RNA Targeting Research Articles

Clinical Significance of HHLA2 as a Novel Therapeutic Target for Colorectal Cancer.

Colorectal cancer (CRC) is a high-indence malignance of the digestive system with a high mortality rate in the world. The results are desired to provide an important theoretical basis for discovering new therapeutic targets for CRC. The expression of human endogenous retrovirus-H-long terminal repeat association protein 2 (HHLA2) in human CRC was detected to explore its correlationship with clinicopathological features and prognosis of patients and its potential in treating CRC. Western blot was employed to detect HHLA2 expression in fresh tissues obtained from 6 CRC patients' excisions, including cancer, paracancer, and normal issues. Immunohistochemical staining was employed to determine HHLA2 expression in paraffin-embedded specimens of 139 patients with colorectal cancer, and its relationship with the clinicopathological profiles and survival was analyzed. Small interfering RNA (siRNA) targeting HHLA2 was used to transfect CRC cells to silent HHLA2. MTT, plate colony formation, cell scratch, and Transwell assay were conducted to observe the proliferation, migration, and invasion of CRC cells. HHLA2 protein was expressed in human colorectal cancer tissues, paracancer tissues and normal tissues, which was significantly upregulated in cancer tissues (P<0.01). HHLA2 expression level in CRC tissues showed a close correlationship with the invasion depth of the tumor (P=0.000), metastasis of regional lymph nodes (P=0.018), clinical stage (P=0.010), and patient survival (P=0.011). Correlation with gender (P=0.873), age (P=0.864), location of the tumor (P=0.768), degree of tumor differentiation (P=0.569) and distant metastasis (P=0.494) exhibited no significance. The survival time of CRC patients with high and low HHLA2 expression groups was 43.231 months and 55.649 months, respectively, with a statistical difference between the two groups (P=0.001). Silencing HHLA2 inhibited proliferation, migration and invasion of CRC cells significantly. HHLA2 is overexpressed in CRC tissues which is associated with poor prognosis of patients. HHLA2 might be recognized as a new candidate for adjuvant diagnosis and prognosis of CRC, as well as a promised new target for immunotherapy of CRC.

Enhancing peroxidase activity of NiCo2O4 nanoenzyme by Mn doping for catalysis of CRISPR/Cas13a-mediated non-coding RNA detection

CRISPR/Cas13a with precise and controllable programming of endonuclease activity has been served as powerful tool for RNA sensing. Although with high sensitivity, existing CRISPR/Cas13a-based biosensors need complex amplification procedure or special equipment that limited quantification capability. Here, Mn-doped NiCo2O4 (Mn/NiCo2O4) nanozyme with enhanced peroxidase activity was synthesized and combined with CRISPR/Cas13a-based reaction to develop a simple, sensitive and universal biosensor for RNA detection, which is achieved through target recognition that activates Cas enzymes to cleave RNA reporter for inhibiting Mn/NiCo2O4 nanozyme to assemble on microplate. The Mn/NiCo2O4 nanozyme assembled on microplate can be monitored through colorimetric and fluorometric approaches. On one hand, Mn/NiCo2O4 nanozyme offers ideal peroxidase activity to catalyze colorimetric reaction, and as low as dozens of amol level of RNA target can be sensitively detected by naked eyes without any amplification procedures. On the other hand, Mn/NiCo2O4 can be also served as a signal amplifier to produce large amount of Co2+, Mn2+and Ni2+ to quench the fluorescence of calcein. The fluorescent approach can achieve higher sensitivity (about 40-fold) than colorimetric method. More importantly, the proposed biosensor can work well for multiple RNA detection in real biological samples, showing a great potential for monitoring non-coding RNA-related diseases.

A resurrected ancestor of Cas12a expands target access and substrate recognition for nucleic acid editing and detection.

