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.
sequencing presentation. providing deep and insightful points about Sanger sequencing, Maxam-gilbert sequencing, Illumina sequencing, and single molecule sequencing.
NEED OF GENETIC SEQUENCING
- Understanding the particular DNA sequence can shed light on a genetic condition and offer hope for the eventual development of treatment.
- An alteration in a DNA sequence can lead to an altered or non functional protein and hence to a harmful effect in a plant or animal.
- Simple point mutations can cause altered protein shape and function.
INTRODUCTION
DEFINITION
HISTORY
METHODS OF DNA SEQUENCING
MAXAM GILBERT METHOD
SANGERS METHOD
AUTOMATED DNA SEQUENCER
PYROSEQUENCING
SHOTGUN SEQUENCING
DNA MICROARRAY
APPLICATION
CONCLUSION
REFRENCES
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.
sequencing presentation. providing deep and insightful points about Sanger sequencing, Maxam-gilbert sequencing, Illumina sequencing, and single molecule sequencing.
NEED OF GENETIC SEQUENCING
- Understanding the particular DNA sequence can shed light on a genetic condition and offer hope for the eventual development of treatment.
- An alteration in a DNA sequence can lead to an altered or non functional protein and hence to a harmful effect in a plant or animal.
- Simple point mutations can cause altered protein shape and function.
INTRODUCTION
DEFINITION
HISTORY
METHODS OF DNA SEQUENCING
MAXAM GILBERT METHOD
SANGERS METHOD
AUTOMATED DNA SEQUENCER
PYROSEQUENCING
SHOTGUN SEQUENCING
DNA MICROARRAY
APPLICATION
CONCLUSION
REFRENCES
The independent study on how Cloud Computing can be used to introduce a new Next Generation Sequencing method in terms of better understanding of the limitations of existing Next Generation Sequencing Methods.
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.
Knowledge of DNA sequences has become indispensable for basic biological research, and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics. Comparing healthy and mutated DNA sequences can diagnose different diseases including various cancers, characterize antibody repertoire, and can be used to guide patient treatment. Having a quick way to sequence DNA allows for faster and more individualized medical care to be administered, and for more organisms to be identified and cataloged.
DNA Sequencing : Maxam Gilbert and Sanger SequencingVeerendra Nagoria
DNA sequencing is a technique to find out the exact arrangement of Nucleotides to make one strand of DNA. DNA sequencing helps in numerous ways from sequence information to paternity testing, mutation detection etc. Traditionally two approaches were used to solve the problem. First is based of enzymes and Second is based on ddNTPs to sequence the DNA using gel electrophoresis technique.
DNA FINGERPRINTING :-
“DNA fingerprinting is a technique that shows the genetic makeup of living things. It is a method of finding the difference between the satellite DNA regions in the genome.”
Content:-
1) Introduction : What is DNA Fingerprinting?
2) Biological samples used
3) Discovery : Who invented DNA Fingerprinting?
4) Procedure : Basic steps and procedure for DNA Fingerprinting
5) Application : Various applications of DNA Fingerprinting
The independent study on how Cloud Computing can be used to introduce a new Next Generation Sequencing method in terms of better understanding of the limitations of existing Next Generation Sequencing Methods.
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.
Knowledge of DNA sequences has become indispensable for basic biological research, and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics. Comparing healthy and mutated DNA sequences can diagnose different diseases including various cancers, characterize antibody repertoire, and can be used to guide patient treatment. Having a quick way to sequence DNA allows for faster and more individualized medical care to be administered, and for more organisms to be identified and cataloged.
DNA Sequencing : Maxam Gilbert and Sanger SequencingVeerendra Nagoria
DNA sequencing is a technique to find out the exact arrangement of Nucleotides to make one strand of DNA. DNA sequencing helps in numerous ways from sequence information to paternity testing, mutation detection etc. Traditionally two approaches were used to solve the problem. First is based of enzymes and Second is based on ddNTPs to sequence the DNA using gel electrophoresis technique.
