Aptamers are single-stranded DNA or RNA molecules that can bind to specific molecular targets with high affinity and specificity. They are identified through an in vitro selection process called Systematic Evolution of Ligands by EXponential enrichment (SELEX). Aptamers have various applications as diagnostic and therapeutic agents. They can serve as biosensors for pathogens by utilizing techniques like electrochemical, fluorescence, and colorimetric detection. Aptamers have been developed against viruses like influenza, HIV, hepatitis C, and others. They show potential for blocking viral fusion and inhibiting viral replication through binding to proteins and enzymes.
Bobs Aptamer Assay Slide Presentation_RRobert Bruce
This document describes the development of an aptamer-based assay for the early detection of lung cancer. Aptamers are oligonucleic acid molecules that bind to specific target molecules and have advantages over antibodies. The current assay takes two days to complete and has high variability. To make it practical for clinical use, the assay needs to be completed in one day with lower variability. Future work will focus on shortening the assay time, optimizing aptamer conjugations and the use of biotinylated antibodies, and refining assay conditions. The goal is to develop a simple, fast assay that can help detect lung cancer early and improve treatment outcomes.
Your Step-by-Step Guide to Electrophoretic Mobility Shift AssayCreative BioMart
The Electrophoretic Mobility Shift Assay (EMSA) is used to detect protein complexes with nucleic acids such as DNA and RNA. It involves incubating a purified protein or cell extract with a radioactively labeled probe, then separating bound and unbound complexes on a gel during electrophoresis. The protein-nucleic acid complexes migrate more slowly than unbound probes. The assay can identify sequence-specific DNA and RNA binding proteins and determine binding specificity using competitive experiments with specific and nonspecific fragments. It is a basic method to study DNA-protein and RNA-protein interactions.
#Aptamer is a term derived from the Latin aptus - fit, and the Greek meros – part. #Aptamers are oligonucleic acid or peptide molecules that bind to a specific target molecule.
Aptamer Hari pankaj vanam aptamer a plethora of opportunitiesVanam Hari Pankaj
This document discusses aptamers, which are short DNA or RNA oligonucleotides that can bind to target molecules like proteins with high affinity and specificity. It begins by defining aptamers and describing their properties. It then discusses the history of aptamers, including the initial development of the SELEX process in the 1990s to isolate aptamers. The document compares the properties of aptamers to antibodies and outlines different types of aptamers and modifications that can improve their stability and function. It also describes the SELEX process in detail and potential applications of aptamers, concluding they are promising for a wide range of therapeutic and diagnostic uses.
Data Integration, Mass Spectrometry Proteomics Software DevelopmentNeil Swainston
This document discusses quantitative proteomics and integrating proteomics data into kinetic modeling in systems biology. It describes using isotopically labeled peptides to quantify proteins simultaneously via mass spectrometry. A method called QconCAT is outlined which uses an artificial protein containing multiple labeled peptides to reference. The document then describes an informatics pipeline to analyze such quantitative proteomics data, identifying peptides, determining concentrations, uploading data to repositories, and linking it with modeling databases to incorporate experimental data into systems biology simulations.
Protein sequencing determines the order of amino acids in a protein. The two major methods are Edman degradation and mass spectrometry. Edman degradation involves labeling the N-terminal amino acid, cleaving it off, and identifying it, repeating the process one amino acid at a time to deduce the sequence. Mass spectrometry involves ionizing and separating protein fragments by mass/charge ratio to determine sequence. Protein sequencing is useful for identifying unknown proteins and characterizing modifications.
This document discusses protein arrays as tools for studying host-pathogen interactions. Protein arrays are similar to DNA microarrays in that proteins or antibodies are attached to a slide to profile protein mixtures, measure binding affinities, and study protein expression levels. They can be used to monitor disease states and for clinical diagnostics. The main types of protein arrays discussed are analytical arrays, functional arrays, and reverse phase arrays. Protein arrays provide a powerful tool for proteomics, biomarker discovery, and analyzing infection responses by profiling antibody and protein signatures.
Aptamers are single-stranded DNA or RNA molecules that can bind to specific molecular targets with high affinity and specificity. They are identified through an in vitro selection process called Systematic Evolution of Ligands by EXponential enrichment (SELEX). Aptamers have various applications as diagnostic and therapeutic agents. They can serve as biosensors for pathogens by utilizing techniques like electrochemical, fluorescence, and colorimetric detection. Aptamers have been developed against viruses like influenza, HIV, hepatitis C, and others. They show potential for blocking viral fusion and inhibiting viral replication through binding to proteins and enzymes.
Bobs Aptamer Assay Slide Presentation_RRobert Bruce
This document describes the development of an aptamer-based assay for the early detection of lung cancer. Aptamers are oligonucleic acid molecules that bind to specific target molecules and have advantages over antibodies. The current assay takes two days to complete and has high variability. To make it practical for clinical use, the assay needs to be completed in one day with lower variability. Future work will focus on shortening the assay time, optimizing aptamer conjugations and the use of biotinylated antibodies, and refining assay conditions. The goal is to develop a simple, fast assay that can help detect lung cancer early and improve treatment outcomes.
Your Step-by-Step Guide to Electrophoretic Mobility Shift AssayCreative BioMart
The Electrophoretic Mobility Shift Assay (EMSA) is used to detect protein complexes with nucleic acids such as DNA and RNA. It involves incubating a purified protein or cell extract with a radioactively labeled probe, then separating bound and unbound complexes on a gel during electrophoresis. The protein-nucleic acid complexes migrate more slowly than unbound probes. The assay can identify sequence-specific DNA and RNA binding proteins and determine binding specificity using competitive experiments with specific and nonspecific fragments. It is a basic method to study DNA-protein and RNA-protein interactions.
#Aptamer is a term derived from the Latin aptus - fit, and the Greek meros – part. #Aptamers are oligonucleic acid or peptide molecules that bind to a specific target molecule.
Aptamer Hari pankaj vanam aptamer a plethora of opportunitiesVanam Hari Pankaj
This document discusses aptamers, which are short DNA or RNA oligonucleotides that can bind to target molecules like proteins with high affinity and specificity. It begins by defining aptamers and describing their properties. It then discusses the history of aptamers, including the initial development of the SELEX process in the 1990s to isolate aptamers. The document compares the properties of aptamers to antibodies and outlines different types of aptamers and modifications that can improve their stability and function. It also describes the SELEX process in detail and potential applications of aptamers, concluding they are promising for a wide range of therapeutic and diagnostic uses.
Data Integration, Mass Spectrometry Proteomics Software DevelopmentNeil Swainston
This document discusses quantitative proteomics and integrating proteomics data into kinetic modeling in systems biology. It describes using isotopically labeled peptides to quantify proteins simultaneously via mass spectrometry. A method called QconCAT is outlined which uses an artificial protein containing multiple labeled peptides to reference. The document then describes an informatics pipeline to analyze such quantitative proteomics data, identifying peptides, determining concentrations, uploading data to repositories, and linking it with modeling databases to incorporate experimental data into systems biology simulations.
Protein sequencing determines the order of amino acids in a protein. The two major methods are Edman degradation and mass spectrometry. Edman degradation involves labeling the N-terminal amino acid, cleaving it off, and identifying it, repeating the process one amino acid at a time to deduce the sequence. Mass spectrometry involves ionizing and separating protein fragments by mass/charge ratio to determine sequence. Protein sequencing is useful for identifying unknown proteins and characterizing modifications.
