PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Combined use of Bacillus strains and Miscanthus for accelerating biodegradation of poly(lactic acid) and poly(ethylene terephthalate)
items: Stimulus–response complexity influences task-set inhibition in task switching
items: In vitro and in vivo activities of the carbonic anhydrase inhibitor, dorzolamide, against vancomycin-resistant enterococci
items: Maternal depressive symptoms and early childhood development: the role of mother–child interactions among mother–child dyads in rural areas of Central and Western China
items: Insomnia partially mediates the relationship between pathological personality traits and depression: a case-control study
items: VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature
items: AbhemC encoding porphobilinogen deaminase plays an important role in chlorophyll biosynthesis and function in albino Ananas comosus var. bracteatus leaves
items: COL1A1 is a prognostic biomarker and correlated with immune infiltrates in lung cancer
items: COVID-19 simulation study—the effect of strict non-pharmaceutical interventions (NPIs) on controlling the spread of COVID-19
items: Effectiveness of isolation policies in schools: evidence from a mathematical model of influenza and COVID-19

Combined use of Bacillus strains and Miscanthus for accelerating biodegradation of poly(lactic acid) and poly(ethylene terephthalate)
type: item
type: AcademicArticle
description: Background The aim of this study was to verify whether the presence of Bacillus strains and of miscanthus influence biodegradation and formed of biofilm of poly(lactic acid) (PLA) and poly(ethylene terephthalate) (PET). Methods The experiment conducted in compost soil showed that strains Bacillus subtilis and Bacillus cereus isolated from heavy metal contaminated environment have biochemical activity and accelerate biodegradation of both plastic materials. Results For PLA film it was found that the carbonyl index dropped by over 15% in the presence of B. subtilis, while the film tensile strength decreased by 35% and the oxygen to carbon O/C ratio was higher by 3% in the presence of B. cereus, and the presence of miscanthus resulted in a loss of weight. For PET film, a decrease in the carbonyl index by 16% was observed following inoculation with B. cereus. The metabolic activity of this strain contributed to the reduction of the film’s tensile strength by 17% and to the increase in the permeability to O2 and CO2. The most intense degradation of PET film was observed in the presence of bacteria and plants. B. subtilis strain combined with miscanthus plantings may be a promising method for accelerating PLA and PET degradation in compost soil.
format: application/pdf
format: text/html
creator: Grażyna B. Dąbrowska
creator: Katarzyna Janczak
creator: Agnieszka Richert
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.10957
publisher: PeerJ Inc.
rights: © 2021 Dąbrowska et al.
abstract: Background The aim of this study was to verify whether the presence of Bacillus strains and of miscanthus influence biodegradation and formed of biofilm of poly(lactic acid) (PLA) and poly(ethylene terephthalate) (PET). Methods The experiment conducted in compost soil showed that strains Bacillus subtilis and Bacillus cereus isolated from heavy metal contaminated environment have biochemical activity and accelerate biodegradation of both plastic materials. Results For PLA film it was found that the carbonyl index dropped by over 15% in the presence of B. subtilis, while the film tensile strength decreased by 35% and the oxygen to carbon O/C ratio was higher by 3% in the presence of B. cereus, and the presence of miscanthus resulted in a loss of weight. For PET film, a decrease in the carbonyl index by 16% was observed following inoculation with B. cereus. The metabolic activity of this strain contributed to the reduction of the film’s tensile strength by 17% and to the increase in the permeability to O2 and CO2. The most intense degradation of PET film was observed in the presence of bacteria and plants. B. subtilis strain combined with miscanthus plantings may be a promising method for accelerating PLA and PET degradation in compost soil.
bibliographic citation: Dąbrowska et al. (2021) Combined use of Bacillus strains and Miscanthus for accelerating biodegradation of poly(lactic acid) and poly(ethylene terephthalate). PeerJ 9:e10957 https://doi.org/10.7717/peerj.10957
date submitted: 2020-10-15
date accepted: 2021-01-27
issued: 2021-03-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dąbrowska
  given name: Grażyna B.
author list: Agent
  family name: Janczak
  given name: Katarzyna
author list: Agent
  family name: Richert
  given name: Agnieszka
doi: 10.7717/peerj.10957
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-30
copyright: ©2021 Dąbrowska et al.
attribution name: Dąbrowska et al.

