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Friday 31 August 2012

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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Tuesday 28 August 2012

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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Monday 27 August 2012

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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Monday 20 August 2012

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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Saturday 18 August 2012

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.

Add caption
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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Thursday 16 August 2012

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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Wednesday 15 August 2012

Newfound gene may help bacteria survive in extreme environments

A newly discovered gene in bacteria may help microbes survive in low-oxygen environments. A bacterial cell with the gene, left, exhibits protective membranes. A cell without the gene, right, produces no membranes.
Image: Paula Welander
In the days following the 2010 Deepwater Horizon oil spill, methane-eating bacteria bloomed in the Gulf of Mexico, feasting on the methane that gushed, along with oil, from the damaged well. The sudden influx of microbes was a scientific curiosity: Prior to the oil spill, scientists had observed relatively few signs of methane-eating microbes in the area.

Now researchers at MIT have discovered a bacterial gene that may explain this sudden influx of methane-eating bacteria. This gene enables bacteria to survive in extreme, oxygen-depleted environments, lying dormant until food — such as methane from an oil spill, and the oxygen needed to metabolize it — become available. The gene codes for a protein, named HpnR, that is responsible for producing bacterial lipids known as 3-methylhopanoids. The researchers say producing these lipids may better prepare nutrient-starved microbes to make a sudden appearance in nature when conditions are favorable, such as after the Deepwater Horizon accident.

The lipid produced by the HpnR protein may also be used as a biomarker, or a signature in rock layers, to identify dramatic changes in oxygen levels over the course of geologic history.

“The thing that interests us is that this could be a window into the geologic past,” says MIT Department of Earth, Atmospheric and Planetary Sciences (EAPS) postdoc Paula Welander, who led the research. “In the geologic record, many millions of years ago, we see a number of mass extinction events where there is also evidence of oxygen depletion in the ocean. It’s at these key events, and immediately afterward, where we also see increases in all these biomarkers as well as indicators of climate disturbance. It seems to be part of a syndrome of warming, ocean deoxygenation and biotic extinction. The ultimate causes are unknown.”

Welander and EAPS Professor Roger Summons have published their results this week in the Proceedings of the National Academy of Sciences.

A sign in the rocks


Earth’s rocky layers hold remnants of life’s evolution, from the very ancient traces of single-celled organisms to the recent fossils of vertebrates. One of the key biomarkers geologists have used to identify the earliest forms of life is a class of lipids called hopanoids, whose sturdy molecular structure has preserved them in sediment for billions of years. Hopanoids have also been identified in modern bacteria, and geologists studying the lipids in ancient rocks have used them as signs of the presence of similar bacteria billions of years ago.

But Welander says hopanoids may be used to identify more than early life forms: The molecular fossils may be biomarkers for environmental phenomena — such as, for instance, periods of very low oxygen.

To test her theory, Welander examined a modern strain of bacteria called Methylococcus capsulatus, a widely studied organism first isolated from an ancient Roman bathhouse in Bath, England. The organism, which also lives in oxygen-poor environments such as deep-sea vents and mud volcanoes, has been of interest to scientists for its ability to efficiently consume large quantities of methane — which could make it helpful in bioremediation and biofuel development.

For Welander and Summons, M. capsulatus is especially interesting for its structure: The organism contains a type of hopanoid with a five-ring molecular structure that contains a C-3 methylation. Geologists have found that such methylations in the ring structure are particularly well-preserved in ancient rocks, even when the rest of the organism has since disappeared.

Welander pored over the bacteria’s genome and identified hpnR, the gene that codes for the protein HpnR, which is specifically associated with C-3 methylation. She devised a method to delete the gene, creating a mutant strain. Welander and Summons then grew cultures of this mutant strain, as well as cultures of wild, unaltered bacteria. The team exposed both strains to low levels of oxygen and high levels of methane over a two-week period to simulate an oxygen-poor environment.

During the first week, there was little difference between the two groups, both of which consumed methane and grew at about the same rate. However, on day 14, the researchers observed the wild strain begin to outgrow the mutant bacteria. When Welander added the hpnR gene back into the mutant bacteria, she found they eventually bounced back to levels that matched the wild strain.

Just getting by to survive

What might explain the dramatic contrast in survival rates? To answer this, the team used electron microscopy to examine the cellular structures in both mutant and wild bacteria. They discovered a stark difference: While the wild type was filled with normal membranes and vacuoles, the mutant strain had none.

The missing membranes, Welander says, are a clue to the lipid’s function. She and Summons posit that the hpnR gene may preserve bacteria’s cell membranes, which may reinforce the microbe in times of depleted nutrients.

“You have these communities kind of just getting by, surviving on what they can,” Welander says. “Then when they get a blast of oxygen or methane, they can pick up very quickly. They’re really poised to take advantage of something like this.”

