PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparative assessment of single-stage and two-stage anaerobic digestion for biogas production from high moisture municipal solid waste
items: Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp
items: Satellite tracking reveals a new migration route of black-necked cranes (Grus nigricollis) in Qinghai-Tibet Plateau
items: Genetic variations in the drug metabolizing enzyme, CYP2E1, among various ethnic populations of Pakistan
items: Population genomics reveals a mismatch between management and biological units in green abalone (Haliotis fulgens)
items: A comparison of COVID-19, SARS and MERS
items: Transcriptomic analysis highlights cochlear inflammation associated with age-related hearing loss in C57BL/6 mice using next generation sequencing
items: Six complete mitochondrial genomes of mayflies from three genera of Ephemerellidae (Insecta: Ephemeroptera) with inversion and translocation of trnI rearrangement and their phylogenetic relationships
items: Evolution of the patella and patelloid in marsupial mammals
items: The changes of morphological and physiological characteristics in hemiparasitic Monochasma savatieri before and after attachment to the host plant

Comparative assessment of single-stage and two-stage anaerobic digestion for biogas production from high moisture municipal solid waste
type: item
type: AcademicArticle
description: Background Anaerobic digestion (AD) is a suitable process for treating high moisture MSW with biogas and biofertilizer production. However, the low stability of AD performance and low methane production results from high moisture MSW due to the fast acidify of carbohydrate fermentation. The effects of organic loading and incineration fly ash addition as a pH adjustment on methane production from high moisture MSW in the single-stage AD and two-stage AD processes were investigated. Results Suitable initial organic loading of the single-stage AD process was 17 gVS L−1 at incineration fly ash (IFA) addition of 0.5% with methane yield of 287 mL CH4 g−1 VS. Suitable initial organic loading of the two-stage AD process was 43 gVS L−1 at IFA addition of 1% with hydrogen and methane yield of 47.4 ml H2 g−1 VS and 363 mL CH4 g−1 VS, respectively. The highest hydrogen and methane production of 8.7 m3 H2 ton−1 of high moisture MSW and 66.6 m3 CH4 ton−1 of high moisture MSW was achieved at organic loading of 43 gVS L−1 at IFA addition of 1% by two-stage AD process. Biogas production by the two-stage AD process enabled 18.5% higher energy recovery than single-stage AD. The 1% addition of IFA into high moisture MSW was useful for controlling pH of the two-stage AD process with enhanced biogas production between 87–92% when compared to without IFA addition. Electricity production and energy recovery from MSW using the coupled incineration with biogas production by two-stage AD process were 9,874 MJ ton−1 MSW and 89%, respectively. Conclusions The two-stage AD process with IFA addition for pH adjustment could improve biogas production from high moisture MSW, as well as reduce lag phase and enhance biodegradability efficiency. The coupled incineration process with biogas production using the two-stage AD process was suitable for the management of MSW with low area requirement, low greenhouse gas emissions, and high energy recovery.
format: application/pdf
format: text/html
creator: Wattananarong Markphan
creator: Chonticha Mamimin
creator: Wantanasak Suksong
creator: Poonsuk Prasertsan
creator: Sompong O-Thong
subject: Microbiology
subject: Mycology
subject: Soil Science
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.9693
publisher: PeerJ Inc.
rights: © 2020 Markphan et al.
abstract: Background Anaerobic digestion (AD) is a suitable process for treating high moisture MSW with biogas and biofertilizer production. However, the low stability of AD performance and low methane production results from high moisture MSW due to the fast acidify of carbohydrate fermentation. The effects of organic loading and incineration fly ash addition as a pH adjustment on methane production from high moisture MSW in the single-stage AD and two-stage AD processes were investigated. Results Suitable initial organic loading of the single-stage AD process was 17 gVS L−1 at incineration fly ash (IFA) addition of 0.5% with methane yield of 287 mL CH4 g−1 VS. Suitable initial organic loading of the two-stage AD process was 43 gVS L−1 at IFA addition of 1% with hydrogen and methane yield of 47.4 ml H2 g−1 VS and 363 mL CH4 g−1 VS, respectively. The highest hydrogen and methane production of 8.7 m3 H2 ton−1 of high moisture MSW and 66.6 m3 CH4 ton−1 of high moisture MSW was achieved at organic loading of 43 gVS L−1 at IFA addition of 1% by two-stage AD process. Biogas production by the two-stage AD process enabled 18.5% higher energy recovery than single-stage AD. The 1% addition of IFA into high moisture MSW was useful for controlling pH of the two-stage AD process with enhanced biogas production between 87–92% when compared to without IFA addition. Electricity production and energy recovery from MSW using the coupled incineration with biogas production by two-stage AD process were 9,874 MJ ton−1 MSW and 89%, respectively. Conclusions The two-stage AD process with IFA addition for pH adjustment could improve biogas production from high moisture MSW, as well as reduce lag phase and enhance biodegradability efficiency. The coupled incineration process with biogas production using the two-stage AD process was suitable for the management of MSW with low area requirement, low greenhouse gas emissions, and high energy recovery.
bibliographic citation: Markphan et al. (2020) Comparative assessment of single-stage and two-stage anaerobic digestion for biogas production from high moisture municipal solid waste. PeerJ 8:e9693 https://doi.org/10.7717/peerj.9693
date submitted: 2019-10-13
date accepted: 2020-07-20
issued: 2020-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Markphan
  given name: Wattananarong
author list: Agent
  family name: Mamimin
  given name: Chonticha
author list: Agent
  family name: Suksong
  given name: Wantanasak
author list: Agent
  family name: Prasertsan
  given name: Poonsuk
author list: Agent
  family name: O-Thong
  given name: Sompong
doi: 10.7717/peerj.9693
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-19
copyright: ©2020 Markphan et al.
attribution name: Markphan et al.

Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp
type: item
type: AcademicArticle
description: Since its emergence in Wuhan, China in late 2019, the origin and evolution of SARS-CoV-2 have been among the most debated issues related to COVID-19. Throughout its spread around the world, the viral genome continued acquiring new mutations and some of them became widespread. Among them, 14408 C>T and 23403 A>G mutations in RdRp and S, respectively, became dominant in Europe and the US, which led to debates regarding their effects on the mutability and transmissibility of the virus. In this study, we aimed to investigate possible differences between time-dependent variation of mutation densities (MDe) of viral strains that carry these two mutations and those that do not. Our analyses at the genome and gene level led to two important findings: First, time-dependent changes in the average MDe of circulating SARS-CoV-2 genomes showed different characteristics before and after the beginning of April, when daily new case numbers started levelling off. Second, this pattern was much delayed or even non-existent for the “mutant” (MT) strain that harbored both 14408 C>T and 23403 A>G mutations. Although these differences were not limited to a few hotspots, it is intriguing that the MDe increase is most evident in two critical genes, S and Orf1ab, which are also the genes that harbor the defining mutations of the MT genotype. The nature of these unexpected relationships warrants further research.
format: application/pdf
format: text/html
creator: Doğa Eskier
creator: Aslı Suner
creator: Gökhan Karakülah
creator: Yavuz Oktay
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
subject: Genomics
subject: Virology
description: doi:10.7717/peerj.9703
publisher: PeerJ Inc.
rights: © 2020 Eskier et al.
abstract: Since its emergence in Wuhan, China in late 2019, the origin and evolution of SARS-CoV-2 have been among the most debated issues related to COVID-19. Throughout its spread around the world, the viral genome continued acquiring new mutations and some of them became widespread. Among them, 14408 C>T and 23403 A>G mutations in RdRp and S, respectively, became dominant in Europe and the US, which led to debates regarding their effects on the mutability and transmissibility of the virus. In this study, we aimed to investigate possible differences between time-dependent variation of mutation densities (MDe) of viral strains that carry these two mutations and those that do not. Our analyses at the genome and gene level led to two important findings: First, time-dependent changes in the average MDe of circulating SARS-CoV-2 genomes showed different characteristics before and after the beginning of April, when daily new case numbers started levelling off. Second, this pattern was much delayed or even non-existent for the “mutant” (MT) strain that harbored both 14408 C>T and 23403 A>G mutations. Although these differences were not limited to a few hotspots, it is intriguing that the MDe increase is most evident in two critical genes, S and Orf1ab, which are also the genes that harbor the defining mutations of the MT genotype. The nature of these unexpected relationships warrants further research.
bibliographic citation: Eskier et al. (2020) Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. PeerJ 8:e9703 https://doi.org/10.7717/peerj.9703
date submitted: 2020-06-17
date accepted: 2020-07-22
issued: 2020-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eskier
  given name: Doğa
author list: Agent
  family name: Suner
  given name: Aslı
author list: Agent
  family name: Karakülah
  given name: Gökhan
author list: Agent
  family name: Oktay
  given name: Yavuz
doi: 10.7717/peerj.9703
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-19
copyright: ©2020 Eskier et al.
attribution name: Eskier et al.

Satellite tracking reveals a new migration route of black-necked cranes (Grus nigricollis) in Qinghai-Tibet Plateau
type: item
type: AcademicArticle
description: Background The black-necked crane (Grus nigricollis) is a vulnerable species and the only species that lives in the plateau. Five migration routes of different populations have been identified, but for cranes wintering in Nyingchi Prefecture, Tibet, the migration route and breeding/summering area are still unknown. The aim of this study was to investigate the spatio-temporal migration patterns of black-necked cranes in this area and to identify important areas for conservation. Methods In 2016, we fitted seven black-necked cranes in Nyingchi with GPS-GSM satellite transmitters to record their migration routes. We used ArcGIS 10.2 to visualize important stopover sites and the ‘ggplot’ function in R to analyze the migration patterns. Results From March 2016 to May 2019, we recorded nine spring migration and four autumn migration tracks from five individuals. Four individuals spent the breeding/summering season in Qinghai Lake, while the other spent the breeding/summering season in the Jinzihai Wetland of Dulan County, Qinghai Province. Detailed spatio-temporal information showed that the spring migration lasted 8.7 ± 4.6 days and covered 1,182.5 ± 90.4 km, while the autumn migration lasted 30 ± 10.6 days and covered 1,455.7 ± 138 km. Basom Lake and the Shazhuyu River were the most important stopover sites during the spring and autumn migrations, respectively. The cranes spent 4.4 ± 3.7 days in Basom Lake and 26.3 ± 10.7 days in the Shazhuyu River. The black-necked cranes mainly migrated during the daytime (>85 % of the fly points), and 81 % (17/21) of all stopover and roosting sites were in the valley or at lakeside swamps. Only 17.7% (516 / 2,914) of the data points for stopover and roosting sites were in protected areas. Main conclusions Our study revealed the breeding/summering areas and migration routes of the black-necked cranes wintering in Nyingchi. These results contribute to a better understanding of the annual spatio-temporal migration patterns and the devel…
format: application/pdf
format: text/html
creator: Ye Wang
creator: Chunrong Mi
creator: Yumin Guo
subject: Animal Behavior
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.9715
