator: Luis M. Martínez
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.9712
publisher: PeerJ Inc.
rights: © 2020 Camí et al.
abstract: Cognitive scientists have paid very little attention to magic as a distinctly human activity capable of creating situations that are considered impossible because they violate expectations and conclude with the apparent transgression of well-established cognitive and natural laws. This illusory experience of the “impossible” entails a very particular cognitive dissonance that is followed by a subjective and complex “magical experience”. Here, from a perspective inspired by visual neuroscience and ecological cognition, we propose a set of seven fundamental cognitive phenomena (from attention and perception to memory and decision-making) plus a previous pre-sensory stage that magicians interfere with during the presentation of their effects. By doing so, and using as an example the deconstruction of a classic trick, we show how magic offers novel and powerful insights to study human cognition. Furthermore, live magic performances afford to do so in tasks that are more ecological and context-dependent than those usually exploited in artificial laboratory settings. We thus believe that some of the mysteries of how the brain works may be trapped in the split realities present in every magic effect.
bibliographic citation: Camí et al. (2020) On the cognitive bases of illusionism. PeerJ 8:e9712 https://doi.org/10.7717/peerj.9712
date submitted: 2020-01-31
date accepted: 2020-07-23
issued: 2020-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Camí
  given name: Jordi
author list: Agent
  family name: Gomez-Marin
  given name: Alex
author list: Agent
  family name: Martínez
  given name: Luis M.
doi: 10.7717/peerj.9712
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-25
copyright: © 2020 Camí et al.
attribution name: Camí et al.

Reviews on common objectives and evaluation indicators for risk communication activities from 2011 to 2017
type: item
type: AcademicArticle
description: Background Risk communication is widely accepted as a significant factor for policy makers, academic researchers, and practitioners in diverse fields. However, there remains a lack of comprehensive knowledge about how risk communication is currently conducted across fields and about the way risk communication is evaluated. Methodology This study systematically searched for materials from three scholarly search engines and one journal with a single search term of “risk communication.” The eligibility assessment selected peer-reviewed articles published in English that evaluated risk communication activities. Emphasis was placed on articles published in recent years accounting for about half of the pre-selected ones. Data on field of study, intervention timing, target audience, communication type, and objectives/evaluation indicators was extracted from the articles. Patterns of objectives/evaluation indicators used in risk communication activities were compared with those of the definitions and purposes of risk communication stated by relevant organizations. Association analysis was conducted based on study fields and objectives/evaluation indicators. Results The screening process yielded 292 articles that were published between 2011 and 2017 in various fields, such as medicine, food safety, chemical substances, and disasters/emergencies. The review process showed that many activities were performed in the medical field, during non-/pre-crisis periods. Recent activities primarily targeted citizens/Non-Profit Organizations (NPOs), and was disseminated in the form of large group or mass communication. While “knowledge increase,” “change in risk perception and concern alleviation,” and “decision making and behavior change” were commonly addressed in practice, “trust-building” and “reduction in psychological distress” were rarely focused. The analysis also indicated that the medical field tends to perform risk communication at the individual or small group level, in contr…
format: application/pdf
format: text/html
creator: Akiko Sato
creator: Kaori Honda
creator: Kyoko Ono
creator: Reiko Kanda
creator: Takehiko I. Hayashi
creator: Yoshihito Takeda
creator: Yoshitake Takebayashi
creator: Tomoyuki Kobayashi
creator: Michio Murakami
subject: Public Health
subject: Science and Medical Education
subject: Environmental Impacts
description: doi:10.7717/peerj.9730
publisher: PeerJ Inc.
rights: © 2020 Sato et al.
