This document summarizes research to bioengineer a new red fluorescent protein tag from a cyanobacteriochrome found in Thermosynechococcus elongatus. The researchers aim to develop a small, photostable red tag as an alternative to commonly used green and yellow fluorescent proteins from jellyfish. They use molecular biology techniques like PCR, site-directed mutagenesis, and transfection of E. coli and mammalian cells to express and purify the mutated protein, which they characterize through spectroscopy and microscopy. The goal is to create a useful new tool for cellular imaging applications.
This document discusses recombinant DNA technology. It describes how recombinant DNA technology involves combining DNA fragments from different organisms. The basic steps are: 1) isolating a gene of interest, 2) inserting the fragment into a carrier DNA molecule to generate recombinant DNA, 3) transferring the recombinant DNA into E. coli host cells, and 4) selecting host cells carrying the recombinant DNA. Key tools used are restriction enzymes, which cut DNA at specific sites; vectors like plasmids, which are self-replicating DNA molecules that act as carriers; and host cells like E. coli bacteria.
Molecular techniques in food microbiologyNajiyaNaju1
This document discusses molecular techniques that are used in food microbiology. It describes several applications of molecular methods including detecting genetically modified foods, food authenticity testing, and microbial contamination detection. Common molecular methods described are PCR, RFLP, PFGE, and DNA microarrays. Specific techniques covered in more depth include real-time PCR, multiplex PCR, plasmid profiling, ribotyping, AFLP, LAMP, FISH, and biosensors. The document provides details on the basic principles and procedures for several of these important molecular analysis methods.
There are three main methods for isolating genes:
1. Using an automated gene machine to synthesize genes from predetermined nucleotide sequences.
2. Gene cloning, which involves inserting a DNA fragment into a vector that is then transferred into a host cell to produce multiple copies.
3. Polymerase chain reaction (PCR), which amplifies a specific DNA sequence using primers that flank the target sequence.
This document discusses recombinant DNA technology. It begins by defining recombinant DNA as DNA molecules formed by combining genetic material from multiple sources using genetic engineering techniques. The key steps involved are isolating genetic material, restriction enzyme digestion, amplification via PCR, ligating DNA molecules, inserting the recombinant DNA into a host, and isolating recombinant cells. The document then discusses each step in more detail and provides examples of applications like insulin production and Bt cotton. It concludes by noting some limitations like potential environmental impacts and vulnerability of cloned populations.
A panel of recombinant monoclonal antibodies against zebrafishShahnaz Yusaf
This document describes the development of 10 recombinant monoclonal antibodies against neural receptors and secreted proteins in zebrafish. The antibodies were generated by expressing the extracellular domains of the target proteins in mammalian cells and using them as antigens. The antibodies were characterized, cloned into expression plasmids, and shown to specifically stain their antigens in fixed zebrafish embryo tissues. The staining patterns matched the known expression patterns of the target genes, demonstrating these antibodies will be useful tools for studying neural development in zebrafish.
Recombinant DNA technology involves recombining DNA segments and allowing recombinant DNA molecules to enter cells and replicate. It was developed in 1973 by scientists Boyer and Cohen. The basic principle is to insert DNA into a vector, introduce it into a host cell where it replicates and produces the gene. Applications include producing human proteins like insulin through genetically engineered bacteria. Safety issues involve ensuring recombinant bacteria do not escape the laboratory and cause epidemics, which is addressed through physical and biological containment methods overseen by regulatory committees.
Recombinant DNA Technology - A Perforated Insight By Rxvichu !!RxVichuZ
Hello friends................................this is me....Vishnu,back after a gap of almost three weeks, with another powerpoint presentation on RECOMBINANT DNA TECHNOLOGY....
Prepared as per Pharmacology syllabus for thrird year Pharm.D students, this 40-slide ppt involves precise details on the following aspects:
1. DEFINITION
2. PRINCIPLES INVOLVED
3. ENZYMES AND VECTORS USED
4. METHODS OF GENE TRANSFER
5. APPLICATIONS OF RECOMBINANT DNA TECHNOLOGY
Not just for Pharm.D , i do sincerely hope that it will be useful for others, on a study or reference cum reading basis too...............
Do post ur feedbacks....
Suggestions for further improvement will be gratefully acknowledged..........
For further details, connect to me in :
Facebook : Rx Vishnu
Gmail: rxvichu623@gmail.com
watsapp and hike: 8086948729
communication: the same number as above.
Keep reading well....study well.................keep rocking!!!
@rxvichu-live 4 more!!!!
:) :)
This document discusses recombinant DNA technology. It describes how recombinant DNA technology involves combining DNA fragments from different organisms. The basic steps are: 1) isolating a gene of interest, 2) inserting the fragment into a carrier DNA molecule to generate recombinant DNA, 3) transferring the recombinant DNA into E. coli host cells, and 4) selecting host cells carrying the recombinant DNA. Key tools used are restriction enzymes, which cut DNA at specific sites; vectors like plasmids, which are self-replicating DNA molecules that act as carriers; and host cells like E. coli bacteria.
Molecular techniques in food microbiologyNajiyaNaju1
This document discusses molecular techniques that are used in food microbiology. It describes several applications of molecular methods including detecting genetically modified foods, food authenticity testing, and microbial contamination detection. Common molecular methods described are PCR, RFLP, PFGE, and DNA microarrays. Specific techniques covered in more depth include real-time PCR, multiplex PCR, plasmid profiling, ribotyping, AFLP, LAMP, FISH, and biosensors. The document provides details on the basic principles and procedures for several of these important molecular analysis methods.
There are three main methods for isolating genes:
1. Using an automated gene machine to synthesize genes from predetermined nucleotide sequences.
2. Gene cloning, which involves inserting a DNA fragment into a vector that is then transferred into a host cell to produce multiple copies.
3. Polymerase chain reaction (PCR), which amplifies a specific DNA sequence using primers that flank the target sequence.
This document discusses recombinant DNA technology. It begins by defining recombinant DNA as DNA molecules formed by combining genetic material from multiple sources using genetic engineering techniques. The key steps involved are isolating genetic material, restriction enzyme digestion, amplification via PCR, ligating DNA molecules, inserting the recombinant DNA into a host, and isolating recombinant cells. The document then discusses each step in more detail and provides examples of applications like insulin production and Bt cotton. It concludes by noting some limitations like potential environmental impacts and vulnerability of cloned populations.
A panel of recombinant monoclonal antibodies against zebrafishShahnaz Yusaf
This document describes the development of 10 recombinant monoclonal antibodies against neural receptors and secreted proteins in zebrafish. The antibodies were generated by expressing the extracellular domains of the target proteins in mammalian cells and using them as antigens. The antibodies were characterized, cloned into expression plasmids, and shown to specifically stain their antigens in fixed zebrafish embryo tissues. The staining patterns matched the known expression patterns of the target genes, demonstrating these antibodies will be useful tools for studying neural development in zebrafish.
Recombinant DNA technology involves recombining DNA segments and allowing recombinant DNA molecules to enter cells and replicate. It was developed in 1973 by scientists Boyer and Cohen. The basic principle is to insert DNA into a vector, introduce it into a host cell where it replicates and produces the gene. Applications include producing human proteins like insulin through genetically engineered bacteria. Safety issues involve ensuring recombinant bacteria do not escape the laboratory and cause epidemics, which is addressed through physical and biological containment methods overseen by regulatory committees.
Recombinant DNA Technology - A Perforated Insight By Rxvichu !!RxVichuZ
Hello friends................................this is me....Vishnu,back after a gap of almost three weeks, with another powerpoint presentation on RECOMBINANT DNA TECHNOLOGY....
Prepared as per Pharmacology syllabus for thrird year Pharm.D students, this 40-slide ppt involves precise details on the following aspects:
1. DEFINITION
2. PRINCIPLES INVOLVED
3. ENZYMES AND VECTORS USED
4. METHODS OF GENE TRANSFER
5. APPLICATIONS OF RECOMBINANT DNA TECHNOLOGY
Not just for Pharm.D , i do sincerely hope that it will be useful for others, on a study or reference cum reading basis too...............
Do post ur feedbacks....
Suggestions for further improvement will be gratefully acknowledged..........
