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.
Saturday, September 15, 2007
Chimp-sized Hominid Walked Upright On Two Legs Six Million Years Ago
Finding: When did hominids begin to walk upright? Recent fossil evidence suggests that a chimp size hominid walked upright on two legs in Kenya's Tugen Hills, over 6 million years ago. That is about 3 million years earlier than "Lucy," the most famous early biped in our lineage.
How the finding occured:
A U.S. research team responsible for analysis of the CT scans of the internal structure of the fossil bone was responsible there is now solid evidence of the earliest upright posture and bipedalism securely dated to six million years.
The fossil the team studied is part of a left thighbone unearthed nearly four years ago by Senut and Pickford at their dig in the Kenyan Lukeino Formation. The fragment includes the intact head of the left thighbone -- the ball that is inserted into the hip socket joint -- plus the bony neck that connects the ball to the thighbone shaft as well as part of the thighbone shaft.
Measurements show that the fossil bone is about the same size as a chimpanzee's. However, CT scans of the interior of the bone reveal that the neck connecting the ball to the shaft is thinner on top than it is on the bottom, a sign the researchers say that the individual from which it came walked on two legs.
How does this compare to modern day apes and humans?
In present day chimps and gorillas, the thicknesses in the upper and lower parts of that bone are approximately equal. In modern humans, the bone on top is thinner than on the bottom by a ratio of one to four or more. The ratio in this fossil is one to three.
The key is the ratio
The ratio in the fossil is evidence for transition to an upright posture and habitual bipedal gait the researchers argue. In addition, because walking upright is the essential mark of a hominid, the ratio is functional evidence that the bones fossilized at Lukeino were from hominids.
Friday, September 14, 2007
Early Man Could Walk but not Run - No Achilles tendon
Finding: The earliest humans almost certainly walked upright on two legs but may have struggled to run at even half the speed of modern man.A new study proposes that if early humans lacked an Achilles tendon, as modern chimps and gorillas do, then their ability to run would have been severely compromised.
Research supports the belief that the earliest humans used efficient bipedal walking rather than chimp-like 'Groucho' walking. But if, as seems likely, early humans lacked an Achilles tendon then whilst their ability to walk would be largely unaffected our work suggests running effectiveness would be greatly reduced with top speeds halved and energy costs more than doubled.
Efficient running would have been essential to allow our ancestors to move from a largely herbivorous diet to the much more familiar hunting activities associated with later humans. What we need to discover now is when in our evolution did we develop an Achilles tendon as knowing this will help unravel the mystery of our origins.
Wednesday, September 12, 2007
Why Genes Of One Parent Are Expressed Over Genes Of The Other: New Ideas In Genomic Imprinting
Finding: Genetic imprinting arises from an 'epigenetic memory' that makes preferences. It appears that imprinting evolved in a stepwise, adaptive way, with each gene or cluster becoming imprinted as the need arose.
How we come to express the genes of one parent over the other is now better understood through studying the platypus and marsupial wallaby -- and it doesn't seem to have originated in association with sex chromosomes.
New research has shed light on the evolution of genomic imprinting, in which specific genes on chromosomes that have been inherited from one parent are expressed in an organism, while the same genes on the chromosome inherited from the other parent are repressed.
Imprinting arises from some kind of 'epigenetic memory' -- modifications to the DNA from one parent, such as the way the chromosomal material is packaged, that do not allow particular genes to be expressed. The reasons why imprinting evolved are not understood. It is known, however, that different patterns of imprinting occur in different classes of mammals, with some classes of mammals exhibiting the phenomenon and others not. Because the evolutionary relationship between mammals is well documented, patterns of imprinting in the different genomes can provide important clues about the evolution of imprinting.
One theory is that imprinted genes arose from sex chromosomes, which can be epigenetically 'shut down' to control the dosage of genes. Another idea is that imprinting arose from an ancestral chromosome that was itself imprinted.
