COMPUTER BIO LOGIC GATES FROM BACTERIA

DNA is often referred to as the building block of life. Now scientists from Imperial College London have demonstrated that DNA (and bacteria) can be used to create the fundamental building blocks of a computer – logic gates. Using DNA and harmless gut bacteria, the scientists have built what they claim are the most advanced biological logic gates ever created by scientists. The research could lead to the development of a new generation of microscopic biological computing devices that, amongst other things, could travel around the body cleaning arteries and destroying cancers.

While previous research had already proven biological logic gates could be made, the Imperial College scientists say the big advantage of their creations is that they behave like their electronic counterparts – replicating the way that electronic logic gates process information by either switching “on” or “off.” Importantly, the new biological logic gates are also modular, meaning they could be fitted together to make different types of logic gates and more complex biological processors.

To create a type of logic gate called an “AND gate,” the team used modified DNA to reprogram Escherichia Coli (E.Coli) bacteria to perform the same switching on and off process as its electronic equivalent when stimulated by chemicals. In a similar way to the way electronic components are made, the team demonstrated that the biological gates could be connected together to form more complex components.

The team also created a “NOT gate” and combined it with the AND gate to produce the more complex “NAND gate.” NAND gates are significant because any Boolean function (AND, OR, NOT, XOR, XNOR), which play a basic role in the design of computer chips, can be implemented by using a combination of NAND gates.

The researchers will now try and develop more complex circuitry that comprises multiple logic gates. To accomplish this they will need to find a way to link multiple biological logic gates together that is similar to the way in which electronic logic gates are linked together to enable complex processing to be carried out.

“We believe that the next stage of our research could lead to a totally new type of circuitry for processing information,” said Professor Martin Buck from the Department of Life Sciences at Imperial College London. “In the future, we may see complex biological circuitry processing information using chemicals, much in the same way that our body uses them to process and store information.”

The team also suggests that these biological logic gates could one day form the building blocks of microscopic biological devices, such as sensors that swim inside arteries, detecting the build up of harmful plaque and rapidly delivering medications to the affected area. Other sensors could detect and destroy cancer cells inside the body, while others could be deployed in the environment to monitor pollution and detect and neutralize dangerous toxins.

Sourced & published by Henry Sapiecha

Researchers attempting to clone

a mammoth by 2017

The last known mammoth lived around 4,500 years ago, but if scientists in Japan are successful then we might be able to meet one soon! Research to resurrect these awesome creatures was shelved when cell nuclei taken from a sample from Siberia were found to be too badly damaged, however a scientific breakthrough in Kobe successfully cloned a mouse from sixteen year old deep frozen tissue, and the research began again in earnest …

Mammoths are a species of the extinct genus Mammuthus, and closely related to modern elephants today. As anyone who’s been awed and amazed by a mammoth skeleton would know, some had long-curved tusks, and in colder regions, long shaggy hair. The last known mammoths died out 4,500 years ago, but in 1997 researchers at Kyoto University began to try and extract DNA from the tissue of a preserved mammoth carcass found in the Siberian permafrost.

Their efforts were thwarted however by damage caused by ice crystals that rendered the cells unviable. The breakthrough came in 2008 when scientist Dr. Teruhiko Wakayama from the RIKEN Center for Developmental Biology in Kobe, Japan, developed a new technique, and successfully managed to clone a mouse from tissue that had been deep frozen for sixteen years.

Now emeritus professor Akira Iritani and his team at Kyoto University are making preparations to fulfill their goal of cloning a live mammoth. They successfully extracted mammoth egg cell nuclei without damage, and used elephant egg cells to fill the gaps.

“Now the technical problems have been overcome, all we need is a good sample of soft tissue from a frozen mammoth,” he told The Daily Telegraph.

In the summer, Iritani will travel to Siberia to search for good mammoth samples. There are an estimated 150 million mammoth remains in Russia’s Siberian permafrost, some whole frozen specimens, others in pieces of bone, tusk, tissue and wool. If he is unsuccessful he will apply to Russian scientists to give him a sample.

If a mammoth embryo is successfully cloned then it will be transplanted into a surrogate African elephant, the mammoth’s closest living relative. Then will follow a gestation period of 22 months, the longest of any land animal.

“The success rate in the cloning of cattle was poor until recently but now stands at about 30 per cent, I think we have a reasonable chance of success and a healthy mammoth could be born in four or five years.” said Iritani.

There are other considerations however; “If a cloned embryo can be created, we need to discuss, before transplanting it into the womb, how to breed [the mammoth] and whether to display it to the public,” Iritani told the Yomiuri Shimbun newspaper. “After the mammoth is born, we’ll examine its ecology and genes to study why the species became extinct and other factors.”