For further details, connect to me in :
Facebook : Rx Vishnu
Gmail: rxvichu623@gmail.com
watsapp and hike: 8086948729
communication: the same number as above.
Keep reading well....study well.................keep rocking!!!
@rxvichu-live 4 more!!!!
:) :)
This document provides an overview of recombinant DNA technology. It defines recombinant DNA technology as procedures that allow DNA from different species to be isolated, cut, and spliced together to form new recombinant molecules. The key steps described are using restriction enzymes to cut DNA at specific sites, inserting genes into bacterial plasmids, transforming bacteria, replicating the recombinant DNA as the bacteria divide, and collecting the amplified genes. Applications discussed include producing insulin, vaccines, human growth hormones, diagnosing infectious diseases, developing novel crop varieties, and industrial strain improvement.
Recombinant DNA Technology and Drug DiscoveryAshok Jangra
In these slide I discuss about the various DNA Technology and their biological importance and modern uses of these technologies. Here I also discussed about the oligonucleotide and new pharmaceutical approaches.
Recombinant DNA refers to DNA molecules formed by combining DNA from different sources. It is produced artificially by joining DNA from different organisms. The pioneers who developed recombinant DNA technology were Paul Berg, Herbert Boyer, and Stanley Cohen in the 1970s. The process involves using restriction enzymes to cut DNA fragments, which are then joined to vector DNA and inserted into host cells where they can be replicated. This allows scientists to modify genes and study their functions.
Gene cloning involves inserting foreign DNA into bacterial plasmids. Restriction enzymes cut DNA at specific sites, creating sticky or blunt ends. Plasmids can replicate independently and accept foreign DNA fragments. The recombinant plasmid is inserted into bacteria via transformation or electroporation. Transformed bacteria are selected using antibiotics or blue-white screening to identify those containing the recombinant plasmid, allowing mass production of the cloned gene.
This document discusses various mechanisms for transforming and transfecting cells, including prokaryotic, eukaryotic, plant, and fungal cells. It describes the history of bacterial transformation and mechanisms such as natural competence, artificial competence using calcium chloride or electroporation, and lipofection. For eukaryotic transfection, it discusses lipofection, dendrimers, and nucleofection. It also outlines various mechanisms for transforming plants, including Agrobacterium, electroporation, viral transformation, and particle bombardment.
Recombinant DNA technology involves linking DNA fragments to self-replicating vectors to create recombinant DNA molecules, which are then replicated in a host cell. DNA is cut with restriction enzymes, isolated, and ligated into a cloning vector before being transformed into a host cell. Recombinant DNA technology is widely used in biotechnology, medicine, and research for applications such as producing insulin, developing drought-resistant crops, and creating recombinant vaccines.
Recombinant DNA technology involves combining DNA molecules from different sources and introducing them into host organisms. Some key points:
- Recombinant DNA is produced by joining DNA fragments from different sources using restriction enzymes and DNA ligase.
- Plasmids and bacterial cells are commonly used as vectors to replicate and express recombinant DNA. Foreign DNA is inserted into plasmids which are then introduced into bacterial cells.
- Restriction enzymes from bacteria are used to cut DNA at specific sequences. This allows insertion of foreign DNA. DNA ligase joins the DNA fragments back together.
- Applications include production of therapeutic proteins, genetic testing, gene therapy, and genetically modified crops. Recombinant DNA technology
The content is about the general description of genetic material and further two techniques of biotechnology. The content includes two topics.
Firstly with introduction to biotechnology it describe about DNA, recombinant DNA (rDNA) technology, history, goals, procedure of rDNA technology, tools, techniques, application, demerits and products of rDNA technology.
Second portion entitiled as Hybridoma technology. this includes the basic principle, production of monoclonal antibodies, merits demerits and drugs from monoclonal antibody.
New pharmaceuticals derived from biotechnology is covered in last. All the content is referred from books and internet sources.
This document discusses various gene transfer techniques called transfection. Transfection is the introduction of foreign DNA into eukaryotic cells, producing transfectants that have incorporated the DNA. Stable transfectants integrate the DNA while transient transfectants express genes briefly without integration. Methods include mechanical techniques like microinjection and bombardment, physical techniques like electroporation and liposomes, and viral vectors. Viruses commonly used include retroviruses, lentiviruses, adenoviruses, and adeno-associated viruses. Non-viral methods discussed are virus-like particles, single-walled carbon nanotubes, and polyamidoamine dendrimers. Overall, the document compares techniques and notes what is needed
Evolution of DNA Sequencing - talk by Jonathan Eisen for the Bodega Workshop ...Jonathan Eisen
This document contains slides for a talk on the evolution of DNA sequencing technologies. It reviews early manual sequencing methods developed by Sanger and others. It then summarizes the development of next-generation sequencing platforms including Roche 454 pyrosequencing, Illumina sequencing by synthesis, and others. The slides describe the key steps in library preparation, cluster generation, sequencing chemistry, and data analysis for various platforms. It provides a historical timeline of major advances that have enabled massive parallel sequencing of DNA.
Recombinant DNA technology allows DNA from different species to be isolated, cut with restriction enzymes, and spliced together to form new recombinant molecules. This involves extracting DNA, cutting it with restriction enzymes to form manageable fragments, inserting fragments into vectors like plasmids, introducing the recombinant vectors into host cells, and amplifying the DNA. Vectors often contain antibiotic resistance genes to select for host cells containing the recombinant DNA. This process allows scientists to isolate and multiply specific genes for study and modification.
Biotechnological tools used for diagnosticSunita Jak
This document discusses several biotechnological tools used for diagnostics:
1. DNA isolation, restriction enzyme digestion, polymerase chain reaction (PCR), gel electrophoresis, and DNA sequencing. PCR is described as artificially multiplying genetic material using primers and DNA polymerase. DNA sequencing methods like Sanger sequencing and Maxam-Gilbert are also outlined. The document concludes by briefly discussing gene cloning techniques like recombinant DNA technology and PCR for preparing copies of DNA fragments.
Plasmids are small, extra-chromosomal DNA molecules capable of replicating independently of chromosomal DNA. They are commonly used as vectors to introduce foreign DNA into host cells. Restriction enzymes cut DNA at specific recognition sequences and are used in molecular cloning. Various techniques like gel electrophoresis, Southern blot, and DNA microarrays can analyze DNA sequences.
Protoplasts are the cells of which cell walls are removed and cytoplasmic membrane is the
outermost layer in such cells.Protoplast can be obtained by specific lytic enzymes to remove
cell wall.Protoplast fusion is a physical phenomenon,during fusion two or more protoplasts
come in contact and adhere with one another either spontaneously or in presence of fusion
inducing agents.
This document summarizes recombinant DNA (rDNA) technology and genetic engineering. It discusses how restriction enzymes and DNA ligases are used to cut and paste DNA from different sources to create recombinant DNA molecules. It also describes genetically modified organisms (GMOs) and provides examples of transgenic organisms. Vectors such as plasmids are used to carry and replicate foreign DNA fragments in bacteria. Selection techniques like antibiotic resistance allow identification of transformed bacteria.
Construction of rDNA molecules and bacterial transformationT. Tamilselvan
Recombinant DNA technology involves introducing genes of interest into the genome of an organism using genetic engineering techniques. This is done by cutting DNA fragments using restriction enzymes, joining the fragments to a vector plasmid, and introducing the recombinant DNA or rDNA into a host cell. The host cell then replicates and produces multiple copies of the rDNA. This allows genes from one species to be introduced into another, such as joining human DNA to E. coli bacteria. The rDNA can then be used to produce beneficial proteins and genetically modified organisms.
This document discusses various chemical agents and methods used for cell transformation through transfection of foreign DNA. It describes factors that affect transfection efficiency, including host cell health and culture conditions as well as DNA quality and quantity. Common transfection methods are also outlined, such as cationic lipids, calcium phosphate, DEAE-Dextran, and magnet-mediated transfection. Each method is briefly explained and its pros and cons discussed.
The document summarizes steps taken to purify a fluorescent protein tag from a cyanobacteriochrome found in Thermosynechococcus elongatus, including:
1) Transforming E. coli with the gene for the cyanobacteriochrome tag and inducing protein expression.
2) Lysing the cells using a microfluidizer and centrifuging to remove cell debris.
