PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Individuals with fibromyalgia have a different gait pattern and a reduced walk functional capacity: a systematic review with meta-analysis
items: Exploring interactions between Beauveria and Metarhizium strains through co-inoculation and responses of perennial ryegrass in a one-year trial
items: Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility
items: The direct and indirect effects of a global pandemic on US fishers and seafood workers
items: Focus on Polish nurses’ health condition: a cross-sectional study
items: Cooperation between arbuscular mycorrhizal fungi and plant growth-promoting bacteria and their effects on plant growth and soil quality
items: Chikungunya virus time course infection of human macrophages reveals intracellular signaling pathways relevant to repurposed therapeutics
items: A machine learning approach for identification of gastrointestinal predictors for the risk of COVID-19 related hospitalization
items: An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2
items: State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data

Individuals with fibromyalgia have a different gait pattern and a reduced walk functional capacity: a systematic review with meta-analysis
type: item
type: AcademicArticle
description: Background The aim of the present study was to perform a systematic review and meta-analysis comparing walking test performance and gait pattern between individuals with and without fibromyalgia (FM). Methodology This systematic review was registered in PROSPERO with the following reference: CRD42018116200.The search for the scientific articles in this systematic review was carried out using the MEDLINE, SCOPUS, PEDRO, CINHAL and WEB OF SCIENCE databases. A combination of three conceptual groups of terms was used: (1) fibromyalgia; (2) walk (performance) tests; and (3) gait analysis. The included articles were analyzed for both functional and pattern of walking data of patients with FM. In order to provide a better estimate of the difference between individuals with and without FM on gait, a meta-analysis was performed on the 6MWT (6-minute walk test). Results Thirty-six studies were analyzed, with a total population of 4.078 participants (3.369 FM and 709 individuals without FM). From a functional point of view, the 6MWT distance covered by the group of individuals without FM was significantly greater than that of the individuals with FM in all the analyzed studies. In addition, when comparing the results obtained in the gait pattern analysis, it was observed that individuals with FM walked slower, with a shorter stride length and lower cadence compare to individuals without FM. Conclusions It is possible to affirm that individuals with FM perform walking tests differently than individuals without FM. It was observed that individuals with FM walk performing a cycle of shorter length and lower frequency, producing a slower gait, which results in a shorter distance traveled, in the same period of time, with respect to healthy subjects.
format: application/pdf
format: text/html
creator: Elio Carrasco-Vega
creator: María Ruiz-Muñoz
creator: Antonio Cuesta-Vargas
creator: Rita Pilar Romero-Galisteo
creator: Manuel González-Sánchez
subject: Anesthesiology and Pain Management
subject: Kinesiology
subject: Rheumatology
subject: Women’s Health
description: doi:10.7717/peerj.12908
publisher: PeerJ Inc.
rights: © 2022 Carrasco-Vega et al.
abstract: Background The aim of the present study was to perform a systematic review and meta-analysis comparing walking test performance and gait pattern between individuals with and without fibromyalgia (FM). Methodology This systematic review was registered in PROSPERO with the following reference: CRD42018116200.The search for the scientific articles in this systematic review was carried out using the MEDLINE, SCOPUS, PEDRO, CINHAL and WEB OF SCIENCE databases. A combination of three conceptual groups of terms was used: (1) fibromyalgia; (2) walk (performance) tests; and (3) gait analysis. The included articles were analyzed for both functional and pattern of walking data of patients with FM. In order to provide a better estimate of the difference between individuals with and without FM on gait, a meta-analysis was performed on the 6MWT (6-minute walk test). Results Thirty-six studies were analyzed, with a total population of 4.078 participants (3.369 FM and 709 individuals without FM). From a functional point of view, the 6MWT distance covered by the group of individuals without FM was significantly greater than that of the individuals with FM in all the analyzed studies. In addition, when comparing the results obtained in the gait pattern analysis, it was observed that individuals with FM walked slower, with a shorter stride length and lower cadence compare to individuals without FM. Conclusions It is possible to affirm that individuals with FM perform walking tests differently than individuals without FM. It was observed that individuals with FM walk performing a cycle of shorter length and lower frequency, producing a slower gait, which results in a shorter distance traveled, in the same period of time, with respect to healthy subjects.
bibliographic citation: Carrasco-Vega et al. (2022) Individuals with fibromyalgia have a different gait pattern and a reduced walk functional capacity: a systematic review with meta-analysis. PeerJ 10:e12908 https://doi.org/10.7717/peerj.12908
date submitted: 2021-04-30
date accepted: 2022-01-18
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carrasco-Vega
  given name: Elio
author list: Agent
  family name: Ruiz-Muñoz
  given name: María
author list: Agent
  family name: Cuesta-Vargas
  given name: Antonio
author list: Agent
  family name: Romero-Galisteo
  given name: Rita Pilar
author list: Agent
  family name: González-Sánchez
  given name: Manuel
doi: 10.7717/peerj.12908
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: ©2022 Carrasco-Vega et al.
attribution name: Carrasco-Vega et al.

