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Syllabus for Fundamental Courses for RGCB PhD Program

BBB 301: Basics of Biochemistry and Biophysics (3 credits)
Module I: The Mole concept-Avogadro number, Solutions-solubility-Concentrations- MolarityNormality-Molality; Acids and bases- Strong and weak acids- Strong and weak bases-pHAcid-Base Titrations, The acid strength-Calculation of pH in different types of solutions: SaltsAcid properties of salts-ion effects on pH, Buffers-pH in a buffer- buffer capacity- titrationsIndicators: Colligative properties: Water structure and the hydrophobic force; Amphipathic
molecules: micelles and the membrane bilayer
Module II: Amino acids, peptides and proteins; Introduction to protein structure: primary and
secondary structures;Protein domains and super secondary structure; The inside and outside
of globular proteins
Module IV: Carbohydrates, Monosaccharides & Disaccharides; Glycoconjugates, Proteoglycans, Glycoproteins, Glycolipids; Lipids: Classification, Fatty acids, Triacylglycerols,
Glycerophospholipids, Sphingolipids, Cholesterol;Properties of lipid aggregates, Micelles and
Bilayers, Liposomes; Electrical properties of membranes; Mechanobiology
Module V: DNA, History of DNA discovery (Griffith/Hershey/Miescher/Levene/Chargaff/
Franklin/ Watson & Crick), Constituents (Purine/Pyrimidines/sugar/phosphate), Types of
structure (role of the grooves), Topology, Denaturation and Re-naturation, Base analogue
uses in diseases; Topoisomerases
Module VI: Glycolysis and Catabolism of Hexoses, Steps involved in glycolysis, Energy
conservation during glycolysis, Energy yield in the conversion of glucose into pyruvate, Entry
of fructose and galactose into glycolysis, Enzymes involved in glycolysis;Citric Acid Cycle,
Evolutionary history of TCA cycle, Steps in citric acid (TCA) cycle, Stoichiometry of citric acid
cycle, Enzymes involved in TCA cycle, Control of TCA cycle, Glyoxalate cycle, Glycolysis
and TCA cycle in human pathology (selected case studies);Pentose Phosphate Pathway,
gluconeogenesis- FA oxidation;Oxidative Phosphorylation; Glycogen Metabolism and its
regulation, Glycogen phosphorylase and Glycogen synthase functions
Module VII: Lipid metabolism- arachidonic acid pathway; Lipid metabolism-Cholesterol
metabolism and regulation; FA synthesis, FA synthase complex; Protein and amino acid
metabolism
Module VIII: Protein-ligand interactions (Protein-Protein; Protein- small molecule), Binding
detection, Measurement of binding parameters: Thermodynamic and kinetic, Binding in
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physiological context- Physiological factors influencing binding; Introduction to Reaction

Kinetics;Enzymology - Steady state Kinetics;Enzyme Inhibition;Enzyme regulatory
mechanisms - Allosteric enzymes, Cooperative enzymes; Post translational
modifications;Enzyme Mechanisms - Catalytic mechanisms;Practical considerations in
Enzymological studies.
MIV 302: Microbiology, Immunology and Virology (3 credits)
Module I: Microbial Morphology & Anatomy, Classification, Microbial growth: Measurement
of growth, growth physiology, cell division, growth kinetics, antibiotics, drug resistance
Module II: Microbial Metabolism: Glycolysis, PPP, ED pathway, Citric acid cycle: Branched
TCA and Reverse TCA, glyoxylate cycle. Metabolism of amino acids: Lipid composition of
microorganisms,
Module III: Microbial Genetics: Genetic analysis of bacteria:Importance and uses of mutation
analysis; DNA transfer, Prokaryotic gene regulation Lac and Trp operons; Basis of fertility
in bacteria. Molecular mechanism of gene transfer by conjugation; Hfrstrains.Chromosomal
DNA transfer by plasmids; Medical Bacteriology, Pathogenicity and virulence, Diseases
caused by parasitic protozoans, their biology and control.
Module IV: Microbes of air/water/soil; Medical, Industrial and Environmental Microbiology;
Sources of industrially important microbes; Metagenomics.
Module V:Immunology- fundamental concepts and anatomy of the immune system :
Components of innate and acquired immunity; Phagocytosis; Major Histocompatibility
Complex - MHC genes, MHC and immune responsiveness and disease susceptibility, HLA
typing
Module VI :Immune responses generated by B and T lymphocytes: Immunoglobulins-basic
structure, classes & subclasses of immunoglobulins, antigenic determinants; Multigene
organization of immunoglobulin genes; Immunoglobulin superfamily; Cell-mediated immune
responses, Antigen-antibody interactions: Precipitation, agglutination and complement
mediated immune reactions; Tumor immunology
Module VII: Vaccinology: Active and passive immunization; Live, killed, attenuated, sub unit
vaccines; Vaccine technology; tolerance, autoimmunity, hypersensitivity
Module VIII: History and principles of virology, virus taxonomy, Virus evolution and
classification, properties of viruses, virus structure; Principal events involved in replication:

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Adsorption, penetration, uncoating nucleic acid and protein synthesis, intracellular trafficking,
assembly, maturation and release, viral-host interaction,
Module IX: Virus structures, animal and plant viruses: Virus structure and morphology,
viruses of veterinary importance and plant viruses: DNA and RNA viruses: Replication:
General strategies, replication of plus stranded RNA virus, negative strand: RNA viruses;
Replication of double stranded RNA virus, and retroviruses: Positive strand virus,.
Retroviruses; Replication of double stranded DNA viruses,;Viral diseases, pathogenesis,
Epidemiology, control, immunology, transformation, evolution, diagnostics, antiviral agents,
emerging diseases.
CDB 303: Cell and Developmental Biology (3 credits)
Module I: Biomembranes: Historical view; Molecular Architecture Models; Importance of
fluidity. Cholesterol, Domains and Microdomains, RAFTS; Intracellular protein traffic:
transport & sorting; Protein Sorting, Trafficking and Targeting the biology of protein
movement into membranes and organelles; Exosomes in biology; Post-translational
mechanism
Module II: Nucleus, chromosome and cell Cycle; Structure, nuclear pores, nucleosome
organization, nucleolus; Cell division (student to be pre-prepared), mechanism of
chromosome segregation; Cell Cycle: Cyclins and cyclin dependent kinases, Regulation of
cyclin - CDK activity retinoblastoma and E2F proteins.
Module III: Cytoskeleton: Microfilaments; Microtubules-structure & dynamics & mitosis; Cell
movements intracellular transport, kinesin and dyenin; Cilia & Flagella
Module IV: Cell Cell signaling & Signal transduction: Cell Signaling in animals: Signaling
from plasma membrane to nucleus including signaling via animal hormones;emphasis on
positioning of cellular machinery, components of various signalling pathways;Downstream
effects of signaling on cell adhesion, cell differentiation, invasion and programmed cell
death;Epithelial-Mesenchymal Transition in Biology: introduce students to issues of polarized
epithelial cell function in the context of normal physiology as well as alterations associated
with disease.
Module V: Plant hormone signaling: Introduction to Plant
Growth Regulators
(Hormones), Plant Hormone Discovery; A Systems Approach to Hormone Interactions; Major
Function of Auxins: Stem Elongation; Cytokinin Functions & Interactions, Brassinosteroids:
Similar to Auxins; Gibberellins: Stem Elongation, Fruit Growth, & Seed, Abscisic Acid,
Strigolactones; Plant Response: Events when Plants Produce Ethylene, Response to

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Mechanical Stress; Apoptosis and Senescence; Mechanism of Leaf Abscission; Mechanism

of Fruit Ripening; Chloroplast and Mitochondrial Biogenesis,Photosynthesis, Peroxisomes.
Module VI: Stem Cell Biology: Germ-line stem cells; Germ Line Stem Cells, Spermatogonial
& Oogonial: Introduction to Stem Cell Biology, Self Renewal & Pluripotency, Asymmetric Cell
Division & Cellular Aging, "Niche" Microenvironment for Stem Cells; Stem Cells in Early
Development; Principles of Embryonic stem cell culture; Pre-implantation embryo
development and culture, embryo hatching. Embryonic Stem Cells; Techniques in the study
of stem cell biology; generation and differentiation of embryonic stem cells as well as induced
pluripotent stem cells, isolation of mouse embryonic fibroblasts, focus formation assay,
teratoma formation assay, the time-lapse microscopy of early embryos and organ cultures.
Module VII: Adult Stem Cells; Hematopoietic Stem Cell, Vascular Endothelial Precursors,
Neural Stem Cell, Pancreatic Stem Cell, Mesenchymal Stem Cell, Liver Regeneration &
Stem Cell; Important functional differences between embryonic, hematopoietic, and adult
stem cells, as well as differences in their biomedical potentials: Tissues engineering,
Chemistry of scaffolds in stem cell research, Scaffolds, synthetic polymers or natural
decellularized tissue, Polymers processing into scaffolds; Salt-leached scaffolds, Freeform
fabricated scaffolds, Nanofiber scaffolds.
MBG 304: Molecular Biology and Genetics (3 credits)
The course content will have problem sets, universal guidelines for nomenclature and
experimental methods. Provision is also made for problem solving, students thoughts or
students presentation in this course.
Module I: Basic Principles of Genetics; Law of segregation; Law of independent assortment;
Chromosomal basis of segregation and independent assortment; Linkage; Crossing over;
multiple allelism; Pleiotropy; Cytoplasmic inheritance; Gene mapping in bacteria:
Transformation, conjugation, transduction and sexduction; Transposable elements
Module II: Chromosome organization and application;Chromosomal disorders; Inborn errors
of metabolism: Phenylketonuria; Neurogenetic disorders: Alzheimers disease; Muscle
genetic disorders: Duchenne Muscular Dystrophy; Genetic disorders of Haematopoitic
systems: Sickle cell anemia; Multifactorial disorders: Mitochondrial syndromes; Management
of genetic disorders
Module III: Genome Organization and application; Organization of bacterial genome;
Structure of eukaryotic chromosomes; Role of nuclear matrix in chromosome organization
and function; Heterochromatin and Euchromatin; DNA reassociation kinetics (Cot curve