abstract: Background Risk communication is widely accepted as a significant factor for policy makers, academic researchers, and practitioners in diverse fields. However, there remains a lack of comprehensive knowledge about how risk communication is currently conducted across fields and about the way risk communication is evaluated. Methodology This study systematically searched for materials from three scholarly search engines and one journal with a single search term of “risk communication.” The eligibility assessment selected peer-reviewed articles published in English that evaluated risk communication activities. Emphasis was placed on articles published in recent years accounting for about half of the pre-selected ones. Data on field of study, intervention timing, target audience, communication type, and objectives/evaluation indicators was extracted from the articles. Patterns of objectives/evaluation indicators used in risk communication activities were compared with those of the definitions and purposes of risk communication stated by relevant organizations. Association analysis was conducted based on study fields and objectives/evaluation indicators. Results The screening process yielded 292 articles that were published between 2011 and 2017 in various fields, such as medicine, food safety, chemical substances, and disasters/emergencies. The review process showed that many activities were performed in the medical field, during non-/pre-crisis periods. Recent activities primarily targeted citizens/Non-Profit Organizations (NPOs), and was disseminated in the form of large group or mass communication. While “knowledge increase,” “change in risk perception and concern alleviation,” and “decision making and behavior change” were commonly addressed in practice, “trust-building” and “reduction in psychological distress” were rarely focused. The analysis also indicated that the medical field tends to perform risk communication at the individual or small group level, in contr…
bibliographic citation: Sato et al. (2020) Reviews on common objectives and evaluation indicators for risk communication activities from 2011 to 2017. PeerJ 8:e9730 https://doi.org/10.7717/peerj.9730
date submitted: 2020-03-09
date accepted: 2020-07-24
issued: 2020-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sato
  given name: Akiko
author list: Agent
  family name: Honda
  given name: Kaori
author list: Agent
  family name: Ono
  given name: Kyoko
author list: Agent
  family name: Kanda
  given name: Reiko
author list: Agent
  family name: Hayashi
  given name: Takehiko I.
author list: Agent
  family name: Takeda
  given name: Yoshihito
author list: Agent
  family name: Takebayashi
  given name: Yoshitake
author list: Agent
  family name: Kobayashi
  given name: Tomoyuki
author list: Agent
  family name: Murakami
  given name: Michio
doi: 10.7717/peerj.9730
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-25
copyright: ©2020 Sato et al.
attribution name: Sato et al.

Reproductive pattern in the solanum mealybug, Phenacoccus solani: A new perspective
type: item
type: AcademicArticle
description: Background The reproductive pattern of most scale insects is ovoviviparity. The solanum mealybug, Phenacoccus solani (Hemiptera: Pseudococcidae), is known as a thelytokous parthenogenetic species, but there is still debate about the reproductive strategies of this species. Methods Here, we investigated the oviposition characteristics of P. solani and used scanning/transmission electron microscopy and RNA-seq to identify the differences between two types of eggs. Results We found that P. solani laid two types of eggs in one batch, with no significant difference in apparent size: one with eyespots that hatched and another without eyespots that failed to hatch. Furthermore, the physiological and molecular differences between the two types of eggs were highly significant. KEGG enrichment analysis revealed significant enrichment for the JAK-STAT, Notch, Hippo, and Wnt signaling pathways and dorsoventral axis formation, wax biosynthesis, cell cycle, insulin secretion, and nitrogen metabolism pathways. The results suggest that the embryo of the egg undergoes development inside the mother and only a short molting period outside the mother. Discussion Ovoviviparous species produce eggs and keep them inside the mother’s body until they are ready to hatch, and the offspring exits the egg shell during or immediately following oviposition. Therefore, we suggest that the reproductive pattern of P. solani can be described as ovoviviparity.
format: application/pdf
format: text/html
creator: Jun Huang
creator: Fuying Zhi
creator: Juan Zhang
creator: Muhammad Hafeez
creator: Xiaowei Li
creator: Jinming Zhang
creator: Zhijun Zhang
creator: Likun Wang
creator: Yaobin Lu
subject: Agricultural Science
subject: Animal Behavior
subject: Developmental Biology
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.9734
publisher: PeerJ Inc.
rights: © 2020 Huang et al.
abstract: Background The reproductive pattern of most scale insects is ovoviviparity. The solanum mealybug, Phenacoccus solani (Hemiptera: Pseudococcidae), is known as a thelytokous parthenogenetic species, but there is still debate about the reproductive strategies of this species. Methods Here, we investigated the oviposition characteristics of P. solani and used scanning/transmission electron microscopy and RNA-seq to identify the differences between two types of eggs. Results We found that P. solani laid two types of eggs in one batch, with no significant difference in apparent size: one with eyespots that hatched and another without eyespots that failed to hatch. Furthermore, the physiological and molecular differences between the two types of eggs were highly significant. KEGG enrichment analysis revealed significant enrichment for the JAK-STAT, Notch, Hippo, and Wnt signaling pathways and dorsoventral axis formation, wax biosynthesis, cell cycle, insulin secretion, and nitrogen metabolism pathways. The results suggest that the embryo of the egg undergoes development inside the mother and only a short molting period outside the mother. Discussion Ovoviviparous species produce eggs and keep them inside the mother’s body until they are ready to hatch, and the offspring exits the egg shell during or immediately following oviposition. Therefore, we suggest that the reproductive pattern of P. solani can be described as ovoviviparity.
