Region Of RNA Research Articles

A riboswitch-controlled TerC family transporter Alx tunes intracellular manganese concentration in Escherichia coli at alkaline pH.

Cells use transition metal ions as structural components of biomolecules and cofactors in enzymatic reactions, making transition metal ions integral cellular components. Organisms optimize metal ion concentration to meet cellular needs by regulating the expression of proteins that import and export that metal ion, often in a metal ion concentration-dependent manner. One such regulation mechanism is via riboswitches, which are 5'-untranslated regions of an mRNA that undergo conformational changes to promote or inhibit the expression of the downstream gene, commonly in response to a ligand. The yybP-ykoY family of bacterial riboswitches shares a conserved aptamer domain that binds manganese ions (Mn2+). In Escherichia coli, the yybP-ykoY riboswitch precedes and regulates the expression of two different genes: mntP, which based on genetic evidence encodes an Mn2+ exporter, and alx, which encodes a putative metal ion transporter whose cognate ligand is currently in question. The expression of alx is upregulated by both elevated concentrations of Mn2+ and alkaline pH. With metal ion measurements and gene expression studies, we demonstrate that the alkalinization of media increases the cytoplasmic manganese pool, which, in turn, enhances alx expression. The Alx-mediated Mn2+ export prevents the toxic buildup of the cellular manganese, with the export activity maximal at alkaline pH. We pinpoint a set of acidic residues in the predicted transmembrane segments of Alx that play a critical role in Mn2+ export. We propose that Alx-mediated Mn2+ export serves as a primary protective mechanism that fine tunes the cytoplasmic manganese content, especially during alkaline stress.IMPORTANCEBacteria use clever ways to tune gene expression upon encountering certain environmental stresses, such as alkaline pH in parts of the human gut and high concentration of a transition metal ion manganese. One way by which bacteria regulate the expression of their genes is through the 5'-untranslated regions of messenger RNA called riboswitches that bind ligands to turn expression of genes on/off. In this work, we have investigated the roles and regulation of alx and mntP, the two genes in Escherichia coli regulated by the yybP-ykoY riboswitches, in alkaline pH and high concentration of Mn2+. This work highlights the intricate ways through which bacteria adapt to their surroundings, utilizing riboregulatory mechanisms to maintain Mn2+ levels amidst varying environmental factors.

Improved constructs for bait RNA display in a bacterial three-hybrid assay.

We have previously developed a transcription-based bacterial three-hybrid (B3H) assay as a genetic approach to probe RNA-protein interactions inside of E. coli cells. This system offers a straightforward path to identify and assess the consequences of mutations in RBPs with molecular phenotypes of interest. One limiting factor in detecting RNA-protein interactions in the B3H assay is RNA misfolding arising from incorrect base-pair interactions with neighboring RNA sequences in a hybrid RNA. To support correct folding of hybrid bait RNAs, we have explored the use of a highly stable stem ("GC clamp") to isolate regions of a hybrid RNA as discrete folding units. In this work, we introduce new bait RNA constructs to 1) insulate the folding of individual components of the hybrid RNA with GC clamps and 2) express bait RNAs that do not encode their own intrinsic terminator. We find that short GC clamps (5 or 7 bp long) are more effective than a longer 13bp GC clamp in the B3H assay. These new constructs increase the number of Hfq-sRNA and -5'UTR interactions that are detectable in the B3H system and improve the signal-to-noise ratio of many of these interactions. We therefore recommend the use of constructs containing short GC clamps for the expression of future B3H bait RNAs. With these new constructs, a broader range of RNA-protein interactions are detectable in the B3H assay, expanding the utility and impact of this genetic tool as a platform to search for and interrogate mechanisms of additional RNA-protein interactions.

SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data.

