SYLLABUS

65 ORIENTATION COURSE IN BIOSCIENCES

th

(OCES 2021-22)

1. PHYSICAL SCIENCES
Module 1.1: PHYSICS, MATHEMATICS and STATISTICS (Code:BS502)
(2 Tests: 150 Marks; Credits: 6) (34 Lectures; 6 AN-Labs and Tutorials)
Course coordinator: M K Ray ([email protected])

PHYSICS 14+1AN

Atomic structure and electromagnetic radiation: Sucheta Chatterjee

Principles of quantization, production and properties of EM (3)+ 1AN
radiation, wave/ particle duality.

Basic Concepts of light and its principles in GD Gupta

spectroscopy and microscopy: (5)
Beer Lambert's law, concept of fluorescence, Life-time and its
measurement; fluorescence quenching, phosphorescence.
Monochromators and optical filters, and lenses. Applications
of fluorescence in structure/organization of nucleic acids,
proteins and membrane. Application of fluorescent proteins in
biology. Basics of lasers and their biological applications.
Principle and applications of optical traps and optical
tweezers.
Concept of interference, diffraction and polarization; CD and
ORD spectra, image formation on retina. Basic concept of light
and its principles in photosynthesis in plants, aquatic life and
marine biota.

Electricity concept in biology: R Makde

Concept of voltage, current and resistance in reference to (6)
membrane potential, ion channels and electrophoresis,
neuronal communication and cardiac function. Concepts and
application of AC and DC in biology.

Concept of accelerator, cyclotron and synchrotron and

their applications in biology and medicine

Mechanical forces in biology: Linear and circular motion

concepts with reference to different types of centrifugation.

Biosensors: Basic principles, applications and limitations

MATHEMATICS

Logarithms: MK Ray
Definition, laws of logarithms, rule for change of base, common (4)
and natural logarithms, characteristic and mantissa, positive
and negative bases. Accuracy and precision, number of
significant digits.

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Linear and polynomial equations:
Linear and quadratic equations and identities, slope, roots,
relation between roots and coefficients (will be covered in
practicals in the context of IRMA assays where polynomials are
relevant)

Permutations and combinations:

Permutation and combination, nCr and nPr notations, factorials

STATISTICS 16+5AN tutorials

Basic concepts: PM Koya

Probability, a priori and posteriori probabilities. Statistical (6)
significance of probabilities, sample and population,
determination of sample size, variables, classification of
variables, nominal, ordinal, interval and ratio, fixed and random
(examples of different biological research for applications of
these concepts)

Population distributions:
Binomial distributions and Poisson distribution – their
properties, parameters and applications in biological
experiments.
Normal and‘t’ distributions–population and sample parameters,
measures of central tendency, measures of dispersion,
variance, degrees of freedom, confidence limits and intervals.

Sampling, estimates and hypothesis testing: Ashok Hadapad

Sampling methods, random sampling and estimates of (5)
population parameters from samples, sample statistics,
hypothesis testing, drawing inferences and confidence limits, P
values. Special cases where variances are unequal, central
limit theorem. (examples of different biological research
problems for applications of these tests)

Pearsons’ product moment correlation coefficient, partial and

multiple correlation, linear regression analysis; Interpretation
of regression coefficients, application of correlation and
regression, multiple regression, logistic regression, outliers,
multicollinearity and missing data, analysis of covariance.
(examples of different biological research problems for
applications of these tests)
Ashok Badigannavar
Nonparametric statistics: (5)
Spearman's coefficient of rank correlation, Chi square test, and
nonparametric methods for hypothesis testing based on ranks.
(examples of different biological research problems for
applications of these tests)
Statistics in diagnostic tests and cohort studies:
ROC curves; Youden’s index, Likelihood ratios; nomogram
analysis, determination of cut-off values. Cohort and case-
control studies, measures of risk (attributable risk, relative and
odds ratio)
5 AN
Tutorials in biostatics

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Module1.2:CHEMISTRY and RADIOCHEMISTRY (Code: BS501)
(1 Test:75 Marks; Credits: 2) (23 Lectures)
Course coordinator: Dr. Santosh Kumar ([email protected])

Introductory lecture – Santosh Kumar

Radioactivity and interaction of radiation with matter: NK Goel
Types of radiation (ionizing and non-ionizing), laws of (5)
radioactive decay, binding energy, nuclear reactions,
interaction of different types of radiation with matter. Track
structure and delta rays; track structures of different radiation
types. Concepts of Bragg’s peak, spread over Bragg’s peak,
radiation exposure and absorption units, radiation weighting
factors; concept of LET; sources of background radiation. Dose
limits of radiation exposures.

Radiation dosimetry: B Sanyal

Basic concepts, physical and chemical dosimetry, dose range (5)
and limitations of dosimetry techniques; scintillation
counting/auto-radiography techniques; personal monitoring
devices and radiation survey instruments; Ionization methods
of radiation dosimetry of internally deposited radionuclides.

Free radical chemistry:

Water radiolysis, free radical generation by radiation and
chemical methods. Fast kinetics, mechanism of reaction,
stability and detection and ESR spectroscopy

Structural chemistry:
Nature of chemical bond, weak interactions and their
implications in biology.

Synthesis mechanisms and bio-organic chemistry: D Goswami

Types of organic reactions, disconnection approach, secondary (6)
metabolites, isolation, characterization and biosynthesis.
Green chemistry and phyto-chemistry.

Active Pharmaceutical Intermediate (API): Importance in

drug manufacturing, Chiral and achiral APIs, Strategies for
cost-effective sustainable synthesis of APIs, Global scenario,
Future of API synthesis.

Radioisotopes: M. Mallia
Concept of tracers, general principles of radionuclide (7)
production, nuclear reactions, production of radioisotopes,
Szillard-Chalmer reaction, separation techniques and
radiochemical purity, examples of production of biologically and
medically useful radioisotopes (reactor produced cyclotron
produced generator produced applying transient and secular
radioactive equilibria)

Radiopharmaceuticals chemistry:
Radiolabelling techniques, therapeutic radiopharmaceuticals,
clinical translation of in vitro to in vivo application; Principle,
applications and limitations of PET-CT, SPECT etc.

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 2.BIOLOGICAL SCIENCES

Module 2.1: BIOCHEMISTRY (Code: BS601)

(1 Test: 75 Marks; Credits: 2) (15 Lectures)
Course coordinator: Dr. Kuber C. Bhainsa ([email protected])

Protein and domain structures, folding and post- Swathi Kota

translational modification: (5)
Basics of protein structures (primary, secondary and tertiary):
soluble, fibrous, intrinsically
Disordered and membrane proteins; Protein ligand interactions;
Protein dynamics, folding, chaperones; Protein engineering:
rational and; directed evolution; Post-transnational
modifications and targeting.

Enzymology: Rajanikant
Enzyme catalysis and kinetics: (5)
Determination of kinetic constants; Enzyme inhibition:
reversible and irreversible. Irreversible inhibition:
Mechanisms and therapeutic use with examples Acetyl choline
esterase inhibitors. Reversible inhibition: Types and
mechanisms, determining inhibitory constants with reference to
their applications in drug designing and therapeutic applications.

Intermediary metabolism: J Kumar

Overview of different pathways-their linkages, key (5)
intermediates, cellular location of the reactions; importance in
human physiology, Diseases linked to metabolic error.

Bioenergetics:
Concepts of enthalpy, entropy, free energy, equilibrium
constant and free energy relationship, sequential reaction
energy coupling, chemical basis of high energy compounds or
bonds, polyphosphates, group transfer and transient signals,
redox reactions in biology.

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Module 2.2:MOLECULAR BIOLOGY (Code: BS608)
(1 Test: 125 Marks, Credits: 4)(28 Lectures)
Course coordinator: Dr. Anand Ballal ([email protected])

DNA replication: Saikat

Regulation of DNA replication in prokaryotes and eukaryotes. Chakraborty
Replication Licensing. Replication stress, fork stalling, reversal and (6)
collapse. Interplay between replication fork progress and dormant
origin. Gene dosage regulation. Replication-Coupled DNA Repair,
Replication-coupled recombinational repair and genomic stability,
break-induced repair (BIR).

Regulation of gene expression: Sheetal Uppal

An overview and comparison of transcription in prokaryotes and (7)
eukaryotes covering the enzymes involved, the process of
transcriptional initiation, elongation and termination.

Gene regulation: Differences in the promoter elements of

prokaryotes eukaryotes. In prokaryotes: Operon concept in brief,
tyrosine phosphorylation, noncoding RNA’s in regulation, antisense
RNAs, secondary structure of mRNAs, riboswitches. In eukaryotes:
Epigenetic changes, chromatin remodelling, stress responsive
alternate splicing, yeast gal gene as template for eukaryotic
regulation.
Mechanistic and structural aspects protein synthesis and its
regulation.

