Techniques based on the principle of selectively amplifying a subset of restriction fragments from a complex mixture of DNA fragments obtained after digestion of genomic DNA with restriction endonucleases.
RAPD markers are decamer DNA fragments.
RAPD is a type of PCR reaction.
as the name suggest it is a fast method when compared to the traditional PCR medthod.
Sanger sequencing is a method of DNA sequencing based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication.
Techniques based on the principle of selectively amplifying a subset of restriction fragments from a complex mixture of DNA fragments obtained after digestion of genomic DNA with restriction endonucleases.
RAPD markers are decamer DNA fragments.
RAPD is a type of PCR reaction.
as the name suggest it is a fast method when compared to the traditional PCR medthod.
Sanger sequencing is a method of DNA sequencing based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication.
What is Genome,Genome mapping,types of Genome mapping,linkage or genetic mapping,Physical mapping,Somatic cell hybridization
Radiation hybridization ,Fish( =fluorescence in - situ hybridization),Types of probes for FISH,applications,Molecular markers,Rflp(= Restriction fragment length polymorphism),RFLPs may have the following Applications;Advantages of rflp,disAdvantages of rflp, Rapd(=Random amplification of polymorphic DNA),Process of rapd, Difference between rflp &rapd
MBB 501 PLANT BIOTECHNOLOGY
INFORMATION ABOUT DIFFERENT DNA MODIFYING ENZYMES
WHAT IS AN ENZYME?
Alkaline Phosphatase
Polynucleotide kinase
Terminal deoxyneucleotidyl transferase
Nucleases
Exonuclease
Bal31 Exonuclease III
Endonuclease
S1 endonulease
Deoxyribonuclease 1 (Dnase 1)
RNase A
RNase H
Restriction Endonuclease
PvuI
PvuII
Different types of endonuclease enzymes
The recognition sequences for some of the most frequently used restriction endonucleases.
Categorization of enzymes
Isoschizomers
Neoschizomers
Isocaudomers
SNP (Single Nucleotide Polymorphic), SNP mapping, SNP profile, SNP types, SNP analysis by gel electropherosis and by mass spectrometry, SNP effects, single strand conformation polymorphism, SNP advantages and disadvantages and application of SNP profile in drug choice
What is Genome,Genome mapping,types of Genome mapping,linkage or genetic mapping,Physical mapping,Somatic cell hybridization
Radiation hybridization ,Fish( =fluorescence in - situ hybridization),Types of probes for FISH,applications,Molecular markers,Rflp(= Restriction fragment length polymorphism),RFLPs may have the following Applications;Advantages of rflp,disAdvantages of rflp, Rapd(=Random amplification of polymorphic DNA),Process of rapd, Difference between rflp &rapd
MBB 501 PLANT BIOTECHNOLOGY
INFORMATION ABOUT DIFFERENT DNA MODIFYING ENZYMES
WHAT IS AN ENZYME?
Alkaline Phosphatase
Polynucleotide kinase
Terminal deoxyneucleotidyl transferase
Nucleases
Exonuclease
Bal31 Exonuclease III
Endonuclease
S1 endonulease
Deoxyribonuclease 1 (Dnase 1)
RNase A
RNase H
Restriction Endonuclease
PvuI
PvuII
Different types of endonuclease enzymes
The recognition sequences for some of the most frequently used restriction endonucleases.
Categorization of enzymes
Isoschizomers
Neoschizomers
Isocaudomers
SNP (Single Nucleotide Polymorphic), SNP mapping, SNP profile, SNP types, SNP analysis by gel electropherosis and by mass spectrometry, SNP effects, single strand conformation polymorphism, SNP advantages and disadvantages and application of SNP profile in drug choice
DNA profiling process, RFLP analysis, STR analysis by PCR, basic principle of dna fingerprinting, advantages and disadvantages of RFLP and STR analysis
this presentation is about the molecular markers as we all know the molecular markers are the DNA sequences it can be easily detected and its inheritance is easily monitored.so the main basics of the molecular markers is the polymorphic nature so it can used as molecular markers.and this will gives you the idea about AFLP, RFLP, RAPD, SNPS,ETC.
Molecular markers- RFLP, RAPD, AFLP, SNP etc.Cherry
Molecular markers are identifiable DNA sequences used to locate genes associated with specific traits or genetic conditions.
