Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules
The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide both because of the Omicron BA.1 mutations (N211 deletion, L212I substitution and EPE 212-214 insertion) and the Omicron BA.2 mutations (V213G substitution). The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it.
Nersisyan et al. (2022) Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules. PeerJ 10:e13354 https://doi.org/10.7717/peerj.13354
Dynamics of human take and animal predation on sea turtle nests in Northwest Costa Rica
Many conservation projects relocate sea turtle eggs to hatcheries to protect the sea turtle nests from the anthropogenic and natural threats they face in the early stages of development. The Rescue Center for Endangered Marine Species (CREMA) manages four sea turtle conservation projects on the nesting beaches of the Southern Nicoya Peninsula in Costa Rica, where the predominant nesting activity is from olive ridley turtles (Lepidochelys olivacea). Two of these nesting projects are based in Costa de Oro and San Miguel, which are adjacent beaches divided by an estuary. In this study, we compared the dynamics and rates of human and animal predation of nests prior to being relocated to the hatchery on both nesting beaches from 2012 to 2018. We hypothesized that human take and animal predation were compensatory threats, meaning that lower human take may result in higher animal predation, and vice versa, resulting in a similar number of nests lost to predation overall. We discuss the community-based conservation programs on both beaches, one of which has been monitored since 1998 (San Miguel) and the other of which has been monitored since 2012 (Costa de Oro). We found that Costa de Oro exhibited high rates of human take with up to 51% of nests being extracted per season, which has decreased since the conservation project was established. Human take was significantly higher than animal predation on both beaches and human take was significantly higher in Costa de Oro. While San Miguel exhibited higher animal predation, the difference was not statistically significant. Higher depredation by animals corresponded to higher overall nest abundance on both beaches. We were unable to find evidence that human take or animal predation increased in the absence of the other threat, suggesting a lack of compensatory effects of predation. Our findings support further analysis of animal predation and a continuation of patrol-based conservation efforts as well as community outreach to attempt to merge cultural values with sea turtle conservation.
Reavis et al. (2022) Dynamics of human take and animal predation on sea turtle nests in Northwest Costa Rica. PeerJ 10:e12925 https://doi.org/10.7717/peerj.12925
Exosomes and ferroptosis: roles in tumour regulation and new cancer therapies
Research on the biological role of exosomes is rapidly developing, and recent evidence suggests that exosomal effects involve ferroptosis. Exosomes derived from different tissues inhibit ferroptosis, which increases tumour cell chemoresistance. Therefore, exosome-mediated regulation of ferroptosis may be leveraged to design anticancer drugs. This review discusses three pathways of exosome-mediated inhibition of ferroptosis: (1) the Fenton reaction; (2) the ferroptosis defence system, including the Xc-GSH-GPX4 axis and the FSP1/CoQ10/NAD(P)H axis; and (3) lipid peroxidation. We also summarize three recent approaches for combining exosomes and ferroptosis in oncology therapy: (1) promoting exosome-inhibited ferroptosis to enhance chemotherapy; (2) encapsulating exosomes with ferroptosis inducers to inhibit cancers; and (3) developing therapies that combine exosomal inhibitors and ferroptosis inducers. This review will contribute toward establishing effective cancer therapies.
Shi et al. (2022) Exosomes and ferroptosis: roles in tumour regulation and new cancer therapies. PeerJ 10:e13238 https://doi.org/10.7717/peerj.13238
Need for split: integrative taxonomy reveals unnoticed diversity in the subaquatic species of Pseudohygrohypnum (Pylaisiaceae, Bryophyta)
We present an integrative molecular and morphological study of subaquatic representatives of the genus Pseudohygrohypnum (Pylaisiaceae, Bryophyta), supplemented by distribution modelling of the revealed phylogenetic lineages. Phylogenetic analyses of nuclear and plastid datasets combined with the assemble species by automatic partitioning (ASAP) algorithm revealed eight distinct species within the traditionally circumscribed P. eugyrium and P. subeugyrium. These species are therefore yet another example of seemingly widely distributed taxa that harbour molecularly well-differentiated lineages with narrower distribution ranges. Studied accessions that were previously assigned to P. eugyrium form three clearly allopatric lineages, associated with temperate regions of Europe, eastern North America and eastern Asia. Remarkably, accessions falling under the current morphological concept of P. subeugyrium were shown to be even more diverse, containing five phylogenetic lineages. Three of these lineages occur under harsh Asian continental climates from cool-temperate to Arctic regions, while the remaining two, referred to P. subeugyrium s.str. and P. purpurascens, have more oceanic North Atlantic and East Asian distributions. Niche identity and similarity tests suggested no similarity in the distributions of the phylogenetically related lineages but revealed the identity of two East Asian species and the similarity of two pairs of unrelated species. A morphological survey confirmed the distinctness of all eight phylogenetic lineages, requiring the description of five new species. Pseudohygrohypnum appalachianum and P. orientale are described for North American and East Asian plants of P. eugyrium s.l., while P. sibiricum, P. subarcticum and P. neglectum are described for the three continental, predominantly Asian lineages of P. subeugyrium s.l. Our results highlight the importance of nontropical Asia as a center of bryophyte diversity. Phylogenic dating suggests that the diversification of subaquatic Pseudohygrohypnum lineages appeared in late Miocene, while mesophilous species of the genus split before Miocene cooling, in climatic conditions close to those where the ancestor of Pseudohygrohypnum appeared. We speculate that radiation of the P. subeugyrium complex in temperate Asia might have been driven by progressive cooling, aridification, and increases in seasonality, temperature and humidity gradients. Our results parallel those of several integrative taxonomic studies of North Asian mosses, which have resulted in a number of newly revealed species. These include various endemics from continental areas of Asia suggesting that the so-called Rapoport’s rule of low diversity and wide distribution range in subpolar regions might not be applicable to bryophytes. Rather, the strong climatic oscillations in these regions may have served as a driving force of speciation and niche divergence.
