Wednesday, August 29, 2007

The Orchid may have been around 84 million years

Finding: The Orchid survived the great extinction 65 million years ago, and flourished to over 25,000 species.
Which came first the mammal or the flower? Well it looks like flowermay have ruled after the dinosaurs died out. So say researchers who have discovered the first fossil orchid, a 15 to 20-million-year-old pollen specimen encased in amber, in the Dominican Republic.

The Orchidaceae family boasts the largest of all flowering plants, but it is poorly understood, because until now there has been no fossil record of its history. Previous speculations put the plants' first appearance at about 45 million years ago.

Harvard University researchers and colleagues compared genetic information from the fossilised Meliorchis caribea with modern-day plants and reconstructed an evolutionary tree. It suggests that the first orchids bloomed about 84 million years ago.

Those that survived the mass extinction 65 million years ago then rapidly proliferated, leading to today's 25,000 or so species.

The Orchid family

Orchidaceae or the Orchid family is the largest and most diverse of the flowering plant (Angiospermae) families, with over 800 described genera and 25,000 species.

Orchids, like the grasses and the palms, which they resemble in some ways—for instance the form of their leaves—are monocotyledons. They have one cotyledon, or embryonic leaf, in contrast to the two of most flowering plants.

Orchids are world wide in distribution, occurring in every habitat, except Antarctica and deserts. The great majority are to be found in the tropics, mostly Asia, South America and Central America. They are found above the Arctic Circle, in southern Patagonia and even on Macquarie Island, close to Antarctica.

Tuesday, August 28, 2007

I'm here & I'm not going away: World's Oldest Bacteria Found Living In Permafrost

Finding: A research team has for the first time ever discovered DNA from living bacteria that are more than half a million years old. Never before has traces of still living organisms that old been found.

What significance does this have?

The exceptional discovery can lead to a better understanding of the aging of cells and might even cast light on the question of life on Mars. All cells decompose with time. But some cells are better than others to postpone the decomposing and thus delay aging and eventually death. And there are even organisms that are capable of regenerate and thereby repair damaged cells. The DNA of these cells are very interesting to the understanding of the process of how cells break down and age.

How the discovery was made

The research team, which consists of experts in, among other things, DNA traces in sediments and organisms, have found ancient bacteria that still contains active and living DNA. So far, it is the oldest finding of organisms containing active DNA and thus life on this earth. The discovery was made after excavations of layers of permafrost in the north-western Canada, the north-eastern Siberia and Antarctica.

Near Death
The project is about examining how bacteria can live after having been frozen down for millions of years. Other researchers has tried to uncover the life of the past and the following evolutionary development by focusing on cells that are in a state of dead-like lethargy.

Still active
We, on the other hand, have found a method that makes is possible to extract and isolate DNA traces from cells that are still active. It gives a more precise picture of the past life and the evolution towards the present because we are dealing with cells that still have a metabolistic function -- unlike "dead" cells where that function has ceased.

After the fieldwork and the isolation of the DNA, the researchers compared the DNA to DNA from a worldwide gene-bank in the US to identify the ancient material. Much in the same way the police compares fingerprints from a crime, the researchers were able to place the DNA more precisely and to place it in a context.

Impact on Darwinian evolution
There is a very long way, of course, from our basic research towards understanding why some cells can become that old. But it is interesting in this context to look at how cells break down and are restored and thus are kept over a very long period. The researchers' methods and results can be used to determine if there was ever life on Mars the way we perceive life on earth.
And then there is the grand perspective in relation to Darwin's evolution theory. It predicts that life never returns to the same genetic level. "But our findings allows us to post the question: are we dealing with a circular evolution where development, so to speak, bites its own tail if and when ancient DNA are mixed with new?

Come Together: Social Habits Of Cells May Hold Key To Fighting Diseases

Finding: Research into Systems Biology have discovered that networking in living cells may determine whether a cell cause diseases.

Scientists in Manchester are working to change the social habits of living cells -- an innovation that could bring about cleaner and greener fuel and help fight diseases such as cancer and diabetes.

As part of a new £18 million project spanning six countries, The Manchester Centre for Integrative Systems Biology at The University of Manchester will spearhead important new research into an emerging field of science and engineering known as Systems Biology*.
Scientists have recently discovered that networking in living cells may determine whether a cell causes diabetes or cancer or helps to maintain our health.

By adjusting and modifying the way cells network, researchers believe it's possible to adjust the behaviour of living cells and reduce the chances of disease occurring.

Using this approach Manchester researchers working on the Systems Biology of Microorganisms (SysMO) research programme will also drive a project that looks at how the yeast used in the production of beer and bread can be turned into an efficient producer of bioethanol.
Other work to be carried out in Manchester includes the investigation of 'lactobacilli'. Some of these occasionally turn into flesh-eating bacteria or cause human diseases such as strep throat and rashes, whereas others are completely safe and are used in the production of cheeses and yoghurts.

It's hoped the work will lead not only to greater understanding of how 'wrong' networks lead to disease, but also to the production of drugs and other foods more efficiently and safely.
Academics will also look at 'pseudomonads' -- soil bacteria that may make people ill but can also be used to degrade nasty compounds in the environment, or to create compounds now being made by chemical industries.

Thermophilic Organisms
Researchers will also focus on 'thermophilic' organisms that live naturally in hot springs, and examine how their networks enable them to survive high and varying temperatures. It's hoped that this research will reveal how to make any living organism cope better with extreme conditions. It may also lead to better performance of detergents and cosmetics.

This is a unique opportunity to begin to understand how networking contributes to the functioning of living cells inside and outside our bodies. It enables us to integrate the best groups from six European countries and will address four concrete issues of energy, the disease-benefit balance, white biotechnology and robustness.

What is Systems Biology?
Systems Biology combines molecular biology and mathematics, which have traditionally been seen as the equivalents of fire and water. This type of research is still viewed as controversial by some in the scientific community.

But researchers involved in SysMO believe this approach will allow them to obtain a very large set of mathematical equations that describe living cells. This may then allow those cells to be engineered in a number of ways, with numerous benefits in the field of medicine and in the commercial world.

