A Momentary Flow

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68 posts tagged DNA

Life doesn’t make trash - A genome is not a blueprint for building a human being, so is there any way to judge whether DNA is junk or not? - Humans are astounding creatures, our unique and highly complex traits encoded by our genome – a vast sequence of DNA ‘letters’ (called nucleotides) directing the building and maintenance of the body and brain. Yet science has served up the confounding paradox that the bulk of our genome appears to be dead wood, biologically inert junk. Could all this mysterious ‘dark matter’ in our genome really be non-functional? Our genome has more than 20,000 genes, relatively stable stretches of DNA transmitted largely unchanged between generations. These genes contain recipes for molecules, especially proteins, that are the main building blocks and molecular machines of our bodies. Yet DNA that codes for such known structures accounts for just over 3 per cent of our genome. What about the other 97 per cent? With the publication of the first draft of the human genome in 2001, that shadow world came into focus. It emerged that roughly half our DNA consisted of ‘repeats’, long stretches of letters sometimes found in millions of copies at seemingly random places throughout the genome. Were all these repeats just junk? To answer this question, hundreds of scientists worldwide joined a massive science project called the Encyclopedia of DNA Elements, or ENCODE. After working hard for almost a decade, in 2012 ENCODE came to a surprising conclusion: rather than being composed mostly of useless junk, 80 per cent of the human genome is in fact functional. (via Is our genome full of junk DNA? – Itai Yanai and Martin Lercher – Aeon)

Life doesn’t make trash
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A genome is not a blueprint for building a human being, so is there any way to judge whether DNA is junk or not?
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Humans are astounding creatures, our unique and highly complex traits encoded by our genome – a vast sequence of DNA ‘letters’ (called nucleotides) directing the building and maintenance of the body and brain. Yet science has served up the confounding paradox that the bulk of our genome appears to be dead wood, biologically inert junk. Could all this mysterious ‘dark matter’ in our genome really be non-functional? Our genome has more than 20,000 genes, relatively stable stretches of DNA transmitted largely unchanged between generations. These genes contain recipes for molecules, especially proteins, that are the main building blocks and molecular machines of our bodies. Yet DNA that codes for such known structures accounts for just over 3 per cent of our genome. What about the other 97 per cent? With the publication of the first draft of the human genome in 2001, that shadow world came into focus. It emerged that roughly half our DNA consisted of ‘repeats’, long stretches of letters sometimes found in millions of copies at seemingly random places throughout the genome. Were all these repeats just junk? To answer this question, hundreds of scientists worldwide joined a massive science project called the Encyclopedia of DNA Elements, or ENCODE. After working hard for almost a decade, in 2012 ENCODE came to a surprising conclusion: rather than being composed mostly of useless junk, 80 per cent of the human genome is in fact functional. (via Is our genome full of junk DNA? – Itai Yanai and Martin Lercher – Aeon)

I Contain Multitudes /Our bodies are a genetic patchwork, possessing variation from cell to cell. Is that a good thing? / Your DNA is supposed to be your blueprint, your unique master code, identical in every one of your tens of trillions of cells. It is why you are you, indivisible and whole, consistent from tip to toe. But that’s really just a biological fairy tale. In reality, you are an assemblage of genetically distinctive cells, some of which have radically different operating instructions. This fact has only become clear in the last decade. Even though each of your cells supposedly contains a replica of the DNA in the fertilized egg that began your life, mutations, copying errors and editing mistakes began modifying that code as soon as your zygote self began to divide. In your adult body, your DNA is peppered by pinpoint mutations, riddled with repeated or rearranged or missing information, even lacking huge chromosome-sized chunks. Your data is hopelessly corrupt. Most genome scientists assume that this DNA diversity, called “somatic mutation” or “structural variation,” is bad. Mutations and other genetic changes can alter the function of the cell, usually for the worse. Disorderly DNA is a hallmark of cancers, and genomic variation can cause a suite of brain disorders and malformations. It makes sense: Cells working off garbled information probably don’t function very well. Most research to date has focused on how aberrant DNA drives disease, but even healthy bodies harbor genetic disorder. In the last few years, some researchers report that anywhere from 10 to 40 percent of brain cells and between 30 and 90 percent of human liver cells are aneuploid, meaning that one entire chromosome is either missing or duplicated. Copy number variations, in which chunks of DNA between 100 and a few million letters in length are multiplied or eliminated, also seem to be widespread in healthy people. (via Our Body as Genetic Patchwork: Helpful or Hurtful? | Simons Foundation)

