Mini DNA replicator could benefit world's poor

A pocket-sized device that runs on two AA batteries and copies DNA as accurately as expensive lab equipment has been developed by researchers in the US.



The device has no moving parts and costs just $10 to make. It runs polymerase chain reactions (PCRs), to generate billions of identical copies of a DNA strand, in as little as 20 minutes. This is much faster than the machines currently in use, which take several hours.

"I hope this will make PCR more available," says Victor Ugaz of Texas A&M University in Texas, US, whose group made the new device. He says the system could enable DNA-based tests to be carried out in the field or in developing countries, where large, expensive laboratory equipment is neither practical nor affordable.

Running a PCR requires treating DNA strands, along with chemical materials needed to make new DNA strands, at three different temperatures. The highest temperature (95°C) causes two strands of a DNA molecule to separate. The lowest temperature (60°C) makes DNA building blocks stick together. Then, holding the temperature in the middle (72°C), allows an enzyme to quickly assemble replica DNA strands.

Facsimile machine

To cycle through these temperatures, a conventional PCR machine heats and cools a large metal block holding multiple tubes containing samples of DNA and the material needed to make copies.

In the new device, created by graduate student Nitin Agrawal, a centimetre-wide loop of tubing wraps in a vertical ring around a set of three metal rods. The rods, together the size of an AA battery, are kept at three different temperatures. With this set-up, the parts of the tube closest to each block are heated differently.

This keeps the liquid flowing through the millimetre-wide tube, and so the DNA and building blocks cycle automatically through the three temperatures needed for PCR. "It's similar to how a lava lamp works," says Ugaz.

As the fluid is heated, it becomes less dense and more buoyant, so it flows upward. When the fluid cools in another part of the loop, it becomes denser and moves down. And because the device only heats the three small blocks of metal, it also runs off just two AA batteries.

Incomplete solution

"This is a significant advance in the proof of the concept," says biomedical engineer Samuel Sia of Columbia University in New York, US. "It shows you can use convection-driven flow to do PCR in a miniaturized format."

The device shows promise for a variety of tests, Sia says, including monitoring levels of HIV virus in a person's body or diagnosing tuberculosis. "There's nothing like this in developing countries," he explains. "There's a great need everywhere in the world for doing DNA- and RNA-based tests."

For the full potential of the device to be realised, however, Sia says that cheap and simple methods of preparing samples, by isolating DNA from cells, will be needed along with miniaturised DNA analysis equipment.

Journal reference: Angewandte Chemie International Edition (DOI: 10.1002/anie.200700306)

Scientists beat internet speed record

Japanese researchers have sent data over the internet at a speed of 9.08GB/s - which would allow a user to download a film in 4 seconds

Jonathan Richards

The prospect of downloading a feature film in seconds came a step closer today after Japanese scientists announced they had achieved a new speed record for transferring data over the internet.

The record - which involved sending a stream of data over a 30,000km network, the equivalent of three quarters of the earth’s circumference - achieved a speed of 9.08 GB/s, about 1,000 times faster than current top of the range broadband connections.

At that speed, a full-length feature film of 1.5 GB would be downloaded in matter of seconds. Most household broadband connections would take more than 40 minutes to download a film.

The benefits were not likely to be felt by regular internet users any time soon, however, because the record was set using a custom-built fibre optic network, which enables speeds far greater than the copper cables through which most homes connect to the internet.

It also used a ‘next generation’ internet protocol called IPv6, which has several benefits over the current protocol, IPv4, but is yet to be widely rolled out.

The researchers led by a team at the University of Tokyo set the record in December last year over a network which stretched from Tokyo to Chicago, on to Amsterdam, and then back to Tokyo via Seattle, a distance of 32, 372km.

For a period 20 minutes on a night they knew net traffic would be at a low - New Year's Eve - they streamed data at a speed of 9.08 GB/s, surpassing the previous record of 8.8 GB/s, which was set in February last year.

