Epigenetics bio proj
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Epigenetics is the study of inheritable changes that occur without altering the DNA sequence. These changes include modifications to gene expression and phenotypes through mechanisms other than the DNA sequence, such as environmental factors. Epigenetic changes can be caused by an individual's choices and environment and can potentially affect their children and grandchildren. Identical twins with the same DNA but different environments and lifestyles can have different epigenetic profiles and health outcomes due to factors like stress levels and diet. While epigenetics research holds promise, it also raises ethical concerns and can potentially cause abnormalities if not carefully studied.
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212 basic molecular genetic studies in atherosclerosis
212 basic molecular genetic studies in atherosclerosisSociety for Heart Attack Prevention and Eradication
This document provides an overview of basic molecular genetic methodologies and their applications in studying atherosclerosis. It describes several key techniques used in molecular genetics research, such as polymerase chain reaction (PCR), gel electrophoresis, Southern blotting, and DNA sequencing. It also discusses methods for detecting genetic variations like single nucleotide polymorphisms. The document then covers applications of these techniques for analyzing specific nucleic acids and genomic studies of atherosclerosis.Basic molecular genetic studies in atherosclerosis
Basic molecular genetic studies in atherosclerosisSociety for Heart Attack Prevention and Eradication
This document provides an overview of basic molecular genetic methodologies and their applications in studying atherosclerosis. It describes several key techniques used in molecular genetics research, such as polymerase chain reaction (PCR), gel electrophoresis, Southern blotting, and DNA sequencing. It also discusses methods for detecting genetic variations like single nucleotide polymorphisms. The document then covers various applications of these techniques in genomic analysis and molecular studies of cardiovascular diseases like atherosclerosis.Structural genomics
Structural genomics aims to sequence and map genomes. Genetic maps show relative gene locations based on recombination rates, while physical maps show direct DNA distances. Genetic maps have low resolution and may differ from physical distances. Physical maps use techniques like restriction mapping and sequencing to order DNA fragments. Sequencing entire genomes requires breaking DNA into small fragments that are then reassembled using overlap or genetic/physical maps. The human genome was first sequenced in 2000 using both map-based and whole genome shotgun approaches. Single nucleotide polymorphisms are also studied to compare individuals.
SAGE (Serial analysis of Gene Expression)
SAGE (Serial Analysis of Gene Expression) is a technique that allows for the rapid and comprehensive analysis of gene expression patterns in a given cell population. It works by isolating mRNA, synthesizing cDNA, ligating short sequence tags to the cDNA, and then counting the number of times each tag is observed to quantify gene expression levels. The tags are concatenated and sequenced to generate vast amounts of data that must be analyzed computationally to identify which genes particular tags correspond to and to compare expression profiles between cell types. SAGE provides an overview of a cell's complete transcriptional activity and has been applied to study differences in cancer vs normal cells and to identify targets of oncogenes and tumor suppressor genes.
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCING
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
Chapter 2 molecular methods in cancer
Molecular methods such as polymerase chain reaction (PCR), real-time PCR, fragment analysis, high-resolution melting analysis, Sanger sequencing, pyrosequencing, and fluorescence in situ hybridization (FISH) are increasingly used in cancer care for diagnosis, prognosis, predicting therapy response, and monitoring minimal residual disease. These techniques detect various biomarkers including mutations, gene fusions, amplifications, and epigenetic changes from samples such as blood, tissue, and bone marrow. The molecular diagnostic tests must demonstrate high analytic validity, clinical validity, and utility to be clinically applicable.
MICROARRAY
Microarray technology allows researchers to analyze the expression levels of thousands of genes simultaneously using DNA probes attached to a solid surface. There are two main types of microarrays: glass cDNA microarrays which involve spotting pre-fabricated cDNA fragments on glass slides; and high-density oligonucleotide arrays which involve the in situ synthesis of oligonucleotides on a chip. The key steps in a microarray experiment are sample preparation and labeling, hybridization of labeled cDNA to the probes, washing, and image analysis to quantify gene expression levels. Microarrays have numerous applications including gene expression profiling, comparative genomics, disease diagnosis, drug discovery, and toxicology research.
Transcriptomics
Transcriptomics is the study of RNA in cells and tissues. The transcriptome refers to the complete set of transcripts in a cell under a specific condition. Understanding the transcriptome reveals the functional elements of the genome and molecular constituents of cells. Techniques for studying the transcriptome include microarray analysis and RNA sequencing. Microarrays measure gene expression levels using fluorescently-labeled cDNA hybridized to probes on an array. RNA sequencing determines expression levels by sequencing individual cDNAs produced from target RNA. Transcriptomics provides insights into development, disease, and varying gene expression under different environmental conditions.
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212 basic molecular genetic studies in atherosclerosis
212 basic molecular genetic studies in atherosclerosisSociety for Heart Attack Prevention and Eradication
This document provides an overview of basic molecular genetic methodologies and their applications in studying atherosclerosis. It describes several key techniques used in molecular genetics research, such as polymerase chain reaction (PCR), gel electrophoresis, Southern blotting, and DNA sequencing. It also discusses methods for detecting genetic variations like single nucleotide polymorphisms. The document then covers applications of these techniques for analyzing specific nucleic acids and genomic studies of atherosclerosis.Basic molecular genetic studies in atherosclerosis
Basic molecular genetic studies in atherosclerosisSociety for Heart Attack Prevention and Eradication
This document provides an overview of basic molecular genetic methodologies and their applications in studying atherosclerosis. It describes several key techniques used in molecular genetics research, such as polymerase chain reaction (PCR), gel electrophoresis, Southern blotting, and DNA sequencing. It also discusses methods for detecting genetic variations like single nucleotide polymorphisms. The document then covers various applications of these techniques in genomic analysis and molecular studies of cardiovascular diseases like atherosclerosis.Structural genomics
Structural genomics aims to sequence and map genomes. Genetic maps show relative gene locations based on recombination rates, while physical maps show direct DNA distances. Genetic maps have low resolution and may differ from physical distances. Physical maps use techniques like restriction mapping and sequencing to order DNA fragments. Sequencing entire genomes requires breaking DNA into small fragments that are then reassembled using overlap or genetic/physical maps. The human genome was first sequenced in 2000 using both map-based and whole genome shotgun approaches. Single nucleotide polymorphisms are also studied to compare individuals.
