PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Transcriptomics analysis of field-droughted pear (Pyrus spp.) reveals potential drought stress genes and metabolic pathways
items: The mRNA and miRNA profiles of goat bronchial epithelial cells stimulated by Pasteurella multocida strains of serotype A and D
items: The use of electromyography and kinematic measurements of the lumbar spine during ergonomic intervention among workers of the production line of a foundry
items: Complete chloroplast genome studies of different apple varieties indicated the origin of modern cultivated apples from Malus sieversii and Malus sylvestris
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

Transcriptomics analysis of field-droughted pear (Pyrus spp.) reveals potential drought stress genes and metabolic pathways
type: item
type: AcademicArticle
description: Drought acts as a major abiotic stress that hinders plant growth and crop productivity. It is critical, as such, to discern the molecular response of plants to drought in order to enhance agricultural yields under droughts as they occur with increasing frequency. Pear trees are among the most crucial deciduous fruit trees worldwide, and yet the molecular mechanisms of drought tolerance in field-grown pear remain unclear. In this study, we analyzed the differences in transcriptome profiles of pear leaves, branches, and young fruits in irrigation vs field-drought conditions over the growing seasons. In total, 819 differentially expressed genes (DEGs) controlling drought response were identified, among which 427 DEGs were upregulated and 392 DEGs were downregulated. Drought responsive genes were enriched significantly in monoterpenoid biosynthesis, flavonoid biosynthesis, and diterpenoid biosynthesis. Fourteen phenylpropanoid, five flavonoid, and four monoterpenoid structural genes were modulated by field drought stress, thereby indicating the transcriptional regulation of these metabolic pathways in fruit exposed to drought. A total of 4,438 transcription factors (TFs) belonging to 30 TF families were differentially expressed between drought and irrigation, and such findings signal valuable information on transcriptome changes in response to drought. Our study revealed that pear trees react to drought by modulating several secondary metabolic pathways, particularly by stimulating the production of phenylpropanoids as well as volatile organic compounds like monoterpenes. Our findings are of practical importance for agricultural breeding programs, while the resulting data is a resource for improving drought tolerance through genetic engineering of non-model, but economically important, perennial plants.
format: application/pdf
format: text/html
creator: Sheng Yang
creator: Mudan Bai
creator: Guowei Hao
creator: Huangping Guo
creator: Baochun Fu
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12921
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Drought acts as a major abiotic stress that hinders plant growth and crop productivity. It is critical, as such, to discern the molecular response of plants to drought in order to enhance agricultural yields under droughts as they occur with increasing frequency. Pear trees are among the most crucial deciduous fruit trees worldwide, and yet the molecular mechanisms of drought tolerance in field-grown pear remain unclear. In this study, we analyzed the differences in transcriptome profiles of pear leaves, branches, and young fruits in irrigation vs field-drought conditions over the growing seasons. In total, 819 differentially expressed genes (DEGs) controlling drought response were identified, among which 427 DEGs were upregulated and 392 DEGs were downregulated. Drought responsive genes were enriched significantly in monoterpenoid biosynthesis, flavonoid biosynthesis, and diterpenoid biosynthesis. Fourteen phenylpropanoid, five flavonoid, and four monoterpenoid structural genes were modulated by field drought stress, thereby indicating the transcriptional regulation of these metabolic pathways in fruit exposed to drought. A total of 4,438 transcription factors (TFs) belonging to 30 TF families were differentially expressed between drought and irrigation, and such findings signal valuable information on transcriptome changes in response to drought. Our study revealed that pear trees react to drought by modulating several secondary metabolic pathways, particularly by stimulating the production of phenylpropanoids as well as volatile organic compounds like monoterpenes. Our findings are of practical importance for agricultural breeding programs, while the resulting data is a resource for improving drought tolerance through genetic engineering of non-model, but economically important, perennial plants.
bibliographic citation: Yang et al. (2022) Transcriptomics analysis of field-droughted pear (Pyrus spp.) reveals potential drought stress genes and metabolic pathways. PeerJ 10:e12921 https://doi.org/10.7717/peerj.12921
date submitted: 2021-04-06
date accepted: 2022-01-20
issued: 2022-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Sheng
author list: Agent
  family name: Bai
  given name: Mudan
author list: Agent
  family name: Hao
  given name: Guowei
author list: Agent
  family name: Guo
  given name: Huangping
author list: Agent
  family name: Fu
  given name: Baochun
doi: 10.7717/peerj.12921
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-18
copyright: ©2022 Yang et al.
attribution name: Yang et al.

