Biophysicists unravel secrets of genetic switch

When an invading bacterium or virus starts rummaging through the contents of a cell nucleus, using proteins like tiny hands to rearrange the host’s DNA strands, it can alter the host’s biological course. The invading proteins use specific binding, firmly grabbing onto particular sequences of DNA, to bend, kink and twist the DNA strands. The invaders also use non-specific binding to grasp any part of a DNA strand, but these seemingly random bonds are weak.

Emory University biophysicists have experimentally demonstrated, for the fist time, how the nonspecific binding of a protein known as the lambda repressor, or C1 protein, bends DNA and helps it close a loop that switches off virulence. The researchers also captured the first measurements of that compaction.

Their results, published in Physical Review E, support the idea that nonspecific binding is not so random after all, and plays a critical role in whether a pathogen remains dormant or turns virulent.

“Our findings are the first direct and quantitative determination of non-specific binding and compaction of DNA,” says Laura Finzi, an Emory professor of biophysics whose lab led the study. “The data are relevant for the understanding of DNA physiology, and the dynamic characteristics of an on-off switch for the expression of genes.”

Lysis plaques of lambda phage on E. coli bacteria.

C1 is the repressor protein of the lambda bacteriophage, a virus that infects the bacterial species E. coli, and a common laboratory model for the study of gene transcription.

The virus infects E. coli by injecting its DNA into the host cell. The viral DNA is then incorporated in the bacterium’s chromosome. Shortly afterwards, binding of the C1 protein to specific sequences on the viral DNA induces the formation of a loop. As long as the loop is closed, the virus remains dormant. If the loop opens, however, the machinery of the bacteria gets hi-jacked: The virus switches off the bacteria’s genes and switches on its own, turning virulent.

“The loop basically acts as a molecular switch, and is very stable during quiescence, yet it is highly sensitive to the external environment,” Finzi says. “If the bacteria is starved or poisoned, for instance, the viral DNA receives a signal that it’s time to get off the boat and spread to a new host, and the loop is opened. We wanted to understand how this C1-mediated, loop-based mechanism can be so stable during quiescence, and yet so responsive to switching to virulence when it receives the signal to do so.”

Transient-loop formation, left, occurs due to non-specific binding of proteins (small orange disks) to DNA (black line). DNA is attached at one end to the glass surface of a microscope flow-chamber and at the other end to a magnetic bead (large gray disk) that reacts to the pulling force of a pair of magnets. The weak, non-specific DNA-protein interactions are disrupted as the force increases. (Graphic by Monica Fernandez.)

Finzi runs one of a handful of physics labs using single-molecule techniques to study the mechanics of gene expression. In 2009, her lab proved the formation of the C1 loop. “We then analyzed the kinetics of loop formation and gained evidence that non-specific binding played a role,” Finzi says. “We wanted to build on that work by precisely characterizing that role.”

Emory undergraduate student Chandler Fountain led the experimental part of the study. He used magnetic tweezers, which can pull on DNA molecules labeled with miniscule magnetic beads, to stretch DNA in a microscope flow chamber. Gradually, the magnets are moved closer to the DNA, pulling it further, so the length of the DNA extension can be plotted against the applied force.

“You get a curve,” Finzi explains. “It’s not linear, because DNA is a spring. Then you put the same DNA in the presence of C1 protein and see how the curve changes. Now, you need more force to get to the same extension because the protein holds onto the DNA and bends it.”

Specifically-bound proteins are shown as orange ovals on a thicker part of the DNA sequence and non-specifically bound proteins are portrayed as gray ovals on regular DNA. Non-specific, transient loops facilitate the coming together of the specifically-bound proteins that mediate formation of the “switch loop”. Once this loop is formed, non-specifically bound protein further stabilize it by increasing the length of the closure in a zipper-like effect. (Graphic by Monica Fernandez.)

 An analysis of the data suggests that, while the specific binding of the C1 protein forms the loop, the non-specific binding acts like a kind of zipper, facilitating the closure of the loop, and keeping it stable until the signal comes to open it.

“The zipper-like effect of the weaker binding sites also allows the genetic switch to be more responsive to the environment, providing small openings that allow it to breathe, in a sense,” Finzi explains. “So the loop is never permanently closed.”

