Regions Of High Variability Research Articles

Comprehensive Analysis of the Immune Response to SARS-CoV-2 Epitopes: Unveiling Potential Targets for Vaccine Development.

SARS-CoV-2 continues to be a major global health threat. In this study, we performed a comprehensive meta-analysis on the epitopes of SARS-CoV-2, revealing its immunological landscape. Furthermore, using Shannon entropy for sequence conservation analysis and structural network-based methods identified candidate epitopes that are highly conserved and evolutionarily constrained in SARS-CoV-2 and other zoonotic coronaviruses. Finally, the population coverage of T cell epitopes was analyzed. The results highlighted regions within each SARS-CoV-2 protein where the immunological activity of antibodies, CD4+, and CD8+ T cell responses was predominantly concentrated. Sequence-based correlation analysis found that epitopes recognized by B cells and CD4+ T cells showed a positive correlation with high viral variability, and these high variability regions were typically linked to robust immune responses. Conversely, epitopes recognized by CD8+ T cells exhibited a negative correlation with high variability. From a structural network degree perspective, no clear correlation was identified between B cell antibody epitopes and CD4+ T cell reactivity with the degree of residue network connectivity. However, a significant positive correlation was observed between CD8+ T cell reactivity and the degree of residue network connectivity. By integrating sequence Shannon entropy and structural network correlation analysis, we pinpointed highly conserved and evolutionarily constrained SARS-CoV-2 candidate epitopes. Furthermore, we utilized immunoinformatics to assess the conservation of SARS-CoV-2 within coronaviruses and the population coverage of these epitopes. Our analysis uncovered key immune responses linked to preventing viral infection and viral clearance, emphasized areas of interest for broad-spectrum SARS-CoV-2 vaccine development, and offered insights for future research and clinical applications.

Application of a localized morphometrics approach to imaging-derived brain phenotypes for genotype-phenotype associations in pediatric mental health and neurodevelopmental disorders.

Quantitative global or regional brain imaging measurements, known as imaging-specific or -derived phenotypes (IDPs), are commonly used in genotype-phenotype association studies to explore the genomic architecture of the brain and how it may be affected by neurological diseases (e.g., Alzheimer's disease), mental health (e.g., depression), and neurodevelopmental disorders (e.g., attention-deficit hyperactivity disorder [ADHD]). For this purpose, medical images have been used as IDPs using a voxel-wise or global approach via principal component analysis. However, these methods have limitations related to multiple testing or the inability to isolate high variation regions, respectively. To address these limitations, this study investigates a localized, principal component analysis-like approach for dimensionality reduction of cross-sectional T1-weighted MRI datasets utilizing diffeomorphic morphometry. This approach can reduce the dimensionality of images while preserving spatial information and enables the inclusion of spatial locality in the analysis. In doing so, this method can be used to explore morphometric brain changes across specific components and spatial scales of interest and to identify associations with genome regions in a multivariate genome-wide association study. For a first clinical feasibility study, this method was applied to data from the Adolescent Brain Cognitive Development (ABCD) study, including adolescents with ADHD (n = 1,359), obsessive-compulsive disorder (n = 1,752), and depression (n = 1,766). Meaningful associations of specific morphometric features with genome regions were identified with the data and corresponded to previous found brain regions in the respective mental health and neurodevelopmental disorder cohorts. In summary, the localized, principal component analysis-like approach can reduce the dimensionality of medical images while still being able to identify meaningful local brain region alterations that are associated with genomic markers across multiple scales. The proposed method can be applied to various image types and can be easily integrated in many genotype-phenotype association study setups.

Sequence analysis of the GP5 protein of porcine reproductive and respiratory syndrome virus in Vietnam from 2007 to 2023.

