Genetics and Epigenetics

Teacher

Dr Yashaswi Nayak

Category

Core Courses

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Course Name : Genetics and Epigenetics

Code(Credit) : CUTM 1454(3-1-0)

Course Objectives

  • Be able to explain and provide examples of how continuous traits are “quantitative traits” and that phenotypic variation may be due to genetic variation within a population and/or environmental variation experienced by individuals within a population.
  • To explain the polygenic theory of genetic variance and the nature of additive alleles, and the assumptions that accompany these ideas and also able to provide competing hypotheses that explain a distribution data set of phenotypes.
  • To discuss epigenetics and its role in cancer, imprinting and X chromosome inactivation.
  • To describe the modifications/mechanisms of DNA marks that result in epigenetic changes and also to discuss the role of epigenetics in environmental exposures.

Course Outcomes

COs Course Outcomes Mapping COs with POs

(High-3, Medium-2, Low-1)

CO1 Students will have an understanding of the role of genetic mechanism in evolution. PO1-3, PO7-1, PO9-2
CO2 Be able to predict the phenotypic classes and their ratios from a monohybrid cross involving dominant and recessive alleles. PO1-3, PO7-1, PO9-2
CO3 Be able to predict the phenotypic classes and their ratios from a cross involving co-dominant or incompletely dominant alleles . PO1-3, PO7-1, PO9-2
CO4 Be able to predict the ratio of a specific genotype and/or phenotype from a cross involving multiple independently assorting genes (with each gene exhibiting only dominant and recessive alleles) . PO1-3, PO7-1, PO9-2

Course Syllabus

Module - 1: Principles of Inheritance (5 h)

Laws of heredity, Co-and incomplete dominance, Gene Linkage and crossing over, Varieties of Gene interractions - lethal genes, multiple alleles, pleiotropic genes, gene epistasis, Structural and numerical alterations of chromosomes and meiotic consequence, Cytoplasmic Inheritance , Sex-chromosome systems; Different mechanisms of sex determination in animals(Drosophila, Man, Bees and Bonellia)

Assignment:

Gene Interaction and Sex Determination in animals

 

Module - 2: Linkage and Crossing over in diploid organisms (5 h)

Sex linkage: Sex linked genes in man, sex chromosome disorders in man, Detection of linkage & Linkage maps: Test cross, test for linkage on the basis of F2 generation, LOD score, gene mapping, three point test cross in Drosophila, construction of linkage maps, Identification of particular linkage groups with specific chromosome, Physical distance and map distance, Interference and coincidence

Assignment:

Two point and Three point Test cross

 

Module - 3: Mitotic recombination and Chromosomal abnormalities (4 h)

Mitotic Recombination, Recombination within gene, Spontaneous and induced mutations, physical and chemical mutagens, chromosomal aberrations, meiotic behaviour of deletion, duplication, inversion and translocation, Euploids and aneuploids-classification, origin, induction, role of polyploidy in evolution.

Practice:

Preparation of Mitotic chromosomes from the given sample

Assignment:

Chromosomal Aberrations

 

Module - 4: Human genetics and Genomics (5 h)

Human genetics - Chromosomal disorder, Some common human syndromes, Twin study, Superfoetation, Polyembryony, Free Martin, Multiple birth, Amniocentesis and Genetic Counselling, Nature and function of genetic material, Chemical compounds causing genetic damage, Gene mapping and genome analysis.

Practice:

To study the karyotyping of chromosomes from the given animal samples.

Assignment:

Chromosomal disorders and human syndromes

 

Module - 5: Epigenetics and Chromatin structures (4 h)

Epigenetics vs Genetics, Epigenetics from phenomena to field : overview and concepts, Basic organization of eukaryotic genome, Histone proteins.

Practice: 

  • To study the chromatin modelling and Chromatin-immunoprecipitation (ChIP)
  • Isolation of total histones, and resolution on SDS-PAGE.

  Assignment:

Chromatin structure and Histone protein

 

Module - 6: Epigenetic marks and chromatin modifications (5 h)

Histone modifications and the histone code, Chromatin remodelling complex and histone variants, DNA Methylation, Acetylation and Deacetylation, Phosphorylation, Ubiquitylation, Deubiquitylation and Phosphorylation.

Practice:

  • Isolation of DNA from animal cell
  • Isolation of nuclei (as a source for studies on structure of chromatin) from rat/mouse liver by discontinuous sucrose-density gradient centrifugation.

 

Module - 7: Dosage compensation and Genomic imprinting (4 h)

Dosage compensation in mammals, Genomic imprinting in mammals, Germline and pleuripotent stem cells, Epigenetics and human disease.