A new Approach to bioscience
Systems biology is a new approach to bioscience that combines theory, computer modelling and experiments. It is revolutionising how bioscientists think and work and will make the outputs on their work more useful, and easier to use in industry and policymaking. Instead of using the traditional biology approach of observation and experiment, systems biology uses computer simulations and modelling to process results, design new, more quantitative experiments and generate predictive solutions

Monday, August 27, 2007

Ancient bacteria could point to life on Mars

Finding: Harsh conditions ok for the survival of Bacteria
Ancient bacteria are able to survive nearly half a million years in harsh, frozen conditions, researchers said on Monday in a study that adds to arguments that permafrost environments on Mars could harbor life. The findings also represent the oldest independently authenticated DNA to date obtained from living cells and could offer clues to better understand ageing.

How long can it live?
"When it can live half a million years on Earth it makes it very promising it could survive on Mars for a very long time," Willerslev said. "Permafrost would be an excellent place to look for life on Mars."

Where did the bacteria live?
The international team, which also included researchers from the United States, Canada, Russia and Sweden, tested the microbes living up to 10 meters deep in permafrost collected from Northern Canada, the Yukon, Siberia and Antarctica.

Repair operations
When a cell dies, its DNA fragments into pieces but the samples studied were all very long strands -- evidence the cells were able to continuously repair genetic material and remain alive.

These cells are active cells repairing DNA to deal with continuous degradation of the genomes. It is the same thing with humans.

What is the mechanism of repair
The scientists do not yet know the mechanism driving the continuous repair but the cells survived by eating nutrients like nitrogen and phosphate lodged in the permafrost.
This is interesting because the temperature on Mars is much colder with more stable temperatures, representing an even better environment to sustain this kind of life, he added.
While most scientists think our neighbor in the solar system is lifeless, the discovery of microbes on Earth that can exist in environments previously thought too hostile has fuelled debate over extraterrestrial life.

Researchers had known these microbes could survive for a long time without food but until now there was little agreement on how long they could live. Knowing this, and eventually pinpointing the key to this longevity, may also help scientists better understand the ageing process, he added.

It is interesting to see why some cells can survive for a very long time, that can be a key for understanding ageing.

Sunday, August 26, 2007

One Species, Many Genomes

Finding: Adaptation to the environment may produce many genomes for the same species
Adaptation to the environment has a stronger effect on the genome than anticipated. Faster growth, darker leaves, a different way of branching - wild varieties of the plant Arabidopsis thaliana are often substantially different from the laboratory strain of this small mustard plant, a favorite of many plant biologists.

Discovering which detailed differences distinguish the genomes of strains from the polar circle or the subtropics, from America, Africa or Asia is being investigated for the first time by research teams from Tübingen, Germany, and California. The results were surprising: The extent of the genetic differences far exceeds the expectations for such a streamlined genome, as the scientists write in Science magazine.

To track down the variation in the genome of the different Arabidopsis strains, the researchers compared the genetic material of 19 wild strains with that of the genome of the lab strain, which was sequenced in the year 2000. Using a very elaborate procedure, they examined every one of the roughly 120 million building blocks of the genome.

For their molecular sleuthing they used almost one billion specially designed DNA probes. The result of this painstaking analysis: on average, every 180th DNA building block is variable. And about four percent of the reference genome either looks very different in the wild varieties, or cannot be found at all. Almost every tenth gene was so defective that it could not fulfill its normal function anymore!

From one - many
Results such as these raise fundamental questions. For one, they qualify the value of the model genomes sequenced so far. There isn’t such a thing as the genome of a species. The insight that the DNA sequence of a single individual is by far not sufficient to understand the genetic potential of a species also fuels current efforts in human genetics.

Still, it is surprising that Arabidopsis has such a plastic genome. In contrast to the genome of humans or many crop plants such as corn, that of Arabidopsis is very much streamlined, and its size is less than a twentieth of that of humans or corn—even though it has about the same number of genes. In contrast to these other genomes, there are few repeats or seemingly irrelevant filler sequences. That even in a minimal genome every tenth gene is dispensable, has been a great surprise.

What does the analysis show?
Detailed analyses showed that genes for basic cellular functions such as protein production or gene regulation rarely suffer knockout hits. Genes that are important for the interaction with other organisms, on the other hand, such as those responsible for defense against pathogens or infections, are much more variable than the average gene. The genetic variability appears to reflect adaptation of local circumstances. It is likely that such variable genes allow plants to withstand dry or wet, hot or cold conditions, or make use of short and long growing seasons.

Such genome analyses of unprecedented details will allow a much better understanding of local adaptation, and this was indeed one of the main reasons for conduction the study. By extending these types of studies to other species we hope to help breeders to produce varieties that are optimally adapted to rapidly changing environmental conditions.

New methods - Direct Sequencing
How environment and genome interact is also the goal of new methods. While the technology used so far can only identify genes that have changed or are lost relative to the reference genome, direct sequencing of the genome of wild strains will allow the detection of new genes. The plan is to decipher the genomes of at least 1001 Arabidopsis varieties. A new instrument, with which the entire genome of a plant can be read in just a few days, is already available. Still missing are the computational algorithms to interpret the anticipated flood of data.

Saturday, August 25, 2007

How Snakes Survive Starvation and still grow

Finding: Snakes are efficient users of their metabolism even lowering it to survive without food.
Starving snakes employ novel survival strategies not seen before in vertebrates, according to research conducted by a University of Arkansas biologist. These findings could be used in conservation strategies to determine the health of snake populations.

These animals take energy reduction to a whole new level.
While scientists knew that some snake species could survive for up to two years without a meal, no studies have examined the physiological changes that take place when a snake goes for prolonged periods without food. Scientists three snake species – the ball python, the ratsnake and the western diamondback rattlesnake – to study their responses to prolonged periods without food.

The 62 snakes studied went about six months without eating – a time period that could well be duplicated in the wild, where food supplies can be scarce. Scientists then looked at physiological, compositional and morphological changes in the snakes.

Low energy demands and can grow even without food
The results showed that the snakes could lower their standard metabolic rates, some by up to 72 percent.

Snakes already had low energy demands. Scientists now know that they can go lower.
Another surprising finding: The snakes continued to grow despite the lack of food – a counterintuitive finding, but a measurement that again does not appear in the research literature.

