Twenty years ago, sequencing the human genome was one of the most ambitious science projects ever attempted. Today, compared to the collection of genomes of the microorganisms living in our bodies, the ocean, the soil and elsewhere, each human genome, which easily fits on a DVD, is comparatively simple. Its 3 billion DNA base pairs and about 20,000 genes seem paltry next to the roughly 100 billion bases and millions of genes that make up the microbes found in the human body.
And a host of other variables accompanies that microbial DNA, including the age and health status of the microbial host, when and where the sample was collected, and how it was collected and processed. Take the mouth, populated by hundreds of species of microbes, with as many as tens of thousands of organisms living on each tooth. Beyond the challenges of analyzing all of these, scientists need to figure out how to reliably and reproducibly characterize the environment where they collect the data.
“There are the clinical measurements that periodontists use to describe the gum pocket, chemical measurements, the composition of fluid in the pocket, immunological measures,” said David Relman, a physician and microbiologist at Stanford University who studies the human microbiome. “It gets complex really fast.”
Excerpt from an article by Emily Singer at Quanta. Continue THERE
The announcement was short. It lasted only a fraction of second — a blink of an eye. But a spacecraft in Earth’s orbit, keeping an eye on such events, captured it on June 3 this year. The announcement may have been brief, but it told us that two exotic dead stars, called neutron stars, have collided with each other. This is a relatively rare event, but it bears good news for the merchants in the Sona bazaar. This collision has created gold — lots of it.
But before you head over to Sona bazaar, you should know that this particular collision happened in a galaxy so far away that it has taken light — traveling at a stupendous speed of 186,000 miles every second — four billion years to reach us! In astronomical terms, this collision happened in a galaxy four billion light-years away. In comparison, light from our Sun gets to us in 8 minutes, and is therefore only 8 light-minutes away. The distance of billions of light-years doesn’t intimidate astronomers, as they routinely study events and objects that are even farther away than this particular galaxy. The significance of this event, however, resides in the fact that for the first time, astronomers have been able to study light from collisions that may help us understand the way elements like gold are created in the universe.
Before we get too caught up in the cosmic glamour, we should remember that almost all of the elements that make our bodies were cooked up inside the stars: the carbon in our DNA, oxygen in our lungs, and iron in our blood. Hydrogen in the water molecule, on the other hand, is a leftover from processes in the early history of the universe. The classic quote from the late astronomer Carl Sagan is indeed true: “We are made up of star stuff”.
Excerpt from an article written by Salman Hameed at the IHT. Continue THERE
Researchers have provided the first comprehensive compendium of mutational processes that drive tumour development. Together, these mutational processes explain most mutations found in 30 of the most common cancer types. This new understanding of cancer development could help to treat and prevent a wide-range of cancers.
Each mutational process leaves a particular pattern of mutations, an imprint or signature, in the genomes of cancers it has caused. By studying 7,042 genomes of people with the most common forms of cancer, the team uncovered more than 20 signatures of processes that mutate DNA. For many of the signatures, they also identified the underlying biological process responsible.
All cancers are caused by mutations in DNA occurring in cells of the body during a person’s lifetime. Although we know that chemicals in tobacco smoke cause mutations in lung cells that lead to lung cancers and ultraviolet light causes mutations in skin cells that lead to skin cancers, we have remarkably little understanding of the biological processes that cause the mutations which are responsible for the development of most cancers.
Read full article HERE
In the past few decades, scientists studying the eating habits of Earth’s creatures have noticed something strange: the babies of several species, from tiger sand sharks to fruit flies, are eating each other.
Thing is, they aren’t freaks of nature. And in fact, the mechanisms behind animal cannibalism are helping scientists ask–and answer–some important evolutionary questions. These three recent studies provide a glimpse into this gruesome diet and what it means for evolution.
Why paternity might still matter after fertilization
Sand tiger sharks have been known to have cannibalistic embryos since the 1980s, when detailed autopsies revealed embryos in the stomachs of other shark embryos. But a new study published in Biological Letters could give some clues as to why.
Female sand tiger sharks aren’t the most faithful–they tend to mate with multiple male partners. And if you’re a male sand tiger shark trying to further your lineage, it’s not just about the speed and strength of sperm. The competition continues even after the eggs turn to embryos. After about five months of gestation, the embryo to first hatch from its egg in utero (the female sand tiger shark has two uteri) begins to feed on its smaller siblings–specifically those fathered by a different male. Some litters may start at 12 but this alpha embryo will eat all but one, leaving its brother or sister from the same mister alive. So despite the litters starting out with various fathers, the offspring that make it through the gestational massacre tend to be from the same father–and they’re large and strong enough to survive potential predators after birth. “It’s exactly the same sort of DNA testing that you might see on Maury Povich to figure out how many dads there are,” Stony Brook University marine biologist and study author Demian Chapman told LiveScience.