The results of the distribution studies suggest that imprinted genes were not located on an ancestrally imprinted chromosome, nor were they associated with sex chromosomes. Rather it appears that imprinting evolved in a stepwise, adaptive way, with each gene or cluster becoming imprinted as the need arose.
The study is also important because despite its evolutionary importance, the platypus remains cytogenetically under-characterised. By linking specific sequences to particular chromosomes, the researchers have pinpointed important markers on the platypus genome.
How we come to express the genes of one parent over the other is now better understood through studying the platypus and marsupial wallaby -- and it doesn't seem to have originated in association with sex chromosomes.
New research has shed light on the evolution of genomic imprinting, in which specific genes on chromosomes that have been inherited from one parent are expressed in an organism, while the same genes on the chromosome inherited from the other parent are repressed.
Imprinting arises from some kind of 'epigenetic memory' -- modifications to the DNA from one parent, such as the way the chromosomal material is packaged, that do not allow particular genes to be expressed. The reasons why imprinting evolved are not understood. It is known, however, that different patterns of imprinting occur in different classes of mammals, with some classes of mammals exhibiting the phenomenon and others not. Because the evolutionary relationship between mammals is well documented, patterns of imprinting in the different genomes can provide important clues about the evolution of imprinting.
One theory is that imprinted genes arose from sex chromosomes, which can be epigenetically 'shut down' to control the dosage of genes. Another idea is that imprinting arose from an ancestral chromosome that was itself imprinted.
The results of the distribution studies suggest that imprinted genes were not located on an ancestrally imprinted chromosome, nor were they associated with sex chromosomes. Rather it appears that imprinting evolved in a stepwise, adaptive way, with each gene or cluster becoming imprinted as the need arose.
The study is also important because despite its evolutionary importance, the platypus remains cytogenetically under-characterised. By linking specific sequences to particular chromosomes, the researchers have pinpointed important markers on the platypus genome.
Thursday, September 6, 2007
Extra Gene Copies Were Enough To Make Early Humans' Mouths Water
Finding: humans carry extra copies of the salivary amylase gene and starches may have been the food that made population growth possible.
What does this mean?
Humans have many more copies of this gene than any of their ape relatives and they use the copies to flood their mouths with amylase, an enzyme that digests starch. The finding bolsters the idea that starch was a crucial addition to the diet of early humans, and that natural selection favored individuals who could make more starch-digesting protein.
If one works - make more, don't wait for improvement to occur
Extra gene copies are an easy way for evolution to ramp up expression of a protein, why wait for chance mutations to improve gene function? Natural selection can favor duplicate copies of a gene that already works well, and enzyme production will increase.
Other primates eat mainly ripe fruits containing very little starch. A new ability to supplement the diet with calorie-rich starches could have fed our large brains and opened up new food supplies that fueled our unrivaled colonization of the planet, Dominy said.
How the research was done
The big mystery of paleoanthropology is what changed? Why did our earliest human ancestors deviate from the pattern we see in living apes to evolve this incredibly large brain, which is very energetically expensive to maintain, and to become a much more efficient bipedal organism?
Starch - not meat
For years, the answer was thought to be the growing importance of meat in the diet, as early humans learned to hunt. But even when you look at modern human hunter-gatherers, meat is a relatively small fraction of their diet. They cooperate with language, use nets; they have poisoned arrows, even, and still it's not that easy to hunt meat. To think that, two to four million years ago, a small-brained, awkwardly bipedal animal could efficiently acquire meat, even by scavenging, just doesn't make a whole lot of sense.
Some anthropologists have begun to suspect the new source of food consisted of starches, stored by plants in the form of underground tubers and bulbs--wild versions of modern-day foods like carrots, potatoes, and onions. Once early humans learned to recognize tuber-forming plants, they opened up a food source unknown to other apes.
Starches and the Homo Erectus
Tubers may have been especially critical for the first widely successful humans, known as Homo erectus, who may have learned to cook with fire. Since this idea was proposed, about a decade ago, researchers have been looking for evidence to support or refute it--no easy task for a theory that concerns highly perishable food consumed two million years ago. But in work earlier this year, scientists found that animals eating tubers and bulbs produce body tissues with an isotopic signature that matches what has been measured in early fossilized humans.
