SPR.pptx
•Download as PPTX, PDF•
0 likes•6 views
This document discusses methods for characterizing protein-protein interactions, including isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), and biolayer interferometry (BLI). It notes that protein interactions control cellular functions and occur with a wide range of binding affinities. SPR is described as an optical method that detects interactions in real-time by measuring changes in surface plasmon resonance. Kinetic analysis of interaction data from these methods provides information about binding constants and rates that is important for understanding interaction mechanisms and affinities. Experimental design considerations like analyte concentration range are also reviewed.
Report
Share
Report
Share
Recommended
GFP For Exploring Protein-Protein Interactions - Nelson Giovanny Rincon Silva
GFP For Exploring Protein-Protein Interactions - Nelson Giovanny Rincon Silva Nelson Giovanny Rincon S
This document describes using green fluorescent protein (GFP) to study protein-protein interactions. GFP from jellyfish has properties that make it useful for this, such as fluorescence and stability. The document discusses fusing GFP to proteins of interest to monitor their interactions. Specifically, it examines fusing GFP to the S-peptide and S-protein fragments of the ribonuclease protein. It describes constructing and purifying these GFP fusion proteins, then using gel retardation and fluorescence polarization assays to measure the interactions and determine binding constants. The assays allow quantifying the fraction of proteins bound versus unbound to study protein binding.Exploring Compound Combinations in High Throughput Settings: Going Beyond 1D ...
The document describes efforts to screen drug combinations in high throughput settings beyond traditional one-dimensional metrics. It discusses the infrastructure and workflows used to screen compound combinations against a library of over 2000 small molecules with diverse mechanisms of action. Quality control of combination screening experiments poses challenges due to the multi-dimensional nature of the data. The researchers are exploring various metrics and analytical approaches to characterize synergistic, additive and antagonistic combination responses across different cell lines and combinations.
defense 2.0
This document summarizes research on engineering bivalent affinity ligands. Key points include:
- A combinatorial bivalent ligand library was generated that identified ligands binding non-overlapping epitopes and maintained thermostability. This library performed better than a monovalent library.
- The best ligands from the bivalent library were sequenced, with 9 found to be bivalent and 1 trivalent. Mutations outside the original library positions were found in some ligands.
- Ligand M2 was identified that bound with low nanomolar affinity and could engage in multi-epitope binding to intrinsically disordered domains of beta-catenin. M2 showed promise as a new binding scaffold.
- Dimer
RecA foscused antibacterial screening
The document discusses the growing problem of antibiotic resistance and potential new approaches to addressing it. It notes that 2 million nosocomial infections occur in the US each year, 70% of which are resistant to at least one drug. 90,000 people die from these infections annually, a nearly 600% increase since 1992. The document then examines RecA, a bacterial protein involved in DNA repair, as a potential new target for antibiotics. It summarizes research investigating various compounds that inhibit RecA's function and could help combat antibiotic resistance.
CYP121 Drug Discovery (M. tuberculosis)
Fragment screening was used to target cytochrome P450 (CYP) enzymes from Mycobacterium tuberculosis. Thermal shift assays identified fragment hits against CYP121, which were validated by NMR. X-ray crystallography showed two binding modes. Fragment growing, merging, and linking yielded elaborated fragments with improved binding affinity down to 2 nM against CYP121, maintaining good ligand efficiency. Future work will further optimize compounds against CYP121 and screen other CYP enzymes to develop selective, potent inhibitors to treat tuberculosis.
''Electrophoretic Mobility Shift Assay'' by KATE, Wisdom Deebeke
This document describes an electrophoretic mobility shift assay (EMSA) presentation. EMSA is a technique used to study interactions between proteins and DNA. It works by detecting a reduction in electrophoretic mobility of DNA when bound to a protein through gel electrophoresis. The presentation aims to describe the basic principles of EMSA, highlight its methods, and discuss applications such as determining binding affinities and studying conformational changes in DNA upon protein binding.
Selection and application of ssDNA aptamers to detect active TB from sputum s...
A paper presentation.
One of the badly-written papers that I've ever read. Seriously.... plenty of speculations and nothing really conclusive.
Selene_Hess_Deciphering Antibiotic Resistance_EDITED
1) Antibiotic resistance in bacteria has evolved due to widespread antibiotic use, necessitating new methods to identify drug targets.
2) The researchers developed a method called CLK-seq that uses microfluidics to crosslink and sequence protein-DNA interactions over time in bacteria like Klebsiella pneumoniae exposed to ciprofloxacin.
3) CLK-seq can determine both the binding locations and kinetics of transcription factor interactions with DNA, allowing identification of gene regulatory sites for antibiotic resistance as potential drug targets.
