Can Hobbyists and Hackers Transform Biotechnology?

For most of us, managing our health means visiting a doctor. The more serious our concerns, the more specialized a medical expert we seek. Our bodies often feel like foreign and frightening lands, and we are happy to let someone with an MD serve as our tour guide. For most of us, our own DNA never makes it onto our personal reading list.

Biohackers are on a mission to change all that. These do-it-yourself biology hobbyists want to bring biotechnology out of institutional labs and into our homes. Following in the footsteps of revolutionaries like Steve Jobs and Steve Wozniak, who built the first Apple computer in Jobs’s garage, and Sergey Brin and Larry Page, who invented Google in a friend’s garage, biohackers are attempting bold feats of genetic engineering, drug development, and biotech research in makeshift home laboratories.

In Biopunk, journalist Marcus Wohlsen surveys the rising tide of the biohacker movement, which has been made possible by a convergence of better and cheaper technologies. For a few hundred dollars, anyone can send some spit to a sequencing company and receive a complete DNA scan, and then use free software to analyze the results. Custom-made DNA can be mail-ordered off websites, and affordable biotech gear is available on Craigslist and eBay.

via Can Hobbyists and Hackers Transform Biotechnology? – Technology Review.

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‘Telepathic’ Genes Recognize Similarities In Each Other

Genes have the ability to recognise similarities in each other from a distance, without any proteins or other biological molecules aiding the process, according to new research. This discovery could explain how similar genes find each other and group together in order to perform key processes involved in the evolution of species.

Scientists Create the First Synthetic Bacterial Genome

A team of 17 researchers at the J. Craig Venter Institute (JCVI) has created the largest man-made DNA structure by synthesizing and assembling the 582,970 base pair genome of a bacterium, Mycoplasma genitalium JCVI-1.0. This work, published online today in the journal Science by Dan Gibson, Ph.D., et al, is the second of three key steps toward the team’s goal of creating a fully synthetic organism. In the next step, which is ongoing at the JCVI, the team will attempt to create a living bacterial cell based entirely on the synthetically made genome.

Programming Biomolecular Self-Assembly Pathways

Nature knows how to make proteins and nucleic acids (DNA and RNA) dance to assemble and sustain life. Inspired by this proof of principle, researchers at the California Institute of Technology have demonstrated that it is possible to program the pathways by which DNA strands self-assemble and disassemble, and hence to control the dynamic function of the molecules as they traverse these pathways.

Molecular Biology Visualization of DNA (Animation)

This is a very informative animation of how DNA is packaged and replicated within the cell nucleus.  [Youtube=http://www.youtube.com/watch?v=5UoKYGKxxMI] 

Nanotechnology innovation may revolutionize gene detection in a single cell

Scientists at Arizona State University’s Biodesign Institute have developed the world’s first gene detection platform made up entirely from self-assembled DNA nanostructures. The results, appearing in the January 11 issue of the journal Science, could have broad implications for gene chip technology and may also revolutionize the way in which gene expression is analyzed in a single cell.

 

Biohacking and programming DNA

Biological engineering does not have to be confined to the laboratories of high-end industry laboratories. Rather, it is desirable to foster a more open culture of biological technology. This talk is an effort to do so; it aims to equip you with basic practical knowledge of biological engineering.  

New clinical trial results show how personalized medicine will alter treatment of genetic disorders

One of the nation’s pre-eminent genetic researchers, Eric Hoffman, PhD, of Children’s Research Institute at Children’s National Medical Center, predicts that in relatively short order, medicine’s next innovation–individualized molecular therapies–will have the unprecedented ability to treat muscular dystrophies, and other disorders.

Human genetic variation — Science’s ‘Breakthrough of the Year’

In 2007, researchers were dazzled by the degree to which genomes differ from one human to another and began to understand the role of these variations in disease and personal traits. Science and its publisher, AAAS, the nonprofit science society, recognize “Human Genetic Variation” as the Breakthrough of the Year, and identify nine other of the year’s most significant scientific accomplishments in the 21 December issue.

Ancient retroviruses spurred evolution of gene regulatory networks in humans and other primates

When ancient retroviruses slipped bits of their DNA into the primate genome millions of years ago, they successfully preserved their own genetic legacy. Today an estimated 8 percent of the human genetic code consists of endogenous retroviruses (ERVs)–the DNA remnants from these so-called “selfish parasites.”

