Low Diversity Research Articles

Premature skewing of T cell receptor clonality and delayed memory expansion in HIV-exposed infants

While preventing vertical HIV transmission has been very successful, HIV-exposed uninfected infants (iHEU) experience an elevated risk to infections compared to HIV-unexposed and uninfected infants (iHUU). Here we present a longitudinal multimodal analysis of infant immune ontogeny that highlights the impact of HIV/ARV exposure. Using mass cytometry, we show alterations in T cell memory differentiation between iHEU and iHUU being significant from week 15 of life. The altered memory T cell differentiation in iHEU was preceded by lower TCR Vβ clonotypic diversity and linked to TCR clonal depletion within the naïve T cell compartment. Compared to iHUU, iHEU had elevated CD56loCD16loPerforin+CD38+CD45RA+FcεRIγ+ NK cells at 1 month postpartum and whose abundance pre-vaccination were predictive of vaccine-induced pertussis and rotavirus antibody responses post 3 months of life. Collectively, HIV/ARV exposure disrupted the trajectory of innate and adaptive immunity from birth which may underlie relative vulnerability to infections in iHEU.

A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts

The gut microbiome plays a crucial role in the health and well-being of animals. It is especially critical for ruminants that depend on this bacterial community for digesting their food. In this study, we investigated the effects of management conditions and supplemental feeding on the gut bacterial microbiota of red deer (Cervus elaphus) in the Bavarian Forest National Park, Germany. Fecal samples were collected from free-ranging deer, deer within winter enclosures, and deer in permanent enclosures. The samples were analyzed by high-throughput sequencing of the 16 S rRNA gene. The results showed that the gut bacterial microbiota differed in diversity, abundance, and heterogeneity within and between the various management groups. Free-ranging deer exhibited lower alpha diversity compared with deer in enclosures, probably because of the food supplementation available to the animals within the enclosures. Free-living individuals also showed the highest beta diversity, indicating greater variability in foraging grounds and plant species selection. Moreover, free-ranging deer had the lowest abundance of potentially pathogenic bacterial taxa, suggesting a healthier gut microbiome. Winter-gated deer, which spent some time in enclosures, exhibited intermediate characteristics between free-ranging and all-year-gated deer. These findings suggest that the winter enclosure management strategy, including supplementary feeding with processed plants and crops, has a significant impact on the gut microbiome composition of red deer. Overall, this study provides important insights into the effects of management conditions, particularly winter enclosure practices, on the gut microbiome of red deer. Understanding these effects is crucial for assessing the potential health implications of management strategies and highlights the value of microbiota investigations as health marker.

Intra- and interspecies variation and population dynamics of Fasciola gigantica among ruminants in Sudan.

Fasciola gigantica is a widespread parasite that causes neglected disease in livestock worldwide. Its high transmissibility and dispersion are attributed to its ability to infect intermediate snail hosts and adapt to various mammalian definitive hosts. This study investigated the variation and population dynamics of F. gigantica in cattle, sheep, and goats from three states in Sudan. Mitochondrial cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 1 (ND1) genes were sequenced successfully to examine intra and interspecific differences. ND1 exhibited higher diversity than COI, with 15 haplotypes and 10 haplotypes, respectively. Both genes had high haplotype diversity but low nucleotide diversity, with 21 and 11 polymorphic sites for ND1 and COI, respectively. Mismatch distribution analysis and neutrality tests revealed that F. gigantica from different host species was in a state of population expansion. Maximum likelihood phylogenetic trees and median networks revealed that F. gigantica in Sudan and other African countries had host-specific and country-specific lineages for both genes. The study also indicated that F. gigantica-infected small ruminants were evolutionarily distant, suggesting deep and historical interspecies adaptation.

Evolutionary relationship of moso bamboo forms and a multihormone regulatory cascade involving culm shape variation.