RNA biology: A Saini

An overview of functional diversity of RNAs, Structure and function (6)
of important non-coding RNAs (tRNAs, rRNAs, snRNAs, snoRNAs).
Secondary and tertiary RNA motifs and their importance. Sub-cellular
trafficking of RNAs. Mechanisms of tRNA maturation. RNA protein
complexes (ribosome, telomerase, spliceosome). RNA interference,
Small and long ncRNAs: biogenesis, mechanism of action and
biotechnological applications. RNA aptamers and SELEX protocol.
DNA/RNA nanostructures and applications.

DNA damage and repair: YS Rajpurohit

Radiation and chemical mutagens induced DNA damages and their (5)
detection. Repair mechanisms in bacteria and higher eukaryotes, cell
cycle specific repair, pathway choice and their regulation. Real time
assessment of DNA repair in in live cells. DNA repair proteins at single
molecular level.

Molecular biology tools: Chitra S Misra

Enzymes in molecular biology and their applications. Cloning and (4)
expression approaches (vectors, affinity tags, expression systems).
Gene knockdown/knockout technologies in prokaryotes and
eukaryotes with a special emphasis on RNAi and CRISPR-Cas
technologies.

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Module 2.3:CELL BIOLOGY& IMMUNOLOGY (Code: BS603)
(1 Test:100 Marks; Credits: 2). (23 Lectures)
Course coordinator: Dr. (Mrs.) Bhavani Shankar([email protected])

Cell cycle and cell death: B Shankar

Predivision stages, G1, S, G2 and M phases and their significance. (4)
Genetic regulation of cell cycle and experimental approaches for cell
cycle regulations. Different modes of cell death and its assessment.

Signal transduction in animal systems: S Ghosh

Receptors (membrane linked and cellular) receptors with enzyme (5)
activity, G proteins, tyrosine kinase related transduction, preview
of three modes of signaling (MAP kinase pathway, NFKB pathway and
JAK/STAT signaling), Radiation induced signal transduction and cell
death pathways, Cytoprotective and cytotoxic pathways, Cross
communication, Bystander effects.

Immunology: D Sharma
Innate and acquired immunity; Cell and organs of the immune (6)
system; Immunocompetent cells and their sub populations; Antigen
presentation; T cell and B cell maturation and activation; Cytokines;
Tolerance and autoimmunity.

Antibodies structure and diversity; affinity and avidity; hybridomas; B. Shankar

T cell receptor, structure and diversity; MHC structure and (3)
polymorphism; MHC restriction; Immuno-deficiency; vaccines and
immune-therapeutics.

Stem Cell Biology: DK Maurya

Stem cell characteristics and regenerative potential; Sources of stem (5)
cells (embryonic, umbilical cord and adult tissues); stemness
associated genes, asymmetric division; Stem cell therapy; Methods
of identification, isolation and characterization.

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Module 2.4: CROP SCIENCE (Code: BS604)
(2 Tests: 125 Marks; Credits: 4) (30 Lectures)
Course coordinator: Dr. (Mrs.) Archana Joshi-Saha ([email protected])

Mendelian genetics, Genetic maps and heteroploids in SK Gupta

crop improvement (3)
Mendelian Genetics, gene interaction, recombination, DNA
markers, simple sequence repeats, SNPs, linkage maps,
MutMap, cytoplasmic inheritance, male sterility, transposible
elements; Gene transfer methods, chromosome engineering for
crop improvement.

Quantitative genetics Ashok Badigannavar

Qualitative Vs quantitative traits, nature of variability, (4)
components of variation; heritability; genetic advance, genotype
x environment interaction and genetic advance. Types of gene
actions and its implications in plant breeding. Hardy-Weinberg
principle and gene frequency. Genetic basis of breeding self- and
cross-pollinated crops.

Principles of plant breeding Suvendu Mondal

Plant Introduction, germplasm exchange and plant quarantine. (8)
Breeding methods in self-pollinated crops-pureline selection,
mass selection, pedigree, bulk and single seed descent method.
Breeding methods in cross pollinated crops: Mass selection,
progeny testing, recurrent selections, synthetics and
composites; heterosis breeding,

Mutation breeding
Nature and classification of mutations, spontaneous mutations
and induced mutations, methodology for mutant screening for
oligogenic and polygenic traits, estimating mutagenic efficiency
and effectiveness. Procedure for release of crop varieties for
commercial cultivation.

Breeding for biotic stress tolerance

Concepts in pathogen resistance; Host defense response to
pathogen invasions-Biochemical and molecular mechanism;
acquired and induced immunity and systemic acquired
resistance (SAR). Host pathogen interaction, gene for gene
hypothesis, Horizontal and vertical resistance in crop plants.
Epigenetic modifications and speed breeding procedures for crop
improvement.

Abiotic stress tolerance Ashish Srivastava

Stress inducing factors-Drought, salinity, heat and heavy metal (5)
toxicity; Physiological and phenological response, genetics of
abiotic stress tolerance and breeding methodologies.

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Radiation in insect pest control Ashok Hadapad
Importance of insect pests, vectors and their management, IPM (2)
concepts, insect resistance in crop plants, mechanism, sources,
screening methodologies and strategies use of radiation and
endosymbionts in pest control-SIT and F1 inherited sterility.
Ashok Hadapad
Soil science (3)
Types of soil, manures and fertilizers, testing and analysis of soil
nutrients, behaviour and fate of pesticides in ecosystem,
pesticide residue analysis, isotope application in soil nutrient
management and reclamation of saline and alkaline soils

Plant tissue culture Sudhir Singh

Methods in plant cell tissue and organ culture, regeneration (5)
pathways-organogenesis and somatic embryogenesis, haploid
production in crop plants and in vitro mutagenesis, apomixis,
secondary metabolites in in vitro culture, plant metabolic
engineering.

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Module 2.5: MICROBIOLOGY & BIOTECHNOLOGY(Code: BS607)
(1 Test: 125 Marks; Credits: 4) (28 Lectures)
Course coordinator. Dr. (Mrs.) Hema Rajaram ([email protected])

Growth, identification and diversity in bacteria: R Shashidhar

Concept of pure culture. Bacterial growth curve- lag, log and (6)
stationary phase; growth advantage in stationary phase (GASP)
phenotype, small colony variant (SCV). Viable but Non-culturable
bacteria (VBNC) and dormant cells.

The 16S rRNA based identification of bacteria. Microbiome in

human health and emerging trends in study of gut microbiota.

Effect of bacteria on plant health (bacterial plant pathogens and Vandan Nagar
beneficial interactions between bacteria and plants). Inter species, (2)
intra species communication in microbes (quorum sensing).

Microbial Genomics: Hiren Joshi

Genomic organization of bacterial viruses, integration into host (3)
genome and packaging (list types of bacterial viruses and explain
one virus eg. lambda).Transformation, transduction and
conjugation.

Types of recombination. Models of recombination, genetics and D Rath

biochemistry of recombination. Artificial genome synthesis and (3)
generation of Mycoplasma laboratorium (synthetic bacterium).

Gene mutation and applied microbiology: D Rath

Discovery of mutations, Types of mutations, molecular events that (6)
cause different types of mutations and their properties. Methods to
detect different types of mutations. Generation, detection and
characterization of conditional mutations and suppressor
mutations. Generation and verification of single gene knock out
library in E. coli (Keio collection).
Introduction to microbial strain development for industrial
applications. Genetic Circuit-Assisted Smart Microbial Engineering
(SME). Use of microbes for production of antibiotics, food
ingredients, enzymes and nutraceuticals.

Antibiotic resistance: challenges and treatment: Vandan Nagar

Antibiotic resistance: Mechanism and challenges. Persister cells. (4)
Novel methods of discovery of new antibiotics (eg. Teixobactin).
Phage therapy. Intracellular pathogenic bacteria, Manipulation of
host immune system by bacterial pathogens (eg. Mycobacterium).

Biofouling: Hiren Joshi

Biofilms: concept, types, measurement and visualization. (4)
Biofouling and bio-corrosion: cause and concern. A case study of
biofouling and bio-corrosion in a nuclear reactor. Detection and
remedial measures.