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analysis); Repetitive and unique sequences; Satellite DNA; DNA melting and buoyant
density; Nucleosome; DNA methylation & Imprinting; Mendelian disorders; Mitochondrial
disorders
Module IV: Genome Maintenance (DNA Replication and Recombination);The Replication of
DNA;Replication initiation, elongation and termination in prokaryotes and eukaryotes;
Enzymes and accessory proteins; Fidelity; Replication of single stranded circular DNA;The
Mutability and Repair of DNA; Photoreactivation; Nucleotide excision repair; Mismatch repair;
SOS repair; Recombination: Homologous and non-homologous;;
Homologous
Recombination at the Molecular Level; Site Specific Recombination and Transposition of
DNA; Defects in Genome Maintenance
Module V: Gene Expression; Mechanisms of Transcription; Prokaryotic Transcription;
Transcription unit; Promoters- Constitutive and Inducible; Operators; Regulatory elements;
Initiation; Attenuation; Termination-Rho-dependent and independent; Anti-termination;
Transcriptional regulation-Positive and negative; Transcript processing; Processing of tRNA
and rRNA; Eukaryotic transcription and regulation; RNA polymerase structure and assembly;
RNA polymeraseI, II, III; Eukaryotic promoters and enhancers; General Transcription factors;
Transcriptional and post-transcriptional gene silencingRNA Splicing; Translation; Translation
machinery; Ribosomes; Composition and assembly; The Genetic Code
Module VI: Eukaryotic GeneRegulation;Transcriptional Regulation in Prokaryotes;
Transcriptional Regulation in Eukaryotes; Regulatory RNAs
Module VII: Epigentics; Control of transcription by DNA methylation, methyl DNA binding
proteins and recruitment of HDACs; Histone methyl transferases; Genomic Imprinting in
Mammals Mechanisms; RNAi Biochemical mechanisms
Module VIII: Molecular Evolution: Ecological Perspective; Population perspective
BBT 305: Basic Biotechniques (3 credits)
Module I: Basic principles of protein detection and quantification: Measurement of total
protein by colorimetry: Biuret, Lowry, bis-cinchinonic acid (BCA) and Bradford assays.
Commercial kits merits and demerits, Amino acid analysis, Spectroscopic methods,
Fluorescence emission methods; Basic principles and Methods of separation and purification
of proteins; Recovery of protein monitoring by SDS PAGE and Western blot. Fundamentals
of chromatography, diverse chromatographic techniques such as Gas chromatography,
HPLC, FPLC, and UPLC etc.

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Module II: Approaches for Protein-protein and protein-ligand interactions: Absorption,

fluorescence and CD spectroscopy: Different spectroscopic techniques, Principles of
absorption spectroscopy, Lambert-Beer law, Application, Instrumentation.
Protein crystallography and Protein infrared spectroscopy: What is x ray crystallography? X
rays, Advantages of knowing crystal structure, process involved in crystal structure
determination, Protein preparation , crystallization, Testing crystals, X- ray data collection,
Structure solution , Molecular Model building
Module III: Proteomics 1: Introduction to Mass Spectrometry, History, Ionizations of
molecules. Mass Analysis, Various kinds of mass spectrometry. Proteome history.
Proteomics 2: Tools of Proteomics: Analytical Protein and Peptide Separations, Protein
Digestion Techniques, Mass Spectrometers for Protein and Peptide Analysis, Protein
Identification by Peptide Mass Fingerprinting, Peptide Sequence Analysis by Tandem Mass
Spectrometry, Protein Identification with Tandem Mass Spectrometry Data.
Proteomics 3: Applications of Proteomics: Mining Proteomes, Protein Expression
Profiling, Identifying ProteinProtein Interactions and Protein Complexes, Mapping Protein
posttranslational Modifications by mass spectrometry: Practical demonstration of mass
spectrometry, ionizations, & peptide analysis by MS: Surface Plasmon Resonance (SPR):
Basics of Plasmon Resonance spectroscopy, Technical aspects and applications.
Module IV: Computational methods in protein analysis: Protein structure confirmation,
superimposition of structures, molecular graphics, Homology modeling: Analyze DNA, RNA,
& Protein sequence using computer software: Basic concepts of sequence similarity, identity
and homology, Sequence patterns and profiles: Database Searching- FASTA, BLAST,
statistical and Biological significance.
Module V: Modern Research Techniques in Genomics: Recombinant DNA manipulation;
protein expression and purification; Restriction digestion and electrophoresis; PCR,
Expression Cloning; Expression vectors (Eukaryotic and prokaryotic, Plasmid isolation and
quality check, GLP; Gene sequencing: Diverse gene sequencing approaches; NGS ;
Microarray methods and data analysis; Methods in Epigenetics ; RNAi approaches in animals
and plants; Bioinformatics approaches to analyze DNA, RNA, and Protein sequence using
BLAST, EMBOSS, Genotyper; Microarray methods and data analysis: Methods in
epigenetics: Chromatin immunoprecipitation, CHIP sequencing, Gene silencing approaches.
Module VI: Radiolabelling based approaches and immunological techniques: Radiation and
radioactivity, Half life and Decay constants; Radiation dose response relations, Radiation
sources, Fundamentals of radiation safety; Radioactive material handling; Radiation
detection and measurements; Radio labeling based approaches in research.

