MSc Programmes – 2018 intake

IBMBB will commence academic activities for its 2018 intake of students for MSc Courses in February 2018. MSc programmes at IBMBB include extensive laboratory training, and its graduates are in high demand with some even receiving job offers before completion of the degree programme. Some of the successful MSc students are able to obtain PhD studentships at the IBMBB. All MSc courses are full time and fee levying.

In keeping with the established objective and the vision in mind our aim is to contribute to human resource development at MSc/MPhil/PhD level in disciplines related to Molecular Life Sciences.In order to achieve these goals the IBMBB conducts two MSc courses.All courses are fee levying programmes.

This is a three semester programme. Each semester will run for 20 weeks. The course is designed to provide an advanced training in branches of molecular life sciences with one semester research project.

Semester 1

  • Cells and genomes
    Universal features of cells, diversity of genomes
  • Cell as a unit of life and functional morphology of the cell
    • Cell membranes, mitochondria, lysosomes and peroxisomes, endoplasmic reticulum, Golgi apparatus, nucleus and associate structures, cytoskeleton and molecular motors
  • Biomolecules and transport across biological membranes  
    • Molecular architecture of living matter: Nucleic acids, proteins, lipids and carbohydrates.
    • Structure and composition of biological membranes: Fluid Mosaic model; transport across biological membranes, kinetics and mechanisms of transport, Na+/K+/ATPase pump, Ca++/ATPase, H+/ATPase, gap junctions and group translocation

     

  • Cell to cell communications and Cell signaling

    • Neural communication

      • Generation and transmission of nerve impulses, Neurotransmitters, Synapses and neuromuscular junction
    • Communication via chemical messengers
      • Peptide and steroid hormones, biogenic amines, eicosanoids and growth factors
      • Endocrine, paracrine and autocrine effects
      • Signaling through G-protein coupled cell-surface receptors
      • Signaling through enzyme-linked cell surface receptors
      • Signaling through cytoplasmic and nuclear receptors
      • Signaling in plants
  • Energy homeostasis in the cell
      • Enzymes : Biological catalysis, kinetics, regulatory enzymes;
      • Bioenergetics and metabolism : Bioenergetics and thermodynamics, Phosphoryl group transfer and ATP, the concept of free energy and biological oxidation-reduction reactions (the redox potential);
      • Intermediary metabolism and its regulation : Carbohydrate metabolism, lipid metabolism and protein metabolism ;
      • Oxidative Phosphorylation: Hormonal regulation and integration of mammalian metabolism

 

  • Cell division, cell cycle and programmed cell death

    • An overview of the cell cycle, Components of the cell cycle control system, M phase
    • Mitosis and meiosis, Cytokinesis, Intracellular control of cell cycle events
    • Programmed cell death
    • Extracellular control of cell division, cell growth and apoptosis

     

  • Cell in its social context
      • Cell junctions, Cell adhesion molecules and cell-cell adhesion
      • Extracellular matrix
      • Integrins

 

  • Isolating and visualizing cells

    • Isolation of cells from tissues
    • Light and phase contrast microscopy in visualising cells
    • Locating specific molecules within a cell using antibodies and fluorescence
    • (Practical demonstration)

     

  • Two of the following Optional Modules

    • Developmental and Reproductive biology
    • Plant development
    • Enzymology

Semester 2

  • Biological Information storage, processing and transfer in the cell

    • DNA Replication: Enzymology of DNA replication, accuracy and fidelity of replication, DNA damage and repair mechanisms.
    • Transcription in prokaryotes and eukaryotes; Eukaryotic transcription factors and their role on regulation on gene expression; tissue specific transcription factors; the role of chromosome structure, remodeling, acetylation/decaetylation and methylation of histone proteins on gene transcription and mechanisms of genomic imprinting.