Exploring interactions between Beauveria and Metarhizium strains through co-inoculation and responses of perennial ryegrass in a one-year trial
type: item
type: AcademicArticle
description: Perennial ryegrass (Lolium perenne L.) possesses a high level of nutritional quality and is widely used as a forage species to establish permanent pastures in southern Chile. However, the productivity of most such pastures is limited by various environmental agents, such as insect pests and drought. In this context, our work stresses the need for elucidating the ability of fungal endophytes to establish interactions with plants, and to understand how these processes contribute to plant performance and fitness. Therefore, we evaluated the colonization and impact of two native strains of the endophytic insect-pathogenic fungus (EIPF) group isolated from permanent ryegrass pastures in southern Chile. Roots and seeds of ryegrass and scarabaeid larvae were collected from nine different ryegrass pastures in the Los Ríos region of southern Chile to specifically isolate EIPFs belonging to the genera Beauveria and Metarhizium. Fungal isolations were made on 2% water agar with antibiotics, and strains were identified by analyzing the entire internal transcribed spacer (ITS) 1-5.8S-ITS2 ribosomal DNA region. Four strains of Beauveria and 33 strains of Metarhizium were isolated only in scarabaeid larvae from ryegrass pastures across four sites. Experimental mini-pastures that were either not inoculated (control) or co-inoculated with conidia of the strains Beauveria vermiconia NRRL B-67993 (P55_1) and Metarhizium aff. lepidiotae NRRL B-67994 (M25_2) under two soil humidity levels were used. Ryegrass plants were randomly collected from the mini-pastures to characterize EIPF colonization in the roots by real-time PCR and fluorescence microscopy. Aboveground biomass was measured to analyze the putative impact of colonization on the mini-pastures’ aboveground phenotypic traits with R software using a linear mixed-effects model and the ANOVA statistical test. Seasonal variation in the relative abundance of EIPFs was observed, which was similar between both strains from autumn to spr…
format: application/pdf
format: text/html
creator: Milena Vera
creator: Sarah Zuern
creator: Carlos Henríquez-Valencia
creator: Carlos Loncoman
creator: Javier Canales
creator: Frank Waller
creator: Esteban Basoalto
creator: Sigisfredo Garnica
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.12924
publisher: PeerJ Inc.
rights: © 2022 Vera et al.
abstract: Perennial ryegrass (Lolium perenne L.) possesses a high level of nutritional quality and is widely used as a forage species to establish permanent pastures in southern Chile. However, the productivity of most such pastures is limited by various environmental agents, such as insect pests and drought. In this context, our work stresses the need for elucidating the ability of fungal endophytes to establish interactions with plants, and to understand how these processes contribute to plant performance and fitness. Therefore, we evaluated the colonization and impact of two native strains of the endophytic insect-pathogenic fungus (EIPF) group isolated from permanent ryegrass pastures in southern Chile. Roots and seeds of ryegrass and scarabaeid larvae were collected from nine different ryegrass pastures in the Los Ríos region of southern Chile to specifically isolate EIPFs belonging to the genera Beauveria and Metarhizium. Fungal isolations were made on 2% water agar with antibiotics, and strains were identified by analyzing the entire internal transcribed spacer (ITS) 1-5.8S-ITS2 ribosomal DNA region. Four strains of Beauveria and 33 strains of Metarhizium were isolated only in scarabaeid larvae from ryegrass pastures across four sites. Experimental mini-pastures that were either not inoculated (control) or co-inoculated with conidia of the strains Beauveria vermiconia NRRL B-67993 (P55_1) and Metarhizium aff. lepidiotae NRRL B-67994 (M25_2) under two soil humidity levels were used. Ryegrass plants were randomly collected from the mini-pastures to characterize EIPF colonization in the roots by real-time PCR and fluorescence microscopy. Aboveground biomass was measured to analyze the putative impact of colonization on the mini-pastures’ aboveground phenotypic traits with R software using a linear mixed-effects model and the ANOVA statistical test. Seasonal variation in the relative abundance of EIPFs was observed, which was similar between both strains from autumn to spr…
bibliographic citation: Vera et al. (2022) Exploring interactions between Beauveria and Metarhizium strains through co-inoculation and responses of perennial ryegrass in a one-year trial. PeerJ 10:e12924 https://doi.org/10.7717/peerj.12924
date submitted: 2021-07-15
date accepted: 2022-01-20
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vera
  given name: Milena
author list: Agent
  family name: Zuern
  given name: Sarah
author list: Agent
  family name: Henríquez-Valencia
  given name: Carlos
author list: Agent
  family name: Loncoman
  given name: Carlos
author list: Agent
  family name: Canales
  given name: Javier
author list: Agent
  family name: Waller
  given name: Frank
author list: Agent
  family name: Basoalto
  given name: Esteban
author list: Agent
  family name: Garnica
  given name: Sigisfredo
doi: 10.7717/peerj.12924
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 Vera et al.
attribution name: Vera et al.

Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility
type: item
type: AcademicArticle
description: Background Impaired meiosis can result in absence of sperm in the seminal fluid. This condition, namely non-obstructive azoospermia (NOA), is one of the reasons of male infertility. Despite the low number of studies on meiosis 1-associated protein (M1AP) in the literature, M1AP is known to be crucial for spermatogenesis. Recently, seven variants (five missense, one frameshift, one splice-site) have been reported in the M1AP gene as associated with NOA, cryptozoospermia and oligozoospermia in two separate studies. However, all missense variants were evaluated as variant of uncertain significance by these studies. Therefore, we aimed to analyze their structural impacts on the M1AP protein that could lead to NOA. Methods We firstly performed an evolutionary conservation analysis for the variant positions. Afterwards, a comprehensive molecular modelling study was performed for the M1AP structure. By utilizing this model, protein dynamics were sampled for the wild-type and variants by performing molecular dynamics (MD) simulations. Results All variant positions are highly conserved, indicating that they are potentially important for function. In MD simulations, none of the variants led to a general misfolding or loss of stability in the protein structure, but they did cause severe modifications in the conformational dynamics of M1AP, particularly through changes in local interactions affecting flexibility, hinge and secondary structure. Conclusions Due to critical perturbations in protein dynamics, we propose that these variants may cause NOA by affecting important interactions regulating meiosis, particularly in wild-type M1AP deficiency since the variants are reported to be homozygous or bi-allelic in the infertile individuals. Our results provided reasonable insights about the M1AP structure and the effects of the variants to the structure and dynamics, which should be further investigated by experimental studies to validate.
format: application/pdf
format: text/html
creator: Umut Gerlevik
creator: Mahmut Cerkez Ergoren
creator: Osman Uğur Sezerman
creator: Sehime Gulsun Temel
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Andrology
subject: Medical Genetics
description: doi:10.7717/peerj.12947
publisher: PeerJ Inc.
rights: © 2022 Gerlevik et al.
abstract: Background Impaired meiosis can result in absence of sperm in the seminal fluid. This condition, namely non-obstructive azoospermia (NOA), is one of the reasons of male infertility. Despite the low number of studies on meiosis 1-associated protein (M1AP) in the literature, M1AP is known to be crucial for spermatogenesis. Recently, seven variants (five missense, one frameshift, one splice-site) have been reported in the M1AP gene as associated with NOA, cryptozoospermia and oligozoospermia in two separate studies. However, all missense variants were evaluated as variant of uncertain significance by these studies. Therefore, we aimed to analyze their structural impacts on the M1AP protein that could lead to NOA. Methods We firstly performed an evolutionary conservation analysis for the variant positions. Afterwards, a comprehensive molecular modelling study was performed for the M1AP structure. By utilizing this model, protein dynamics were sampled for the wild-type and variants by performing molecular dynamics (MD) simulations. Results All variant positions are highly conserved, indicating that they are potentially important for function. In MD simulations, none of the variants led to a general misfolding or loss of stability in the protein structure, but they did cause severe modifications in the conformational dynamics of M1AP, particularly through changes in local interactions affecting flexibility, hinge and secondary structure. Conclusions Due to critical perturbations in protein dynamics, we propose that these variants may cause NOA by affecting important interactions regulating meiosis, particularly in wild-type M1AP deficiency since the variants are reported to be homozygous or bi-allelic in the infertile individuals. Our results provided reasonable insights about the M1AP structure and the effects of the variants to the structure and dynamics, which should be further investigated by experimental studies to validate.
bibliographic citation: Gerlevik et al. (2022) Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility. PeerJ 10:e12947 https://doi.org/10.7717/peerj.12947
date submitted: 2021-03-12
date accepted: 2022-01-25
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gerlevik
  given name: Umut
author list: Agent
  family name: Ergoren
  given name: Mahmut Cerkez
author list: Agent
  family name: Sezerman
  given name: Osman Uğur
author list: Agent
  family name: Temel
  given name: Sehime Gulsun
doi: 10.7717/peerj.12947
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 Gerlevik et al.
attribution name: Gerlevik et al.

