PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
items: Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean
items: High-performance pipeline for MutMap and QTL-seq
items: Sensitivity of soil hydrogen uptake to natural and managed moisture dynamics in a semiarid urban ecosystem
items: A comparative study of the capability of MSCs isolated from different human tissue sources to differentiate into neuronal stem cells and dopaminergic-like cells
items: An ODE model of yaws elimination in Lihir Island, Papua New Guinea
items: International football players with cerebral palsy maintained their physical fitness after a self-training program during the COVID-19 lockdown
items: Geometric morphometrics as a tool to understand biogeographical and evolutionary patterns in crane fly genus Ischnotoma Skuse (Diptera, Tipulidae)
items: Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease
items: Positively selected genes in the hoary bat (Lasiurus cinereus) lineage: prominence of thymus expression, immune and metabolic function, and regions of ancient synteny

Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
type: item
type: AcademicArticle
description: Background The Tropical Andes is the world’s most biodiverse hotspot. This region contains >1,000 amphibian species, more than half of which are endemic. Herein we describe two new glassfrog species (Centrolenidae: Hyalinobatrachium) that we discovered within relatively unexplored and isolated localities of the Ecuadorian Andes. Methods We employed morphological, acoustic, and molecular methods to test the hypothesis that Hyalinobatrachium mashpi sp. nov and H. nouns sp. nov. are species new to science. Following standard methods, we generated mitochondrial sequences (16S) of 37 individuals in the genus Hyalinobatrachium. We inferred the phylogenetic relationships of the two new species in comparison to all other glassfrogs using Maximum Likelihood. In addition to describing the call of H. mashpi sp. nov., we performed a discriminant analysis of principal components (DAPC) with the advertisement call characteristics of several congeners. Results Based on an integrative taxonomy approach, we describe two new species. Morphological traits and the inferred phylogeny unambiguously place the new taxa in the genus Hyalinobatrachium. Both species are distinguished from other glassfrogs mainly by their dorsal coloration (i.e., dorsum lime green with small light yellow spots, head usually with interorbital bar) and transparent pericardium (i.e., the heart is visible through the ventral skin). The new species exhibit a high morphological similarity (i.e., cryptic) and occur within relatively close geographical proximity (closest aerial distance = 18.9 km); however, their uncorrected p distance for the mitochondrial gene 16S is 4.6–4.7%, a value that greatly exceeds the genetic distance between closely related species of centrolenid frogs. The DAPC revealed that the advertisement call of H. mashpi sp. nov. is acoustically distinct. Discussion Our findings are congruent with several previous studies that report a high degree of endemism in the Toisán mountain range, which appea…
format: application/pdf
format: text/html
creator: Juan M. Guayasamin
creator: Rebecca M. Brunner
creator: Anyelet Valencia-Aguilar
creator: Daniela Franco-Mena
creator: Eva Ringler
creator: Anderson Medina Armijos
creator: Carlos Morochz
creator: Lucas Bustamante
creator: Ross J. Maynard
creator: Jaime Culebras
subject: Biodiversity
subject: Conservation Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13109
publisher: PeerJ Inc.
rights: © 2022 Guayasamin et al.
abstract: Background The Tropical Andes is the world’s most biodiverse hotspot. This region contains >1,000 amphibian species, more than half of which are endemic. Herein we describe two new glassfrog species (Centrolenidae: Hyalinobatrachium) that we discovered within relatively unexplored and isolated localities of the Ecuadorian Andes. Methods We employed morphological, acoustic, and molecular methods to test the hypothesis that Hyalinobatrachium mashpi sp. nov and H. nouns sp. nov. are species new to science. Following standard methods, we generated mitochondrial sequences (16S) of 37 individuals in the genus Hyalinobatrachium. We inferred the phylogenetic relationships of the two new species in comparison to all other glassfrogs using Maximum Likelihood. In addition to describing the call of H. mashpi sp. nov., we performed a discriminant analysis of principal components (DAPC) with the advertisement call characteristics of several congeners. Results Based on an integrative taxonomy approach, we describe two new species. Morphological traits and the inferred phylogeny unambiguously place the new taxa in the genus Hyalinobatrachium. Both species are distinguished from other glassfrogs mainly by their dorsal coloration (i.e., dorsum lime green with small light yellow spots, head usually with interorbital bar) and transparent pericardium (i.e., the heart is visible through the ventral skin). The new species exhibit a high morphological similarity (i.e., cryptic) and occur within relatively close geographical proximity (closest aerial distance = 18.9 km); however, their uncorrected p distance for the mitochondrial gene 16S is 4.6–4.7%, a value that greatly exceeds the genetic distance between closely related species of centrolenid frogs. The DAPC revealed that the advertisement call of H. mashpi sp. nov. is acoustically distinct. Discussion Our findings are congruent with several previous studies that report a high degree of endemism in the Toisán mountain range, which appea…
bibliographic citation: Guayasamin et al. (2022) Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes. PeerJ 10:e13109 https://doi.org/10.7717/peerj.13109
date submitted: 2021-10-19
date accepted: 2022-02-22
issued: 2022-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guayasamin
  given name: Juan M.
