PH.D. Degree Course (Autonomous)

In Biochemistry

REGULATIONS, CURRICULAM AND SYLLABUS

AFTER REVISION 2017-2018

DEPARTMENT OF BIOCHEMISTRY

SCHOOL OF LIFE SCIENCES

BHARATHIDASAN UNIVERSITY

TIRUCHIRAPPALLI 620 024

Curriculum Structure

S.No. Course Name of the Course Credits

1 Course – I Research Methodology 4

2 Course II

(Any one)

1.Biochemistry of Signal Transduction and

Regulation

2.Molecular Endocrinology/Chromatin and

Epigenetics

3.Principles and Application of Molecular

Techniques

4.Advanced techniques in Lipid Biology

4

3 Course III

(Any One)

1.Cellular and Molecular Neuroscience

2.Neurogerontology

3.Nanotechnology

4.Nanoscience

5.Reproductive Biology

6.Neuroscience

7.RNAi Technology

8.MicroRNA Technology

9.Biochemical Aspects of Cancer

10.Lipid Metabolomics

11.Yeast Lipidology

12.Cancer Biology

4

Programme Outcomes

• Research Granduands of Science and Technology are well equipped with

Research & Development Competences expressive of their Creative

Knowledge, Inventive Skill, Resolute Attitude and Innovative Pursuits in their

chosen fields.

• Research Granduands are Seasoned to the demanding Research Environment and

explicitly Spirited enough to the occasion in their scientific/technological quests

with exemplary qualities of productive contribution to society, nation and world

in the arena of Science and Technology.

• Research Graduands are ready to espouse Leadership Responsibilities in their

chosen fields of Science and Technology with demonstrated perfection and

benchmark contribution.

• Research Graduants Collate information from a variety of sources and Enrich a coherent

understanding of the subject concerned pertaining to Novel investigation on the

problems in everyday life.

BCMPH01- RESEARCH METHODOLOGY

Unit I:

Research Methodology: Introduction: meaning of research; objectives of research; types

of research; research approaches; significances of research; Components of a research,

research methods; importance of knowing how research is done; Computer application in

scientific research: Finding scientific articles. Defining the research problem; What is the

research problem? Selecting the problem; Techniques involved in defining the problem;

Research design; Need for research Design; different types of research designs; basic

principles of experimental designs.year books, & monographs, journals, conference

proceedings, abstracting & indexing journals, index & References cards, internet,

magazines.

Unit II:

Data Collection: Primary and secondary Data collection. Sampling: Sampling and

Population, Techniques sampling selection, Characteristics of a good sample, Sampling

errors and how to reduce them. Techniques of Data Collection: Data schedule,

Observation, Opinionnaire, Questionnaire, Interview schedules, Bibliometrics,

Webometrics. Report writing; Preparation of manuscript- plan of the report, review of

literature & its use in designing a research work, designing of methodology,

interpretation of data & thesis layout.Scientificwriting.Characteristic of scientific writing,

essential features of an abstract, presentation of data, writing of results

&discussions.Bibliography, oral presentation; precautions for writing research reports;

conclusions.

Unit III:

Descriptive Statistics: Tabulation, organization and graphical representation of

quantitative data. Measures of central tendencies: Mean Median and Mode. Measures of

ariability: Range. Q.D; S.D; A.D; and Coefficient of Variation Measures of Relative

Position: Percentiles, Percentile Ranks, Standards Scores, Stanine Scores, T- Scores

Normal Probability Distribution, properties of normal curve, applications of normal

curve, Hypothesis testing: What is Hypothesis? Basic concepts concerning testing of

hypothesis; procedure for hypothesis testing; Probability; Markov models and Hidden

Markov Models; Probability distribution; Binomial; Poisson; Normal distribution and

Multiple testing Methods ANOVA; Test of significance-t-test; F-test.

Unit IV: Bioinformatics: Origin and overview of bioinformatics. Applications of

bioinformatics. Research in bioinformatics, Biological Databases: Literature databases,

Sequence databases, Structure databases, Structural classification databases, Metabolic

pathways database, Pattern and Motif searches: PROSITE, BLOCKS, PRINTS, PFAM.

Sequence alignment: Pairwise sequence alignment - Local and Global alignments.

Dotplot -Dynamic programming methods. Scoring or Substitution matrices - Database

searching -FASTA and BLAST searches - Multiple sequence alignment. ClustalW. T-

Coffee .Tools for Drug discovery / drug design

Unit V:

Genomics and Proteomics: Genome features of Prokaryote and Eukaryote. - Genome

projects: HGP, E.coli, A.thaliana and Human-Genomic variations (SNP). Genome

expression (Microarray). Comparative Genomics: MUMMER,Etc.

Proteomics: Protein sequence and structure characterization - Proteomics tools in Expasy

server. Primary Structure Prediction by Computing there pi, Secondary structure

prediction: GOR and Chou Fasman – Tertiary structure prediction: Homology modeling.

Ab initio Modelling, Protein Structure and Function Determination, Protein structure

visualization tools: RasMol and Swiss PDB Viewer, online Analyzing Tools.

UNIT VI:

Introduction to Presentation Tools- Features and functions, creating presentation,

master page, adding animation, customizing presentation, showing presentation, printing

handouts.

References:

1. Kothari. C.R. 2004 Research Methodology – Methods and Techniques,New Age

International(P)Ltd

2. E Balagurusamy.Programming in ANSI C Tata McGraw Hill

3. RandaL.Schwartz,tomphoenix,learningperl,third edition

4. Research Methodology . Methods &Techniques : Kothari, C.R.

5. Tests, Measurements and Research Methods in BehaviouralSciences . Singh, A.K.

6. Statistical Methods . Y.P. Aggarwal.

COURSE OUTCOME:

Understand and apply research approaches, techniques and strategies in the

appropriate manner for managerial decision making

Demonstrate knowledge and understanding of data analysis and interpretation

in relation to the research process

Develop necessary critical thinking skills in order to evaluate different research

approaches utilized in the service industries

Students will be able to describe basic approaches to qualitative research

Students will be able to identify and critiquearticles based on different research

methods

Students will be able to Write a research proposal suitable for submission to a

research funding body

Students will be able to Choose appropriate quantitative or qualitative method to

collect data.

Design an appropriate mixed-method research study to answer a health-related

research question

BCMPH3:1-YEAST LIPIDOLOGY

OBJECTIVES:

This course will cover basic concepts and technologies in membrane and lipid

biochemistry. The major objective will be to critically evaluate the current literature on

the biophysical properties, molecular architecture, bio-assembly, and various functions of

cellular membranes, as well as the mechanisms involved in the translocation of

membrane proteins and lipids from the sites of synthesis to their subcellular residence(s).

Selected topics on the structure, physical state, biosynthesis, assembly, and function of

membrane-associated molecules in transmembrane signaling and other cellular processes

will be discussed. The course will be primarily literature-based, using both assigned

reviews and original papers. The technical approaches and experimental strategies used in

studies that have contributed significantly to advancing the basic understanding of

important aspects of membrane biochemistry and membrane biology will be emphasized.

Unit 1

Lipids: The essential biomolecules-classification and its biological functions. –Recent

trends in lipid research- Yeast (Saccharomyces cerevisiae) as a model system for lipid

research- Lipid composition of yeast subcellular membranes. Comparison of yeast to

human genome system. Importance of yeast lipidomics in understanding regulation of

human diseases. Lipid as a biomarker.

Unit 2

Lipid Metabolism in Yeast - Biosynthesis and degradation of membrane phospholipids:

Phosphatidyl choline, phosphatidyl ethanolamine, phosphatidylinositol, phosphatidyl

serine, phosphatidyl glycerol and cardiolipin. Biosynthesis and catabolic pathways of

neutral lipids: Diacylglycerol, Triacyglycerol, sterol, steryl esters. Structure and

biosynthesis of Sphingolipids and glycosphingolipids.

Unit 3

Genetic and Biochemical mechanisms for the regulation of phospholipid synthesis-

inositol choline responsive elements, Transcription factors INO1, INO2 and OPI3.

Regulation by inositol and zinc, Regulation by CTP, Adenosine Homocysteine and S-

Adenosine Methionine (SAM) and transcriptional factors. Role of phosphaticacid

phosphatase (PAP) and diacylglycerol kinase (DAG) in the regulation of lipid

homeostasis. Relationship of phospholipid metabolism to phospholipid transport and

membrane trafficking.

