Biotechnology by Owen Borville September 14, 2024
Biotechnology is the use of biological agents for technological advancement. Biotechnology was once used for breeding crops and livestock before the discovery of DNA structure in 1953, and scientific advancement allowed for more advancement in the field.
The main application of biotechnology are in medicine (including vaccine and antibiotic production) and agriculture (genetic modification of crops and livestock to increase yield). Industrial applications are in fermentation, cleaning oil spills, and biofuels production).
DNA and RNA must be extracted or isolated from cells in order to study or manipulate them.
A lysis buffer is a solution of mostly detergent enzymes that breaks cell membranes and nuclear membranes and releases cell contents. Lipid molecules are broken. Enzymes like proteases and ribonucleasis (RNAses) break down proteins and RNA.
Gel Electrophoresis Nucleic acids are negatively charged ions and an electric field can mobilize them. Gel electrophoresis is a technique that scientists use to separate molecules on the basis of size, using this charge. Nucleic acids can be separated as whole chromosomes, or fragments.
Polymerase chain reaction (PCR) is a technique that scientists use to amplify specific DNA regions for further analysis. Used to clone gene fragments, analyze genetic diseases, identify contaminant foreign DNA in sample, and amplifying DNA for sequencing, determining paternity, and detecting genetic diseases. The PCR Cycle contains three steps: denaturation, annealing, and DNA synthesis. The PCR Cycle is repeated continuously, doubling DNA molecules each time.
Reverse transcriptase PCR (RT-PCR) is a PCR technique that involves converting RNA to DNA by reverse transcriptase enzyme. The first step is to recreate the original DNA template strand (called cDNA) by applying DNA nucleotides to the mRNA. Then after the cDNA is made, then regular PCR can be used to amplify it.
A probe is a small DNA fragment used to determine if the complementary sequence is present in a DNA sample, by using radioactive of fluorescent dyes to aid detection.
Nucleic acid fragments are transferred from the gel into a nylon membrane with a procedure called blotting.
Southern blotting is when DNA is transferred to a nylon membrane and Northern blotting is when RNA is transferred to a nylon membrane.
Molecular Cloning of DNA Fragments Cloning small genome fragments allows researchers to manipulate and study specific genes and their protein products, or non-coding regions in isolation.
A plasmid, or vector, is a small circular DNA molecule that replicates independently of the chromosomal DNA. Plasmids occur naturally in bacteria populations and have genes that can contribute to favorable traits of the organism, like antibiotic resistance, the ability to be unaffected by antibiotics.
The DNA fragment of the human genome or genome of another organism is called foreign DNA, or transgene. The bacterium's DNA is the host DNA.
The multiple cloning site (MCS) is the site that multiple restriction endonucleases can recognize. The MCS is a short DNA sequence containing multiple sites that different commonly available restriction endonucleases can cut.
Restriction endonucleases recognize specific DNA sequences and cut them in a predictable manner and are naturally produced by bacteria as a defense mechanism against foreign DNA.
Recombinant DNA are plasmid molecules with foreign DNA inserted into them or combined with them thus they are created artificially. They are also called chimeric molecules because the origin of different molecule parts of the molecules can be traced back to different species of biological organisms or even to chemical synthesis.
Recombinant proteins are proteins expressed from recombinant DNA molecules, but not all recombinant plasmids are capable of expressing genes.
Cellular cloning is when unicellular organisms, such as bacteria and yeast, naturally produce clones of themselves when they replicate asexually by binary fission. The nuclear DNA replicates by the process of mitosis and creates an exact replica of the genetic material.
Reproductive cloning is a method scientists use to clone or identically copy an entire multicellular organism. While most multicellular organisms reproduce sexually, advances in biotechnology have allowed artificially induced mammal asexual reproduction in the laboratory.
Parthenogenesis occurs when an embryo grows and develops without egg fertilization, a form of asexual reproduction. Combining an egg cell haploid nucleus with a diploid nucleus from a donor of the same species, it will become a zygote genetically identical to the donor.
