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Telomeric G-quadruplexes (G4s) are non-canonical DNA structures composed of TTAGGG repeats. They are extensively studied both as biomolecules key for genome stability and as promising building blocks and functional elements in synthetic biology and nanotechnology. This is why it is extremely important to understand how the interaction between G4s is affected by their topology. We used small-angle x-ray scattering to investigate the end-to-end stacking of antiparallel telomeric G-quadruplexes formed by the sequence AG3(T2AG3)3. To represent the experimental data, we developed a highly efficient coarse-grained fitting tool, which successfully described the samples as an equilibrium mixture of monomeric and dimeric G4 species. Our findings indicate that the antiparallel topology prevents the formation of long multimeric structures under self-crowding conditions, unlike the hybrid/parallel structures formed by the same DNA sequence. This result supports the idea that the stacking of monomeric G-quadruplexes is strongly affected by the presence of diagonal loops. [ABSTRACT FROM AUTHOR]

Experimentally, in the presence of the crowding agent polyethylene glycol (PEG), sodium ions compact double-stranded DNA more readily than potassium ions. Here, we have used molecular dynamics simulations and the "ion binding shells model" of DNA condensation to provide an explanation for the observed variations in condensation of short DNA duplexes in solutions containing different monovalent cations and PEG; several predictions are made. According to the model we use, externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, the number of externally bound Na+ ions is larger than the number of K+ ions over a wide range of chloride concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation that is at least 0.2kBT per base pair more favorable in solution with NaCl than with KCl at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+ depends noticeably on the DNA sequence; we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. Counter-intuitively, the addition of a small amount of a crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA–DNA attraction, shifting the equilibrium away from the DNA condensed phase. [ABSTRACT FROM AUTHOR]

In this study, a novel electrochemical biosensor was developed for the sensitive and selective detection of the Acinetobacter baumannii gene sequence. The biosensor was created by immobilizing a capture probe specific to the A. baumannii gene on the surface of chitosan-gold modified pencil graphite electrodes. Following solid-state hybridization on the Chit-Au/PGE surface, the target DNA sequence of the A. baumannii was detected by measuring the guanine signal using square wave voltammetry (SWV). All experimental parameters impacting sensor response are examined in order to improve hybridization efficacy, and the electrochemical biosensor's performance. The limit of detection (LOD) for the A. baumannii gene sequence was calculated and found to be 1.93 nM. Three different non-complementary DNA sequences were used to evaluate the assay selectivity, but no interference effect was obtained. Additionally, the potential applicability of the biosensor to real samples was tested in artificial serum media. The suggested electrochemical test procedure is simple, approachable, and quick, making it a convenient approach for the screening of DNA sequence. [Display omitted] • Pencil graphite electrodes were modified with chitosan-Au composite. • CHIT-Au/PGEs were used for electrochemical biosensing of A. baumannii gene • The [Fe(CN) 6 ]3-/4- oxidation signal was measured by SWV technique. • The proposed electrochemical assay is simple, rapid, and accessible. [ABSTRACT FROM AUTHOR]

Aim Methods Results Conclusion In Japan, despite low nationwide hepatitis C (HCV) incidence, new infections among people who inject drugs (PWID) and men who have sex with men (MSM) hinder HCV elimination. We explored HCV transmission dynamics and screened HCV recombination within these populations.This cross‐sectional study recruited HCV‐infected patients from Osaka National Hospital, Osaka, Japan, from January 2010 to September 2023. Data from questionnaires and medical records were analyzed. Serum samples collected before anti‐HCV treatment underwent HCV RNA extraction, and sequencing of full core (576 bp) and NS5B (267 bp) regions using the Sanger method. Genotype distribution was determined by phylogenetic analysis, and recombinant screening was conducted.A total of 115 patients were categorized into non‐MSM PWID (31), MSM PWID (15), MSM non‐PWID (25), and non‐MSM non‐PWID (44). Positive amplification rates were 99.1% (114/115) for the full‐core region, and 96.5% (111/115) for NS5B. No intergenotypic recombination was detected. The predominant genotype in non‐MSM PWID was 2a (58%), whereas genotype 1b was most common in MSM PWID, MSM non‐PWID, and non‐MSM non‐PWID groups (79%, 64%, and 68%, respectively). Nucleotide sequence similarity of 94.75%–100% was found in HCV strains from MSM PWID and MSM non‐PWID in both full‐core and NS5B regions, whereas strains from non‐MSM PWID and non‐MSM non‐PWID were distinct.The findings suggest that the transmission route in PWID is determined by MSM status, whereas MSM groups showed the same transmission route regardless of PWID. HCV control measures should be focused not only on PWID, but also on MSM to achieve HCV elimination in Japan. [ABSTRACT FROM AUTHOR]

With the advent of gene editing technologies like CRISPR/Cas9, it has become possible to edit genomic regions of interest for research and therapeutic purposes. These technologies have also been adapted to alter gene expression without changing their DNA sequence, allowing epigenetic edits. While genetic editors make edits by cutting the genome at specified regions, epigenetic editors leverage the same targeting mechanism but act based on the epigenetic modifier fused to them, such as a methyltransferase. Here, we discuss two recently employed epigenetic editors (epi‐editors) that silenced target genes involved in disease to mitigate their effects. Neumann et al. reported the construction of an epigenetic editor called CHARM that could methylate and silence the prion gene in mouse brains and subsequently switch itself off. Additionally, Capelluti et al. developed an epi‐editor called EvoETR that knocked down Pcsk9 in the murine liver to reduce LDL levels. We aim to highlight the design principles underlying the design of these epi‐editors to inform future editor designs. [ABSTRACT FROM AUTHOR]

Cytosine base editing is a powerful tool for making precise single nucleotide changes in cells and model organisms like zebrafish, which are valuable for studying human diseases. However, current base editors struggle to edit cytosines in certain DNA contexts, particularly those with GC and CC pairs, limiting their use in modelling disease-related mutations. Here we show the development of zevoCDA1, an optimized cytosine base editor for zebrafish that improves editing efficiency across various DNA contexts and reduces restrictions imposed by the protospacer adjacent motif. We also create zevoCDA1-198, a more precise editor with a narrower editing window of five nucleotides, minimizing off-target effects. Using these advanced tools, we successfully generate zebrafish models of diseases that were previously challenging to create due to sequence limitations. This work enhances the ability to introduce human pathogenic mutations in zebrafish, broadening the scope for genomic research with improved precision and efficiency. Cytosine base editing is crucial for modeling human diseases in zebrafish. Here, the authors present zevoCDA1 and zevoCDA1-198, optimized editors that improve editing efficiency and precision, allowing zebrafish modeling for disease-related mutations which were previously limited by DNA sequence contexts. [ABSTRACT FROM AUTHOR]

Sublingual immunotherapy (SLIT) has received considerable attention as a method for allergen immunotherapy (AIT). However, the mechanism of SLIT, especially its timing, has not been thoroughly investigated. We evaluated therapeutic and prophylactic SLIT in an allergic airway inflammation model and evaluated their efficacies. Mice were intranasally exposed to Dermatophagoides farinae (Der f) extract and received SLIT before (prophylactic model) and after (therapeutic model) intranasal exposure of Der f. We investigated airway responsiveness, airway inflammation, allergen-specific antibodies, lung histology and single-cell RNA sequencing (scRNA-seq) and T-cell receptor sequencing were also investigated. SLIT in the therapeutic model was effective; however, the effects of SLIT in the prophylactic model were stronger and immune tolerance was maintained for three months. ScRNA-seq of lung CD4+CD25+ T cells revealed that the expansion of induced T regulatory (iTreg) cells was greater in the prophylactic model than that in the therapeutic model. Additionally, the TCR repertoire of iTregs from the prophylactic model was abundant, sharing many clones with the TCR repertoire of effector T cells. These data suggest that the prophylactic model of AIT is extremely effective and persistent, and may respond to allergen diversity, and provide evidence for the clinical recommendation of preventive AIT. [ABSTRACT FROM AUTHOR]