Unit4

Lipid Droplets (LD): Structure and function of lipid droplets. Storage of neutral lipids in

lipid droplets. Role of Triacyglycerol and steryl esters in lipid droplet. Contributions of

Dga1p and Lro1p to Triacyglycerol synthesis, Are1p and Are2p sterol esterification. Role

and mechanism of lipid droplet proteins- Fat lipid dystrophy (FLD1), lipin (PAH1).

Mechanism of Lipid droplet degradation/lipolysis- Lipolytic enzymes-Lipid droplet

hydrolase (LDH1), Triacylgycerol lipases1 (TGL1, 2, 3, 4, and 5), Serine ester hydrolases

(YEH1, 2)

Unit 5

Systems biology of lipid metabolism: Application and function of yeast based data bases

and software - High-throughput screening in lipids:Saccharomyces Genome Database

(SGD, http://www.yeastgenome.org),YEASTRACT(Yeast Search for Transcriptional

Regulators and Consensus Tracking), NCBI-BLAST, Multiple sequence alignment-

Clustal W, JAVA Shade, Praline. Tools for predicting hydrophobicity - TMpred,

Phobius, SOSUI,TMHMM, Top Pred 2.0, HM-MTOP.

Unit 6

Recent updates and technologies involved in yeast lipidology.

COURSE OUTCOME:

1. Yeast and humans share a significant fraction of their functional pathways

that control key aspects of eukaryotic cell biology, including the cell

cycle, metabolism , programmed cell death], protein folding, quality

control and degradation, vesicular transport, and many key signaling

pathways, such as mitogen-activated protein kinase (MAPK) , target of

rapamycin (TOR) [34], and insulin/IGF-I signaling pathways. So study

about basic model is favoured by the course.

2. Lipidology is the scientific study of lipids. Compared to other biomedical

fields, lipidology was originally less popular since the constant handling

of oils, smears, and greases was unappealing and separation was difficult.

But the field is popular after chromatographic studies.

3. The course favours familiarity of lipid metabolism in yeast model.

4. It helps to understand biochemistry of lipids better and thus annotating

genomes, but also understanding genetic polymorphisms and the post

genetic effects induced by drugs,food and toxins. It helps ro know how

to identify and quantify thousands of cellular lipid molecular species and

their interactions with other lipids, proteins and other metabolites in yeast

model.

5. Complement course which gave huge progress in genomics and

proteomics and constitute the family of system biology with reference to

yeast.

6. Spatial and temporal alterations in the content and composition of

different lipid molecular species is acquired.

7. To completely understand the major biomolecule lipid and to analyse its

role, basic knowledge is bestowed.

8. Understanding in content which is particularly relevant to human diseases

and the role of lipids in various physiological processes, pathology, and

disease.

BCPHD104-ADVANCED TECHNIQUES IN LIPID BIOLOGY

OBJECTIVES:

This course will cover basic concepts and technologies in membrane and lipid

biochemistry. The major objective will be to critically evaluate the current literature on

the biophysical properties, molecular architecture, bio-assembly, and various functions of

cellular membranes, as well as the mechanisms involved in the translocation of

membrane proteins and lipids from the sites of synthesis to their subcellular residence(s).

Selected topics on the structure, physical state, biosynthesis, assembly, and function of

membrane-associated molecules in transmembrane signaling and other cellular processes

will be discussed. The course will be primarily literature-based, using both assigned

reviews and original papers. The technical approaches and experimental strategies used in

studies that have contributed significantly to advancing the basic understanding of

important aspects of membrane biochemistry and membrane biology will be emphasized.

Unit 1

Chromatographic techniques in lipids: Chromatography principle, instrumentation and

application of Thin layer chromatography (TLC), TLC blotting: application to microscale

analysis of lipids and as a new approach to lipid-protein interaction. Hydrophilic

interaction

Liquid Chromatography (HILC), High performance thin layer chromatography (HPTLC),

High performance liquid chromatography (HPLC), Reverse phase high performance

liquid chromatography (RPHLC) and Column chromatography, Ion exchange and spin

column chromatography , Gas chromatography-Applications of chromatography in

analyzing fatty acid profiles.

Unit 2

Principle, instrumentation and application of UV, visible spectrophotometry and

spectroflourimetry. Basic principle and application of mass spectra, Quantification of

lipids by Electrospray ionization mass spectrometry (ESI-MS), and Fourier transformer

mass spectrometry (FT MS).Matrix-assisted laser desorption/ionization-time of flight

mass spectrometry (MALDI-TOF MS). Application of various spectrometries in

analyzing and characterizing lipids and proteins.

Unit 3

Centrifugation - Preparative and Analytical centrifugation, Sub cellular

fractionation. Determination of relative molecular mass– sedimentation velocity and

sedimentation equilibrium. Application of centrifugation in characterizing lipid related

proteins. Units of radio activity. Detection and measurement of radio activity and their

half life. Types of scintillation counting (Solid and liquid), quenching and quench

correction, scintillation cocktails and sample preparation, Cerenkov counting.

Application of radio isotopes in lipid biology. Autoradiography. Radiation hazards,

radiation dosimetry.

Unit 4

Fluorescence studies of lipids - Fluorescence based analysis of distribution of

lipids in membranes and sub cellular organelles. Bimolecular fluorescence

Complementation analysis. Application of Green fluorescent protein (GFP) and Red

fluorescent protein (RFP) tagging in cellular localization. Application of fluorescent dyes

to differentiate subcellular organelles and storage of neutral lipids and phospholipids-

Filipin, Oil red O, Nile Red, Rhodamine B, BODIPY, DAPI and Annexin VStaining.

Unit 5

Microscopical studies in lipid research- fluorescence microcopy, confocal

microcopy,Transmission electron microscopy (TEM),scanning electron

microscope (SEM), Stimulated emission depletion (STED) microscopy, coherent anti-

Stokes Raman (CARS) Microscopy, Cryo-electron microscopy, BF-Bright field and DIC-

Different interference contrast. Image acquisition and analysis softwares in various

microscopical techniques. Applications and importance of fluorescence microscopy in

lipid droplet studies.

Unit 6

Recent updates and technologies involved in yeast lipidology.

COURSE OUTCOME:

1. Yeast and humans share a significant fraction of their functional pathways

that control key aspects of eukaryotic cell biology, including the cell

cycle, metabolism , programmed cell death], protein folding, quality

control and degradation, vesicular transport, and many key signaling

pathways, such as mitogen-activated protein kinase (MAPK) , target of

rapamycin (TOR) [34], and insulin/IGF-I signaling pathways. So study

about basic model is favoured by the course.

2. Lipidology is the scientific study of lipids. Compared to other biomedical

fields, lipidology was originally less popular since the constant handling

of oils, smears, and greases was unappealing and separation was difficult.

But the field is popular after chromatographic studies.

3. The course favours familiarity of lipid metabolism in yeast model.

4. It helps to understand biochemistry of lipids better and thus annotating

genomes, but also understanding genetic polymorphisms and the post

genetic effects induced by drugs,food and toxins. It helps ro know how

to identify and quantify thousands of cellular lipid molecular species and

their interactions with other lipids, proteins and other metabolites in yeast

model.

5. Complement course which gave huge progress in genomics and

proteomics and constitute the family of system biology with reference to

yeast.

6. Spatial and temporal alterations in the content and composition of

different lipid molecular species is acquired.

7. To completely understand the major biomolecule lipid and to analyse its

role, basic knowledge is bestowed.

8. Understanding in content which is particularly relevant to human diseases

and the role of lipids in various physiological processes, pathology, and

disease.

(BCPHD103)-CELL SIGNALLING

Objectives

i. Helps to distinguish the key principles of biochemical metabolic concepts

ii. Students will learn the signalling pathways that will help them in further

studies.

iii. Students grasp the basic need of the signalling molecules and the

consequesnce on their absence.

iv. Students will be exposed to most of the actions of the biological system,which

they will study in depth with signalling molecules.

v. Students can able to understand the function of specific anabolic and catabolic

pathways and how these pathways are controlled and interrelated

Unit I:

Regulation of transcription and translation in prokaryotes: Positive and negative control,

repressor and inducer, concept of operon, lac-, andtrpoperons, attenuation, regulons.

Regulation in eukaryotes- gene families, regulatory strategies in eukaryotes, gene

alteration, regulation of synthesis of primary transcripts, hormonal control, transcription

factors, transcription factors: targets of signaling pathways, DNA binding motifs in pro-

and eukaryotes Helix turn, helix, zinc fingers, leucine zippers/ b zip, helix loop helix

motifs. Regulation at the level of translation in prokaryotes and eukaryotes.