Recommended
GFP For Exploring Protein-Protein Interactions - Nelson Giovanny Rincon Silva
GFP For Exploring Protein-Protein Interactions - Nelson Giovanny Rincon Silva Nelson Giovanny Rincon S
This document describes using green fluorescent protein (GFP) to study protein-protein interactions. GFP from jellyfish has properties that make it useful for this, such as fluorescence and stability. The document discusses fusing GFP to proteins of interest to monitor their interactions. Specifically, it examines fusing GFP to the S-peptide and S-protein fragments of the ribonuclease protein. It describes constructing and purifying these GFP fusion proteins, then using gel retardation and fluorescence polarization assays to measure the interactions and determine binding constants. The assays allow quantifying the fraction of proteins bound versus unbound to study protein binding.Exploring Compound Combinations in High Throughput Settings: Going Beyond 1D ...
The document describes efforts to screen drug combinations in high throughput settings beyond traditional one-dimensional metrics. It discusses the infrastructure and workflows used to screen compound combinations against a library of over 2000 small molecules with diverse mechanisms of action. Quality control of combination screening experiments poses challenges due to the multi-dimensional nature of the data. The researchers are exploring various metrics and analytical approaches to characterize synergistic, additive and antagonistic combination responses across different cell lines and combinations.
defense 2.0
This document summarizes research on engineering bivalent affinity ligands. Key points include:
- A combinatorial bivalent ligand library was generated that identified ligands binding non-overlapping epitopes and maintained thermostability. This library performed better than a monovalent library.
- The best ligands from the bivalent library were sequenced, with 9 found to be bivalent and 1 trivalent. Mutations outside the original library positions were found in some ligands.
- Ligand M2 was identified that bound with low nanomolar affinity and could engage in multi-epitope binding to intrinsically disordered domains of beta-catenin. M2 showed promise as a new binding scaffold.
- Dimer
RecA foscused antibacterial screening
The document discusses the growing problem of antibiotic resistance and potential new approaches to addressing it. It notes that 2 million nosocomial infections occur in the US each year, 70% of which are resistant to at least one drug. 90,000 people die from these infections annually, a nearly 600% increase since 1992. The document then examines RecA, a bacterial protein involved in DNA repair, as a potential new target for antibiotics. It summarizes research investigating various compounds that inhibit RecA's function and could help combat antibiotic resistance.
CYP121 Drug Discovery (M. tuberculosis)
Fragment screening was used to target cytochrome P450 (CYP) enzymes from Mycobacterium tuberculosis. Thermal shift assays identified fragment hits against CYP121, which were validated by NMR. X-ray crystallography showed two binding modes. Fragment growing, merging, and linking yielded elaborated fragments with improved binding affinity down to 2 nM against CYP121, maintaining good ligand efficiency. Future work will further optimize compounds against CYP121 and screen other CYP enzymes to develop selective, potent inhibitors to treat tuberculosis.
''Electrophoretic Mobility Shift Assay'' by KATE, Wisdom Deebeke
This document describes an electrophoretic mobility shift assay (EMSA) presentation. EMSA is a technique used to study interactions between proteins and DNA. It works by detecting a reduction in electrophoretic mobility of DNA when bound to a protein through gel electrophoresis. The presentation aims to describe the basic principles of EMSA, highlight its methods, and discuss applications such as determining binding affinities and studying conformational changes in DNA upon protein binding.
Selection and application of ssDNA aptamers to detect active TB from sputum s...
A paper presentation.
One of the badly-written papers that I've ever read. Seriously.... plenty of speculations and nothing really conclusive.
Selene_Hess_Deciphering Antibiotic Resistance_EDITED
1) Antibiotic resistance in bacteria has evolved due to widespread antibiotic use, necessitating new methods to identify drug targets.
2) The researchers developed a method called CLK-seq that uses microfluidics to crosslink and sequence protein-DNA interactions over time in bacteria like Klebsiella pneumoniae exposed to ciprofloxacin.
3) CLK-seq can determine both the binding locations and kinetics of transcription factor interactions with DNA, allowing identification of gene regulatory sites for antibiotic resistance as potential drug targets.
S. prasanth kumar young scientist awarded presentation
The document summarizes research on the coat protein of the Tomato yellow leaf curl viral (TYLCV) disease, which causes significant damage to tomato crops in India. Key findings include:
1) Sequence analysis found mutations in the coat protein that provide insights into the evolutionary divergence of Indian virus isolates and their ability to systematically infect plants.
2) Structural modeling predicted the coat protein binds double-stranded DNA through interactions facilitated by surface loops and neutral patches on the protein.
3) Docking simulations showed the coat protein binds plant DNA through electrostatic and van der Waals interactions, helping the virus infect tomato and other plants.
Tessa Poster for IP
1. 22Rv1 prostate cancer cells were treated with enzalutamide to generate resistant cells (22Rv1-R).
2. Microscopy showed no morphological differences between 22Rv1 and 22Rv1-R cells. Western blot analysis revealed higher MDR1 expression in 22Rv1-R cells.
3. MTT assay demonstrated 22Rv1-R cell viability remained stable in increasing enzalutamide concentrations, indicating resistance, while 22Rv1 cell viability decreased.
