A methyl group from S-adenosyl-methionine (SAM) is transferred to the C5 position of the pyrimidine ring of cytosine residues by DNMTs in genomic CpG dinucleotides.
https://www.creative-biogene.com/Services/Drug-Discovery-Services/DNA-Methyltransferase-Screening-and-Profiling.html
Dna methylation ppt
definition of Dna methylation ppt
discovery of Dna methylation ppt
types of Dna methylation ppt
history of Dna methylation ppt
process of Dna methylation ppt
mechanism of Dna methylation ppt
methylation in cancer
cytosine methylation
genomic imprinting
A methyl group from S-adenosyl-methionine (SAM) is transferred to the C5 position of the pyrimidine ring of cytosine residues by DNMTs in genomic CpG dinucleotides.
https://www.creative-biogene.com/Services/Drug-Discovery-Services/DNA-Methyltransferase-Screening-and-Profiling.html
Dna methylation ppt
definition of Dna methylation ppt
discovery of Dna methylation ppt
types of Dna methylation ppt
history of Dna methylation ppt
process of Dna methylation ppt
mechanism of Dna methylation ppt
methylation in cancer
cytosine methylation
genomic imprinting
Ibica2014 p(8) visualizing and identifying the dna methylationAboul Ella Hassanien
DNA methylation is an epigenetic mechanism that cells use to control
gene expression. DNA methylation has become one of the hottest topics in cancer
research, especially for abnormally hypermethylated tumor suppressor genes
or hypomethylaed oncogenes research. The analysis of DNA methylation data
determines the differential hypermethlated or hypomethylated genes that are candidate
to be cancer biomarkers. Visualization the DNA methylation status may
lead to discover new relationships between hypomethylated and hypermethylated
genes, therefore this paper applied a mathematical modelling theory called formal
concept analysis for visualizing DNA methylation status.
Epigenetics can be used to explain the phenomena that cannot be explained by genetics/genomics, such as the differences between monozygotic twins, which are considered to be genetically identical.
Sequencing based approaches for profiling dna methylationsciencelearning123
DNA methylation, one of the most studied epigenetic modifications, refers to the addition of a methyl group to the fifth carbon of cytosine (C) catalyzed by DNA methyltransferases (Dnmts), forming 5-methylcytosine (5mC). DNA methylation predominantly occurs in CpGs but is also found in non-CpG contexts.
The role of DNA methylation in complex diseasesJordana Bell
A 1-hour lecture to 4th-year undergraduate and/or MSc students in human genetics, focusing on exploring the role of DNA methylation in human complex disease.
The Role of DNA Methylation in Coronary Artery DiseaseBardia Farivar
Epigenetic studies have identified DNA methylation in coronary artery disease (CAD). How the critical genes interact at the cellular level to cause CAD is still unknown. The discovery of DNA methylation inspired researchers to explore relationships in genomic coding and disease phenotype. In the past two decades, there have been many findings regarding the relationship between DNA methylation and CAD development, and the DNA methylation of critical genes have been found to be significantly changed during CAD, including DNA methylation at homocysteine, Alu and long Interspersed Element 1 (LINE-1) repetitive elements.
The extraction of DNA involves three main steps that are cell lysis, protein separation, and DNA purification. Cell lysis is usually performed by incubation of cell in buffer containing detergent and protease. Cellular proteins are salted out or phase separated using organic solvents. Finally DNA is isolated and purified either by alcohol precipitation or adsorption with silica and elution.
Induction of transformation by a deoxyribonucleic acid fraction isolated from...Babita Neupane
This is a highlight of the one of the groundbreaking paper of early 1940's in field of molecular biology.
Induction of transformation by a deoxyribonucleic acid fraction isolated from Pneumococcus Type III. Avery, O.T., Macleod, C. M., McCarty, M. (1944) The journal of experimental medicine 79(2):137-58.
