Summer Training 2025

Mastering Nucleic Acid Extraction

• DNA and RNA extraction from different sources; clinical, plant, and environmental samples.

•  Learning to overcome challenges in working with degraded or low-yield samples.  

Amplification Strategies – Polymerase Chain Reaction

• Standard, reverse transcription, multiplex, and nested PCR techniques.

• Optimizing reaction set-up and adjusting thermal profile.

• Learning how to use PCR for different applications for mutation detection and genome analysis.

• Troubleshoot agarose gel electrophoresis and interpret the results. 

Real-Time PCR (qPCR) for Quantitative Analysis

• Fluorescent chemistries (SYBR Green, TaqMan, HRM) for precise quantification.

• Optimizing reaction conditions, threshold & Ct values

• Absolute quantification vs Relative qunatification.

• Data interpretation, validation, and statistical analysis using qPCR software.

• High-Resolution Melting (HRM) curve analysis for SNP genotyping. 

DNA Sequencing Technologies

• How to choose the right technology

• Capillary Electrophoresis & Next-generation sequencing (NGS)  

Applications

• Detection of pathogens using multiplex PCR, qPCR diagnostics.

• Antibiotic resistance gene analysis for clinical microbiology applications.

• Pharmacogenomics and its role in predicting drug response.

• Understanding cancer epidemiology, risk factors, symptoms, types & stages.  

• The role of molecular biology in cancer diagnosis & treatment.  

• Studying the genes whose mutation contributes to the causation of cancer.  

• Ras genes mutation triggering the development of different types of human tumors.  

• P53 mutations & programmed cell death.  

• Prognostic Implication of FLT3 Gene Mutations in Acute Myeloid Leukemia  

• In vitro anti-cancer effect of different treatments in Breast cancer cell line  

• Diagnostic role of BCR-ABL in Acute Lymphatic Leukemia  

• In Vivo Cancer Models to Guide Precision Medicine & study Efficacy of Cancer Therapy  

• BRCA1 and BRCA2 genes mutations & breast cancer development  

• Identifying gene expression patterns associated with drug response  

• Calculating minimal residual disease (MRD)  

• Understanding major molecular response (MMR)  

• Identifying prognosis relevant genes  

• Current approaches and challenges in managing and monitoring treatment response in cancer patients  

• Targeted mutation detection in clinical cancer settings: formaldehyde fixed paraffin embedded (FFPE) tumor tissues 

(I) Semen Analysis to evaluate male fertility

•  Physical examination to assess the volume, viscosity, and color of semen.

• Chemical analysis to measure parameters such as pH and sperm concentration..

• Microscopic examination for evaluating sperm morphology, motility, and vitality. 

• Sperm DNA Fragmentation (SDF) & Sperm Chromatin Dispensation (SCD).

(II) Preimplantation Genetic Testing - PGT

• Identification and selection of genetically viable embryos.

• Genetic analysis when one or both parents carry a known genetic mutation associated with specific hereditary disorders. 

• Enabling parents to select embryos that do not carry the mutations associated with certian diseases (cystic fibrosis, Tay-Sachs disease, and sickle cell anemia)

• Assess the overall chromosomal health of embryos, identifying issues such as aneuploidy (an abnormal number of chromosomes), which can lead to miscarriage or developmental problems.

• Types of chromosomal abnormalities—numerical (e.g., aneuploidy) and structural (e.g., translocations, deletions). 

• Karyotyping and reading the chromosomes banding.

• Genomic techniques for detection of copy number variations (CNVs), single nucleotide polymorphisms (SNPs), and other mutations. 

Principles of nucleic acid extraction

• Understanding essential principles for optimizing yield and purity of extracted nucleic acids.

• DNA extraction using the silica-based method along with troubleshooting tips.

Polymerase Chain Reaction (PCR)

• Principle, reaction setup and thermal profiling.

• Troubleshooting Tips; no amplification, the primer design and non-specific bands. 

Agarose Gel Electrophoresis 

• Gel electrophoresis steps and how it works.

• Used buffers, electrophoresis device system & electrical separation.

• Staining agents used to visualize the DNA bands under UV light.

• How to read the results.

•  Introduction to animal cell culture .

•  Cell counting using hemocytometer.

•  Adherent vs. suspension cells. 

•  Examples of commonly used cell lines. 

•  Cytotoxicity assays: include screening for cytostatic and cytotoxic anticancer drugs and the measurement of cell proliferation.

• Principle of the MTT Assay. 

• Definition and importance of cytotoxicity assays in research. 

• Seed cells in 96-well plates. 

• Measure absorbance using ELISA reader. 

• Handling food samples and maintaining their integrity

• Step-by-step microbiological testing: E. coli, Salmonella, S. aureus, and more.

• Working with selective media: Baird-Parker, XLD, EMB, VRBG.

• Generating professional microbiological reports.

• Interpreting test results accurately.

• Good Laboratory Practices (GLP)

• Sterilization, safety, and workflow optimization in microbiology labs.

• Interview Preparation: Common questions for microbiologist roles in the food industry.

• Introduction to NCBI Databases: GenBank, PubMed, BLAST

• Introduction to EMBL-EBI Databases: Ensembl, UniProt

• ⁠Principles & Tools for Primer Design

• Tools & Algorithms for Sequence Alignment

• ⁠Phylogenetic Tree Analysis

• ⁠Overview of Snap Gene Software

• ⁠Introduction to Galaxy Platform

• ⁠Data Analysis Tools in Galaxy

• ⁠Analyzing Biological Data

• ⁠Using KEGG for Pathway Analysis

Isolation & Microscopic Examination

•  Isolation of bacterial colonies from clinical samples.

• Understand the different streaking techniques (e.g., quadrant streaking) to obtain pure cultures of microorganisms, facilitating the observation of colony morphology on culture media.

•  Complete Gram Staining Procedure to differentiate between Gram-positive and Gram-negative bacteria. 

Biochemical Identification Tests

• Catalase - Oxidase - Coagulase -  Urease -Citrate Test

• MIO (Motility-Indole-Ornithine)  

•  TSI (Triple Sugar Iron) Agar Test

Antibiotic Susceptibility Testing

• Use standard antibiotic sensitivity discs to evaluate bacterial resistance or susceptibility. 

• Learning how to measure zones of inhibition and interpret results in alignment with clinical guidelines.

Diagnostic Labs Workflow 

• Integrating results from laboratory procedures into a structured diagnostic workflow. 

• Learning how to interpret findings and correlate microbiological data, leading to the accurate scientific identification of unknown bacteria.

• Preparation of a Professional Mini Lab Report; by documenting findings in a concise lab report format, focusing on clarity, organization, and professionalism.