Unit II:

Signal transduction: definition, signals, ligands and receptors. Endocrine, paracrine and

autocrinesignaling. Sensory Transduction : Nerve impulse transmission – Nerve cells,

synapses, reflex arc structure, Resting membrane potential, Nernst equation, action

potential, voltage gated ion-channels, impulse transmission, neurotransmitters,

neurotransmitter receptors. Rod and cone cells in the retina, biochemical changes in the

visual cycle, photochemical reaction and regulation of rhodopsin. Odor receptors.

Chemistry of muscle contraction – actin and myosin filaments, theories involved in

muscle contraction, mechanism of muscle contraction, energy sources for muscle

contraction.

Unit III:

Receptors and signaling pathways: cell signaling, cell surface receptors. G Protein

coupled receptors- structure, mechanism of signal transmission, regulatory GTPases,

heterotrimeric G proteins and effector molecules of G Proteins. Signaling molecules-

cAMP, cGMP, metabolic pathways for the formation of inositol triphosphate from

phosphatidyl inositol diphosphate, Ca2+, DAG and NO as signaling molecules, ryanodine

and other Ca2+ receptors, phosphoregulation of inositol and the calcium channel

activation. Ser/Thr-specific protein kinases and phosphatases.Receptor tyrosine kinases,

Role of phosphotyrosine in SH2 domain binding. Signal transmission via Ras proteins

and MAP kinase pathways.

Unit IV:

Signaling by nuclear receptors: ligands, structure and functions of nuclear receptors,

nuclear functions for hormones/metabolites - orphan receptors; cytoplasmic functions and

crosstalk with signaling molecules, signaling pathway of the steroid hormone

receptors.Cytokine receptors- structure and activation of cytokine receptors, Jak-Stat path

way, Janus kinases, Stat proteins.

Unit V:

Regulation of the cell cycle: Overview of the cell cycle, cell cycle control mechanisms,

Cyclin-dependent protein kinases (CDKs), regulation of cell cycle by proteolysis, G1/S

Phase transition, G2/M Phase transition, cell cycle control of DNA replication, DNA

damage check points. Cancer, types of cancer, factors causing cancer-physical, chemical

and biological agents. Errors in function of signal proteins and tumerogenesis.Oncogenes,

proto-oncogenes and tumor suppressor genes.Tumor suppressor protein p53 and its role

in tumor suppression.Tumor suppressor APC and Wnt/ -Catenin signaling.

Unit VI:

Signal transduction in Health and Disease: Cancer, Neurodegeneration, Diabetes and

Obesity and Inflammation

Recommended Books:

1) Molecular biology- David Freifelder, Narosa Publishing House Pvt.

Limited, 2005

2) Biochemistry of Signal Transduction and Regulation. 3rd Edition. Gerhard

Krauss, 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 3-

527-30591-2

3) Molecular Biology of the Cell, 4th edition, Bruce Alberts. New

York: Garland Science; 2002. ISBN-10: 0-8153-3218-1ISBN-10: 0-8153-4072-9

4) Molecular Cell Biology, 4th edition, Harvey Lodish.New York: W. H.

Freeman; 2000. ISBN-10: 0-7167-3136-3

5) Principles of cell and molecular biology- Lewis Kleinsmith, 2nd edition,

illustrated, HarperCollins, 1995.

COURSE OUTCOME:

1. Help understand the key principles of biochemical metabolic concepts

2. Students will learn the signalling pathways that will help them in further studies.

3. Students learn the basic need of the signalling molecules and the consequesnce on

their absence.

4. Students will be exposed to most of the actions of the biological system,which they

will study in depth with signalling molecules.

5. Students can able to understand the function of specific anabolic and catabolic

pathways and how these pathways are controlled and interrelated

6. How current research has provided us with an understanding of the molecular basis

of the control of metabolism

7. "How to communicate scientific information effectively in writing Hypothesis-

based experimental design"

8. The course aims to give participants a basic knowledge of mechanisms of signal

transduction and the significance of signal transduction in physiology and

pathophysiology.

BCMPH02-PRINCIPLES AND APPLICATIONS OF MOLECULAR

TECHNIQUES

Objectives:

1. To understand basic principles of molecular techniques.

2. It deals with protein – protein interaction and extraction.

3. It imparts the knowledge of genome size and its current state.

4. To explain modern techniques to investigate interactions between

macromolecules (DNA, RNA and proteins).

UNIT I:

Protein separation, Protein identification, Protein quantification, Protein sequence

analysis, Structural proteomics, Interaction proteomics, Protein modification, and

Cellular proteomics. Sample handling and storage: Preparation of Sample, Subcellular

fractionation, Density gradients, Affinity, Protein fractionation, Ultrafiltration.

Purification: Removal of interfering compounds, Salts, DNA, lipids, Protein

solubilisation, Disulfide bonds, chaotropes, detergents, etc. Detection and quantitation:

Chemical tagging, fluorescence, negative staining, Radio-labelling.

UNIT II:

Protein Expression system: transfection, transformation, transduction, induction,

detection and purification of expressed transgenes. Protein/peptide chemical Synthesis:

Biotinylated product, Antibody Production & Engineering Protein Interactome:

Methodology for detection, protein-protein interactions. Protein Arrays: protein

polynucleotide, interactions with other Biomolecules, Signalling Complex, Liposome,

reconstitution of membrane protein in lipid vesicles.

UNIT III:

X-ray crystallography and nuclear magnetic resonance - Tandem mass

spectrometry combined with reverse phase chromatography or 2-D electrophoresis -

Affinity chromatography – fluorescence resonance energy transfer (FRET), Surface

Plasmon Resonance (SPR) - X-ray Tomography. Proteome analysis:Algorithms for

proteomics, Protein expression profiling, protein arrays, Protein microarrays. Advantages

and disadvantages of DNA and protein microarrays.

UNIT IV:

Genome size: Number of genes, gene related sequences, organellar DNA.

Experimental techniques for gene location: Hybridization tests to tests to determine

expressed sequences, cDNA sequencing, and mapping of ends of transcripts, location of

exon-intron boundaries. Gene inactivation and functional analysis, gene over expression

and assessment of function. Reporter genes and immunocytochemistry in locating gene

expression in cells and tissues. Comparative genomics in the study of human disease

genes. Current state of the human genetic map.

UNIT V:

Physical, Chemical and biological properties of Free Radicals. Types of Free

Radicals, Biological sources of Free Radicals. Anti oxidants – Enzymatic and non-

enzymatic antioxidants, Mechanism of Free Radicals scavenging by antioxidants.

Balance and imbalance between Free Radicals and Antioxidants. Free Radicals induced

Macromolecular damage. Free Radicals in Oxidative Stress and diseases (Cancer,

Myocardial Infarction, Neurological disorders, Diabetes Mellitus). Free Radicals and

Apoptosis. Methods for the determination of Free Radicals, Antioxidants and Free

Radical mediated damaged products by Spectrophotometry, Spectroflourymetry, HPLC,

EPR Spectroscopy and by various staining methods.

UNIT VI:

Molecular Techniques for diagnosis - PCR- RFLP, ARMS-PCR, ELISA,

Multiplex-PCR, SSCP, CSGE, DGGE, DHPLC, MALDI-TOF and DNA Sequencing.

Reference:

1. Twyman, R. M. Principles of proteomics. BIOS Scientific Publishers, New York.

2004.

2. Liebler, D. C. Introduction to Proteomics: Tools for the New Biology. Humana

Press, Totowa, NJ. 2002.

3. Westermeier, R. and T. Naven. Proteomics in Practice: A Laboratory Manual of

Proteome

4. Analysis. Weinheim: Wiley-VCH, 2002.

5. Cantor & Smith, 1999, Genomics, John-Willey & Sons.

6. T.A. Brown, 1999, Genomes, John-Willey & Sons.

7. R. Durbin, S. Eddy, A. Krogh, G. Mitchison, 1998, Biological sequences analysis.

8. P. Clote, R. Backofen, 2000, Computational Molecular Biology. Wiley, West

Sussex.

9. M.J. Bishop, 1999, Genetic Database, Academic press, London.

10. Andreas M. Papas, 1999, Antioxidant Status, Diet, Nutrition and Health, CRC

Press, London.

11. Molecular Diagnostics for the Clinical Laboratorian, 2nd ed.; William B.

Coleman and Gregory J. Tsongalis, (Eds.); Humana Press 2005 ISBN:

1588293564.

12. http://www.justmed.eu/files/MolecularDiagnosticsFundamentalsMethodsandClini

calApplications.pdf.

COURSE OUTCOME

1. This course is to discipline to student’s knowledge of main engines of

implementation and transmission of a genetic material at molecular and cellular

levels.

