A DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is a collection of microscopic DNA spots, commonly representing single genes, arrayed on a solid surface by covalent attachment to chemically suitable matrices.
DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system. Qualitative or quantitative measurements with DNA microarrays utilize the selective nature of DNA-DNA or DNA-RNA hybridization under high-stringency conditions and fluorophore-based detection. DNA arrays are commonly used for expression profiling, i.e., monitoring expression levels of thousands of genes simultaneously, or for comparative genomic hybridization.
Microarray technology is often used for gene expression profiling. It makes use of the sequence resources created by the genome sequencing projects and other sequencing efforts to answer the question, what genes are expressed in a particular cell type of an organism, at a particular time, under particular conditions?
For instance, they allow comparison of gene expression between normal and diseased (e.g., cancerous) cells. There are several names for this technology - DNA microarrays, DNA arrays, DNA chips, gene chips, others. Sometimes a distinction is made between these names but in fact they are all synonyms as there are no standard definitions for which type of microarray technology should be called by which name.
Microarrays exploit the preferential binding of complementary nucleic acid sequences. A microarray is typically a glass slide, on to which DNA molecules are attached at fixed locations (spots or features). There may be tens of thousands of spots on an array, each containing a huge number of identical DNA molecules (or fragments of identical molecules), of lengths from twenty to hundreds of nucleotides. The spots on a microarray are either printed on the microarrays by a robot, or synthesized by photo-lithography (similar to computer chip productions) or by ink-jet printing. There are commercially available microarrays, however many academic labs produce their own microarrays.
Microarrays that contain all of the about 6000 genes of the yeast genome have been available since 1997. The latest generations of commercial microarrays represent the entire human genome, more than 30,000 genes, on two microarrays.
Friday, September 28, 2007
Tuesday, September 25, 2007
Genetic Carrying Handles: Cloning Vectors
In order to clone a gene, its DNA sequence must be attached to some kind of carrier, also made of DNA, that can take it into the cell. Biologists call these carriers vectors. A vector acts like a handle for the DNA, and it also contains other tools such as an origin of replication and a selective marker.
The origin of replication is a sequence of DNA that the host cell recognizes that allows it to make more copies of the clone DNA sequence. This origin sequence is where the cell begins copying the vector and the attached clone DNA. The selective marker is a specific DNA sequence that is used by biologists to tell if the clone has entered the cell, and they are usually genes that confer antibiotic resistance to the cell.
The most common media used for this process is actually very similar to chicken soup, but the carbohydrate agarose is added to convert the media into a semi-solid substance, since bacterial colonies are much easier to detect on a semi-solid surface. Agarose is much like gelatin, but it comes from seaweed and unlike gelatin, most bacteria cannot digest it. Antibiotics are often added to the media, to kill any cells that do not possess the antibiotic resistant selective marker gene, which is in the clone DNA. This way, biologists can ensure that all the remaining cells have in fact taken up the clone DNA and its vector.
These cells are called transfected cells. Antibiotics are not the only way to identify transfected cells. Biologists sometimes use selective markers that turn cells a different colour or even to make them glow. Common proteins that do this include luciferase, which makes fireflies glow or green fluorescent protein, which comes from certain species of jellyfish. Green fluorescent protein also comes in other colours!
The origin of replication is a sequence of DNA that the host cell recognizes that allows it to make more copies of the clone DNA sequence. This origin sequence is where the cell begins copying the vector and the attached clone DNA. The selective marker is a specific DNA sequence that is used by biologists to tell if the clone has entered the cell, and they are usually genes that confer antibiotic resistance to the cell.
The most common media used for this process is actually very similar to chicken soup, but the carbohydrate agarose is added to convert the media into a semi-solid substance, since bacterial colonies are much easier to detect on a semi-solid surface. Agarose is much like gelatin, but it comes from seaweed and unlike gelatin, most bacteria cannot digest it. Antibiotics are often added to the media, to kill any cells that do not possess the antibiotic resistant selective marker gene, which is in the clone DNA. This way, biologists can ensure that all the remaining cells have in fact taken up the clone DNA and its vector.