Serine integrases are phage- (or mobile element-) encoded enzymes that catalyse site-specific recombination reactions between a short DNA sequence on the phage genome (attP) and a corresponding host genome sequence (attB), thereby integrating the phage DNA into the host genome. Each integrase has its unique pair of attP and attB sites, a feature that allows them to be used as orthogonal tools for genome modification applications. In the presence of a second protein, the Recombination Directionality Factor (RDF), integrase catalyses the reverse excisive reaction, generating new recombination sites, attR and attL. In addition to promoting attR x attL reaction, the RDF inhibits attP x attB recombination. This feature makes the directionality of integrase reactions programmable, allowing them to be useful for building synthetic biology devices. In this report, we describe the degree of orthogonality of both integrative and excisive reactions for three related integrases (ϕC31, ϕBT1, and TG1) and their RDFs. Among these, TG1 integrase is the most active, showing near complete recombination in both attP x attB and attR x attL reactions, and the most directional in the presence of its RDF. Our findings show that there is varying orthogonality among these three integrases – RDF pairs. ϕC31 integrase was the least selective, with all three RDFs activating it for attR x attL recombination. Similarly, ϕC31 RDF was the least effective among the three RDFs in promoting the excisive activities of the integrases, including its cognate ϕC31 integrase. ϕBT1 and TG1 RDFs were noticeably more effective than ϕC31 RDF at inhibiting attP x attB recombination by their respective integrases, making them more suitable for building reversible genetic switches. AlphaFold-Multimer predicts very similar structural interactions between each cognate integrase – RDF pair. The binding surface on the RDF is much more conserved than the binding surface on the integrase, an indication that specificity is determined more by the integrase than the RDF. Overall, the observed weak integrase/RDF orthogonality across the three enzymes emphasizes the need for identifying and characterizing more integrase – RDF pairs. Additionally, the ability of a particular integrase's preferred reaction direction to be controlled to varying degrees by non-cognate RDFs provides a path to tunable, non-binary genetic switches. [ABSTRACT FROM AUTHOR]

Gene expression emerges from DNA sequences through the interaction of transcription factors (TFs) with DNA cis-regulatory sequences. In eukaryotes, TFs bind to transcription factor binding sites (TFBSs) with differential affinities, enabling cell-specific gene expression. In this view, DNA enables TF binding along a continuum ranging from low to high affinity depending on its sequence composition; however, it is not known whether evolution has entailed a further level of entanglement between DNA-protein interaction. Here we found that the composition and length (22 bp) of the DNA sequence interposed between the CRX and NRL retinal TFs in the proximal promoter of RHODOPSIN (RHO) largely controls the expression levels of RHO. Mutagenesis of CRX-NRL DNA linking sequences (here termed "DNA-linker") results in uncorrelated gene expression variation. In contrast, mutual exchange of naturally occurring divergent human and mouse Rho cis-regulatory elements conferred similar yet species-specific Rho expression levels. Two orthogonal DNA-binding proteins targeted to the DNA-linker either activate or repress the expression of Rho depending on the DNA-linker orientation relative to the CRX and NRL binding sites. These results argue that, in this instance, DNA itself contributes to CRX and NRL activities through a code based on specific base sequences of a defined length, ultimately determining optimal RHO expression levels. [ABSTRACT FROM AUTHOR]

Ectomycorrhizal (ECM) fungi are important tree symbionts within forests. The biogeography of ECM fungi remains to be investigated because it is challenging to observe and identify species. Because most ECM plant taxa have a Holarctic distribution, it is difficult to evaluate the extent to which host preference restricts the global distribution of ECM fungi. To address this issue, we aimed to assess whether host preference enhances the endemism of ECM fungi that inhabit dipterocarp rainforests. Highly similar sequences of 175 operational taxonomic units (OTUs) for ECM fungi that were obtained from Lambir Hill's National Park, Sarawak, Malaysia, were searched for in a nucleotide sequence database. Using a two‐step binomial model, the probability of presence for the query OTUs and the registration rate of barcode sequences in each country were simultaneously estimated. The results revealed that the probability of presence in the respective countries increased with increasing species richness of Dipterocarpaceae and decreasing geographical distance from the study site (i.e. Lambir). Furthermore, most of the ECM fungi were shown to be endemic to Malaysia and neighbouring countries. These findings suggest that not only dispersal limitation but also host preference are responsible for the high endemism of ECM fungi in dipterocarp rainforests. Moreover, host preference likely determines the areas where ECM fungi potentially expand and dispersal limitation creates distance–decay patterns within suitable habitats. Although host preference has received less attention than dispersal limitation, our findings support that host preference has a profound influence on the global distribution of ECM fungi. [ABSTRACT FROM AUTHOR]

Aim: To date a vicariant event through the mutualistic relationship of a hylid frog and its bromeliad host found across two isolated mountain ranges as part of an island–continental split and to use this information to calibrate a molecular dating analysis of hylids. Location: South America. Time Period: Pliocene. Major Taxa Studied: Treefrogs, Arboranae. Methods: Pliocene tectonic movements sank a portion of a mountain range that connected present‐day Trinidad (island) and northern Venezuela, eventually isolating populations of the golden tree frog Phytotriades auratus and its host bromeliad Glomeropitcairnia erectiflora on both sides of a saltwater barrier. We estimated the submersion rate timing of the vicariant event, then employed ecological niche modelling to establish the distribution of the frog and its host to the Pliocene. We generated nucleotide sequence data for the hylid on each side of the marine barrier and proposed a biogeographic calibration for the split between populations. Using Bayesian phylogenetic analysis, we evaluated the impact of incorporating this biogeographic calibration on estimates of treefrog divergence times. Results: A relatively continuous, high‐elevation mountain range existed before the Pliocene and the opening of the Gulf of Paria (4.45 ± 0.85 Ma). Phytotriades auratus and G. erectiflora would have been distributed across the Paria and Northern Range mountains as a single population since the Pliocene. Divergence times among treefrogs (Arboranae) were older than those inferred using fossil calibrations alone, with mean age estimates for subfamilies and genera being ~2 and ~1.2 million years older, respectively. Main Conclusions: Our study presents a biogeographic calibration based on a vicariant model that connects the evolution of the populations of a hylid through geology and ecological data. The implementation of this date as a molecular clock calibration reduces the uncertainty in date estimates for the shallower nodes in the phylogeny of Arboranae. [ABSTRACT FROM AUTHOR]

The crowing of male Gallus exhibits diverse sound patterns. This is believed to be related to the phenotypic diversity of vocal organs, one of which is influenced by the nucleotide diversity of the associated genes. The SOX9 gene, involved in cartilaginous tissue growth and development, is reported to contribute e in the development of larynx and syrinx. This study aimed to characterize the CDS regions of exons 1 and 2 of the SOX9 gene in junglefowl to assess its diversity. Genomic DNA was extracted from ten individuals of G. varius from Lombok and Sumbawa. The CDS regions of SOX9 gene exons 1 and 2 were amplified using two primer pairs. Additionally, the CDS regions of SOX9 gene exons 1 and 2 from 54 junglefowl SRA data in an online repository were mapped and analyzed. The study identified all nucleotide sequences as CDS regions of SOX9 gene exons 1 and 2. Six shared, and 24 unique haplotypes were constructed. A putative amino acid sequence common to all Gallus species was also identified. The diversity observed in the CDS regions of SOX9 gene exons 1 and 2 nucleotide sequence showed a different level with the diversity observed in its amino acid sequence. [ABSTRACT FROM AUTHOR]