The new discovery is a separate line of evidence pointing to the importance of starch in human beginnings. When early humans mastered fire, cooking starchy vegetables would have made them even easier to eat, he added. At the same time it would have made extra amylase gene copies an even more valuable trait.
We roast tubers, and we eat French fries and baked potatoes," Dominy said. "When you cook, you can afford to eat less overall, because the food is easier to digest. Some marginal food resource that you might only eat in times of famine, now you can cook it and eat it. Now you can have population growth and expand into new territories.
What does this mean?
Humans have many more copies of this gene than any of their ape relatives and they use the copies to flood their mouths with amylase, an enzyme that digests starch. The finding bolsters the idea that starch was a crucial addition to the diet of early humans, and that natural selection favored individuals who could make more starch-digesting protein.
If one works - make more, don't wait for improvement to occur
Extra gene copies are an easy way for evolution to ramp up expression of a protein, why wait for chance mutations to improve gene function? Natural selection can favor duplicate copies of a gene that already works well, and enzyme production will increase.
Other primates eat mainly ripe fruits containing very little starch. A new ability to supplement the diet with calorie-rich starches could have fed our large brains and opened up new food supplies that fueled our unrivaled colonization of the planet, Dominy said.
How the research was done
- The researchers sampled saliva from 50 European-American undergraduates and found as many as 15 copies of the amylase gene per person. By comparison, all 15 chimpanzees they sampled had exactly 2 copies each. Students with more copies of the gene also had higher concentrations of the enzyme in their spit.
- Diet -Next, studies involving groups of humans with differing diets took place. They found a similar correspondence between the amount of starch in a group's diet and the average number of amylase gene copies its individuals possessed.
- The Yakut of the Arctic, whose traditional diet centers around fish, had fewer copies than the related Japanese, whose diet includes starchy foods like rice. The same pattern existed for two Tanzanian tribes--the Datog, who raise livestock, and the Hadza, who primarily gather tubers and roots. The Hadza had more copies of the gene than the Datog.
Even though they're closely related genetically and live close to each other geographically, still there are big differences in the average number of copies in these populations. Geography and relatedness are not driving these differences. It's diet. - In pondering human origins anthropologists have long been stumped by the sudden, nearly simultaneous increases in our brain size, body size, and geographic range, while other apes changed little. Early humans simply must have found some source of better nutrition to make it all possible.
The big mystery of paleoanthropology is what changed? Why did our earliest human ancestors deviate from the pattern we see in living apes to evolve this incredibly large brain, which is very energetically expensive to maintain, and to become a much more efficient bipedal organism?
Starch - not meat
For years, the answer was thought to be the growing importance of meat in the diet, as early humans learned to hunt. But even when you look at modern human hunter-gatherers, meat is a relatively small fraction of their diet. They cooperate with language, use nets; they have poisoned arrows, even, and still it's not that easy to hunt meat. To think that, two to four million years ago, a small-brained, awkwardly bipedal animal could efficiently acquire meat, even by scavenging, just doesn't make a whole lot of sense.
Some anthropologists have begun to suspect the new source of food consisted of starches, stored by plants in the form of underground tubers and bulbs--wild versions of modern-day foods like carrots, potatoes, and onions. Once early humans learned to recognize tuber-forming plants, they opened up a food source unknown to other apes.
Starches and the Homo Erectus
Tubers may have been especially critical for the first widely successful humans, known as Homo erectus, who may have learned to cook with fire. Since this idea was proposed, about a decade ago, researchers have been looking for evidence to support or refute it--no easy task for a theory that concerns highly perishable food consumed two million years ago. But in work earlier this year, scientists found that animals eating tubers and bulbs produce body tissues with an isotopic signature that matches what has been measured in early fossilized humans.
The new discovery is a separate line of evidence pointing to the importance of starch in human beginnings. When early humans mastered fire, cooking starchy vegetables would have made them even easier to eat, he added. At the same time it would have made extra amylase gene copies an even more valuable trait.