author list: Agent
  family name: Brunner
  given name: Rebecca M.
author list: Agent
  family name: Valencia-Aguilar
  given name: Anyelet
author list: Agent
  family name: Franco-Mena
  given name: Daniela
author list: Agent
  family name: Ringler
  given name: Eva
author list: Agent
  family name: Medina Armijos
  given name: Anderson
author list: Agent
  family name: Morochz
  given name: Carlos
author list: Agent
  family name: Bustamante
  given name: Lucas
author list: Agent
  family name: Maynard
  given name: Ross J.
author list: Agent
  family name: Culebras
  given name: Jaime
doi: 10.7717/peerj.13109
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-18
copyright: © 2022 Guayasamin et al.
attribution name: Guayasamin et al.

Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean
type: item
type: AcademicArticle
description: Background Soybean is the main oilseed crop grown in the world; however, drought stress affects its growth and physiology, reducing its yield. The objective of this study was to characterize the physiological, metabolic, and genetic aspects that determine differential resistance to water deficit in soybean genotypes. Methods Three soybean genotypes were used in this study, two lineages (L11644 and L13241), and one cultivar (EMBRAPA 48-C48). Plants were grown in pots containing 8 kg of a mixture of soil and sand (2:1) in a greenhouse under sunlight. Soil moisture in the pots was maintained at field capacity until the plants reached the stage of development V4 (third fully expanded leaf). At this time, plants were subjected to three water treatments: Well-Watered (WW) (plants kept under daily irrigation); Water Deficit (WD) (withholding irrigation until plants reached the leaf water potential at predawn of −1.5 ± 0.2 MPa); Rewatered (RW) (plants rehydrated for three days after reached the water deficit). The WW and WD water treatments were evaluated on the eighth day for genotypes L11644 and C48, and on the tenth day for L13241, after interruption of irrigation. For the three genotypes, the treatment RW was evaluated after three days of resumption of irrigation. Physiological, metabolic and gene expression analyses were performed. Results Water deficit inhibited growth and gas exchange in all genotypes. The accumulation of osmolytes and the concentrations of chlorophylls and abscisic acid (ABA) were higher in L13241 under stress. The metabolic adjustment of lineages in response to WD occurred in order to accumulate amino acids, carbohydrates, and polyamines in leaves. The expression of genes involved in drought resistance responses was more strongly induced in L13241. In general, rehydration provided recovery of plants to similar conditions of control treatment. Although the C48 and L11644 genotypes have shown some tolerance and resilience responses to severe water de…
format: application/pdf
format: text/html
creator: Adinan Alves da Silva
creator: Cíntia Oliveira Silva
creator: Vanessa do Rosario Rosa
creator: Michel Filiphy Silva Santos
creator: Kacilda Naomi Kuki
creator: Maximiller Dal-Bianco
creator: Rafael Delmond Bueno
creator: Juraci Alves de Oliveira
creator: Danielle Santos Brito
creator: Alan Carlos Costa
creator: Cleberson Ribeiro
subject: Agricultural Science
subject: Biochemistry
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13118
publisher: PeerJ Inc.
rights: © 2022 Alves da Silva et al.