This document discusses protein arrays as tools for studying host-pathogen interactions. Protein arrays are similar to DNA microarrays in that proteins or antibodies are attached to a slide to profile protein mixtures, measure binding affinities, and study protein expression levels. They can be used to monitor disease states and for clinical diagnostics. The main types of protein arrays discussed are analytical arrays, functional arrays, and reverse phase arrays. Protein arrays provide a powerful tool for proteomics, biomarker discovery, and analyzing infection responses by profiling antibody and protein signatures.
Peptide Mass Fingerprinting (PMF) and Isotope Coded Affinity Tags (ICAT)Suresh Antre
Analytical technique for identifying unknown protein. The peptide mass are compared to database containing the theoretical peptide masses of all known protein sequences.
De novo peptide sequencing is performed without prior knowledge of the amino acid sequence. It uses computational approaches to deduce the peptide sequence directly from mass spectrometry spectra. The main principle is to use mass differences between fragment ions like y and b ions to calculate amino acid residues. While it can identify previously unknown sequences, there is uncertainty in the complete sequence and difficulty determining directionality sometimes. Creative Proteomics offers de novo sequencing services using high-performance mass spectrometry and computational algorithms.
Aptamers - New Class of Oligonucleotide for Therapeutic and Diagnostic Useajithnandanam
http://technologyinscience.blogspot.com/2014/01/aptamers-new-class-of-oligonucleotide.html
Aptamers are single-stranded RNA or DNA oligonucleotides 15 to 60 base in length that bind with high affinity to specific molecular targets; most aptamers to proteins bind with Kds (equilibrium constant) in the range of 1 pM to 1 nM similar to monoclonal antibodies. These nucleic acid ligands bind to nucleic acid, proteins, small organic compounds, and even entire organisms. Aptamers have many potential uses in intracellular processes studies, medicine and technology. Aptamers are often identified using a technique called SELEX (Systematic Evolution of Ligands by EXponential enrichment). By this techniques aptamers(oligos) having high affinity and specificity to the target is isolated from the sequence pool after several rounds of selection.
(a) While in the ER, only N-linked glycosylation can occur, which attaches carbohydrates to asparagine amino acids. There are 25 asparagine amino acids, so 25 carbohydrates will be attached in the ER.
(b) While in the Golgi apparatus, both N-linked and O-linked glycosylation can occur. N-linked glycosylation attaches 25 carbohydrates (same as in ER). O-linked glycosylation attaches carbohydrates to serine and threonine amino acids, of which there are 25 each, for a total of 50. Therefore, the total number of carbohydrates attached in the Golgi apparatus is 25 (N-linked)
This document provides an overview of proteomics, including protein modification and sequencing. It defines the proteome and proteomics, giving a brief history. It describes the main types of proteomics including expression and interaction proteomics. It also outlines some of the key tools and methods used in proteomics, including protein structure databases and the main methods for protein sequencing like N-terminal sequencing. The document concludes by defining and describing different types of protein modification like trimming and covalent attachments. It also lists some related proteomics tools.
In Situ Polymerase Chain Reaction (In situ PCR) is a powerful method that detects minute quantities of rare or single-copy number nucleic acid sequences in frozen or paraffin-embedded cells or tissue sections for the localization of those sequences within the cells. The principle of this method involves tissue fixing (to preserve the cell morphology) and subsequent treatment with proteolytic digestion (to provide access for the PCR reagents to the target DNA). The target sequences are amplified by those reagents and then detected by standard immunocytochemical protocols. In situ PCR combines the sensitivity of PCR or RT-PCR amplification along with the ability to perform morphological analysis on the same sample, and thus it is an attractive tool in diagnostic applications. One of the most prominent applications is the detection of infectious disease agents including HIV-1, HBV, HPV, HHV-6, CMV, and EBV.
Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015Alain van Gool
An overview of the proteomics, glycomics and metabolomics expertise and capabilities within the Translational Metabolic Laboratory of the Radboudumc. We're interested in collaboration with academic and industrial partners, either bilateral or as part of multi-partner consortia.
This document provides an overview of common proteomics techniques. It describes proteomics as the study of proteins including their roles, structures, localization, interactions and other factors. The key techniques discussed include molecular techniques like DNA microarrays and yeast two-hybrid analysis, separation techniques like gel electrophoresis and chromatography, protein identification methods like mass spectroscopy and Edman sequencing, and protein structure determination methods like NMR, X-ray crystallography and computational prediction. The document provides examples and details of several of these techniques.
DNA- based biosensors
DNA- based biosensors
Limitations
Poor detection limit
Non-specificity
Inefficient electrode regeneration
Sophisticated electrode preparation
It lacked specificity towards As(III)
Aptamers - based biosensors
Aptamers are single-stranded DNA or RNA molecules that can bind to a number of target analytes, including proteins and peptides with high affinity and specificity.
Commercial potential for use as biosensors.
Aptamers - based biosensors
Aptamers - based biosensors
Possible mode of interaction of arsenic site with aptamer
Aptamers - based biosensors
Aptamers - based biosensors
Protein-based biosensors
Most protein-based biosensors developed for As(III) or As(V) are based on the inhibition phenomenon.
Interaction between protein and arsenic species
Characteristics of cell free arsenic biosensors with detection limits and induction period/response time
Conclusion
A number of arsenic biosensors have been developed based on whole-cell biosensor to biomolecules based biosensors.
However, whole-cell biosensor has successfully utilized in the analysis of arsenic in groundwater and soil, but has some limitations.
Biomolecules based biosensors has quick response capacity and better detection limits.
Further challenges
Development of biosensors that could detect arsenic in complex matrices including health related matrices such as blood, urine, etc. and water with high TDS and salinity including seawater.
Article info
Thank you All
This document provides an overview of therapeutic aptamers. It defines aptamers as oligonucleotide molecules that bind to specific target molecules. Aptamers are produced using SELEX to select sequences with high affinity for target proteins. They have various therapeutic applications, such as inhibiting thrombin formation, amyloid-β propagation in Alzheimer's, and HIV integrase enzyme. Aptamers can also be used for targeted drug delivery by conjugating drugs to aptamers that bind cell surface proteins like nucleolin. The document discusses aptamer structure, production, modifications to improve stability, and advantages for therapeutic use.
Measuring apoptosis in real time with a new luminescent methodMourad FERHAT, PhD
We developed a homogeneous luminogenic annexin V binding assay to detect apoptosis in real time using a multimode plate reader. The detection reagent has two different annexin V fusion proteins engineered to contain complementing domains of a binary luciferase, a substrate for luciferase and a cell impermeable fluorogenic DNA dye to detect necrotic cells. The method allow real-time monitoring of Cellular apoptosis and necrosis in microwell plates without washing steps with a highly sensitive luminescent signal. The AnnexinV luminescent method is amenable to High throughput and is a good alternative to FACS, low-throughput Annexin V-FITC based method.
Fredric Sanger determined the first protein sequence in 1953, which was insulin. There are two main methods for protein sequencing - N-terminal sequencing including the Sanger method and Edman degradation, and C-terminal sequencing using carboxypeptidases. Protein sequences can be predicted from DNA sequences after determining the gene sequence. Comparing protein sequences between organisms can provide information about evolutionary relationships and how organisms have diverged over time as mutations cause amino acid changes. Work has been done in Pakistan on sequencing various proteins.
Proteomics 2 d gel, mass spectrometry, maldi tofnirvarna gr
This document discusses proteomics techniques including 2D gel electrophoresis and mass spectrometry. It provides an overview of 2D gel electrophoresis, describing the key steps of sample preparation, running the first and second dimensions, visualizing and analyzing the results. Mass spectrometry techniques for proteomics including MALDI-TOF and electrospray ionization are also summarized. The document outlines several applications of these proteomics approaches such as protein identification, characterization of post-translational modifications, and organism identification.