SAGE (Serial analysis of Gene Expression)
SAGE (Serial Analysis of Gene Expression) is a technique that allows for the rapid and comprehensive analysis of gene expression patterns in a given cell population. It works by isolating mRNA, synthesizing cDNA, ligating short sequence tags to the cDNA, and then counting the number of times each tag is observed to quantify gene expression levels. The tags are concatenated and sequenced to generate vast amounts of data that must be analyzed computationally to identify which genes particular tags correspond to and to compare expression profiles between cell types. SAGE provides an overview of a cell's complete transcriptional activity and has been applied to study differences in cancer vs normal cells and to identify targets of oncogenes and tumor suppressor genes.
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCING
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
Chapter 2 molecular methods in cancer
Molecular methods such as polymerase chain reaction (PCR), real-time PCR, fragment analysis, high-resolution melting analysis, Sanger sequencing, pyrosequencing, and fluorescence in situ hybridization (FISH) are increasingly used in cancer care for diagnosis, prognosis, predicting therapy response, and monitoring minimal residual disease. These techniques detect various biomarkers including mutations, gene fusions, amplifications, and epigenetic changes from samples such as blood, tissue, and bone marrow. The molecular diagnostic tests must demonstrate high analytic validity, clinical validity, and utility to be clinically applicable.
MICROARRAY
Microarray technology allows researchers to analyze the expression levels of thousands of genes simultaneously using DNA probes attached to a solid surface. There are two main types of microarrays: glass cDNA microarrays which involve spotting pre-fabricated cDNA fragments on glass slides; and high-density oligonucleotide arrays which involve the in situ synthesis of oligonucleotides on a chip. The key steps in a microarray experiment are sample preparation and labeling, hybridization of labeled cDNA to the probes, washing, and image analysis to quantify gene expression levels. Microarrays have numerous applications including gene expression profiling, comparative genomics, disease diagnosis, drug discovery, and toxicology research.
Transcriptomics
Transcriptomics is the study of RNA in cells and tissues. The transcriptome refers to the complete set of transcripts in a cell under a specific condition. Understanding the transcriptome reveals the functional elements of the genome and molecular constituents of cells. Techniques for studying the transcriptome include microarray analysis and RNA sequencing. Microarrays measure gene expression levels using fluorescently-labeled cDNA hybridized to probes on an array. RNA sequencing determines expression levels by sequencing individual cDNAs produced from target RNA. Transcriptomics provides insights into development, disease, and varying gene expression under different environmental conditions.
Snp
A single-nucleotide polymorphism (SNP) is a variation in a single DNA building block (nucleotide) that differs between members of a species. SNPs are the most common type of genetic variation among humans, with around 0.1% of bases differing between individuals. They can occur in coding regions, where they may alter the resulting protein, or non-coding regions. SNPs are significant for mapping genes and studying an individual's predisposition to diseases like cancer or response to medications. They can be identified by comparing DNA sequences from many individuals or through laboratory techniques like SNP genotyping.
Molecular marker and its application to genome mapping and molecular breeding
Molecular markers are genetic elements that can be used to follow chromosomes or chromosomal segments during genetic analysis. Molecular markers include molecular techniques like single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). SSRs, also known as microsatellites, are tandem repeats of short DNA motifs that are highly polymorphic due to replication slippage errors. SNPs are single base pair changes that are the most common type of genetic variation. Both SNPs and SSRs are useful molecular markers that can be detected through polymerase chain reaction (PCR) and are important tools for genome mapping and molecular breeding applications.
STRUCTURAL GENOMICS, FUNCTIONAL GENOMICS, COMPARATIVE GENOMICS
Structural genomics is a field that aims to determine the 3D structures of all proteins encoded by a genome. It involves determining structures on a large scale using techniques like X-ray crystallography and NMR. This allows identification of novel protein folds and potential drug targets. Comparative genomics compares genomic features between organisms and provides insights into evolution and conserved sequences and functions. It is a key tool in fields like medicine and agriculture.
Genome organisation
Genetic Organisation:
All cellular activities are encoded within a cell’s DNA.
The sequence of bases within a DNA molecule represents the genetic information of the cell.
Segments of DNA molecules are called genes, and individual genes contain the instructional code necessary for synthesizing various proteins, enzymes, or stable RNA molecules.
Functional genomics
Functional genomics uses genome-wide experimental approaches to assess gene function on a large scale. It analyzes gene expression through techniques like transcriptomics and proteomics. Transcriptomics analyzes gene expression profiles through RNA sequencing or microarray analysis. Microarray analysis involves hybridizing fluorescently-labeled cDNA or cRNA to microarrays containing DNA probes to measure gene expression levels across thousands of genes simultaneously. Functional genomics provides a global understanding of gene function and molecular interactions through integrated omics approaches.