Meaning what?
This suggests that there must be a strong selective advantage to growing longer. It also means the snakes have become extremely efficient in their ability to use available resources.

To illustrate the strategies employed by snakes to combat starvation, look at an economic analogy of supply and demand.

When you’re cut off from resources, you are an organism that still needs to expend energy. The “demand” end is met by decreasing their metabolic rate. The “supply” end must be met by frugal use of resources they have at hand for energy, which comes from within.
The body composition of snakes includes water, ash, protein, fats and carbohydrates. Scientists found that the snakes used up selected fat stores first during starvation, but he also found crucial differences between the snake species. The ratsnakes, which typically have a more abundant rodent supply in their natural environment, began to break down proteins faster than the pythons or rattlesnakes.

The protein use was higher in the snakes less well adapted to starvation. Snakes are relatively new on the world scene, having been around for about 100 million years. Yet they currently comprise about half of all reptile species.

Snakes appear to be very evolutionarily successful. Understanding the physiology that allows them to succeed in low-energy environments will help scientists further their understanding of the snakes’ evolution and their adaptation to their current ecosystems.

Why Were Prehistoric Insects Huge?

Finding: More than 300 million years ago, there was 31 to 35 percent oxygen in the air. That means that the respiratory systems of the insects could be smaller and still deliver enough oxygen to meet their demands, allowing the creatures to grow much larger.

A recent study was conducted to help determine why insects, once dramatically larger than they are today, have seen such a remarkable reduction in size over the course of history. Insects breathe through a network of air filled tubes that deliver oxygen directly to the cells. These tracheal tubes, especially in the leg, take up more room in larger beetles.

There were hundreds of ideas to explain the small size, but none of them could be proven. One theory was that it was an insect’s respiratory system that limited its size. So a study was launched an extensive study using beetles and fruit flies.

The study, much of which was performed at Illinois’ Argonne National Laboratory, involved the examination of various beetles’ respiratory systems, using new x-ray beam technology to help determine how they breathe.

Friday, August 24, 2007

It's not just genes that sets us apart

U.S. geneticists believe they know why humans are so different from chimps, although sharing most of the same genes: it's how the genes are used.

After studying the regulatory sequences adjacent to 6,280 genes in the DNA of chimps, humans and the rhesus macaque, scientists determined the differences center mainly on traits involving brains and diet. It's rather like the same set of notes being played in very different ways.

Positive selection, the process by which genetic changes that aid survival and reproduction spread throughout a species, has targeted the regulation of many genes known to be involved in the brain and nervous system and in nutrition.

Although many studies have looked for significant differences in the coding regions of genes relating to neural system development and failed to find any, the Duke team believes its study is the first to take a genome-wide look at the evolution of regulatory sequences in different organisms.

Thursday, August 23, 2007

The Chimp Genome Reveals A Retroviral Invasion In Primate Evolution

What functions are done in DNA?
It's been known for a long time that only 2%-3% of human DNA codes for proteins. Much of the rest of our genomes is often referred to as junk DNA. It consists of retroelements: genomic elements that are transcribed into RNA, reverse-transcribed into DNA, and then reinserted into a new spot in the genome. Human endogenous retroviruses make up one class of these retroelements. Retroviruses can insert themselves into the host's DNA in either soma (nonreproductive cells) or the germline (sperm or egg).

If the virus invades a nonreproductive cell, infection may spread, but viral DNA will die with the host. A retrovirus is called endogenous when it invades the germline and gets passed on to offspring. Because endogenous retroviruses can alter gene function and genome structure, they can influence the evolution of their host species. Over 8% of our genome is made of these infectious. It is these remnants infections that scientists believe occurred before Old World and New World monkeys diverged (2.5 billion years ago).

Are there any retrovirus in other animals but not found in Humans?
In a new study scientists scanned finished chimpanzee genome sequence for endogenous retroviral elements, and found one called PTERV1 that does not occur in humans. Searching the genomes of a subset of apes and monkeys revealed that the retrovirus had integrated into the germline of African great apes and Old World monkeysbut did not infect humans and Asian apes (orangutan, siamang, and gibbon). This undermines the notion that an ancient infection invaded an ancestral primate lineage, since great apes (including humans) share a common ancestor with Old World monkeys.

Are the sequences common to an ancestor?
Scientists have found over 100 copies of PTERV1 in each African ape (chimp and gorilla) and Old World monkey (baboon and macaque) species. They compared the sites of viral integration in each of these primates and found that few if any of these insertion sites were shared among the primates. It appears then that the sequences have not been conserved from a common ancestor, but are specific to each lineage.

What is PTERV1?
PTERV1 contains three structural genes: gag, pol, and env and regulatory sequences called long terminal repeats (LTRs). To further explore the evolutionary history of the retroviral elements, the scientists compared the sequences of gag and pol, as well as the LTR sequences, for each infected primate species. The sequence history, they discovered, did not comport with the established evolutionary history of the primates themselves. Divergence between macaque and baboon was significantly greater than between gorilla and chimp even though slightly more evolutionary time separates gorilla and chimp than macaque and baboon.

What does a retrovirus produce?
When a retrovirus reproduces, identical copies of LTR sequences are created on either side of the retroviral element; the divergence of LTR sequences within a species can be used to estimate the age of an initial infection. Scientists estimate that gorillas and chimps were infected about 34 million years ago, and baboon and macaque about 1.5 million years ago. The disconnect between the evolutionary history of the retrovirus and the primates, they, could be explained if the Old World monkeys were infected by "several diverged viruses" while gorilla and chimpanzee were infected by a single, though unknown, source.

Not all primates are infected
As for how this retroviral infection bypassed orangutans and humans, the authors offer a number of possible scenarios but dismiss geographic isolation: even though Asian and African apes were mostly isolated during the Miocene era (spanning 24 to 5 million years ago), humans and African apes did overlap.

It could be that African apes evolved a susceptibility to infection, for example, or that humans and Asian apes evolved resistance. A better understanding of the evolutionary history and population genetics of great apes will help identify the most likely scenarios. And knowing how these retroviral elements infiltrated some apes while sparing others could provide valuable insights into the process of evolution itself.

Wednesday, August 22, 2007

Human Ape Split may have occurred 13 million years ago

Ten million-year-old fossils discovered in Ethiopia show that humans and apes probably split six or seven million years earlier than widely thought, according to landmark study released Wednesday.

