nccs.res.in BET 2014 Syllabus Biotechnology Eligibility Test : National Centre for Cell Science

Name of the Organisation : Department of Biotechnology DBT National Centre for Cell Science, Pune
Type of Announcement : Syllabus
Designation : Biotechnology Eligibility Test BET 2014
Reference Number : —

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Syllabus for DBT-JRF BET examination
General Comments: Question paper will have two parts, Part-A (Aptitude & General Biotechnology) and Part-B (General plus specialized branches in Biotechnology). Part-A will have all compulsory 75 MCQ questions, out of which 25 will be of analytical aptitude, comprehension and quantitative reasoning type and 50 will be from General Biotechnology. There will be 200 questions in Part B, out of which only 50 questions need to be answered. Questions in Part B will also include general biotechnology in addition to the specialized areas listed below.

PART-A: Aptitude & General Biotechnology
Aptitude:
Questions may include Comprehension based, where a written paragraph is given for the students to read and then questions based on that paragraph is asked. They may be designed to test non-verbal reasoning capacity (e.g., by finding the odd one out in a series of abstract pictures), they may also be of quantitative type; designed to test the students ability to comprehend large numbers and do simple calculations.

General Biotechnology :
1) Biomolecular structure and function :
a) Covalent structure of Amino acids, proteins, nucleic acids, carbohydrates and lipids.
b) Forces that stabilize biomolecules: electrostatic and van der Waal’s interaction, hydrogen bonding. Interactions with solvents, Hydrophobic effect.
c) Protein Structure: Structural characteristics of ?-helix, ?-sheet and ?-turn. Ramachandran plot. Protein domains and domain architecture. Quaternary structure of proteins.
d) Conformation of Nucleic acids: Structural characteristics of A, B and Z-DNA. 3D structure of t-RNA, ribozymes and riboswitches
e) Basic Thermodynamics: Laws of thermodynamics. Concepts of ?G, ?H and ?S.
f) Physical properties of water and their role in biology. Concepts of pH, ionic strength and buffers.
g) Chemical kinetics: Concepts of order and molecularity of a chemical reaction. Derivation of first and second order rate equation, measurement of rate constants. Concept of activation energy.
h) Enzymology: Introduction to enzymes. Types of enzymatic reaction mechanisms, Michaelis-Menten kinetics. Competitive, Non-competitive and Un-competitive inhibition. Bi-substrate reaction kinetics. Allostery.

2) Methods in Biotechnology :
a) Concepts of precision and accuracy in experimental measurements. Concept of signal to noise ratio.
b) Biostatistics: Measures of Central Tendency. Fundamental ideas of probability and probability distributions: Binomial, Poisson and Gaussian distributions. Concept of the Central Limit Theorem. Hypothesis testing: Use of Student’s t and 2 tests. Correlation and regression. Basic concepts of design of Experiments.
c) Biochemical Methods: Chromatography: Ion exchange, Gel Filtration and Affinity chromatography. Electrophoresis: Native and SDS-PAGE. Isoelectric focusing. 2D-PAGE and its applications.
d) UV/Vis spectrophotometry. Beer-Lambert’s law and its use in determination of protein/ nucleic acid concentration.
e) Fluorescence Spectroscopy: Basic concepts of excitation and emission. Quenching, Stern-Volmer Plots. Theory and applications of FRET and fluorescence lifetime measurements.
f) Fundamentals of CD, IR and Raman spectroscopy and their use in the study of biomolecular conformation.
g) Centrifugation: Basic concepts of centrifugation. Calculation of g value from RPM. Density gradient centrifugation. Sedimentation velocity and Sedimentation equilibrium. Separation of sub-cellular components and macromolecules using high speed and ultracentrifugation.
h) Microscopy: Bright field, phase contrast, fluorescence, confocal, and electron microscopy.
i) Fundamentals of X-ray, NMR and cryo-electron microscopy for determination of biomolecular structure.

3) Organization of structure and functions of prokaryotic and eukaryotic cells :
a) Cell wall and Cell Membrane: physical structure of model membranes in prokaryotes and eukaryotes, lipid bilayer, membrane proteins, other constituents; diffusion, osmosis, active transport, regulation of intracellular transport and electrical properties.
b) Structural organization and functions of cell organelles: nucleus, mitochondria, Golgi bodies, endoplasmic reticulum, lysosomes, Chloroplast, peroxisomes, vacuoles. Cytoskeletons structure and motility function.
c) Organization of genomes: genes and chromosomes, Operon, unique and repetitive DNA, interrupted genes, gene families, structure of chromatin and chromosomes, heterochromatin, euchromatin, transposons.
d) Cell division and cell cycle: Mitosis and meiosis, their regulation, Cell cycle and its regulation, Apoptosis, Necrosis and Autophagy.
e) Cell transformation and cancer, oncogenes and proto-oncogenes, tumor suppressor genes, metastasis. Therapeutic interventions of uncontrolled cell growth.