TAP-tagging is a protein purification technique that involves creating a fusion protein with a TAP tag to study protein-protein interactions. The TAP tag contains protein A and a calmodulin binding peptide separated by a TEV protease site. This allows two-step affinity purification of associated protein complexes under physiological conditions. TAP-tagging was developed in the 1990s and has been widely used to map protein interaction networks in yeast and identify new protein complexes involved in processes like pre-mRNA splicing.
The document discusses several nucleic acid techniques used in clinical laboratories, including polymerase chain reaction (PCR), reverse transcription PCR (RT-PCR), real-time PCR, electrophoresis, and DNA sequencing. It provides details on how each technique works, such as using thermostable DNA polymerase and primers to amplify specific DNA regions in PCR. RT-PCR is used to amplify RNA by first converting it to cDNA. Real-time PCR detects fluorescence during amplification to quantify levels of target DNA. Electrophoresis separates nucleic acid fragments by size in an electric field in agarose or polyacrylamide gels.
The western blot is a technique used to detect specific proteins in a sample. It involves separating proteins by size using gel electrophoresis, transferring them to a membrane, and using antibodies to detect the target protein. The key steps are sample preparation, gel electrophoresis, blotting, blocking, antibody probing, and detection. Western blotting allows researchers to identify proteins from complex mixtures and is widely used in molecular biology and medical diagnosis, such as detecting HIV, HBV, and HSV infections.
New tools bring greater understanding to cellular metabolism research Mourad FERHAT, PhD
Presentation of Promega Solutions in the field of cellular Metabolism research. Discover new bioluminescent assays for the detection of several metabolites and metabolic process such as : Glucose Uptake, Glucose consumption, Lactate secretion and Glutamine/Glutamate metabolism.
- The document describes an experiment to produce and purify green fluorescent protein (GFP) from E. coli bacteria and then crystallize the purified GFP.
- GFP was expressed in E. coli bacteria containing a plasmid with the GFP gene. The bacteria were induced to produce GFP, which was then purified using nickel affinity and hydrophobic interaction chromatography.
- Bradford assays and SDS-PAGE were used to analyze the purified GFP samples and determine concentration and purity. Finally, purified GFP was crystallized using vapor diffusion.
Creative Bioarray offers various kinase assay technologies to support drug discovery research objectives. These include radiometric assays, which are the gold standard but labor intensive, and fluorescence-based assays that are better suited for high-throughput screening. Each technology has strengths and weaknesses depending on the research goal, and Creative Bioarray can support customers through selecting the appropriate assay and interpreting results.
Recent advances in enzyme assays can be divided into two categories: assays using labelled substrates and assays using sensors to detect unmodified substrates. Labelled substrates include fluorogenic and chromogenic substrates that generate a detectable signal upon enzyme cleavage. FRET substrates separate a fluorophore-quencher pair upon cleavage. Isotopically labelled substrates allow detection of enantioselectivity. Assays using sensors can detect natural substrates, making them cheaper and more versatile. Examples include electrochemical detection of lipase activity and fluorescence-based detection of alcohol dehydrogenases. The trend is to assemble many assays in parallel for high-throughput enzyme profiling and fingerprinting.
Peptide Mass Fingerprinting (PMF) and Isotope Coded Affinity Tags (ICAT)Suresh Antre
Analytical technique for identifying unknown protein. The peptide mass are compared to database containing the theoretical peptide masses of all known protein sequences.
De novo peptide sequencing is performed without prior knowledge of the amino acid sequence. It uses computational approaches to deduce the peptide sequence directly from mass spectrometry spectra. The main principle is to use mass differences between fragment ions like y and b ions to calculate amino acid residues. While it can identify previously unknown sequences, there is uncertainty in the complete sequence and difficulty determining directionality sometimes. Creative Proteomics offers de novo sequencing services using high-performance mass spectrometry and computational algorithms.
Aptamers - New Class of Oligonucleotide for Therapeutic and Diagnostic Useajithnandanam
http://technologyinscience.blogspot.com/2014/01/aptamers-new-class-of-oligonucleotide.html
Aptamers are single-stranded RNA or DNA oligonucleotides 15 to 60 base in length that bind with high affinity to specific molecular targets; most aptamers to proteins bind with Kds (equilibrium constant) in the range of 1 pM to 1 nM similar to monoclonal antibodies. These nucleic acid ligands bind to nucleic acid, proteins, small organic compounds, and even entire organisms. Aptamers have many potential uses in intracellular processes studies, medicine and technology. Aptamers are often identified using a technique called SELEX (Systematic Evolution of Ligands by EXponential enrichment). By this techniques aptamers(oligos) having high affinity and specificity to the target is isolated from the sequence pool after several rounds of selection.
(a) While in the ER, only N-linked glycosylation can occur, which attaches carbohydrates to asparagine amino acids. There are 25 asparagine amino acids, so 25 carbohydrates will be attached in the ER.
(b) While in the Golgi apparatus, both N-linked and O-linked glycosylation can occur. N-linked glycosylation attaches 25 carbohydrates (same as in ER). O-linked glycosylation attaches carbohydrates to serine and threonine amino acids, of which there are 25 each, for a total of 50. Therefore, the total number of carbohydrates attached in the Golgi apparatus is 25 (N-linked)
This document provides an overview of proteomics, including protein modification and sequencing. It defines the proteome and proteomics, giving a brief history. It describes the main types of proteomics including expression and interaction proteomics. It also outlines some of the key tools and methods used in proteomics, including protein structure databases and the main methods for protein sequencing like N-terminal sequencing. The document concludes by defining and describing different types of protein modification like trimming and covalent attachments. It also lists some related proteomics tools.
In Situ Polymerase Chain Reaction (In situ PCR) is a powerful method that detects minute quantities of rare or single-copy number nucleic acid sequences in frozen or paraffin-embedded cells or tissue sections for the localization of those sequences within the cells. The principle of this method involves tissue fixing (to preserve the cell morphology) and subsequent treatment with proteolytic digestion (to provide access for the PCR reagents to the target DNA). The target sequences are amplified by those reagents and then detected by standard immunocytochemical protocols. In situ PCR combines the sensitivity of PCR or RT-PCR amplification along with the ability to perform morphological analysis on the same sample, and thus it is an attractive tool in diagnostic applications. One of the most prominent applications is the detection of infectious disease agents including HIV-1, HBV, HPV, HHV-6, CMV, and EBV.
Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015Alain van Gool
An overview of the proteomics, glycomics and metabolomics expertise and capabilities within the Translational Metabolic Laboratory of the Radboudumc. We're interested in collaboration with academic and industrial partners, either bilateral or as part of multi-partner consortia.
This document provides an overview of common proteomics techniques. It describes proteomics as the study of proteins including their roles, structures, localization, interactions and other factors. The key techniques discussed include molecular techniques like DNA microarrays and yeast two-hybrid analysis, separation techniques like gel electrophoresis and chromatography, protein identification methods like mass spectroscopy and Edman sequencing, and protein structure determination methods like NMR, X-ray crystallography and computational prediction. The document provides examples and details of several of these techniques.
DNA- based biosensors
DNA- based biosensors
Limitations
Poor detection limit
Non-specificity
Inefficient electrode regeneration
Sophisticated electrode preparation
It lacked specificity towards As(III)
Aptamers - based biosensors
Aptamers are single-stranded DNA or RNA molecules that can bind to a number of target analytes, including proteins and peptides with high affinity and specificity.
Commercial potential for use as biosensors.
