Tag Archive: DNA


This illustration shows Tribolium castaneum telomerase catalytic subunit, TERT (Emskorda / CC BY-SA 3.0)

The human body consists of fifty trillion cells, and each cell has 46 chromosomes which are the structures in the nucleus containing our hereditary material, the DNA. The ends of all chromosomes are protected by so-called telomeres.

The telomeres serve to protect the chromosomes in much the same way as the plastic sheath on the end of a shoelace. But each time a cell divides, the telomeres become a little bit shorter and eventually end up being too short to protect the chromosomes.

Each cell has a ‘multi-ride ticket,’ and each time the cell divides, telomeres will use up one ride. Once there are no more rides left, the cell will not divide any more, and will ‘retire.’ But some special cells in the body can activate telomerase, which again can elongate the telomeres.

Sex cells, or other stem cells, which must be able to divide more than normal cells, have this feature. Unfortunately, cancer cells have discovered the trick, and it is known that they also produce telomerase and thus keep themselves artificially young. The telomerase gene therefore plays an important role in cancer biology, and it is precisely by identifying cancer genes that the researchers imagine that you can improve the identification rate and the treatment.

“We have discovered that differences in the telomeric gene are associated both with the risk of various cancers and with the length of the telomeres. The surprising finding was that the variants that caused the diseases were not the same as the ones which changed the length of the telomeres. This suggests that telomerase plays a far more complex role than previously assumed,” said Dr Stig Bojesen from the University of Copenhagen, Denmark, first author of a paper published in Nature Genetics.

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The Genomic Instability Group led by researcher Óscar Fernández-Capetillo at the Spanish National Cancer Research Centre (CNIO), has for the first time obtained a panoramic photo of the proteins that take part in human DNA division, a process known as replication.

The research article, published today in the journal Cell Reports, is the result of a collaborative study in which other CNIO groups have also participated, including the Proteomics Unit led by Javier Muñoz and the DNA Replication Group led by Juan Méndez.

DNA replication is the chemical process that sustains cell division, and thus one of the biological mechanisms targeted by most chemotherapeutic agents in order to destroy tumour cells.

To date, multiple independent molecular studies carried out over the last decades have given a general idea of the proteins involved in the replication process. “We suspected that there might be several dozen proteins that control this process meticulously, thus ensuring the correct duplication of our genome as an indispensible step prior to cell division,” explains Fernández-Capetillo.

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Fluorescent dyes track the presence of the RNA molecules and the genes they  affect in the developing mouse brain.

Specific DNA once dismissed as junk plays an important role in brain development and might be involved in several devastating neurological diseases, UC San Francisco scientists have found.

Their discovery in mice is likely to further fuel a recent scramble by researchers to identify roles for long-neglected bits of DNA within the genomes of mice and humans alike.

While researchers have been busy exploring the roles of proteins encoded by the genes identified in various genome projects, most DNA is not in genes. This so-called junk DNA has largely been pushed aside and neglected in the wake of genomic gene discoveries, the UCSF scientists said.

In their own research, the UCSF team studies molecules called long noncoding RNA (lncRNA, often pronounced as “link” RNA), which are made from DNA templates in the same way as RNA from genes.

“The function of these mysterious RNA molecules in the brain is only beginning to be discovered,” said Daniel Lim, MD, PhD, assistant professor of neurological surgery, a member of the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF, and the senior author of the study, published online April 11 in the journal Cell Stem Cell.

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DNA Double Helix

Pretty much anything can be a computer, if it can compute logical functions, store data, and transmit information — even living cells. A team at Stanford University has accomplished one of the the final tasks necessary to turn cells into working computers: They’ve created a biological transistor, called a transcriptor, that uses DNA and RNA instead of electrons and responds to logical functions.

Drew Endy, an assistant professor of bioengineering, has previously made other vital contributions to biocomputing. Last year, his lab developed a “biological Internet” that can transmit genetic information between cells, as well as a rewritable data storage system for DNA.

