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
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.
BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
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.
BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
Genomic library and shotgun sequencing. It includes the topics about genomic library,construction method, its uses and applications, shotgun sequencing, difference between random and whole genome sequencing, its advantages and disadvantages etc.
A physical map of a chromosome or a genome that shows the physical locations of genes and other DNA sequences of interest. Physical maps are used to help scientists identify and isolate genes by positional cloning.
According to the ICSM (Intergovernmental Committee on Surveying and Mapping), there are five different types of maps: General Reference, Topographical, Thematic, Navigation Charts and Cadastral Maps and Plans.
Sanger sequencing is one of the DNA sequencing methods used to identify and determine the sequence (Nucleotide) of DNA .This is an enzymatic method of sequencing developed by Fred Sanger.
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.
This presentation covers a general introduction to expression vector, its components, types, and its application. Then it covers some of the expression system with examples.
Genomic library and shotgun sequencing. It includes the topics about genomic library,construction method, its uses and applications, shotgun sequencing, difference between random and whole genome sequencing, its advantages and disadvantages etc.
A physical map of a chromosome or a genome that shows the physical locations of genes and other DNA sequences of interest. Physical maps are used to help scientists identify and isolate genes by positional cloning.
According to the ICSM (Intergovernmental Committee on Surveying and Mapping), there are five different types of maps: General Reference, Topographical, Thematic, Navigation Charts and Cadastral Maps and Plans.
Sanger sequencing is one of the DNA sequencing methods used to identify and determine the sequence (Nucleotide) of DNA .This is an enzymatic method of sequencing developed by Fred Sanger.
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.
This presentation covers a general introduction to expression vector, its components, types, and its application. Then it covers some of the expression system with examples.
Molecular markers for measuring genetic diversity Zohaib HUSSAIN
Molecular markers for measuring genetic diversity
Introduction:
The molecular basis of the essential biological phenomena in plants is crucial for the effective conservation, management, and efficient utilization of plant genetic resources (PGR).
Determining genetic diversity can be based on morphological, biochemical, and molecular types of information. However, molecular markers have advantages over other kinds, where they show genetic differences on a more detailed level without interferences from environmental factors, and where they involve techniques that provide fast results detailing genetic diversity
Comparison of different methods
Morphological characterization does not require expensive technology but large tracts of land are often required for these experiments, making it possibly more expensive than molecular assessment. These traits are often susceptible to phenotypic plasticity; conversely, this allows assessment of diversity in the presence of environmental variation.
Biochemical analysis is based on the separation of proteins into specific banding patterns. It is a fast method which requires only small amounts of biological material. However, only a limited number of enzymes are available and thus, the resolution of diversity is limited.
Molecular analyses comprise a large variety of DNA molecular markers, which can be employed for analysis of variation. Different markers have different genetic qualities (they can be dominant or co-dominant, can amplify anonymous or characterized loci, can contain expressed or non-expressed sequences, etc.).
Genetic marker
The concept of genetic markers is not a new one; in the nineteenth century, Gregor Mendel employed phenotype-based genetic markers in his experiments. Later, phenotype-based genetic markers for Drosophila melanogaster led to the founding of the theory of genetic linkage. A genetic marker is an easily identifiable piece of genetic material, usually DNA that can be used in the laboratory to tell apart cells, individuals, populations, or species. The use of genetic markers begins with extracting proteins or chemicals (for biochemical markers) or DNA (for molecular markers) from tissues of the plant (for example, seeds, foliage, pollen, sometimes woody tissues).
Molecular markers In genetics, a molecular marker (identified as genetic marker) is a fragment of DNA that is associated with a certain location within the genome. Molecular markers which detect variation at the DNA level such as nucleotide changes: deletion, duplication, inversion and/or insertion. Markers can exhibit two modes of inheritance, i.e. dominant/recessive or co-dominant. If the genetic pattern of homozygotes can be distinguished from that of heterozygotes, then a marker is said to be co-dominant. Generally co-dominant markers are more informative than the
Taxonomy is the branch of science concerned with the classification of organisms. A taxonomic designation is more than just a name. Ideally, it reflects evolutionary history and the relationship between organisms. Traditionally, taxonomic classification has relied upon morphological features and physiological characteristics. However, for bacterial taxonomy, phenotypic approaches have proven insufficient. Unrelated bacteria can exhibit identical traits, closely related bacteria can have divergent features, and methods for accurate identification may be too cumbersome for routine use. In contrast, molecular taxonomy approaches use data derived from hereditary material and provide a robust view of genetic relatedness. Advances in technology have been accompanied by improvements in the cost, speed, and availability of molecular methods. Here, we provide a brief history of approaches to prokaryotic classification and describe how molecular taxonomy is redefining our understanding of bacterial evolution and the tree of life.
