DNA microarrays contain thousands of DNA sequences attached to a solid surface in defined positions. Each DNA spot represents a single gene. The document describes the basic protocol for a DNA microarray experiment which involves isolating mRNA from samples, labeling the mRNA, hybridizing it to the microarray, and scanning the microarray to quantify gene expression levels. It also discusses various types of microarrays classified by their probes, such as cDNA, oligonucleotide, and SNP microarrays, as well as parameters that affect microarray fabrication.
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.
Microarray -types, DNA chip, Principle and application of microarray, Preparation of DNA Chip, Affymetrix chip, microarray in genomics and proteomics, advantages and limitations of microarray
Next Generation Sequencing (NGS) Is A Modern And Cost Effective Sequencing Technology Which Enables Scientists To Sequence Nucleic Acids At Much Faster Rate. In This Presentation, You Will Learn About What is NGS, Idea Behind NGS, Methodology And Protocol, Widely Adapted NGS Protocols, Applications And References For Further Study.
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.
Microarray -types, DNA chip, Principle and application of microarray, Preparation of DNA Chip, Affymetrix chip, microarray in genomics and proteomics, advantages and limitations of microarray
Next Generation Sequencing (NGS) Is A Modern And Cost Effective Sequencing Technology Which Enables Scientists To Sequence Nucleic Acids At Much Faster Rate. In This Presentation, You Will Learn About What is NGS, Idea Behind NGS, Methodology And Protocol, Widely Adapted NGS Protocols, Applications And References For Further Study.
DNA microarray:
A DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is a collection of microscopic DNA spots, commonly representing single genes, arrayed on a solid surface by covalent attachment to a chemical matrix. DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system. Qualitative or quantitative measurements with DNA microarrays utilize the selective nature of DNA-DNA or DNA-RNA hybridization under high-stringency conditions and fluorophore-based detection. DNA arrays are commonly used for expression profiling, i.e., monitoring expression levels of thousands of genes simultaneously.
The DNA microarray is a tool used to determine whether the DNA from a particular individual contains a mutation in genes like BRCA1 and BRCA2. The chip consists of a small glass plate encased in plastic. Some companies manufacture microarrays using methods similar to those used to make computer microchips.
Hello There,
DNA Footprinting Is A Molecular Biology Technique With Wide Applications In Many Areas Of Biological Sciences And Importantly It Is Used For Crime Detection In Forensic Sciences. In This Presentation, You Will Learn What It Is, The Technology, Protocol, Pictorial Representation, Applications And References For Further Study.
High throughput next generation sequencing and robust transcriptome analysis help with gene expression profiling, gene annotation or discovery of non-coding RNA.
The DNA microarray is a tool used to determine whether the DNA from a particular individual contains a mutation in genes like BRCA1 and BRCA2. The chip consists of a small glass plate encased in plastic. Some companies manufacture microarrays using methods similar to those used to make computer microchips.
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles of a specific DNA sequence, known as probes.
This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000’s of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. We first cover the history of microarrays and the antecedent technologies that led to their development. We then discuss the methods of manufacture of microarrays and the most common biological applications. The chapter ends with a brief discussion of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies.
DNA microarray:
A DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is a collection of microscopic DNA spots, commonly representing single genes, arrayed on a solid surface by covalent attachment to a chemical matrix. DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system. Qualitative or quantitative measurements with DNA microarrays utilize the selective nature of DNA-DNA or DNA-RNA hybridization under high-stringency conditions and fluorophore-based detection. DNA arrays are commonly used for expression profiling, i.e., monitoring expression levels of thousands of genes simultaneously.
The DNA microarray is a tool used to determine whether the DNA from a particular individual contains a mutation in genes like BRCA1 and BRCA2. The chip consists of a small glass plate encased in plastic. Some companies manufacture microarrays using methods similar to those used to make computer microchips.
Hello There,
DNA Footprinting Is A Molecular Biology Technique With Wide Applications In Many Areas Of Biological Sciences And Importantly It Is Used For Crime Detection In Forensic Sciences. In This Presentation, You Will Learn What It Is, The Technology, Protocol, Pictorial Representation, Applications And References For Further Study.
High throughput next generation sequencing and robust transcriptome analysis help with gene expression profiling, gene annotation or discovery of non-coding RNA.
The DNA microarray is a tool used to determine whether the DNA from a particular individual contains a mutation in genes like BRCA1 and BRCA2. The chip consists of a small glass plate encased in plastic. Some companies manufacture microarrays using methods similar to those used to make computer microchips.
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles of a specific DNA sequence, known as probes.
This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000’s of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. We first cover the history of microarrays and the antecedent technologies that led to their development. We then discuss the methods of manufacture of microarrays and the most common biological applications. The chapter ends with a brief discussion of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies.