     

  • Molecular basis of abnormal cell growth and metastasis
  • Protein, DNA and RNA based techniques
  • Bioinformatics
  • Implication of genomics and proteomics on health and Agriculture
  • Research methodology and biostatistics
    • Hypothesis driven and inductive research
    • Null hypothesis, Statistical significance
    • Literature review
    • General and specific objectives
    • Validation and quality assurance of methodology
    • Analysis of numerical data – parametric and non parametric tests
    • descriptive statistics, comparison of two groups, comparison of three groups or more
    • regression and correlation
  • Ethical issues in scientific research and ethical, legal and social implications of Genetic, genomic and reproductive technologies
    • Ethical issues in animal and human experimentation, Informed consent and confidentiality
    • Ethical, legal and social implications of genetic research, genetic testing, assisted reproductive technology, reproductive and therapeutic cloning

     

Optional Modules

  • Developmental and Reproductive biology

    • Gametogenesis
    • Fertilization and implantation
    • Sex determination and sexual differentiation
    • Reproductive messengers
    • Reproductive maturation
    • Follicular development, ovulation and the corpus luteum
    • Neuroendocrine regulation and function of the male and female reproductiive systems
    • Pregnancy, parturition and labour, lactation
    • Reproductive senescence
    • Universal mechanisms of animal development
    • Basic anatomical features, Regulatory genes and lessons from mutations
    • Positional value, Assymetric cell division
    • Regulation of development: morphogens, sequential induction, intrinsic and
    • extracellular inhibitors  
  • Enzymology:
    • General mechanisms of enzyme action
    • Competitive and non-competitive inhibition
    • Enzyme kinetics
    • Classification of enzymes
    • Classification of co-factors
    • Detail mechanism of enzyme action of selected enzymes
    • Enzyme assays
    • Purification of enzymes
    • Sequencing of enzymes
    • Allosterases, Industrial enzymes, Isozymes
    • Clinical enzymology
    • Multi enzyme complexes
    • Proteolytic activation, Covalent modification
  • Plant Development:

    • An introduction to flowering plant
    • Flowering plant life cycle
    • Cellular level development
    • Mechanisms controlling cell fate
    • Cell intrinsic information – genetic involvement
    • Cell e xtrinsic information – Different genes involved in the development under different conditions
    • Coordination of development : E ffects of different genes during the transition from embryonic to post-embryonic development
This is a three semester course of 20 weeks duration each. The course is designed to provide a strong foundation in molecular and cellular immunology and a research component. The research component is organized to offer training in research methodologies.

Semester 1

  • Overview of the Immune System :

    • Introduction to the immune system: Innate and adaptive immunity, General properties of the immune responses.
    • Cells, tissues and organs of the immune system: Hematopoiesis, Cells of the immune system;
      Lymphocytes, Antigen presenting cells; dendritic cells & mononuclear phagocytes and granulocytes
    • Anatomy and functions of primary, secondary & tertiary lymphoid tissues: Bone marrow, Thymus, Lymph nodes and lymphatic system, spleen, Cutaneous immune system and mucosal immune system
    • Pathways and mechanisms of lymphocyte recirculation and homing: Recirculation of naïve T lymphocytes and B lymphocytes, Cell adhesion molecules & Migration of lymphocytes to sites of inflammation
    • Evolution of immunity

     

  • Molecular Immunology :

    • Molecules of the immune system:
      • Acute phase proteins: C-reactive protein, serum amyloid A, fribrinogen, mannose-binding protein and complement components
      • Cytokines: Properties of cytokines, cytokine receptors, cytokine antagonists, secretion, cytokine network, cytokine-related diseases & therapeutic uses
      • The complement system: Functions of complement, components, regulation of complement system, biological sequences and deficiencies
    • Antigens: Immunogenicity vs antigenicity, Factors that influence immunogenicity, haptens and pattern recognition receptors
    • Immunoglobulins: Structure & function, Organization and expression of immunoglobulin genes, Monoclonal antibodies, Antibody cloning and engineering
    • The Major Histocompatibility Complex: The general organization and inheritance, MHC molecules and genes, Genomic map of MHC genes and MHC and disease susceptibility
    • T-cell Receptors and accessory membrane molecules, Antigen processing and presentation

     

