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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]

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]

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]

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]

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]

The TREX-2 complex of eukaryotes is responsible for the export of a wide range of mRNAs from the nucleus to the cytoplasm. Previously, we showed that a subunit of the D. melanogaster TREX-2 complex, the PCID2 protein, has a domain that specifically interacts with RNA. However, it remains unknown whether other components of the complex are involved in interaction with and recognition of the target mRNA. In the present study, we determined the role of Xmas-2, the core structural subunit of the complex, in the specific recognition of ras2 mRNA fragments. In this work, we showed that Xmas-2 interacts with ras2 mRNA independently of other subunits of the complex. We showed that RNA-binding domains are located in both the N-terminal domain and the C-terminal domain of Xmas-2. However, the interaction of the protein with ras2 mRNA fragments is independent of RNA sequence and structure and is nonspecific. Thus, the Xmas-2 subunit is not involved in the recognition of specific RNA sequences by the complex. [ABSTRACT FROM AUTHOR]

Systemic lupus erythematosus (SLE) is a prime example of how the interplay between genetic and environmental factors can trigger systemic autoimmunity, particularly in young women. Although clinical disease can take years to manifest, risk is established by the unique genetic makeup of an individual. Genome-wide association studies have identified almost 200 SLE-associated risk loci, yet unravelling the functional effect of these loci remains a challenge. New analytic tools have enabled researchers to delve deeper, leveraging DNA sequencing and cell-specific and immune pathway analysis to elucidate the immunopathogenic mechanisms. Both common genetic variants and rare non-synonymous mutations can interact to increase SLE risk. Notably, variants strongly associated with SLE are often located in genome super-enhancers that regulate MHC class II gene expression. Additionally, the 3D conformations of DNA and RNA contribute to genome regulation and innate immune system activation. Improved therapies for SLE are urgently needed and current and future knowledge from genetic and genomic research should provide new tools to facilitate patient diagnosis, enhance the identification of therapeutic targets and optimize testing of agents. This Review explores the genetic basis of systemic lupus erythematosus, including the role of enhancers in the MHC region, the 3D structure of DNA and various pathway-specific mechanisms. These findings enhance disease understanding and inform improved diagnosis and treatment strategies. Key points: Identification of both common and rare monogenic DNA sequence variants associated with systemic lupus erythematosus (SLE) have advanced understanding of critical immune pathways contributing to SLE pathogenesis. Common genetic variants and rare non-synonymous mutations might synergize to augment the risk of developing SLE. Genetic variants that confer a strong association with SLE risk map to critical genome super-enhancers that regulate the expression of MHC class II genes. 3D conformations of DNA and RNA contribute to genome regulation and innate immune system activation. Ancestry-specific genetic risk scores based on relevant immune system pathways might improve the assessment of the risk of SLE. Consideration of patient-specific genetic variants in clinical trial design should increase the success of drug development programmes. [ABSTRACT FROM AUTHOR]

Naked mole-rats, Heterocephalus glaber , are champion hypoxia-tolerant rodents that live under low oxygen conditions in their subterranean burrows. Detrimental effects of low oxygen can be mitigated through metabolic rate depression (MRD), metabolic reorganization, and global downregulation of nonessential cellular processes. Recent research has progressively implicated epigenetic modifications – rapid, reversible changes to gene expression that do not alter the DNA sequence itself – as major players in implementing and maintaining MRD. N6-adenosine (m6A) methylation is the most prevalent mammalian RNA modification and is responsible for pre-mRNA processing and mRNA export from the nucleus. Hence, m6A -mediated conformational changes alter the cellular fate of transcripts. The present study investigated the role of m6A RNA methylation responses to 24 h of hypoxia exposure in H. glaber cardiac tissue. Total protein levels of m6A writers/readers/erasers, m6A demethylase activity, and total m6A quantification were measured under normoxic vs. hypoxic conditions in H. glaber heart. While there was no change in either demethylase activity or total m6A content, many proteins of the m6A pathway were downregulated during hypoxia. Overall, m6A may not be a signature hypoxia-responsive characteristic in H. glaber heart, but downregulation of the protein machinery involved in m6A cycling points to an alternate biological involvement. Further research will explore other forms of RNA modifications and other epigenetic mechanisms to determine the controls on hypoxia endurance in this subterranean mammal. • Broadly, total protein levels of RNA m6A machinery decreased during hypoxia. • There was no change in demethylase activity or total m6A in normoxia vs. hypoxia. • There was a marked upregulation in eIF3a protein expression during hypoxia. • Upregulation of eIF3a may link to AMPK activation and/or mTOR inhibition. [ABSTRACT FROM AUTHOR]