The information about how the C1 genetic switch works may provide insights into the workings of other genetic switches.

“Single-molecule techniques have opened a new era in the mechanics of biological processes,” Finzi says. “I hope this kind of experiment will lead to better understanding of how our own DNA is compacted into chromosomes, and how it unravels locally to become expressed.”
source: http://esciencecommons.blogspot.in/2012/08/biophysicists-unravel-secrets-of.html
 

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Moving Toward Regeneration

After transplantation of healthy tissue and subsequent decapitation, planarian stem cells (shown in blue, top panel) leave the graft (shown in green, middle panel) and migrate towards the amputation site while proliferating and producing progeny (magenta). This wound-induced migration rescues the lethally irradiated host animal and eventually the stem cell compartment is completely repopulated with fully functional stem cells (shown in blue, bottom panel).

The skin, the blood, and the lining of the gut—adult stem cells replenish them daily. But stem cells really show off their healing powers in planarians, humble flatworms fabled for their ability to rebuild any missing body part. Just how adult stem cells build the right tissues at the right times and places has remained largely unanswered.
Now, in a study published in an upcoming issue of Development, researchers at the Stowers Institute for Medical Research describe a novel system that allowed them to track stem cells in the flatworm Schmidtea mediterranea. The team found that the worms’ stem cells, known as neoblasts, march out, multiply, and start rebuilding tissues lost to amputation.
“We were able to demonstrate that fully potent stem cells can mobilize when tissues undergo structural damage,” says Howard Hughes Medical Institute and Stowers Investigator Alejandro Sánchez Alvarado, Ph.D., who led the study. “And these processes are probably happening to both you and me as we speak, but are very difficult to visualize in organisms like us.”
Stem cells hold the potential to provide an unlimited source of specialized cells for regenerative therapy of a wide variety of diseases but delivering human stem cell therapies to the right location in the body remains a major challenge. The ability to follow individual neoblasts opens the door to uncovering the molecular cues that help planarian stem cells navigate to the site of injury and ultimately may allow scientists to provide therapeutic stem cells with guideposts to their correct destination.
“Human counterparts exist for most of the genes that we have found to regulate the activities of planarian stem cells,” says Sánchez Alvarado. “But human beings have these confounding levels of complexity. Planarians are much simpler making them ideal model systems to study regeneration.”
Scientists had first hypothesized in the late 1800s that planarian stem cells, which normally gather near the worms’ midlines, can travel toward wounds. The past century produced evidence both for and against the idea. Sánchez Alvarado, armed with modern tools, decided to revisit the question.
For the new study, first author Otto C. Guedelhoefer, IV, Ph.D., a former graduate student in Sánchez Alvarado’s lab, exposed S. mediterranea to radiation, which killed the worms’ neoblasts while leaving other types of cells unharmed. The irradiated worms would wither and die within weeks unless Guedelhoefer transplanted some stem cells from another worm. The graft’s stem cells sensed the presence of a wound—the transplant site—migrated out of the graft, reproduced and rescued their host. Unlike adult stem cells in humans and other mammals, planarian stem cells remain pluripotent in fully mature animals and remain so even as they migrate.
But when Guedelhoefer irradiated only a part of the worm’s body, the surviving stem cells could not sense the injury and did not mobilize to fix the damage, which showed that the stem cells normally stay in place. Only when a fair amount of irradiated tissue died did the stem cells migrate to the injured site and start to rebuild. Next, Guedelhoefer irradiated a worm’s body part and cut it with a blade. The surviving stem cells arrived at the scene within days.
To perform the experiments, Guedelhoefer adapted worm surgery and x-ray methods created sixty to ninety years ago. “Going back to the old literature was essential and saved me tons of time,” says Guedelhoefer, currently a postdoctoral fellow at the University of California, Santa Barbara. He was able to reproduce and quantify results obtained in 1949 by F. Dubois, a French scientist, who first developed the techniques for partially irradiating planarians with x-rays.
But Guedelhoefer went further. He pinpointed the locations of stem cells and studied how far they dispersed using RNA whole-mount in situ hybridization (WISH), specifically adapted to planarians in Sánchez Alvarado’s lab. Using WISH, he observed both original stem cells and their progeny by tagging specific pieces of mRNA . The technique allowed him to determine that pluripotent stem cells can travel and produce different types of progeny at the same time.
“In other systems, most migrating stem cell progeny are not pluripotent,” says Guedelhoefer. “For the most part, blood stem cells in humans stay in the bone marrow but their progeny leave and turn into a few other cell types.” But in planarians, it looks like those two things are completely separate. Stem cells can move and maintain the full potential to turn into other types of cells.”
Next, Sánchez Alvarado looks forward to implementing genetic screens and transplantation experiments to disrupt or enhance the cellular behaviors the team observed, to figure out the “rules of engagement” for stem cell migration, he says.
“Why can some animals regenerate whole body parts but you and I are not good at it?” says Sánchez Alvarado. “Can we write an extra rule or erase one? Is it possible, for instance, to get rid of cancer while gaining regenerative properties? These are questions we’d love to have answers to.”