In this study, from the perspective of image processing, we propose the iDNA-ITLM model, using a novel data enhance strategy by continuously self-replicating a short DNA sequence into a longer DNA sequence and then embedding it into a high-dimensional matrix to enlarge the receptive field, for identifying DNA methylation sites. Our model consistently outperforms the current state-of-the-art sequence-based DNA methylation site recognition methods when evaluated on 17 benchmark datasets that cover multiple species and include three DNA methylation modifications (4mC, 5hmC, and 6mA). The experimental results demonstrate the robustness and superior performance of our model across these datasets. In addition, our model can transfer learning to RNA methylation sequences and produce good results without modifying the hyperparameters in the model. The proposed iDNA-ITLM model can be considered a universal predictor across DNA and RNA methylation species. [ABSTRACT FROM AUTHOR]

Several Amaranthus hybridus L. biotypes present single and triple amino acid substitutions in EPSPS (5‐enolypyruvylshikimate‐3‐phosphate synthase). In resistant and tolerant species to glyphosate, differential susceptibility and alterations in the EPSPS sequence could cause modifications in their morphological–structural characteristics, an issue that is unknown for biotypes of A. hybridus. The aim of the work was to determine the susceptibility to glyphosate, the presence of mutations in EPSPS and the growth form in four biotypes of this weed from north‐central Argentina. To carry out this, a dose–response assay was conducted, to determine the presence of mutations in the EPSPS, DNA was extracted, amplified and sequenced, and finally, to evaluate the morphological–structural variations, the growth form was analysed. Our findings revealed that Ah03, Ah07 and Ah36 biotypes had resistance factors of 22 to 118. The EPSPS sequence remains unaltered in the Ah39 biotype, leading it to be considered a susceptible biotype. Biotypes Ah03 and Ah36 had heterozygous changes in the DNA sequence resulting in amino acid substitutions at positions 102, 103 and 106 being considered resistant biotypes, whereas in Ah07 some individuals showed unaltered DNA sequences and others exhibited heterozygous changes. The growth form was quantitatively different between biotypes, standing the most susceptible biotype that produced more seeds and required less thermal time for the appearance of the terminal inflorescence. The present investigation provides new evidence that resistant biotypes with the triple DNA mutation exhibit variations in the growth form compared to susceptible biotypes of this weed. [ABSTRACT FROM AUTHOR]

Brucellosis and Tuberculosis, both of which are contagious diseases, have presented significant challenges to global public health security in recent years. Delayed treatment can exacerbate the conditions, jeopardizing patient lives. Currently, no vaccine has been approved to prevent these two diseases simultaneously. In contrast to traditional vaccines, mRNA vaccines offer advantages such as high efficacy, rapid development, and low cost, and their applications are gradually expanding. This study aims to develop multi-epitope mRNA vaccines argeting Brucella melitensis and Mycobacterium tuberculosis H37Rv (L4 strain) utilizing immunoinformatics approaches. The proteins Omp25, Omp31, MPT70, and MPT83 from the specified bacteria were selected to identify the predominant T- and B-cell epitopes for immunological analysis. Following a comprehensive evaluation, a vaccine was developed using helper T lymphocyte epitopes, cytotoxic T lymphocyte epitopes, linear B-cell epitopes, and conformational B-cell epitopes. It has been demonstrated that multi-epitope mRNA vaccines exhibit increased antigenicity, non-allergenicity, solubility, and high stability. The findings from molecular docking and molecular dynamics simulation revealed a robust and enduring binding affinity between multi-epitope peptides mRNA vaccines and TLR4. Ultimately, Subsequently, following the optimization of the nucleotide sequence, the codon adaptation index was calculated to be 1.0, along with an average GC content of 54.01%. This indicates that the multi-epitope mRNA vaccines exhibit potential for efficient expression within the Escherichia coli(E. coli) host. Analysis through immune modeling indicates that following administration of the vaccine, there may be variation in immunecell populations associated with both innate and adaptive immune reactions. These types encompass helper T lymphocytes (HTL), cytotoxic T lymphocytes (CTL), regulatory T lymphocytes, natural killer cells, dendritic cells and various immune cell subsets. In summary, the results suggest that the newly created multi-epitope mRNA vaccine exhibits favorable attributes, offering novel insights and a conceptual foundation for potential progress in vaccine development. [ABSTRACT FROM AUTHOR]

The latest pandemic resulting from the novel SARS-CoV-2 coronavirus has significantly affected public health, the worldwide economy, and social life. Metal organic frameworks (MOFs) are currently being implemented in biosensors for rapid and accurate detection of viruses thanks to their exceptional properties. This research aims to develop a Zeolitic Imidazolate Framework-8 (ZIF-8) based fluorescent biosensor for facile and rapid COVID-19 RNA sequence detection. ZIF-8 was characterized using several tests, such as FT-IR, TGA, and PXRD, to examine the MOF's crystalline structure and thermal stability. The results demonstrated high crystallinity and thermal stability up to a temperature of 550 °C. The experimental study showed that ZIF-8 is an excellent fluorescence quencher, with 78.39% quenching efficiency. Analyzing the adsorption mechanism of probe DNA into ZIF-8 revealed that they can form electrostatic and π–π stacking interactions, forming a P-DNA@ZIF-8 complex and that PET is more dominant than FRET in the quenching mechanism. This ZIF-8 biosensing platform showed high sensitivity towards COVID-19 RNA with an ultra-low limit of detection of 6.24 pM, a rapid detection time of 8 min, and high selectivity to COVID-19 RNA. Indeed, ZIF-8 experienced much lower fluorescence recovery when tested on two mismatched RNAs. The experimental results show the potential use of ZIF-8 as a novel biosensor for a rapid and sensitive COVID-19 diagnosis. [ABSTRACT FROM AUTHOR]

Thyroid cancer (TC) represents one of the most prevalent endocrine malignancies, with a rising incidence worldwide. Epigenetic alterations, which modify gene expression without altering the underlying DNA sequence, have garnered significant attention in recent years. Increasing evidence underscores the pivotal role of epigenetic modifications, including DNA methylation, RNA methylation, and histone methylation, in the pathogenesis of TC. This review provides a comprehensive overview of these reversible and environmentally influenced epigenetic modifications, highlighting their molecular mechanisms and functional roles in TC. Additionally, the clinical implications, challenges associated with studying these epigenetic modifications, and potential future research directions are explored. [ABSTRACT FROM AUTHOR]

The document from Frontiers in Veterinary Science presents morphological characteristics of feces from two bird species, A. rufipectus and L. nycthemera, along with a sampling table detailing the longitude, latitude, and time of each sample collection. It also includes alpha diversity indices for each sample and Blastn alignments with nucleotide sequence accession numbers for various fungal species. The research provides valuable insights into the microbial diversity of bird feces, contributing to our understanding of avian health and ecology. [Extracted from the article]

Homologous recombination during meiosis is critical for chromosome segregation and also gives rise to genetic diversity. Genetic exchange between homologous chromosomes during meiosis is mediated by the recombinase Dmc1, which is capable of recombining DNA sequences with mismatches. The Hop2-Mnd1 complex mediates Dmc1 activity. Here, we reveal a regulatory role for Hop2-Mnd1 in restricting substrate selection. Specifically, Hop2-Mnd1 upregulates Dmc1 activity with DNA substrates that are either fully homologous or contain DNA mismatches, and it also acts against DNA strand exchange between substrates solely harboring microhomology. By isolating and examining salient Hop2-Mnd1 separation-of-function variants, we show that suppressing illegitimate DNA recombination requires the Dmc1 filament interaction attributable to Hop2-Mnd1 but not its DNA binding activity. Our study provides mechanistic insights into how Hop2-Mnd1 helps maintain meiotic recombination fidelity. Homologous recombination ensures chromosome segregation and genetic diversity. Here, the authors reveal a role for the Hop2-Mnd1 complex in maintaining Dmc1-mediated recombination fidelity by preventing illegitimate DNA exchanges. [ABSTRACT FROM AUTHOR]