Extracellular vesicles (EVs), or exosomes, play important roles in physiological and pathological cellular communication and have gained substantial traction as biological drug carriers. EVs contain both short and long non-coding RNAs that regulate gene expression and epigenetic processes. To fully capitalize on the potential of EVs as drug carriers, it is important to study and understand the intricacies of EV function and EV RNA-based communication. Here we developed a genetically encodable RNA-based biomaterial, termed EXO-Probe, for tracking EV RNAs. The EXO-Probe comprises an EV-loading RNA sequence (EXO-Code), fused to a fluorogenic RNA Mango aptamer for RNA imaging. This fusion construct allowed the visualization and tracking of EV RNA and colocalization with markers of multivesicular bodies; imaging RNA within EVs, and non-destructive quantification of EVs. Overall, the new RNA-based biomaterial provides a useful and versatile means to interrogate the role of EVs in cellular communication via RNA trafficking to EVs and to study cellular sorting decisions. The system will also help lay the foundation to further improve the therapeutic efficacy of EVs as drug carriers. [Display omitted] [ABSTRACT FROM AUTHOR]

• The current study focused on the prediction of 5-methylcytosine (m5C) sites in RNA sequence • A novel method of feature generation has been proposed by incorporating statistical moments for features reduction. • The LSTM model revealed the maximum accuracy score in independent set test and k-fold cross validation as well. • A webserver, m5c-iDeep, is freely available online for the enhancement of research in m5C sites detection. 5-Methylcytosine (m5c) is a modified cytosine base which is formed as the result of addition of methyl group added at position 5 of carbon. This modification is one of the most common PTM that used to occur in almost all types of RNA. The conventional laboratory methods do not provide quick reliable identification of m5c sites. However, the sequence data readiness has made it feasible to develop computationally intelligent models that optimize the identification process for accuracy and robustness. The present research focused on the development of in-silico methods built using deep learning models. The encoded data was then fed into deep learning models, which included gated recurrent unit (GRU), long short-term memory (LSTM), and bi-directional LSTM (Bi-LSTM). After that, the models were subjected to a rigorous evaluation process that included both independent set testing and 10-fold cross validation. The results revealed that LSTM-based model, m5c-iDeep, outperformed revealing 99.9 % accuracy while comparing with existing m5c predictors. In order to facilitate researchers, m5c-iDeep was also deployed on a web-based server which is accessible at https://taseersuleman-m5c-ideep-m5c-ideep.streamlit.app/. [ABSTRACT FROM AUTHOR]

A colorimetric and rapid signal amplified microRNA (miRNA) detection system based on autocatalytic entropy-driven circuit (AEDC) is reported. The target miRNA-21 (miR-21) was firstly hybridized with the sticky end of the triple-stranded hybrid complex (S, which consisting of a reporter strand (P), a byproduct strand (R) and an assistant strand (Q)), and P strand, which contained the G-quadruplex sequence that was released through the toehold-mediated strand displacement reaction. The G-quadruplex sequence interacted with hemin to form the peroxidase-mimicking DNAzymes and catalyzed the H2O2-mediated oxidation of colorless 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS2−) to the green ABTS•−. Meanwhile, fuel strand (F) hybridized with S to release the target miR-21 and the waste duplex DNA product F-Q was formed, which brings the two split mimic target DNA sequences into proximity to form the intact mimic target DNA sequence (analogue of miR-21). The obtained mimic target DNA as well as the released miR-21 can be cyclically used to trigger autocatalytic EDC reaction, leading to the rapidly enhanced formation of mimic target DNA with the concomitant generation of a higher colorimetric signal. Finally, a colorimetric and rapid miR-21 system based on the hairpin-free AEDC reaction was successfully fabricated. This system also has been applied for the miRNA determination in serum, exhibiting the potential application in the clinical diagnosis. [ABSTRACT FROM AUTHOR]