Dr Kei Hiraki, professor of computing science at the University of Tokyo who led the research, said: "These records are final for the 10GB/s network era because they represent more than 98% of the upper limit of network capacity.”

The increased speed had resulted from "several technical improvements," Dr Hiraki said, including more precise "pacing" of data and better "buffering capability," which resulted in less "packet loss."

The 'path' used for the record was custom-built fibre optic network used by universities and government agencies for research purposes.

A spokeswoman for internet2, a US-based consortium which helped develop the network, said that it was currently in the process of being upgraded to allow speeds of 100GB, which would allow films to be downloaded in fractions of a second.

"In order to deliver those kinds of speeds to consumers, however, you're talking about a significant investment in the existing infrastructure, and that's something that has to come from the network providers," the spokeswoman said.

Dr Hiraki said that he expected to achieve speeds of 40GB within 2 years, and 100GB in 6 years.

Asked whether he was already working on the next record attempt, he said: "Of course. But the method is still confidential."

Blogger Bar :: Firefox Add-ons

Blogger Bar :: Firefox Add-ons

Hey guys don't use this one use the Google Bar instead.

Find it under Add Ons on the Mozilla.org website.

Craig

Fact or Fiction?: Living People Outnumber the Dead

Fact or Fiction?: Living People Outnumber the Dead

Booming population growth among the living, according to one rumor, outpaces the dead

By Ciara Curtin

LIVING VERSUS DEAD: The Earth may seem crowded with 6.5 billion people but it would take 100 billion living to come close to outnumbering all who have ever lived. The human population has swelled so much that people alive today outnumber all those who have ever lived, says a factoid whose roots stretch back to the 1970s. Some versions of this widely circulating rumor claim that 75 percent of all people ever born are currently alive. Yet, despite a quadrupling of the population in the past century, the number of people alive today is still dwarfed by the number of people who have ever lived. In 2002 Carl Haub, a demographer at the Population Reference Bureau, a nongovernmental organization in Washington, D.C., updated his earlier estimate of the number of people that have ever existed. To calculate this, he studied the available population data to determine the human population growth rates during different historical periods, and used them to determine the number of people who have ever been born.

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For most of history, the population grew slowly, if at all. According to the United Nations' Determinants and Consequences of Population Trends, the first Homo sapiens appeared around 50,000 years ago, though this figure is debatable. Little is known about this distant past and how many of us there might have been, but by the time of the agricultural revolution in the Middle East in 9000 B.C., Earth held an estimated five million people. Between the rise of farming and the height of Roman rule,population growth was sluggish; at less than a tenth of a percent per year, it crawled to about 300 million by A.D. 1. Then the total fell as plagues wiped out large swathes of people. (The "black death" in the 14th century wiped out at least 75 million.) As a result, by 1650 the world population had only increased to about 500 million. By 1800, though, thanks to improved agriculture and sanitation, it doubled to more than one billion. And, in 2002 when Haub last made these calculations, the planet's population had exploded, reaching 6.2 billion.

To calculate how many people have ever lived, Haub followed a minimalist approach, beginning with two people in 50000 B.C.—his Adam and Eve. Then, using his historical growth rates and population benchmarks, he estimated that slightly over 106 billion people had ever been born. Of those, people alive today comprise only 6 percent, nowhere near 75 percent. "[It is] almost surely true people alive today are some small fraction of [all] people," says Joel Cohen, a professor of populations at the Rockefeller and Columbia Universities in New York City. For this myth ever to be valid there would have to be more than 100 billion people living on Earth. "How cozy," Cohen says. "It just doesn't seem plausible," he adds. Today there are more than 6.5 billion people walking on Earth, according to United Nations estimates. Recently, the population has been increasing by about 1.2 percent each year, down from the late 1960s peak of a 2.1 percent yearly growth rate. Some industrialized countries, especially France and Japan, have very low birth rates and their populations are actually dwindling, Haub notes. In developing nations populations continue to grow, but some countries, such as India, are experiencing a slowdown in their growth rate. Cohen doubts that a doubling of today's population, to 13 billion, will occur, never mind approaching anywhere near 100 billion. Not even the U.N.'s highest projection predicts that much growth, he says. For 2050, the world body's estimates range from 7.3 billion to 10.7 billion people. The median, and most likely, projection of 8.9 billion relies on a gradual slowing of the growth rate. And the U.N. predicts the world population will stabilize at 10 billion inhabitants sometime after 2200. At this rate, the living will never outnumber the dead

