PROJECTS IN BIOINFORMATICS

  • WHOLE-GENOME SEQUENCING

  • SMALL RNA SEQUENCING

ABSTRACT #1

  • Whole-Genome Sequencing Project

    This research project aimed to sequence the genomes of two strains of Escherichia coli, MM294 and O157:H7, using Illumina sequencing technology. The study was successful in all aspects of the procedure, including DNA culturing and extraction, DNA library construction, sequencing run, and genome analysis using various Illumina applications. The results showed that both strains had acceptable DNA yields and concentrations, and the sequencing run had an acceptable Q30 score. The genome analysis revealed differences between the two strains in terms of taxonomic classification, serotyping, virulence genes, resistance genes, and plasmid replicons. Despite some limitations with the IGV genome viewing app, the study provided a significant amount of data on each sample, most of which aligning with expectations, and can be considered a success overall.

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Culture plates of MM294 and O157:H7

SUMMARY OF FINDINGS

Using Illumina sequencing technology, whole-genomes of two strains of Escherichia coli, MM294 and O157:H7, were analyzed and compared. The results showed that both strains had acceptable DNA yields and concentrations, with MM294 yielding 13.3 μg and O157:H7 yielding 9.9 μg of DNA. The sequencing run had an acceptable Q30 score of 84.76% for MM294 and 82.35% for O157:H7.

Genome analysis revealed differences between the two strains in terms of taxonomic classification, serotyping, virulence genes, resistance genes, and plasmid replicons. Notably, O157:H7 contained genes for Shiga toxins, associated with severe disease outcomes, while MM294 lacked these genes. Moreover, resistance genes were identified in both strains, including genes for resistance to multiple antibiotics such as tetracycline and streptomycin.

Virulence genes that have been associated with severe disease outcomes were also investigated. In particular, intimin-encoding gene eae and enterohemolysin-encoding gene ehxA were identified in O157:H7. The study provides valuable insights into genomic differences between these two important E. coli strains, shedding light on their potential virulence and antibiotic resistance mechanisms.

ABSTRACT #2

  • Small RNA Sequencing Project

    This cutting-edge small RNA sequencing project aimed to identify and compare small RNA molecules in animals and plants. Samples were taken from various sources, including human brain cells, baby hamster kidney cells, and different plant species. Using state-of-the-art laboratory procedures, including RNA extraction, library construction, and sequencing, the samples were quality-checked throughout the process. The sequencing run was highly successful, producing high-quality reads and low error rates. The project revealed significant conservation of miRNA between animals and plants, providing insights into evolutionary history dating back as far as 1870 million years ago. These strong results highlight the power of bioinformatics in unlocking the secrets of genetic diversity and evolution.

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hsa-mir-3168 was the most significant miRNA precursor hit across plant and animal species

SUMMARY OF FINDINGS

Using Illumina sequencing technology, small RNA molecules were analyzed from a diverse set of organisms spanning two kingdoms. Samples were taken from human brain cells, baby hamster kidney cells, arugula, lime basil, orchid, and sweet basil. The sequencing run generated 136 million high-quality reads, with an average read length of 18-22 nt.

The data analysis revealed significant conservation of miRNA between animals and plants, as well as high conservation within each kingdom. Notably, miR-21 and miR-156 were conserved across both animal and plant samples.

Additionally, several miRNAs were identified that were specific to each organism or tissue type. Of particular interest, miR-9 was specific to human brain cells and miR-167 to sweet basil.

Findings such as these provide insight into the evolutionary history of small RNAs, revealing conserved miRNAs between animals and plants as well as unique miRNAs specific to each organism or tissue type. Additionally, this research highlights the utility of small RNA sequencing and bioinformatics approaches in better understanding the complex world of gene expression and regulation.