RNA molecules perform a variety of functions in cells, many of which rely on their secondary and tertiary structures. Chemical probing methods coupled with high-throughput sequencing have significantly accelerated the mapping of RNA structures, and increasingly large datasets of transcriptome-wide RNA chemical probing data are becoming available. Analogously to what has been done for decades in the protein world, this RNA structural information can be leveraged to aid the discovery of structural similarity to a known RNA (or RNA family), which, in turn, can inform about the function of transcripts. We have previously developed SHAPEwarp, a sequence-agnostic method for the search of structurally homologous RNA segments in a database of reactivity profiles derived from chemical probing experiments. In its original implementation, however, SHAPEwarp required substantial computational resources, even for moderately sized databases, as well as significant Linux command line know-how. To address these limitations, we introduce here SHAPEwarp-web, a user-friendly web interface to rapidly query large databases of RNA chemical probing data for structurally similar RNAs. Aside from featuring a completely rewritten core, which speeds up by orders of magnitude the search inside large databases, the web server hosts several high-quality chemical probing databases across multiple species. SHAPEwarp-web is available fromhttps://shapewarp.incarnatolab.com.

The outbreak of teak leaf blight disease caused by Alternaria alternata in the semi‐arid Bundelkhand region of India

AbstractTectona grandis is a vital hardwood tree species with substantial industrial and economic importance. From 2020 to 2021, an unusual leaf blight disease was observed in T. grandis saplings planted in the Nursery of the Central Agroforestry Research Institute (CAFRI), Jhansi, India. Disease incidence was recorded as 50%–70% with 40%–82% severity over two consecutive years on over 1000 saplings. The leaf blight disease was extensive, leading to defoliation of young leaves and mortality of teak saplings in the nursery. The pathogen was identified as Alternaria alternata following standard laboratory procedures and sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA). The pathogenicity of two isolates, A. alternata TgAa1 and TgAa2, was proven under greenhouse conditions. Phylogenetic analysis revealed the close association of TgAa1 and TgAa2 with other pathogenic A. alternata strains in the NCBI database. A. alternata is considered a severe foliar pathogen, known to cause leaf spot and leaf blight diseases in many annual and perennial plant species. Correct diagnosis and prevention are emphasized to contain the spread of teak leaf blight to other regions in India. This is the first report of A. alternata causing Tectona grandis leaf blight in the Bundelkhand region of India.

Analysis of RNA translation with a deep learning architecture provides new insight into translation control.

Accurate annotation of coding regions in RNAs is essential for understanding gene translation. We developed a deep neural network to directly predict and analyze translation initiation and termination sites from RNA sequences. Trained with human transcripts, our model learned hidden rules of translation control and achieved a near perfect prediction of canonical translation sites across entire human transcriptome. Surprisingly, this model revealed a new role of codon usage in regulating translation termination, which was experimentally validated. We also identified thousands of new open reading frames in mRNAs or lncRNAs, some of which were confirmed experimentally. The model trained with human mRNAs achieved high prediction accuracy of canonical translation sites in all eukaryotes and good prediction in polycistronic transcripts from prokaryotes or RNA viruses, suggesting a high degree of conservation in translation control. Collectively, we present a general and efficient deep learning model for RNA translation, generating new insights into the complexity of translation regulation.

Cooperative binding of bivalent ligands yields new insights into the guanidine-II riboswitch.

Riboswitches are involved in regulating the gene expression in bacteria. They are located within the untranslated regions of bacterial messenger RNA and function as switches by adjusting their shape, depending on the presence or absence of specific ligands. To decipher the fundamental aspects of bacterial gene control, it is therefore important to understand the mechanisms that underlie these conformational switches. To this end, a combination of an experimental binding study, molecular simulations and machine learning has been employed to obtain insights into the conformational changes and structural dynamics of the guanidine-II riboswitch. By exploiting the design of a bivalent ligand, we were able to study ligand binding in the aptamer dimer at the molecular level. Spontaneous ligand-binding events, which are usually difficult to simulate, were observed and the contributing factors are described. These findings were further confirmed by in vivo experiments, where the cooperative binding effects of the bivalent ligands resulted in increased binding affinity compared to the native guanidinium ligand. Beyond ligand binding itself, the simulations revealed a novel, ligand-dependent base-stacking interaction outside of the binding pocket that stabilizes the riboswitch.

Recognition of Davidsoniella virescens on Fagus sylvatica Wood in Poland and Assessment of Its Pathogenicity.