3) Purifying the fluorescent tag protein using a chitin bead column.
4) Analyzing purity using SDS-PAGE gel electrophoresis and a spectrophotometer.
This document provides the timetable and protocols for a practical course on making and analyzing tRNA synthetases in vivo and using cell-free protein synthesis. Over two weeks, students will perform site-directed mutagenesis to produce mutant aminoacyl-tRNA synthetases, express their proteins in E. coli cells and purify the proteins, and use cell-free synthesis to attempt incorporating a phosphotyrosine analogue into a target protein using their mutant synthetases and suppressor tRNA. The document outlines the experimental steps, including mutagenesis, transformation, plasmid preparation, sequencing, protein expression and purification, cell-free reaction set up, and analysis by SDS-PAGE. Safety procedures are also described to handle
This document provides an overview of recombinant DNA technology. It defines recombinant DNA technology as procedures that allow DNA from different species to be isolated, cut, and spliced together to form new recombinant molecules. The key steps described are using restriction enzymes to cut DNA at specific sites, inserting genes into bacterial plasmids, transforming bacteria, replicating the recombinant DNA as the bacteria divide, and collecting the amplified genes. Applications discussed include producing insulin, vaccines, human growth hormones, diagnosing infectious diseases, developing novel crop varieties, and industrial strain improvement.
Recombinant DNA Technology and Drug DiscoveryAshok Jangra
In these slide I discuss about the various DNA Technology and their biological importance and modern uses of these technologies. Here I also discussed about the oligonucleotide and new pharmaceutical approaches.
Recombinant DNA refers to DNA molecules formed by combining DNA from different sources. It is produced artificially by joining DNA from different organisms. The pioneers who developed recombinant DNA technology were Paul Berg, Herbert Boyer, and Stanley Cohen in the 1970s. The process involves using restriction enzymes to cut DNA fragments, which are then joined to vector DNA and inserted into host cells where they can be replicated. This allows scientists to modify genes and study their functions.
Gene cloning involves inserting foreign DNA into bacterial plasmids. Restriction enzymes cut DNA at specific sites, creating sticky or blunt ends. Plasmids can replicate independently and accept foreign DNA fragments. The recombinant plasmid is inserted into bacteria via transformation or electroporation. Transformed bacteria are selected using antibiotics or blue-white screening to identify those containing the recombinant plasmid, allowing mass production of the cloned gene.
This document discusses various mechanisms for transforming and transfecting cells, including prokaryotic, eukaryotic, plant, and fungal cells. It describes the history of bacterial transformation and mechanisms such as natural competence, artificial competence using calcium chloride or electroporation, and lipofection. For eukaryotic transfection, it discusses lipofection, dendrimers, and nucleofection. It also outlines various mechanisms for transforming plants, including Agrobacterium, electroporation, viral transformation, and particle bombardment.
Recombinant DNA technology involves linking DNA fragments to self-replicating vectors to create recombinant DNA molecules, which are then replicated in a host cell. DNA is cut with restriction enzymes, isolated, and ligated into a cloning vector before being transformed into a host cell. Recombinant DNA technology is widely used in biotechnology, medicine, and research for applications such as producing insulin, developing drought-resistant crops, and creating recombinant vaccines.
Recombinant DNA technology involves combining DNA molecules from different sources and introducing them into host organisms. Some key points:
- Recombinant DNA is produced by joining DNA fragments from different sources using restriction enzymes and DNA ligase.
- Plasmids and bacterial cells are commonly used as vectors to replicate and express recombinant DNA. Foreign DNA is inserted into plasmids which are then introduced into bacterial cells.
- Restriction enzymes from bacteria are used to cut DNA at specific sequences. This allows insertion of foreign DNA. DNA ligase joins the DNA fragments back together.
- Applications include production of therapeutic proteins, genetic testing, gene therapy, and genetically modified crops. Recombinant DNA technology
The content is about the general description of genetic material and further two techniques of biotechnology. The content includes two topics.
Firstly with introduction to biotechnology it describe about DNA, recombinant DNA (rDNA) technology, history, goals, procedure of rDNA technology, tools, techniques, application, demerits and products of rDNA technology.
Second portion entitiled as Hybridoma technology. this includes the basic principle, production of monoclonal antibodies, merits demerits and drugs from monoclonal antibody.
New pharmaceuticals derived from biotechnology is covered in last. All the content is referred from books and internet sources.
This document discusses various gene transfer techniques called transfection. Transfection is the introduction of foreign DNA into eukaryotic cells, producing transfectants that have incorporated the DNA. Stable transfectants integrate the DNA while transient transfectants express genes briefly without integration. Methods include mechanical techniques like microinjection and bombardment, physical techniques like electroporation and liposomes, and viral vectors. Viruses commonly used include retroviruses, lentiviruses, adenoviruses, and adeno-associated viruses. Non-viral methods discussed are virus-like particles, single-walled carbon nanotubes, and polyamidoamine dendrimers. Overall, the document compares techniques and notes what is needed
Evolution of DNA Sequencing - talk by Jonathan Eisen for the Bodega Workshop ...Jonathan Eisen
This document contains slides for a talk on the evolution of DNA sequencing technologies. It reviews early manual sequencing methods developed by Sanger and others. It then summarizes the development of next-generation sequencing platforms including Roche 454 pyrosequencing, Illumina sequencing by synthesis, and others. The slides describe the key steps in library preparation, cluster generation, sequencing chemistry, and data analysis for various platforms. It provides a historical timeline of major advances that have enabled massive parallel sequencing of DNA.
Recombinant DNA technology allows DNA from different species to be isolated, cut with restriction enzymes, and spliced together to form new recombinant molecules. This involves extracting DNA, cutting it with restriction enzymes to form manageable fragments, inserting fragments into vectors like plasmids, introducing the recombinant vectors into host cells, and amplifying the DNA. Vectors often contain antibiotic resistance genes to select for host cells containing the recombinant DNA. This process allows scientists to isolate and multiply specific genes for study and modification.
Biotechnological tools used for diagnosticSunita Jak
This document discusses several biotechnological tools used for diagnostics:
1. DNA isolation, restriction enzyme digestion, polymerase chain reaction (PCR), gel electrophoresis, and DNA sequencing. PCR is described as artificially multiplying genetic material using primers and DNA polymerase. DNA sequencing methods like Sanger sequencing and Maxam-Gilbert are also outlined. The document concludes by briefly discussing gene cloning techniques like recombinant DNA technology and PCR for preparing copies of DNA fragments.
Plasmids are small, extra-chromosomal DNA molecules capable of replicating independently of chromosomal DNA. They are commonly used as vectors to introduce foreign DNA into host cells. Restriction enzymes cut DNA at specific recognition sequences and are used in molecular cloning. Various techniques like gel electrophoresis, Southern blot, and DNA microarrays can analyze DNA sequences.
Protoplasts are the cells of which cell walls are removed and cytoplasmic membrane is the
outermost layer in such cells.Protoplast can be obtained by specific lytic enzymes to remove
cell wall.Protoplast fusion is a physical phenomenon,during fusion two or more protoplasts
come in contact and adhere with one another either spontaneously or in presence of fusion
inducing agents.
This document summarizes recombinant DNA (rDNA) technology and genetic engineering. It discusses how restriction enzymes and DNA ligases are used to cut and paste DNA from different sources to create recombinant DNA molecules. It also describes genetically modified organisms (GMOs) and provides examples of transgenic organisms. Vectors such as plasmids are used to carry and replicate foreign DNA fragments in bacteria. Selection techniques like antibiotic resistance allow identification of transformed bacteria.
Construction of rDNA molecules and bacterial transformationT. Tamilselvan
Recombinant DNA technology involves introducing genes of interest into the genome of an organism using genetic engineering techniques. This is done by cutting DNA fragments using restriction enzymes, joining the fragments to a vector plasmid, and introducing the recombinant DNA or rDNA into a host cell. The host cell then replicates and produces multiple copies of the rDNA. This allows genes from one species to be introduced into another, such as joining human DNA to E. coli bacteria. The rDNA can then be used to produce beneficial proteins and genetically modified organisms.