Stimulus–response complexity influences task-set inhibition in task switching
type: item
type: AcademicArticle
description: Previous studies have found that inhibiting a task set plays an important role in task switching. However, the impact of stimulus–response (S–R) complexity on this inhibition processing has not been explored. In this study, we applied the backward inhibition paradigm (switching between tasks A, B, and C, presented in sets of three) in order to investigate inhibition performance under different S–R complexities caused by corresponding S–R mappings. The results showed that the difficult condition resulted in a greater switch cost than the moderate and easy conditions. Furthermore, we found a significant n−2 repetition cost under the easy S–R complexity that was reversed under the difficult S–R complexity. To verify stability of the reversed n−2 repetition cost in the difficult condition, we recruited another independent sample to conduct an additional experiment with the difficult condition. These results replicated the reversed n−2 repetition cost. These findings suggest that S–R complexity affects task-set inhibition in task switching because the effect of the task-set inhibition was insignificant when the S–R complexity increased; it was only significant under the easy condition. This result was caused by the different cognitive resource assignments.
format: application/pdf
format: text/html
creator: Li Zhao
creator: Saisai Hu
creator: Yingying Xia
creator: Jinyu Li
creator: Jingjing Zhao
creator: Ya Li
creator: Yonghui Wang
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.10988
publisher: PeerJ Inc.
rights: © 2021 Zhao et al.
abstract: Previous studies have found that inhibiting a task set plays an important role in task switching. However, the impact of stimulus–response (S–R) complexity on this inhibition processing has not been explored. In this study, we applied the backward inhibition paradigm (switching between tasks A, B, and C, presented in sets of three) in order to investigate inhibition performance under different S–R complexities caused by corresponding S–R mappings. The results showed that the difficult condition resulted in a greater switch cost than the moderate and easy conditions. Furthermore, we found a significant n−2 repetition cost under the easy S–R complexity that was reversed under the difficult S–R complexity. To verify stability of the reversed n−2 repetition cost in the difficult condition, we recruited another independent sample to conduct an additional experiment with the difficult condition. These results replicated the reversed n−2 repetition cost. These findings suggest that S–R complexity affects task-set inhibition in task switching because the effect of the task-set inhibition was insignificant when the S–R complexity increased; it was only significant under the easy condition. This result was caused by the different cognitive resource assignments.
bibliographic citation: Zhao et al. (2021) Stimulus–response complexity influences task-set inhibition in task switching. PeerJ 9:e10988 https://doi.org/10.7717/peerj.10988
date submitted: 2020-07-13
date accepted: 2021-02-01
issued: 2021-03-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Li
author list: Agent
  family name: Hu
  given name: Saisai
author list: Agent
  family name: Xia
  given name: Yingying
author list: Agent
  family name: Li
  given name: Jinyu
author list: Agent
  family name: Zhao
  given name: Jingjing
author list: Agent
  family name: Li
  given name: Ya
author list: Agent
  family name: Wang
  given name: Yonghui
doi: 10.7717/peerj.10988
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-30
copyright: © 2021 Zhao et al.
attribution name: Zhao et al.

In vitro and in vivo activities of the carbonic anhydrase inhibitor, dorzolamide, against vancomycin-resistant enterococci
type: item
type: AcademicArticle
description: Vancomycin-resistant enterococci (VRE) are a serious public health threat and a leading cause of healthcare-associated infections. Bacterial resistance to antibiotics recommended for the treatment of enterococcal infections complicates the management of these infections. Hence, there is a critical need for the discovery of new anti-VRE agents. We previously reported carbonic anhydrase inhibitors (CAIs) as new potent VRE inhibitors. In the present study, the activity of the CAI, dorzolamide was evaluated against VRE both in vitro and in vivo. Dorzolamide exhibited potent activity against a panel of clinical VRE isolates, with minimum inhibitory concentration (MIC) values ranging from 1 µg/mL to 8 µg/mL. A killing kinetics experiment determined that dorzolamide exhibited a bacteriostatic effect against VRE, which was similar to the drug of choice (linezolid). Dorzolamide interacted synergistically with gentamicin against four strains of VRE, and exhibited an additive interaction with gentamicin against six VRE strains, reducing gentamicin’s MIC by several folds. Moreover, dorzolamide outperformed linezolid in an in vivo VRE colonization reduction mouse model. Dorzolamide significantly reduced the VRE burden in fecal samples of mice by 2.9-log10 (99.9%) and 3.86-log10 (99.99%) after 3 and 5 days of treatment, respectively. Furthermore, dorzolamide reduced the VRE count in the cecal (1.74-log10 (98.2%) reduction) and ileal contents (1.5-log10 (96.3%)) of mice, which was superior to linezolid. Collectively, these results indicate that dorzolamide represents a promising treatment option that warrants consideration as a supplement to current therapeutics used for VRE infections.
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creator: Nader S. Abutaleb
creator: Ahmed E.M. Elhassanny
creator: Daniel P. Flaherty
creator: Mohamed N. Seleem
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.11059
publisher: PeerJ Inc.
rights: © 2021 Abutaleb et al.