The ruminant microbiome plays a key role in the health, feed utilization and environmental impact of ruminant production systems. Microbiome research provides insights to reduce the environmental footprint and improve meat and milk production from ruminants. However, the microbiome composition depends on the ruminant species, habitat and diet, highlighting the importance of having a good representation of ruminant microbiomes in their local environment to translate research findings into beneficial approaches. This information is currently lacking. In this study, we examined the metadata of farmed ruminant microbiome studies to determine global representativeness and summarized information by ruminant species, geographic location, body site, and host information. We accessed data from the International Nucleotide Sequence Database Collaboration via the National Center for Biotechnology Information database. We retrieved 47,628 sample metadata, with cattle accounting for more than two-thirds of the samples. In contrast, goats, which have a similar global population to cattle, were underrepresented with less than 4% of the total samples. Most samples originated in Western Europe, North America, Australasia and China but countries with large ruminant populations in South America, Africa, Asia, and Eastern Europe were underrepresented. Microbiomes from the gastrointestinal tract were the most frequently studied, comprising about 87% of all samples. Additionally, the number of samples from other body sites such as the respiratory tract, milk, skin, reproductive tract, and fetal tissue, has markedly increased over the past decade. More than 40% of the samples lacked basic information and many were retrieved from generic taxonomic classifications where the ruminant species was manually recovered. The lack of basic information such as age, breed or sex can limit the reusability of the data for further analysis and follow-up studies. This requires correct taxonomic assignment of the ruminant host and basic metadata information using accepted ontologies adapted to host-associated microbiomes. Repositories should require this information as a condition of acceptance. The results of this survey highlight the need to encourage studies of the ruminant microbiome from underrepresented ruminant species and countries worldwide. This shortfall in information poses a challenge for the development of microbiome-based strategies to meet sustainability requirements, particularly in areas with expanding livestock production systems. [ABSTRACT FROM AUTHOR]

Background: Rotavirus B (RVB) causes diarrhea in humans and pigs. Although various RVB strains were identified in humans and various animals globally, little is known about the epidemiology RVB infection in Africa. In this study, we attempted to examine the prevalence of RVB infection in pig populations in Zambia. Methods: Metagenomic analyses were conducted on pig feces collected in Zambia to detect double stranded RNA viruses, including RVB. To clarify the prevalence of RVB infection in pig populations in Zambia, 147 fecal samples were screened for the RVB detection by RT-qPCR. Full genome sequence of a detected RVB was determined by Sanger sequencing and genetically analyzed. Results: The metagenomic analyses revealed that RVB sequence reads and contigs of RVB were detected from one fecal sample collected from pigs in Zambia. RT-qPCR screening detected RVB genomes in 36.7% (54/147) of fecal samples. Among 54 positive samples, 13 were positive in non-diarrheal samples (n = 48, 27.1%) and 41 in diarrheal samples (n = 99, 41.4%). Genetic analyses demonstrated that all the segments of ZP18-18, except for VP4, had high nucleotide sequence identities (80.6–92.6%) with all other known RVB strains detected in pigs. In contrast, the VP4 sequence of ZP18-18 was highly divergent from other RVB strains (< 64.6% identities) and formed a distinct lineage in the phylogenetic tree. Notably, the VP8 subunit of the VP4 showed remarkably low amino acid identities (33.3%) to those of known RVB strains, indicating that the VP8 subunit of ZP18-18 was unique among RVB strains. According to the whole genome classification for RVB, ZP18-18 was assigned to a genotype constellation, G18-P[9]-I12-R4-C4-M4-A8-N10-T5-E4-H7 with the newly established VP4 genotype P[9]. Conclusions: This current study updates the geographical distribution and the genetic diversity of RVB. Given the lack of information regarding RVB in Africa, further RVB surveillance is required to assess the potential risk to humans and animals. [ABSTRACT FROM AUTHOR]

Chromosomal heteromorphisms (CHs) are morphological variations predominantly found in constitutive heterochromatic regions of the genome, primarily composed of tandemly repetitive sequences of satellite DNA. Although not completely devoid of genes, these regions are typically not transcribed into proteins and lack obvious phenotypic impact. Nonetheless, their clinical importance is increasingly under scrutiny, with several studies aiming to assess their influence on human diseases and susceptibilities, especially as they are seemingly part of the long noncoding RNAs in certain tissues. This article summarizes the classification methods of human heterochromatic CHs documented in the literature over the last two decades. Multiple scoring systems have been identified, and previous approaches for CH assessment and reporting in genetic diagnosis have shown inconsistencies. Owing to the current heterogeneity in the classification of CHs, data analysis may be biased, impacting the quality of clinical reports and human genetic research. This review highlights the need for a universal scoring system, which is essential for scientific reproducibility and the accurate identification and clinical evaluation of human CHs. Standardizing chromosomal heteromorphisms for better genetic insights: In 2004, the Human Genome Project revealed the complete human DNA sequence, showing that most of our genome consists of noncoding and repetitive DNA sequences. Researchers reviewed various classification systems for chromosomal heteromorphisms to address this knowledge gap. They conducted a literature review using PubMed/MEDLINE, focusing on studies from 2000 to 2024 that described or used classification systems for CHs. This review included 18 studies and identified three main classification methods: Linear Measurement, Twice the Size of the Homologous, and 16p Size Comparison. The results showed inconsistencies in evaluating CHs due to different methodologies and lack of standard sizes for heterochromatic regions. Researchers concluded that standardizing CH classification is crucial for accurate genetic diagnosis and scientific reproducibility. Future research should focus on developing clear guidelines and advanced detection technologies to better understand CHs and their clinical implications. "This summary was initially drafted using artificial intelligence, then revised and fact-checked by the author." [ABSTRACT FROM AUTHOR]

Objectives: Oropouche virus (OROV) causes systemic infections including the nervous and blood systems, posing a significant and growing public health challenge. However, a comprehensive review of the bibliometric analysis of OROV is still lacking. Therefore, the objective of this study was to provide insight into the research dynamics and current hotspots of OROV. Methods: This study used bibliometric analysis to explore the current status of research related to OROV. 148 publications from 1961 to 2024 were retrieved from the Scopus database. Countries, authors, institutions, journals, references, and keywords were visualized using VOSviewer, CiteSpace, R studio, and Bibliometrix. Microsoft Excel was used for statistical analysis. Results: Brazil is the country with the highest number of publications, total cited frequency, and the most extensive international collaboration. The most popular journal in this field is the American Journal of Tropical Medicine and Hygiene. Instituto Evandro Chagas is the institution with the highest number of publications, and Eurico Arruda is involved in the highest number of publications. Keyword co-occurrence analysis showed that Oropouche bunyavirus, virology, bunyavirus, priority journal, and nucleotide sequence are the main research hotspots in this field. Conclusion: Our study provides a comprehensive overview of the research trends and key areas of focus in OROV. The field is currently experiencing rapid growth, as evidenced by the rising number of annual publications, which not only highlights increased research activity but also lays a solid foundation for further in-depth investigations. This trend offers valuable insights for developing effective strategies for outbreak prevention and control in public health. Presently, researchers are concentrating on the detailed study of Bunyavirus infections, employing both virological and genetic approaches to elucidate their complex pathogenic mechanisms. [ABSTRACT FROM AUTHOR]