Davidsoniella virescens is so far only known in North America. However, recently in southern Poland, blackish growth consisting of fungal mycelia and sporulation structures was found on the wood of Fagus sylvatica. As a result of isolation, 17 cultures of this fungus were obtained. All cultures produced an intense sweet odor. This fungus, both in situ and in vitro, abundantly produced perithecia with long necks and asexual stage. Particularly characteristic was the production of variable endoconidia in two types of phialophores differing mainly in the width of the collarette. The nucleotide sequences for five gene fragments of representative cultures were used in phylogenetic analyses: 18S; the internal transcribed spacer regions ITS1 and ITS2, including the 5.8S gene (ITS); 28S region of the ribosomal RNA (rRNA), β-tubulin 2 (TUB2) and translation elongation factor 1-α (TEF1). Based on morphological and phylogenetic analyses, the fungus on European beech in Poland was identified as Davidsoniella virescens. The optimal temperature for radial colony growth was 20 °C. However, the differences between colony diameter at 25 °C compared to that at the optimal temperature were not statistically significant. Six D. virescens isolates were used for pathogenicity assay. They were inoculated into wounds on stems of two-year-old seedlings of Fagus sylvatica and Acer saccharum (36 seedlings of each tree species). Final evaluation was performed 4 months after inoculation. No external symptoms were observed in any A. saccharum seedling, neither in the crown nor on the stem. However, 13.9% of F. sylvatica seedlings showed wilting symptoms throughout the entire crown within 3-6 weeks after inoculation. Moreover, after 4 months on the stems of 30.6% beech seedlings, necrotic lesions with a length of 1.3 to 7.2 cm were formed, without any symptoms of wilting. The most noticeable internal symptom was the discoloration of the wood, which was observed in all inoculated seedlings of both tree species. All D. virescens isolates caused greater wood discoloration in F. sylvatica than in A. saccharum. Most of the differences found in the extent of discoloration between host plants were statistically significant. The discoloration caused by all D. virescens isolates in F. sylvatica was significantly greater than in the control. However, none of the isolates tested on A. saccharum caused significantly greater wood discoloration compared to the control. Pathogenicity tests showed that the D. virescens isolates identified in southern Poland may pose a greater threat to native European beech than to foreign sugar maple.

Investigating Enterocytozoon bieneusi in pigs farmed in Zhejiang Province, China: Occurrence, genotype identification, evolutionary analysis, and zoonotic risk assessment

Enterocytozoon bieneusi is a widespread intracellular fungus that can infect both humans and animals, making it a significant zoonotic threat. In the current study, a total of 208 fecal samples were assayed to investigate the prevalence of E. bieneusi in pigs reared in Zhejiang Province, China. Employing polymerase chain reaction (PCR) amplification techniques specifically designed to target the internal transcribed spacer (ITS) region of the small subunit ribosomal RNA (rRNA) gene, the results revealed that 78 samples (37.5 %) tested positive for the presence of E. bieneusi. A total of 19 different genotypes of E. bieneusi were detected. Nine of these genotypes were already known: EbpC (n = 36), KIN-1 (n = 10), PigEbITS7 (n = 8), EbpA (n = 6), Henan III (n = 3), PigEbITS5 (n = 2), Henan-IV (n = 1), EbpD (n = 1), and TypeIV (n = 1), and 10 were novel: ZJP-I to ZJP-X (one each). The present investigation revealed that all the nine known genotypes identified in pigs here, have also been previously discovered in humans. Additionally, the novel genotypes of E. bieneusi discovered here were all classified as belonging to Group 1. These findings suggest the potential for cross-species transmission between humans and pigs.

Revealing Brownish Mycena Diversity in China: New Discoveries and Taxonomic Insights.

Within the genus Mycena, species exhibiting brownish basidiomata present considerable challenges in identification due to similar coloration. This study underscores the significance of pileipellis types and cheilocystidia characteristics as critical in delimiting brownish Mycena species. To clarify the principal taxonomic characters and their utility in distinguishing between brownish Mycena species, a morphological taxonomy and phylogenetic analysis were performed. Five new species from China were introduced and characterized through a comprehensive morphological anatomy and phylogenetic substantiation: M. campanulatihemisphaerica sp. nov., M. digitifurcata sp. nov., M. kunyuensis sp. nov., M. limitis sp. nov., and M. oryzifluens sp. nov. Discussions of these taxa are supplemented with morphological illustrations. The phylogenetic relationships were inferred using Bayesian Inference and Maximum Likelihood methods based on sequences from the internal transcribed spacer and the large subunit regions of nuclear ribosomal RNA. With the addition of these five new species, the worldwide count of brownish Mycena increases to 94, and a key to the 29 known species of brownish Mycena from China is presented.

