GENOMICS

Seminar
On
GENOMICS
Submitted
By MUKESH KUMAR DILANIA
M.Sc. III Semester (Botany)
GUIDED BY : HOD PRINCIPLE
Mr. Amarnath Nishad. Miss R. Kuldeep. Dr. Komal Sarava

INTRODUCATION
 Genomics is the study of mapping, sequencing and analysis of the genome. It is the
scientific discipline of genomes of cells studies through high-throughout sequencing.
Its helps to understand the structure, function and co-ordinated regulations of all
genes in an organism.
 A genome is the entire DNA of genes of an organism. Genes carry information of
making all the proteins required by the organisms. These proteins determine, among,
other things, how the organism looks, how well its body metabolizer food or fights
infection and even how it behaves.
DEFINITION
“Genomics the branch of molecular biology concerned with the
structure, function, evolution, and mapping of genomes.”

HISTORY
 1971- Wu and Taylor determine the first ever DNA
sequence.
 1977-Sanger et al. sequence the first ever (DNA based)
virus genome.
 1955- First complete bacterial genome sequence
(Haemophilus influenzae)
 1996- First complete eukaryotic.
genome(Saccharomyces cerevisiae)
 1998- First animal Genome. (Caenorhabditis elegans)

GENE SEQUENCING
• The determination of the order of various
gene along the length of a chromosome is
called gene sequencing.
• It is gives a high resolution genetic maps
of chromosomes. here, exact genes have
not been plotted on the chromosomes.

Method of Gene Sequencing
DIRECTED GENE SEQUENCING
 In the directed gene sequencing, any one DNA fragment
of the genome is chosen for DNA sequencing and then
the fragment coming next to it as in intact, chromosomes
is subjected to DNA sequencing. Thus the DNA is
proceeded in one or fragment. Hence, this method is
also known as ordered sequencing.
 In one method of ordered gene sequencing, BAC library
is made from the genomic DNA and then individual DNA
fragment of the genome are sequencing from the first
clone, then the second clone and so on.

FIG : Ordered gene sequencing using
BAC vector

TYPES OF GENOMICS
1. Structural Genomics
2. Functional Genomics
1. Structural Genomics:
 The Structural genomics is the study of the structure of all genes that make up a
genome and their arrangement in the chromosome.
 It includes DNA sequencing and genome annotation.
 The determination of nucleotide sequence of genomic DNA is called DNA
sequencing.
2. Functional Genomics:
 The functional genomics is the study of functions of all genes and their roles in
regulating metabolic pathways at different stages of development.
 The functions of genes are discovered with high-throughput techniques using
gene conting and sequence comparison with data of a related organism.

GENOME SEQUENCING PROJECTS
 Projects to map and sequence all the DNA in different species of
organism are called genome projects.
 The genome projects of many mammals, plants, insects, pathogenic
microbes, etc. Have been conducted by many national and
international agencies to know all about their genes.
 Human Genome Project
 The human genome project(HGP) is a project to map and
sequence the 3 billion nucleotides contained in the human
genome and to identify all the genes present and it. It is under
the control of an international body, Human genome
organization(HUGO). It was started in 1990 and completed in
2003

THERE ARE CURRENTLY TWO HUMAN GENOME PROJECTS.
* International HGP
* Celera Genomics HGP
* International HGP
• This project was planned in 1986 by Charles Delisi, who was the director of the US department of
Energy (DOE). The DOE and national institute of health (NIH) hand in hand started this project in 1990.
• The 1987 report stated boldly, “The ultimate goal of this initiative is to understand the human genome”
And “Knowledge of the human genome is necessary for the progress of medicine and other health
sciences as knowledge of human anatomy”.
* Celera Genomics HGP
• Celera Genomics is a US Biotechnology company that takes the commercial potential of
human genome.
• This company took effort to sequence the human genome in 1998. It was a privately
funded project co- ordinated by Craig venter.
• It was aimed at sequencing commercially through gene identification for discovery of new
drugs.

Benefits from Genome Sequencing
Projects
 It provides insights on genome organization and
evolution, and the mechanisms involved therein.
 A better understanding of human genetic diseases
should facilitate their management/cure.
 The pathogenicity of microorganism would be better
understood. This should facilitate protection from such
diseases.
• REFERENCE :
• Book Of Biotechnology – V. Kumarsen.

Seminar
On
PROTEOMICS
Submitted
By RAVINDRANATH RANA

INTRODUCTION
 Proteomics = proteos -protein .
 Omics – The study.
 Proteomic is the study of the proteome .the protein complement of the
genome.
 Proteomisc is a new biological science.
 Proteomics words derived from proteome.
 The terms "proteome" is used to describe the set of protein expressed
from the transcriptome of cell .
 But the terms proteome has been devised to describe the protein
specified by genome of an organism .