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Module 2.6: CANCER BIOLOGY (Code: BS606)
(1 Test: 100 marks; Credits: 2) (23 lectures)
Course Coordinator: Dr. B. S. Patro ([email protected])

Introduction to cancer biology: BS Patro

Evolutionary perspective of cancer; carcinogens (biological, (2)
chemical and physical), etiology of cancer: DNA repair, genome
integrity and epigenetics

Cellular and molecular biology of cancer: Amit Kumar

Hallmarks of cancer; oncogenesis and tumour suppression; (6)
hormones and cancer; signalling pathways in cancer, cell cycle
control, deregulated cell death process; telomerase,
immortalisation, senescence. Tumor anatomy and hypoxia

Cancer cell metabolism:

Altered glucose metabolism; altered metabolic enzyme
expression: mutation of oncogenic isocitrate dehydrogenase,
fumarate hydratase, succinate dehydrogenase mutation, arginine
succinate synthase 1; upregulated glutaminolysis and serine
addiction; metabolic symbiosis; metabolic dependencies and
collateral lethality.

Tumor metastasis, invasion and dormancy: Saikat Chakraborty

Benign and malignant tumor; stages and grading of tumor; (4)
systemic spread of cancer cells: disseminated and circulating
tumor cells; epithelial-to-mesenchymal transition (EMT) during
development and metastasis; cellular and molecular drivers of
metastasis; the role of hematopoietic and stromal cells in
metastatic progression; metastatic latency.

Tumormicro-environment: Rahul Checker

Cancer associated stroma, angiogenesis; cancer immunology: (6)
tumour resistance to immune mediated control and elimination.

Treatment modalities and recent advances in cancer

therapy:
Chemotherapy (natural, dietary and synthetic drugs),
immunotherapy (antibody and cell-based therapy); nanoparticle-
based cancer imaging and therapy; cancer stem cells: role in
cancer relapse after chemo/radiotherapy, targeting CSC;
metastasis treatment; development of personalized medicine.

Cytogenetics:
BL Das
Constitutional anomalies: Numerical and structural, causes and
(5)
their implications in human health. Chromosomal disorders.

Molecular Genetics
Non-Mendelian inheritance of single gene disorders, monitoring
and screening of human population, copy number variations,
association studies,
Genome Mapping: somatic cell hybrids, radiation hybrids, contigs,
chromosome walking.

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Module 2.7: BIOINFORMATICS (Code: BS602)
(1 Test: 125 Marks; Credits: 4) (22 Lectures + 6 days practical)
Course coordinator: Dr. D. Rath ([email protected])

Introduction to databases: Bhanu Prakash

Primary and Derived databases: GenBank, EMBL/EBI, DDBJ, PDB, (1)
Swiss-Prot. PRINTS, BLOCKS, rDNA databases. Specialized
databases e.g. BioCyc etc.

Sequence analysis/alignment techniques: A Das

Pair wise sequence alignment: local and global alignment, (7+2AN)
consensus sequence (sequence logo), motifs, patterns, frequency
matrices (PAM, BLOSUM), PSSM, log odds score, penalty,
introduction to graphical, dynamic programming (Needleman-
Wunsch and Smith-Waterman algorithm) and heuristic methods,
database similarity searches-BLAST/FASTA algorithms.

Multiple sequence alignment, clustering, dendrogram/tree Bhanu Prakash

construction, molecular phylogeny. (2+1AN)

Genomics and high-throughput analysis: Vinay Jain

Next generation sequencing (NGS) and different platforms (3+1AN)
(pyrosequencing, ion-torrent, Illumina, SOliD, SMRT, Nanopore),
exome sequencing, transcriptome sequencing, NGS data quality
assessment and introduction to de-novo or reference-based
assembly, comparative genomics, microarrays and applications.

Bioinformatics applications in proteomics: B Basu

Introduction to mass spectrometry-based proteomics, MASCOT, (4+1AN)
protein sequence database and their use, gel based and gel free
quantitative proteomic approaches, interpretation and validation of
proteomics results, functional proteomics.

Structural biology and structural bioinformatics: S Bihani

Theory and practices of protein crystallography, introduction to the (5+1AN)
protein structural databases (PDB, CATH, SCOP etc.).
Instrumentation: structural/functional genomics initiatives,
evolution of structural motifs and molecular evolution
(convergent/divergent evolution), structure prediction methods
with particular focus on homology/comparative modelling and
threading, structural validation approaches, protein structures in
biotechnology (rational drug design/protein engineering etc.).

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Module 2.8: RADIATION BIOLOGY(Code: BS609)
(2 Tests: 125 Marks; Credits: 4) (28 Lectures)
Course Coordinator: Dr.(Mrs.) Anu Ghosh ([email protected])

Introduction to radiation biology Anu Ghosh

Radiation-induced free radical generation in biological systems; (6)
radiation units; direct and indirect effect; concepts of LET and RBE.
Survival curves of different radiation types; concept of D10, D0, Dq,
extrapolation number, linear quadratic model of radiation damage.

Effects of radiation on microbes & plants:

Radiation response and molecular mechanisms of extreme
radioresistance in microbes, Internal and external radiation
exposure to plants. Effect of radiation on photosynthesis and
respiration. Bio-indicator plants.

Radiation injury and radioprotection Rahul Checker

Biological effects of free radicals; biological defense against free (5)
radicals. O2 effect, radiosensitive and resistant tissues, acute
radiation syndromes – bone marrow syndrome, gastrointestinal
syndrome and cerebrovascular system syndrome. Sub-lethal and
potentially lethal damage and recovery, physical, chemical and
biological factors modifying radiation damage. Chemical and cell-
based radio-protection.

Heavy metal radionuclides BN Pandey

Chemical and radiobiological toxicity of internalized radio-nuclides (2)
and their mechanisms of interaction with biomolecules. Biological
strategies for decorporation and medical management of
internalized radio-nuclides.

Radio-sensitization and radiotherapy of cancer: BS Patro

Basic concepts, concept of four Rs in radiation biology, chemical (5)
radio-sensitizers and their applications in radiotherapy of cancer.
Particle beam therapy. End points for in vitro and in vivo cell
survival. Dose fractionation, biologically effective dose for
teletherapy, IGRT, IMRT, brachytherapy, MFD and CHART. Radio-
resistance of tumor cells: cellular and molecular mechanisms of
radio-resistance. Hyperthermia and modification of radiation
injury.

Bio-dosimetry for radiation exposure: Vivek Kumar

Dose response relationship, utero exposure, risk estimation of (5)
genetic diseases and malformations. Biological dosimetry: partial
and whole-body exposure, calibration curves, cytogenetic and
molecular end points: dicentrics, translocations, CBMN assay,
pancentromeric, telomeric and whole chromosome FISH,
premature chromosome condensation, HPRT assay, comet assay,
gamma-H2AX foci.

Radiation risk assessment, low dose radiation effects and BN Pandey

bystander effect: (5)
Epidemiological studies in radiation risk assessment. Estimation of
radiation risk estimation at population level; radiobiology of major
radiological incidents/nuclear accidents (A-bomb survivors, Mayak
Plant, Chernobyl and Fukushima, Mayapuri Incident). High
background radiation areas and low dose radiation effects; concept
of DDRF, LNT and radiation hormesis. Radiation induced bystander
and abscopal effects.

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Module 2.9: FOOD TECHNOLOGY (Code: BS605)
(1 Test: 100 Marks; Credits: 2) (21 Lectures)
Course coordinator: Dr. S. Gautam ([email protected])
Introductory lecture: Dr. S Gautam
Food processing & preservation Sweetie
 Post- harvest losses of food: Causes and impact, Kanatt
 Processing and preservation: Basic concepts, Conventional and (3)
advance methods (hurdle technologies, Pasteurization,
sterilization, canning and retort, extrusion processing -type and
components of extrusion and applications of technology).
 Effects of processing on nutritional and other quality parameters
of food
 Emerging technologies: Applications of UV, microwave, infrared,
radio waves, ultrasonic waves in food processing, high pressure,
ozone processing, Ohmic heating and pulse electric field in food
processing

Radiation processing of food for Safety, Security and Sweetie

International trade Kanatt
(2)
(A) Overview and Basic concept of food irradiation
Applications of food irradiation and underlying mechanism
Dose limit, regulatory approval and labelling
Wholesomeness and safety of irradiated food
Global and Indian scenario of food irradiation

(B) Interaction of radiation with food components Vanshika

 Radiation sources used (Gamma/ E- beam/ X-rays): Production Adiani
and decay, Concept of half-life and energy level, Comparative (6)
advantages and limitations of these radiation sources, Basic
principles of food irradiation dosimetry

(C) Effect of radiation processing on major (carbohydrate, protein,

Fat) and minor food ingredients (Vitamins etc.)
 Effects of radiation processing on different quality parameters of
food
 Detection of irradiated food

Radiation processing plant:

Design, throughput, regulatory approvals and safety

Microbial spoilage of Food Sachin

 Food spoilage-causes and factors, spoilage microorganisms, food Hajare
borne pathogens (3)
 Methods for rapid detection of microorganism in food
 Radiation inactivation of microorganisms, target theory, concept
of decimal reduction, D10 value, 12-D concept, factors affecting
radiation sensitivity of microorganisms.

