STS stands for sequence tagged site which is short DNA sequence, generally between 100 and 500 bp in length, that is easily recognizable and occurs only once in the chromosome or genome being studied.
Genomics C elegan genome and model organismiqraakbar8
The C. elegans genome is about 100 million base pairs long and consists of six pairs of chromosomes in hermaphrodites or five pairs of autosomes with XO chromosome in male C. elegans and a mitochondrial genome. The genome contains an estimated 20,470 protein-coding genes.
STS stands for sequence tagged site which is short DNA sequence, generally between 100 and 500 bp in length, that is easily recognizable and occurs only once in the chromosome or genome being studied.
Genomics C elegan genome and model organismiqraakbar8
The C. elegans genome is about 100 million base pairs long and consists of six pairs of chromosomes in hermaphrodites or five pairs of autosomes with XO chromosome in male C. elegans and a mitochondrial genome. The genome contains an estimated 20,470 protein-coding genes.
Bioinformatics in biotechnology by kk sahu KAUSHAL SAHU
Introduction
Bioinformatics – definition
History
Required skills
Core areas of bioinformatics
Components of bioinformatics
Nomenclature system in bioinformatics
Biological databases
Types of database
Bioinformatics tools
Applications of bioinformatics
Conclusion
References
Lecture delivered by T. Ashok Kumar, Head, Department of Bioinformatics, Noorul Islam College of Arts and Science, Kumaracoil, Thuckalay, INDIA. UGC Sponsored National Workshop on BIOINFORMATICS AND GENOME ANALYSIS for College Teachers on August 11 & 12, 2014. Organized by Centre for Bioinformatics, Department of Zoology, NMCC.
Gene mapping, describes the methods used to identify the locus of a gene and the distances between genes. The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome. Molecular markers come in all forms.
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
Introduction
History
How are new drug discovered?
Bioinformatics in drug discovery
Tools for drug discovery
Successful drug
Software for drug discovery
Conclusion
References
Introduction
History
Genetic mapping
DNA Markers
Physical mapping
Importance
Drawback
Conclusion
References
uses genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.
Genetic techniques include cross-breeding experiments or, in the case of humans, the examination of family histories (pedigrees).
this is done by me and my team mates of Wayamba University Sri Lanka for our project.From now we decided to allow download this file.I would be greatful if you could send your comments..
And I'm willing to help you in similar works.I'm in final year of my degree(.BSc Biotechnology)..
pubudu_gokarella@yahoo.com
Bioinformatics in biotechnology by kk sahu KAUSHAL SAHU
Introduction
Bioinformatics – definition
History
Required skills
Core areas of bioinformatics
Components of bioinformatics
Nomenclature system in bioinformatics
Biological databases
Types of database
Bioinformatics tools
Applications of bioinformatics
Conclusion
References
Lecture delivered by T. Ashok Kumar, Head, Department of Bioinformatics, Noorul Islam College of Arts and Science, Kumaracoil, Thuckalay, INDIA. UGC Sponsored National Workshop on BIOINFORMATICS AND GENOME ANALYSIS for College Teachers on August 11 & 12, 2014. Organized by Centre for Bioinformatics, Department of Zoology, NMCC.
Gene mapping, describes the methods used to identify the locus of a gene and the distances between genes. The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome. Molecular markers come in all forms.
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
Introduction
History
How are new drug discovered?
Bioinformatics in drug discovery
Tools for drug discovery
Successful drug
Software for drug discovery
Conclusion
References
Introduction
History
Genetic mapping
DNA Markers
Physical mapping
Importance
Drawback
Conclusion
References
uses genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.
Genetic techniques include cross-breeding experiments or, in the case of humans, the examination of family histories (pedigrees).
this is done by me and my team mates of Wayamba University Sri Lanka for our project.From now we decided to allow download this file.I would be greatful if you could send your comments..
And I'm willing to help you in similar works.I'm in final year of my degree(.BSc Biotechnology)..
pubudu_gokarella@yahoo.com
Two approaches (clone by clone & whole genome shotgun).
Types of DNA sequencing ( 1st, next and 3rd).
Crop genomes sequenced . (Example :Arabidopsis,Rice, Pigeon pea)
Genome project of Human and methods of sequencing human genome; Genome project of Rice and its post genome sequencing era; Arabidopsis genome project: Why Rice and Arabidopsis chosen for genome project?
