The document discusses omics technology and its various applications in the field of nutrition. It defines omics as the comprehensive study of biological systems using techniques like genomics, transcriptomics, proteomics and metabolomics. Nutrigenomics applies these omics approaches to study how food and dietary components influence gene expression. Key applications mentioned include using nutrigenomics to develop foods that can prevent and treat diseases by modulating gene expression, and analyzing gene-diet interactions that could increase risk of conditions like diabetes.
Genomics, Transcriptomics, Proteomics, Metabolomics - Basic concepts for clin...Prasenjit Mitra
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This set of slides gives an overview regarding the various omics technologies available and how they can be used for improvement in clinical setting or research
Genomics, Transcriptomics, Proteomics, Metabolomics - Basic concepts for clin...Prasenjit Mitra
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This set of slides gives an overview regarding the various omics technologies available and how they can be used for improvement in clinical setting or research
In shotgun sequencing the genome is broken randomly into short fragments (1 to 2 kbp long) suitable for sequencing. The fragments are ligated into a suitable vector and then partially sequenced. Around 400â500 bp of sequence can be generated from each fragment in a single sequencing run. In some cases, both ends of a fragment are sequenced. Computerized searching for overlaps between individual sequences then assembles the complete sequence.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones).
Metabolome refers to the complete set of chemical compounds involved in an organism's metabolism (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites)
Metabolomics is the scientific study of chemical processes involving metabolites. Metabolomics is a relatively new member to the â-omicsâ family of systems biology technologies.
With the DNA sequences of more than 90 genomes completed, as well as a draft sequence of the human genome, a major challenge in modern biology is to understand the expression, function, and regulation of the entire set of proteins encoded by an organismâthe aims of the new field of proteomics. This information will be invaluable for understanding how complex biological processes occur at a molecular level, how they differ in various cell types, and how they are altered in disease states. The term proteomics describes the study and characterization of a complete set of proteins present in a cell, organ, or organism at a given time.
In general, proteomic approaches can be used (a) for proteome profiling, (b) for comparative expression analysis of two or more protein samples, (c) for the localization and identification of posttranslational modifications, and (d) for the study of protein-protein interactions. The human genome harbours 26000â31000 protein-encoding genes; whereas the total number of human protein products, including splice variants and essential posttranslational modifications (PTMs), has been estimated to be close to one million. It is evident that most of the functional information on the genes resides in the proteome, which is the sum of multiple dynamic processes that include protein phosphorylation, protein trafficking, localization, and protein-protein interactions. Moreover, the proteomes of mammalian cells, tissues, and body fluids are complex and display a wide dynamic range of proteins concentration one cell can contain between one and more than 100000 copies of a single protein.
A rapidly emerging set of key technologies is making it possible to identify large numbers of proteins in a mixture or complex, to map their interactions in a cellular context, and to analyze their biological activities. Mass spectrometry has evolved into a versatile tool for examining the simultaneous expression of more than 1000 proteins and the identification and mapping of posttranslational modifications. High-throughput methods performed in an array format have enabled large-scale projects for the characterization of protein localization, protein-protein interactions, and the biochemical analysis of protein function. Finally, the plethora of data generated in the last few years has led to approaches for the integration of diverse data sets that greatly enhance our understanding of both individual protein function and elaborate biological processes.
Functional proteomics, methods and toolsKAUSHAL SAHU
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INTRODUCTION
HISTORY
DEFINITION
PROTEOMICS
FUNCTIONAL PROTEOMICS
PROTEOMICS SOFTWARE
PROTEOMICS ANALYSIS
TOOLS FOR PROTEOM ANALYSIS
DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS
APLLICATIONS
LIMITATIONS
CONCLUSION
Personalized Medicine and the Omics Revolution by Professor Mike SnyderThe Hive
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Personalized medicine is expected to benefit from the combination of genomic information with the global monitoring of molecular components and physiological states. To ascertain whether this can be achieved, we determined the whole genome sequence of an individual at high accuracy and performed an integrated Personal Omics Profiling (iPOP) analysis, combining genomic, transcriptomic, proteomic, metabolomic, and autoantibodyomic information, over a 38-month period that included healthy and two virally infected states. Our iPOP analysis of blood components revealed extensive, dynamic and broad changes in diverse molecular components and biological pathways across healthy and disease conditions. Importantly, genomic information was also used to estimate medical risks, including Type 2 Diabetes, whose onset was observed during the course of our study. Our study demonstrates that longitudinal personal omics profiling can relate genomic information to global functional omics activity for physiological and medical interpretation of healthy and disease states.