Genome assembly
This document discusses different methods for genome sequencing and assembly, including restriction enzyme fingerprinting, marker sequences, and hybridization assays. It focuses on using marker sequences like sequence-tagged sites (STS), expressed sequence tags (ESTs), untranslated regions (UTRs), and single nucleotide polymorphisms (SNPs) to map genomes. Large-insert cloning vectors like BACs and PACs can be used with restriction enzyme fingerprinting and FPC software to assemble contigs and map genomes at a large scale. Marker sequences provide a dense set of physical markers to build accurate physical maps of genomes.
Molecular methods
This document discusses various molecular methods used in molecular genetics and molecular biology. It begins by categorizing common techniques into diagnostic methods, analysis and sequencing, microarray methods, and proteomics. Several key diagnostic techniques are then described in more detail, including gel electrophoresis, hybridization, PCR, immunoprecipitation, and karyotyping. Recombinant DNA technology basics like cloning genes, cDNA, and purposes of cloning are explained. Other analysis methods such as sequencing, microarrays, RNA-Seq, and techniques like RNAi, knockout methods, and liposomes are also summarized.
Gene mapping and sequencing
This document discusses gene mapping and sequencing. It begins by defining genomics and genetic markers such as RFLP, SSLP, and SNP that are used to track inheritance. Gene mapping involves determining the locus and distance between genes on chromosomes, which is important for diagnosing genetic diseases. There are two main types of gene mapping: linkage mapping which measures recombination frequency to determine if genes are linked, and physical mapping which precisely locates DNA sequences on chromosomes using techniques like fluorescence in situ hybridization. The document also discusses methods for gene sequencing, including Sanger sequencing and Maxam-Gilbert sequencing, as well as newer techniques like shotgun sequencing and Illumina sequencing.
SAGE- Serial Analysis of Gene Expression
Serial Analysis of Gene Expression (SAGE) is a method to quantify gene expression in cells. It involves extracting short sequence tags from mRNA transcripts and concatenating them for efficient sequencing. This allows simultaneous analysis of thousands of transcripts. SAGE provides quantitative gene expression data without prior knowledge of genes and can identify differentially expressed genes between cell types or conditions. While powerful, it requires substantial sequencing and computational analysis of large datasets.
Massively Parallel Signature Sequencing (MPSS)
Lynx Therapeutics' Massively Parallel Signature Sequencing (MPSS) is an early high-throughput DNA sequencing technique. It works by attaching cDNA from an mRNA sample to beads, determining short sequence signatures from many beads in parallel, and using the signatures to count the number of individual mRNA molecules from each gene. This digital gene expression data allows MPSS to accurately quantify genes expressed at low levels by analyzing transcripts from virtually all genes simultaneously. The technique involves converting mRNA to cDNA, attaching oligonucleotide tags, PCR amplification on beads, and using fluorescent probes to determine short sequences in increments of four nucleotides from millions of beads in parallel.
Analysis of gene expression
Gene expression can be analyzed by determining mRNA levels and analyzing proteins. mRNA levels are usually determined by hybridizing probes to mRNA or cDNA, as in Northern blots which separate mRNA by size, or microarrays which analyze thousands of genes simultaneously. Protein analysis includes ELISA and Western blots to detect specific proteins, and proteomics uses techniques like gel electrophoresis and mass spectrometry to study the entire proteome.
Techniques in proteomics
This document provides an overview of common proteomics techniques. It describes proteomics as the study of proteins including their roles, structures, localization, interactions and other factors. The key techniques discussed include molecular techniques like DNA microarrays and yeast two-hybrid analysis, separation techniques like gel electrophoresis and chromatography, protein identification methods like mass spectroscopy and Edman sequencing, and protein structure determination methods like NMR, X-ray crystallography and computational prediction. The document provides examples and details of several of these techniques.
Functional genomics
This document provides an overview of functional genomics and methods for transcriptome analysis. It discusses two main approaches - sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. For sequence-based approaches, it describes how ESTs can provide gene discovery and expression information but have limitations. It outlines the SAGE methodology and gene index construction to organize EST data. For microarrays, it summarizes the basic workflow including sample preparation, hybridization, image analysis and data normalization to identify differentially expressed genes through statistical tests.
Human genome, genetic mapping, cloning, and cryonics
This document discusses the science of cryonics, which is the process of preserving humans in extremely cold temperatures after death with the goal of future revival. It explains that cryonics was first proposed by Robert Ettinger in the 1960s based on the idea that future medical advances may allow revival after freezing. The document outlines the cryonics process which involves replacing water in the body with antifreeze chemicals to prevent ice damage before freezing the body. It notes that the goal of cryonics is to use future nanotechnology and repair techniques to potentially revive frozen patients. The oldest cryonics patient currently preserved is from 1967.
GENOMIC MAPPING:FISH(Fluorescent in situ hybridization )
Genomic mapping is a graphic representation of the arrangement of genes or DNA sequences on chromosome & used to identify and record the location of gene & distances between genes on chromosome.
There are mainly two kinds of genome maps are known : 1.Genetic or linkage maps & 2. Physical maps
Where Physical map provides detail of the actual physical distance between genetic markers, as well as the exact location of genes.
An example of Physical mapping is FISH. FISH is a powerful technique for detecting RNA or DNA sequences in cells, tissues & tumors
Comparitive genomic hybridisation
Comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells
Dhanu
DNA sequencing determines the order of bases in a DNA sample. Two major early methods are the Maxam-Gilbert chemical cleavage method using double-stranded DNA and the Sanger chain termination method using single-stranded DNA. The Sanger method involves primer annealing, complementary strand synthesis using labeled chain terminators, and resolution on a polyacrylamide gel to read the sequence. Bacteria protect their DNA from foreign DNA through modification and restriction. Modification involves host-specific methylation while restriction enzymes cut foreign DNA at specific recognition sequences. There are four classes of restriction enzymes that differ in subunit composition, cofactor requirements, and cleavage position relative to the recognition site.