Moso bamboo (Phyllostachys edulis) known as Mao Zhu (MZ) in Chinese exhibits various forms with distinct morphological characteristics. However, the evolutionary relationship among MZ forms and the mechanisms of culm shape variation are still lacking. Here, the main differences among MZ forms were identified as culm shape variation, which were confirmed by analysing MZ forms (799 bamboo culms) and MZ (458 bamboo culms) populations. To unravel the genetic basis underlying the morphological variations, 20 MZ forms were subjected to whole-genome resequencing. Further analysis yielded 3 230 107 high-quality SNPs and uncovered low genetic diversity and high genotype heterozygosity associated with MZ forms' formation. By integrating the SNP data of 427 MZ individuals representing 15 geographic regions, the origins of eight MZ forms were successfully traced using the phylogenetic tree and the identified common heterozygous loci. Meanwhile, transcriptomic analysis was performed using shoots from MZ and its two forms with culm shape variation. The results, combined with genomic analyses, demonstrated that hormone signalling related genes played crucial roles in culm variation. Co-expression network analysis uncovered genes associated with multiple plant hormone signal transduction, especially auxin and cytokinin were involved in culm shape variation. Furthermore, the regulatory relationships of a specific transcription factor and their target genes associated with auxin and ethylene signalling were validated by yeast one-hybrid, electrophoretic mobility shift assays, and dual-luciferase reporter. Overall, this study provides important insights into the culm shape variation formation in bamboo, which facilitates to breed new varieties with novel culms.

Benthic macroinvertebrate response to estuarine emergent marsh restoration across a delta-wide environmental gradient

Benthic invertebrates play vital roles in estuarine ecosystems, but like other taxa they have been excluded from former marshlands by diking and land use conversion. Dike removal is one way of restoring marsh, but the response of benthic invertebrates has been little studied. Also understudied is variation in benthic invertebrate communities across entire deltas, particularly in the Pacific Northwest of North America where deltas receive high flows and sediment loads for their size. Our goals were to evaluate invertebrate response to large-scale dike removal on the Nisqually River Delta in Puget Sound, Washington, U.S.A., characterize delta-wide invertebrate community variation, and relate invertebrate response and spatial variation to environmental conditions. We sampled invertebrates annually from one year before to three years after dike removal in restoring marsh, previously restored marsh, undisturbed reference marsh, and adjacent tidal flats. Marine taxa immediately colonized the area recently restored to tidal inundation and population size grew exponentially thereafter for several of them. Community composition and diversity recovered completely, and density and biomass were approaching recovery three years later. Invertebrate communities converged between restoring and pre-existing marsh (previously restored and reference), suggesting an influence of reestablished connectivity. Just offshore from the dike line, invertebrates declined one year after dike removal but then rebounded indicating resilience to short-term disturbance. Dike removal effects were not detected farther offshore. Near the offshore edge of the delta, invertebrate biomass and body size were greater than elsewhere and a diverse assemblage of crustaceans, polychaetes, and bivalves was present. Farther inshore, tidal flats were dominated by a few species of small-bodied polychaetes and had higher density but lower biomass and diversity. Facultative detritivores, which can also filter feed, were the dominant feeding guild everywhere on the tidal flats. Density, biomass, diversity, and community composition on the marsh were more similar to the inner than outer tidal flats. Environmental variables most associated with invertebrate community variation were elevation, salinity, and sediment grain size and organic content. Our results are relevant to assessing performance and setting expectations for future restorations and have broad implications for the role of benthic invertebrates in estuarine ecosystems.

Feeding practices and dietary intake in Brazilian children with Down syndrome: A cross-sectional study.