Meet the speaker, Professor Michael Snyder (Stanford):
Michael Snyder is the Stanford Ascherman Professor, Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine. He received his Ph.D. from the California Institute of Technology and postdoctoral training at Stanford University. He is a leader in the field of functional genomics and proteomics, and one of the major participants of the ENCODE project. His laboratory study was the first to perform a large-scale functional genomics project in any organism, and has launched many technologies in genomics and proteomics. These including the development of proteome chips, high resolution tiling arrays for the entire human genome, methods for global mapping of transcription factor binding sites (ChIP-chip now replaced by ChIP-seq), paired end sequencing for mapping of structural variation in eukaryotes, de novo genome sequencing of genomes using high throughput technologies and RNA-Seq. These technologies have been used for characterizing genomes, proteomes and regulatory networks. Seminal findings from the Snyder laboratory include; the discovery that much more of the human genome is transcribed and contains regulatory information than was previously appreciated, and a high diversity of transcription factor binding occurs both between and within species. He has also combined different state-ofâthe-art omics technologies to perform the first longitudinal detailed integrative personal omics profile (iPOP) of person and used this to assess disease risk and monitor disease states for personalized medicine. He is a co-founder of several biotechnology companies including; Protometrix (now part of Life Technologies), Affomix (now part of Illumina), Excelix, and Personalis, and he presently serves on the board of a number of companies.
In shotgun sequencing the genome is broken randomly into short fragments (1 to 2 kbp long) suitable for sequencing. The fragments are ligated into a suitable vector and then partially sequenced. Around 400â500 bp of sequence can be generated from each fragment in a single sequencing run. In some cases, both ends of a fragment are sequenced. Computerized searching for overlaps between individual sequences then assembles the complete sequence.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones).
Metabolome refers to the complete set of chemical compounds involved in an organism's metabolism (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites)
Metabolomics is the scientific study of chemical processes involving metabolites. Metabolomics is a relatively new member to the â-omicsâ family of systems biology technologies.
With the DNA sequences of more than 90 genomes completed, as well as a draft sequence of the human genome, a major challenge in modern biology is to understand the expression, function, and regulation of the entire set of proteins encoded by an organismâthe aims of the new field of proteomics. This information will be invaluable for understanding how complex biological processes occur at a molecular level, how they differ in various cell types, and how they are altered in disease states. The term proteomics describes the study and characterization of a complete set of proteins present in a cell, organ, or organism at a given time.
In general, proteomic approaches can be used (a) for proteome profiling, (b) for comparative expression analysis of two or more protein samples, (c) for the localization and identification of posttranslational modifications, and (d) for the study of protein-protein interactions. The human genome harbours 26000â31000 protein-encoding genes; whereas the total number of human protein products, including splice variants and essential posttranslational modifications (PTMs), has been estimated to be close to one million. It is evident that most of the functional information on the genes resides in the proteome, which is the sum of multiple dynamic processes that include protein phosphorylation, protein trafficking, localization, and protein-protein interactions. Moreover, the proteomes of mammalian cells, tissues, and body fluids are complex and display a wide dynamic range of proteins concentration one cell can contain between one and more than 100000 copies of a single protein.