abstract: Vancomycin-resistant enterococci (VRE) are a serious public health threat and a leading cause of healthcare-associated infections. Bacterial resistance to antibiotics recommended for the treatment of enterococcal infections complicates the management of these infections. Hence, there is a critical need for the discovery of new anti-VRE agents. We previously reported carbonic anhydrase inhibitors (CAIs) as new potent VRE inhibitors. In the present study, the activity of the CAI, dorzolamide was evaluated against VRE both in vitro and in vivo. Dorzolamide exhibited potent activity against a panel of clinical VRE isolates, with minimum inhibitory concentration (MIC) values ranging from 1 µg/mL to 8 µg/mL. A killing kinetics experiment determined that dorzolamide exhibited a bacteriostatic effect against VRE, which was similar to the drug of choice (linezolid). Dorzolamide interacted synergistically with gentamicin against four strains of VRE, and exhibited an additive interaction with gentamicin against six VRE strains, reducing gentamicin’s MIC by several folds. Moreover, dorzolamide outperformed linezolid in an in vivo VRE colonization reduction mouse model. Dorzolamide significantly reduced the VRE burden in fecal samples of mice by 2.9-log10 (99.9%) and 3.86-log10 (99.99%) after 3 and 5 days of treatment, respectively. Furthermore, dorzolamide reduced the VRE count in the cecal (1.74-log10 (98.2%) reduction) and ileal contents (1.5-log10 (96.3%)) of mice, which was superior to linezolid. Collectively, these results indicate that dorzolamide represents a promising treatment option that warrants consideration as a supplement to current therapeutics used for VRE infections.
bibliographic citation: Abutaleb et al. (2021) In vitro and in vivo activities of the carbonic anhydrase inhibitor, dorzolamide, against vancomycin-resistant enterococci. PeerJ 9:e11059 https://doi.org/10.7717/peerj.11059
date submitted: 2020-11-26
date accepted: 2021-02-12
issued: 2021-03-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abutaleb
  given name: Nader S.
author list: Agent
  family name: Elhassanny
  given name: Ahmed E.M.
author list: Agent
  family name: Flaherty
  given name: Daniel P.
author list: Agent
  family name: Seleem
  given name: Mohamed N.
doi: 10.7717/peerj.11059
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-30
copyright: ©2021 Abutaleb et al.
attribution name: Abutaleb et al.

Maternal depressive symptoms and early childhood development: the role of mother–child interactions among mother–child dyads in rural areas of Central and Western China
type: item
type: AcademicArticle
description: Background The associations among maternal depressive symptoms (MDS), mother–child interactions and early child development are poorly understood. This study aimed to explore the role of mother–child interactions on the associations between MDS and child development. Methods A cross-sectional study with a multistage sampling method was conducted in rural areas of Central and Western China. MDS, child development outcomes (communication, gross motor function, fine motor function, problem solving and personal social skills) and mother–child interactions were assessed by The Edinburgh Postpartum Depression Scale, the Chinese version of the Ages and Stages Questionnaires and the Multiple Indicator Cluster Surveys, respectively. Regression-based statistical mediation and moderation were conducted using the PROCESS macro for SPSS. Results A total of 2,548 participants (mothers: 1,274; children: 1,274) were included in our analyses. MDS was negatively associated with child development outcomes and mother–child interactions partly mediated these associations. The proportion of the mediating effect of mother–child interactions was 7.7% for communication, 8.2% for gross motor, 10.3% for fine motor, 10.1% for problem-solving and 9.5% for personal social domains. In addition, the interaction effects of MDS and mother–child interactions on the communication domain were significant (β = 0.070, 95% CI 0.016, 0.124; p = 0.011). The associations between MDS and child communication abilities were weaker at the high level (simple slope = −0.019, t = − 0.458, p = 0.647) of mother–child interactions than at the mean level (simple slope = −0.089, t = − 3.190, p = 0.002) and the low level (simple slope = −0.158, t = − 4.231, p < 0.001). Similar moderating effects were not observed in the other child development outcomes. Conclusion Our results suggest the important role of mother–child interactions on the associations between MDS and early childhood development. Due to the cross-sectional…
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creator: Xiaoli Liu
creator: Chenlu Yang
creator: Yuning Yang
creator: Xiaona Huang
creator: Yinping Wang
creator: Yaqing Gao
creator: Qiying Song
creator: Yan Wang
creator: Hong Zhou
subject: Epidemiology
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.11060
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background The associations among maternal depressive symptoms (MDS), mother–child interactions and early child development are poorly understood. This study aimed to explore the role of mother–child interactions on the associations between MDS and child development. Methods A cross-sectional study with a multistage sampling method was conducted in rural areas of Central and Western China. MDS, child development outcomes (communication, gross motor function, fine motor function, problem solving and personal social skills) and mother–child interactions were assessed by The Edinburgh Postpartum Depression Scale, the Chinese version of the Ages and Stages Questionnaires and the Multiple Indicator Cluster Surveys, respectively. Regression-based statistical mediation and moderation were conducted using the PROCESS macro for SPSS. Results A total of 2,548 participants (mothers: 1,274; children: 1,274) were included in our analyses. MDS was negatively associated with child development outcomes and mother–child interactions partly mediated these associations. The proportion of the mediating effect of mother–child interactions was 7.7% for communication, 8.2% for gross motor, 10.3% for fine motor, 10.1% for problem-solving and 9.5% for personal social domains. In addition, the interaction effects of MDS and mother–child interactions on the communication domain were significant (β = 0.070, 95% CI 0.016, 0.124; p = 0.011). The associations between MDS and child communication abilities were weaker at the high level (simple slope = −0.019, t = − 0.458, p = 0.647) of mother–child interactions than at the mean level (simple slope = −0.089, t = − 3.190, p = 0.002) and the low level (simple slope = −0.158, t = − 4.231, p < 0.001). Similar moderating effects were not observed in the other child development outcomes. Conclusion Our results suggest the important role of mother–child interactions on the associations between MDS and early childhood development. Due to the cross-sectional…
