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

New packaging would indicate

when food is spoiled

By Ben Coxworth

13:09 January 13, 2011

Prof. Andrew Mills with food packaged in his smart plastic (Photo: University of Strathcly...

Prof. Andrew Mills with food packaged in his smart plastic (Photo: University of Strathclyde)

Given that German scientists have already developed packaging film that kills food-inhabiting bacteria, it only makes sense that Scottish scientists should be developing the next step in the process – food packaging that changes color when the food is going bad. The “intelligent plastic” film, which is being created at Glasgow’s University of Strathclyde, is intended to take the guesswork out of whether or not the food packaged within it is still safe to eat.

The new plastic is intended to be used in conjunction with modified atmosphere packaging, an existing process in which the shelf life of food is lengthened by replacing the air inside its packaging with a protective gas mixture – often, most or all of the oxygen is drawn out and replaced with nitrogen or carbon dioxide.

Such packaging typically includes inserted labels that indicate freshness. TheStrathclyde team see their plastic as being a less expensive alternative to those labels, as it could simply be integrated into the production of the packaging, instead of having to be made and inserted separately.

While the researchers are keeping zip-locked about just how their plastic would know when food was going off, they have stated that it would react not only to food that has been left too long, but also to food that has become tainted due to damaged packaging or lack of refrigeration.

“We hope that this will reduce the risk of people eating food which is no longer fit for consumption and help prevent unnecessary waste of food,” said project leader Prof. Andrew Mills. “We also hope it will have a direct and positive impact on the meat and seafood industries.”

Sourced & published by Henry Sapiecha

‘Killer paper’ could prolong shelf life of foods

By Ben Coxworth

16:04 January 19, 2011


Silver is a known killer of harmful bacteria, and has already been incorporated into things such as antibacterial keyboardswashing machineswater filters, and plastic coatings for medical devices. Now, scientists have added another potential product to the list: silver nanoparticle-impregnated “killer paper” packaging, that could help keep food from spoiling.

Led by Aharon Gedanken from Israel’s Bar-Ilan University, the team discovered that paper could be covered with silver nanoparticles through the application of ultrasonic radiation – a process known as ultrasonication. It involves the formation and subsequent collapse of acoustic bubbles near a solid surface, which creates microjets that throw the desired nanoparticles onto that surface. To the team’s knowledge, this was only the second time that ultrasonication had ever been attempted on paper.

Unlike previous attempts at creating antibacterial paper, this one-step method was reportedly quite effective, and produced a smooth, homogenous, long-lasting coating. By varying the nanoparticle concentration and the application time, the thickness of the coating could be varied as needed. When exposed to E. coli and S. aureus bacteria, both of which cause food poisoning, the paper killed them all off within three hours.

The scientists stated that the ultrasonication process could also be used to apply other nanomaterials to paper, which could be used to tweak its hydrophobicity, conductivity, or texture.

While the addition of ionic silver to foods has been used in the past to ward off bacteria, the paper would reportedly serve as a longer-term solution, as it would act as a slow-release reservoir for the silver. Germany’s Fraunhofer Institute for Process Engineering and Packaging has previously looked into the use of sorbic acid-coated plastic as an antibacterial food wrap.

The killer paper research was recently published in the journal Langmuir.

Sourced & published by Henry Sapiecha

NASA announces discovery

of radical new life form – on Earth

By Ben Coxworth

12:27 December 2, 2010


In a press conference held today, scientists working with NASA announced the discovery of a new microorganism right here on Earth that employs a survival strategy never seen before in any other life form. Found in Northern California’s highly-saline Mono Lake, the GFAJ-1 bacteria exists in an environment that has very little phosphorous, an element that had previously been considered essential for all living things in order to build DNA. To cope with this problem, the bacteria is able to substitute highly-toxic arsenic for phosphorous, in its cell components. The fact that a microbe is able to survive in such a fashion opens up the possibilities for where life could exist on other planets, and will require a rethink on NASA’s part regarding its search for extraterrestrial life forms.

Until this announcement, it had been assumed that carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur were required for any terrestrial organism to grow. Phosphorous is considered to be an essential part of the backbone of DNA and RNA. Arsenic, on the other hand, is highly poisonous to most life forms – it is, however, chemically-similar to phosphorous.

Felisa Wolfe-Simon, a NASA Astrobiology Research Fellow in residence at the U.S. Geological Survey, led a team that first discovered GFAJ-1 in the salty, alkaline mud of Mono Lake. Mud from the lake was taken back to her lab, and placed in a medium that (like the lake) had very little phosphorous, but lots of arsenic. The bacteria was observed growing in the mud, despite everything. When analyzed, the GFAJ-1 were found to be using the arsenic as phosphorous.