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background The black-necked crane (Grus nigricollis) is a vulnerable species and the only species that lives in the plateau. Five migration routes of different populations have been identified, but for cranes wintering in Nyingchi Prefecture, Tibet, the migration route and breeding/summering area are still unknown. The aim of this study was to investigate the spatio-temporal migration patterns of black-necked cranes in this area and to identify important areas for conservation. Methods In 2016, we fitted seven black-necked cranes in Nyingchi with GPS-GSM satellite transmitters to record their migration routes. We used ArcGIS 10.2 to visualize important stopover sites and the ‘ggplot’ function in R to analyze the migration patterns. Results From March 2016 to May 2019, we recorded nine spring migration and four autumn migration tracks from five individuals. Four individuals spent the breeding/summering season in Qinghai Lake, while the other spent the breeding/summering season in the Jinzihai Wetland of Dulan County, Qinghai Province. Detailed spatio-temporal information showed that the spring migration lasted 8.7 ± 4.6 days and covered 1,182.5 ± 90.4 km, while the autumn migration lasted 30 ± 10.6 days and covered 1,455.7 ± 138 km. Basom Lake and the Shazhuyu River were the most important stopover sites during the spring and autumn migrations, respectively. The cranes spent 4.4 ± 3.7 days in Basom Lake and 26.3 ± 10.7 days in the Shazhuyu River. The black-necked cranes mainly migrated during the daytime (>85 % of the fly points), and 81 % (17/21) of all stopover and roosting sites were in the valley or at lakeside swamps. Only 17.7% (516 / 2,914) of the data points for stopover and roosting sites were in protected areas. Main conclusions Our study revealed the breeding/summering areas and migration routes of the black-necked cranes wintering in Nyingchi. These results contribute to a better understanding of the annual spatio-temporal migration patterns and the devel…
bibliographic citation: Wang et al. (2020) Satellite tracking reveals a new migration route of black-necked cranes (Grus nigricollis) in Qinghai-Tibet Plateau. PeerJ 8:e9715 https://doi.org/10.7717/peerj.9715
date submitted: 2020-03-25
date accepted: 2020-07-23
issued: 2020-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Ye
author list: Agent
  family name: Mi
  given name: Chunrong
author list: Agent
  family name: Guo
  given name: Yumin
doi: 10.7717/peerj.9715
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-19
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Genetic variations in the drug metabolizing enzyme, CYP2E1, among various ethnic populations of Pakistan
type: item
type: AcademicArticle
description: Genetic polymorphism in cytochrome P450 (CYP) monooxygenase genes is an important source of interindividual variability of drug response. CYP enzyme activities may change as a result of such polymorphisms which then, may affect drug metabolism. This would result in a change in the severity and frequency of adverse effects in addition to the non-responder phenomenon. CYP2E1, a member of CYP superfamily, affects the metabolism of several clinically important drugs such as halothane, paracetamol, etc. Genetic variation in CYP2E1 is known to cause significant inter-individual differences in drug response and adverse effects. The degree of genetic variation is found to be different in different populations around the world. The frequencies of two important polymorphisms in the CYP2E1*7C, NC_000010.10:g.135340548A>G (rs2070672) and CYP2E1, NC_000010.10:g.135339244G>C (rs3813865), are not known in the Pakistani population. In the present investigation, 636 healthy human volunteers were screened for these two single nucleotide polymorphism. Our results indicate that about 18% (rs2070672) and 28% (rs3813865) of the Pakistani population has a genotype containing at least one low activity allele. A significant interethnic variation in the frequencies of both the polymorphisms was observed. These results suggest that pharmacogenetics screening for low activity genotypes would be a helpful tool for clinicians when they prescribe medications metabolized by CYP2E1, as a significant fraction of the Pakistani population is expected to have a variable response to these drugs.
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creator: Sagheer Ahmed
creator: Nadeem Altaf
creator: Mahnoor Ejaz
creator: Zaira Zulfiqar
creator: Kholood Janjua
creator: Dana Festila
creator: Nicula Cristina
subject: Genetics
subject: Pharmacology
subject: Medical Genetics
subject: Population Biology
description: doi:10.7717/peerj.9721
publisher: PeerJ Inc.
rights: © 2020 Ahmed et al.
abstract: Genetic polymorphism in cytochrome P450 (CYP) monooxygenase genes is an important source of interindividual variability of drug response. CYP enzyme activities may change as a result of such polymorphisms which then, may affect drug metabolism. This would result in a change in the severity and frequency of adverse effects in addition to the non-responder phenomenon. CYP2E1, a member of CYP superfamily, affects the metabolism of several clinically important drugs such as halothane, paracetamol, etc. Genetic variation in CYP2E1 is known to cause significant inter-individual differences in drug response and adverse effects. The degree of genetic variation is found to be different in different populations around the world. The frequencies of two important polymorphisms in the CYP2E1*7C, NC_000010.10:g.135340548A>G (rs2070672) and CYP2E1, NC_000010.10:g.135339244G>C (rs3813865), are not known in the Pakistani population. In the present investigation, 636 healthy human volunteers were screened for these two single nucleotide polymorphism. Our results indicate that about 18% (rs2070672) and 28% (rs3813865) of the Pakistani population has a genotype containing at least one low activity allele. A significant interethnic variation in the frequencies of both the polymorphisms was observed. These results suggest that pharmacogenetics screening for low activity genotypes would be a helpful tool for clinicians when they prescribe medications metabolized by CYP2E1, as a significant fraction of the Pakistani population is expected to have a variable response to these drugs.