Papaya trees showing disease symptoms caused by root-knot nematodes (Meloidogyne spp.) were detected in a tropical fruit farm in Vero Beach, FL, USA. Roots were severely galled containing a high population density of root-knot nematode eggs. The nematode species causing damage was identified as M. incognita based on the morphometrics of body, stylet, and tail length of the second-stage juveniles, and morphological characteristics of female perineal patterns. Molecular analyses using both species-specific and universal primers also confirmed the species identity. A pathogenicity test confirmed M. incognita reproduction on papaya by producing nematode females and egg masses within the root galls. This report documents the first confirmed detection of M. incognita in papaya in Florida, USA, providing detailed information on the nematode's morphology characteristics and DNA sequence data. [ABSTRACT FROM AUTHOR]

Reproducible laboratory research relies on correctly identified reagents. We have previously described gene research papers with wrongly identified nucleotide sequence(s), including papers studying miR‐145. Manually verifying reagent identities in 36 recent miR‐145 papers found that 56% and 17% of papers described misidentified nucleotide sequences and cell lines, respectively. We also found 5 cell line identifiers in miR‐145 papers with misidentified nucleotide sequences and cell lines, and 18 cell line identifiers published elsewhere, that did not represent indexed human cell lines. These 23 identifiers were described as non‐verifiable (NV), as their identities were unclear. Studying 420 papers that mentioned 8 NV identifier(s) found 235 papers (56%) that referred to 7 identifiers (BGC‐803, BSG‐803, BSG‐823, GSE‐1, HGC‐7901, HGC‐803, and MGC‐823) as independent cell lines. We could not find any publications describing how these cell lines were established. Six cell lines were sourced from cell line repositories with externally accessible online catalogs, but these cell lines were not indexed as claimed. Some papers also stated that short tandem repeat (STR) profiles had been generated for three cell lines, yet no STR profiles could be identified. In summary, as NV cell lines represent new challenges to research integrity and reproducibility, further investigations are required to clarify their status and identities. [ABSTRACT FROM AUTHOR]

Nucleic acid‐based vaccines allow scalable, rapid, and cell‐free vaccine production in response to an emerging disease such as the current COVID‐19 pandemic. Here, we objected to the design of a multiepitope mRNA vaccine against the structural proteins of SARS‐CoV‐2. Through an immunoinformatic approach, promising epitopes were predicted for the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins. Fragments rich in overlapping epitopes were selected based on binding affinities with HLA classes I and II for the specific presentation to B and T lymphocytes. Two constructs were designed by fusing the fragments in different arrangements via GG linkers. Construct 1 showed better structural properties and interactions with toll‐like receptor 2 (TLR‐2), TLR‐3, and TLR‐4 during molecular docking and dynamic simulation. A 50S ribosomal L7/L12 adjuvant was added to its N‐terminus to improve stability and immunogenicity. The final RNA sequence was used to design a trans‐amplifying RNA (taRNA) vaccine in a split‐vector system. It consists of two molecules: a nonreplicating RNA encoding a trans‐acting replicase to amplify the second one, a trans‐replicon (TR) RNA encoding the vaccine protein. Overall, the immune response simulation detected that activated B and T lymphocytes and increased memory cell formation. Macrophages and dendritic cells proliferated continuously, and IFN‐γ and cytokines like IL‐2 were released highly. [ABSTRACT FROM AUTHOR]

Sri Lankan cassava mosaic virus (SLCMV) is one of the viruses that cause cassava mosaic disease. Strong mosaic symptoms on a cassava plant in the Northern Territory tested positive in begomovirus specific PCR testing. The DNA sequence of the amplicon was 96.38% similar (over 528 bp) to SLCMV, a result confirmed by sequencing genomic DNA. This is the first record of SLCMV in Australia, and outside of Asia. [ABSTRACT FROM AUTHOR]