Molecular Biology research evolves through the development of the technologies used for carrying them out. It is not possible to research on a large number of genes using traditional methods
1. Introduction:
A few life scientists may mourn the passing of the days when the concept of “one gene, one protein" controlled their professional lives. But most of the colleagues have welcomed the arrival of DNA chips and microarrays that offer researchers the opportunity to run thousands of samples simultaneously in a single experiment under virtually identical conditions. The pharmaceutical industry in particular values the use of microarray technology to screen increasing numbers of molecules in smaller volumes as drug candidates. Alex Szabo, the vice president of Strata gene, says “There’s tremendous excitement about the technology. Everyone realizes that it’s one of the key technologies in the genomic era”.
Microarray technology seems tailor-made for the type of exploration necessary to follow up the initial work on sequencing the genes of humans and other organisms. The professor of Biochemistry, Patrick Brown, at Stanford University says that “Genome projects give you, in a sense, a list of the words in the genome vocabulary”. Jeff Mooney, Business technology manager of Corning Microarray Technologies, extend his thought as “If you want to learn what words mean in a foreign language you look at how they are used. It’s the same of genes. Microarrays as a way of seeing how genes express themselves will be the most widely used application of arrays”. The more we look at the human genome, the more questions people have. Microarray platforms help to answer general and specific questions.
Beyond this, researchers see use of microarrays in such areas as genotyping, studying disease pathways, analysing Single Nucleotide Polymorphisms (SNPs), and examining proteins. “Expression arrays offer researchers the promise of finding the fundamental causes of disease and identifying new, more precise strategies to diagnose, treat, prevent and ultimately cure disease” says Stephen Fodor, Chairman and CEO of Affymetrix, Inc., the first major manufacturer of arrays.
Plenty of vendors have joined Affymetrix in the microarray marketplace. “There are tens, if not hundreds, of companies out there trying to find the next technology” says Andrew Farquharson, executive vice president of Operon Technologies, Inc. Some new comers, such as Nimblegen Systems, Inc., aim to follow the model pioneered by Affymetrix and Incyte Genomics, producing microarrays for core facilities in large industrial and academic departments. Others, such as Corning, plant to enter the market with “theme arrays” targeted at specific diseases. Yet more, including Agilent Technologies and German company Graffinity Pharamaceutical Design, GmbH, provide specific services such as fingerprinting arrays designed and used by individual researchers. CLONTECH Laboratories, subsidiary of BD Bioscience and British firm BioRobotics, Ltd., provide the basic tools necessary for individual researchers to carry out the entire process of producing microarrays, including fingerprinting.
A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface.
The core principle behind microarrays is hybridization between two DNA strands, the property of complementary nucleic acid sequences to specifically pair with each other by forming hydrogen bonds between complementary nucleotide base pairs.
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(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.
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.
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.
2. DNA Microarray
DNA microarrays are microscope slides that are
printed with thousands of tiny spots in defined
positions, with each spot containing a known DNA
sequence or gene.
These slides are referred to as gene chips or DNA
chips.
DNA microarrays are solid supports, usually of glass
or silicon, upon which DNA is attached in an
organized pre-determined grid fashion.
Each spot of DNA, called a probe, represents a
single gene.
A microarray is a laboratory tool used to detect the
expression of thousands of genes at the same time.
3.
4. A basic protocol for a DNA microarray is as follows:
Isolate and purify mRNA from samples of
interest. Since we are interested in comparing
gene expression, one sample usually serves as
control, and another sample would be the
experiment (healthy vs. disease, etc)
Reverse transcribe and label the mRNA. In order
to detect the transcripts by hybridization, they need
to be labeled, and because starting material maybe
limited, an amplification step is also used.
Hybridize the labeled target to the microarray. This step
involves placing labeled cDNAs onto a DNA microarray where
it will hybridize to their synthetic complementary DNA probes
attached on the microarray. A series of washes are used to
remove non-bound sequences.
Scan the microarray and quantitate the signal. The
fluorescent tags on bound cDNA are excited by a laser
and the fluorescently labeled target sequences that bind to
a probe generate a signal. The total strength of the signal
depends upon the amount of target sample binding to the
probes present on that spot
7. Parameters affecting fabrication of microarrays.
Spot density and array geometry.
Probe density is defined as number of probes located on a given surface while
hybridised density is defined as the number of target located on a given surface
Hybridisation efficiency is defined as the ratio between hybridised and probe
density
8. Classification of microarray based on the
mode of preparation
1. The spotted array on glass: spotted arrays are arrays made on
poly-lysine coated glass microscope slides. This provides binding of
high-density DNA by using slotted pins. It allows fluorescent labeling
of the sample.
2. Self-assembled arrays: these are fiber optic arrays made by the
deposition of DNA synthesized on small polystyrene beads. The
beads are deposited on the etched ends of the array. Different DNA
can be synthesized on different beads and applying a mixture of
beads to the fiber optic cable will make a randomly assembled array.
3. In-situ synthesized arrays: these arrays are made by chemical
synthesis on a solid substrate. In the chemical synthesis, photolabile
protecting groups are combined with photolithography to perform the
action. These arrays are used in expression analysis, genotyping,
and sequencing. Affymetrix for instance produces microarrays
routinely with millions of probes on 1.28 cm2 surface. There is
almost no space between the spots and spotsizes are below 10 mm.
9.
10.