I Contain Multitudes
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Our bodies are a genetic patchwork, possessing variation from cell to cell. Is that a good thing?
/
Your DNA is supposed to be your blueprint, your unique master code, identical in every one of your tens of trillions of cells. It is why you are you, indivisible and whole, consistent from tip to toe. But that’s really just a biological fairy tale. In reality, you are an assemblage of genetically distinctive cells, some of which have radically different operating instructions. This fact has only become clear in the last decade. Even though each of your cells supposedly contains a replica of the DNA in the fertilized egg that began your life, mutations, copying errors and editing mistakes began modifying that code as soon as your zygote self began to divide. In your adult body, your DNA is peppered by pinpoint mutations, riddled with repeated or rearranged or missing information, even lacking huge chromosome-sized chunks. Your data is hopelessly corrupt. Most genome scientists assume that this DNA diversity, called “somatic mutation” or “structural variation,” is bad. Mutations and other genetic changes can alter the function of the cell, usually for the worse. Disorderly DNA is a hallmark of cancers, and genomic variation can cause a suite of brain disorders and malformations. It makes sense: Cells working off garbled information probably don’t function very well. Most research to date has focused on how aberrant DNA drives disease, but even healthy bodies harbor genetic disorder. In the last few years, some researchers report that anywhere from 10 to 40 percent of brain cells and between 30 and 90 percent of human liver cells are aneuploid, meaning that one entire chromosome is either missing or duplicated. Copy number variations, in which chunks of DNA between 100 and a few million letters in length are multiplied or eliminated, also seem to be widespread in healthy people. (via Our Body as Genetic Patchwork: Helpful or Hurtful? | Simons Foundation)

Less than 10% of human DNA has functional role, claim scientists - Large stretches may be no more than biological baggage, say researchers after comparing genome with that of other mammals - More than 90% of human DNA is doing nothing very useful, and large stretches may be no more than biological baggage that has built up over years of evolution, Oxford researchers claim. The scientists arrived at the figure after comparing the human genome with the genetic makeup of other mammals, ranging from dogs and mice to rhinos and horses. The researchers looked for sections of DNA that humans shared with the other animals, which split from our lineage at different points in history. When DNA is shared and conserved across species, it suggests that it does something valuable. Gerton Lunter, a senior scientist on the team, said that based on the comparisons, 8.2% of human DNA was “functional”, meaning that it played an important enough role to be conserved by evolution. “Scientifically speaking, we have no evidence that 92% of our genome is contributing to our biology at all,” Lunter told the Guardian. Researchers have known for some time that only 1% of human DNA is held in genes that are used to make crucial proteins to keep cells – and bodies – alive and healthy. The latest study, reported in the journal Plos Genetics, suggests that a further 7% of human DNA is equally vital, regulating where, when, and how genes are expressed. But if much of our DNA is so worthless, why do we still carry it around? “It’s not true that nature is parsimonious in terms of needing a small genome. Wheat has a much larger genome than we do,” Lunter said. “We haven’t been designed. We’ve evolved and that’s a messy process. This other DNA really is just filler. It’s not garbage. It might come in useful one day. But it’s not a burden.” (via Less than 10% of human DNA has functional role, claim scientists | Science | The Guardian)