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Human nutrition and Functional Foods: Sahyog
 Macro & micronutrients, RDA, consequences of improper intake of Jamdar
the nutrients, glycemic index, glycemic load (5)
 Overview of diet related diseases
 Dietary intervention and gut microbiota
 Specialized food (e.g. sports-food, space food, high-altitude food,
emergency rations)
 Functional foods, probiotics, prebiotics.
 Nanotechnology in food and nutrigenomics

Non-nutritional parameters of the food:

 Food texture, Color and flavors
 Use of food additives
 Food flavour: isolation and encapsulation.

Food packaging and coating applications: Packaging and biopolymer Sachin

material and their properties, natural and non-natural ingredients, active Hajare
packaging, Intelligent or smart packaging, MAP, edible film and coatings. (2)
Food package labelling

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3.0 Laboratory Techniques in Life Sciences (Code: BS592)
(65 days includes ~70 lectures; Credits: 16)550 marks (200 marks viva+350 marks
written test at the end of each practical)
Course coordinators: Dr. (Mrs.) Bhakti Basu ([email protected]) & Dr. Dibakar
Goswami ([email protected])

3.1) Cell Biology Techniques

Chromosomal analysis with mammalian cells metaphase preparation, K. S. Shettigar
micronuclei, G-banding, chromosomal aberrations, cytogenetic effects of (4 days)
radiation.
Immunology: ELISA, isolation of lymphocytes from lymphoid tissues and Kavitha
peripheral blood, immunophenotyping of T and B cells, E-rosettes and PFC (5 days)
assays, tissue culture methods, blast transformation, cytokine assays.
Flow cytometry
Radio-immunoassay and related procedures and tracer distribution in MKRay
animals (5 days)
3.2) General techniques
Confocal microscopy G Pai (1 day)

TLC, GC-MS, mass spectrometry, ESR, IR Jyoti Tripathi (1 day)

NMR/ FT-NMR D. Goswami (1 day)

Affinity purification of tagged proteins, Polyacrylamide Gel Electrophoresis, Bhakti Basu
Electrophoretic resolution of proteins (1D & 2D), western blotting (5 days)
&immunodetection

Pulse field gel electrophoresis (PFGE) Swati Kota (2 days)

Enzyme and cell Immobilization, permeabilization Jitendra Kumar

(4 days)
3.3) Molecular Biology and Microbiology
Transduction, conjugation, repair of UV induced Gargi Bindal (5 days)
damage, screening of markers

Isolation and Purification of DNA from Plants (difference in protocol of DNA Ashish Srivastava
isolation from bacteria and mammalian cell-demonstration) & MicroRNA (4 days)
isolation and characterization demonstration of Southern Hybridization

Total RNA From Mammalian Cells, Polymerase Chain Reaction, Amp-FLP, Vinay Jain (3 days)
silver staining, cDNA synth, RT-PCR

Microbiology: Enumeration of bacteria –plating techniques, radiation Vandan Nagar (3 days)

survival curve
3.4) Radiation Techniques
Radiation Biology & Radiation Measurements: S.T. Mehetre,
Radioisotope tracer techniques and radiation measurements, GM counting Poulomi Mukherjee,
system, counting statistics; half-life, absorption and scattering, isotope Darshana. Shalaskar
dilution, crystal scintillation counting (8 days)
Chemical dosimetry& ESR B. Sanyal (1 day)
Food Irradiation S. R. Kanatt
Hurdle technology (water activity, antioxidants, packaging & gamma (3 days)
irradiation), analysis (microbial, chemical & sensory)

Plant tissue culture and biotransformation Sudhir Singh & H. Tak

(5 days)

Drug delivery/liposome preparation Neena Shetake

(2 days)

SEM Celin Acharya (1 day)

TEM Anand Ballal (1 day)

Stem cell culture DK Maurya (2 days)

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4.0 SEMINARS (Code: BS594)
(200 marks; Credits: 4)
Course coordinator: Dr. B. N. Pandey ([email protected])

This module is designed for cultivating the art of communication and presentation
in the trainees and helps towards value addition to the professional ability and
personality development of the trainees

4.1 Paper Seminar (100 marks; Credits: 2)

Seminar on a selected paper published by reputed scientists. The purpose of the

paper seminar is to prepare the trainee to acquire skills in the presentation of
published research work. Aspects such as analysis of the experimental data,
details discussion on the results and hypothesis presented and drawing of
meaningful conclusions are expected to be inculcated during the process. In
addition, the trainee is encouraged to point out the strengths and lacunae if any
in the publication and suggest feasible steps to enhance the quality of the
publication.

4.2 Review Seminar (100 marks; Credits: 2)

Seminar on a review to be presented by trainees. Broad

areas/processes/topics/concepts of current research interest are communicated
to the trainees for choosing a topic for review. The seminar committee allocates
the review topic to the trainee from amongst the topics submitted by him/her
based upon the suitability, interests and aptitude of the trainee. The trainee is
expected to review as many papers as feasible on the specified topic and submit
a brief summary on the review topic assigned followed by an open defense. A
senior HBNI faculty in Biosciences is assigned as a mentor to each trainee to guide
them.

16
5.0 Research Methodology
(1 Test: 100 marks; non-credits course) (Total no of lecturers: 20)
Course coordinator: Dr. Kuber Bhainsa ([email protected])

Topic Lectures
Scientific research and documentation Dr. SS Kumar
Scientific research: Definition, characteristic, types and need of (5)
research, Identification of problem, Literature survey and assessment
of its current status, formulating objectives, approach to solve the
problem, designing the experiment, actual investigation to achieve the
objectives, results and discussion.
Documentation and writing: Types of report; research paper, project
reports, thesis, Seminar presentation. Preparation of manuscript for
publication- research, review paper and thesis writing.

Application of computer in research, data handling and Bhanu

presentation Prakash
Use of word processing, spreadsheet and database software. Plotting of (5)
graphs. Internet and its application: Email, WWW, Web browsing,
acquiring technical skills, drawing inferences from data, multimedia and
power points.

Occupational safety, health and environment at work place Rajdeep, BSC

Regulatory framework of BARC, Atomic Energy Act 1962, Atomic Energy (5)
Factory Rules, Radiation Protection Rules, Surveillance of occupational
health, Medical care and management of Internal contamination.
Radiation safety, Fire safety, Electrical safety and Chemical safety.

IPR and research ethics - Ethical issues – ethical committees - As suggested

Commercialization - Copy right - Royalty - Intellectual property rights by Head,
and patent law – Trade Related aspects of Intellectual Property Rights TTCD (5)
- Reproduction of published material - Plagiarism - Citation and
acknowledgement - Reproducibility and accountability

17
6.0 AUDIT LECTURES
(Non-credits course) (Total no of lecturers: 9)
Course coordinator: Dr. Sudhir Singh ([email protected])

Reactor Science 5
Basic concepts of nuclear energy (As per Head,
Properties of nuclei, binding energy, cross section, nuclear fission RPDD)
process and energy release, fission products, fission product activity,
fission gammas, Neutron flux
Interaction of neutrons with matter
Neutron reactions, production of neutrons, nuclear reactions with
thermal and fast neutrons
Concept of a nuclear reactor
Chain reaction, multiplication factor, four factor formula, nuclear
reactor materials, fissile, fertile, fissionable nuclides, fuel,
moderator, coolant, structural materials, concepts of irradiation,
burn up, criticality
Exposition to different reactor systems
Indian nuclear power programme, thorium utilisation (AHWR)

Biosciences
Bio safety and animal ethics Amit Kumar
(4)

18
7.0 ELECTIVE COURSES (BS701 - BS715)

(Each elective course will include 20 lectures and 2weeks practical. Exam will be
held at the end of the week following the completion of each elective.
(Four tests: 125 marks for each elective; 6 credits for each elective; Total: 500
marks; 24 credits)

Code Title Name of

coordinator
BS701 Advances in enzyme technology Archana Mishra
BS702 Assessment of health effects from exposure to low levels of B. L. Das
ionizing radiation
BS703 Biology of stress and adaptive response in bacteria Hema Rajaram
BS704 Challenges for sustainable and clean environment S.T. Mehetre
BS705 Food borne pathogens R. Shashidhar
BS706 Immunological methods in biochemical and chemical analysis M. K. Ray
BS707 Molecular markers and genomics for crop improvement S. K. Gupta
BS708 Oxidative stress and redox modifiers in disease management Santosh Kumar
BS709 Cancer-hallmarks, pathogenesis, microenvironment and Bhavani Shankar
therapeutics
BS710 Plant genetic engineering Himanshu Tak
BS711 Advances in genome biology Y.S. Rajpurohit
BS712 Principle and practices in structural biology Mukesh Kumar
BS713 Advanced instrumentation for bioanalysis and imaging Kuber C. B.
BS714 Molecular biology methods in tuberculosis and thyroid cancer Savita Kulkarni
BS715 Principles and practices of Mutation Breeding S. Mondal

NB: The Trainees are to make choice of four (4) electives.

