Fast nanopore sequencing data analysis with SLOW5

Nanopore sequencing depends on the FAST5 file format, which does not allow efficient parallel analysis. Here we introduce SLOW5, an alternative format engineered for efficient parallelization and acceleration of nanopore data analysis. Using the example of DNA methylation profiling of a human genome, analysis runtime is reduced from more than two weeks to approximately 10.5 h on a typical high-performance computer. SLOW5 is approximately 25% smaller than FAST5 and delivers consistent improvements on different computer architectures.

Interrogation of the microenvironmental landscape in spinal ependymomas reveals dual functions of tumor-associated macrophages

Spinal ependymomas are the most common spinal cord tumors in adults, but their intratumoral cellular heterogeneity has been less studied, and how spinal microglia are involved in tumor progression is still unknown. Here, our single-cell RNA-sequencing analyses of three spinal ependymoma subtypes dissect the microenvironmental landscape of spinal ependymomas and reveal tumor-associated macrophage (TAM) subsets with distinct functional phenotypes. CCL2+ TAMs are related to the immune response and exhibit a high capacity for apoptosis, while CD44+ TAMs are associated with tumor angiogenesis. By combining these results with those of single-cell ATAC-sequencing data analysis, we reveal that TEAD1 and EGR3 play roles in regulating the functional diversity of TAMs. We further identify diverse characteristics of both malignant cells and TAMs that might underlie the different malignant degrees of each subtype. Finally, assessment of cell-cell interactions reveal that stromal cells act as extracellular factors that mediate TAM diversity. Overall, our results reveal dual functions of TAMs in tumor progression, providing valuable insights for TAM-targeting immunotherapy.

6-Shogaol Mitigates Sepsis-Associated Hepatic Injury through Transcriptional Regulation

Sepsis-associated liver dysfunction presents a significant public health problem. 6-Shogaol is the key bioactive component in dry ginger, which has antioxidant and anti-inflammation capacity. The present study aims to investigate the preventive effect of 6-shogaol on sepsis-induced liver injury. 6-Shogaol was administered to mice for 7 consecutive days before being intraperitoneally injected with lipopolysaccharide (LPS). After 24 h, mice were sacrificed, and biochemical and transcriptomic analyses were performed. Our results demonstrated that 6-shogaol prevented LPS-induced impairment in antioxidant enzymes and elevation in malondialdehyde level in the liver. The hepatic inflammatory response was significantly suppressed by 6-shogaol through suppressing the MAPK/NFκB pathway. RNA-sequencing data analysis revealed that 41 overlapped genes between the LPS vs. control group and 6-shogaol vs. LPS group were identified, among which 36 genes were upregulated, and 5 genes were downregulated for the LPS vs. control group. These overlapped genes are enriched in inflammation-related pathways, e.g., TNF and NFκB. The mRNA expression of the overlapped genes was also verified in the LPS-induced BRL-3A cell model. In summary, 6-shogaol shows great potential as a natural chemopreventive agent to treat sepsis-associated hepatic disorders.

Microbiome Associated with Slovak Traditional Ewe’s Milk Lump Cheese

Worldwide consumers increasingly demand traditional/local products, to which those made from ewe’s milk belong. In Slovakia, dairy products made from ewe’s milk have a long tradition. A total of seventeen farmhouse fresh ewe’s milk lump cheeses from various local farm producers in central Slovakia were sampled at farms and then analyzed. Based on the sequencing data analysis, the phylum Firmicutes dominated (60.92%) in ewe’s lump cheeses, followed with the phylum Proteobacteria (38.23%), Actinobacteria (0.38%) and Bacteroidetes (0.35%). The phylum Firmicutes was represented by six genera, among which the highest amount possessed the genus Streptococcus (41.13%) followed with the genus Lactococcus (8.54%), Fructobacillus (3.91%), Enterococcus (3.18%), Staphylococcus (1.80%) and the genus Brochotrix (0.08%). The phylum Proteobacteria in ewe’s lump cheeses involved eight Gram-negative genera: Pseudomonas, Acinetobacter, Enterobacter, Ewingella, Escherichia-Shigella, Pantoea and Moraxella. The phylum Bacteroidetes involved three genera: Bacteroides, Sphingobacterium and Chrysobacterium. Results presented are original; the microbiome of Slovak ewe’s milk lump cheese has been not analyzed at those taxonomic levels up to now.

Next Generation Sequencing Data Analysis and its Applications in Agriculture

Next Generation sequencing (NGS) technologies are revolutionizing the acquisition of genomic data at relatively low cost. NGS technologies are rapidly changing approaches to complex genomic studies and generating a vast amount of data. New and more powerful bioinformatics proposals and tools are needed to handle such large biological collections of such huge amounts of data provided by NGS data analysis. In addition, specialized software tools and advanced computational resources are required for data integration. In this article, we are describing here the main computational approach for next generation sequencing data analysis and its role in agriculture for crop improvement.