The direct and indirect effects of a global pandemic on US fishers and seafood workers
type: item
type: AcademicArticle
description: The United States’ fishing and seafood industries experienced major shifts in consumer demand and social-distancing restrictions starting in March 2020, when the early stages of the COVID-19 pandemic were unfolding. However, the specific effects on fishers and seafood processors are less well known. Fishermen and seafood workers are potentially at risk during a pandemic given existing tight working quarters, seasonal work, and long hours. To address these concerns, and given a lack of data on the sector, we reviewed news articles, scientific articles, and white papers to assess the various effects of COVID-19 on US seafood workers. Here, we show that most COVID-19 cases among seafood workers occurred during summer 2020 and during the beginning of 2021. These cases were documented across coastal areas, with Alaska experiencing the largest number of cases and outbreaks. Seafood workers were about twice as likely to contract COVID-19 as workers in other parts of the overall US food system. We also documented a number of indirect effects of the pandemic. New social-distancing restrictions and policies limited crew size, resulting in longer hours and more physical taxation. Because of changes in demand and the closure of some processing plants because of COVID-19 outbreaks, economic consequences of the pandemic were a primary concern for fishers and seafood workers, and safety measures allowed for seafood price variation and losses throughout the pandemic. We also highlight a number of inequities in COVID-19 responses within the seafood sector, both along racial and gender lines. All of these conditions point to the diverse direct and indirect effects of the COVID-19 pandemic on fishers and seafood workers. We hope this work sets the foundation for future work on the seafood sector in relation to the COVID-19 pandemic, improving the overall workplace, and collecting systematic social and economic data on workers.
format: application/pdf
format: text/html
creator: Easton R. White
creator: Jill Levine
creator: Amanda Moeser
creator: Julie Sorensen
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.13007
publisher: PeerJ Inc.
rights: © 2022 White et al.
abstract: The United States’ fishing and seafood industries experienced major shifts in consumer demand and social-distancing restrictions starting in March 2020, when the early stages of the COVID-19 pandemic were unfolding. However, the specific effects on fishers and seafood processors are less well known. Fishermen and seafood workers are potentially at risk during a pandemic given existing tight working quarters, seasonal work, and long hours. To address these concerns, and given a lack of data on the sector, we reviewed news articles, scientific articles, and white papers to assess the various effects of COVID-19 on US seafood workers. Here, we show that most COVID-19 cases among seafood workers occurred during summer 2020 and during the beginning of 2021. These cases were documented across coastal areas, with Alaska experiencing the largest number of cases and outbreaks. Seafood workers were about twice as likely to contract COVID-19 as workers in other parts of the overall US food system. We also documented a number of indirect effects of the pandemic. New social-distancing restrictions and policies limited crew size, resulting in longer hours and more physical taxation. Because of changes in demand and the closure of some processing plants because of COVID-19 outbreaks, economic consequences of the pandemic were a primary concern for fishers and seafood workers, and safety measures allowed for seafood price variation and losses throughout the pandemic. We also highlight a number of inequities in COVID-19 responses within the seafood sector, both along racial and gender lines. All of these conditions point to the diverse direct and indirect effects of the COVID-19 pandemic on fishers and seafood workers. We hope this work sets the foundation for future work on the seafood sector in relation to the COVID-19 pandemic, improving the overall workplace, and collecting systematic social and economic data on workers.
bibliographic citation: White et al. (2022) The direct and indirect effects of a global pandemic on US fishers and seafood workers. PeerJ 10:e13007 https://doi.org/10.7717/peerj.13007
date submitted: 2021-12-08
date accepted: 2022-02-03
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: White
  given name: Easton R.
author list: Agent
  family name: Levine
  given name: Jill
author list: Agent
  family name: Moeser
  given name: Amanda
author list: Agent
  family name: Sorensen
  given name: Julie
doi: 10.7717/peerj.13007
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 White et al.
attribution name: White et al.

Focus on Polish nurses’ health condition: a cross-sectional study
type: item
type: AcademicArticle
description: Background The nursing profession carries with it many negative factors and a high risk of developing chronic diseases, including overweight and obesity. According to statistics, the health condition of this professional group is much worse than that of the average population of the same age. As the largest and most trusted professional group in the world, nurses are critical to the health of any nation. The aim of the study was to assess the Polish nurse’s health condition based on real measurements of parameters important for the occurrence of metabolic diseases. Methods This is the cross-sectional, conducted among two age groups of Polish nurses (<50 years and ≥50 years). Study included the measurements with DXA, the assessment of glucose concentration and lipid profile, the measurement of blood pressure and socio-demographic data of the surveyed nurses. Results The majority of respondents above 50 years old were nurses with elevated total cholesterol (79.3%), elevated LDL cholesterol (72.8%), 42.4% of studied nurses had hypertension. Conclusion Individual, local and national measures to prevent and support the health of this professional group are needed.
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format: text/html
creator: Anna Bartosiewicz
creator: Edyta Łuszczki
creator: Pawel Jagielski
creator: Lukasz Oleksy
creator: Artur Stolarczyk
creator: Katarzyna Dereń
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Nursing
subject: Public Health
description: doi:10.7717/peerj.13065
publisher: PeerJ Inc.
rights: © 2022 Bartosiewicz et al.
abstract: Background The nursing profession carries with it many negative factors and a high risk of developing chronic diseases, including overweight and obesity. According to statistics, the health condition of this professional group is much worse than that of the average population of the same age. As the largest and most trusted professional group in the world, nurses are critical to the health of any nation. The aim of the study was to assess the Polish nurse’s health condition based on real measurements of parameters important for the occurrence of metabolic diseases. Methods This is the cross-sectional, conducted among two age groups of Polish nurses (<50 years and ≥50 years). Study included the measurements with DXA, the assessment of glucose concentration and lipid profile, the measurement of blood pressure and socio-demographic data of the surveyed nurses. Results The majority of respondents above 50 years old were nurses with elevated total cholesterol (79.3%), elevated LDL cholesterol (72.8%), 42.4% of studied nurses had hypertension. Conclusion Individual, local and national measures to prevent and support the health of this professional group are needed.