The properties of Cas12a nucleases constrict the range of accessible targets and their applications. In this study, we applied ancestral sequence reconstruction (ASR) to a set of Cas12a orthologs from hydrobacteria to reconstruct a common ancestor, ReChb, characterized by near-PAMless targeting and the recognition of diverse nucleic acid activators and collateral substrates. ReChb shares 53% sequence identity with the closest Cas12a ortholog but no longer requires a T-rich PAM and can achieve genome editing in human cells at sites inaccessible to the natural FnCas12a or the engineered and PAM-flexible enAsCas12a. Furthermore, ReChb can be triggered not only by double-stranded DNA but also by single-stranded RNA and DNA targets, leading to non-specific collateral cleavage of all three nucleic acid substrates with similar efficiencies. Finally, tertiary and quaternary structures of ReChb obtained by cryogenic electron microscopy reveal the molecular details underlying its expanded biophysical activities. Overall, ReChb expands the application space of Cas12a nucleases and underscores the potential of ASR for enhancing CRISPR technologies.

Marker-dependent cleavage of RNA by binary (split) DNAzyme (BiDz) and binary DNA machines (biDNM).

Oligonucleotide gene therapy (OGT) can be used to suppress specific RNA in cells and thus have been explored for gene therapy. Despite extensive effort, there is no clinically significant OGT for treating cancer. Low efficiency of OGT is one of the problems. Earlier, we proposed to address this problem by suppressing most vital genes in cancer cells e.g. housekeeping genes. To achieve specific activation of the OGT agents in cancer but not in normal cells, we designed binary (split) DNAzyme (BiDz), which is activated by cancer-related nucleic acid sequences. This work is devoted to BiDz optimization using cancer marker-related sequence as an activator and three folded RNA targets. To achieve efficient binding of folded RNA, the BiDz design was equipped with RNA binding/unwinding arms, a construction that was dabbed 'BiDz machines' (BiDM). BiDM was designed to have improved both iRNA cleavage rates and RNA recognition in comparison with BiDz. Further development of DNA nanotechnology-inspired agents can advance OGT technology in treating cancer, viral infections, and genetic disorders.

Bifunctional SnO2/NiO/rGO nanocomposite electrode for hydrogen evolution reaction and detection of winter wheat cold-resistant RNA.

Aconvenient, non-toxic, and low-cost tin dioxide (SnO2)/nickel oxide (NiO)/reduced graphene oxide (rGO) nanocatalytic electrode was investigated, which can effectively promote the hydrogen evolution reaction and can also be used to construct a sensitive winter wheat cold-tolerant RNA sensor. Due to the good synergy and photocurrent generation between SnO2 and NiO, which accelerates the electron transfer and catalyzes the hydrolysis reaction, the resultant data for the hydrogen evolution reaction in alkaline environment of this material are very impressive, with cathodic current densities of up to 10mAcm-2. The marvelous heterostructures and photovoltaic properties form a signal amplification system, which enables the nanocomposites to have an excellent linear sensitivity in low-concentration RNA solutions. The single-stranded complementary RNA of the target RNA was immobilized on the surface of the nanocomposites, which enabled the materials to recognize the target RNA under enzyme-free conditions. The test results showed that the modified electrode materials had good single detection performance in a wide linear range from 0.1nM to 2mM, with the limit of detection (LOD) of 0.078nM. The developed nanocomposite electrode has good performance in hydrogen evolution and winter wheat cold-resistant RNA detection, and is a bifunctional device with superior performance.

Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping.

RNA molecules form complex networks of molecular interactions that are central to their function and to cellular architecture. But these interaction networks are difficult to probe in situ. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a method for elucidating the biomolecules near an RNA of interest, within its native context. O-MAP uses RNA-fluorescence in situ hybridization-like oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA in situ, enabling nearby molecules to be enriched by streptavidin pulldown. This induces exceptionally precise biotinylation that can be easily optimized and ported to new targets or sample types. Using the noncoding RNAs 47S, 7SK and Xist as models, we develop O-MAP workflows for discovering RNA-proximal proteins, transcripts and genomic loci, yielding a multiomic characterization of these RNAs' subcellular compartments and new regulatory interactions. O-MAP requires no genetic manipulation, uses exclusively off-the-shelf parts and requires orders of magnitude fewer cells than established methods, making it accessible to most laboratories.