Aptamers - based biosensors
Aptamers - based biosensors
Possible mode of interaction of arsenic site with aptamer
Aptamers - based biosensors
Aptamers - based biosensors
Protein-based biosensors
Most protein-based biosensors developed for As(III) or As(V) are based on the inhibition phenomenon.
Interaction between protein and arsenic species
Characteristics of cell free arsenic biosensors with detection limits and induction period/response time
Conclusion
A number of arsenic biosensors have been developed based on whole-cell biosensor to biomolecules based biosensors.
However, whole-cell biosensor has successfully utilized in the analysis of arsenic in groundwater and soil, but has some limitations.
Biomolecules based biosensors has quick response capacity and better detection limits.
Further challenges
Development of biosensors that could detect arsenic in complex matrices including health related matrices such as blood, urine, etc. and water with high TDS and salinity including seawater.
Article info
Thank you All
This document provides an overview of therapeutic aptamers. It defines aptamers as oligonucleotide molecules that bind to specific target molecules. Aptamers are produced using SELEX to select sequences with high affinity for target proteins. They have various therapeutic applications, such as inhibiting thrombin formation, amyloid-β propagation in Alzheimer's, and HIV integrase enzyme. Aptamers can also be used for targeted drug delivery by conjugating drugs to aptamers that bind cell surface proteins like nucleolin. The document discusses aptamer structure, production, modifications to improve stability, and advantages for therapeutic use.
Measuring apoptosis in real time with a new luminescent methodMourad FERHAT, PhD
We developed a homogeneous luminogenic annexin V binding assay to detect apoptosis in real time using a multimode plate reader. The detection reagent has two different annexin V fusion proteins engineered to contain complementing domains of a binary luciferase, a substrate for luciferase and a cell impermeable fluorogenic DNA dye to detect necrotic cells. The method allow real-time monitoring of Cellular apoptosis and necrosis in microwell plates without washing steps with a highly sensitive luminescent signal. The AnnexinV luminescent method is amenable to High throughput and is a good alternative to FACS, low-throughput Annexin V-FITC based method.
Fredric Sanger determined the first protein sequence in 1953, which was insulin. There are two main methods for protein sequencing - N-terminal sequencing including the Sanger method and Edman degradation, and C-terminal sequencing using carboxypeptidases. Protein sequences can be predicted from DNA sequences after determining the gene sequence. Comparing protein sequences between organisms can provide information about evolutionary relationships and how organisms have diverged over time as mutations cause amino acid changes. Work has been done in Pakistan on sequencing various proteins.
Proteomics 2 d gel, mass spectrometry, maldi tofnirvarna gr
This document discusses proteomics techniques including 2D gel electrophoresis and mass spectrometry. It provides an overview of 2D gel electrophoresis, describing the key steps of sample preparation, running the first and second dimensions, visualizing and analyzing the results. Mass spectrometry techniques for proteomics including MALDI-TOF and electrospray ionization are also summarized. The document outlines several applications of these proteomics approaches such as protein identification, characterization of post-translational modifications, and organism identification.
TAP-tagging is a protein purification technique that involves creating a fusion protein with a TAP tag to study protein-protein interactions. The TAP tag contains protein A and a calmodulin binding peptide separated by a TEV protease site. This allows two-step affinity purification of associated protein complexes under physiological conditions. TAP-tagging was developed in the 1990s and has been widely used to map protein interaction networks in yeast and identify new protein complexes involved in processes like pre-mRNA splicing.
The document discusses several nucleic acid techniques used in clinical laboratories, including polymerase chain reaction (PCR), reverse transcription PCR (RT-PCR), real-time PCR, electrophoresis, and DNA sequencing. It provides details on how each technique works, such as using thermostable DNA polymerase and primers to amplify specific DNA regions in PCR. RT-PCR is used to amplify RNA by first converting it to cDNA. Real-time PCR detects fluorescence during amplification to quantify levels of target DNA. Electrophoresis separates nucleic acid fragments by size in an electric field in agarose or polyacrylamide gels.
The western blot is a technique used to detect specific proteins in a sample. It involves separating proteins by size using gel electrophoresis, transferring them to a membrane, and using antibodies to detect the target protein. The key steps are sample preparation, gel electrophoresis, blotting, blocking, antibody probing, and detection. Western blotting allows researchers to identify proteins from complex mixtures and is widely used in molecular biology and medical diagnosis, such as detecting HIV, HBV, and HSV infections.
New tools bring greater understanding to cellular metabolism research Mourad FERHAT, PhD
Presentation of Promega Solutions in the field of cellular Metabolism research. Discover new bioluminescent assays for the detection of several metabolites and metabolic process such as : Glucose Uptake, Glucose consumption, Lactate secretion and Glutamine/Glutamate metabolism.
- The document describes an experiment to produce and purify green fluorescent protein (GFP) from E. coli bacteria and then crystallize the purified GFP.
- GFP was expressed in E. coli bacteria containing a plasmid with the GFP gene. The bacteria were induced to produce GFP, which was then purified using nickel affinity and hydrophobic interaction chromatography.
- Bradford assays and SDS-PAGE were used to analyze the purified GFP samples and determine concentration and purity. Finally, purified GFP was crystallized using vapor diffusion.
Creative Bioarray offers various kinase assay technologies to support drug discovery research objectives. These include radiometric assays, which are the gold standard but labor intensive, and fluorescence-based assays that are better suited for high-throughput screening. Each technology has strengths and weaknesses depending on the research goal, and Creative Bioarray can support customers through selecting the appropriate assay and interpreting results.
Recent advances in enzyme assays can be divided into two categories: assays using labelled substrates and assays using sensors to detect unmodified substrates. Labelled substrates include fluorogenic and chromogenic substrates that generate a detectable signal upon enzyme cleavage. FRET substrates separate a fluorophore-quencher pair upon cleavage. Isotopically labelled substrates allow detection of enantioselectivity. Assays using sensors can detect natural substrates, making them cheaper and more versatile. Examples include electrochemical detection of lipase activity and fluorescence-based detection of alcohol dehydrogenases. The trend is to assemble many assays in parallel for high-throughput enzyme profiling and fingerprinting.
This document discusses proteomic methodologies for studying protein phosphorylation. It begins with an introduction to protein phosphorylation and its importance in regulating cellular processes. It then describes the workflow for analyzing phosphorylation through proteomics, including isolating phosphoproteins, identifying phosphorylation sites via mass spectrometry, and comparing normal and treated phosphoproteomes. Key methods discussed are 2D gel electrophoresis, phosphoprotein staining, silver staining, spot excision, in-gel digestion, and liquid chromatography-tandem mass spectrometry for identifying phosphorylation sites. The document emphasizes that proteomic analysis is needed to fully understand phosphorylation dynamics and signaling pathways.
1. Molecular testing in lung cancer has identified several new biomarkers in recent years, including ALK, ROS1, MET exon 14 skipping, NTRK fusions, and KRAS G12C mutations.
2. Next-generation sequencing has become a widely used testing method that allows for parallel testing of multiple genes and biomarkers. RNA sequencing is generally preferred over DNA sequencing for detection of fusions.
3. Single gene assays remain important options, especially for established biomarkers like EGFR mutations, but targeted NGS panels provide a more comprehensive approach and have been validated in large testing programs.
High throughput screening (HTS) is a process used in drug discovery to quickly test large numbers of chemical compounds and biological agents for biological activity against a disease state or condition of interest. The goal of HTS is to identify "hits" or "leads" that show desired activity at low concentrations and have a new chemical structure. Cell-based assays are an important type of HTS that uses live cells to more accurately model biological systems and provide information on bioavailability, cytotoxicity, and effects on biochemical pathways. Key elements of cell-based assays include a cellular component, a target molecule to detect cellular responses, and instrumentation to conduct and analyze the assay.