A molecular marker is a specific gene fragment present at a specific position called ‘locus’ (pleural loci) in the genome of a cell.
In the pool of unknown DNA or in a whole chromosome, these molecular markers help in identification of particular sequence of DNA at particular location.
Molecular marker General introduction by K. K. SAHU Sir.KAUSHAL SAHU
Introduction
Molecular marker
Characterstics of molecular marker
Types of molecular marker
. Non PCR Based
. PCR Based
RFLP
RAPD
AFLP
SSR
SNP
Conclusion
References
TYPES OF MOLECULAR MARKERS,ITS ADVANTAGES AND DISADVANTAGESANFAS KT
Types of molecular markers (genetics)
ITS ADVANTAGES AND DISADVANTAGES
What is a genetic marker?
RFLP: Restriction fragment length polymorphism
AFLP: Amplified fragment length polymorphism
RAPD: Random amplification of polymorphic DNA
ISSR: Inter simple sequence repeat
STR: Short tandem repeats
SCAR: Sequence characterized amplified region
SNP: Single nucleotide polymorphism
SSR: Simple sequence repeat
Molecular Markers and Their Application in Animal Breed.pptxTrilokMandal2
Molecular markers have had a significant impact on breed development and conservation efforts, transforming genetics and offering vital insights into genetic diversity, lineage tracing, and genotype characterization. The importance of molecular markers in improving genetic gains, facilitating breeding programs, and preserving genetic diversity for the long-term sustainability of the animal population has been underlined in this review paper. Emerging advancements in molecular marker technology show enormous potential for improving and conserving breeds. Deeper insights into the genetic basis of complex traits will be provided through GWAS, CRISPR/Cas9, gene editing technologies, and sequencing technologies, resulting in faster genetic gains. Breeders and conservationists will be able to make more informed judgments thanks to these technologies. In conclusion, molecular markers have had a significant impact on breed conservation and enhancement. Their innovations have changed the industry and given both conservationists and breeders vital knowledge. We can pave the road for more effective and sustainable genetic improvement and the preservation of biodiversity for future generations by combining the power of molecular markers with conventional breeding and conservation techniques.
Similar to molecular marker RFLP, and application (20)
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
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
1. Molecular Marker
RFLP
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )
3. INTRODUCTION
Restriction Fragment Length Polymorphism (RFLP) is a
technique in which organisms may be differentiated by analysis of
patterns derived from cleavage of their DNA.
If two organisms differ in the distance between sites of cleavage
of a particular restriction endonuclease, the length of the
fragments produced will differ when the DNA is digested with a
restriction enzyme.
The similarity of the patterns generated can be used to
differentiate species from one another .
First developed in the 1970s, it still has many uses.
4. RFLP
RFLP stands for "restriction fragment length
polymorphism."
The first two words refer to the process of DNA
fragmenting with specially applied enzymes.
Once this takes place, the DNA strands break up into
various lengths.
Polymorphism in Greek word means "many shapes."
This word references the multiple shapes, or lengths, that
can result in a definitive match distinctive to each human
being.
5. Analysis technique
1. Extraction
The first step is extraction of the DNA from the
sample, be it blood, saliva, semen or some other
biological sample .
2. Production of Restriction Fragments
The purified DNA is then cut into fragments by
RESTRICTION ENZYMES.
6. 3. Electrophoresis
• The restriction fragments have negative charge and can be
separated by a technique called GEL ELECTROPHORESIS, which
separates the pieces of DNA based on their size.
• with the smaller fragments migrating farther than the larger
fragments.
7. 4. DNA transfer by Southern blotting
• DNA transfer is called ‘Southern blotting’. In this method, the
gel is first denatured in a basic solution and placed in a tray.
• A porous nylon or nitrocellulose membrane is laid over the gel,
and the whole weighted down. All the DNA restriction
fragments in the gel transfer as single strands by capillary
action to the membrane.
• All fragments retain the same pattern on the membrane as on
the gel.
8. 5. DNA hybridization
• The membrane with the target DNA is incubated with the
DNA probe.
• Incubation conditions are such that if strands on the
membrane are complementary to those of the probe,
hybridization will occur and labelled duplexes formed.