The mRNA and miRNA profiles of goat bronchial epithelial cells stimulated by Pasteurella multocida strains of serotype A and D
type: item
type: AcademicArticle
description: Pasteurella multocida (P. multocida) is a zoonotic bacterium that predominantly colonizes the respiratory tract and lungs of a variety of farmed and wild animals, and causes severe respiratory disease. To investigate the characteristics of the host immune response induced by P. multocida strains of serotype A and D, high-throughput mRNA-Seq and miRNA-Seq were performed to analyze the changes in goat bronchial epithelial cells stimulated by these two serotypes of P. multocida for 4 h. Quantitative RT-PCR was used to validate the randomly selected genes and miRNAs. The results revealed 204 and 117 differentially expressed mRNAs (|log2(Fold-change)| ≥ 1, p-value < 0.05) in the P. multocida serotype A and D stimulated groups, respectively. Meanwhile, the number of differentially expressed miRNAs (|log2(Fold-change)| > 0.1, p-value < 0.05) were 269 and 290, respectively. GO and KEGG enrichment analyses revealed 13 GO terms (p-value < 0.05) and four KEGG pathways (p-value < 0.05) associated with immunity. In the serotype A-stimulated group, the immune-related pathways were the GABAergic synapse and Toll-like receptor signaling pathways, while in the serotype D-stimulated group, the immune-related pathways were the phagosome and B cell receptor signaling pathways. Based on the predicted results of TargetScan and miRanda, the differentially expressed mRNA–miRNA network of immune-related GO terms and KEGG pathways was constructed. According to the cell morphological changes and the significant immune-related KEGG pathways, it was speculated that the P. multocida serotype D strain-stimulated goat bronchial epithelial cells may induce a cellular immune response earlier than serotype A-stimulated cells. Our study provides valuable insight into the host immune response mechanism induced by P. multocida strains of serotype A and D.
format: application/pdf
format: text/html
creator: Qi An
creator: Si Chen
creator: Luyin Zhang
creator: Zhenxing Zhang
creator: Yiwen Cheng
creator: Haotian Wu
creator: Ang Liu
creator: Zhen Chen
creator: Bin Li
creator: Jie Chen
creator: Yiying Zheng
creator: Churiga Man
creator: Fengyang Wang
creator: Qiaoling Chen
creator: Li Du
subject: Cell Biology
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.13047
publisher: PeerJ Inc.
rights: © 2022 An et al.
abstract: Pasteurella multocida (P. multocida) is a zoonotic bacterium that predominantly colonizes the respiratory tract and lungs of a variety of farmed and wild animals, and causes severe respiratory disease. To investigate the characteristics of the host immune response induced by P. multocida strains of serotype A and D, high-throughput mRNA-Seq and miRNA-Seq were performed to analyze the changes in goat bronchial epithelial cells stimulated by these two serotypes of P. multocida for 4 h. Quantitative RT-PCR was used to validate the randomly selected genes and miRNAs. The results revealed 204 and 117 differentially expressed mRNAs (|log2(Fold-change)| ≥ 1, p-value < 0.05) in the P. multocida serotype A and D stimulated groups, respectively. Meanwhile, the number of differentially expressed miRNAs (|log2(Fold-change)| > 0.1, p-value < 0.05) were 269 and 290, respectively. GO and KEGG enrichment analyses revealed 13 GO terms (p-value < 0.05) and four KEGG pathways (p-value < 0.05) associated with immunity. In the serotype A-stimulated group, the immune-related pathways were the GABAergic synapse and Toll-like receptor signaling pathways, while in the serotype D-stimulated group, the immune-related pathways were the phagosome and B cell receptor signaling pathways. Based on the predicted results of TargetScan and miRanda, the differentially expressed mRNA–miRNA network of immune-related GO terms and KEGG pathways was constructed. According to the cell morphological changes and the significant immune-related KEGG pathways, it was speculated that the P. multocida serotype D strain-stimulated goat bronchial epithelial cells may induce a cellular immune response earlier than serotype A-stimulated cells. Our study provides valuable insight into the host immune response mechanism induced by P. multocida strains of serotype A and D.