Less than 10% of human DNA has functional role, claim scientists
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Large stretches may be no more than biological baggage, say researchers after comparing genome with that of other mammals
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More than 90% of human DNA is doing nothing very useful, and large stretches may be no more than biological baggage that has built up over years of evolution, Oxford researchers claim. The scientists arrived at the figure after comparing the human genome with the genetic makeup of other mammals, ranging from dogs and mice to rhinos and horses. The researchers looked for sections of DNA that humans shared with the other animals, which split from our lineage at different points in history. When DNA is shared and conserved across species, it suggests that it does something valuable. Gerton Lunter, a senior scientist on the team, said that based on the comparisons, 8.2% of human DNA was “functional”, meaning that it played an important enough role to be conserved by evolution. “Scientifically speaking, we have no evidence that 92% of our genome is contributing to our biology at all,” Lunter told the Guardian. Researchers have known for some time that only 1% of human DNA is held in genes that are used to make crucial proteins to keep cells – and bodies – alive and healthy. The latest study, reported in the journal Plos Genetics, suggests that a further 7% of human DNA is equally vital, regulating where, when, and how genes are expressed. But if much of our DNA is so worthless, why do we still carry it around? “It’s not true that nature is parsimonious in terms of needing a small genome. Wheat has a much larger genome than we do,” Lunter said. “We haven’t been designed. We’ve evolved and that’s a messy process. This other DNA really is just filler. It’s not garbage. It might come in useful one day. But it’s not a burden.” (via Less than 10% of human DNA has functional role, claim scientists | Science | The Guardian)

How spit protects us from poison in coffee -Johns Hopkins University Original Study -
Saliva and common proteins from blood and muscle appear to protect human cells from powerful DNA-destroying toxins in tea, coffee, and liquid smoke flavoring, new research shows. The findings suggest that our bodies naturally launch multiple defenses against these toxins—plant chemicals called pyrogallol-like polyphenols (PLPs)—and could explain why they don’t cripple cells and cause the illness that would be expected from their presence in human diets. Last year, researchers demonstrated that PLPs could do significant damage by breaking strands of DNA, the carrier of genetic information. The effect of the toxins was so strong—in some cases producing 20 times the damage of chemotherapy drugs delivered to cancer patients—that the researchers immediately thought to find out why there wasn’t more damage, and to look for ways that cells might be fighting back. “If these chemicals are so widespread—they’re in flavorings, tea, coffee—and they damage DNA to such a high degree,” says Scott Kern, professor of oncology and pathology at Johns Hopkins University School of Medicine, “we thought there must be defense mechanisms that protect us on a daily basis from plants we choose to eat.” In the new study, published in Food and Chemical Toxicology, Kern and colleagues found that an enzyme in saliva called alpha-amylase, the blood protein albumin, and the muscle protein myoglobin all protect cells from DNA breakage by tea, coffee, and isolated PLPs. (via How spit protects us from poison in coffee | Futurity)

How spit protects us from poison in coffee
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Johns Hopkins University Original Study
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Saliva and common proteins from blood and muscle appear to protect human cells from powerful DNA-destroying toxins in tea, coffee, and liquid smoke flavoring, new research shows. The findings suggest that our bodies naturally launch multiple defenses against these toxins—plant chemicals called pyrogallol-like polyphenols (PLPs)—and could explain why they don’t cripple cells and cause the illness that would be expected from their presence in human diets. Last year, researchers demonstrated that PLPs could do significant damage by breaking strands of DNA, the carrier of genetic information. The effect of the toxins was so strong—in some cases producing 20 times the damage of chemotherapy drugs delivered to cancer patients—that the researchers immediately thought to find out why there wasn’t more damage, and to look for ways that cells might be fighting back. “If these chemicals are so widespread—they’re in flavorings, tea, coffee—and they damage DNA to such a high degree,” says Scott Kern, professor of oncology and pathology at Johns Hopkins University School of Medicine, “we thought there must be defense mechanisms that protect us on a daily basis from plants we choose to eat.” In the new study, published in Food and Chemical Toxicology, Kern and colleagues found that an enzyme in saliva called alpha-amylase, the blood protein albumin, and the muscle protein myoglobin all protect cells from DNA breakage by tea, coffee, and isolated PLPs. (via How spit protects us from poison in coffee | Futurity)

