Posts Tagged ‘DNA’
A man wrongly accused and charged with raping a woman was the “innocent victim” of an avoidable mistake, the forensics watchdog said today.
Adam Scott was arrested and held in custody for months after a plastic tray containing a sample of his DNA was re-used in the analysis of a swab from a rape victim in Manchester by private firm LGC Forensics.
Forensic science regulator Andrew Rennison said Mr Scott, from Devon, was an “innocent victim of avoidable contamination“.
It also emerged that the same error happened at least once before, on October 12 last year, the report added.
“The contamination was the result of human error by a technician who failed to follow basic procedures for the disposal of plastic trays used as part of a validated DNA extraction process,” he said…
“These errors were compounded by the failure at LGC to consider the possibility of contamination despite concerns expressed by the investigating officer about the reliability of the DNA profile.”
He went on: “It is unlikely that the case against Mr Scott would ever have proceeded to trial and, in the absence of any further evidence, the case would probably have been discontinued.
“However, this is of little comfort to Mr Scott who was charged on October 23 2011 and remanded in custody on this case until it was withdrawn on March 7 2012…”
LGC said it “deeply regrets the incident of contamination”, blah, blah, blah.
Results from the best science in the world still must run the gauntlet of human beings who may or may not be capable of maintaining legitimate standards. The procedures for checking quality in this case were as useless as the test.
Using the latest-generation Atacama Large Millimeter Array (ALMA), which is an advanced system of 64 radio-telescope antennas in northern Chile, scientists at the European Southern Observatory have discovered a simple form of sugar orbiting a small binary star. Known as 16293-2422, that star is only 400 light-years away, and has about the same mass as the Sun. The finding could shed light on how the building blocks of life can originate spontaneously in deep space, even without a planet to support them.
The molecule found was glycolaldehyde (C2H4O2), not dissimilar to the table sugar (C12H22O11) we’re familiar with, and one of the building blocks of DNA and RNA. Glycolaldehyde has been found inside distant cloud dust as early as in 2000 but, crucially, this marks the first time that scientists have detected it in the right place and at the right time for life to blossom in its vicinity…
Most chemical reactions on Earth occur in liquid water, but in interstellar space the complex molecules appear to form on the surface of tiny dust particles. Smaller molecules such as water, formaldehyde, methane, ammonia, carbon dioxide or methanol coat the surfaces and interiors of the grains in the dust clouds. Then, when a shock wave hits the dust, it provides the energy to assemble more complex molecules (such as sugars) from the simpler ones and then free them from the dust grains.
One of the open questions on the origins of life on Earth is the mystery of how, based on our ample fossil record, life seems to have originated very shortly after the right conditions arose on our planet. This finding might help explain why, as there is mounting evidence now that prebiotic chemistry – the formation of the molecular building blocks necessary for the creation of life – occurs in interstellar clouds long before those clouds collapse to form a new planetary system.
Cripes! Another fascinating area of study – incorporating astrophysics, astrochemistry, prebiotic chemistry and leading to organic life and evolution.
It boggles the mind.
The genetic “control panel” of the human body that regulates the activity of our 23,000 genes has been revealed for the first time in a scientific tour de force that could revolutionise the understanding and treatment of hundreds of diseases.
Scientists have once and for all swept away any notion of “junk DNA” by showing that that the vast majority of the human genome does after all have a vital function by regulating the genes that build and maintain the body.
Junk DNA was a term coined 40 years ago to describe the part of the genome that does not contain any genes, the individual instructions for making the body’s vital proteins. Now, this vast genetic landscape could hold hidden clues to eradicating human disease, scientists said.
Hundreds of researchers from 32 institutes around the world collaborated on the immense effort to decipher the hidden messages within the 98 per cent of the human genome without any genes and was thought, therefore, to have no function.