The handful of teeth from the earliest direct ancestors of modern gorillas ever found -- one canine and eight molars -- also leave virtually no doubt, the study's authors and experts said, that both humans and modern apes did indeed originate from Africa.

The near total absence to date of traces on the continent of apes from this period had led many scientists to conclude that the shared line from which humans and living great apes emerged had taken a long evolutionary detour through Eurasia.

The Last common ancestor - out of Africa
But the study, published in the British journal Nature, demonstrates that the Last Common Ancestor (of both man and ape) was strictly an African phenomenon. Tthe fossils are viewed as "a critically important discovery," a view echoed by several other scientists who had read the paper or seen the artifacts.

The most startling implication of the find, the scientists agree, is that our human progenitors diverged from today's great apes -- including gorillas, orangutans and chimpanzees -- several million years earlier than widely accepted research based on molecular genetics had previously asserted.

The trail in the hunt for physical evidence of our human ancestors goes cold some six or seven million years ago.

The anthropological past
Orrorin was discovered in Kenya in 2000 and nicknamed "Millennium Man" and it goes back 5.8 to 6.1 million years, while Sahelanthropus, found in 2001 later in Chad, is considered by most experts to extend the human family tree another one million years into the past.

Beyond that, however, fossils of early humans from the Miocene period, 23 to five million years ago, disappear. Fossils of early apes especially during the critical period of 14 to eight million years ago were virtually non-existant -- until now.

"We know nothing about how the human line actually emerged from apes," the authors of the paper noted.
But the new fossils, dubbed "Chororapithecus abyssinicus" by the team of Japanese and Ethiopian paleoanthropologists who found them, place the early ancestors of the modern day gorilla 10 to 10.5 million years in the past, suggesting that the human-ape split occurred before that.

The line: Orangutan, Gorrilla, Chimpanzee - Human

There is broad agreement that chimpanzees were the last of the great apes to split from the evolutionary line leading to man, after gorillas and, even earlier, orangutans.

Conventional scientific wisdom, based on genetic "distances" measured by molecular geneticists, had placed the divergence between chimps and humans some five to six million years ago. Orangutans are thought to have parted company with our ancestors 13 to 14 million years ago.
"If the new discovery is in the gorilla lineage, then this will definitely substantially push back the split time between apes and humans," Halie-Selassie at Kent State told AFP.

When did the split take place?
The scientists leading the team that found the fossils calculated that the human-orangutan split could easily have been as old as 20 million years.

They determined that the teeth belonged to gorilla ancestors based on unique shared characteristics of the molars, which had evolved for a diet of fibrous foods such as stems and leaves.

The match is not exact, however, and could prompt some scientists to challenge the findings.
The teeth fragments, found in barren scrubland some 170 kilometres (100 miles) east of Ethiopia's capital Addis Ababa, almost went unnoticed.
Asfaw recalled the chance discovery.

"It was our last day of field survey in February 2006, and our sharp-eyed field assistant, Kampiro, found the first ape tooth, a canine," he said.
"He picked it up and showed it to me, and I knew that this was something new -- Ethiopia's first fossil great ape."

Tuesday, August 21, 2007

How close are we to creating artificial life?

Around the world, a few scientists are trying to create life from scratch ...they're getting closer.
Some experts expect an announcement within 3 to 10 years from someone in the now little-known field of "wet artificial life."

That first cell of synthetic life—made from the basic chemicals in DNA— i.e., creating protocells has the potential to shed new light on our place in the universe, this will remove one of the few fundamental mysteries about creation in the universe and our role.

It's going to be a big deal and everybody's going to know about it, we're talking about a technology that could change our world in pretty fundamental ways—in fact, in ways that are impossible to predict.

Several scientists believe man-made life forms will one day offer the potential for solving a variety of problems, from fighting diseases to locking up greenhouse gases to eating toxic waste.
Bedau figures there are three major hurdles to creating synthetic life:

  • A container, or membrane, for the cell to keep bad molecules out, allow good ones, and the ability to multiply.
  • A genetic system that controls the functions of the cell, enabling it to reproduce and mutate in response to environmental changes.
  • A metabolism that extracts raw materials from the environment as food and then changes it into energy.
some of the steps under way will be : creating a cell membrane then getting nucleotides, which are the building blocks of DNA to form a working genetic system.

His idea is that once the container is made, if scientists add nucleotides in the right proportions, then Darwinian evolution could simply take over. It's a cleaver ploy we may not be smart enough to design things, but we let evolution do the hard work and then we figure out what happened.

One scientist is attacking that problem by going outside of natural genetics. Normal DNA consists of four bases—adenine, cytosine, guanine and thymine (known as A,C,G,T)—molecules that spell out the genetic code in pairs. Instead of 4 pair, one scientist is trying to add eight new bases to the genetic alphabet.

Monday, August 20, 2007

DNA Replication Behavior- from Low to High

DNA replication is considered the heart of the DNA process. Recent findings by scientists at the Genome Institute of Singapore (GIS) may be paving the way for more efficient analyses and tests related to the replication of cells, and ultimately, to the better understanding of human biology, such as in stem cell research.

Where does duplication occur?
Faithful duplication of the genome ensures that daughter cells inherit a complete set of genetic materials identical to parent cells. This duplication occurs in the section of the cell cycle known as the S-phase. Extensive research on the budding yeast revealed that the replication process is started at hundreds of origins in the S-phase.

Is the replication process efficient?
Many previous studies focused on the replication timing and initiation sites, but not on the efficiency. So it was believed that the replication efficiency decreased as the S-phase progressed.
But now they know better. In a recently published paper scientists described how they were able to determine the replication timing and efficiency at the various loci in the genome. Now replication efficiency is low at the beginning of the S-phase, but the efficiency increased at the later stage of this phase.

Sunday, August 19, 2007

Genes changes linked to an organism's survivability

Studies from biologists have found that a simple interaction between just two genes determines the patterns of fur coloration that camouflage mice against their background, protecting them from many predators. The work marks one of the few instances in which specific genetic changes have been linked to an organism's ability to survive in the wild.