Sourced & published by Henry Sapiecha

Faster DNA Analysis

at Room Temperature

Science (Aug. 12, 2010) — DNA microarrays are one of the most powerful tools in molecular biology today. The devices, which can be used to probe biological samples and detect particular genes or genetic sequences, are employed in everything from forensic analysis to disease detection to drug development.

Now Paul Li and colleagues at Simon Fraser University in Burnaby, Canada have combined DNA microarrays with microfluidic devices, which are used for the precise control of liquids at the nanoscale. In an upcoming issue of the journal Biomicrofluidics, which is published by the American Institute of Physics (AIP), Li and his colleagues describe how the first combined device can be used for probing and detecting DNA.

The key to Li’s result: gold nanoparticles. Suspended in liquid and mixed with DNA, the nanometer-scale spheres of gold act as mini magnets that adhere to each of the DNA’s twin strands. When the DNA is heated, the two strands separate, and the gold nanoparticles keep them apart, which allows the single strands to be probed with other pieces of DNA that are engineered to recognize particular sequences.

Li, whose work is funded by the Natural Sciences and Engineering Research Council of Canada, is applying for a patent for his technique. He sees a host of benefits from the combination of DNA microarrays and microfluidics.

“It’s faster and requires a relatively small sample,” he says, adding in his paper that “the whole procedure is accomplished at room temperature in an hour and apparatus for high temperature… is not required”

Sourced & published by Henry Sapiecha

Scientists Uncover

Transfer of Genetic Material

Between Blood-Sucking Insect

and Mammals

Science(Apr. 30, 2010) — Researchers at The University of Texas at Arlington have found the first solid evidence of horizontal DNA transfer, the movement of genetic material among non-mating species, between parasitic invertebrates and some of their vertebrate hosts.

The findings are published in the April 28 issue of the journal Nature, one of the world’s foremost scientific journals.

Genome biologist Cédric Feschotte and postdoctoral researchers Clément Gilbert and Sarah Schaack found evidence of horizontal transfer of transposon from a South American blood-sucking bug and a pond snail to their hosts. A transposon is a segment of DNA that can replicate itself and move around to different positions within the genome. Transposons can cause mutations, change the amount of DNA in the cell and dramatically influence the structure and function of the genomes where they reside.

“Since these bugs frequently feed on humans, it is conceivable that bugs and humans may have exchanged DNA through the mechanism we uncovered. Detecting recent transfers to humans would require examining people that have been exposed to the bugs for thousands of years, such as native South American populations,” Feschotte said.

Data on the insect and the snail provide strong evidence for the previously hypothesized role of host-parasite interactions in facilitating horizontal transfer of genetic material. Additionally, the large amount of DNA generated by the horizontally transferred transposons supports the idea that the exchange of genetic material between hosts and parasites influences their genomic evolution.

“It’s not a smoking gun, but it is as close to it as you can get,” Feschotte said

The infected blood-sucking triatomine, causes Chagas disease by passing trypanosomes (parasitic protozoa) to its host. Researchers found the bug shared transposon DNA with some hosts, namely the opossum and the squirrel monkey. The transposons found in the insect are 98 percent identical to those of its mammal hosts.

The researchers also identified members of what Feschotte calls space invader transposons in the genome of Lymnaea stagnalis, a pond snail that acts as an intermediate host for trematode worms, a parasite to a wide range of mammals.

The long-held theory is that mammals obtain genes vertically, or handed down from parents to offspring. Bacteria receive their genes vertically and also horizontally, passed from one unrelated individual to another or even between different species. Such lateral gene transfers are frequent in bacteria and essential for rapid adaptation to environmental and physiological challenges, such as exposure to antibiotics.

Until recently, it was not known horizontal transfer could propel the evolution of complex multicellular organisms like mammals. In 2008, Feschotte and his colleagues published the first unequivocal evidence of horizontal DNA transfer.

Millions of years ago, tranposons jumped sideways into several mammalian species. The transposon integrated itself into the chromosomes of germ cells, ensuring it would be passed onto future generations. Thus, parts of those mammals’ DNA did not descend from their common ancestors, but were acquired laterally from another species.

The actual means by which transposons can spread across widely diverse species has remained a mystery.

“When you are trying to understand something that occurred over thousands or millions of years ago, it is not possible to set up a laboratory experiment to replicate what happened in nature,” Feschotte said.

Instead, the researchers made their discovery using computer programs designed to compare the distribution of mobile genetic elements among the 102 animals for which entire genome sequences are currently available. Paul J. Brindley of George Washington University Medical Center in Washington, D.C., contributed tissues and DNA used to confirm experimentally the computational predictions of Feschotte’s team.

When the human genome was sequenced a decade ago, researchers found that nearly half of the human genome is derived from transposons, so this new knowledge has important ramifications for understanding the genetics of humans and other mammals.

Feschotte’s research is representative of the cutting edge research that is propelling UT Arlington on its mission of becoming a nationally recognized research institution.

Sourced and published by Henry Sapiecha 2nd May 2010