Dr. S. MANIKANDAN, M.Sc., Ph.D
Lecturer in Botany
Thiruvalluvar University Model Constituent College,
Tittagudi 606 106, Tamil Nadu, India.
Email id: drgsmanikandan@gmail.com
this is a presentation on molecular markers that include what is molecular marker, it's types, biochemical markets (alloenzyme), it's classification, data analysis and it's applications
Introduction- PTERIDOPHYTES
Pteridophytes in the broad interpretation of the term are vascular plants (plants with xylem & phloem) that reproduce & disperse via spores, because they produce neither flowers nor seeds, they are refered to as CRYPTOGAMS.
The 305 genera & 13,000 species of pteridophytes found throughout the world.
The pteridophyte includes Clubmosses,SPike-mosses, Quilworts,Horsetails,Ferns.
FERNS -Adiantum (Maiden-hair fern)
(Family-Pteridaceae)
A.pedatum, A. raddianum(Delta-maiden hair),
Asplenium, (FAMILY-ASPLENACEAE)- Asplenium nidus
(Birds nest fern),
Blechnum, (family-blechnaceae) , Cyrotomium, (family-dryopteridaceae), Davalia, (family-davalliaceae), Doryopteris
(family-pteridaceae), Nephrolepis,(family-lomariopsidaceae) -N. biserrata furcans, N. exallata mucosa, Pityrogramma
(family-pteridaceae), P.calomelanos (silver fern), P.chrysophylla (golden fern), Platycerium family-polypodiaceae
P. bifurcatum, P.willinckii (silver staghorn),Polypodium(family-polypodiaceae), Polystichum (family-dryopteridaceae),Pteris
(family- pteridaceae), CONCLUSION
Introduction -Remote means – far away ; Sensing means – believing or observing or acquiring some information.
Remote sensing means acquiring information of things from a distance with sensors. (without touching the things)
Sensors are like simple cameras except that they not only use visible light but also other bands of the electromagnetic spectrum such as infrared, microwaves and ultraviolet regions.
Distance of Remote Sensing, Definition of remote sensing - Remote Sensing is:
“The art and science of obtaining information about an object without being in direct contact with the object” (Jensen 2000).
India’s National Remote Sensing Agency (NRSA) defined as : “Remote sensing is the technique of deriving information about objects on the surface of the earth without physically coming into contact with them.”
Remote Sensing Process, - (A) Energy Source or Illumination.
(B) Radiation and the Atmosphere.
(C) Interaction with the Target.
(D) Recording of Energy by the Sensor.
(E) Transmission, Reception, & Processing.
(F) Interpretation and Analysis.
(G) Application.
Remote sensing platforms , History of Remote Sensing, Applications of remote sensing - In Agriculture, In Geology, Applications of National Priority.
INTRODUCTION -
The source of sugar can be stems or underground roots.
Two principle source of sugar are Sugarcane & sugar beet.
Also called as industrial plants
The sources of storage sugars are;
Stems- Sugarcane, Sugar maple
Roots- Beets, carrots
Flowers- palm
SUGARCANE (Saccharum officinarum)
SYSTEMATIC POSIYION –
Class- Liliopsida
Order- Poales
Family- Poaceae
Genus- Saccharum
Species- officinarum
Vernacular name- Ganna
Botanical & ecological description of sugarcane, SUGARCANE GROWING REGIONS, Cultivation of sugarcane, Processing of sugarcane, Uses of sugarcane
Sugar beet (Beta vulgaris) - SYSTEMATIC POSITION-
Family-Amaranthaceae
Genus- Beta
Species- vulgaris
Vernacular name- chukandar
Cultivation of Sugar beet, harvesting of Sugar beet, Processing of sugar extraction from Sugar beet, By-products of Sugar beet, Uses of sugar beet,
PALMYRA PALM- Manufacture OF Jaggery
Sweet potato (Ipomoea batatas) -
SYSTEMATIC POSITION-
Class - Magnoliopsida
Order- Solanales
Family-Convolvulaceae
Genus –Ipomoea
Species- batatas
USES OF SWEET POTATO,
Stevia rebaudiana- USEs OF STEVIA
Other sugars, Importance of sugar
Introduction,In some fungi ,true sexual cycle comprising of nuclear fusion and meiosis is absent.
These fungi derive the benefits of sexuality through a cycle know as parasexuaL cycle.
First Reported by- Gudio Pontecorvo and J.A.Roper(1952)
Parasexual cycle was reported in
Aspergillus nidulans,the imperfect stage of Emericella nidulans.
Since then parasexual cycle has been discovered not only in several members of Deutromycetes but also in fungi belonging to Ascomycetes and Basidiomycetes.
DEFINETION - Parasexuality is defined as a cycle in which Plasmogamy, Karyogamy and Meiosis [Haploidization] take place in sequence but not at a specified time or at specified points in the life cycle of an organism.