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent 13 of porcine reproductive and respiratory syndrome (PRRS), which is one of the most economically 14 devastating viruses in the Vietnamese swine industry. With a view toward determining the 15 genetic variation among PRRSV strains in Vietnam, we examined 271 PRRSV GP5 protein 16 sequences obtained from strains isolated in Vietnam from 2007 to 2023, for which we constructed 17 phylogenetic trees. Additionally, a collection of 52 PRRSV-1 strains and 80 PRRSV-2 strains 18 isolated in different years were specifically selected for nucleotide and amino acid homology analysis 19 and amino acid sequence alignment. The results revealed 76.1%-100.0% nucleotide and 20 75.2%-100.0% amino acid homologies for the PRRSV-1 GP5 gene, and 81.8%-100.0% nucleotide 21 and 81.1%-100.0% amino acid homologies for the PRRSV-2 GP5 gene. Amino acid mutation sites 22 in PRRSV-2 were found to be primarily distributed in the signal peptide region, antigenic sites, two 23 T-cell antigen regions, two highly variable regions (HVRs), and in the vicinity of the neutralizing 24 epitope, with a deletion mutation occurring in the neutralizing epitope, whereas amino acid mutations 25 in the PRRSV-1 sequences were found to occur predominantly in two T-cell epitopes. Genetic 26 analysis revealed that PRRSV-1 strains in Vietnam are of subtype 1 (Global), whereas PRRSV-2 27 strains are categorized into sublineages L1A, L5A, and L8E, with L8E being the predominantly 28 prevalent strain at present. Recombination analyses indicated that no significant recombination 29 events have occurred in any of the assessed 271 Vietnamese PRRSV strains. Our 30 analyses of 271 Vietnamese PRRSV strains have yielded valuable insights regarding the 31 epidemiological trends and genetic dynamics of PRRSV in Vietnam, and will provide a theoretical 32 basis for formulating prevention and control measures for PRRS and the development of PRRS 33 vaccines.

BO-GRNN: Machine Learning for Underwater Acoustic Source Localization

This article proposes a Bayesian optimization-based generalized regression neural network (BO-GRNN) framework for underwater source localization in shallow water environment. Specially, by leveraging kernel regression analysis, BO-GRNN fits a conditional probability density function using training and test samples to infer the source location of unseen test samples. Furthermore, BO-GRNN models the objective function as a Gaussian process (GP) based on observed samples, utilizing an acquisition function to sample around the best objective function values and high variance regions. By evaluating these samples and updating the GP iteratively, the optimal hyperparameters are identified, ultimately improving the training efficiency and localization performance of the GRNN. Simulation experiments and error analysis validate this framework’s effectiveness. Further validation using SWellEx-96 experimental data demonstrates the superior localization performance of this framework, even with limited data snapshots. This framework estimates the range and depth of underwater sources within a 10 km range, achieving mean absolute errors of less than 0.15 km for range and 0.2 m for depth. Compared to GRNN, this framework demonstrates a 5 times improvement in training efficiency. These advantages make BO-GRNN an efficient, accurate, and robust solution for underwater source localization.

An improved method for upscaling 2D images using adaptive edge sharpening and an optimized directional anisotropic diffusion filter

Image upscaling employs various polynomial techniques, including bicubic and Lanczos, to minimize computing load for various real-time applications. Polynomial interpolation, on the other hand, results in blurring artifacts in high resolution (HR) images due to edge degradation. Many other interpolation approaches, including edge-based and dictionary learning-based schemes, result in blurring in the image’s high frequency (HF) region. As a result, a novel post-processing technique is proposed that uses the Lanczos method to upscale the low resolution (LR) image. To eliminate blur along the image’s edge, the edge component of the interpolated image is retrieved. Adaptive sharpening is used to make the edges more prominent, as predicting pixels in the high variance region is challenging. After the edge is extracted, the smooth region is filtered with an optimized directional anisotropic diffusion (ODAD) filter to preserve texture details and geometric regularity. The sharpened edge image is aggregated with the ODAD filtered image to generate an improved HR (IHR) image. The IHR is then scaled up and down to reduce blurring even further, resulting in a blurred HR image (BHR). The residual image is obtained by subtracting the BHR from the IHR images, which represent the undetected HF. Finally, the residual image and the IHR image are combined to generate the final restored image, which includes all prediction loss details. The results of the experiments show that the proposed algorithm outperforms existing methodologies, particularly in terms of visuality and parameter-wise measurement.

A qPCR Assay for the Quantification of Selected Genotypic Variants of Spodoptera frugiperda Multiple Nucleopolyhedrovirus (Baculoviridae).