Pre‐Defined Stem‐Loop Structure Library for the Discovery of L‐RNA Aptamers that Target RNA G‐Quadruplexes

L‐RNA aptamers have been developed to target G‐quadruplexes (G4s) and regulate G4‐mediated gene expression. However, the aptamer selection process is laborious and challenging, and aptamer identification is subjected to high failure rate. By analyzing the previously reported G4‐binding L‐RNA aptamers, we found that the stem‐loop (SL) structure is favored by G4 binding. Herein, we present a robust and effective G4‐SLSELEX‐Seq platform specifically for G4 targets by introducing a pre‐defined stem‐loop structure library during SELEX process. Using G4‐SLSELEX‐Seq, we rapidly identified an L‐RNA aptamer, L‐Apt1‐12 for EBNA1 RNA G4 (rG4) in just three selection rounds. L‐Apt1‐12 maintained the stem‐loop structure initially introduced, and possessed a unique G‐triplex motif that is important for the strong binding affinity and specificity to EBNA1 rG4. Notably, L‐Apt1‐12 effectively downregulated endogenous EBNA1 protein expression in human cancer cells and showed selective toxicity towards EBV‐positive cancer cells, highlighting its potential for targeted therapy against EBV‐associated cancers. Furthermore, we demonstrate the robustness and generality of G4‐SLSELEX‐Seq by selecting L‐RNA aptamers for another two G4 targets‐APP rG4 and HCV‐1a rG4, also obtaining high‐affinity aptamers in three selection rounds. These findings demonstrated G4‐SLSELEX‐Seq can be a robust and efficient platform for the selection of L‐RNA aptamers targeting rG4.

Pre-Defined Stem-Loop Structure Library for the Discovery of L-RNA Aptamers that Target RNA G-Quadruplexes.

L-RNA aptamers have been developed to target G-quadruplexes (G4s) and regulate G4-mediated gene expression. However, the aptamer selection process is laborious and challenging, and aptamer identification is subjected to high failure rate. By analyzing the previously reported G4-binding L-RNA aptamers, we found that the stem-loop (SL) structure is favored by G4 binding. Herein, we present a robust and effective G4-SLSELEX-Seq platform specifically for G4 targets by introducing a pre-defined stem-loop structure library during SELEX process. Using G4-SLSELEX-Seq, we rapidly identified an L-RNA aptamer, L-Apt1-12 for EBNA1 RNA G4 (rG4) in just three selection rounds. L-Apt1-12 maintained the stem-loop structure initially introduced, and possessed a unique G-triplex motif that is important for the strong binding affinity and specificity to EBNA1 rG4. Notably, L-Apt1-12 effectively downregulated endogenous EBNA1 protein expression in human cancer cells and showed selective toxicity towards EBV-positive cancer cells, highlighting its potential for targeted therapy against EBV-associated cancers. Furthermore, we demonstrate the robustness and generality of G4-SLSELEX-Seq by selecting L-RNA aptamers for another two G4 targets-APP rG4 and HCV-1a rG4, also obtaining high-affinity aptamers in three selection rounds. These findings demonstrated G4-SLSELEX-Seq can be a robust and efficient platform for the selection of L-RNA aptamers targeting rG4.

Adaptation of a Model Spike Aptamer for Isothermal Amplification-Based Sensing.

Isothermal amplification (IA) techniques like rolling circle amplification (RCA) and loop-mediated isothermal amplification (LAMP) have gained significant attention in recent years due to their ability to rapidly amplify DNA or RNA targets at a constant temperature without the need for complex thermal cycling equipment. Such technologies, combined with colorimetric systems rendering visual confirmation of the amplification event, are ideal for the development of point-of-need detection methods suitable for field settings where access to specialized laboratory equipment is limited. The utility of these technologies, thus far limited to DNA and RNA targets, could be broadened to a wide range of targets by using aptamers. Composed of DNA or RNA themselves, aptamers can bind to substances, including proteins, metabolites, and inorganic substances. Their nucleic acid nature can potentially allow them to serve as a bridge, extending the reach of DNA/RNA-centric technologies to the broader molecular world. Indeed, the change in aptamer conformation occurring during ligand interaction can be used to elaborate ligand-responding RCA or LAMP templates. By using an existing aptamer targeting SARS-CoV-2 Spike protein as a model, we explored the possibility of establishing ligand-responsive IA systems. Our study used aptamers with simple sequence modifications as templates in LAMP assays and hyperbranched RCA (HRCA) by exploiting the dynamic nature of the model aptamer to trigger these IA systems. Importantly, our work uniquely demonstrates that this aptamer's dynamic response to ligand binding can regulate both RCA and LAMP processes. This novel approach of using aptamer conformational changes to trigger LAMP paves the way for new aptamer-based detection assays. Our system detects 50 nM of Spike protein, with LAMP occurring within 30 min in the presence of Spike. The colorimetric readout showed clear results, allowing for the detection of Spike protein presence.

