A blot, in molecular biology and genetics, is a method of transferring proteins, DNA or RNA, onto a carrier (for example, a nitrocellulose, polyvinylidene fluoride (PVDF) or nylon membrane). In many instances, this is done after a gel electrophoresis, transferring the molecules from the gel onto the blotting membrane, and other times adding the samples directly onto the membrane. After the blotting, the transferred proteins, DNA or RNA are then visualized by colorant staining (for example, silver staining of proteins), autoradiographic visualization of radioactive labelled molecules (performed before the blot), or specific labelling of some proteins or nucleic acids. The latter is done with antibodies or hybridization probes that bind only to some molecules of the blot and have an enzyme joined to them. After proper washing, this enzymatic activity (and so, the molecules we search in the blot) is visualized by incubation with proper reactive, rendering either a colored deposit on the blot or a chemiluminiscent reaction which is registered by photographic film.
Southern blot
A Southern blot is a method routinely used in molecular biology for detection of a specific DNA sequence in DNA samples. Southern blotting combines transfer of electrophoresis-separated DNA fragments to a filter membrane and subsequent fragment detection by probe hybridization.[1]
Western blot
A Western blot is used for the detection of specific proteins in complex samples. Proteins are first separated by size using electrophoresis before being transferred to an appropriate blotting matrix (usually PVDF or nitrocellulose) and subsequent detection with antibodies.
Eastern blot
The Eastern blot is used for the detection of specific posttranslational modifications of proteins. Proteins are separated by gel electrophoresis before being transferred to a blotting matrix whereupon posttranslational modifications are detected by specific substrates (cholera toxin, concanavalin, phosphomolybdate, etc.) or antibodies.
ChIP-Seq was considered one of the most popular methods to study protein-DNA interactions and can be used , to identify the binding sites of transcription factors ( activators or repressors) or to determine the distributions of histones ( histone modifications) with specific post-translational modifications throughout the genome.
This is technique used widely for protein separation from a mixture and is very easy and less costly method. Slides cover all essential points about EMSA and it is quite interesting to know that how it detect and separate different proteins and their mobility shift assay.
ChIP-Seq was considered one of the most popular methods to study protein-DNA interactions and can be used , to identify the binding sites of transcription factors ( activators or repressors) or to determine the distributions of histones ( histone modifications) with specific post-translational modifications throughout the genome.
This is technique used widely for protein separation from a mixture and is very easy and less costly method. Slides cover all essential points about EMSA and it is quite interesting to know that how it detect and separate different proteins and their mobility shift assay.
This lecture is intended as an introduction to the fundamental concepts associated with plasmid DNA. Plasmids can be applied as vectors in Genetic Engineering for the production of recombinant proteins as well as the construction of genomic libraries for DNA sequencing projects.
The technique of molecular biology like DNA isolation, RNA isolation, PCR, Western blot, RFLP, etc was developed with development in science. This presentation includes the method of DNA and RNA isolation and their Quantification techniques.
WHAT IS BLOTTING?
Blotting is a technique for detecting any macromolecules that we deal with like DNA, RNA or proteins, which are initially present in a complex mixture.
TYPES OF BLOTTING:
Southern Blotting
Northern Blotting
Western Blotting
NORTHERN BLOTTING
A northern blotting is a laboratory method used to detect specific RNA molecules among a mixture of RNA (mRNA).
The technique was developed in 1979 by James Alwine and his colleagues.
Northern blotting can be used to analyze a sample of RNA from a particular tissue or cell type in order to measure the expression of particular genes.
Northern blotting involves the use of electrophoresis to separate RNA samples by size, and detection with a hybridization probe complementary to part of or the entire target sequence.
The term ‘northern blot’ actually refers specifically to the capillary transfer of RNA from the electrophoresis gel to the blotting membrane. However the entire process is commonly referred to as northern blotting.
PROCEDURE
1.RNA isolation:
2.Separation of RNA using gel electrophoresis:
3.BLOTTING:
4.Hybridization with labelled probe:
5.WASHING OFF EXCESS PROBES
This presentation contains information about restriction enzymes, its nomenclature, restriction digestion, and its application. This also contains information about the chemicals used in restriction and also explains the general procedure of restriction digestion of DNA
RNA splicing is a form of RNA processing in which a newly made precursor messenger RNA (mRNA) is transformed into a mature RNA by removing the non-coding sequences termed introns.