This document discusses various chemical agents and methods used for cell transformation through transfection of foreign DNA. It describes factors that affect transfection efficiency, including host cell health and culture conditions as well as DNA quality and quantity. Common transfection methods are also outlined, such as cationic lipids, calcium phosphate, DEAE-Dextran, and magnet-mediated transfection. Each method is briefly explained and its pros and cons discussed.
The document summarizes steps taken to purify a fluorescent protein tag from a cyanobacteriochrome found in Thermosynechococcus elongatus, including:
1) Transforming E. coli with the gene for the cyanobacteriochrome tag and inducing protein expression.
2) Lysing the cells using a microfluidizer and centrifuging to remove cell debris.
3) Purifying the fluorescent tag protein using a chitin bead column.
4) Analyzing purity using SDS-PAGE gel electrophoresis and a spectrophotometer.
This document provides the timetable and protocols for a practical course on making and analyzing tRNA synthetases in vivo and using cell-free protein synthesis. Over two weeks, students will perform site-directed mutagenesis to produce mutant aminoacyl-tRNA synthetases, express their proteins in E. coli cells and purify the proteins, and use cell-free synthesis to attempt incorporating a phosphotyrosine analogue into a target protein using their mutant synthetases and suppressor tRNA. The document outlines the experimental steps, including mutagenesis, transformation, plasmid preparation, sequencing, protein expression and purification, cell-free reaction set up, and analysis by SDS-PAGE. Safety procedures are also described to handle
The researchers aimed to bioengineer a new red fluorescent protein tag from cyanobacteriochromes in Thermosynechococcus elongatus. They transfected Jurkat cells with plasmids containing fluorescent protein tags for visualization under advanced microscopes. Electroporation and the plasmid pAcGFP1-Tubulin were found to be most efficient for transfection. Future goals include optimizing expression of their engineered 569 fluorescent tag in mammalian cells.
Next generation-sequencing.ppt-convertedShweta Tiwari
The advance version, sequences the whole genome efficiently with high speed and high throughput sequencing at reduce cost is termed as Next Generation Sequencing (NGS) or massively parallel sequencing (MPS).
Foreign genes can be expressed in both prokaryotic and eukaryotic systems. Recombinant proteins have many pharmaceutical and industrial uses. Prokaryotic expression is faster and cheaper but some eukaryotic proteins may lack proper processing. Eukaryotic systems like yeast, insect cells and mammalian cells allow for proper post-translational modifications but are more complex and expensive. The choice of expression system depends on the desired protein properties and costs involved.
The document discusses developing a DNA vaccine for fish using chitosan nanoparticles to deliver plasmid DNA encoding the OMP38 gene of Vibrio anguillarum. Key points:
- Chitosan nanoparticles were developed to deliver the pVAOMP38 plasmid and protect it from nuclease degradation. Studies showed the nanoparticles maintained plasmid integrity.
- The pVAOMP38 plasmid was transfected into seabass kidney cells in vitro and shown to express.
- Fish were vaccinated by feeding with chitosan-pVAOMP38 nanoparticles, chitosan-empty vector, or chitosan alone. The fish were later challenged with V. anguillarum to evaluate vaccine efficiency.
This document discusses the use of fluorescent proteins in current biological research. It begins with an overview of the development of optical microscopy and fluorescence techniques. It then focuses on the green fluorescent protein (GFP) and how it has been used as a molecular tag to study protein expression and interactions in living cells through techniques like gene delivery, transfection, viral infection, FRET, and optogenetics. The document concludes that fluorescent proteins have revolutionized cell biology by enabling the real-time visualization and control of molecular pathways and signaling processes in living systems.
Recombinant protein expression and purification Lecturetest
The document discusses recombinant protein expression and engineering. It describes:
1) Cloning or synthesizing the gene of interest, making an expression construct, transfecting cells, purifying the recombinant protein.
2) Factors to consider like the protein's origin (prokaryotic/eukaryotic), required post-translational modifications, and available expression systems.
3) A case study expressing recombinant human alpha-1-acid glycoprotein in E. coli, including vector construction, periplasmic extraction, affinity purification, and yield.
Analysis of Peroxisomal Lipid Metabolism in the Oleaginous Microalga Nannochloropsis and Development of Synthetic Biology Tools for Genetic Engineering
Describe the application of DNA profiling in paternity tests and forensic investigations
Analyze DNA profiles to draw conclusions about paternity tests and forensic investigations.
Western blotting is a technique used to detect specific proteins in a sample:
1) Proteins are first separated by electrophoresis and then transferred to a membrane for detection.
2) Antibodies are used to detect the target protein(s) on the membrane through binding.
3) An enzyme-linked secondary antibody is used to visualize the bound primary antibodies, allowing visualization of bands that correspond to the target proteins.
GEL ELECTROPHORESIS WITH BLOT TECHNIQUES.pptxDheeraj Saini
This document provides an overview of gel electrophoresis and blotting techniques. It describes how gel electrophoresis uses a gel matrix to separate macromolecules like DNA, RNA, and proteins based on size and charge when an electric current is applied. The document then discusses different types of gel electrophoresis including agarose gel electrophoresis, polyacrylamide gel electrophoresis, and starch gel electrophoresis. It also summarizes common blotting techniques like Southern blotting for detecting DNA, Northern blotting for detecting RNA, and Western blotting for detecting proteins. The document provides details on the basic principles and procedures for each technique.
The document describes a new fluorescent biosensor platform called Nomad that can measure changes in intracellular second messenger concentrations after GPCR activation in live cells. The Nomad biosensors localize to the plasma membrane but undergo a conformational change and vesicularization upon increases in second messengers like cAMP, calcium, or DAG. This allows their redistribution to be detected using high-content screening. The biosensors come in three versions corresponding to different second messengers and can be multiplexed to simultaneously measure different signaling pathways and receptor internalization. The Nomad biosensors provide a robust, homogeneous, and reagent-free assay for high-throughput screening of GPCR activity.
The document describes a microarray study to analyze gene expression in atherosclerotic plaques and correlate it with factors related to plaque vulnerability. Specimens will be obtained from human carotid/coronary arteries and atherosclerotic plaques in mouse models. Gene expression will be profiled using microarrays and correlated with histopathology, pH, temperature, spectroscopy and other variables. The goal is to identify genes associated with vulnerable plaques and rupture. Plaques from influenza-infected and drug-treated mice will also be analyzed to study effects on gene expression and plaque structure.
132 gene expression in atherosclerotic plaquesSHAPE Society
This document discusses microarray studies to analyze gene expression in atherosclerotic plaques and correlate it with factors related to plaque vulnerability. It begins with background on the history and applications of DNA microarrays. Key steps discussed include probe design, sample preparation including tissue collection, labeling RNA samples, hybridizing samples to a microarray chip, scanning and analyzing image data. The document outlines creating a custom microarray based on selected genes and correlating gene expression with temperature, pH, spectroscopy and histopathology of plaques. It will also analyze gene expression in influenza-infected mice and mice where plaques are induced to rupture with drugs. Human carotid artery specimens from surgery will be analyzed from symptomatic and asymptomatic patients.
The document describes a microarray study to analyze gene expression in atherosclerotic plaques and correlate it with factors related to plaque vulnerability. Specimens will be obtained from human carotid/coronary arteries and atherosclerotic plaques in mouse models. Gene expression will be profiled using microarrays and correlated with histopathology, pH, temperature, spectroscopy and other variables. Plaques from influenza-infected and drug-treated mice will also be analyzed to identify genes associated with plaque rupture. The goal is to better understand plaque vulnerability and identify potential drug targets.
This document provides an overview of DNA cloning including:
1. The basic steps in DNA cloning including isolation of vector and gene source DNA, insertion into the vector, and introduction into cells.
2. Uses of polymerase chain reaction and restriction enzymes in cloning.
3. Applications of cloning such as recombinant protein production, genetically modified organisms, DNA fingerprinting, and gene therapy.