The results, Welander says, are especially exciting from a geological perspective. If 3-methylhopanoids do indeed allow bacteria to survive in times of low oxygen, then a spike of the related lipid in the rock record could indicate a dramatic decrease in oxygen in Earth’s history, enabling geologists to better understand periods of mass extinctions or large ocean die-offs.

“The original goal was [to] make this a better biomarker for geologists,” Welander says. “It’s very meticulous [work], but in the end we also want to make a broader impact, such as learning how microorganisms deal with hydrocarbons in the environment.”

David Valentine, a professor of microbial geochemistry at the University of California at Santa Barbara, says the group’s target lipid is akin to cholesterol, which plays an important role in the membranes of human and animal cells. He says the gene identified by the group may play a similar role in bacteria.

“This work demonstrates an important unity in biology,” Valentine says. “Their results are a needed step in providing context for interpreting the distribution of these biomarkers in the geological record.”

source: http://web.mit.edu/newsoffice/2012/gene-helps-bacteria-survive-in-extreme-conditions-0726.html
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Researchers build a toolbox for synthetic biology

MIT and BU researchers designed new transcription factors that can bind to DNA and turn on specific genes.
Graphic: Christine Daniloff/iMol
For about a dozen years, synthetic biologists have been working on ways to design genetic circuits to perform novel functions such as manufacturing new drugs, producing fuel or even programming the suicide of cancer cells.

Achieving these complex functions requires controlling many genetic and cellular components, including not only genes but also the regulatory proteins that turn them on and off. In a living cell, proteins called transcription factors often regulate that process.

So far, most researchers have designed their synthetic circuits using transcription factors found in bacteria. However, these don’t always translate well to nonbacterial cells and can be a challenge to scale, making it harder to create complex circuits, says Timothy Lu, assistant professor of electrical engineering and computer science and a member of MIT’s Research Laboratory of Electronics.

Lu and his colleagues at Boston University (BU), Harvard Medical School and Massachusetts General Hospital (MGH) have now come up with a new method to design transcription factors for nonbacterial cells (in this case, yeast cells). Their initial library of 19 new transcription factors should help overcome the existing bottleneck that has limited synthetic biology applications, Lu says.

The project is part of a larger, ongoing effort to develop genetic “parts” that can be assembled into circuits to achieve specific functions. Through this endeavor, Lu and his colleagues hope to make it easier to develop circuits that do exactly what a researcher wants.

“If you look at a parts registry, a lot of these parts come from a hodgepodge of different organisms. You put them together into your organism of choice and hope that it works,” says Lu, corresponding author of a paper describing the new transcription factor design technique in the Aug. 3 issue of the journal Cell.

Lead authors of the paper include Ahmad Khalil, assistant professor of biomedical engineering at BU, Lu, and BU postdoc Caleb Bashor. Other authors are Harvard grad student Cherie Ramirez; BU research assistant Nora Pyenson; Keith Joung, associate chief of pathology for research at MGH; and James Collins, BU professor of biomedical engineering.

Binding DNA


Recent advances in designing proteins that bind to DNA gave the researchers the boost they needed to start building a new library of transcription factors.

Transcription factors include a section that recognizes and latches on to a specific DNA sequence called a promoter. The protein then recruits an enzyme called RNA polymerase, which starts copying the gene into messenger RNA, the molecule that carries genetic instructions to the rest of the cell.

In many transcription factors, the DNA-binding section consists of proteins known as zinc fingers, which target different DNA sequences depending on their structure. The researchers based their new zinc fingers designs on the structure of a naturally occurring zinc finger protein. “By modifying specific amino acids within that zinc finger, you can get them to bind with new target sequences,” Lu says.

The researchers attached the new zinc fingers to existing activator segments, allowing them to create many combinations of varying strength and specificity. They also designed transcription factors that work together, so that a gene can only be turned on if the factors bind each other.

Andrew Ellington, a professor of biochemistry at the University of Texas at Austin, says the work is an important step toward creating more complex circuits in nonbacterial cells. “They’ve created a bunch of new transcription factors, and they’ve done it in a modular way, creating additional tools people can use to fashion new circuitry,” says Ellington, who was not part of the research team.

Toward greater complexity

Such transcription factors should make it easier for synthetic biologists to design circuits to perform tasks such as sensing a cell’s environmental conditions.

In this paper, the researchers built some simple circuits in yeast, but they plan to develop more complex circuits in future studies. “We didn’t build a massive 10- or 15-transcription factor circuit, but that’s something that we’re definitely planning to do down the road,” Lu says. “We want to see how far we can scale the type of circuits we can build out of this framework.”