bibliographic citation: Bartosiewicz et al. (2022) Focus on Polish nurses’ health condition: a cross-sectional study. PeerJ 10:e13065 https://doi.org/10.7717/peerj.13065
date submitted: 2021-11-01
date accepted: 2022-02-14
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bartosiewicz
  given name: Anna
author list: Agent
  family name: Łuszczki
  given name: Edyta
author list: Agent
  family name: Jagielski
  given name: Pawel
author list: Agent
  family name: Oleksy
  given name: Lukasz
author list: Agent
  family name: Stolarczyk
  given name: Artur
author list: Agent
  family name: Dereń
  given name: Katarzyna
doi: 10.7717/peerj.13065
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 Bartosiewicz et al.
attribution name: Bartosiewicz et al.

Cooperation between arbuscular mycorrhizal fungi and plant growth-promoting bacteria and their effects on plant growth and soil quality
type: item
type: AcademicArticle
description: The roles of arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) in improving nutrition uptake and soil quality have been well documented. However, few studies have explored their effects on root morphology and soil properties. In this study, we inoculated Elymus nutans Griseb with AMF and/or PGPR in order to explore their effects on plant growth, soil physicochemical properties, and soil enzyme activities. The results showed that AMF and/or PGPR inoculation significantly enhanced aboveground and belowground vegetation biomass. Both single and dual inoculations were beneficial for plant root length, surface area, root branches, stem diameter, height, and the ratio of shoot to root, but decreased root volume and root average diameter. Soil total nitrogen, alkaline phosphatase, and urease activities showed significant growth, and soil electrical conductivity and pH significantly declined under the inoculation treatments. Specific root length showed a negative correlation with belowground biomass, but a positive correlation with root length and root branches. These results indicated that AMF and PGPR had synergetic effects on root morphology, soil nutrient availability, and plant growth.
format: application/pdf
format: text/html
creator: Lu Yu
creator: Hui Zhang
creator: Wantong Zhang
creator: Kesi Liu
creator: Miao Liu
creator: Xinqing Shao
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.13080
publisher: PeerJ Inc.
rights: © 2022 Yu et al.
abstract: The roles of arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) in improving nutrition uptake and soil quality have been well documented. However, few studies have explored their effects on root morphology and soil properties. In this study, we inoculated Elymus nutans Griseb with AMF and/or PGPR in order to explore their effects on plant growth, soil physicochemical properties, and soil enzyme activities. The results showed that AMF and/or PGPR inoculation significantly enhanced aboveground and belowground vegetation biomass. Both single and dual inoculations were beneficial for plant root length, surface area, root branches, stem diameter, height, and the ratio of shoot to root, but decreased root volume and root average diameter. Soil total nitrogen, alkaline phosphatase, and urease activities showed significant growth, and soil electrical conductivity and pH significantly declined under the inoculation treatments. Specific root length showed a negative correlation with belowground biomass, but a positive correlation with root length and root branches. These results indicated that AMF and PGPR had synergetic effects on root morphology, soil nutrient availability, and plant growth.
bibliographic citation: Yu et al. (2022) Cooperation between arbuscular mycorrhizal fungi and plant growth-promoting bacteria and their effects on plant growth and soil quality. PeerJ 10:e13080 https://doi.org/10.7717/peerj.13080
date submitted: 2021-08-30
date accepted: 2022-02-16
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Lu
author list: Agent
  family name: Zhang
  given name: Hui
author list: Agent
  family name: Zhang
  given name: Wantong
author list: Agent
  family name: Liu
  given name: Kesi
author list: Agent
  family name: Liu
  given name: Miao
author list: Agent
  family name: Shao
  given name: Xinqing
doi: 10.7717/peerj.13080
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 Yu et al.
attribution name: Yu et al.