Definition :- That's just not protein biochemistry ,
PROTEOME : “Is the complement protein found in a single cell in a
particular environment / is complete collection of protein encoded by
genome of an organism.”
PROTEOMICS : “Is the study of composition ,structure ,function
and interaction of the protein directing the activities of each living cell.”

HISTORY
 The term proteomic was first coined in 1994 by an "Australian "
postulated fellow named “, "Mark Willkines".
D E F I N I N G P ROT E O M I C S :
• large scale study of protein usually by biochemical methods it is date back
to the late 1970.
• In 1990 biological mass spectrometry emarged as a powerful analytical
methode that removed most of the limitations of proteins analysis.
• Today the term proteomic covers much of the functional analysis of gene
product including large scale identification or localization study of protein.

AIMS OF PROTEOMICS
• It's aims to study the dynamics protein, protein products of
the genome and their interaction .
• Major two techniques used in proteomics:-
1. 2D - gel electrophoresis technique -separation of complex
protein mixture .
2. Mass spectrometry -- Identification and structure analysis .

PROTEIN STRUCTURE
• Proteins are large molecules or macro molecules their composition are C,H,O,N
molecules but some time S, Zn ,Cu, P etc.
• Constiny of one or more long chain of amio acid residue.
• Protein performe a vast array of function whithin organism including - Catalysing ,
metabolic reactions , DNA replication, Responding to stimuli and transporting
molecules from one location to another .
=>> Protein structure divide into 4 types-
1. Primary structure.
2. Secondary structure
3. Tertiary structure
4. Quaternary structure

CLASSIFICATION OF PROTEOMICS
1. Expression Proteomics
2. Structure Proteomics
3. Functional Proteomics
1. Expression Proteomics:
• Expression proteomic is the quantitative study of protein expression
between the sample which differ by some variable is know as
expression protein.
• This type of proteomics can help identify the may protein found in a
particular sample and protein differentially expressed the related
sample.
• E.g. When comparing diseased and healthy tissue technologies such
as 2D page and mass spectrometry used here.

2.Structural Proteomics :
• The structural proteomics deal with the study of structure and nature of
protein present in a particular cell organelles.
• The structure of protein complex are know as structural proteomics.
• Structural analysis can aid identification of the function of newly discovered
gene.
3.Functional Proteomics:
• Functional proteomics represent a wide ranging term for many specific
directed proteomics methodology.
• The characterization of protein -protein interaction are used to determined
protein functions and to demonstrated protein assemble in longer complex.

PROTEOMICS TECHNIQUES
1. TYPICAL PROTEOME EXPERIMENT

PROTEOMICS TECHNIQUES
1. MAJORTECHNIQUE IN PROTEOME EXPERIMENT

Genomics VS Proteomics
• Proteomics can be classified into structural functional and expression proteomics
• a)Structural proteomics: is the study of the structure of proteins and their location in the cell
• b)Functional proteomics: study of function of all proteins which primarily include protein-protein
interaction and interaction of proteins with other biomolecules.
• c) Expression proteomics: is the study of identification and quantification or expression level of
proteins of the cell at different developmental stages or at different environmental conditions
• Techniques in genomics include.
• a) gene sequencing strategies like directed gene sequencing, whole genome short gun
sequencing,
• b)Construction of ESTs (expressed sequence Tags),
• c) Identification of single nucleotide polymorphisms (SNPs),
• d) Analysis and interpretation of sequenced data using different databases and software.
• Techniques in proteomics include

• Genomics
• Proteomics
• Genomics is the study of genome of an organism. Genome represents the entire genes
of an organism or a cell type.
• Proteomics is the study of proteome of an organism. Proteome refers to the entire
protein set coded by the genome of an organism or a cell type.
• Genomics include mapping, sequencing and analysis of genome.
• Proteomics include characterization of all proteins of an organism or study of structure
and function of proteins.
• Genomics can be broadly classified into structural and functional genomics
• a)Structural genomics: is the study of the structure of all genes and its relative position
on the chromosome.
• b)Functional genomics: study of function of all genes or the role of these genes in
regulating metabolic activities of the cell.

• a) protein extraction, electrophoretic separation, digestion of separated
proteins into small fragments using trypsin, mass spectroscopy to find out
amino acid sequences and finally protein identification using standard
databases.
• b) Protein 3D structure prediction using software.
• c) Protein expression study using protein microarray.
• Thrust areas in Genomics: Genome Sequencing projects of many
organisms including Human Genome Project
• Proteome database development like SWISS-2D PAGE and software
development for computer aided drug design
REFERENCE : Biotechnology – V. Kumarsen.
Biotechnology – R. C. Dubey.