bibliographic citation: Huang et al. (2020) Reproductive pattern in the solanum mealybug, Phenacoccus solani: A new perspective. PeerJ 8:e9734 https://doi.org/10.7717/peerj.9734
date submitted: 2020-04-30
date accepted: 2020-07-25
issued: 2020-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Jun
author list: Agent
  family name: Zhi
  given name: Fuying
author list: Agent
  family name: Zhang
  given name: Juan
author list: Agent
  family name: Hafeez
  given name: Muhammad
author list: Agent
  family name: Li
  given name: Xiaowei
author list: Agent
  family name: Zhang
  given name: Jinming
author list: Agent
  family name: Zhang
  given name: Zhijun
author list: Agent
  family name: Wang
  given name: Likun
author list: Agent
  family name: Lu
  given name: Yaobin
doi: 10.7717/peerj.9734
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-25
copyright: ©2020 Huang et al.
attribution name: Huang et al.

Mitochondrial destiny in type 2 diabetes: the effects of oxidative stress on the dynamics and biogenesis of mitochondria
type: item
type: AcademicArticle
description: Background One reason for the development of insulin resistance is the chronic inflammation in obesity. Materials & Methods Scientific articles in the field of knowledge on the involvement of mitochondria and mitochondrial DNA (mtDNA) in obesity and type 2 diabetes were analyzed. Results Oxidative stress developed during obesity contributes to the formation of peroxynitrite, which causes cytochrome C-related damage in the mitochondrial electron transfer chain and increases the production of reactive oxygen species (ROS), which is associated with the development of type 2 diabetes. Oxidative stress contributes to the nuclease activity of the mitochondrial matrix, which leads to the accumulation of cleaved fragments and an increase in heteroplasmy. Mitochondrial dysfunction and mtDNA variations during insulin resistance may be connected with a change in ATP levels, generation of ROS, mitochondrial division/fusion and mitophagy. This review discusses the main role of mitochondria in the development of insulin resistance, which leads to pathological processes in insulin-dependent tissues, and considers potential therapeutic directions based on the modulation of mitochondrial biogenesis. In this regard, the development of drugs aimed at the regulation of these processes is gaining attention. Conclusion Changes in the mtDNA copy number can help to protect mitochondria from severe damage during conditions of increased oxidative stress. Mitochondrial proteome studies are conducted to search for potential therapeutic targets. The use of mitochondrial peptides encoded by mtDNA also represents a promising new approach to therapy.
format: application/pdf
format: text/html
creator: Daria Skuratovskaia
creator: Alexandra Komar
creator: Maria Vulf
creator: Larisa Litvinova
subject: Biochemistry
subject: Genetics
subject: Diabetes and Endocrinology
subject: Medical Genetics
subject: Metabolic Sciences
description: doi:10.7717/peerj.9741
publisher: PeerJ Inc.
rights: © 2020 Skuratovskaia et al.
abstract: Background One reason for the development of insulin resistance is the chronic inflammation in obesity. Materials & Methods Scientific articles in the field of knowledge on the involvement of mitochondria and mitochondrial DNA (mtDNA) in obesity and type 2 diabetes were analyzed. Results Oxidative stress developed during obesity contributes to the formation of peroxynitrite, which causes cytochrome C-related damage in the mitochondrial electron transfer chain and increases the production of reactive oxygen species (ROS), which is associated with the development of type 2 diabetes. Oxidative stress contributes to the nuclease activity of the mitochondrial matrix, which leads to the accumulation of cleaved fragments and an increase in heteroplasmy. Mitochondrial dysfunction and mtDNA variations during insulin resistance may be connected with a change in ATP levels, generation of ROS, mitochondrial division/fusion and mitophagy. This review discusses the main role of mitochondria in the development of insulin resistance, which leads to pathological processes in insulin-dependent tissues, and considers potential therapeutic directions based on the modulation of mitochondrial biogenesis. In this regard, the development of drugs aimed at the regulation of these processes is gaining attention. Conclusion Changes in the mtDNA copy number can help to protect mitochondria from severe damage during conditions of increased oxidative stress. Mitochondrial proteome studies are conducted to search for potential therapeutic targets. The use of mitochondrial peptides encoded by mtDNA also represents a promising new approach to therapy.