DNA FINGERPRINTING :-
“DNA fingerprinting is a technique that shows the genetic makeup of living things. It is a method of finding the difference between the satellite DNA regions in the genome.”
Content:-
1) Introduction : What is DNA Fingerprinting?
2) Biological samples used
3) Discovery : Who invented DNA Fingerprinting?
4) Procedure : Basic steps and procedure for DNA Fingerprinting
5) Application : Various applications of DNA Fingerprinting
Similar to MSC IV SEMESTER_DNA Profiling - DNA Sequencing.pdf (20)
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.
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 .
This report details the geological observations and interpretations made during a field investigation of the Kaptai Rangamati road-cut section, located in southeastern Bangladesh. The purpose of this report is to document the exposed rock units, their characteristics, and the geological structures present within the road cut.
word2vec, node2vec, graph2vec, X2vec: Towards a Theory of Vector Embeddings o...Subhajit Sahu
Below are the important points I note from the 2020 paper by Martin Grohe:
- 1-WL distinguishes almost all graphs, in a probabilistic sense
- Classical WL is two dimensional Weisfeiler-Leman
- DeepWL is an unlimited version of WL graph that runs in polynomial time.
- Knowledge graphs are essentially graphs with vertex/edge attributes
ABSTRACT:
Vector representations of graphs and relational structures, whether handcrafted feature vectors or learned representations, enable us to apply standard data analysis and machine learning techniques to the structures. A wide range of methods for generating such embeddings have been studied in the machine learning and knowledge representation literature. However, vector embeddings have received relatively little attention from a theoretical point of view.
Starting with a survey of embedding techniques that have been used in practice, in this paper we propose two theoretical approaches that we see as central for understanding the foundations of vector embeddings. We draw connections between the various approaches and suggest directions for future research.
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.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
FAIRSpectra - Towards a common data file format for SIMS imagesAlex Henderson
Presentation from the 101st IUVSTA Workshop on High performance SIMS instrumentation and machine learning / artificial intelligence methods for complex data.
This presentation describes the issues relating to storing and sharing data from Secondary Ion Mass Spectrometry experiments, and some potential solutions.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
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.
5. VAC course: Basics of Bioinformatics 23rd-26th August, 20223
Maxam-Gilbert Sequencing Method:
Developed by Allan Maxam and Walter
Gilbert in the late 1970s
Chemical Cleavage: The DNA molecule is
first chemically modified at specific bases
to create cleavage points. Four different
reactions are performed, each targeting a
specific type of base (A+G, C, G, T).
Fragment Separation: The labeled
fragments are separated by gel
electrophoresis.
Sequence Determination: The sequence of
the DNA is determined by reading the
order of bands on the gel. Each band
corresponds to a cleavage site, revealing the
positions of the specific modified bases and
their respective sequence positions in the
DNA.
6. How Sanger Sequencing Works? (Classic Sanger Method)
https://www.youtube.com/watch?v=-QIMkQ4E_wE
7. VAC course: Basics of Bioinformatics 23rd-26th August, 20223
Sanger Sequencing Method:
The Sanger sequencing method, developed by Frederick
Sanger around the same time, became more widely adopted
due to its technical advantages.
1.Primer Annealing: A short DNA primer is annealed to
the single-stranded DNA template. DNA synthesis begins
from the primer using a DNA polymerase enzyme.
2.DNA Synthesis with Chain Terminators: DNA synthesis
is carried out using a mix of regular deoxynucleotides
(dNTPs) and chain-terminating dideoxynucleotides
(ddNTPs). The ddNTPs lack a 3' hydroxyl group,
preventing further elongation of the DNA
3.Fragment Separation: The DNA synthesis reactions
generate a series of fragments of varying lengths, each
terminating with a ddNTP. The fragments are separated
by gel electrophoresis, similar to the Maxam-Gilbert
method.
