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.

Scientists create ‘designer enzymes’

Chemists from UCLA and the University of Washington have succeeded in creating “designer enzymes,” a major milestone in computational chemistry and protein engineering.

Designer enzymes will have applications for defense against biological warfare, by deactivating pathogenic biological agents, and for creating more effective medications.

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Craig Venter: On the verge of creating synthetic life

Can we create new life out of our digital universe?” asks Craig Venter. And his answer is, yes, and pretty soon. He walks the TED2008 audience through his latest research into “fourth-generation fuels” — biologically created fuels with CO2 as their feedstock. His talk covers the details of creating brand-new chromosomes using digital technology, the reasons why we would want to do this, and the bioethics of synthetic life. A fascinating Q&A with TED’s Chris Anderson follows .  

Newly Engineered Genetic Switches Enhance Production Of Proteins, Pharmaceuticals

Bacteria have evolved complex mechanisms called quorum sensing systems that provide for cell-to-cell communication, an adaptation that allows them to wait until their population grows large enough before mounting an attack on a host or competing for nutrients. Lianhong Sun, a chemical engineer at the University of Massachusetts Amherst, has engineered one of these systems to create genetic switches that could lower the cost of producing therapeutic proteins and pharmaceuticals.
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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.
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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.

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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.  

Scientists synthesize memory in yeast cells

Harvard Medical School researchers have successfully synthesized a DNA-based memory loop in yeast cells, findings that mark a significant step forward in the emerging field of synthetic biology.

After constructing genes from random bits of DNA, researchers in the lab of Professor Pamela Silver, a faculty member in Harvard Medical School’s Department of Systems Biology, not only reconstructed the dynamics of memory, but also created a mathematical model that predicted how such a memory “device” might work.

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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.

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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.”

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Scientists develop tiny implantable biocomputers

Researchers at Harvard University and Princeton University have made a crucial step toward building biological computers, tiny implantable devices that can monitor the activities and characteristics of human cells. The information provided by these “molecular doctors,” constructed entirely of DNA, RNA, and proteins, could eventually revolutionize medicine by directing therapies only to diseased cells or tissues.
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Scientists equip bacteria with custom chemo-navigational system

Using an innovative method to control the movement of Escherichia coli in a chemical environment, Emory University scientists have opened the door to powerful new opportunities in drug delivery, environmental cleanup and synthetic biology. Their findings are published online in the Journal of the American Chemical Society and will be published in a future print issue.
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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.

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Scientists unlock mystery of embryonic stem cell signaling pathway

A newly discovered small molecule called IQ-1 plays a key role in preventing embryonic stem cells from differentiating into one or more specific cell types, allowing them to instead continue growing and dividing indefinitely, according to research performed by a team of scientists who have recently joined the stem-cell research efforts at the Keck School of Medicine of the University of Southern California.
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Scientists create mice with enhanced color vision

Researchers at the Johns Hopkins School of Medicine and their colleagues have found that mice simply expressing a human light receptor in addition to their own can acquire new color vision, a sign that the brain can adapt far more rapidly to new sensory information than anticipated.

This work, appearing March 23 in Science, also suggests that when the first ancestral primate inherited a new type of photoreceptor more than 40 million years ago, it probably experienced immediate color enhancement, which may have allowed this trait to spread quickly.
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First complete computer model of human metabolism

Researchers at the University of California, San Diego, have constructed the first complete computer model of human metabolism. Available free on the Web, the model is a major step forward in the fledging field of systems biology, and it will help researchers uncover new drug pathways and understand the molecular basis of cancer and other diseases.

Read rest of this story on Technology Review site.

Scientists develop new procedure to differentiate human embryonic stem cells

Scientists have developed a new procedure for the differentiation of human embryonic stem cells, with which they have created the first transplantable source of lung epithelial cells.

The method involves the use of protein markers under the control of cell-specific promoters to convert undifferentiated human embryonic stem cells into highly-specialized cells. The human embryonic stem cells were cultured on specially coated dishes and transfected with a lung epithelial gene regulator of a drug selection gene.
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Researchers replace organ in adult mice using ‘single-parent’ stem cells

Researchers at the University of Pennsylvania School of Veterinary Medicine have derived uniparental embryonic stem cells – created from a single donor’s eggs or two sperm – and, for the first time, successfully used them to repopulate a damaged organ with healthy cells in adult mice. Their findings demonstrate that single-parent stem cells can proliferate normally in an adult organ and could provide a less controversial alternative to the therapeutic cloning of embryonic stem cells.
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The Incredible, Medical Egg

Genetically modified chickens that produce medicines in their eggs may be the drug factories of the future. The chicken egg has a storied history in medicine. Even today, millions of ordinary fertilized eggs are each punctured with a drill and injected with flu virus to make vaccines. Now, scientists at the same research institute that cloned Dolly the sheep have produced a genetically modified rooster whose female descendants lay eggs that produce medicines in place of a protein in egg whites.