They have concluded in a series of 30 research papers published simultaneously today, in Nature, Science and other journals, that this so-called junk DNA is in fact an elaborate patchwork of regulatory sequences that act as a huge operating system for controlling the genome…
“We see that 80 per cent of the genome is actively doing something. We found that a much bigger part of the genome – a surprising amount in fact – is involved in controlling when and where proteins are produced,” Dr. Ewen Birney said.
Defects in this part of the genome could be responsible for a range of illnesses, from diabetes and Crohn’s disease to disorders of the immune system, such as lupus. Knowing about them could lead to a fundamental reappraisal of what goes wrong in scores of difficult conditons, said John Stamatoyannopoulous of Washington University in Seattle, another leader of the consortium.
Bravo! As happens so often, study and experimentation pries away prominence of a small body of knowledge only to open the door to new studies magnitudes larger and broader. Gonna need more molecular biologists, gang.
Unlike the Crime Scene Investigators from the popular TV series, these detectives are hired to look for evidence of rogue wood from stores increasingly worried about being duped by a global trade in illegal timber now worth billions.
They take wood samples into their lab and put them through DNA tests that can pinpoint the species and origin of a piece of timber. They also track timber and timber products from forest to shop to ensure clients’ shipments are legal.
“This is like CSI meets save the planet,” says Jonathan Geach, executive director of Double Helix Tracking Technologies, the Singapore company that has developed and commercialized DNA testing for wood, the only firm in the world to do so…
The money earned from a trade that Interpol estimates at up to $30 billion annually is untaxed and often run by organized gangs to fund crime and conflict. The logging increases global warming with heightened carbon emissions, and landslides through loss of watersheds. It causes loss of livelihoods in forest communities and dents global timber prices.
Until now, the battle against trade in illegal timber has been waged with regulations and preventive measures, and has not met with much success. Now it is increasingly focused on using the criminal justice system and law enforcement techniques.
Retailers such as Kingfisher, Marks & Spencer and Australian timber wholesaler Simmonds Lumber are either already using the technology or looking to add it to their existing timber sourcing practices…
As new U.S. laws started to bite over the past two years, and with tougher laws set for Europe in 2013, the number of clients is growing, says Kevin Hill, DoubleHelix’s founder.
Within two years, the aim is to license Lowe’s DNA extraction technique to accredited laboratories globally, as the $150 billion timber industry comes under increasing pressure to stamp out illegal wood.
As much as I hate the phrase, this is a true win-win situation for consumers and sellers alike. Contractors and end users will have verified questions like sustainability. Lumbering interests and mills will profit from sales with guaranteed quality, legality.
RTFA for many details about the economics and science. Interesting stuff.
By now you’ve probably read about the paper which reports that there seem to have been three waves of humans migrating into the New World prior to the arrival of Europeans. A major aspect of this result is that it does not emerge out of a vacuum, but rather comes close to settling an old question in linguistics…
The late Joseph Greenberg generated a series of audacious phylogenies of languages of the world. Greenberg’s attempts received mixed reviews. It seems that there is little controversy about some of his classifications of African languages, but linguists of American native dialects rejected his division of the languages of the New World into three broad families, Eskimo-Aleut, Na-Dene, and Amerind…The linguistic trichotomy also lent itself to a narrative of three migrations…
Despite all this drama, the scientific isn’t too hard to understand. Aside from the nifty statistics one problem is that many of these native groups have European and African admixture, but there are workarounds to that (e.g., just pull out genomic segments which are indigenous, and use those)…
On a big picture note this puts the lie to the idea that before agriculture hunter-gatherer societies were subject purely to differentiation in situ. The Eskimo-Aleut and Na-Dene erupted into a settled landscape, and dispossessed the indigenous groups of their lands…The First Americans “struck back” in this case, shoving aside the pioneers of northern living who had likely originated more recently from the margins of eastern Asia. Of course, the Eskimo-Aleut and related peoples were not First Americans only, rather, it was the old (First American) and new (Asian) ganging up upon the not so old or new (Asian).