The process of RNA splicing involves the removal of non-coding sequences or introns and joining of the coding sequences or exons.
RNA splicing takes place during or immediately after transcription within the nucleus in the case of nucleus-encoded genes.
In eukaryotic cells, RNA splicing is crucial as it ensures that an immature RNA molecule is converted into a mature molecule that can then be translated into proteins. The post-transcriptional modification is not necessary for prokaryotic cells.
This presentation gives an easy introduction to ChIP-seq analyses and is part of a bioinformatics workshop. The accompanying websites are available at http://sschmeier.github.io/bioinf-workshop/#!galaxy-chipseq/
This lecture is intended as an introduction to the fundamental concepts associated with plasmid DNA. Plasmids can be applied as vectors in Genetic Engineering for the production of recombinant proteins as well as the construction of genomic libraries for DNA sequencing projects.
The technique of molecular biology like DNA isolation, RNA isolation, PCR, Western blot, RFLP, etc was developed with development in science. This presentation includes the method of DNA and RNA isolation and their Quantification techniques.
WHAT IS BLOTTING?
Blotting is a technique for detecting any macromolecules that we deal with like DNA, RNA or proteins, which are initially present in a complex mixture.
TYPES OF BLOTTING:
Southern Blotting
Northern Blotting
Western Blotting
NORTHERN BLOTTING
A northern blotting is a laboratory method used to detect specific RNA molecules among a mixture of RNA (mRNA).
The technique was developed in 1979 by James Alwine and his colleagues.
Northern blotting can be used to analyze a sample of RNA from a particular tissue or cell type in order to measure the expression of particular genes.
Northern blotting involves the use of electrophoresis to separate RNA samples by size, and detection with a hybridization probe complementary to part of or the entire target sequence.
The term ‘northern blot’ actually refers specifically to the capillary transfer of RNA from the electrophoresis gel to the blotting membrane. However the entire process is commonly referred to as northern blotting.
PROCEDURE
1.RNA isolation:
2.Separation of RNA using gel electrophoresis:
3.BLOTTING:
4.Hybridization with labelled probe:
5.WASHING OFF EXCESS PROBES
This presentation contains information about restriction enzymes, its nomenclature, restriction digestion, and its application. This also contains information about the chemicals used in restriction and also explains the general procedure of restriction digestion of DNA
RNA splicing is a form of RNA processing in which a newly made precursor messenger RNA (mRNA) is transformed into a mature RNA by removing the non-coding sequences termed introns.
The process of RNA splicing involves the removal of non-coding sequences or introns and joining of the coding sequences or exons.
RNA splicing takes place during or immediately after transcription within the nucleus in the case of nucleus-encoded genes.
In eukaryotic cells, RNA splicing is crucial as it ensures that an immature RNA molecule is converted into a mature molecule that can then be translated into proteins. The post-transcriptional modification is not necessary for prokaryotic cells.
This presentation gives an easy introduction to ChIP-seq analyses and is part of a bioinformatics workshop. The accompanying websites are available at http://sschmeier.github.io/bioinf-workshop/#!galaxy-chipseq/
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Concept: reannealing nucleic acids to identify sequence of interest.
Separates DNA/RNA in an agarose gel, then detects specific bands using probe and hybridization.
Hybridization takes advantage of the ability of a single stranded DNA or RNA molecule to find its complement, even in the presence of large amounts of unrelated DNA.
Allows detection of specific bands (DNA fragments or RNA molecules) that have complementary sequence to the probe.
Size bands and quantify abundance of molecule.
Southern blotting is a laboratory technique used to detect specific DNA sequences in DNA samples. It involves several steps:
Restriction Digestion: DNA from a biological sample (such as blood or tissue) is broken into smaller fragments using restriction enzymes, which cut the DNA at specific sequences.
Electrophoresis: The DNA fragments are separated based on their molecular weights using gel electrophoresis. This process allows smaller fragments to move faster than larger fragments.
Transfer to Membrane: The DNA fragments are transferred from the gel onto a solid membrane, typically a positively charged nylon membrane, using capillary action.
Hybridization: The membrane is then exposed to a DNA probe labeled with a radioactive, fluorescent, or chemical tag. The probe is designed to be complementary to the target DNA sequence, allowing it to bind to the specific DNA fragment on the membrane.
