Bio-chips, also known as lab-on-a-chip devices, can provide portable, low-cost, and low-power platforms for integrating sensors and other components. DNA microarrays allow high-throughput screening by placing probes for thousands of genes on a single chip. mRNA is extracted from experimental and control samples, converted to fluorescent cDNA, and hybridized on the chip. The fluorescent intensities indicate gene expression levels. Protein microarrays similarly attach thousands of proteins to a chip and detect binding with probes to study protein interactions, expression levels, and functions.
Creative Bioarray introduces the tissue array technology and the procedure of making TMAs. Pre-made tissue array and custom tissue array are both provided. In addition, related services are also available.
Please note: This presentation accompanies a recorded webinar at:
https://www1.gotomeeting.com/register/347794241
Biomarkers for studying gene regulation and cell function can be efficiently analyzed by multiplexed methods. Dr. Jim Lazar from OriGene Technologies will provide an overview of four different but related detection technologies that can be used to analyze genetic variants, microRNA expression, transcription factor binding, and protein expression on the Luminex xMAP platform. OriGene’s broad panel of assays and tools for discovery, analysis and validation of multiple classes of important biomarkers will allow researcher to develop more accurate descriptions of biologically complex systems.
Creative Bioarray introduces the tissue array technology and the procedure of making TMAs. Pre-made tissue array and custom tissue array are both provided. In addition, related services are also available.
Please note: This presentation accompanies a recorded webinar at:
https://www1.gotomeeting.com/register/347794241
Biomarkers for studying gene regulation and cell function can be efficiently analyzed by multiplexed methods. Dr. Jim Lazar from OriGene Technologies will provide an overview of four different but related detection technologies that can be used to analyze genetic variants, microRNA expression, transcription factor binding, and protein expression on the Luminex xMAP platform. OriGene’s broad panel of assays and tools for discovery, analysis and validation of multiple classes of important biomarkers will allow researcher to develop more accurate descriptions of biologically complex systems.
Presented by Dr. Miller at the 40th Annual Symposium "Diagnostic and Clinical Challenges of 20th Century Microbes", held on Nov 18, 2010 in Philadelphia.
Presented by Dr. Miller at the 40th Annual Symposium "Diagnostic and Clinical Challenges of 20th Century Microbes", held on Nov 18, 2010 in Philadelphia.
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.
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.
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
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
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.
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.
whole genome analysis
history
needs
steps involved
human genome data
NGS
pyrosequencing
illumina
SOLiD
Ion torrent
PacBio
applications
problems
benefits
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
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Gopinath Rebala
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Encryption in Microsoft 365 - ExpertsLive Netherlands 2024Albert Hoitingh
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The Art of the Pitch: WordPress Relationships and SalesLaura Byrne
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Topics covered:
UI automation Introduction,
UI automation Sample
Desktop automation flow
Pradeep Chinnala, Senior Consultant Automation Developer @WonderBotz and UiPath MVP
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
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Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
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This video focuses on the notifications, alerts, and approval requests using Slack for Bonterra Impact Management. The solutions covered in this webinar can also be deployed for Microsoft Teams.
Interested in deploying notification automations for Bonterra Impact Management? Contact us at sales@sidekicksolutionsllc.com to discuss next steps.
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Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
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And...
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Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
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LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
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During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
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3. White lines correspond to metal electrodes that
connect to individual nanowire devices. The
position of the microfluidic channel used to
deliver sample is highlighted in blue and has a
total size of 6 mm × 500 μm, length × width.
The image field is 4.4 × 3.5 mm.
(B) Optical image of one row of
addressable device elements from the
region highlighted by the red-dashed
box in A. The red arrow highlights the
position of a device. The image field is
500 × 400 μm.
C) Scanning electron
microscopy image of one
silicon nanowire device.
The electrode contacts are
visible at the upper right
and lower left regions of the
image. (Scale bar: 500 nm.)
4. Bio-chips
•
•
•
•
Portable,
low cost in high volumes,
low power,
can be integrated with other components
Chii-Wann Lin et al, DEVELOPMENT OF MICROMACHINED ELECTROCHEMICAL SENSOR
AND PORTABLE METER SYSTEM, a Proceedings of the 20th Annual International Conference of the IEEE
Engineering in Medicine and Biology Society, Vol. 20, No 4,1998
4
5. System architectures
• Chips – flat platforms, sensors below or above the chip
T. Vo-Dinh et al. , Sensors and Actuators, B 74 (2001) 2-11
5
6.
7. Schematic diagram of an integrated DNA biochip system
Vo-Dinh T, Alarie JP, Isola N, Landis D, Wintenberg AL, Ericson, MN (1999) Anal Chem 71 :
358–363
7
8. fluorescence detection of Cy5-labeled Streptavidin using a 4X4
photodiode array IC biochip. Excitation by a 12 mW He±Ne laser
(632.8 nm).
