RAMBALDIS

fuckyeahmolecularbiology:

Ancient Viral DNA in the Human Genome

Traces of ancient viruses, which infected our ancestors millions of years ago, are more widespread throughout our modern-day genomes than was previously thought.

The new research sheds light on the origins of a large proportion of our genetic material, much of which is still not understood. Only about 1.5% of human genes code for a useful protein product, that we’ve discovered; half of the rest is labeled “junk DNA” - although new research indicates it has a variety of purposes - while the other half was introduced by viruses or parasites, like the ancient ones studied here.

The senior author on the study (published in the Proceedings of National Academy of Sciences), Dr. Robert Belshaw from Oxford University’s Zoology Department, said: “This is the story of an epidemic within every animal’s genome, a story which has been going on for 100 million years and which continues today.

“Much of the dark matter in our genome plays by its own rules, in the same way as an epidemic of an infectious disease but operating over millions of years.

Learning the rules of this ancient game will help us understand their role in health and disease.”

Not only do these viruses exist within our genomes, but some of are even helpful, Dr. Belshaw insists. Protein syncytin, for example - derived from a virus - helps develop the human placenta.

The study believes that unlocking the secrets of these viruses is essential to understanding the full complexity of the human genome.

Image: SEM image of Influenza A virus.

fuckyeahmolecularbiology:

Super Synthetic: Why Your Cells Might Be Smarter Than Your Calculator

Synthetic biologists have programmed a mammalian cell to calculate basic logical operations thanks to a highly complex artificial gene network.

A team of researchers from ETH Zurich headed by Martin Fussenegger, a professor of biotechnology and bioengineering at ETH Zurich’s Department of Biosystems in Basel, has constructed a gene network that can perform logical operations and, as a result, initiate specific metabolic steps. “We have developed the first real cellular calculator,” says Fussenegger.

Using biological components, the researchers developed a set of different elements that can be interconnected in different combinations and subsequently perform logical operations. These circuit elements, which are known as “logic gates” in the jargon, use the apple molecule phloretin and the antibiotic erythromycin as input signals. The calculations performed are based on Boolean logic.

“By combining several logic gates, we have achieved an unprecedented level of complexity in the synthetic gene network in cells,” stresses Professor Fussenegger. Even more remarkably, the bio-computer can process two different input and output signals in parallel. This sets the bio-computer apart from digital electronics, as this only works with electrons.

“Of course, our cell calculator is nowhere near as efficient as a PC,” says the ETH-Zurich professor. “By nature, however, a cell can process many different metabolic products in parallel.”

By combining and interconnecting several logic gates, the biotechnologists ultimately obtained a “half-adder” and “half-subtractor”: Both central circuit elements in computer technology. A half-adder is a basic digital circuit that adds up two binary numbers; the half-subtractor, on the other hand, deducts them. These two elements are found in every digital calculator, where they perform most calculations. In cell-structure experiments, the two bio-computer components produced solid results.

Scientists hope that these “cell calculators” can be widely used for a variety of applications, including monitoring and regulating a patient’s metabolism to help with diseases like diabetes. While still a far cry from medical applications, Professor  Fussenegger is optimistic. “It’s [just] wonderful that a mammalian cell can calculate like that!” he beams.

For more about synthetic cells, read here and here.

ikenbot:

What Is Sand Made Of?

Image: Magnified sand under 250x microscope

Simply put, sand is made of tiny particles of worn-down rock. These particles are picked up by wind, water or the ice in glaciers and left as sediment in the ocean or as sand dunes on land.

The composition of sand varies and depends on the local rocks, but the most common material is silica — more often known as quartz. Coral, lava rock and gypsum are other materials often found in sand. The size and texture of sand particles varies and can offer insight into where it came from. A very small grain of sand, for example, is easier for the wind to blow around and may have traveled a long distance. The roundness of the sand may provide a clue as to how it was formed. Bodies of water with strong bottom currents produced different particles of sand than the particles produced by sand that is transported by rivers or streams, which tend to be very round. The International Sand Collectors Society offers a chart with size classes (in millimeters) for sand and mud [source: Sand Collectors]

Sand dunes form when a lot of loose sand is in an area that also has little vegetation to stand in the way. With enough wind and some sort of obstacle to serve as a sort of blocking or gathering point for the blowing sand, the particles gather and form a dune. Sand dunes reproduce when two crescent-shaped dunes collide, thanks to a little encouragement from their matchmaker friend the wind. When a small dune runs into a larger one — a very slow process that can take as long as a year — the smaller one can pass through it. If the sand dune is unstable, the horns at each end of the crescent shape will break off and become two even smaller dunes. Researchers refer to this process as “breeding.”

The tallest sand dunes in North America are at the base of the Sangre de Cristo Mountains in Colorado. Visitors to the Great Sand Dunes National Park can see how the massive dunes formed from sediments deposited in a deep valley. Scientists have discovered that a huge lake probably once covered the valley and receded from climate change. The large sheet of sand blew with the southwest wind accumulated into a natural pocket formed by a combination of three mountain passes. Opposing wind directions helped create the vertical shape of the dunes [source: National Park Service].

ucsdhealthsciences:

How Infectious Disease May Have Shaped Human Origins
Inactivation of two genes may have allowed escape from bacterial pathogens, researchers say

Roughly 100,000 years ago, human evolution reached a mysterious bottleneck: Our ancestors had been reduced to perhaps five to ten thousand individuals living in Africa. In time, “behaviorally modern” humans would emerge from this population, expanding dramatically in both number and range, and replacing all other co-existing evolutionary cousins, such as the Neanderthals.

The cause of the bottleneck remains unsolved, with proposed answers ranging from gene mutations to cultural developments like language to climate-altering events, among them a massive volcanic eruption.

Add another possible factor: infectious disease.

In a paper published in the June 4, 2012 online Early Edition of The Proceedings of the National Academy of Sciences, an international team of researchers, led by scientists at the University of California, San Diego School of Medicine, suggest that inactivation of two specific genes related to the immune system may have conferred selected ancestors of modern humans with improved protection from some pathogenic bacterial strains, such as Escherichia coli K1 and Group B Streptococci, the leading causes of sepsis and meningitis in human fetuses, newborns and infants.  

“In a small, restricted population, a single mutation can have a big effect, a rare allele can get to high frequency,” said senior author Ajit Varki, MD, professor of medicine and cellular and molecular medicine and co-director of the Center for Academic Research and Training in Anthropogeny at UC San Diego. “We’ve found two genes that are non-functional in humans, but not in related primates, which could have been targets for bacterial pathogens particularly lethal to newborns and infants. Killing the very young can have a major impact upon reproductive fitness. Species survival can then depend upon either resisting the pathogen or on eliminating the target proteins it uses to gain the upper hand.” More here

In the above photo, Escherichia coli bacteria, like these in a false-color scanning electron micrograph by Thomas Deerinck at UC San Diego’s National Center for Microscopy and Imaging Research, cause a variety of often life-threatening conditions, particularly among the young. Varki and colleagues suggest a genetic change 100,000 or so years ago conferred improved protection from these microbes, and likely altered human evolutionary development.