What does the research show?
The work shows how changes in just a few genes can greatly alter an organism's appearance. It also illuminates the pathway by which these two genes interact to produce distinctive coloration. The result is that now there's reason to believe this simple pathway may be evolutionarily conserved across mammals that display lighter bellies and darker backs, from mice to tuxedo cats to German Shepherds.

What was studied?
Researchers studied Peromyscus, a mouse that is the most widespread mammal in North America. Within the last several thousand years, these mice have migrated from mainland Florida to barrier islands and dunes along the Atlantic and Gulf coasts, where they now live on white sand beaches. In the process, the beach mice's coats have become markedly lighter than that of their mainland brethren.

What did the research show?
Nature provides a tremendous amount of variation in color patterns among organisms, ranging from leopard spots to zebra stripes; these patterns help individuals survive. But it has been difficult to understand how these adaptive color patterns are generated. The research helped identify the genetic changes producing a simple color pattern that helps camouflage mice inhabiting the sandy dunes of Florida's Gulf and Atlantic coasts. These 'beach mice' have evolved a lighter pigmentation than their mainland relatives, a coloration that helps camouflage them from predators that include owls, herons, and hawks.

Previous research has shown that such predators, all of which hunt by sight, will preferentially catch darker mice on the white sand beaches, providing a powerful opportunity for natural selection to evolve increased camouflage.

Which Genes were involved?
Through a detailed genomic analysis, researchers identified two pigmentation genes, for the melanocortin-1 receptor (Mc1r) and an agouti signaling protein (Agouti) that binds to this receptor and turns it off. Conclusion: A single amino-acid mutation in Mc1r gene can weaken the receptor's activity, or a mutation in the Agouti gene can increase the amount of protein present without changing the protein's sequence, also reducing Mc1r activity and yielding lighter pigmentation.

Research findings
What do the genes do? Both genes affect the type and amount of melanin in individual hairs. If both genes are turned on, the mouse is dark in color. If a mutation occurs, which changes either gene this leads to a somewhat blonder mouse, but when the combination of mutations occur in both genes this produces a mouse very light in color.

Does temperature affect evolution?

Where does evolution occur in a temperate area or in a hot area?
It turns out that new species originate more frequently in temperate regions than in the tropics. Steamy and wet they may be, but tropical hotspots of biodiversity are not the hottest as far as evolution is concerned. Scientists looked at pairs of "sister" species - pairs that evolved from an immediate common ancestor - and estimated how long ago the sisters diverged from each other.

In hot areas
Near the equator, sister species split on average about 3.4 million years ago, whereas those in temperate regions split roughly 1.7 million years ago. It is true that tropical zones do host a greater species diversity, but that's because fewer species have gone extinct there.

In cold areas
In very high latitudes - above the Arctic Circle - the sister species split even more recently, with none of those reviewed separating more than a million years ago.

Dramatic climatic changes in temperate regions over the past hundreds of thousands of years may have driven evolution harder.

Friday, August 17, 2007

Retracing Evolution With First Atomic Structure Of An Ancient Protein

Can you show any evidence of evolution by looking at the atomic structure of a protein? Scientists say yes. They have determined for the first time the atomic structure of an ancient protein. This reveals in detail how genes evolved their functions.

Recreating ancient progenitors of protein
The workhorses of the cell are proteins. But a detailed study showing how proteins have evolved has not been possible and has eluded evolutionary biologists. This was due because ancient proteins have not been available for direct study. So scientists used state-of-the-art computational and molecular techniques to re-create the ancient progenitors of an important human protein.

Looking at the Atoms
The challenge: can you use only the atoms of ancient proteins to trace changes in the atomic architecture? Two different groups of scientists worked together to trace how changes in the protein's atomic architecture over millions of years caused it to evolve a crucial new function -- uniquely responding to the hormone that regulates stress.

The ultimate level of detail
This is the ultimate level of detail and you can see exactly how evolution tinkered with the ancient structure to produce a new function that is crucial to our own bodies today.
The researchers focused on the glucocorticoid receptor (GR), a protein in humans and other vertebrates that allows cells to respond to the hormone cortisol, which regulates the body's stress response. The scientists' goal was to understand the process of evolution behind the GR's ability to specifically interact with cortisol.

How it was done
Scientists used computational techniques and a large database of modern receptor sequences to determine the ancient GR's gene sequence from a time just before and just after its specific relationship with cortisol evolved. The ancient genes existed more than 400 million years ago -- were then synthesized, expressed, and their structures determined using X-ray crystallography, a state-of-the art technique that allows scientists to see the atomic architecture of a molecule.

The structures allowed the scientists to identify exactly how the new function evolved. They found that just seven historical mutations, when introduced into the ancestral receptor gene in the lab, recapitulated the evolution of GR's present-day response to cortisol. They were even able to deduce the order in which these changes occurred, because some mutations caused the protein to lose its function entirely if other "permissive" changes, which otherwise had a negligible effect on the protein, were not in place first.

Thursday, August 16, 2007

In evolutions playground, Humans left chimps behind

What is the difference between humans and chimps?
MICRO-RNA, the snippets of RNA that control gene expression, could be the difference.

Variation between individuals, in traits ranging from pigment to behaviour, is the raw material of evolution. The difference can be down to very subtle changes: the genes involved may code for exactly the same proteins but make them at other places and times. So could micro-RNA be the determining factor?

What do Micro-RNA's do?
Micro-RNAs are a mere 22 nucleotides long and block the messenger RNA that translates DNA into protein. This allows them to fine-tune gene expression. Micro-RNA has only recently been studied because it was discovered withing the last few years. But it has been shown to determine what cell types form, and, for example, whether sheep become muscular or puny.

Now, researchers at the Hubrecht Laboratory in Utrecht, the Netherlands, have combed painstakingly through the RNA in human and chimp brains, and found 447 new micro-RNAs, more than doubling the number discovered so far. Some were expressed very rarely.

What accounts for the differences between Chimps and Humans?
The brain has 10,000 cell types, so it is possible because of all these micro-RNAs. Many were unique to chimps and humans, and some only to humans. So while we share most of our DNA with chimps, the small genetic changes through Micro RNA that fine-tune its expression might account for the radical differences in our brains. This is the playground of evolution.