Synthetic biology circuits can be analog or digital, just like electrical circuits. Digital circuits include logic functions such as AND and OR gates, which allow cells to make unequivocal decisions such as whether to undergo programmed cell suicide. Analog functions are useful for sensors that take continuous measurements of a specific molecule in the cell or its environment. By combining those circuits, researchers can create more complex systems in which a digital decision is triggered once the sensor reaches a certain threshold.

In addition to building more complex circuits, the researchers are planning to try their new transcription factors in other species of yeast, and eventually in mammalian cells, including human cells. “What we’re really hoping at the end of the day is that yeast are a good launching pad for designing those circuits,” Lu says. “Working on mammalian cells is slower and more tedious, so if we can build verified circuits and parts in yeast and them import them over, that would be the ideal situation. But we haven’t proven that we can do that yet.”

The research was funded by the Howard Hughes Medical Institute, National Institutes of Health, the Office of Naval Research, the Defense Advanced Research Projects Agency and the National Science Foundation.

source: http://web.mit.edu/newsoffice/2012/synthetic-biology-tools-0803.html
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Monday 13 August 2012

“Selfish” DNA in animal mitochondria offers possible tool to study aging

Caenorhabditis briggsae
Researchers at Oregon State University have discovered, for the first time in any animal species, a type of “selfish” mitochondrial DNA that is actually hurting the organism and lessening its chance to survive – and bears a strong similarity to some damage done to human cells as they age.
The findings, just published in the journal PLoS One, are a biological oddity previously unknown in animals. But they may also provide an important new tool to study human aging, scientists said.
Such selfish mitochondrial DNA has been found before in plants, but not animals. In this case, the discovery was made almost by accident during some genetic research being done on a nematode, Caenorhabditis briggsaea type of small roundworm.
“We weren’t even looking for this when we found it, at first we thought it must be a laboratory error,” said Dee Denver, an OSU associate professor of zoology. “Selfish DNA is not supposed to be found in animals. But it could turn out to be fairly important as a new genetic model to study the type of mitochondrial decay that is associated with human aging.”
DNA is the material that holds the basic genetic code for living organisms, and through complex biological processes guides beneficial cellular functions. Some of it is also found in the mitochondria, or energy-producing “powerhouse” of cells, which at one point in evolution was separate from the other DNA.
The mitochondria generally act for the benefit of the cell, even though it is somewhat separate. But the “selfish” DNA found in some plant mitochondria – and now in animals – has major differences. It tends to copy itself faster than other DNA, has no function useful to the cell, and in some cases actually harms the cell. In plants, for instance, it can affect flowering and sometimes cause sterility.
“We had seen this DNA before in this nematode and knew it was harmful, but didn’t realize it was selfish,” said Katie Clark, an OSU postdoctoral fellow. “Worms with it had less offspring than those without, they had less muscle activity. It might suggest that natural selection doesn’t work very well in this species.”
That’s part of the general quandary of selfish DNA in general, the scientists said. If it doesn’t help the organism survive and reproduce, why hasn’t it disappeared as a result of evolutionary pressure? Its persistence, they say, is an example of how natural selection doesn’t always work, either at the organism or cellular level. Biological progress is not perfect.
In this case, the population sizes of the nematode may be too small to eliminate the selfish DNA, researchers said.
What’s also interesting, they say, is that the defects this selfish DNA cause in this roundworm are surprisingly similar to the decayed mitochondrial DNA that accumulates as one aspect of human aging. More of the selfish DNA is also found in the worms as they age.
Further study of these biological differences may help shed light on what can cause the mitochondrial dysfunction, Denver said, and give researchers a new tool with which to study the aging process.

source: http://oregonstate.edu/ua/ncs/archives/2012/aug/%E2%80%9Cselfish%E2%80%9D-dna-animal-mitochondria-offers-possible-tool-study-aging
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Sunday 12 August 2012

Toward 'universal' vaccine: Scientists describe antibodies that protect against large variety of flu viruses

A team led by scientists at the Scripps Research Institute and Crucell Vaccine Institute has described three human antibodies that provide broad protection against influenza B virus strains. The work was published in Science Express, the advance online issue of the journal Science, on Aug. 9, 2012. Image courtesy of the Wilson lab, the Scripps Research Institute

The isolation of the new broadly neutralizing antibodies, which was reported the journal Science's advance online edition, Science Express, on August 9, paves the way for researchers to develop a universal antibody-based flu therapy for use in severe infections or to protect hospital staff during an outbreak. Importantly, these antibodies may provide key clues to the design of an active universal flu vaccine—designed to protect long-term against flu viruses, not just against the current season's strains. "To develop a truly universal flu vaccine or therapy, one needs to be able to provide protection against influenza A and influenza B viruses, and with this report we now have broadly neutralizing antibodies against both," said Ian A. Wilson, the Hansen Professor of Structural Biology at Scripps Research, who was senior investigator for the new study with Crucell's Jaap Goudsmit and Robert Friesen. One of the newly discovered antibodies will be of special interest to flu researchers, because it appears to protect against essentially all influenza B and influenza A strains. "It's the only one in the world that we know of that has been found to do this," said Wilson. Looking for the Missing Pieces Influenza B viruses are considered less dangerous than Influenza A viruses, and have been less intensively studied because they have less capacity to mutate into deadly pandemic strains. However, influenza B viruses account for a significant part of the annual flu illness burden in humans.