Generally parasexual cycle occurs in those fungi in which true sexual cycle does not take place.
Parasexualcycle also know as Somatic recombination. PASEXUALITY ALSO REPORTED IN SOME ORGANISMS- Aspergillus nigar, Penicillium crysogenum, STEPS OF PARASEXUAL CYCLE - 1) ESTABLISHMENT OF HETEROKARYOSIS, 2) Formation of Heterozygous DIPLOIDS, 3) occasional mitotic crossing-over during multiplication of diploid nuclei, 4)occasional haplodization through aneuploidy , COMPARISION BETWEEN SEXUAL AND PARASEXUAL CYCLE, IMPORTANCE OF PARASEXUALITY, C0NCLUSION
Environmental management: Introduction and scopeRashmi Yadav
What is Environment ? The sum total of all surroundings of a living organism, including natural forces & other living things which provide conditions for development & growth as well as of danger & damages.
INTRODUCTION, Environmental management ,DEFINITION – “Environmental management system refers to the management of an organization's environmental programs in a comprehensive, systematic, planned and documented manner. It includes the organizational structure, planning & resources for developing, implementing and maintaining policy for environmental protection.”
Characteristics of environmental management, Two main standards- BS7750,ISO 14001, Schemes of environmental management- Eco management and Audit schemes(EMS), Why have an EMS? Scope of environmental management, Importance of environmental management, Role of remote sensing in environmental management
Introduction,Definition, Cycling elements, Types of biogeochemical cycle- Gaseous cycle and sedimentary cycle Nitrogen cycle, steps of Nitrogen cycle- Nitrogen fixation, Nitrification, Assimilation Ammonification, and Denitrification and ecological function of nitrogen, use of nitrogen cycle phosphorus cycle, steps of phosphorus cycle, biological functions of phosphorus cycle and other functions of phosphorus and conclusion
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
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.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
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.
Richard's aventures in two entangled wonderlandsRichard 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.
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.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...
Genome mapping
1.
2. The haploid set of chromosomes
in a gamete or microorganisms, or
in each cell of multicellular
organisms.
It is encoded either in DNA or for
many types of viruses, in RNA.
Each genome contains all of the
information needed to build and
maintain that organisms.
3. “A graphic representation of the
arrangement of genes or DNA
sequences on chromosome”.
The human genome map
completed in 1996 locates 5264
markers for gene.
A genome map are used to
identify and record the location
of gene & distances between
genes on chromosome. Genome mapping by
Fluorescent fingerprinting
4. The two main kinds of genome maps are known ;
1. Genetic or linkage maps &
2. Physical maps
Both maps are a collection of genetic markers
5. Genetic maps illustrate the order of genes on a
chromosomes and the relative distances between those
genes.
Genetic maps are based on recombination, the exchange
of DNA sequences between non-sister chromatids
during meiosis.
6. A genetic map is prepared on the basis of recombination data
between carefully selected genetic markers usually ordered
into suitable crosses.
Recombination frequency=No. of recombinant progeny 100%
Total No. of progeny
7. But in case of humans, linkage
maps have to be prepared using
family pedigree data.
In such maps, the distances
between genes are shown in terms
of map units or centiMorgans
(cM).
The chief problem of linkage
mapping is the non availability of a
sufficient number of genetic
markers to cover the entire genome.
8. A Physical map provides detail of the actual physical
distance between genetic markers, as well as the exact
location of genes.
There are three most important techniques used to
create a physical map :
Somatic cell hybridization
Radiation hybridization
Fluorescent in situ hybridization
9. Also called somatic cell fusion or protoplast fusion.
Development of hybrid plants through the fusion of
somatic protoplasts of two different plant species is called
somatic hybridization.
Somatic hybridization involves the following 4 steps;
1. Isolation of protoplast.
2. Fusion of the protoplasts of the desired species.
3. Selection of somatic hybrid cells.
4. Culture of the hybrid cells and regeneration of the hybrid
plants from them.
11. is a method for high resolution
mapping.
In radiation hybrid mapping uses
radiation such as x- ray, to break
the DNA into fragments.
The amount of radiation can be
adjusted to create smaller or larger
fragments.
This technique is not affected by
increased or decreased
recombination frequency.
12. FISH is a powerful technique for detecting RNA or DNA sequences in
cells, tissues & tumors.
FISH provides a unique link among the studies of cell biology,
cytogenetics, & molecular genetics.
FISH allows very precise spatial resolution of morphological & genomic
structures.
The technique is rapid, simple to implement and offers great probe
stability.
13. Types of probes for FISH
Locus specific probes– binds to a particular region of a
chromosome.
This type of probe is useful when researchers have isolated a
small portion of gene and want to determine on which
chromosome the gene is located.