Detection: The bound probe is detected using methods such as X-ray film, phosphorimaging, or chemiluminescent substrates, depending on the type of label used.
Southern blotting is used in various applications, including:
Identifying specific DNA sequences in DNA samples
Studying gene rearrangements and mutations
Analyzing viral and bacterial infections
Forensic analysis and personal identification
Gene mapping and restriction enzyme mapping
Identifying methylated sites in genes.
This technique is named after its inventor, Dr. Edwin Southern, who first published it in 1975.
This is all about southern blotting
Nucleic Acids
DNA
Eukaryotic Chromosomes
The Histones
Deoxynucleic acid ( DNA )
Importance of Nucleotides
Base pairing
Denaturation and Renaturation
Determination GC content
Prokaryotic DNA synthesis
Prokaryotic DNA Replication
Transcription
Coding Strand and Template Strand
Steps of RNA synthesize
Macromolecules of life (Nucleic acids & Proteins)Amany Elsayed
Macromolecules of life (Nucleic acids & Proteins)
The Fibrous Proteins
The Collagens
The Globular Proteins
Structure and Function of Myoglobin
Minor Hemoglobin’s
Biological value of proteins
Nitrogen Balance
Protein Deficiency
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.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
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.
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.
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.
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.
2. 2
There are different blotting procedures
depending on the type of molecule being
transferred:-
• When DNA fragments are
transferred the procedure is called a Southern
blot, named after the person who first developed
it, Edward Southern.
•With Northern blotting, RNA molecules are
transferred
•and with Western blotting, protein molecules are
transferred.
3. 3
Probe
◘ A probe (a piece of nucleic acid with identical
and specific sequence to the organism or gene of
interest) can then hybridize (join) to the
biological molecules (DNA, RNA or protein) with
an identical sequence on the membrane.
◘ The hybridization between the blotted DNA
and probe is visualized by labelling the probe in
some way.
4. 4
DNA probe joins together (hybridizes) with target DNA
blotted on a membrane.
General principle
•All blotting procedures begin with a standard process
called gel electrophoresis. During this step, DNA,
RNA, or proteins are loaded on to an agarose or
polyacylamide gel (that functions like a molecular
sieve) and are then run through an electric field.
•Transfer is initiated when the nylon or nitrocellulose
membrane is laid on top of the gel and biological
molecules are transferred from the gel to the
membrane .
ا تتنقل بتبدأفوق محطوط بيبقي اللي الغشاء الي الجل من النوويه الحماض
الجل
•It is used to verify the presence or absence of a
specific nucleotide sequence in DNA from different
sources .
انا معين تتابع غياب او وجود احدد عشان اصال دا الموضوع بستخدم
عايزه
• DNA is isolated from each source and then digested
with a specific restriction enzyme .
5. 5
• The DNA restriction fragments are loaded onto an agarose
gel and the fragments separated by electrophoresis
according to size .
• The fragments visible with Ethidium bromide under UV-
light
• The DNA is then transferred from the agarose gel to a
membrane ( nylon or nitrocellulose ) and denatured to
produce single strands .
تكامل يعمل وعشان الغشاء علي مزدوج شريط بيبقي ايه ان الدي بستخدم لما طبعا
وتهجينلشريط يتحول الزم البروب وبين بينه مااالول الزم كدا عشان مفرد
مفرد لشريط يتحول
• A nucleic acid probe is labeled , usually by incorporating
radioactivity or tagging the molecule with a fluorescent dye .
ال الزمبروعشا مشعة صبغة او مشعة بماده متعلم يكون باحطه لما مكانه احدد ن
الشاشه تحت
• The labeled probe is added and it binds to complementary
DNA on the membrane .
• To detect the position of the labeled probe , the membrane
is covered with an x-ray film and after development the
position of the probe becomes visible.
للجهاز وانقله راي لالكس فيلم علي الغشاء بنقل دا فات اللي كل بخلص ما اول
ارتباط نتيجه طالعة اللي المشعة الماده هيظهرلي اللي) تهجين (انا اللي التتابع
. البروب مع عايزه
7. 7
• This Technique is used to study gene expression by
detection of RNA ( or isolated mRNA ) in a sample .
• with northern blotting it is possible to observe cellular
control over structure and function by determining the
particular gene expression levels during differentiation ,
morphogenesis , as well as abnormal or diseased
conditions .
Northern blotting
• starting with extraction of total RNA from a
homogenized tissue sample .