Chikungunya virus time course infection of human macrophages reveals intracellular signaling pathways relevant to repurposed therapeutics
type: item
type: AcademicArticle
description: Background Chikungunya virus (CHIKV) is a mosquito-borne pathogen, within the Alphavirus genus of the Togaviridae family, that causes ~1.1 million human infections annually. CHIKV uses Aedes albopictus and Aedes aegypti mosquitoes as insect vectors. Human infections can develop arthralgia and myalgia, which results in debilitating pain for weeks, months, and even years after acute infection. No therapeutic treatments or vaccines currently exist for many alphaviruses, including CHIKV. Targeting the phagocytosis of CHIKV by macrophages after mosquito transmission plays an important role in early productive viral infection in humans, and could reduce viral replication and/or symptoms. Methods To better characterize the transcriptional response of macrophages during early infection, we generated RNA-sequencing data from a CHIKV-infected human macrophage cell line at eight or 24 hours post-infection (hpi), together with mock-infected controls. We then calculated differential gene expression, enriched functional annotations, modulated intracellular signaling pathways, and predicted therapeutic drugs from these sequencing data. Results We observed 234 pathways were significantly affected 24 hpi, resulting in six potential pharmaceutical treatments to modulate the affected pathways. A subset of significant pathways at 24 hpi includes AGE-RAGE, Fc epsilon RI, Chronic myeloid leukemia, Fc gamma R-mediated phagocytosis, and Ras signaling. We found that the MAPK1 and MAPK3 proteins are shared among this subset of pathways and that Telmisartan and Dasatinib are strong candidates for repurposed small molecule therapeutics that target human processes. The results of our analysis can be further characterized in the wet lab to contribute to the development of host-based prophylactics and therapeutics.
format: application/pdf
format: text/html
creator: Madison Gray
creator: Israel Guerrero-Arguero
creator: Antonio Solis-Leal
creator: Richard A. Robison
creator: Bradford K. Berges
creator: Brett E. Pickett
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Virology
subject: Infectious Diseases
description: doi:10.7717/peerj.13090
publisher: PeerJ Inc.
rights: © 2022 Gray et al.
abstract: Background Chikungunya virus (CHIKV) is a mosquito-borne pathogen, within the Alphavirus genus of the Togaviridae family, that causes ~1.1 million human infections annually. CHIKV uses Aedes albopictus and Aedes aegypti mosquitoes as insect vectors. Human infections can develop arthralgia and myalgia, which results in debilitating pain for weeks, months, and even years after acute infection. No therapeutic treatments or vaccines currently exist for many alphaviruses, including CHIKV. Targeting the phagocytosis of CHIKV by macrophages after mosquito transmission plays an important role in early productive viral infection in humans, and could reduce viral replication and/or symptoms. Methods To better characterize the transcriptional response of macrophages during early infection, we generated RNA-sequencing data from a CHIKV-infected human macrophage cell line at eight or 24 hours post-infection (hpi), together with mock-infected controls. We then calculated differential gene expression, enriched functional annotations, modulated intracellular signaling pathways, and predicted therapeutic drugs from these sequencing data. Results We observed 234 pathways were significantly affected 24 hpi, resulting in six potential pharmaceutical treatments to modulate the affected pathways. A subset of significant pathways at 24 hpi includes AGE-RAGE, Fc epsilon RI, Chronic myeloid leukemia, Fc gamma R-mediated phagocytosis, and Ras signaling. We found that the MAPK1 and MAPK3 proteins are shared among this subset of pathways and that Telmisartan and Dasatinib are strong candidates for repurposed small molecule therapeutics that target human processes. The results of our analysis can be further characterized in the wet lab to contribute to the development of host-based prophylactics and therapeutics.
bibliographic citation: Gray et al. (2022) Chikungunya virus time course infection of human macrophages reveals intracellular signaling pathways relevant to repurposed therapeutics. PeerJ 10:e13090 https://doi.org/10.7717/peerj.13090
date submitted: 2021-12-17
date accepted: 2022-02-18
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gray
  given name: Madison
author list: Agent
  family name: Guerrero-Arguero
  given name: Israel
author list: Agent
  family name: Solis-Leal
  given name: Antonio
author list: Agent
  family name: Robison
  given name: Richard A.
author list: Agent
  family name: Berges
  given name: Bradford K.
author list: Agent
  family name: Pickett
  given name: Brett E.
doi: 10.7717/peerj.13090
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 Gray et al.
attribution name: Gray et al.

A machine learning approach for identification of gastrointestinal predictors for the risk of COVID-19 related hospitalization
type: item
type: AcademicArticle
description: Background and aim COVID-19 can be presented with various gastrointestinal symptoms. Shortly after the pandemic outbreak, several machine learning algorithms were implemented to assess new diagnostic and therapeutic methods for this disease. The aim of this study is to assess gastrointestinal and liver-related predictive factors for SARS-CoV-2 associated risk of hospitalization. Methods Data collection was based on a questionnaire from the COVID-19 outpatient test center and from the emergency department at the University Hospital in combination with the data from internal hospital information system and from a mobile application used for telemedicine follow-up of patients. For statistical analysis SARS-CoV-2 negative patients were considered as controls in three different SARS-CoV-2 positive patient groups (divided based on severity of the disease). The data were visualized and analyzed in R version 4.0.5. The Chi-squared or Fisher test was applied to test the null hypothesis of independence between the factors followed, where appropriate, by the multiple comparisons with the Benjamini Hochberg adjustment. The null hypothesis of the equality of the population medians of a continuous variable was tested by the Kruskal Wallis test, followed by the Dunn multiple comparisons test. In order to assess predictive power of the gastrointestinal parameters and other measured variables for predicting an outcome of the patient group the Random Forest machine learning algorithm was trained on the data. The predictive ability was quantified by the ROC curve, constructed from the Out-of-Bag data. Matthews correlation coefficient was used as a one-number summary of the quality of binary classification. The importance of the predictors was measured using the Variable Importance. A 2D representation of the data was obtained by means of Principal Component Analysis for mixed type of data. Findings with the p-value below 0.05 were considered statistically significant. Results A total …
format: application/pdf
format: text/html
creator: Peter Lipták
creator: Peter Banovcin
creator: Róbert Rosoľanka
creator: Michal Prokopič
creator: Ivan Kocan
creator: Ivana Žiačiková
creator: Peter Uhrik
creator: Marian Grendar
creator: Rudolf Hyrdel
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
subject: Data Mining and Machine Learning
subject: COVID-19
description: doi:10.7717/peerj.13124
publisher: PeerJ Inc.