This document discusses materials and methods used in a study involving the chemical fipronil and zinc. Twenty male albino rats were divided into four groups of five rats each: a control group, a zinc group that received zinc supplementation, a fipronil group exposed to the insecticide fipronil, and a combination group exposed to both zinc and fipronil. Biochemical assays were conducted to assess oxidative stress markers like superoxide dismutase, catalase, glutathione peroxidase, glutathione-S-transferase, glutathione, lipid peroxidation, and total protein in the rats. Chemicals used including fipronil and zinc sulfate were obtained from reputable suppliers. Kits for the biochemical assays were purchased from a diagnostic
Proteomics in VSC for crop improvement programmeSumanthBT1
Proteomics techniques such as gel electrophoresis and mass spectrometry are used to separate and identify proteins. Two-dimensional gel electrophoresis separates proteins by size and charge, while MALDI-TOF mass spectrometry relies on mass spectrometry to analyze proteins and peptides. Protein-protein interactions can be studied using techniques like yeast two-hybrid systems and co-immunoprecipitation. Databases such as UniProt, PDB, and KEGG provide information on protein sequences, structures, and pathways.
Similar to Congreso de Biotecnología Arequipa Perú June 2011 (20)
This student worksheet contains questions about a pGLO bacteria transformation experiment. It asks the student to define terms related to the experiment such as GFP, transgenic, E. coli, plasmids, ampicillin, and arabinose. It also asks how the student will know if the experiment was successful.
The Spiller Lab at Rutgers University studies transgenic organisms. Their goal is to create a transgenic bacteria that glows in the dark by taking the GFP gene from jellyfish and inserting it into E. coli bacteria. The GFP gene will be inserted into the bacterial DNA using a plasmid called pGLO. This will allow the bacteria to produce green fluorescent protein and glow, while also conferring resistance to ampicillin, allowing the bacteria to grow on nutrient plates containing the antibiotic.
1. The document provides instructions for a PGLO lab practice involving transforming E. coli bacteria with plasmid DNA.
2. The instructions include labeling micro test tubes, spreading bacteria on agar plates, heat shocking bacteria to allow plasmid entry, and incubating plates overnight to allow bacterial growth.
3. Students are asked to cut out descriptions of 12 steps and match them to diagrams showing how to complete the bacterial transformation protocol.
The document is a worksheet that asks a student to determine which of 10 animals are most closely related by matching them in pairs. It provides the names of 10 animals - African elephant, kangaroo, horseshoe crab, dugong, crocodile, mountain gorilla, ring-tailed lemur, nine-banded armadillo, three-toed sloth, brown recluse spider, emperor penguin, and possum. The student is instructed to match the animals in pairs of the most closely related.
Manatees are large, slow-moving aquatic mammals that inhabit coastal waters and rivers. They can grow up to 13 feet long and weigh over 1,300 pounds. Despite their massive size, manatees are graceful swimmers that typically glide at 5 miles per hour but can burst up to 15 miles per hour. Manatees give birth underwater and mothers help their calves reach the surface for their first breath. Manatees are herbivores that consume large amounts of water plants. They are classified as endangered due to hunting and accidental collisions with boats.
The document provides instructions for an activity where students are asked to match animals based on which are most closely related. It lists 12 animals and has students work with a partner to determine relationships between the animals. It then has them write down the correct matches.
Elephants have evolved over millions of years from small forest-dwelling animals to the large land mammals we know today. Early elephant ancestors were about the size of a dog and lived in forests in Africa and Asia as far back as 60 million years ago. Over generations, natural selection led to elephants growing larger in size to survive in more open grassland habitats, developing trunks and tusks, and living in herds for protection and survival.
Dugongs are large marine mammals that graze on seagrasses along coastlines from East Africa to Australia. They can stay underwater for up to six minutes and breathe either by fully surfacing or standing on their tails. Dugongs spend most of their time alone or in small groups but sometimes gather in large herds, and mothers care for calves for around 18 months. Although now protected, dugongs were historically hunted for their meat and other products, and their populations remain vulnerable.
Birds have different types of beaks adapted for eating different kinds of food. The worksheet matches bird beaks to tools that represent their beak functions and has students hypothesize what each bird eats based on its beak. To test their hypotheses, students will need to research each bird species to determine if their predictions about the birds' diets match the actual types of food each bird eats in the wild.
This document describes the beaks, diets, and habitats of various bird species from around the world. It discusses African spoonbills, lesser flamingos, yellow-naped amazon parrots, speckled pigeons, white-faced whistling ducks, griffon vultures, red-billed hornbills, hammerkops, Egyptian geese, chestnut mandibled toucans, blue and yellow macaws, king penguins, and Magellanic penguins. Each entry provides details about the bird's taxonomy, geographical range, habitat, and diet that is adapted to its particular beak type.
Este documento proporciona instrucciones para un taller sobre la transformación de bacterias con el plásmido pGLO y la posterior purificación de la proteína GFP. El taller se llevará a cabo en dos días, comenzando con la transformación bacteriana con pGLO para inducir la resistencia a ampicilina y la expresión de GFP, seguido del cultivo bacteriano y la inducción de GFP con arabinosa.
Are you interested in the pGLO™ experiment? Learn more about this hands-on laboratory activity with a FREE download of BioRad’s pGLO™ experiment power point.
The document discusses engineering a red fluorescent protein tag from the cyanobacterium Thermosynechococcuselongatus for use as an easily detectable protein marker. The tag would respond to different light wavelengths and could be used to study protein expression and transformation in T. elongatus cells. Existing green fluorescent protein tags from jellyfish require a different light wavelength to be detected. The engineered red tag would use the GAF domain protein and phycocyanobilin chromophore from T. elongatus to fluorescently label and image proteins when expressed in host cells.
This document summarizes a student research project on bioengineering fluorescent protein tags from cyanobacteriochromes found in Thermosynechococcus elongatus BP-1. The student presented on expressing genes from T. elongatus that produce cyanobacteriochromes, which are light-sensitive blue/green pigments, in E. coli cells. The goal was to engineer red fluorescent cyanobacteriochromes by using a two-plasmid system involving genes for heme oxygenase and reductase in E. coli cells containing the cyanobacteriochrome genes.
The researcher expressed the wrong fluorescent protein from Thermosynechococcus elongatus, with the pelleted proteins being blue instead of the expected yellow. Through DNA sequencing and comparison to published sequences, they determined the expressed protein was gene 0569 instead of the target gene 0911. Contamination of samples or mislabeling likely occurred. The researcher took steps to verify the correct gene, such as sequencing plasmid DNA from older stock and improving lab techniques, to obtain the expected yellow fluorescent protein in future expressions.
Stay informed! Mills CBST is funded by the National Science Foundation, Chemical, Bioengineering, Environmental, and Transport Systems (CBET) division. This highlight describes in detail the work of Mills CBST, led by Dr. Susan Spiller.