Fedosov et al. (2022) Need for split: integrative taxonomy reveals unnoticed diversity in the subaquatic species of Pseudohygrohypnum (Pylaisiaceae, Bryophyta). PeerJ 10:e13260 https://doi.org/10.7717/peerj.13260
Taxonomic revision of the Pheidole megacephala species-group (Hymenoptera, Formicidae) from the Malagasy Region
Background The Malagasy Region, one of the top megadiversity regions, hosts one of the highest numbers of endemic and threatened organisms on earth. One of the most spectacular examples of ant radiation on the island has occurred in the hyperdiverse genus Pheidole. To this date, there are 135 described Madagascan Pheidole divided into 16 species-groups, and 97% of Malagasy species are endemic to the island. This study is a taxonomic revision of the Pheidole megacephala group, one of only two species-groups comprising a combination of native, endemic taxa and widely distributed introduced species. Methods The diversity of the Malagasy members of the megacephala group was assessed via application of qualitative morphological and DNA sequence data. Qualitative, external morphological characteristics (e.g., head shape, gaster sculpture, body colouration) were evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. Mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were analyzed to test the putative species previously delimited by morphological analyses. Results We recognize three species belonging to the megacephala group: P. megacephala (Fabricius, 1793), P. megatron Fischer & Fisher, 2013 and P. spinosa Forel, 1891 stat. nov. Pheidole spinosa is redescribed and elevated to the species level. The following names are recognized as junior synonyms of P. spinosa: P. megacephala scabrior Forel, 1891 syn. nov., P. picata Forel, 1891 syn. nov., P. picata gietleni Forel, 1905 syn. nov., P. picata bernhardae Emery, 1915 syn. nov., and P. decepticon Fischer & Fisher, 2013 syn. nov. The results are supplemented with an identification key to species for major workers of the megacephala group, high-resolution images for major and minor workers, and comments on the distribution and biology of all Malagasy members of the group. Our study revealed that Pheidole megacephala, a species listed among the 100 worst invasive species worldwide, occurs in both natural and disturbed sites in the Malagasy region. The two remaining members of the megacephala group, most likely endemic to this region, are also present in anthropogenic habitats and often co-occur with P. megacephala. It appears that the Malagasy members of the group are generalists and dominant in anthropogenic habitats. Additionally, we documented the presence of supermajors in colonies of P. spinosa—a phenomenon previously not known for this group.
Salata et al. (2022) Taxonomic revision of the Pheidole megacephala species-group (Hymenoptera, Formicidae) from the Malagasy Region. PeerJ 10:e13263 https://doi.org/10.7717/peerj.13263
Radar remote sensing-based inversion model of soil salt content at different depths under vegetation
Excessive soil salt content (SSC) seriously affects the crop growth and economic benefits in the agricultural production area. Prior research mainly focused on estimating the salinity in the top bare soil rather than in deep soil that is vital to crop growth. For this end, an experiment was carried out in the Hetao Irrigation District, Inner Mongolia, China. In the experiment, the SSC at different depths under vegetation was measured, and the Sentinel-1 radar images were obtained synchronously. The radar backscattering coefficients (VV and VH) were combined to construct multiple indices, whose sensitivity was then analyzed using the best subset selection (BSS). Meanwhile, four most commonly used algorithms, partial least squares regression (PLSR), quantile regression (QR), support vector machine (SVM), and extreme learning machine (ELM), were utilized to construct estimation models of salinity at the depths of 0–10, 10–20, 0–20, 20–40, 0–40, 40–60 and 0–60 cm before and after BSS, respectively. The results showed: (a) radar remote sensing can be used to estimate the salinity in the root zone of vegetation (0-30 cm); (b) after BSS, the correlation coefficients and estimation accuracy of the four monitoring models were all improved significantly; (c) the estimation accuracy of the four regression models was: SVM > QR > ELM > PLSR; and (d) among the seven sampling depths, 10–20 cm was the optimal inversion depth for all the four models, followed by 20–40 and 0–40 cm. Among the four models, SVM was higher in accuracy than the other three at 10–20 cm (RP2 = 0.67, RMSEP = 0.12%). These findings can provide valuable guidance for soil salinity monitoring and agricultural production in the arid or semi-arid areas under vegetation.