SERMACSposterDr.V
This document summarizes a study investigating estradiol-conjugated DNA methylating compounds. Three compounds were synthesized and tested for their ability to bind DNA and estrogen receptors, induce DNA methylation, and cause toxicity in breast cancer cells. Compound 2a was found to be the most toxic, producing the highest levels of N3-methyladenine DNA adducts. Fluorescent assays showed compound binding to DNA and varying binding affinities to estrogen receptors. Overall, the results help explain how these compounds can selectively target and damage estrogen receptor-positive breast cancer cells through DNA methylation.
Day3 troublshooting
Solve your western blot problems with these troubleshooting tips, covering common causes of no signal, high background, multiple bands, and more.
iGEM jamboree presentation final
This document summarizes John Errico's iGEM project on engineering a contact-dependent inhibition system for pathogen detection. The system uses a bacterial defense mechanism called contact-dependent inhibition (CDI) that involves the delivery of toxic proteins to other bacteria on contact. Errico aims to modify this system to produce a secondary messenger like cAMP upon contact with a specific protein, and use this to trigger gene expression for pathogen detection. The document outlines the key components of CDI systems, the steps taken to engineer a prototype system, potential issues encountered, and ideas for future applications of the customizable approach.
2015 07 09__epigenetic_profiling_environmental_health_sciences_v42
Next Generation Epigenetic Profiling for Environmental Health Sciences
The document discusses next generation epigenetic profiling technologies and their applications in environmental health sciences. It provides an overview of epigenetics and biology, next generation epigenetic profiling technologies like methylation arrays and sequencing, and applications in areas like nutrition, circadian rhythms, temperature stress, and small molecules. The technologies allow genome-wide analysis of epigenetic marks at higher resolution and lower cost than previous methods. This enables studying how environmental exposures may influence human health by altering epigenetic regulation of genes.
Structure based computer aided drug design
The document discusses structure-based computer-aided drug design. It describes the drug discovery process and challenges involved in predicting how small molecules bind to protein targets. Key steps in molecular docking include describing the receptor and ligand, sampling possible binding configurations, and scoring the interactions to estimate binding affinity. Genetic and simulated annealing algorithms are commonly used to sample configurations. The accuracy of docking depends on factors like receptor and ligand flexibility.
single chain fragment variable antibody(ScFv)
Single chain fragment variable (ScFv) antibodies are antibody fragments consisting of a single monomeric variable heavy chain that is able to bind specifically to antigens. They are also known as nanobodies and are produced from the variable domains of camelid heavy chain antibodies that lack light chains. Nanobodies have several advantages over traditional antibodies including small size, high stability, and ability to penetrate tissues. They are being researched and developed for various diagnostic and therapeutic applications including cancer imaging and treatment, viral infections, and cardiovascular diseases.
Deshpande et al. Retrovirology (2016)
This document summarizes a study examining the genetic attributes associated with the exceptional sensitivity of an HIV-1 clade C envelope protein to autologous broadly neutralizing plasma antibodies. The researchers identified an envelope that was significantly more sensitive to neutralization by contemporaneous plasma than two other envelopes. Sequence analysis found mutations in the V3/C3 region of the sensitive envelope. Chimeric envelope experiments determined that replacing the V3/C3 region of a resistant envelope with the sensitive envelope conferred enhanced neutralization sensitivity, indicating this region plays a role in exposure of epitopes targeted by plasma antibodies. Fine mapping identified a proline to isoleucine substitution at position 326 in the V3 loop that modulated neutralization susceptibility.
Deshpande et al.,Retrovirology 2016
This study examined the genetic attributes associated with the enhanced sensitivity of an HIV-1 clade C envelope protein (HVTR-PG80v2.eJ7) to autologous broadly neutralizing plasma antibodies from an elite neutralizer. The researchers found that mutations in the V3/C3 region of the envelope protein were associated with its increased sensitivity to neutralization by autologous plasma antibodies. Depletion experiments showed that these mutations altered the envelope conformation to better expose epitopes targeted by both neutralizing and non-neutralizing antibodies in the plasma. Therefore, distinct vulnerabilities associated with antibody evasion could be linked to mutations in the V3/C3 region of the HIV envelope.
zdockTeaching.ppt
This document discusses protein docking, which is the computational determination of protein complex structures from individual protein structures. It describes challenges in protein docking like large search spaces and protein flexibility. The document outlines an integrated approach to protein docking that uses shape complementarity functions, desolvation energies, electrostatic interactions, and post-processing techniques. Evaluation on benchmark datasets shows a 60% success rate when 10 predictions are submitted. Future work proposed includes developing an automatic docking server and improving post-processing methods.
MIT Amgen Scholar Presentation
This study aims to investigate how the charge distribution on protein surfaces affects protein-polymer interactions. The researchers will:
1. Express GFP proteins with varying charge distributions through site-directed mutagenesis.
2. Synthesize model polymers using RAFT polymerization and conjugate them to the GFP proteins.
3. Use techniques like turbidity measurements and DLS to analyze how the proteins interact with cationic, anionic, and neutral polymers depending on the proteins' charge distributions.