Alphabaculoviruses are lethal dsDNA viruses of Lepidoptera that have high genetic diversity and are transmitted in aggregates within proteinaceous occlusion bodies. This mode of transmission has implications for their efficacy as biological insecticides. A Nicaraguan isolate of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV-NIC) comprising nine genotypic variants has been the subject of considerable study due to the influence of variant interactions on the insecticidal properties of mixed-variant occlusion bodies. As part of a systematic study on the replication and transmission of variant mixtures, a tool for the accurate quantification of a selection of genotypic variants was developed based on the quantitative PCR technique (qPCR). First, primer pairs were designed around a region of high variability in four variants named SfNic-A, SfNic-B, SfNic-C and SfNic-E to produce amplicons of 103-150 bp. Then, using cloned purified amplicons as standards, amplification was demonstrated over a dynamic range of 108-101 copies of each target. The assay was efficient (mean ± SD: 98.5 ± 0.8%), reproducible, as shown by low inter- and intra-assay coefficients of variation (<5%), and specific to the target variants (99.7-100% specificity across variants). The quantification method was validated on mixtures of genotype-specific amplicons and demonstrated accurate quantification. Finally, mixtures of the four variants were quantified based on mixtures of budded virions and mixtures of DNA extracted from occlusion-derived virions. In both cases, mixed-variant preparations compared favorably to total viral genome numbers by quantification of the polyhedrin (polh) gene that is present in all variants. This technique should prove invaluable in elucidating the influence of variant diversity on the transmission and insecticidal characteristics of this pathogen.

Comparative chloroplast genomes: insights into the identification and phylogeny of rapid radiation genus Rhodiola.

Rhodiola L. is a genus exhibiting rapid radiation and represents a typical case for studying plastid gene adaptation in species that spread from high altitudes to low altitudes. In this study, 23 samples of 18 Rhodiola species were collected from the Qinghai-Tibetan Plateau and five scattered alpine areas, and the plastid genomes (plastomes) of these species were sequenced, annotated, and compared between high-altitude and widely distributed groups. The plastomes of Rhodiola were found to be highly conserved in terms of gene size, content, and order but highly variable in several lineage-specific features, such as codon usage bias, IR boundary shifting, and distinct repeat sequence structures binding to SSRs. Codon usage in the genes of photosystem II exhibited an obvious preference, reflecting significant environmental adaptation pressures. In this study, three repeat regions compounded with trinucleotide and mononucleotide repeats were found for the first time in R. forrestii, R. himalensis, and R. yunnanensis. High-variability regions such as ndhF, ycf1, trnH-psbA, and rpoC1-rpoB were screened, laying the foundation for the precise identification of these species. The phylogenetic analysis revealed the occurrence of cyto-nuclear discordance, likely originating from the frequent interspecific hybridization events observed within Rhodiola species during rapid radiation. Dioecious and hermaphrodite species can be broadly categorized into two subclades, probably they have different environmental adaptation strategies in response to climate change. In addition, the phylogenetic tree supported the monophyly of R. forrestii and R. yunnanensis, which compose R. Sect. Pseudorhodiola. In conclusion, plastome data enrich the genetic information available for the Rhodiola genus and may provide insight into species migration events during climate change.

Structure and biological activity in vitro of Flagellin and its mutants from Escherichia coli Nissle 1917.

Bacterial flagellin is a potent immunomodulatory agent. Previously, we successfully obtained flagellin from Escherichia coli Nissle 1917 (FliCEcN) and constructed two mutants with varying degrees of deletion in its highly variable regions (HVRs). We found that there was a difference in immune stimulation levels between the two mutants, with the mutant lacking the D2-D3 domain pair of FliCEcN having a better adjuvant effect. Therefore, this study further analyzed the structural characteristics of the aforementioned FliCEcN and its two mutants and measured their levels of Caco-2 cell stimulation to explore the impact of different domains in the HVRs of FliCEcN on its structure and immune efficacy. This study utilized AlphaFold2, SERS (Surface-enhanced Raman spectroscopy), and CD (circular dichroism) techniques to analyze the structural characteristics of FliCEcN and its mutants, FliCΔ174-506 and FliCΔ274-406, and tested their immune effects by stimulating Caco-2 cells in vitro. The resultsindicate that the D2andD3 domainsof FliCEcNhave more complex interactionscomparedtothe D1-D2 domainpair., and thesedomains alsoplay a role in molecular docking with TLR5 (Toll-like receptor 5). Furthermore, FliCΔ274-406 hasmore missing side chain and characteristic amino acid peaks than FliCΔ174-506. The FliCEcN group was found to stimulatehigherlevelsofIL-10 (interleukin 10) secretion, while the FliCΔ174-506 and FliCΔ274-406 groups had higher levels of IL-6 (interleukin 6) and TNF-α (tumor necrosis factor-α) secretion. In summary, the deletion of different domains in the HVRs of FliCEcN affects its structural characteristics, its interaction with TLR5, and the secretion of immune factors by Caco-2 cells.