Studies investigating the quality of the diet and dietary intake of children with Down syndrome (DS) are required because the features attributed to the syndrome can affect growth, development and quality of life. This cross-sectional study was conducted with 77 Brazilian children with DS between 5 and 36months of age receiving care at the multidisciplinary outpatient clinic of the University Hospital. Participants' sociodemographic, dietary and anthropometric data were collected from the care protocols. Dietary data were collected from 24-h recalls and dietary practices were assessed according to the WHO dietary guidelines. Associations between inadequate feeding practices and demographic variables were assessed using logistic regression models. Fruits, milk or infant formula, vegetables, beans and meat were among the five most consumed foods by the children investigated. Overall, we observed a high number of cases of early weaning (50.6%), low minimum dietary diversity (MDD; 40.3%), inadequate consistency for age (64.9%), early presence of ultra-processed foods (76.6%), sugars and sweets (33.8%) in the diet of the children with DS. In the associations of inadequate feeding practices by age group, low MDD [odds ratio (OR): 18.6; 95% confidence interval (CI): 3.4; 57.1] and inadequate consistency (OR: 6.65; 95% CI: 1.8; 24.7) were more frequent among children aged below 12months while this relationship was inverse for early introduction of sugar and sweets (OR: 0.04; 95% CI: 0.01; 0.29). Our findings showed a high number of cases of inadequate dietary practices in children with DS investigated, which could adversely affect the long-term health of this population.

Microbial community structure of plant-based meat alternatives

A reduction in animal-based diets has driven market demand for alternative meat products, currently raising a new generation of plant-based meat alternatives (PBMAs). It remains unclear whether these substitutes are a short-lived trend or become established in the long term. Over the last few years, the trend of increasing sales and diversifying product range has continued, but publication activities in this field are currently limited mainly to market research and food technology topics. As their popularity increases, questions emerge about the safety and nutritional risks of these novel products. Even though all the examined products must be heated before consumption, consumers lack experience with this type of product and thus further research into product safety, is desirable. To consider these issues, we examined 32 PBMAs from Austrian supermarkets. Based on 16S rRNA gene amplicon sequencing, the majority of the products were dominated by lactic acid bacteria (either Leuconostoc or Latilactobacillus), and generally had low alpha diversity. Pseudomonadota (like Pseudomonas and Shewanella) dominated the other part of the products. In addition to LABs, a high diversity of different Bacillus, but also some Enterobacteriaceae and potentially pathogenic species were isolated with the culturing approach. We assume that especially the dominance of heterofermentative LABs has high relevance for the product stability and quality with the potential to increase shelf life of the products. The number of isolated Enterobacteriaceae and potential pathogens were low, but they still demonstrated that these products are suitable for their presence.

Multi-Strategy Improved Dung Beetle Optimization Algorithm and Its Applications

The dung beetle optimization (DBO) algorithm, a swarm intelligence-based metaheuristic, is renowned for its robust optimization capability and fast convergence speed. However, it also suffers from low population diversity, susceptibility to local optima solutions, and unsatisfactory convergence speed when facing complex optimization problems. In response, this paper proposes the multi-strategy improved dung beetle optimization algorithm (MDBO). The core improvements include using Latin hypercube sampling for better population initialization and the introduction of a novel differential variation strategy, termed “Mean Differential Variation”, to enhance the algorithm’s ability to evade local optima. Moreover, a strategy combining lens imaging reverse learning and dimension-by-dimension optimization was proposed and applied to the current optimal solution. Through comprehensive performance testing on standard benchmark functions from CEC2017 and CEC2020, MDBO demonstrates superior performance in terms of optimization accuracy, stability, and convergence speed compared with other classical metaheuristic optimization algorithms. Additionally, the efficacy of MDBO in addressing complex real-world engineering problems is validated through three representative engineering application scenarios namely extension/compression spring design problems, reducer design problems, and welded beam design problems.

Molecular-level carbon traits underlie the multidimensional fine root economics space.

Carbon influences the evolution and functioning of plants and their roots. Previous work examining a small number of commonly measured root traits has revealed a global multidimensionality of the resource economics traits in fine roots considering carbon as primary currency but without considering the diversity of carbon-related traits. To address this knowledge gap, we use data from 66 tree species from a tropical forest to illustrate that root economics space co-varies with a novel molecular-level traits space based on nuclear magnetic resonance. Thinner fine roots exhibit higher proportions of carbohydrates and lower diversity of molecular carbon than thicker roots. Mass-denser fine roots have more lignin and aromatic carbon compounds but less bioactive carbon compounds than lighter roots. Thus, the transition from thin to thick fine roots implies a shift in the root carbon economy from 'do-it-yourself' soil exploration to collaboration with mycorrhizal fungi, while the shift from light to dense fine roots emphasizes a shift from acquisitive to conservative root strategy. We reveal a previously undocumented role of molecular-level carbon traits that potentially undergird the multidimensional root economics space. This finding offers new molecular insight into the diversity of root form and function, which is fundamental to our understanding of plant evolution, species coexistence and adaptations to heterogeneous environments.