Alphoid or centromeric repeat probes – are
generated from repetitive sequences found in the middle of
each chromosome
Whole chromosome probes- are actually collections
of smaller probes, each of which binds to a different sequence
along the length of a given chromosome.
14.
15. FISH has a large number of applications in molecular
biology and medical science including;
• Gene mapping
• Diagnosis of chromosomal abnormalities
• Studies of cellular structure and function
In clinical research;
• Prenatal diagnosis, Cancer diagnosis
• Molecular cytogenetic of birth defects & mental retardation
• Diagnosis of infectious diseases &
• Detection of aberrant gene expression
16. In laboratory research FISH can be used for;
• To study the evolution of genomes
• Analyzing nuclear organization
• Visualization of chromosomal territories and chromatin in
interphase cells etc.
Chromosome painting –
17. In genetics, a molecular marker is a
fragment of DNA that is associated
with a certain location within the
genome.
Molecular markers are used to identify
a particular sequence of DNA in a pool
of unknown DNA.
Isozymes (electrophoretic variants of
enzymes) and DNA sequences are
used as molecular markers in
chromosome mapping.
18. A molecular genetic marker may can be divided into
two classes ;
a) An Biochemical marker which detect variation at
the gene product level such as changes in proteins
and amino acids.
b) Molecular markers which detect variation at the
DNA level such as Nucleotide changes, Deletion,
Duplication.
19. A RFLP is a genetic marker that can be
examined by cleaving the DNA into
fragments with a restriction enzymes.
A restriction enzyme cuts the DNA
molecule at every occurrence of a
particular sequences called
restriction site.
For example, HindII enzyme cuts at
GTGCAC or GTTAAC.
If we apply a restriction enzyme on
DNA, it is cut at every occurrence of
the restriction site into a million
restriction fragments each a few
thousands nucleotide long.
20.
21. Identification and isolation of any gene known to be linked with an RFLP locus.
In paternity cases or criminal cases to determine the sources of DNA sample.
Identification of the most important loci affecting a quantitative trait.
Determination of chromosome segments alteration of which is likely to yield the
best results.
Diagnostic in genetically inherited disease.
Identifying hybrids.
Pedigree analysis.
Genetic screening.
22. The number of RFLP loci is very large so that
even very small segments of the chromosomes
can be mapped.
Even quantitative trait loci can be mapped
which is virtually impossible through
conventional techniques.
It is rapid as compared to conventional linkage
mapping.
The RFLP acts as a screening marker for some
genetic diseases even in the absence of gene,
e.g. HbS gene screening.
23. Expensive
Requires relatively large amount of DNA.
Low levels of polymorphism in some species.
Need a suitable probe library.
Time consuming especially with single copy probes.
Costly
24. It is a PCR based technology.
In 1991 Welsh and Maclelland
developed this technique.
This procedure detects nucleotide
sequence polymorphism in DNA.
It detects dominant variation in the
genome.
It is used to analyse genetic diversity of
an individual by random primers.
26. Gene mapping
DNA amplification finger printing.
Study of closely related species.
They are quick and easy to assay, because PCR is involved.
Only low quantities of template DNA are required.
RAPD have a very high genomic abundance and are
randomly distributed throughout the genome.
Pure DNA is not needed.
27. • Markers are dominant i.e. they can’t distinguish whether a
DNA sequence is amplified from a locus that is
homozygous or heterozygous.
• PCR is an enzymatic reaction, therefore, the quality and
concentration of template DNA, conc. of PCR components
and the PCR cycling conditions may greatly influence the
outcome.
• Mismatches between the primer and the template may
results in the total absence of PCR product as well as
merely decreased amount of the product.
Thus, the RAPD results can be difficult to interpret.
29. RFLP RAPD
1. Large quantity of purified DNA
required.
1. Quantity of DNA required for analysis
is small.
2. Different species specific probes are
required.
2. Same primers with arbitrary sequence
can be used for different species
3.Comparatively slower processing due to
more steps involved.
3. Fewer steps in procedure therefore it is
rapid (Five times quicker than RFLP)
4. Technique comparatively more reliable 4. Technique comparatively less reliable
30. 5. Can detect allelic variants 5. Cannot detect allelic variants
6. 1-3 loci detected 6. 1-10 loci detected
7. Method involves:
a) digestion of extracted DNA by
restriction enzymes,
b) gel electrophoresis of fragments,
c) southern blot by specific probes
and detection of specific sequences
7. Method involves:
a) extraction of DNA,
b) amplification by PCR using
random primers,
c) gel electrophoresis of amplified
DNA and visualization of markers
RFLP RAPD
31. Genome mapping – Wikipedia the free encyclopedia
Biotechnology – B. D. Singh
Genetics principle and analysis – Daniel L. Hartl
- Elizabeth W. Jones
Biotechnology – S. S. Purohit
Biotechnology (Applying the genetic revolution)-
David P. Clark & Nanette J. Pazdernik