rnomics

[rnomics]

PIP-seq – particle-templated instant partition sequencing

Understanding how our immune cells respond to different environmental factors is key to developing better treatments for diseases. A recent study has introduced a groundbreaking #RNA sequencing method called Particle-Templated Instant Partition Sequencing (PIP-Seq) that offers a more detailed look at specific immune cells in the lungs, especially after exposure to harmful substances. What ... https://www.rna-seqblog.com/pip-seq-particle-templated-instant-partition-sequencing/?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

scDist – robust identification of perturbed cell types in single-cell #RNA-seq data

Single-cell transcriptomics is a powerful technique that allows scientists to study how individual cells behave in different diseases. By looking at the #RNA within single cells, researchers can see how various cell types change and how these changes might contribute to the progression of diseases like COVID-19 or responses to treatments like immunotherapy. However, ... https://www.rna-seqblog.com/scdist-robust-identification-of-perturbed-cell-types-in-single-cell-rna-seq-data/?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

Modified #RNA sequencing method reveals how small #RNAs boost immune response to tuberculosis

Tuberculosis kills about 1.3 million people each year, making it one of the most lethal infectious diseases in the world. Now, molecular biologist Yohei Kirino, PhD and his research team at Thomas Jefferson University has found that certain #RNA molecules in people with tuberculosis are drastically different than those in healthy people. The findings, published in ... https://www.rna-seqblog.com/modified-rna-sequencing-method-reveals-how-small-rnas-boost-immune-response-to-tuberculosis/?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

Genes, Vol. 15, Pages 1165: Schistosoma japonicum sja-let-7 Inhibits the Growth of Hepatocellular Carcinoma Cells via Cross-Species Regulation of Col1α2

Liver fibrosis, a critical precursor to hepatocellular carcinoma (HCC), results from chronic liver injury and significantly contributes to HCC progression. Schistosomiasis, a neglected tropical disease, is known to cause liver fibrosis; however, this process can be modulated by schistosome-derived #miRNAs. Previous studies from our laboratory have demonstrated that Schistosoma japonicum extracellular vesicles (EVs) deliver sja-let-7 to hepatic stellate cells, leading to the inhibition of Col1α2 expression and alleviation of liver fibrosis. Given the well-documented antifibrotic and antiproliferative properties of the let-7 #miRNA family, this study aims to preliminarily investigate the effects of the sja-let-7/Col1α2 axis on BALB/c mice and HCC cell line SNU387, providing a basis for the potential application of parasite-derived molecules in HCC therapy. In the present study, schistosome-induced fibrosis datasets were analyzed to identify the role of Col1α2 in extracellular matrix organization. Pan-#cancer analysis revealed that Col1α2 is upregulated in various #cancers, including HCC, with significant associations with immune cell infiltration and clinical parameters, highlighting its diagnostic importance. Functional assays demonstrated that transfection with sja-let-7 mimics significantly reduced Col1α2 expression, inhibited HCC cell proliferation, migration, and colony formation. These findings suggest that sja-let-7, by targeting Col1α2, has the potential to serve as a therapeutic agent in HCC treatment. This study indicates the pivotal role of Col1α2 in liver fibrosis and HCC, and the promising therapeutic application of helminth-derived #miRNAs. https://www.mdpi.com/2073-4425/15/9/1165?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

JoF, Vol. 10, Pages 631: Two Sugarcane Expansin Protein-Coding Genes Contribute to Stomatal Aperture Associated with Structural Resistance to Sugarcane Smut

Sporisorium scitamineum is a biotrophic fungus responsible for inducing sugarcane smut disease that results in significant reductions in sugarcane yield. Resistance mechanisms against sugarcane smut can be categorized into structural, biochemical, and physiological resistance. However, structural resistance has been relatively understudied. This study found that sugarcane variety ZZ9 displayed structural resistance compared to variety GT42 when subjected to different inoculation methods for assessing resistance to smut disease. Furthermore, the stomatal aperture and density of smut-susceptible varieties (ROC22 and GT42) were significantly higher than those of smut-resistant varieties (ZZ1, ZZ6, and ZZ9). Notably, S. scitamineum was found to be capable of entering sugarcane through the stomata on buds. According to the #RNA sequencing of the buds of GT42 and ZZ9, seven Expansin protein-encoding genes were identified, of which six were significantly upregulated in GT42. The two genes c111037.graph_c0 and c113583.graph_c0, belonging to the α-Expansin and β-Expansin families, respectively, were functionally characterized, revealing their role in increasing the stomatal aperture. Therefore, these two sugarcane Expansin protein-coding genes contribute to the stomatal aperture, implying their potential roles in structural resistance to sugarcane smut. Our findings deepen the understanding of the role of the stomata in structural resistance to sugarcane smut and highlight their potential in sugarcane breeding for disease resistance. https://www.mdpi.com/2309-608X/10/9/631?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