rights: © 2022 Lipták et al.
abstract: Background and aim COVID-19 can be presented with various gastrointestinal symptoms. Shortly after the pandemic outbreak, several machine learning algorithms were implemented to assess new diagnostic and therapeutic methods for this disease. The aim of this study is to assess gastrointestinal and liver-related predictive factors for SARS-CoV-2 associated risk of hospitalization. Methods Data collection was based on a questionnaire from the COVID-19 outpatient test center and from the emergency department at the University Hospital in combination with the data from internal hospital information system and from a mobile application used for telemedicine follow-up of patients. For statistical analysis SARS-CoV-2 negative patients were considered as controls in three different SARS-CoV-2 positive patient groups (divided based on severity of the disease). The data were visualized and analyzed in R version 4.0.5. The Chi-squared or Fisher test was applied to test the null hypothesis of independence between the factors followed, where appropriate, by the multiple comparisons with the Benjamini Hochberg adjustment. The null hypothesis of the equality of the population medians of a continuous variable was tested by the Kruskal Wallis test, followed by the Dunn multiple comparisons test. In order to assess predictive power of the gastrointestinal parameters and other measured variables for predicting an outcome of the patient group the Random Forest machine learning algorithm was trained on the data. The predictive ability was quantified by the ROC curve, constructed from the Out-of-Bag data. Matthews correlation coefficient was used as a one-number summary of the quality of binary classification. The importance of the predictors was measured using the Variable Importance. A 2D representation of the data was obtained by means of Principal Component Analysis for mixed type of data. Findings with the p-value below 0.05 were considered statistically significant. Results A total …
bibliographic citation: Lipták et al. (2022) A machine learning approach for identification of gastrointestinal predictors for the risk of COVID-19 related hospitalization. PeerJ 10:e13124 https://doi.org/10.7717/peerj.13124
date submitted: 2021-09-01
date accepted: 2022-02-24
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lipták
  given name: Peter
author list: Agent
  family name: Banovcin
  given name: Peter
author list: Agent
  family name: Rosoľanka
  given name: Róbert
author list: Agent
  family name: Prokopič
  given name: Michal
author list: Agent
  family name: Kocan
  given name: Ivan
author list: Agent
  family name: Žiačiková
  given name: Ivana
author list: Agent
  family name: Uhrik
  given name: Peter
author list: Agent
  family name: Grendar
  given name: Marian
author list: Agent
  family name: Hyrdel
  given name: Rudolf
doi: 10.7717/peerj.13124
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 Lipták et al.
attribution name: Lipták et al.

An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2
type: item
type: AcademicArticle
description: Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
format: application/pdf
format: text/html
creator: Sk. Sarif Hassan
creator: Vaishnavi Kodakandla
creator: Elrashdy M. Redwan
creator: Kenneth Lundstrom
creator: Pabitra Pal Choudhury
creator: Tarek Mohamed Abd El-Aziz
creator: Kazuo Takayama
creator: Ramesh Kandimalla
creator: Amos Lal
creator: Ángel Serrano-Aroca
creator: Gajendra Kumar Azad
creator: Alaa A.A. Aljabali
creator: Giorgio Palù
creator: Gaurav Chauhan
creator: Parise Adadi
creator: Murtaza Tambuwala
creator: Adam M. Brufsky
creator: Wagner Baetas-da-Cruz
creator: Debmalya Barh
creator: Vasco Azevedo
creator: Nikolas G. Bazan
creator: Bruno Silva Andrade
creator: Raner José Santana Silva
creator: Vladimir N. Uversky
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.13136
publisher: PeerJ Inc.
rights: © 2022 Hassan et al.
abstract: Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
bibliographic citation: Hassan et al. (2022) An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 10:e13136 https://doi.org/10.7717/peerj.13136
date submitted: 2021-09-16
date accepted: 2022-02-27
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hassan
  given name: Sk. Sarif
author list: Agent
  family name: Kodakandla
  given name: Vaishnavi
author list: Agent
  family name: Redwan
  given name: Elrashdy M.