Surprisingly, the infected hosts and their primate descendants also appear to have benefited from this genetic invasion, new evidence suggests. The ancient retroviruses–distant relatives of the human immunodeficiency virus (HIV)–helped a gene called p53 become an important “master gene regulator” in primates, according to a study published this week in the online early edition of Proceedings of the National Academy of Sciences.

Gene regulation, not just genes, is what sets humans apart from primates

The striking differences between humans and chimps aren’t so much in the genes we have, which are 99 percent the same, but in the way those genes are used, according to new research from a Duke University team.

It’s rather like the same set of notes being played in very different ways.

In two major traits that set humans apart from chimps and other primates – those involving brains and diet – gene regulation, the complex cross-talk that governs when genes are turned on and off, appears to be significantly different.

Biologists discover a reason why chromosomes break, often leading to cancer

In the past ten years, researchers in genome stability have observed that many kinds of cancer are associated with areas where human chromosomes break. They have hypothesized – but never proven – that slow or altered replication led to the chromosomes breaking.

In a Tufts University study published in the Aug. 3 journal “Molecular Cell,” two molecular biologists have used yeast artificial chromosomes to prove the hypothesis. The Tufts researchers have found a highly flexible DNA sequence that increases fragility and stalls replication, which then causes the chromosome to break.

Bioengineers Devise ‘Dimmer Swith’ To Regulate Gene Expression In Mammal Cells

Three Boston University biomedical engineers have created a genetic dimmer switch that can be used to turn on, shut off, or partially activate a gene’s function. Professor James Collins, Professor Charles Cantor and doctoral candidate Tara Deans invented the switch, which can be tuned to produce large or small quantities of protein, or none at all

This switch helps advance the field of synthetic biology, which rests on the premise that complex biological systems can be built by arranging components or standard parts, as an electrician would to build an electric light switch. Much work in the field to date uses bacteria or yeast, but the Boston University team used more complex mammalian cells, from hamsters and mice. The switch has several new design features that extend possible applications into areas from basic research to gene therapy.

Risk genes for multiple sclerosis uncovered

A large-scale genomic study has uncovered new genetic variations associated with multiple sclerosis (MS), findings that suggest a possible link between MS and other autoimmune diseases. The study, led by an international consortium of clinical scientists and genomics experts, is the first comprehensive study investigating the genetic basis of MS. Findings appear in the July 29 online edition of the New England Journal of Medicine.

Caffeine and exercise can team up to prevent skin cancer

Regular exercise and little or no caffeine has become a popular lifestyle choice for many Americans. But a new Rutgers study has found that it may not be the best formula for preventing sun-induced skin damage that could lead to cancer. Low to moderate amounts of caffeine, in fact, along with exercise can be good for your health.

Mutating the entire genome

Genes account for only 2.5 percent of DNA in the human genetic blueprint, yet diseases can result not only from mutant genes, but from mutations of other DNA that controls genes. University of Utah researchers report in the journal Nature Genetics that they have developed a faster, less expensive technique for mutating those large, non-gene stretches of DNA.

 

 

 

Ancient retrovirus sheds light on HIV pandemic

Human resistance to a retrovirus that infected chimpanzees and other nonhuman primates 4 million years ago ironically may be at least partially responsible for the susceptibility of humans to HIV infection today.

“This ancient virus is a battle that humans have already won. Humans are not susceptible to it and have probably been resistant throughout millennia,” said senior author Michael Emerman, Ph.D., a member of the Human Biology and Basic Sciences divisions at the Hutchinson Center. “However, we found that during primate evolution, this innate immunity to one virus may have made us more vulnerable to HIV.”

Serious diseases genes revealed

A major advance in understanding the genetics behind several of the world’s most common diseases has been reported.The landmark Wellcome Trust study analysed DNA from the blood of 17,000 people to find genetic differences. They found new genetic variants for depression, Crohn’s disease, coronary heart disease, hypertension, rheumatoid arthritis and type 1 and 2 diabetes.

The remarkable findings, published in Nature, have been hailed as a new chapter in medical science.