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements.

In the SARS-CoV-2 lineage, RNA elements essential for its viral life cycle, including genome replication and gene expression, have been identified. Still, the precise structures and functions of these RNA regions in coronaviruses remain poorly understood. This lack of knowledge points out the need for further research to better understand these crucial aspects of viral biology and, in time, prepare for future outbreaks. In this research, the in silico analysis of the cis RNA structures that act in the alpha-, beta-, gamma-, and deltacoronavirus genera has provided a detailed view of the presence and adaptation of the structures of these elements in coronaviruses. The results emphasize the importance of these cis elements in viral biology and their variability between different viral variants. Some coronavirus variants in some groups, depending on the cis element (stem-loop1 and -2; pseudoknot stem-loop1 and -2, and s2m), exhibited functional adaptation. Additionally, the conformation flexibility of the s2m element in the SARS variants was determined, suggesting a coevolution of this element in this viral group. The variability in secondary structures suggests genomic adaptations that may be related to replication processes, genetic regulation, as well as the specific pathogenicity of each variant. The results suggest that RNA structures in coronaviruses can adapt and evolve toward different viral variants, which has important implications for viral adaptation, pathogenicity, and future therapeutic strategies.

Long non-coding intergenic RNA, LINC00273 induces cancer metastasis and stemness via miRNA sponging in triple negative breast cancer

LncRNAs and miRNAs, being the master regulators of gene expression, are crucial functional mediators in cancer. Our study unveils the critical regulatory role of the metastatic long non-coding RNA LINC00273 as the master regulator of oncogenes involved in cancer metastasis, stemness, and chemoresistance via its miRNA sponging mechanism. M2 (a salt of bis-Schiff base) mediated G quadruplex (G4) stabilization at the LINC00273 gene promoter remarkably inhibits LINC00273 transcription. Therefore, low-level LINC00273 transcripts are unable to efficiently sponge the miRNAs, which subsequently become available to bind and downregulate their target oncogenes. We have observed significantly different global transcriptomic scenarios in LINC00273 upregulated and downregulated circumstances in MDA-MB-231 triple-negative breast cancer model. Additionally, we have found the G4 sequence in the LINC00273 RNA to play a critical role in miRNA sequestration. miRNAs (miR-6789-5p, miR200b, miR-125b-5p, miR-4268, miR3978) have base pairing complementarity within the G4 region of LINC00273 RNA and the 3′-UTR (untranslated region) of MAPK12, TGF-β1, and SIX-1 transcripts. We have reported TGF-β1, SIX-1, and MAPK12 to be the direct downstream targets of LINC00273. The correlation between abnormal expression of lncRNA LINC00273 and TNBC aggressiveness strongly evidenced in our study shall accelerate the development of lncRNA-based anti-metastatic therapeutics.

Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance.

The ompD transcript, encoding an outer membrane porin in Salmonella, harbors a controlling element in its coding region that base-pairs imperfectly with a 'seed' region of the small regulatory RNA (sRNA) MicC. When tagged with the sRNA, the ompD mRNA is cleaved downstream of the pairing site by the conserved endoribonuclease RNase E, leading to transcript destruction. We observe that the sRNA-induced cleavage site is accessible to RNase E in vitro upon recruitment of ompD into the 30S translation pre-initiation complex (PIC) in the presence of the degradosome components. Evaluation of substrate accessibility suggests that the paused 30S PIC presents the mRNA for targeted recognition and degradation. Ribonuclease activity on PIC-bound ompD is critically dependent on the recruitment of RNase E into the multi-enzyme RNA degradosome, and our data suggest a process of substrate capture and handover to catalytic sites within the degradosome, in which sequential steps of seed matching and duplex remodelling contribute to cleavage efficiency. Our findings support a putative mechanism of surveillance at translation that potentially terminates gene expression efficiently and rapidly in response to signals provided by regulatory RNA.