abstract: Background Soybean is the main oilseed crop grown in the world; however, drought stress affects its growth and physiology, reducing its yield. The objective of this study was to characterize the physiological, metabolic, and genetic aspects that determine differential resistance to water deficit in soybean genotypes. Methods Three soybean genotypes were used in this study, two lineages (L11644 and L13241), and one cultivar (EMBRAPA 48-C48). Plants were grown in pots containing 8 kg of a mixture of soil and sand (2:1) in a greenhouse under sunlight. Soil moisture in the pots was maintained at field capacity until the plants reached the stage of development V4 (third fully expanded leaf). At this time, plants were subjected to three water treatments: Well-Watered (WW) (plants kept under daily irrigation); Water Deficit (WD) (withholding irrigation until plants reached the leaf water potential at predawn of −1.5 ± 0.2 MPa); Rewatered (RW) (plants rehydrated for three days after reached the water deficit). The WW and WD water treatments were evaluated on the eighth day for genotypes L11644 and C48, and on the tenth day for L13241, after interruption of irrigation. For the three genotypes, the treatment RW was evaluated after three days of resumption of irrigation. Physiological, metabolic and gene expression analyses were performed. Results Water deficit inhibited growth and gas exchange in all genotypes. The accumulation of osmolytes and the concentrations of chlorophylls and abscisic acid (ABA) were higher in L13241 under stress. The metabolic adjustment of lineages in response to WD occurred in order to accumulate amino acids, carbohydrates, and polyamines in leaves. The expression of genes involved in drought resistance responses was more strongly induced in L13241. In general, rehydration provided recovery of plants to similar conditions of control treatment. Although the C48 and L11644 genotypes have shown some tolerance and resilience responses to severe water de…
bibliographic citation: Alves da Silva et al. (2022) Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean. PeerJ 10:e13118 https://doi.org/10.7717/peerj.13118
date submitted: 2021-08-19
date accepted: 2022-02-23
issued: 2022-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alves da Silva
  given name: Adinan
author list: Agent
  family name: Oliveira Silva
  given name: Cíntia
author list: Agent
  family name: do Rosario Rosa
  given name: Vanessa
author list: Agent
  family name: Silva Santos
  given name: Michel Filiphy
author list: Agent
  family name: Naomi Kuki
  given name: Kacilda
author list: Agent
  family name: Dal-Bianco
  given name: Maximiller
author list: Agent
  family name: Delmond Bueno
  given name: Rafael
author list: Agent
  family name: Alves de Oliveira
  given name: Juraci
author list: Agent
  family name: Santos Brito
  given name: Danielle
author list: Agent
  family name: Costa
  given name: Alan Carlos
author list: Agent
  family name: Ribeiro
  given name: Cleberson
doi: 10.7717/peerj.13118
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-18
copyright: © 2022 Alves da Silva et al.
attribution name: Alves da Silva et al.

High-performance pipeline for MutMap and QTL-seq
type: item
type: AcademicArticle
description: Summary Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5–8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies. Availability The new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq).
format: application/pdf
format: text/html
creator: Yu Sugihara
creator: Lester Young
creator: Hiroki Yaegashi
creator: Satoshi Natsume
creator: Daniel J. Shea
creator: Hiroki Takagi
creator: Helen Booker
creator: Hideki Innan
creator: Ryohei Terauchi
creator: Akira Abe
subject: Bioinformatics
subject: Computational Biology
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.13170
publisher: PeerJ Inc.
rights: © 2022 Sugihara et al.
abstract: Summary Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5–8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies. Availability The new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq).
bibliographic citation: Sugihara et al. (2022) High-performance pipeline for MutMap and QTL-seq. PeerJ 10:e13170 https://doi.org/10.7717/peerj.13170
date submitted: 2022-01-13
date accepted: 2022-03-04
issued: 2022-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sugihara
  given name: Yu
author list: Agent
  family name: Young
  given name: Lester
author list: Agent
  family name: Yaegashi
  given name: Hiroki
author list: Agent
  family name: Natsume
  given name: Satoshi
author list: Agent
  family name: Shea
  given name: Daniel J.
author list: Agent
  family name: Takagi
  given name: Hiroki
author list: Agent
  family name: Booker
  given name: Helen
author list: Agent
  family name: Innan
  given name: Hideki
author list: Agent
  family name: Terauchi
  given name: Ryohei
author list: Agent
  family name: Abe
  given name: Akira
doi: 10.7717/peerj.13170
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-18
copyright: ©2022 Sugihara et al.
attribution name: Sugihara et al.

Sensitivity of soil hydrogen uptake to natural and managed moisture dynamics in a semiarid urban ecosystem
type: item
type: AcademicArticle
description: The North American Monsoon season (June–September) in the Sonoran Desert brings thunderstorms and heavy rainfall. These rains bring cooler temperature and account for roughly half of the annual precipitation making them important for biogeochemical processes. The intensity of the monsoon rains also increase flooding in urban areas and rely on green infrastructure (GI) stormwater management techniques such as water harvesting and urban rain gardens to capture runoff. The combination of increased water availability during the monsoon and water management provide a broad moisture regime for testing responses in microbial metabolism to natural and managed soil moisture pulses in drylands. Soil microbes rely on atmospheric hydrogen (H2) as an important energy source in arid and semiarid landscapes with low soil moisture and carbon availability. Unlike mesic ecosystems, transient water availability in arid and semiarid ecosystems has been identified as a key limiting driver of microbe-mediated H2 uptake. We measured soil H2 uptake in rain gardens exposed to three commonly used water harvesting practices during the monsoon season in Tucson AZ, USA. In situ static chamber measurements were used to calculate H2 uptake in each of the three water harvesting treatments passive (stormwater runoff), active (stored rooftop runoff), and greywater (used laundry water) compared to an unaltered control treatment to assess the effects of water management practices on soil microbial activity. In addition, soils were collected from each treatment and brought to the lab for an incubation experiment manipulating the soil moisture to three levels capturing the range observed from field samples. H2 fluxes from all treatments ranged between −0.72 nmol m−2 s−1 and −3.98 nmol m−2 s−1 over the monsoon season. Soil H2 uptake in the greywater treatment was on average 53% greater than the other treatments during pre-monsoon, suggesting that the increased frequency and availability of water in the g…
format: application/pdf
format: text/html
creator: Vanessa Buzzard
creator: Dana Thorne
creator: Juliana Gil-Loaiza
creator: Alejandro Cueva
creator: Laura K. Meredith
subject: Soil Science
subject: Biosphere Interactions
subject: Biogeochemistry
description: doi:10.7717/peerj.12966
publisher: PeerJ Inc.