Seminar
On
Molecular Marker for
integression of useful traits.
Submitted
By ISHA Pandey

WHAT IS A GENETIC MAPPING
Genome Mapping
• mapping the entire genome of an organism is know as genome mapping.
• identifying the genes present on the genome & detecting their presence on the
chromosome is called gene mapping.
• the genome mapping is of two types-
• * Linkage Mapping
• * Genetic Mapping
* Linkage Mapping, homologous chromosome is done by making a linkage map from
the help of crossing over.
• mapping the distance, sequence& position of genes present in the chromosome is
called genetic mapping.
* Genetic Mapping is of three types-

1. Cytogenetic Mapping- In this, mapping of DNA or plasmid present in the
cytoplasm of prokaryotic organisms is done.
2. Physical Mapping- In this ,mapping of the distance of the genes present
in the chromosome is done.
• this of three type-
1) Chromosome Jumping.
2) Chromosome Walking.
3) Fluorescent In Situ Hybridization.
3. Molecular Mapping- In this ,mapping of the base sequence of genes
present in chromosome such as adenine, guanine, thymine, cytosine are
mapped.

*Molecular Marker-
• The variant DNA fragment that gives some in information about genes of interest is called
molecular marker.
• A molecular marker (identified as genetic marker) is a fragment of DNA that is associated
with a certain location within the genome .molecular markers are used in molecular biology
&biotechnology to identify a particular sequence of DNA in a pool of unknown DNA.
• Molecular markers are used to construct chromosome maps, cytogenetic maps, &
physical maps of chromosome.
• Such molecular marker are very useful to evaluate phenotypic variability among the
individuals of a species, to construct chromosome maps& to distinguish pne species from
other species.
• Nowadays DNA fragments are used in gene mapping as a marker gene (producing mutant
character)
• Molecular marker means DNA fragment are sequence, this marker may be unknown or
known.
• Unknown marker is DNA fragment whose sequence, other character & function are
unknown.
• The know marker is DNA fragment whose sequence, other character & function are know.
• When molecular marker is a different structure in different individuals of a species, it is called
polymorphic marker.
MOLECULAR MARKER

Molecular markers are of the following types-
1) Restriction Fragment Length Polymorphism-
• The RFLP is a non-PCR based method. The variation in
the restriction DNA fragments length s between
individuals of species is called restriction fragment length
polymorphism.
TYPES OF MOLECULAR MARKER

Fig : Various Step Of RFLP Analysis

Advantage and Disadvantage OF RFLP
• ADVANTAGE-
• High reproducibility.
• Detect coupling phase of DNA.
• Reliable marker in linkage & breeding analysis.
• Easily determine a linked trait present in both homozygous &
heterozygous.
• DISADVANTAGE-
• Require large quantities of high molecular weight of DNA.
• Time consuming.
• Expensive process.
• Labor intensive.(hard work)

USE OF RFLP
• RFLP method is used to construct
chromosome map of human being, rice,
wheat, maize & microbes.
• DNA finger printing.
• Single gene disease in man, plants & animals
can be identified with RFLP markers.
• Studies of gene flow.
• Used in phylogenetic studies.

2) Random Amplified Polymorphic DNAs-
• the RAPD is a PCR (polymerase chain reaction)
based method to detect variations between individuals
of a species by selective amplification of their genome.
• The method was developed by J. G. K. williams
et.al.in 1991.
• Its use when we do not know about target sequence.

• RAPDs
• ADVANTAGE
• Quick & easy to assay.
• Low quantities of template DNA required.
• Dominant markers.
• In expensive.
• Do not require any specific knowledge of the target.
• DISADVANTAGE
• Low reproducibility
• Highly sensitive & complicated procedure.
• PCR cycling conditions greatly influence the outcome.

• Uses of RAPD
1)RAPDs are used as genetic markers for
constructing genetic maps of higher
organisms. e.g.-helianthus, pines, rice, etc.
2) RAPD analysis helps us to identify
genes of high economic value through
comparison of RAPD fragments. Eg.-rice
,wheat, barley, maize, pea, etc.
3) RAPD analysis distinguishes one
individual from others of a species as
fingerprinting analysis.
4) RAPD markers helps to determine
specific genes in chromosomes.

3) Variable Number Of Tandem Repeats-
• The variation in the number of tandem repeats
between two or more individuals is called variable
number of tandem repeats.