Building a system with logic gates that can compute true-false answers from biochemical information is the third component in creating a biological computer.

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The term “survival of the fittest” refers to natural selection in biological systems, but Darwin’s theory may apply more broadly than that. New research from the U.S. Department of Energy’s Brookhaven National Laboratory shows that this evolutionary theory also applies to technological systems.

Computational biologist Sergei Maslov of Brookhaven National Laboratory worked with graduate student Tin Yau Pang from Stony Brook University to compare the frequency with which components “survive” in two complex systems: bacterial genomes and operating systems on Linux computers.

Their work is published in the Proceedings of the National Academy of Sciences. Maslov and Pang set out to determine not only why some specialized genes or computer programs are very common while others are fairly rare, but to see how many components in any system are so important that they can’t be eliminated. “If a bacteria genome doesn’t have a particular gene, it will be dead on arrival,” Maslov said. “How many of those genes are there? The same goes for large software systems. They have multiple components that work together and the systems require just the right components working together to thrive.’”

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PSA: DNA

Public Service Announcement

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.

“These developments will more readily enable one to create programmable cells with decision-making capabilities for a variety of applications,” says James Collins, a synthetic biologist at Boston University in Massachusetts who was not involved in the study.

Collins developed the genetic ‘toggle switch’ that helped to kick-start the field of synthetic biology more than a decade ago. A wide range of computational circuits for cells have been developed since, including a simple counter that Collins and his team devised in 2009.

But “to make this a really rigorous engineering discipline, we need to move towards frameworks that allow you to program cells in a more scalable fashion,” says Timothy Lu, a synthetic biologist at MIT who led the latest research. “We wanted to show you can assemble a bunch of simple parts in a very easy fashion to give you many types of logical functions.”

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DNA tags label rioters and other criminals so cops can find them “at a less confrontational time for officers.”

DNA Gun In Action

Riots are a tough nut for law enforcement in part because of the sheer number of people involved–it’s impossible to stop and arrest every person involved in a skirmish. That’s why cops have some pretty high-tech methods for catching suspects, from facial recognition software to debilitating sonic cannons. But none is as bizarre as this new DNA gun from a UK security firm.

The SelectaDNA High Velocity System works like it sounds–it shoots people with pellets containing a unique DNA fingerprint. Unlike rubber-pellet guns, Tasers or tear gas canisters, the technology does not deter or disable the suspect–he or she can get away seemingly unscathed. But later, authorities can track down the suspect and arrest him or her “at a less confrontational time for officers,” according to the company. Portable readers equipped with ultraviolet light scanners would be able to verify the synthetic DNA.

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ll 154 Shakespeare sonnets were spelled out in DNA to demonstrate the vast potential of genetic data storage.

William Shakespeare

His words have touched the lovelorn and been pored over by brooding teenagers for more than four hundred years, but now some of the most romantic poems ever penned have been written into the code of life.

The entire collection of Shakespeare’s 154 sonnets has been spelled out in DNA by scientists in Cambridge to demonstrate the vast potential of genetic storage. Huge quantities of information could be written into specks of DNA and archived for tens of thousands of years, the researchers claim.

Alongside the Bard’s sonnets, the scientists made strands of DNA that stored part of an audio file of Martin Luther King’s 1963 speech “I have a dream”, and the seminal research paper that first described the double helical nature of DNA by Francis Crick and James Watson, a decade earlier.

Written in DNA, one of Shakespeare’s sonnets weighs 0.3 millionths of a millionth of a gram. One gram of DNA could hold as much information as more than a million CDs, the researchers said.

Nick Goldman and Ewan Birney at the European Bioinformatics Institute in Hinxton, near Cambridge, came up with the idea in a pub in Hamburg. They wondered what alternatives might exist to the expensive hard disks and magnetic tapes used to store the growing datasets that are becoming ever more common in biology.