2. The methods of change of a genetic material and constructing of transgene

organisms with the given properties.

3. Students can be understood Know the natural function of restriction

endonucleases and how a normal bacterial cell protects its DNA from their

activity.

4. Understand the value of and the processes involved with the polymerase chain

reaction (PCR).

5. To understand the function of creative use of modern tools and techniques for

manipulation and analysis of genomic sequences.

6. This technique can use to train students in strategizing research methodologies

employing genetic engineering techniques.

7. Understand the similarities and differences between how genetic information is

passed on in eukaryotes and prokaryotes.

8. Students can observe the Identify the fundamental differences between genetically

engineered crops and non-genetically engineered crops.

BCPHD102- NEUROGERONTOLOGY

Objectives:

To introduce basic concepts about the organization, structure, and function of the

human central nervous system; To enable students to apply these fundamental principles

toward understanding nervous system function and dysfunction and toward clinical

problem-solving in relation to disorders that affect the nervous system, with emphasis on

the central nervous system.

Unit I:

Gerontology: Define Aging, factors that favor aging process (role of free radicals, calorie

restriction and aging genes); theories of aging; neurobiology of aging.

Unit II:

Neuron Anatomy: Gross anatomy of human and rat Brain: - Function of spinal cord,

meninges, cerebrum, cerebellum, hippocampus and thalamus; sympathetic and

parasympathetic nervous system location, distribution and function; functional

organization of motor system; CSF- formation, circulation, absorption and functions.

Classification of neurons; structure and function of dendrites, axons, glial cells,

astrocytes, oligodendrocytes, schwann cells and microglial cells.

Unit III:

Synaptogenesis: Synaptic transmission- properties of chemical and electrical synapses;

calcium hypothesis: control of transmitter release; synthesis and trafficking of neuronal

proteins. Synaptic transmission at nerve-muscle synapses and central synapses; Ligand

gated channels; second messengers and synaptic transmission; short term and long term

synaptic plasticity.

Unit IV:

Neurotransmitters and its function: Definitions, classification and functions of

Neurotransmitter, neurohormones& neuromodulators; Role of nitric oxide, neuroactive

peptides, opiate peptides and brain gut peptide.

Role of acetylcholine in neuromuscular transmission; end plate potential; nicotinic and

muscarinic acetylcholine receptors and their classification; structure, agonist and

antagonists of acetylcholine. Clinical Neurochemistry- Anti-ChE agents and their

classifications; cholinergic projections in the brain; cholinergic neurons and Alzheimer’s

disease.

Unit: V

Learning, Memory and Cognition: Learning, Memory and Cognition, Methods in

neurobiology research, tools and techniques in neurobiology (EEG, CT, MRI, PET,

SPECT); introduction and organization of sleep and wakefulness, slow wave sleep factor,

learning and memory, REM sleep physiology and relevant brain anatomy-orexin,

narcolepsy and control of sleep and wakefullness.

Unit: VI

Neurodegenetrative disorders: Definitions - Multiple sclerosis, Parkinson’s disease,

Huntington’s disease, amyloidosis, multiple myeloma, tauopathy, amyotrophic lateral

sclerosis, Pick’s disease, neuroblastoma, cerebral amyloid angiopathy, mild cognitive

impairment.

Biochemistry of Alzheimer’s disease(AD): What is Alzheimer’s disease? Causes, signs,

symptoms and biomarkers of AD; amyloid precursor protein and its processing, structure

of APP, alpha, beta and gamma secretases (localization, biological function and mode of

action); beta-amyloid plaques; tau phosphorylation and neurofibrillary tangles; β-amyloid

degrading enzymes.

References:

1. Neurobiology – From molecular basis to disease Volume (1&2) by ROBERT A.

MEYERS

2. Medical Physiology – GUYTON

3. Medical Physiology – BROWN

4. Human physiology - Vander Sherman Lucia

COURSE OUTCOME

1. Neurogerontology tells the story of how the aging brain affects all aspects of

cognition and physical performance.

2. It comprehensively links the principles and substance of neuroscience with

gerontology and psychology.

3. Neurogerontology explores the functional relationships between the central

nervous system and psychological phenomena of aging, including perception,

arousal, learning, cognition, and motor behavior.

4. Understand how the interaction of cells and neural circuits leads to higher level

activities such as cognition and behavior

5. The course helps to understand the degenerative disorders like Alzheimers,

Parkinson's and Huntington's etc.,

6. Relate the properties of individual cells to their function in organized neural

circuits and systems

7. Understand the properties of cells that make up the nervous system including the

propagation of electrical signals used for cellular communication

8. Neuroscience is the scientific study of the brain and nervous system, whose

ultimate goal is to understand higher brain function at a variety of levels.

BCPHD102:1- CONCEPTS IN NEUROCHEMISTRY

Objectives:

To introduce basic concepts about the organization, structure, and function of the

human central nervous system; To enable students to apply these fundamental principles

toward understanding nervous system function and dysfunction and toward clinical

problem-solving in relation to disorders that affect the nervous system, with emphasis on

the central nervous system.

PRE-REQUISITE:

Neuroscience is a stand-alone course but it is expected that students have a basic

understanding of human anatomy and physiology and the basic vocabulary of the

anatomical sciences.

Unit-I

CNS Overview: Introduction to the Brain; Overview of brain systems and general

principles of their functional organization: From cortical maps and subcortical loops to

the micro-structure of brain circuits and their interconnections. CNS Organization; CNS

Topography; Neuroembryology. VASCULATURE: Metabolism, Cerebral blood flow,

CSF; Blood Supply; Stroke.

Unit-II

CELL BIOLOGY OF NEURONS AND GLIA: Nucleus and gene expression and

regulation, Protein synthesis & translational control (including RNAi), Protein sorting &

trafficking (signal peptides, Golgi, secretory and endocytic pathways), Cytoskeleton &

transport (cytoskeleton, actin, microtubules, intermediate filaments, dendritic and axonal

localization/transport, motors and adaptor), Signaling Pathways. Mitochondria, energy

homeostasis and free radicals/energy metabolism in the neuron, Overview of glial cell

biology & myelination (types of glia, morphology and function, myelination in CNS and

PNS).

Unit-III

ELECTRICAL PROPERTIES OF NEURONS: Overview of membrane structure &

membrane transport, membrane potential, Ion channels and Ion Channel activity

(electrochemical gradient), Action potentials, Propagation of action potentials along

axons, Modulating action potential, Electrophysiological techniques for studying action

potentials and ion channels.

Unit-IV

SYNAPTIC TRANSMISSION: Overview of synaptic communication/structure of the

synapse, Neural Signaling: -Neurotransmitters; Action potentials: - Resting potential;

Excitatory; Inhibitory; Threshold; Depolarization; Hyperpolarization; Synapse:

Formation; Synaptic communication; Neural circuits, synaptic plasticity: LTP/LTD,

Spike Time dependent plasticity. Mechanism of neurotransmitter release, postsynaptic

response: electronic properties of dendrites, basic integration, Ionotropic (v) metabotropic

receptors, Neurochemical transmission: Glutamate, GABA, Glycine, Acetylcholine

(Synthesis, storage, release and inactivation), Dopamine, Norepinephrine, epinephrine,

serotonin, histamine, Neuropeptides & atypical neurotransmitters, Electrical synapses

(gap junctions).

Unit-V

DEVELOPMENT & PLASTICITY: Overview of nervous system development/

comparative embryology, Neural induction, Regionalization, Neurogenesis & migration,

Mechanisms of axon guidance & target cell recognition, Synapse formation &

elimination, Neuronal Death.

Unit-VI

TRUAMA AND DISEASE: Development disorders; Degenerative disorders;

Psychiatric disorders; Injury disorders; Others like Epilepsy; Visual Pathways; Occular

Movements; Vascular syndromes; Sensory and Motor Syndromes.

TEXTBOOK

1. J. W. Baynes, M. H. Dominiczak, Medical Biochemistry, 2nd ed., Elsevier

Mosby, Philadelphia, New York, Toronto, 2005.

2. G. Siegel, R.W. Albess, S. Brady, D. Price, Basic Neurochemistry, 7th Edition,

Amsterdam. Tokio, 2006.

3. George J Siegel, MD, Editor-in-Chief, Bernard W Agranoff, MD, R Wayne

Albers, PhD, Stephen K Fisher, PhD, and Michael D Uhler, PhD. Basic

Neurochemistry, 6th edition Philadelphia: Lippincott-Raven; 1999.

4. Dale purves , George j. Augustine, David fitzpatrick , William c. Hall, Anthony-

samuellamantia , James o. Mcnamara , S. Mark williams. Neurosciencethird

edition Publishers Sunderland, Massachusetts U.S.A, 2004.