bibliographic citation: An et al. (2022) The mRNA and miRNA profiles of goat bronchial epithelial cells stimulated by Pasteurella multocida strains of serotype A and D. PeerJ 10:e13047 https://doi.org/10.7717/peerj.13047
date submitted: 2021-10-25
date accepted: 2022-02-11
issued: 2022-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: An
  given name: Qi
author list: Agent
  family name: Chen
  given name: Si
author list: Agent
  family name: Zhang
  given name: Luyin
author list: Agent
  family name: Zhang
  given name: Zhenxing
author list: Agent
  family name: Cheng
  given name: Yiwen
author list: Agent
  family name: Wu
  given name: Haotian
author list: Agent
  family name: Liu
  given name: Ang
author list: Agent
  family name: Chen
  given name: Zhen
author list: Agent
  family name: Li
  given name: Bin
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Zheng
  given name: Yiying
author list: Agent
  family name: Man
  given name: Churiga
author list: Agent
  family name: Wang
  given name: Fengyang
author list: Agent
  family name: Chen
  given name: Qiaoling
author list: Agent
  family name: Du
  given name: Li
doi: 10.7717/peerj.13047
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-18
copyright: ©2022 An et al.
attribution name: An et al.

The use of electromyography and kinematic measurements of the lumbar spine during ergonomic intervention among workers of the production line of a foundry
type: item
type: AcademicArticle
description: Purpose Workers who perform repetitive movements are exposed to many risk factors leading to the occurrence of lumbar back pain. The aim of the research was to answer the question whether the ergonomic instruction conducted by a physiotherapist would change the tested range of motion of the segments of lumbar spine and the symmetry of the work of the torso and upper limbs muscles during work performed by foundry employees. Methods The study included 12 foundry production line workers with musculoskeletal pain. The workstation was built in the laboratory that perfectly simulates work on the production line. The workers performed two activities from their daily work, i.e. transferring and moving a casting. They were then given ergonomic instruction by a physiotherapist and performed the assigned tasks again. During the activities, the electromyographic signal from five muscles was recorded in terms of symmetry of their work. The maximum angular ranges of the motor segments of the lumbar spine were measured using gyroscopes. Results After the ergonomic instruction, the contralateral imbalance of muscle activity decreased statistically significantly during the first phase (p = 0.0004), second phase (p = 0.0002) and the third phase (p = 0.0069) of transferring the casting. While moving the casting , only erector spinae showed statistically significantly (p = 0.0131) more symmetrical work after the ergonomic instruction. During the transfer of the casting, statistically significantly lower values of the ranges of motion between the segments were obtained after carrying out the ergonomic instruction for the left (p = 0.0231) and right (p = 0.0032) lateral flexion. The ranges of movement between the segments differed statistically significantly for the flexion (p = 0.0117), extension (p = 0.0469) and left (p = 0.0031) and right lateral flexion movements (p = 0.0012). Conclusion Conducting ergonomic instruction consisting in teaching the correct performance of a movement tas…
format: application/pdf
format: text/html
creator: Anna Błaszczyk
creator: Małgorzata B. Ogurkowska
subject: Kinesiology
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.13072
publisher: PeerJ Inc.
rights: © 2022 Błaszczyk and Ogurkowska
abstract: Purpose Workers who perform repetitive movements are exposed to many risk factors leading to the occurrence of lumbar back pain. The aim of the research was to answer the question whether the ergonomic instruction conducted by a physiotherapist would change the tested range of motion of the segments of lumbar spine and the symmetry of the work of the torso and upper limbs muscles during work performed by foundry employees. Methods The study included 12 foundry production line workers with musculoskeletal pain. The workstation was built in the laboratory that perfectly simulates work on the production line. The workers performed two activities from their daily work, i.e. transferring and moving a casting. They were then given ergonomic instruction by a physiotherapist and performed the assigned tasks again. During the activities, the electromyographic signal from five muscles was recorded in terms of symmetry of their work. The maximum angular ranges of the motor segments of the lumbar spine were measured using gyroscopes. Results After the ergonomic instruction, the contralateral imbalance of muscle activity decreased statistically significantly during the first phase (p = 0.0004), second phase (p = 0.0002) and the third phase (p = 0.0069) of transferring the casting. While moving the casting , only erector spinae showed statistically significantly (p = 0.0131) more symmetrical work after the ergonomic instruction. During the transfer of the casting, statistically significantly lower values of the ranges of motion between the segments were obtained after carrying out the ergonomic instruction for the left (p = 0.0231) and right (p = 0.0032) lateral flexion. The ranges of movement between the segments differed statistically significantly for the flexion (p = 0.0117), extension (p = 0.0469) and left (p = 0.0031) and right lateral flexion movements (p = 0.0012). Conclusion Conducting ergonomic instruction consisting in teaching the correct performance of a movement tas…
bibliographic citation: Błaszczyk et al. (2022) The use of electromyography and kinematic measurements of the lumbar spine during ergonomic intervention among workers of the production line of a foundry. PeerJ 10:e13072 https://doi.org/10.7717/peerj.13072
date submitted: 2021-08-20
date accepted: 2022-02-15
issued: 2022-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Błaszczyk
  given name: Anna
author list: Agent
  family name: Ogurkowska
  given name: Małgorzata B.