Exploring the Association between Anxiety, Depression, and Gut Microbiota during Pregnancy: Findings from a Pregnancy Cohort Study in Shijiazhuang, Hebei Province, China

Negative emotions and gut microbiota during pregnancy both bear significant public health implications. However, the relationship between them has not been fully elucidated. This study, utilizing data from a pregnancy cohort, employed metagenomic sequencing to elucidate the relationship between anxiety, depression, and gut microbiota’s diversity, composition, species, and functional pathways. Data from 87 subjects, spanning 225 time points across early, mid, and late pregnancy, were analyzed. The results revealed that higher anxiety and depression scores significantly corresponded to lower alpha diversity (including the Shannon entropy and the Simpson index). Anxiety and depression scores, along with categorical distinctions of anxiety/non-anxiety and depression/non-depression, were found to account for 0.723%, 0.731%, 0.651%, and 0.810% of the variance in gut-microbiota composition (p = 0.001), respectively. Increased anxiety was significantly positively associated with the abundance of Oscillibacter sp. KLE 1745, Oscillibacter sp. PEA192, Oscillibacter sp. KLE 1728, Oscillospiraceae bacterium VE202 24, and Treponema socranskii. A similar association was significantly noted for Oscillibacter sp. KLE 1745 with elevated depression scores. While EC.3.5.3.1: arginase appeared to be lower in the anxious group than in the non-anxious group, vitamin B12-related enzymes appeared to be lower in the depression group than in the non-depression group. The changes were found to be not statistically significant after post-multiple comparison adjustment.

Seasonal covariations of diet-gut microbiota in the adaptation of the newly reintroduced Père David's deer (Elaphurus davidianus) to the northern habitat

Milu (Père David's deer, Elaphurus davidianus), once extinct in the wild, was one of the few indigenous large herbivores of the wetland ecosystem in China. The reintroduction of milu in northern China has just started and is expected to restore not only that species, but also the ecosystem. To acquire insights into the adaptive process of the milu population first rewilded in the northern habitat and provide knowledge for the on-going and future reintroduction attempts, we used DNA metabarcoding to analyze the diets and gut microbiota of those milu in the first year after releasing. The results showed strong seasonality in both diet and gut microbiota. Significant higher dietary diversity was detected in in autumn than summer and winter. Woody dietary components increased continuously from summer to winter. A significant correspondence was found between the dietary and microbial diversities. Enrichment of metabolic pathways involved in lipid and amino acid metabolism was identified in summer, and of those involved in carbohydrate and glycan metabolism was identified in winter. Pathways related to metabolism of certain amino acid were differently abundant in the breeding season. The study indicated the contribution of foraging and gut microbial seasonality to the overwintering, reproduction and environmental adaption of the reintroduced milu. The enrichment of opportunistic pathogen Treponema and lower microbial diversity indicated higher health risk in winter, and thus disease prevention measures were suggested. Pre- and post-release food evaluation and monitoring was recommended to ensure food sufficiency in the reintroductions.

Distribution and genetic diversity of cobitid species in Iran (Teleostei: Cobitidae)

Several species of Cobitis have been reported within Iran, but only four are recognized as valid. The geographical distribution and genetic diversity of these species are not well-known. Two new populations of C. saniae and C. avicennae were reported herein based on their morphological and phylogenetic characters from the Mahabad River, a tributary of the Urmia Lake basin, and the Razavar River, a tributary of the Karkheh drainage, respectively. The genetic diversity and genetic structure of populations of C. saniae, C. avicennae, and C. faridpaki were analysed using the DNA sequences of the mitochondrial COI gene. COI sequences from various watersheds in Iran, Azerbaijan, and Georgia were used. A moderate to high level haplotype diversity and low nucleotide diversity were found in most of the populations of all three species. The AMOVA test and pairwise FST comparison revealed significant genetic structure and genetic distance between the Urmia Lake basin and other C. saniae populations. The results highlight the importance of conserving these species and their habitats, particularly in the Urmia Lake basin, where significant genetic differentiation was observed.

Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring

BackgroundGenome-wide comparisons of populations are widely used to explore the patterns of nucleotide diversity and sequence divergence to provide knowledge on how natural selection and genetic drift affect the genome. In this study we have compared whole-genome sequencing data from Atlantic and Pacific herring, two sister species that diverged about 2 million years ago, to explore the pattern of genetic differentiation between the two species.ResultsThe genome comparison of the two species revealed high genome-wide differentiation but with islands of remarkably low genetic differentiation, as measured by an FST analysis. However, the low FST observed in these islands is not caused by low interspecies sequence divergence (dxy) but rather by exceptionally high estimated intraspecies nucleotide diversity (π). These regions of low differentiation and elevated nucleotide diversity, termed high-diversity regions in this study, are not enriched for repeats but are highly enriched for immune-related genes. This enrichment includes genes from both the adaptive immune system, such as immunoglobulin, T-cell receptor and major histocompatibility complex genes, as well as a substantial number of genes with a role in the innate immune system, e.g. novel immune-type receptor, tripartite motif and tumor necrosis factor receptor genes. Analysis of long-read based assemblies from two Atlantic herring individuals revealed extensive copy number variation in these genomic regions, indicating that the elevated intraspecies nucleotide diversities were partially due to the cross-mapping of short reads.ConclusionsThis study demonstrates that copy number variation is a characteristic feature of immune trait loci in herring. Another important implication is that these loci are blind spots in classical genome-wide screens for genetic differentiation using short-read data, not only in herring, likely also in other species harboring qualitatively similar variation at immune trait loci. These loci stood out in this study because of the relatively high genome-wide baseline for FST values between Atlantic and Pacific herring.

The impact of herbicide-resistant canola systems on the weed community dynamics in the Canadian Prairies

Increased adoption of no-till and extensive cultivation of herbicide-resistant (HR) crops in low diversity rotations are some of the transformations that occurred during the 1970s-2000s in western Canada. How these transformations in canola-based crop rotations impacted weed communities are not comprehensively studied. Historical data analysis of weed survey data ( Saskatchewan, Manitoba and Alberta) in canola crops and a canola rotation field experiment were used to understand how tillage, herbicide-resistant cropping systems, and frequency of canola in the rotation can impact weed abundance, composition, and diversity in the Canadian prairies. Weed survey data revealed that the frequency of many weed species declined in years after 1995 compared with before 1995, the year HR cultivars were introduced. Gallium spurium (false cleavers) and volunteer wheat (Triticum aestivum L.) were the only species showing a continuous increase in frequency throughout the surveyed years. Species richness showed no trajectories but varied depending on climatic conditions. Glyphosate-resistant (G.R.) systems were associated with green foxtail irrespective of their frequency in the rotation. Wild oat was predominant in the longer rotations with glufosinate and imidazolinone-resistant canola. In the field study, weeds associated with pre-herbicide weed control timing were relatively controlled when herbicides were applied (glyphosate and glufosinate), except for foxtail barley (Hordium Jubatum L), which was not controlled in most HR systems. Overall, both weed survey data and field experiment data revealed greater control of most weed species due to growing of HR canola cultivars.

The diversity of the microbiome impacts chronic lymphocytic leukemia development in mice and humans.