1. Bioengineering fluorescent tags from phytochromes found in Thermosynechococcus elongatus Mills CBST Research Project 2011 Presented by Rosa Meza-Acevedo, Alexandria Magallan Tianling Ou, with support from Susan C. Spiller, PI
2. Mills College Center for Biophotonics, Science and Technology (CBST) Bioengineer a fluorescent tag Easy-to-detect protein marker Respond to different wavelengths of light Reporter of protein expression Photographs made at CBST – UC Davis
3. Bioengineering A Fluorescent Tag “DNA for fluorescent tag” can be bioengineered. In our work, we have engineered a nucleic acid sequence that will be translated into the fluorescent protein that we want. Modified from: http://www.biology.duke.edu/model-system/ymsg/cloning.html
4. Introduce the Bioengineered Fluorescent Tagged protein into a living cell Transfection Plasmid with new DNA & tag Nucleus Modified from: http://www.biology.duke.edu/model-system/ymsg/cloning.html
5. Transfected Eukaryotic Cell Containing Bioengineered Plasmid with Fluorescent tag Modified from: http://www.biology.duke.edu/model-system/ymsg/cloning.html
6. Our Research Goal Bioengineer a small, red fluorescent tag from a cyanobacteriochrome found in Thermosynechococcus elongatus Develop this tag to be useful in cellular imaging techniques in vitro and eventually in vivo
7. Our Research Goal Bioengineer a new red fluorescent tag Red illumination of the cytoskeleton Images modified from: cbst.ucdavis.edu
29. Schematic model of the GAF domain and its associated chromophore Chromophore in the GAF binding pocket of protein
30. Procedure PCR genomic DNA Restriction enzyme and Ligation Site-Directed Mutagenesis Protein Purification Transformation Protein Expression Visualization! SDS-PAGE gel and Transblot Transfection
31. PCR genomic DNA: Genomic DNA from T. elongatusand primers are used in PCR to capture GAF domain only, with the appropriate restriction enzyme recognition sequences at each end. -- Genomic DNA gift from Dr. Ikeuchi, University of Tokyo, and Dr. J. Clark Lagarias, University of California, Davis
32. Restriction Enzyme and Ligation After we obtain the GAF domain with recognition sites at each end from PCR, it is digested with the restriction enzymes, and then ligated by annealing to the sticky ends of the pBAD plasmid, which has been prepared by digesting with the same enzyme. pBAD + inserted GAF domain (569)
33. Rolling Circle Site-Directed Mutagenesis: Mutating Cysteine Aspartate Absorb light in the red region Prevent photoreversibility Fluorescence Mutated plasmid
34. Mutation of Cysteine (C) in the GAF domain of 569T TGTGAT GGGTTGGCCACAAGCTCGAGATCAGGTAATTGATTGAGCAGGCAGCC AAATGTGCAGATTGCTTACGTCAGGCTGCGGTGCAGTTAAGTGAGTTG CGCGATCGCCAAGCCATTTTTGAGACCCTTGTGGCAAAGGGCCGTGA ACTATTGGCCTGCGATCGTGTCATTGTCTATGCCTTTGATGACAACTAT GTGGGAACAGTCGTAGCCGAGTCGGTGGCAGAAGGATCCCTGTTTCC GCGAACACTGGGTAGAGGCCTACCGCCAGGGCCGCATTCAAGCCACG ACGGATATTTTCAAGGCAGGGCTAACGGAGTGTCACCTGAATCAACTC CGGCCCCTCAAGGTTCGGGCAAATCTTGTCGTGCCGATGGTGATCGA CGACCAACTTTTTGGTCTCCTGATTGCCCACCAGTGCAGTGAACCACG CCAGTGGCAGGAGATCGAGATTGACCAATTCAGTGAACTGGCGAGCA CCGGCAGCCTTGTCCTGGAGCGTCTCCATTTCCTTGAGCAGCCCGGG
41. Protein Purification Mechanical Cell Lysis Extract crude protein from cells Centrifuge to separate soluble protein from cells Next Step: Chitin binding www.diversified-equipment.com Microfluidizer http://www.microfluidicscorp.com/
44. SDS-PAGE The process of using an electric current to separate bands of proteins. Determine the purity of the isolated protein. Pure protein is indicated by a single band of a particular size The size of the protein can be determined
45. SDS – sodium dodecyl sulfate Charged groups Anionic detergent Proteins denature Negative charge on proteins Hydrophobic regions http://www.bio.davidson.edu/courses/genomics/method/SDSPAGE/SDSPAGE.html#SDS
46. PAGE – PolyAcrylamide Gel Electrophoresis Gel restrains large molecules from migrating as fast as smaller molecules Two gel layers 12% Resolving – pH 8.8 4% Stacking – pH 6.68
47. Preparing PolyAcrylimide Gel http://upload.wikimedia.org/wikipedia/commons/7/75/SDS-PAGE_Acrylamide_gel.png- Modified
48. Running Gel-Electrophoresis Glass gel cassettes Blue = Negative Red = Positive Protein Sample Inner chamber Outer Chamber Electrode assembly Lid Mini Tank Power Source http://upload.wikimedia.org/wikipedia/commons/4/46/SDS-PAGE_Electrophoresis.png - Modified
51. Transfection The process of introducing nucleic acids into eukaryotic cells Opening transient pores in the cell membrane to allow the uptake of material There are biochemical methods and physical methods
52. Physical Method of Transfection: Electroporation Use of high-voltage electric pulse to perturb the cell membrane and form transient pores, introducing DNA Highly efficient for the introduction of foreign genes in tissue culture cells, especially mammalian cells
54. Transfection to Jurkat Cells http://www.clontech.com/images/pt/PT3827-5.pdf Plasmid we currently use for transfection Jurkat Cells that are transfected by pDsRed-Monmer-Actin
56. A video from CBST, taken on a deconvolution microscope
Editor's Notes
project based on a bacterium that can produce cyanobacteriochromes. The Thermosynechococcus elongatus. I will refer to this bacterium as T. elongatus as short. Thermo SIN A CO COCK uss
We are part of a group called Mills College Center for Biophotonics, Science and Technology in Oakland, California. The main goal of this group is to bioengineer fluorescent proteins. Definition: Biophotonics = the study of the interaction of light with biological material- where “light” includes all forms of radiant energy whose quantum unit is the photonCells pic – Image to your left is Human lymphocyte cell, called a Jurkat E6-1 Cell in the middle is a Jurkat labeled with GFP, Cell on the right is a Jurkat labeled with DsRed-Monomer.Mouse picFluorescent tags are easy to detect protein markers that can be inserted into a living organism. Different fluorescent tags respond to certain excitation wavelengths of light. For example, in the image to your right there are 6 genetically engineered rats. Of the 6, 3 are fluorescing bright green under UV light because they are expressing www.teachengineering.org/view_activity.php?ur...a green fluorescent protein otherwise known as GFP. GFP was cloned from jellyfish over 30 years ago. It’s primary use is to report successful protein expression. Under UV light, we can see that the rats that are fluorescing green are the rats that have successfully synthesized the bioengineered tag. Most times these tags will include additional genetic changes, so the glow factor serves as a reporter of which rat has these changes in their DNA. GFP is a widely used fluorescent protein in bio imaging, however, each year new fluorescent proteins are being developed to improve bio imaging techniques.
DNA RNA ProteinSite directed mutagenesis is used to make a specific amino acid change by altering DNA at the appropriate location on the geneThe changed codon results in a changed protein after transcription and translationRestriction enzyme digestion---we cut the plasmid open and the ends of our PCR product so that the sticky ends match and orientation of our insert will be correct.Here (below, in the box) we need to show one of our genescut out the GAF domainmutate it to achieve flourescence. Then in the next slide this piece of DNA is added to the protein of interest. Make the tag look red to make our point later about our goalem out of plasmids and then reinsert them into dna.WORK ON THIS
DNA RNA ProteinSite directed mutagenesis is used to make a specific amino acid change by altering DNA at the appropriate location on the geneThe changed codon results in a changed protein after transcription and translationRestriction enzyme digestion---we cut them out of plasmids and then reinsert them into dna.WORK ON THIS
DNA RNA ProteinSite directed mutagenesis is used to make a specific amino acid change by altering DNA at the appropriate location on the geneThe changed codon results in a changed protein after transcription and translationRestriction enzyme digestion---we cut them out of plasmids and then reinsert them into dna.WORK ON THIS
Add a red fluorescent tag to the cytoskeleton of a lymphocyte to … traffic controlIlluminating features of traffic control…maybe add an image
Add a red fluorescent tag to the cytoskeleton of a lymphocyte to … traffic controlIlluminating features of traffic control…maybe add an image
These truncated cyanobacteriochromes have much shorter amino acids sequence than previously characterized Infrared Fluorescent Proteins (IFPs). For instance, 569 has a sequence of 174 amino acids, while the GFP has over 200 amino acids.Red wavelengths will panatrate through tissues farther than green wavelength. SmuRF:SmuRF stands for small unexpected red fluorescent tag, which is our goal of protein tag.Red wavelengths will panatrate through tissues farther than green wavelength.
Currently, scientists use market fluorescent tags such as GFP for their imaging protocols. These tags have an emission spectrum that is close to UV light. This limits the capacity to work in vivo however, as UV light damages living cells. In addition, these fluorescent tags are subject to photobleaching. Because most scientific experiments using fluorescent tags require a specific amount of time under light in order to excite these molecules into fluorescence. However, prolonged exposure eventually results in the destruction of these same cells. This presents a major issue in visualization.Modifications have been made to GFP and the family of jellyfish proteins to lengthen its wavelength of emission up to about orange. Also, market fluorescent tags have a longer amino acid sequence. The longer the amino acid sequence, the more obstruction=more chances of structural damage to the cellProduce Reactive oxygen molecule which causes chemical damage to the cell
One of the major goals in new fluorescent tag development is to construct a fluorescent protein that has better imaging properties than those found in marketed fluorescent tags. Currently, we are working with fluorescent tags found in proteins from cyanobacteria. These proteins fluoresce a brighter red color which is better for bio imaging. Bright red fluorescent tags can be seen under a wider range of microscopes for cellular AND subcellular views which means there is an increased capacity to image the entire animal travels through tissue (red light). Also, these tags are not subject to photobleaching, and with a shorter amino acid sequence they are less obstructive to the proteinsModifications have been made to GFP and the family of jellyfish proteins to lengthen its wavelength of emission up to about orange.