Genes, Vol. 15, Pages 1161: Simultaneous Visualization of R-Loops/#RNA:DNA Hybrids and Replication Forks in a DNA Combing Assay

R-loops, structures that play a crucial role in various biological processes, are integral to gene expression, the maintenance of genome stability, and the formation of epigenomic signatures. When these R-loops are deregulated, they can contribute to the development of serious health conditions, including #cancer and neurodegenerative diseases. The detection of R-loops is a complex process that involves several approaches. These include S9.6 antibody- or #RNAse H-based immunoprecipitation, non-denaturing bisulfite footprinting, gel electrophoresis, and electron microscopy. Each of these methods offers unique insights into the nature and behavior of R-loops. In our study, we introduce a novel protocol that has been developed based on a single-molecule DNA combing assay. This innovative approach allows for the direct and simultaneous visualization of #RNA:DNA hybrids and replication forks, providing a more comprehensive understanding of these structures. Our findings confirm the transcriptional origin of the hybrids, adding to the body of knowledge about their formation. Furthermore, we demonstrate that these hybrids have an inhibitory effect on the progression of replication forks, highlighting their potential impact on DNA replication and cellular function. https://www.mdpi.com/2073-4425/15/9/1161?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

Biology, Vol. 13, Pages 688: The Human Pathogen Mycobacterium tuberculosis and the Fish Pathogen Mycobacterium marinum Trigger a Core Set of Late Innate Immune Response Genes in Zebrafish Larvae

Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum is #evolutionarily one of the closest non-tuberculous species related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen, we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study, we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina #RNA deep sequencing (#RNAseq). Bacterial aggregates carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post-infection. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the inflammatory response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week after infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. The generated extensive transcriptome data sets will be of great use to add translational value to zebrafish as a model for infection of tuberculosis using the M. marinum infection system. In addition, we identify new marker genes such as dusp8 and CD180 that are induced by M. tuberculosis infection in zebrafish and in human macrophages at later stages of infection that can be further investigated. https://www.mdpi.com/2079-7737/13/9/688?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

SmithHunter: a workflow for the identification of candidate smith#RNAs and their targets

Smith#RNAs (Small MITochondrial Highly-transcribed #RNAs) are a novel class of small #RNA molecules that are encoded in the mitochondrial genome and regulate the expression of nuclear transcripts. Initial evidenc... https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-05909-0?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

Microorganisms, Vol. 12, Pages 1820: Profile of Bacterial Communities in Copper Mine Tailings Revealed through High-Throughput Sequencing

Mine-tailing dumps are one of the leading sources of environmental degradation, often with public health and ecological consequences. Due to the complex ecosystems generated, they are ideal sites for exploring the bacterial diversity of specially adapted microorganisms. We investigated the concentrations of trace metals in solid copper (Cu) mine tailings from the Ovejería Tailings Dam of the National Copper Corporation of Chile and used high-throughput sequencing techniques to determine the microbial community diversity of the tailings using 16S #rRNA gene-based amplicon sequence analysis. The concentrations of the detected metals were highest in the following order: iron (Fe) > Cu > manganese (Mn) > molybdenum (Mo) > lead (Pb) > chromium (Cr) > cadmium (Cd). Furthermore, 16S #rRNA gene-based sequence analysis identified 12 phyla, 18 classes, 43 orders, 82 families, and 154 genera at the three sampling points. The phylum Proteobacteria was the most dominant, followed by Chlamydiota, Bacteroidetes, Actinobacteria, and Firmicutes. Genera, such as Bradyrhizobium, Aquabacterium, Paracoccus, Caulobacter, Azospira, and Neochlamydia, showed high relative abundance. These genera are known to possess adaptation mechanisms in high concentrations of metals, such as Cd, Cu, and Pb, along with nitrogen-fixation capacity. In addition to their tolerance to various metals, some of these genera may represent pathogens of amoeba or humans, which contributes to the complexity and resilience of bacterial communities in the studied Cu mining tailings. This study highlights the unique microbial diversity in the Ovejería Tailings Dam, including the discovery of the genus Neochlamydia, reported for the first time for heavy metal resistance. This underscores the importance of characterizing mining sites, particularly in Chile, to uncover novel bacterial mechanisms for potential biotechnological applications. https://www.mdpi.com/2076-2607/12/9/1820?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

Applied Microbiology, Vol. 4, Pages 1268-1282: Addition of Chicken Litter Compost Changes Bacteriobiome in Fallow Soil