1. High throughput screening (HTS) is a process for screening large numbers of biological compounds against selected targets using automated equipment. It aims to accelerate the drug discovery process.
2. The key steps in HTS include target identification, reagent preparation, assay development, screening compound libraries, data analysis and management. HTS assays can be biochemical, cellular, or involve measuring second messengers.
3. HTS has various applications in natural product drug discovery, including identifying inhibitors of human thrombin from plant extracts. Euphane triterpenes isolated from Lantana camara leaves showed potent thrombin inhibitory activity.
This document summarizes and compares different methods for detecting apoptosis in cells, including morphological changes, membrane asymmetry, protease activity, and DNA modifications.
For morphological changes, methods like confocal microscopy and phase contrast microscopy allow visualization of features like blebbing and apoptotic bodies. Electron microscopy also enables detection of nuclear density changes. Advantages are low cost and providing information for further studies, while disadvantages include lack of objectivity and difficulty quantifying apoptosis.
Membrane asymmetry detection uses annexin V binding to phosphatidylserine exposed on the outer membrane of apoptotic cells. This can be analyzed via flow cytometry or fluorescence microscopy and distinguishes apoptotic from necrotic cells. Advantages are rapid accurate quantification
Simplified receptor based pharmacophore approach to retrieve potent ptp lar i...rajmaha9
Simplified Receptor Based Pharmacophore Approach to Retrieve Potent PTP-LAR Inhibitors Using Apoenzyme
M. Elizabeth Sobhia*
Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S.
Nagar, Punjab 160062, India
Abstract: The design of biological active compounds from the apoenzyme is still a challenging task. Herein a simple yet efficient technique is reported to generate a receptor based pharmacophore solely using a ligand-free protein crystal structure. Human leukocyte antigen-related phosphatase (PTP-LAR) is an apoenzyme and a receptor like transmembrane phosphatase that has emerged as a drug target for diabetes, obesity and cancer. The prior knowledge of the active residues responsible for the mechanism of action of the protein was used to generate the LUDI interaction map. Then, the complement negative image of the binding site was used to generate the pharmacophore features. A unique strategy was
followed to design a pharmacophore query maintaining crucial interactions with all the active residues, essential for the enzyme inhibition. The same query was used to screen several databases consisting of the Specs, IBS, iniMaybridge, NCI and an in-house PTP inhibitor databases. In order to overcome the common bioavailability problem associated with phosphatases, the hits obtained were filtered by Lipinski’s Rule of Five, SADMET properties and validated by docking studies in Glide and GOLD. These docking studies not only suggest the essential ligand binding interactions but also the binding patterns necessary for the LAR inhibition. The ligand pharmacophore mapping studies further validated the
screened protocol and supported that the final screened molecules, presumably, showed potent inhibitory activity.
Subsequently, these molecules were subjected to Derek toxicity predictions and nine new molecules with different
scaffold were obtained as non-toxic PTP-LAR inhibitors. The present prospective strategy is a powerful technique to
identify potent inhibitors using the protein 3D structure alone and is a valid alternative to other structure-based and
random docking approaches.
This document provides information about Nanosyn, a contract research organization that offers various drug discovery services including high throughput screening, assay development, and medicinal chemistry services. It describes Nanosyn's microfluidic-based detection technology which allows simultaneous detection of enzyme substrates and products in a single sample run. This provides accurate and reproducible results. The technology also tolerates autofluorescent compounds and enables identification of both inhibitors and activators.
Use of fluorescence lifetime technology to provide efficient protection from ...Dmitry Gakamsky
This article describes novel data analysis of fluorescence lifetime-based protein kinase assays to identify and correct for compound interference in several practical cases. This ability, together with inherent advantages of fluorescence lifetime technology (FLT) as a homogeneous, antibody-free format indepen- dent of sample concentration, volume, excitation intensity, and geometry, makes fluorescence lifetime a practical alternative to the established ‘‘gold standards’’ of radiometric and mobility shift (Caliper) assays. The analysis is based on a photochemical model that sets constraints on the values of fluorescence lifetimes in the time responses of the assay. The addition of an exponential component with free floating lifetime to the constrained model, in which the lifetimes are constants predetermined from control mea- surements and the preexponential coefficients are ‘‘floating’’ parameters, allows the relative concentra- tion of phosphorylated and nonphosphorylated substrates to be calculated even in the presence of compound fluorescence. The method is exemplified using both simulated data and experimental results measured from mixtures of dye-labeled phosphorylated and nonphosphorylated kinase substrates. A change of the fluorescence lifetime is achieved by the phosphorylated substrate-specific interaction with a bifunctional ligand, where one binding site interacts with the phosphate group and the other interacts with the dye.
This document provides an overview of the schedule and topics for a course on metabolic networks. The course covers various topics related to metabolism, including enzyme assays, mass spectrometry techniques, primary metabolism, glycogen metabolism, metabolic networks in humans, flux analysis, and biochemical databases. Homework discussions are scheduled every other Friday. Guest lecturers will discuss biochemical databases and tools for modeling metabolism on the last two class meetings. The course includes no class on Veteran's Day and Thanksgiving.
This document discusses various biophysical and biochemical techniques used to analyze biotech products, including proteins. It describes techniques such as circular dichroism spectroscopy, fluorescence spectroscopy, calorimetry, sedimentation velocity, and western blotting that can provide information on a protein's secondary structure, tertiary structure, stability, and post-translational modifications. It also discusses analytical methods like chromatography, electrophoresis, mass spectrometry, and spectroscopy that can analyze a protein's purity, heterogeneity, conformation, and interactions with other molecules. The techniques allow characterization of biotech products to ensure quality, identity, stability and activity.
Cell-based Reporter Assays: Measure 45 Signaling Pathway Activity in Any Cel...Qiagen - Egypt
Would you like to measure signaling pathway activity in your favorite cell? Learn how to successfully apply convenient and robust reporter assays to your RNA interference, gene over-expression, protein, or small molecule studies. The Cignal Reporter Assays are an excellent tool for studying pathway signaling activity in cells that are amenable to transfection, available for studying numerous pathways including (ROS, Wnt, NF-kB, Notch, cAMP/PKA, TGFbeta, and the Cignal Lenti Reporter Assays combines the power of a lentiviral delivery system with our robust transcription factor reporter technology, enabling you to study signal pathways in virtually any cell type. You can find a technology overview, protocol tutorial, and application examples in the following presentation.
Cell-based Reporter Assays: Measure 45 Signaling Pathway Activity in Any Cell...QIAGEN
Would you like to measure signaling pathway activity in your favorite cell? Learn how to successfully apply convenient and robust reporter assays to your RNA interference, gene over-expression, protein, or small molecule studies. The Cignal Reporter Assays are an excellent tool for studying pathway signaling activity in cells that are amenable to transfection, available for studying numerous pathways including (ROS, Wnt, NF-kB, Notch, cAMP/PKA, TGFbeta, and the Cignal Lenti Reporter Assays combines the power of a lentiviral delivery system with our robust transcription factor reporter technology, enabling you to study signal pathways in virtually any cell type. You can find a technology overview, protocol tutorial, and application examples in the following presentation.