Helen Sang of the Roslin Institute in Edinburgh, Scotland, and her colleagues used lentivirus to introduce a gene into freshly fertilized chicken embryos that trigger the production of various drugs rather than the protein ovalbumin, which normally makes up roughly 54 percent of egg whites. The researchers screened the resultant cockerels for one that produced the new gene in its semen. They then bred him with normal hens to produce a flock of chickens that carried the inserted gene thereby producing medicines in their egg’s whites.

Read rest of the story at Scientific American

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.
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Fighting HIV by Building a New Killer Frankenstein Virus

In order to find out how one of the world’s most devastating diseases overcomes state-of-the-art drugs, scientists led by Dr. Vineet KewalRamani at National Cancer Institute (NCI) are biohacking and re-engineering the HIV virus. Dr. KewalRamani and his collegues have combined pieces of HIV and another virus to create a deadly new hybrid—a tenacious little microbe that knows all the tricks of its parent pathogens. Discovering where, and how, HIV hides in the body will be a critical step towards a cure for the disease—or at least a better treatment.

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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.

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Immune cell communication key to hunting viruses

Immunologists at the Kimmel Cancer Center at Thomas Jefferson University in Philadelphia have used nanotechnology to create a novel “biosensor” to solve in part a perplexing problem in immunology: how immune system cells called killer T-cells hunt down invading viruses.

They found that surprisingly little virus can turn on the killer T-cells, thanks to some complicated communication among so-called “antigen presenting” proteins that recognize and attach to the virus, in turn, making it visible to the immune system. T-cell receptors then “see” the virus, activating the T-cells.
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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.
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Researchers make nanosheets that mimic protein formation

How to direct and control the self-assembly of nanoparticles is a fundamental question in nanotechnology.

University of Michigan researchers have discovered a way to make nanocrystals in a fluid assemble into free-floating sheets the same way some protein structures form in living organisms.
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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.
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Scientists report full humanization of yeast glycosylation pathway

For the first time, scientists have engineered yeast cells capable of producing a broad repertoire of recombinant therapeutic proteins with fully human sugar structures (glycosylation). These sugar structures ensure a glycoprotein’s biological activity and half-life and to date, have necessitated the expression of therapeutic glycoproteins in mammalian hosts. The accomplishment reported today has the potential to eliminate the need for mammalian cell culture, while improving control over glycosylation, and improving performance characteristics of many therapeutic proteins. Continue reading “Scientists report full humanization of yeast glycosylation pathway”

Creating new life forms in laboratory

Ever since chemist Stanley Miller created organic compounds from simple building blocks like water, methane, and ammonia, the idea of creating life and thus peering into its possible origins, has fascinated biologists.

Is it possible to build a “protocell” or the most primitive life form from scratch? A cadre of pioneer scientists are trying to do just that. This fascinating quest and current advances in steps of creating life are described in a recent New Scientist article.

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Researchers develop all-in-one remote control gene expression tool derived from HIV

In an article appearing online today in the journal Nature Methods, researchers at the EPFL (Ecole Polytechnique Fédérale de Lausanne) unveil a powerful new tool that will facilitate genetic research and open up new avenues for the clinical treatment of genetic disease.

An all-in-one tool like this – efficiently combining techniques that each previously required separate delivery – will likely see wide use in genetic research and in clinical gene therapy applications. It is particularly applicable for use in stem cells, embryonic cells and tissues and organs that are amenable to genetic transduction.
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Creating first synthetic life form

Work on the world’s first human-made species is well under way at a research complex in Rockville, Md., and scientists in Canada have been quietly conducting experiments to help bring such a creature to life.

Robert Holt, head of sequencing for the Genome Science Centre at the University of British Columbia, is leading efforts at his Vancouver lab to play a key role in the production of the first synthetic life form — a microbe made from scratch.

The project is being spearheaded by U.S. scientist Craig Venter, who gained fame in his former job as head of Celera Genomics, which completed a privately-owned map of the human genome in 2000.
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