Text and Image via POPSci. Continue THERE
In the mid-2000s, David Markovitz, a scientist at the University of Michigan, and his colleagues took a look at the blood of people infected with HIV. Human immunodeficiency viruses kill their hosts by exhausting the immune system, allowing all sorts of pathogens to sweep into their host’s body. So it wasn’t a huge surprise for Markovitz and his colleagues to find other viruses in the blood of the HIV patients. What was surprising was where those other viruses had come from: from within the patients’ own DNA.
HIV belongs to a class of viruses called retroviruses. They all share three genes in common. One, called gag, gives rise to the inner shell where the virus’s genes are stored. Another, called env, makes knobs on the outer surface of the virus, that allow it to latch onto cells and invade them. And a third, called pol, makes an enzyme that inserts the virus’s genes into its host cell’s DNA.
It turns out that the human genome contains segments of DNA that match pol, env, and gag. Lots of them. Scientists have identified 100,000 pieces of retrovirus DNA in our genes, making up eight percent of the human genome. That’s a huge portion of our DNA when you consider that protein coding genes make up just over one percent of the genome.
Excerpt form an article written by Carl Zimmer. Continue HERE
Through an un-usual DNA collection method, American artist Heather Dewey-Hagborg creates portrait sculptures from the analyses of genetic material collected in public places. From cigarette butts to hair samples, she works using random traces left behind from un-suspecting strangers. In a statement by Dewey-Hagborg, ‘Stranger Visions’ calls attention to the impulse toward genetic determinism and the potential for a culture of genetic surveillance. Using DNA facial modeling software and a 3D printer, physical models are conceived – reconstructed from ethnic profiles, eye color and hair color.
Text and Images via DesignBoom
Many extinct species—from the passenger pigeon to the woolly mammoth—might now be reclassified as “bodily, but not genetically, extinct.” They’re dead, but their DNA is recoverable from museum specimens and fossils, even those up to 200,000 years old.
Thanks to new developments in genetic technology, that DNA may eventually bring the animals back to life. Only species whose DNA is too old to be recovered, such as dinosaurs, are the ones to consider totally extinct, bodily and genetically.
But why bring vanished creatures back to life? It will be expensive and difficult. It will take decades. It won’t always succeed. Why even try?
Excerpt from an article written by Stewart Brand for National Geographic News. Continue THERE
Synthetic biologists have developed DNA modules that perform logic operations in living cells. These ‘genetic circuits’ could be used to track key moments in a cell’s life or, at the flick of a chemical switch, change a cell’s fate, the researchers say. Their results are described this week in Nature Biotechnology.
Synthetic biology seeks to bring concepts from electronic engineering to cell biology, treating gene functions as components in a circuit. To that end, researchers at the Massachusetts Institute of Technology (MIT) in Cambridge have devised a set of simple genetic modules that respond to inputs much like the Boolean logic gates used in computers.
Excerpt from an article written by Roland Pease at Nature. Continue HERE
The most disruptive force on the planet resides in DNA. Biotech companies and academic researchers are just beginning to unlock the potential of piecing together life from scratch. Champions of synthetic biology believe that turning genetic code into Lego-like blocks to build never-before-seen organisms could solve the thorniest challenges in medicine, energy, and environmental protection. But as the hackers who cracked open the potential of the personal computer and the Internet proved, the most revolutionary discoveries often emerge from out-of-the-way places, forged by brilliant outsiders with few resources besides boundless energy and great ideas.
In Biopunk, Marcus Wohlsen chronicles a growing community of DIY scientists working outside the walls of corporations and universities who are committed to democratizing DNA the way the Internet did information. The “biohacking” movement, now in its early, heady days, aims to unleash an outbreak of genetically modified innovation by making the tools and techniques of biotechnology accessible to everyone. Borrowing their idealism from the worlds of open-source software, artisinal food, Internet startups and the Peace Corps, biopunks are devoted advocates for open-sourcing the basic code of life. They believe in the power of individuals with access to DNA to solve the world’s biggest problems.
You’ll meet a new breed of hackers who aren’t afraid to get their hands wet, from entrepreneurs who aim to bring DNA-based medical tools to the poorest of the poor to a curious tinkerer who believes a tub of yogurt and a jellyfish gene could protect the world’s food supply. These biohackers include:
• A duo who started a cancer drug company in their kitchen
• A team who built an open-source DNA Xeroxing machine
• A woman who developed a genetic test in her apartment for a deadly disease that has stricken her family
Along with the potential of citizen science to bring about radical change, Wohlsen explores the risks of DIY bioterrorism; the possibility of cv gone awry; and whether the ability to design life from scratch on a laptop might come sooner than we think.
Text and Image via Marcus Wohlsen.