Spatial and Geographic Information Science
Chen et al. (2022) Radar remote sensing-based inversion model of soil salt content at different depths under vegetation. PeerJ 10:e13306 https://doi.org/10.7717/peerj.13306
Analysis of professional soccer players in competitive match play based on submaximum intensity periods
The main objective of this study is to analyse sub-maximum intensity periods (SubMIP’s) manifested by professional soccer players during official matches (number of events and time spent in each event), according to the player position, match halve and match, and also to group the players according to their SubMip values during the competition. Methods We collected a total of 247 individual records of 14 players using Global Positioning System (GPS) during 15 official league matches (Azerbaijan Premier League 2019–2020). We calculated both the number of SubMIPs events and the time each player spent in the SubMIPs zone (threshold of 85% MIP). We analysed the possible independence of the variables with the Kruskal–Wallis test and the possible specific relationships between the groups using a post-hoc analysis with Dunn’s test. In order to explore the possible distribution of physical demands in homogeneous groups, a cluster analysis was performed. Results The statistical analysis showed significant differences between the individual variables in the number of events and in the time spent by the player above the threshold in distance covered at speed >19.8 km/h (HSR), distance covered at speed >25.2 km/h (Sprint), acceleration density (AccDens), mean metabolic power (MetPow), metres per minute (Mmin) and high metabolic load distance >25.5 W/kg (HMLD). Differences were also found according to the playing position in MetPow, Mmin and between halves in AccDens, MetPow, Mmin. In the clustering based on the time spent by the player in SubMIPs, three main groups were described: (1) the centroid was located in lower values in each of the variables; (2) there were an accentuation of the AccDens variable; (3) all the variables, except AccDens, were accentuated. Conclusions The main differences with regard to SubMIPs were related to the player’s individual physical performance and not to position. However, the player’s position could act as an attractor and show significant differences during matches.
Caro et al. (2022) Analysis of professional soccer players in competitive match play based on submaximum intensity periods. PeerJ 10:e13309 https://doi.org/10.7717/peerj.13309
Integrated bioinformatics analysis for the identification of hub genes and signaling pathways related to circANRIL
Background Antisense noncoding RNA in the INK4 locus (ANRIL) is located on human chromosome 9p21, and modulation of ANRIL expression mediates susceptibility to some important human disease, including atherosclerosis (AS) and tumors, by affecting the cell cycle circANRIL and linear ANRIL are isoforms of ANRIL. However, it remains unclear whether these isoforms have distinct functions. In our research, we constructed a circANRIL overexpression plasmid, transfected it into HEK-293T cell line, and explored potential core genes and signaling pathways related to the important differential mechanisms between the circANRIL-overexpressing cell line and control cells through bioinformatics analysis. Methods Stable circANRIL-overexpressing (circANRIL-OE) HEK-293T cells and control cells were generated by infection with the circANRIL-OE lentiviral vector or a negative control vector, and successful transfection was confirmed by conventional flurescence microscopy and quantitative real-time PCR (qRT-PCR). Next, differentially expressed genes (DEGs) between circANRIL-OE cells and control cells were detected. Subsequently, Gene Ontology (GO) biological process (BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explore the principal functions of the significant DEGs. A protein–protein interaction (PPI) network and competing endogenous RNA (ceRNA) network were constructed in Cytoscape to determine circularRNA (circRNA)- microRNA(miRNA)-messenger RNA (mRNA) interactions and hub genes, and qRT-PCR was used to verify changes in the expression of these identified target genes. Results The successful construction of circANRIL-OE cells was confirmed by plasmid sequencing, visualization with fluorescence microscopy and qRT-PCR. A total of 1745 DEGs between the circANRIL-OE group and control were identified, GO BP analysis showed that these genes were mostly related to RNA biosynthesis and processing, regulation of transcription and signal transduction. The KEGG pathway analysis showed that the up regulated DEGs were mainly enriched in the MAPK signaling pathway. Five associated target genes were identified in the ceRNA network and biological function analyses. The mRNA levels of these five genes and ANRIL were detected by qRT-PCR, but only COL5A2 and WDR3 showed significantly different expression in circANRIL-OE cells.