Read rest of the article at BBC Newssite

Nobel laureate James Watson receives his personal genome sequence

The $1 million, two-month project is a collaboration of 454 Life Sciences and the BCM Human Genome Sequencing Center (HGSC), said Dr. Richard Gibbs, director of the HGSC and a scientific advisor to the Connecticut-based company. The announcement, aside from its meaning to Watson, is significant because it demonstrates that it will be possible in the future to sequence anyone’s genome – a goal toward which many sequencing firms are working. The time and cost will decrease as the technology improves.

Dr. Watson will receive a DVD with his genomic sequence. He will decide which of his data will be published.

Mechanism of microRNAs deciphered

Over 30% of our genes are under the control of small molecules called microRNAs. They prevent specific genes from being turned into protein and regulate many crucial processes like cell division and development, but how they do so has remained unclear. Now researchers from the European Molecular Biology Laboratory (EMBL) have developed a new method that uncovered the mode of action of microRNAs in a test tube. The study, which is published in the current online issue of Nature, reveals that microRNAs block the initiation of translation, the earliest step in the process that turns genetic information stored on messenger RNAs into proteins.

Remarkable advance in muscle restoration in an animal model of Duchenne muscular dystrophy

Using a new type of drug that targets a specific genetic defect, researchers at the University of Pennsylvania School of Medicine, along with colleagues at PTC Therapeutics Inc. and the University of Massachusetts Medical School, have for the first time demonstrated restoration of muscle function in a mouse model of Duchenne’s muscular dystrophy (DMD). The research appears ahead of print in an advanced online publication of Nature.

Major genetic study identifies clearest link yet to obesity risk

Scientists have identified the most clear genetic link yet to obesity in the general population as part of a major study of diseases funded by the Wellcome Trust, the UK’s largest medical research charity. People with two copies of a particular gene variant have a 70% higher risk of being obese than those with no copies.

Cells Selectively Absorb Short Nanotubes

DNA-wrapped single-walled carbon nanotubes (SWCNTs) shorter than about 200 nanometers readily enter into human lung cells and so may pose an increased risk to health, according to scientists at the National Institute of Standards and Technology (NIST).

Nanotube length threshold: NIST experiments using human lung cells demonstrate that DNA-wrapped single-walled carbon nanotubes longer than about 200 nanometers are excluded from cells, while shorter lengths are able to penetrate the cell interior (dark lines in the fluorescence image above).Credit: NIST

Tiny particles pave way for new bedside diagnostics

MIT researchers have created an inexpensive method to screen for millions of different biomolecules (DNA, proteins, etc.) in a single sample-a technology that could make possible the development of low-cost clinical bedside diagnostics.

The work, based on tiny customizable particles, could also be used for disease monitoring, drug discovery or genetic profiling. Even though the particles are thinner than the width of a human hair, each is equipped with a barcoded ID and one or more probe regions that turn fluorescent when they detect specific targets in a test sample.

Oxidative damage in newly synthesized DNA plays a role in Parkinson’s disease

Oxygen is the quintessential two-edged sword of molecular biology: essential for (animal) life, but at the same time a perennial source of damage to macromolecules. Reactive oxygen species (ROS), arising from both external sources and the intrinsic metabolic machinery of the cell itself, have been implicated in many aspects of cellular aging.

Of particular interest to human beings, especially those living in the rapidly aging post-industrial Western nations, is the relationship between oxidative damage and neurodegenerative illness. While most of the age-related neurodegenerative diseases are caused by accumulation of protein aggregates, it is becoming evident that ROS play an important role in exacerbating the underlying pathologies: e.g., DNA oxidation arises early in the pathogenesis of Alzheimer’s disease; and oxidative damage to a key anti-oxidant defense protein may generate a pernicious positive-feedback loop in the initiating events of Parkinson’s disease.

Read rest of the story at Ouroboros site.

Mapping the Cancer Genome

Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies.

“If we wish to learn more about cancer, we must now concentrate on the cellular genome.” Nobel laureate Renato Dulbecco penned those words more than 20 years ago in one of the earliest public calls for what would become the Human Genome Project. “We are at a turning point,” Dulbecco, a pioneering cancer researcher, declared in 1986 in the journal Science. Discoveries in preceding years had made clear that much of the deranged behavior of cancer cells stemmed from damage to their genes and alterations in their functioning. “We have two options,” he wrote. “Either try to discover the genes important in malignancy by a piecemeal approach, or & sequence the whole genome.”