bibliographic citation: Liu et al. (2021) Maternal depressive symptoms and early childhood development: the role of mother–child interactions among mother–child dyads in rural areas of Central and Western China. PeerJ 9:e11060 https://doi.org/10.7717/peerj.11060
date submitted: 2020-11-27
date accepted: 2021-02-13
issued: 2021-03-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiaoli
author list: Agent
  family name: Yang
  given name: Chenlu
author list: Agent
  family name: Yang
  given name: Yuning
author list: Agent
  family name: Huang
  given name: Xiaona
author list: Agent
  family name: Wang
  given name: Yinping
author list: Agent
  family name: Gao
  given name: Yaqing
author list: Agent
  family name: Song
  given name: Qiying
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Zhou
  given name: Hong
doi: 10.7717/peerj.11060
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-30
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Insomnia partially mediates the relationship between pathological personality traits and depression: a case-control study
type: item
type: AcademicArticle
description: Background and Objective Personality disorders are frequently associated with insomnia and depression, but little is known about the inter-relationships among these variables. Therefore, this study examined these inter-relationships and the possible mediating effect of insomnia on the association between specific personality pathologies and depression severity. Methods There were 138 study participants, including 69 individuals with depression and 69 healthy controls. The main variables were measured by the Hamilton Depression Rating Scale-24 (HAMD-24), Athens Sleep Insomnia Scale (AIS), and the Personality Diagnostic Questionnaire (PDQ-4+). Multivariate linear regression and mediation analysis were conducted. Results With the exception of the antisocial personality score, all the PDQ-4+ scores and AIS scores were significantly higher in the depression group than in the healthy control group (p < 0.001). In the total sample, all personality pathology scores (p < 0.001), except the antisocial personality score, had significant positive correlations with the AIS scores and HAMD-24 scores, and the AIS scores and HAMD-24 scores were positively correlated (r = 0.620, p < 0.001). Regression analysis revealed that borderline personality, passive-aggressive personality, and insomnia positively predicted the severity of depression, after adjusting for sociodemographic covariates, and that insomnia partially mediated the associations of borderline personality and passive-aggressive personality with depression severity. Conclusions Borderline personality, passive-aggressive personality, and insomnia tend to increase the severity of depression, and the effect of borderline and passive-aggressive personality on depression severity may be partially mediated by insomnia. This is the first study to report these findings in a Chinese sample, and they may help researchers to understand the pathways from specific personality pathologies to the psychopathology of depression better, whi…
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creator: Fenglan Chen
creator: Xiujin Lin
creator: Yuli Pan
creator: Xuan Zeng
creator: Shengjie Zhang
creator: Hong Hu
creator: Miaoyu Yu
creator: Junduan Wu
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.11061
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Background and Objective Personality disorders are frequently associated with insomnia and depression, but little is known about the inter-relationships among these variables. Therefore, this study examined these inter-relationships and the possible mediating effect of insomnia on the association between specific personality pathologies and depression severity. Methods There were 138 study participants, including 69 individuals with depression and 69 healthy controls. The main variables were measured by the Hamilton Depression Rating Scale-24 (HAMD-24), Athens Sleep Insomnia Scale (AIS), and the Personality Diagnostic Questionnaire (PDQ-4+). Multivariate linear regression and mediation analysis were conducted. Results With the exception of the antisocial personality score, all the PDQ-4+ scores and AIS scores were significantly higher in the depression group than in the healthy control group (p < 0.001). In the total sample, all personality pathology scores (p < 0.001), except the antisocial personality score, had significant positive correlations with the AIS scores and HAMD-24 scores, and the AIS scores and HAMD-24 scores were positively correlated (r = 0.620, p < 0.001). Regression analysis revealed that borderline personality, passive-aggressive personality, and insomnia positively predicted the severity of depression, after adjusting for sociodemographic covariates, and that insomnia partially mediated the associations of borderline personality and passive-aggressive personality with depression severity. Conclusions Borderline personality, passive-aggressive personality, and insomnia tend to increase the severity of depression, and the effect of borderline and passive-aggressive personality on depression severity may be partially mediated by insomnia. This is the first study to report these findings in a Chinese sample, and they may help researchers to understand the pathways from specific personality pathologies to the psychopathology of depression better, whi…
bibliographic citation: Chen et al. (2021) Insomnia partially mediates the relationship between pathological personality traits and depression: a case-control study. PeerJ 9:e11061 https://doi.org/10.7717/peerj.11061
date submitted: 2020-07-20
date accepted: 2021-02-13
issued: 2021-03-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Fenglan
author list: Agent
  family name: Lin
  given name: Xiujin
author list: Agent
  family name: Pan
  given name: Yuli
author list: Agent
  family name: Zeng
  given name: Xuan
author list: Agent
  family name: Zhang
  given name: Shengjie
author list: Agent
  family name: Hu
  given name: Hong
author list: Agent
  family name: Yu
  given name: Miaoyu
author list: Agent
  family name: Wu
  given name: Junduan
doi: 10.7717/peerj.11061
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-30
copyright: © 2021 Chen et al.
attribution name: Chen et al.