author list: Agent
  family name: Lundstrom
  given name: Kenneth
author list: Agent
  family name: Pal Choudhury
  given name: Pabitra
author list: Agent
  family name: Abd El-Aziz
  given name: Tarek Mohamed
author list: Agent
  family name: Takayama
  given name: Kazuo
author list: Agent
  family name: Kandimalla
  given name: Ramesh
author list: Agent
  family name: Lal
  given name: Amos
author list: Agent
  family name: Serrano-Aroca
  given name: Ángel
author list: Agent
  family name: Azad
  given name: Gajendra Kumar
author list: Agent
  family name: Aljabali
  given name: Alaa A.A.
author list: Agent
  family name: Palù
  given name: Giorgio
author list: Agent
  family name: Chauhan
  given name: Gaurav
author list: Agent
  family name: Adadi
  given name: Parise
author list: Agent
  family name: Tambuwala
  given name: Murtaza
author list: Agent
  family name: Brufsky
  given name: Adam M.
author list: Agent
  family name: Baetas-da-Cruz
  given name: Wagner
author list: Agent
  family name: Barh
  given name: Debmalya
author list: Agent
  family name: Azevedo
  given name: Vasco
author list: Agent
  family name: Bazan
  given name: Nikolas G.
author list: Agent
  family name: Andrade
  given name: Bruno Silva
author list: Agent
  family name: Santana Silva
  given name: Raner José
author list: Agent
  family name: Uversky
  given name: Vladimir N.
doi: 10.7717/peerj.13136
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 Hassan et al.
attribution name: Hassan et al.

State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data
type: item
type: AcademicArticle
description: Anthropogenic changes in the natural environment have led to alarming rates of biodiversity loss, resulting in a more urgent need for conservation. Although there is an increasing cognizance of the importance of incorporating biodiversity data into conservation, the accuracy of the inferences generated from these records can be highly impacted by gaps and biases in the data. Because of the Philippines’ status as a biodiversity hotspot, the assessment of potential gaps and biases in biodiversity documentation in the country can be a critical step in the identification of priority research areas for conservation applications. In this study, we systematically assessed biodiversity data on animal and plant taxa found in the Philippines by examining the extent of metadata gaps, taxonomic biases, and spatial biases in DNA barcode data while using species occurrence data as a backdrop of the ‘Philippines’ biodiversity. These barcode and species occurrence datasets were obtained from public databases, namely: GenBank, Barcode of Life Data System and Global Biodiversity Information Facility. We found that much of the barcode data had missing information on either records and publishing, geolocation, or taxonomic metadata, which consequently, can limit the usability of barcode data for further analyses. We also observed that the amount of barcode data can be directly associated with the amount of species occurrence data available for a particular taxonomic group and location–highlighting the potential sampling biases in the barcode data. While the majority of barcode data came from foreign institutions, there has been an increase in local efforts in recent decades. However, much of the contribution to biodiversity documentation only come from institutions based in Luzon.
format: application/pdf
format: text/html
creator: Carmela Maria P. Berba
creator: Ambrocio Melvin A. Matias
subject: Biodiversity
subject: Bioinformatics
subject: Genetics
subject: Data Science
description: doi:10.7717/peerj.13146
publisher: PeerJ Inc.
rights: © 2022 Berba and Matias
abstract: Anthropogenic changes in the natural environment have led to alarming rates of biodiversity loss, resulting in a more urgent need for conservation. Although there is an increasing cognizance of the importance of incorporating biodiversity data into conservation, the accuracy of the inferences generated from these records can be highly impacted by gaps and biases in the data. Because of the Philippines’ status as a biodiversity hotspot, the assessment of potential gaps and biases in biodiversity documentation in the country can be a critical step in the identification of priority research areas for conservation applications. In this study, we systematically assessed biodiversity data on animal and plant taxa found in the Philippines by examining the extent of metadata gaps, taxonomic biases, and spatial biases in DNA barcode data while using species occurrence data as a backdrop of the ‘Philippines’ biodiversity. These barcode and species occurrence datasets were obtained from public databases, namely: GenBank, Barcode of Life Data System and Global Biodiversity Information Facility. We found that much of the barcode data had missing information on either records and publishing, geolocation, or taxonomic metadata, which consequently, can limit the usability of barcode data for further analyses. We also observed that the amount of barcode data can be directly associated with the amount of species occurrence data available for a particular taxonomic group and location–highlighting the potential sampling biases in the barcode data. While the majority of barcode data came from foreign institutions, there has been an increase in local efforts in recent decades. However, much of the contribution to biodiversity documentation only come from institutions based in Luzon.
bibliographic citation: Berba et al. (2022) State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data. PeerJ 10:e13146 https://doi.org/10.7717/peerj.13146
date submitted: 2021-09-23
date accepted: 2022-03-01
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Berba
  given name: Carmela Maria P.
author list: Agent
  family name: Matias
  given name: Ambrocio Melvin A.
doi: 10.7717/peerj.13146
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 Berba and Matias
attribution name: Berba and Matias

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