38 posts tagged DNA
Big data sets create ‘tree of life’ confusion
The genomics revolution has given experts mountains of DNA data to reconstruct the evolution of all living beings, but the vast information has led to contradictory conclusions.
“It has become common for top-notch studies to report genealogies that strongly contradict each other in where certain organisms sprung from, such as the place of sponges on the animal tree or of snails on the tree of mollusks,” says Antonis Rokas, associate professor of biological sciences, at Vanderbilt University.
In a study published online by the journal Nature, Rokas and graduate student Leonidas Salichos analyze the reasons for these differences and propose a suite of novel techniques that can resolve the contradictions and provide greater accuracy in deciphering the deep branches of life’s tree.
“The study by Salichos and Rokas comes at a critical time when scientists are grappling with how best to detect the signature of evolutionary history from a deluge of genetic data. These authors provide intriguing insights into our standard analytical toolbox, and suggest it may be time to abandon some of our most trusted tools when it comes to the analysis of big data sets. This significant work will certainly challenge the community of evolutionary biologists to rethink how best to reconstruct phylogeny,” says Michael F. Whiting, program director of systematics and biodiversity science at the National Science Foundation, which funded the study.
Computers Made Out of DNA, Slime and Other Strange Stuff
Most designs for molecular computers are based on human notions of what a computer should be. Yet as researchers applied mathematician Hajo Broersma of the Netherlands’ University of Twente wrote of their work, “the simplest living systems have a complexity and sophistication that dwarfs manmade technology” — and they weren’t even designed to be that way. Evolution generated them. In the NASCENCE project, short for “NAnoSCale Engineering for Novel Computation using Evolution,” Broersma and colleagues plant to exploit evolution’s ability to use combinations of molecules and their emergent properties in unexpected, incredibly powerful ways. They hope to develop a system that interfaces a digital computer with nano-scale particle networks, then use the computer to set algorithmic goals towards which evolution will guide the particles. “We want to develop alternative approaches for situations or problems that are challenging or impossible to solve with conventional methods and models of computation,” they write. One imagines computer chips with geometries typically seen in molecular structures, such as the E. coli ribosome and RNA seen here; success, predict Broersma’s team, could lay “the foundations of the next industrial revolution.” (via Computers Made Out of DNA, Slime and Other Strange Stuff | Wired Science | Wired.com)
Organism With Seven Sexes Plays DNA Roulette
It’s been more than 50 years since scientists discovered that the single-celled organism Tetrahymena thermophila has seven sexes. But researchers only recently determined how each cell’s sex, or mating type, is determined.
The seven sexes, as it turns out, are randomly determined by a series of cut and paste genetic recombination events. These assemble one complete gene pair and delete all others, according to the paper, published in PLoS Biology.
“We found a pair of genes that have a specific sequence, which is different for each mating type,” professor emeritus Eduardo Orias of UC Santa Barbara said in a press release. “They are very similar genes — clearly related to one another, going back probably to a common ancestor — but they have become different. And each is different in a specific way that determines the mating type of the cell.
The discovery doesn’t just shed light on Tetrahymena. Better understanding of DNA rearrangements could have potential human health implications ranging from tissue transplantation to cancer.
One potential benefit is the ability of an organism to distinguish its own tissues from those of another. That ability is a first-line defense against infection and illness, but it can also cause problems, like rejection of transplanted organs.
As a single-celled organism, the “parents” associated with Tetrahymena reproduction are actually two nuclei: one that contains the genetic information for progeny cells, and another that’s referred to as the “working copy.”
“It’s completely random, as if they had roulette wheel with six numbers and wherever the marble ends up is what they get,” Orias said.
“Tetrahymena has about as many genes as the human genome. For thousands of those genes you can recognize the sequence similarity to corresponding genes in the human genome with the same biological function. That’s what makes it a valuable organism to investigate important biological questions.”
Image: Tetrahymena thermophila; Ciliate Genome Sequence Reveals Unique Features of a Model Eukaryote. Robinson R, PLoS Biology Vol. 4/9/2006, e304; Wikimedia Commons
Misguided Nostalgia for Our Paleo Past
The first thing you have to do to study 4,000-year-old DNA is take off your clothes.