These cells are called transfected cells. Antibiotics are not the only way to identify transfected cells. Biologists sometimes use selective markers that turn cells a different colour or even to make them glow. Common proteins that do this include luciferase, which makes fireflies glow or green fluorescent protein, which comes from certain species of jellyfish. Green fluorescent protein also comes in other colours!
Sunday, September 23, 2007
Bacterial artificial chromosome
A bacterial artificial chromosome (BAC) is a DNA construct, based on a fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually E. coli. F-plasmids play a crucial role because they contain partition genes that promote the even distribution of plasmids after bacterial cell division. The bacterial artificial chromosome's usual insert size is 150 kbp, with a range from 100 to 300 kbp. A similar cloning vector, called a PAC has also been produced from the bacterial P1-plasmid.
BACs are often used to sequence the genetic code of organisms in genome projects, for example the Human Genome Project. A short piece of the organism's DNA is amplified as an insert in BACs, and then sequenced. Finally, the sequenced parts are rearranged in silico, resulting in the genomic sequence of the organism.
Wednesday, September 19, 2007
Bats and Humans share a common Gene for communication
Finding: The FOXP2 gene found in humans and bats allows human language evolution and bat echo location.
Discoveries that mutations in the FoxP2 gene lead to speech defects and that the gene underwent changes around the time language evolved both implicate FOXP2 in the evolution of human language.
No genetic variation exists among many vertebrates
Recently, patterns of gene expression in birds, humans and rodents have suggested a wider role in the production of vocalisations. But many reports have established that FOXP2 shows very little genetic variation across even distantly related vertebrates - from reptiles to mammals -- providing few extra clues as to the gene's role.
Genetic Variation does exist with echo locating bats
A new study, undertaken by a joint of team of British and Chinese scientists, has found that this gene shows unparalleled variation in echolocating bats. The results, appearing in a study report that FOXP2 sequence differences among bat lineages correspond well to contrasting forms of echolocation.
Bats like people need coordination of mouth and face for communication
Like speech, bat echolocation involves producing complex vocal signals via sophisticated coordination of the mouth and face. The involvement of FOXP2 in the evolution of echolocation adds weighty support to the theory that FOXP2 functions in the sensory-motor coordination of vocalisations.
Discoveries that mutations in the FoxP2 gene lead to speech defects and that the gene underwent changes around the time language evolved both implicate FOXP2 in the evolution of human language.
No genetic variation exists among many vertebrates
Recently, patterns of gene expression in birds, humans and rodents have suggested a wider role in the production of vocalisations. But many reports have established that FOXP2 shows very little genetic variation across even distantly related vertebrates - from reptiles to mammals -- providing few extra clues as to the gene's role.
Genetic Variation does exist with echo locating bats
A new study, undertaken by a joint of team of British and Chinese scientists, has found that this gene shows unparalleled variation in echolocating bats. The results, appearing in a study report that FOXP2 sequence differences among bat lineages correspond well to contrasting forms of echolocation.
Bats like people need coordination of mouth and face for communication
Like speech, bat echolocation involves producing complex vocal signals via sophisticated coordination of the mouth and face. The involvement of FOXP2 in the evolution of echolocation adds weighty support to the theory that FOXP2 functions in the sensory-motor coordination of vocalisations.
Tuesday, September 18, 2007
New Method Can Reveal Ancestry Of All Genes Across Many Different Genomes
Finding: A new method has been developed that can reveal the ancestry of all genes across many different genomes. First applied to 17 species of fungi, the approach has unearthed some surprising clues about why new genes pop up in the first place and the biological nips and tucks that bolster their survival.
The problem
The wheels of evolution turn on genetic innovation as new genes with new functions appear, allowing organisms to grow and adapt in new ways. But deciphering the history of how and when various genes appeared, for any organism, has been a difficult and largely intractable task. Having the ability to trace the history of genes on a genomic scale opens the doors to a vast array of interesting and largely unexplored scientific questions. Although the principles laid out in the study pertain to fungi, they could have relevance to a variety of other species as well.
What we know
It has been recognized for decades that new genes first arise as carbon copies of existing genes. It is thought that this replication allows one of the gene copies to persist normally, while giving the other the freedom to acquire novel biological functions. Though the importance of this so-called gene duplication process is well appreciated it is the grist for the mill of evolutionary change the actual mechanics have remained murky, in part because scientists have lacked the tools to study it systematically.