Comparative analysis of chloroplast genomes of Pulsatilla species reveals evolutionary and taxonomic status of newly discovered endangered species Pulsatilla saxatilis

BackgroundPulsatilla saxatilis, a new species of the genus Pulsatilla has been discovered. The morphological information of this species has been well described, but its chloroplast genome characteristics and comparison with species of the same genus remain to be reported.ResultsOur results showed that the total length of chloroplast (cp.) genome of P. saxatilis is 162,659 bp, with a GC content of 37.5%. The cp. genome contains 134 genes, including 90 known protein-coding genes, 36 tRNA genes, and 8 rRNA genes. P. saxatilis demonstrated similar characteristics to other species of genus Pulsatilla. Herein, we compared cp. genomes of 10 species, including P. saxatilis, and found that the cp. genomes of the genus Pulsatilla are extremely similar, with a length of 162,322–163,851 bp. Furthermore, The SSRs of Pulsatilla ranged from 10 to 22 bp in length. Among the four structural regions of the cp. genome, most long repeats and SSRs were detected in the LSC region, followed by that in the SSC region, and least in IRA/ IRB regions. The most common types of long repeats were forward and palindromic repeats, followed by reverse repeats, and only a few complementary repeats were found in 10 cp. genomes. We also analyzed nucleotide diversity and identified ccsA_ndhD, rps16_trnK-UUU, ccsA, and rbcL, which could be used as potential molecular markers for identification of Pulsatilla species. The results of the phylogenetic tree constructed by connecting the sequences of high variation regions were consistent with those of the cp. gene phylogenetic tree, and the species more closely related to P. saxatilis was identified as the P. campanella.ConclusionIt was determined that the closest species to P. saxatilis is P. campanella, which is the same as the conclusion based on pollen grain characteristics, but different from the P. chinensis determined based on morphological characteristics. By revealing information on the chloroplast characteristics, development, and evolution of the cp. genome and the potential molecular markers, this study provides effective molecular data regarding the evolution, genetic diversity, and species identification of the genus Pulsatilla.

Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom.

Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687-152,759 bp in length. Each genome contains 126-132 genes, including 81-87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61-64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae.

Characterization of single nucleotide polymorphisms in chloroplast genomes of Musaceae Juss.

Musaceae Juss., also called the bananas and plantains family contains essential food crops with critical economic value and nutritional and medicinal properties. In this study, complete chloroplast genomes of 55 species of Musaceae, including all three genera of Musa, Musella, and Ensete, were used to characterize single nucleotide polymorphisms. Also, nucleotide diversity among surveyed species was observed. The results showed regions of high genetic variability in the chloroplast genome and genes carrying multiple single-nucleotide polymorphisms specific for species and genera, such as ycf1, ycf2, ndhF, matK, accD, infA, and petL. A biased nucleotide conversion toward G, C, and T suggests a trend in the evolution of the Musaceae chloroplast genomes. Phylogenetic analysis revealed a close relationship between Ensete and Musella genera and confirmed the existence of two clades in the genus Musa. This study summarizes nucleotide diversity, focusing on single-nucleotide polymorphisms, which are helpful for further studies on population genetics and developing molecular markers in Musaceae.

Natural variation in a short region of the Acidovorax citrulli type III-secreted effector AopW1 is associated with differences in cytotoxicity and host adaptation.