19
 Annexure-II
COURSE STRUCTURE - BIOSCIENCES
FOUNDATION COURSES
S. No Subject Title Course Code Hours Credits Marks
1 Chemistry & Radiochemistry BS 501 23 2 75
2 Physics, Maths & Statistics BS 502 40 4 150
FOUNDATION TOTAL 65 6 225
CORE COURSES
S. No Subject Title Course Hours Credits Marks
Code
1 Biochemistry BS 601 15 2 75
2 Bioinformatics BS 602 30 4 125
3 Cell Biology BS 603 23 2 100
4 Crop Science BS 604 30 4 125
5 Food Technology BS 605 21 2 100
6 Cancer Biology BS 606 23 2 100
7 Microbiology & Biotechnology BS 607 28 4 125
8 Molecular Biology BS 608 28 4 125
9 Radiation Biology BS 609 30 4 125
CORE TOTAL 228 28 1000
ELECTIVES (any 4)
S. No Subject Title Course Code Hours Credits Marks
1 Advances in enzyme technology BS 701 20+2W* 6 125
Assessment of health effects from exposure to low levels of ionizing 20+2W* 6 125
2 BS 702
radiation
3 Biology of stress and adaptive responses in bacteria BS 703 20+2W* 6 125
4 Challenges for sustainable and clean environment BS 704 20+2W* 6 125
5 Food borne pathogens BS 705 20+2W* 6 125
6 Immunological methods in biochemical and chemical analysis BS 706 20+2W* 6 125
7 Molecular markers and genomics for crop improvement BS 707 20+2W* 6 125
8 Oxidative stress and redox modifiers in disease management BS 708 20+2W* 6 125
Cancer- hallmarks, pathogenesis, microenvironment and therapeutics 20+2W* 6 125
9 BS 709
(previously Overview of Cancer)
10 Plant genetic engineering BS 710 20+2W* 6 125
11 Advances in genome biology BS 711 20+2W* 6 125
12 Principle and practices in structural biology BS 712 20+2W* 6 125
13 Advanced instrumentation for bionalysis and imaging BS 713 20+2W* 6 125
14 Molecular biology methods in tuberculosis and thyroid cancer BS 714 20+2W* 6 125
15 Principles and practices of Mutation Breeding BS 715 20+2W* 6 125
ELECTIVES TOTAL 80+8W 24 500
* Two weeks: 20 lectures; 10 afternoon practical (6 credits each)
THEORY TOTAL 372+8W 60 1700
NON-SUBJECT ASSIGNMENTS
S.No. Subject Title Course Code Credits Marks
1 Viva Voce (Mid-Term & Final) BS 591 2 200
2 Laboratory Techniques in Life Sciences BS 592 16 550
3 Seminars BS 594 4 200
TOTAL 22 950
CREDIT
Course Credit Marks Total contact hours
1 Foundation course 6 225 65
2 Core Course 28 1000 228
3 Laboratory techniques in life sciences 16 550 NA
4 Seminars 4 200 NA
5 Research Methodology* 0 100 20
6 Audit lectures* 0 NA 9
7 Elective courses 24 500 80
8 Viva Voce(Mid-Term & Final) 2 200 NA
Total 80 2775 402
*Non-credit courses; 50% marks required

20
 BS701: Advances in Enzyme Technology

Course Coordinator: Dr. Archana Mishra, EMT, NABTD

S. No. Lecturer Topics

1 Dr. Archana Mishra, NABTD Industrial applications of enzymes; stabilization of

enzymes and bioprocess development

Nanotechnology in the field of biosensors

2 Dr. K. C. Bhainsa, NABTD Proteins / enzymes for remediation

Bionanotechnology in the field of bioremediation

3 Dr. Jitendra Kumar, NABTD Biosensors: concept and methods, its application in
agriculture, food, environment and medical.

4 Shri S. Bhanu Prakash, Computational enzymology and Non-aqueous

NABTD enzymology

5 Dr. K. C. Bhainsa, NABTD Advances in biomaterials and their bioengineering

applications

21
 BS702: ASSESSMENT OF HEALTH RISK FROM EXPOSURE TO LOW LEVELS OF IONIZING
RADIATION

Co-coordinator Dr. (Mrs) Birajalaxmi Das, RBHSD

Syllabus for Radiobiology elective course

1. Low doses of ionizing radiation, an overview – Definition of low dose, units of radiation dose,
Sources of exposure to radiation in humans - natural and man-made, detection of ionizing radiation –
physical and biological. Overview of various high level natural radiation areas of the world.

2. Research Methodology – Steps involved in planning and designing a research study Formulating
answerable questions, testable hypothesis, study designs & experiment, data collection &
management, statistical analysis, conclusions, replication

3. Heritable genetic effect of radiation in human population. Genetic diseases, Mendelian,

multifactorial and chromosomal Diseases, Risk estimation of different cl asses of genetic diseases,
Doubling dose estimates, concept of mutation component.

4. Introduction to Epidemiological methods - Collection of epidemiologic data, types of

epidemiological studies, cohort and case control studies, statistical power, Analysis of epidemiologic
data, Linear relative risk model, Interpretation of epidemiological data, assessment of association and
dose response relationship.

5. Atom Bomb survivor studies - Description of cohorts and statistical methods, dosimetry, cancer
data (solid, site specific), benign neoplasms and non-neoplastic disease.
6. Medical Radiation studies - Medical uses of radiation, Radiotherapy for malignant and benign
diseases, diagnostics, evaluation of risks for specific cancer sites. Medical and Dental occupational
exposures.
7. Occupational Radiation studies - Workers of Nuclear Industry, Chernobyl clean-up & Mayak facility,
Air-line & aerospace employees, Fukushima accident and its after effects.
8. Environmental Radiation studies - Population living around nuclear facilities, population exposed
atmospheric testing, fall out or other environmental release of radiation, Population exposed
Chernobyl accident, and population natural background radiation.
9. Integration of Biology and Epidemiology - DNA damage response and cancer risk, etiology of
cancer at different sites, dose and dose rate effects on tumor induction, Role of immune system in
cancer, effects of low doses of radiation on the immune system, other forms of cellular and animal
response to radiation, genetic susceptibility to cancer.
10. Risk Assessment –models and methods - Risk assessment methodology, risk models, variables
that modify the dose response relationship. Estimating Cancer Risk: Measures of risk and choice of
cancer end points, risk calculations

11. Recent advances in adaptation, bystander effects etc. and their impact in risk assessment.
Hands on Training (Practical):
(One week)
Introduction to statistical packages and Analysis of sample data. Preparation & exploration of data,
data visualization using graphical tools, data analysis - hands on training.

Faculty members: co-ordinator Dr. (Mrs) Birajalaxmi Das, Other faculty members:
Dr (Mrs.) Birajalaxmi Das, Dr (Mrs.) Anu Ghosh, Dr. (Mrs.) Bhavani Shankar, Dr. Vivek Kumar PR and
P. K. M Koya

22
 BS703: Biology of Stress and Adaptive Response in Bacteria

Course Coordinator: Dr. Hema Rajaram, MBD

Lectures Lecturers Contact Hours

1. General features of organization and

regulation of bacterial stress response Hema Rajaram 1
Introduction to cyanobacteria and genetic
manipulations for assessment of tolerance

2. Heat-shock and cold-shock response Hema Rajaram 2

3. Stationary Phase response Hema Rajaram 1

4. Toxin-antitoxin systems for stress management Hema Rajaram 1

5. Salinity, osmotic stress Response and potassium signalling Anand Ballal 3

6. Enzymatic Management of Cyanobacterial Oxidative Stress M. Banerjee 2

7. Multiple stress tolerances of Deinococcu radiodurans

and its assessment Bhakti Basu 4

8. Biochemical characteristics of SSB and its role in DNA repair A.K. Ujaoney 1

9. DNA damage and repair in cyanobacteria Hema Rajaram 1

10. Microbial responses to heavy metal toxicity and uranium bioremediation

Celin Acharya 3
11. Biotechnological Applications Hema Rajaram 1
------------------
20 hours