To find broadly protective antibodies against Influenza B, the team at Crucell generated a large collection of flu antibodies from the immune cells of volunteers who had been given a seasonal flu vaccine. The researchers then screened this collection for antibodies that could bind to a wide variety of influenza B strains. Three of the antibodies they found in this manner—CR8033, CR8071, and CR9114—protected mice against normally lethal doses of the two major influenza B strains. CR9114 also protected mice against influenza A viruses, including the H1N1 subtype that killed about 17,000 people in a 2009 pandemic. The fact that these antibodies protected against a variety of flu strains suggested they mark functionally important sites, or "epitopes," on the virus that are relatively unchanging (conserved) from one flu strain to the next. Wilson's team at Scripps Research characterized the newly discovered antibodies' binding sites on influenza viruses using electron microscopy and X-ray crystallography techniques. They found that CR8033 binds to a highly conserved epitope—a functionally important site—on the "head" of the hemagglutinin protein, a structure that studs the outer coat of flu viruses and allows the viruses to stick to vulnerable cells. CR8071 binds to the base of the hemagglutinin head. Most antibodies that bind to the hemagglutinin head and neutralize influenza do so by blocking the virus's attachment to host cells. "The unique thing about these two antibodies is that they neutralize flu viruses chiefly by preventing virus particles from exiting infected cells," said Nick Laursen, a research associate in Wilson's laboratory who was a lead author of the study. A Weak Point on the Virus Antibody CR9114 turned out to bind to a site on the hemagglutinin stem. "It prevents the hemagglutinin protein from undergoing the shape-change needed for the virus to fuse to the outer membrane of a host cell," said Cyrille Dreyfus, a Wilson lab research associate who also was a lead author of the study. "This appears to be a real weak point of the virus, because this epitope is highly conserved among influenza A subtypes as well as influenza B." Wilson notes that in a study published in 2009 his laboratory determined the structure of another Crucell antibody that broadly neutralizes influenza A viruses by binding to essentially the same site on the hemagglutinin stem—but in a subtly different way, so that it fails to get a grip on influenza B viruses, too. "With some tweaking of that antibody's binding domains, we might have been able to get a broader effect like CR9114's," Wilson said. The viral epitope to which CR9114 binds will now be studied extensively by researchers as a target for vaccines and therapies, because it is the only one found so far that is broadly vulnerable to neutralization on both influenza A and B viruses. Remarkably, CR9114 performed poorly against influenza B viruses in initial lab-dish tests known as microneutralization assays, which test the ability of an antibody to protect cells from viral infection. Yet CR9114 was clearly effective under more realistic conditions in mice, even at low doses. Because it attacks the stem rather than the head of flu virus hemagglutinins, CR9114 also failed to show effects in a widely used test known as the hemagglutinin-inhibition assay. "As we move towards design of a universal flu vaccine, we need to find more inclusive assays to screen for antibodies such as CR9114, which may be highly effective but have novel mechanisms for neutralization that cannot be detected by the current methods used in influenza vaccine development," Goudsmit said.

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Killing cancer: stories from the cutting edge of science