The real deal – in a computer simulation
Step aside, DNA—new synthetic compounds called XNAs can also store and copy genetic information, a new study says. And, in a “big advancement,” these artificial compounds can also be made to evolve in the lab, according to study co-author John Chaput of the Biodesign Institute at Arizona State University.
Nucleotides, the building blocks of DNA are composed of four bases—A, G, C, and T. Attached to the bases are sugars and phosphates.
First, researchers made XNA building blocks to six different genetic systems by replacing the natural sugar component of DNA with one of six different polymers, synthetic chemical compounds…The team—led by Vitor Pinheiro…then evolved enzymes, called polymerases, that can make XNA from DNA, and others that can change XNA back into DNA.
This copying and translating ability allowed for genetic sequences to be copied and passed down again and again—artificial heredity.
Last, the team determined that HNA, one of the six XNA polymers, could respond to selective pressure in a test tube…As would be expected for DNA, the stressed HNA evolved into different forms.
This shows that “beyond heredity, specific XNAs have the capacity for Darwinian evolution,” according to the study…
All of XNA’S actions are “completely controlled by experimentalists—it’s 100 percent unnatural,” study co-author Chaput noted…But such control means that scientists can “use [XNA] to ask very basic questions in biology,” such as about the origins of life, Chaput said.
For instance, “it’s possible that life didn’t begin with DNA and proteins like we see today—it may have begun with something much, much simpler,” he said.
A scientist could potentially evolve XNA to discover various functions that would have been important for early life.
I love it. Opening biochemistry to the inventiveness of humankind. Practical and experimental modeling beyond computer models.
A paedophile who abducted four young girls from the street in the 1980s and 1990s and sexually abused them has appeared in court after cold-case detectives linked his DNA to the crimes.
David Bryant, a 65-year-old grandfather from Ulverston, Cumbria, was due to be sentenced at Newcastle crown court on Friday but the case was adjourned until next week.
The court heard that Bryant carried out separate attacks on young girls in Hampshire and Tyneside. He has admitted four counts of kidnap and four of sexual assault.
Mark Giuliani, for the prosecution, told the court: “A familiar feature of this offending is how the defendant targeted young girls out playing near their homes…
The prosecution told the court that Bryant was convicted of three sex offences against women between 1975 and 1984.
How many more cases could be solved if politicians felt like spending the money on computational analysis to link evidence already on file — instead of the crap that governments assign higher priority. Like wars, standing armies sufficient to “show the flag”, the war on drugs, subsidies to keep the prices of commodities higher than need be.
Day of Discovery
The first complete genome-sequencing of “Otzi,” Italy’s prehistoric iceman, is revealing a wealth of details about the man who roamed the Alps 5,300 years ago and could unleash a frenzy of activity among scientists thanks to open data.
Over the last 20 years, scientists have painstakingly collected data from the stomach, bowels and teeth of the 45-year old man, who was found sticking out of a glacier by German climbers in 1991 in the Tyrolean Alps on the Austro-Italian border.
But for the first time since the Copper-age individual was unearthed, his complete genetic profile has been reconstituted, revealing a very modern predisposition for cardiovascular diseases, lactose intolerance, and brown eyes that betray near-Eastern origins.
“He is more closely related to modern Sardinian or Corsican populations than, for instance, mainland Italy further to the south,” Angela Graefen, a human genetics researcher at the Eurac Institute for the Mummies and the Iceman in Bolzano, Italy, told Reuters…
“His ancestors were more plausibly from the first wave of migrants from the Near East. The genome group stuck in the isolated regions which were less affected by human migrations, Mediterranean islands but also remote Alpine valleys.”
Otzi, a hunter who was felled by an arrow while climbing the high mountains, was also predisposed to arteriosclerosis and heart diseases, conditions thought to be more linked to modern risk factors such as being overweight, smoking or drinking…
The research helps flesh out a picture of the iceman, who had brown hair, type-O blood, the lactose intolerance that was common among Neolithic agrarian societies. He also was the first-known carrier of Lyme disease, a bacterial infection spread by ticks.