The document summarizes various methods used to measure apoptosis and cell viability, including membrane integrity assays, functional assays, DNA labeling assays, and morphological assays. Membrane integrity assays like trypan blue exclusion, annexin V binding, and LDH leakage determine cell viability based on plasma membrane integrity. Functional assays like MTT, XTT, and Alamar Blue measure cell metabolism. DNA labeling assays use fluorescent conjugates to label cells, while morphological assays examine changes in cell morphology during apoptosis. The document provides details on the principles, materials, and procedures for several common assays used to measure apoptosis and cell viability.
ELISA (enzyme-linked immunosorbent assay) is a biochemical technique used to detect the presence of antigens or antibodies in a biological sample. It uses antibodies and color changing enzymes to identify a substance in the sample. There are different types of ELISA including sandwich, indirect, and competitive ELISA. ELISA is widely used in areas like immunology, diagnostics, and food testing due to its accuracy, sensitivity, and ability to analyze multiple samples at once.
The document summarizes work using synthetic protein scaffolds to study the effect of enzyme scaffolding on the rate of product formation in biochemical pathways. Key points:
- Proteins involved in the resveratrol pathway were successfully expressed and purified except CFP proteins due to contamination.
- A FRET assay will be used to determine if scaffold assembly was successful by observing higher YFP and lower CFP fluorescence intensities.
- Understanding how kinetic parameters of enzymes in pathways relate to increased product yield from scaffolding is important for biofuels and pharmaceuticals.
- Future work will purify remaining proteins, perform FRET and HPLC to quantify resveratrol production from scaffolded versus non-sc
Creative Bioarray provides an extensive range of high quality RNA samples which are ideal for Northern blotting, ribonuclease protection assay, SI nuclease assay, RT-PCR/Q-PCR analysis, rapid amplification of cDNA ends (RACE) and purification of mRNA for library construction.
https://www.creative-bioarray.com/products/rna-list-22.htm
Immunohistochemistry uses antibodies to detect antigens in tissue samples in order to localize proteins and study biological processes. It has various applications including cancer prognosis, tumor identification, and research. The process involves deparaffinizing tissue, antigen retrieval, blocking, primary/secondary antibody incubation, signal development using enzymes, counterstaining, and mounting slides. Different methods like direct, indirect, PAP, ABC, and LSAB are used depending on the desired sensitivity and specificity. Careful antibody selection and protocol optimization are important for obtaining high quality results.
A fluorescent compound has the property of absorbing light energy at a range of specific wavelengths. This absorption of light causes electron to rise from the ground state to a higher energy level (excited state). The excited electron quickly decays to its ground state while releasing the excess energy in the form of photon of light. This transition of energy is called fluorescence.
https://www.creative-bioarray.com/support/fluorochromes-in-flow-cytometry.htm
Caco-2 cells are the most widely used cell line for predicting intestinal drug absorption as they form polarized monolayers with tight junctions and microvilli like intestinal cells. Other cell lines used include MDCK, HT29-MTX, 2/4/A1, TC-7, LLC-PK1, IEC-18 and T84, but they have limitations such as lack of transporters, unstable monolayers, or poor differentiation. While cell models show good correlation with passive drug permeability, correlations with active transport are more variable. Extensive studies are still needed to fully characterize intestinal drug transport mechanisms in these models.
Comparison of caco 2 with other cell-based models for intestinal permeability...Creative-Bioarray
The use of cell cultures provides a method to predict drug permeability by utilizing cell monolayers in a two-chamber diffusion system to simulate the passage of drugs from the intestinal lumen into the blood.
Cell cycle refers to the set of events through which a cell grows, replicates its genome, and ultimately divides into two daughter cells through the process of mitosis.
https://www.creative-bioarray.com/cell-cycle-assays.htm
Creative Bioarray is offering Caco-2 permeability assay to help determine the absorption and the bioavailability of drug candidates, facilitating the lead optimization process in drug discovery.
https://www.creative-bioarray.com/Services/caco-2-permeability-assay.htm
A broad range of reprogramming systems is available including mRNA reprogramming, dox-inducible human 4F2A reprogramming and lentivirus reprogramming. These technologies have been adopted and developed in close collaboration with leading iPS cell pioneers. Our extensive range of products allows for customization of individual transcription factors, cell culture conditions, and delivery systems for the optimization of reprogramming parameters.
https://www.creative-bioarray.com/Services/Custom-iPS-Cell-Services.htm
Cell proliferation assays are used to monitor the dynamic growth of a cell population or to detect daughter cells in a growing population.
On the other hand, cell viability assays assess how healthy the cells are by measuring markers of cellular activity.
https://www.creative-bioarray.com/products/cell-viability,-proliferation-and-cytotoxicity-list-226.htm
Cell cycle regulation is controlled by cyclins, cyclin-dependent kinases (CDKs), and CDK inhibitors. Cyclins bind to and activate CDKs to promote cell cycle progression. CDK inhibitors like p16 and p21 inhibit CDK activity to induce cell cycle arrest. Checkpoints like the DNA damage checkpoint ensure DNA integrity before replication or division. Dysregulation of these regulators can lead to uncontrolled cell growth and cancer.
By using flow cytometry, staining dyes are needed. Creative Bioarray can choose different dyes to perform the assays, including propidium iodide (PI), BrdU, 7-amino actinomycin-D (7-AAD), Hoechst 33342 and 33258, and 4’6’-diamidino-2-phenylindole (DAPI), based on the customer’s applications or requirements.
https://www.creative-bioarray.com/cell-cycle-assays.htm
Induced Pluripotent Stem Cells (iPSCs) are a type pf pluripotent stem cell artificially derived, and often referred to as programmed, from adult somatic cells using the expression of certain genes in culture.
https://www.creative-bioarray.com/products/ipsc-reprogramming-kit-list-239.htm
A fluorescent compound has the property of absorbing light energy at a range of specific wavelengths. This absorption of light causes electron to rise from the ground state to a higher energy level (excited state). The excited electron quickly decays to its ground state while releasing the excess energy in the form of photon of light. This transition of energy is called fluorescence.
https://www.creative-bioarray.com/support/fluorochromes-in-flow-cytometry.htm
Histology Services provides various histology and microscopy services including immunohistochemistry, immunofluorescence, fluorescent in situ hybridization, transmission electron microscopy, and other services to help scientists with life science research. Their services offer flexible and customized solutions to help clients reach research milestones faster and more efficiently while saving on infrastructure costs. They have established proprietary protocols and techniques to enhance sensitivity and quality for applications such as cell and tissue sample preparation, probe design and labeling, hybridization, and imaging.
Creative Bioarray offers 35 human cell systems with over 160 different cell types. Moreover, we also provide our customers with primary cells from over 13 types of other animals.
https://www.creative-bioarray.com/products/primary-cell-types-list-14.htm?page=1
Drug transporters mediate the uptake and efflux of a broad variety of drugs and drug metabolites. Most uptake transporters are members of the solute carrier (SLC) family, while most efflux transporters are members of the ATP-binding cassette (ABC) transporter family.
https://www.creative-bioarray.com/services/drug-transporters.htm
Acroscell provides ready-to-use beating human induced pluripotent stem cells (iPSC)-derived cardiomyocytes. Generated from mature cells that have been genetically reprogramed to a pluripotent stem cell state, induced pluripotent stem cells (iPSCs) can be readily expanded and induced to specialize or differentiate into cardiomyocytes in vitro.
https://www.creative-bioarray.com/acroscell/ipsc-derived-cardiomyocytes.html
PAMPA provides a simplified approach to permeability by addressing just a single transport mechanism. This avoids the complexities of active transport and metabolism, enabling ranking of the compounds on a single permeability factor.
https://dda.creative-bioarray.com/parallel-artificial-membrane-permeability-assay.html
Creative Bioarray's SuperQuick® angiogenesis assay kit provides a robust method to determine angiogenesis (in vitro) in less than 18 hrs. This assay kit provides a simple, easy to perform, semi-quantitative tool for assessing angiogenesis.
https://www.creative-bioarray.com/superquick-angiogenesis-assay-kit-item-csk-xa001-5627.htm
Immuno-Oncology (I-O) is an emerging and evolving treatment modality that includes immunotherapies designed to utilize the body’s own immune system to fight diseases. The last 30 years of I-O research has progressed considerably with approvals for the use of various I-O therapies including vaccines, cytokines, tumor-directed monoclonal antibodies, and immune checkpoint inhibitors.
https://www.creative-bioarray.com/immuno-oncology.htm
“An Outlook of the Ongoing and Future Relationship between Blockchain Technologies and Process-aware Information Systems.” Invited talk at the joint workshop on Blockchain for Information Systems (BC4IS) and Blockchain for Trusted Data Sharing (B4TDS), co-located with with the 36th International Conference on Advanced Information Systems Engineering (CAiSE), 3 June 2024, Limassol, Cyprus.