We roast tubers, and we eat French fries and baked potatoes," Dominy said. "When you cook, you can afford to eat less overall, because the food is easier to digest. Some marginal food resource that you might only eat in times of famine, now you can cook it and eat it. Now you can have population growth and expand into new territories.
Tuesday, September 4, 2007
Genome Study Shines Light On Genetic Link To Height
Finding: Inheriting the 'C'-containing copy of the HMGA2 gene -- a 'C' written in the DNA code instead of a 'T' often makes people taller: one copy can add about a half centimeter in height while two copies can add almost a full centimeter.
Why do tall people get to be tall?
Nearly a century ago it was thought that many genes likely influence how tall a person grows, but little progress was made to find the genes, until now.
Methodology
Using a new "genome-wide association" method, the research team searched the human genome for single letter differences in the genetic code that appear more often in tall individuals compared to shorter individuals. By analyzing DNA from nearly 35,000 people, the researchers zeroed in on a difference in the HMGA2 gene -- a 'C' written in the DNA code instead of a 'T'. This gene change can account for the difference in tallnes.
The study is the first convincing result that explains how DNA can affect normal variation in human height. Height is a complex trait, involving a variety of genetic and non-genetic factors, it can teach us about the genetic framework of other complex traits -- such as diabetes, cancer and other common human diseases.
In addition to being a textbook example of a complex trait, height is a common reason children are referred to medical specialists. Although short stature by itself typically does not signal cause for concern, delayed growth can sometimes reflect a serious underlying health condition.
DNA accounts for 90% of growth
Nearly 90% of the variation in height among most human populations can be attributed to DNA. The remainder is due to environmental and lifestyle factors, such as nutrition. Although a few genes have been uncovered through studies of rare, single-gene stature disorders, most do not seem to be associated with height in the general population. Recent advances, including the completion of the HapMap project and the availability of large-scale research tools, enabled the scientists to take a systematic approach to understand how common genetic differences can impact a person's height.
After scrutinizing the initial data, the scientists identified a single letter change -- known as a single nucleotide polymorphism or SNP -- in the HMGA2 gene as the most promising result. They collaborated with additional researchers to study this SNP through a second phase of analysis that encompassed nearly 30,000 individuals: adults and children from the Avon Longitudinal Study of Parents and Children (ALSPAC) and the Exeter Family Study of Childhood Health (EFSOCH),
Unlike most other complex traits, height is something that can be easily defined and measured in very large numbers of people. Soon the scientific community will have access to many more large-scale genomic data sets, making it feasible to identify additional genes involved in height."
What the Gene does
While surprisingly little is known about how genes hardwire humans for growth, some initial clues have already surfaced as a result of the HMGA2 discovery. The gene is active in the first months of fetal growth and shuts off shortly before birth, suggesting it orchestrates growth-related events early in human development. Moreover, it appears to influence the overall longitudinal growth of the skeleton, as scientists found that the T-to-C change in the gene's DNA sequence correlates with an increased length of both the limbs and spine in young children. HMGA2 has also been implicated in certain forms of cancer. Thus, further studies may help dissect the relationship between normal growth and the deranged growth central to cancer.
Why do tall people get to be tall?
Nearly a century ago it was thought that many genes likely influence how tall a person grows, but little progress was made to find the genes, until now.
Methodology
Using a new "genome-wide association" method, the research team searched the human genome for single letter differences in the genetic code that appear more often in tall individuals compared to shorter individuals. By analyzing DNA from nearly 35,000 people, the researchers zeroed in on a difference in the HMGA2 gene -- a 'C' written in the DNA code instead of a 'T'. This gene change can account for the difference in tallnes.
The study is the first convincing result that explains how DNA can affect normal variation in human height. Height is a complex trait, involving a variety of genetic and non-genetic factors, it can teach us about the genetic framework of other complex traits -- such as diabetes, cancer and other common human diseases.