Preliminary results showed the proteins were successfully expressed and conjugated to polymers while maintaining structure. Turbidity data also indicated how charge affects protein aggregation with polyelectrolytes. Overall, this work could help understand how
Coebp
The document lists research projects at the University of Manchester's Centre of Excellence in Biopharmaceuticals, including studies on mechanisms of protein aggregation, concentrated protein solutions, protein solution rheology, detection of protein contaminants, immunogenicity of protein aggregates, predictive modelling of protein solubility, higher order protein structure, controllable protein expression in bacteria, CHO cell line development, differentiation of single stem cells, and molecular organisation and function of glycoprotein polymer gels. Contact information is provided for each project leader.
Exploring protein-protein interactions by Weak Affinity Chromatography (WAC) ...
This is a presentation of the method of weak affinity chromatography and its application in a case study. The presentation was held at the Drug Discovery Chemistry meeting in San Diego on April 2-4, 2024, by Björn Walse, CEO of SARomics Biostructures.
Specificity and Evolvability in Eukaryotic Protein Interaction Networks
The document discusses the evolution of protein interaction networks by comparing networks across species. It finds that interactions change at a fast rate, with around 1% to 3% of interactions turning over per million years. Less specific interactions mediated by promiscuous domains evolve faster than more specific interactions. Functions related to immune response and transport show evidence of positive selection for fast interaction turnover. This dynamic interaction evolution may allow networks to search for optimal solutions to biological problems through mutations at the protein and network levels.
Nicb Research Overview
The NICB (National Institute for Cellular Biotechnology) is located on the Dublin City University (DCU) campus in Dublin, Ireland. It is a leading multidisciplinary centre of translational research in fundamental and applied cellular biotechnology, molecular cell Biology, ocular diseases and biological chemistry. It includes a multidisciplinary team of Cell and Molecular Biologists, Biotechnologists, Chemists and Informatics specialists.
The NICB prioritises translational research involving collaborations with industry and with clinicians, and is committed to educating people from all backgrounds in the area of Biomedical Science.
This slideshare summarises the main research areas of the NICB, including:
Molecular basis for biopharmaceutical production by animal cells
Cancer – drug resistance, invasion and biomarkers
Tissue Engineering/Stem Cell Therapy – ocular diseases, diabetes
Using animal cells as research tools and models for disease research
Non biopsy diagnosis of acute rejection of Renal allograft
This document discusses non-invasive methods for diagnosing acute rejection in renal transplant patients. Currently, graft biopsy is the gold standard but it is invasive and detects rejection at a late stage. The presentation evaluates various potential biomarkers being studied through genomics, proteomics, and metabolomics approaches. Several individual studies are highlighted that found biomarkers like urinary MCP-1, VEGF, cytokines, and certain metabolites that showed potential for detecting early acute rejection non-invasively. Magnetic resonance imaging is also discussed as a non-invasive imaging technique being researched. In summary, the ideal non-invasive biomarker has yet to be identified but a combination of markers may provide a more realistic approach for different clinical scenarios.
my paper 2015
This document describes a new blood test using gold nanoparticles and dynamic light scattering to detect early stage cancers. The test analyzes the protein corona that forms on the nanoparticles when mixed with blood serum. It was discovered that serum from prostate cancer patients forms a corona with higher levels of immunoglobulin G (IgG) compared to non-cancer controls. Two studies showed the test has 90-95% specificity and 50% sensitivity for early prostate cancer, improving on PSA testing. The increased IgG is believed to be from autoantibodies produced against tumors. The simple test requires only a few drops of blood and provides rapid results, making it suitable for cancer screening.
Amy_Wood_CV _2015
Amy Wood has over 10 years of experience in molecular biology, protein production and purification, and cancer research. She holds a PhD in Molecular Biology/Immunology from the University of Birmingham and has worked in both academic and industrial settings. Her career has focused on developing cancer therapies through protein expression, structural analysis, and investigating protein-protein interactions.
2013-11-26 DTL FIH symposium, Leiden
1) The document discusses the use of protein and metabolite biomarkers in personalized healthcare, noting that over 100 biomarkers are now included in drug labels and 16 companion diagnostics are needed.
2) It describes how companion diagnostics can help determine a drug's metabolism, efficacy, or safety for a patient. Systems biology approaches that integrate multi-omic data are important for developing personalized treatment approaches.
3) The Radboud Center for Proteomics, Glycomics and Metabolomics performs various 'omics analyses including proteomics, glycoproteomics, metabolomics, and top-down proteomics to discover and validate biomarkers for personalized healthcare applications like diagnosing rare diseases, detecting inborn errors of metabolism, and characterizing
Compexometric titration/Chelatorphy titration/chelating titration
Classification
Metal ion ion indicators
Masking and demasking reagents
Estimation of Magnisium sulphate
Calcium gluconate
Complexometric Titration/ chelatometry titration/chelating titration, introduction, Types-
1.Direct Titration
2.Back Titration
3.Replacement Titration
4.Indirect Titration
Masking agent, Demasking agents
formation of complex
comparition between masking and demasking agents,
Indicators/Metal ion indicators/ Metallochromic indicators/pM indicators,
Visual Technique,PM indicators (metallochromic), Indicators of pH, Redox Indicators
Instrumental Techniques-Photometry
Potentiometry
Miscellaneous methods.