Communications Mining Series - Zero to Hero - Session 1DianaGray10
This session provides introduction to UiPath Communication Mining, importance and platform overview. You will acquire a good understand of the phases in Communication Mining as we go over the platform with you. Topics covered:
• Communication Mining Overview
• Why is it important?
• How can it help today’s business and the benefits
• Phases in Communication Mining
• Demo on Platform overview
• Q/A
Enchancing adoption of Open Source Libraries. A case study on Albumentations.AIVladimir Iglovikov, Ph.D.
Presented by Vladimir Iglovikov:
- https://www.linkedin.com/in/iglovikov/
- https://x.com/viglovikov
- https://www.instagram.com/ternaus/
This presentation delves into the journey of Albumentations.ai, a highly successful open-source library for data augmentation.
Created out of a necessity for superior performance in Kaggle competitions, Albumentations has grown to become a widely used tool among data scientists and machine learning practitioners.
This case study covers various aspects, including:
People: The contributors and community that have supported Albumentations.
Metrics: The success indicators such as downloads, daily active users, GitHub stars, and financial contributions.
Challenges: The hurdles in monetizing open-source projects and measuring user engagement.
Development Practices: Best practices for creating, maintaining, and scaling open-source libraries, including code hygiene, CI/CD, and fast iteration.
Community Building: Strategies for making adoption easy, iterating quickly, and fostering a vibrant, engaged community.
Marketing: Both online and offline marketing tactics, focusing on real, impactful interactions and collaborations.
Mental Health: Maintaining balance and not feeling pressured by user demands.
Key insights include the importance of automation, making the adoption process seamless, and leveraging offline interactions for marketing. The presentation also emphasizes the need for continuous small improvements and building a friendly, inclusive community that contributes to the project's growth.
Vladimir Iglovikov brings his extensive experience as a Kaggle Grandmaster, ex-Staff ML Engineer at Lyft, sharing valuable lessons and practical advice for anyone looking to enhance the adoption of their open-source projects.
Explore more about Albumentations and join the community at:
GitHub: https://github.com/albumentations-team/albumentations
Website: https://albumentations.ai/
LinkedIn: https://www.linkedin.com/company/100504475
Twitter: https://x.com/albumentations
GraphSummit Singapore | The Art of the Possible with Graph - Q2 2024Neo4j
Neha Bajwa, Vice President of Product Marketing, Neo4j
Join us as we explore breakthrough innovations enabled by interconnected data and AI. Discover firsthand how organizations use relationships in data to uncover contextual insights and solve our most pressing challenges – from optimizing supply chains, detecting fraud, and improving customer experiences to accelerating drug discoveries.
Unlock the Future of Search with MongoDB Atlas_ Vector Search Unleashed.pdfMalak Abu Hammad
Discover how MongoDB Atlas and vector search technology can revolutionize your application's search capabilities. This comprehensive presentation covers:
* What is Vector Search?
* Importance and benefits of vector search
* Practical use cases across various industries
* Step-by-step implementation guide
* Live demos with code snippets
* Enhancing LLM capabilities with vector search
* Best practices and optimization strategies
Perfect for developers, AI enthusiasts, and tech leaders. Learn how to leverage MongoDB Atlas to deliver highly relevant, context-aware search results, transforming your data retrieval process. Stay ahead in tech innovation and maximize the potential of your applications.
#MongoDB #VectorSearch #AI #SemanticSearch #TechInnovation #DataScience #LLM #MachineLearning #SearchTechnology
Climate Impact of Software Testing at Nordic Testing DaysKari Kakkonen
My slides at Nordic Testing Days 6.6.2024
Climate impact / sustainability of software testing discussed on the talk. ICT and testing must carry their part of global responsibility to help with the climat warming. We can minimize the carbon footprint but we can also have a carbon handprint, a positive impact on the climate. Quality characteristics can be added with sustainability, and then measured continuously. Test environments can be used less, and in smaller scale and on demand. Test techniques can be used in optimizing or minimizing number of tests. Test automation can be used to speed up testing.
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.
Full-RAG: A modern architecture for hyper-personalizationZilliz
Mike Del Balso, CEO & Co-Founder at Tecton, presents "Full RAG," a novel approach to AI recommendation systems, aiming to push beyond the limitations of traditional models through a deep integration of contextual insights and real-time data, leveraging the Retrieval-Augmented Generation architecture. This talk will outline Full RAG's potential to significantly enhance personalization, address engineering challenges such as data management and model training, and introduce data enrichment with reranking as a key solution. Attendees will gain crucial insights into the importance of hyperpersonalization in AI, the capabilities of Full RAG for advanced personalization, and strategies for managing complex data integrations for deploying cutting-edge AI solutions.
Introducing Milvus Lite: Easy-to-Install, Easy-to-Use vector database for you...Zilliz
Join us to introduce Milvus Lite, a vector database that can run on notebooks and laptops, share the same API with Milvus, and integrate with every popular GenAI framework. This webinar is perfect for developers seeking easy-to-use, well-integrated vector databases for their GenAI apps.
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.
Why You Should Replace Windows 11 with Nitrux Linux 3.5.0 for enhanced perfor...SOFTTECHHUB
The choice of an operating system plays a pivotal role in shaping our computing experience. For decades, Microsoft's Windows has dominated the market, offering a familiar and widely adopted platform for personal and professional use. However, as technological advancements continue to push the boundaries of innovation, alternative operating systems have emerged, challenging the status quo and offering users a fresh perspective on computing.
One such alternative that has garnered significant attention and acclaim is Nitrux Linux 3.5.0, a sleek, powerful, and user-friendly Linux distribution that promises to redefine the way we interact with our devices. With its focus on performance, security, and customization, Nitrux Linux presents a compelling case for those seeking to break free from the constraints of proprietary software and embrace the freedom and flexibility of open-source computing.
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
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.
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.
UiPath Test Automation using UiPath Test Suite series, part 5DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 5. In this session, we will cover CI/CD with devops.
Topics covered:
CI/CD with in UiPath
End-to-end overview of CI/CD pipeline with Azure devops
Speaker:
Lyndsey Byblow, Test Suite Sales Engineer @ UiPath, Inc.
