University College London- United Kingdom, London
Research student at the Respiratory Laboratory
Project: ''Characterization of novel vaccine candidates against Streptococcus pneumoniae''
March 2023 - August 2023
- A previously uncharacterized pneumococcal surface-exposed antigen (SP_X) was identified to be studied as a vaccine candidate followed by generating the knockout mutant of that candidate. Characterization of the function of the protein was then performed by investigating the mutant's phenotype.
- Pneumococcal stock was prepared using TSB (tryptic soy broth) liquid culture
- Bacterial plating and counting of colony-forming units
- Serum deposition assay was performed using sera from mice immunized with pneumococcal antigens to assess the antigens surface exposure.
- Bacterial DNA extraction by using the Promega Wizard Genomic DNA Purification Kit followed by the quantification of the DNA with a nanodrop OneC microvolume spectrophotometer.
- Overlap extension PCR was used to generate the mutants
- Primers were designed for sp_X deletion
- Gel electrophoresis was performed to confirm the successful amplification of the PCR products
- The bacterial transformation was performed using CSP1 (competence stimulating peptide)
- Sanger sequencing was performed using the DNA extracted from the clones and the external primers
- A Western Blot was performed using anti-mouse antibodies against the protein of interest (SP_X) to confirm the absence of the expression of the protein in mutants
- Confocal microscopy was used to evaluate any structural changes between the mutant and WT (wild type) and to further confirm the absence of the desired protein in the knockout mutant strains
- Growth assays were performed to measure possible changes in the proliferation rate of the mutants
- A complement deposition assay was performed to assess if the desired protein ( Sp_X) was important to complement binding as a mechanism of evasion from complement-mediated killing
University of Greenwich- United Kingdom, London
Research student at the Exogenix laboratory
Project: ''The investigation of the multifunctional protein ALiX. Its role in intracellular trafficking using CRISPR Cas9 Technology''
December 2021- April 2022
-The focus of this innovative dissertation was on gene editing and the intracellular delivery of siRNA through the improvement of drug delivery mechanisms. A CRISPR sequence was identified against the target gene (ALiX), and sub-cloned it into a Cas9 and sgRNA expressed plasmid. The influence of CRISPR technology in medicine both from the perspective of therapeutic design as well as research and development in the future was observed.
- The transcript variant 2 for ALiX was introduced in benchling to select the most suitable CRISPR sequence with the highest off-target value.
- The plasmid containing Cas9 enzyme was extracted from pure E.Coli culture and the concentration and purity were obtained using BioDrop
- A restriction enzyme (BbSI) was used to cut the plasmid followed by the alignment of the strands
- A gene cleanse was performed along with additional agarose gel electrophoresis with both cut and uncut plasmid for comparison
- Gibson assembly was used to clone the fragments into the vector followed by a bacterial transformation process
- The screening of the samples was performed by a PCR
References available upon request