Ibica2014 p(8) visualizing and identifying the dna methylationAboul Ella Hassanien
DNA methylation is an epigenetic mechanism that cells use to control
gene expression. DNA methylation has become one of the hottest topics in cancer
research, especially for abnormally hypermethylated tumor suppressor genes
or hypomethylaed oncogenes research. The analysis of DNA methylation data
determines the differential hypermethlated or hypomethylated genes that are candidate
to be cancer biomarkers. Visualization the DNA methylation status may
lead to discover new relationships between hypomethylated and hypermethylated
genes, therefore this paper applied a mathematical modelling theory called formal
concept analysis for visualizing DNA methylation status.
Epigenetics can be used to explain the phenomena that cannot be explained by genetics/genomics, such as the differences between monozygotic twins, which are considered to be genetically identical.
Sequencing based approaches for profiling dna methylationsciencelearning123
DNA methylation, one of the most studied epigenetic modifications, refers to the addition of a methyl group to the fifth carbon of cytosine (C) catalyzed by DNA methyltransferases (Dnmts), forming 5-methylcytosine (5mC). DNA methylation predominantly occurs in CpGs but is also found in non-CpG contexts.
The role of DNA methylation in complex diseasesJordana Bell
A 1-hour lecture to 4th-year undergraduate and/or MSc students in human genetics, focusing on exploring the role of DNA methylation in human complex disease.
The Role of DNA Methylation in Coronary Artery DiseaseBardia Farivar
Epigenetic studies have identified DNA methylation in coronary artery disease (CAD). How the critical genes interact at the cellular level to cause CAD is still unknown. The discovery of DNA methylation inspired researchers to explore relationships in genomic coding and disease phenotype. In the past two decades, there have been many findings regarding the relationship between DNA methylation and CAD development, and the DNA methylation of critical genes have been found to be significantly changed during CAD, including DNA methylation at homocysteine, Alu and long Interspersed Element 1 (LINE-1) repetitive elements.
The extraction of DNA involves three main steps that are cell lysis, protein separation, and DNA purification. Cell lysis is usually performed by incubation of cell in buffer containing detergent and protease. Cellular proteins are salted out or phase separated using organic solvents. Finally DNA is isolated and purified either by alcohol precipitation or adsorption with silica and elution.
Induction of transformation by a deoxyribonucleic acid fraction isolated from...Babita Neupane
This is a highlight of the one of the groundbreaking paper of early 1940's in field of molecular biology.
Induction of transformation by a deoxyribonucleic acid fraction isolated from Pneumococcus Type III. Avery, O.T., Macleod, C. M., McCarty, M. (1944) The journal of experimental medicine 79(2):137-58.
This is an internship report on molecular biology techniques, which was performed at PERD center under the guidance of Dr. Anshu Srivastava. This pdf contains all the basic information which is a preliminary requisite to know while approaching the molecular biology experimentally.
DTNB (5,5'-Dithio-bis (2-nitrobenzoic acid) also known as Ellman’s reagent for determination of total sulfhydryl groups, protein-bound sulfhydryl groups, and free sulfhydryl groups in biological samples.
UiPath Test Automation using UiPath Test Suite series, part 6DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 6. In this session, we will cover Test Automation with generative AI and Open AI.
UiPath Test Automation with generative AI and Open AI webinar offers an in-depth exploration of leveraging cutting-edge technologies for test automation within the UiPath platform. Attendees will delve into the integration of generative AI, a test automation solution, with Open AI advanced natural language processing capabilities.
Throughout the session, participants will discover how this synergy empowers testers to automate repetitive tasks, enhance testing accuracy, and expedite the software testing life cycle. Topics covered include the seamless integration process, practical use cases, and the benefits of harnessing AI-driven automation for UiPath testing initiatives. By attending this webinar, testers, and automation professionals can gain valuable insights into harnessing the power of AI to optimize their test automation workflows within the UiPath ecosystem, ultimately driving efficiency and quality in software development processes.