Practice: 

  • Identification of inactivated X chromosomes as barr body from the given sample
  • Preparation and study of metaphase chromosomes from mouse bone marrow

Assignment:

Epigenetics and human disease

 

Reference and Textbooks

  • Gardner, E.J., Simmons, M.J., Snustad, D.P.  (2008). Principles of Genetics.  VIII Edition. Wiley India.
  • Snustad, D.P., Simmons, M.J. (2009). Principles of Genetics. V Edition. John Wiley and Sons Inc.
  • Klug, W.S., Cummings, M.R., Spencer, C.A. (2012). Concepts of Genetics X Edition. Benjamin Cummings.
  • Russell, P. (2009).  Genetics- A Molecular Approach.  III Edition.  Benjamin Cummings.
  • Griffiths, A.J.F., Wessler, S.R., Lewontin, R.C. and Carroll, S.B.
  • Introduction to Genetic Analysis. IX Edition. W. H. Freeman and Co.
  • Ridley, M. (2004). Evolution. III Edition. Blackwell Publishing
  • Barton, N. H., Briggs, D. E. G., Eisen, J. A.Goldstein, D. B. and Patel, N. H. (2007).   Cold Spring, Harbour Laboratory Press.
  • Hall, B.  and Hallgrimsson,  B.  (2008). Evolution.  IV Edition.  Jones  and  BartlettPublishers
  • Campbell, N. and Reece J.  B. (2011).  Biology.  IX Edition, Pearson, Benjamin,Cummings.
  • Douglas, J. Futuyma (1997). Evolutionary Biology. Sinauer Associates.
  • Epigenetics, C. David Allis and Thomas Jenuwein, (2007)Cold Spring Harbor Laboratory Press, New York, USA .
  • Molecular Biology of Gene, Watson et al., (5th Ed. 2004), Pearson Education, Delhi, INDIA
  • Genetics by P.K Gupta.

Session Plan

Session 1

Laws of heredity, Co-and incomplete dominance

Online source: Mendelian Inheritance (and Terminology)

You tube source: Genetics - Exceptions to Mendelism

Session 2

Gene Linkage and crossing over

Online source : Genetic linkage slideshare

You tube link: Gene linkage and crossing over

Session 3

Varieties of Gene interractions - lethal genes, multiple alleles, pleiotropic genes, gene epistasis

Online source :https://www2.estrellamountain.edu/faculty/farabee/biobk/BioBookgeninteract.html

You tube link  1 : Genetic epistasis

You tube link 2 : Pleiotropy

Session 4

Structural and numerical alterations of chromosomes and meiotic consequence.

Online source : Atlas Genetics

You tube link  :Chromosome Nondisjunction Animation

Session 5

 Cytoplasmic Inheritance , Sex-chromosome systems; Different mechanisms of sex determination in animals(Drosophila, Man, Bees and Bonellia)

Online source :1. Mechanism of sex determination

Online source :2. Cytoplasmic Inheritance

 

You tube link  :  1. Sex Determination

You tube link  :  2.Sex Linkage and Cytoplasmic Inheritance

Session 6

Sex linkage: Sex linked genes in man, sex chromosome disorders in man,

Online source 1 : Sex Linked Inheritance 

Online source : The X chromosome

 

You tube link  :  1. Sex Linked Trait

Session 7

Detection of linkage & Linkage maps: Test cross, test for linkage on the basis of F2 generation

Online source :1. Genetic Recombination

 

You tube link  :  1. Gene Linkage and Genetic Maps

You tube link  :  2.Linkage and Mapping 

Session 8

LOD score, gene mapping, three point test cross in Drosophila, construction of linkage maps

Online source :1. Gene Mapping

Online source : 2. Calculation of Recombination Distance

You tube link  :  1. Three point testcross

Session 9

Identification of particular linkage groups with specific chromosome

Coursera source 1 : Linkage to Association Gene-Mapping

Online source 2 : Calculation of Recombination Distance

Online source 3: Gene mapping

You tube link  :  1. Three point testcross

Session 10

Physical distance and map distance, Interference and coincidence,

Online source :Interference

You tube link  :  Interference and Coincidence

Session 11

Mitotic Recombination, Recombination within gene.

Coursera source :Recombination (G)

Online source : Mitotic Recombination

You tube link  : Mitotic recombination

Session 12

Spontaneous and induced mutations, physical and chemical mutagens

Online source :Spontaneous and Induced Mutations

You tube link : Types of Mutagens-Phycial, Chemical (Base analog-5-bromo uracil) & Biological

Session 13

Chromosomal aberrations, meiotic behavior of deletion, duplication, inversion and translocation.

Online source :An Introduction to Chromosomal Aberrations

You tube link: Chromosomal aberrations

Session 14

Euploids and aneuploids-classification, origin, induction, role of polyploidy in evolution .

Online source :An Introduction to Genetic Analysis.