bibliographic citation: Ahmed et al. (2020) Genetic variations in the drug metabolizing enzyme, CYP2E1, among various ethnic populations of Pakistan. PeerJ 8:e9721 https://doi.org/10.7717/peerj.9721
date submitted: 2019-11-28
date accepted: 2020-07-23
issued: 2020-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahmed
  given name: Sagheer
author list: Agent
  family name: Altaf
  given name: Nadeem
author list: Agent
  family name: Ejaz
  given name: Mahnoor
author list: Agent
  family name: Zulfiqar
  given name: Zaira
author list: Agent
  family name: Janjua
  given name: Kholood
author list: Agent
  family name: Festila
  given name: Dana
author list: Agent
  family name: Cristina
  given name: Nicula
doi: 10.7717/peerj.9721
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-19
copyright: © 2020 Ahmed et al.
attribution name: Ahmed et al.

Population genomics reveals a mismatch between management and biological units in green abalone (Haliotis fulgens)
type: item
type: AcademicArticle
description: Effective fishery management strategies should be based on stock delimitation and knowledge of the spatial scale at which species are distributed. However, a mismatch often occurs between biological and management units of fishery resources. The green abalone (Haliotis fulgens) supports an important artisanal fishery in the west coast of the Baja California Peninsula (BCP), Mexico, which has shown a declining tendency despite the several management measures. Thus, the aim of this study was to characterize the spatial patterns of neutral genomic variation of green abalone along the BCP to test whether the genomic structure patterns support the current green abalone management areas. To test this hypothesis, a set of 2,170 putative neutral single nucleotide polymorphisms discovered by a double digest restriction-site associated DNA approach was used on 10 locations along the BCP. The results revealed a population structure with three putative groups: Guadalupe Island and northern and southern BCP locations. The contemporary gene flow might be explained by local oceanographic features, where it is bidirectional within the southern region but with a predominant southward flow from the northern region. These findings indicated that the administrative areas did not match the biological units of H. fulgens fishery; hence, the stock assessment and management areas should be revised.
format: application/pdf
format: text/html
creator: Paulina Mejía-Ruíz
creator: Ricardo Perez-Enriquez
creator: Jorge Alberto Mares-Mayagoitia
creator: Fausto Valenzuela-Quiñonez
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Evolutionary Studies
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.9722
publisher: PeerJ Inc.
rights: © 2020 Mejía-Ruíz et al.
abstract: Effective fishery management strategies should be based on stock delimitation and knowledge of the spatial scale at which species are distributed. However, a mismatch often occurs between biological and management units of fishery resources. The green abalone (Haliotis fulgens) supports an important artisanal fishery in the west coast of the Baja California Peninsula (BCP), Mexico, which has shown a declining tendency despite the several management measures. Thus, the aim of this study was to characterize the spatial patterns of neutral genomic variation of green abalone along the BCP to test whether the genomic structure patterns support the current green abalone management areas. To test this hypothesis, a set of 2,170 putative neutral single nucleotide polymorphisms discovered by a double digest restriction-site associated DNA approach was used on 10 locations along the BCP. The results revealed a population structure with three putative groups: Guadalupe Island and northern and southern BCP locations. The contemporary gene flow might be explained by local oceanographic features, where it is bidirectional within the southern region but with a predominant southward flow from the northern region. These findings indicated that the administrative areas did not match the biological units of H. fulgens fishery; hence, the stock assessment and management areas should be revised.
bibliographic citation: Mejía-Ruíz et al. (2020) Population genomics reveals a mismatch between management and biological units in green abalone (Haliotis fulgens). PeerJ 8:e9722 https://doi.org/10.7717/peerj.9722
date submitted: 2019-12-13
date accepted: 2020-07-23
issued: 2020-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mejía-Ruíz
  given name: Paulina
author list: Agent
  family name: Perez-Enriquez
  given name: Ricardo
author list: Agent
  family name: Mares-Mayagoitia
  given name: Jorge Alberto
author list: Agent
  family name: Valenzuela-Quiñonez
  given name: Fausto
doi: 10.7717/peerj.9722
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-19
copyright: © 2020 Mejía-Ruíz et al.
attribution name: Mejía-Ruíz et al.