Tumour-treating electrical fields, a Victorian gout remedy, and an anti-cancer 'virus’. Meet the scientists tackling our most feared disease in some truly innovative ways.
Despite the billions spent in pursuit of cures , it remains essentially mysterious. We do have a far better idea of what might give us cancer. Fewer people smoke, dietary awareness has increased and many known carcinogens have been removed from the environment. Yet the disease goes on killing much as it has always done. “If you look at the death rate from cancer, there’s no dramatic change over the last five decades,” says the cancer specialist David Agus, author of The End of Illness. A realist might say we are losing the battle against cancer except where we are winning it.
But there are grounds for optimism. New technologies are opening new avenues of possibility. And at the cutting edge of the battle against cancer are dozens of projects currently under way all over the world. Some are lavishly funded, some operate on shoestrings, some are pursuing simple objectives, others are pushing the frontiers of science. What they have in common is a belief that humans can do far ­better against our most feared disease. Here are just some of them.
Prof Tim Illidge: the magic bullet
In his laboratory in Manchester’s Christie Institute, one of the largest cancer treatment centres in Europe, Prof Tim Illidge is busy developing what he hopes will become a “magic bullet” against certain cancers. He is a pioneer in the use of radio-immunotherapy, or training the body’s immune system to recognise – and destroy – cancer cells.
Immunotherapy — altering cells in a laboratory to make them better at fighting cancer — has been known about for some time. The problem with it is that as tumours become more advanced, they become less visible to the attacking cells. Radio-immunotherapy adds the refinement of precisely targeted radioactive molecules that can spot and “zap” cancer cells without damaging healthy tissues.
Prof Illidge gives the example of Mel, a retired ambulance driver who was faced with an aggressive course of chemotherapy. “Instead, by attaching a radioactive molecule to an anti-cancer antibody, we used his immune system to kill the tumour cells,” Prof Illidge says. “It’s significantly better for patients as it’s quicker with fewer side effects. We call it the 'magic bullet’. Mel was delighted, and even managed to keep his ponytail.”
Prof Jim Mccaul: the 19th-century gout cure
Just as nothing can be too futuristic in cancer treatment, so nothing can be too old-fashioned. Prof Jim McCaul, a head and neck cancer specialist at Bradford Royal Infirmary, is conducting a trial using a 19th-century gout remedy.
Lugol’s Iodine was invented by French physician Jean Lugol in 1827, and has been used for everything from cleaning cuts to purifying water. One of its more interesting features is an ability to stain healthy cells – those capable of storing glycogen – to a chocolatey-brown colour, while leaving cancerous or pre-cancerous cells a paler hue. The importance of this discovery is that surgeons operating on mouth and throat cancers currently have no reliable way of knowing how much tissue to remove. Pre-cancerous cells may be left behind or perfectly healthy ones cut out.
The iodine trial, believes Prof McCaul, could lead to the current 10mm margin around the cancer being reduced to 2mm. “It’s a simple idea,” he says, “but it can take a lot of the guesswork out of surgery. We have tests going on in 12 sites and the results are encouraging. Previously, we would have expected to have 32 per cent of patients left with pre-cancerous cells. That’s down to four per cent.”
Prof Jay Bradner: the miraculous molecule
Every cancer pioneer builds on the work of others. Prof Jay ­Bradner, a myeloma (bone marrow cancer) specialist at the Dana-Farber Institute in Boston, took as his starting point the breakthrough discovery in the Eighties that all cancer was tied into genetics. The problem might be inherited or the result of exposure to outside agents such as smoke or radioactivity, but in the end the cancer resulted from abnormalities in the genes. Little wonder, then, that the Human Genome Project, which set out to map the body’s 20,000-plus genes – and reveal the exact method by which the genes went wrong – prompted such excitement.
It didn’t turn out to be so simple. The genetic coding of a malignant cell could look completely normal. Something else must be making it malfunction. Many researchers, including Prof Bradner, believe that the epigenome – basically the gene’s on-off switch – may hold the key.
“You might ask yourself, with all the things cancer’s trying to do to kill our patient, how does it remember it’s cancer?” Prof Bradner said in a recent TED talk. “When it winds up its genome, divides into two cells and unwinds again, why does it not turn into an eye, into a liver, as it has all the genes necessary to do this? The reason is that cancer places little molecular bookmarks, little Post-it Notes, that remind the cell: “I’m cancer; I should keep growing.” Prof Bradner’s response? To develop a molecule that would “prevent the Post-it Note from sticking” and trick cancer cells into forgetting they were cancer.
Focusing their research on a very rare but virulent cancer, midline carcinoma, Prof Bradner and his team eventually came up with JQ1, a molecule to target the protein that causes it. And as they watched their molecule in action under the microscope, their excitement only increased: “The cancer cells, small, round and rapidly dividing, grew these arms and extensions,” said Prof Bradner. “They were changing shape. In effect, the cancer cell was forgetting it was cancer and becoming a normal cell.”
