Genetics and Epigenetics
Teacher
Dr Yashaswi Nayak
Category
Core Courses
Course Attendees
Still no participant
Course Reviews
Still no reviews
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,
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'?
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
You tube link : Genome Organization | Molecular Biology
Session 25
Histone proteins
Online source : DNA Packaging: Nucleosomes and Chromatin
You tube link : Histone | Chromatin | Nucleosome | DNA Packaging
Session 26
Practice - 3 (2 h)
To study the chromatin modelling and Chromatin-immunoprecipitation (ChIP)
Online source 1: Extraction, purification and analysis of histones
Online source 2: Extracting histones for the specific purpose of label-free MS
Youtube source 1: The principle of SDS PAGE-a full and clear explanation of the technique and how does it work
Youtube source 2: Separating Proteins using SDS Polyacrylamide Gel Electrophoresis
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
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 […]