Complex titration with EDTA.
Pests of Storage_Identification_Dr.UPR.pdf
InIndia-post-harvestlosses-unscientificstorage,insects,rodents,micro-organismsetc.,accountforabout10percentoftotalfoodgrains
Graininfestation
Directdamage
Indirectly
•theexuviae,skin,deadinsects
•theirexcretawhichmakefoodunfitforhumanconsumption
About600speciesofinsectshavebeenassociatedwithstoredgrainproducts
100speciesofinsectpestsofstoredproductscauseeconomiclosses
More Related Content
Similar to SPR.pptx
S. prasanth kumar young scientist awarded presentation
The document summarizes research on the coat protein of the Tomato yellow leaf curl viral (TYLCV) disease, which causes significant damage to tomato crops in India. Key findings include:
1) Sequence analysis found mutations in the coat protein that provide insights into the evolutionary divergence of Indian virus isolates and their ability to systematically infect plants.
2) Structural modeling predicted the coat protein binds double-stranded DNA through interactions facilitated by surface loops and neutral patches on the protein.
3) Docking simulations showed the coat protein binds plant DNA through electrostatic and van der Waals interactions, helping the virus infect tomato and other plants.
Tessa Poster for IP
1. 22Rv1 prostate cancer cells were treated with enzalutamide to generate resistant cells (22Rv1-R).
2. Microscopy showed no morphological differences between 22Rv1 and 22Rv1-R cells. Western blot analysis revealed higher MDR1 expression in 22Rv1-R cells.
3. MTT assay demonstrated 22Rv1-R cell viability remained stable in increasing enzalutamide concentrations, indicating resistance, while 22Rv1 cell viability decreased.
SERMACSposterDr.V
This document summarizes a study investigating estradiol-conjugated DNA methylating compounds. Three compounds were synthesized and tested for their ability to bind DNA and estrogen receptors, induce DNA methylation, and cause toxicity in breast cancer cells. Compound 2a was found to be the most toxic, producing the highest levels of N3-methyladenine DNA adducts. Fluorescent assays showed compound binding to DNA and varying binding affinities to estrogen receptors. Overall, the results help explain how these compounds can selectively target and damage estrogen receptor-positive breast cancer cells through DNA methylation.
Day3 troublshooting
Solve your western blot problems with these troubleshooting tips, covering common causes of no signal, high background, multiple bands, and more.
iGEM jamboree presentation final
This document summarizes John Errico's iGEM project on engineering a contact-dependent inhibition system for pathogen detection. The system uses a bacterial defense mechanism called contact-dependent inhibition (CDI) that involves the delivery of toxic proteins to other bacteria on contact. Errico aims to modify this system to produce a secondary messenger like cAMP upon contact with a specific protein, and use this to trigger gene expression for pathogen detection. The document outlines the key components of CDI systems, the steps taken to engineer a prototype system, potential issues encountered, and ideas for future applications of the customizable approach.
2015 07 09__epigenetic_profiling_environmental_health_sciences_v42
Next Generation Epigenetic Profiling for Environmental Health Sciences
The document discusses next generation epigenetic profiling technologies and their applications in environmental health sciences. It provides an overview of epigenetics and biology, next generation epigenetic profiling technologies like methylation arrays and sequencing, and applications in areas like nutrition, circadian rhythms, temperature stress, and small molecules. The technologies allow genome-wide analysis of epigenetic marks at higher resolution and lower cost than previous methods. This enables studying how environmental exposures may influence human health by altering epigenetic regulation of genes.
Structure based computer aided drug design
The document discusses structure-based computer-aided drug design. It describes the drug discovery process and challenges involved in predicting how small molecules bind to protein targets. Key steps in molecular docking include describing the receptor and ligand, sampling possible binding configurations, and scoring the interactions to estimate binding affinity. Genetic and simulated annealing algorithms are commonly used to sample configurations. The accuracy of docking depends on factors like receptor and ligand flexibility.
single chain fragment variable antibody(ScFv)
Single chain fragment variable (ScFv) antibodies are antibody fragments consisting of a single monomeric variable heavy chain that is able to bind specifically to antigens. They are also known as nanobodies and are produced from the variable domains of camelid heavy chain antibodies that lack light chains. Nanobodies have several advantages over traditional antibodies including small size, high stability, and ability to penetrate tissues. They are being researched and developed for various diagnostic and therapeutic applications including cancer imaging and treatment, viral infections, and cardiovascular diseases.
Deshpande et al. Retrovirology (2016)
This document summarizes a study examining the genetic attributes associated with the exceptional sensitivity of an HIV-1 clade C envelope protein to autologous broadly neutralizing plasma antibodies. The researchers identified an envelope that was significantly more sensitive to neutralization by contemporaneous plasma than two other envelopes. Sequence analysis found mutations in the V3/C3 region of the sensitive envelope. Chimeric envelope experiments determined that replacing the V3/C3 region of a resistant envelope with the sensitive envelope conferred enhanced neutralization sensitivity, indicating this region plays a role in exposure of epitopes targeted by plasma antibodies. Fine mapping identified a proline to isoleucine substitution at position 326 in the V3 loop that modulated neutralization susceptibility.