Genetic engineering is the alteration of an organism's genotype using recombinant DNA technology (foreign DNA) to modify an organism's DNA to achieve desirable traits.
A genetically modified organism (GMO) is the organism that receives the recombinant DNA. If the foreign DNA comes from a different species, the host organism is transgenic. Scientists have genetically modified bacteria, plants, and animals since the 1970's for medical, agricultural, industrial, and academic purposes. GMOs from plants are common in processed foods.
Gene targeting is the use of recombinant DNA vectors to alter a particular gene's expression, either by introducing mutations in a gene, or by eliminating a certain gene's expression by deleting a part or all of the gene sequence from the organism's genome.
Genetic diagnosis by genetic testing is the process of testing for suspected genetic defects before administering treatment.
Gene therapy is a genetic engineering technique used to cure diseases that involves introducing a good gene at a random location in the genome to aid the cure of a disease that is caused by a mutated gene. The good gene is usually introduced into diseased cells as part of a vector transmitted by a virus that can infect the host cell and deliver the foreign DNA.
Modern vaccination techniques use the genes of microorganisms cloned into vectors to mass produce the desired antigen, then introduce the antigen to the body to stimulate immune response. Antibiotics are a biotechnological product and microorganisms naturally produce them in order to survive.
Transgenic animals are animals that have been modified to express recombinant DNA from foreign DNA. Transgenic plants are plants that have received recombinant DNA from other species. Ti plasmids (tumor inducing) plasmids are derived from Agrobacterium tumefaciens that scientists have used to introduce foreign DNA into plant cells for antibiotic resistance.
The bacterium Bacillus thuringiensis (Bt) is an organic insecticide used to protect plants. The Flavr Savr tomato was the first GM crop on the market in 1994.
The Genome and Genetic Maps
Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. Genome mapping is the process of locating genes on each chromosome. A genetic map is an illustration that lists genes and their location on a chromosome. A genetic marker is a gene or sequence on a chromosome that co-segregates or shows genetic linkage with a specific trait. A physical map is a representation of physical distance in nucleotides between genes or genetic markers and present more details of smaller chromosome regions.
Linkage analysis is a procedure during study of genetic maps that analyzes the recombination frequency between genes to determine if they are linked or show independent assortment. Exchanging DNA between homologous chromosome pairs is called genetic recombination, which occurs by crossing over DNA between homologous DNA strands, such as non-sister chromatids.
Scientists use genetic markers to generate genetic maps, including: Restriction fragment length polymorphism (RFLP) is the variation between individuals in the length of DNA fragments, which restriction endonucleases generate. Variable number of tandem repeats (VNTRs) are repeated sets of nucleotides present in DNA’s non-coding regions. Microsatellite polymorphism is the variation between individuals in the sequence and number of microsatellite DNA repeats. Single nucleotide polymorphism (SNP) is the variation between individuals in a single nucleotide.
Physical maps for genetics are made using three methods: Cytogenic mapping uses information from microscopic analysis of stained chromosome sections.
Radiation hybrid mapping uses information obtained by fragmenting the chromosome with x-rays, breaking the DNA into fragments.
Sequence mapping resulted from DNA sequencing technology that allowed for creating detailed physical maps with distances measured in terms of the number of base pairs.
Creating genomic libraries and complimentary DNA (cDNA) libraries has accelerated the physical mapping process. STS (sequence-tagged site) is a unique sequence in the genome with a known exact chromosome location. An expressed sequence tag (EST) is a short STS that is identified with cDNA.
Whole Genome Sequencing is a process that determines an entire genome's DNA sequence. Whole-exome sequencing is a lower cost alternative to whole genome sequencing where the doctor only sequences the DNA's coding, exon-producing regions.