Fig : Step Involved In VNTRs Analysis

• VNTRs analysis is useful for identification of
polygenic markers.
• It is an efficient method for the study of gene
mutations in human genome & others.
• It is used in mapping point mutations in genomes
of populations.
• It is useful to distinguish one individual from
others via DNA fingerprinting.
• Genomes of individuals can be characterized by
using VNTRs analysis.
USES OF VNTRS

4) Simple Sequence Repeats -
• Simple sequence repeats are 1-6 base pair
long sequences distributed along the
chromosome.
• There are also known as micro-satellites.

USES OF SSRS ANALYSIS
• SSRs analysis is used to identify genes
associated with specific traits.
• It is used in the construction of genetic
maps.
• It is used for the identification of
polymorphic genes.
• It distinguishes one organism from others
based on the difference inthe DNAs.

5) Amplified Fragment Length Polymorphism-
• The AFLP is a method to detect polymorphism
in the DNA throughout the genome.
• AFLP method was developed by VOS et.al in
1995.
• It is very useful to detect substitution variations
in the genomes.

• AFLP is used in DNA fingerprinting to
distinguish one individual from others without
the knowledge of their genomes.
• AFLP is used to construct high density genetic
maps of genomes of plants & animals.
• AFLP is used to identify mutation in the
genome.
Uses of AFLP

Seminar
On
MICROARRAYS
Submitted
By KANCHU MARKAM

INTRODUCTION
 A DNA microarray is a collection of microscopic DNA
spots to a solid surface.
 Each DNA spot contains picomoles of a specific DNA
sequence , known as probes.
 A microarray is a pattern of s s DNA probes which are
immobilized on a surface called a chip or a solid.
 The core principle behind microarrays is hybridization
between two DNA strands.
 Microarrays use hybridization to detect a specific DNA or
RNA in a sample.
 RNA microarray uses a million different prob

HISTORY
• Microarrays technology evolved from southern blotting.
• The concept of microarray first proposed in the late 1980 by
Augenlicht and his colleagues.
PRINCIPLE
• The core principle behind microarray is hybridization.
• Sample are labeled using fluorescent dyes.
• At least two sample are hybridized to chip.
• Complementary nucleic acid sequences get pair via hydrogen
bonds.
• Washing of non specific bonding sequences.
• [Sample preparation and labeling] [Hybridization]
• [Washing] [Image acquisition and data analysis]
•

TYPES OF BASED CHIP /MICROARRAYS
There are two types of DNA chip / microarrays-
(1) cDNA Based chip/ microarray
(2) Oligonucleotide Based chip / microarray
(1) cDNA Based chip/ microarray
• This type of chips are prepared by using cDNA.
• It is a called cDNA chips or cDNA microarray or probe DNA .
• The cDNAs are amplified by using PCR .
• Than these immobilized on a solid support made up of nylon filter of
glass slide.
• Small volume of this DNA preparation is spotted on solid surface
making physical contain between these two.
• DNA is delivered mechanically or in a or robotic manner.
• When one DNA spotting is done, the pin is washed and loaded with
fresh DNA to start the second cycle.

(2) Oligonucleotide Based Chip/Microarray
• In oligonucleotide microarray short DNA oligonucleotide are
spotted onto the arry.
• The main feature of Oligonucleotide is that each gene is
normally represented by more than one probe .
• The ensemble of probes mapping to different regions of the
gene is usually called probe set.
• Commercial oligonucleotide chips are available (ex: Affymetrix,
inc, gene chip system.)

APPLICATION
(1) Gene Expression Analysis-
• The process of measuring gene expression via cDNA is called
expression analysis.
• Not all the genes in the human genome are active at all times.
• Thousand genes are simultaneously assessed.
• Study the effects of certain treatment, Diseases, and development
stages on gene expression.
(2) Diseases Diagnosis-
• Help to investigate about different Diseases-
• E.g. Earlier cancers classified on the basis of the organs in which
the tumors development.
• Now, classify the types of car the patterns of gene activity in timer
cars.

(3) Extensive application in pharmacogenetics:
• Comparative analysis of the genes.
• Help the identification of the specific proteins produce
by diseased cell.
• Help to produce very effective drugs.
(4) Toxicological Research:
• A rapid platform for the research of the impact of
toxins on the cell and their passing on to the progeny.
• Important for toxicogenomic studies.