Genes from 17 different species
Driven by the recent explosion of whole genome sequence data, the authors of the new study were able to assemble a natural history of more than 100,000 genes belonging to a group of fungi known as the Ascomycota. From this, the researchers gained a detailed view of gene duplication across the genomes of 17 different species of fungi, including the laboratory model Saccharomyces cerevisiae, commonly known as baker's yeast.
Methodology - Synergy
The basis for the work comes from a new method termed "SYNERGY", which first author Ilan Wapinski and his coworkers developed to help them reconstruct the ancestry of each fungal gene.
By tracing a gene's lineage through various species, the method helps determine in which species the gene first arose, and if -- and in what species -- it became duplicated or even lost altogether. SYNERGY draws its strength from the use of multiple types of data, including the evolutionary or "phylogenetic" tree that depicts how species are related to each other, and the DNA sequences and relative positions of genes along the genome.
Perhaps most importantly, the method does not tackle the problem of gene origins in one fell swoop, as has typically been done, but rather breaks it into discrete, more manageable bits. Instead of treating all species at once, SYNERGY first focuses on a pair of the most recently evolved species -- those at the outer branches of the tree -- and works, two-by-two, toward the more ancestral species that comprise the roots.
From this analysis scientists were able to identify a set of core principles that govern gene duplication in fungi. The findings begin to paint a picture of how new genes are groomed over hundreds of millions of years of evolution.
The problem
The wheels of evolution turn on genetic innovation as new genes with new functions appear, allowing organisms to grow and adapt in new ways. But deciphering the history of how and when various genes appeared, for any organism, has been a difficult and largely intractable task. Having the ability to trace the history of genes on a genomic scale opens the doors to a vast array of interesting and largely unexplored scientific questions. Although the principles laid out in the study pertain to fungi, they could have relevance to a variety of other species as well.
What we know
It has been recognized for decades that new genes first arise as carbon copies of existing genes. It is thought that this replication allows one of the gene copies to persist normally, while giving the other the freedom to acquire novel biological functions. Though the importance of this so-called gene duplication process is well appreciated it is the grist for the mill of evolutionary change the actual mechanics have remained murky, in part because scientists have lacked the tools to study it systematically.
Genes from 17 different species
Driven by the recent explosion of whole genome sequence data, the authors of the new study were able to assemble a natural history of more than 100,000 genes belonging to a group of fungi known as the Ascomycota. From this, the researchers gained a detailed view of gene duplication across the genomes of 17 different species of fungi, including the laboratory model Saccharomyces cerevisiae, commonly known as baker's yeast.
Methodology - Synergy
The basis for the work comes from a new method termed "SYNERGY", which first author Ilan Wapinski and his coworkers developed to help them reconstruct the ancestry of each fungal gene.
By tracing a gene's lineage through various species, the method helps determine in which species the gene first arose, and if -- and in what species -- it became duplicated or even lost altogether. SYNERGY draws its strength from the use of multiple types of data, including the evolutionary or "phylogenetic" tree that depicts how species are related to each other, and the DNA sequences and relative positions of genes along the genome.
Perhaps most importantly, the method does not tackle the problem of gene origins in one fell swoop, as has typically been done, but rather breaks it into discrete, more manageable bits. Instead of treating all species at once, SYNERGY first focuses on a pair of the most recently evolved species -- those at the outer branches of the tree -- and works, two-by-two, toward the more ancestral species that comprise the roots.
From this analysis scientists were able to identify a set of core principles that govern gene duplication in fungi. The findings begin to paint a picture of how new genes are groomed over hundreds of millions of years of evolution.
Monday, September 17, 2007
History of Bacteria evolution
Finding: The evolutionary history of bacteria has been worked out.
Unlike other organisms that tend to pass their genes on to the next generation of their own species, bacteria often exchange genetic material with totally unrelated species a process called lateral gene transfer.
Researchers did not believe that they could work out the evolutionary history of bacteria. But now, thanks to the availability of sequenced genomes for groups of related bacteria, and a new analytical approach, researchers at have been able to demonstrate that constructing a bacterial family tree is indeed possible.