Nuclear speckles are nuclear membraneless organelles in higher eukaryotic cells playing a vital role in gene expression. Using an in situ reverse transcription-based sequencing method, we study nuclear speckle-associated human transcripts. Our data indicate the existence of three gene groups whose transcripts demonstrate different speckle localization properties: stably enriched in nuclear speckles, transiently enriched in speckles at the pre-messenger RNA stage, and not enriched. We find that stably enriched transcripts contain inefficiently excised introns and that disruption of nuclear speckles specifically affects splicing of speckle-enriched transcripts. We further reveal RNA sequence features contributing to transcript speckle localization, indicating a tight interplay between transcript speckle enrichment, genome organization, and splicing efficiency. Collectively, our data highlight a role of nuclear speckles in both co-and posttranscriptional splicing regulation. Last, we show that genes with stably enriched transcripts are over-represented among genes with heat shock-up-regulated intron retention, hinting at a connection between speckle localization and cellular stress response. [ABSTRACT FROM AUTHOR]

DNA walkers have attracted considerable attention in biosensing and bioimaging. Compared with the conventional single leg-based DNA walker, the bipedal DNA walker has remarkable advantages, with improved sensitivity and fast kinetics, and can work efficiently in a crowded cellular environment. However, most reported bipedal DNA walkers are powered by exogenous supplementation, and elaborate DNA sequence designs, auxiliary additives or extra carriers are often needed. A highly integrated bipedal DNA walker that can address robustness, sensitivity and consistency issues in a single system is highly desirable but remains a great challenge. We herein report a novel bipedal DNA nanowalker system through simple assembly of a DNA substrate, hairpin functionalized-AuNPs (AuNPs-H2), and a blocked Mn2+-dependent DNAzyme hairpin (H1) on degradable MnO2 nanosheets, which holds great potential for living cell operation. Highly integrated features enable the simultaneous delivery of core components of the bipedal DNA walker, including a walking track (AuNPs-H2), a walking strand (H1 cleaved by APE1), and a driving force (Mn2+-dependent DNAzyme cleavage) as a whole, thereby enhancing the control of the spatiotemporal distribution of these components at the intracellular target sites. The redox reaction between the MnO2 nanosheets and GSH inside the cells not only consumed the intracellular GSH to improve the biostability of the walking track but also generated abundant Mn2+ as a cofactor of the DNAzyme. As a proof of concept, the developed nanowalker was demonstrated to work efficiently for monitoring base excision repair (BER)-related human apurinic/apyrimidinic endonuclease 1 (APE1) in living cells, highlighting the great potential of the bipedal DNA nanowalker in biological systems. [ABSTRACT FROM AUTHOR]

Human cytomegalovirus (HCMV) infection can lead to congenital infections and severe complications, particularly in immunocompromised individuals. Current serological tests for diagnosing HCMV infection often face limitations in sensitivity and specificity. Developing multi‐epitope antigens for serological assays offers the potential for enhancing diagnostic accuracy. This study aimed to design a novel multi‐epitope antigen for HCMV infection diagnosis using immunoinformatic approaches. Five tegument proteins (universal protein resource [UniProt] ID: Po8318, Po6725, F5HC97, Q6RX10, and F5HC05) were selected based on their antigenic properties and literature review. Six linear B‐cell epitopes were predicted within conserved regions of each antigen sequence and linked with appropriate linkers. The designed multi‐epitope antigen underwent thorough evaluation for physicochemical properties, solubility, antigenicity, and cross‐reactivity. Additionally, the three‐dimensional structure of the antigen was predicted, refined, and validated. The nucleotide sequence of the designed antigen was optimized for successful expression in Escherichia coli and inserted into a pET23a (+) vector. Immunoinformatic analysis revealed that the multi‐epitope antigen exhibits stability, antigenicity, and lacks cross‐reactivity. Our findings suggest that this multi‐epitope antigen is a promising candidate for diagnosing HCMV infection. However, further validation through laboratory testing is required to confirm its diagnostic efficacy. [ABSTRACT FROM AUTHOR]

The CUT and homeodomain are ubiquitous DNA binding elements often tandemly arranged in multiple transcription factor families. However, how the CUT and homeodomain work concertedly to bind DNA remains unknown. Using ONECUT2, a driver and therapeutic target of advanced prostate cancer, we show that while the CUT initiates DNA binding, the homeodomain thermodynamically stabilizes the ONECUT2-DNA complex through allosteric modulation of CUT. We identify an arginine pair in the ONECUT family homeodomain that can adapt to DNA sequence variations. Base interactions by this ONECUT family-specific arginine pair as well as the evolutionarily conserved residues are critical for optimal DNA binding and ONECUT2 transcriptional activity in a prostate cancer model. The evolutionarily conserved base interactions additionally determine the ONECUT2-DNA binding energetics. These findings provide insights into the cooperative DNA binding by CUT-homeodomain proteins. CUT and HOX are conserved DNA binding elements prevalent in human transcription factors. Here, the authors use an integrative approach to study the mechanism of CUT-HOX cross-talk towards DNA binding by the prostate cancer target ONECUT2. [ABSTRACT FROM AUTHOR]

The continuous emergence of new illegal compounds, particularly psychoactive chemicals, poses significant challenges for current drug detection methods. Developing new protocols and kits for each new drug requires substantial time, effort, and dedicated manpower. Whole-cell bacterial bioreporters have been proven capable of detecting diverse hazardous compounds in both laboratory and field settings, identifying not only single compounds but also chemical families. We present the development of a microbial bioreporter for the detection of cocaine, the nervous system stimulant that is the second-most widely used illegal drug in the US. Escherichia coli was transformed with a plasmid containing a bacterial luxCDABEG bioluminescence gene cassette, activated by a cocaine-responsive signaling cascade. The engineered bioreporter is demonstrated to be a sensitive and specific first-generation detection system for cocaine, with detection thresholds of 17 ± 8 μg/L and 130 ± 50 μg/L in a buffer solution and in urine, respectively. Further improvement of the sensor's performance was achieved by altering the nucleotide sequence of the PBen gene promoter, the construct's sensing element, using accelerated site-directed evolution. The applicability of ready-to-use paper strips with immobilized bioreporter cells was demonstrated for cocaine detection in aqueous solutions. [ABSTRACT FROM AUTHOR]

CRISPR/Cas9 has been applied to edit the genome of various organisms, but our understanding of editing outcomes at specific sites after Cas9-mediated DNA cleavage is still limited. Several deep learning-based methods have been proposed for repair outcome prediction; however, there is still room for improvement in terms of performance regarding frameshifts and model interpretability. Here, we present DeepIndel, an end-to-end multi-label regression model for predicting repair outcomes based on the BERT-base module. We demonstrate that our model outperforms existing methods in terms of accuracy and generalizability across various metrics. Furthermore, we utilized Deep SHAP to visualize the importance of nucleotides at various positions for DNA sequence and found that mononucleotides and trinucleotides in DNA sequences surrounding the cut site play a significant role in repair outcome prediction. [ABSTRACT FROM AUTHOR]

Prediction of chromatin interactions from DNA sequence has been a significant research challenge in the last couple of years. Several solutions have been proposed, most of which are based on encoder-decoder architecture, where 1D sequence is convoluted, encoded into the latent representation, and then decoded using 2D convolutions into the Hi-C pairwise chromatin spatial proximity matrix. Those methods, while obtaining high correlation scores and improved metrics, produce Hi-C matrices that are artificial - they are blurred due to the deep learning model architecture. In our study, we propose the HiCDiffusion, sequence-only model that addresses this problem. We first train the encoder-decoder neural network and then use it as a component of the diffusion model - where we guide the diffusion using a latent representation of the sequence, as well as the final output from the encoder-decoder. That way, we obtain the high-resolution Hi-C matrices that not only better resemble the experimental results - improving the Fréchet inception distance by an average of 11 times, with the highest improvement of 56 times - but also obtain similar classic metrics to current state-of-the-art encoder-decoder architectures used for the task. [ABSTRACT FROM AUTHOR]