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature
type: item
type: AcademicArticle
description: Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in …
format: application/pdf
format: text/html
creator: Olivier Zablocki
creator: Michelle Michelsen
creator: Marie Burris
creator: Natalie Solonenko
creator: Joanna Warwick-Dugdale
creator: Romik Ghosh
creator: Jennifer Pett-Ridge
creator: Matthew B. Sullivan
creator: Ben Temperton
subject: Bioinformatics
subject: Ecology
subject: Genomics
subject: Marine Biology
subject: Virology
description: doi:10.7717/peerj.11088
publisher: PeerJ Inc.
rights: © 2021 Zablocki et al.
abstract: Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in …
bibliographic citation: Zablocki et al. (2021) VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature. PeerJ 9:e11088 https://doi.org/10.7717/peerj.11088
date submitted: 2020-11-06
date accepted: 2021-02-19
issued: 2021-03-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zablocki
  given name: Olivier
author list: Agent
  family name: Michelsen
  given name: Michelle
author list: Agent
  family name: Burris
  given name: Marie
author list: Agent
  family name: Solonenko
  given name: Natalie
author list: Agent
  family name: Warwick-Dugdale
  given name: Joanna
author list: Agent
  family name: Ghosh
  given name: Romik
author list: Agent
  family name: Pett-Ridge
  given name: Jennifer
author list: Agent
  family name: Sullivan
  given name: Matthew B.
author list: Agent
  family name: Temperton
  given name: Ben
doi: 10.7717/peerj.11088
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-30
copyright: ©2021 Zablocki et al.
attribution name: Zablocki et al.

AbhemC encoding porphobilinogen deaminase plays an important role in chlorophyll biosynthesis and function in albino Ananas comosus var. bracteatus leaves
type: item
type: AcademicArticle
description: Background The chimeric leaves of Ananas comosus var. bracteatus are composed of normal green parts (Grs) and albino white parts (Whs). Although the underlying mechanism of albinism in A. comosus var. bracteatus leaves is not fully understood, it is likely associated with the chlorophyll (Chl) biosynthesis. In this biosynthetic process, porphobilinogen deaminase (PBGD) plays a crucial role by catalyzing the conversion of porphobilinogen (PBG) to uroporphyrinogen III (Urogen III). Therefore, its encoding gene AbhemC was investigated here in association with Chl biosynthesis and albinism in chimeric A. comosus var. bracteatus leaves. Methods The Chl content, main Chl biosynthesis precursor content, and main enzyme activity were determined and compared between the Whs and Grs of A. comosus var. bracteatus leaves. In addition, AbhemC was cloned and its transcriptional expression and prokaryotic protein expression were analyzed. Furthermore, RNAi-mediated silencing of AbhemC was produced and assessed in tobacco plants. Results The concentration of Chl a and Chl b in the Grs was significantly higher than that in the Whs, respectively. Additionally, the content of the Chl biosynthesis precursor Urogen III decreased significantly in the Whs compared with the Grs. Thus, the transition of PBG to Urogen III may be the first rate-limiting step leading to albinism in the chimeric leaves of A. comosus var. bracteatus. The gene AbhemC comprised 1,135 bp and was encoded into a protein with 371 amino acids; phylogenetically, AbhemC was most closely related to hemC of pineapple. Prokaryotic expression and in vitro enzyme activity analysis showed that the cloned mRNA sequence of AbhemC was successfully integrated and had PBGD activity. Compared with control plants, transgenic tobacco leaves with pFGC5941-AbhemC-RNAi vector were substantially less green with significantly reduced hemC expression and Chl content, as well as reduced PBGD enzyme activity and significantly decreased conten…
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creator: Yanbin Xue
creator: Xia Li
creator: Meiqin Mao
creator: Yehua He
creator: Mark Owusu Adjei
creator: Xuzixin Zhou
creator: Hao Hu
creator: Jiawen Liu
creator: Xi Li
creator: Jun Ma
subject: Biochemistry
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11118
publisher: PeerJ Inc.
rights: © 2021 Xue et al.