  • The Immune Response :
    • Innate immunity: Innate immune response, features and components of the innate immune system; barriers; anatomic, physiologic, phagocytic & inflammatory, circulating effector cells, circulating effector proteins and cytokines
    • Inflammatory response, mediators of inflammation, Role of innate immunity in local and systemic defense against microbes and Role of innate immunity in stimulating adaptive immune responses
    • Adaptive immunity
      • T-cell maturation, activation and differentiation; B-cell generation, activation and differentiation, Regulation of B-cell development & immune effector functions and Immunological tolerance of lymphocytes
      • Effector mechanisms of Cell-Mediated immunity
      • Effector mechanisms of Humoral immunity
      • Collaboration between innate & adaptive immunity and Regulation of the immune effector response

     

  • Antigen-Antibody interactions: Principles and Applications and Immunological techniques:
    • Antibody affinity and avidity, Cross reactivity, Immunoassays & immunodiagnosis
    • Antigen-Antibody interactions: Precipitation reactions, Agglutination reactions, Radioimmunoassay, ELISA, Western blotting, Immunoprecipitation, Immunofluorescence
    • Identification of cell populations: Flow cytometry & fluorescence, Immunohistochemistry, Immunoelectronmicroscopy
    • Isolation of cell populations: Fluorescent activated cell sorting (FACS), density-dependent centrifugations, panning
    • Functional assays: Complement activity, phagocytic assay, lymphocyte proliferation, cytotoxicity, Assays for antibody and cytokine production

     

  • Other topics:
    Philosophy of Science, Research Methodology & Biostatistics, Ethical, Legal and Social Implications of Science, Introduction to Information Technology

Semester 2

  • Immunopathology (Immunedisorders)
    • Autoimmune diseases: Spectrum of autoimmune diseases, Organ-specific and systemic autoimmune diseases, genetic factors and pathogenesis, animal models, aetiology, mechanisms of induction of autoimmunity and therapeutic approaches
    • Immunodeficiencies: Primary immunodeficiencies: Lymphoid immunodeficiencies, immuno-deficiency of myeloid lineage, defects in complement proteins, experimental models of immunodeficiencies, AIDS and other acquired or secondary immunodeficiencies
    • Hypersensitivity: IgE-mediated (Type I) hypersensitivity, Antibody-mediated (Type II) hypersensitivity, Immune complex-mediated (Type III) hypersensitivity and Type IV or delayed-type hypersensitivity (DTH)
  • Immunity in Defense and Disease

    • Immune mechanisms induced by microbes:
      • Immunity to extracellular and intracellular bacteria; mechanisms of immunity related to bacterial surface structures, First and second line defenses, antigen specific protective mechanisms
      • Immunity to viruses ; innate immune responses, host defense involving B and T cells, strategies for evading immune defenses, immunopathology
      • Immunity to fungi
    • Immunity to parasites (protozoans & nematodes); Features of parasitic infections, effector mechanisms, role of T cells in development of immunity, escape mechanisms, immunopathological consequences, Immerging infectious diseases
    • Immunity to tumours; tumor antigens, immune response to tumors, evasion of immune response by tumors, immunotherapy for tumors
  • Immunomodulation
    • Immunotherapy
    • Vaccinology: Principles of vaccinology; active and passive immunization, Designing vaccines for active immunization: whole-organism vaccines, different types of antigens used as vaccines, purified macromolecules, recombinant vector vaccines, DNA vaccines and multivalent subunit vaccines
    • Safety and effectiveness of vaccines; vaccines of the future
    • Immunization programmes, Combination vaccines and Regulatory mechanisms in Sri Lanka
    • Global vaccine initiative and Elimination programmes in Sri Lanka

Optional Modules

    • Recombinant DNA Techonology :

      • Structure of DNA, Structure of genes, Extraction of DNA, DNA manipulation enzymes and their applications, Restrctiction Endonucleases and their applications, DNA sequencing and Polymerase Chain Reaction (PCR)
      • DNA cloning: Constrcution of genomic DNA libraries; Construction of cDNA libraries: isolation of mRNA, synthesis of cDNA and cloning of cDNA; screening of libraries; cloning DNA fragments into plasmid vectors; Genetic transformation and gene expression in prokaryotic & eukaryotic cells

       

    • Cancer Immunology :
      • Cancer: origin and terminology & malignant transformation of cells, Tumors of the immune system, Immune response to tumors, Tumor evasion of the immune system, Tumor antigens & markers, Oncogenes and cancer genetics, Cancer immunotherapy, Cancer Epidemiology, Therapies available in Sri Lanka, Current diagnostics & Research needs

 

  • Special topics :
    • Philosophy of Science
    • Research Methodology & Biostatistics
    • Introduction to Information Technology and Bioinformatics
    • Ethical, Legal and Social Implications of Science
Full time (week days, 09.00 – 17.00) , two year programme providing advance training and a strong foundation in Bioinformatics. This programe will be jointly offered by the Institute of Biochemistry, Molecular Biology and Biotechnology (IBMBB), University of Colombo and the University of Colombo School of Computing (UCSC).