Exploring the Regulatory Landscape of Dementia: Insights from Non-Coding RNAs.

Dementia, a multifaceted neurological syndrome characterized by cognitive decline, poses significant challenges to daily functioning. The main causes of dementia, including Alzheimer's disease (AD), frontotemporal dementia (FTD), Lewy body dementia (LBD), and vascular dementia (VD), have different symptoms and etiologies. Genetic regulators, specifically non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are known to play important roles in dementia pathogenesis. MiRNAs, small non-coding RNAs, regulate gene expression by binding to the 3' untranslated regions of target messenger RNAs (mRNAs), while lncRNAs and circRNAs act as molecular sponges for miRNAs, thereby regulating gene expression. The emerging concept of competing endogenous RNA (ceRNA) interactions, involving lncRNAs and circRNAs as competitors for miRNA binding, has gained attention as potential biomarkers and therapeutic targets in dementia-related disorders. This review explores the regulatory roles of ncRNAs, particularly miRNAs, and the intricate dynamics of ceRNA interactions, providing insights into dementia pathogenesis and potential therapeutic avenues.

Effects of Scallop Mantle Toxin on Intestinal Microflora and Intestinal Barrier Function in Mice.

Previous studies have shown that feeding mice with food containing mantle tissue from Japanese scallops results in aggravated liver and kidney damage, ultimately resulting in mortality within weeks. The aim of this study is to evaluate the toxicity of scallop mantle in China's coastal areas and explore the impact of scallop mantle toxins (SMT) on intestinal barrier integrity and gut microbiota in mice. The Illumina MiSeq sequencing of V3-V4 hypervariable regions of 16S ribosomal RNA was employed to study the alterations in gut microbiota in the feces of SMT mice. The results showed that intestinal flora abundance and diversity in the SMT group were decreased. Compared with the control group, significant increases were observed in serum indexes related to liver, intestine, inflammation, and kidney functions among SMT-exposed mice. Accompanied by varying degrees of tissue damage observed within these organs, the beneficial bacteria of Muribaculaceae and Marinifilaceae significantly reduced, while the harmful bacteria of Enterobacteriaceae and Helicobacter were significantly increased. Taken together, this article elucidates the inflammation and glucose metabolism disorder caused by scallop mantle toxin in mice from the angle of gut microbiota and metabolism. SMT can destroy the equilibrium of intestinal flora and damage the intestinal mucosal barrier, which leads to glucose metabolism disorder and intestinal dysfunction and may ultimately bring about systemic toxicity.

An interpretable deep learning model predicts RNA–small molecule binding sites

The intricate interplay between RNA molecules and small ligands plays a pivotal role in regulating biological processes, underscoring the necessity for accurate prediction models of RNA–small molecule binding sites. In this study, we develop CapBind, a novel interpretive deep learning framework utilizing a Capsule Network architecture, to precisely identify RNA–small molecule binding sites. This framework stands out for its multifaceted approach, which leverages both the sequence and structural information of RNA as input features, allowing for a thorough understanding of the complex interactions between RNA and small molecules. Leveraging multi-source bioinformatics data, including the distribution of RNA secondary structures, our model characterizes sequence and structural features with unparalleled depth. Through a unified alignment of these multi-source feature representations, we achieve dimensional homogeneity in the potential feature maps for both types of biological data. The crux of our methodology lies in the deployment of a multi-level Capsule Network, engineered to identify the nuanced interactions of RNA sequences with small molecules. The essence of our approach resides in the implementation of a multi-layered Capsule Network. Utilizing a sophisticated routing mechanism, this network demonstrates unparalleled efficacy in learning and identifying the intricate interactions between RNA sequences and small molecules. This mechanism enables dynamic adjustment of information flow across multiple levels, thereby capturing subtle features and patterns that might elude conventional neural network architectures. The experimental results demonstrate the superior performance of our model, particularly highlighting its progress in evaluation metrics compared to current state-of-the-art models. Case studies further validate the model’s precision in identifying binding sites, offering potential insights into gene expression pathways and novel therapeutic avenues for neurodegenerative diseases. Moreover, an extensive interpretability analysis of our silicon model reveals the internal interaction mechanisms between specific RNA regions and small molecules, contributing valuable perspectives for drug design and molecular biology research. These findings underscore the model’s predictive accuracy and biological applicability, establishing our approach as a significant leap forward in the computational prediction of RNA–small molecule binding sites.