5. Siegel, George and R. Wayne Albers, Scott Brady and Donald Price Basic

Neurochemistry, 7th edition: Molecular, Cellular and Medical Aspects Academic

Press/2005.

6. Haines, Duane Neuroanatomy - An Atlas of Structures, Sections and Systems, 5th

edition Lippincott Williams and Wilkins/2000.

REFERENCE BOOKS

1. Afifi and Bergman, Functional Neuroanatomy, Text and Atlas, McGrawHill, 2nd

Edition, 2005.

2. Haines, Neuroanatomy: An Atlas of Structures, Sections and Systems, 7th ed. Ed.

Lippincott William and Wilkins, 2007.

3. Blumenfeld, Neuroanatomy Through Clinical Cases (Paperback), Sinauer

Associates; 2nd edition (2010).

COURSE OUTCOME:

1. Neurochemistry is the scientific study of the chemical interactions of the

brain and nervous system.

2. Ultimate goal is to understand higher brain function at a variety of levels.

3. Understand the properties of cells that make up the nervous system

including the propagation of electrical signals used for cellular

communication.

4. Relate the properties of individual cells to their function in organized

neural circuits and systems.

5. Understand how the interaction of cells and neural circuits leads to higher

level activities such as cognition and behaviour.

6. An understanding of the influence of family, community, and society in

the care of people with neurological disorder.Evaluate and discuss primary

research literature and evaluate the validity of hypotheses generated by

others.

7. This course is providing you with the requisite skills to effectively

communicate scientific and medical information to diverse audiences.

8. Understanding pathophysiology, work-up, and treatments for Disease

Specific Knowledge.

(17ASPHD20)-CELLULAR AND MOLECULAR NEUROSCIENCE

Objectives:

To understand the basics of development of brain and neuronatomy

Molecular mechanism of neural plasticity

Regenerative neuroscience and neurological disease

Unit I: Brain development and Neuroanotomy: Brain development, neural tube

patterning, neuroanatomy,organization of nervous system- concept of CNS, ANS and

PNS, Types- structural classification of neurons and glial cells.

Unit II: Neuronal communications: Synapses, Action potential, ion channels, Synaptic

integration- Types of synapsis,. Neurotransmitters- Types: Acetylcholine/ Cholinergic

pathways, Biological amine- Amine acid- ATP & Adenosine- Neuropeptides- Serotonin

and Histamine - biosynthesis and metabolism.

Unit III: Neural plasticity and memory: Concepts and theories in memory

machineries- Fractionation- Classification of memory- Explicit & implicit memory-

modulation of brain circuits- Molecular mechanism of memory formation- Stress and

emotions in memory impairments associated with aging. Cognition- Genetic aspects-

animal models. Imprinting- Organizational theory- heredity- Based on the environment-

genetic view- impact of hormones- Maternal program- Impact of environment of

cognition.

Unit IV: Neurological disease: Introduction to neurodegenerative disease- neurological

disorders- neuromuscular disorders- Prion disease, Ataxias, Huntington’s disease-

Alzheimer’s disease and Parkinson’s disease, stroke, epilepsy, cerebral malaria,

meningitis and multiple sclerosis.

Unit V:Adult Neurogenesis: Neurogenesis- history and neural stem cell niches,

regulation of neurogenesis, functional implication of adult neurogenesis, neural stem cell

transplantation, fate mapping of neural stem cells.

Techniques: Brain imaging-MRI, fMRI, CT scan, Live Imaging techniques. EEG,

neuronal cell culture, Cryosections, Histology, Immunohistochemistry, RT-PCR, Gene

and protein arrays, Confocal imaging, stereology microscope, FACS, Gel

Electrophoresis, Western blot, ELISA, Stereotaxic Patch-clamp, Rotorad, Morris water

Maze, Y and radaial arm-Mazes and elevated plus maze.

Unit VI: basics and principle of confocal, 2 photon microscopes and FACS for cell fate

analysis using online based books and PubMed articles

Course outcome

Students have improved their knowledge on Brain development, neuro anatomy,

Synapses, Action potential, Neural plasticity, Cognition, Neurological diseases,

Ataxia, Neural Stem cells, Adult neurogenesis and Brain imaging techniques

Reference:

1. Eric Kandel, James Schwartz and Thomas Jessell. Principels of neural science, c

Graw Hill Publication

2. Peter S. Haeper and Max Perutz. Neurodegerative diseases; Molecular aspects,

Oxford University press.

3. Dale Purves- Principles of cognitive neuroscience (2007)

4. Neural Plasticity and memory- Federico Bermudez- Rattoni (2007)

5. Matt Carter Jennifer C. Shieh. Guide to Research Techniques in Neuroscience.

Academic Press is an Imprint of Elsevier (2010)

6. https://nba.uth.tmc.edu/neuroscience/

7. https://www.coursera.org/courses?languages=en&query=neuroscience

8. https://en.wikipedia.org/wiki/Neuroscience

BCPHD01-Molecular Endocrinology

Objectives:

The objectives of this course are to introduce the basic principles, organs and

systems in mammalian (human) endocrinology. Students will be able to identify the

organs involved in endocrine function, will know the major hormones that are produced

by these organs and will know the physiological effect of these hormones. In addition,

students will be introduced to the molecular mechanisms of action of many of these

mediators and will start to appreciate biochemical and signaling events at the cellular and

whole animal level. An understanding of appropriate key human endocrine disorders will

also be discussed.

Unit -I

Introduction to hormones, Definition and classification.Mechanism of action of hormones

and its regulation.Hypothalamic and pituitary hormones- Anterior pituitary hormones:

biological actions regulation and disorders of growth hormones. Posterior pituitary

hormones – biological actions and regulation of vasopressin.Diabetes insipidus and Hypo

and Hyper pituitarism.

Unit II

Thyroid hormones –transport, metabolic fate and biological actions.Hypo and Hyper

thyroidism.Hormonal regulation of calcium and phosphate metabolism.Secrection and

biological actions of PTH, Calcitonin.Hypo and hyper calcemia.Adrenal cortical

hormones.regulation, transport, and biological effects. Adrenal medullary hormones –

secretion, regulation, and biological effects of catecholamines.

Unit III

Gonadal hormones: Regulation, transport and biological actions of androgens.

Regulation, metabolism and biological effects of osterogen and progesterone - menstrual

cycle- Pregnancy.Pancreatic hormones – synthesis, regulation, transport, and biological

actions mechanism of Glucagons, somatostatin and insulin.Introduction and biological

action of gastrointestinal hormones.

Unit IV

Signal transduction – Hormone – receptor interactions, biochemistry of receptor

activation. Signal transduction through cytoplasmic and nuclear receptors.Endocrine,

paracrine and autocrine signaling. Sensory Transduction: Nerve cells, synapses, ion

channels, neurotransmitters, neurotransmitter receptors and impulse transmission.

Receptors and signaling pathways – cell surface receptors: G-protein coupled receptors,

receptor kinases (tyr, ser/thr).

Unit V

Second messengers – cyclic nucleotides, role of cGMP in visual transduction, cAMP and

CREB.Involvement of protein-protein interaction in signaling pathways.Metabolic

pathways for the formation of Inositol triphosphate from phosphatidyl inositol

diphosphate, formation of DAG, Ca2+ channel activation, phosphoregulation of inositol,

activation and translocation of protein kinase C in cell membrane. The Ras-raf MAP

kinase cascade.Crosstalk in signaling pathways.

Unit VI:

Signal transduction in Health and Disease: Cancer, Neurodegeneration, Diabetes and

Obesity and Inflammation

References:

1. Harper’s Biochemistry – 24th

Edition.

2. Metabolic regulation – A Molecular Approach.

3. Text Book of Endocrinology – R.M Williams.

4. Williams Textbook of Endocrinology – Wilson and Foster 8th ed.

5. Mechanisms of hormone action – Autind and Short.

6. Stryer, L. Biochemistry. W. H. Freeman & Co.

7. Voet, D. and Voet, J.G., Biochemistry, John Wiley & Sons.

8. Lehninger, Principles of Biochemistry, Kalyani Publishers.

9. Thomas M. Devlin. Biochemistry with Clinical Correlations.

10. Helmrich, Biochemistry of cell signaling, Oxford Univ. Press.

11. Gomperts, Signal transduction.

COURSE OUTCOME:

1. To introduce the basic principles, organs and systems in mammalian

(human) endocrinology

2. To identify the organs involved in endocrine function

3. To know the major hormones that are produced by endocrine organs and

will know the physiological effect of these hormones

4. To introduce the molecular mechanisms of action of many of these

mediators and will start to appreciate biochemical and signaling events at

the cellular and whole animal level.