Introduction
History
Tumor suppressor gene- pRB
- RB gene
- Role of RB in regulation of cell cycle
- Tumor associated with RB gene mutation
Tumor suppressor gene- p53
- What is p53 gene?
- Function of p53 gene
- How it regulates cell cycle
- What happen if p53 gene inactivated
- Cancer associated with p53 mutation
- Conclusion
- References
Introduction
Definition
History
Two hit hypothesis
Functions
Mutation in tumor suppressor genes
What is mutation
Inherited mutation of TSGs
Acquired mutation of TSGs
What is Oncogenes?
TSGs and Oncogenes : Brakes and accelerators
Stop and go signal
Examples of TSGs:
RB-The retinoblastoma gene
P53 protein
TSGs &cell suicide
Conclusion
References
Introduction
Protein synthesis
Synthesis of secretory proteins on membrane-bound ribosomes
Processing of newly synthesized proteins in the ER
Synthesis of integral membrane protein on membrane bound ribosomes
Maintenance of membrane asymmetry
Conclusion
Reference
Introduction
Definition
Factors required for Translation
Formation of aminoacyl t-RNA
1)Activation of amino acid
2) Transfer of amino acid to t-RNA
Translation involves following steps:-
1)Initiation
2)Elongation
3)Termination
Conclusion
Reference
Introduction
Definition
History
central dogma
Major components
mRNA,tRNA,rRNA
Energy source
Amino acids
Protien factor
Enzymes
Inorganic ions
Step involves in translation:
Aminoacylation of tRNA
Initiation
Elongation
termination
Importance of translation
Conclusion
Reference
Introduction
Protein modifications
Folding
Chaperon mediated
Enzymatic
Cleavage
Addition of functional groups
Chemical groups
Hydrophobic groups
Proteolysis
Conclusion
Reference
INTRODUCTION
HISTORY
WHAT IS TRANSCRIPTION
PROKARYOTIC TRANSCRIPTION
STEPS OF TRANSCRIPTION
HOW TRANSCRIPTION OCCURS
PROCESS OF TRANSCRIPTION
Initiation
Elongation
Termination
CONCLUSION
REFRENCES
Enzyme Kinetics and thermodynamic analysisKAUSHAL SAHU
Introduction
Kinetics and thermodynamicSG
Thermodynamic in enzymatic reactions
balanced equations in chemical reactions
changes in free energy determine the direction & equilibrium state of chemical reactions
the rates of reactions
Factors effecting enzymatic activity
(i) Enzyme concentration.
(ii) Substrate concentration.
(iii)Temperature
(iv) pH.
(v) Activators.
(vi)Inhibitors
Michaelis-menten equation
CONCLUSIONS
REFERENECES
Recepter mediated endocytosis by kk ashuKAUSHAL SAHU
INTRODUCTION
DEFINITION OF RECEPTOR MEDIATED ENDOCYTOSIS
WHAT TYPE OF LIGANDS ENTER BY RME?
FORMATION OF CLATHRIN-COATED VESICLES
TRISKELIONS
ROLE OF DYNAMIN IN THE FORMATION OF CLATHRIN-COATED VESICLES
ROLE OF PHOSPHOLIPIDS IN THE FORMATION OF COATED VESICLES
ENDOCYTIC PATHWAY
LDLs AND CHOLESTROL METABOLISM
CONCLUSION
REFERENCES
The delivery of newly synthesized protein to their proper cellular destination, usually referred to as protein targeting or sorting.
The mode of protein transport depends chiefly on the location in the cell cytoplasm of the polysomes involved in protein synthesis.
There are two modes of protein sorting:-
1) Co - translational Transportation.
2) Post - translational Transportation.
Prokaryotic translation machinery by kk KAUSHAL SAHU
Introduction
Definition
Factors required for Translation
Formation of aminoacyl t-RNA
1)Activation of amino acid
2) Transfer of amino acid to t-RNA
Translation involves following steps:-
1)Initiation
2)Elongation
3)Termination
Conclusion
Reference
Nucleophilic Addition of carbonyl compounds.pptxSSR02
Nucleophilic addition is the most important reaction of carbonyls. Not just aldehydes and ketones, but also carboxylic acid derivatives in general.