Faster, low cost sequencing technologies needed to drive era of personalized medicine

DNA testing is transforming health care and medicine, but current technologies only give a snapshot of an individual’s genetic makeup. Any patient wanting a complete picture of their inherited DNA, or genome, would drop their jaw at the sight of the bill — to the current tune of $10 million or more charged for every human or mammalian-sized genome sequenced.

The NHGRI, part of the National Institutes of Health (NIH), has set an ambitious target of $1,000 or less – a cost 10,000 times lower than current technology – to make genome sequencing a routine diagnostic tool in medical care. The reduced cost may allow doctors to tailor medical treatments to an individual’s genetic profile for diagnosing, treating, and ultimately preventing many common diseases such as cancer, heart disease, diabetes and obesity.

Scientists discover new class of RNA

The last few years have been very good to ribonucleic acid (RNA). Decades after DNA took biology by storm, RNA was considered little more than a link in a chain–no doubt a necessary link, but one that, by itself, had little to offer. But with the discoveries of RNA interference and microRNAs, this meager molecule has been catapulted to stardom as a major player in genomic activity.

Now, a team of scientists led by David Bartel, a professor in MIT’s Department of Biology, has discovered an entirely new class of RNA molecules.

Scientists map key landmarks in human genome

Dana-Farber Cancer Institute researchers have developed a powerful method for charting the positions of key gene-regulating molecules called nucleosomes throughout the human genome. The mapping tool could help uncover important clues for understanding and diagnosing cancer and other diseases, the scientists say. Moreover, it may shed light on the role of nucleosomes in the process of “reprogramming” an adult cell to its original embryonic state, which is a critical operation in cloning.

Nanoparticle assembly enters the fast lane

The speed of nanoparticle assembly can be accelerated with the assistance of the molecule that carries life’s genetic instructions, DNA, a team of researchers at the U.S. Department of Energy’s Brookhaven National Laboratory recently found. Nanoparticles, particles with dimensions on the order of billionths of a meter, could potentially be used for more efficient energy generation and data storage, as well as improved methods for diagnosing and treating disease. Learning how to control and tailor the assembly of these miniscule particles into larger functional systems remains a major challenge for scientists.

Buildup of damaged DNA in cells drives aging

The accumulation of genetic damage in our cells is a major contributor to how we age, according to a study being published today in the journal Nature by an international group of researchers. The study found that mice completely lacking a critical gene for repairing damaged DNA grow old rapidly and have physical, genetic and hormonal profiles very similar to mice that grow old naturally. Furthermore, the premature aging symptoms of the mice led to the discovery of a new type of human progeria, a rare inherited disease in which affected individuals age rapidly and die prematurely.

Regulating the nuclear architecture of the cell

An organelle called the nucleolus resides deep within the cell nucleus and performs one of the cell’s most critical functions: it manufactures ribosomes, the molecular machines that convert the genetic information carried by messenger RNA into proteins that do the work of life.

Gary Karpen and Jamy Peng, researchers in the Life Sciences Division of the Department of Energy’s Lawrence Berkeley National Laboratory, have now discovered two pathways that regulate the organization of the nucleolus and other features of nuclear architecture, maintaining genome stability in the fruit fly Drosophila melanogaster.

DNA Repair Teams’ Motto: ‘To Protect and Serve’

When you dial 911 you expect rescuers to pull up at your front door, unload and get busy—not park the truck down the street and eat donuts. It’s the same for a cell—just before it divides, it recruits protein complexes that repair breakage that may have occurred along the linear DNA chains making up your 46 chromosomes. Without repair, damage caused by smoking, chemical mutagens, or radiation might be passed on to the next generation.

However, in 2005, investigators at the Salk Institute for Biological Studies observed that before cell division some of these cellular paramedics inexplicably idle at undamaged chromosome ends, known as telomeres. Apparently the telomeres’ disheveled appearance —resembling that of broken DNA strands—raises a red flag.

Now, in a study published in the Nov. 17 issue of Cell, that same team led by Jan Karlseder, Ph.D, Hearst Endowment Assistant Professor in the Molecular and Cell Biology Laboratory, reveals why those repair crews are parked at the ends of chromosomes and in doing so answer fundamental questions about how chromosomal stability is maintained.