Background: Epigenetics denotes heritable alterations in gene expression patterns independent of changes in DNA sequence. Epigenetic therapy seeks to reprogram malignant cells to a normal phenotype and has been extensively investigated in oncology. This study conducts a bibliometric analysis of epigenetic therapy in cancer, providing a comprehensive overview of current research, identifying trends, and highlighting key areas of investigation. Methods: Publications concerning epigenetic inhibitors in cancer spanning 2004 to 2023 were retrieved from the Web of Science Core Collection (WoSCC). Co-occurrence analysis using VOSviewer assessed current status and focal points. Evolutionary trends and bursts in the knowledge domain were analyzed using CiteSpace. Bibliometrix facilitated topic evolution and revealed trends in keywords. National, institutional, and author affiliations and collaborations were also examined. Results: A total of 2,153 articles and reviews on epigenetic therapy in oncology were identified, demonstrating a consistent upward trend over time. The United States (745 papers), University of Texas MD Anderson Cancer Center (57 papers), and Stephen B. Baylin (27 papers) emerged as the most productive country, institution, and author, respectively. Keyword co-occurrence analysis identified five primary clusters: tumor, DNA methylation, epigenetic therapy, expression, and immunotherapy. In the past 5 years, newly emerging themes with increased centrality and density include "drug resistance," "immunotherapy," and "combination therapy." The most cited publication reviewed current understanding of potential causes of epigenetic diseases and proposed future therapeutic strategies. Conclusion: In the past two decades, the importance of epigenetic therapy in cancer research has become increasingly prominent. The United States occupies a key position in this field, while China, despite having published a large number of related papers, still has relatively limited influence. Current research focuses on the "combination therapy" of epigenetic drugs. Future studies should further explore the sequencing and scheduling of combination therapies, optimize trial designs and dosing regimens to improve clinical efficacy. [ABSTRACT FROM AUTHOR]

Ancient Platycladus orientalis holds significant ecological, landscape, historical, and cultural value. In northern China, leaf blight has significantly impacted the growth and ornamental value of ancient P. orientalis. In this study, 26 blight leaf samples of ancient P. orientalis were collected in Beijing, China. Phylogenetic analysis based on the concatenated internal transcribed spacer (ITS), β-tubulin (tub2), and RNA polymerase second largest subunit (rpb2) DNA sequence data combined with fungal morphological characteristics revealed three taxa of Nothophoma, i.e. N. platycladus, N. spiraeae, and N. juglandis. Of which, N. platycladus is a species new to science. Koch's postulates indicated that all these three species of Nothophoma could cause leaf blight of P. orientalis. [ABSTRACT FROM AUTHOR]

DNA splice junction classification is a crucial job in computational biology. The challenge is to predict the junction type (IE, EI, or N) from a given DNA sequence. Predicting junction type is crucial for understanding gene expression patterns, disease causes, splicing regulation, and gene structure. The location of the regions where exons are joined, and introns are removed during RNA splicing is very difficult to determine because no universal rule guides this process. This study presents a two-layer hybrid approach inspired by ensemble learning to overcome this challenge. The first layer applies the grey wolf optimizer (GWO) for feature selection. GWO's exploration ability allows it to efficiently search a vast feature space, while its exploitation ability refines promising areas, thus leading to a more reliable feature selection. The selected features are then fed into the second layer, which employs a classification model trained on the retrieved features. Using cross-validation, the proposed method divides the DNA splice junction dataset into training and test sets, allowing for a thorough examination of the classifier's generalization ability. The ensemble model is trained on various partitions of the training set and tested on the remaining held-out fold. This process is performed for each fold, comprehensively evaluating the classifier's performance. We tested our method using the StatLog DNA dataset. Compared to various machine learning models for DNA splice junction prediction, the proposed GWO+SVM ensemble method achieved an accuracy of 96%. This finding suggests that the proposed ensemble hybrid approach is promising for DNA splice junction classification. The implementation code for the proposed approach is available at https://github.com/EFHamouda/DNA-splice-junction-prediction. [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]