Prof Yoram Palti: the tumour-treating hat
The key feature of cancer is mitosis, the phenomenon of errant cells dividing and multiplying to form a tumour. One of the core goals of cancer researchers has been to find a way to stop this, and prevent cancer’s ability to spread. Prof Yoram Palti, founder of a small cancer treatment company, Novocure Ltd, based in Haifa, Israel, has developed the idea of using electrical fields that can disrupt the abnormal behaviour of chromosomes in the affected cells and prevent them splitting.
The company’s TTF (tumour-treating fields) device consists of a battery pack and electrode pads that are worn under a hat for 20 hours a day. Roger Stupp, a prominent American researcher who has championed it, says: “When I first saw it I thought it was completely voodoo, goofy, nuts.” Yet trials suggest TTF can significantly slow the spread of brain cancers, and the company is developing a new range for breast and lung cancers.
Danny Hillis: could proteins unlock cancer?
Danny Hillis, a self-described “inventor, entrepreneur and computer geek”, admits cutting an unlikely figure in the rarefied world of cancer research. Yet his capacity for fresh thinking – as an engineering student at Harvard, Hillis pioneered the concept of parallel computers that is now the basis for most supercomputers – prompted his conviction that the world is thinking about cancer in entirely the wrong way. Rather than being seen as something to be treated with drugs and procedures, Hillis believes cancer should be prevented at source. How? One answer Hillis, a flamboyant Californian, offers, is proteomics, the study of proteins.
Hillis believes proteins hold the real secret of cancer. The trillions of cells in the human body, he says, are in constant conversation, working co-operatively almost like the operating system of an advanced computer. The proteins are the main carriers of information within the system. When they relay false information, the body reacts wrongly and gets sick. This, essentially, is what causes cancer. Proteomics can give us a means of “listening in” on what the body cells are saying, and knowing when something is going wrong.
Hillis is no lone wolf. The pioneering oncologist Dr David Agus shares his view that “cancer” is not one disease and that the conditions that fall under it are far more varied than the medical establishment is prepared to admit. The problem for disciples of proteomics is that not everyone has the same kind of protein network, meaning that a way has to be found to “map” the human body on an individualised basis. Scientists at Applied Minds, the research and development company that Hillis co-founded in the Los Angeles suburb of Burbank, are busy searching for the answer.
Prof John bell: the anti-cancer virus
A man-made virus that can attack cancer cells has long been a dream of medical researchers – but for decades has remained just that. The possibility first arose from a celebrated 1951 case of a young girl with leukaemia who contracted chickenpox, sending the cancer into remission. The euphoria that followed soon subsided as complications became apparent, notably the tendency of the immune system to fight off the virus.
New hope is emerging with the development in Ottawa, Canada, of JX-595, an engineered virus that appears to overcome the early problems. It is based on the vaccina virus, used in the development of smallpox vaccine. Unlike previous anti-cancer viruses it has few ill effects on the healthy parts of the body and can be administered into the bloodstream, rather than directly into the tumour.
“We are very excited,” says Prof John Bell at the University of Ottawa, the project’s lead researcher, “because this is the first time in medical history that a viral therapy has been shown to consistently and selectively replicate in cancer tissue after infusion into humans.”
Dr Timothy Ley: whole genome sequencing
Sometimes cancer seems to know exactly who it is after. Last year it went after Dr Lukas Wartman, a renowned leukaemia specialist at Washington University. Dr Wartman, 34, had already fought off two youthful bouts of leukaemia. His chances of surviving a third were virtually non-existent.
But he had one advantage: his colleagues at the university’s pioneering genome institute. Last July, the unit’s assistant director, Dr Timothy Ley, set the team to work on a very special project, fully sequencing the genes of Dr Wartman’s cancer cells, his healthy cells, and his RNA, a close chemical cousin to DNA. It had never been tried on this type of cancer before, and it required the institute’s scanning machines and supercomputer to run around the clock. But they found the problem – a rogue gene that was producing large amounts of a certain protein, spurring the cancer’s growth.
Astonishingly, although it was only approved for kidney cancer, there was an available drug to attack this gene. Dr Wartman’s leukaemia is now in remission.
Whole genome sequencing is a complex, uncertain and expensive undertaking. When the Apple boss Steve Jobs had run out of other options to combat his pancreatic cancer, he underwent a similar process to Dr Wartman, reputedly costing him $100,000. Yet simpler variations of the procedure are becoming available, and Dr Ley believes the big advances are still to come. “This is the most powerful diagnostic tool we’ve ever had,” he says. “The more sequencing we do, the more we understand these mutations.”