First lifeforms to pass on artificial DNA engineered by US scientists -Organisms carrying beefed-up DNA code could be designed to churn out new forms of drugs that could otherwise not be made - The first living organism to carry and pass down to future generations an expanded genetic code has been created by American scientists, paving the way for a host of new life forms whose cells carry synthetic DNA that looks nothing like the normal genetic code of natural organisms. Researchers say the work challenges the dogma that the molecules of life making up DNA are “special”. Organisms that carry the beefed-up DNA code could be designed to churn out new forms of drugs that otherwise could not be made, they have claimed. “This has very important implications for our understanding of life,” said Floyd Romesberg, whose team created the organism at the Scripps Research Institute in La Jolla, California. “For so long people have thought that DNA was the way it was because it had to be, that it was somehow the perfect molecule.” From the moment life gained a foothold on Earth the diversity of organisms has been written in a DNA code of four letters. The latest study moves life beyond G, T, C and A – the molecules or bases that pair up in the DNA helix – and introduces two new letters of life: X and Y. Romesberg started out with E coli, a bug normally found in soil and carried by people. Into this he inserted a loop of genetic material that carried normal DNA and two synthetic DNA bases. Though known as X and Y for simplicity, the artificial DNA bases have much longer chemical names, which themselves abbreviate to d5SICS and dNaM. In living organisms, G, T, C and A come together to form two base pairs, G-C and T-A. The extra synthetic DNA forms a third base pair, X-Y, according to the study in Nature. These base pairs are used to make genes, which cells use as templates for making proteins. Romesberg found that when the modified bacteria divided they passed on the natural DNA as expected. But they also replicated the synthetic code and passed that on to the next generation. That generation of bugs did the same. (via First lifeforms to pass on artificial DNA engineered by US scientists | World news | The Guardian)

First lifeforms to pass on artificial DNA engineered by US scientists
-
Organisms carrying beefed-up DNA code could be designed to churn out new forms of drugs that could otherwise not be made
-
The first living organism to carry and pass down to future generations an expanded genetic code has been created by American scientists, paving the way for a host of new life forms whose cells carry synthetic DNA that looks nothing like the normal genetic code of natural organisms. Researchers say the work challenges the dogma that the molecules of life making up DNA are “special”. Organisms that carry the beefed-up DNA code could be designed to churn out new forms of drugs that otherwise could not be made, they have claimed. “This has very important implications for our understanding of life,” said Floyd Romesberg, whose team created the organism at the Scripps Research Institute in La Jolla, California. “For so long people have thought that DNA was the way it was because it had to be, that it was somehow the perfect molecule.” From the moment life gained a foothold on Earth the diversity of organisms has been written in a DNA code of four letters. The latest study moves life beyond G, T, C and A – the molecules or bases that pair up in the DNA helix – and introduces two new letters of life: X and Y. Romesberg started out with E coli, a bug normally found in soil and carried by people. Into this he inserted a loop of genetic material that carried normal DNA and two synthetic DNA bases. Though known as X and Y for simplicity, the artificial DNA bases have much longer chemical names, which themselves abbreviate to d5SICS and dNaM. In living organisms, G, T, C and A come together to form two base pairs, G-C and T-A. The extra synthetic DNA forms a third base pair, X-Y, according to the study in Nature. These base pairs are used to make genes, which cells use as templates for making proteins. Romesberg found that when the modified bacteria divided they passed on the natural DNA as expected. But they also replicated the synthetic code and passed that on to the next generation. That generation of bugs did the same. (via First lifeforms to pass on artificial DNA engineered by US scientists | World news | The Guardian)

Scientists hail synthetic chromosome advance
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Scientists have created the first synthetic chromosome for yeast in a landmark for biological engineering. Previously synthetic DNA has been designed and made for simpler organisms such as bacteria. As a form of life whose cells contain a nucleus, yeast is related to plants and animals and shares 2,000 genes with us. So the creation of the first of yeast’s 16 chromosomes has been hailed as “a massive deal” in the emerging science of synthetic biology. The genes in the original chromosome were replaced with synthetic versions and the finished manmade chromosome was then successfully integrated into a yeast cell. The new cell was then observed to reproduce, passing a key test of viability. Yeast is a favoured target for this research because of its well-established use in key industries such as brewing and baking and its potential for future industrial applications. One company in California has already used synthetic biology to create a strain of yeast that can produce artemisinin, an ingredient for an anti-malarial drug. The synthesis of chromosome III in yeast was undertaken by an international team and the findings are published in the journal Science (yeast chromosomes are normally designated by Roman numerals). (via BBC News - Scientists hail synthetic chromosome advance)