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a naturally occurring genetic defense system in bacteria and archaea. It is comprised of a series of DNA sequence repeats with spacers derived from previous exposures to plasmid or phage. Further understanding and applications of CRISPR system have revolutionized our capacity for gene or genome editing of prokaryotes and eukaryotes. The CRISPR systems are classified into 3 distinct types: type I, type II, and type III, each of which possesses an associated signature protein, Cas3, Cas9, and Cas10, respectively. As the CRISPR loci originated from earlier independent exposures of foreign genetic elements, it is likely that their associated signature proteins may have evolved rapidly. Also, their functional domain structures might have experienced different selective pressures, and therefore, they have differentially diverged in their amino acid sequences. We employed genomic, phylogenetic, and structure-function constraint analyses to reveal the evolutionary distribution, phylogenetic relationship, and structure-function constraints of Cas3, Cas9, and Cas10 proteins. Results reveal that all 3 Cas-associated proteins are highly represented in the phyla Bacteroidetes, Firmicutes, and Proteobacteria, including both pathogenic and non-pathogenic species. Genomic analysis of homologous proteins demonstrates that the proteins share 30% to 50% amino acid identity; therefore, they are low to moderately conserved and evolved rapidly. Phylogenetic analysis shows that 3 proteins originated monophyletically; however, the evolution rates were different among different branches of the clades. Furthermore, structure-function constraint analysis reveals that both Cas3 and Cas9 proteins experiences low to moderate levels of negative selection, and several protein domains of Cas3 and Cas9 proteins are highly conserved. To the contrary, most protein domains of Cas10 proteins experience neutral or positive selection, which supports rapid genetic divergence and less structure-function constraints. [ABSTRACT FROM AUTHOR]

Background: Biotransformation of steroid compounds into therapeutic products using microorganisms offers an eco-friendly and economically sustainable approach to the pharmaceutical industry rather than a chemical synthesis way. The biotransformation efficiency of progesterone into the anticancer compound testololactone using Penicillium chrysogenum Ras3009 has been investigated. Besides, maximization of testololactone formation was achieved by studying the kinetic modelling and impact of some fermentation conditions on the biotransformation process. Results: The fungal strain Ras3009 was selected among twelve fungal strains as the most runner for the transformation of 81.18% of progesterone into testololactone. Ras3009 was identified phenotypically and genotypically as Penicillium chrysogenum, its 18 S rRNA nucleotide sequence was deposited in the GenBank database by the accession number OR480104. Studying the impact of fermentation conditions on biotransformation efficiency indicated a positive correlation between substrate concentration and testololactone formation until reaching the maximum velocity vmax. Kinetic studies revealed that vmax was gL− 1hr− 1 with high accuracy, giving R2 of 0.977. The progesterone transformation efficiency generally increased with time, reaching a maximum of 100% at 42 h with testololactone yield (Ypt/s) 0.8700 mg/mg. Moreover, the study indicated that the enzymatic conversion by P. chrysogenum Ras3009 showed high affinity to the substrate, intracellularly expressed, and released during cell disruption, leading to higher efficiency when using whole microbial cell extract. Conclusions: Fungi can be promising biocatalysts for steroid transformation into valuable chemicals and pharmaceutical compounds. The study revealed that the new fungal isolate P. chrysogenum Ras3009 possesses a great catalytic ability to convert progesterone into testololactone. Kinetic modelling analysis and optimization of the fermentation conditions lead to higher transformation efficiency and provide a better understanding of the transformation processes. [ABSTRACT FROM AUTHOR]

Background: Sclerotium rolfsii Sacc. is one of the potential soil-borne plant pathogens due to its significant loss in terms of yield and quality in several crop plants. In soybean the pathogen is associated with collar rot disease. Methods: Sixteen samples which were showing collar rot symptoms were collected from different soybean growing regions of the country and were subjected for isolation and purification. Molecular detection was carried out using ITS1/4 primers followed by phylogenetic analysis was performed using the MEGA 11 bioinformatics tool. Further, the biochemical test was made for oxalic acid production to determine the variability across the isolate. Result: DNA was amplified for ITS rDNA region at 650-700 bp in all the sixteen isolates. BLAST detection of nucleotide sequence of sixteen isolates framed mainly into two distinct phylogenetic clusters. Cluster B consisted of two isolates (MPSe 1 and MHSa 3) whereas, Cluster A contains the remaining fourteen isolates. There was a variation with respect to oxalic acid production among the isolates which was in the rage of 1.15 to 2.23 mg/ml. [ABSTRACT FROM AUTHOR]

Background: Nipah virus is a deadly infectious virus that was first isolated and identified from Malaysia. Since then, a number of Nipah virus outbreaks have been reported from Bangladesh and India. Transmission of the disease occurs through Pteropus genus fruit bats. The case fatality rate of this infection is very high when compared with other viral zoonoses. At present, there are no approved vaccines or drugs available to prevent or treat this infection. A number of studies are ongoing to develop an efficient vaccine candidate to combat this deadly virus. The majority of them concentrate on the structural and non-structural proteins, which are the main targets of neutralizing antibodies. Materials and Methods: Here, we analyzed the genome sequence identity of two Nipah virus strains, Indian and Malaysian, and also the amino acid identity between the two structural proteins (Attachment glycoprotein G and Fusion protein F) and one non-structural protein (W protein) of those two strains. Results and Discussion: It was found that there is a considerable amount of nucleotide sequence homology between the initial strain that originated from Malaysia and the strain that is now found in India. Furthermore, the Structural and Non-structural proteins of these two strains exhibit a high degree of similarity. Conclusion: Hence, a vaccine candidate designed using either NiV M or NiV B can be effectively used as a potent vaccine. [ABSTRACT FROM AUTHOR]

The water‐lily clade represents the second earliest‐diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the "core Nymphaeaceae"—comprising the genera Euryale, Nymphaea and Victoria—is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length‐variable introns and intergenic spacers are known to contain most of the sequence variability within the water‐lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software‐driven DNA sequence alignment, followed by a motif‐based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the subgenus Nymphaea is sister to all other subgenera of Nymphaea. Our results also clarify many evolutionary relationships within the Nymphaea subgenera Brachyceras, Hydrocallis and Nymphaea. In closing, we discuss whether the phylogenetic reconstructions obtained through our motif‐based alignment adjustments are in line with morphological evidence on water‐lily evolution. [ABSTRACT FROM AUTHOR]

Objectives: PD‐1 plays a crucial role in the immune dysregulation of rheumatoid arthritis (RA), but the specific characteristics of PD‐1+CD4+ T cells remain unclear and require further investigation. Methods: Circulating PD‐1+CD4+ T cells from RA patients were analysed using flow cytometry. Plasma levels of soluble PD‐1 (sPD‐1) were measured using enzyme‐linked immunosorbent assay (ELISA). Single‐cell RNA sequence data from peripheral blood mononuclear cells (PBMCs) and synovial tissue of patients were obtained from the GEO and the ImmPort databases. Bioinformatics analyses were performed in the R studio to characterise PD‐1+CD4+ T cells. Expression of CCR7, KLF2 and IL32 in PD‐1+CD4+ T cells was validated by flow cytometry. Results: RA patients showed an elevated proportion of PD‐1+CD4+ T cells in peripheral blood, along with increased plasma sPD‐1 levels, which positively correlated with TNF‐α and erythrocyte sedimentation rate. Bioinformatic analysis revealed PD‐1 expression on CCR7+CD4+ T cells in PBMCs, and on both CCR7+CD4+ T cells and CXCL13+CD4+ T cells in RA synovium. PD‐1 was co‐expressed with CCR7, KLF2, and IL32 in peripheral CD4+ T cells. In synovium, PD‐1+CCR7+CD4+ T cells had higher expression of TNF and LCP2, while PD‐1+CXCL13+CD4+ T cells showed elevated levels of ARID5A and DUSP2. PD‐1+CD4+ T cells in synovium also appeared to interact with B cells and fibroblasts through BTLA and TNFSF signalling pathways. Conclusion: This study highlights the increased proportion of PD‐1+CD4+ T cells and elevated sPD‐1 levels in RA. The transcriptomic profiles and signalling networks of PD‐1+CD4+ T cells offer new insights into their role in RA pathogenesis. [ABSTRACT FROM AUTHOR]