bibliographic citation: Skuratovskaia et al. (2020) Mitochondrial destiny in type 2 diabetes: the effects of oxidative stress on the dynamics and biogenesis of mitochondria. PeerJ 8:e9741 https://doi.org/10.7717/peerj.9741
date submitted: 2020-04-13
date accepted: 2020-07-26
issued: 2020-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Skuratovskaia
  given name: Daria
author list: Agent
  family name: Komar
  given name: Alexandra
author list: Agent
  family name: Vulf
  given name: Maria
author list: Agent
  family name: Litvinova
  given name: Larisa
doi: 10.7717/peerj.9741
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-25
copyright: ©2020 Skuratovskaia et al.
attribution name: Skuratovskaia et al.

The role of textiles as fomites in the healthcare environment: a review of the infection control risk
type: item
type: AcademicArticle
description: Background Infectious diseases are a significant threat in both healthcare and community settings. Healthcare associated infections (HCAIs) in particular are a leading cause of complications during hospitalisation. Contamination of the healthcare environment is recognised as a source of infectious disease yet the significance of porous surfaces including healthcare textiles as fomites is not well understood. It is currently assumed there is little infection risk from textiles due to a lack of direct epidemiological evidence. Decontamination of healthcare textiles is achieved with heat and/or detergents by commercial or in-house laundering with the exception of healthcare worker uniforms which are laundered domestically in some countries. The emergence of the COVID-19 pandemic has increased the need for rigorous infection control including effective decontamination of potential fomites in the healthcare environment. This article aims to review the evidence for the role of textiles in the transmission of infection, outline current procedures for laundering healthcare textiles and review studies evaluating the decontamination efficacy of domestic and industrial laundering. Methodology Pubmed, Google Scholar and Web of Science were searched for publications pertaining to the survival and transmission of microorganisms on textiles with a particular focus on the healthcare environment. Results A number of studies indicate that microorganisms survive on textiles for extended periods of time and can transfer on to skin and other surfaces suggesting it is biologically plausible that HCAIs and other infectious diseases can be transmitted directly through contact with contaminated textiles. Accordingly, there are a number of case studies that link small outbreaks with inadequate laundering or infection control processes surrounding healthcare laundry. Studies have also demonstrated the survival of potential pathogens during laundering of healthcare textiles, which may increase…
format: application/pdf
format: text/html
creator: Lucy Owen
creator: Katie Laird
subject: Microbiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.9790
publisher: PeerJ Inc.
rights: © 2020 Owen and Laird
abstract: Background Infectious diseases are a significant threat in both healthcare and community settings. Healthcare associated infections (HCAIs) in particular are a leading cause of complications during hospitalisation. Contamination of the healthcare environment is recognised as a source of infectious disease yet the significance of porous surfaces including healthcare textiles as fomites is not well understood. It is currently assumed there is little infection risk from textiles due to a lack of direct epidemiological evidence. Decontamination of healthcare textiles is achieved with heat and/or detergents by commercial or in-house laundering with the exception of healthcare worker uniforms which are laundered domestically in some countries. The emergence of the COVID-19 pandemic has increased the need for rigorous infection control including effective decontamination of potential fomites in the healthcare environment. This article aims to review the evidence for the role of textiles in the transmission of infection, outline current procedures for laundering healthcare textiles and review studies evaluating the decontamination efficacy of domestic and industrial laundering. Methodology Pubmed, Google Scholar and Web of Science were searched for publications pertaining to the survival and transmission of microorganisms on textiles with a particular focus on the healthcare environment. Results A number of studies indicate that microorganisms survive on textiles for extended periods of time and can transfer on to skin and other surfaces suggesting it is biologically plausible that HCAIs and other infectious diseases can be transmitted directly through contact with contaminated textiles. Accordingly, there are a number of case studies that link small outbreaks with inadequate laundering or infection control processes surrounding healthcare laundry. Studies have also demonstrated the survival of potential pathogens during laundering of healthcare textiles, which may increase…
bibliographic citation: Owen et al. (2020) The role of textiles as fomites in the healthcare environment: a review of the infection control risk. PeerJ 8:e9790 https://doi.org/10.7717/peerj.9790
date submitted: 2020-05-18
date accepted: 2020-07-31
issued: 2020-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Owen
  given name: Lucy
author list: Agent
  family name: Laird
  given name: Katie