You tube link: 1-  Changes in chromosome number (Euploidy and Aneuploidy)

You tube link: 2-Euploidy, polyploidy part -1

Session 15

Practice 1 (2h)

Preparation of Mitotic chromosomes from the given sample

Youtube source: Mitosis

Online source: Mitotic Chromosome preparation from bone marrow

Session 16

Human genetics - Chromosomal disorder, Some common human syndromes

Online source: Genetic Diseases (Disorder Definition, Types, and Examples)

You tube link:   Genetic Disorders And Diseases

Session 17

Twin study, Superfoetation, Polyembryony, Free Martin, Multiple birth

Online source: 1. Twin Study

Online source:2. Superfetation – Getting Pregnant while Pregnant

 

You tube link: 1.  What are 'twin studies'?

You tube link: 2. Formation of Twins

Session 18

Amniocentesis and Genetic Counselling

Online source: 1. Amniocentesis  

Online source:2. genetic counselling

You tube link:   Amniocentesis

Session 19

Nature and function of genetic material, Chemical compounds causing genetic damage.

Online source: Chemical Mutagen

You tube link:  Mutagens and carcinogens | Biomolecules

Session 20

Gene mapping and genome analysis

Coyrsera source : Genetic Mapping 

You tube link : Gene mapping/How to decode  

Session-21

Practice 2 (2 h)

To study the karyotyping of chromosomes from the given animal samples.

Online Source: Karyotyping

You Tube Link : What is Karyotyping ?

Session 22

Epigenetics and chromatin structure; Epigenetics vs Genetics

Online source : Epigenetics and chromatin

You tube link : Epigenetics Overview

Session 23

Epigenetics from phenomena to field : overview and concepts

coursera source : Introduction to the concepts of epigenetic control

Online source: Concept of Epigenetics

You tube link : Epigenetics Overview

Session 24

Basic organization of eukaryotic genome

Online source : General organizations in Eukaryotes

You tube link : Genome Organization | Molecular Biology

Session 25

Session 26

Session 27

Practice - 4 (2 h)

 Isolation of total histones, and resolution on SDS-PAGE.

Online source: Chromatin Immunoprecipitation (ChIP) Protocol

Youtube source: Chromatin Immunoprecipitation: ChIP step by step

Session 28

Histone modifications and the histone code

Online source : Regulation of chromatin by histone modifications

You tube link : Histone modifications (Introduction)

Session 29

Chromatin remodelling complex and histone variants

Coursera source : Chromatin remodelling

You tube link : Chromatin Remodeling in Eukaryotes

Session 30

DNA Methylation

Coursera source : Histone acetylation and histone methylation

Online source 1: Histone acetylation

Online source 2: Histone methylation

You tube link : DNA Methylation

Session 31

Acetylation and Deacetylation

Coursera source : Histone acetylation and histone methylation

Online source 1 : Histone deacetylation

You tube link : Histone acetylation and histone methylation

Session 32

Phosphorylation, Ubiquitylation, Deubiquitylation and Phosphorylation

Online source : Global analysis of phosphorylation and ubiquitylation crosstalk in protein degradation

You tube link : What is ubiquitin?

Session 33

Practice -4 (2 h)

Isolation of DNA from animal cell

Online Source : DNA Extraction and Purification

You Tube Link : DNA extraction from Blood

Session 34

Practice -5 (2h)

 Isolation of nuclei (as a source for studies on structure of chromatin) from rat/mouse liver by discontinuous sucrose-density gradient centrifugation.

Online Source : Cell Separation Media Methodology and applications

You Tube Link : Sucrose Density Gradient High Speed Centrifugation

Session 35

Dosage compensation and Genomic imprinting :Dosage compensation in mammals

Online source : Dosage Compensation in Mammals

You tube link : Evolution of Dosage compensation

Session 36

Genomic imprinting in mammals

Coursera source : Genomic Imprinting

Online source: Genomic imprinting

You tube link : Genomic imprinting

Session 37

Germline and pleuripotent stem cells

Online source : Germline and Pluripotent Stem Cells

You tube link :  What is a pluripotent stem cell?

Session 38

Epigenetics and human disease

Online source : 1. Role of Epigenetics in Biology and Human Diseases

Online source :2. Epigenetics and Human Disease

You tube link :  Epigenetics basics

Session 39

Practice -6 (2 h)

Identification of inactivated X chromosomes as barr body from the given sample

Online Source : Barr Body detection (sex chromatin body)

Session 40

Practice -7 (2 h)

Preparation and study of metaphase chromosomes from mouse bone marrow

Online Source: Mitotic chromosome preparations from bone marrow

Case Studies

Case Studies

Our Main Teachers

Dr Yashaswi Nayak

Associate Professor
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Associate Professor, Department of Zoology (School of Applied Sciences) CUTM – Bhubaneswar Dr. Yashaswi Nayak presently serving in Centurion University of Technology and Management as faculty and Head of the Department of Zoology has around sixteen years of teaching experience and possess specialization in Poultry management , vermicomposting processes. Her area of interest is Fishery […]