“What I’ve presented to you today is a microbe, doing something different than life as we knew it,” said Wolfe-Simon. “We’ve cracked open the door to what’s possible for life elsewhere in the universe, and that’s profound.”

“I find this result delightful, because it makes me have to expand my notion of what environmental constituents might enable habitability,” added Pamela Conrad, of NASA’s Jet Propulsion Laboratory. “We still don’t know everything there is to know about what might make a habitable environment on another planet.”

The research was published today in the journal Science.

All images courtesy NASA.

Sourced & published by Henry Sapiecha


Bacteria Can Have a ‘Sense of Smell’

Science (Aug. 17, 2010) — Bacteria are well-known to be the cause of some of the most repugnant smells on earth, but now scientists have revealed this lowest of life forms actually has a sense of smell of its own.


A team of marine microbiologists at Newcastle University have discovered for the first time that bacteria have a molecular “nose” that is able to detect airborne, smell-producing chemicals such as ammonia.

Published in Biotechnology Journal, their study shows how bacteria are capable of ‘olfaction’ — sensing volatile chemicals in the air such as ammonia produced by rival bacteria present in the environment.

Led by Dr Reindert Nijland, the research also shows that bacteria respond to this smell by producing a biofilm — or ‘slime’ — the individual bacteria joining together to colonise an area in a bid to push out any potential competitor.

Biofilm is a major cause of infection on medical implants such as heart valves, artificial hips and even breast implants. Also known as ‘biofouling’ it costs the marine industry millions every year, slowing ships down and wasting precious fuel. But it also has its advantages. Certain biofilms thrive on petroleum oil and can be used to clean up an oil spill.

Dr Nijland, who carried out the work at Newcastle University’s Dove Marine Laboratory, said the findings would help to further our understanding of how biofilms are formed and how we might be able to manipulate them to our advantage.

“This is the first evidence of a bacterial ‘nose’ capable of detecting potential competitors,” he said.

“Slime is important in medical and industrial settings and the fact that the cells formed slime on exposure to ammonia has important implications for understanding how biofilms are formed and how we might be able to use this to our advantage.

“The next step will be to identify the nose or sensor that actually does the smelling.”

This latest discovery shows that bacteria are capable of at least four of the five senses; a responsiveness to light — sight — contact-dependent gene expression — touch — and a response to chemicals and toxins in their environment either through direct contact — taste — or through the air — smell.

Ammonia is one of the simplest sources of nitrogen — a key nutrient for bacterial growth. Using rival bacteria Bacillus subtilis and B.licheniformus, both commonly found in the soil, the team found that each produced a biofilm in response to airborne ammonia and that the response decreased as the distance between the two bacterial colonies increased.

Project supervisor Professor Grant Burgess, director of the Dove Marine Laboratory, said that understanding the triggers that prompt this sort of response had huge potential.

“The sense of smell has been observed in many creatures, even yeasts and slime moulds, but our work shows for the first time that a sense of smell even exists in lowly bacteria.

“From an evolutionary perspective, we believe this may be the first example of how living creatures first learned to smell other living creatures.

“It is an early observation and much work is still to be done but, nevertheless, this is an important breakthrough which also shows how complex bacteria are and how they use a growing number of ways to communicate with each other.

“Bacterial infections kill millions of people every year and discovering how your bacterial enemies communicate with each other is an important step in winning this war. This research provides clues to so far unknown ways of bacterial communication.”

Sourced & published by Henry Sapiecha

Plastic Antibody Works in First Tests

in Living Animals

Science (June 11, 2010) — Scientists are reporting the first evidence that a plastic antibody — an artificial version of the proteins produced by the body’s immune system to recognize and fight infections and foreign substances — works in the bloodstream of a living animal.


The discovery, they suggest in a report in the Journal of the American Chemical Society, is an advance toward medical use of simple plastic particles custom tailored to fight an array of troublesome “antigens.”

Those antigens include everything from disease-causing viruses and bacteria to the troublesome proteins that cause allergic reactions to plant pollen, house dust, certain foods, poison ivy, bee stings and other substances.