What will you get from this session?
1. Insights into integrating generative AI.
2. Understanding how this integration enhances test automation within the UiPath platform
3. Practical demonstrations
4. Exploration of real-world use cases illustrating the benefits of AI-driven test automation for UiPath
Topics covered:
What is generative AI
Test Automation with generative AI and Open AI.
UiPath integration with generative AI
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
DevOps and Testing slides at DASA ConnectKari Kakkonen
My and Rik Marselis slides at 30.5.2024 DASA Connect conference. We discuss about what is testing, then what is agile testing and finally what is Testing in DevOps. Finally we had lovely workshop with the participants trying to find out different ways to think about quality and testing in different parts of the DevOps infinity loop.
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdfPaige Cruz
Monitoring and observability aren’t traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current company’s observability stack.
While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
I, a former op, would like to extend an invitation to all application developers to join the observability party will share these foundational concepts to build on:
Essentials of Automations: The Art of Triggers and Actions in FMESafe Software
In this second installment of our Essentials of Automations webinar series, we’ll explore the landscape of triggers and actions, guiding you through the nuances of authoring and adapting workspaces for seamless automations. Gain an understanding of the full spectrum of triggers and actions available in FME, empowering you to enhance your workspaces for efficient automation.
We’ll kick things off by showcasing the most commonly used event-based triggers, introducing you to various automation workflows like manual triggers, schedules, directory watchers, and more. Plus, see how these elements play out in real scenarios.
Whether you’re tweaking your current setup or building from the ground up, this session will arm you with the tools and insights needed to transform your FME usage into a powerhouse of productivity. Join us to discover effective strategies that simplify complex processes, enhancing your productivity and transforming your data management practices with FME. Let’s turn complexity into clarity and make your workspaces work wonders!
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
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
Guy Korland, CEO and Co-founder of FalkorDB, will review two articles on the integration of language models with knowledge graphs.
1. Unifying Large Language Models and Knowledge Graphs: A Roadmap.
https://arxiv.org/abs/2306.08302
2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs:
https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/
Threats to mobile devices are more prevalent and increasing in scope and complexity. Users of mobile devices desire to take full advantage of the features
available on those devices, but many of the features provide convenience and capability but sacrifice security. This best practices guide outlines steps the users can take to better protect personal devices and information.
zkStudyClub - Reef: Fast Succinct Non-Interactive Zero-Knowledge Regex ProofsAlex Pruden
This paper presents Reef, a system for generating publicly verifiable succinct non-interactive zero-knowledge proofs that a committed document matches or does not match a regular expression. We describe applications such as proving the strength of passwords, the provenance of email despite redactions, the validity of oblivious DNS queries, and the existence of mutations in DNA. Reef supports the Perl Compatible Regular Expression syntax, including wildcards, alternation, ranges, capture groups, Kleene star, negations, and lookarounds. Reef introduces a new type of automata, Skipping Alternating Finite Automata (SAFA), that skips irrelevant parts of a document when producing proofs without undermining soundness, and instantiates SAFA with a lookup argument. Our experimental evaluation confirms that Reef can generate proofs for documents with 32M characters; the proofs are small and cheap to verify (under a second).
Paper: https://eprint.iacr.org/2023/1886
Pushing the limits of ePRTC: 100ns holdover for 100 daysAdtran
At WSTS 2024, Alon Stern explored the topic of parametric holdover and explained how recent research findings can be implemented in real-world PNT networks to achieve 100 nanoseconds of accuracy for up to 100 days.
In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
We will explore the capabilities of AI in understanding XML markup languages and autonomously creating structured XML content. Additionally, we will examine the capacity of AI to enrich plain text with appropriate XML markup. Practical examples and methodological guidelines will be provided to elucidate how AI can be effectively prompted to interpret and generate accurate XML markup.
