Double meaning in genetic code

Scientists discover double meaning in genetic code:

Scientists discover double meaning in genetic code

Scientists discover double meaning in genetic code

Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

A research team led by Dr. John Stamatoyannopoulos, University of Washington associate professor of genome sciences and of medicine, made the discovery. The findings are reported in the Dec. 13 issue of Science. The work is part of the Encyclopedia of DNA Elements Project, also known as ENCODE. The National Human Genome Research Institute funded the multi-year, international effort. ENCODE aims to discover where and how the directions for biological functions are stored in the human genome.

Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long.

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

The genetic code uses a 64-letter alphabet called codons. The UW team discovered that some codons, which they called duons, can have two meanings, one related to protein sequence, and one related to gene control. These two meanings seem to have evolved in concert with each other. The gene control instructions appear to help stabilize certain beneficial features of proteins and how they are made.

The discovery of duons has major implications for how scientists and physicians interpret a patient’s genome and will open new doors to the diagnosis and treatment of disease.

“The fact that the genetic code can simultaneously write two kinds of information means that many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously,” said Stamatoyannopoulos.

Source:  sciencedaily.com

Supreme Court addresses software patent

Supreme Court agrees to address key issue: Can software be patented?

 

Supreme Court agrees to address key issue: Can software be patented?

Supreme Court agrees to address key issue: Can software be patented?

 

Over the past few years, two aspects of patent law in the United States have come under increasing scrutiny. First, there’s been the rise of patent trolls who scoop up broad patents on particular methods or ways of performing an activity, then sue a number of companies (or even the end users) of that technology, claiming that their rights have been violated. Second, there’ve been an increasing number of lawsuits over the topic of software patents and the question of what is — or isn’t — patentable.

Now, the Supreme Court has agreed to take a case — Alice Corporation Pty. Ltd v CLS Bank International — that deals directly with the question of what is, or isn’t, patentable. Lower courts have been tangling with this issue for years — the question of specific software patents was at the heart of Google’s recent court spat with Oracle, which ended in a win for Google but may be lost on appeal.

Rise of the patent trolls

The central problem with software patents is the gray area between “Doing X on a computer” (clearly unpatentable) and the development of a new method of performing a task or function. The pro-patent argument is that a person who discovers a new algorithm or method of doing things in software has clearly invented something and is entitled to patent it. The anti-patent argument is that such “inventions’ are nothing but an application of mathematics. Mathematics cannot be patented in the US, so why should software carry patents?

Patent trolls, meanwhile, have inadvertently given a great deal of ammunition to the anti-software patents crowd by launching massive lawsuit campaigns to assert ownership over such mundane tasks as connecting a printer to a network. Companies now acquire huge war chests of patents specifically to use against other companies that engage in patent warfare. This is generally seen as one reason Google acquired Motorola several years ago, and Microsoft earns more from its patent licensing fees from Android than it does from Windows Phone.

One final thing to note is that patents and copyrights are two entirely different things. If software can’t be patented, Microsoft still retains a coypright on the code of Windows, Oracle still has a copyright on Java, and it would still be illegal to copy a program without an appropriate license. Lower courts have had little luck creating a clear-cut example of when a software invention is or is not patentable, so the hope is that the Supreme Court will issue clearer rules.

Hidden Genetic Code

A hidden genetic code for better designer genes:

 

A hidden genetic code for better designer genes

A hidden genetic code for better designer genes

 

Scientists routinely seek to reprogram bacteria to produce proteins for drugs, biofuels and more, but they have struggled to get those bugs to follow orders. But a hidden feature of the genetic code, it turns out, could get bugs with the program. The feature controls how much of the desired protein bacteria produce, a team from the Wyss Institute for Biologically Inspired Engineering at Harvard University reported in the September 26 online issue of Science.

The findings could be a boon for biotechnologists, and they could help synthetic biologists reprogram bacteria to make new drugs and biological devices.

By combining high-speed “next-generation” DNA sequencing and DNA synthesis technologies, Sri Kosuri, Ph.D., a Wyss Institute staff scientist, George Church, Ph.D., a core faculty member at the Wyss Institute and professor of genetics at Harvard Medical School, and Daniel Goodman, a Wyss Institute graduate research fellow, found that using more rare words, or codons, near the start of a gene removes roadblocks to protein production.

“Now that we understand how rare codons control gene expression, we can better predict how to synthesize genes that make enzymes, drugs, or whatever you want to make in a cell,” Kosuri said.

To produce a protein, a cell must first make working copies of the gene encoding it. These copies, called messenger RNA (mRNA), consist of a specific string of words, or codons. Each codon represents one of the 20 different amino acids that cells use to assemble proteins. But since the cell uses 61 codons to represent 20 amino acids, many codons have synonyms that represent the same amino acid.

In bacteria, as in books, some words are used more often than others, and molecular biologists have noticed over the last few years that rare codons appear more frequently near the start of a gene. What’s more, genes whose opening sequences have more rare codons produce more protein than genes whose opening sequences do not.

No one knew for sure why rare codons had these effects, but many biologists suspected that they function as a highway on-ramp for ribosomes, the molecular machines that build proteins. According to this idea, called the codon ramp hypothesis, ribosomes wait on the on-ramp, then accelerate slowly along the mRNA highway, allowing the cell to make proteins with all deliberate speed. But without the on-ramp, the ribosomes gun it down the mRNA highway, then collide like bumper cars, causing traffic accidents that slow protein production. Other biologists suspected rare codons acted via different mechanisms. These include mRNA folding, which could create roadblocks for ribosomes that block the highway and slow protein production.