Sequencing strategies include:
The chain termination method or dideoxy method (developed by Frederick Sanger) involves DNA replication of a single-stranded template by using a primer and a regular deoxynucleotide (dNTP), which is a monomer, or a single DNA unit. The primer and dNTP mix with a small proportion of fluorescently labeled dideoxynucleotides (ddNTPs). Chain termination is a DNA sequencing technique that uses (ddNTPs) to terminate the growing DNA strand. The DNA polymerase enzyme incorporates ddNTPs into the DNA strand during replication, which terminates the strand because the ddNTPs lack a hydroxyl group needed to form a bond with the next nucleotide. The fragments of different lengths are separated on a gel and read by a laser to produce a chromatogram. A computer converts the letters to produce the final sequence. Using dideoxynucleotides, the DNA fragment can terminate at different points. The DNA separates on the basis of size, and these bands can be read based on the fragments’ size.
Shotgun sequencing method involves randomly breaking up the genome into small DNA fragments that are sequenced individually. A computer program looks for overlaps in the DNA sequences, using them to reassemble the fragments in their correct order to reconstitute the genome. A larger sequence that is assembled from overlapping shorter sequences is called a contig.
Pairwise-end sequencing requires analyzing each fragment’s end for overlap. Pairwise-end sequencing is, therefore, more difficult than shotgun sequencing, but it is easier to reconstruct the sequence because there is more available information.
Next-generation sequencing (deep sequencing or massively parallel sequencing), is a group of automated techniques used for rapid DNA sequencing. These automated low-cost sequencers can generate sequences of hundreds of thousands or millions of short fragments (25 to 500 base pairs) in the time frame of one day. These sequencers use sophisticated software to get through the difficult process of assembling all of the fragments in order.
A model organism is a species that researchers use as a model to understand the biological processes in other species that the model organism represents. Having entire genomes sequenced helps with the research efforts in these model organisms.
Genome annotation is the process of attaching biological information to gene sequences. Annotating gene sequences helps with basic experiments in molecular biology, such as designing PCR primers and RNA targets.
DNA microarrays are methods that scientists use to detect gene expression and genome regions by analyzing different DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and sequences. The DNA microarray is a collection of microscopic DNA spots, or probes, attached to a solid surface, or chip. The chip is then exposed to DNA or RNA from a sample, such as cells or tissue. The probes detect and quantify the relative abundance of transcripts in the sample. Applications include genetic diagnosis, biofilm research, and cancer research.
Predicting disease with genomics: Most of the common diseases, such as heart disease, are multi-factored or polygenic, which is a phenotypic characteristic that involves two or more genes, and also involves environmental factors such as diet.
Pharmacogenomics, or toxicogenomics, involves evaluating drug effectiveness and safety on the basis of information from an individual's genomic sequence. Pharmacogenomics can help doctors predict drug effectiveness on a particular patient based on genomics, determine the best dose level, and find the best medication for a patient.
Metagenomics is the study of the collective genomes of multiple species that grow and interact in an environmental niche. Metagenomics can be used to identify new species more rapidly and to analyze the effect of pollutants on the environment. Metagenomics is the study of the structure and function of entire nucleotide sequences isolated and analyzed from all the organisms (typically microbes) in a bulk sample.
Metagenomics is often used to study a specific community of microorganisms, such as those residing on human skin, in the soil or in a water sample. Metagenomics provides a means for studying microbial communities in their own environment. Complex ecological interactions, including lateral gene transfer, phage-host dynamics, and metabolic complementation—can now be studied with the lens of metagenomics. All genomic DNA from a particular environment is cut into fragments and ligated into a cloning vector. Each color represents DNA from a different species. The fragments are sequenced, and regions of overlap are used to determine the genomic sequences.
The genomics of microorganisms is being used to find better ways to harness biofuels from algae and cyanobacteria. The main sources of fuel today are coal, oil, wood, and other plant products, such as ethanol. However, there is a need for more alternative renewable sources of energy, such as with the microbial community, which is one of the largest sources of genes, enzymes, and organic material that can help with medical vaccines, disease treatment, and environmental cleanup.
Mitochondria are cellular organelles with their own DNA that mutates rapidly. Mitochondrial genomics is commonly used to trace genealogy, because mitochondrial DNA often passes through the mother during the fertilization process.