5. The underlying pathologies of important endocrine diseases will be

discussed.

6. The module will provide a basic understanding of the molecular

mechanisms of hormone action and will include a description of the main

hormone receptors and their signal transduction pathways.

7. The subject helps in understanding the insights on endocrine disrupters.

8. The synergestic activity of the endocrine organs can be explored.

BC 201 - BIOCHEMISTRY OF SIGNAL TRANSDUCTION AND REGULATION

Objectives

vi. Helps to distinguish the key principles of biochemical metabolic concepts

vii. Students will learn the signaling pathways that will help them in further

studies.

viii. Students grasp the basic need of the signaling molecules and the consequence

on their absence.

ix. Students will be exposed to most of the actions of the biological system,

which they will study in depth with signaling molecules.

x. Students can able to understand the function of specific anabolic and catabolic

pathways and how these pathways are controlled and interrelated

Unit - I

Regulation of transcription and translation in prokaryotes:Positive and negative

control, repressor and inducer, concept of operon, lac-, and trp operons, attenuation,

regulons. Regulation in eukaryotes- gene families, regulatory strategies in eukaryotes,

gene alteration, regulation of synthesis of primary transcripts, hormonal control,

transcription factors, transcription factors: targets of signaling pathways, DNA binding

motifs in pro- and eukaryotes, Helix turn, helix, zinc fingers, leucine zippers/ b zip, helix

loop helix motifs. Regulation at the level of translation in prokaryotes and eukaryotes.

Unit- II

Signal transduction: definition, signals, ligands and receptors. Endocrine, paracrine and

autocrine signaling. Sensory Transduction : Nerve impulse transmission – Nerve cells,

synapses, reflex arc structure, Resting membrane potential, action potential, voltage gated

ion-channels, impulse transmission, neurotransmitters, neurotransmitter receptors. Rod

and cone cells in the retina, biochemical changes in the visual cycle, photochemical

reaction and regulation of rhodopsin. Odor receptors. Chemistry of muscle contraction –

actin and myosin filaments, theories involved in muscle contraction, mechanism of

muscle contraction, energy sources for muscle contraction.

Unit - III

Receptors and signaling pathways: cell signaling, cell surface receptors. G Protein

coupled receptors- structure, mechanism of signal transmission, regulatory GTPases,

heterotrimeric G proteins and effector molecules of G Proteins. Receptor tyrosine

kinases, Role of phosphotyrosine in SH2 domain binding. Signal transmission via Ras

proteins and MAP kinase pathways. Signaling molecules- cAMP, cGMP, metabolic

pathways for the formation of inositol triphosphate from phosphatidyl inositol

diphosphate, Ca2+, DAG and NO as signaling molecules, ryanodine and other Ca2+

receptors, phosphoregulation of inositol and the calcium channel activation. Ser/Thr-

specific protein kinases and phosphatases.

Unit - IV

Signaling by nuclear receptors:ligands, structure and functions of nuclear receptors,

nuclear functions for hormones/metabolites - orphan receptors; cytoplasmic functions and

crosstalk with signaling molecules, signaling pathway of the steroid hormone receptors.

Cytokine receptors- structure and activation of cytokine receptors, Jak-Stat path way,

Janus kinases, Stat proteins.

Unit - V

Regulation of the cell cycle: Overview of the cell cycle, cell cycle control mechanisms,

Cyclin-dependent protein kinases (CDKs), regulation of cell cycle by proteolysis, G1/S

Phase transition, G2/M Phase transition, cell cycle control of DNA replication, DNA

damage check points. Cancer, types of cancer, factors causing cancer-physical, chemical

and biological agents. Errors in function of signal proteins and tumerogenesis.Oncogenes,

proto-oncogenes and tumor suppressor genes.Tumor suppressor protein p53 and its role

in tumor suppression.Tumor suppressor APC and Wnt/-Catenin signaling.

Unit VI:

Signal transduction in Health and Disease: Cancer, Neurodegeneration, Diabetes and

Obesity and Inflammation

Recommended Books:

1. Molecular biology- David Freifelder, Narosa Publishing House Pvt. Limited,

2005

2. Biochemistry of Signal Transduction and Regulation. 3rd Edition. Gerhard

Krauss, 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 3-

527-30591-2

3. Molecular Biology of the Cell, 4th edition, Bruce Alberts. New York: Garland

Science; 2002. ISBN-10: 0-8153-3218-1ISBN-10: 0-8153-4072-9

4. Molecular Cell Biology, 4th edition, Harvey Lodish.New York: W. H. Freeman;

2000. ISBN-10: 0-7167-3136-3

5. Principles of cell and molecular biology- Lewis Kleinsmith, 2nd edition,

illustrated, HarperCollins, 1995.

COURSE OUTCOME:

1. Help understand the key principles of biochemical metabolic concepts

2. Students will learn the signalling pathways that will help them in further studies.

3. Students learn the basic need of the signalling molecules and the consequesnce on

their absence.

4. Students will be exposed to most of the actions of the biological system,which they

will study in depth with signalling molecules.

5. Students can able to understand the function of specific anabolic and catabolic

pathways and how these pathways are controlled and interrelated

6. How current research has provided us with an understanding of the molecular basis

of the control of metabolism

7. "How to communicate scientific information effectively in writing Hypothesis-

based experimental design"

8. The course aims to give participants a basic knowledge of mechanisms of signal

transduction and the significance of signal transduction in physiology and

pathophysiology.

BCPHD011-CHROMATIN AND EPIGENETICS

Objective:

This an elective course for Biochemistry majors. The objective of this course is to

provide students with a solid foundation in both the principles of epigenetics and

experimental research by emphasizing the use of primary research articles and focusing

on developing analytical scientific reading and writing skills to focuson the current

questions in epigeneticsandhowtheyare beingaddressedexperimentally.

Unit-I

Chromatin structure: DNA and histones, nucleosome, organization of nucleosome in

chromatin, chromosomal architecture, modulation of chromosome structure, histones,

chromatin and nuclear assembly, transcription in chromatin, chromatin remodeling

machines.

Unit-II

Epigenetics: Introductionto epigenetics,basicconceptoverviewandbriefhistoryof thefield,

Epigenetic modifications and gene expression: DNA methylation, DNA acetylation,

Lostintranslation:Non-codingRNAsinEpigenetics.

Unit-III

Linking Epigenetic modifications: Chromatin remodelingand transcription, Model

animal systems for studying epigenetic regulation, Genomic imprinting in mammals,

multiple layers of epigenetic regulation; genome-wide analysis of epigenetic markers.

Unit-IV

Epigenetics and the environment: Gene-environment interactions, environmental

epigenomics, interplay of genome rearrangement and environment during development,

Epigeneticprogrammingincellrenewalandpluripotency.

Unit-V

Epigenetics in disease:

Epidemiology of health, epigenetics and endocrine diseases, Environmental

epigenetics and obesity, Epigenetics and cancer, Epigenome and aging, epigenetics and

cardiovascular disease, epigenetics and brain, Epigenetics and microRNA, Epigenetics in

drug discovery.

Unit VI:

The Histone Code: Biochemistry of Modifying Enzymes, Binding Proteins and

RNAs in Chromatin Regulation (protein-protein, protein-nucleic acids interactions,

complex purification)

Text Book:

Chromatin and Gene Regulation: Molecular Mechanisms in Epigenetics by B. M.

Turner (2008)

Reference book:

1. Epigenetics and Chromatin edited by Philippe Jeanteur (2008)

2. Epigenetics: The Death of the Genetic Theory of Disease Transmission by Joel D.

Wallach, Ma Lan, Gerhard N. Schrauzer (2014)

3. epigenetic epidemiology edited by Karin B. Michels - 2012

4. Epigenetics in human diseases edited by TrygveTollefsbol (2012)

COURSE OUTCOME:

1. Understand differences between Mendelian and epigenetic inheritance

2. Understand DNA methylation regulates gene expression

3. Understand how chromatin modifications and remodelling regulate gene

expression

4. Understand the role of non-coding RNAs in epigenetic regulation

5. Understand how epigenetic modifications are propagated

6. Understand the research process from hypothesis generation to final

presentation of results

7. Be able to generate testable research questions from observations.

8. Be able to design a controlled experiment to test a hypothesisand to present

findings of a primary research paper and indicate their significance/limit

BCPHD105-REPRODUCTIVE BIOLOGY

Number of credits: 4

Objectives:

Study the molecular mechanisms of human reproduction.