A tale of scale & speed: How the US Navy is enabling software delivery from l...sonjaschweigert1
Rapid and secure feature delivery is a goal across every application team and every branch of the DoD. The Navy’s DevSecOps platform, Party Barge, has achieved:
- Reduction in onboarding time from 5 weeks to 1 day
- Improved developer experience and productivity through actionable findings and reduction of false positives
- Maintenance of superior security standards and inherent policy enforcement with Authorization to Operate (ATO)
Development teams can ship efficiently and ensure applications are cyber ready for Navy Authorizing Officials (AOs). In this webinar, Sigma Defense and Anchore will give attendees a look behind the scenes and demo secure pipeline automation and security artifacts that speed up application ATO and time to production.
We will cover:
- How to remove silos in DevSecOps
- How to build efficient development pipeline roles and component templates
- How to deliver security artifacts that matter for ATO’s (SBOMs, vulnerability reports, and policy evidence)
- How to streamline operations with automated policy checks on container images
A tale of scale & speed: How the US Navy is enabling software delivery from l...
Technologies to study kinases
1.
2. 哎呀小小草 POWERPOINT
Kinases are arguably one of the most important drug targets due
to the roles their dysregulation, mutations, and overexpression
play in all major pathologies, including metabolic, cardiovascular,
degenerative, inflammatory, and infectious diseases. Finding the
best method for kinase screening and profiling can be a challenging
task and will depend on your research objective, the type of kinase,
availability of an antibody, the size of the kinase substrate and the
analytical instruments available.
3. Creative Bioarray provides a comprehensive set of assay
technologies to solve all of your research objectives - from
target discovery to compound screening, profiling and hit
confirmation. Our breadth of expertise and experience in
kinase research enables our scientists to support you
every step of the way through the drug discovery process.
Kinase Assays
Creative Bioarray
https://dda.creative-bioarray.com/
1-631-626-9181
Email: info@creative-bioarray.com
6. Radiometric kinase assay using 32P-labelled ATP or
33P-labelled ATP is one of the oldest techniques used
to study protein phosphorylation. They rely on the
transfer of radioactive phosphate groups from ATP to
the substrate by a kinase, allowing detection of
activity. The radiolabeled phosphate incorporated into
the substrate is directly proportional to the kinase
activity.
Radiometric Assay
7. Advantages
Radiometric assay formats are the gold
standard for kinase screening, which can
produce reproducible, high-quality data
and directly measure enzyme activity.
Limitations
They are labor intensive and require safe
disposal of radioactive materials, so they
are usually not suitable for high-throughput
screening.
8.
9. Fluorescence resonance energy
transfer (FRET) involves the
transfer of non-radiative energy
from a donor fluorophore to a
close-proximity acceptor
fluorophore. When the donor
and acceptor are spatially close
to each other, the acceptor
molecule will quench any
fluorescence emission from the
donor molecule.
Fluorescence Resonance Energy Transfer (FRET) Assay
The first step of the FRET kinase assay is to
incubate the FRET labeled substrate with ATP and
kinase, resulting in the transfer of γ-phosphate to
the substrate peptide. In the second reaction step,
a site-specific protease is added to the mixture. If
the protease cleaves a non-phosphorylated peptide,
the fluorescent donor and acceptor will be
sufficiently separated to disrupt the FRET, thus
generating a fluorescent signal that can be
measured as a ratio of donor emission to acceptor
emission.
10. Advantages of FRET
HTS friendly
Homogenous reaction
Limitations of FRET
Uses synthetic peptide substrate
Requires counter screening against coupling enzyme
Demonstrates a high false-positive rate for fluorescent compounds
Substrate requires modification for fluorophore labeling
11.
12. Time-resolved fluorescence (TRF) uses fluorophores
with a long decay time, and monitors the fluorescence
as a function of time after excitation by a flash of light.
Lanthanide ions, such as europium, samarium, and
terbium, are often used in this technology due to their
longer emission lifetimes (hundreds of microseconds
compared to several nanoseconds for conventional
organic fluorophores).
Time Resolved Fluorescence (TRF)
13. Advantages &
Limitations
The advantage of this technology is that contaminating
fluorescent molecules which contribute to background
noise have a shorter decay time than lanthanide ions,
so the signal is much cleaner. There are several
commercially available TRF assays, mainly based either
on ELISA assay or combined with FRET assay.
14.
15. Fluorescence polarization (FP), a technique that monitors
molecular movement and rotation, is a widely used
detection method for kinase inhibitors in HTS. The principle
of this assay is that smaller molecules rotate faster than
larger molecules. A fluorescently labeled peptide substrate
in the solution rotates quickly and so will have a low
fluorescence polarization. When the phosphorylation
reaction is initiated by addition of a kinase and ATP, any
phosphorylated peptide substrates will be recognized by
the phospho-antibody. The binding of the antibody will slow
down the rotation of the molecule (high fluorescence
polarization), and this change in speed can be measured.
Fluorescence Polarization (FP) Assay
16. Advantages &
Limitations
Since this is a one-step assay without additional
washing steps, it is very suitable for screening a large
number of kinase inhibitor candidates. However, one
of the major drawbacks for this and other
fluorescence-based assays, is that unused fluorescent
compounds and labeled substrates may produce high
background signals and false positives.
17.
18. Luminescence-based assay uses firefly protein
luciferase to measure the amount of ATP. In the
presence of ATP, luciferase converts the substrate
luciferin into oxyluciferin, which releases yellow-green
photon of light with a spectral maximum of 560 nm.
Although this format shows low sensitivity at low ATP
concentrations, this effect can be counteracted by using
a two-step detection method including 1) stopping the
kinase reaction and depleting the remaining ATP, and 2)
adding reagents to convert ADP to ATP, which is
measured using the coupled luciferase reaction.
Luminescence detection methods can accommodate
fluorescent compounds, but the inhibitory effect of the
compounds on luciferase must be considered.
Luminescence Detection
19.
20. The mobility shift assay takes advantage of the fact
that a phosphorylated peptide substrate is more
negatively charged than the same substrate in the
unphosphorylated state. Therefore, when a mixture of
these peptides is subjected to gel electrophoresis, the
phosphorylated and unphosphorylated substrates will
have different mobility.
Mobility Shift Assay
21. Advantages & Limitations
Since the difference in charge between the peptide
and the substrate is key, the result of mobility shift
assay is greatly affected by the size and sequence of
the substrate. Therefore, this assay is not suitable for
the analysis of larger peptides or whole protein, and
works best when the peptide substrate contains only
specific phosphorylation site sequences.
22.
23. Cell-based functional kinase screening provides a
reliable, quantitative mean for determining the functional
inhibitory effects of drug candidates on kinase targets of
interest in a physiologically relevant cellular environment.
This allows for a more predictive characterization of the
organism’s physiological response to the drug, and
greatly reduces the chances of false positive/negative
data.
Cell-based ELISA Assay
Enzyme-linked immunosorbent assay (ELISA) can be
used to quantitate kinase levels and assess their activity.
In this format, the substrate is captured by the membrane
and detected by a specific anti-phosphorylated substrate
antibody. The detection can also be very sensitive when
using antibodies labeled with highly fluorescent dyes.
24. Advantages & Limitations
ELISA is popular because it is generally fast,
inexpensive, easy to accommodate multiple samples,
and does not require highly specialized equipment.
However, the requirement of separation with multiple
washing steps limits the use of ELISA in HTS. In
addition, the development of high-quality phospho-
specific antibodies presents another challenge.
25. A large number of commercially available kinase assays have been developed in recent years based
on the technologies described above. Each technology has its strengths and weaknesses, and the
most appropriate assay will depend on the aim of the project. For high-throughput screening drug
discovery projects, methods that can be easily automated and miniaturized, such as the
fluorescence-based assays, are the most suitable. For projects that require a more in-depth profile of
the kinase function, a more robust assay such as radiometric assay will provide more reliable results.
Conclusion