93 posts tagged genetics
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)
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)
An international team of researchers led by the University of Arizona (UA) has sequenced the complete genome of African rice. The genetic information will enhance scientists’ and agriculturalists’ understanding of the growing patterns of African rice, and help development of new rice varieties that are better able to cope with increasing environmental stressors to help solve global hunger challenges, the researchers say. The research paper was published in Nature Genetics (open access). The 9 billion-people question “Rice feeds half the world, making it the most important food crop,” said Rod A. Wing, director of the Arizona Genomics Institute at the UA . “Rice will play a key role in helping to solve what we call the 9-billion-people question.” The 9 billion-people question refers to predictions that the world’s population will increase to more than 9 billion people — many of whom will live in areas where access to food is extremely scarce — by the year 2050. The question lies in how to grow enough food to feed the world’s population and prevent the host of health, economic and social problems associated with hunger and malnutrition. Now, with the completely sequenced African rice genome, scientists and agriculturalists can search for ways to cross Asian and African species to develop new varieties of rice with the high-yield traits of Asian rice and the hardiness of African rice. “African rice is once more at the forefront of cultivation strategies that aim to confront climate change and food availability challenges,” said Judith Carney, a professor in the Department of Geography and the Institute of the Environment and Sustainability at the University of California, Los Angeles, and author of “Black Rice.” The book describes the historical importance of African rice, which was brought to the United States during the period of transatlantic slavery. Carney is also a co-author on the Nature Genetics paper, and her book served as one of the inspirations behind sequencing the African rice genome.
The Game Theory of Life
-Applying game theory to the behavior of genes provides a new view of natural selection.
In what appears to be the first study of its kind, computer scientists report that an algorithm discovered more than 50 years ago in game theory and now widely used in machine learning is mathematically identical to the equations used to describe the distribution of genes within a population of organisms. Researchers may be able to use the algorithm, which is surprisingly simple and powerful, to better understand how natural selection works and how populations maintain their genetic diversity. By viewing evolution as a repeated game, in which individual players, in this case genes, try to find a strategy that creates the fittest population, researchers found that evolution values both diversity and fitness. Some biologists say that the findings are too new and theoretical to be of use; researchers don’t yet know how to test the ideas in living organisms. Others say the surprising connection, published Monday in the advance online version of the Proceedings of the National Academy of Sciences, may help scientists understand a puzzling feature of natural selection: The fittest organisms don’t always wipe out their weaker competition. Indeed, as evidenced by the menagerie of life on Earth, genetic diversity reigns.
“It’s a very different way to look at selection,” said Stephen Stearns, an evolutionary biologist at Yale University who was not involved in the study. “I always find radically different ways of looking at a problem interesting.” (via Game Theory Makes New Predictions for Evolution | Simons Foundation)
Genetic anomaly which switches on blonde hair is not linked to any other traits, scientists conclude
The fair-haired have long endured accusations that they are less intelligent than brunettes, to the extent that an unexpected show of stupidity is now referred to as a “blonde moment”. But blondes should take heart. Scientists have discovered that hair colour is determined by a single letter of the genetic code – and it is completely unrelated to any other inherited trait. It means that being blonde has no link to either intelligence or being gregarious. So if blondes really do have more fun, or come across as ditzy, the driving force is likely to be nurture not nature. Scientists at Stanford University found that switching a single letter of DNA can turn brunettes to blondes. “The genetic mechanism that controls blond hair doesn’t alter the biology of any other part of the body,” said lead researcher Professor David Kingsley. “It’s clear that this hair colour change is occurring through a regulatory mechanism that operates only in the hair. “The change that causes blond hair is, literally, only skin deep “We’ve been trying to track down the genetic and molecular basis of naturally occurring traits, such as hair and skin pigmentation, to get insight into the general principles by which traits evolve.” The gene switch which turns on blonde hair also played no part in eye colour, the scientists found, suggesting that blue eyes and fair hair are not genetically linked. “This particular genetic variation in humans is associated with blonde hair, but it isn’t associated with eye colour or other pigmentation traits,” Prof Kingsley added.
Tigers need diverse gene pool to survive
Stanford University Original Study
New research shows that increasing genetic diversity among the 3,000 or so tigers left on the planet, though interbreeding and other methods, may be the key to their survival as a species. Iconic symbols of power and beauty, wild tigers may roam only in stories someday soon. Their historical range has been reduced by more than 90 percent. But conservation plans that focus only on increasing numbers and preserving distinct subspecies ignore genetic diversity, according to the study. In fact, following that approach, the tiger could vanish entirely. “Numbers don’t tell the entire story,” says Elizabeth Hadly, professor in environmental biology at Stanford University and senior fellow at the Stanford Woods Institute for the Environment. She is a coauthor of the study, which appears in the Journal of Heredity.
That research shows that the more gene flow there is among tiger populations, the more genetic diversity is maintained and the higher the chances of species survival become. In fact, it might be possible to maintain tiger populations that preserve about 90 percent of genetic diversity. (via Tigers need diverse gene pool to survive | Futurity)
From genetic and genomic testing to new techniques in human assisted reproduction, various technologies are providing parents with more of a say about the children they have and “stirring the pot of ‘designer baby’ concerns,” writes Thomas H. Murray, President Emeritus of The Hastings Center, in a commentary in Science. Murray calls for a national conversation about how much discretion would-be parents should have. “Preventing a lethal disease is one thing; choosing the traits we desire is quite another,” he writes. He discusses public hearings two weeks ago by the United States Food and Drug Administration to consider whether to permit human testing of a new method of assisted reproduction – mitochondrial manipulation – that would prevent the transmission of certain rare diseases and perhaps address some causes of female infertility. At issue is the safety of the technology, as well as its ethical implications. Mitochondrial manipulation creates an embryo with the nuclear DNA from the prospective mother and father (which contains most of the genetic material) and the mitochondrial DNA (containing 37 genes) from a donor without mitochondrial defects. Among the ethical concerns is that daughters produced by this procedure could pass down the mitochondrial DNA to their children. “Up to now, the United States has not allowed such genetic changes across generations,” Murray writes.