They knew that DNA was an incredibly efficient and compact way to store information, and set about devising a way to turn the molecules into digital memory: capable of encoding the 1s and 0s used to store words, images, music and video on computers.

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A team of Scottish researchers say that they have made a breakthrough discovery, locating the moment in evolutionary history when intelligence and the ability to reason first appeared in our earliest ancestors. They also say that the root cause of many brain disorders can also be traced back to the same genetic events.

According to Seth Grant, the lead researcher on the study and a professor of molecular neuroscience at University of Edinburgh: “One of the greatest scientific problems is to explain how intelligence and complex behaviours arose during evolution.”

Grant and his colleagues say this happened around 500 million years ago as a result of a sudden increase in the number of brain genes possessed by our early invertebrate ancestors. The researchers say that these simple ocean-dwelling animals experienced a ‘genetic accident’ that resulted in an unintended multiplication in the number of brain genes that they possessed. In the millions of years that followed, these extra intelligence genes provided survival benefits to the animals that inherited them and gave rise to increasingly sophisticated behaviors. In humans, these abilities reached their peak with our unique abilities to analyze situations, understand abstract concepts and learn complicated skills.

The study results, which have been published as two papers in the journal Nature Neuroscience, also point to a direct link between the evolution of complex behavior and the origins of a number of brain disorders. The scientists say that the same genes that gave us our enhanced cognitive abilities are also to blame for a variety of common brain diseases.

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PSA: DNA

Public Service Announcement: DNA

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The DNA Replication Complex, an assembly of proteins that synthesizes new DNA before cell division.  It consists of Helicase, Primase, Single-strand binding proteins, and DNA polymerase III.  Because DNA strands can only be copied in one direction, the complex must pull out loops of one strand and replicate it in fragments.  At this moment there are hundreds of trillions of these molecular machines in constant activity within your body.

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The notion that police can identify a suspect based on the tiniest drop of blood or trace of tissue has long been a staple of TV dramas, but scientists at Harvard have taken the idea a step further. Using just a single human cell, they can reproduce an individual’s entire genome.

As described in a Dec. 21 paper in Science, a team of researchers, led by Xiaoliang Sunney Xie, the Mallinckrodt Professor of Chemistry and Chemical Biology, and made up of postdoctoral fellow Chenghang Zong, graduate student Alec Chapman, and former graduate student Sijia Lu, developed a method — dubbed MALBAC, short for Multiple Annealing and Looping-based Amplification Cycles — that requires just one cell to reproduce an entire DNA molecule.

More than three years in the making, the breakthrough technique offers the potential for early cancer treatment by allowing doctors to obtain a genetic “fingerprint” of a person’s cancer from circulating tumor cells. It also could lead to safer prenatal testing for a host of genetic diseases.

“If you give us a single human cell, we report to you 93 percent of the genome that contains three billion base pairs, and if there is a single base mutation, we can identify it with 70 percent detectability, with no false positives detected,” Xie said. “This is a major development.”

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Origin of Life Needs a Rethink, Scientists Argue

Scientists trying to unravel the mystery of life’s origins have been looking at it the wrong way, a new study argues.

Instead of trying to recreate the chemical building blocks that gave rise to life 3.7 billion years ago, scientists should use key differences in the way that living creatures store and process information, suggests new research detailed in the Journal of the Royal Society Interface.

“In trying to explain how life came to exist, people have been fixated on a problem of chemistry, that bringing life into being is like baking a cake, that we have a set of ingredients and instructions to follow,” said study co-author Paul Davies, a theoretical physicist and astrobiologist at Arizona State University. “That approach is failing to capture the essence of what life is about.”

Living systems are uniquely characterized by two-way flows of information, both from the bottom up and the top down in terms of complexity, the scientists write in the article. For instance, bottom up would move from molecules to cells to whole creatures, while top down would flow the opposite way. The new perspective on life may reframe the way that scientists try to uncover the origin of life and hunt for strange new life forms on other planets.