ALKBH5 Regulates Corneal Neovascularization by Mediating FOXM1 M6A Demethylation.

This study aims to explore the regulatory role and potential mechanisms of ALKBH5-mediated N6-methyladenosine (m6A) demethylation modification in corneal neovascularization (CNV). A mouse CNV model was established through corneal alkali burns. Total m6A levels were measured using an m6A RNA methylation quantification kit. The mRNA expression of candidate m6A-related enzymes was quantified by quantitative RT-PCR. Small interfering RNA targeting ALKBH5 was injected subconjunctivally into alkali-burned mice. The CNV area, corneal epithelial thickness, and pathological changes were evaluated. Protein expression was detected by western blot and immunofluorescence. Human umbilical vein endothelial cells (HUVECs) were treated with IL-6. Plasmid transfection knocked down ALKBH5 or overexpressed FOXM1 in IL-6-induced HUVECs. The assays of CCK8, wound healing, and tube formation evaluated the cell proliferation, migration, and tube formation abilities, respectively. The dual-luciferase assay examined the binding between ALKBH5 and FOXM1. Methylated RNA immunoprecipitation-qPCR detected the m6A levels of FOXM1. Significant CNV was observed on the seventh day. Total m6A levels were reduced, and ALKBH5 expression was increased in CNV corneas and IL-6-induced HUVECs. ALKBH5 knockdown alleviated corneal neovascularization and inflammation and countered IL-6-induced promotion of cell proliferation, migration, and tube formation in HUVECs. ALKBH5 depletion increased m6A levels and decreased VEGFA and CD31 expression both in vivo and in vitro. This knockdown in HUVECs elevated m6A levels on FOXM1 mRNA while reducing its mRNA and protein expression. Notably, FOXM1 overexpression can reverse ALKBH5 depletion effects. ALKBH5 modulates FOXM1 m6A demethylation, influencing CNV progression and highlighting its potential as a therapeutic target.

DDX RNA helicases: key players in cellular homeostasis and innate antiviral immunity.

RNA helicases are integral in RNA metabolism, performing important roles in cellular homeostasis and stress responses. In particular, the DExD/H-box (DDX) helicase family possesses a conserved catalytic core that binds structural features rather than specific sequences in RNA targets. DDXs have critical roles in all aspects of RNA metabolism including ribosome biogenesis, translation, RNA export, and RNA stability. Importantly, functional specialization within this family arises from divergent N and C termini and is driven at least in part by gene duplications with 18 of the 42 human helicases having paralogs. In addition to their key roles in the homeostatic control of cellular RNA, these factors have critical roles in RNA virus infection. The canonical RIG-I-like receptors (RLRs) play pivotal roles in cytoplasmic sensing of viral RNA structures, inducing antiviral gene expression. Additional RNA helicases function as viral sensors or regulators, further diversifying the innate immune defense arsenal. Moreover, some of these helicases have been coopted by viruses to facilitate their replication. Altogether, DDX helicases exhibit functional specificity, playing intricate roles in RNA metabolism and host defense. This review will discuss the mechanisms by which these RNA helicases recognize diverse RNA structures in cellular and viral RNAs, and how this impacts RNA processing and innate immune responses.

All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies.