4) Cellular processes :
a) DNA replication, repair and recombination (Unit of replication, enzymes involved, replication origin and replication fork, fidelity of replication, extrachromosomal replicons, DNA damage and repair mechanisms, homologous and site-specific recombination).

b) Transcription of various types of RNAs and their processing and modifications. Transcription factors and machinery including RNA polymerases, formation of initiation complex, elongation and termination of transcription. Regulation of transcription: activators (enhancers) and repressors, Locus control regions. Structure and function of different types of RNA and mRNPs. RNA transport, localization and function.

c) Protein synthesis, processing and transport of proteins: Ribosome, mRNA structure, genetic code, aminoacylation of tRNA, aminoacyl tRNA synthetase. Mechanism of translation: Initiation, elongation and termination factors and translational proof-reading. Regulation of Translation- global vs mRNA-specific. Translation inhibitors, Posttranslational modifications of proteins. Protein trafficking and transport.

d) Control of gene expression at transcription and translation level: Regulation of gene expression in viruses, prokaryotes and eukaryotes, role of chromatin, chromatin remodelling and gene silencing, Epigenetic regulation.

e) Host-pathogen interaction: Recognition and entry processes of different pathogens like bacteria, viruses and protozoans into animal and plant host cells, alteration of host cell behavior by pathogens, virus-induced cell transformation, pathogen-induced diseases in animals and plants, cell-cell fusion in both normal and abnormal cells.

f) Cell signaling: Hormones and their receptors, cell surface receptor, signaling through G-protein coupled receptors, signal transduction pathways, second messengers, regulation of signaling pathways, bacterial and plant two-component systems, light signaling in plants, bacterial chemotaxis and quorum sensing.

g) Cellular communication: General principles of cell communication, cell adhesion and roles of different adhesion molecules, tight junctions, communicating junctions, extracellular matrix, integrins, neurotransmission and its regulation. Regulation of hematopoiesis, differentiation and development.

h) Innate and adaptive immune system: Cells and molecules involved in innate and adaptive immunity, antigens, antigenicity and immunogenicity. B and T cell epitopes, structure and function of antibody molecules. generation of antibody diversity, monoclonal antibodies, antibody engineering, antigen-antibody interactions, MHC molecules, antigen processing and presentation, activation and differentiation of B and T cells, B and T cell receptors, humoral and cell-mediated immune responses, primary and secondary immune modulation, the complement system, Toll-like receptors, cellmediatedeffector functions, inflammation, hypersensitivity and autoimmunity, immune response during bacterial (tuberculosis), parasitic (malaria) and viral (HIV) infections, congenital and acquired immunodeficiencies, vaccines.

5) Recombinant DNA Technology :
a) Enzymes used in Recombinant DNA technology.
b) Isolation and purification of DNA (genomic and plasmid) and RNA. Various methods of separation, characterization of nucleic acids including Southern and Northern hybridizations.
b) Molecular cloning of DNA or RNA fragments in bacterial and eukaryotic systems. Expression of recombinant proteins using bacterial, animal and plant vectors and their purification. Western blotting.
c) Generation of genomic and cDNA libraries. Plasmid, phage, cosmid, BAC and YAC vectors. In vitro mutagenesis and deletion techniques, gene knock out in bacterial and eukaryotic organisms.
d) Isolation and amplification of specific nucleic acid sequences, PCR, RT PCR and qRT PCR
e) DNA sequencing methods, strategies for genome sequencing.
f) Methods for analysis of gene expression at RNA and protein level, large scale expression, such as micro array based techniques.
g) Analysis of DNA polymorphism: RFLP, RAPD and AFLP techniques.
h) Biosafety regulations and IPR.

6. Genetics, Phylogeny & Evolution :
a) Chromosomal inheritance: Principles of Mendelian inheritance, codominance, incomplete dominance, gene interactions, pleiotropy, genomic imprinting, linkage and cross-over, sex-linked inheritance, Population Genetics and Hardy-Weinberg equilibrium.
b) Extrachromosomal inheritance: Maternal inheritance (mitochondria and chloroplast)
c) Gene concept: Allele, multiple alleles, pseudoalleles.
d) Genetic analysis: Linkage maps, mapping with molecular markers, tetrad analysis, gene transfer in bacteria: transformation, conjugation, transduction, sex-duction, fine structure analysis of gene.
e) Mutation: Spontaneous, induced, lethal, conditional, reversion, mutagenic suppression, germinal and somatic mutation, insertion, deletion, duplication, translocation, transposition, ploidy.
f) DNA finger printing and its applications, DNA bar coding, marker assisted selection and QTL mapping.
g) Species concept in archaea, bacteria and eukarya.
h) Phylogenetic analysis and evolutionary relationship among taxa, MLST.