Composting is an environmentally friendly process, turning animal waste into fertilizer. Chicken litter compost (CLC) improves soil properties, increasing crop yields. However, the CLC effect on the soil microbiome is understudied. This study aimed to compare bacteriobiome diversity in fallow arable Chernozem with and without CLC addition in a field experiment in the Novosibirsk region, Russia, using 16S #rRNA gene metabarcoding. Pseudomonadota, Actinomycetota and Acidobacteriota were the most OTU-rich phyla, together accounting for >50% of the total number of sequence reads. CLC-related shifts in the bacteriobiome structure occurred at all taxonomic levels: the Bacillota abundance was 10-fold increased due to increased Bacilli, both being indicator taxa for the CLC-soil. The main Actinomycetota classes were the indicators for the CLC-soil (Actinobacteria) and no-CLC soil (Thermoleophilia, represented Gaiella). Both Bacillota and Actinomycetota phyla were the ultimate constituents of the CLC added, persisting in the soil for five months of fallowing. The no-CLC soil indicator phyla were Acidobacteriota (represented by Acidobacteria_Group3) and Verrucomicrobiota. Future metabarcoding studies of chicken litter application in agricultural soils, including cropped studies, should address the soil microbiome at the species/strain levels in more detail, as well as how it is affected by specific crops, preferably accompanied by a direct methodology revealing the microbiota functions. https://www.mdpi.com/2673-8007/4/3/87?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

Biomedicines, Vol. 12, Pages 2001: Epigenetic Regulation of DNA Methylation and #RNA Interference in Gastric #cancer: A 2024 Update

Gastric #cancer (GC) remains a significant public health concern because of its lethality, underscoring the need for deeper insights into its molecular mechanisms. Recent studies have increasingly highlighted the role of epigenetic modifications as critical players in #cancer progression. Despite their importance, research specifically addressing epigenetic factors in GC is relatively scarce. This paper seeks to bridge that gap by examining recent literature that elucidates the epigenetic landscape associated with GC. The investigation of long noncoding #RNAs (l#ncRNAs) has revealed their substantial involvement in gene dysregulation and epigenetic alterations within GC tumors. Notably, l#ncRNAs such as LINC00853 and LINC01266 have been identified as significant contributors to the epigenetic modulation of gene expression. Furthermore, the overexpression of KAT5 and GPX4 has been shown to mitigate the antiproliferative effects resulting from the depletion of circRHOT1, suggesting a complex interplay between these molecules in GC pathophysiology. Another pivotal aspect of epigenetic regulation in GC involves modifications in N6-methyladenosine (m6A), which play crucial roles in #mRNA maturation processes such as splicing, export, degradation, and translation. m6A modifications are known for their influence on various #cancer-related pathways, thus presenting a potential avenue for targeted interventions. Our findings indicate that the most pronounced instances of epigenetic dysregulation in GC can be traced back to the effects of long l#ncRNAs and alterations in m6A modification patterns. This underscores the urgent need for comprehensive investigations into these epigenetic factors, as a deeper understanding could lead to enhanced diagnostic markers and innovative therapeutic strategies. The integration of genetic and epigenetic considerations is essential for advancing the field of GC research. This synthesis of recent findings concerning epigenetic regulation offers valuable insights that could inform future studies and therapeutic developments. There is a critical need for ongoing research to elucidate the complexities of epigenetic modifications in GC, ultimately improving patient outcomes through tailored interventions. https://www.mdpi.com/2227-9059/12/9/2001?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

NASC-seq2 – principles of transcription at the resolution of individual bursts

Imagine a factory where products are made in short, intense bursts rather than in a continuous flow. In the world of biology, something similar happens with gene expression, a process known as "transcriptional bursting."... https://www.rna-seqblog.com/nasc-seq2/?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

RNA Sequencing reveals molecular mechanism behind MS and other autoimmune diseases

A Yale-led study reveals a mechanism that triggers loss of immune regulation associated with multiple sclerosis and other diseases — and a target for treatment. More than two decades ago, a research team in the lab of David Hafler, a Yale researcher who at the time was at Harvard, discovered a type of T cell ... https://www.rna-seqblog.com/rna-sequencing-reveals-molecular-mechanism-behind-ms-and-other-autoimmune-diseases/?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

New approach to DNA computing uses Nanopore #RNA sequencing to perform calculations and solve puzzles

Scientists from the USA have developed new methods for DNA computing with which they can store data, perform calculations and solve Sudoku puzzles. A team from North Carolina State University and Johns Hopkins University claims to have developed the first DNA-based method that can store, retrieve, calculate, delete and repeatedly overwrite data. The scientists ... https://www.rna-seqblog.com/new-approach-to-dna-computing-uses-nanopore-rna-sequencing-to-perform-calculations-and-solve-puzzles/?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

IJMS, Vol. 25, Pages 9543: Maximal Genetic Code Symmetry Is a Physicochemical Purine–Pyrimidine Symmetry Language for Transcription and Translation in the Flow of Genetic Information from DNA to Proteins