Qin et al. (2022) Integrated bioinformatics analysis for the identification of hub genes and signaling pathways related to circANRIL. PeerJ 10:e13135 https://doi.org/10.7717/peerj.13135
Effect of steady-state aerobic exercise intensity and duration on the relationship between reserves of heart rate and oxygen uptake
Background The percentages of heart rate (%HRR) or oxygen uptake (%V̇O2R) reserve are used interchangeably for prescribing aerobic exercise intensity due to their assumed 1:1 relationship, although its validity is debated. This study aimed to assess if %HRR and %V̇O2R show a 1:1 relationship during steady-state exercise (SSE) and if exercise intensity and duration affect their relationship. Methods Eight physically active males (age 22.6 ± 1.2 years) were enrolled. Pre-exercise and maximal HR and V̇O2 were assessed on the first day. In the following 4 days, different SSEs were performed (running) combining the following randomly assigned durations and intensities: 15 min, 45 min, 60% HRR, 80% HRR. Post-exercise maximal HR and V̇O2 were assessed after each SSE. Using pre-exercise and post-exercise maximal values, the average HR and V̇O2 of the last 5 min of each SSE were converted into percentages of the reserves (%RES), which were computed in a 3-way RM-ANOVA (α = 0.05) to assess if they were affected by the prescription parameter (HRR or V̇O2R), exercise intensity (60% or 80% HRR), and duration (15 or 45 min). Results The %RES values were not affected by the prescription parameter (p = 0.056) or its interactions with intensity (p = 0.319) or duration and intensity (p = 0.117), while parameter and duration interaction was significant (p = 0.009). %HRRs and %V̇O2Rs did not differ in the 15-min SSEs (mean difference [MD] = 0.7 percentage points, p = 0.717), whereas %HRR was higher than %V̇O2R in the 45-min SSEs (MD = 6.7 percentage points, p = 0.009). Conclusion SSE duration affects the %HRR-%V̇O2R relationship, with %HRRs higher than %V̇O2Rs in SSEs of longer duration.
Ferri Marini et al. (2022) Effect of steady-state aerobic exercise intensity and duration on the relationship between reserves of heart rate and oxygen uptake. PeerJ 10:e13190 https://doi.org/10.7717/peerj.13190
Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods
The tremendous boost in next generation sequencing and in the “omics” technologies makes it possible to characterize the human gut microbiome—the collective genomes of the microbial community that reside in our gastrointestinal tract. Although some of these microorganisms are considered to be essential regulators of our immune system, the alteration of the complexity and eubiotic state of microbiota might promote autoimmune and inflammatory disorders such as diabetes, rheumatoid arthritis, Inflammatory bowel diseases (IBD), obesity, and carcinogenesis. IBD, comprising Crohn’s disease and ulcerative colitis, is a gut-related, multifactorial disease with an unknown etiology. IBD presents defects in the detection and control of the gut microbiota, associated with unbalanced immune reactions, genetic mutations that confer susceptibility to the disease, and complex environmental conditions such as westernized lifestyle. Although some existing studies attempt to unveil the composition and functional capacity of the gut microbiome in relation to IBD diseases, a comprehensive picture of the gut microbiome in IBD patients is far from being complete. Due to the complexity of metagenomic studies, the applications of the state-of-the-art machine learning techniques became popular to address a wide range of questions in the field of metagenomic data analysis. In this regard, using IBD associated metagenomics dataset, this study utilizes both supervised and unsupervised machine learning algorithms, (i) to generate a classification model that aids IBD diagnosis, (ii) to discover IBD-associated biomarkers, (iii) to discover subgroups of IBD patients using k-means and hierarchical clustering approaches. To deal with the high dimensionality of features, we applied robust feature selection algorithms such as Conditional Mutual Information Maximization (CMIM), Fast Correlation Based Filter (FCBF), min redundancy max relevance (mRMR), Select K Best (SKB), Information Gain (IG) and Extreme Gradient Boosting (XGBoost). In our experiments with 100-fold Monte Carlo cross-validation (MCCV), XGBoost, IG, and SKB methods showed a considerable effect in terms of minimizing the microbiota used for the diagnosis of IBD and thus reducing the cost and time. We observed that compared to Decision Tree, Support Vector Machine, Logitboost, Adaboost, and stacking ensemble classifiers, our Random Forest classifier resulted in better performance measures for the classification of IBD. Our findings revealed potential microbiome-mediated mechanisms of IBD and these findings might be useful for the development of microbiome-based diagnostics.
Bakir-Gungor et al. (2022) Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods. PeerJ 10:e13205 https://doi.org/10.7717/peerj.13205