Myocardial fibroblasts play a crucial role in heart structure and function. In recent years, significant progress has been made in understanding the epigenetic regulation of myocardial fibroblasts, which is essential for cardiac development, homeostasis, and disease progression. In healthy hearts, cardiac fibroblasts (CFs) play a crucial role in synthesizing the extracellular matrix (ECM) when in a dormant state. However, under pathological and environmental stress, CFs transform into activated fibroblasts known as myofibroblasts. These myofibroblasts produce an excess of ECM, which promotes cardiac fibrosis. Although multiple molecular mechanisms are associated with CF activation and myocardial dysfunction, emerging evidence highlights the significant involvement of epigenetic regulation in this process. Epigenetics refers to the heritable changes in gene expression that occur without altering the DNA sequence. These mechanisms have emerged as key regulators of myocardial fibroblast function. This review focuses on recent advancements in the understanding of the role of epigenetic regulation and emphasizes the impact of epigenetic modifications on CF activation. Furthermore, we present perspectives and prospects for future research on epigenetic modifications and their implications for myocardial fibroblasts. [ABSTRACT FROM AUTHOR]

Plant rhabdoviruses cause considerable economic losses and are a threat to the agriculture of Solanaceae plants. Two novel virus isolates belonging to the family Rhabdoviridae are identified by high-throughput sequencing (HTS) in Russian eggplant cultivars grown in the Volga river delta region for the first time. The phylogenetic inference of L protein (polymerase) shows that these virus isolates belong to Alphanucleorhabdovirus physostegia (Physostegia chlorotic mottle virus—PhCMoV), and their minus-sense RNA genomes have the typical gene order 3′-nucleocapsid (N)—X protein (X)—phosphoprotein (P)—Y protein (Y)—matrix protein (M)—glycoprotein (G)—polymerase (L)-5′ observed in some plant-infecting alphanucleorhabdoviruses. One of the PhCMoV isolates from the eggplant cultivar Almaz is genetically very similar to the Russian PhCMoV isolate from tomato and grouped in a subclade together with four isolates from Belgium, Germany, the Netherlands, and France. However, another eggplant-infecting isolate from the Russian cultivar Boggart is the most divergent compared with the other 45 virus genomes of European PhCMoV isolates. Thus, our comparative analysis reveals that two virus isolates from Russia may either share a close evolutionary relationship with European isolates or significantly diverge from all known virus isolates. The potential to use the protein sequence comparative analysis of accessory polypeptides, along with the early developed strategy of the nucleotide sequence comparison of the RNA genomes, is shown. [ABSTRACT FROM AUTHOR]

Wheat streak mosaic virus is one of the most widespread viruses in cereal crops, causing severe losses and dramatically affecting worldwide wheat production. Currently, four distinct clades of WSMV have been grouped and named: A (Mexico), B (Europe, Asia, Russia, the USA), C (Iran), and D (The USA, Argentina, Brazil, Australia, Canada, Türkiye). In this study, we determined the nearly complete and partial nucleotide sequences of WSMV type B isolates collected from wheat found in the European part of Türkiye using high throughput sequencing. Excluding the poly(A) tail, the genome of isolate S34Edirne (GenBank acc.no. MZ405098) consisted of 9360 nucleotides and contained a single large open reading frame encoding a polyprotein of 3033 amino acids. The partial sequence of WSMV in wheat isolate (GenBank acc.no. ON364116) is 3348 nt long. The characteristic lack of a GGA (Gly2761) codon within coat protein (CP) of the polyprotein of S34Edirne complete nucleotide sequence is typical for the clade B, WSMV-ΔE isolates, which are widely found throughout the European continent. Sequence comparisons revealed that WSMV Turkish wheat isolate is the most closely related to Czech isolate, with highly similar nucleotide and amino acid identities at 98.83 and 99.13%, respectively. The result of this study indicates that the nearly complete and partial genome sequences of S34Edirne and S34_Edirne24 isolates should be placed into clade B of the European WSMV-ΔE isolates. [ABSTRACT FROM AUTHOR]

There is a high demand for natural agrochemicals to control postharvest phytopathogens in fruit. In this study, the Colletotrichum magnum strain was isolated from Maradol papaya fruits showing symptoms of anthracnose, identified based on its morphological characteristics and confirmed by an analysis of its 5.8S ribosomal DNA sequence. The antifungal activity of aqueous and ethanol extracts from Acacia pennatula, Acalypha gaumeri, Bonellia flammea, Calea urticifolia and Croton chichenensis was evaluated against Colletotrichum magnum by agar dilution bioassay at a concentration of 1 mg mL−1 and recording mycelial growth inhibition (MGI), sporulation inhibition (SI) and spore germination inhibition (SGI) were recorded. The extracts that caused MGI of C. magnum by more than 30% were re-evaluated. It was concluded that the aqueous and ethanol extracts from B. flammea stem bark were the most effective in the MGI (91.53–94.49%), SI (99.32–99.65%), and SGI (91.65–100%) of C. magnum at a 3% (w/v) concentration. A serial dilution of the aqueous extract of B. flammea demonstrated that 2.35% and 3% (w/v) were highly effective against C. magnum in vitro, and both concentrations were randomly applied to postharvest Maradol papaya fruit by dip. The results found that both concentrations caused an anthracnose disease severity of 0.92–0.97% in papaya fruits, which was lower than the commercial fungicide Tecto 60®. The aqueous extract from B. flammea stem bark represents a promising opportunity for developing a natural biopesticide to effectively control anthracnose in papaya fruits induced by C. magnum. [ABSTRACT FROM AUTHOR]

G‐Quadruplexes (G4s) are highly dynamic and polymorphic nucleic acid structures that can adopt a variety of conformations. When exposed to oxidative conditions, more specifically singlet oxygen, the guanosine nucleobases can be oxidized, which in turn can affect the conformation and folding of the G4. Based on this peculiar phenomenon, it is rationalized that G4s can serve as quantification sensors for the production of singlet oxygen. Here, a method for determining the quantum yield of singlet oxygen generation for visible as well as UV‐light excited photosensitizers, using a short G4 DNA sequence, readily available from common DNA companies, as a biological and water‐soluble probe, is presented. [ABSTRACT FROM AUTHOR]

A fluorescent and photoelectrochemical (PEC) dual-mode biosensor based on target biorecognition-triggered cyclic amplification was constructed for Kana detection. With the assistance of the catalyzed reaction of exonuclease III, a Kana-aptamer DNA duplex was designed for conducting the cyclic release of G-rich DNA sequence as well as output DNA S2. The released G-rich sequence triggers the fluorescence (FL) of thioflavin T (ThT), the intensity of which is positively correlated with the Kana concentration. The linear range is 0.2 to 30 nM, and the detection limit reaches 0.07 nM. Simultaneously, the released output DNA S2 was captured by Fe3O4@CdTe-probe ssDNA and then combined with methylene blue to realize the transduction of polarity-reversed PEC signal, leading to the sensitive detection of Kana with a linear range of 0.2 to 40 nM and a calculated detection limit of 0.2 nM. The outstanding performance endows the dual-mode biosensor a promising prospect for practical application. [ABSTRACT FROM AUTHOR]