The gut microbiota play a critical role in maintaining a healthy human body and their dysregulation is associated with various diseases. In this study, we investigated the influence of the gut microbiome diversity on chronic lymphocytic leukemia (CLL) development. Stool sample analysis of 59 CLL patients revealed individual and heterogeneous microbiome compositions, but allowed for grouping of patients according to their microbiome diversity. Interestingly, CLL patients with a lower microbiome diversity and an enrichment of bacteria linked to poor health suffered from a more advanced or aggressive form of CLL. In the Eμ-TCL1 mouse model of CLL, we observed a faster course of disease when mice were housed in high hygiene conditions. Shotgun DNA sequencing of fecal samples showed that this was associated with a lower microbiome diversity which was dominated by Mucispirillum and Parabacteroides genera in comparison to mice kept under lower hygiene conditions. In conclusion, we applied taxonomic microbiome analyses to demonstrate a link between the gut microbiome diversity and the clinical course of CLL in humans, as well as the development of CLL in mice. Our novel data serve as a basis for further investigations to decipher the pathological and mechanistic role of intestinal microbiota in CLL development.

Swarm and UNOISE outperform DADA2 and Deblur for denoising high-diversity marine seafloor samples

Abstract The performance of sequence variant resolution analytic tools for metabarcoding has not yet been adequately benchmarked for high-diversity environmental samples. We therefore evaluated the sequence variant tools DADA2, Deblur, Swarm and UNOISE, using high-diversity seafloor samples, resulting in comparisons of 1800 sequence variant tables. The evaluation was based on 30 sediment grab samples, for which three replica samples were collected. Each replica sample was extracted using five common DNA extraction kits, resulting in 450 DNA extracts which were 16S rRNA gene sequenced (V3-V4), using Illumina. Assessments included variation across replica samples, extraction kits and denoising methods, in addition to applying prior knowledge about alpha diversity correlations towards the cosmopolitan marine archaeon Nitrosopumilus with high diversity, and the sulfide oxidizing Sulfurovum with low diversity. DADA2 displayed the highest variance between replicates (Manhattan distance 1.14), while Swarm showed the lowest variance (Manhattan distance 0.93). For the analysis based on prior biological knowledge, UNOISE displayed the highest alpha diversity (Simpson’s D) correlation towards Nitrosopumilus (Spearman rho = 0.85), while DADA2 showed the lowest (Spearman rho = 0.10). Deblur completely eliminated Nitrosopumilus from the dataset. For Sulfurovum, on the other hand, all the methods showed comparable results. In conclusion, our evaluations show that Swarm and UNOISE performed better than DADA2 and Deblur for high-diversity seafloor samples.

Correlation of Oral Microbiota With Different Immune Responses to Antiretroviral Therapy in People Living With HIV

Abstract Both HIV infection and antiretroviral therapy (ART) affect the oral microbiome. Whether successful treatment with ART in people living with HIV (PLWH), which leads to a significant decline in viral loads and immune reconstitution, is associated with changes in or recovery of the oral microbiome remains unknown. Therefore, we performed a cross-sectional study of 118 PLWH receiving regular ART and 40 healthy controls (HCs). Among the 118 PLWH, 18 immunological non-responders (INRs; <200 CD4+ T cells/μL) and 30 immunological responders (IRs; ≥500 CD4+ T cells/μL) were identified. The oral microbiota composition of all participants was analyzed using 16S rRNA gene sequencing of throat swab samples. Relative abundance of bacterial genera was compared between IRs and INRs, and Pearson correlations between bacterial abundance and peripheral blood immune cell counts were evaluated. The INR group showed lower alpha diversity than the IR and HC groups, which displayed similar alpha diversity. The genera Alloprevotella, Prevotella and Neisseria were more abundant in PLWH than in HC, whereas the genera Rothia, Streptococcus and Fusobacterium were more abundant in HC than in PLWH. The genus Rothia was more abundant in the INR group, whereas Prevotella, Alloprevotella, Porphyromonas and Haemophilus were more abundant in the IR group. The genera Rothia and Alloprevotella were negatively and positively associated with CD4+ T cell counts, respectively. Thus, an increased abundance of Rothia in the oral microbiome is associated with unfavorable outcomes regarding immune reconstitution in PLWH receiving regular ART, whereas Prevotella, Alloprevotella, Porphyromonas and Haemophilus are associated with favorable outcomes.