(5) Gene ID:
• Small microarray to check IDs of organisms in food and feed (like
cymo) and mycoplasma in cell culture .
• Mostly combining PCR and microarray technology.
(6) Advantages:
• Provide data for thousands genes.
• One experiment instead of many.
• Fast and easy to obtain results.
• Hugs step doser to discovering course for Diseases and cancer.
• Different parts of DNA can be used to study gene expression.
REFERENCE :
By - B.D. SINGH – Biotechnology Expanding Horizons

Seminar
On
BIOINFORMATICS
Submitted
By RESHMA SHEIKH

INTRODUCTION
• Translation of billion of character in DNA sequences that make the genome
into biologically meaningful information has given birth to a new field of
science called ‘Bioinformatics’.
• The term bioinformatics has been derived by combining biology and
informatics.
• “Bioinformatics (Biological information) is derived from the analysis of
a range of physical of biological characteristic of person.”
• A more precise definition of bioinformatics is a application of information
science (mathematics, Statics and computer sciences) to increase outer
understanding of biology.
• The biological information is collect from the computer hardware and
software for biodegradation of biological information such as the storage of
an invasive material that can be used to recycle an organic material.
• Bioinformatics is ‘MIS’ for molecular biology information.

HISTORY
• Bioinformatics has a long history that began in Mendel’s period when the
result of his experiments on plant hybridization were announced
recordically.
• In 1959 V.M. Ingram compared the amino acid sequences of sickle cell
haemoglobin with normal haemoglobin and found that two haemoglobin to
each other.
• IN 1962, Zuckerkandl and Pauling proposed the theory of ‘Molecular
Evolution.
• Marvin Carruthers and Leory Hood made a huge leap in bioinformatics
when they invented a method for automated DNA sequencing.

TYPES OF SEQUENCING USED IN BIOINFORMATICS
DNA Sequencing :
• Finding the base sequence of the DNA fragment is known as DNA sequencing.
• The light of database file has been sent to the database and sent to nucleotide database queries and analysis.
• BLAST and FASTA interface are very useful to analyze the DNA sequences by similarity searching.
• Genomic DNA and duplicate DNA for DNA analyzes are used as query.
RNA Sequencing :
• Finding the base sequencing of the RNA fragment is known as RNA sequencing.
• BLAST and FASTA interface are very useful to analyze the DNA sequences by similarity searching.
Protein Sequencing :
• The protein sequence of protein that detects the amino acid sequence is important for proteins.
• BLAST and FASTA interface are very useful to analyze.

Nomenclature
IUPAC (International Union of Pure and Applied Chemistry) has recommended
a nomenclature system.
Numerical data related to nucleotide and amino acid sequence can be
converted to digital from and is named.

Database
Database is a huge collection of electronic environments of data from a single
subject.
Database is heart of bioinformatics.
There were a total of 281 and their number are increasing rapidly.

Some Indian Database
• GM Crops Database – This Database, developed at NRC on plant
Biotechnology, New Delhi, is an interactive web resource storing information
on biosafety of transgenics.
• Including over 800 publication on the subject.
• Vanshanudhan – This database has been developed by NRC on
Plant Biotechnology, New Delhi scientist as an outcome of Indian
rice genome initiative. It contains information on the 59.298 rice
genes.

Database Retrieval and Analysis Tools
• Research and Analysis tools are required
for the use of database.
• Often these programs are called data
mining tools.
• There are several database retrieval tools
such as :

Database Retrieval and Analysis Tools
BLAST (Basic local Alignment Search Tool)
ENTREZ
OMIM (Online Mendalian Inheritance in Man)
PubMed (Publishers on Medicine)
TAXONOMY
LOCUS LINK
PROSITE
SRS (Sequence Retrieval System)

Uses of Bioinformatics Programs and its Used in Analysis:
I. Uses of Bioinformatics Program-
I. Discovery Of Genes
II. Identification of Functional Domains of Proteins
Detection of Noncoding RNA
Genome Annotation

II. Use of Bioinformatics Tools in Analysis
i. Processing Raw Information
ii. Genes
iii. Proteins
iv. Regulatory Sequence
Phylogenetic Relationship

CONCLUSION
• Bioinformatics deals with the use of computerized molecular biology with
the maintenance and data usage.
• This is a information technology.
• It is also called computational molecular biology.
• DNA Sequencing, DNA Fingerprinting and all Biological data stored and
analysis by Bioinformatics techniques.
• Genomics, Proteomics. Molecular marker and Microaarys all data analysis
and stored in computer software and Hardware by Bioinformation
Technology.
• They all technology developed to know all type of genomic and biological
information and their processing in plants and animal body.
REFERENCE : Biotechnology – V. Kumarsen.
Biotechnology – R. C. Dubey.
Biotechnology – B. D. Singh.

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