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Module VII: Research methods in cellomics: Cell culture techniques (Basics); Primary cells
and cell lines, Culture methods, Enzymatic , mechanical, Explant approaches, Cell culture
requirements, Media , FBS etc, Contamination and Cell culture lab requirements, GLP. Gene
delivery approaches: Transfection techniques, Electroporation, Lipid based transfection
methods, Dextran, CaCl2 methods. Microinjection, Viral gene delivery methods, Retroviral,
Adenoviral and Lentiviral transfection protocols.
Module VIII: Cell imaging: Basics of Microscopy: Bio-imaging; Introduction to important
concepts. Digital vs. analog images. Light microscopy; History, Latest developments and
trends. Basics of optics, resolution and Super resolution : Theories and techniques of
Fluorescent and confocal microscopy: Fluorescence microscopes and components, Live cell
fluorescence imaging, Multidimensional imaging: TEM, SEM, Scanning probe microscopy
(AFM) and Raman Confocal imaging: Principles, Components of Equipments, Image
formation principles, Sample preparation and image analysis, Advanced application in
imaging; Application and principles of FRET, FRAP, FLIM, Photo activation etc.
Cell analysis and cell separation techniques (FACS): Flow cytometry, Principles of diverse
flow cytometers and sorting approaches, Detection methods and compensation in flow
cytometry. Immunophenotyping; Sterile sorting of live cells; Commercial sorters and variants;.
Sample preparation for FACS
Module IX: Medical imaging approaches: Whole animal imaging approaches: Optical
imaging, CT, MRI, SPECT, MRI analysis of animal models of human diseases: Animal
models of angiogenesis and cancer: In vivo models, Developmental studies using animal
models, Angiogenesis studies in tissues, Principles and practices in angiogenesis research.

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BRM 306: Research methodology, Bio-Statistics and Bioethics (3 credits)

Module I: Fundamentals of Research
Definition and meaning of research, importance of research, characteristics of research,
steps in research, types of research (Descriptive vs. Analytical; Applied vs. Fundamental;
Quantitative vs. Qualitative; Conceptual vs. Empirical).
Module II: Research Problems
Meaning of research problems, sources of research problems, characteristics of good
research problems, criteria for selection and formulation of research problems or Research
Design. Meaning, Needs and features of a good research design. Critical literature review,
Identifying gap areas from literature review and development of working hypothesis.
Module III: Research design and methods
Need for a research design, Basic Principles, Features of good design, Important concepts
relating to research design, Observation and Facts, Laws and Theories, Prediction and
explanation, Induction, Deduction, Development of Models; Developing a research plan,
Exploration, Description, Diagnosis, and Experimentation; Determining experimental and
sample designs
Module IV: Data Collection and analysis (Bio-statistics):
Execution of the research, sampling, decision on number of groups, major parameters and
strategies for observation and collection of data, Methods of data collection, Sampling
Methods, Data Processing and Analysis strategies - Data Analysis with Statistical Packages,
Generalization and Interpretation
Module V: Writing reports
Structure and components of research report, types of reports, layout of research report, how
to write a research report, referencing in academic writing. Introduction to bibliography
software such as end note, reference manager, mendeley, refworks etc.
Module VI: Research ethics
Research Integrity and Research Misconduct; The Ethics of Human Subjects Research;
Responsible Conduct of Research with Animals; Intellectual Property and Data Ownership,
Responsible Authorship; Conflict of Interest, Mentoring; Data management;
Workshop: The Lab: An interactive video from the Department of Health and Human Service
Office of Research Integrity ( http://ori.hhs.gov/TheLab )

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