M.Phil Molecular Biology and Genetics

Course for PhD in Molecular Biology: Total Credit Hours 20 +40

Course ID	Subject/Module	Credit Hours	Marks
Mol: 301	Research Methodology and Biostatistics	2	100
Mol: 302	Advance Human Genetics	3	100
Mol: 303	Computational Biology and Bioinformatics	3	100
Mol: 304	Modern DNA typing techniques	3	100
Mol: 401	Recombinant DNA Technology	3	100
Mol: 402	Advance Genomics	3	100
Mol: 403	Advance Proteomics	3	100
Total Credit hours taught course		20	700
Thesis/Research		40
Total PhD Credit hours		60

Mol: 301: Advance Human Genetics
Introduction to Genomics - information flow in biology, Central Dogma of Life, DNA sequence data, genome information resources Proteomics - protein sequence and structural data, protein information resources and data bases. Computational Genomics - Internet basics, biological data analysis and application, sequence data bases, NCBI model, file format. Sequence alignment & data base search - Protein primary sequence analysis, DNA sequence Analysis, FASTA algorithm, BLAST, multiple sequence alignment, DATA base searching using BLAST and FASTA. DNA Typing: DNA polymorphisms: the basis of DNA typing, Microsatellite analysis , Short tandem repeat analysis, Mitochondrial DNA analysis. High-throughput analysis of gene function - DNA microarrays, Protein arrays.. Single Nucleotide Polymorphisms -, Mapping disease-associated SNPs. The Hardy-Weinberg Equation allele frequencies, Basics and concept. Basics of Allele Genotyping and frequency. Applications in genetics Human disease, now and future.

Mol: 302: Computational Biology and Bioinformatics
Introduction to Genomics - information flow in biology, DNA sequence data, Experimental approach to genome sequence data, genome information resources.
Functional Proteomics - protein sequence and structural data, protein information resources and Secondary data bases. Computational Genomics - Internet basics, biological data analysis and application, sequence data bases, NCBI model, file format. Sequence alignment & data base search - Protein primary sequence analysis, DNA sequence analysis, pair wise sequence alignment, FASTA algorithm, BLAST, multiple sequence alignment, DATA base searching using BLAST and FASTA. Structural data bases - Small molecules data bases, protein information resources, protein data bank.

Mol: 303: Modern DNA Typing Techniques
DNA Typing: DNA polymorphisms: the basis of DNA typing, Minisatellite analysis, Polymerase chain reaction based analysis, Short tandem repeat analysis, Mitochondrial DNA analysis, Y chromosome analysis, randomly amplified polymorphic DNA (RAPD) analysis. Proteomics and beyond: Analysis of the transcriptome, Proteomics-Expression analysis &characterization of proteins, Metabolomics & global biochemical networks. High-throughput analysis of gene function - DNA microarrays, Protein arrays, Mass spectrometry. Single Nucleotide Polymorphisms - The nucleolar proteome, Mapping disease-associated SNPs. NGS concepts and utilization.

Mol: 401: Recombinant DNA Technology
Gene Recombination and Gene transfer: Bacterial Conjugation, Transformation, Transduction, Episomes, Plasmids, Microinjection, Electroporation, Microprojectile, Shot Gun method, Ultrasonication, Liposome fusion, Microlaser. Changing genes: site-directed mutagenesis and Protein engineering: Primer extension is a simple method for site directed mutation, PCR based site directed mutagenesis, Random mutagenesis, Use of Phage display techniques to facilitate the selection of mutant peptides, Gene shuffling, production of chimeric proteins.
Genetic engineering in animals: Production of transgenic mice, ES cells can be used for gene targeting in mice, Application of gene targeting, using Yeast to study Eikaryotic gene function, Therapeutic products produced by genetic engineering blood proteins, human hormones, immune modulators and vaccines, Transgenic animals, production of proteins of pharmaceutical value. Genetic engineering in plants: use of Agrobacterium tumefaciens and Arhizogenes, Ti plasmid, strategies of gene transfer to plant cells, Direct DNA transfer to plants, Gene targeting in plants, use of plant viruses as episomal expression vectors.

Mol: 402: Advance Genomics
Classical genetics and positional cloning. An overview of classical screening strategies (forward genetics) in model systems including D. melanogaster and C. elegans. Strengths and limitations. Introduction to genomic technologies and historical perspective. Advances in microarray and deep sequencing techologies. Latest technological advances. Overview of their use in the hapmap and genome sequencing projects. methods in genomic analyses. Generation and handling of genomic datasets. Most common, and useful tools of analyses. Pitfalls, and significance considerations. Chromatin immunoprecipitation (ChIP) & genomic methods in molecular genetics. Functional genomic methods and analyses of transcription factors binding sites and targets Mapping the three-dimensional architecture of genomes with 3C-related technologies. Overview of the structural organization of the genome. Methods for genome-wide profiling. An updated perspective on what these new technologies have uncovered, and future directions for improvements. Advanced genetic technologies in the mouse. Brief historical overview of technologies. Conditional gene expression/inactivation. Mutagenesis screens in the mouse. Recent advance in genomics. Genomics of alternative splicing. Overview of alternative splicing. Implications in human diseases. Genome-wide analyses. MicroRNAs: methods in target prediction & functional validation. Overview of miRNA target recognition. MicroRNA, and prediction target databases. Functional validation strategies. Genetic networking of miRNAs. SiRNA & shRNA libraries for functional genomic screens. Design and implementation of experiments utilizing genome-wide RNAi approaches to examine gene function.

Mol: 403: Advance Proteomics
Proteomics and phosphoproteomics. Advanced proteomics and protein chemistry. Complex analyses using MS/MS, LCMS/MS, MuDPIT, PTM analysis using mass spectrometry. Proofing and validation of PTMs. Metabolomics. Profiling of metabolites and small bio-molecules in development and cancer. Genomics workshop: prospects and overview of the most recent advances. Overview of highlights from the current literature; discussion of tendencies, relevant publications, major current