With Art.sy, a visitor can enter an artist, artwork, artistic movement or medium into a search bar and the site will generate a list of artists and works that have been deemed related in some way. “There are a lot of people who may know who Warhol is, but they have no idea who Ray Johnson is. The ability to make those connections is what this is about,” said Cwilich, Art.sy’s Chief Operating Officer, on a recent segment of The Takeaway with John Hockenberry.
The endeavor is a true collaboration between computer scientists and art historians. (This is even evident in Art.sy’s leadership. Cleveland, Art.sy’s 25-year-old chief executive officer, is a computer science engineer, and Cwilich is a former executive from Christie’s Auction House.) To create a Web site that could generate fine-art recommendations, the Art.sy team had to first tackle the Art Genome Project. Essentially, a number of art historians have identified 800-and-counting “genes,” or characteristics, that apply to different pieces of art. These genes are words that describe the medium being used, the artistic style or movement, a concept (i.e., war), content, techniques and geographic regions, among other things. All the images that are tagged with a specific gene—say, “American Realism” or “Isolation/Alienation”—are then linked within the search technology.
Text and Image via The Smithsonian. Continue HERE
Back in 2001, the Human Genome Project gave us a nigh-complete readout of our DNA. Somehow, those As, Gs, Cs, and Ts contained the full instructions for making one of us, but they were hardly a simple blueprint or recipe book. The genome was there, but we had little idea about how it was used, controlled or organized, much less how it led to a living, breathing human.
That gap has just got a little smaller. A massive international project called ENCODE – the Encyclopedia Of DNA Elements – has moved us from “Here’s the genome” towards “Here’s what the genome does”. Over the last 10 years, an international team of 442 scientists have assailed 147 different types of cells with 24 types of experiments. Their goal: catalog every letter (nucleotide) within the genome that does something. The results are published today in 30 papers across three different journals, and more.
For years, we’ve known that only 1.5 percent of the genome actually contains instructions for making proteins, the molecular workhorses of our cells. But ENCODE has shown that the rest of the genome – the non-coding majority – is still rife with “functional elements”. That is, it’s doing something.
Excerpt from an article by Discover. Continue HERE
According to EteRNA: By playing EteRNA, you will participate in creating the first large-scale library of synthetic RNA designs. Your efforts will help reveal new principles for designing RNA-based switches and nanomachines — new systems for seeking and eventually controlling living cells and disease-causing viruses. By interacting with thousands of players and learning from real experimental feedback, you will be pioneering a completely new way to do science. Join the global laboratory!
EteRNA is starting with simple shapes like “the finger” and “the cross” to make sure you can nail the fundamentals. And then we’ll be moving on to elaborate shapes like trees. And then molecules that switch folds when they sense a specific other piece of RNA. This might take a few weeks, or it might take a year — we want to make sure we can ace these exercises.
After that, we will embark on one of a few epic projects – perhaps we’ll make the first RNA random-access memory for a computer. Or switches that enables cells to fluoresce if they start expressing cancer genes. Or how about a nanomotor? Or a nanoLED display? There are lots of options, and we’ll let you propose your own and choose.
Finally, you’ll start seeing a few other kinds of puzzles popping up in later stages: The ability to play with RNAs in three dimensions. The ability to see natural RNAs from bacteria, viruses, and humans; and challenges to predict their properties. Stay tuned.
The apples have been ‘contaminated’ with DNA which has been genetically engineered to encode for the Universal Declaration of Human Rights.
The project has bio-engineered a bacteria which has the Universal Declaration of Human Rights encoded into its DNA sequence. The DNA has been extracted and apples grown near The Hague, which houses the International Court of Justice, have been ‘contaminated’ with the synthetic DNA. They are currently being sent to genomics laboratories around the world, which have been asked to sequence the declaration and also to eat the fruit.
Blighted By Kenning
Click HERE to see documentation and correspondence relating to trying to exhibit a Genetically Modified Organism (GMO) in the UK and Netherlands.
Text and Image via Charlotte Jarvis
The music legend apparently orders workers to complete an extreme clean of all her dressing rooms on tour so that any hair, skin or saliva belonging to the 53-year-old cannot be captured.
Concert promoter Alvaro Ramos, who is overseeing the Portuguese leg of Madonna’s MDNA tour, told Britain’s Daily Mirror: “We have to take extreme care, like I have never seen for any other artist.
“We cannot even look at the dressing room after it is ready, or even open the door.”
He added: “We can only enter after her sterilization team has left the room. There will not be any of Madonna’s DNA, any hair or anything. They will clean up everything. In the end, it is all to protect her and make her feel comfortable.”
Text and Image via Herald Sun
A team of scientists from the University of Virginia and University of North Carolina in the US have discovered a previously unidentified type of small circular DNA molecule occurring outside the chromosomes in mouse and human cells. The circular DNA is 200-400 base pairs in length and consists of non-repeating sequences. The new type of extra-chromosomal circular DNA (eccDNA) has been dubbed microDNA. Unlike other forms of eccDNA, in microDNA the sequences of base pairs are non-repetitive and are usually found associated with particular genes. This suggests they may be produced by micro-deletions of small sections of the chromosomal DNA.