source:http://www.newswise.com/articles/moving-toward-regeneration

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Teen Googles his way to new cancer testing method

Fifteen-year-old Jack Andraka took INTEL ISEF 2012 science fair honours this year for the development of a cancer-testing method found to be 168 times faster, 26,000 times cheaper and 400 times more sensitive than the current gold-medal standard.

His work was impressive enough to earn the Maryland high school student a total of $100,500 in grants and prizes at the 2012 Intel Science Fair.

Even more impressive is the source he credits for much of his success: Google.

"I definitely could not have done this research and project without the use of the internet", Andraka told BBC News in an interview published this week.

"I basically went to Google and was looking up cancer statistics, also looking at a bunch of different documents on like, single walled carbon nanotubes and pancreatic cancer biology," he told the BBC.

Andraka was able to find enough information using search engines and free online science papers to invent his procedure, which is now being hailed as "revolutionary" by the American Cancer Society and science publications around the world.

The test uses a method similar to that of a diabetic testing strip, with a dipstick sensor that can test either blood or urine for the presence of mesothelin in the body -- a chemical known to be a biomarker for early-stage pancreatic cancer.

As Forbes reports, this method could also affect how other types of cancer are diagnosed and treated in the future.

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The Laser Beam as a “3D Painter”

3D pattern, produced by photografting (180 µm wide). Fluorescent molecules are attached to the hydrogel, resulting in a microscopic 3D pattern.

There are many ways to create three dimensional objects on a micrometer scale. But how can the chemical properties of a material be tuned at micrometer  precision? Scientists at the Vienna University of Technology developed a method to attach molecules at exactly the right place. When biological tissue is grown, this method can allow the positioning of chemical signals, telling living cells where to attach. The new technique also holds promise for sensor technology: A tiny three dimensional “lab on a chip” could be created, in which accurately positioned molecules react with substances from the environment.

Materials Science and Chemistry
“3D-photografting” is the name of the new method. Two research teams from the Vienna University of Technology collaborated closely to develop it: Professor Jürgen Stampfl’s materials science team and Professor Robert Liska’s research group for macromolecular chemistry.

Both research groups have already attracted considerable attention in the past, developing new kinds of 3D-printers. However, for the applications on which the scientists are working on now, 3D-printing would not have been useful: “Putting together a material from tiny building blocks with different chemical properties would be extremely complicated”, says Aleksandr Ovsianikov. “That is why we start from a three dimensional scaffold and then attach the desired molecules at exactly the right positions.”

Molecules in the Hydrogel – Locked into Position by the Laser
The scientists start with a so-called hydrogel – a material made of macromolecules, arranged in a loose meshwork. Between those molecules, large pores remain, through which other molecules or even cells can migrate.
Specially selected molecules are introduced into the hydrogel meshwork, then certain points are irradiated with a laser beam. At the positions where the focused laser beam is most intense, a photochemically labile bond is broken. That way, highly reactive intermediates are created which locally attach to the hydrogel very quickly. The precision depends on the laser’s lens system, at the Vienna University of Technology a resolution of 4 µm could be obtained. “Much like an artist, placing colors at certain points of the canvas, we can place molecules in the hydrogel – but in three dimensions and with high precision”, says Aleksandr Ovsianikov.