Deshpande et al.,Retrovirology 2016
This study examined the genetic attributes associated with the enhanced sensitivity of an HIV-1 clade C envelope protein (HVTR-PG80v2.eJ7) to autologous broadly neutralizing plasma antibodies from an elite neutralizer. The researchers found that mutations in the V3/C3 region of the envelope protein were associated with its increased sensitivity to neutralization by autologous plasma antibodies. Depletion experiments showed that these mutations altered the envelope conformation to better expose epitopes targeted by both neutralizing and non-neutralizing antibodies in the plasma. Therefore, distinct vulnerabilities associated with antibody evasion could be linked to mutations in the V3/C3 region of the HIV envelope.
zdockTeaching.ppt
This document discusses protein docking, which is the computational determination of protein complex structures from individual protein structures. It describes challenges in protein docking like large search spaces and protein flexibility. The document outlines an integrated approach to protein docking that uses shape complementarity functions, desolvation energies, electrostatic interactions, and post-processing techniques. Evaluation on benchmark datasets shows a 60% success rate when 10 predictions are submitted. Future work proposed includes developing an automatic docking server and improving post-processing methods.
MIT Amgen Scholar Presentation
This study aims to investigate how the charge distribution on protein surfaces affects protein-polymer interactions. The researchers will:
1. Express GFP proteins with varying charge distributions through site-directed mutagenesis.
2. Synthesize model polymers using RAFT polymerization and conjugate them to the GFP proteins.
3. Use techniques like turbidity measurements and DLS to analyze how the proteins interact with cationic, anionic, and neutral polymers depending on the proteins' charge distributions.
Preliminary results showed the proteins were successfully expressed and conjugated to polymers while maintaining structure. Turbidity data also indicated how charge affects protein aggregation with polyelectrolytes. Overall, this work could help understand how
Coebp
The document lists research projects at the University of Manchester's Centre of Excellence in Biopharmaceuticals, including studies on mechanisms of protein aggregation, concentrated protein solutions, protein solution rheology, detection of protein contaminants, immunogenicity of protein aggregates, predictive modelling of protein solubility, higher order protein structure, controllable protein expression in bacteria, CHO cell line development, differentiation of single stem cells, and molecular organisation and function of glycoprotein polymer gels. Contact information is provided for each project leader.
Exploring protein-protein interactions by Weak Affinity Chromatography (WAC) ...
This is a presentation of the method of weak affinity chromatography and its application in a case study. The presentation was held at the Drug Discovery Chemistry meeting in San Diego on April 2-4, 2024, by Björn Walse, CEO of SARomics Biostructures.
Specificity and Evolvability in Eukaryotic Protein Interaction Networks
The document discusses the evolution of protein interaction networks by comparing networks across species. It finds that interactions change at a fast rate, with around 1% to 3% of interactions turning over per million years. Less specific interactions mediated by promiscuous domains evolve faster than more specific interactions. Functions related to immune response and transport show evidence of positive selection for fast interaction turnover. This dynamic interaction evolution may allow networks to search for optimal solutions to biological problems through mutations at the protein and network levels.
Nicb Research Overview
The NICB (National Institute for Cellular Biotechnology) is located on the Dublin City University (DCU) campus in Dublin, Ireland. It is a leading multidisciplinary centre of translational research in fundamental and applied cellular biotechnology, molecular cell Biology, ocular diseases and biological chemistry. It includes a multidisciplinary team of Cell and Molecular Biologists, Biotechnologists, Chemists and Informatics specialists.
The NICB prioritises translational research involving collaborations with industry and with clinicians, and is committed to educating people from all backgrounds in the area of Biomedical Science.
This slideshare summarises the main research areas of the NICB, including:
Molecular basis for biopharmaceutical production by animal cells
Cancer – drug resistance, invasion and biomarkers
Tissue Engineering/Stem Cell Therapy – ocular diseases, diabetes
Using animal cells as research tools and models for disease research
Non biopsy diagnosis of acute rejection of Renal allograft
This document discusses non-invasive methods for diagnosing acute rejection in renal transplant patients. Currently, graft biopsy is the gold standard but it is invasive and detects rejection at a late stage. The presentation evaluates various potential biomarkers being studied through genomics, proteomics, and metabolomics approaches. Several individual studies are highlighted that found biomarkers like urinary MCP-1, VEGF, cytokines, and certain metabolites that showed potential for detecting early acute rejection non-invasively. Magnetic resonance imaging is also discussed as a non-invasive imaging technique being researched. In summary, the ideal non-invasive biomarker has yet to be identified but a combination of markers may provide a more realistic approach for different clinical scenarios.
my paper 2015
This document describes a new blood test using gold nanoparticles and dynamic light scattering to detect early stage cancers. The test analyzes the protein corona that forms on the nanoparticles when mixed with blood serum. It was discovered that serum from prostate cancer patients forms a corona with higher levels of immunoglobulin G (IgG) compared to non-cancer controls. Two studies showed the test has 90-95% specificity and 50% sensitivity for early prostate cancer, improving on PSA testing. The increased IgG is believed to be from autoantibodies produced against tumors. The simple test requires only a few drops of blood and provides rapid results, making it suitable for cancer screening.