abstract: Background The chimeric leaves of Ananas comosus var. bracteatus are composed of normal green parts (Grs) and albino white parts (Whs). Although the underlying mechanism of albinism in A. comosus var. bracteatus leaves is not fully understood, it is likely associated with the chlorophyll (Chl) biosynthesis. In this biosynthetic process, porphobilinogen deaminase (PBGD) plays a crucial role by catalyzing the conversion of porphobilinogen (PBG) to uroporphyrinogen III (Urogen III). Therefore, its encoding gene AbhemC was investigated here in association with Chl biosynthesis and albinism in chimeric A. comosus var. bracteatus leaves. Methods The Chl content, main Chl biosynthesis precursor content, and main enzyme activity were determined and compared between the Whs and Grs of A. comosus var. bracteatus leaves. In addition, AbhemC was cloned and its transcriptional expression and prokaryotic protein expression were analyzed. Furthermore, RNAi-mediated silencing of AbhemC was produced and assessed in tobacco plants. Results The concentration of Chl a and Chl b in the Grs was significantly higher than that in the Whs, respectively. Additionally, the content of the Chl biosynthesis precursor Urogen III decreased significantly in the Whs compared with the Grs. Thus, the transition of PBG to Urogen III may be the first rate-limiting step leading to albinism in the chimeric leaves of A. comosus var. bracteatus. The gene AbhemC comprised 1,135 bp and was encoded into a protein with 371 amino acids; phylogenetically, AbhemC was most closely related to hemC of pineapple. Prokaryotic expression and in vitro enzyme activity analysis showed that the cloned mRNA sequence of AbhemC was successfully integrated and had PBGD activity. Compared with control plants, transgenic tobacco leaves with pFGC5941-AbhemC-RNAi vector were substantially less green with significantly reduced hemC expression and Chl content, as well as reduced PBGD enzyme activity and significantly decreased conten…
bibliographic citation: Xue et al. (2021) AbhemC encoding porphobilinogen deaminase plays an important role in chlorophyll biosynthesis and function in albino Ananas comosus var. bracteatus leaves. PeerJ 9:e11118 https://doi.org/10.7717/peerj.11118
date submitted: 2020-09-24
date accepted: 2021-02-25
issued: 2021-03-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xue
  given name: Yanbin
author list: Agent
  family name: Li
  given name: Xia
author list: Agent
  family name: Mao
  given name: Meiqin
author list: Agent
  family name: He
  given name: Yehua
author list: Agent
  family name: Owusu Adjei
  given name: Mark
author list: Agent
  family name: Zhou
  given name: Xuzixin
author list: Agent
  family name: Hu
  given name: Hao
author list: Agent
  family name: Liu
  given name: Jiawen
author list: Agent
  family name: Li
  given name: Xi
author list: Agent
  family name: Ma
  given name: Jun
doi: 10.7717/peerj.11118
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-30
copyright: ©2021 Xue et al.
attribution name: Xue et al.

COL1A1 is a prognostic biomarker and correlated with immune infiltrates in lung cancer
type: item
type: AcademicArticle
description: Objective Lung cancer (LC) is one of the top ten malignant tumors and the first leading cause of cancer-related death among both men and women worldwide. It is imperative to identify immune-related biomarkers for early LC diagnosis and treatment. Methods Three Gene Expression Omnibus (GEO) datasets were selected to acquire the differentially expressed genes(DEGs) between LC and normal lung samples through GEO2R tools of NCBI. To identify hub genes, the DEGs were performed functional enrichment analysis, the protein–protein interaction (PPI) network construction, and Lasso regression. Then, a nomogram was constructed to predict the prognosis of patients with carcinoma based on hub genes. We further evaluated the influence of COL1A1 on clinical prognosis using GSE3141, GSE31210, and TCGA database. Also, the correlations between COL1A1 and cancer immune infiltrates and the B7-CD28 family was investigated via TIMER and GEPIA. Further analysis of immunohistochemistry shown that the COL1A1 expression level is positively correlated with CD276 expression level. Results By difference analysis, there were 340 DEGs between LC and normal lung samples. Then, we picked out seven hub genes, which were identified as components of the risk signature to divide LC into low and high-risk groups. Among them, the expression of COL1A1 is highly correlated with overall survival(OS) and progression-free survival (PFS) (p < 0.05). Importantly, there is a moderate to strong positive relationships between COL1A1 expression level and infiltration level of CD4+ T cells, Macrophage, Neutrophil, and Dendritic cell, as well as CD276 expression level. Conclusion These findings suggest that COL1A1 is correlated with prognosis and immune infiltrating levels, including CD4+ T cells, Macrophage, Neutrophil, and Dendritic cell, as well as CD276 expression level, indicating COL1A1 can be a potential immunity-related biomarker and therapeutic target in LC.
format: application/pdf
format: text/html
creator: Qishun Geng
creator: Zhibo Shen
creator: Lifeng Li
creator: Jie Zhao
subject: Bioinformatics
subject: Immunology
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.11145
publisher: PeerJ Inc.
rights: © 2021 Geng et al.