Genomics can also be used in agriculture to increase crop yield and quantity by searching for desirable traits with genomic data and linking traits to genes.
Proteomics: Proteins are the final products of genes that help perform the functions of genes. All enzymes except ribozymes are proteins and proteins regulate molecules, some help transport oxygen, and some proteins are antibodies. A proteome is the entire set of proteins that a cell type produces and proteomes are included in genomes.
Proteomics is the study of proteomes' function and proteomics complements genomics. While the genome is constant, the proteome varies within an organism. Proteomics is the study of the interactions, function, composition, and structures of proteins and their cellular activities. Proteomics provides a better understanding of the structure and function of the organism than genomics. Proteomics aims to identify the subcellular location of each protein. This information can be used to create a 3-D protein map of the cell, providing novel information about protein regulation.
Metabolomics involves studying small molecule metabolites in an organism. The metabolome is the complete set of metabolites that are related to an organism's genetic makeup. Metabolomics offers an opportunity to compare genetic makeup and physical characteristics, as well as genetic makeup and environmental factors. The goal of metabolome research is to identify, quantify, and catalogue all the metabolites in living organisms' tissues and fluids. Metabolomics is an emerging field and is broadly defined as the comprehensive measurement of all metabolites and low-molecular-weight molecules in a biological specimen.
Techniques for protein analysis include mass spectrometry, x-ray crystallography, nuclear magnetic resonance (NMR), protein microarrays, along with computer software.
Systems biology, which includes genomic and proteomic-scale analysis, is the study of whole biological systems (genomes and proteomes), based on interactions within the system. Proteins are naturally unstable and more difficult to research proteomic analysis than genomic analysis.
Genomes and proteomes are used to study the genetic basis of diseases, the most prominent of which is cancer. Protein expression can indicate disease processes and an individual protein is a biomarker. A set of proteins with altered expression levels is a protein signature.
A false negative is an incorrect test result that should have been positive and this is the current problem with biomarkers for early cancer detection. Many cancer cases are undetected, so that biomarkers are unreliable. However, protein signatures may be more reliable than biomarkers for cancer detection.
Biotechnology is the use of biological agents for technological advancement. Biotechnology was once used for breeding crops and livestock before the discovery of DNA structure in 1953, and scientific advancement allowed for more advancement in the field.
The main application of biotechnology are in medicine (including vaccine and antibiotic production) and agriculture (genetic modification of crops and livestock to increase yield). Industrial applications are in fermentation, cleaning oil spills, and biofuels production).
DNA and RNA must be extracted or isolated from cells in order to study or manipulate them.
A lysis buffer is a solution of mostly detergent enzymes that breaks cell membranes and nuclear membranes and releases cell contents. Lipid molecules are broken. Enzymes like proteases and ribonucleasis (RNAses) break down proteins and RNA.
Gel Electrophoresis Nucleic acids are negatively charged ions and an electric field can mobilize them. Gel electrophoresis is a technique that scientists use to separate molecules on the basis of size, using this charge. Nucleic acids can be separated as whole chromosomes, or fragments.
Polymerase chain reaction (PCR) is a technique that scientists use to amplify specific DNA regions for further analysis. Used to clone gene fragments, analyze genetic diseases, identify contaminant foreign DNA in sample, and amplifying DNA for sequencing, determining paternity, and detecting genetic diseases. The PCR Cycle contains three steps: denaturation, annealing, and DNA synthesis. The PCR Cycle is repeated continuously, doubling DNA molecules each time.
Reverse transcriptase PCR (RT-PCR) is a PCR technique that involves converting RNA to DNA by reverse transcriptase enzyme. The first step is to recreate the original DNA template strand (called cDNA) by applying DNA nucleotides to the mRNA. Then after the cDNA is made, then regular PCR can be used to amplify it.
A probe is a small DNA fragment used to determine if the complementary sequence is present in a DNA sample, by using radioactive of fluorescent dyes to aid detection.
Nucleic acid fragments are transferred from the gel into a nylon membrane with a procedure called blotting.