doi: 10.7717/peerj.9790
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-25
copyright: ©2020 Owen and Laird
attribution name: Owen and Laird

CircHIPK3 regulates cardiac fibroblast proliferation, migration and phenotypic switching through the miR-152-3p/TGF-β2 axis under hypoxia
type: item
type: AcademicArticle
description: Background The occurrence of pathological cardiac fibrosis is attributed to tissue hypoxia. Circular RNAs play significant regulatory roles in multiple cardiovascular diseases and are involved in the regulation of physiological and pathophysiological processes. CircHIPK3 has been identified as the one of the most crucial regulators in cardiac fibrosis. However, the mechanisms by which circHIPK3 regulates cardiac fibrosis under hypoxia remain unclear. Our study aimed to determine circHIPK3 expression in cardiac fibroblasts (CFs) and investigate the functions of circHIPK3 in hypoxia environment. Methods The expression level of circHIPK3 in CFs under hypoxia (1% O2) was analyzed by qRT-PCR. The role of circHIPK3 on the proliferation and migration of CFs were determined by EdU, cell wound scratch assay and cell cycle. The expression of proteins associated with phenotypic transformation in CFs in vitro was examined by immunofluorescence assay and western blot. Bioinformatics analysis, dual luciferase activity assay and RNA fluorescent in situ hybridization assay revealed that miR-152-3p was identified as a target of circHIPK3 and that TGF-β2 was targeted by miR-152-3p. Results CircHIPK3 expression was significantly upregulated in CFs in a hypoxic environment. In vitro, overexpressing circHIPK3 obviously promoted CF proliferation, migration and phenotypic changes under hypoxia, but those processes were suppressed by circHIPK3 silencing. CircHIPK3 acted as an endogenous miR-152-3p sponge and miR-152-3p aggravated circHIPK3 silencing induced inhibition of CF proliferation, migration, phenotypic transformation and TGF-β2 expression in vitro. In summary, circHIPK3 plays a pivotal role in the development of cardiac fibrosis by targeting the miR-152-3p/TGF-β2 axis. Conclusions These findings demonstrated that circHIPK3 acted as a miR-152-3p sponge to regulate CF proliferation, migration and phenotypic transformation through TGF-β2, revealing that modulation of circHIPK3 express…
format: application/pdf
format: text/html
creator: Weiwei Liu
creator: Yan Wang
creator: Zhimei Qiu
creator: Ranzun Zhao
creator: Zhijiang Liu
creator: Wenming Chen
creator: Junbo Ge
creator: Bei Shi
subject: Cell Biology
subject: Cardiology
description: doi:10.7717/peerj.9796
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: Background The occurrence of pathological cardiac fibrosis is attributed to tissue hypoxia. Circular RNAs play significant regulatory roles in multiple cardiovascular diseases and are involved in the regulation of physiological and pathophysiological processes. CircHIPK3 has been identified as the one of the most crucial regulators in cardiac fibrosis. However, the mechanisms by which circHIPK3 regulates cardiac fibrosis under hypoxia remain unclear. Our study aimed to determine circHIPK3 expression in cardiac fibroblasts (CFs) and investigate the functions of circHIPK3 in hypoxia environment. Methods The expression level of circHIPK3 in CFs under hypoxia (1% O2) was analyzed by qRT-PCR. The role of circHIPK3 on the proliferation and migration of CFs were determined by EdU, cell wound scratch assay and cell cycle. The expression of proteins associated with phenotypic transformation in CFs in vitro was examined by immunofluorescence assay and western blot. Bioinformatics analysis, dual luciferase activity assay and RNA fluorescent in situ hybridization assay revealed that miR-152-3p was identified as a target of circHIPK3 and that TGF-β2 was targeted by miR-152-3p. Results CircHIPK3 expression was significantly upregulated in CFs in a hypoxic environment. In vitro, overexpressing circHIPK3 obviously promoted CF proliferation, migration and phenotypic changes under hypoxia, but those processes were suppressed by circHIPK3 silencing. CircHIPK3 acted as an endogenous miR-152-3p sponge and miR-152-3p aggravated circHIPK3 silencing induced inhibition of CF proliferation, migration, phenotypic transformation and TGF-β2 expression in vitro. In summary, circHIPK3 plays a pivotal role in the development of cardiac fibrosis by targeting the miR-152-3p/TGF-β2 axis. Conclusions These findings demonstrated that circHIPK3 acted as a miR-152-3p sponge to regulate CF proliferation, migration and phenotypic transformation through TGF-β2, revealing that modulation of circHIPK3 express…
bibliographic citation: Liu et al. (2020) CircHIPK3 regulates cardiac fibroblast proliferation, migration and phenotypic switching through the miR-152-3p/TGF-β2 axis under hypoxia. PeerJ 8:e9796 https://doi.org/10.7717/peerj.9796
date submitted: 2020-06-04
date accepted: 2020-08-01
issued: 2020-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Weiwei
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Qiu
  given name: Zhimei
author list: Agent
  family name: Zhao
  given name: Ranzun
author list: Agent
  family name: Liu
  given name: Zhijiang
author list: Agent
  family name: Chen
  given name: Wenming
author list: Agent
  family name: Ge
  given name: Junbo
author list: Agent
  family name: Shi
  given name: Bei
doi: 10.7717/peerj.9796
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-25
copyright: © 2020 Liu et al.