10. MICROARRAYS
It is a 2D array on a solid substrate (usually a glass slide or silicon thinfilm cell) that assays large number of biological material using highthroughput screening methods. Types of microarrays include:
• DNA microarrays,
• oligonucleotide microarrays
• MMChips, for surveillance of microRNA populations
• Protein microarrays
• Tissue microarrays
• Cellular microarrays (also called transfection microarrays)
• Chemical compound microarrays
• Antibody microarrays
• Carbohydrate arrays (glycoarrays)
12. Example of a DNA Array
(note green, yellow red colors;
also note that only part of the total
array is depicted)
13. Example of a DNA Array
(note green, yellow red colors;
also note that only part of the total
array is depicted)
http://www.biomed.miami.edu/arrays/images/agilent_array.jpg
41,000+ unique human genes
and transcripts represented, all
with public domain annotations
14. an arrayed series of thousands of microscopic spots of
DNA oligonucleotides, called probes, each containing
picomoles of a specific DNA sequence. This can be a short section
of a gene or other DNA element that are used as probes to hybridi
a cDNA or cRNA sample (called target)
the probes are attached to a solid surface by a covalent
bond to a chemical matrix (via epoxy-silane, amino-silane,
lysine, polyacrylamide or others). The solid surface can be
glass or a silicon chip
15. • Probe-target hybridization is usually
detected and quantified by detection of
fluorophore-, or chemiluminescence-labeled
targets to determine relative abundance of
nucleic acid sequences in the target. Since
an array can contain tens of thousands of
probes, a microarray experiment can
accomplish many genetic tests in parallel.
16. Colloquially known as an Affy chip when an Affymetrix chip is used.
Other microarray platforms, such as Illumina, use microscopic beads,
instead of the large solid support.
Affymetrix
Agilent Technologies
Applied
CombiMatrix
Eppendorf
GE Healthcare
Genetix
Greiner Bio-One
Illumina, Inc.
Kreatech
Micronit Microfluidics
Nanogen, Inc.
NimbleGen
Ocimum Biosolutions
Roche Diagnostics
SCHOTT Nexterion
STMicroelectronics
17. • DNA microarrays can be used to measure
changes in gene expression levels, to detect
single nucleotide polymorphisms (SNPs) ,
to genotype or resequence mutant genomes.
18. Step 1: Create a DNA array (gene
“chip”) by placing single-stranded
DNA/ Oligonucleotides for each
gene to be assayed into a separate
“well” on the chip.
19. DNA Array: Single-stranded copy DNA Oligonucleotides for
each gene in a different well.
cDNA
gene 1
cDNA
gene 2
cDNA
gene 3
cDNA
gene 4
cDNA
gene 5
20. Step 2: Extract mRNA from biological tissues
subjected to an experimental treatment and
from the same tissue subjected to a control
treatment. Or from normal and from
pathological tissue
21. • Step 3- Make single-stranded DNA from the
mRNA using “color coded” nucleotides.
22. Extract mRNA from Control Cells
Make single-stranded cDNA
using green nucleotides (e.g.
Quantum dots)
cDNA = complementary DNA (DNA synthesized from RNA)
Extract mRNA from
Experimental/pathological Cells
Make single-stranded cDNA
using red nucleotides (e.g.
Quantum dots)
23. Step 4: After making many DNA copies of
the RNA, extract an equal amount of cDNA
from the controls & experimentals and
place it into a container.
29. Step 9: Allow to hybridize, then wash away
all single-stranded DNA.
30. Result:
(1)
(2)
(3)
(4)
Some wells have no color-coded cDNA (no mRNA in either type of cell)
Some wells have only red (i.e., expressed only in experimental cells)
Some wells have only green (i.e., expressed only in control cells)
Some wells have both red and green in various mixtures (expressed
in both experimental and control cells)
31. Step 10: Scan with a laser set to detect the
color & process results on computer.
32. Results:
The colors denote the degree of expression in the
experimental versus the control cells.
Gene not expressed in control or
in experimental cells
Only in
control
cells
Mostly in
control
cells
Mostly in
Only in
Same in
experimental experimental
both cells
cells
cells
35. Part1
Protein Microarray
1. High throughput
analysis of hundreds of
thousands of proteins.
2. Proteins are
immobilized on glass
chip.
3. Various probes
(protein, lipids, DNA,
peptides, etc) are used.
36. Protein Array VS DNA Microarray
Target:
Binding:
Stability:
Surface:
Printing:
Amplification:
Proteins
(Big, 3D)
3D affinity
Low
Glass
Arrayer
Cloning
DNA
(Small, 2D)
2D seq
High
Glass
Arrayer
PCR
37. Protein Array Fabrication
Protein substrates
Polyacrylamide or
agarose gels
Glass
Nanowells
Proteins deposited
on chip surface by
robots
Benfey & Protopapas, 2005
38. Protein Attachment
Diffusion
Protein suspended in
random orientation, but
presumably active
Adsorption/Absorption
Some proteins inactive
Covalent attachment
Some proteins inactive
Affinity
Orientation of protein
precisely controlled
Diffusion
Adsorption/
Absorption
Covalent
Affinity
Benfey & Protopapas, 2005
39. Protein Interactions
Different capture molecules
must be used to study
different interactions
Examples
Antibodies (or antigens) for
detection
Proteins for protein-protein
interaction
Enzyme-substrate for
biochemical function
Antigen–
antibody
Protein–
protein
Aptamers
Enzyme–
substrate
Receptor–
ligand
Benfey & Protopapas, 2005
40. Expression Array
Probes (antibody) on surface recognize
target proteins.
Identification of expressed proteins from
samples.
Typical quantification method for large # of
expressed proteins.
41.
42.
43.
44.
45. Interaction Array
Probes (proteins, peptides, lipids) on
surface interact with target proteins.
Identification of protein interactions.
High throughput discovery of interactions .
46. Functional Array
Probes (proteins) on surface react with
target molecules .
Reaction products are detected.
Main goal of proteomics.
57. Technical Challenges in Protein Chips
1. Poor control of immobilized protein activity.
2. Low yield immobilization.
3. High non-specific adsorption.
4. Fast denaturation of Protein.
5. Limited number of labels – low mutiplexing