 
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Friday 10 August 2012

Stars and hexagons! DNA code shapes gold nanoparticles

University of Illinois chemists found that DNA can shape gold nanoparticle growth similarly to the way it shapes protein synthesis, with different letters of the genetic code producing gold circles, stars and hexagons. (Credit: Li Huey Tan, Zidong Wang and Yi Lu)
DNA holds the genetic code for all sorts of biological molecules and traits. But University of Illinois researchers have found that DNA’s code can similarly shape metallic structures.

The team found that DNA segments can direct the shape of gold nanoparticles – tiny gold crystals that have many applications in medicine, electronics and catalysis. Led by Yi Lu, the Schenck Professor of Chemistry at the U. of I., the team published its surprising findings in the journal Angewandte Chemie.

“DNA-encoded nanoparticle synthesis can provide us a facile but novel way to produce nanoparticles with predictable shape and properties,” Lu said. “Such a discovery has potential impacts in bio-nanotechnology and applications in our everyday lives such as catalysis, sensing, imaging and medicine.”

Gold nanoparticles have wide applications in both biology and materials science thanks to their unique physicochemical properties. Properties of a gold nanoparticle are largely determined by its shape and size, so it is critical to be able to tailor the properties of a nanoparticle for a specific application.

“We wondered whether different combinations of DNA sequences could constitute ‘genetic codes’ to direct the nanomaterial synthesis in a way similar to their direction of protein synthesis,” said Zidong Wang, a recent graduate of Lu’s group and the first author of the paper.

Gold nanoparticles are made by sewing tiny gold seeds in a solution of gold salt. Particles grow as gold in the salt solution deposits onto the seeds. Lu’s group incubated the gold seeds with short segments of DNA before adding the salt solution, causing the particles to grow into various shapes determined by the genetic code of the DNA.

The DNA alphabet comprises four letters: A, T, G and C. The term genetic code refers to the sequence of these letters, called bases. The four bases and their combinations can bind differently with facets of gold nanoseeds and direct the nanoseeds’ growth pathways, resulting in different shapes.

In their experiments, the researchers found that strands of repeating A’s produced rough, round gold particles; T’s, stars; C’s, round, flat discs; G’s, hexagons. Then the group tested DNA strands that were a combination of two bases, for example, 10 T’s and 20 A’s. They found that many of the bases compete with each other resulting in intermediate shapes, although A dominates over T.

Next, the researchers plan to investigate exactly how DNA codes direct nanoparticle growth. They also plan to apply their method to synthesize other types of nanomaterials with novel applications.

source: http://news.illinois.edu/news/12/0808nanoparticles_YiLu.html
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New Perspectives On the Function of the Golgi Apparatus

Golgi stacks (labelled with Man1-YFP) and import sites (labelled with the ER tethering factor TIP20-CFP) colocalize even when Golgi stacks are mobile. Both fluorescently-tagged proteins were coexpressed together with the ER marker RFP-p24d5 in tobacco.
Cell biologists at the University of Heidelberg have recently obtained data which can explain the different way the Golgi apparatus functions in higher plant and mammalian cells. In contrast to mammalian cells the Golgi apparatus -- a membrane system in the cytoplasm, which participates in a variety of metabolic pathways -- consists in higher plants of hundreds of small Golgi stacks which move along the endoplasmic reticulum (ER) in a stop-and-go fashion. Prof. David G. Robinson and his research group at the Centre for Organismal Studies of the University of Heidelberg have now been able to provide a mechanistic explanation for the highly ordered and efficient transport of vesicles between the ER and Golgi stacks.
Their results have just been published in the journal Frontiers in Plant Science.
The Golgi apparatus is one of the most important and variable of the organelles belonging to the endomembrane system. One of its essential functions is to modify and sort macromolecules which are destined for either the lysosome (or the vacuole in plants) of for the extracellular milieu. Whereas in mammalian cells the Golgi apparatus is a complex permanently fixed in the vicinity of the nucleus, in higher plants it is subdivided into hundreds of small mobile Golgi stacks. "A consequence of this morphological difference is that vesicle transport between the ER and the Golgi stacks needs to be highly efficient and strictly regulated in order that vesicles do not get lost during Golgi movement," explained Prof. Robinson.
In order to investigate this process, the Heidelberg scientists looked for so-called ER-import sites (ERIS): special domains of the ER where incoming vesicles from the Golgi stacks fuse with the ER. "In this regard, one of the most important problems to be addressed was the spatio-temporal relationship of ERIS to the domain(s) of the ER responsible for export (ERES) and to the mobile Golgi stacks," said Prof. Robinson. In order to identify ERIS, The Heidelberg team used fluorescently-tagged proteins that were known to participate in the process of vesicle fusion. These included so-called tethering factors, responsible for the long-range capture of vesicles, as well as SNARE proteins which are involved in the actual fusion process with the ER membrane.
It turns out that both classes of protein are restricted to domains which lie immediately beneath the the Golgi stacks. "Even more surprising was the discovery that the export domains (ERES) were also present at this position, and that both moved in parallel with the Golgi stacks," declared Prof. Robinson. By having the import and export machineries so tightly coupled to the Golgi stack, it is now clear how the higher plant cell can effectively accomplish vesicle transfer between the ER and the Golgi apparatus without loss during the fast Golgi movement. "This aspect of the higher plant endomembrane system differs totally from animal cells and is a unique and totally new feature among organisms possessing a nucleus and internal membranes" emphasized Prof. Robinson.
source: http://www.uni-heidelberg.de/presse/news2012/pm20120809_golgi_en.html