Carbonyls undergo addition reactions with a large range of nucleophiles.
Comparing the relative basicity of the nucleophile and the product is extremely helpful in determining how reversible the addition reaction is. Reactions with Grignards and hydrides are irreversible. Reactions with weak bases like halides and carboxylates generally don’t happen.
Electronic effects (inductive effects, electron donation) have a large impact on reactivity.
Large groups adjacent to the carbonyl will slow the rate of reaction.
Neutral nucleophiles can also add to carbonyls, although their additions are generally slower and more reversible. Acid catalysis is sometimes employed to increase the rate of addition.
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Toxic effects of heavy metals : Lead and Arsenicsanjana502982
Heavy metals are naturally occuring metallic chemical elements that have relatively high density, and are toxic at even low concentrations. All toxic metals are termed as heavy metals irrespective of their atomic mass and density, eg. arsenic, lead, mercury, cadmium, thallium, chromium, etc.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
3. Introduction
Genome mapping, also called gene mapping, is the creation of a genetic
map assigning DNA fragments to chromosomes.
A genome map helps scientists navigate around the genome. Like road
maps and other familiar maps, a genome map is a set of landmarks that
tells people where they are, and helps them get where they want to go.
In most living things, the genome is made of a chemical called DNA.
Each one of earth's species has its own distinctive genome.
4. Definition
The technique of locating the gene is called genome mapping.
It describes the order of genes or other markers and the spacing
between them on each chromosome.
The first genome of a living organism was Haemophilus
influenza in 1995.
5. History
1953 – Watson-crick structure of DNA published.
1975 – F. Sanger and independently A. Maxam & W.Gilbert, develop
methods for sequencing DNA.
1981 – Human mitochondrial DNA sequenced ; 16,569 bp.
1995 – First complete sequence of a bacterial genome, Haemophilus
influenza, by TIGR.
1996 – Completion of yeast genome, first eukaryotic genome
sequence.
1 dec. 1999 – Sequence of first complete human chromosome
published.
6. Genes & Genomes
Genes can be defined as the “functional part of
DNA”. It is a small defined section of the entire
genome sequences and each gene has a specific
unique purpose.
Genome can be defined as the “total genetic
constituent of an organism”.
8. Mapping techniques
Two types of techniques are their :- 1 )Genetic mapping
2) Physical mapping
Genetic mapping
Genetic mapping is based on the use of genetic techniques to construct maps
showing the positions of genes and other sequence features on a genome.
The first genetic maps, constructed in the early decades of the 20th century for
organisms such as the fruit fly, used genes as markers.
9. DNA markers for genetic mapping
Genes are very useful markers but they are by no means ideal. One problem,
especially with larger genomes such as those of vertebrates and flowering
plants, is that a map based entirely on genes is not very detailed.
We need other types of marker.
Mapped features that are not genes are called DNA markers
There are three types of DNA sequence feature that satisfy this requirement:
restriction fragment length polymorphisms (RFLPs), simple sequence length
polymorphisms (SSLPs), and single nucleotide polymorphisms (SNPs).
10. RFLPs - RFLPs were the first type of DNA marker to be studied. RFLPs can
be used to measure recombination rates which can lead to a genetic map with
the distance between RFLP loci measured in centi Morgans. Analysis of RFLP
variation in genomes was a vital tool in genome mapping and genetic disease
analysis. There are thought to be about 105 RFLPs in the human genome, but
of course for each RFLP there can only be two alleles.
SSLPs - SSLPs are arrays of repeat sequences that display length variations,
different alleles containing different numbers of repeat units. Unlike RFLPs,
SSLPs can be multi-allelic.
11. SNPs - These are positions in a genome where some individuals have one
nucleotide (e.g. a G) and others have a different nucleotide (e.g. a C). There
are vast numbers of SNPs in every genome. In the human genome there are
at least 1.42 million SNPs.
12. Physical mapping
Physical mapping uses molecular biology
techniques to examine DNA molecules directly
in order to construct maps showing the
positions of sequence features, including genes.
13. Physical mapping techniques
a)Fluorescence in situ
hybridization (FISH)
In situ hybridization is a version of hybridization
analysis in which an intact chromosome is
examined by probing it with a labeled DNA
molecule. The position on the chromosome at
which hybridization occurs provides information
about the map location of the DNA sequence
used as the probe.