• RNA separated by gel electrophoresis .
• A nylon membrane with a positive charge is the
most effective for use in northern blotting since
the negatively charged nucleic acids have a high
affinity for them .
• The transfer buffer contains Formamide
because it lowers the annealing temperature of
the probe – RNA interaction preventing RNA
degradation by high temperatures .
8. 8
• After the probe has been labeled , it is hybridized
to the RNA on the membrane .
• The membrane is washed to ensure that the
probe has bound specifically .
• The hybrid signals are then detected by X-ray
film and can be quantified by densitometry .
Advantages & Disadvantages of Northern
blotting
• Northern blotting is able to detect small changes
in gene expression that microarrays cannot
• A problem in Northern blotting is often sample
degradation by RNases ( Both endogenous to the
sample and through through environmental
contamination ) .
9. 9
Western blotting
• ◘ • Steps :-
1- Sample preparation .
2- Electrophoresis .
3- Transfer.
4- Blocking .
5- Detection.
بقي هنبدأ دي قبل اللي المحاضرات في خطوتين اول اخدنا احنا
. الثالثة الخطوة من الوقتي
◘ Transfer
• To make The proteins accessible to antibody
detection , they are moved from within the gel
onto a nitrocellulose or polyvinylidene
difluoride ( PVDF ) membrane similar to
Southern blot DNA transfer .
البر ان هيكون هنا االختالف ولكن فاتت اللي الطريقة نفسوب
هيبقي
( Anti body )
10. 10
• Another method for transferring the
proteins is called electro blotting and uses
an electric current to pull proteins from the
gel into the PVDF or nitrocellulose
membrane .
• As a result of this “ blotting “ process , the
proteins are exposed on a thin surface layer
for detection .
• Protein binding is based upon
hydrophobic interaction , as well as
charged interactions between the
membrane and protein.
• Nitrocellulose membrane are cheaper
than PVDF , but are far more Fragile and
do not stand up well to repeated probings.
هشاشه اكثر بيكون
11. 11
Blocking
• Steps must be taken to prevent interactions between the
membrane and the antibody used for detection of the target
protein .
• Blocking of non-specific binding is achieved by placing the
membrane in a dilute solution of protein , typically Bovine
serum albumin ( BSA) or non-fat dry milk ( both are
inexpensive ) , with a minute ( percentage of detergent such
as Tween 20 .
12. 12
Detection
Two steps :-
1- ◘ primary Antibody
• After blocking a diluted solution of
primary antibody ( generally between
0.5 and 5 micrograms/ml ) is
incubated with the membrane under
gentle agitation .
• The solution is composed of
buffered saline solution with a small
percentage of detergent , and
sometimes with powdered milk or
BSA .
• The Antibody solution and the
membrane can be incubated together
from 30 minutes to Overnight .
13. 13
2- ◘ Secondary Antibody
• After rinsing the membrane to remove unbound
primary antibody .
وبين بينها ما تفاعل هيحصل االولية المضادة االجسام بضيف لما
مع دي االجسام تفاعل بيمنع بلوكنج بضيف كدا عشان الغشاء
االجسام بسيب كدا وبعد بس البروتين مع تتفاعل ويخليها الغشاء
الغشاء هغسل وبعدين معين لوقت البروتين مع تتفاعل المضاده
ا المضادة االجسام اضيف واؤجعاالجسام في هتشبك اللي لثانوية
األولية المضادة
• The membrane is exposed to another antibody ,
directed at a specific portion of the primary
antibody .
• This is known as secondary antibody , and due
to its targeting properties , tends to be referred to
as “ Antimouse” “ Anti-goat “ etc ,
- Antibodies come from animal sources ( or
animal sourced hybridoma cultures ) ; an
anti-mouse secondary will bind to just about
any mouse-sourced primary anti body
14. 14
• The secondary antibody is usually linked to
biotin or to a reporter enzyme such as alkaline
phosphatase or horseradish peroxidase .
• This means that several secondary antibodies
will bind to one primary antibody and enhance
the signal .
15. 15
Eastern blotting
• it is a technique to detect protein post
translational modification and is an extension of
the biochemical technique of western blotting .
المحاضرة تمت
Q.A
لما اال هتتفهم مش عشان تذاكروا ما بعد ليها فيديوهات تسمعوا ياريت
االول بعينيكم تشوفوها☺