Genome annotation
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Molecular Technology
Genomic DNA and cDNA can be used to produce target DNA for cloning. Genomic DNA contains introns and other noncoding sequences, while cDNA is produced from mRNA and does not contain introns. Probes, which are DNA or RNA fragments labeled with radioactive or fluorescent tags, can be used to detect complementary nucleotide sequences in DNA or RNA samples. Southern blotting is a technique used to detect specific DNA fragments and involves cleavage of DNA, electrophoresis, transfer to a membrane, and detection using a labeled probe. Factors limiting the effectiveness of gene therapy include problems integrating DNA into the genome long-term and immune responses against foreign DNA.
Protein – DNA interactions, an overview
This document discusses protein-DNA interactions and various methods used to study them. It begins by introducing how proteins interact with DNA and RNA to influence their structure and function, playing crucial roles in processes like replication, transcription, and recombination. It then discusses DNA-binding proteins (DBPs) that constitute around 10% of protein-coding genes and regulate gene expression by binding to DNA. The document outlines different types of protein-DNA interactions and various detection methods used to study these interactions like chromatin immunoprecipitation assays, electrophoretic mobility shift assays, and DNA footprinting. It concludes that identifying DNA-binding proteins and their interaction mechanisms provides insights into gene expression and functions.
Vntr marker
This document discusses variable number tandem repeats (VNTRs), specifically microsatellites and minisatellites. It defines VNTRs as sequences with a variable number of tandem repeats of short DNA motifs. Microsatellites have repeat units of 1-10 bp while minisatellites have larger repeat units of 9-65 bp. Minisatellites can be detected using Southern blots with probes targeting the core repeat sequence, while microsatellites are detected using PCR. VNTRs are highly polymorphic due to variations in the number of repeats, making them useful for applications like forensic analysis, genetic mapping, and varietal identification.
Chromatin
1st ChIP-SAGE uses ChIP to purify chromatin, then crosslinks are reversed and linkers are ligated to DNA ends before digestion with NlaIII and MmeI to produce 21-22 bp sequence tags for cloning and sequencing.
2nd Deposition of histone variants like H2A.Z and H3.3 mark boundaries of regulatory regions in genomes and create hierarchical nucleosome stability.
3rd Interpreting ChIP experiments requires considering antibody specificity, chromatin preparation methods, and that results reflect average modification states across cells.
More Related Content
What's hot
Snp
A single-nucleotide polymorphism (SNP) is a variation in a single DNA building block (nucleotide) that differs between members of a species. SNPs are the most common type of genetic variation among humans, with around 0.1% of bases differing between individuals. They can occur in coding regions, where they may alter the resulting protein, or non-coding regions. SNPs are significant for mapping genes and studying an individual's predisposition to diseases like cancer or response to medications. They can be identified by comparing DNA sequences from many individuals or through laboratory techniques like SNP genotyping.
Molecular marker and its application to genome mapping and molecular breeding
Molecular markers are genetic elements that can be used to follow chromosomes or chromosomal segments during genetic analysis. Molecular markers include molecular techniques like single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). SSRs, also known as microsatellites, are tandem repeats of short DNA motifs that are highly polymorphic due to replication slippage errors. SNPs are single base pair changes that are the most common type of genetic variation. Both SNPs and SSRs are useful molecular markers that can be detected through polymerase chain reaction (PCR) and are important tools for genome mapping and molecular breeding applications.
STRUCTURAL GENOMICS, FUNCTIONAL GENOMICS, COMPARATIVE GENOMICS
Structural genomics is a field that aims to determine the 3D structures of all proteins encoded by a genome. It involves determining structures on a large scale using techniques like X-ray crystallography and NMR. This allows identification of novel protein folds and potential drug targets. Comparative genomics compares genomic features between organisms and provides insights into evolution and conserved sequences and functions. It is a key tool in fields like medicine and agriculture.
Genome organisation
Genetic Organisation:
All cellular activities are encoded within a cell’s DNA.
The sequence of bases within a DNA molecule represents the genetic information of the cell.
Segments of DNA molecules are called genes, and individual genes contain the instructional code necessary for synthesizing various proteins, enzymes, or stable RNA molecules.
Functional genomics
Functional genomics uses genome-wide experimental approaches to assess gene function on a large scale. It analyzes gene expression through techniques like transcriptomics and proteomics. Transcriptomics analyzes gene expression profiles through RNA sequencing or microarray analysis. Microarray analysis involves hybridizing fluorescently-labeled cDNA or cRNA to microarrays containing DNA probes to measure gene expression levels across thousands of genes simultaneously. Functional genomics provides a global understanding of gene function and molecular interactions through integrated omics approaches.
Genome assembly
This document discusses different methods for genome sequencing and assembly, including restriction enzyme fingerprinting, marker sequences, and hybridization assays. It focuses on using marker sequences like sequence-tagged sites (STS), expressed sequence tags (ESTs), untranslated regions (UTRs), and single nucleotide polymorphisms (SNPs) to map genomes. Large-insert cloning vectors like BACs and PACs can be used with restriction enzyme fingerprinting and FPC software to assemble contigs and map genomes at a large scale. Marker sequences provide a dense set of physical markers to build accurate physical maps of genomes.