A rapidly emerging set of key technologies is making it possible to identify large numbers of proteins in a mixture or complex, to map their interactions in a cellular context, and to analyze their biological activities. Mass spectrometry has evolved into a versatile tool for examining the simultaneous expression of more than 1000 proteins and the identification and mapping of posttranslational modifications. High-throughput methods performed in an array format have enabled large-scale projects for the characterization of protein localization, protein-protein interactions, and the biochemical analysis of protein function. Finally, the plethora of data generated in the last few years has led to approaches for the integration of diverse data sets that greatly enhance our understanding of both individual protein function and elaborate biological processes.
Functional proteomics, methods and toolsKAUSHAL SAHU
Â
INTRODUCTION
HISTORY
DEFINITION
PROTEOMICS
FUNCTIONAL PROTEOMICS
PROTEOMICS SOFTWARE
PROTEOMICS ANALYSIS
TOOLS FOR PROTEOM ANALYSIS
DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS
APLLICATIONS
LIMITATIONS
CONCLUSION
Personalized Medicine and the Omics Revolution by Professor Mike SnyderThe Hive
Â
Personalized medicine is expected to benefit from the combination of genomic information with the global monitoring of molecular components and physiological states. To ascertain whether this can be achieved, we determined the whole genome sequence of an individual at high accuracy and performed an integrated Personal Omics Profiling (iPOP) analysis, combining genomic, transcriptomic, proteomic, metabolomic, and autoantibodyomic information, over a 38-month period that included healthy and two virally infected states. Our iPOP analysis of blood components revealed extensive, dynamic and broad changes in diverse molecular components and biological pathways across healthy and disease conditions. Importantly, genomic information was also used to estimate medical risks, including Type 2 Diabetes, whose onset was observed during the course of our study. Our study demonstrates that longitudinal personal omics profiling can relate genomic information to global functional omics activity for physiological and medical interpretation of healthy and disease states.
Meet the speaker, Professor Michael Snyder (Stanford):
Michael Snyder is the Stanford Ascherman Professor, Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine. He received his Ph.D. from the California Institute of Technology and postdoctoral training at Stanford University. He is a leader in the field of functional genomics and proteomics, and one of the major participants of the ENCODE project. His laboratory study was the first to perform a large-scale functional genomics project in any organism, and has launched many technologies in genomics and proteomics. These including the development of proteome chips, high resolution tiling arrays for the entire human genome, methods for global mapping of transcription factor binding sites (ChIP-chip now replaced by ChIP-seq), paired end sequencing for mapping of structural variation in eukaryotes, de novo genome sequencing of genomes using high throughput technologies and RNA-Seq. These technologies have been used for characterizing genomes, proteomes and regulatory networks. Seminal findings from the Snyder laboratory include; the discovery that much more of the human genome is transcribed and contains regulatory information than was previously appreciated, and a high diversity of transcription factor binding occurs both between and within species. He has also combined different state-ofâthe-art omics technologies to perform the first longitudinal detailed integrative personal omics profile (iPOP) of person and used this to assess disease risk and monitor disease states for personalized medicine. He is a co-founder of several biotechnology companies including; Protometrix (now part of Life Technologies), Affomix (now part of Illumina), Excelix, and Personalis, and he presently serves on the board of a number of companies.
The 'omics' revolution: How will it improve our understanding of infections a...WAidid
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This slideset explains the âOmicsâ technology and its role in the study of infections and vaccination. It is a revolution as it offers powerful tools to interrogate the animal / human immune response to vaccines and infections.
Data analysis & integration challenges in genomicsmikaelhuss
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Presentation given at the Genomics Today and Tomorrow event in Uppsala, Sweden, 19 March 2015. (http://connectuppsala.se/events/genomics-today-and-tomorrow/) Topics include APIs, "querying by data set", machine learning.
Resolving Ambiguity in Target ID Screens - CRISPR-Cas9 Based Essentiality Pro...Candy Smellie
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Pathfinder Target Essentiality Assay Service
A new CRISPRâCas9 based medium throughput assay service for validation of target gene essentiality
Can be used to resolve ambiguous screening results
Can also provide information on drug target suitability
This assay developed at Horizon will enable you to identify genes essential for the growth of specific cancer cell lines.