Bacterial fruit blotch, caused by Acidovorax citrulli, is a serious disease of melon and watermelon. The strains of the pathogen belong to two major genetic groups: group I strains are strongly associated with melon, while group II strains are more aggressive on watermelon. A. citrulli secretes many protein effectors to the host cell via the type III secretion system. Here we characterized AopW1, an effector that shares similarity to the actin cytoskeleton-disrupting effector HopW1 of Pseudomonas syringae and with effectors from other plant-pathogenic bacterial species. AopW1 has a highly variable region (HVR) within amino acid positions 147 to 192, showing 14 amino acid differences between group I and II variants. We show that group I AopW1 is more toxic to yeast and Nicotiana benthamiana cells than group II AopW1, having stronger actin filament disruption activity, and increased ability to induce cell death and reduce callose deposition. We further demonstrated the importance of some amino acid positions within the HVR for AopW1 cytotoxicity. Cellular analyses revealed that AopW1 also localizes to the endoplasmic reticulum, chloroplasts, and plant endosomes. We also show that overexpression of the endosome-associated protein EHD1 attenuates AopW1-induced cell death and increases defense responses. Finally, we show that sequence variation in AopW1 plays a significant role in the adaptation of group I and II strains to their preferred hosts, melon and watermelon, respectively. This study provides new insights into the HopW1 family of bacterial effectors and provides first evidence on the involvement of EHD1 in response to biotic stress.

Bayesian optimization with Gaussian process surrogate model for source localization.

Source localization with a geoacoustic model requires optimizing the model over a parameter space of range and depth with the objective of matching a predicted sound field to a field measured on an array. We propose a sample-efficient sequential Bayesian optimization strategy that models the objective function as a Gaussian process (GP) surrogate model conditioned on observed data. Using the mean and covariance functions of the GP, a heuristic acquisition function proposes a candidate in parameter space to sample, balancing exploitation (sampling around the best observed objective function value) and exploration (sampling in regions of high variance in the GP). The candidate sample is evaluated, and the GP conditioned on the updated data. Optimization proceeds sequentially until a fixed budget of evaluations is expended. We demonstrate source localization for a shallow-water waveguide using Monte Carlo simulations and experimental data from an acoustic source tow. Compared to grid search and quasi-random sampling strategies, simulations and experimental results indicate the Bayesian optimization strategy converges on optimal solutions rapidly.

Genetic variation and recombination analysis of the GP5 (GP5a) gene of PRRSV-2 strains in China from 1996 to 2022.

Porcine reproductive and respiratory syndrome virus (PRRSV) has been prevalent in China for more than 25 years and remains one of the most significant pathogens threatening the pig industry. The high rate of mutation and frequent recombination of PRRSV have exacerbated its prevalence, particularly with the emergence of highly pathogenic PRRSV (HP-PRRSV) has significantly increased the pathogenicity of PRRSV, posing a serious threat to the development of Chinese pig farming. To monitor the genetic variation of PRRSV-2 in China, the GP5 sequences of 517 PRRSV-2 strains from 1996 to 2022 were analyzed and phylogenetic trees were constructed. Furthermore, a total of 60 PRRSV strains, originating from various lineages, were carefully chosen for nucleotide and amino acid homologies analysis. The results showed that the nucleotide homologies of the PRRSV GP5 gene ranged from 81.4 to 100.0%, and the amino acid homologies ranged from 78.1 to 100.0%. Similarly, the PRRSV GP5a gene showed 78.0 ~ 100.0% nucleotide homologies and 70.2 ~ 100.0% amino acid homologies. Amino acid sequence comparisons of GP5 and GP5a showed that some mutations, such as substitutions, deletions, and insertions, were found in several amino acid sites in GP5, these mutations were primarily found in the signal peptide region, two highly variable regions (HVRs), and near two T-cell antigenic sites, while the mutation sites of GP5a were mainly concentrated in the transmembrane and intramembrane regions. Phylogenetic analysis showed that the prevalent PRRSV-2 strains in China were divided into lineages 1, 3, 5, and 8. Among these, strains from lineage 8 and lineage 1 are currently the main prevalent strains, lineage 5 and lineage 8 have a closer genetic distance. Recombination analysis revealed that one recombination event occurred in 517 PRRSV-2 strains, this event involved recombination between lineage 8 and lineage 1. In conclusion, this analysis enhances our understanding of the prevalence and genetic variation of PRRSV-2 in China. These findings provide significant insights for the development of effective prevention and control strategies for PRRS and serve as a foundation for future research in this field.