Southern blotting is when DNA is transferred to a nylon membrane and Northern blotting is when RNA is transferred to a nylon membrane.
Molecular Cloning of DNA Fragments Cloning small genome fragments allows researchers to manipulate and study specific genes and their protein products, or non-coding regions in isolation.
A plasmid, or vector, is a small circular DNA molecule that replicates independently of the chromosomal DNA. Plasmids occur naturally in bacteria populations and have genes that can contribute to favorable traits of the organism, like antibiotic resistance, the ability to be unaffected by antibiotics.
The DNA fragment of the human genome or genome of another organism is called foreign DNA, or transgene. The bacterium's DNA is the host DNA.
The multiple cloning site (MCS) is the site that multiple restriction endonucleases can recognize. The MCS is a short DNA sequence containing multiple sites that different commonly available restriction endonucleases can cut.
Restriction endonucleases recognize specific DNA sequences and cut them in a predictable manner and are naturally produced by bacteria as a defense mechanism against foreign DNA.
Recombinant DNA are plasmid molecules with foreign DNA inserted into them or combined with them thus they are created artificially. They are also called chimeric molecules because the origin of different molecule parts of the molecules can be traced back to different species of biological organisms or even to chemical synthesis.
Recombinant proteins are proteins expressed from recombinant DNA molecules, but not all recombinant plasmids are capable of expressing genes.
Cellular cloning is when unicellular organisms, such as bacteria and yeast, naturally produce clones of themselves when they replicate asexually by binary fission. The nuclear DNA replicates by the process of mitosis and creates an exact replica of the genetic material.
Reproductive cloning is a method scientists use to clone or identically copy an entire multicellular organism. While most multicellular organisms reproduce sexually, advances in biotechnology have allowed artificially induced mammal asexual reproduction in the laboratory.
Parthenogenesis occurs when an embryo grows and develops without egg fertilization, a form of asexual reproduction. Combining an egg cell haploid nucleus with a diploid nucleus from a donor of the same species, it will become a zygote genetically identical to the donor.
Genetic engineering is the alteration of an organism's genotype using recombinant DNA technology (foreign DNA) to modify an organism's DNA to achieve desirable traits.
A genetically modified organism (GMO) is the organism that receives the recombinant DNA. If the foreign DNA comes from a different species, the host organism is transgenic. Scientists have genetically modified bacteria, plants, and animals since the 1970's for medical, agricultural, industrial, and academic purposes. GMOs from plants are common in processed foods.
Gene targeting is the use of recombinant DNA vectors to alter a particular gene's expression, either by introducing mutations in a gene, or by eliminating a certain gene's expression by deleting a part or all of the gene sequence from the organism's genome.
Genetic diagnosis by genetic testing is the process of testing for suspected genetic defects before administering treatment.
Gene therapy is a genetic engineering technique used to cure diseases that involves introducing a good gene at a random location in the genome to aid the cure of a disease that is caused by a mutated gene. The good gene is usually introduced into diseased cells as part of a vector transmitted by a virus that can infect the host cell and deliver the foreign DNA.
Modern vaccination techniques use the genes of microorganisms cloned into vectors to mass produce the desired antigen, then introduce the antigen to the body to stimulate immune response. Antibiotics are a biotechnological product and microorganisms naturally produce them in order to survive.
Transgenic animals are animals that have been modified to express recombinant DNA from foreign DNA. Transgenic plants are plants that have received recombinant DNA from other species. Ti plasmids (tumor inducing) plasmids are derived from Agrobacterium tumefaciens that scientists have used to introduce foreign DNA into plant cells for antibiotic resistance.
The bacterium Bacillus thuringiensis (Bt) is an organic insecticide used to protect plants. The Flavr Savr tomato was the first GM crop on the market in 1994.
The Genome and Genetic Maps
Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. Genome mapping is the process of locating genes on each chromosome. A genetic map is an illustration that lists genes and their location on a chromosome. A genetic marker is a gene or sequence on a chromosome that co-segregates or shows genetic linkage with a specific trait. A physical map is a representation of physical distance in nucleotides between genes or genetic markers and present more details of smaller chromosome regions.