Cancer cure patented

Cancer cure patented
Submitted by Vidura Panditaratne on Thu,:16. SciTech | United States | Non-geographical | News

Breast Cancer cellBreast Cancer cell

A group of researchers claim that they are patenting a possible cure for cancer involving nothing more than sugar and short-chain fatty acid combination. [ Chemistry & Biology]

The Johns Hopkins researchers cautioned that their double-punch molecule, described in the December issue of the journal Chemistry & Biology, has not yet been tested on animals or humans.

Nevertheless, they believe it represents a promising new strategy for fighting the deadly disease, and have already filed an application for a U.S. patent covering this class of compounds.

"For a long time, cancer researchers did not pay much attention to the use of sugars in fighting cancer," Department of Biomedical Engineering postdoctoral fellow said. "But we found that when the right sugar is matched with the right chemical partner, it can deliver a powerful double-whammy against cancer cells."

Sampathkumar and his colleagues built upon 20-year-old findings that a short-chain fatty acid called butyrate can slow the spread of cancer cells. In the 1980s, researchers discovered that butyrate, which is formed naturally at high levels in the digestive system by symbiotic bacteria that feed on fibre, can restore healthy cell functioning.

Efforts to use butyrate as a general drug for tumours elsewhere in the body have been hindered by the high doses of the compound needed to effectively eradicate cancer leading scientists to try and make butyrate more potent by modifying it or joining it to other compounds.

The results have been disappointing because the molecular partner added to butyrate to improve delivery to the cancer cells often produced unsafe side effects.

In some of the less successful experiments, designed to avoid toxic side effects, researchers used innocuous sugar molecules such as glucose to carry butyrate into the cells.

"We didn't think they chose the right partner molecule," said Kevin J. Yarema, an assistant professor of biomedical engineering who supervised the project. "Our insight was to select the sugar partner to serve not just as a passive carrier but as additional ammunition in the fight against cancer."

The researchers focused on a sugar called N-acetyl-D-mannosamine, or ManNAc, for short, and created a hybrid molecule by linking ManNAc with butyrate.

The hybrid easily penetrates a cell's surface, then is split apart by enzymes inside the cell.

Once inside the cell, ManNAc is processed into another sugar known as sialic acid that plays key roles in cancer biology, while butyrate orchestrates the expression of genes responsible for halting the uncontrolled growth of cancer cells.

Although the study of the exact molecular mechanism is in its early stages, the researchers believe the separate chemical components work together to bolster the cancer-fighting power of butyrate.

The double attack triggers cellular suicide, also called apoptosis, in the cancer cells.

To find out whether this butyrate-ManNAc hybrid alone would produce the positive results, the researchers tested three other sugar-butyrate combinations and a butyrate salt compound with no sugar attached.

The four other formulas and the butyrate-ManNAc hybrid were each added to lab dishes containing cancer cells.

After three to five days, cancer growth had slowed in all of the dishes.

After 15 days, cancer growth had resumed in dishes treated with four of the compounds, but in samples treated with the butyrate-ManNAc hybrid, all of the cancer cells had died.

The researchers also wanted to find out whether administering the two parts of the hybrid independently would achieve the same result, but in these experiments, the cancer cells did not self-destruct.

The researchers suspect this is because the hybrid molecules more easily penetrate the surface of the cell than the individual chemicals.

Once the components are inside, the researchers believe the partners help enzymes to resume the normal assembly of sugar molecules and correct aberrant gene expression patterns, two processes that go awry when cancer occurs.