RNA modifications are essential for human health - too much or too little of them leads to serious illnesses ranging from neurodevelopmental disorders to cancer. Technical advances in RNA modification sequencing are beginning to uncover the RNA targets of diverse RNA-modifying enzymes that are dysregulated in disease. However, the emerging transcriptome-wide maps of modified nucleosides installed by these enzymes should be considered as first drafts. In particular, a range of technical artefacts lead to false negatives- modified sites that are overlooked owing to technique-dependent, and often sequence-context-specific, 'blind spots'. In this Review, we discuss potential sources of false negatives in sequencing-based RNA modification maps, propose mitigation strategies and suggest guidelines for transparent reporting of sensitivity to detect modified sites in profiling studies. Important considerations for recognition and avoidance of false negatives include assessment and reporting of position-specific sequencing depth, identification of protocol-dependent RNA capture biases and applying controls for false negatives as well as for false positives. Despite their limitations, emerging maps of RNA modifications reveal exciting and largely uncharted potential for post-transcriptional control of all aspects of RNA function.

Site-Specific Integration by Circular Donor Improves CRISPR/Cas9-Mediated Homologous Recombination in Human Cell Lines

The technology for obtaining the high-efficiency expression of target proteins through site-specific recombination has made progress. However, using the CRISPR/Cas9 system for site-specific integration of long fragments and the expression of active proteins remains a challenge. This study optimized the linear DNA circularization system, eliminated the prokaryotic plasmid backbone on the traditional foreign gene vector, and generated a homologous arm-free circular donor template with a single guide RNA target site (sgRNA TS). This strategy significantly increased the co-transfection efficiency of the 1.6 kb template and Cas9 plasmid by 1.15-fold, and the average knock-in (KI) efficiency of the 4.7 kb long-fragment template for the two target gene sites increased by 1.3-fold. Subsequently, we used rhBCHE as a reporter gene to efficiently integrate the 5.4 kb fragment containing the gene of interest (GOI) into specific sites in the HEK293T cell line to detect the expression of the circular template at different target sites. Overall, this study further verifies that the length of the circular donor is more conducive to non-homologous integration, and more importantly, we provide a simple and optimized strategy for the construction of long-fragment site integration cell lines.

Sustainable synthesis of MOF for COVID-19 detection using a 23 factorial design

The emergence of the COVID-19 pandemic has underscored the urgent requirement for rapid and accurate diagnostic methods to detect the virus and control its spread. Metal Organic Frameworks (MOFs) have gained significant interest in biosensing applications because of their exceptional properties. This study investigates the microwave synthesis of zeolitic imidazolate framework-8 (ZIF-8) and explores its potential as a fluorescent biosensor for detecting COVID-19 RNA sequences. The microwave method enables a rapid, eco-friendly, and efficient synthesis of ZIF-8. Characterization tests including PXRD, FE-SEM, TGA, and FT-IR confirmed the high crystallinity and thermal stability of ZIF-8. To optimize the biosensor’s performance, a 23 factorial design is pursued. The factorial design allows determining the individual and simultaneous effects of the control parameters such as ZIF-8 concentration, buffer pH, and solution temperature on the quenching efficiency. The results demonstrate that the parameters combination of 25 °C, pH 8.0, and 0.7 mg/mL ZIF-8 concentration results in the highest quenching percentage of 72.41 %. The study of the quenching mechanism confirms that the P-DNA can form electrostatic and π-π stacking interactions with ZIF-8, to produce a P-DNA@ZIF-8 complex. It is also found that photoinduced electron transfer is more dominant than fluorescence resonance energy transfer in the quenching mechanism. The biosensor showed a high sensitivity towards the target COVID-19 RNA with a very low detection limit of 12.02 pM, a fast detection time of 40 minutes, and high selectivity to the target RNA. This study shows the potential of ZIF-8 as a feasible and environmentally friendly material for swiftly and accurately detecting COVID-19 RNA sequences.