Researchers Create DNA Logic Circuits That Work in Test Tubes

Computers and liquids are not very compatible, as many a careless coffee-drinking laptop owner has discovered. But a new breakthrough by researchers at the California Institute of Technology could result in future logic circuits that literally work in a test tube–or even in the human body.

In the current issue of the journal Science, a Caltech group led by computer scientist Erik Winfree reports that they have created DNA logic circuits that work in salt water, similar to an intracellular environment. Such circuits could lead to a biochemical microcontroller, of sorts, for biological cells and other complex chemical systems. The lead author of the paper is Georg Seelig, a postdoctoral scholar in Winfree’s lab.

Living to be 100 programmed at birth?

A study from the University of Chicago has been getting a lot of press attention lately. They found that your chances of living to 100 may depend on how young your mother was when she gave birth to you with chances doubled if mom was under 25. The reports do not give the explanation why.

Dr. Steven Palter, a specialist in Obstetrics and Gynecology and Reproductive Endocrinology and Infertility, has written in his blog docinthemachine about an interesting theory of reproductive aging and human longevity. The findings are based on data presented in recent American Society for Reproductive Medicine meeting by Dr. Keefe of U. Florida on the telemore and its role in reproductive aging.

Read rest of this interesting story at docinthemachine blog.

How to Resurrect an Extinct Retrovirus

French researchers have resurrected a retrovirus that became trapped in the human genome about five million years ago. Pieced together from existing sequences in human DNA, the reconstructed virus was able to infect mammalian cells weakly, suggesting that it works similarly to the extinct organism.

Researchers show that DNA gets kinky easily at the nanoscale

Scientists have answered a long-standing molecular stumper regarding DNA: How can parts of such a rigid molecule bend and coil without requiring large amounts of force? According to a team of researchers from the United States and the Netherlands, led by a physicist from the University of Pennsylvania, DNA is much more flexible than previously believed when examined over extremely small lengths. They used a technique called atomic force microscopy to determine the amount of energy necessary to bend DNA over nano-size lengths (about a million times smaller than a printed letter).

Researchers find smallest cellular genome

The smallest collection of genes ever found for a cellular organism comes from tiny symbiotic bacteria that live inside special cells inside a small insect.

The bacteria Carsonella ruddii has the fewest genes of any cell. The bacteria’s newly sequenced genome, the complete set of DNA for the organism, is only one-third the size of the previously reported “smallest” cellular genome.

Technique reveals inner lives of red blood cells

For the first time, researchers at MIT can see every vibration of a cell membrane, using a technique that could one day allow scientists to create three-dimensional images of the inner workings of living cells.

Studying cell membrane dynamics can help scientists gain insight into diseases such as sickle cell anemia, malaria and cancer. Using a technique known as quantitative phase imaging, researchers at MIT’s George R. Harrison Spectroscopy Laboratory can see cell membrane vibrations as tiny as a few tens of nanometers (billionths of a meter).

Researchers develop DNA switch to interface living organisms with computers

Researchers at the University of Portsmouth, UK, have developed an electronic switch based on DNA – a world-first bio-nanotechnology breakthrough that provides the foundation for the interface between living organisms and the computer world.

The new technology is called a ‘nanoactuator’ or a molecular dynamo. The device is invisible to the naked eye – about one thousandth of a strand of human hair.

A new mechanism of aging discovered

We all age, it’s a fact of life, like death and taxes, and there’s nothing we can do about it. But, how is it possible that of two middle-aged mice, one is already grey, balding and frail? Some mice that age three times faster than normal are revealing to scientists why we grow old.

Researchers have discovered that genetic mutations in the powerhouses of our cells — mitochondria — appear to trigger cells to die and speed up the aging process. Inducing these kinds of mitochondrial mutations leads to premature aging in mice, which live only about half as long as normal mice.

Genetic repair mechanism clears the way for sealing DNA breaks

Scientists investigating an important DNA-repair enzyme now have a better picture of the final steps of a process that glues together, or ligates, the ends of DNA strands to restore the double helix.

Jumping gene could provide non-viral alternative for gene therapy

A jumping gene first identified in a cabbage-eating moth may one day provide a safer, target-specific alternative to viruses for gene therapy, researchers say.