A comparison of COVID-19, SARS and MERS
type: item
type: AcademicArticle
description: In mid-December 2019, a novel atypical pneumonia broke out in Wuhan, Hubei Province, China and was caused by a newly identified coronavirus, initially termed 2019 Novel Coronavirus and subsequently severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of 19 May 2020, a total of 4,731,458 individuals were reported as infected with SARS-CoV-2 among 213 countries, areas or territories with recorded cases, and the overall case-fatality rate was 6.6% (316,169 deaths among 4,731,458 recorded cases), according to the World Health Organization. Studies have shown that SARS-CoV-2 is notably similar to (severe acute respiratory syndrome coronavirus) SARS-CoV that emerged in 2002–2003 and Middle East respiratory syndrome coronavirus (MERS-CoV) that spread during 2012, and these viruses all contributed to global pandemics. The ability of SARS-CoV-2 to rapidly spread a pneumonia-like disease from Hubei Province, China, throughout the world has provoked widespread concern. The main symptoms of coronavirus disease 2019 (COVID-19) include fever, cough, myalgia, fatigue and lower respiratory signs. At present, nucleic acid tests are widely recommended as the optimal method for detecting SARS-CoV-2. However, obstacles remain, including the global shortage of testing kits and the presentation of false negatives. Experts suggest that almost everyone in China is susceptible to SARS-CoV-2 infection, and to date, there are no effective treatments. In light of the references published, this review demonstrates the biological features, spread, diagnosis and treatment of SARS-CoV-2 as a whole and aims to analyse the similarities and differences among SARS-CoV-2, SARS-CoV and MERS-CoV to provide new ideas and suggestions for prevention, diagnosis and clinical treatment.
format: application/pdf
format: text/html
creator: Tingting Hu
creator: Ying Liu
creator: Mingyi Zhao
creator: Quan Zhuang
creator: Linyong Xu
creator: Qingnan He
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.9725
publisher: PeerJ Inc.
rights: © 2020 Hu et al.
abstract: In mid-December 2019, a novel atypical pneumonia broke out in Wuhan, Hubei Province, China and was caused by a newly identified coronavirus, initially termed 2019 Novel Coronavirus and subsequently severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of 19 May 2020, a total of 4,731,458 individuals were reported as infected with SARS-CoV-2 among 213 countries, areas or territories with recorded cases, and the overall case-fatality rate was 6.6% (316,169 deaths among 4,731,458 recorded cases), according to the World Health Organization. Studies have shown that SARS-CoV-2 is notably similar to (severe acute respiratory syndrome coronavirus) SARS-CoV that emerged in 2002–2003 and Middle East respiratory syndrome coronavirus (MERS-CoV) that spread during 2012, and these viruses all contributed to global pandemics. The ability of SARS-CoV-2 to rapidly spread a pneumonia-like disease from Hubei Province, China, throughout the world has provoked widespread concern. The main symptoms of coronavirus disease 2019 (COVID-19) include fever, cough, myalgia, fatigue and lower respiratory signs. At present, nucleic acid tests are widely recommended as the optimal method for detecting SARS-CoV-2. However, obstacles remain, including the global shortage of testing kits and the presentation of false negatives. Experts suggest that almost everyone in China is susceptible to SARS-CoV-2 infection, and to date, there are no effective treatments. In light of the references published, this review demonstrates the biological features, spread, diagnosis and treatment of SARS-CoV-2 as a whole and aims to analyse the similarities and differences among SARS-CoV-2, SARS-CoV and MERS-CoV to provide new ideas and suggestions for prevention, diagnosis and clinical treatment.
bibliographic citation: Hu et al. (2020) A comparison of COVID-19, SARS and MERS. PeerJ 8:e9725 https://doi.org/10.7717/peerj.9725
date submitted: 2020-03-29
date accepted: 2020-07-24
issued: 2020-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Tingting
author list: Agent
  family name: Liu
  given name: Ying
author list: Agent
  family name: Zhao
  given name: Mingyi
author list: Agent
  family name: Zhuang
  given name: Quan
author list: Agent
  family name: Xu
  given name: Linyong
author list: Agent
  family name: He
  given name: Qingnan
doi: 10.7717/peerj.9725
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-19
copyright: © 2020 Hu et al.
attribution name: Hu et al.

Transcriptomic analysis highlights cochlear inflammation associated with age-related hearing loss in C57BL/6 mice using next generation sequencing
type: item
type: AcademicArticle
description: Background In our aging society, age-related hearing loss (AHL) is the most common sensory disorder in old people. Much progress has been made in understanding the pathological process of AHL over the past few decades. However, the mechanism of cochlear degeneration during aging is still not fully understood. Methods Next generation sequencing technique was used to sequence the whole transcriptome of the cochlea of C57BL/6 mice, a mouse model of AHL. Differentially expressed genes (DEGs) were identified using the Cuffdiff software. GO and KEGG pathway enrichment analyses of the DEGs were implemented by using the GOseq R package and KOBAS software, respectively. Results A total of 731 genes (379 up- and 352 down-regulated) were revealed to be differentially expressed in the cochlea of aged mice compared to the young. Many genes associated with aging, apoptosis, necroptosis and particularly, inflammation were identified as being significantly modulated in the aged cochlea. GO and KEGG analyses of the upregulated DEGs revealed that the most enriched terms were associated with immune responses and inflammatory pathways, whereas many of the downregulated genes are involved in ion channel function and neuronal signaling. Real-time qPCR showed that H2O2 treatment significantly induced the expression of multiple inflammation and necroptosis-related genes in HEI-OC1 cells. Conclusion Using next generation sequencing, our transcriptomic analysis revealed the differences of gene expression pattern with age in the cochlea of C57BL/6 mice. Our study also revealed multiple immune and inflammatory transcriptomic changes during cochlear aging and provides new insights into the molecular mechanisms underlying cochlear inflammation in AHL.
format: application/pdf
format: text/html
creator: Zhongwu Su
creator: Hao Xiong
creator: Yi Liu
creator: Jiaqi Pang
creator: Hanqing Lin
creator: Weijian Zhang
creator: Yiqing Zheng
subject: Bioinformatics
subject: Otorhinolaryngology
description: doi:10.7717/peerj.9737
publisher: PeerJ Inc.