Wednesday, August 15, 2007

Why Are There So Many More Species Of Insects? Because Insects Have Been Here Longer

J. B. S. Haldane once famously quipped that "God is inordinately fond of beetles." Results of a study suggest that this fondness was expressed not by making so many, but rather by allowing them to persist for so long.

In a study appearing in the American Naturalist, scientists show that many insect groups like beetles and butterflies have fantastic numbers of species because these groups are so old. In contrast, less diverse groups, like mammals and birds, are evolutionarily younger.

This is a surprisingly simple answer to a fundamental biological puzzle. They accumulated data from molecular phylogenies (which date the evolutionary relationships among species using genetic information) and from the fossil record to ask whether groups with more species today had accumulated species at faster rates.

Animals as diverse as mollusks, insects, spiders, fish, amphibians, reptiles, birds, and mammals appear to have accumulated new species at surprisingly similar rates over evolutionary time. Groups with more species were simply those that had survived longer. Their analyses thus identify time as a primary determinant of species diversity patterns across animals.

Given the unprecedented extinction rates that the Earth's biota are currently experiencing, these findings are also quite sobering. We are rapidly losing what it has taken nature hundreds of millions of years to construct, and only time can repair it.

Tuesday, August 14, 2007

Stopping Cancer Cells From Reading Their Own DNA

There are three primary ways of treating cancer at present, and these have fundamentally changed little in 30 years. If there are tumours, surgery can be used to cut out the cancerous tissue, It the cells are malignang, then radiation therapy is the method. Chemotherapy is used to keep the cancerous cells from dividing. But a new approach using a molecular technique to prevent interference in the DNA copy metric.

The approach uses the information from tumor cells and block them from copying DNA sequences. This will cut off the genetic information flow that tumours need to grow.

The enzyme called Topoisomerase IB plays a key role in some of the molecular metric involved in the processes of DNA and RNA copying during cell division. These are responsible for reading the genetic code and making sure it is encoded correctly in the daughter cell. In healthy cells this process works normally, but in cancer cells it does not work well at all. If one can specifically target these molecular metrics in cancer cells one can prevent the cancer cells from growing into a larger tumor.

This molecular copying metric is constructed largely out of proteins. It works by effectly walking along the DNA double helix reading the genetic code so that it can be copied accurately into new DNA during division. Other components is responsible for slicing and assembling the DNA itself.

Monday, August 13, 2007

Genetic evidence for evolution

If there is evolution, is there any evidence for it at the genetic level?

The answer is yes. Scientists who have been studying genetic changes occurring in the human genome over the last 15,000 to 100,000 years, have found that over this relatively short period of time the human genome has changed by as much as 10 percent.

Evidence withing the Human Genome
A scientific study identifies small, gradual changes (microevolution) that demonstrate species divergence from a common ancestor millions of years ago (macroevolution). The study makes human-to-human comparisons throughout the complete human genome instead of comparing a human to mice or chimpanzees. By this procedure humans can be seen changing over time, due to our ancestors being exposed to – among other selective pressures – different climates as they spread across the globe.

Evidence for Change
Early humans had problems digesting lactose after the age of one. Lactose is an enzyme found in milk. Befor the domestication of animals (about 20,000 years ago) humans could not digest milk after infancy. But some time after humans began migrating and domesticating animals, humans began to develop a gene that allowed us to tolerate consuming milk into adulthood. In other words as humans have populated the world, there has been strong selective pressure at the genetic level for mutations that allow digestion of a new food source or tolerate infection by a pathogen that the population may not have faced in a previous environment.

Sunday, August 12, 2007

Trilobite variation declined after the Cambrian Explosion

From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on. So a highly variable species will evolve more rapidly than others.

Is that statement true?

Paleontologists for decades have suspected that highly variable species evolved more rapidly than others, and several studies have approached questions pertaining to it--but this is the first to convincingly document it in any group.

Most studies have focused on the variability that occurs between species rather than within them, but one recent study analyzed 982 species of trilobites, ancient relatives of spiders and horseshoe crabs.

When did Trilobites live?
Trilobites have been extinct for over 250 million years. They were once the most common creatures in the world's oceans. They ranged in size from nearly microscopic to more than a foot long, though most of the 17,000 known species measured from one to four inches. They were very diverse.

Trilobites were among the creatures that emerged 500 million years ago, during what paleontologists call "the Cambrian explosion," or "the Cambrian radiation." Before this time, life on Earth was limited mostly to bacteria, algae, single-celled organisms and only the simplest animal groups. But during the Cambrian Period, more complex creatures with skeletons, eyes and limbs emerged with amazing suddenness.

What does the research show?

So the question is what fueled the Cambrian radiation, and why was that event so singular? The answer: It appears that organisms displayed "rampant" within-species variation in the 'warm afterglow' of the Cambrian explosion, but not later.

A study focused on actively evolving characteristics during the Cambrian time. The trilobite head alone displayed many different characteristics. There were differences in ornamentation, number and placement of spines, and the shape of head segments. Overall, approximately 35 percent of the 982 trilobite species exhibited some variation in some aspect of their appearance that was evolving. But more than 70 percent of early and middle Cambrian species exhibited variation, while only 13 percent of later trilobite species did so.

Conclusion: There's hardly any variation in the post-Cambrian. Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn't vary in the post-Cambrian trilobites.

Why does variation withing a species decline through time?
Paleontologists have proposed two ideas to account for why variation within species declined through time.

1)Ecological. In the very early Cambrian seas, fewer organisms existed than today, which meant that they faced less competition for food. You didn't really have to be tightly specialized to make a living in the Cambrian. But as evolution gave rise to more varieties of organisms, ecological communities became more diverse. You had to be very fine-tuned to your particular niche to make a living and to beat out competitors for a limited resource. More organizms in the ocean meant that there must be more genetic variation in order to survive.

2) The genomic hypothesis offers a second explanation for the decline of within-species variation over time. According to this idea, internal processes in the organism were the key factors. Various developmental processes interact with one another to control the growth and formation of body parts as any organism progresses from egg to adult.

It's been suggested that early on in evolutionary history, in the Cambrian Period, the degree to which these different developmental processes interacted with each other within the organism was a lot less. As a result, the constraints on what the final organism looked like were relatively low.