Here is how they do it
Scientists propose an approach that begins by scouring genomes for a set of genes that serve as reliable indicators of bacterial evolution. This method has important implications for biologists studying the evolutionary history of organisms by establishing a foundation for charting the evolutionary events, such as lateral gene transfer, that shape the structure and substance of genomes.
In this study, the researchers chose the ancient bacterial group called gamma Proteobacteria, an ecologically diverse group (including Escherichia coli and Salmonella species) with the most documented cases of lateral gene transfer and the highest number of species with sequenced genomes.
Why use bacteria at all?
Bacteria promise to reveal a wealth of information about genomic evolution, because so many clusters of related bacterial genomes have been sequenced--allowing for broad comparative analysis among species--and because their genomes are small and compact.
The results support the ability of their method to reconstruct the important evolutionary events affecting genomes. Their approach promises to elucidate not only the evolution of bacterial genomes but also the diversification of bacterial species events that have occurred over the course of about a billion years of evolution.
Unlike other organisms that tend to pass their genes on to the next generation of their own species, bacteria often exchange genetic material with totally unrelated species a process called lateral gene transfer.
Researchers did not believe that they could work out the evolutionary history of bacteria. But now, thanks to the availability of sequenced genomes for groups of related bacteria, and a new analytical approach, researchers at have been able to demonstrate that constructing a bacterial family tree is indeed possible.
Here is how they do it
Scientists propose an approach that begins by scouring genomes for a set of genes that serve as reliable indicators of bacterial evolution. This method has important implications for biologists studying the evolutionary history of organisms by establishing a foundation for charting the evolutionary events, such as lateral gene transfer, that shape the structure and substance of genomes.
In this study, the researchers chose the ancient bacterial group called gamma Proteobacteria, an ecologically diverse group (including Escherichia coli and Salmonella species) with the most documented cases of lateral gene transfer and the highest number of species with sequenced genomes.
Why use bacteria at all?
Bacteria promise to reveal a wealth of information about genomic evolution, because so many clusters of related bacterial genomes have been sequenced--allowing for broad comparative analysis among species--and because their genomes are small and compact.
The results support the ability of their method to reconstruct the important evolutionary events affecting genomes. Their approach promises to elucidate not only the evolution of bacterial genomes but also the diversification of bacterial species events that have occurred over the course of about a billion years of evolution.
Sunday, September 16, 2007
Human - Chimpanzee split occured 5-7 million years ago
Finding- New research indicates that the split between chimpanzees and humans occured 5 to 7 million years ago. This improves the time differential which previously had a 10 million year range 3-13 million years. Now the differential is 2 million years.
How it was done:
Scientists analyzed the largest data set yet of genes that code for proteins and also used an improved computational approach that they developed, which takes into account more of the variability -- or statistical error--in the data than any other previous study. Gene studies are needed to address this problem because the interpretation of the earliest fossils of humans at the ape/human boundary are controversial and because almost no fossils of chimpanzees have been discovered.
The science team examined 167 different gene sequence sets from humans, chimpanzees, macaques, and mice.
No previous study has taken into account all of the error involved in estimating time with the molecular-clock method. The new statistical technique is a multifactor bootstrap-resampling approach.
Nucleotide arrangement
The scientists estimated the time of divergence between species by studying the sequential arrangement of nucleotides that make up the chain-like DNA molecules of each species. The number of mutations in the DNA sequence of a species, compared with other species, is a gauge of its rate of evolutionary change.
Calibration - rate of one species with that of another species
The minimum time of divergence
By calibrating this rate with the known time of divergence of a species on another branch of the tree-like diagram that shows relationships among species, scientists can estimate the time when the species they are studying evolved. In this case, the calibration time the scientists used was the split of Old World monkeys -- including baboons, macaques, and others -- from the branch of the phylogenetic tree that led to humans and apes, which fossil studies have shown is at least 24 million years ago. Using this calibration time, the team estimated that the human-chimp divergence occurred at least 5 million years ago, proportionally about one-fifth of the calibration time.