rights: © 2022 Buzzard et al.
abstract: The North American Monsoon season (June–September) in the Sonoran Desert brings thunderstorms and heavy rainfall. These rains bring cooler temperature and account for roughly half of the annual precipitation making them important for biogeochemical processes. The intensity of the monsoon rains also increase flooding in urban areas and rely on green infrastructure (GI) stormwater management techniques such as water harvesting and urban rain gardens to capture runoff. The combination of increased water availability during the monsoon and water management provide a broad moisture regime for testing responses in microbial metabolism to natural and managed soil moisture pulses in drylands. Soil microbes rely on atmospheric hydrogen (H2) as an important energy source in arid and semiarid landscapes with low soil moisture and carbon availability. Unlike mesic ecosystems, transient water availability in arid and semiarid ecosystems has been identified as a key limiting driver of microbe-mediated H2 uptake. We measured soil H2 uptake in rain gardens exposed to three commonly used water harvesting practices during the monsoon season in Tucson AZ, USA. In situ static chamber measurements were used to calculate H2 uptake in each of the three water harvesting treatments passive (stormwater runoff), active (stored rooftop runoff), and greywater (used laundry water) compared to an unaltered control treatment to assess the effects of water management practices on soil microbial activity. In addition, soils were collected from each treatment and brought to the lab for an incubation experiment manipulating the soil moisture to three levels capturing the range observed from field samples. H2 fluxes from all treatments ranged between −0.72 nmol m−2 s−1 and −3.98 nmol m−2 s−1 over the monsoon season. Soil H2 uptake in the greywater treatment was on average 53% greater than the other treatments during pre-monsoon, suggesting that the increased frequency and availability of water in the g…
bibliographic citation: Buzzard et al. (2022) Sensitivity of soil hydrogen uptake to natural and managed moisture dynamics in a semiarid urban ecosystem. PeerJ 10:e12966 https://doi.org/10.7717/peerj.12966
date submitted: 2021-07-09
date accepted: 2022-01-28
issued: 2022-03-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buzzard
  given name: Vanessa
author list: Agent
  family name: Thorne
  given name: Dana
author list: Agent
  family name: Gil-Loaiza
  given name: Juliana
author list: Agent
  family name: Cueva
  given name: Alejandro
author list: Agent
  family name: Meredith
  given name: Laura K.
doi: 10.7717/peerj.12966
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-17
copyright: © 2022 Buzzard et al.
attribution name: Buzzard et al.

A comparative study of the capability of MSCs isolated from different human tissue sources to differentiate into neuronal stem cells and dopaminergic-like cells
type: item
type: AcademicArticle
description: Background Neurodegenerative diseases are characterized by progressive neuronal loss and degeneration. The regeneration of neurons is minimal and neurogenesis is limited only to specific parts of the brain. Several clinical trials have been conducted using Mesenchymal Stem Cells (MSCs) from different sources to establish their safety and efficacy for the treatment of several neurological disorders such as Parkinson’s disease, multiple sclerosis and amyotrophic lateral sclerosis. Aim The aim of this study was to provide a comparative view of the capabilities of MSCs, isolated from different human tissue sources to differentiate into neuronal stem cell-like cells (NSCs) and possibly into dopaminergic neural- like cells. Methods Mesenchymal stem cells were isolated from human bone marrow, adipose, and Wharton’s jelly (WJ) tissue samples. Cells were characterized by flow cytometry for their ability to express the most common MSC markers. The differentiation potential was also assessed by differentiating them into osteogenic and adipogenic cell lineages. To evaluate the capacity of these cells to differentiate towards the neural stem cell-like lineage, cells were cultured in media containing small molecules. Cells were utilized for gene expression and immunofluorescence analysis at different time points. Results Our results indicate that we have successfully isolated MSCs from bone marrow, adipose tissue, and Wharton’s jelly. WJ-MSCs showed a slightly higher proliferation rate after 72 hours compared to BM and AT derived MSCs. Gene expression of early neural stem cell markers revealed that WJ-MSCs had higher expression of Nestin and PAX6 compared to BM and AT-MSCs, in addition to LMX expression as an early dopaminergic neural marker. Immunofluorescence analysis also revealed that these cells successfully expressed SOX1, SOX2, Nestin, TUJ1, FOXA2 and TH. Conclusion These results indicate that the protocol utilized has successfully differentiated BM, AT and WJ-MSCs into NS…
format: application/pdf
format: text/html
creator: Nidaa A. Ababneh
creator: Ban Al-Kurdi
creator: Fatima Jamali
creator: Abdalla Awidi
subject: Biochemistry
subject: Bioengineering
subject: Cell Biology
subject: Neuroscience
description: doi:10.7717/peerj.13003
publisher: PeerJ Inc.