FTO blocks RNA translational activity via the loss of N6-methyladenosine methylation at 5' UTR regulated by RBM5 in cisplatin-resistant NSCLC.

N6-methyladenosine (m6A) methylation has been widely regarded in numerous biological functions including CR. Nonetheless, the molecular process of m6A methylation behind CR in non-small cell lung cancer (NSCLC) has no apparent significance. We identified in this study that the expression of FTO alpha-ketoglutarate dependent dioxygenase (FTO) was downregulated in CR NSCLC tissues and cells in vivo and in vitro. Additionally, RIP-seq indicated that loss of FTO contributed to the elevated m6A methylation at 5'-untranslated region of RNAs which were closely connected with tumor resistance and malignancy, and FTO exerted to exclude the recruitment of eIF3A to these target genes in CR NSCLC. Moreover, FTO-enriched transcripts displayed a reduced translational capability in CR NSCLC compared to the regular NSCLC cells. Finally, we also identified RNA binding motif protein 5 (RBM5) that could specially interact with FTO in regular NSCLC compared to CR NSCLC. Deficiency of RBM5 resulted in the abnormal recognition of transcripts by FTO, and led to the translation silencing of genes associated with CR such as ATP7A, ERCC1, CD99, CDKN3, XRCC5, and NOL3. Taken together, our data characterized FTO as a novel translation regulator and revealed the molecular mechanism on gene translation through the synergistic effects with RBM5 and m6A methylation in CR NSCLC cells.

Molecular Detection and Phylogenetic Analysis of the alkB Gene in Klebsiella oxytoca Strains Isolated from the Gut of Tenebrio molitor.

The challenge in polystyrene disposal has caused researchers to look for urgent innovative and ecofriendly solutions for plastic degradation. Some insects have been reported to use polystyrene as their sole carbon source, and this has been linked to the presence of microbes in their guts that aid in plastic digestion. Thus, this study focuses on the molecular detection and phylogenetic analysis of the alkane-1-monooxygenase (alkB) gene in Klebsiella oxytoca strains isolated from the gut of Tenebrio molitor. The alkB gene encodes for alkane-1-monooxygenase, an enzyme involved in the oxidation of inactivated alkanes. This gene can be used as a marker to assess bacteria's ability to biodegrade polystyrene. Three bacterial strains were isolated from the guts of T. molitor mealworms and were confirmed using polymerase chain reaction (PCR) of the 16S ribosomal RNA gene. The primers used in the amplification of the 16S ribosomal RNA region were designed using NCBI, a bioinformatics tool. To detect the presence of the alkB gene in the isolated bacterial strains, a set of primers used in the amplification of this gene was manually designed from the conserved regions of the alkB nucleotide sequences of eleven bacterial species from GenBank. TCOFFE online tool was used to align the alkB sequences of the bacteria, while Jalview and ConSurf were used to view the alignment. The amplified alkB gene was then sequenced using the Sanger sequencing technique, blasted on NCBI to look for similar sequences, and a phylogenetic tree was constructed. Based on the 16S ribosomal RNA gene sequences, the isolated bacterial strains were confirmed to be Klebsiella oxytoca NBRC 102593, Klebsiella oxytoca JCM 1665, and Klebsiella oxytoca ATCC 13182. The alkB gene sequence identical to fourteen alkB gene sequences derived from Actinobacteria whole genome was detected in Klebsiella oxytoca for the first time to the best of our knowledge. The novel nucleotide sequence was published in the NCBI database under accession number OP959069. This gene sequence was found to be for the enzyme alkane-1-monooxygenase and may be one of the enzymes responsible for polystyrene degradation by the putative Klebsiella oxytoca ATCC 13182 in T. molitor.

Major Group-B Enterovirus populations deleted in the noncoding 5' region of genomic RNA modulate activation of the type I interferon pathway in cardiomyocytes and induce myocarditis.