Chemical Signals for Cells
This method can be used to artificially grow biological tissue. Like a climbing plant clinging to a rack, cells need some scaffold at which they attach. In a natural tissue, the extracellular matrix does the trick by using specific amino acid sequences to signal the cells, where they are supposed to grow.
In the lab, scientists are trying to use similar chemical signals. In various experiments, cell  attachment could be guided on two dimensional surfaces, but in order to grow larger tissues with a specific inner structure (such as capillaries), a truly three dimensional technique is required.

Micro Sensors Detect Molecules
Depending on the application, different molecules can be used. 3D photografting is not only useful for bio-engineering but also for other fields, such as photovoltaics or sensor technology. In a very small space, molecules can be positioned which attach to specific chemical substances and allow their detection. A microscopic three-dimensional “lab on a chip” becomes possible.

source: http://www.tuwien.ac.at/en/news/news_detail/article/7719/

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Simplifying genetic codes to look back in time

(A) Electron density maps. Upper panel: Alanine introduced by the GCU codon in the universal genetic code. Lower panel: Alanine introduced by the UGG codon in the simplified code. (B) Activity of proteins synthesized by the simplified and universal codes from the gene for each code. Copyright : Tokyo Institute of Technology

Daisuke Kiga and co-workers at the Department of Computational Intelligence and Systems Science at Tokyo Institute of Technology, together with researchers across Japan, have shown that simpler versions of the universal genetic code, created by knocking out certain amino acids, can still function efficiently and accurately in protein synthesis [1]. The researchers conducted experiments altering the genetic codein a test tube. They removed the amino acid tryptophan and discovered that the resulting simplified code could still generate proteins as before. By knocking out individual amino acids and observing the effects, scientists will be able to understand how early primordial organisms may have functioned and evolved. There will be also numerous applications for simplified genetic strains in laboratory experiments, which could potentially prevent non-natural genetically modified materials from entering the natural world


All current life forms on Earth have 20 amino acids in their genetic code. However, scientists believe that this was not always the case, and that organisms evolved from simpler genetic codes with fewer amino acids. Amino acids are linked in accordance with codons – a 3-letter combination of the four base nucleotides (G, A, T and C) in a genetic code. There are 64 possible codons, and so most amino acids are produced by several different codons, except for tryptophan and methionine, which are generated by just one codon each. Tryptophan is thought to be the most recent amino acid to become part of the universal genetic code.

Kiga and his team took the codon for tryptophan, and reassigned it to code for the amino acid alanine instead. They discovered the resulting simplified code could still generate proteins as before. The researchers also reassigned another codon originally for the amino acid cysteine and replaced it with serine. This simplified code without cysteine was able to synthesise an active enzyme.

By knocking out individual amino acids and observing the effects, scientists will be able to understand how early primordial organisms may have functioned and evolved. There are also numerous applications for simplified genetic codes in laboratory experiments and clinical trials.

Before emergence of the current universal genetic code, primitive organisms that may have used only 19 amino acids could benefit from horizontal gene transfer, where cells transfer genetic material between one another. This is a key method used by bacteria to develop resistance to drugs. An organism with the current universal genetic code for 20 amino acids would have competitive advantages in its ability to synthesise proteins, but could not engage in genetic transfer with the rest of the population. Only when a suitably large gene pool of organisms with 20 amino acids is available could horizontal transfer occur between these life forms and they could then thrive. This implies that organisms with a simpler genetic code could be used as a barrier in laboratory experiments, preventing new genetically modified strains from escaping to the natural world.


source: http://www.researchsea.com/html/article.php/aid/7386/cid/3/research/simplifying_genetic_codes_to_look_back_in_time.html
 

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Indian Biotech industry growing at 15% annually, abundant job opportunities

"With the Indian Biotechnology segment growing at 15% per year, career opportunities in fields such as bio-pharmacy, bio-service, bio-agriculture, bio-industrial and bio-informatics is burgeoning", informed G S Krishnan, Managing Director, Novozymes South Asia Pvt. Ltd

He informed candidates that most jobs are currently available in the private sector and for research & development, marketing, sales/business development and customer support profiles.