attribution name: Liu et al.

On the spillover effect and optimal size of marine reserves for sustainable fishing yields
type: item
type: AcademicArticle
description: Marine reserves are an essential component of modern fishery management. Marine reserves, which represent a management tradeoff between harvesting and conservation, are fundamental to maintenance of fisheries. Finding optimal reserve sizes that improve fishing yields is not only of theoretical interest, but also of practical importance to facilitate decision making. Also, since the migratory behavior of some species influences the spillover effect of a marine reserve, this is a key consideration when assessing performance of marine reserves. The relationship between optimal reserve size and migration rate/mode has not been well studied, but it is fundamental to management success. Here, I investigate optimal reserve size and its management outcome with different levels of spillover via a simple two-patch mathematical model. In this model, one patch is open to fishing, and the other is closed. The two-patch model is aggregated by single-population dynamics when the migration rate is sufficiently larger than the growth rate of a target species. At this limit, I show that an optimal reserve size exists when pre-reserve fishing occurs at fishing mortality larger than fMSY, the fishing mortality at the maximum sustainable yield (MSY). Also, the fishing yield at an optimal reserve size becomes as large as MSY at the limit. Numerical simulations at various migration rates between the two patches suggest that the maximum harvest under management with a marine reserve is achieved at this limit. This contrasts with the conservation benefit which is maximized at an intermediate migration rate. Numerical simulations show that the above-mentioned condition for an optimal reserve size to exist derived from the aggregated model is necessary when the migration rate is not sufficiently large, and that a moderate migration rate is further necessary for an optimal reserve size to exist. However, high fishing mortality reduces this requirement.
format: application/pdf
format: text/html
creator: Nao Takashina
subject: Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Mathematical Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.9798
publisher: PeerJ Inc.
rights: © 2020 Takashina
abstract: Marine reserves are an essential component of modern fishery management. Marine reserves, which represent a management tradeoff between harvesting and conservation, are fundamental to maintenance of fisheries. Finding optimal reserve sizes that improve fishing yields is not only of theoretical interest, but also of practical importance to facilitate decision making. Also, since the migratory behavior of some species influences the spillover effect of a marine reserve, this is a key consideration when assessing performance of marine reserves. The relationship between optimal reserve size and migration rate/mode has not been well studied, but it is fundamental to management success. Here, I investigate optimal reserve size and its management outcome with different levels of spillover via a simple two-patch mathematical model. In this model, one patch is open to fishing, and the other is closed. The two-patch model is aggregated by single-population dynamics when the migration rate is sufficiently larger than the growth rate of a target species. At this limit, I show that an optimal reserve size exists when pre-reserve fishing occurs at fishing mortality larger than fMSY, the fishing mortality at the maximum sustainable yield (MSY). Also, the fishing yield at an optimal reserve size becomes as large as MSY at the limit. Numerical simulations at various migration rates between the two patches suggest that the maximum harvest under management with a marine reserve is achieved at this limit. This contrasts with the conservation benefit which is maximized at an intermediate migration rate. Numerical simulations show that the above-mentioned condition for an optimal reserve size to exist derived from the aggregated model is necessary when the migration rate is not sufficiently large, and that a moderate migration rate is further necessary for an optimal reserve size to exist. However, high fishing mortality reduces this requirement.