Objective: High-risk neuroblastoma patients often have poor outcomes despite multi-treatment options. The risk stratification of high-risk MYCN-not-amplified (HR-MYCN-NA) patients remains difficult. This study aims to identify a gene set signature that can help further stratify HR-MYCN-NA patients for a potential personalized therapeutic strategy. Methods: Three microarrays and one single-cell RNA sequence dataset were acquired and analyzed. Firstly, the prognostic-related genes (PRGs) in HR-MYCN-NA tumor cells were identified using TARGET-NB and GSE137804 datasets. Then, the prognostic model was established by LASSO-Cox regression, and verified in external cohort (GSE49710, GSE45547). Moreover, a time-dependent receiver operating characteristic curve (ROC) and area under the ROC (AUC) was used to assess survival prediction. A nomogram was established to predict the 1-, 3- and 5-year overall survival (OS) of HR-MYCN-NA patients. Results: In the training set, a five-PRGs signature, which include GAL, GFRA3, MARCKS, PSMD13, and ZNHIT3 genes, was identified and successfully stratified HR-MYCN-NA patients into ultra-high risk (UHR) and high-risk (HR) subtypes (HR = 4.29, P < 0.001). ROC curve analysis confirmed its predictive power (AUC = 0.74–0.82), suggesting a good predictive efficacy. Consistently, high-risk scores also predicted worse OS (HR = 2, P = 0.033) in the external validation dataset (AUC = 0.67–0.71). Moreover, the overall C-index of the nomogram was 0.75 (P < 0.001), which indicated good agreement between the observed and predicted survival rates. Further integrating the five PRGs signature with clinical factors, these 5 gene signature (HR = 4.45, P < 0.001) and tumor grade (HR = 4.15, P = 0.02) were found to be independent prognostic factors for HR-MYCN-NA patients. Conclusion: The novel five PRGs signature could well predict the survival of HR-MYCN-NA patients, which may provide constructive information for these subsets. [ABSTRACT FROM AUTHOR]

The origin of translation is one of the most difficult problems of molecular evolution. Identifying molecular systems that translate an RNA sequence into a peptide sequence in the absence of ribosomes and enzymes is a challenge. Recently, single‐nucleotide translation via coupling of 5′ phosphoramidate‐linked amino acids to 2′/3′‐aminoacyl transfer‐NMPs, as directed by the sequence of an RNA template, was demonstrated for three of the four canonical nucleotides. How single‐nucleotide translation could be expanded to include all four bases and to produce longer peptides without translocation along the template strand remained unclear. Using transfer strands of increasing length containing any of the four bases that interrogate adjacent positions along the template, we now show that pentapeptides can be produced in coupling reactions and subsequent hydrolytic release in situ. With 2′/3′‐aminoacylated mono‐, di‐, tri‐ and tetranucleotides we thus show how efficient translation can be without biomacromolecules. [ABSTRACT FROM AUTHOR]

This article explores the significance of developing new techniques and technical advances in experimental botany to enhance our understanding of plant biology. It specifically focuses on the importance of microscopy and gene editing technology in plant research. The article highlights the different branches of microscopy and their advantages and limitations, as well as specific research articles that utilize microscopy techniques to study autophagosomes, peptide-receptor binding, and redox dynamics. It also discusses the use of CRISPR/Cas9 gene editing technology in plants and provides resources for planning and performing gene editing experiments. The article emphasizes the need for a combination of advanced methods in plant biology research and acknowledges the contributions of previous methodologies to scientific progress. [Extracted from the article]

Background: MicroRNA isoforms (isomiRs), tRNA-derived fragments (tRFs), and rRNA-derived fragments (rRFs) represent most of the small non-coding RNAs (sncRNAs) found in cells. Members of these three classes modulate messenger RNA (mRNA) and protein abundance and are dysregulated in diseases. Experimental studies to date have assumed that the subcellular distribution of these molecules is well-understood, independent of cell type, and the same for all isoforms of a sncRNA. Results: We tested these assumptions by investigating the subcellular distribution of isomiRs, tRFs, and rRFs in biological replicates from three cell lines from the same tissue and same-sex donors that model the same cancer subtype. In each cell line, we profiled the isomiRs, tRFs, and rRFs in the nucleus, cytoplasm, whole mitochondrion (MT), mitoplast (MP), and whole cell. Using a rigorous mathematical model we developed, we accounted for cross-fraction contamination and technical errors and adjusted the measured abundances accordingly. Analyses of the adjusted abundances show that isomiRs, tRFs, and rRFs exhibit complex patterns of subcellular distributions. These patterns depend on each sncRNA's exact sequence and the cell type. Even in the same cell line, isoforms of the same sncRNA whose sequences differ by a few nucleotides (nts) can have different subcellular distributions. Conclusions: SncRNAs with similar sequences have different subcellular distributions within and across cell lines, suggesting that each isoform could have a different function. Future computational and experimental studies of isomiRs, tRFs, and rRFs will need to distinguish among each molecule's various isoforms and account for differences in each isoform's subcellular distribution in the cell line at hand. While the findings add to a growing body of evidence that isomiRs, tRFs, rRFs, tRNAs, and rRNAs follow complex intracellular trafficking rules, further investigation is needed to exclude alternative explanations for the observed subcellular distribution of sncRNAs. [ABSTRACT FROM AUTHOR]