rights: © 2022 Ababneh et al.
abstract: Background Neurodegenerative diseases are characterized by progressive neuronal loss and degeneration. The regeneration of neurons is minimal and neurogenesis is limited only to specific parts of the brain. Several clinical trials have been conducted using Mesenchymal Stem Cells (MSCs) from different sources to establish their safety and efficacy for the treatment of several neurological disorders such as Parkinson’s disease, multiple sclerosis and amyotrophic lateral sclerosis. Aim The aim of this study was to provide a comparative view of the capabilities of MSCs, isolated from different human tissue sources to differentiate into neuronal stem cell-like cells (NSCs) and possibly into dopaminergic neural- like cells. Methods Mesenchymal stem cells were isolated from human bone marrow, adipose, and Wharton’s jelly (WJ) tissue samples. Cells were characterized by flow cytometry for their ability to express the most common MSC markers. The differentiation potential was also assessed by differentiating them into osteogenic and adipogenic cell lineages. To evaluate the capacity of these cells to differentiate towards the neural stem cell-like lineage, cells were cultured in media containing small molecules. Cells were utilized for gene expression and immunofluorescence analysis at different time points. Results Our results indicate that we have successfully isolated MSCs from bone marrow, adipose tissue, and Wharton’s jelly. WJ-MSCs showed a slightly higher proliferation rate after 72 hours compared to BM and AT derived MSCs. Gene expression of early neural stem cell markers revealed that WJ-MSCs had higher expression of Nestin and PAX6 compared to BM and AT-MSCs, in addition to LMX expression as an early dopaminergic neural marker. Immunofluorescence analysis also revealed that these cells successfully expressed SOX1, SOX2, Nestin, TUJ1, FOXA2 and TH. Conclusion These results indicate that the protocol utilized has successfully differentiated BM, AT and WJ-MSCs into NS…
bibliographic citation: Ababneh et al. (2022) A comparative study of the capability of MSCs isolated from different human tissue sources to differentiate into neuronal stem cells and dopaminergic-like cells. PeerJ 10:e13003 https://doi.org/10.7717/peerj.13003
date submitted: 2021-10-27
date accepted: 2022-02-03
issued: 2022-03-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ababneh
  given name: Nidaa A.
author list: Agent
  family name: Al-Kurdi
  given name: Ban
author list: Agent
  family name: Jamali
  given name: Fatima
author list: Agent
  family name: Awidi
  given name: Abdalla
doi: 10.7717/peerj.13003
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-17
copyright: ©2022 Ababneh et al.
attribution name: Ababneh et al.

An ODE model of yaws elimination in Lihir Island, Papua New Guinea
type: item
type: AcademicArticle
description: Yaws is a chronic infection that affects mainly the skin, bone and cartilage and spreads mostly between children. The new approval of a medication as treatment in 2012 has revived eradication efforts and now only few known localized foci of infection remain. The World Health Organization strategy mandates an initial round of total community treatment (TCT) with single-dose azithromycin followed either by further TCT or by total targeted treatment (TTT), an active case-finding and treatment of cases and their contacts. We develop the compartmental ODE model of yaws transmission and treatment for these scenarios. We solve for disease-free and endemic equilibria and also perform the stability analysis. We calibrate the model and validate its predictions on the data from Lihir Island in Papua New Guinea. We demonstrate that TTT strategy is efficient in preventing outbreaks but, due to the presence of asymptomatic latent cases, TTT will not eliminate yaws within a reasonable time frame. To achieve the 2030 eradication target, TCT should be applied instead.
format: application/pdf
format: text/html
creator: Presley Kimball
creator: Jacob Levenson
creator: Amy Moore
creator: Jan Rychtar
creator: Dewey Taylor
subject: Epidemiology
subject: Global Health
subject: Health Policy
subject: Infectious Diseases
subject: Computational Science
description: doi:10.7717/peerj.13018
publisher: PeerJ Inc.
rights: © 2022 Kimball et al.
abstract: Yaws is a chronic infection that affects mainly the skin, bone and cartilage and spreads mostly between children. The new approval of a medication as treatment in 2012 has revived eradication efforts and now only few known localized foci of infection remain. The World Health Organization strategy mandates an initial round of total community treatment (TCT) with single-dose azithromycin followed either by further TCT or by total targeted treatment (TTT), an active case-finding and treatment of cases and their contacts. We develop the compartmental ODE model of yaws transmission and treatment for these scenarios. We solve for disease-free and endemic equilibria and also perform the stability analysis. We calibrate the model and validate its predictions on the data from Lihir Island in Papua New Guinea. We demonstrate that TTT strategy is efficient in preventing outbreaks but, due to the presence of asymptomatic latent cases, TTT will not eliminate yaws within a reasonable time frame. To achieve the 2030 eradication target, TCT should be applied instead.