“Right now, we’re focusing on searching for life that’s identical to us, with the same molecules,” said Chris McKay, an astrobiologist at the NASA Ames Research Center who was not involved in the study. “Their approach potentially lays down a framework that allows us to consider other classes of organic molecules that could be the basis of life.”

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The justices’ decision will likely resolve an ongoing battle between scientists who believe that genes carrying the secrets of life should not be exploited for commercial gain and companies that argue that a patent is a reward for years of expensive research that moves science forward. The current case involves Myriad Genetics Inc. of Salt Lake City, which has patents on two genes linked to increased risk of breast and ovarian cancer.

Myriad’s BRACAnalysis test looks for mutations on the breast cancer predisposition gene, or BRCA. Those mutations are associated with much greater risks of breast and ovarian cancer. But the American Civil Liberties Union challenged those patents, arguing that genes couldn’t be patented, and in March 2010, a New York district court agreed. But the U.S. Court of Appeals for the Federal Circuit has now twice ruled that genes can be patented, in Myriad’s case because the isolated DNA has a “markedly different chemical structure” from DNA within the body. Among the ACLU’s plaintiffs are geneticists who said they were not able to continue their work because of Myriad’s patents, as well as breast cancer and women’s health groups, patients and groups of researchers, pathologists and laboratory professionals.

“It’s wrong to think that something as naturally occurring as DNA can be patented by a single company that limits scientific research and the free exchange of ideas,” said Chris Hansen, staff attorney with the ACLU Speech, Privacy and Technology Project. A call to a Myriad spokeswoman was not immediately returned, but in court papers the company’s lawyers said without being able to patent and profit from their work, they would not be able to fund the type of medical breakthroughs doctors depend on. The company also said that deciding now that genes can’t be patented would throw into chaos current research and profits structures for drug-makers and medical research companies, who have gotten more than 40,000 DNA-related patents from the Patent and Trademark Office for almost 30 years, according to court papers.

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Scientists have discovered for the first time how humans – and other mammals – have evolved to have intelligence.

Researchers have identified the moment in history when the genes that enabled us to think and reason evolved.

This point 500 million years ago provided our ability to learn complex skills, analyse situations and have flexibility in the way in which we think.

Professor Seth Grant, of the University of Edinburgh, who led the research, said: “One of the greatest scientific problems is to explain how intelligence and complex behaviours arose during evolution.”

The research, which is detailed in two papers in Nature Neuroscience, also shows a direct link between the evolution of behaviour and the origins of brain diseases.

Scientists believe that the same genes that improved our mental capacity are also responsible for a number of brain disorders.

“This ground breaking work has implications for how we understand the emergence of psychiatric disorders and will offer new avenues for the development of new treatments,” said John Williams, Head of Neuroscience and Mental Health at the Wellcome Trust, one of the study funders.

The study shows that intelligence in humans developed as the result of an increase in the number of brain genes in our evolutionary ancestors.

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“Ever since a monk called Mendel started breeding pea plants we’ve been learning about our genomes. In 1953, Watson, Crick and Franklin described the structure of the molecule that makes up our genomes: the DNA double helix. Then, in 2001, scientists wrote down the entire 3-billion letter code contained in the average human genome. Now they’re trying to interpret that code; to work out how it’s used to make different types of cells and different people. The ENCODE project, as it’s called, is the latest chapter in the story of you.”

DNA strand, over a page of TGAC base pairs

A bioengineer and geneticist at Harvard’s Wyss Institute have successfully stored 5.5 petabits of data — around 700 terabytes — in a single gram of DNA, smashing the previous DNA data density record by a thousand times.

The work, carried out by George Church and Sri Kosuri, basically treats DNA as just another digital storage device. Instead of binary data being encoded as magnetic regions on a hard drive platter, strands of DNA that store 96 bits are synthesized, with each of the bases (TGAC) representing a binary value (T and G = 1, A and C = 0).