Molecular methods
This document discusses various molecular methods used in molecular genetics and molecular biology. It begins by categorizing common techniques into diagnostic methods, analysis and sequencing, microarray methods, and proteomics. Several key diagnostic techniques are then described in more detail, including gel electrophoresis, hybridization, PCR, immunoprecipitation, and karyotyping. Recombinant DNA technology basics like cloning genes, cDNA, and purposes of cloning are explained. Other analysis methods such as sequencing, microarrays, RNA-Seq, and techniques like RNAi, knockout methods, and liposomes are also summarized.
Gene mapping and sequencing
This document discusses gene mapping and sequencing. It begins by defining genomics and genetic markers such as RFLP, SSLP, and SNP that are used to track inheritance. Gene mapping involves determining the locus and distance between genes on chromosomes, which is important for diagnosing genetic diseases. There are two main types of gene mapping: linkage mapping which measures recombination frequency to determine if genes are linked, and physical mapping which precisely locates DNA sequences on chromosomes using techniques like fluorescence in situ hybridization. The document also discusses methods for gene sequencing, including Sanger sequencing and Maxam-Gilbert sequencing, as well as newer techniques like shotgun sequencing and Illumina sequencing.
SAGE- Serial Analysis of Gene Expression
Serial Analysis of Gene Expression (SAGE) is a method to quantify gene expression in cells. It involves extracting short sequence tags from mRNA transcripts and concatenating them for efficient sequencing. This allows simultaneous analysis of thousands of transcripts. SAGE provides quantitative gene expression data without prior knowledge of genes and can identify differentially expressed genes between cell types or conditions. While powerful, it requires substantial sequencing and computational analysis of large datasets.
Massively Parallel Signature Sequencing (MPSS)
Lynx Therapeutics' Massively Parallel Signature Sequencing (MPSS) is an early high-throughput DNA sequencing technique. It works by attaching cDNA from an mRNA sample to beads, determining short sequence signatures from many beads in parallel, and using the signatures to count the number of individual mRNA molecules from each gene. This digital gene expression data allows MPSS to accurately quantify genes expressed at low levels by analyzing transcripts from virtually all genes simultaneously. The technique involves converting mRNA to cDNA, attaching oligonucleotide tags, PCR amplification on beads, and using fluorescent probes to determine short sequences in increments of four nucleotides from millions of beads in parallel.
Analysis of gene expression
Gene expression can be analyzed by determining mRNA levels and analyzing proteins. mRNA levels are usually determined by hybridizing probes to mRNA or cDNA, as in Northern blots which separate mRNA by size, or microarrays which analyze thousands of genes simultaneously. Protein analysis includes ELISA and Western blots to detect specific proteins, and proteomics uses techniques like gel electrophoresis and mass spectrometry to study the entire proteome.
Techniques in proteomics
This document provides an overview of common proteomics techniques. It describes proteomics as the study of proteins including their roles, structures, localization, interactions and other factors. The key techniques discussed include molecular techniques like DNA microarrays and yeast two-hybrid analysis, separation techniques like gel electrophoresis and chromatography, protein identification methods like mass spectroscopy and Edman sequencing, and protein structure determination methods like NMR, X-ray crystallography and computational prediction. The document provides examples and details of several of these techniques.
Functional genomics
This document provides an overview of functional genomics and methods for transcriptome analysis. It discusses two main approaches - sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. For sequence-based approaches, it describes how ESTs can provide gene discovery and expression information but have limitations. It outlines the SAGE methodology and gene index construction to organize EST data. For microarrays, it summarizes the basic workflow including sample preparation, hybridization, image analysis and data normalization to identify differentially expressed genes through statistical tests.
Human genome, genetic mapping, cloning, and cryonics
This document discusses the science of cryonics, which is the process of preserving humans in extremely cold temperatures after death with the goal of future revival. It explains that cryonics was first proposed by Robert Ettinger in the 1960s based on the idea that future medical advances may allow revival after freezing. The document outlines the cryonics process which involves replacing water in the body with antifreeze chemicals to prevent ice damage before freezing the body. It notes that the goal of cryonics is to use future nanotechnology and repair techniques to potentially revive frozen patients. The oldest cryonics patient currently preserved is from 1967.
GENOMIC MAPPING:FISH(Fluorescent in situ hybridization )
Genomic mapping is a graphic representation of the arrangement of genes or DNA sequences on chromosome & used to identify and record the location of gene & distances between genes on chromosome.
There are mainly two kinds of genome maps are known : 1.Genetic or linkage maps & 2. Physical maps
Where Physical map provides detail of the actual physical distance between genetic markers, as well as the exact location of genes.
An example of Physical mapping is FISH. FISH is a powerful technique for detecting RNA or DNA sequences in cells, tissues & tumors
Comparitive genomic hybridisation
Comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells
Dhanu
DNA sequencing determines the order of bases in a DNA sample. Two major early methods are the Maxam-Gilbert chemical cleavage method using double-stranded DNA and the Sanger chain termination method using single-stranded DNA. The Sanger method involves primer annealing, complementary strand synthesis using labeled chain terminators, and resolution on a polyacrylamide gel to read the sequence. Bacteria protect their DNA from foreign DNA through modification and restriction. Modification involves host-specific methylation while restriction enzymes cut foreign DNA at specific recognition sequences. There are four classes of restriction enzymes that differ in subunit composition, cofactor requirements, and cleavage position relative to the recognition site.