Major 5'-terminally deleted (5'TD) RNA forms of group-B coxsackievirus (CVB-5'TD) has been associated with myocarditis in both mice and humans. Although it is known that interferon-β (IFN-β) signaling is critical for an efficient innate immune response against CVB-induced myocarditis, the link between CVB-5'TD RNA forms and type I IFN signaling in cardiomyocytes remains to be explored. In a mouse model of CVB3/28-induced myocarditis, major early-emerging forms of CVB-5'TD RNA have been characterized as replicative viral populations that impair IFN-β production in the heart. Synthetic CVB3/28 RNA forms mimicking each of these major 5'TD virus populations were transfected in mice and have been shown to modulate innate immune responses in the heart and to induce myocarditis in mice. Remarkably, transfection of synthetic viral RNA with deletions in the secondary structures of the 5'-terminal CVB3 RNA domain I, modifying stem-loops "b", "c" or "d", were found to impair IFN-β production in human cardiomyocytes. In addition, the activation of innate immune response by Poly(I:C), was found to restore IFN-β production and to reduce the burden of CVB-5'TD RNA-forms in cardiac tissues, thereby reducing the mortality rate of infected mice. Overall, our results indicate that major early-emerging CVB3 populations deleted in the domain I of genomic RNA, in the 5' noncoding region, modulate the activation of the type I IFN pathway in cardiomyocytes and induce myocarditis in mice. These findings shed new light on the role of replicative CVB-5'TD RNA forms as key pathophysiological factors in CVB-induced human myocarditis.

Occurrence and distribution of cyst nematodes, Heterodera spp. (Tylenchida: Heteroderidae) associated with black cabbage, Brassica oleracea var. acephala L. (Brassicales: Brassicaceae) in the Eastern Black Sea Region of Türkiye

This study was conducted during 2021-2022 to detect and determine distribution and population of cyst nematodes, Heterodera spp. (Tylenchida: Heteroderidae) in black cabbage Brassica oleracea var. acephala L. (Brassicales: Brassicaceae) production areas of the Eastern Black Sea Region of Türkiye. For it, a total of 77 samples were taken from 53 districts belonging to the Artvin, Giresun, Ordu, Rize, and Trabzon provinces in the region. Soil samples were taken from around the root of the kale plants. Nematodes were extracted by using the centrifugal flotation technique. The nematodes were identified using morphological features and molecular analysis based on Polymerase Chain Reaction (PCR) method. For molecular analysis, the ribosomal DNA region including the gene region of 28S ribosomal RNA (rRNA) (ITS1, 5.8S, ITS2) was amplified using primer sets TW81/AB28. Additionally, a species-specific primer set (Car-F/Car-R) covering the Cytochrome Oxidase I (cox1) region of mitochondrial DNA (mtDNA) was used. As a result of the analysis, cyst nematodes Heterodera cruciferae Franklin, 1945, Heterodera carotae Jones, 1950 and Heterodera fici Kirjanova, 1954 species were identified in the kale production areas in the region. Heterodera carotae is the first record of the cyst nematode species in Türkiye. Heterodera cruciferae, H. carotae, and H. fici were detected from the total collected soil samples at 16.9%, 3.9%, and 1.3% relative frequency, respectively. Among all, Giresun was the most infected province with 35.3% infection rate, followed by Trabzon with 26.3%, Ordu with 21.1% and Rize with 13.3%.

RNase E searches for cleavage sites in RNA by linear diffusion: direct evidence from single-molecule FRET.

The ability of obstacles in cellular transcripts to protect downstream but not upstream sites en masse from attack by RNase E has prompted the hypothesis that this mRNA-degrading endonuclease may scan 5'-monophosphorylated RNA linearly for cleavage sites, starting at the 5' end. However, despite its proposed regulatory importance, the migration of RNase E on RNA has never been directly observed. We have now used single-molecule FRET to monitor the dynamics of this homotetrameric enzyme on RNA. Our findings reveal that RNase E slides along unpaired regions of RNA without consuming a molecular source of energy such as ATP and that its forward progress can be impeded when it encounters a large structural discontinuity. This movement, which is bidirectional, occurs in discrete steps of variable length and requires an RNA ligand much longer than needed to occupy a single RNase E subunit. These results indicate that RNase E scans for cleavage sites by one-dimensional diffusion and suggest a possible molecular mechanism.