Semester 1

    • Foundations in Bioinformatics
    • Introduction to Bioinformatics
        • History and scope of bioinformatics
        • Use of computational resources by molecular biologists/ life scientists
        • Awareness of Tools for Bioinformatics
        • Trends in Bioinformatics (By visiting scholars)

       

    • Introduction to computing
        • Components of a computer system
        • Computing Architectures
        • Operating Systems
        • Internet, web architecture and search engines
        • Tools for report writing
        • Introduction to programming languages and paradigms

       

    • Biocomputing
        • Programming for Bioinformatics
          • Syntax, data types, structuring code, Operators, Control statements, loops, Input-Output statements etc….
          • String matching algorithms
        • Data Base Management Systems
          • Flat files
          • Relational Databases
          • How the database forms an integral component in a computer tool / Business application
          • XML
        • Data mining, Neural Nets and Genetic Algorithms

       

    • Cellular and Molecular Biology and Biochemistry
      • Cell as a unit of life in detail
      • Biomolecules
      • Chromosome structure and function
      • Gene organisation
      • Genomes
      • Biological information storage in the cell and usage for life
        • DNA replication, transcription and translation
        • Genetic code
      • Protein structure and properties in detail – active sites/ domains, protein folding, routing, secretion
      • Enzymes as catalysts

 

  • Sequence Analysis
    • Collecting and storing sequences
    • Sequence Analysis
    • Pairwise alignment of sequences (EMBOSS)
    • Local and Global Alignments (DNA and Protein) metabolism
    • Multiple sequence alignments
    • Optimisation of sequence analysis
    • Database searching for similar sequences
    • Algorithms in primary sequence analysis
    • Genome wide analysis
    • Genomic polymorphisms
    • Gene prediction and annotation

     

Semester 2

  • Cellular and Molecular Biology and Biochemistry
    • Energy metabolism
    • Metabolic pathways and intermediary metabolism
    • Cell-to-cell communication
    • Ligand-receptor interaction
    • Signal transduction
    • Molecular evolution and phylogenetic relationships
    • Basic Molecular Biological Techniques

     

  • Statistics for Bioinformatics
      • Introduction to R
      • Basic Mathematics
      • Descriptive Statistics
      • Estimation theory
      • Linear and non-linear Modelling
      • Multivariate Data Analysis

     

  • Phylogenetic Approaches
      • Definition and history
      • Distance computation
      • Phylogeny construction, analysis of significance of branches and clades (EMBnet)
      • Methods in phylogenetic analysis
      • Evaluation methods in phylogenetic analysis

     

  • Structural and Functional Analysis
    • Definition of structural elements in DNA
    • Definition of structural elements in proteins
    • Motif, domains
    • Analysis of homology, identification of motifs and domains
    • RNA secondary structure prediction
    • Structure and function
    • Protein Structure Determination
    • Protein Structure Prediction
      • Homology modeling
      • de novo modeling
      • Threading
    • Subcellular localisation of proteins
    • Use of structural information

Semester 3

  • Advance topics in Bioinformatics
    • Systems Biology and Pathway Analysis
    • Microarray Data analysis
    • Machine Learning in Biocomputing
    • Integration of data resources
    • Bioinformatics algorithms – design and complexity
    • Simulation software in Biocomputing
    • Next Generation Sequence Analysis
    • Other current topics
  • Advance Statistics for Bioinformatics
      • Linear and non-linear Modelling – II
      • Multivariate analysis – II
      • Statistics for population genetics
      • Advance statistical approaches

     

  • Research Methodology
  • Research seminars on selected topics

Semester 4

  • Research Project