Genome annotation
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
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Molecular marker and its application to genome mapping and molecular breeding
Molecular marker and its application to genome mapping and molecular breeding
STRUCTURAL GENOMICS, FUNCTIONAL GENOMICS, COMPARATIVE GENOMICS
STRUCTURAL GENOMICS, FUNCTIONAL GENOMICS, COMPARATIVE GENOMICS
Human genome, genetic mapping, cloning, and cryonics
Human genome, genetic mapping, cloning, and cryonics
GENOMIC MAPPING:FISH(Fluorescent in situ hybridization )
GENOMIC MAPPING:FISH(Fluorescent in situ hybridization )
Similar to Epigenetics bio proj
Molecular Technology
Genomic DNA and cDNA can be used to produce target DNA for cloning. Genomic DNA contains introns and other noncoding sequences, while cDNA is produced from mRNA and does not contain introns. Probes, which are DNA or RNA fragments labeled with radioactive or fluorescent tags, can be used to detect complementary nucleotide sequences in DNA or RNA samples. Southern blotting is a technique used to detect specific DNA fragments and involves cleavage of DNA, electrophoresis, transfer to a membrane, and detection using a labeled probe. Factors limiting the effectiveness of gene therapy include problems integrating DNA into the genome long-term and immune responses against foreign DNA.
Protein – DNA interactions, an overview
This document discusses protein-DNA interactions and various methods used to study them. It begins by introducing how proteins interact with DNA and RNA to influence their structure and function, playing crucial roles in processes like replication, transcription, and recombination. It then discusses DNA-binding proteins (DBPs) that constitute around 10% of protein-coding genes and regulate gene expression by binding to DNA. The document outlines different types of protein-DNA interactions and various detection methods used to study these interactions like chromatin immunoprecipitation assays, electrophoretic mobility shift assays, and DNA footprinting. It concludes that identifying DNA-binding proteins and their interaction mechanisms provides insights into gene expression and functions.
Vntr marker
This document discusses variable number tandem repeats (VNTRs), specifically microsatellites and minisatellites. It defines VNTRs as sequences with a variable number of tandem repeats of short DNA motifs. Microsatellites have repeat units of 1-10 bp while minisatellites have larger repeat units of 9-65 bp. Minisatellites can be detected using Southern blots with probes targeting the core repeat sequence, while microsatellites are detected using PCR. VNTRs are highly polymorphic due to variations in the number of repeats, making them useful for applications like forensic analysis, genetic mapping, and varietal identification.
Chromatin
1st ChIP-SAGE uses ChIP to purify chromatin, then crosslinks are reversed and linkers are ligated to DNA ends before digestion with NlaIII and MmeI to produce 21-22 bp sequence tags for cloning and sequencing.
2nd Deposition of histone variants like H2A.Z and H3.3 mark boundaries of regulatory regions in genomes and create hierarchical nucleosome stability.
3rd Interpreting ChIP experiments requires considering antibody specificity, chromatin preparation methods, and that results reflect average modification states across cells.
212 basic molecular genetic studies in atherosclerosis
Basic molecular genetic studies of atherosclerosis involve analyzing genes and genetic variations using various techniques. Key techniques discussed are PCR to amplify DNA, gel electrophoresis to separate DNA fragments by size, DNA sequencing to determine nucleotide order, and DNA microarrays where many genes are attached to a chip to analyze expression levels. These techniques are furthering our understanding of genetic factors contributing to atherosclerosis development and progression.
Molecular genetics
This document provides an overview of basic molecular genetic methodologies and their applications in studying atherosclerosis. It describes several key techniques used in molecular genetics research, such as polymerase chain reaction (PCR), gel electrophoresis, Southern blotting, and DNA sequencing. It also discusses methods for detecting genetic variations like single nucleotide polymorphisms. The document then covers various applications of these techniques in genomic analysis and molecular studies of cardiovascular diseases like atherosclerosis.
Recombinant dna technology
Recombinant DNA (rDNA) molecules are DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in the genome.
Molecular genetic diagnosis
This document discusses molecular genetic diagnosis techniques. It begins by describing how techniques like karyotyping, Southern blotting, and Sanger sequencing revolutionized genetic diagnosis in the late 20th century. It then covers the various indications for genetic testing, including inherited conditions, prenatal testing, and acquired conditions like cancer. The rest of the document details specific molecular analysis techniques used, such as PCR, Sanger sequencing, pyrosequencing, restriction fragment length analysis, FISH, MLPA, Southern blotting, and next generation sequencing. It provides examples of the medical applications of these various techniques.
Blotting
The document describes various blotting techniques used to detect DNA, RNA, and proteins. It discusses Southern blotting, which is used to detect specific DNA sequences through separation, transfer, and hybridization. The overall steps involve DNA fragmentation, gel electrophoresis, transfer to a membrane, hybridization with a probe, washing, and detection. Northern blotting is similar but detects RNA and uses formaldehyde during gel electrophoresis. Western blotting detects specific proteins by separating proteins by size on a gel, transferring them to a membrane, labeling with antibodies, washing, and detecting the bound antibodies. These techniques allow for detection of specific biomolecules.
Molecular markers- RFLP, RAPD, AFLP, SNP etc.
Molecular markers are identifiable DNA sequences used to locate genes associated with specific traits or genetic conditions.
A molecular marker is a specific gene fragment present at a specific position called ‘locus’ (pleural loci) in the genome of a cell.
In the pool of unknown DNA or in a whole chromosome, these molecular markers help in identification of particular sequence of DNA at particular location.
Construction and screening of genomic library
This document discusses the construction and screening of genomic libraries. It explains that a genomic library contains DNA fragments that represent an organism's entire genome. The library is constructed by isolating, purifying, and fragmenting genomic DNA, then cloning the fragments into suitable vectors. Common vectors for large DNA fragments include lambda phage, YACs, and BACs. The library can then be screened to identify clones containing genes of interest using various methods like hybridization, PCR, or screening for gene expression and complementation. Hybridization methods for screening include colony hybridization and plaque hybridization.