Throwing light on the current market situation, Krishnan said that demand at the entry level in the biotechnology industry may not be encouraging. The reason being, the industry is still at a nascent stage in India. However, this situation will improve if candidates can equip themselves with higher professional/specialized degrees to qualify further in this segment. A fresher can seek junior research associate positions or lab technicians in the Research & Development (R&D) function, he added.

"Many pharmaceutical companies have established R&D centers in India and are considering tapping India's talent. Graduates with good academic results, relevant experience and strong soft skills can look forward to a range of positions in the field", remarked Lawrence Ganti, Director - Head, Merck Serono India

In view of Krishnan, the Industrial Biotech segment is another promising domain where candidates can focus for lucrative career opportunities in multiple industries such as textile, detergent, food, feed, leather, and is growing at 11% per year in India.

Another upcoming area in the biotechnology industry is bioinformatics, which has registered 10% growth and holds promising career opportunities for candidates with knowledge of computer and statistics.

According to industry experts, analytical and communication skills are very crucial together with right qualification to have a successful career in the biotechnology industry.

source: http://economictimes.indiatimes.com/news/news-by-industry/jobs/indian-biotech-industry-growing-at-15-annually-abundant-job-opportunities/articleshow/15390536.cms

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Molecular code cracked

Scientists have cracked a molecular code that may open the way to destroying or correcting defective gene products, such as those that cause genetic disorders in humans.
The code determines the recognition of RNA molecules by a superfamily of RNA-binding proteins called pentatricopeptide repeat (PPR) proteins.
When a gene is switched on, it is copied into RNA.  This RNA is then used to make proteins that are required by the organism for all of its vital functions.  If a gene is defective, its RNA copy and the proteins made from this will also be defective.  This forms the basis of many terrible genetic disorders in humans.
RNA-binding PPR proteins could revolutionise the way we treat disease.  Their secret is their versatility - they can find and bind a specific RNA molecule, and have the capacity to correct it if it is defective, or destroy it if it is detrimental. They can also help ramp up production of proteins required for growth and development.
The new paper in PLOS Genetics describes for the first time how PPR proteins recognise their RNA targets via an easy-to-understand code.  This mechanism mimics the simplicity and predictability of the pairing between DNA strands described by Watson and Crick 60 years ago, but at a protein/RNA interface.

A molecular model of a PPR protein recognising a specific RNA molecule. The identity of specific amino acid residues in the protein (coloured sticks) determines the sequence of the RNA molecule it can bind.

This exceptional breakthrough comes from an international, interdisciplinary research team including UWA researchers Professor Ian Small and Aaron Yap from the ARC Centre for Excellence in Plant Energy Biology and Professor Charlie Bond and Yee Seng Chong from UWA's School of Chemistry and Biochemistry, along with Professor Alice Barkan's team at the University of Oregon.  This research was publicly funded by the ARC and the WA State Government in Australia and the NSF in the USA.
"Many PPR proteins are vitally important, but we don't know what they do.  Now we've cracked the code, we can find out," said ARC Plant Energy Biology Director Ian Small.
"What's more, we can now design our own synthetic proteins to target any RNA sequence we choose - this should allow us to control the expression of genes in new ways that just weren't available before.  The potential is really exciting."
"This discovery was made in plants but is applicable across many species as PPR proteins are found in humans and animals too," says Professor Bond.

source: http://www.news.uwa.edu.au/201208174922/international/molecular-code-cracked

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Artificial jellyfish swims in a heartbeat

Using recent advances in marine biomechanics, materials science, and tissue engineering, a team of researchers at Harvard University and the California Institute of Technology (Caltech) have turned inanimate silicone and living cardiac muscle cells into a freely swimming “jellyfish.”
The finding serves as a proof of concept for reverse engineering a variety of muscular organs and simple life forms. It also suggests a broader definition of what counts as synthetic life in an emerging field that has primarily focused on replicating life’s building blocks.
The researchers’ method for building the tissue-engineered jellyfish, dubbed “Medusoid,” was published in a Nature Biotechnology paper on July 22.
An expert in cell- and tissue-powered actuators, coauthor Kevin Kit Parker has previously demonstrated bioengineered constructs that can grip, pump, and even walk. The inspiration to raise the bar and mimic a jellyfish came out of his own frustration with the state of the cardiac field.