The non-ideal accuracy and insufficient selectivity of CRISPR/Cas9 systems is a serious problem for their use as a genome editing tool. It is important to select the target sequence correctly so that the CRISPR/Cas9 system does not cut similar sequences. This requires an understanding of how and why mismatches in the target sequence can affect the efficiency of the Cas9/sgRNA complex. In this work, we studied the catalytic activity of the Cas9 enzyme to cleave DNA substrates containing nucleotide mismatch at different positions relative to the PAM in the "seed" sequence. We show that mismatches in the complementarity of the sgRNA/DNA duplex at different positions relative to the protospacer adjacent motif (PAM) sequence tend to decrease the cleavage efficiency and increase the half-maximal reaction time. However, for two mismatches at positions 11 and 20 relative to the PAM, an increase in cleavage efficiency was observed, both with and without an increase in half-reaction time. Thermodynamic parameters were obtained from molecular dynamics results, which showed that mismatches at positions 8, 11, and 20 relative to the PAM thermodynamically stabilize the formed complex, and a mismatch at position 2 of the PAM fragment exerts the greatest stabilization compared to the original DNA sequence. The weak correlation of the thermodynamic binding parameters of the components of the Cas9/sgRNA:dsDNA complex with the cleavage data of DNA substrates containing mismatches indicates that the efficiency of Cas9 operation is mainly affected by the conformational changes in Cas9 and the mutual arrangement of sgRNA and substrates. [ABSTRACT FROM AUTHOR]

Objective: Modern neurobiology focuses on understanding and preventing neurodegeneration by detecting cellular changes early. Changes in astrocyte ultramorphology may indicate early neurodegeneration, associated with decreased synaptic plasticity and astrocyte aging. While high-resolution techniques like EM and SPM can study these structures, they can't use fluorescence microscopy for complete 3D analysis. We suggest using fluorescent dye-conjugated nanoantibodies for astrocyte labeling, allowing detailed ultramorphological research with electron, optical, and scanning probe microscopy, plus optical probe nanotomography. Methods: Hippocampi from male C57BL/6 mice were stained using commercial or GFAP-specific VHH-E9 nanoantibodies. The VHH-E9 antibodies were created by synthesizing a nucleotide sequence with added histidines and cysteine, then cloning it into the pET22 plasmid at XbaI and BamHI sites. Escherichia coli Rosetta-gami (DE3) cells were transformed to produce the pET22-VHHE9 strain. The nanoantibodies were produced via autoinduction and conjugated with a fluorophore. Astrocyte morphology was analyzed using the Sholl test with FiJi software. Results and Discussion: Traditional immunoglobulins can cause visualization inaccuracies due to the distance between the label and target protein. Nanoantibody conjugates, being smaller, reduce these errors. Immunostainings with both types showed similar efficiency, as Sholl profiles from different samples aligned within error margins. This supports the effectiveness of the sample preparation method and VHH-E9 nanoantibodies. It also suggests potential for developing similar procedures with fluorescent contrast agents, like semiconductor nanocrystals. Conclusions: To study astrocyte changes in early neurodegenerative stages, we propose combining high-resolution microscopy, optical microspectroscopy, and 3D ultrastructure restoration. Our method, OPNT, uses fluorescence microscopy for localization data, and SPM/UMT for ultrastructure. This involves creating UMT sections for simultaneous OM/SPM analysis and reconstructing them into a 3D array. We efficiently reconstruct 3D astrocyte ultramorphology and developed an immunostaining procedure using camel VHH-E9 nanoantibodies specific to GFAP, highlighting its efficiency and potential with fluorescent semiconductor nanocrystals. [ABSTRACT FROM AUTHOR]

In this study, we apply k-polar generalized neutrosophic logic to the ideal of BCK-algebra and consequently introduce the notion of a k-polar generalized neutrosophic ideal in BCK-algebra with an example. We provide conditions for a k-polar generalized neutrosophic set to be a k-polar generalized neutrosophic ideal. We prove that every k-polar generalized neutrosophic ideal is a kpolar generalized neutrosophic subalgebra, but the converse is not true, which can be illustrated with an example. Furthermore, we prove that a k-polar generalized neutrosophic set is a k-polar generalized neutrosophic ideal if and only if its corresponding cut sets are ideals of the BCK algebra. [ABSTRACT FROM AUTHOR]

Identifying similar DNA sequences is crucial in various biological research endeavors. This paper delves into the intricate workings of a specific algorithm designed for this purpose. We provide a systematic explanation, exploring how the algorithm handles user input, reads stored DNA sequences, utilizes the Word2Vec model for vector representation, and calculates sequence similarity using diverse metrics like Cosine Similarity and Neutrosophic Distance. Additionally, the paper explores the incorporation of neutrosophic values to account for uncertainty in the comparisons. Finally, we discuss the extraction of results, including matched sequences, similarity scores, and accuracy measures. This in-depth exploration provides a clear understanding of the algorithm's capabilities and fosters its effective application in DNA sequence analysis. [ABSTRACT FROM AUTHOR]

Tumor‐specific microRNA (miRNA) imaging strategies are critical for investigating mechanisms associated with cancer progression; however, nonspecific signal leakage and false‐positive signaling limit their selectivity and efficiency. In this paper, an endogenously activated and self‐reinforced DNA lipid nanodevice (LND) for spatial‐specific and high‐contrast imaging of miRNAs in living cells and animals is presented. The LND is functionalized on cholesterol‐based lipid micelles (CLMs) containing smart response and self‐fueling DNA components that display redox‐activatable and autocatalytic miRNA probing activities, respectively. The LNDs are initially silenced and selectively activated using glutathione, an endogenous microenvironmental factor overexpressed in tumor cells, to prevent nonspecific signal leakage. Subsequently, an autocatalytic DNA circuit is used for tumor‐specific and high‐contrast miRNA imaging. It is demonstrated that robust CLM nanoparticles can be easily assembled from a cholesterol‐conjugated G‐rich DNA sequence by stirring in a buffered solution, enabling the LND to enter cells naturally. In addition, in vitro and in vivo data illustrate that the enhanced biostability of DNA components on the surface of LNDs can be realized for minimizing false‐positive signals, making the system ideal for miRNA imaging in living mice. This smart LND technique has great potential for precise biomedical imaging and clinical diagnosis. [ABSTRACT FROM AUTHOR]

SUMMARY: Deep learning offers new approaches to investigate the mechanisms underlying complex biological phenomena, such as subgenome dominance. Subgenome dominance refers to the dominant expression and/or biased fractionation of genes in one subgenome of allopolyploids, which has shaped the evolution of a large group of plants. However, the underlying cause of subgenome dominance remains elusive. Here, we adopt deep learning to construct two convolutional neural network (CNN) models, binary expression model (BEM) and homoeolog contrast model (HCM), to investigate the mechanism underlying subgenome dominance using DNA sequence and methylation sites. We apply these CNN models to analyze three representative polyploidization systems, Brassica, Gossypium, and Cucurbitaceae, each with available ancient and neo/synthetic polyploidized genomes. The BEM shows that DNA sequence of the promoter region can accurately predict whether a gene is expressed or not. More importantly, the HCM shows that the DNA sequence of the promoter region predicts dominant expression status between homoeologous gene pairs retained from ancient polyploidizations, thus predicting subgenome dominance associated with these events. However, HCM fails to predict gene expression dominance between new homoeologous gene pairs arising from the neo/synthetic polyploidizations. These results are consistent across the three plant polyploidization systems, indicating broad applicability of our models. Furthermore, the two models based on methylation sites produce similar results. These results show that subgenome dominance is associated with long‐term sequence differentiation between the promoters of homoeologs, suggesting that subgenome expression dominance precedes and is the driving force or even the determining factor for sequence divergence between subgenomes following polyploidization. Significance Statement: Our study demonstrates that deep learning models can predict subgenome dominance in ancient polyploids but not in newly synthesized polyploids, highlighting the importance of long‐term sequence divergence. These findings provide valuable insights into the evolutionary mechanisms of polyploidy and offer a novel approach for studying complex genomic interactions. [ABSTRACT FROM AUTHOR]