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Saturday 4 August 2012

Structural analysis opens the way to new anti-influenza drugs

Different inhibitors (yellow, grey) fill the cave-like active site of the cap-snatching protein (the endonuclease, in green) differently, even though they all bind to the active site’s two metal ions (magenta).Credit: EMBL/Cusack
Researchers at the European Molecular Biology Laboratory (EMBL) in Grenoble, France, have determined the detailed 3-dimensional structure of part of the flu virus’ RNA polymerase, an enzyme that is crucial for influenza virus replication. This important finding is published today in PLoS Pathogens. The research was done on the 2009 pandemic influenza strain but it will help scientists to design innovative drugs against all the different influenza strains, and potentially lead to a new class of anti-flu drugs in the next 5-10 years.
The scientists focused on the endonuclease part of the viral RNA polymerase. The endonuclease is responsible for a unique mechanism called ‘cap-snatching’ that allows the virus to trick its host cell into producing viral proteins. In human cells the translation of messenger RNA (mRNA) strands into proteins requires a special structure, called the “cap”, at the beginning of each mRNA. When the influenza virus infects a host cell its endonuclease “snatches” that cap from the cell’s own mRNA. Another part of its RNA polymerase then uses it as the starting point for synthesizing viral mRNA. With the correct cap structure at the beginning, viral mRNA can then hijack the protein-production machinery of the infected cell to make viral proteins, which assemble into new viruses that will spread the infection.
The team led by Stephen Cusack, Head of EMBL Grenoble, analyzed crystals of endonuclease from the 2009 pandemic influenza strain using the high intensity X-ray beams at the European Synchrotron Radiation Facility (ESRF). The researchers were able to determine the 3D atomic structure of the enzyme and to visualize how several different small molecule inhibitors bind to and block its active site. If the active site of the endonuclease is blocked by an inhibitor the enzyme cannot bind its normal substrate, the host cell mRNA, and viral replication is prevented.
The active site of the endonuclease is shaped like a cave with two metal ions at the bottom. Cusack and colleagues found that all the inhibitors they studied bind to those two metal ions but, depending on their shapes, different inhibitors bind differently to the amino-acids of the cave’s walls.
“Based on this detailed structural information we can now design new synthetic chemicals which bind even more tightly to the endonuclease active site and thus will potentially be more potent inhibitors of influenza virus replication,” explains Stephen Cusack. “We can even try to build in anti-drug resistance by making sure the inhibitors only contact those amino acids that the virus cannot mutate since they are essential for the normal activity of the polymerase.”
Because the cap-snatching mechanism is common to all influenza strains, new potent endonuclease inhibitors should be effective against seasonal flu, novel pandemic strains or highly pathogenic H5N1 bird flu. EMBL scientists are working with EMBL’s spin-off company Savira pharmaceuticals, in partnership with Roche, to further develop influenza inhibitors. Promising candidates will be tested first for efficacy in cell culture, ultimately moving into clinical trials on humans.
This research was partly funded by the European commission, through the FP7 research grant awarded to the FluPharm project.
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3D movie at ‘ultraresolution’ shows how cell’s machinery bends membrane inwards

Scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, have combined the power of two kinds of microscope to produce a 3-dimensional movie of how cells ‘swallow’ nutrients and other molecules by engulfing them. The study, published today in Cell, is the first to follow changes in the shape of the cell’s membrane and track proteins thought to influence those changes. It also provides ample data to investigate this essential process further.
This ‘swallowing’, called endocytosis, is involved in a variety of crucial tasks. It is used by brain cells relaying information to each other, for instance, and is also hijacked by many viruses, which use it to invade their host’s cells. When a cell is about to swallow some molecules, a dent appears in the cell’s membrane, and gradually expands inwards, pinching off to form a little pouch, or vesicle, that transports molecules into the cell.
To investigate how the cell’s machinery pulls in the membrane and forms the vesicle, researchers led by Marko Kaksonen and John Briggs employed a method they developed two years ago to faithfully follow the exact same molecules first under a light microscope and then with the higher resolution of an electron microscope. This enabled them to combine two sets of data that so far could only be obtained in isolation: the timing and sequence with which different components of the cell’s machinery arrive at the vesicle-to-be, and the 3D changes to membrane shape that ultimately form that vesicle. They discovered, for instance, that the first proteins to arrive on the inside of the cell’s membrane are not able to start bending it inwards until a network of the cell’s scaffolding protein, actin, forms and starts pulling on the membrane.
The data used to make the video is freely available to the scientific community and will, Kaksonen and Briggs believe, provide valuable information to others trying to develop physical models of how this process works. The EMBL scientists themselves are probing the roles of individual proteins in this process, by perturbing them, and would like to extend the current work in yeast to human cells.
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