Transcriptomics,techniqes, applications.pdf
The analysis of global gene expression and transcription factor regulation, global approaches to alternative splicing and its regulation, long noncoding RNAs, gene expression models of signalling pathways, from gene expression to disease phenotypes, introduction to isoform sequencing, systematic and integrative analysis of gene expression to identify feature genes underlying human diseases.
Genetic engineering and Recombinant DNA
Genetic engineering involves altering the DNA of living organisms using biotechnology. It includes techniques like changing single DNA base pairs, deleting or adding genes, or combining DNA from different species. Recombinant DNA technology is used to create recombinant DNA molecules by manipulating DNA in vitro and introducing them into host organisms. This allows bacteria to be engineered to produce human insulin through inserting the human insulin gene into bacterial plasmids. Genomic libraries can be created by ligating fragmented genomic or cDNA into plasmid vectors to transform bacteria and clone the entire genome.
Pcr
The document summarizes several molecular biology techniques used to analyze DNA, including PCR, RFLP, DGGE, FISH, and clone libraries. PCR is used to amplify a targeted region of DNA using primers. RFLP and DGGE separate DNA fragments of different lengths after restriction enzyme digestion or denaturation to identify sequences. FISH uses fluorescent probes to directly image specific organisms in samples. Clone libraries create collections of DNA fragments for sequencing.
Introduction to epigenetics and study design
This document provides an introduction to the integration of epidemiology and epigenetics in studying epigenome-wide association studies (EWAS). It discusses that EWAS require subject matter knowledge, pressing biological questions, determinants of epigenetic variation, and appropriate study design and analysis while focusing on DNA methylation. It also reviews different study designs for EWAS including experimental, cohort, case-control, twin, and family-based studies. Key concepts in epidemiology that are important for EWAS such as confounding, selection bias, information bias, and matching are also discussed.
Dna mapping
This document provides information on various genetic mapping techniques. It discusses locus, genome, linked genes, genetic distance, and recombination frequency. It then describes genetic mapping and the different types of maps - genetic/linkage maps and physical maps. Genetic maps are based on recombination frequencies while physical maps use techniques like in situ hybridization. Restriction mapping and DNA footprinting are also summarized as methods to determine the order and location of genes and restriction sites on chromosomes. Transposable elements in eukaryotes are classified into Class I and II based on their mechanism of transposition via RNA intermediates or direct DNA-to-DNA movement.
Genome editing
genome editing is the emerging branch which includes the specific and precise engineering of genomic regions
molecular biology Molecular markers (1).pptx
Molecular markers are used to identify DNA sequences and are based on natural DNA polymorphisms like substitutions, additions, or patterns. There are five key characteristics of suitable molecular markers: being polymorphic, co-dominant inheritance, random and frequent distribution, easy and cheap detection, and reproducibility. Common types of markers include RFLPs, AFLPs, RAPDs, VNTRs, microsatellites, SNPs, STRs, and others. These markers have various advantages and disadvantages and can be used for applications like characterization, genetic diagnostics, and forensic analysis.
genetic_enginnering_merged.pdf
This document provides an overview of the 3 credit hour course "Recombinant DNA technology" with a course code of BioT 3115. The course covers topics such as introduction to gene manipulation, cloning vectors and hosts, DNA library techniques, PCR, DNA sequencing and mutagenesis, and applications of recombinant DNA technology in fields like medicine, agriculture, industry and environment. It also discusses key enzymes used for gene manipulation like restriction enzymes, DNA ligases and topoisomerases.
Cancer genome
This document discusses cancer genomics and tumor sequencing. It explains that tumor genotyping helps clinicians individualize cancer treatments by matching patients to the best treatment based on their tumor's DNA alterations. Next generation sequencing methods have made it possible to sequence entire cancer genomes and identify additional targets for new cancer therapies. Large-scale projects like The Cancer Genome Atlas and the International Cancer Genome Consortium are analyzing hundreds of cancer genomes to better understand the molecular changes driving different cancer types.
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212 basic molecular genetic studies in atherosclerosis
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Jenna pauly
Genetically modified foods are foods that have been modified by scientists by changing or adding new genes. Scientists genetically modify foods to protect against pests, add nutrients, help foods thrive in different environments, and protect from disease. Common genetically modified foods include bananas, tomatoes, corn, and soybeans. The genetic modification process involves isolating a desired gene, inserting it into a transfer vector like a plasmid, transforming the plant by transferring the plasmid into the plant's chromosomes using Agrobacterium tumefaciens bacteria. While genetically modified foods aim to benefit agriculture, some argue they could spread unknown diseases, lead to pest resistance, transfer allergens, or interfere with nature.
Annie reich
The Honolulu Technique is one of three cloning methods that can produce live cloned offspring from adult animal cells. It was developed by scientists at the University of Hawaii who successfully cloned mice over five generations. The technique involves removing the nucleus from a donor cell, transferring it into an egg, stimulating the egg to divide, and implanting the cloned embryo into a surrogate mother. While it is more successful than other cloning methods and may help treat diseases, it is also expensive, reduces genetic diversity, and requires many attempts due to mutations.
Brian bullock
The document outlines the process used to sequence the human genome. It describes how DNA was broken into fragments, placed in bacterial chromosomes to be replicated, cut into fingerprints, and then reassembled by mapping overlapping sequences of letters to complete the genome sequence. The project took 7 years to complete at a cost of $3 billion and led to discoveries that could help map genes associated with diseases and develop new medical treatments and cures.