They compared the ability of the four best-characterized jumping genes, or transposons, to insert themselves into a cell’s DNA and produce a desired change, such as making the cell resistant to damage from radiation therapy.

They found the piggyBac transposon was five to 10 times better than the other circular pieces of DNA at making a home and a difference in several mammalian cell lines, including three human ones.

Researchers identify gene as protector of DNA, enemy of tumors

A single gene plays a pivotal role launching two DNA damage detection and repair pathways in the human genome, suggesting that it functions as a previously unidentified tumor suppressor gene, researchers at The University of Texas M. D. Anderson Cancer Center report in Cancer Cell.

The advance online publication also reports that the gene – called BRIT1 – is under-expressed in human ovarian, breast and prostate cancer cell lines.

Human embryonic stem cells display a unique pattern of chemical modification to DNA

Scientists have found that the DNA of human embryonic stem cells is chemically modified in a characteristic, predictable pattern. This pattern distinguishes human embryonic stem cells from normal adult cells and cell lines, including cancer cells. The study, which appears online today in Genome Research, should help researchers understand how epigenetic factors contribute to self-renewal and developmental pluripotence, unique characteristics of human embryonic stem cells that may one day allow them to be used to replace diseased or damaged cells with healthy ones in a process called therapeutic cloning.

DNA damage study probes inflammation, disease link

New research at MIT may help scientists better understand the chemical associations between chronic inflammation and diseases such as cancer and atherosclerosis. The work could lead to drugs that break the link between the two.

Scientists Discover a Genetic Code for Organizing DNA

DNA – the long, thin molecule that carries our hereditary material – is compressed around protein scaffolding in the cell nucleus into tiny spheres called nucleosomes. The bead-like nucleosomes are strung along the entire chromosome, which is itself folded and packaged to fit into the nucleus. What determines how, when and where a nucleosome will be positioned along the DNA sequence?

Dr. Eran Segal and research student Yair Field of the Computer Science and Applied Mathematics Department at the Weizmann Institute of Science have succeeded, together with colleagues from Northwestern University in Chicago, in cracking the genetic code that sets the rules for where on the DNA strand the nucleosomes will be situated. Their findings appeared today in Nature.

Engineers Use DNA to Direct Nanowire Assembly and Growth

A growing number of engineers are using nature’s engineer – DNA – to create nanomaterials that can be used in everything from medical devices to computer circuits. A team from Brown University and Boston College is the first to use DNA to direct construction and growth of complex nanowires. Their work appears in Nanotechnology.

Scientists publishes first human microbiome analysis

For the first time, scientists have defined the collective genome of the human gut, or colon. Up to 100 trillion microbes, representing more than 1,000 species, make up a motley "microbiome" that allows humans to digest much of what we eat, including some vitamins, sugars, and fiber, an accomplishment that has far-reaching implications for clinical diagnosis and treatment of many human diseases.

In a study published in the June 2 issue of Science, scientists at The Institute for Genomic Research (TIGR) and their colleagues describe and analyze the colon microbiome, which includes more than 60,000 genes–twice as many as found in the human genome. Some of these microbial genes code for enzymes that humans need to digest food, suggesting that bacteria in the colon co-evolved with their human host, to mutual benefit.

Mice that lives 20 percent longer

The canny world of advertising has caught on to the free radical theory of aging, marketing a whole array of antioxidants for preventing anything from wrinkles to dry hair to reducing the risk of heart disease — promising to help slow the hands of time.

Nevertheless, numerous studies of people taking antioxidant pills have failed to show a benefit, and the supplements may even be harmful. A study earlier this year hinted that high doses of the antioxidant vitamin E may raise the risk of heart disease, while earlier research has found that beta carotene, another popular antioxidant, puts smokers at higher risk of lung cancer. But that doesn’t mean the free radical theory of aging is wrong, “We think that it is fundamental to the understanding and the implications of aging,” says University of Washington pathologist, Peter Rabinovitch.

Working with genetically engineered mice — to produce a natural antioxidant enzyme called catalase — Rabinovitch’s group found that, on average, the mice live longer. But don’t go running to the medicine cabinet for your bottle of Vitamin C or other antioxidant supplement, only naturally-occurring antioxidants seem to offer a dip in the fountain of youth, and so far, only in mice.