Slime Mould Algorithm Based on a Gaussian Mutation for Solving Constrained Optimization Problems

The slime mould algorithm may not be enough and tends to trap into local optima, low population diversity, and suffers insufficient exploitation when real-world optimization problems become more complex. To overcome the limitations of SMA, the Gaussian mutation (GM) with a novel strategy is proposed to enhance SMA and it is named as SMA-GM. The GM is used to increase population diversity, which helps SMA come out of local optima and retain a robust local search capability. Additionally, the oscillatory parameter is updated and incorporated with GM to set the balance between exploration and exploitation. By using a greedy selection technique, this study retains an optimal slime mould position while ensuring the algorithm’s rapid convergence. The SMA-GM performance was evaluated by using unconstrained, constrained, and CEC2022 benchmark functions. The results show that the proposed SMA-GM has a more robust capacity for global search, improved stability, a faster rate of convergence, and the ability to solve constrained optimization problems. Additionally, the Wilcoxon rank sum test illustrates that there is a significant difference between the optimization outcomes of SMA-GM and each compared algorithm. Furthermore, the engineering problem such as industrial refrigeration system (IRS), optimal operation of the alkylation unit problem, welded beam and tension/compression spring design problem are solved, and results prove that the proposed algorithm has a better optimization efficiency to reach the optimum value.

HPV16 Genomes: In Silico Analysis of E6 and E7 Oncoproteins in 20 South American Variants

Background: Human papillomavirus (HPV) is the main risk factor for the development of squamous cell cervical cancer, and E6 oncoprotein and E7 oncoprotein are important components of the viral genome and its oncogenic potential. It is known that different viral variants of HPV16 have different pathology and impact on the development of neoplasia, although few studies have been performed on South American variants. Objective: Therefore, the present study aimed to analyze in silico the genomic diversity of HPV16 in 20 complete genome variants of South America in the National Center for Biotechnology Information (NCBI) database. Methods: We performed a descriptive study to characterize the polymorphic regions of the E6 and E7 genes in HPV16 variants, using software for genomic data and single nucleotide polymorphism (SNP) analysis and others for phylogenetic analysis. Results: The variants analyzed included six SNPs linked to cancer (A131G, G145T, C335T, T350G, C712A, and T732C) and significant variation (798 nucleotide substitutions). Despite this, the variants showed low genetic diversity. Eighteen variants of unclear significance (VUS) were identified, 10 of which were in the coding E6 regions and 8 in the coding E7 regions. The prevalence of lineage D variants is of concern due to their pathology in cervical cancer and requires more research and epidemiological vigilance regarding their prevalence in the population. Conclusion: study may contribute to future research on South American variants of HPV16, their pathogenicity, and the development of treatments.

Phyllosphere fungal diversity generates pervasive nonadditive effects on plant performance.

Plants naturally harbor diverse microbiomes that can dramatically impact their health and productivity. However, it remains unclear how fungal microbiome diversity, especially in the phyllosphere, impacts intermicrobial interactions and consequent nonadditive effects on plant productivity. Combining manipulative experiments, field collections, culturing, microbiome sequencing, and synthetic consortia, we experimentally tested for the first time how foliar fungal community diversity impacts plant productivity. We inoculated morning glories (Ipomoea hederifolia L.) with 32 phyllosphere consortia of either low or high diversity or with single fungal taxa, and measured effects on plant productivity and allocation. We found the following: (1) nonadditive effects were pervasive with 56% of fungal consortia interacting synergistically or antagonistically to impact plant productivity, including some consortia capable of generating acute synergism (e.g. > 1000% increase in productivity above the additive expectation), (2) interactions among 'commensal' fungi were responsible for this nonadditivity in diverse consortia, (3) synergistic interactions were approximately four times stronger than antagonistic effects, (4) fungal diversity affected the magnitude but not frequency or direction of nonadditivity, and (5) diversity affected plant performance nonlinearly with the highest performance in low-diversity treatments. These findings highlight the importance of interpreting plant-microbiome interactions under a framework that incorporates intermicrobial interactions and nonadditive outcomes to understand natural complexity.