Amy_Wood_CV _2015
Amy Wood has over 10 years of experience in molecular biology, protein production and purification, and cancer research. She holds a PhD in Molecular Biology/Immunology from the University of Birmingham and has worked in both academic and industrial settings. Her career has focused on developing cancer therapies through protein expression, structural analysis, and investigating protein-protein interactions.
2013-11-26 DTL FIH symposium, Leiden
1) The document discusses the use of protein and metabolite biomarkers in personalized healthcare, noting that over 100 biomarkers are now included in drug labels and 16 companion diagnostics are needed.
2) It describes how companion diagnostics can help determine a drug's metabolism, efficacy, or safety for a patient. Systems biology approaches that integrate multi-omic data are important for developing personalized treatment approaches.
3) The Radboud Center for Proteomics, Glycomics and Metabolomics performs various 'omics analyses including proteomics, glycoproteomics, metabolomics, and top-down proteomics to discover and validate biomarkers for personalized healthcare applications like diagnosing rare diseases, detecting inborn errors of metabolism, and characterizing
Similar to SPR.pptx (20)
S. prasanth kumar young scientist awarded presentation
S. prasanth kumar young scientist awarded presentation
2015 07 09__epigenetic_profiling_environmental_health_sciences_v42
2015 07 09__epigenetic_profiling_environmental_health_sciences_v42
Exploring protein-protein interactions by Weak Affinity Chromatography (WAC) ...
Exploring protein-protein interactions by Weak Affinity Chromatography (WAC) ...
Specificity and Evolvability in Eukaryotic Protein Interaction Networks
Specificity and Evolvability in Eukaryotic Protein Interaction Networks
Non biopsy diagnosis of acute rejection of Renal allograft
Non biopsy diagnosis of acute rejection of Renal allograft
Recently uploaded
Compexometric titration/Chelatorphy titration/chelating titration
Classification
Metal ion ion indicators
Masking and demasking reagents
Estimation of Magnisium sulphate
Calcium gluconate
Complexometric Titration/ chelatometry titration/chelating titration, introduction, Types-
1.Direct Titration
2.Back Titration
3.Replacement Titration
4.Indirect Titration
Masking agent, Demasking agents
formation of complex
comparition between masking and demasking agents,
Indicators/Metal ion indicators/ Metallochromic indicators/pM indicators,
Visual Technique,PM indicators (metallochromic), Indicators of pH, Redox Indicators
Instrumental Techniques-Photometry
Potentiometry
Miscellaneous methods.
Complex titration with EDTA.
Pests of Storage_Identification_Dr.UPR.pdf
InIndia-post-harvestlosses-unscientificstorage,insects,rodents,micro-organismsetc.,accountforabout10percentoftotalfoodgrains
Graininfestation
Directdamage
Indirectly
•theexuviae,skin,deadinsects
•theirexcretawhichmakefoodunfitforhumanconsumption
About600speciesofinsectshavebeenassociatedwithstoredgrainproducts
100speciesofinsectpestsofstoredproductscauseeconomiclosses
Gadgets for management of stored product pests_Dr.UPR.pdf
Insectsplayamajorroleinthedeteriorationoffoodgrainscausingbothquantitativeandqualitativelosses
Wellprovedthatnogranariescanbefilledwithgrainswithoutinsectsastheharvestedproducecontainegg(or)larvae(or)pupae(or)adultinsectinthembecauseoffieldcarryoverinfestationwhichcannotbeavoidedindevelopingcountrieslikeIndia
Simpletechnologiesfortimelydetectionofinsectsinthestoredproduceandtherebyplantimelycontrolmeasures
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...Scintica Instrumentation
Targeting Hsp90 and its pathogen Orthologs with Tethered Inhibitors as a Diagnostic and Therapeutic Strategy for cancer and infectious diseases with Dr. Timothy Haystead.Randomised Optimisation Algorithms in DAPHNE
Slides from talk:
Aleš Zamuda: Randomised Optimisation Algorithms in DAPHNE .
Austrian-Slovenian HPC Meeting 2024 – ASHPC24, Seeblickhotel Grundlsee in Austria, 10–13 June 2024
https://ashpc.eu/
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
The cost of acquiring information by natural selection
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
It's based on the first part of this research paper:
The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
Direct Seeded Rice - Climate Smart Agriculture
Direct Seeded Rice - Climate Smart AgricultureInternational Food Policy Research Institute- South Asia Office
PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
ESR spectroscopy in liquid food and beverages.pptx
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Micronuclei test.M.sc.zoology.fisheries.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
Ozturkcan, S., Berndt, A., & Angelakis, A. (2024). Mending clothing to support sustainable fashion. Presented at the 31st Annual Conference by the Consortium for International Marketing Research (CIMaR), 10-13 Jun 2024, University of Gävle, Sweden.