Further emphasis will be placed on the role of AI in developing XSLT, or schemas such as XSD and Schematron. We will address the techniques and strategies adopted to create prompts for generating code, explaining code, or refactoring the code, and the results achieved.
The discussion will extend to how AI can be used to transform XML content. In particular, the focus will be on the use of AI XPath extension functions in XSLT, Schematron, Schematron Quick Fixes, or for XML content refactoring.
The presentation aims to deliver a comprehensive overview of AI usage in XML development, providing attendees with the necessary knowledge to make informed decisions. Whether you’re at the early stages of adopting AI or considering integrating it in advanced XML development, this presentation will cover all levels of expertise.
By highlighting the potential advantages and challenges of integrating AI with XML development tools and languages, the presentation seeks to inspire thoughtful conversation around the future of XML development. We’ll not only delve into the technical aspects of AI-powered XML development but also discuss practical implications and possible future directions.
The Art of the Pitch: WordPress Relationships and SalesLaura Byrne
Clients don’t know what they don’t know. What web solutions are right for them? How does WordPress come into the picture? How do you make sure you understand scope and timeline? What do you do if sometime changes?
All these questions and more will be explored as we talk about matching clients’ needs with what your agency offers without pulling teeth or pulling your hair out. Practical tips, and strategies for successful relationship building that leads to closing the deal.
Removing Uninteresting Bytes in Software FuzzingAftab Hussain
Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process.
In this work, we equipped AFL, a popular fuzzer, with DIAR and examined two critical Linux libraries -- Libxml's xmllint, a tool for parsing xml documents, and Binutil's readelf, an essential debugging and security analysis command-line tool used to display detailed information about ELF (Executable and Linkable Format). Our preliminary results show that AFL+DIAR does not only discover new paths more quickly but also achieves higher coverage overall. This work thus showcases how starting with lean and optimized seeds can lead to faster, more comprehensive fuzzing campaigns -- and DIAR helps you find such seeds.
- These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.
Maruthi Prithivirajan, Head of ASEAN & IN Solution Architecture, Neo4j
Get an inside look at the latest Neo4j innovations that enable relationship-driven intelligence at scale. Learn more about the newest cloud integrations and product enhancements that make Neo4j an essential choice for developers building apps with interconnected data and generative AI.
2. • Epigenetics- The heritable changes in gene function that occur independently to the DNA
sequence.
• DNA Methylation- A biochemical process critical to human development that in this case
involves the addition of a methyl group to the 5 position of the cytosine pyrimidine ring.
• Dinucleotide- a nucleotide consisting of two units each composed of a phosphate, a pentose, and
a nitrogen base.
• Bisulphite- a salt or ester of sulphurous acid containing the monovalent group -HSO3 or the ion
HSO3-.
• Sulphonation- The addition of bisulphite to the 5-6 double bond of cytosine.
• Hydrolic Deamination- Hydrolytic deamination of the resulting cytosine-bisulphite derivative to
give a uracil-bisulphite derivative.
• Alkali Desulphonation- Removal of the sulphonate group by an alkali treatment, to give uracil.
• Nucleotides- molecules that when joined together make up the basic elements of DNA and RNA.
• PCR Amplification- to amplify a single or a few copies of a piece of DNA across several orders
of magnitude, generating thousands to millions of copies of a particular DNA sequence.
• Cloning- to processes used to create copies of DNA fragments (molecular cloning), cells (cell
cloning), or organisms
• Sequencing- several methods and technologies that are used for determining the order of the
nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA.
• Denaturation- a process in which proteins or nucleic acids lose the tertiary structure and
secondary structure which is present in their native state, by application of some external stress
or compound such as a strong acid or base.
3.