abstract: Objective Lung cancer (LC) is one of the top ten malignant tumors and the first leading cause of cancer-related death among both men and women worldwide. It is imperative to identify immune-related biomarkers for early LC diagnosis and treatment. Methods Three Gene Expression Omnibus (GEO) datasets were selected to acquire the differentially expressed genes(DEGs) between LC and normal lung samples through GEO2R tools of NCBI. To identify hub genes, the DEGs were performed functional enrichment analysis, the protein–protein interaction (PPI) network construction, and Lasso regression. Then, a nomogram was constructed to predict the prognosis of patients with carcinoma based on hub genes. We further evaluated the influence of COL1A1 on clinical prognosis using GSE3141, GSE31210, and TCGA database. Also, the correlations between COL1A1 and cancer immune infiltrates and the B7-CD28 family was investigated via TIMER and GEPIA. Further analysis of immunohistochemistry shown that the COL1A1 expression level is positively correlated with CD276 expression level. Results By difference analysis, there were 340 DEGs between LC and normal lung samples. Then, we picked out seven hub genes, which were identified as components of the risk signature to divide LC into low and high-risk groups. Among them, the expression of COL1A1 is highly correlated with overall survival(OS) and progression-free survival (PFS) (p < 0.05). Importantly, there is a moderate to strong positive relationships between COL1A1 expression level and infiltration level of CD4+ T cells, Macrophage, Neutrophil, and Dendritic cell, as well as CD276 expression level. Conclusion These findings suggest that COL1A1 is correlated with prognosis and immune infiltrating levels, including CD4+ T cells, Macrophage, Neutrophil, and Dendritic cell, as well as CD276 expression level, indicating COL1A1 can be a potential immunity-related biomarker and therapeutic target in LC.
bibliographic citation: Geng et al. (2021) COL1A1 is a prognostic biomarker and correlated with immune infiltrates in lung cancer. PeerJ 9:e11145 https://doi.org/10.7717/peerj.11145
date submitted: 2020-11-16
date accepted: 2021-03-03
issued: 2021-03-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Geng
  given name: Qishun
author list: Agent
  family name: Shen
  given name: Zhibo
author list: Agent
  family name: Li
  given name: Lifeng
author list: Agent
  family name: Zhao
  given name: Jie
doi: 10.7717/peerj.11145
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-30
copyright: ©2021 Geng et al.
attribution name: Geng et al.

COVID-19 simulation study—the effect of strict non-pharmaceutical interventions (NPIs) on controlling the spread of COVID-19
type: item
type: AcademicArticle
description: Background From the beginning of 2020, COVID-19 infection has changed our lives in many aspects and introduced limitations in the way people interact and communicate. In this paper, we are evaluating the effect of non-pharmaceutical interventions (NPI) in limiting the spread of the Severe Acute Respiratory Syndrome Coronavirus 2 pandemic during a wedding ceremony from Irbid, Northern Jordan. Agent-based modeling was used in a real wedding event that occurred at the beginning of the spread of the pandemic in Jordan. Two infected nationals of Jordan, who arrived in Jordan about a week before the event, initiated the spread of the pandemic within the contact community. Methods In this work, a strict national NPI that the government implemented is developed by using an abstract model with certain characteristics similar to the Jordanian community. Thus, the Jordanian community is represented in terms of ages, occupations, and population movements. After that, the extent of the impact of the NPI measures on the local community is measured. Results We observed the deterioration of the state of society while the epidemic is spreading among individuals in the absence of preventive measures. Also, the results show that the herd immunity case was an epidemic, with a high level of spread among the community with 918 cases during a short interval of time. On the other hand, the preventive measures scenario shows a totally controlled spread with only 74 cases applied on the same interval of time. Furthermore, a convergence in the actual results of the real system with the hypothetical system were detected in the case of applying the strict NPI measures. Finally, strict NPI at the community level following social gatherings seem to be effective measures to control the spread of the COVID- 19 pandemic.
format: application/pdf
format: text/html
creator: Amal Alzu’bi
creator: Sanaa Abu Alasal
creator: Khalid A. Kheirallah
creator: Valerie Watzlaf
subject: Infectious Diseases
subject: Public Health
subject: Computational Science
description: doi:10.7717/peerj.11172
publisher: PeerJ Inc.
rights: © 2021 Alzu’bi et al.
abstract: Background From the beginning of 2020, COVID-19 infection has changed our lives in many aspects and introduced limitations in the way people interact and communicate. In this paper, we are evaluating the effect of non-pharmaceutical interventions (NPI) in limiting the spread of the Severe Acute Respiratory Syndrome Coronavirus 2 pandemic during a wedding ceremony from Irbid, Northern Jordan. Agent-based modeling was used in a real wedding event that occurred at the beginning of the spread of the pandemic in Jordan. Two infected nationals of Jordan, who arrived in Jordan about a week before the event, initiated the spread of the pandemic within the contact community. Methods In this work, a strict national NPI that the government implemented is developed by using an abstract model with certain characteristics similar to the Jordanian community. Thus, the Jordanian community is represented in terms of ages, occupations, and population movements. After that, the extent of the impact of the NPI measures on the local community is measured. Results We observed the deterioration of the state of society while the epidemic is spreading among individuals in the absence of preventive measures. Also, the results show that the herd immunity case was an epidemic, with a high level of spread among the community with 918 cases during a short interval of time. On the other hand, the preventive measures scenario shows a totally controlled spread with only 74 cases applied on the same interval of time. Furthermore, a convergence in the actual results of the real system with the hypothetical system were detected in the case of applying the strict NPI measures. Finally, strict NPI at the community level following social gatherings seem to be effective measures to control the spread of the COVID- 19 pandemic.
bibliographic citation: Alzu’bi et al. (2021) COVID-19 simulation study—the effect of strict non-pharmaceutical interventions (NPIs) on controlling the spread of COVID-19. PeerJ 9:e11172 https://doi.org/10.7717/peerj.11172
date submitted: 2020-11-15
date accepted: 2021-03-07
issued: 2021-03-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alzu’bi
  given name: Amal
author list: Agent
  family name: Abu Alasal
  given name: Sanaa
author list: Agent
  family name: Kheirallah
  given name: Khalid A.
author list: Agent
  family name: Watzlaf
  given name: Valerie
doi: 10.7717/peerj.11172
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-30
copyright: © 2021 Alzu’bi et al.
attribution name: Alzu’bi et al.