High expression of LINC00467 promotes proliferation and metastasis of lung adenocarcinoma cells by suppressing autophagy via inhibiting the AMPK/mTOR pathway

To investigate the regulatory effects of LINC00467 on proliferation and metastasis of lung adenocarcinoma cells and the involvement of autophagy in its regulatory mechanism. LINC00467 expression levels in lung adenocarcinoma tissues and their correlation with the patients' survival outcomes were analyzed using data from TCGA database. LINC00467 expression was also examined using qRT-PCR in human bronchial epithelial cells 16HBE and lung adenocarcinoma cell lines A549 and H1299. In A549 and H1299 cells transfected with a short hairpin RNA targeting LINC00467 (shLINC00467), the effects of 3-methyladenine (3-MA, an autophagy inhibitor) and BML-275 (an AMPK inhibitor) treatment on cell proliferation, migration, and expressions of LC3 and the AMPK/mTOR pathway proteins were tested using colony formation assay, wound-healing and Transwell assays, immunofluorescence staining and Western blotting. GSEA enrichment analysis was conducted to analyze the correlation between LINC00467 and the autophagy pathway. The expression level of LINC00467 was significantly higher in lung adenocarcinoma tissues than in the adjacent tissues (P < 0.001) and increased progressively with the clinical stage (P < 0.05), and its high expression was associated with a poor overall survival (P= 0.049) and a high first progression rate (P=0.026) of the patients. LINC00467 expression was also significantly higher in A549 and H1299 cells than in 16HBE cells. In A549 and H1299 cells, LINC00467 knockdown significantly decreased colony-forming, migration and invasion abilities of the cells, lowered p-mTOR/mTOR and p62 expressions, and increased p-AMPK/AMPK expressions and LC3Ⅱ/Ⅰ ratio, and these effects were strongly attenuated by application of either 3-MA or BML-275. GSEA analysis suggested an inhibitory effect on LINC00467 on the autophagy pathway (|NES| > 1, P < 0.05, FDR < 0.25). High expressions of LINC00467 promote proliferation and metastasis of lung adenocarcinoma cells possibly by inhibiting cell autophagy mediated by the AMPK/mTOR signaling pathway.

Recent Progress of Antisense Oligonucleotide Therapy for Superoxide-Dismutase-1-Mutated Amyotrophic Lateral Sclerosis: Focus on Tofersen.

Amyotrophic lateral sclerosis (ALS) is a refractory neurodegenerative disease characterized by the degeneration and loss of motor neurons, typically resulting in death within five years of onset. There have been few effective treatments, making the development of robust therapies an urgent challenge. Genetic mutations have been identified as contributors to ALS, with mutations in superoxide dismutase 1 (SOD1), which neutralizes the harmful reactive oxygen species superoxide, accounting for approximately 2% of all ALS cases. To counteract the toxic gain of function caused by SOD1 mutations, therapeutic strategies aimed at suppressing SOD1 gene expression have shown promise. Antisense oligonucleotide (ASO) is an artificially synthesized, short, single-stranded DNA/RNA molecule that binds to target RNA to alter gene expression, representing a next-generation therapeutic approach. In 2023, tofersen became the first ASO drug approved by the FDA for ALS. Administered intrathecally, tofersen specifically binds to SOD1 mRNA, inhibiting the production of toxic SOD1 protein, thereby improving biomarkers of ALS. The long-term efficacy and safety of tofersen require further validation, and the development of more optimized treatment protocols is essential. A series of studies and therapeutic developments related to SOD1 mutations have advanced the understanding of ALS pathophysiology and significantly contributed to treatment strategies for central nervous system disorders. This review focuses on an overview of SOD1 mutations and the development process of tofersen, aiming to deepen the understanding of advancements in ALS research and discuss future challenges and directions for ASO therapy.

Molecular Identification of Genes Resistant to Antibiotics in Staphylococcus aureus Isolated from Sub-clinical Animals Affected by Mastitis

Background and Aim: Mastitis is a prevalent and costly disease that significantly impacts the dairy industry, affecting both sheep's health and milk quality. In order to determine the bacterial causes of subclinical mastitis in Iraq and its susceptibility to antibiotics, the study aims to molecularly detect resistant Staphylococcus aureus isolated from sheep infected with mastitis. Methods: Molecular assay and phylogenetic study to detect Staph aureus isolates by using 16 Sr RNA and resistance virulence genes (aac-aph, tetk) by the conventional method of PCR. Two hundred samples were collected from the subclinical mastitis of infected ewes, Samples were reserved on an icebox and transported to the laboratories. Milk samples were cultured on Blood Agar and Mannitol Salt Agar (7.5%) plates. The culture plates were then incubated at 37°C for 24 hours. Results: The PCR assay revealed amplification of the 16S rRNA gene in all 20 isolates, amplification of the aac-aph gene in 19 isolates, and the tetK gene in all 20 isolates. The PCR products of 20 positive samples for (16 Sr RNA) target genes were sequenced, evaluated, and dropped on the Genbank-NCBI under the accession number, which became a reference to Iraq and the world. According to the current study, Staphylococcus aureus is commonly found in milk. To combat drug resistance, antimicrobial drug use should be normalized, and antimicrobial resistance surveillance should be conducted regularly. Conclusion: PCR-product of 8 positive samples for 16sr RNA target gene were sequenced, analyzed, and deposited on the Genbank-NCBI under the accession number and became a reference to Iraq and the Middle East and the world.