But the full-genome sequencing also opens far more possibilities for researchers around the globe than the 2008 sequencing of his mitochondrial DNA — which is passed down through the mother’s line.
“This is more information than we could probably study in a lifetime,” Eurac’s Graefen said. “That’s why we have made the data public on a special browser so that a specialist in any field can look this up.”
“There are millions of genes out there which have yet to be identified. In the future, when we know what a particular gene is for, we can check what it was like 5,000 years ago,” she said.
I never miss a story about Otzi. I’ve hiked the region where he was found – and I wish I had found him.
Archaic DNA sequencing is such an interesting study. Yet another aspect of computational analysis I’d love to focus on – if I was starting out as a geek, nowadays.
The medical world is holding its breath, waiting for the revolution. It will be here any minute. Definitely by the end of the decade. Or perhaps it will take a little longer than that, but seriously, it’s right around the corner. More or less.
That’s the genomics revolution, with its promise of treatment focused on the individual rather than the group. At last, patients will be more than the product of their age, sex, ethnicity, illnesses and bad habits; treatments will be aimed like a laser at their personal genetic particulars, and if those genes are not quite what they should be, then those genes will be fixed.
…A particularly readable and comprehensive vision can be found in Dr. Eric J. Topol’s new book, “The Creative Destruction of Medicine.”
Dr. Topol, a cardiologist and researcher at the Scripps Research Institute with the energy of 10 (if his prose style and his honor-laden biography are any indication), dispenses in short order with our current population-based medical strategies. They are wasteful and inexact, he points out, often marginally beneficial to the group and downright harmful to the individual.
He presents an array of far better ideas, a few now actually being practiced in rudimentary form. These include pharmacogenomics, in which specific genes that govern responses to medications are routinely assayed, and cancer treatments that probe tumors for specific genetic targets rather than relying on standard chemotherapy…
In “Am I My Genes?,” the psychiatrist and ethicist Dr. Robert L. Klitzman plunges readers into the world of genomic medicine as it exists today: a barely mapped terrain of immense overlapping uncertainties. Many thousands of patients are bravely stumbling along in there…
Although written for an academic audience, this book should make compelling reading for anyone considering genetic testing for…many conditions: It provides an instant community of fellow travelers along with a sophisticated moderator. Dr. Klitzman moves through all the basic landmarks, including the big ones: “Do I want to know?,” “Whom should I tell?” and “Why me..?”
And that is exactly the phenomenon that fascinates H. Sebastian Seung, a professor of computational neuroscience at M.I.T. whose “Connectome” lays out the newest research into why we think the way we do. For Dr. Seung, it is self-evident that you are more than your genes. The real you sits firmly within your skull, and while your brain’s 100 billion nerve cells may carry your genes, the “you” they form is shaped by the ways they connect to one another…
As a newborn, Dr. Seung writes, you are pretty much just a product of your genes and some initial random connections, but every second of your first few years adds to the cumulative web of connections that form you. By the time you are a toddler you have more synapses, or connections among your neurons, than you ever will again: In some ways the adult you is just an edited 2-year old, one of many eminently pleasing thoughts he sets forth.
This is complicated stuff, and it is a testament to Dr. Seung’s remarkable clarity of exposition that the reader is swept along with his enthusiasm, as he moves from the basics of neuroscience out to the farthest regions of the hypothetical, sketching out a spectacularly illustrated giant map of the universe of man.
All added to the list. I may have to resume my practice back when I only edited and wrote for one blog. Take a chunk of Friday off to catch up with my reading.
Problem is – this site of mine is especially satisfying because readership and followers are within the margin of error for 50/50 women and men – and depending on the time of day here in the Rockies and time zones around the world, the audience varies from 18% to 68% US-based. The rest of the world is onboard just about all the time.