I am standing with Oddný Ósk Sverrisdóttir in the airlock room next to the ancient-DNA laboratory at Uppsala University, in Sweden, preparing to see how she and her colleagues examine the bones of human beings and the animals they domesticated thousands of years ago. These scientists are looking for signs of changes in the genes that allow us to consume dairy products past the age of weaning, when all other mammals lose the ability to digest lactose, the sugar present in milk. After that time, dairy products can cause stomach upsets. But in some groups of humans, particularly those from Northern Europe and parts of Africa, lactase—the enzyme that breaks down lactose—lingers throughout life, allowing them to take advantage of a previously unusable food source. Sverrisdóttir and her Ph.D. supervisor, Anders Götherström, study how and when this development occurred, and how it is related to the domestication of cows for their meat and milk. They examine minute changes in genes obtained from radiocarbon-dated bones from archaeological sites around Europe. (via Misguided Nostalgia for Our Paleo Pasts - The Chronicle Review - The Chronicle of Higher Education)
These 3-D Portraits Were Created Using Only A Person’s DNA
Stranger Visions is an art project which tries to determine what we look like based on a single strand of hair.
How much information about ourselves do we leave behind in public, as we shed saliva, hair, and sweat throughout the day? It’s a question that drives the artwork of Heather Dewey-Hagborg, whose project Stranger Visions reconstructs the faces of the anonymous as 3-D printed sculptures, using genetic detritus found in chewing gum, cigarette butts, and wads of hair around New York City. (via 7 | These 3-D Portraits Were Created Using Only A Person’s DNA | Co.Exist: World changing ideas and innovation)
Music doesn’t go along at a single, mechanical speed. Notes of various lengths mix to create a specific, complex rhythm. New research suggests protein synthesis works the same way. The sequence of events is elegant: proteins are assembled when ribosomes match mRNA sequences up with specific tRNA molecules. Those tRNAs carry specific amino acids that link together in a chain to form a specific protein.
But multiple RNA sequences can encode the same amino acid—some that are translated quickly, and some slowly. Although they all result in proteins with identical composition, the choice of mRNA sequence can dramatically change the rate at which the protein is made.
Research from Stanford University biology Professor Judith Frydman and researcher Sebastian Pechmann now reveals that this protein synthesis “rhythm” may be evolutionarily adjusted to control the folding of the new protein chain as it emerges from the ribosome.
The finding may explain how RNA sequences define the final, folded form of a protein—a fundamental problem in molecular biology, since proteins need to fold in order to function.
“For around 50 years, there has been a conceptual gap between the sequence and the final structure,” says Pechmann, a postdoctoral scholar in the Frydman Lab. “There’s been the sense that there’s much more information in the sequence than can be deciphered at the moment.”
It has been one of the toughest problems in genetics. How do investigators figure out not just what genes are involved in causing a disease, but what turns those genes on or off? What makes one person with the genes get the disease and another not? Now, in a pathbreaking paper, researchers at the Johns Hopkins University School of Medicine and the Karolinska Institute in Sweden report a way to evaluate one gene-regulation system: chemical tags that tell genes to be active or not. Their test case was of patients with rheumatoid arthritis, a crippling autoimmune disease that affects 1.5 million Americans. It was an investigation of epigenetics, a popular area of molecular biology that looks for modifications of genes that can help determine disease risk. “This is one of the first studies that looks for an epigenetic disease association in a really rigorous fashion,” said Dr. Bradley Bernstein of Harvard, who was not associated with the study. Kun Zhang of the University of California, San Diego, made a similar observation. “I am quite impressed with their level of rigor and sophistication,” he said. In previous genomic studies, researchers with papers in leading journals “have made major claims, but after a few months or a year they were retracted,” he said. Those investigators, Dr. Zhang added, “did not treat their data very carefully.”
Computer files stored accurately on DNA in new breakthrough Scientists have recorded data including Shakespearean sonnets and an MP3 file on strands of DNA, in a breakthrough which could see millions of records stored on a handful of molecules rather than computer drives.
By translating computerised files into DNA similar to that found in plants and animals, the researchers claim it is possible to store a billion books’ worth of data for thousands of years in just a small test tube. Although the method is expensive, it could still be much more efficient than hard drives or magnetic tape for long-term storage of large sets of data such as government records, the scientists said. Within a decade, they expect the technique to have become cheap enough that DNA storage could become cost-efficient for the public to store lifelong keepsakes like wedding videos. Dr Nick Goldman of the European Bioinformatics Institute, who led the study, said: “We already know that DNA is a robust way to store information because we can extract it from bones of woolly mammoths, which date back tens of thousands of years, and make sense of it. “It’s also incredibly small, dense and does not need any power for storage, so shipping and keeping it is easy.” (via Computer files stored accurately on DNA in new breakthrough - Telegraph)