To read the data stored in DNA, you simply sequence it — just as if you were sequencing the human genome — and convert each of the TGAC bases back into binary. To aid with sequencing, each strand of DNA has a 19-bit address block at the start (the red bits in the image below) — so a whole vat of DNA can be sequenced out of order, and then sorted into usable data using the addresses.

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Lab Research Shows Stress Damages DNA

Why do humans and their primate cousins get more stress-related diseases than any other member of the animal kingdom? The answer, says Stanford neuroscientist Robert Sapolsky, is that people, apes and monkeys are highly intelligent, social creatures with far too much spare time on their hands. ”Primates are super smart and organized just enough to devote their free time to being miserable to each other and stressing each other out,” he said. “But if you get chronically, psychosocially stressed, you’re going to compromise your health. So, essentially, we’ve evolved to be smart enough to make ourselves sick.”

A professor of biological sciences and of neurology and neurological sciences, Sapolsky has spent more than three decades studying the physiological effects of stress on health. His pioneering work includes ongoing studies of laboratory rats and wild baboons in the African wilderness. All vertebrates respond to stressful situations by releasing hormones, such as adrenalin and glucocorticoids, which instantaneously increase the animal’s heart rate and energy level. “The stress response is incredibly ancient evolutionarily,” Sapolsky said. “Fish, birds and reptiles secrete the same stress hormones we do, yet their metabolism doesn’t get messed up the way it does in people and other primates.”

To understand why, he said, “just look at the dichotomy between what your body does during real stress—for example, something is intent on eating you and you’re running for your life—versus what your body does when you’re turning on the same stress response for months on end for purely psychosocial reasons.”

In the short term, he explained, stress hormones are “brilliantly adapted” to help you survive an unexpected threat. “You mobilize energy in your thigh muscles, you increase your blood pressure and you turn off everything that’s not essential to surviving, such as digestion, growth and reproduction,” he said. “You think more clearly, and certain aspects of learning and memory are enhanced. All of that is spectacularly adapted if you’re dealing with an acute physical stressor—a real one.”

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The technique uses two proteins adapted from viruses to “flip” the DNA bits.

Though it is at an early stage, the advance could help pave the way for computing and memory storage within biological systems.

A team reporting in Proceedings of the National Academy of Sciences say the tiny information storehouses may also be used to study cancer and aging.

The team, from Stanford University’s bioengineering department, has been trying for three years to fine-tune the biological recipe they use to change the bits’ value.

The bits comprise short sections of DNA that can, under the influence of two different proteins, be made to point in one of two directions within the chromosomes of the bacterium E. coli.

The data are then “read out” as the sections were designed to glow green or red when under illumination, depending on their orientation.

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Scientists have identified the gene which may have driven the crucial step in evolution where man learned to talk.

By duplicating itself two and a half million years ago the gene could have given early human brains the power of speech and invention, leaving cousins such as chimpanzees behind.

The gene, known as SRGAP2, helps control the development of the neocortex – the part of the brain responsible for higher functions like language and conscious thought.

Having an extra copies slowed down the development of the brain, allowing it to forge more connections between nerve cells and in doing so grow bigger and more complex, researchers said.

In a study published in the Cell journal, the scientists reported that the gene duplicated about 3.5 million years ago to create a “daughter” gene, and again a million years later creating a “granddaughter” copy.

Although humans and chimpanzees separated six million years ago, we still share 96 per cent of our genome and the gene is one of only about 30 which have copied themselves since that time.

The first duplication was relatively inactive but the second occurred at about the time when primitive Homo separated from its brother Australopithecus species and began developing more sophisticated tools and behaviours.

Evan Eichler at the University of Washington, who led the research, said the benefit of the duplication would have been instant, meaning human ancestors could have distanced themselves from rival species within a generation.

He said: “This innovation could not have happened without that incomplete duplication. Our data suggest a mechanism where incomplete duplication of this gene created a novel function ‘at birth’.”

Source: Telegraph

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