Linkage analysis is a procedure during study of genetic maps that analyzes the recombination frequency between genes to determine if they are linked or show independent assortment. Exchanging DNA between homologous chromosome pairs is called genetic recombination, which occurs by crossing over DNA between homologous DNA strands, such as non-sister chromatids.
Scientists use genetic markers to generate genetic maps, including: Restriction fragment length polymorphism (RFLP) is the variation between individuals in the length of DNA fragments, which restriction endonucleases generate. Variable number of tandem repeats (VNTRs) are repeated sets of nucleotides present in DNA’s non-coding regions. Microsatellite polymorphism is the variation between individuals in the sequence and number of microsatellite DNA repeats. Single nucleotide polymorphism (SNP) is the variation between individuals in a single nucleotide.
Physical maps for genetics are made using three methods: Cytogenic mapping uses information from microscopic analysis of stained chromosome sections.
Radiation hybrid mapping uses information obtained by fragmenting the chromosome with x-rays, breaking the DNA into fragments.
Sequence mapping resulted from DNA sequencing technology that allowed for creating detailed physical maps with distances measured in terms of the number of base pairs.
Creating genomic libraries and complimentary DNA (cDNA) libraries has accelerated the physical mapping process. STS (sequence-tagged site) is a unique sequence in the genome with a known exact chromosome location. An expressed sequence tag (EST) is a short STS that is identified with cDNA.
Whole Genome Sequencing is a process that determines an entire genome's DNA sequence. Whole-exome sequencing is a lower cost alternative to whole genome sequencing where the doctor only sequences the DNA's coding, exon-producing regions.
Sequencing strategies include:
The chain termination method or dideoxy method (developed by Frederick Sanger) involves DNA replication of a single-stranded template by using a primer and a regular deoxynucleotide (dNTP), which is a monomer, or a single DNA unit. The primer and dNTP mix with a small proportion of fluorescently labeled dideoxynucleotides (ddNTPs). Chain termination is a DNA sequencing technique that uses (ddNTPs) to terminate the growing DNA strand. The DNA polymerase enzyme incorporates ddNTPs into the DNA strand during replication, which terminates the strand because the ddNTPs lack a hydroxyl group needed to form a bond with the next nucleotide. The fragments of different lengths are separated on a gel and read by a laser to produce a chromatogram. A computer converts the letters to produce the final sequence. Using dideoxynucleotides, the DNA fragment can terminate at different points. The DNA separates on the basis of size, and these bands can be read based on the fragments’ size.
Shotgun sequencing method involves randomly breaking up the genome into small DNA fragments that are sequenced individually. A computer program looks for overlaps in the DNA sequences, using them to reassemble the fragments in their correct order to reconstitute the genome. A larger sequence that is assembled from overlapping shorter sequences is called a contig.
Pairwise-end sequencing requires analyzing each fragment’s end for overlap. Pairwise-end sequencing is, therefore, more difficult than shotgun sequencing, but it is easier to reconstruct the sequence because there is more available information.
Next-generation sequencing (deep sequencing or massively parallel sequencing), is a group of automated techniques used for rapid DNA sequencing. These automated low-cost sequencers can generate sequences of hundreds of thousands or millions of short fragments (25 to 500 base pairs) in the time frame of one day. These sequencers use sophisticated software to get through the difficult process of assembling all of the fragments in order.
A model organism is a species that researchers use as a model to understand the biological processes in other species that the model organism represents. Having entire genomes sequenced helps with the research efforts in these model organisms.
Genome annotation is the process of attaching biological information to gene sequences. Annotating gene sequences helps with basic experiments in molecular biology, such as designing PCR primers and RNA targets.
DNA microarrays are methods that scientists use to detect gene expression and genome regions by analyzing different DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and sequences. The DNA microarray is a collection of microscopic DNA spots, or probes, attached to a solid surface, or chip. The chip is then exposed to DNA or RNA from a sample, such as cells or tissue. The probes detect and quantify the relative abundance of transcripts in the sample. Applications include genetic diagnosis, biofilm research, and cancer research.