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...Advanced-Concepts-Team
Presentation in the Science Coffee of the Advanced Concepts Team of the European Space Agency on the 07.06.2024.
Speaker: Diego Blas (IFAE/ICREA)
Title: Gravitational wave detection with orbital motion of Moon and artificial
Abstract:
In this talk I will describe some recent ideas to find gravitational waves from supermassive black holes or of primordial origin by studying their secular effect on the orbital motion of the Moon or satellites that are laser ranged.8.Isolation of pure cultures and preservation of cultures.pdf
Isolation of pure culture, its various method.
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...
A proprietary approach developed by bringing together the best of learning theories from Psychology, design principles from the world of visualization, and pedagogical methods from over a decade of training experience, that enables you to: Learn better, faster!
Recently uploaded (20)
Compexometric titration/Chelatorphy titration/chelating titration
Compexometric titration/Chelatorphy titration/chelating titration
Gadgets for management of stored product pests_Dr.UPR.pdf
Gadgets for management of stored product pests_Dr.UPR.pdf
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
The cost of acquiring information by natural selection
The cost of acquiring information by natural selection
aziz sancar nobel prize winner: from mardin to nobel
aziz sancar nobel prize winner: from mardin to nobel
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
ESR spectroscopy in liquid food and beverages.pptx
ESR spectroscopy in liquid food and beverages.pptx
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...
8.Isolation of pure cultures and preservation of cultures.pdf
8.Isolation of pure cultures and preservation of cultures.pdf
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...
SPR.pptx
- 1. Characterization of ProteinInteractions by ITC,SPRand BLI Sangho Lee Department of BiologicalSciences Sungkyunkwan University
- 2. Outline • Protein interactions: why bother? • Optical methods: SPRandBLI
- 3. Protein interactions – why bother?
- 4. Protein interactions control the lives ofcells Escherichiacoli drawn to molecular scaleby DavidGoodsell
- 6. LowAffinity Antigen:antibody Weakinteractions suchas ubiquitin:ubiquitinreceptor Most proteininteractions Moderate Affinity HighAffinity 104<Ka<108 M-1 Range of binding constants 103M-1 104M-1 108 M-1 >109M-1 Kd<10-4 M (mM) Ka<104 M-1 Protein interactions: binding affinity range 10-4 <Kd<10-8 M (mM –nM) Kd>10-9 M (nM) Ka>109 M-1
- 7. Dissociation constant: Kd 𝐾𝑑 𝑃𝐿 𝑃+ 𝐿 𝑘𝑜𝑓𝑓 [𝑃] 𝐿 𝐾𝑑 = [𝑃𝐿] = 𝑘𝑜 𝑛 M
- 9. Protein:DNA interaction Mixed-lineage leukemia: A type of childhood leukemia in which a piece of chromosome 11 has been translocated (broken off and attached itself to another chromosome). Children with this type of leukemia have a particularly poor prognosis (outlook). They do not respond at all well to the standard therapies for ALL (acute lymphoblastic or lymphocytic leukemia) and often suffer from early relapse after chemotherapy. On both the clinical and laboratory chromosome 11 childhood leukemia levels, appears therefore to be adistinctive diseaseand not asubset of ALL.Armstrong andcoworkers (Nature, Jan2002) named it "mixed-lineage leukemia.“ [MedicineNet.com] Heatabsorbed
- 10. Protein:cofactor interaction CAP:catabolite activator protein (dimer) cAMP:cyclic AMP
- 12. Surface plasmon resonance (SPR):Theory [Patching, Biochim. Biophys. Acta (2014)] Ligands
- 13. Surface plasmon resonance (SPR):Sensorgram [BiaCore]
- 14. Surface plasmon resonance (SPR):Components Microfluidics SensorChip DetectionSystem [BiaCore]
- 15. Surface plasmon resonance (SPR):Sensor chips SensorChip CM5 SensorChip CM4 SensorChip C1 Sensor Chip HP A SensorChip L1 CMdextran +Lipophilic Tail SensorChip NTA SensorChip CM3 SensorChip SA SensorChip AU [BiaCore]
- 16. Kinetic analysis: Why important? 100 pM 1nM 10nM 10pM 1 M 1mM 100 M Kd 100nM 10 M k o n (M -1 s - 1 ) 104 107 106 105 103 102 0.0001 0.001 0.1 1 -1 -1 kon(M s) koff(s-1) Kd = A B C 0.01 koff(s-1) [BiaCore]
- 17. Kinetic analysis: Sameaffinity, different kinetics Compare sensorgrams for three different interactions • Same1 nM affinity (Kd) • Different kinetics 2 0 100 4 6 8 h % blocked target 0 [BiaCore] 𝑘𝑑 𝐾𝑑= 𝑘𝑎
- 18. Thingsto consider: Analyteconcentration • Run analyses over a wide range of analyte concentrations, ideally 100-fold or more: The range should span 10x below the Kdto 10x above theKd. • Accurate analyte concentration iscritical! • Include azero-concentration sample in the analyses. [BiaCore] Toohighconcentration Toolow concentration Optimized