rights: © 2020 Su et al.
abstract: Background In our aging society, age-related hearing loss (AHL) is the most common sensory disorder in old people. Much progress has been made in understanding the pathological process of AHL over the past few decades. However, the mechanism of cochlear degeneration during aging is still not fully understood. Methods Next generation sequencing technique was used to sequence the whole transcriptome of the cochlea of C57BL/6 mice, a mouse model of AHL. Differentially expressed genes (DEGs) were identified using the Cuffdiff software. GO and KEGG pathway enrichment analyses of the DEGs were implemented by using the GOseq R package and KOBAS software, respectively. Results A total of 731 genes (379 up- and 352 down-regulated) were revealed to be differentially expressed in the cochlea of aged mice compared to the young. Many genes associated with aging, apoptosis, necroptosis and particularly, inflammation were identified as being significantly modulated in the aged cochlea. GO and KEGG analyses of the upregulated DEGs revealed that the most enriched terms were associated with immune responses and inflammatory pathways, whereas many of the downregulated genes are involved in ion channel function and neuronal signaling. Real-time qPCR showed that H2O2 treatment significantly induced the expression of multiple inflammation and necroptosis-related genes in HEI-OC1 cells. Conclusion Using next generation sequencing, our transcriptomic analysis revealed the differences of gene expression pattern with age in the cochlea of C57BL/6 mice. Our study also revealed multiple immune and inflammatory transcriptomic changes during cochlear aging and provides new insights into the molecular mechanisms underlying cochlear inflammation in AHL.
bibliographic citation: Su et al. (2020) Transcriptomic analysis highlights cochlear inflammation associated with age-related hearing loss in C57BL/6 mice using next generation sequencing. PeerJ 8:e9737 https://doi.org/10.7717/peerj.9737
date submitted: 2020-03-24
date accepted: 2020-07-26
issued: 2020-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Zhongwu
author list: Agent
  family name: Xiong
  given name: Hao
author list: Agent
  family name: Liu
  given name: Yi
author list: Agent
  family name: Pang
  given name: Jiaqi
author list: Agent
  family name: Lin
  given name: Hanqing
author list: Agent
  family name: Zhang
  given name: Weijian
author list: Agent
  family name: Zheng
  given name: Yiqing
doi: 10.7717/peerj.9737
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-19
copyright: © 2020 Su et al.
attribution name: Su et al.

Six complete mitochondrial genomes of mayflies from three genera of Ephemerellidae (Insecta: Ephemeroptera) with inversion and translocation of trnI rearrangement and their phylogenetic relationships
type: item
type: AcademicArticle
description: As a small order of Pterygota (Insecta), Ephemeroptera has almost 3,500 species around the world. Ephemerellidae is a widely distributed common group of Ephemeroptera. However, the relationship among Ephemerellidae, Vietnamellidae and Teloganellidae is still in dispute. In this study, we sequenced six complete mitogenomes of three genera from Ephemerellidae (Insecta: Ephemeroptera): Ephemerella sp. Yunnan-2018, Serratella zapekinae, Serratella sp. Yunnan-2018, Serratella sp. Liaoning-2019, Torleya grandipennis and T. tumiforceps. These mitogenomes were employed to reveal controversial phylogenetic relationships among the Ephemeroptera, with emphasis on the phylogenetic relationships among Ephemerellidae. The lengths of the six mayfly mitogenomes ranged from 15,134 bp to 15,703 bp. Four mitogenomes of Ephemerella sp. Yunnan-2018, Serratella zapekinae, Serratella sp. Yunnan-2018 and Serratella sp. Liaoning-2019 had 22 tRNAs including an inversion and translocation of trnI. By contrast, the mitogenomes of T. tumiforceps and T. grandipennis had 24 tRNAs due to an extra two copies of inversion and translocation of trnI. Within the family Ephemerellidae, disparate gene rearrangement occurred in the mitogenomes of different genera: one copy of inversion and translocation trnI in the genera Ephemerella and Serratella, and three repeat copies of inversion and translocation of trnI in the genus Torleya. A large non-coding region (≥200 bp) between trnS1 (AGN) and trnE was detected in T. grandipennis and T. tumiforceps. Among the phylogenetic relationship of the Ephemeroptera, the monophyly of almost all families except Siphlonuridae was supported by BI and ML analyses. The phylogenetic results indicated that Ephemerellidae was the sister clade to Vietnamellidae whereas Teloganellidae was not a sister clade of Ephemerellidae and Vietnamellidae.
format: application/pdf
format: text/html
creator: Xiao-Dong Xu
creator: Yi-Yang Jia
creator: Si-Si Cao
creator: Zi-Yi Zhang
creator: Kenneth B. Storey
creator: Dan-Na Yu
creator: Jia-Yong Zhang
subject: Entomology
subject: Genomics
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9740
publisher: PeerJ Inc.
rights: © 2020 Xu et al.