Predicting disease with genomics: Most of the common diseases, such as heart disease, are multi-factored or polygenic, which is a phenotypic characteristic that involves two or more genes, and also involves environmental factors such as diet.
Pharmacogenomics, or toxicogenomics, involves evaluating drug effectiveness and safety on the basis of information from an individual's genomic sequence. Pharmacogenomics can help doctors predict drug effectiveness on a particular patient based on genomics, determine the best dose level, and find the best medication for a patient.
Metagenomics is the study of the collective genomes of multiple species that grow and interact in an environmental niche. Metagenomics can be used to identify new species more rapidly and to analyze the effect of pollutants on the environment. Metagenomics is the study of the structure and function of entire nucleotide sequences isolated and analyzed from all the organisms (typically microbes) in a bulk sample.
Metagenomics is often used to study a specific community of microorganisms, such as those residing on human skin, in the soil or in a water sample. Metagenomics provides a means for studying microbial communities in their own environment. Complex ecological interactions, including lateral gene transfer, phage-host dynamics, and metabolic complementation—can now be studied with the lens of metagenomics. All genomic DNA from a particular environment is cut into fragments and ligated into a cloning vector. Each color represents DNA from a different species. The fragments are sequenced, and regions of overlap are used to determine the genomic sequences.
The genomics of microorganisms is being used to find better ways to harness biofuels from algae and cyanobacteria. The main sources of fuel today are coal, oil, wood, and other plant products, such as ethanol. However, there is a need for more alternative renewable sources of energy, such as with the microbial community, which is one of the largest sources of genes, enzymes, and organic material that can help with medical vaccines, disease treatment, and environmental cleanup.
Mitochondria are cellular organelles with their own DNA that mutates rapidly. Mitochondrial genomics is commonly used to trace genealogy, because mitochondrial DNA often passes through the mother during the fertilization process.
Genomics can also be used in agriculture to increase crop yield and quantity by searching for desirable traits with genomic data and linking traits to genes.
Proteomics: Proteins are the final products of genes that help perform the functions of genes. All enzymes except ribozymes are proteins and proteins regulate molecules, some help transport oxygen, and some proteins are antibodies. A proteome is the entire set of proteins that a cell type produces and proteomes are included in genomes.
Proteomics is the study of proteomes' function and proteomics complements genomics. While the genome is constant, the proteome varies within an organism. Proteomics is the study of the interactions, function, composition, and structures of proteins and their cellular activities. Proteomics provides a better understanding of the structure and function of the organism than genomics. Proteomics aims to identify the subcellular location of each protein. This information can be used to create a 3-D protein map of the cell, providing novel information about protein regulation.
Metabolomics involves studying small molecule metabolites in an organism. The metabolome is the complete set of metabolites that are related to an organism's genetic makeup. Metabolomics offers an opportunity to compare genetic makeup and physical characteristics, as well as genetic makeup and environmental factors. The goal of metabolome research is to identify, quantify, and catalogue all the metabolites in living organisms' tissues and fluids. Metabolomics is an emerging field and is broadly defined as the comprehensive measurement of all metabolites and low-molecular-weight molecules in a biological specimen.
Techniques for protein analysis include mass spectrometry, x-ray crystallography, nuclear magnetic resonance (NMR), protein microarrays, along with computer software.
Systems biology, which includes genomic and proteomic-scale analysis, is the study of whole biological systems (genomes and proteomes), based on interactions within the system. Proteins are naturally unstable and more difficult to research proteomic analysis than genomic analysis.
Genomes and proteomes are used to study the genetic basis of diseases, the most prominent of which is cancer. Protein expression can indicate disease processes and an individual protein is a biomarker. A set of proteins with altered expression levels is a protein signature.
A false negative is an incorrect test result that should have been positive and this is the current problem with biomarkers for early cancer detection. Many cancer cases are undetected, so that biomarkers are unreliable. However, protein signatures may be more reliable than biomarkers for cancer detection.