bibliographic citation: Kimball et al. (2022) An ODE model of yaws elimination in Lihir Island, Papua New Guinea. PeerJ 10:e13018 https://doi.org/10.7717/peerj.13018
date submitted: 2021-10-18
date accepted: 2022-02-06
issued: 2022-03-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kimball
  given name: Presley
author list: Agent
  family name: Levenson
  given name: Jacob
author list: Agent
  family name: Moore
  given name: Amy
author list: Agent
  family name: Rychtar
  given name: Jan
author list: Agent
  family name: Taylor
  given name: Dewey
doi: 10.7717/peerj.13018
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-17
copyright: ©2022 Kimball et al.
attribution name: Kimball et al.

International football players with cerebral palsy maintained their physical fitness after a self-training program during the COVID-19 lockdown
type: item
type: AcademicArticle
description: Background The COVID-19 global pandemic caused a complete stop in sport participation which meant a detraining period for athletes. High-level athletes had to train at home guided by their coaches and conditioning trainers in an effort to maintain their physical fitness. The aim of maintaining the training adaptations and physical fitness during the COVID-19 mandatory lockdown was especially important for CP athletes, in which the detraining period was expected to cause early declines in motor function, poor coordination and muscle weakness due to their disability. Methods The present study assessed the effect of a guided self-training program on international CP football players’ physical fitness during the COVID-19 mandatory lockdown. Fifteen CP football players from the Spanish National Team participated in the study. An experimental design with a pre- (T1) and a post-intervention (T2) assessment was carried out, with a 12-week period of players’ self-training (divided in two periods of 6 weeks) which combined strength and endurance training. Physical performance assessment consisted in the free countermovement jump (CMJ), 5, 10 and 20-m sprint, the modified agility T-test (MAT) and a dribbling test. The Kruskal–Wallis test was used for between-group comparisons, while the Student’s paired t test or the Fisher Pitman permutation test, based on the normality of the data, were used for within-group comparisons. Results The results showed no differences between sport classes (FT1, FT2 and FT3) in physical fitness change after the training program (Chi2 = 0.16 to 1.73; p = 0.42 to 0.92). Within-group comparisons showed an increase of jump height in the CMJ (4.19 cm [2.46, 5.93]; p < 0.001) and a maintenance of the 5, 10 and 20-m sprint, MAT and dribbling ability (<0.01 to 0.09 s; p = 0.19 to 0.97). Discussion To the authors’ knowledge, this is the first study that examined the physical fitness adaptations to a training program with CP football players. The results sh…
format: application/pdf
format: text/html
creator: Iván Peña-González
creator: José Manuel Sarabia
creator: Agustín Manresa-Rocamora
creator: Manuel Moya-Ramón
subject: COVID-19
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.13059
publisher: PeerJ Inc.
rights: © 2022 Peña-González et al.
abstract: Background The COVID-19 global pandemic caused a complete stop in sport participation which meant a detraining period for athletes. High-level athletes had to train at home guided by their coaches and conditioning trainers in an effort to maintain their physical fitness. The aim of maintaining the training adaptations and physical fitness during the COVID-19 mandatory lockdown was especially important for CP athletes, in which the detraining period was expected to cause early declines in motor function, poor coordination and muscle weakness due to their disability. Methods The present study assessed the effect of a guided self-training program on international CP football players’ physical fitness during the COVID-19 mandatory lockdown. Fifteen CP football players from the Spanish National Team participated in the study. An experimental design with a pre- (T1) and a post-intervention (T2) assessment was carried out, with a 12-week period of players’ self-training (divided in two periods of 6 weeks) which combined strength and endurance training. Physical performance assessment consisted in the free countermovement jump (CMJ), 5, 10 and 20-m sprint, the modified agility T-test (MAT) and a dribbling test. The Kruskal–Wallis test was used for between-group comparisons, while the Student’s paired t test or the Fisher Pitman permutation test, based on the normality of the data, were used for within-group comparisons. Results The results showed no differences between sport classes (FT1, FT2 and FT3) in physical fitness change after the training program (Chi2 = 0.16 to 1.73; p = 0.42 to 0.92). Within-group comparisons showed an increase of jump height in the CMJ (4.19 cm [2.46, 5.93]; p < 0.001) and a maintenance of the 5, 10 and 20-m sprint, MAT and dribbling ability (<0.01 to 0.09 s; p = 0.19 to 0.97). Discussion To the authors’ knowledge, this is the first study that examined the physical fitness adaptations to a training program with CP football players. The results sh…
bibliographic citation: Peña-González et al. (2022) International football players with cerebral palsy maintained their physical fitness after a self-training program during the COVID-19 lockdown. PeerJ 10:e13059 https://doi.org/10.7717/peerj.13059
date submitted: 2021-12-13
date accepted: 2022-02-13
issued: 2022-03-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peña-González
  given name: Iván
author list: Agent
  family name: Sarabia
  given name: José Manuel
author list: Agent
  family name: Manresa-Rocamora
  given name: Agustín
author list: Agent
  family name: Moya-Ramón
  given name: Manuel
doi: 10.7717/peerj.13059
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-17
copyright: © 2022 Peña-González et al.