Molecular Identification of Genes Resistant to Antibiotics in Staphylococcus aureus Isolated from Sub-clinical Animals Affected by Mastitis

Background and Aim: Mastitis is a prevalent and costly disease that significantly impacts the dairy industry, affecting both sheep's health and milk quality. In order to determine the bacterial causes of subclinical mastitis in Iraq and its susceptibility to antibiotics, the study aims to molecularly detect resistant Staphylococcus aureus isolated from sheep infected with mastitis. Methods: Molecular assay and phylogenetic study to detect Staph aureus isolates by using 16 Sr RNA and resistance virulence genes (aac-aph, tetk) by the conventional method of PCR. Two hundred samples were collected from the subclinical mastitis of infected ewes, Samples were reserved on an icebox and transported to the laboratories. Milk samples were cultured on Blood Agar and Mannitol Salt Agar (7.5%) plates. The culture plates were then incubated at 37°C for 24 hours. Results: The PCR assay revealed amplification of the 16S rRNA gene in all 20 isolates, amplification of the aac-aph gene in 19 isolates, and the tetK gene in all 20 isolates. The PCR products of 20 positive samples for (16 Sr RNA) target genes were sequenced, evaluated, and dropped on the Genbank-NCBI under the accession number, which became a reference to Iraq and the world. According to the current study, Staphylococcus aureus is commonly found in milk. To combat drug resistance, antimicrobial drug use should be normalized, and antimicrobial resistance surveillance should be conducted regularly. Conclusion: PCR-product of 8 positive samples for 16sr RNA target gene were sequenced, analyzed, and deposited on the Genbank-NCBI under the accession number and became a reference to Iraq and the Middle East and the world.

Detachable DNA Assembly Module to Dissect Tumor Cells Heterogeneity via RNA Pinpoint Screening.

Differential RNA expression is becoming increasingly valuable in evaluating tumor heterogeneity for a better understanding of malignant tumors and guiding personalized therapy. However, traditional techniques for analyzing cellular RNA are mainly focused on determining the absolute level of RNA, which may lead to inaccuracies in understanding tumor heterogeneity, primarily due to i) the subtle differences in certain RNA types that have similar total concentrations and ii) the existence of variations in RNA expression across different samples. Herein, a detachable DNA assembly module is proposed that is capable not only of quantifying the expression level of target RNA but also of innovatively evaluating its proportion within its RNA family population through a sequential assembly and disassembly route. Using the let-7 family as an experimental model, a significant difference is discovered in let-7a proportion between normal mammary epithelial cells and breast cancer cells, a characteristic that is often missed in bulk analysis of traditional techniques. By combining concentration and proportion information, the detachable DNA assembly module demonstrates markedly higher efficiency in discerning among various types of cells compared to traditional techniques. This innovative assembly module is expected to offer a new perspective to highlight tumor heterogeneity and guide personalized therapy.

Mechanistic Studies of Small Molecule Ligands Selective to RNA Single G Bulges.

Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated Molecular Dynamics (GaMD) simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity-relationship (SAR) studies and transverse relaxation measurements by NMR spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Strikingly, small structure perturbations on these key contributors, such as the addition of a methyl group that disrupts the planarity of the ligand resulted in > 100-fold reduction in the binding affinity. Our work deepened the understanding of RNA-small molecule interactions and integrated a new generalizable platform for the rational design of selective small-molecule RNA binders.