bibliographic citation: Takashina (2020) On the spillover effect and optimal size of marine reserves for sustainable fishing yields. PeerJ 8:e9798 https://doi.org/10.7717/peerj.9798
date submitted: 2020-06-02
date accepted: 2020-08-02
issued: 2020-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Takashina
  given name: Nao
doi: 10.7717/peerj.9798
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-25
copyright: ©2020 Takashina
attribution name: Takashina

Distribution characteristics of serum β2-microglobulin between viral and bacterial lower respiratory tract infections: a retrospective study
type: item
type: AcademicArticle
description: Background Lower respiratory tract infection (LRTI) is one of the leading cause of death in children under 5 years old around the world between 1980 and 2016. Distinguishing between viral and bacterial infection is challenging when children suffered from LRTI in the absence of pathogen detection. The aim of our study is to analyze the difference of serum β2-microglobulin (β2-MG) between viral LRTI and bacterial LRTI in children. Methods This retrospective study included children with LRTI caused by a single pathogen from Yancheng Third People’s Hospital, Yancheng, China, between January 1, 2016 and December 31, 2019. Participants were divided into the younger group (1 year old ≤ age < 3 years old) and the older group (3 years old ≤ age < 5 years old) for subgroup analysis. Results A total of 475 children with LRTI caused by common respiratory pathogens were identified. In the younger group as well as the older group, the serum level of β2-MG in respiratory syncytial virus, influenza A virus and influenza B virus groups were significantly increased compared to that in the Mycoplasma pneumoniae group. Compared with Streptococcus pneumoniae infection group, the serum β2-MG level of respiratory syncytial virus, influenza A virus and influenza B virus groups were significantly higher in children between 1 and 3 years old. Conclusions The serum β2-MG may distinguish viral infection from bacterial infection in children with LRTI.
format: application/pdf
format: text/html
creator: Xulong Cai
creator: Qiaolan Xu
creator: Chenrong Zhou
creator: Li Zhou
creator: Qijun Yong
creator: Qing Mu
creator: Yan Cheng
creator: Jiena Wang
creator: Jingjing Xie
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
subject: Pediatrics
subject: Respiratory Medicine
description: doi:10.7717/peerj.9814
publisher: PeerJ Inc.
rights: © 2020 Cai et al.
abstract: Background Lower respiratory tract infection (LRTI) is one of the leading cause of death in children under 5 years old around the world between 1980 and 2016. Distinguishing between viral and bacterial infection is challenging when children suffered from LRTI in the absence of pathogen detection. The aim of our study is to analyze the difference of serum β2-microglobulin (β2-MG) between viral LRTI and bacterial LRTI in children. Methods This retrospective study included children with LRTI caused by a single pathogen from Yancheng Third People’s Hospital, Yancheng, China, between January 1, 2016 and December 31, 2019. Participants were divided into the younger group (1 year old ≤ age < 3 years old) and the older group (3 years old ≤ age < 5 years old) for subgroup analysis. Results A total of 475 children with LRTI caused by common respiratory pathogens were identified. In the younger group as well as the older group, the serum level of β2-MG in respiratory syncytial virus, influenza A virus and influenza B virus groups were significantly increased compared to that in the Mycoplasma pneumoniae group. Compared with Streptococcus pneumoniae infection group, the serum β2-MG level of respiratory syncytial virus, influenza A virus and influenza B virus groups were significantly higher in children between 1 and 3 years old. Conclusions The serum β2-MG may distinguish viral infection from bacterial infection in children with LRTI.
bibliographic citation: Cai et al. (2020) Distribution characteristics of serum β2-microglobulin between viral and bacterial lower respiratory tract infections: a retrospective study. PeerJ 8:e9814 https://doi.org/10.7717/peerj.9814
date submitted: 2020-05-27
date accepted: 2020-08-04
issued: 2020-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Xulong
author list: Agent
  family name: Xu
  given name: Qiaolan
author list: Agent
  family name: Zhou
  given name: Chenrong
author list: Agent
  family name: Zhou
  given name: Li
author list: Agent
  family name: Yong
  given name: Qijun
author list: Agent
  family name: Mu
  given name: Qing
author list: Agent
  family name: Cheng
  given name: Yan
author list: Agent
  family name: Wang
  given name: Jiena
author list: Agent
  family name: Xie
  given name: Jingjing
doi: 10.7717/peerj.9814
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-25
copyright: © 2020 Cai et al.
attribution name: Cai et al.

