Transcriptomics analysis of field-droughted pear (Pyrus spp.) reveals potential drought stress genes and metabolic pathways
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.
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
The mRNA and miRNA profiles of goat bronchial epithelial cells stimulated by Pasteurella multocida strains of serotype A and D
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.
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
The use of electromyography and kinematic measurements of the lumbar spine during ergonomic intervention among workers of the production line of a foundry
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 task reduced the contralateral imbalance of muscle activity and changes the ranges of movement of L1-S1 segments. The task of optimizing the load on the musculoskeletal system, including the lumbar spine, should be carried out by means of appropriate ergonomic instruction and multi-pronged measures, including analysis of the health of employees, their working environment and physical activity outside the workplace. Electromyography and measurements of the range of movement of the lumbar spine appear to be good tools for the evaluation of workplace ergonomics.
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
Complete chloroplast genome studies of different apple varieties indicated the origin of modern cultivated apples from Malus sieversii and Malus sylvestris
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.
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
Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes
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 appears to be isolated from the main Andean cordillera for some amphibian groups. We recommend that both H. mashpi sp. nov. and H. nouns sp. nov. be listed as Endangered, following IUCN criteria. These new species provide another example of cryptic diversity in the Andes—further evidence that the region fosters much more biodiversity than we have the resources to catalog. Threatened by mining and other exploitative industries, these glassfrogs and many other yet-to-be-discovered Andean species highlight the dire need for effective conservation measures—especially in northwestern Ecuador.
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
Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean
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 deficit, greater efficiency was observed in the L13241 genotype through adjustments in morphological, physiological, genetic and metabolic characteristics that are combined in the same plant. This study contributes to the advancement in the knowledge about the resistance to drought in cultivated plants and provides bases for the genetic improvement of the soybean culture.
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
High-performance pipeline for MutMap and QTL-seq
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).
Sugihara et al. (2022) High-performance pipeline for MutMap and QTL-seq. PeerJ 10:e13170 https://doi.org/10.7717/peerj.13170
Sensitivity of soil hydrogen uptake to natural and managed moisture dynamics in a semiarid urban ecosystem
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 greywater treatment resulted in higher H2 uptake during the dry season. H2 uptake was significantly correlated with soil moisture (r = −0.393, p = 0.001, df = 62) and temperature (r = 0.345, p = 0.005, df = 62). Our findings suggest that GI managed residential soils can maintain low levels of H2 uptake during dry periods, unlike unmanaged systems. The more continuous H2 uptake associated with GI may help reduce the impacts of drought on H2 cycling in semiarid urban ecosystems.
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
A comparative study of the capability of MSCs isolated from different human tissue sources to differentiate into neuronal stem cells and dopaminergic-like cells
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 NSC-like cells. WJ-MSCs possess a higher potential to transdifferentiate into NSC and dopaminergic-like cells. Thus, it might indicate that this protocol can be used to induce MSC into neuronal lineage, which provides an additional or alternative source of cells to be used in the neurological cell-based therapies.
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
An ODE model of yaws elimination in Lihir Island, Papua New Guinea
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.
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