This result suggests that the DNA found in tissue cells may exhibit more variation than previously thought, and the implication of this is that sequencing of the DNA in blood cells (which are the cells usually used for sequencing) may give misleading results if micro-deletions have occurred in the DNA of other tissues but not in blood cells. Examples in which this might be important are in genetic sequencing for autism or schizophrenia, which could be caused by incorrect functioning of certain genes in brain tissue. Many cancers are also caused by incorrect functioning of genes; in this case tumor suppressor genes, and sequencing of blood cell DNA could also give misleading results.
Excerpts from an article via PhysOrg
Researchers today unveiled a DNA nanorobot that can track down leukemia cells and kill them on sight, unleashing a therapeutic payload that causes the cancerous cells to self-destruct. Incredibly, this molecular assassin can accomplish this assignment while leaving healthy cells unharmed.
Leading researchers in the field of nanotechnology are calling the clam-like bots (which are assembled from the same components that make up your genetic code) a major milestone in the field of smart drugs. This level of praise has been hard-earned, and a long time coming; it’s taken the field of DNA nanotechnology thirty years to get where it is today. Find out how scientists got here, and how DNA nanotechnology — once considered by many to be a pipe dream — is now poised to change the future of medicine and technology forever.
What is DNA Nanotechnology?
Nanotechnologies are materials, structures, or devices intentionally designed by scientists to function on a scale of less than 100 nanometers. As a point of reference, a water molecule is about 1 nanometer across, while a single strand of hair has a diameter of about 100,000 nanometers. Researchers use a variety of molecules to create nanotechnologies (carbon nanotubes, for example, are popular in nanotech); but DNA nanotechnologists work with — you guessed it — DNA.
Continue at io9
ANCIENT HISTORY: The layers of sediment excavated in Denisova Cave (top left) and its surroundings have yielded such artifacts as chipping tools (top right), a fragment of a pinky bone, and a molar. DNA in the bone and molar led to the identification of a new hominin group, the Denisovans.Photos: Courtesy of David Reich (top left, top right, bottom right); Courtesy of the Max Planck Institute for Evolutionary Anthropology (bottom left, middle right)
Perched in the Altai Mountains of southern Siberia, and overlooking the Anui River and its surrounding forest, is the Denisova Cave. It is not a particularly large natural structure, but its high ceilings, central limestone chimney, and location near abundant food sources have made it an inviting shelter for humans and animals for tens of thousands of years.
“It’s kind of a magical cave,” says David Reich, an HMS professor of genetics who traveled to the site this past summer. It was a rugged trip, covering 5,500 miles on a 48-hour journey that began in Boston, touched London and Moscow, and finished with a bumpy 10-hour van ride to the Denisova Cave, near Russia’s border with Kazakhstan. But Reich, whose affiliation with the Broad Institute of MIT and Harvard means he’s more often surrounded by gene sequencers than Stone Age tools, took the opportunity to step inside this remote refuge to witness the resting spot of ancient DNA that had been preserved in bone fragments buried deep in cave sediments.
For the past year, Reich and an international team of evolutionary geneticists have been coaxing information from that DNA. What they’ve found has changed our understanding of human history.
DOWN TO EARTH: Excavation of Denisova Cave, a site overseen by the Russian Academy of Sciences, is an ongoing venture involving international teams of researchers. Photo: Courtesy of David Reich
Text and Images via Harvard Medicine. Continue HERE
The claim by Ion Torrent on Tuesday that a reasonably affordable machine capable of mapping an individual’s complete genetic makeup for $1,000 will be ready by the end of the year has technology geeks in a tizzy.
The $1,000 genome has been hotly sought ever since a crude map of the human genome was first published in 2001. The Carlsbad, Calif. biotech company, part of Life Technologies, will sell its device to research labs and medical clinics for $99,000 to $149,000, compared to the current price of about $750,000 for existing sequencers, Reuters reported on its website Tuesday. According to Reuters, a doctor will be able to sequence a patient’s entire genome for $1,000, compared to the current rate of $3,000 just to test for breast cancer gene mutations, for example. And the company says its new machine can complete the genome analysis within a day, rather than the two months previously needed.
It’s widely believed this type of genetic analysis will revolutionize medicine, that patients will learn their risk profile for potential diseases by having their DNA read right in the doctor’s office. Drugs and vaccines will be designed to fit our genes, in order to maximize efficacy and minimize any side-effects. Newborn babies would have someone peek at their genes so parents could take steps to prevent genetic risks from becoming realities.
Text by Art Caplan, Ph.D. Continue HERE