Engaging inexpensive hands-on activities using Chlamydomonas reinhardtii (a green micro-alga) beads to teach the interplay of photosynthesis and cellular respiration to K4–K16 Biology students
type: item
type: AcademicArticle
description: Background Photosynthesis and cellular respiration play major roles in energy metabolism and are important Life Science topics for K16 Biology students. Algae beads are used for photosynthesis and cellular respiration labs. Currently there are a few companies that sell biology educational kits for making algae beads using non-motile green micro-algae to introduce students to photosynthesis. These kits are expensive and, do not come with detailed guidelines for trouble shooting and customizations for different grade levels. Chlamydomonas reinhardtii is a motile green micro-alga and is an excellent model system for photosynthesis studies. In this article, we are presenting the work conducted in the student-driven, American Society of Plant Biologists-funded, Plant-BLOOME educational outreach project. This project is a supervised collaborative effort of three undergraduates and one high school student. We have generated a protocol which can be used to make Chlamydomonas beads. We have used these beads to design two simple and inexpensive plant biology hands-on activities. These laboratory activities have been customized to teach the interplay of photosynthesis and cellular respiration to K4–K16 Biology students. Methods Chlamydomonas beads were used for two different laboratory activities that involved monitoring pH changes over time using a pH indicator. Our first activity centers on making and, using light-powered algae bead bracelets to monitor dramatic color/pH changes over time when exposed to darkness or light. Our second activity employs strain-specific algae beads with approximately equal cell numbers to conduct comparative photosynthesis and cellular respiration studies in two Chlamydomonas strains namely, wild type, 4A+ and, a high light-sensitive, photosynthetic mutant, 10E35/lsr1a. Results We optimized our experimental protocol using algae beads in a 5.5 mL screw capped glass vials before performing the same experiment in algae bead bracelets. We found that…
format: application/pdf
format: text/html
creator: Mautusi Mitra
creator: Sara Michelle Broom
creator: Kysis Pinto
creator: Sovi-Mya Doan Wellons
creator: Ariel Dominique Roberts
subject: Biochemistry
subject: Plant Science
subject: Science and Medical Education
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.9817
publisher: PeerJ Inc.
rights: © 2020 Mitra et al.
abstract: Background Photosynthesis and cellular respiration play major roles in energy metabolism and are important Life Science topics for K16 Biology students. Algae beads are used for photosynthesis and cellular respiration labs. Currently there are a few companies that sell biology educational kits for making algae beads using non-motile green micro-algae to introduce students to photosynthesis. These kits are expensive and, do not come with detailed guidelines for trouble shooting and customizations for different grade levels. Chlamydomonas reinhardtii is a motile green micro-alga and is an excellent model system for photosynthesis studies. In this article, we are presenting the work conducted in the student-driven, American Society of Plant Biologists-funded, Plant-BLOOME educational outreach project. This project is a supervised collaborative effort of three undergraduates and one high school student. We have generated a protocol which can be used to make Chlamydomonas beads. We have used these beads to design two simple and inexpensive plant biology hands-on activities. These laboratory activities have been customized to teach the interplay of photosynthesis and cellular respiration to K4–K16 Biology students. Methods Chlamydomonas beads were used for two different laboratory activities that involved monitoring pH changes over time using a pH indicator. Our first activity centers on making and, using light-powered algae bead bracelets to monitor dramatic color/pH changes over time when exposed to darkness or light. Our second activity employs strain-specific algae beads with approximately equal cell numbers to conduct comparative photosynthesis and cellular respiration studies in two Chlamydomonas strains namely, wild type, 4A+ and, a high light-sensitive, photosynthetic mutant, 10E35/lsr1a. Results We optimized our experimental protocol using algae beads in a 5.5 mL screw capped glass vials before performing the same experiment in algae bead bracelets. We found that…
bibliographic citation: Mitra et al. (2020) Engaging inexpensive hands-on activities using Chlamydomonas reinhardtii (a green micro-alga) beads to teach the interplay of photosynthesis and cellular respiration to K4–K16 Biology students. PeerJ 8:e9817 https://doi.org/10.7717/peerj.9817
date submitted: 2020-06-03
date accepted: 2020-08-05
issued: 2020-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mitra
  given name: Mautusi
author list: Agent
  family name: Broom
  given name: Sara Michelle
author list: Agent
  family name: Pinto
  given name: Kysis
author list: Agent
  family name: Wellons
  given name: Sovi-Mya Doan
author list: Agent
  family name: Roberts
  given name: Ariel Dominique
doi: 10.7717/peerj.9817
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-25
copyright: ©2020 Mitra et al.
attribution name: Mitra et al.

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