Metabolic syndrome is a growing concern in developed societies and due to its polygenic nature, the genetic component is only slowly being elucidated. Common mitochondrial DNA sequence variants have been associated with symptoms of metabolic syndrome and may, therefore, be relevant players in the genetics of metabolic syndrome. We investigate the effect of mitochondrial sequence variation on the metabolic phenotype in conplastic rat strains with identical nuclear but unique mitochondrial genomes, challenged by high-fat diet. We find that the variation in mitochondrial rRNA sequence represents risk factor in the insulin resistance development, which is associated with diacylglycerols accumulation, induced by tissue-specific reduction of the oxidative capacity. These metabolic perturbations stem from the 12S rRNA sequence variation affecting mitochondrial ribosome assembly and translation. Our work demonstrates that physiological variation in mitochondrial rRNA might represent a relevant underlying factor in the progression of metabolic syndrome. Detailed characterization of mtDNA haplotypes uncovers the impact of mitochondrial rRNA variations on mitochondrial translation and oxidative capacity and their metabolic consequences including insulin resistance development induced by high-fat diet. [ABSTRACT FROM AUTHOR]

We report the design of a single RNA sequence capable of adopting one of two ribozyme folds and catalyzing the cleavage and/or ligation of the respective substrates. The RNA is able to change its conformation in response to its environment, hence it is called chameleon ribozyme (CHR). Efficient RNA cleavage of two different substrates as well as RNA ligation by CHR is demonstrated in separate experiments and in a one pot reaction. Our study shows that sequence variants of the hairpin ribozyme intersect with the hammerhead ribozyme and that rather short RNA molecules can have comprehensive conformational flexibility, which is an important feature for the emergence of new functional folds in early evolution. [ABSTRACT FROM AUTHOR]

During an investigation of fungal diversity from freshwater environments in different regions in Jiangxi Province, China, four interesting species were collected. Morphology coupled with combined gene analysis of an ITS, LSU, SSU, and rpb2 DNA sequence data showed that they belong to the family Pleurotheciaceae. Four new species, Pleurotheciella ganzhouensis, Pla. irregularis, Pla. verrucosa, and Pleurothecium jiangxiense are herein described. Pleurotheciella ganzhouensis is characterized by its capsule-shaped conidia and short conidiophores, while Pla. irregularis has amorphous conidiophores and 3-septate conidia. Pleurotheciella verrucosa has cylindrical or verrucolose conidiogenous cells, 1-septate, narrowly fusiform, meniscus or subclavate conidia. Pleurothecium jiangxiense characterized in having conidiogenous cells with dense cylindrical denticles and short conidiophores. Pleurothecium obovoideum was transferred to Neomonodictys based on phylogenetic evidence. All species are compared with other similar species and comprehensive descriptions, micrographs, and phylogenetic data are provided. [ABSTRACT FROM AUTHOR]

Synonymous codons were originally viewed as interchangeable, with no phenotypic consequences. However, substantial evidence has now demonstrated that synonymous substitutions can perturb a variety of gene expression and protein homeostasis mechanisms, including translational efficiency, translational fidelity, and cotranslational folding of the encoded protein. To date, most studies of synonymous codon-derived perturbations have focused on effects within a single gene. Here, we show that synonymous codon substitutions made far within the coding sequence of Escherichia coli plasmid-encoded chloramphenicol acetyltransferase (cat) can significantly increase expression of the divergent upstream tetracycline resistance gene, tetR. In four out of nine synonymously recoded cat sequences tested, expression of the upstream tetR gene was significantly elevated due to transcription of a long antisense RNA (asRNA) originating from a transcription start site within cat. Surprisingly, transcription of this asRNA readily bypassed the native tet transcriptional repression mechanism. Even more surprisingly, accumulation of the TetR protein correlated with the level of asRNA, rather than total tetR RNA. These effects of synonymous codon substitutions on transcription and translation of a neighboring gene suggest that synonymous codon usage in bacteria may be under selection to both preserve the amino acid sequence of the encoded gene and avoid DNA sequence elements that can significantly perturb expression of neighboring genes. Avoiding such sequences may be especially important in plasmids and prokaryotic genomes, where genes and regulatory elements are often densely packed. Similar considerations may apply to the design of genetic circuits for synthetic biology applications. [ABSTRACT FROM AUTHOR]