A tool for rapid, automated characterization of population epigenomics in plants

Epigenetic variation in plant populations is an important factor in determining phenotype and adaptation to the environment. However, while advances have been made in the molecular and computational methods to analyze the methylation status of a given sample of DNA, tools to profile and compare the methylomes of multiple individual plants or groups of plants at high resolution and low cost are lacking. Here, we describe a computational approach and R package (sounDMR) that leverages the benefits of long read nanopore sequencing to enable robust identification of differential methylation from complex experimental designs, as well as assess the variability within treatment groups and identify individual plants of interest. We demonstrate the utility of this approach by profiling a population of Arabidopsis thaliana exposed to a demethylating agent and identify genomic regions of high epigenetic variability between individuals. Given the low cost of nanopore sequencing devices and the ease of sample preparation, these results show that high resolution epigenetic profiling of plant populations can be made more broadly accessible in plant breeding and biotechnology.

Summer Rice–Winter Potato Rotation Suppresses Various Soil-Borne Plant Fungal Pathogens

Growing potatoes (Solanum tuberosum) using the idle rice fields in Southern China and the Indo-Gangetic Plains of India in the winter season through the rice–potato rotation (RC) system could support future food security. However, the modulation capacity of the RC system on soilborne fungal pathogens is still unclear. In the current study, a pot experiment was designed and conducted to monitor the dynamics of soil fungal community composition between the potato monoculture (CC) system and the RC system, where the two systems were set with the same soil conditions: autoclaving with fertilization; autoclaving without fertilization; autoclave-free with fertilization; and autoclave-free without fertilization. Then, the uncultivated soil (CK) and root-zone soil samples of conditions under the two systems were collected, and then soil physiochemical properties and enzymatic activities were determined. Next, the high-variable region (V5–V7) of fungal 18S rRNA genes of the samples were amplified and sequenced through the PCR technique and the Illumina Miseq platform, respectively. Finally, the fungal species diversity and composition, as well as the relative abundance of fungal pathogens annotated against the Fungiuld database in soil samples, were also investigated. The results showed that the RC could significantly (p &lt; 0.05) increase soil fungal species diversity and decrease the relative abundance of soil fungal pathogens, where the RC could suppress 23 soil fungal pathogens through cultivating the rice during the summer season and 93.75% of the remaining pathogens through winter-season cultivation. Seven-eighths of the conditions under RC have lower pathogenic MGIDI indices (6.38 to 7.82) than those of the CC (7.62 to 9.63). Notably, both rice cultivation and winter planting reduced the abundance of the pathogenic strain ASV24 under the Colletotrichum genus. The bipartite fungal network between the pathogens and the non-pathogens showed that the pathogenic members could be restricted through co-occurring with the non-pathogenic species and planting crops in the winter season. Finally, the redundancy analysis (RDA) indicated that soil pH, electronic conductivity, available phosphorus content, and various enzyme activities (cellulase, urease, sucrase, acid phosphatase, catalase, polyphenol oxidase) could be the indicators of soil fungal pathogens. This experiment demonstrated that the rice–potato rotation system outperformed the potato monoculture on suppressing soilborne fungal pathogenic community.

Circulation and Cross‐Shelf Exchanges in the Northern Shelf of the Southwestern Atlantic: Dynamics

AbstractThe strong interaction between the Brazil Current and the adjacent shelf is clearly visible in satellite‐derived products (sea surface temperature, salinity, and chlorophyll‐a concentration). Assessments of circulation features and cross‐shelf exchanges from these products are, however, limited to the surface layer. Here we analyze the regional circulation and dynamics using the results of a suite of process‐oriented, high‐resolution numerical experiments. Passive tracers and Lagrangian floats characterize the exchanges between the shelf and the open ocean, identifying regions of high variability, and assessing the contribution of small‐scale eddies to the cross‐shelf mass exchanges. We estimate that 0.2–0.4 Sv of the shelf transport variability between 34°S and 25°S comes from ocean internal variability which represents ∼50%–70% of the total variability. Between 25°S and 21°S, internal ocean variability represents more than 90% of the shelf transport variability. We find that generation of cyclonic eddies is more frequent (&gt;15% of the time) at the shelfbreak bights. The core of these eddies contains fresher, colder, and more nutrient‐rich shelf waters. Maps of satellite chlorophyll‐a concentration suggest that the horizontal and vertical exchanges of mass associated with these eddies are a critical element of the primary production cycle.