attribution name: Peña-González et al.

Geometric morphometrics as a tool to understand biogeographical and evolutionary patterns in crane fly genus Ischnotoma Skuse (Diptera, Tipulidae)
type: item
type: AcademicArticle
description: Background The geometric morphometric analysis is applied for the first time for the family Tipulidae to distinguish evolutionary and biogeographical patterns on Ischnotoma species from Neotropical and Australian regions. We included 45 recognized species of the genus, representing its three subgenera I. (Icriomastax), I. (Ischnotoma), and I. (Neotipula). This paper aims to test if the three subgenera are recoverable using this set of morphometric data. Methods Twenty-two landmarks were selected on the wing, mostly located on the radial and medial veins. A Regression Analysis, Principal Components Analysis (PCA), a Shape Coordinates PCA and a Canonical Variate Analysis (CVA) were used to test the variations among individuals, wing shape and groups. Results For all analyses, the species of Ischnotoma (Neotipula) has a strong dissociation from the remaining species and the CVA shows a complete separation of the three subgenera. This study represents the first insight for a new assessment of Ischnotoma and the first step to giving a possible new status for I. (Neotipula).
format: application/pdf
format: text/html
creator: Jéssica Gouvêa
creator: Leonardo H. Gil-Azevedo
subject: Biogeography
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.13123
publisher: PeerJ Inc.
rights: © 2022 Gouvêa and Gil-Azevedo
abstract: Background The geometric morphometric analysis is applied for the first time for the family Tipulidae to distinguish evolutionary and biogeographical patterns on Ischnotoma species from Neotropical and Australian regions. We included 45 recognized species of the genus, representing its three subgenera I. (Icriomastax), I. (Ischnotoma), and I. (Neotipula). This paper aims to test if the three subgenera are recoverable using this set of morphometric data. Methods Twenty-two landmarks were selected on the wing, mostly located on the radial and medial veins. A Regression Analysis, Principal Components Analysis (PCA), a Shape Coordinates PCA and a Canonical Variate Analysis (CVA) were used to test the variations among individuals, wing shape and groups. Results For all analyses, the species of Ischnotoma (Neotipula) has a strong dissociation from the remaining species and the CVA shows a complete separation of the three subgenera. This study represents the first insight for a new assessment of Ischnotoma and the first step to giving a possible new status for I. (Neotipula).
bibliographic citation: Gouvêa et al. (2022) Geometric morphometrics as a tool to understand biogeographical and evolutionary patterns in crane fly genus Ischnotoma Skuse (Diptera, Tipulidae). PeerJ 10:e13123 https://doi.org/10.7717/peerj.13123
date submitted: 2021-08-04
date accepted: 2022-02-24
issued: 2022-03-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gouvêa
  given name: Jéssica
author list: Agent
  family name: Gil-Azevedo
  given name: Leonardo H.
doi: 10.7717/peerj.13123
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-17
copyright: ©2022 Gouvêa and Gil-Azevedo
attribution name: Gouvêa and Gil-Azevedo

Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease
type: item
type: AcademicArticle
description: Background The disease caused by Barley yellow mosaic virus (BaYMV) infection is a serious threat to autumn-sown barley (Hordeum vulgare L.) production in Europe, East Asia and Iran. Due to the rapid diversification of BaYMV strains, it is urgent to discover novel germplasm and genes to assist breeding new varieties with resistance to different BaYMV strains, thus minimizing the effect of BaYMV disease on barley cropping. Methods A natural population consisting of 181 barley accessions with different levels of resistance to BaYMV disease was selected for field resistance identification in two separate locations (Yangzhou and Yancheng, Jiangsu Province, China). Additive main effects and multiplicative interaction (AMMI) analysis was used to identify accessions with stable resistance. Genome-wide association study (GWAS) of BaYMV disease resistance was broadly performed by combining both single nucleotide polymorphisms (SNPs) and specific molecular markers associated with the reported BaYMV disease resistance genes. Furthermore, the viral protein genome linked (VPg) sequences of the virus were amplified and analyzed to assess the differences between the BaYMV strains sourced from the different experimental sites. Results Seven barley accessions with lower standardized Area Under the Disease Progress Steps (sAUDPS) index in every environment were identified and shown to have stable resistance to BaYMV disease in each assessed location. Apart from the reported BaYMV disease resistance genes rym4 and rym5, one novel resistance locus explaining 24.21% of the phenotypic variation was identified at the Yangzhou testing site, while two other novel resistance loci that contributed 19.23% and 19.79% of the phenotypic variation were identified at the Yancheng testing site, respectively. Further analysis regarding the difference in the VPg sequence of the predominant strain of BaYMV collected from these two testing sites may explain the difference of resistance loci differential…
format: application/pdf
format: text/html
creator: Yuhan Pan
creator: Juan Zhu
creator: Yi Hong
creator: Mengna Zhang
creator: Chao Lv
creator: Baojian Guo
creator: Huiquan Shen
creator: Xiao Xu
creator: Rugen Xu
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13128
publisher: PeerJ Inc.