It can be used to definitively resolve ambiguous screening results.
Or to provide information on target suitability â by testing essentiality in ânormalâ cells, or in cancer subtypes different to the proposed patient population
Blueprints to blue sky â analyzing the challenges and solutions for IHC compa...Candy Smellie
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Manual assessment of biomarker expression is associated with significant inter- and intra reader variability. In some cases there are also limitations when it comes to sensitivity and specificity of manual biomarker assessment.
In one example to the left, the âpureâ contribution of inter-reader variability associated with Ki67 assessment was quantified across 20 tumors and 126 participating labs. In that study, it was demonstrated how image analysis can be used to significantly reduce inter-reader variability.
In a another study, the National Danish Validation study of Her2, it was demonstrated how improved sensitivity/specificity of quantitative HER2 protein expression wrt gene amplification lead to significant cost savings in reflex testing.
By automating aspects of stain quality control, it will become scalable to he point where EQA organizations may be able and willing to offer more frequent â perhaps even on-demand â proficiency testing and calibration services.
It is possible that objective and quantitative standards will contribute to improve compliance with protocol recommendations.
In clinical multi-center trials it will be easier to standardize and monitor data from each center.
And it is our hope tha larger diagnostic pathology labs will be able to benefit from such a method by closely monitoring drift in staining quality for biomarkers.
Challenges and opportunities in personal omics profilingSenthil Natesan
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The term ââomicââ is derived from the Latin suffix ââomeââ meaning mass or many. Thus, OMICS involve a mass (large number) of measurements per endpoint. (Jackson et al., 2006)
The functional state of a cell can be explained by the integrated set of different OMICS data, called molecular signature or biomarker.The same fact can be exploited to find out difference between diseased and normal.
For diagnosis of a diseases in future, personal OMICS profiling (POP) is indispensible.
The POP further confer advantage to produce personal drugs, based on POP.
Conferencia de la Dra. Ana MarĂa Roa, BiĂłloga Molecular, sobre EpigenĂŠtica, impartida en la Universidad Popular Carmen de Michelena de Tres Cantos el 1 de marzo de 2013.
MĂĄs informaciĂłn en:
http://www.universidadpopularc3c.es/index.php/actividades/conferencias/event/448-conferencia-una-revision-de-los-conocimientos-fundamentales-de-la-biologia-de-la-celula-la-epigenetica
this is done by me and my team mates of Wayamba University Sri Lanka for our project.From now we decided to allow download this file.I would be greatful if you could send your comments..
And I'm willing to help you in similar works.I'm in final year of my degree(.BSc Biotechnology)..
pubudu_gokarella@yahoo.com
TOXICOLOGY STUDY IS VERY ESSENTIAL FOR DRUG DISCOVERY. INTERNATIONAL COUNCIL FOR HARMONIZATION (ICH) HAS IMPLEMENTED SOME BASIC RULES AND REGULATION REGARDING THE TOXICITY STUDY ON ANIMAL DURING PRE-CLINICAL TRIAL, WHICH IS A PART OF DRUG DISCOVERY PROCESS. HERE SOME OF THE BASIC TEST ARE DISCUSSED ALONG WITH SOME BASIC CONCEPTS OF GENETICS. HOPE THIS WILL HELP THE STUDENTS TO UNDERSTAND THE TOPIC.
The study of nucleic acids began with the discovery of DNA, progressed to the study of genes and small fragments, and has now exploded to the field of genomics. Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. The advances in genomics have been made possible by DNA sequencing technology. [Source: https://opentextbc.ca/biology/chapter/10-3-genomics-and-proteomics/]
-Basic Concepts in Genetics
-What is Epigenetic?
-History of Epigenetic
-How do epigenetics work?
-Epigenetics and the Environment
-Epigenetic Inheritance
-Epigenetics in Psychiatry
DevOps and Testing slides at DASA ConnectKari Kakkonen
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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.