T.Elongatus is a cyano bacteria. Cyanobacteria makes cyanobacteriochromes. These cyanobacteriochromes are homologous to plant phytochromes. They also show photoreversibility. Photoreversibility is the ability for the chromophore to absorb light energy and convert the protein to which it is covalently bound into inactive and active forms in response to different wavelengthsModel organism for investigating photosynthesis. Thermophilic unicellular rod shaped cyanobacterium that lives in hot sprinfs Define the importance of a “stable” protein: easier to work with in the lab and to replicate and also bc they have to exist under higher temperatures.Plants use phytochromes as sensors to modify their growth and development, constituting “shade avoidance syndrome”---for example, when a plant is shaded by another plant in a canopy, the phytochrome species will interconvert between red and far red, thus initiating transcriptional signaling cascades. This signaling cascade will then cause the plant to elongate and project its leaves into regions of sunlight.
There are 5 cyanobacteriochromes but over the summer we focused our experiments on 2: 569 and 899. Both of these exhibit multiple protein domains, which are units of protein structure. We are only interested in the GAF domainEach of these phytochrome-like proteins consist of a protein + bilin chromophore. Protein domain consists of several different domains but we are interested in the GAF domain because it is known to bind to the chromophore.Each of these phytochrome-like proteins consist of a protein + bilin chromophore. Protein domain consists of several different domains but we are interested in the GAF domain because it is known to bind to the chromophore. (CHROMPHORE ABSORBS THE PHOTONS TO GIVE IT LIGHT SENSING CAPABILITIES SO PROTEIN CAN BECOME REACTIVE) (ENERGY CAUSES CHROMOPHORE TO ROTATE THUS CHANGING SHAPE OF PROTEIN MAKING IT CATALYTICALLY ACTIVE---SAS)So, now that I have explained what site directed mutagenesis is, we can talk more about our cyanobacteriochromes of interest which are 569 and 899. Both of them have undergone what we call a truncation, which will be represented later with a T, and a truncation mutation, represented as TM. The important thing to remember is that we are only working with the GAF domain which is why we need a truncation to shorten the DNA sequence of the cyanobacteriochromeAdd the phylogentic tree of cyanobacteriochrome.We decided to use the GAF domain only because it is the smallest part/within the protein that could bind the chromophore. The chromophore is absolutely essential for sensitivity to photons. Our project engineers regions of the GAF domain in order to choose the particular wavelength we wish to capture. For example, we wish to absorb red photons in order to fluorescent longer red photons.
class II Phr proteins. or cyanobacteriochromes, all contain the six Amino Acid identifying motif = XDXCFX (green). This means - any nucleic acid (X), aspartate, X, cysteine, phenylalanine, X.
Here is the schematic model of the GAF domain of cyanobacteriochrome. You can see that the GAF domain folds the binding pocket of protein (purple ribbons), within which the bilin (chromophore) binds covalently, making the cyanobacteriochrome.
The next few slides are going to show you the procedures that we used to extract proteins from these cyanobacteriochromes. First, we would go over a procedure call protein expression and then we will follow that with a procedure call protein purification. PCR genomic DNA with primers to capture the GAF domain DNA sequence Insert our PCR product into a transformation vector built upon pBAD by doing restriction enzyme digest and ligation Site directed mutagenesis to change amino acid cysteine in the class II GAF motif to aspartate to make it fluorescence Transform E. coli bacteria with two plasmids pBAD + insert and pPL from Lagarias protein expression in the E. coli system using the plasmids we constructed protein purification to confirm the fluorescence (Wavelength, brightness) SDS-PAGE gel to see the purity and size of the protein Dry the gel for records Transblotting to nitrocellulose paper to demonstrate if the chromophore is covalently attached to the binding pocket Construct another plasmid in which we are going to put our tag next to actin or tubulin and the plasmid will be appropiate for transfecting jurkat cells.\\ Transfection Restriction Enzyme digest to construct the plasmid vector for transforming E. coli or transfecting jurkat cells
Since we know that the GAF domain binds to the chromophore, in order to induce a conformational change in the structure of the protein, we have a to do a procedure called site directed mutagenesis. Here, site directed mutagenesis is used to make a specific amino acid change by altering DNA at the appropriate location on the gene. In this image, you can see the sequence of the GAF domain, boxed in red is the specific location in that we are interested in. It is at this location where we make a mutation of the cysteine base to a aspartate base. The change of this codon result in a conformational change in the protein, thus preventing photoreversibility. This worked was publish in Biochemistry 2008.
Restriction Enzyme:Restriction enzymes are DNA-cutting enzymes found in bacteria.Recognition site for the enzyme at either end of the
We use PCR in this procedure as well.Our designed primers are going to start PCR, making a new plasmid that contains our mutation, and then another restriction enzyme will degrade our old plasmid.Sited directed mutagenesis is used to change cysteine to aspartate in the class II motif of the GAF domain. This particular cysteine is required for the blue/green photoreversibility of native cyanobacteriochromes, but results in bright red fluorescence when changed to aspartate. Since all class II Phr proteins. or cyanobacteriochromes, contain the six Amino Acid identifying motif = XDXCFX (green). This means - X, aspartate, X, cysteine, phenylalanine, X is mutated to - X, asparate, X, aspartate, phenylalanine, X.
Since we know that the GAF domain binds to the chromophore, in order to induce a conformational change in the structure of the protein, we have a to do a procedure called site directed mutagenesis. Here, site directed mutagenesis is used to make a specific amino acid change by altering DNA at the appropriate location on the gene. In this image, you can see the sequence of the GAF domain, boxed in red is the specific location in that we are interested in. It is at this location where we make a mutation of the cysteine base to a aspartate base. The change of this codon result in a conformational change in the protein, thus preventing photoreversibility. This worked was publish in Biochemistry 2008. The mutation in the published work was Cysteine 499 in the tlr0924 gene, the cysteine in tll0569 is homologous, but in a different position in the nucleic acid sequence. It is, however, part of the same motif that is present in all Class II GAF domains, class II Phr proteins or cyanobacteriochromes, XDXCFX (green)This is the sequence of 569
this image is an example of another cyanobacteriochrome that has undergone site directed mutagenesis. The protein, Tlr0924, is described in our paper Biochemistry, June 2008In the tube, the mutation made changed the cyanobacteriochrome’s conformation causing it to appear this turquoise (blue green) color. In addition of being turquoise to the naked eye, it also absorbs red wavelengths as you can see it by this spectrophotometer graph.
If you remember earlier in this presentation, we went over how transfection is used to insert a bioengineered plasmid into a eukaryotic cell. Now, we are inserting a bioengineered plasmid with a red fluorescent tag instead of a green fluorescent tag into a E. coli cell. The process is the same in an eukaryotic cell but because we are using E. coli is called transformation instead of transfection. We are going to use E. coli as our protein manufacturer. The E.coli strain that we use in the laboratory is not pathogenic, like the strains you may hear about in the news recently
We have the stock of E.coli (LMG194) that contains pPL-PCB plasmids. The pPL plasmids contain two enzymes that will make our bilin chromophore in the E.coli, from the E.coli’s own supply of HEME, After the second transformation, E.coli has two plasmids, pBAD and pPL. They are under the control of chemicals IPTG and L-arabinose, LMG194 will express from both plasmids when these chemicals are added. As the protein that we engineered is expressed, it will covalently bind the bilin, which is made from the E.coli’s HEME. When the protein binds to the bilin, it becomes sensitive/reactive to the photons.