Effectiveness of isolation policies in schools: evidence from a mathematical model of influenza and COVID-19
type: item
type: AcademicArticle
description: Background Non-pharmaceutical interventions such as social distancing, school closures and travel restrictions are often implemented to control outbreaks of infectious diseases. For influenza in schools, the Center of Disease Control (CDC) recommends that febrile students remain isolated at home until they have been fever-free for at least one day and a related policy is recommended for SARS-CoV-2 (COVID-19). Other authors proposed using a school week of four or fewer days of in-person instruction for all students to reduce transmission. However, there is limited evidence supporting the effectiveness of these interventions. Methods We introduced a mathematical model of school outbreaks that considers both intervention methods. Our model accounts for the school structure and schedule, as well as the time-progression of fever symptoms and viral shedding. The model was validated on outbreaks of seasonal and pandemic influenza and COVID-19 in schools. It was then used to estimate the outbreak curves and the proportion of the population infected (attack rate) under the proposed interventions. Results For influenza, the CDC-recommended one day of post-fever isolation can reduce the attack rate by a median (interquartile range) of 29 (13–59)%. With 2 days of post-fever isolation the attack rate could be reduced by 70 (55–85)%. Alternatively, shortening the school week to 4 and 3 days reduces the attack rate by 73 (64–88)% and 93 (91–97)%, respectively. For COVID-19, application of post-fever isolation policy was found to be less effective and reduced the attack rate by 10 (5–17)% for a 2-day isolation policy and by 14 (5–26)% for 14 days. A 4-day school week would reduce the median attack rate in a COVID-19 outbreak by 57 (52–64)%, while a 3-day school week would reduce it by 81 (79–83)%. In both infections, shortening the school week significantly reduced the duration of outbreaks. Conclusions Shortening the school week could be an important tool for controlling influenza…
format: application/pdf
format: text/html
creator: Adam A.C. Burns
creator: Alexander Gutfraind
subject: Mathematical Biology
subject: Epidemiology
subject: Health Policy
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.11211
publisher: PeerJ Inc.
rights: © 2021 Burns and Gutfraind
abstract: Background Non-pharmaceutical interventions such as social distancing, school closures and travel restrictions are often implemented to control outbreaks of infectious diseases. For influenza in schools, the Center of Disease Control (CDC) recommends that febrile students remain isolated at home until they have been fever-free for at least one day and a related policy is recommended for SARS-CoV-2 (COVID-19). Other authors proposed using a school week of four or fewer days of in-person instruction for all students to reduce transmission. However, there is limited evidence supporting the effectiveness of these interventions. Methods We introduced a mathematical model of school outbreaks that considers both intervention methods. Our model accounts for the school structure and schedule, as well as the time-progression of fever symptoms and viral shedding. The model was validated on outbreaks of seasonal and pandemic influenza and COVID-19 in schools. It was then used to estimate the outbreak curves and the proportion of the population infected (attack rate) under the proposed interventions. Results For influenza, the CDC-recommended one day of post-fever isolation can reduce the attack rate by a median (interquartile range) of 29 (13–59)%. With 2 days of post-fever isolation the attack rate could be reduced by 70 (55–85)%. Alternatively, shortening the school week to 4 and 3 days reduces the attack rate by 73 (64–88)% and 93 (91–97)%, respectively. For COVID-19, application of post-fever isolation policy was found to be less effective and reduced the attack rate by 10 (5–17)% for a 2-day isolation policy and by 14 (5–26)% for 14 days. A 4-day school week would reduce the median attack rate in a COVID-19 outbreak by 57 (52–64)%, while a 3-day school week would reduce it by 81 (79–83)%. In both infections, shortening the school week significantly reduced the duration of outbreaks. Conclusions Shortening the school week could be an important tool for controlling influenza…
bibliographic citation: Burns et al. (2021) Effectiveness of isolation policies in schools: evidence from a mathematical model of influenza and COVID-19. PeerJ 9:e11211 https://doi.org/10.7717/peerj.11211
date submitted: 2020-11-20
date accepted: 2021-03-14
issued: 2021-03-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Burns
  given name: Adam A.C.
author list: Agent
  family name: Gutfraind
  given name: Alexander
doi: 10.7717/peerj.11211
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-03-30
copyright: © 2021 Burns and Gutfraind
attribution name: Burns and Gutfraind

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