Laboratory Work 6 hours each day for 10 working days (60 hours)

To be conducted by all the above faculty members with help from Dr. PrashanthRaghavan, Ms.
Pratiksha, Dr. A. Narasimha, Dr. Kriti, Mr. Arvind Kumar, Mr. Akhilesh Potnis and Ms. Divya TV

23
 BS704: Challenges for Clean and Sustainable Environment
Course Co-ordinator: Dr. S.T. Mehetre
Course Outline: Theory: 20 hrs

Description Lecturer hours

Introduction to sustainability Dr ST Mehetre 05
Introduction and concept of sustainability
Sustainability in view of climate change. Carbon credit and its
relevance.
Practical ways to implement sustainability. Successful examples of
environment management, pollution control, waste management
Concept of solid waste management with special reference to Dr ST Mehetre 02
Nisargruna Biogas plant
Composting technology as an alternative to air pollution by Dr PK Mukherjee 02
burning crop residues, dry leaves etc
Environmental pollution management with respect to Heavy Dr Darshana Salaskar 02
metals bioremediation
Environmental pollution management with respect to chemical Dr ST Mehetre 02
pesticides
Role of biopesticides and biofertilizers in clean environment Dr PK Mukherjee 03
Dr ST Mehetre 02
Role of nanoparticles for environment management Dr Poulomi Mukherjee 02

Practical’s: 05 No
Description Resource person No of hours
Analysis of different gases including methane by Dr ST Mehetre 03
gas chromatography
Pesticide residue analysis by GC, HPLC, TLC Dr ST Mehetre 05
Fate and behaviour of heavy metal under rice Dr Darshana Salaskar 05
ecosystem
Demonstration of composting technology Dr Poulomi Mukherjee, 02
Darshana
Development of biopesticide formulation Dr PK Mukherjee 05
Dr ST Mehetre

Field visits
1. Nisargruna biogas plant at Nursery, TSH, BARC Hospital and outside location
2. Composting site at Anushaktinagar, Mandala, Kamgarnagar etc
3. Field visit where carbon credit/environmental management concept is used (Godrej supports
carbon credit, farmer engaged in organic farming, society managing own waste).

24
 BS705: FOOD-BORNE PATHOGENS
Course coordinator: Shashidhar R - [email protected]

Sl. Theory Lectures No. of

No. Lectures
1 Introduction to food-borne pathogens and epidemiology 1
Important pathogens; economics of outbreak; epidemiology; world centers for
monitoring these pathogens
2 Detection and typing of food-borne pathogens 1
Biochemical, Molecular (PCR & Microarray) and Immunological detection; Typing -
serology, DNA based - PFGE, RFLP, MLS
3 Food-borne Bacterial pathogens 10
Classification, source ,distribution, detection, pathogenicity, cure and importance in
food industry with respect to Salmonella species, Vibrio species, Listeria
monocytogenes, Campylobacter species, Yersinia enterocolitica, Escherichia coli,
Bacillus cereus, Clostridium species, Shigella species and Staphylococcus aureus
4 Food-borne viruses and prions Norwalk 1
viruses, Hepatitis A, Hepatitis E, Rotaviruses, Prions
5 Mycotoxins 1
Aflatoxins from Aspergillus flavus and A. parasiticus; Ochratoxins from A. ochraceus
and Fumonisins from Fusarium species
6 Protozoan 1
Cyclospora cayetanensis, Cryptosporidum parvum, Anisakis simplex, Taenia saginata,
T. solium, Toxoplasma gondii, Trichinella spiralis
7 Molecular mechanisms of pathogenicity–Salmonella, L. monocytogenes 2
Adhesion, Invasion and Survival inside host cell
8 Molecular stress response of food-borne pathogens 2
Extreme environments of food, Survival strategies of pathogens in extreme heat, acid
and saline conditions, VBNC, Detection of VBNC, Importance of VBNC in context with
food borne pathogens
9 Emerging and uncommon food-borne pathogens 1
Enterobacter sakazakii, Aeromonas species, Mycobacterium paratuberculosis,
Arcobacter species, Antibiotic / food processing resistant strains and variants of already
known pathogens
10 HACCP 1
Principles of HACCP; Implication of HACCP; Radiation processing and HACCP
Sl. Practicals No. of
No Practicals
1 Isolation and characterization of bacterial pathogens (Salmonella species, Vibrio 10 AN
species, Listeria monocytogenes, Yersinia enterocolitica, Escherichia coli, and
Staphylococcus aureus); Rapid detection of Salmonella using nested PCR; Molecular
characterization of Salmonella; Detection of aflatoxin
Faculty: R Shashidhar, M N Karani, S N Jamdar, S N Hajare
Teachers:
1. Dr. Shashidhar R – 8 classes
2. Dr. Sachin Hajare- 2 classes
3. Dr. Sweetie Kanatt - 3 classes
4. Dr. Vandan Nagar - -7 classes
5. Mrs. Arati Kakatar- Practicals.

25
 BS706: Immunological methods in biochemical and chemical analysis
Course Coordinator: Dr. MK Ray, RMC

S. No. Lecturer Topics

1 Dr(Mrs) Savita Kulkarni Antigen- antibody interactions in immunoassays
2 Dr ( Mrs) Archana Damle Production of polyclonal and monoclonal antibodies
3 Shri M K Ray Radioiodination, Data analysis, QC-QA in immunoassay
4 Smt Smita Gawandi Standards in immunoassay, Immunization of lab animals
5 Smt Bharati Jain Protein chips and affinity purification
6 Shri Avik Chakraborty AMA assay, ATA
7 Shri J Kumarasamy Immobilization of antibodies, Separation Methods in
immunoassay, Scatchard plot, Nanobodies
8 Smt Chandrakala Gholve Tg asays, ATA, Scatchard plot
9 Dr(Mrs) Savita Kulkarni Non-isotopic Immunoassays, SCFV antibodies, Abzymes
and phage display

26
 BS707: Molecular markers and genomics for crop improvement
Coordinator: Dr. S K Gupta

Lecture title Number of lectures Delivered by

1. Introduction to molecular markers and application in 2 BKD/JS

plant breeding

2. Methods and principles of PCR 1 SKG

3. Different methods of DNA extraction from plant tissues 1 SKG

4. Different types of molecular markers (RAPD, ISSR, SSR, 3 SKG

AFLP, ILP and SNPs)

5. Reverse Genetics: TILLING (Targented Induced Local 2 JS

Lesions IN Genomics)

6. Calculation of similarity index, UPGMA, Cluster 2 AJS

analysis, dendrogram construction

7. Next generation sequencing (NGS) & Genotyping by

1 JGM
sequencing (GBS) technologies for crop improvement
2 SS
8. Quantitative or real-time PCR
2 SM
9. Epigenetics in crop improvement
1 JS
10. QTLs (Quantitative Trait Loci) and their role in plant
breeding

11. Marker assisted selection (MAS) and Marker 2 BKD/AB

assisted Breeding

(Background selection, foreground selection)

12. Genome –wide association mapping in plants 1 AB

Practical (2 weeks) (BKD, JS, SKG, AJS, SS, SM, GV, AS, PD)

 Different molecular markers techniques: ISSR, SSR & ILP

 PCR & Agarose gel electrophoresis, PAGE & Silver staining, Capillary electrophoresis, RT-PCR
 SSR and ILP marker development/primer designing
 Scoring of molecular markers data and analysis
 Software demonstrations: NTSYS, Joinmap, QTL Cartographer, Structure analysis
 Detecting polymorphism without gel (low resolution melting/high resolution melting curve
analysis)
 Automated DNA extraction, DNA quantification and TILLING

BKD: Dr. BK Das, JGM: Dr. JG Manjaya, JS: Dr. J Souframanian, SKG: Dr. SK Gupta, SS: Dr. S Singh, AJS: Dr. AJ
Saha, SM: Dr. S. Mondal, AB: Dr. A Badiganawar, GV: G Vishwakarma, AS: A Shitre, PD: P Dhansekhar

27
 BS708: OXIDATIVE STRESS AND REDOX MODIFIERS IN DISEASE MANAGEMENT
Coordinator: Dr. S. Santosh Kumar

SI. Theory Lectures No. of Lectures (20)

NO. 4 MARKS PER
LECTURE
1. Introduction and Significance SSK (1)
ROS/RNS and their physiological significance in healthy state
2. Detection and measurement of free radicals and their actions SSK (2)
ESR and pulse radiolysis-their applications
Finger printing for DNA, proteins and lipids
Biochemical methods for radical scavenging and molecular
damage by free radicals
3. Reactive species as useful biomolecules SSK (1)
Radical enzymes SRK (1)
Fruit ripening and wound response
Role in biological defense mechanisms
Lipoxygenases and cyclooxygenases
4. Natural antioxidants and their dietary source SRao (1)
Antioxidants from different sources
5. Antioxidants in prevention and therapy of human ailments DKM (4)
Cardiovascular ailments
Diabetes and other metabolic diseases SSK (1)
Diseases of the nervous system
Cancer
Ageing and diseases associated with it
Respiratory ailments
6. Antioxidants and Food SRK (4)
Types and effects of rancidity
Measurement of oxidative rancidity
Methods to prevent oxidation
Natural and synthetic antioxidants and their extraction methods
Measuring of antioxidant activity in foods
Novel antioxidants in food preservation
Role of antioxidants inn radiation preservation of foods
Application of antioxidants in food products of animal and plant
origin
Functionality of natural antioxidants during food preservation
7. Role of cellular redox in regulation of immune responses DS (2)
8. Manufacturing Resource Planning (MRP) and its role in food SRao (1)
preservation
9. Natural compounds as novel natural antimicrobials SPC (1)
10. Generally Recognized As Safe (GRAS) food preservatives SPC (1)
SI. Practicals 20 MARKS
NO.