Brain hubs defined in the group do not overlap with regions of high inter-individual variability

Connector ‘hubs’ are brain regions with links to multiple networks. These regions are hypothesized to play a critical role in brain function. While hubs are often identified based on group-average functional magnetic resonance imaging (fMRI) data, there is considerable inter-subject variation in the functional connectivity profiles of the brain, especially in association regions where hubs tend to be located. Here we investigated how group hubs are related to locations of inter-individual variability. To answer this question, we examined inter-individual variation at group-level hubs in both the Midnight Scan Club and Human Connectome Project datasets. The top group hubs defined based on the participation coefficient did not overlap strongly with the most prominent regions of inter-individual variation (termed ‘variants’ in prior work). These hubs have relatively strong similarity across participants and consistent cross-network profiles, similar to what was seen for many other areas of cortex. Consistency across participants was further improved when these hubs were allowed to shift slightly in local position. Thus, our results demonstrate that the top group hubs defined with the participation coefficient are generally consistent across people, suggesting they may represent conserved cross-network bridges. More caution is warranted with alternative hub measures, such as community density (which are based on spatial proximity to network borders) and intermediate hub regions which show higher correspondence to locations of individual variability.

Temporal variability of a soundscape near a mid-oceanic atoll in the northern Indian ocean

Soundscape ecology in the context of physical oceanographic features is an emerging area of research revealing interactions between physically, biologically and anthropogenically driven sounds and their sources. Soundscapes can shape and reveal distributions of a range of species, from fish larvae to whales, within marine ecosystems. The northern Indian Ocean is a region of high environmental variability driven by seasonally reversing monsoonal winds. The mid-oceanic islands within these waters consist of steep slopes forming a crucial interface between shallow reef and deep oceanic habitats. Studies on soundscape are limited in these waters. The aim of this study was to characterize major sound sources off the southern and northern side of the Kavaratti atoll in Lakshadweep islands, India, located at the northern part of the Laccadive-Maldives-Chagos Ridge. A first look at shallow water soundscapes are provided here using passive acoustic monitoring, and how they correlate with satellite-derived oceanographic variables. Geophonic and biophonic sources across different frequency bands are identified with three major choruses – a dusk fish chorus, a midnight chorus that is speculated to be produced by myctophids, and a snapping shrimp night chorus. Low frequency biophonic choruses peaked in inter-monsoon months (January to March), while low frequency geophonic sound levels peaked during monsoon months (June to October) and increased with wind speed. The dusk fish chorus and the midnight chorus (at the south site) decreased with increasing sea surface salinity, while the snapping shrimp chorus (at the south site) increased with increasing sea surface salinity. Snapping shrimp chorus levels increased with decreasing wind speed. The dusk fish chorus peaked during full and waning moon, and the midnight and snapping shrimp choruses peaked during new moon periods. The sources and patterns described in this study will help compare with future soundscape and sound pressure level measurements within this region. This will be useful in the context of a changing climate and for planning future developmental projects on the islands. Reef choruses link with peak larval recruitment, spawning, or feeding activities, and further investigation into the peak calling times reported here will help uncover the function of choruses. Expanding the collection of passive acoustic monitoring data and oceanographic measurements over longer timescales will significantly advance ‘soundscape oceanography’.

Contemporary oceanic radiocarbon response to ocean circulation changes

Radiocarbon (14C) is a valuable tracer of ocean circulation, owing to its natural decay over thousands of years and to its perturbation by nuclear weapons testing in the 1950s and 1960s. Previous studies have used 14C to evaluate models or to investigate past climate change. However, the relationship between ocean 14C and ocean circulation changes over the past few decades has not been explored. Here we use an Ocean-Sea-ice model (NEMO) forced with transient or fixed atmospheric reanalysis (JRA-55-do) and atmospheric 14C and CO2 boundary conditions to investigate the effect of ocean circulation trends and variability on 14C. We find that 14C/C (∆14C) variability is generally anti-correlated with potential density variability. The areas where the largest variability occurs varies by depth: in upwelling regions at the surface, at the edges of the subtropical gyres at 300 m depth, and in Antarctic Intermediate Water and North Atlantic Deep Water at 1000 m depth. We find that trends in the Atlantic Meridional Overturning Circulation may influence trends in ∆14C in the North Atlantic. In the high-variability regions the simulated variations are larger than typical ocean ∆14C measurement uncertainty of 2–5‰ suggesting that ∆14C data could provide a useful tracer of circulation changes.