11. APPLICATIONS OF RFLP
APPLICATION OF RFLP IN FORENSIC
APPLICATION OF RFLP IN DISEASE PROGNOSIS
APPLICATION OF RFLP IN GENETIC COUNSELING
APPLICATION OF RFLP IN PEDIGREE
APPLICATION OF RFLP IN VARIETAL
12. APPLICATION OF RFLP IN FORENSIC
RFLP was one of the first applications of DNA analysis
to forensic investigation.
Any type of organism can be identified by examination
of DNA sequences unique to that species.
To identify individuals, forensic scientists scan 13 DNA
regions, that vary from person to person and use the data
to create a DNA profile of that individual.
There is an extremely small chance that another person
has the same DNA profile for a particular set of 13
regions.
Using samples from blood, bone, hair, and other body
tissues and products.
13. Some Examples of RFLP Uses for Forensic Identification
• In criminal cases, this generally involves obtaining samples from
crime-scene evidence and a suspect, extracting the DNA, and
analyzing it for the presence of a set of specific DNA regions.
• A series of probes bound to a DNA sample creates a distinctive
pattern for an individual.
• Forensic scientists compare these DNA profiles to determine
whether the suspect's sample matches the evidence sample.
• If the sample profiles don't match, the person did not contribute
the DNA at the crime scene.
• If the patterns match, the suspect may have contributed the
evidence sample.
• determine paternity; that is, who the father of the child really
is.
14. APPLICATION OF RFLP IN
DISEASE PROGNOSIS
• RFLP allows an investigator to a potentially defective
DNA sequence, it can be used effectively in the
diagnosis of diseases in which a specific mutational site.
• Diagnoses utilizing RFLP linkage analysis can be
extended further by comparing genotypes between a
known whose status is unknown, the approach is
applicable to single gene disorders inherited as
autosomal dominant , or x-linked traits .
• Cloned genes can be modified with specific mutational
changes at specific sites by using the technique of site
directed mutagenesis.
16. APPLICATION OF RFLP IN
GENETIC COUNSELING
• If a particular RFLP is usually associated with
a particular genetic disease, then the presence
or absence of that RFLP can be used to counsel
people about their risk of developing or
transmitting the disease.
17. APPLICATION OF RFLP IN PEDIGREE
• In humans, one mating (one pair of parents) rarely has enough
children to give reliable ratios. In that case one can still do pedigree
analysis. Modern pedigree analysis is much more sophisticated than
anything we can do.
• The pedigree shows the inheritance of a RFLP marker through three
generations in a single family. A total of 8 alleles (numbered to the
left of the blots) are present in the family. The RFLPs of each
member of the family are placed directly below his (squares) or her
(circles) symbol and RFLP numbers.
18. APPLICATION OF RFLP IN VARIETAL
• RFLP analysis is now a standard, well-tested procedure for
estimation of genetic diversity.
• We have evaluated RFLP markers as tools for assessing genetic
variation and determining the relationships among different
populations from a wide range of geographical origins and
representing Species.
• RFLP uses in Verify varietal identity and stability.
19. ADVANTAGES OF RFLPS
Highly robust methodology with good transferability between
laboratories.
Co-dominantly inherited and, as such, can estimate
heterozygosity.
No sequence information required.
Because based on sequence homology, highly recommended
for phylogenetic analysis between related species.
Well suited for constructing genetic linkage maps .
20. DISADVANTAGES OF RFLPs
Large amounts of DNA required.
Low levels of polymorphism in some species.
Need a suitable probe library.
Time consuming, especially with single-copy
probes.
Costly
Distribution of probes to collaborating
laboratories required.
21. CONCLUSIONS
• The actual analysis time is lengthy and
complicated, but is also less prone to error.
• RFLP analysis is most common techniques
used in a variety of scientific areas, including
genetics and forensics.
• Takes advantage of differences in DNA
between individuals that result in different
fragments when digested with restriction
enzymes.
22. REFERENCES
• BOOKS
Cell and molecular biology by Gerald karp 6th
edition.
• PDF FAILS ( Date- 140313,Time -08:00 PM )
1. 18591_restriction fragment length polymorphism(1).pdf
2. Mol Markers Vol1III RFLPs(1).pdf