Similar to the way a human heart moves blood throughout the body, jellyfish propel themselves through the water by pumping. In figuring out how to take apart and then rebuild the primary motor function of a jellyfish, the aim was to gain new insights into how such pumps really worked.
“It occurred to me in 2007 that we might have failed to understand the fundamental laws of muscular pumps,” says Parker, Tarr Family Professor of Bioengineering and Applied Physics at the Harvard School of Engineering and Applied Sciences (SEAS) and a Core Faculty Member at the Wyss Institute for Biologically Inspired Engineering at Harvard. “I started looking at marine organisms that pump to survive. Then I saw a jellyfish at the New England Aquarium and I immediately noted both similarities and differences between how the jellyfish and the human heart pump.”
To build the Medusoid, Parker collaborated with Janna Nawroth, a doctoral student in biology at Caltech and lead author of the study, who performed the work as a visiting researcher in Parker’s lab. They also worked with Nawroth’s adviser, John Dabiri, a professor of aeronautics and bioengineering at Caltech, who is an expert in biological propulsion.
“A big goal of our study was to advance tissue engineering," says Nawroth. “In many ways, it is still a very qualitative art, with people trying to copy a tissue or organ just based on what they think is important or what they see as the major components—without necessarily understanding if those components are relevant to the desired function or without analyzing first how different materials could be used.”
It turned out that jellyfish, believed to be the oldest multi-organ animals in the world, were an ideal subject, as they use muscles to pump their way through water, and their basic morphology is similar to that of a beating human heart.
To reverse engineer a medusa jellyfish, the investigators used analysis tools borrowed from the fields of law enforcement biometrics and crystallography to make maps of the alignment of subcellular protein networks within all of the muscle cells within the animal. They then conducted studies to understand the electrophysiological triggering of jellyfish propulsion and the biomechanics of the propulsive stroke itself.
Based on such understanding, it turned out that a sheet of cultured rat heart muscle tissue that would contract when electrically stimulated in a liquid environment was the perfect raw material to create an ersatz jellyfish. The team then incorporated a silicone polymer that fashions the body of the artificial creature into a thin membrane that resembles a small jellyfish, with eight arm-like appendages.
Using the same analysis tools, the investigators were able to quantitatively match the subcellular, cellular, and supracellular architecture of the jellyfish musculature with the rat heart muscle cells.
The artificial construct was placed in container of ocean-like salt water and shocked into swimming with synchronized muscle contractions that mimic those of real jellyfish. (In fact, the muscle cells started to contract a bit on their own even before the electrical current was applied.)
“I was surprised that with relatively few components—a silicone base and cells that we arranged—we were able to reproduce some pretty complex swimming and feeding behaviors that you see in biological jellyfish,” says Dabiri.
Their design strategy, they say, will be broadly applicable to the reverse engineering of muscular organs in humans.
“As engineers, we are very comfortable with building things out of steel, copper, concrete," says Parker. “I think of cells as another kind of building substrate, but we need rigorous quantitative design specs to move tissue engineering to a reproducible type of engineering. The jellyfish provides a design algorithm for reverse engineering an organ's function and developing quantitative design and performance specifications. We can complete the full exercise of the engineer's design process: design, build, and test.”
In addition to advancing the field of tissue engineering, Parker adds that he took on the challenge of building a creature to challenge the traditional view of synthetic biology which is “focused on genetic manipulations of cells.” Instead of building just a cell, he sought to “build a beast.”
Looking forward, the researchers aim to further evolve the artificial jellyfish, allowing it to turn and move in a particular direction, and even incorporating a simple “brain” so it can respond to its environment and replicate more advanced behaviors like heading toward a light source and seeking energy or food.
source: http://wyss.harvard.edu/viewpressrelease/90/artificial-jellyfish-swims-in-a-heartbeat

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Writing the Book in DNA

              George Church and Sriram Kosuri discuss the benefits of using DNA as a storage medium and the approach they developed.