The btuB riboswitch is a regulatory RNA sequence controlling gene expression of the outer membrane B12 transport protein BtuB by specifically binding coenzyme B12 (AdoCbl) as its natural ligand. The B12 sensing riboswitch class is known to accept various B12 derivatives, leading to a division into two riboswitch subclasses, dependent on the size of the apical ligand. Here we focus on the role of side chains b and e on affinity and proper recognition, i. e. correct structural switch of the btuB RNA, which belongs to the AdoCbl‐binding class I. Chemical modification of these side chains disturbs crucial hydrogen bonds and/or electrostatic interactions with the RNA, its effect on both affinity and switching being monitored by in‐line probing. Chemical modifications at sidechain b of vitamin B12 show larger effects indicating crucial B12‐RNA interactions. When introducing the same modification to AdoCbl the influence of any side‐chain modification tested is reduced. This renders the impact of the adenosyl‐ligand for B12‐btuB riboswitch recognition clearly beyond the known role in affinity. [ABSTRACT FROM AUTHOR]

Oligodendrocyte (OL) differentiation from oligodendrocyte precursor cells (OPCs) is considered to result in two populations: premyelinating and myelinating OLs. Recent single‐cell RNA sequence data subdivided these populations into newly formed (NFOLs), myelin‐forming (MFOLs), and mature (MOLs) oligodendrocytes. However, which newly proposed population corresponds to premyelinating or myelinating OLs is unknown. We focused on the NFOL‐specific long non‐coding oligodendrocyte 1 gene (LncOL1) and sought to label NFOLs under the control of the LncOL1 promoter using a tetracycline‐controllable gene induction system. We demonstrated that LncOL1 was expressed by premyelinating OLs and that the MFOL‐specific gene, Ctps, was not, indicating that NFOLs correspond to premyelinating OLs and that MFOLs and MOLs correspond to myelinating OLs. We then generated a LncOL1‐tTA mouse in which a tetracycline transactivator (tTA) cassette was inserted downstream from the LncOL1 transcription initiation site. By crossing the LncOL1‐tTA mice with tetO reporter mice, we generated LncOL1‐tTA::tetO‐yellow fluorescent protein (YFP) double‐transgenic (LncOL1‐YFP) mice. Although LncOL1 is non‐coding, YFP was detected in LncOL1‐YFP mice, indicating successful tTA translation. Unexpectedly, we found that the morphology of LncOL1‐tTA‐driven YFP+ cells was distinct from that of LncOL1+ premyelinating OLs and that the labeled cells instead appeared as myelinating OLs. We demonstrated from their RNA expression that YFP‐labeled OLs were MFOLs, but not MOLs. Using the unique property of delayed YFP induction, we sought to determine whether MFOLs are constantly supplied from OPCs and differentiate into MOLs, or whether MFOLs pause their differentiation and sustain this stage in the adult brain. To achieve this objective, we irradiated adult LncOL1‐YFP brains with X‐rays to deplete dividing OPCs and their progeny. The irradiation extinguished YFP‐labeled OLs, indicating that adult OPCs differentiated into MOLs during a single period. We established a new transgenic mouse line that genetically labels MFOLs, providing a reliable tool for investigating the dynamics of adult oligodendrogenesis. [ABSTRACT FROM AUTHOR]