To see which ideas were correct, the three researchers used a high-speed, multiplexed method that they’d reported in August in The Proceedings of the National Academy of Sciences.

First, they tested how well rare codons activated genes by mass-producing 14,000 snippets of DNA with either common or rare codons; splicing them near the start of a gene that makes cells glow green, and inserting each of those hybrid genes into different bacteria. Then they grew those bugs, sorted them into bins based on how intensely they glowed, and sequenced the snippets to look for rare codons.

They found that genes that opened with rare codons consistently made more protein, and a single codon change could spur cells to make 60 times more protein.

“That’s a big deal for the cell, especially if you want to pump out a lot of the protein you’re making,” Goodman said.

The results were also consistent with the codon-ramp hypothesis, which predicts that rare codons themselves, rather than folded mRNA, slow protein production. But the researchers also found that the more mRNA folded, the less of the corresponding protein it produced — a result that undermined the hypothesis.

To put the hypothesis to a definitive test, the Wyss team made and tested more than 14,000 mRNAs – including some with rare codons that didn’t fold well, and others that folded well but had no rare codons. By quickly measuring protein production from each mRNA and analyzing the results statistically, they could separate the two effects.

The results showed clearly that RNA folding, not rare codons, controlled protein production, and that scientists can increase protein production by altering folding, Goodman said.

The new method could help resolve other thorny debates in molecular biology. “The combination of high-throughput synthesis and next-gen sequencing allows us to answer big, complicated questions that were previously impossible to tease apart,” Church said.

“These findings on codon use could help scientists engineer bacteria more precisely than ever before, which is tremendous in itself, and they provide a way to greatly increase the efficiency of microbial manufacturing, which could have huge commercial value as well,” said Wyss Institute Founding Director Don Ingber, M.D., Ph.D. “They also underscore the incredible value of the new automated technologies that have emerged from the Synthetic Biology Platform that George leads, which enable us to synthesize and analyze genes more rapidly than ever before.”

Quantum encryption Unbreakable

With quantum encryption, in which a message gets encoded in bits represented by particles in different states, a secret message can remain secure even if the system is compromised by a malicious hacker.

Cryptography

Cryptography

 

No matter how complex they are, most  secret codes turn out to be breakable. Producing the ultimate secure code may require encoding a secret message inside the quantum relationship between atoms, scientists say.  Now cryptographers have taken “quantum encryption” a step further by showing how a secret message can remain secure even if the system is compromised by a malicious hacker.Artur Ekert, director of the Center for Quantum Technologies at the National University of Singapore, presented the new findings here at the annual meeting of the American Association for the Advancement of Science.  Ekert, speaking Saturday (Feb. 18), described how  decoders can adjust for a compromised encryption device, as long as they know the degree of compromise.  The subject of subatomic particles is a large step away from the use of papyrus, the ancient writing material employed in the first known cryptographic device. That device, called a scytale, was used in 400 B.C. by Spartan military commanders to send coded messages to one another. The commanders would wrap strips of papyrus around a wooden baton and write the message across the strips so that it could be read only when the strips were wrapped around a baton of matching size. Later, the technique of substitution was developed, in which the entire alphabet would be shifted, say, three characters to the right, so than an “a” would be replaced by “d,” and “b” replaced by “e,” and so on. Only someone who knew the substitution rule could read the message. Julius Caesar employed such a cipher scheme in the first century B.C.  Over time, ciphers became more and more complicated, so that they were harder and harder to crack. Harder, but not impossible.  “When you look at the history of cryptography, you come up with a system, and sooner or later someone else comes up with a way of breaking the system,” Ekert said. “You may ask yourself: Is it going to be like this forever? Is there such a thing as the perfect cipher?”  The closest thing to a perfect cipher involves what’s called a one-time pad.  “You just write your message as a sequence of bits and you then add those bits to a key and obtain a cryptogram,” Ekert said.”If you take the cryptogram and add it to the key, you get plain text. In fact, one can prove that if the keys are random and as long as the messages, then the system offers perfect security.”  “If the keys are as long as the message, then you need a secure way to distribute the key,” Ekert said.  The nature of physics known as quantum mechanics seems to offer the best hope of knowing whether a key is secure.  Quantum mechanics says that certain properties of subatomic particles can’t be measured without disturbing the particles and changing the outcome. In essence, a particle exists in a state of indecision until a measurement is made, forcing it to choose one state or another. Thus, if someone made a measurement of the particle, it would irrevocably change the particle.  If an encryption key were encoded in bits represented by particles in different states, it would be immediately obvious when a key was not secure because the measurement made to hack the key would have changed the key.  This, of course, still depends on the ability of the two parties sending and receiving the message to be able to independently choose what to measure, using a truly random number generator — in other words, exercising free will — and using devices they trust.   But what if a hacker were controlling one of the parties, or tampering with the encryption device?  Ekert and his colleagues showed that even in this case, if the messaging parties still have some free will, their code could remain secure as long as they know to what degree they are compromised.  In other words, a random number generator that is not truly random can still be used to send an undecipherable secret message, as long as the sender knows how random it is and adjusts for that fact.  “Even if they are manipulated, as long as they are not stupid and have a little bit of free will, they can still do it,”.