Lecturers
SSK- S. Santosh Kumar; DS- Deepak Sharma; DKM- DK. Maurya; SRK- SR. Kanatt
SPC- SP. Chawla SRao – Shobita Rao

28
 Practicals

------------------------------------------------------------------------------------------------------------
Radiation induced plasmid relaxation assay
DPPH & ABTS Radical scavenging
Lipid peroxidation (Thiobarbituric acid reactive substances & lipid hydroperoxides); Protein oxidation
DNA damage by radiation and peroxyl radicals – possible prevention by an antioxidant
Electron Spin Resonance, Pulse radiolysis,
Nuclear levels of redox sensitive transcription factors
DNA fragmentation – by radiation and peroxyl radicals and possible prevention
ROS generation and quenching in cells
Expression of antioxidant enzymes
Estimation of GSH/GSSG Levels
Food related antioxidant assays
------------------------------------------------------------------------------------------------------------

SPC- SP. Chawla

SSK- S. Santosh Kumar
SRK- SR. Kanatt
DKM – DK. Maurya
DS- Deepak Sharma

29
 BS709: Cancer-Hallmarks, Pathogenesis, Microenvironment and Therapeutics
(previously overview of cancer)
Co-coordinator- Dr. Bhavani Shankar)

Genetics and pathophysiology: Genetic basis of cancer, germline mutations, nature of cancer,
Hallmarks of cancer, pathophysiology of neoplasia, sequential changes during cancer pathogeneisis,
Epidemiology of Cancer, Clinical manifestations of cancer. (4)

Molecular characteristics and Oncogenesis: Causes and prevention, Genetic changes in neoplasia and
multi-step tumorigenesis, Oncogenes, tumor suppressor genes, Tumor Viruses, Physical, chemical and
viral carcinogenesis, characteristics of neoplastic cells, role of tumor microenvironment, Inflammation
and cancer, Interactions of pathways in cancer. (6)

Tumor immunology: Immunosurveillance, Anti-tumor immunity (cells involved and mechanism),

Evason of the immune system by tumor, Tumor antigens, Immunotherapy and Tumor vaccines
(5)

Animal Models in Cancer Research: Spontaneous cancer, tumors following exposure to environmental
factors or chemicals, subcutaneous, i.v models orthotopic models and models for study of metastasis
(2)

Cancer Therapeutics: Traditional and emerging therapies; Rationale behind new state-of-the-art
cancer treatments (3)

Practicals
Clonogenic and proliferation assays
Cell cycle and cytotoxicity
Immunohistochemistry
Animal models

The lecturers for this elective course will be Dr. Susan Cherian (Medical Division), Dr. Bhavani
Shankar, Dr. B.N. Pandey, and Dr. H. D. Sarma (RB&HSD)

30
 BS710: PLANT GENETIC ENGINEERING
Coordinator: Dr. Himanshu Tak
Sl. Theory Lectures No. of
No. Lectures
1 Plant cell and tissue culture systems for genetic transformation. 2 TRG
Requirements of in vitro cultures, nutrient media, plant growth regulators, in vitro
propagation systems and their applications
2 Plant gene structure and organization, isolation and cloning. 2 HT
3 Plant expression vectors, promoters, enhancer elements. 2 HT
Popularly used vectors, cis and trans acting factors, types and role of promoters,
enhancers
4 Selectable marker and reporter genes. 2 SS
Antibiotic resistant marker genes, Herbicide marker genes, Reporter genes, removal
of marker genes, alternate selectable marker systems
5 Methods of plant genetic transformation. 2 HT
(i) Direct gene transfer methods, particle bombardment, electroporation, sonication,
electrophoresis, liposome delivery, microinjection, whisker mediated transfer;
(ii)Agrobacterium-mediated, strains, virulence genes, mechanism of T -DNA transfer
and integration, different methods of Agro- transformation, vectors used in Agro
transformation
6 Enhancing and stabilizing transgene expression, genome editing techniques in 3 HT
plants
Transgene silencing – mechanism and control, CRISPR-CAS9, TALEN and ZFN
mediated genome editing.
7 Genetic manipulation for biotic and abiotic stress tolerance. 2 SS
Disease resistance (viral, fungal, bacterial), insect resistance, abiotic (salinity,
drought, cold) tolerance
8 Molecular farming. 2 TRG
Host systems and methods, technology and products, strategies for increasing
recombinant protein production, downstream processing
9 Plant metabolic engineering for quality improvement. 2 SS
Biosynthetic pathway modulation, nutritional quality improvement, functional
foods. Ripening related genes, expression and control, genes for nutritional quality.
10 Plant Proteomics through genetic engineering. 2 HT
Commonly used vectors for protein overexpression, Protein purification techniques,
purification of proteins from inclusion bodies
11 Bioethics and biosafety of transgenic plants 1 SS
Guidelines and regulation of biosafety, field trials and release of transgenic crops and
commercial aspects.
Sl. Practicals No. of
No Practicals
1 Transformation by electroporation and confirmation through colony PCR; Plant 10 days
explant preparation for transformation and Agrobacterium-mediated TRG, HT
transformation using GUS reporter gene; Histochemical localization of GUS in and SS
transformed tissues; Extraction of DNA from transformed tissues and confirmation
of transgene integration (PCR / Southern); RNA isolation and quantitative real time
PCR; Confirmation and quantification of transgene expression by Western analysis;
Overexpression and purification of plant proteins, Particle bombardment mediated
genetic transformation.
Faculty: T R Ganapathi, Sudhir Singh, Himanshu Tak.

31
 BS711: Advances in Genome Biology

Coordinator: Dr. Y. S. Rajpurohit

Other faculties:
Dr. HS Misra
Dr. Sudhir Singh
Dr. Swati K.
Sri Rajesh Chaurasia

1. Genome structure with certain examples 3

2. Genome packaging in bacteria, plants and animals 3
3. Genome maintenance and integrity 3
4. Mechanisms of genome segregation 3
5. Factors affecting genome dynamics 3
6. Various approaches for creating genomic alteration in plant and bacterial systems,
particularly ploidy 3
7. Usefulness of genomic perturbation in quality and strain improvements and harmful
implication in mammalian cells 2
Total - 20

Laboratory experiments (6 days)

1. Pulsed field gel electrophoresis to analyse genome from plants, animals and multipartite
genome harboring bacteria.
2. Visualization of real time dynamics of genome segregation in bacterial and mammalian
cells during stressed growth by fluorescence microscopy (Time lapse).
3. Isolation of protoplast of plants with different levels of ploidy and visualization of DNA
organization in these crop plants by DNA staining and fluorescence microscopy.