Saturday, August 11, 2007

A Complete primate gene study

U.S. scientists have completed what's believed the most comprehensive assessment of gene copy number variations across human and non-human primate species.

A study provides an overview of genes and gene families that have undergone major copy number expansions and contractions during approximately 60 million years of evolutionary time.

Primates first appeared on Earth about 90 million years ago, and today roughly 300 primate species exist. To survey the differences in gene copy number among those species, researchers used DNA microarrays containing more than 24,000 human genes to perform comparative genomic hybridization experiments. DNA comparisons were made using samples from humans with those of nine other primate species: chimpanzee, gorilla, bonobo, orangutan, gibbon, macaque, baboon, marmoset, and lemur. This allowed them to identify specific genes and gene families that, through evolutionary time, have undergone lineage-specific copy number gains and losses.
The scientists said they discovered differences potentially associated with cognition, reproduction, immune function, and susceptibility to genetic disease.

Friday, August 10, 2007

Shrinking Genomes

Scientists generally believe that insertions of retroelements, or"jumping genes," once established in a population, are irreversible and are maintained throughout evolution. This unidirectional theory of retroelement evolution, which calls for ever-expanding genome size, is challenged by work that appears in the September issue of Genome Research.

Deletion of Genome elements from Rhesus to Humans
Researchers performed a whole-genome comparison of the human, chimpanzee, and Rhesus monkey sequences, and they identified 37 instances where a retroelement was present in Rhesus (a more primitive primate species) but absent in either humans or chimpanzees. This indicated that these retroelements had been deleted during the evolution of the more recent primate species.

Mediation by short identical sequences
Intriguingly, the scientists further demonstrated that these deletions were mediated by short identical sequences that flank the retroelements. They extended the study to random, non-retroelement sequences and showed that deletions caused by short identical DNAsequences were a widespread genomic phenomenon. In fact, thousands of insertion-deletion sequence differences between the human and chimpanzee genomes were likely mediated by short identical sequences.

The work strongly suggests an important role for short, non-adjacent, identical segments of DNA in genomic deletions and it lends insight into deletion mechanisms that help to counterbalance genome expansion in primates.

Conclusion: Genes don't get bigger with more complex species, they get smaller.

Thursday, August 9, 2007

Ecological Biogeography

Unlike historical biogeographers, ecological biogeographers make extensive use of current population information. They study the ways in which species develop and interact in the presence of other species and different environments. Many ecological biogeographers mimic Darwin: they study island communities as a type of experimental system to test hypotheses about species development.

Much of ecological biogeography is concerned with species richness, the number of different species an area supports. In specific, ecological biographers have developed the species richness equilibrium model.

The model begins with an uninhabited "island" that can be either a literal island or an area of like habitats completely surrounded by unlike habitats. All species available to colonize the new area are called the "species pool." As more and more new species enter the new area, the species pool becomes smaller and smaller, and the immigration rate (the probability that any given species moving into the area will be a new species) decreases.

At the same time, the island becomes more and more crowded and supplies become scarce, causing the extinction rate to increase. The point at which the extinction rate and the immigration rate balance is called the equilibrium point. The model predicts that changes in extinction and immigration rates will tend toward the equilibrium point, which is different for every island, depending on resources and degree of separation from other areas. This is shown graphically in the figure below.

Wednesday, August 8, 2007

Historical biogeographers

Historical biogeographers also make use of a tool called an area cladogram. This diagram is made by taking a taxonomic tree, which shows various species and their relatedness, and replacing the species names with the geographic location in which those species are found. This new tree allows scientists to determine how the differences in environments have effected the evolutionary history of different species of common origin. A sample area cladogram is shown below:

Tuesday, August 7, 2007

The Dynamics Of Transcription In Living Mammalian Cells

Transcription is the transfer of DNA’s genetic information through the synthesis of complementary molecules of messenger RNA. It forms the basis of all cellular activities. But the dynamics of the process is not well understood. Scientist do not know how efficient it is or how long it takes. But researchers at the Albert Einstein College of Medicine have measured the stages of transcription in real time. Their unexpected and surprising findings have fundamentally changed the way transcription is understood.

The study focused on the ensyme responsible for transcription, RNA polymerase II. During transcription, numbers of RNA polymerase II molecules assemble on DNA and then synthesize RNA by sequentially recruiting complementary RNA nucleotides.

3 phases of Transcription

To visualize the transcription process, the researchers used living mammalian cells, each of which contained 200 copies of an artificial gene that they had inserted into one of the cell’s chromosomes. Then, by attaching fluorescent tags to RNA polymerase II, they were able to closely monitor all three phases of the transcription process:
  • binding of the enzyme molecules to DNA,
  • initiation (when the enzyme links the first few RNA nucleotides together) and
  • elongation (construction of the rest of the RNA molecule).
The result of the observation
As they observed the RNA polymerase II molecules attaching to DNA and making new RNA, they saw many cases where enzyme molecules attached — and then promptly fell off.

Transcription is inefficient
During the first two phases the transcription process is really inefficient. It turns out that only one percent of polymerases that bind to the gene actually remain on to help in synthesizing an RNA molecule.

Transcription may be inefficient for a reason. All the factors needed for transcription have to come together at the right time and the right place, so there’s a lot of falling off and adding on of polymerases until everything is precisely coordinated.

The researchers observed that
  • the binding phase of transcription lasted six seconds and
  • initiation phase lasted 54 seconds.
  • the elongation phase lasted 517 seconds (about eight minutes).
Pausing and Elongation
The “lead” polymerase on the growing polymerase II enzyme sometimes “paused” for long periods, retarding transcription in the same way that a Sunday driver on a narrow road slows down all traffic behind him.
But in the absence of pausing, elongation proceeded much faster — about 70 nucleotides synthesized per second — than has previously been reported.

These two phenomena — pausing and rapid RNA synthesis during elongation — may be crucial for regulating gene expression. Once the ‘paused’ polymerase starts up again, in a very short time you could synthesize a new batch of messenger RNA molecules that might suddenly be needed for making large amounts of a particular protein.