 Although George Church's next book doesn't hit the shelves until Oct. 2, it has already passed an enviable benchmark: 70 billion copies -- roughly triple the sum of the top 100 books of all time.
And they fit on your thumbnail.
That's because Church, a founding core faculty member of the Wyss Institute for Biologically Inspired Engineering at Harvard University and the Robert Winthrop Professor of Genetics at Harvard Medical School, and his team encoded in DNA the book, Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves in DNA, which they then decoded and copied.
Biology's databank, DNA has long tantalized researchers with its potential as a storage medium: fantastically dense, stable, energy-efficient and proven to work over a timespan of some 3.5 billion years. While not the first project to demonstrate the potential of DNA storage, Church's team married next-generation sequencing technology with a novel strategy to encode 1,000 times the largest amount of data previously stored in DNA.
The team reports its results in the Aug. 17 issue of the journal Science.
The researchers used binary code to preserve the text, images and formatting of the book. While the scale is roughly what a 5 1/4-inch floppy disk once held, the density of the bits is nearly off the charts: 5.5 petabits, or 1 million gigabits, per cubic millimeter. "The information density and scale compare favorably with other experimental storage methods from biology and physics," said Sriram Kosuri, a senior scientist at the Wyss Institute and senior author on the paper. The team also included Yuan Gao, a former Wyss postdoc who is now an associate professor of biomedical engineering at Johns Hopkins University.

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And where some experimental media -- like quantum holography -- require incredible cold temperatures and tremendous energy, DNA is stable at room temperature. "You can drop it wherever you want, in the desert or your backyard, and it will be there 400,000 years later," Church said.
Reading and writing in DNA is slower than in other media, however, which makes it better suited for archival storage of massive amounts of data, rather than for quick retrieval or data processing. "Imagine that you had really cheap video recorders everywhere," Church said. "Just paint walls with video recorders. And for the most part they just record and no one ever goes to them. But if something really good or really bad happens you want to go and scrape the wall and see what you got. So something that's molecular is so much more energy efficient and compact that you can consider applications that were impossible before."
About four grams of DNA theoretically could store the digital data humankind creates in one year.
Although other projects have encoded data in the DNA of living bacteria, the Church team used commercial DNA microchips to create standalone DNA. "We purposefully avoided living cells," Church said. "In an organism, your message is a tiny fraction of the whole cell, so there's a lot of wasted space. But more importantly, almost as soon as a DNA goes into a cell, if that DNA doesn't earn its keep, if it isn't evolutionarily advantageous, the cell will start mutating it, and eventually the cell will completely delete it."
In another departure, the team rejected so-called "shotgun sequencing," which reassembles long DNA sequences by identifying overlaps in short strands. Instead, they took their cue from information technology, and encoded the book in 96-bit data blocks, each with a 19-bit address to guide reassembly. Including jpeg images and HTML formatting, the code for the book required 54,898 of these data blocks, each a unique DNA sequence. "We wanted to illustrate how the modern world is really full of zeroes and ones, not As through Zs alone," Kosuri said.
The team discussed including a DNA copy with each print edition of Regenesis. But in the book, Church and his co-author, the science writer Ed Regis, argue for careful supervision of synthetic biology and the policing of its products and tools. Practicing what they preach, the authors decided against a DNA insert -- at least until there has been far more discussion of the safety, security and ethics of using DNA this way. "Maybe the next book," Church said.
source: http://wyss.harvard.edu/viewpressrelease/93/writing-the-book-in-dna

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GBioFin Entrepreneurship Certification Programme

GBio Fin invites applications for GECP 2012 Online. The students are required to send their Resume, Colored Photograph and an Innovative Idea related to Biotechnology/BioScience. The selection of the candidate will be made through his academic performance record , Innovative idea and Telephonic Interview.

Through GECP students will be taught about Entrepreneurship and its related fields. The students will also be guided for making business plan and presentation in an Entrepreneurship Competition.

Last date to apply is 15th September 2012, kindly send all the required documents at
GECP@BIOFIN.NET

GECP is an online cum distance mode programme started by GBioFin for Entrepreneurship promotion in Biotechnology.

There is no fee for GECP 2012.

A Certificate will be provided after the completion of GECP.

Deadline: 15th September 2012

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