Faculties

Dr H. S. Misra, Dr. Swati and Dr Y. S. Rajpurohit -PFGE of bacteria, plants and mammalian genomes.
Genome segregation studies in D. radiodurans and E. coli.
Dr. Sudhir Singh- Brasicca, Tobacco and banana protoplast isolation and FM studies with DAPI and PI
staining
Dr Rajesh Chaurasia- Mammalian cells exposure to gamma, colchicines, cisplatine, doxorubicin
treatment and monitoring in vitro defect on nucleoid size during recovery periods

32
 BS712: Principles and practices in Structural Biology
Coordinator: Dr. Mukesh Kumar

Topic No. of lecture- Faculty

/tutorial- hours
1. Introduction to three dimensional structures of 2 Dr. Subhash C. Bihani
proteins and nucleic acids,
Methods for determining 3D structures of biological
macromolecules

2. Methods of protein expression and purification 2 Dr. Vishal Prashar

3. Crystal symmetry, Macromolecular crystallisation

and crystal characterization 2 Dr. Gagan D. Gupta

4. X-ray sources and diffraction theory

2 Dr. Gagan D. Gupta
5. Methods of diffraction data collection, data
processing 2 Dr. Amit Das

6. Methods for solving the Phase problem

2 Dr. Amit Das
7. Crystallographic refinement
2 Dr. Mukesh Kumar
8. Electron density maps, model building and
validation 2 Dr. Vishal Prashar

9. Structure-based drug design

2 Dr. Subhash C. Bihani
10. Biophysical techniques for characterisation of
proteins, protein-ligand interactions: principles of 2 Dr. Lata Panicker
CD, fluorescence spectroscopy, etc.

Laboratory experiments: 10
a) Protein expression and purification
b) Protein crystallization
c) Crystal mounting, diffraction data collection and Dr. Amit Das
processing Dr. Gagan D. Gupta
d) Structure solution and refinement Dr. Lata Panicker
e) Interpretation of electron density maps, model Dr. Subhash C. Bihani
building and validation Dr. Vishal Prashar
f) Biophysical methods in structural biology: CD,
fluorescence, etc.

Total 20 lectures-
hours
10 tutorial-
hours
Tutorials will be conducted with the help from Ms. Shweta Kumari and Ms. Rimanshee Arya.

33
 BS713: Advanced Instrumentation for Bioanalysis and Imaging
Coordinator - Dr. Kuber Bhainsa ([email protected])

Theory Faculty and number of lecture

Current perspective on advanced instrumentation Dr. Kuber Bhainsa (2 Lecturers)
for bioanalysis and imaging
Principle and application of the Instruments:
Liquid Chromatography Mass Spectrometry (LCMS) Dr. Sumit Gupta and Smt. Jyoti Tripathi
(2 lecturers)

Inductively Coupled Plasma Spectrophotometer Dr. Kuber Bhainsa (5 lecturers) , Dr.

(ICP), X-ray Diffraction (Powder), Scanning Electron Jitendra Kumar (2 lectures) , Bhanu
Microscopy (SEM) and Rheometer Prakash (2 lectures) and

Atomic Force Microscopy (AFM) Dr. Hema Rajaram (2 Lectuers)

Transmission Electron Microscopy (TEM) Dr. Anand Ballal/ Dr. Alka Gupta (2
Lecturers)

Confocal Laser Scanning Microscopy (CLSM) Dr. B. N. Pandey (3 lecturers)

Practical 10 Afternoons, For all the instruments

put together to be carried out in the
respective lab.

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 BS714: Molecular biology methods in tuberculosis and thyroid cancer
Course Coordinator: Dr. Savita Kulkarni

Lectures:
1. Introduction to TB - its evolution and comparison to other infectious diseases. [2] SPK, MKR

2. Importance of molecular diagnostic methods aiding clinical diagnosis in infectious diseases and
cancer. [1] SB

3. Molecular biology techniques in diagnosis of tuberculosis. [2] SPK

4. Understanding of Molecular epidemiology in tuberculosis. [2] SG, PKG

5. Importance of Phylogeny in tuberculosis. [1] SG

6. Drug used in tuberculosis and Molecular mechanisms of drug resistance in TB [2] MKR, PKG

7. Drug discovery in tuberculosis. (Synthetic and natural compounds ) [2] MKR

8. Introduction to thyroid cancer. [1] AAD

9. Molecular methods of diagnosis of thyroid cancer including circulating tumour cells.

[2] AAD, AC

10. Molecular mechanisms of resistance to treatment in thyroid cancers. [2] AC, DT

11. Genetic, epigenetic and post-translational modification in thyroid cancer and their role in thyroids
cancer prognosis. [3] AC, DT

---------------------------------------------------------------------------------------------------------------------------
Total [20]
Laboratory experiments:
1. Spoligotyping for different strains of M.tuberculosis (Tuberculosis )
2. Mycobacterial Interstitial Repeat Units (MIRU) typing (Tuberculosis )
3. RFLP(Tuberculosis )
4. Single target PCR and multiplex PCR (Tuberculosis )
5. Real time Quantitative PCR for TB and Thyroglobulin (Tuberculosis and thyroid cancer)
6. REMA assay and radiorespirometry assay for Drug resistance detection(Tuberculosis )
7. Mutant Allele Specific Amplification (MASA) ( thyroid cancer)
8. Mutator assay (thyroid cancer )
9. Single strand length Polymorphism (SSCP) ( thyroid cancer )
10. In situ hybridization (Thyroid cancer )

Faculty:
Dr (Smt.) Savita Kulkarni (SPK)
Dr (Smt.) Archana Damle (AAD)
Dr. Sandip Basu (SB)
Mr. Muktikanta Ray (MKR)
Mr. Avik Chakraborty (AC)
Mr. Pramod Kumar Gupta (PG)
Mr. Sujay Gaikwad (SG)
Mr. Devavrat Tripathi (DT)

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 BS715: Principles and Practices of Mutation Breeding
Course Coordinator: Dr. Suvendu Mondal ([email protected])

Title Sub-Titles No. of Name of

Lecture Lecturer
Principles of Molecular basis of mutagenesis, Mechanism of mutation in dry 2 BKD
Mutation seed and wet tissue, Different types of mutagen (physical and
Breeding chemical) and their mode of action.
Types of mutations, Double stranded DNA break, Repair and 2 AJS
Associated mutations in plants.

Practices of Methodology & Screening techniques in mutation breeding, 2 JGM

Mutation Genetics of mutated traits, Stabilization of mutants in self and
Breeding cross pollinated crops.
Successful examples of mutation breeding for qualitative and 1 JGM
quantitative traits.

In vitro Principles of mutation breeding of vegetative propagated crops, 1 HT

mutagenesis methodology for in vitro mutagenesis, Dissociation of
chimeras and selection of mutants.
Methods for screening in vitro mutants, Artificial selection, 1 HT
Haploid mutagenesis. Somatic embryogenesis for mutant
induction.
Advanced Ion beam radiation mutagenesis, Electron beam and/or Proton 2 AMB
techniques of beam radiation mutagenesis, Space /Cosmic radiation, VCP
inducing Advantages/Disadvantages compared to gamma rays.
mutations in
plants
Molecular Techniques for mutation detection and screening (TILLING, 2 JS
techniques and Eco-TILLING, de-TILLING, HRM based TILLING,
methods for Transposon induced mutagenesis/insertional mutagenesis, Use
mutation of molecular marker techniques in mutation detection.
detection and Site directed mutagenesis in plants (CRISPR-CAS, ZFN, 1 AJS/SM
screening in TALEN etc.)
plants
Molecular characterization of mutants: Mut-Map, Mut-Map+ 1 SM
Molecular approaches to identify novel mutants in crop plants, 1 AB
Gene tagging of mutated traits using molecular markers.
Epigenetics Generation of epimutants, Mode of actions of epimutagens and 1 SM
their application, Methods of dissecting epigenetic behavior of
quantitative traits.
Statistical Handling the field data, analysis and interpretation. 1 AMB
analysis on Design of experiment for mutant germplasm, mutant lines and
mutant their derivatives.
population
Achievements Research experience of mutation breeding at BARC 1 JS
on Mutation
Breeding Research on mutation breeding at IAEA, Vienna and world 1 AMB
perspective.

Practicals Irradiation of seeds, Determination of LD50 dose/GR50 /GR30 BKD, JGM, SM, AB,
calculation, Analyzing dose-response curve, Calculation of JS, AJS, VJD, PGB,
mutation frequency. Comparative study of electron beam and PD, GV
gamma rays mutagenesis.
Field /Laboratory screening of mutants
In vitro mutagenesis experiments
Practical on TILLING, HRM and high throughput mutant
screening.
Practical on nondestructive techniques for screening of
mutants.

36
SJJ: Dr. S. Jambhulkar; JGM: Dr. J. Manjaya; AMB: Dr. Anand Badigannavar; BKD: Dr. B. K. Das; AJS: Dr.
Archana Joshi Saha; JS: Dr. J. Souframanien; SM: Dr. Suvendu Mondal; VCP: Dr. V.C. Petwal; AB: Dr.
Ashok Badigannavar; VJD: Dr. Vinod J. Dhole; HT: Dr. Himanshu Tak, PD: Shri P. Dhansekar; AS: Shri
Abhijit Shitre, PGB: Ms. Poonam G. Bhad; GV: Shri Gautam Vishwakarma

37