Natural products are molecules that fulfil a range of important ecological functions. Many natural products have been exploited for pharmaceutical and agricultural applications. In contrast to many other specialised metabolites, the products of modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) systems can often (partially) be predicted from the DNA sequence of the biosynthetic gene clusters. This is because the biosynthetic pathways of NRPS and PKS systems adhere to consistent rulesets. These universal biosynthetic rules can be leveraged to generate biosynthetic models of biosynthetic pathways. While these principles have been largely deciphered, software that leverages these rules to automatically generate visualisations of biosynthetic models has not yet been developed. To enable high-quality automated visualisations of natural product biosynthetic pathways, we developed RAIChU (Reaction Analysis through Illustrating Chemical Units), which produces depictions of biosynthetic transformations of PKS, NRPS, and hybrid PKS/NRPS systems from predicted or experimentally verified module architectures and domain substrate specificities. RAIChU also boasts a library of functions to perform and visualise reactions and pathways whose specifics (e.g., regioselectivity, stereoselectivity) are still difficult to predict, including terpenes, ribosomally synthesised and posttranslationally modified peptides and alkaloids. Additionally, RAIChU includes 34 prevalent tailoring reactions to enable the visualisation of biosynthetic pathways of fully maturated natural products. RAIChU can be integrated into Python pipelines, allowing users to upload and edit results from antiSMASH, a widely used BGC detection and annotation tool, or to build biosynthetic PKS/NRPS systems from scratch. RAIChU's cluster drawing correctness (100%) and drawing readability (97.66%) were validated on 5000 randomly generated PKS/NRPS systems, and on the MIBiG database. The automated visualisation of these pathways accelerates the generation of biosynthetic models, facilitates the analysis of large (meta-) genomic datasets and reduces human error. RAIChU is available at https://github.com/BTheDragonMaster/RAIChU and https://pypi.org/project/raichu. Scientific contribution RAIChU is the first software package capable of automating high-quality visualisations of natural product biosynthetic pathways. By leveraging universal biosynthetic rules, RAIChU enables the depiction of complex biosynthetic transformations for PKS, NRPS, ribosomally synthesised and posttranslationally modified peptide (RiPP), terpene and alkaloid systems, enhancing predictive and analytical capabilities. This innovation not only streamlines the creation of biosynthetic models, making the analysis of large genomic datasets more efficient and accurate, but also bridges a crucial gap in predicting and visualising the complexities of natural product biosynthesis. [ABSTRACT FROM AUTHOR]

Macrobrachium rosenbergii, or giant river prawn, is the most economically crucial cultured freshwater crustacean. A predominant challenge in developing crustacean aquaculture is reproduction management, particularly ovary maturation, where identifying regulative mechanisms at the molecular level is critical. Ovary is the primary tissue for studying gene and protein expressions involved in crustacean growth and reproduction. Despite significant interest in M. rosenbergii, its gene discovery has been at a relatively small scale compared to other genera. In this study, comprehensive transcriptomic sequencing data for different maturation stages of the ovary of M. rosenbergii were observed. The 20 female M. rosenbergii samples evaluated were categorised into four maturation stages, 1 to 4. A total of 817,793,14, 841,670,70, 914,248,78 and 878,085,88 raw reads were obtained from stages 1, 2, 3 and 4, respectively. The assembled unique sequences (unigenes) post-clustering (n = 98013) was 131,093,546 bp with an average size of 1,338 bp. The BLASTX unigene search against National Centre for Biotechnology Information (NCBI), non-redundant (NR), nucleotide sequence (NT), Kyoto Encyclopaedia of Genes and Genomes Orthology (KO), Swiss-Prot, Protein Family (PFAM), Gene Ontology (GO), and euKaryotic Orthologous Groups (KOG) databases yielded 27,680 (28.24%), 7,449 (7.59%), 13,026 (13.29%), 22,606 (23.06%), 29,907 (30.51%), 30,025 (30.63%) and 14,368 (14.65%) significant matches, respectively, totalling to 37,338 annotated unigenes (38.09%). The differentially expressed genes (DEG) analysis conducted in this study led to identifying cyclin B, insulin receptor (IR), oestrogen sulfotransferase (ESULT) and vitellogenin (Vg), which are critical in ovarian maturation. Nevertheless, some M. rosenbergii ovarian maturation-related genes, such as small ubiquitin-like modifier (SUMO)-activating enzyme subunit 1, E3 ubiquitin-protein ligase RNF25, and neuroparsin, were first identified in this study. The data obtained in the present study could considerably contribute to understanding the gene expression and genome structure in M. rosenbergii ovaries throughout its developmental stage. [ABSTRACT FROM AUTHOR]