Spermatogenesis:

Theory Sex determination and differentiation: Mechanism of Sex determination,

differentiation of gonad and the genital tract. Stem cell renewal in testis,

Spermatogenesis: structural and molecular events, experimental approaches to study

spermatogenesis; Seminiferous epithelial cycle; Sertoli cell: structure and function.

Steroidogenesis:

Leydig cell: generation of Leydig cell, steroidogenesis; Leydig and Sertoli cell

proliferation during foetal and postnatal development; Regulation of testicular functions.

Epididymal maturation of spermatozoa; Capacitation, Signal transduction pathway in

acrosome reaction.

Male sterility:

Male sterility: azoospermia, oligozoospermia, asthenozoospermia, varicocele; Genetic

basis for male infertility, Mutational analysis in genes for hormones, receptor and gamete

development. Follicular development and selection; Role of extra-and intra-gonadal

factors in folliculogenesis; Oocyte maturation and its regulation;

Female Reproductive system:

Ovulation: factors involved in follicular rupture; Luteinization and luteolysis; Follicular

atresia. Regulation of reproductive cycle in female: menstrual cycle in human, estrous

cycle in rat, estrous behaviour in cycling animals; Female reproductive disorder:

amenorrhea, polycystic ovary.

Fertilization and contraception:

Fertilization: A comparative account on pre-fertilization events in oviparous animals

(echinoderms-amphibians-mammals), activation of egg, candidate molecules involved in

fertilization; Contraception leading to prevention of polyspermy: surgical, hormonal and

immunocontraception.

Recommended Books:

1. The Physiology of Reproduction, Vol 1 and 2, Ernst Knobil and Jimmy D. Neil, (ed),

Raven Press.

2. Male Reproductive Function, Christina Wang, (Ed), Kluwer Academic Publishers.

3. The ovary, (Ed), Solly Zuckerman Zuckerman, Barbara J. Weir, T. G. Baker.

Academic Press.

4. The ovary, Peter C.K. Leung and Eli Y. Adashi, (ed), Elsevier (Academic Press), 2004.

5. Cell and Molecular Biology of Testis, (Ed), Claude Desjardins and Larry L. Ewing.

Oxford University Press, USA

COURSE OUTCOME

1. Reproductive Biology covers clinical subjects such as the pathophysiology of

reproduction (e.g. sterility, infertility and abnormal pregnancy, and reproductive

tract infections), age-associated changes and disorders of the reproductive tract

(e.g. peri- and postmenopausal periods, urinary incontinence and other pelvic

floor disorders, impact of hormone replacement therapy), reproductive tissue

cancers (e.g. prostate, ovary, uterus, cervix, breast), and the impact of

environmental and occupational hazards on reproduction.

2. Through practices in genetics and genomics, students will scrutinize the different

cells, tissues and organs involved in animal reproduction, exploring the

inheritance of traits as well as disorders and diseases.

3. Students will study the requirements for reproduction, including the production of

sufficient numbers of viable gametes, fertilization, implantation in a receptive

uterus, formation of a placenta that can sustain and nurture a baby, and delivery at

full term.

4. This course is designed to give the student a clear understanding of the

pathophysiology of the menstrual cycle, fertilization, implantation, ovum growth

development, differentiation and associated abnormalities.

5. Disorders of fetal development including the principles of teratology and the

mechanism of normal and abnormal parturition will be covered as well as the

pathophysiology of the breast and disorders of lactation.

6. Fetal asphyxia and its consequences will be reviewed with emphasis on the

technology currently available for its detection. In addition the conclusion of the

reproductive cycle, menopause, and the use of hormonal replacement will be

covered.

7. Students will explore how reproductive biology impacts other aspects of health,

exploring implications of early life exposures for later health and of the biology of

reproductive cancers.

8. Social and ethical implications of reproductive technologies and research will be

discussed within appropriate topics.

BCMPHGP3:4-NANOTECHNOLOGY

Objectives:

1. Introduces the students with the basics of nanotechnology that includes

nanomaterials and devices.

2. Elaborates on the biological aspects of nanotechnology like synthesis methods

and applications.

3. To evaluate the potential risks and benefits of nanotechnology to the

environment and to human health and safety.

4. Pre-clinical characterization of nanomaterials intended for cancer therapeutics and

diagnostics.

Unit I:

Introduction: History of Nanotechnology and Nanobiotechnology, scope and

Applications. Introduction and overview of Quantum concepts. Nanomaterials and

Nanobiomaterials: Structures and properties of Carbon based, metal based and

bionanomaterials: Fullerenes, Bucky Ball, Nanotubes, Quantum Dots, Magnetic, Nano

Shells, Dendrimers, Nanocarriers, Nanocrystals, Nanowires, Nanomembranes, hybrid

biological/inorganic, protein & DNA based nanostructures. Introduction & overview of

1st, 2nd and 3rd generationbiomaterials.

Unit II:

Characterization of Nanostructures: UV-Visible spectroscopy, Electron Microscopy-

Scanning electron microscopy (SEM), Atomic Force microscopy (AFM), Transmission

electron microscopy (TEM), Scanning Probe microscopy (SPM), Scanning tunnel

microscopy (STM); Fourier Transform infrared spectroscopy (FTIR); X-ray

spectroscopy.

Unit III:

Nano Synthesis and Fabrication: Introduction & overview of Nanofabrication: Bottom

up-self assembly and Top down approaches using processes like Ball milling, Sol-gel

Process, Chemical

Vapour deposition (CVD). Plasma or flame spraying synthesis, Ion-Bean sculpting

electrodeposition and various lithography techniques. Nanolithography and Soft

lithography. Biosensors: types, applications and developments. Biosensor in modern

medicine.

Unit IV:

Application of Nanobiotechnology: Medical Nanobiotechnology: Diagnostics: Imaging:

Benefits and Applications. Nanotherpeutics: cancer treatment – Nanotechnology based

chemotherapy (Smart Bomb), Pebbles, wound care products, Implantable materials for

vascular interventions, Implantables materials for orthopaedics and dentistry. Active

implantable devices and biomics. Nanosurgery. Pharmaceutical Nanobiotechnology:

Drug delivery – Nanoparticles used as drug delivery systems, types of drug loading, drug

release (sustained and targeted release mechanism), Biodegradable polymers. Application

in the field of Nano Surgery and Tissue Engineering.

Unit V:

BioMEMS and NEMS: Micro & Nano-Electromechanical systems – Fabrication process

– choice of materials – advantages and limits of various approaches, Applications,

Thermal Radiations, Magnetic, Chemical and Mechanical Transducers –Sensing and

Actuators. Nano Safety Issues: Nanotoxicology: Toxicology health effects caused by

Nanoparticles, Ethics, Challenges and Future.

Unit VI:

Recent technologies involved in synthesis of nanoparticles and its activity in invitro and

Invivo studies. Targeted drug delivery based on nanomaterial technology.

References:

1. Introduction to Nanotechnology - Charles P. Poole, Frank J. Owens, John Wiley

& sons, (2003)

2. Nanotechnology-fundamentals and applications-Karkare, I.K International

publishing house pvt. Ltd, (2008)

3. Nanotechnology - Richard Booker &Eary Boysen, Wiley India (P) ltd, (2005)

4. Salata O.V. Applications of nanoparticles in biology and medicine. Journal of

Nanobiotechnology, 2:3, (2004).

5. Bernard H.A Relim, Microbial Bionanotechnology, (2006)

6. https://www.pdfdrive.net/introduction-to-nanomaterials-and-nanotechnology-

e7096944.html

7. http://elibrary.bsu.az/books_250/N_229.pdf

8. http://www.hailienene.com/resources/nano-technology.pdf

COURSE OUTCOME:

1.Students can able to Know what it takes to have a career in nanotechnology

2.Understand the need to increase Nanotechnology awareness 3.Understand the

definition of Nanotechnology

4.Know the processing of Nanoparticles and Nanomaterials

5.Know the application of Nanotechnology and nanomaterials

6.Understand the fundamental principles of nanotechnology and their application

to biomedical engineering.

7.Apply and transfer interdisciplinary systems engineering approaches to the field

of bio- and nanotechnology projects

8.Practice and explain state-of-the-art characterization methods for nanomaterials,

understanding and critiquing nanomaterial safety and handling methods required

during characterization

BCPHD104-CANCER BIOLOGY

Objectives:

1. Identify and eliminate or to reduce probable causes of cancer.

2. To understand the mechanisms of cancer development and progression.

3. The ultimate aim is to translate basic findings into diagnostics, treatments and

ultimate cures.