abstract: As a small order of Pterygota (Insecta), Ephemeroptera has almost 3,500 species around the world. Ephemerellidae is a widely distributed common group of Ephemeroptera. However, the relationship among Ephemerellidae, Vietnamellidae and Teloganellidae is still in dispute. In this study, we sequenced six complete mitogenomes of three genera from Ephemerellidae (Insecta: Ephemeroptera): Ephemerella sp. Yunnan-2018, Serratella zapekinae, Serratella sp. Yunnan-2018, Serratella sp. Liaoning-2019, Torleya grandipennis and T. tumiforceps. These mitogenomes were employed to reveal controversial phylogenetic relationships among the Ephemeroptera, with emphasis on the phylogenetic relationships among Ephemerellidae. The lengths of the six mayfly mitogenomes ranged from 15,134 bp to 15,703 bp. Four mitogenomes of Ephemerella sp. Yunnan-2018, Serratella zapekinae, Serratella sp. Yunnan-2018 and Serratella sp. Liaoning-2019 had 22 tRNAs including an inversion and translocation of trnI. By contrast, the mitogenomes of T. tumiforceps and T. grandipennis had 24 tRNAs due to an extra two copies of inversion and translocation of trnI. Within the family Ephemerellidae, disparate gene rearrangement occurred in the mitogenomes of different genera: one copy of inversion and translocation trnI in the genera Ephemerella and Serratella, and three repeat copies of inversion and translocation of trnI in the genus Torleya. A large non-coding region (≥200 bp) between trnS1 (AGN) and trnE was detected in T. grandipennis and T. tumiforceps. Among the phylogenetic relationship of the Ephemeroptera, the monophyly of almost all families except Siphlonuridae was supported by BI and ML analyses. The phylogenetic results indicated that Ephemerellidae was the sister clade to Vietnamellidae whereas Teloganellidae was not a sister clade of Ephemerellidae and Vietnamellidae.
bibliographic citation: Xu et al. (2020) Six complete mitochondrial genomes of mayflies from three genera of Ephemerellidae (Insecta: Ephemeroptera) with inversion and translocation of trnI rearrangement and their phylogenetic relationships. PeerJ 8:e9740 https://doi.org/10.7717/peerj.9740
date submitted: 2020-05-07
date accepted: 2020-07-26
issued: 2020-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Xiao-Dong
author list: Agent
  family name: Jia
  given name: Yi-Yang
author list: Agent
  family name: Cao
  given name: Si-Si
author list: Agent
  family name: Zhang
  given name: Zi-Yi
author list: Agent
  family name: Storey
  given name: Kenneth B.
author list: Agent
  family name: Yu
  given name: Dan-Na
author list: Agent
  family name: Zhang
  given name: Jia-Yong
doi: 10.7717/peerj.9740
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-19
copyright: ©2020 Xu et al.
attribution name: Xu et al.

Evolution of the patella and patelloid in marsupial mammals
type: item
type: AcademicArticle
description: The musculoskeletal system of marsupial mammals has numerous unusual features beyond the pouch and epipubic bones. One example is the widespread absence or reduction (to a fibrous “patelloid”) of the patella (“kneecap”) sesamoid bone, but prior studies with coarse sampling indicated complex patterns of evolution of this absence or reduction. Here, we conducted an in-depth investigation into the form of the patella of extant marsupial species and used the assembled dataset to reconstruct the likely pattern of evolution of the marsupial patella. Critical assessment of the available literature was followed by examination and imaging of museum specimens, as well as CT scanning and histological examination of dissected wet specimens. Our results, from sampling about 19% of extant marsupial species-level diversity, include new images and descriptions of the fibrocartilaginous patelloid in Thylacinus cynocephalus (the thylacine or “marsupial wolf”) and other marsupials as well as the ossified patella in Notoryctes ‘marsupial moles’, Caenolestes shrew opossums, bandicoots and bilbies. We found novel evidence of an ossified patella in one specimen of Macropus rufogriseus (Bennett’s wallaby), with hints of similar variation in other species. It remains uncertain whether such ossifications are ontogenetic variation, unusual individual variation, pathological or otherwise, but future studies must continue to be conscious of variation in metatherian patellar sesamoid morphology. Our evolutionary reconstructions using our assembled data vary, too, depending on the reconstruction algorithm used. A maximum likelihood algorithm favours ancestral fibrocartilaginous “patelloid” for crown clade Marsupialia and independent origins of ossified patellae in extinct sparassodonts, peramelids, notoryctids and caenolestids. A maximum parsimony algorithm favours ancestral ossified patella for the clade [Marsupialia + sparassodonts] and subsequent reductions into fibrocartilage in didelphids, d…
format: application/pdf
format: text/html
creator: Alice L. Denyer
creator: Sophie Regnault
creator: John R. Hutchinson
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.9760
publisher: PeerJ Inc.
rights: © 2020 Denyer et al.