doi: 10.7717/peerj.13072
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-18
copyright: ©2022 Błaszczyk and Ogurkowska
attribution name: Błaszczyk and Ogurkowska

Complete chloroplast genome studies of different apple varieties indicated the origin of modern cultivated apples from Malus sieversii and Malus sylvestris
type: item
type: AcademicArticle
description: Background Apple is one of the most important temperate deciduous fruit trees worldwide, with a wide range of cultivation. In this study, we assessed the variations and phylogenetic relationships between the complete chloroplast genomes of wild and cultivated apples (Malus spp.). Method We obtained the complete chloroplast genomes of 24 apple varieties using next-generation sequencing technology and compared them with genomes of (downloaded from NCBI) the wild species. Result The chloroplast genome of Malus is highly conserved, with a genome length of 160,067–160,290 bp, and all have a double-stranded circular tetrad structure. The gene content and sequences of genomes of wild species and cultivated apple were almost the same, but several mutation hotspot regions (psbI-atpA, psbM-psbD, and ndhC-atpE) were detected in these genomes. These regions can provide valuable information for solving specific molecular markers in taxonomic research. Phylogenetic analysis revealed that Malus formed a new clade and four cultivated varieties clustered into a branch with M. sylvestris and M. sieversii, which indicated that M. sylvestris and M. sieversii were the ancestor species of the cultivated apple.
format: application/pdf
format: text/html
creator: Xueli Li
creator: Zhijie Ding
creator: Haoyu Miao
creator: Jinbo Bao
creator: Xinmin Tian
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13107
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background Apple is one of the most important temperate deciduous fruit trees worldwide, with a wide range of cultivation. In this study, we assessed the variations and phylogenetic relationships between the complete chloroplast genomes of wild and cultivated apples (Malus spp.). Method We obtained the complete chloroplast genomes of 24 apple varieties using next-generation sequencing technology and compared them with genomes of (downloaded from NCBI) the wild species. Result The chloroplast genome of Malus is highly conserved, with a genome length of 160,067–160,290 bp, and all have a double-stranded circular tetrad structure. The gene content and sequences of genomes of wild species and cultivated apple were almost the same, but several mutation hotspot regions (psbI-atpA, psbM-psbD, and ndhC-atpE) were detected in these genomes. These regions can provide valuable information for solving specific molecular markers in taxonomic research. Phylogenetic analysis revealed that Malus formed a new clade and four cultivated varieties clustered into a branch with M. sylvestris and M. sieversii, which indicated that M. sylvestris and M. sieversii were the ancestor species of the cultivated apple.
bibliographic citation: Li et al. (2022) Complete chloroplast genome studies of different apple varieties indicated the origin of modern cultivated apples from Malus sieversii and Malus sylvestris. PeerJ 10:e13107 https://doi.org/10.7717/peerj.13107
date submitted: 2021-10-21
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: Li
  given name: Xueli
author list: Agent
  family name: Ding
  given name: Zhijie
author list: Agent
  family name: Miao
  given name: Haoyu
author list: Agent
  family name: Bao
  given name: Jinbo
author list: Agent
  family name: Tian
  given name: Xinmin
doi: 10.7717/peerj.13107
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-18
copyright: © 2022 Li et al.
attribution name: Li et al.

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.

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