4. Seek new diagnostic tests for the malignant disease in early stage.

Unit I:

Introduction, historical perspective, classification carcinogenesis, cancer initiation,

promotion & progression, pathways of spread- Epidemology: Cancer incidence,

Geographical and environmental factors, Age, Genetic Predisposition of cancer, Non-

Hereditary predisposing condition- molecular basis of cancer: Essential Alterations for

malignant transformation, the normal cell cycle, cell division- mitosis & meiosis, self

sufficiency in growth signals.

Unit II:

Oncogenes, identification of oncogenes, retroviruses and oncogenes, detection of

oncogenes, growth factors and growth factor receptor that are

oncogenes.Oncogenes/proto oncogene activity. Growth factors related to transformation.

Unit III:

Tumor suppressor genes cancer cell cycles DNA viruses/ cell immortalization tumor

suppressor gene pathway DNA methylation, epigenetic silencing of suppressor genes,

evasion of apoptosis.

Unit IV:

DNA repair defects and genomic instability in cancer cells, limitless replicative potential:

telomerase, development of sustained angiogenesis- invasion and metastasis, invasion of

extracellular matrix- vascular dissemination and homing of tumor cells, molecular

genetic of metastasis development, stromal microenvironment and carcinogenesis,

dysregulation of cancer, associated genes, chromosomal changes, gene amplification,

epigenetic changes, molecular profiles of cancer cells.

Unit V:

Tumor progression and heterogeneity agents and their cellular interaction-chemical

carcinogenesis, radiation carcinogenesis, microbial carcinogenesis- host defence against

tumor immunity clinical features of tumor.

Unit VI:

Recent technology to detect cancer diseases and advanced technology to cure cancer

diseases. Targeted drug delivery methods to cure cancer.

References:

1. Cancer biology- Raymond W. Ruddon, Oxford University Press, 3rd edition

(1995)

2. Molecular Biology of cancer- F. Macdonald, Taylor & Francis, 2nd edition (2004)

3. http://csbl.bmb.uga.edu/mirrors/JLU/DragonStar2017/download/introduction-to-

cancer-biology.pdf

4. http://www.nhri.org.tw/NHRI_ADM/userfiles/file/1010510.pdf

5. https://books.google.co.in/books/about/The_Biology_of_Cancer_Second_Edition.

html?id=MzMmAgAAQBAJ

6. Margaret A. Knowles, Peter J Selby, An Introduction to Cellular and Molecular

Biology of Cancer, 4th Edition, Oxford Medical Publication, 1991.

7. https://oncouasd.files.wordpress.com/2014/09/cancer-principles-and-practice-of-

oncology-6e.pdf

8. https://archive.org/details/biologyofcancera00burc.

COURSE OUTCOME

1. Understanding how cancer develops and progress

2. To understand how the gene mutations, drive the growth and spread of cancer

3. To understand and differentiate the normal cells and cancer cells

4. To understand the signalling pathways in cancer cells

5. To understand the proteins and basic biomolecule components involving in the

metastasis.

6. To understand how the angiogenesis, induce formation of new capillary blood

vessels.

7. To understand the role of viruses and microorganisms in development of cancer

cells

8. To understand the environmental factor that bestow cancer and also detection and

diagnosis of cancer

BC202-BIOCHEMISTRY OF SIGNAL TRANSDUCTION AND REGULATION

Objectives:

1. Provides a comprehensive account of cell signaling and signal transduction.

2. To examine in detail on the biochemical basis of the transmission of molecular

signals from a cell's exterior to its interior and how this can bring about changes

in cellular behavior and gene expression.

3. The course emphasizes the biochemical concepts underlying signal transduction

and the types of experimental analysis that are employed to study signaling

pathways.

4. An understanding of signaling in relation to tumor cell biology.

Unit I:

Regulation of transcription and translation in prokaryotes: Positive and negative control,

repressor and inducer, concept of operon, lac-, and trpoperons, attenuation, regulons.

Regulation in eukaryotes- gene families, regulatory strategies in eukaryotes, gene

alteration, regulation of synthesis of primary transcripts, hormonal control, transcription

factors, transcription factors: targets of signaling pathways, DNA binding motifs in pro-

and eukaryotes Helix turn, helix, zinc fingers, leucine zippers/ b zip, helix loop helix

motifs. Regulation at the level of translation in prokaryotes and eukaryotes.

Unit II:

Signal transduction: definition, signals, ligands and receptors. Endocrine, paracrine and

autocrine signaling. Sensory Transduction : Nerve impulse transmission – Nerve cells,

synapses, reflex arc structure, Resting membrane potential, Nernst equation, action

potential, voltage gated ion-channels, impulse transmission, neurotransmitters,

neurotransmitter receptors. Rod and cone cells in the retina, biochemical changes in the

visual cycle, photochemical reaction and regulation of rhodopsin. Odor receptors.

Chemistry of muscle contraction – actin and myosin filaments, theories involved in

muscle contraction, mechanism of muscle contraction, energy sources for muscle

contraction.

Unit III:

Receptors and signaling pathways: cell signaling, cell surface receptors. G Protein

coupled receptors- structure, mechanism of signal transmission, regulatory GTPases,

heterotrimeric G proteins and effector molecules of G Proteins. Signaling molecules-

cAMP, cGMP, metabolic pathways for the formation of inositol triphosphate from

phosphatidyl inositol diphosphate, Ca2+, DAG and NO as signaling molecules, ryanodine

and other Ca2+ receptors, phospho-regulation of inositol and the calcium channel

activation. Ser/Thr-specific protein kinases and phosphatases. Receptor tyrosine kinases,

Role of phosphotyrosine in SH2 domain binding. Signal transmission via Ras proteins

and MAP kinase pathways.

Unit IV:

Signaling by nuclear receptors: ligands, structure and functions of nuclear receptors,

nuclear functions for hormones/metabolites - orphan receptors; cytoplasmic functions and

crosstalk with signaling molecules, signaling pathway of the steroid hormone receptors.

Cytokine receptors- structure and activation of cytokine receptors, Jak-Stat path way,

Janus kinases, Stat proteins.

Unit V:

Regulation of the cell cycle: Overview of the cell cycle, cell cycle control mechanisms,

Cyclin-dependent protein kinases (CDKs), regulation of cell cycle by proteolysis, G1/S

Phase transition, G2/M Phase transition, cell cycle control of DNA replication, DNA

damage check points.

Cancer, types of cancer, factors causing cancer-physical, chemical and biological agents.

Errors in function of signal proteins and tumerogenesis. Oncogenes, proto-oncogenes and

tumor suppressor genes. Tumor suppressor protein p53 and its role in tumor suppression.

Tumor suppressor APC and Wnt/-Catenin signaling.

Unit VI:

Current research in oncogenes and suppressor genes, recent scenario of signaling

pathways in Interleukins and cell surface receptors.

References:

1. Molecular biology- David Freifelder, Narosa Publishing House Pvt. Limited,

2005

2. Biochemistry of Signal Transduction and Regulation. 3rd Edition. Gerhard

Krauss, 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 3-

527-30591-2

3. http://www.beck-shop.de/fachbuch/leseprobe/9783527313976_Excerpt_001.pdf

4. Molecular Biology of the Cell, 4th edition, Bruce Alberts. New York: Garland

Science; 2002. ISBN-10: 0-8153-3218-1ISBN-10: 0-8153-4072-9

5. Molecular Cell Biology, 4th edition, Harvey Lodish.New York: W. H. Freeman;

2000. ISBN-10: 0-7167-3136-3

6. Principles of cell and molecular biology- Lewis Kleinsmith, 2nd edition,

illustrated, HarperCollins, 1995.

7. http://www2.nsysu.edu.tw/wzhlab/ch03%20protein%20structure%20and%20func

tion.

8. http://www.wormbook.org/chapters/www_cellcyclereguln/cellcyclereguln.pdf

COURSE OUTCOME:

9. Help understand the key principles of biochemical metabolic concepts

10. Students will learn the signalling pathways that will help them in further studies.

11. Students learn the basic need of the signalling molecules and the consequesnce on

their absence.

12. Students will be exposed to most of the actions of the biological system,which they

will study in depth with signalling molecules.

13. Students can able to understand the function of specific anabolic and catabolic

pathways and how these pathways are controlled and interrelated

14. How current research has provided us with an understanding of the molecular basis

of the control of metabolism

15. "How to communicate scientific information effectively in writing Hypothesis-

based experimental design"

16. The course aims to give participants a basic knowledge of mechanisms of signal

transduction and the significance of signal transduction in physiology and

pathophysiology.