7. Genomics and Proteomics :
a) Introduction to Genomics: Structure and organization of prokaryotic and eukaryotic genomes – nuclear, mitochondrial and chloroplast genomes; Computational analysis of sequences- finding genes and regulatory regions; Gene annotation; Similarity searches; Pairwise and multiple alignments; Alignment statistics; Prediction of gene function using homology, context, structures, networks; Genetic variationpolymorphism, deleterious mutation; Phylogenetics; Tools for genome analysis– PCR, RFLP, DNA fingerprinting, RAPD, Automated DNA sequencing; Linkage and pedigree analysis; Construction of genetic maps; Physical maps, FISH to identify chromosome landmarks.

b) Genome sequencing: Human genome project-landmarks on chromosomes generated by various mapping methods; BAC libraries and shotgun libraries preparation; Physical map-cytogenetic map, contig map, restriction map, DNA sequence; DNA sequencing and sequence assembly; Model organisms and other genome projects; Comparative genomics of relevant organisms such as pathogens and non-pathogens; Evolution of a pathogen. Taxonomic classification of organisms using molecular markers -16S rRNA typing/sequencing.

c) DNA Microarray technology: Basic principles and design: cDNA and oligonucleotide arrays; Applications: Global gene expression analysis, Comparative transcriptomics, Differential gene expression; Genotyping/SNP detection; Detection technology; Computational analysis of microarray data.

d) Proteomics: Outline of a typical proteomics experiment; Identification and analysis of proteins by 2D analysis; Spot visualization and picking; Tryptic digestion of protein and peptide fingerprinting; Mass spectrometry; ion source (MALDI, spray sources); analyzer (ToF, quadrupole, quadrupole ion trap) and detector; clinical proteomics and disease biomarkers; Prions; proteins in disease; Protein-protein interactions: Solid phase ELISA, pull-down assays (using GST-tagged protein), far western analysis, by surface plasmon resonance technique, Yeast two hybrid system, Phage display; Protein interaction maps; Protein arrays-definition, applications- diagnostics, expression profiling.

8. IPR, Biosafety & Bioethics :
a) Types of IP: Patents, Trademarks, Copyright & Related Rights, Industrial Design, Traditional Knowledge, Geographical Indications, Protection of New GMOs; International framework for the protection of IP. IP as a factor in R&D; IPs of relevance to Biotechnology and few Case Studies; Introduction to History of GATT, WTO, WIPO and TRIPS

b) Invention in context of “prior art”; Patent databases; Searching International Databases; Country-wise patent searches (USPTO, EPO, India etc.); Analysis and report formation

c) Types of patents; Indian Patent Act 1970; Recent Amendments; Filing of a patent application; Precautions before patenting-disclosure/non-disclosure; WIPO Treaties; Budapest Treaty; PCT and Implications; Role of a Country Patent Office; Procedure for filing a PCT application

d) Patent application- forms and guidelines, fee structure, time frames; Types of patent applications: provisional and complete specifications; PCT and convention patent applications; International patenting-requirement, procedures and costs; Financial assistance for patenting-introduction to existing schemes; Publication of patents-gazette of India, status in Europe and US Patenting by research students, lecturers and scientists-University/organizational rules in India and abroad, credit sharing by workers, financial incentives, Patent infringement- meaning, scope, litigation, case studies and examples.

e) Biosafety: Introduction; Historical Background; Introduction to Biological Safety Cabinets; Primary Containment for Biohazards; Biosafety Levels; Biosafety Levels of Specific Microorganisms; Recommended Biosafety Levels for Infectious Agents and Infected Animals; Biosafety guidelines – Government of India; Definition of GMOs & LMOs; Roles of Institutional Biosafety Committee, RCGM, GEAC etc. for GMO applications in food and agriculture; Environmental release of GMOs; Risk Analysis; Risk Assessment; Risk management and communication; Overview of National Regulations and relevant International Agreements including Cartagena Protocol.

f) Bioethics: Concepts; Philosophical considerations; Epistemology of Science; Ethical Terms; Principles & Theories; Relevance to Biotechnology; Ethics and the Law Issues: Genetic Engineering, Stem Cells, Cloning, Medical techniques, Trans-humanism, Bioweapons; Research concerns – Animal Rights, Ethics of Human Cloning, Reproduction and Stem Cell Research; Emerging issues: Biotechnology’s Impact on Society; DNA on the Witness Stand – Use of genetic evidence in civil and criminal court cases; Challenges to Public Policy – To Regulate or Not to Regulate; Improving public understanding of biotechnology products to correct misconceptions.