rights: © 2022 Pan et al.
abstract: Background The disease caused by Barley yellow mosaic virus (BaYMV) infection is a serious threat to autumn-sown barley (Hordeum vulgare L.) production in Europe, East Asia and Iran. Due to the rapid diversification of BaYMV strains, it is urgent to discover novel germplasm and genes to assist breeding new varieties with resistance to different BaYMV strains, thus minimizing the effect of BaYMV disease on barley cropping. Methods A natural population consisting of 181 barley accessions with different levels of resistance to BaYMV disease was selected for field resistance identification in two separate locations (Yangzhou and Yancheng, Jiangsu Province, China). Additive main effects and multiplicative interaction (AMMI) analysis was used to identify accessions with stable resistance. Genome-wide association study (GWAS) of BaYMV disease resistance was broadly performed by combining both single nucleotide polymorphisms (SNPs) and specific molecular markers associated with the reported BaYMV disease resistance genes. Furthermore, the viral protein genome linked (VPg) sequences of the virus were amplified and analyzed to assess the differences between the BaYMV strains sourced from the different experimental sites. Results Seven barley accessions with lower standardized Area Under the Disease Progress Steps (sAUDPS) index in every environment were identified and shown to have stable resistance to BaYMV disease in each assessed location. Apart from the reported BaYMV disease resistance genes rym4 and rym5, one novel resistance locus explaining 24.21% of the phenotypic variation was identified at the Yangzhou testing site, while two other novel resistance loci that contributed 19.23% and 19.79% of the phenotypic variation were identified at the Yancheng testing site, respectively. Further analysis regarding the difference in the VPg sequence of the predominant strain of BaYMV collected from these two testing sites may explain the difference of resistance loci differential…
bibliographic citation: Pan et al. (2022) Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease. PeerJ 10:e13128 https://doi.org/10.7717/peerj.13128
date submitted: 2021-10-01
date accepted: 2022-02-25
issued: 2022-03-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Yuhan
author list: Agent
  family name: Zhu
  given name: Juan
author list: Agent
  family name: Hong
  given name: Yi
author list: Agent
  family name: Zhang
  given name: Mengna
author list: Agent
  family name: Lv
  given name: Chao
author list: Agent
  family name: Guo
  given name: Baojian
author list: Agent
  family name: Shen
  given name: Huiquan
author list: Agent
  family name: Xu
  given name: Xiao
author list: Agent
  family name: Xu
  given name: Rugen
doi: 10.7717/peerj.13128
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-17
copyright: © 2022 Pan et al.
attribution name: Pan et al.

Positively selected genes in the hoary bat (Lasiurus cinereus) lineage: prominence of thymus expression, immune and metabolic function, and regions of ancient synteny
type: item
type: AcademicArticle
description: Background Bats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat (Lasiurus cinereus) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor. Methods To better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML. Results Of 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch (P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov–Smirnov test (P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1-like gene family may indicate evo…
format: application/pdf
format: text/html
creator: Robert S. Cornman
creator: Paul M. Cryan
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.13130
publisher: PeerJ Inc.
rights: © 2022 Cornman and Cryan
abstract: Background Bats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat (Lasiurus cinereus) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor. Methods To better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML. Results Of 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch (P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov–Smirnov test (P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1-like gene family may indicate evo…
bibliographic citation: Cornman et al. (2022) Positively selected genes in the hoary bat (Lasiurus cinereus) lineage: prominence of thymus expression, immune and metabolic function, and regions of ancient synteny. PeerJ 10:e13130 https://doi.org/10.7717/peerj.13130
date submitted: 2021-09-23
date accepted: 2022-02-25
issued: 2022-03-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cornman
  given name: Robert S.
author list: Agent
  family name: Cryan
  given name: Paul M.
doi: 10.7717/peerj.13130
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-17
copyright: © 2022 Cornman and Cryan
attribution name: Cornman and Cryan

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