4. • DNA Methylation provides instructions to gene
expression elements of physiology that tell it where and
when a gene should be expressed. DNA Methylation
normally occurs in conjunction with 5’-CpG-3’
dinucleotides which are located in concentrated regions
of repetitive genomic sequences associated with gene
promoters. DNA Methylation is established early in
human development and can be targeted by certain types
of cancer. Bisulphite conversion, PCR amplification, and
cloning/sequencing are used to show resolution of a
single nucleotide for methylation in the DNA molecule.
5. • DNA samples are prepared by incubating the genomic
DNA with bisulphite DNA Lysis Buffer in a total volume
of 18 microliters for 1 hr at 37°C.
• DNA Denaturation begins with denaturing the 2
micrograms of DNA used in this experiment in a volume
of 20 microliters by adding 2 microliters of freshly
prepared 3M NaOH to a final concentration of 0.3 M.
• Incubate the samples for 15 minutes in a water bath at
37°C followed by an incubation at 90°C for 2 min in a
heat block. Immediately place the tubes on ice for 5 mins.
• Centrifuge the tubes at 4°C for 10 s at 10,000 grams to
ensure the DNA is at the bottom of the test tubes.
6. • Prepare fresh solutions of Quinol and saturated sodium
metabisulphite. Inverting the reagent/H2O mixture with
minimum mixing and aeration with result in the desired
saturated sodium bisulphite solution.
• pH may need to be adjusted to 10 M NaOH.
• Add saturated metabisulphite and Quionol to the denatured
DNA in a final volume of 240 microliters to a final
concentration of 2.31 M bisulphite/0.5 mM Quinol, pH 5.0.
Gently mix and centrifuge.
• Overlay the samples with mineral oil then incubate for 4-16
hours. The length of the bisulphite treatment is dependent on
the quantity and quality of the DNA being converted. Poor
DNA should be incubated for only 4 hours.
• Centrifuge the tubes to ensure all the liquid is at the bottom
then recover the bisulphite treated DNA layer from the oil
layer by carefully pipetting it from the bottom being careful to
not get mineral oil.
7. • Remove any free bisulphite ions by passing through a
desalting column. Different desalting columns can be
used to eluted the ions in 50 microliters of milli-Q water
depending on the quantity and quality of the DNA.
• Desulphonate the bisulphite adduct to remove the uracil
ring. Incubate the samples at 37°C.
• Centrifuge briefly.
• Neutralize the solution with ammonium acetate, pH 7.0 to
a final concentration of 3M.
• Ethanol-precipitate the DNA by adding 100% ice cold
ethanol and mix well by inversion. Leave overnight then
centrifuge, air dry afterwards for approx. 20 minutes.
• Re-suspend the DNA pellet. Leave at room temp. approx.
2 hours and occasionally vortex the tubes.
• Immediately start PCR Amplification or store for 1-10
years.
8. • Primer Design: Effective design of PCR bisulphite
conversion-specific primers are crucial to ensure that the
amplification of the DNA is unbiased.
9. • To test for proportional PCR amplification use a 50:50
Methylated/Unmethylated fully bisulphite converted control
sample and amplify with the bisulphite conversion-specific
primers under the optimized PCR reaction conditions.
• Prepare PCR amplification reaction mixutres in 100 microliter
aliquots.
• Across 10 tubes set the run reaction gradient to +/- 3°C in a
temperature gradient thermocycler.
• Test the methylated and umethylated amplicons for appropriate
proportions by digesting the methylated DNA in an
informative restriction enzyme such as Taq 1.
• Ensure proportional PCR amplification has been completed, if
not, adjust MgCl2 concentration.
• PCR amplification now can be performed.
10.
11.
12.
13.
14.
15.
16.
17. • New sequencing techniques are evolving to produce
similar resolution results to bisulphite genomic
sequencing.
• Third generation single molecule sequencing has the
potential to allow for analysis of both primary DNA and
methylation without the need for bisulphite sequencing.
• Bisulphite genome sequencing is still the main protocol in
methylation analysis.
• Modification of the process only occurs when minor
problems arise.