Jacob price
The Human Genome Project was a 13-year project completed in 2003 that mapped and analyzed all of the genes in the human genome. It found that there are approximately 20,500 genes in the human body, less than originally predicted. The project provided detailed information about human genes and their structure, organization, and function, representing the basic set of instructions for human development and function.
Polymerase chain reaction
PCR (polymerase chain reaction) is a process that allows specific DNA sequences to be replicated millions of times, invented by Dr. Kary Banks Mullis in 1983. A thermocycler machine automates temperature changes to denature, anneal, and extend DNA during PCR cycles. This allows small amounts of DNA to be amplified for research, forensics, and other applications by creating multiple copies of the targeted DNA sequence.
Alec wood genemapping
Gene mapping involves using genetic maps to find links between genes and diseases transmitted from parents to children, and has been useful in locating genes believed to cause common disorders such as asthma, heart disease, diabetes, cancer, and psychiatric conditions. Researchers use linkage to determine chromosome regions likely containing risk genes, ruling out low-chance areas, and then use association studies on candidate genes to test for connections to conditions. It is hoped that gene mapping can help find cures and prevent diseases from becoming prominent.
Geneticsnotes ch9 bio
Gregor Mendel conducted experiments with pea plants in the 1850s and 1860s to study inheritance of traits. He observed that traits were inherited in predictable patterns, with dominant traits masking recessive traits in the offspring of crosses. His work established the fundamental laws of genetics, including segregation of alleles, independent assortment of traits, and dominance. Mendel's work laid the foundation for the field of molecular genetics and our modern understanding of genes and inheritance.
Geneticsnotes ch9 bio
Gregor Mendel conducted experiments with pea plants in the 1850s and 1860s to study inheritance of traits. He observed that traits were inherited in predictable patterns, with one trait (factor) being dominant and the other recessive. This led to his laws of inheritance including dominance, segregation, and independent assortment. His work established the field of genetics and provided evidence that traits are passed from parents to offspring via discrete units later known as genes.
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Epigenetics bio proj
- 2. What is Epigenetics? • Epigenetics is the study of inheritable changes that can occur without a change in the DNA sequence.
- 3. • Epigenetics are the changes of gene expressions and the cells phenotypes. • They are caused not by the DNA sequence but other mechanisms. • EPIGENETICS literally means ~epi (above) ~genetics. • This refers to changes in the genome.
- 5. • Epigenetics goes deeper then just your genes they depend on your social aspects, environment, and even your diet. • The choices you make will affect your children and even your grandchildren.
- 7. • Epigenetics is really easy to see in identical twins. • If two twins with the same DNA were seperated early on in life and one went to live in New York and the other on the beach. The one in New York would have a stressful lifa and may end up having asthma due to the environment, while the other would be living a stress-free life, it all depends on the area, the people and your diet.
- 8. • Even if you make bad decisions for yourself, your children may be have some of that in them due to your mistake • Diet is especially important, because not making healthy choices can lead to cancer and cause trouble to you in the future. • The twin on the beach may do yoga every morning and will be healthy and fit, she won’t have cancer.
- 9. Ethical concerns • Epigenetics is moving at a rapid rate. • Intriguing research is being done, primarily done on animals • Epigenetics show up faster than mutations • Researchers have found out that epigenetic changes can be reversible • People began calling epigenetics the new “Lamarckism.”
- 10. Advantages • One human testing it mainly works on identical twins. • Researchers are very picky and are adopting epigenetics, to se if the methods will answer any biological questions.
- 11. Disadvantages • Epigeneticss can cause abnormilities • Cardiac hypertrophy • Heart failure
- 12. 5-mC intact. The uracils are amplified as thymines, and 5-mC residues are amplified as cytosines in PCR. Comparison of sequence information between the reference genome and bisulfite-treated DNA can provide single-nucleotide resolution information about cytosine methylation patterns. Sequence-Specific Enzyme Digestion Restriction enzymes are used to generate DNA •High enzyme turnover •Determination of methylation status is limited by the enzyme recognition site fragments for methylation •Well-studied •Overnight protocols analysis. Some restriction •Easy-to-use •Lower throughput enzymes are methylation- •Availability of recombinant sensitive (i.e., digestion is enzymes impaired or blocked by methylated DNA). When used in conjunction with an isoschizomer that has the same recognition site but is methylation insensitive, information about methylation status can be obtained. Additionally, the use of methylation- dependent restriction enzymes (i.e., requires methylated DNA for cleavage to occur) can be used to fragment DNA for sequencing analysis. Methylated DNA Fragmented genomic DNA Immunoprecipitation (restriction enzyme •Relatively fast •Dependent on antibody specificity digestion or sonication) is •Compatible with array-based •May require more than one 5-mC for antibody binding denatured and analysis •Requires DNA denaturation immunoprecipitated with •Applicable for high •Resolution depends on the size of the immunoprecipitated DNA and for microarray antibodies specific for 5- throughput sequencing experiments, depends on probe design mC. The enriched DNA •Data from repeat sequences may be overrepresented fragments can be analyzed by PCR for locus-specific studies or by microarrays (MeDIP-chip) and massively parallel sequencing (MeDIP- seq) for whole genome studies. Methylated DNA-Binding Instead of relying on Proteins antibodies for DNA •Well-studied •May require high DNA input enrichment, affinity-based •Does not require •May require a long protocol assays use proteins that denaturation •Requires salt elutions specifically bind methylated •Compatible with array-based •Does not give single base methylation resolution data or unmethylated CpG sites analysis in fragmented genomic DNA •Applicable for high (restriction enzyme throughput sequencing digestion or sonication). The enriched DNA fragments can be analyzed by PCR for locus-specific studies or by microarrays and massively parallel