Monday, August 6, 2007

Biogeorgraphic Distributions

The geographic distributions of species can be of a number of types
Consider the distribution of three species of toucans in the genus Ramphastos.
• Endemic distributions
Two of the species, R. vitellinus and R. cluminatus , have endemic distributions: they are limited to a particular area. Endemic distributions can be more or less widespread.
• Cosmopolitan distributions
The extreme case of species that are found on all continents of the globe are called cosmopolitan. The pigeon, for example, is found on all continents except Antarctica; on a strict definition, the pigeon (pictured opposite) might not be allowed to be cosmopolitan, but the term is usually intended less strictly - and the pigeon is called a cosmopolitan species.
• Disjunct distributions
Other species, like R. ariel , are not confined to a single area, but are distributed in more than one region with a gap between them: these are called disjunct distributions.
Maps can be drawn for a taxonomic group at any Linnaean level: just as species have geographic distributions, so too do genera, families, orders. Biogeography aims to explain the distributions of the higher taxa too, in addition to those of species; and different explanatory processes are often appropriate at different levels.
Short-term movements of individuals influence the distributions of populations and species, whereas slower acting geological processes may control the biogeography of higher taxa.

Sunday, August 5, 2007

Genetic Chromosome Breaking

Researchers in genome stability have observed that many kinds of cancer are associated with areas where human chromosomes break. Its been hypothesized, but not proven, that slow or altered replication led to the chromosomes breaking.

But now a study at Tufts University two molecular biologists have used yeast artificial chromosomes to prove that hypothesis. They found a highly flexible DNA sequence that increases fragility and stalls replication, which then causes the chromosome to break.

Cancer Causing Areas
The area in question is an area that has a tumor suppressor gene -- a gene whose absence can cause tumors. If you delete that gene or delete part of that gene so it doesn't work anymore, that can lead to tumors. The fact that there is fragility in the same region that this gene is located is a bad coincidence. Fragility can cause deletions and deletions can cause cancer, so you want to understand the fragility because that might be what's causing cancer.

DNA structure leads to fragility
Past research had predicted the flexibility of the DNA helix in this particular common fragile site by calculating the twist angle between consecutive base pairs and found that there were several points of high flexibility, suggesting that the flexibility was connected to the fragility.
Freudenreich and Zhang used yeast artificial chromosomes to test this idea because it allowed them to look at the region in a more detailed way than looking at human chromosomes and to monitor the replication process. They expect the results will be similar when tested in human cells based on previous research using yeast chromosomes.

How the research was conducted
Two regions of predicted high flexibility, plus a region near a cancer cell breakpoint and a control region were tested to see whether any of these regions could cause breakage of a yeast chromosome. They found that one did. This is the first known sequence element within a human common fragile site shown to increase chromosome breakage. What is intriguing is that the sequence that breaks, in addition to being flexible, is predicted to form an abnormal DNA structure." The result is that when replication stalls, chromosomes can break.

How did the chromosomes break?
From past studies, they hypothesized that breakage was connected to replication. Replication is just the duplication of DNA in side the cells as they divide, the DNA inside those cells must duplicate. The research showed that the chromosomes were breaking because replication was stalled.

The problem arises when they do not heal correctly and instead are deleted or rearranged, Cancer cells almost always have some sort of deletions or rearrangements. Something is wrong with their chromosomes that then messes up the genes that are in those areas.

Replication process stalled
The researchers also noticed that this particular sequence was an AT-rich region, where the DNA was composed mostly of the bases adenine (A) and thymine (T), rather than the other bases cytosine (C) or guanine (G). Freudenreich and Zhang found the longer the AT-repeat, the more the replication process was stalled, something they would like to follow up on with further research.

Some researchers believe that the longer the repeat, the more the abnormal the DNA structure forms, and the more fragile the chromosome becomes. What is still up in the air is whether people with longer repeats are more prone to deleting that tumor suppressor gene and getting cancer as a result. Does this correlation between chromosome breaks and cancer has a medical consequence.

Friday, August 3, 2007

BioGeorgraphy and Range Limitations?

What factors limit the geographic range of a species?
Ecological factors
The distributional limits of a species are set by its ecological attributes:

• Fundamental niches
If a species is able to tolerate a certain range of physical factors such as temperature, humidity, and so on and it has the capacity in theory live anywhere within these tolerance limits, this is its fundamental niche.

• Realized niches - Competing species
However, if there are competing species that occupy part of this range the competition may be too strong to permit both species to exist. The near extinction of the red squirrel in Britain due to competition from the grey squirrel is a good example. Each species' realized niche will be smaller than its physiology makes possible. In other words each species will occupy a smaller range than it otherwise would in the absence of competition.

Thursday, August 2, 2007

Genetic Factors Strongly Shape How Peers Are Chosen

The company we keep may be more influenced by genetics than previously thought. Researchers report that as individuals develop, genes become more important in influencing how they choose their peer groups. The findings offer insight into which individuals may be at risk for future substance use or other externalizing behaviors such as conduct and antisocial personality disorder.

The study involved 1,800 male twin pairs from mid-childhood to early adulthood, between 1998 and 2004.

Through a series of interviews, researchers found that genetic factors increasingly impact how male twins make choices as they mature and develop their own social groups. Their finding include that the path from genes to behaviors like drug use and antisocial behaviors is not entirely direct or biological. Rather an important part of this pathway involves the genetics, which influences our own social environment, which in turn impacts on our risk for a whole host of deviant behaviors. Results demonstrate clearly that a complete understanding of the pathway from genes to antisocial behaviors, including drug abuse, has to take into account self-selection into deviant versus benign environments. The effects of peers in adolescence can be quite powerful, either encouraging or discouraging deviant behaviors. Peers also provide access to substances of abuse.

Wednesday, August 1, 2007

Molecular evolution

Molecular evolution is the process of evolution at the scale of DNA, RNA, and proteins.

Some of the key topics that spurred development of the field have been
  • the evolution of enzyme function,
  • the use of nucleic acid divergence as a "molecular clock" to study species divergence,
  • and the origin of non-functional or junk DNA.

Recent advances in genomics, including whole-genome sequencing, high-throughput protein characterization, and bioinformatics have led to a dramatic increase in studies on the topic. In the 2000s, some of the active topics have been the role of gene duplication in the emergence of novel gene function, the extent of adaptive molecular evolution versus neutral drift, and the identification of molecular changes responsible for various human characteristics especially those pertaining to infection, disease, and cognition.