In the report, Kenneth Shea, Yu Hosino, and colleagues refer to previous research in which they developed a method for making plastic nanoparticles, barely 1/50,000th the width of a human hair, that mimic natural antibodies in their ability to latch onto an antigen. That antigen was melittin, the main toxin in bee venom. They make the antibody with molecular imprinting, a process similar to leaving a footprint in wet concrete. The scientists mixed melittin with small molecules called monomers, and then started a chemical reaction that links those building blocks into long chains, and makes them solidify. When the plastic dots hardened, the researchers leached the poison out. That left the nanoparticles with tiny toxin-shaped craters.

Their new research, together with Naoto Oku’s group of the University Shizuoka Japan, established that the plastic melittin antibodies worked like natural antibodies. The scientists gave lab mice lethal injections of melittin, which breaks open and kills cells. Animals that then immediately received an injection of the melittin-targeting plastic antibody showed a significantly higher survival rate than those that did not receive the nanoparticles. Such nanoparticles could be fabricated for a variety of targets, Shea says. “This opens the door to serious consideration for these nanoparticles in all applications where antibodies are used,” he adds.

Sourced and published by Henry Sapiecha 12th June 2010

Microbes galore in seas; “spaghetti” mats Pacific

HUGE MATS OF TOXIC BACTERIA ON SEA BEDS


By Alister Doyle, Environment CorrespondentPosted 2010/04/18 at 1:09 pm EDT

OSLO, Apr. 18, 2010 (Reuters) — The ocean depths are home to myriad species of microbes, mostly hard to see but including spaghetti-like bacteria that form whitish mats the size of Greece on the floor of the Pacific, scientists said on Sunday.


The survey, part of a 10-year Census of Marine Life, turned up hosts of unknown microbes, tiny zooplankton, crustaceans, worms, burrowers and larvae, some of them looking like extras in a science fiction movie and underpinning all life in the seas.

“In no other realm of ocean life has the magnitude of Census discovery been as extensive as in the world of microbes,” said Mitch Sogin of the Marine Biological Laboratory in Woods Hole, Massachusetts, head of the marine microbe census.

The census estimated there were a mind-boggling “nonillion” — or 1,000,000,000,000,000,000,000,000,000,000 (30 zeroes) — individual microbial cells in the oceans, weighing as much as 240 billion African elephants, the biggest land animal.

Getting a better idea of microbes, the “hidden majority” making up 50 to 90 percent of biomass in the seas, will give a benchmark for understanding future shifts in the oceans, perhaps linked to climate change or pollution.

Among the biggest masses of life on the planet are carpets on the seabed formed by giant multi-cellular bacteria that look like thin strands of spaghetti. They feed on hydrogen sulphide in oxygen-starved waters in a band off Peru and Chile.

“Fishermen sometimes can’t lift nets from the bottom because they have more bacteria than shrimp,” Victor Gallardo, vice chair of the Census Scientific Steering Committee, told Reuters. “We’ve measured them up to a kilo (2.2 lbs) per square meter.”

GHOSTLY MATS

The census said they carpeted an area the size of Greece — about 130,000 sq km (50,000 sq miles) or the size of the U.S. state of Alabama. Toxic to humans, the bacteria are food for shrimp or worms and so underpin rich Pacific fish stocks.

The bacteria had also been found in oxygen-poor waters off Panama, Ecuador, Namibia and Mexico as well as in “dead zones” under some salmon farms. They were similar to ecosystems on earth that thrived from 2.5 billion to 650 million years ago.

Overall in the oceans, up to a billion microbe species may await identification under the Census, an international 10-year project due for completion in October 2010.

Tiny life was found everywhere, including at thermal vents with temperatures at 150 Celsius (300F) or in rocks 1,626 meters (5,335 ft) below the sea floor. Many creatures lack names or are hard to pronounce like loriciferans, polychaetes or copepods.

One major finding was that rare microbes are often found in samples where they can be outnumbered 10,000 to one by more common species. Isolated microbes may be lying in wait for a change in conditions that could bring a population boom.

Ann Bucklin, head of the Census of Marine Zooplankton that include tiny transparent crustaceans or jellyfish, said the seas were barely studied even by the census.

“Seventy percent of the oceans are deeper than 1,000 meters,” Bucklin, of the University of Connecticut, told Reuters. “The deep layer is the source of the hidden diversity.”

Paul Snelgrove, of Memorial University in Canada, said one sample in the South Atlantic in an area the size of a small bathroom — 5.4 square meters — turned up 700 species of copepod, a type of crustacean, 99 percent of them unfamiliar.

Just finding Latin names for each find will be hard. Scientists had rejected the idea of raising funds by letting people pay to have a marine “bug” named after them.

Sourced and published by Henry Sapiecha 21st April 2010