Slack (or Teams) Automation for Bonterra Impact Management (fka Social Soluti...Jeffrey Haguewood
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Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
We believe integration and automation are essential to user experience and the promise of efficient work through technology. Automation is the critical ingredient to realizing that full vision. We develop integration products and services for Bonterra Case Management software to support the deployment of automations for a variety of use cases.
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.
Dev Dives: Train smarter, not harder â active learning and UiPath LLMs for do...UiPathCommunity
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đĽ Speed, accuracy, and scaling â discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Miningâ˘:
See how to accelerate model training and optimize model performance with active learning
Learn about the latest enhancements to out-of-the-box document processing â with little to no training required
Get an exclusive demo of the new family of UiPath LLMs â GenAI models specialized for processing different types of documents and messages
This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath.
Speakers:
đ¨âđŤ Andras Palfi, Senior Product Manager, UiPath
đŠâđŤ Lenka Dulovicova, Product Program Manager, UiPath
Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf91mobiles
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91mobiles recently conducted a Smart TV Buyer Insights Survey in which we asked over 3,000 respondents about the TV they own, aspects they look at on a new TV, and their TV buying preferences.
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
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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.
Accelerate your Kubernetes clusters with Varnish CachingThijs Feryn
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A presentation about the usage and availability of Varnish on Kubernetes. This talk explores the capabilities of Varnish caching and shows how to use the Varnish Helm chart to deploy it to Kubernetes.
This presentation was delivered at K8SUG Singapore. See https://feryn.eu/presentations/accelerate-your-kubernetes-clusters-with-varnish-caching-k8sug-singapore-28-2024 for more details.
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
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As AI technology is pushing into IT I was wondering myself, as an âinfrastructure container kubernetes guyâ, how get this fancy AI technology get managed from an infrastructure operational view? Is it possible to apply our lovely cloud native principals as well? What benefitâs both technologies could bring to each other?
Let me take this questions and provide you a short journey through existing deployment models and use cases for AI software. On practical examples, we discuss what cloud/on-premise strategy we may need for applying it to our own infrastructure to get it to work from an enterprise perspective. I want to give an overview about infrastructure requirements and technologies, what could be beneficial or limiting your AI use cases in an enterprise environment. An interactive Demo will give you some insides, what approaches I got already working for real.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
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Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
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Today, after several years of existence, an extremely active community and an ultra-dynamic ecosystem, Kubernetes has established itself as the de facto standard in container orchestration. Thanks to a wide range of managed services, it has never been so easy to set up a ready-to-use Kubernetes cluster.
However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks.
In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.
Software Delivery At the Speed of AI: Inflectra Invests In AI-Powered QualityInflectra
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In this insightful webinar, Inflectra explores how artificial intelligence (AI) is transforming software development and testing. Discover how AI-powered tools are revolutionizing every stage of the software development lifecycle (SDLC), from design and prototyping to testing, deployment, and monitoring.
Learn about:
⢠The Future of Testing: How AI is shifting testing towards verification, analysis, and higher-level skills, while reducing repetitive tasks.
⢠Test Automation: How AI-powered test case generation, optimization, and self-healing tests are making testing more efficient and effective.
⢠Visual Testing: Explore the emerging capabilities of AI in visual testing and how it's set to revolutionize UI verification.
⢠Inflectra's AI Solutions: See demonstrations of Inflectra's cutting-edge AI tools like the ChatGPT plugin and Azure Open AI platform, designed to streamline your testing process.
Whether you're a developer, tester, or QA professional, this webinar will give you valuable insights into how AI is shaping the future of software delivery.
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
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In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
Generating a custom Ruby SDK for your web service or Rails API using Smithyg2nightmarescribd
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Have you ever wanted a Ruby client API to communicate with your web service? Smithy is a protocol-agnostic language for defining services and SDKs. Smithy Ruby is an implementation of Smithy that generates a Ruby SDK using a Smithy model. In this talk, we will explore Smithy and Smithy Ruby to learn how to generate custom feature-rich SDKs that can communicate with any web service, such as a Rails JSON API.
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