An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
Hassan et al. (2022) An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 10:e13136 https://doi.org/10.7717/peerj.13136
State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data
Anthropogenic changes in the natural environment have led to alarming rates of biodiversity loss, resulting in a more urgent need for conservation. Although there is an increasing cognizance of the importance of incorporating biodiversity data into conservation, the accuracy of the inferences generated from these records can be highly impacted by gaps and biases in the data. Because of the Philippines’ status as a biodiversity hotspot, the assessment of potential gaps and biases in biodiversity documentation in the country can be a critical step in the identification of priority research areas for conservation applications. In this study, we systematically assessed biodiversity data on animal and plant taxa found in the Philippines by examining the extent of metadata gaps, taxonomic biases, and spatial biases in DNA barcode data while using species occurrence data as a backdrop of the ‘Philippines’ biodiversity. These barcode and species occurrence datasets were obtained from public databases, namely: GenBank, Barcode of Life Data System and Global Biodiversity Information Facility. We found that much of the barcode data had missing information on either records and publishing, geolocation, or taxonomic metadata, which consequently, can limit the usability of barcode data for further analyses. We also observed that the amount of barcode data can be directly associated with the amount of species occurrence data available for a particular taxonomic group and location–highlighting the potential sampling biases in the barcode data. While the majority of barcode data came from foreign institutions, there has been an increase in local efforts in recent decades. However, much of the contribution to biodiversity documentation only come from institutions based in Luzon.
Berba et al. (2022) State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data. PeerJ 10:e13146 https://doi.org/10.7717/peerj.13146
Computational bioacoustics with deep learning: a review and roadmap
Animal vocalisations and natural soundscapes are fascinating objects of study, and contain valuable evidence about animal behaviours, populations and ecosystems. They are studied in bioacoustics and ecoacoustics, with signal processing and analysis an important component. Computational bioacoustics has accelerated in recent decades due to the growth of affordable digital sound recording devices, and to huge progress in informatics such as big data, signal processing and machine learning. Methods are inherited from the wider field of deep learning, including speech and image processing. However, the tasks, demands and data characteristics are often different from those addressed in speech or music analysis. There remain unsolved problems, and tasks for which evidence is surely present in many acoustic signals, but not yet realised. In this paper I perform a review of the state of the art in deep learning for computational bioacoustics, aiming to clarify key concepts and identify and analyse knowledge gaps. Based on this, I offer a subjective but principled roadmap for computational bioacoustics with deep learning: topics that the community should aim to address, in order to make the most of future developments in AI and informatics, and to use audio data in answering zoological and ecological questions.
Stowell (2022) Computational bioacoustics with deep learning: a review and roadmap. PeerJ 10:e13152 https://doi.org/10.7717/peerj.13152
Immediate and cumulative effects of upper-body isometric exercise on the cornea and anterior segment of the human eye
Objectives The execution of isometric resistance training has demonstrated to cause changes in the ocular physiology. The morphology of the cornea and anterior chamber is of paramount importance in the prevention and management of several ocular diseases, and thus, understating the impact of performing isometric exercise on the eye physiology may allow a better management of these ocular conditions. We aimed to determine the short-term effects of 2-minutes upper-body isometric effort at two different intensities on corneal and anterior eye morphology. Methods Eighteen healthy young adults performed a 2-minutes isometric biceps-curl exercise against two loads relative to their maximum strength capacity (high-intensity and low-intensity) in a randomized manner. An Oculus Pentacam was used to measure the corneal morphology and anterior chamber parameters in both experimental conditions at baseline, during the isometric effort (after 30, 60, 90 and 120 seconds), and after 30 and 120 seconds of passive recovery. Results We found that isometric effort causes an increase in pupil size (P < 0.001), and a decrease in the iridocorneal angle (P = 0.005), anterior chamber volume (P < 0.001) and K-flat (P < 0.001) during isometric effort, with these effects being more accentuated in high-intensity condition (P < 0.005 in all cases).Performing 2-minutes upper-body isometric effort did not alter anterior chamber depth, central corneal thickness, corneal volume, and K-steep (P > 0.05 in all cases). Conclusions Our data exhibit that performing 2-minutes of upper-body isometric exercise modifies several parameters of the corneal morphology and anterior eye biometrics, with these changes being greater for the high-intensity exercise condition. The findings of this study may be of relevance for the prevention and management of corneal ectasias and glaucoma.
Vera et al. (2022) Immediate and cumulative effects of upper-body isometric exercise on the cornea and anterior segment of the human eye. PeerJ 10:e13160 https://doi.org/10.7717/peerj.13160
Relationship between circadian genes and memory impairment caused by sleep deprivation
Background Sleep deprivation (SD)-induced cognitive impairment is highly prevalent worldwide and has attracted widespread attention. The temporal and spatial oscillations of circadian genes are severely disturbed after SD, leading to a progressive loss of their physiological rhythms, which in turn affects memory function. However, there is a lack of research on the role of circadian genes and memory function after SD. Therefore, the present study aims to investigate the relationship between circadian genes and memory function and provide potential therapeutic insights into the mechanism of SD-induced memory impairment. Methods Gene expression profiles of GSE33302 and GSE9442 from the Gene Expression Omnibus (GEO) were applied to identify differentially expressed genes (DEGs). Subsequently, both datasets were subjected to Gene Set Enrichment Analysis (GSEA) to determine the overall gene changes in the hippocampus and brain after SD. A Gene Oncology (GO) analysis and Protein-Protein Interaction (PPI) analysis were employed to explore the genes related to circadian rhythm, with their relationship and importance determined through a correlation analysis and a receiver operating characteristic curve (ROC), respectively. The water maze experiments detected behavioral changes related to memory function in SD rats. The expression of circadian genes in several critical organs such as the brain, heart, liver, and lungs and their correlation with memory function was investigated using several microarrays. Finally, changes in the hippocampal immune environment after SD were analyzed using the CIBERSORT in R software. Results The quality of the two datasets was very good. After SD, changes were seen primarily in genes related to memory impairment and immune function. Genes related to circadian rhythm were highly correlated with engagement in muscle structure development and circadian rhythm. Seven circadian genes showed their potential therapeutic value in SD. Water maze experiments confirmed that SD exacerbates memory impairment-related behaviors, including prolonged escape latencies and reduced numbers of rats crossing the platform. The expression of circadian genes was verified, while some genes were also significant in the heart, liver, and lungs. All seven circadian genes were also associated with memory markers in SD. The contents of four immune cells in the hippocampal immune environment changed after SD. Seven circadian genes were related to multiple immune cells. Conclusions In the present study, we found that SD leads to memory impairment accompanied by changes in circadian rhythm-related genes. Seven circadian genes play crucial roles in memory impairment after SD. Naïve B cells and follicular helper T cells are closely related to SD. These findings provide new insights into the treatment of memory impairment caused by SD.
Ke et al. (2022) Relationship between circadian genes and memory impairment caused by sleep deprivation. PeerJ 10:e13165 https://doi.org/10.7717/peerj.13165
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