abstract: The musculoskeletal system of marsupial mammals has numerous unusual features beyond the pouch and epipubic bones. One example is the widespread absence or reduction (to a fibrous “patelloid”) of the patella (“kneecap”) sesamoid bone, but prior studies with coarse sampling indicated complex patterns of evolution of this absence or reduction. Here, we conducted an in-depth investigation into the form of the patella of extant marsupial species and used the assembled dataset to reconstruct the likely pattern of evolution of the marsupial patella. Critical assessment of the available literature was followed by examination and imaging of museum specimens, as well as CT scanning and histological examination of dissected wet specimens. Our results, from sampling about 19% of extant marsupial species-level diversity, include new images and descriptions of the fibrocartilaginous patelloid in Thylacinus cynocephalus (the thylacine or “marsupial wolf”) and other marsupials as well as the ossified patella in Notoryctes ‘marsupial moles’, Caenolestes shrew opossums, bandicoots and bilbies. We found novel evidence of an ossified patella in one specimen of Macropus rufogriseus (Bennett’s wallaby), with hints of similar variation in other species. It remains uncertain whether such ossifications are ontogenetic variation, unusual individual variation, pathological or otherwise, but future studies must continue to be conscious of variation in metatherian patellar sesamoid morphology. Our evolutionary reconstructions using our assembled data vary, too, depending on the reconstruction algorithm used. A maximum likelihood algorithm favours ancestral fibrocartilaginous “patelloid” for crown clade Marsupialia and independent origins of ossified patellae in extinct sparassodonts, peramelids, notoryctids and caenolestids. A maximum parsimony algorithm favours ancestral ossified patella for the clade [Marsupialia + sparassodonts] and subsequent reductions into fibrocartilage in didelphids, d…
bibliographic citation: Denyer et al. (2020) Evolution of the patella and patelloid in marsupial mammals. PeerJ 8:e9760 https://doi.org/10.7717/peerj.9760
date submitted: 2020-01-16
date accepted: 2020-07-28
issued: 2020-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Denyer
  given name: Alice L.
author list: Agent
  family name: Regnault
  given name: Sophie
author list: Agent
  family name: Hutchinson
  given name: John R.
doi: 10.7717/peerj.9760
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-19
copyright: ©2020 Denyer et al.
attribution name: Denyer et al.

The changes of morphological and physiological characteristics in hemiparasitic Monochasma savatieri before and after attachment to the host plant
type: item
type: AcademicArticle
description: Background Monochasma savatieri is an endangered hemiparasitic medicinal plant with a variety of antioxidant, antimicrobial and anti-inflammatory properties. Despite the urgent need to understand the parasitic biology of M. savatieri, parasite-host associations have long been neglected in studies of M. savatieri. Methods We conducted a pot cultivation experiment to analyze changes in the growth traits, physiological performance and anatomical structures of M. savatieri grown with the potential host Gardenia jasminoides E., before and after the establishment of the parasite-host association. Results Prior to the establishment of the parasite-host association, the presence of the host had no significant effect on the maximum root length, leaf indexes or total dry weight of M. savatieri seedlings, but had significant positive effect on seedling height, number of roots or number of haustoria. When it was continuously grown without a host, M. savatieri growth was rather slow. The establishment of the parasite-host association enhanced the growth of M. savatieri, and higher levels of photosynthetic pigments, increased antioxidant enzyme activity and lower malondialdehyde accumulation were observed in M. savatieri with an established parasite-host association. Furthermore, an analysis of the anatomical structures of M. savatieri showed that the establishment of the parasite-host association enabled better development of the seedling vegetative organs than that in seedlings without parasite-host associations. Conclusions Our study demonstrates the physiological and anatomical changes that occurred in M. savatieri after connection with a host and suggests that the enhanced growth and development of M. savatieri were highly dependent on the parasite-host association.
format: application/pdf
format: text/html
creator: Lanlan Chen
creator: Zaibiao Zhu
creator: Qiaosheng Guo
creator: Jun Guo
creator: Zhigang Huang
creator: Hui Zhang
subject: Agricultural Science
subject: Developmental Biology
subject: Ecology
subject: Plant Science
subject: Histology
description: doi:10.7717/peerj.9780
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Background Monochasma savatieri is an endangered hemiparasitic medicinal plant with a variety of antioxidant, antimicrobial and anti-inflammatory properties. Despite the urgent need to understand the parasitic biology of M. savatieri, parasite-host associations have long been neglected in studies of M. savatieri. Methods We conducted a pot cultivation experiment to analyze changes in the growth traits, physiological performance and anatomical structures of M. savatieri grown with the potential host Gardenia jasminoides E., before and after the establishment of the parasite-host association. Results Prior to the establishment of the parasite-host association, the presence of the host had no significant effect on the maximum root length, leaf indexes or total dry weight of M. savatieri seedlings, but had significant positive effect on seedling height, number of roots or number of haustoria. When it was continuously grown without a host, M. savatieri growth was rather slow. The establishment of the parasite-host association enhanced the growth of M. savatieri, and higher levels of photosynthetic pigments, increased antioxidant enzyme activity and lower malondialdehyde accumulation were observed in M. savatieri with an established parasite-host association. Furthermore, an analysis of the anatomical structures of M. savatieri showed that the establishment of the parasite-host association enabled better development of the seedling vegetative organs than that in seedlings without parasite-host associations. Conclusions Our study demonstrates the physiological and anatomical changes that occurred in M. savatieri after connection with a host and suggests that the enhanced growth and development of M. savatieri were highly dependent on the parasite-host association.
bibliographic citation: Chen et al. (2020) The changes of morphological and physiological characteristics in hemiparasitic Monochasma savatieri before and after attachment to the host plant. PeerJ 8:e9780 https://doi.org/10.7717/peerj.9780
date submitted: 2019-12-16
date accepted: 2020-07-30
issued: 2020-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Lanlan
author list: Agent
  family name: Zhu
  given name: Zaibiao
author list: Agent
  family name: Guo
  given name: Qiaosheng
author list: Agent
  family name: Guo
  given name: Jun
author list: Agent
  family name: Huang
  given name: Zhigang
author list: Agent
  family name: Zhang
  given name: Hui
doi: 10.7717/peerj.9780
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-19
copyright: © 2020 Chen et al.
attribution name: Chen et al.

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