This is how is it done. We use E.coli as our protein manufacturer because its genome is known and it is easy to work with in a lab. After transforming E.coli with our plasmid that has our red fluorescent tag, we grow our bacteria in a flask. This culture is allowed to grow overnight in order to have the optimal amount of bacteria. After this, we will induce protein expression by adding two chemicasl that would turn on the promoter within both of our plasmids, thus causing the expression of our protein of interest. If protein expression is successful, we should expect to see the non-mutated protein as a yellow color, while our mutated protein should be a bright blue color because it is absorbing red light.Using Escherichia coli (E. coli) as our Protein ManufacturerWhen expression of both plasmids has been initiated with IPTG and L-arabonse, the E.coli cells are incubated with shaking at 37 celcius degree for 18 – 24 hours. After expression for 18 -24 hours, E.coli cells are collected by centrifuging.
These are results of a recent protein expression completed this summer. Here we can see that 569T and 899T, our non-mutated protein, does show a bright yellow color while our mutated protein, 569TM shows bright blue color. If these pellets were exposed to red exciting light, we would expect to see our 569TM fluoresce red in longer wavelengths. T stands for truncated, and TM stands for truncated and mutated. Add a new pic for this
After protein expression, we have to lyse the cells open in order to purify the protein. This image to your right is called Microfluidizer which is used to mechanically lyse the cells. There are several steps to this process but to overview once the cell is properly lyse, it will be centrifuge to further extract parts of the cell that we are not interested in. This leads us to one of the final steps in protein purification called column chitin binding.
The supernatant from centrifugation is dripped over the chitin beads in the column.As we can see in this image, the chitin beads that have been successfully bound to the protein are now blue. The next step is to completely cleave this bound protein from our chitin beads which is a step that we are currently working on.
Here is a closer image of how the beads binds to the protein. We can see that the protein expressed by E. coli has a chitin binding domain. This domain will attach to the chitin bead. Other proteins and cellular components from E. coli are washed away from the column after the chitin beads grasp onto our engineered protein. After they are washed successfully, then we can then cleave the chitin binding domain from our protein of interest so the only part we are left with is our most purified form of the protein.
First we will look at SDS, an anionic detergent, that is able to denature a protein to its primary structure without breaking the amino acid chain.With the presence of negatively charged sulfate ions, the entire linearized protein is covered with a net negative charge. This charge ensures that proteins of similar size are able to migrate at about the same rate. It also allows for the proteins to travel from the negative anode pole to the positive cathode pole when an electric current is applied to the gel.
The polyacrylamide gel is meant to provide obstacles for the migrating protein. Smaller proteins can move through the gel faster because they are able to maneuver through the polymer easier than large proteins.The gel is SDS-PAGE is composed of two layers. When making the gel, the resolving gel, or stacking gel, is added first. It is composed of 12% acrylamide and has a pH of 8.8. It is in this bottom layer of the gel where we will see more separation between the bands. The increase amount of acrylamide provides narrow channels in which the proteins can travel, here is where we will see smaller bands move further down the gel.The stacking gel is added last and forms the upper layer. It is composed of 4% acrylamide and has a pH of 6.68. This gel is more porous, allowing for the proteins of different size to become “stacked” against each other when the come to the interface of the resolving gel. As they are stacked, the proteins are then able to start their migration through the resolving gel at the same time.
Here are the general steps in preparing the acrylamide gel. Using gel glass plates and a casting frame. The two plates will be place on top of one another.The resolving gel will be added first to the small space between the plates. Water will soon be added to prevent mixture with the air and create a flat surface at the top of the gel.After polymerizing for 45 minutes the stacking gel is added.Immediately after the stacking gel is poured the comb, which forms the gel into wells, is inserted between the plates. This is where the proteins will be loaded.Once polymerization has occurred, the gel is ready to use.
We place the gel plates facing toward each other in the electrode assembly, which is then lowered into the mini tank.Running buffer is added to the inner chamber between the two plates, as well as in the outer chamber. Buffer in these two regions allows for an electric current to flow through the gels.Now that the buffer is added, the samples can be loaded into the wells. Once this is complete. The mini tank is covered with a lid that is attached to the power source. An electric current travels through the negative anode end, into the inner chamber, down the gels, out through the outer chamber, and back through the positive anode end to the power source.We would like to visually show you this process through a short video.**show video
Here is a sample of one of our results after drying the gel. You can see the ladders which show the relative sizes of the proteins.We can determine the purity of the protein by the one band position that is seen across the gel. Each protein is relatively the same size. We also compare the our proteins to our control chp1. chp1 is a protein that is slightly smaller than the sample proteins used in this gel.In our lab we want to know if bilin chromophore is covalently bound to our protien, therefore we perform one more test based on the polyacrylamide gel.(Information on hand….do not state in presentation)12/27Lane 1: Ladder used to relate compartative sizes of proteinsLane 2: Cph1 – bacterial phytochrome that we use as a control. We compare protein size. What you see here are the proteins before truncation (shortened) to GAF only domain of the 924 gene.Lane 3: Full length 924 without mutationLane 4: Full length with mutation (924) of cystine to aspartateLane 5: LadderLane 6: Full length protein with cystine mutated to alanineLane 7: BlankLane 8: 924 with cystine to aspartate mutation, but with no chromophore (apoprotein)
To determine the presence of the chromophore, we transfer the proteins from the gel to nitrocellulose using Bio-Rad transblotting equipment.The nitrocellulose is incubated overnight in zinc acetate causing proteins which bind the bilin chromophore to fluoresce in ultraviolet light.After SDS-PAGE has linearized the proteins and positioned them on the gel, only covalently bound bilins will have travelled with those proteins during electrophoresis.Zinc acetate – determines if the chromophore is still present. In this particular transblot you can see that the chromphore is present in three of the proteins - the control and two of the cyanobacteriochromes.Now that we know have confirmed that our proteins have bilin covalently bound to them, we can then transfect our plasmids into the mammalian system.
Transfection: The process of introducing nucleic acids into eukaryotic cells by nonviral methods. Transfection of animal cells typically involves opening transient pores or "holes" in the cell membrane, to allow the uptake of genetic material. There are two methods for transfectionbiochemical methods, such as using calcium phosphatephysical methods, such as electroporation
The mechanism is based on the use of an electrical pulse to perturb the cell membrane and form transient pores that allow passage of nucleic acids into the cell (Shigekawa and Dower, 1988). This procedure is highly efficient for the introduction of foreign genes in tissue culture cells, especially mammalian cells. In addition, electroporation often requires more cells than chemical methods because of substantial cell death, and extensive optimization often is required to balance transfection efficiency and cell viability.
General Process of Transfection:Plasmid combines with Tranfection ReagentCombined plasmid and reagent complex enter the cellDNA released in the cellNucleofector:The Nucleofector™ Technology is a novel transfection technology especially designed for the needs of primary cells and difficult-to-transfect cell lines. It is a non-viral method which is based on a unique combination of electrical parameters and cell-type specific solutions.It allows transfected DNA to directly enter the nucleus. Transfection reagentEppendorf tubesDropperSpecial Cuvette
pDsRed-Monomer-Actin Vector: This plasmid encodes DsRed-Monomer, a monomeric mutant of the Discosoma sp. red fluorescent protein DsRed. The pDsRed-Monomer-Actin fusion protein incorporates into growing actin filaments, allowing visualization of the actin cytoskeleton in living or fixed cells.This plasmid contains all the correct origins of replication and promoter regions to be active in both e.coli and mammalian cells. G418- antibiotic mixture – Neo, allowing the selection of Jurkat cells that actually incorporated the plasmids.Jurkat Cell: Jurkat Cells are an immortalized line of T lymphocyte cells that are used to study acute T cell leukemia, T cell signaling, and the expression of various chemokine receptors susceptible to viral entry, particularly HIV. Jurkat cells are also useful in science because of their ability to produce interleukin 2. Their primary use, however, is to determine the mechanism of differential susceptibility of cancers to drugs and radiation.The cells are Jurkat cells, which are cancerous white blood cells.Graph:The Jurkat cells are expressing DsRed-Monomer actin in its cytoskeleton. Goal:We will test our cyanobacteriochrome sequence by replacing DsRed-Monomer with our bioengineered red fluorescent tag (???)
The Deconvolution fluorescence microscope at CBST is used for rapid live and fixed cell fluorescence microscopy. It can capture time elapse images showing the red fluorescent cytoskeleton in 2 to 3 dimensions.