4.Sequence Determination: The sequence is deduced by
analyzing the order of bands on the gel, with the last band
in each lane indicating the nucleotide at the corresponding
position in the DNA sequence.
8. VAC course: Basics of Bioinformatics 23rd-26th August, 20223
•Principle: Both methods rely on chemical modifications and
subsequent separation to determine DNA sequence.
•Read Length: Sanger sequencing generally provided longer read
lengths compared to Maxam-Gilbert sequencing.
•Throughput: Sanger sequencing was more amenable to automation and
higher throughput due to the use of a single reaction mix with chain-
terminating nucleotides.
•Labor Intensity: Maxam-Gilbert sequencing involved more complex
chemical reactions and separate reactions for each base type, making it
more labor-intensive.
•Widespread Adoption: Sanger sequencing gained wider adoption due to
its simpler reaction setup and more streamlined process.
•Advancement: Both methods laid the groundwork for DNA sequencing
but have been largely replaced by high-throughput Next-Generation
Sequencing (NGS) methods due to their speed, scalability, and lower c
9. Next Generation Sequencing - A Step-By-Step Guide to DNA Sequencing
https://www.youtube.com/watch?v=WKAUtJQ69n8
12. Unit 4: DNA database and quality assurance
• NDNAD, CODIS, and other databases,
• DNA Lab Quality Assurance and Quality Control, Forensic DNA
Advisory Groups: US DOJ, SWGDAM, AAFS, ENFSI DNA WG, and
ISFG DNA. National and International accredited bodies, quality
standards, certification, and legal Admissibility of DNA Evidence.
• National bodies for DNA profiling: CDFD, CCMB, LaCONES.
23. VAC course: Basics of Bioinformatics 23rd-26th August, 20223
https://www.icmr.gov.in/cnextgenseq.html
24.
25.
26. Based on 19 studies review
• DNA databases are an effective deterrence
and detection tool
• DNA databases are more effective in studying
the crimes committed by unidentified
offenders than other criminological data
sources
• Combining the DNA database and the police
recorded crime database gives a more
complete view on criminal networks than the
police database alone
• DNA databases do increase the probability of
identification, arrest and prosecution in cases
of property crimes
33. direct matching between known
and unknown sample profiles
profiles from missing persons
and their relatives
unidentified human remains
34. Current scenario in India
• huge requirement for these types of
databases which may help in stopping
different types of fraud like ration
card fraud, voter identity card fraud,
driving license fraud etc
• The database may help the Indian
police to differentiate the criminals
and non criminals.
36. • The DNA Technology (Use and
Application) Regulation Bill, 2019
was introduced in Lok Sabha by the
Minister for Science and
Technology, Mr. Harsh Vardhan, on
July 8, 2019.
• Use of DNA Data: offences under
the Indian Penal Code, 1860, and
for civil matters such as paternity
suits.
• DNA testing for matters related
to establishment of individual
identity.
37. Collection of DNA
arrested persons: written consent if the offence carries a
punishment of up to seven years
more than seven years of imprisonment or death,
consent is not required
person is a victim, or relative of a missing person, or a
minor or disabled person, the authorities are required
to obtain the written consent.
Magistrate who may order
38. DNA Data Bank
National DNA Data Bank and Regional DNA Data
Banks, for every state, or two or more states
maintain indices for the following categories of
data: (i) a crime scene index, (ii) a suspects’ or
undertrials’ index, (iii) an offenders’ index, (iv)
a missing persons’ index, and (v) an unknown
deceased persons’ index.
39. Removal of DNA profiles
(i) of a suspect if a police report is filed or
court order given
(ii) of an undertrial if a court order is given
iii)on written request, for persons who are
not a suspect, offender or undertrial, from
the crime scene or missing persons’ index.
40.
41. This Photo by Unknown Author is licensed under CC BY-SA