In addition to being a textbook example of a complex trait, height is a common reason children are referred to medical specialists. Although short stature by itself typically does not signal cause for concern, delayed growth can sometimes reflect a serious underlying health condition.
DNA accounts for 90% of growth
Nearly 90% of the variation in height among most human populations can be attributed to DNA. The remainder is due to environmental and lifestyle factors, such as nutrition. Although a few genes have been uncovered through studies of rare, single-gene stature disorders, most do not seem to be associated with height in the general population. Recent advances, including the completion of the HapMap project and the availability of large-scale research tools, enabled the scientists to take a systematic approach to understand how common genetic differences can impact a person's height.
After scrutinizing the initial data, the scientists identified a single letter change -- known as a single nucleotide polymorphism or SNP -- in the HMGA2 gene as the most promising result. They collaborated with additional researchers to study this SNP through a second phase of analysis that encompassed nearly 30,000 individuals: adults and children from the Avon Longitudinal Study of Parents and Children (ALSPAC) and the Exeter Family Study of Childhood Health (EFSOCH),
Unlike most other complex traits, height is something that can be easily defined and measured in very large numbers of people. Soon the scientific community will have access to many more large-scale genomic data sets, making it feasible to identify additional genes involved in height."
What the Gene does
While surprisingly little is known about how genes hardwire humans for growth, some initial clues have already surfaced as a result of the HMGA2 discovery. The gene is active in the first months of fetal growth and shuts off shortly before birth, suggesting it orchestrates growth-related events early in human development. Moreover, it appears to influence the overall longitudinal growth of the skeleton, as scientists found that the T-to-C change in the gene's DNA sequence correlates with an increased length of both the limbs and spine in young children. HMGA2 has also been implicated in certain forms of cancer. Thus, further studies may help dissect the relationship between normal growth and the deranged growth central to cancer.
Monday, September 3, 2007
A new way to study evolutionary paths
Finding: There is a new way to shed light on macroevolutionary research.
A team of scientists developed a novel methodological approach in evolutionary studies. Using the method they named 'genomic phylostratigraphy', its authors shed new and unexpected light on some of the long standing macroevolutionary issues, which have been puzzling evolutionary biologists since Darwin.
Problems with using Fossils
The only direct method of research in evolutionary history involves analyzing the fossil remains of once living organisms, excavated in various localities throughout of the world. However, that approach often cannot provide the full evolutionary pathway of some species, as it requires uncovering of many fossils from various stages of its evolutionary history. As the fossil record is imperfect, the evolution research fundamentally hinges on luck factor in discovering the adequate paleontological sites.
New Approach - Snapshots of the evolutionary path
However, the RBI team proposed a novel and interesting approach to bypass this obstacle. Namely, they suggested that the genome of every extant species carries the ‘snapshots’ of evolutionary epochs that species went trough. What's even more important, they also developed the method which enables evolution researchers to readily convert those individual 'snapshots’ into the full-length 'evolutionary movie' of a species.
The approach on flies
Applying their new methodology on the fruit fly genomic data they tackled some of the most intriguing evolutionary puzzles - some of which distressed even Darwin himself. First, they demonstrated that parts of the living organism exposed to the environment – so called ‘ectoderm’ - are more prone to evolutionary changes. Further, they explained the evolutionary origin of the ‘germ layers’, the primary tissue forms that form during the first days after the conception of a new animal, and from which subsequently all other tissues are developed. Finally, they discovered the potential genetic trigger for the 'Cambrian explosion', a major global evolutionary event on the planet, when some 540 million years ago almost all animal forms known today suddenly 'appeared'.
A team of scientists developed a novel methodological approach in evolutionary studies. Using the method they named 'genomic phylostratigraphy', its authors shed new and unexpected light on some of the long standing macroevolutionary issues, which have been puzzling evolutionary biologists since Darwin.
Problems with using Fossils
The only direct method of research in evolutionary history involves analyzing the fossil remains of once living organisms, excavated in various localities throughout of the world. However, that approach often cannot provide the full evolutionary pathway of some species, as it requires uncovering of many fossils from various stages of its evolutionary history. As the fossil record is imperfect, the evolution research fundamentally hinges on luck factor in discovering the adequate paleontological sites.