11. (A) Unmodified DNA
is randomly
immobilised to
surfaces meaning
that some DNA
strands can
participate in
hybridisation (I) while
other cannot (II).
(B) Immobilisation of
DNA using end
modifications (I) can
also result in intra
chain bonds (II).
(C) Molecular organisation of end modified probes
directly immobilised to the active groups on the solid
support (I) or displaced from the surface using a
linker (II) or a dendrimeric linker (III).
Immobilisation
of DNA to
surfaces.
12.
13.
14. A grid alignment (also known as addressing or spot finding or gridding) is
one of the processing steps in microarray image analysis that registers a set
of unevenly spaced, parallel, and perpendicular lines (a template) with the
image content representing a two-dimensional (2D) array of spots.
Grid alignment methods: Manual grid alignment, semiautomated grid
alignment and fully automated grid alignment.
Grid alignment
15. Foreground and background detection.
The outcome of grid alignment is an approximation of spot locations. The
next task is to identify pixels that belong to foreground (signal) of
expected spot shape and to background. This task involves image
segmentation and clustering.
Image segmentation is associated with the problem of partitioning an
image into spatially contiguous regions with similar properties (e.g., color
or texture)
image clustering refers to the problem of partitioning an image into
sets of pixels with similar properties (e.g., intensity, color, or texture) but
not necessarily connected.
16. (1) circular signal area outside of allowed location
and radius deviations,
(2) small signal with respect to background
(3) disconnected signal areas
(4) inconsistent intensity probability distributions.
quality assurance of the microaray image is
the process of elimination of the grid cells with
unreliable microarray information. This is done
by running the screening algorithm which performs
four types of quality assurance.
Quality assurance
Normalization of microarray data is aimed to correct for
the systematic measurement errors and bias in the
observed data. The errors and bias may be introduced by
several factors such as difference in probe labeling,
concentration of target DNA/ RNA sequence, efficiency of
hybridization, instrumental noise due to scanners or
printers etc.
17. Classification of microarray based on the
types of probes used
1. DNA microarrays: DNA microarray is also known as gene chip, DNA chip,
or biochip. It either measures DNA or uses DNA as a part of its detection
system. There are four different types of DNA microarrays:
cDNA microarrays
oligo DNA microarrays –
In this type, the spotted probes contains of short, chemically synthesized
sequences, 20-25 mers/gene.
specificity is high and cross hybridization can be inhibited.
BAC microarrays - A BAC clone chip is a DNA microarray whose probe is
a template amplified by PCR. The template is a genome region
incorporated into a comprehensive BAC (bacterial artificial chromosome)
clone which various research institutions used in decoding the genome
sequence of various organisms.
SNP microarrays. - SNP array is a type of DNA microarray which is used
to detect polymorphisms within a population
19. Analytical microarrays
Analytical microarrays are typically used to profile a
complex mixture of proteins in order to measure binding
affinities, specificities, and protein expression levels of
the proteins in the mixture.
Antibody microarrays are the most common analytical
microarray
In this technique, a library of antibodies, aptamers, or
affibodies is arrayed on a glass microscope slide. The
array is then probed with a protein solution.
20.
21. Functional Microarrays
functional protein arrays are composed of
arrays containing full-length functional
proteins or protein domains.
These protein chips are used to study the
biochemical activities of an entire proteome
in a single experiment.
They are used to study numerous protein
interactions, such as protein–protein,
protein–DNA, protein–RNA, protein–
phospholipid, and protein–small molecule
interactions
22.
23. In RPA, cells are isolated from
various tissues of interest and are
lysed. The lysate is arrayed onto a
nitrocellulose slide using a contact
pin microarrayer.
The slides are then probed with
antibodies against the target protein
of interest, and the antibodies are
typically detected with
chemiluminescent, fluorescent, or
colorimetric assays
Several such multiprotein samples
are spotted on the microarray, which
is then probed with a single target
molecule.
Reverse Phase Microarrays
25. An ideal surface for protein microarray fabrication has to be capable of
immobilizing proteins and preserving their three‐dimensional (3‐D) conformation.
26.
27. 3. Tissue microarrays: tissue microarray paraffin blocks that are formed by
separating cylindrical tissue cores from various donors and embedding it into
a single microarray. This is mainly used in pathology.
4. Cellular microarrays: they are also called transfection microarrays or living-
cell-microarrays, and are used for screening large-scale chemical and
genomic libraries and systematically investigating the local cellular
microenvironment.
5. Chemical compound microarrays: this is used for drug screening and drug
discovery. This microarray has the capacity to identify and evaluate small
molecules and so it is more useful than the other technologies used in the
pharmaceutical industry.
6. Carbohydrate arrays: they are also called glycoarrays. Carbohydrate arrays
are used in screening proteomes that are carbohydrate binding. They can also
be utilized in calculating protein binding affinities and automization of solid-
support synthesis for glycans.
7. Phenotype microarrays: phenotype microarrays or PMs are mainly used in
drug development. They quantitatively measure thousands of cellular
phenotypes all at once. It is also used in functional genomics and toxicological
testing.