Until now, research has not taken into consideration the physicochemical purine–pyrimidine symmetries of the genetic code in the transcription and translation processes of proteinogenesis. Our Supersymmetry Genetic Code table, developed in 2022, is common and unique for all #RNA and DNA living species. Its basic structure is a purine–pyrimidine symmetry net with double mirror symmetry. Accordingly, the symmetry of the genetic code directly shows its organisation based on the principle of nucleotide Watson–Crick and codon–anticodon pairing. The maximal purine–pyrimidine symmetries of codons show that each codon has a strictly defined and unchangeable position within the genetic code. We discovered that the physicochemical symmetries of the genetic code play a fundamental role in recognising and differentiating codons from #mRNA and the anticodon #tRNA and aminoacyl-#tRNA synthetases in the transcription and translation processes. These symmetries also support the wobble hypothesis with non-Watson–Crick pairing interactions between the translation process from #mRNA to #tRNA. The Supersymmetry Genetic Code table shows a specific arrangement of the second base of codons, according to which it is possible that an anticodon from #tRNA recognises whether a codon from #mRNA belongs to an amino acid with two or four codons, which is very important in the purposeful use of the wobble pairing process. Therefore, we show that canonical and wobble pairings essentially do not lead to misreading and errors during translation, and we point out the role of physicochemical purine–pyrimidine symmetries in decreasing disorder according to error minimisation and preserving the integrity of biological processes during proteinogenesis. https://www.mdpi.com/1422-0067/25/17/9543?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

Nutrients, Vol. 16, Pages 2956: Dietary Pattern’s Role in Hepatic Epigenetic and Dietary Recommendations for the Prevention of NAFLD

NAFLD has emerged as a significant public health concern, with its prevalence increasing globally. Emphasizing the complex relationship between dietary patterns and epigenetic modifications such as DNA methylation or #miRNA expression can exert a positive impact on preventing and managing metabolic disorders, including NAFLD, within the 2030 Sustainable Development Goals. This review aims to evaluate the influence of dietary patterns on hepatic epigenetic gene modulation and provide dietary recommendations for the prevention and management of NAFLD in the general population. Methods: Comprehensive screening and eligibility criteria identified eleven articles focusing on epigenetic changes in NAFLD patients through dietary modifications or nutrient supplementation. Results and Discussion: Data were organized based on study types, categorizing them into evaluations of epigenetic changes in NAFLD patients through dietary pattern modifications or specific nutrient intake. Conclusions: The study highlights the importance of dietary interventions in managing and preventing NAFLD, emphasizing the potential of dietary patterns to influence hepatic epigenetic gene modulation. This study provides valuable insights and recommendations to mitigate the risk of developing NAFLD: (i) eat a primarily plant-based diet; (ii) increase consumption of high-fiber foods; (iii) consume more polyunsaturated and monounsaturated fatty acids; (iv) limit processed foods, soft drinks, added sugars, and salt; and (v) avoid alcohol. https://www.mdpi.com/2072-6643/16/17/2956?utm_source=dlvr.it&utm_medium=tumblr

[rnomics]

#ncRNA, Vol. 10, Pages 48: Circulating #miRNAs in the Plasma of Post-COVID-19 Patients with Typical Recovery and Those with Long-COVID Symptoms: Regulation of Immune Response-Associated Pathways

Following the acute phase of SARS-CoV-2 infection, certain individuals experience persistent symptoms referred to as long COVID. This study analyzed the patients categorized into three distinct groups: (1) individuals presenting rheumatological symptoms associated with long COVID, (2) patients who have successfully recovered from COVID-19, and (3) donors who have never contracted COVID-19. A notable decline in the expression of miR-200c-3p, miR-766-3p, and miR-142-3p was identified among patients exhibiting rheumatological symptoms of long COVID. The highest concentration of miR-142-3p was found in healthy donors. One potential way to reduce #miRNA concentrations is through antibody-mediated hydrolysis. Not only can antibodies possessing #RNA-hydrolyzing activity recognize the #miRNA substrate specifically, but they also catalyze its hydrolysis. The analysis of the catalytic activity of plasma antibodies revealed that antibodies from patients with long COVID demonstrated lower hydrolysis activity against five fluorescently labeled oligonucleotide sequences corresponding to the Flu-miR-146b-5p, Flu-miR-766-3p, Flu-miR-4742-3p, and Flu-miR-142-3p #miRNAs and increased activity against the Flu-miR-378a-3p #miRNA compared to other patient groups. The changes in #miRNA concentrations and antibody-mediated hydrolysis of #miRNAs are assumed to have a complex regulatory mechanism that is linked to gene pathways associated with the immune system. We demonstrate that all six #miRNAs under analysis are associated with a large number of signaling pathways associated with immune response-associated pathways. https://www.mdpi.com/2311-553X/10/5/48?utm_source=dlvr.it&utm_medium=tumblr