14. b) Sequence tagged site (STS) mapping
To generate a detailed physical map of a large genome we need,
ideally, a high-resolution mapping procedure that is rapid and not
technically demanding.
At present the most powerful physical mapping technique, and
the one that has been responsible for generation of the most
detailed maps of large genomes, is STS mapping(olson et al).
A STS is simply a short DNA sequence, generally between 100
and 500 bp in length.
15. Genomic databases
•Genomes Server -this server gives access to a hundreds of
complete genome sequences, including those from archaea, bacteria,
eukaryota, organelles, plasmids and viruses.
•Karyn's Genomes - contains general information about organisms
whose genomes are completely sequenced. The main aim of the database is
to provide a short and concise explanation as to why it is important to obtain
these organisms genomic sequences.
•FlyBase - the database for Drosophila melanogaster is one of the best-
curated genetic databases.
16. •MGD- the 'Mouse Genome Database' is one of the most
comprehensively curated genetic databases.
•RGD- the 'Rat Genome Database' curates and integrates rat
genetic and genomic data and provides access to this data to support
research using the rat as a genetic model for the study of human
disease.
•Plant databases- MaizeDB is the database for genetic data on
maize. The 'Plant Genome Information Resource' (PGDIC) provides
access to many different plant genome databases, including
chlamydomonas, cotton, alfalfa, wheat, barley, rye, rice, millet,
sorghum and species of solanaceae and trees. MENDEL is a plant-wide
database for plant genes.
17. •GOLD – genome online database is a World Wide Web resource for
comprehensive access to information regarding genome sequencing project.
18. •MBGD– microbial genome database is a database for comparative
analysis of completely sequenced microbial genomes, the no. of which is
now growing rapidly.
19. TOOLS
The Bioinformatics tools are the software programs for the saving, retrieving
and analysis of Biological data and extracting the information from them.
This tool compares nucleotide or protein sequences to genomic sequence
databases and calculates the statistical significance of matches.
BLAST (BASIC LOCAL ALIGNMENT SEARCH TOOL)
It is a program for sequence similarity searching developed at the NCBI.
It identifies genes and genetic features.
20. FASTA (FAST-ALL)
FASTA is a DNA and protein sequence alignment software package.
It is used for a fast protein or fast nucleotide comparison.
EMBOSS
EMBOSS (The European Molecular Biology Open Software Suite) is a new,
free open source software analysis package specially developed for the
needs of the molecular biology user community.
with in EMBOSS you will find around 100 programs (applications) for
sequence alignment, database searching with sequence patterns, nucleotide
sequence pattern analysis etc.
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/
21. Clustalw
ClustalW is a general purpose multiple sequence alignment program for
DNA or proteins.
It produces biologically meaningful multiple sequence alignments of
divergent sequences, calculates the best match for the selected
sequences, and lines them up so that the identities, similarities and
differences can be seen.
RasMol
It is a powerful research tool to display the structure of DNA, proteins, and
smaller molecules. Protein Explorer, a derivative of RasMol, is an easier to
use program.
22. SVA
Sequence Variant Analyzer (SVA) is a tool developed to analyze genetic
variants from whole-genome sequencing studies.
Software: SequenceVariantAnalyzer
URL: http://www.svaproject.org/
23. Human genome project
The Human Genome Project (HGP) was a 13-year project coordinated by
the U.S. Department of Energy and the National Institutes of Health.
Project goals were-
to identify all the approximately 20,000-25,000 genes in human DNA
.
determine the sequences of the 3 billion chemical base pairs that make up human
DNA.
store this information in databases,.
improve tools for data analysis.
24. Conclusion
Current & potential applications of genome research will
address national needs in molecular medicine, waste control
and environmental cleanup, biotechnology, energy sources,
and risk assessment.
The knowledge of genome mapping would lead to better
medical management of the diseases and pharmaceuticals
discovery.
25. References
C.S.V. Murthy, Bioinformatics. First edition
David W. Mount, Bioinformatics:sequence & genome analysis.
2nd edition
B.D.Singh, Biotechnology. Expanding Horizons. 1st edition
Websites-
www.genomenewsnetwork.org
www.ncbi.nlm.nih.gov
www.genome.gov
www.tigr.org/