Other supporting evidence
The maximum time of divergence
This time is consistent with the findings of several research groups that have used the molecular-clock method to estimate the split of humans and chimpanzees since the first attempt in 1967. But this is only a minimum estimate, because it was based on a minimum calibration time. To obtain a maximum limit on the human-chimp divergence, the team used as a calibration point the maximum estimate, based on fossil studies, of the divergence of Old-World monkeys and the branch leading to humans -- 35 million years ago. Calculations using this date yielded a time for the human-chimp split of approximately 7 million years ago, which again was proportionally about one-fifth of the calibration time.
What else can be gathered from knowing the origin of the divergence?
Besides knowing when we divereged, a fact worth knowing, this divergence time also has considerable importance because it is used to establish how fast genes mutate in humans and to date the historical spread of our species around the globe.
Knowing the timescale of human evolution, and how we changed through time in relation to our environment, could provide valuable clues for understanding the evolution of intelligent life.
This research does not pinpoint the precise time of the split, it tells us that proportional differences on branches in family trees should be considered when proposing new times. For example, we now know that a 10-to-12-million-year human-chimp split would infer a divergence of Old World monkeys from our lineage that is too old (50-to-60-million years ago) to reconcile with the current fossil record of primates.
What then is the next step?
Although some additional improvement is possible by including more genes and more species, the greatest opportunity now for further narrowing this estimate of 5-to-7-million years will be the discovery of new fossils and the improvement in geologic dating of existing fossils.
How it was done:
Scientists analyzed the largest data set yet of genes that code for proteins and also used an improved computational approach that they developed, which takes into account more of the variability -- or statistical error--in the data than any other previous study. Gene studies are needed to address this problem because the interpretation of the earliest fossils of humans at the ape/human boundary are controversial and because almost no fossils of chimpanzees have been discovered.
The science team examined 167 different gene sequence sets from humans, chimpanzees, macaques, and mice.
No previous study has taken into account all of the error involved in estimating time with the molecular-clock method. The new statistical technique is a multifactor bootstrap-resampling approach.
Nucleotide arrangement
The scientists estimated the time of divergence between species by studying the sequential arrangement of nucleotides that make up the chain-like DNA molecules of each species. The number of mutations in the DNA sequence of a species, compared with other species, is a gauge of its rate of evolutionary change.
Calibration - rate of one species with that of another species
The minimum time of divergence
By calibrating this rate with the known time of divergence of a species on another branch of the tree-like diagram that shows relationships among species, scientists can estimate the time when the species they are studying evolved. In this case, the calibration time the scientists used was the split of Old World monkeys -- including baboons, macaques, and others -- from the branch of the phylogenetic tree that led to humans and apes, which fossil studies have shown is at least 24 million years ago. Using this calibration time, the team estimated that the human-chimp divergence occurred at least 5 million years ago, proportionally about one-fifth of the calibration time.
Other supporting evidence
The maximum time of divergence
This time is consistent with the findings of several research groups that have used the molecular-clock method to estimate the split of humans and chimpanzees since the first attempt in 1967. But this is only a minimum estimate, because it was based on a minimum calibration time. To obtain a maximum limit on the human-chimp divergence, the team used as a calibration point the maximum estimate, based on fossil studies, of the divergence of Old-World monkeys and the branch leading to humans -- 35 million years ago. Calculations using this date yielded a time for the human-chimp split of approximately 7 million years ago, which again was proportionally about one-fifth of the calibration time.
What else can be gathered from knowing the origin of the divergence?
Besides knowing when we divereged, a fact worth knowing, this divergence time also has considerable importance because it is used to establish how fast genes mutate in humans and to date the historical spread of our species around the globe.
Knowing the timescale of human evolution, and how we changed through time in relation to our environment, could provide valuable clues for understanding the evolution of intelligent life.
This research does not pinpoint the precise time of the split, it tells us that proportional differences on branches in family trees should be considered when proposing new times. For example, we now know that a 10-to-12-million-year human-chimp split would infer a divergence of Old World monkeys from our lineage that is too old (50-to-60-million years ago) to reconcile with the current fossil record of primates.
What then is the next step?
Although some additional improvement is possible by including more genes and more species, the greatest opportunity now for further narrowing this estimate of 5-to-7-million years will be the discovery of new fossils and the improvement in geologic dating of existing fossils.
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