New Approach - Snapshots of the evolutionary path
However, the RBI team proposed a novel and interesting approach to bypass this obstacle. Namely, they suggested that the genome of every extant species carries the ‘snapshots’ of evolutionary epochs that species went trough. What's even more important, they also developed the method which enables evolution researchers to readily convert those individual 'snapshots’ into the full-length 'evolutionary movie' of a species.
The approach on flies
Applying their new methodology on the fruit fly genomic data they tackled some of the most intriguing evolutionary puzzles - some of which distressed even Darwin himself. First, they demonstrated that parts of the living organism exposed to the environment – so called ‘ectoderm’ - are more prone to evolutionary changes. Further, they explained the evolutionary origin of the ‘germ layers’, the primary tissue forms that form during the first days after the conception of a new animal, and from which subsequently all other tissues are developed. Finally, they discovered the potential genetic trigger for the 'Cambrian explosion', a major global evolutionary event on the planet, when some 540 million years ago almost all animal forms known today suddenly 'appeared'.
Sunday, September 2, 2007
Ancient Pig DNA Study Sheds New Light On Colonization Of Europe By Early Farmers
Finding: The earliest domesticated pigs in Europe, which many archaeologists believed to be descended from European wild boar, were actually introduced from the Middle East by Stone Age farmers.
The research involved mitochondrial DNA from ancient and modern pig remains. Its findings also suggest that the migration of an expanding Middle Eastern population, who brought their 'farming package' of domesticated plants, animals and distinctive pottery styles with them, actually 'kickstarted' the local domestication of the European wild boar.
While archaeologists already know that agriculture began about 12,000 years ago in the central and western parts of the Middle East, spreading rapidly across Europe between 6,800 -- 4000BC, many outstanding questions remain about the mechanisms of just how it spread. This research sheds new and important light on the actual process of the establishment of farming in Europe.
Many archaeologists believe that farming spread through the diffusion of ideas and cultural exchange, not with the direct migration of people. However, the discovery and analysis of ancient Middle Eastern pig remains across Europe reveals that although cultural exchange did happen, Europe was definitely colonised by Middle Eastern farmers.
A combination of rising population and possible climate change in the 'fertile crescent', which put pressure on land and resources, made them look for new places to settle, plant their crops and breed their animals and so they rapidly spread west into Europe.
The domestic pigs that were derived from the European wild boar must have been considered vastly superior to those originally from Middle East. In fact, the European domestic pigs were so successful that over the next several thousand years they spread across the continent and even back into the Middle East where they overtook the indigenous domestic pigs. For whatever reason, European pigs were the must have farm animal.
The research involved mitochondrial DNA from ancient and modern pig remains. Its findings also suggest that the migration of an expanding Middle Eastern population, who brought their 'farming package' of domesticated plants, animals and distinctive pottery styles with them, actually 'kickstarted' the local domestication of the European wild boar.
While archaeologists already know that agriculture began about 12,000 years ago in the central and western parts of the Middle East, spreading rapidly across Europe between 6,800 -- 4000BC, many outstanding questions remain about the mechanisms of just how it spread. This research sheds new and important light on the actual process of the establishment of farming in Europe.
Many archaeologists believe that farming spread through the diffusion of ideas and cultural exchange, not with the direct migration of people. However, the discovery and analysis of ancient Middle Eastern pig remains across Europe reveals that although cultural exchange did happen, Europe was definitely colonised by Middle Eastern farmers.
A combination of rising population and possible climate change in the 'fertile crescent', which put pressure on land and resources, made them look for new places to settle, plant their crops and breed their animals and so they rapidly spread west into Europe.
The domestic pigs that were derived from the European wild boar must have been considered vastly superior to those originally from Middle East. In fact, the European domestic pigs were so successful that over the next several thousand years they spread across the continent and even back into the Middle East where they overtook the indigenous domestic pigs. For whatever reason, European pigs were the must have farm animal.
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