Thursday 19 May 2011

The DNA time machine

Were they deformed modern humans or a different prehistoric species to us?
 ~~> The query about the hobbit-sized individuals who lived on the Indonesian island of Flores until about 13,000 years ago is among the most hotly debated in archaeology.
        Finding more of their diminutive bones in the giant, cold cave where the first hobbit remains were discovered years ago could help clinch the most widely accepted view about them, that they were a brand spanking new species. But getting a quantity of their ancient DNA would provide the definitive proof so lots of crave - if it turned out to be a kind of human DNA seldom seen before.
        DNA degrades with time, in hot climates. But know-how to study ancient genetic material has advanced quickly in recent years. And when DNA can be extracted from bones or teeth or hair or other remains, it opens up a fascinating new window on the past, says Dr Jeremy Austin, deputy director of the Australian Centre for Ancient DNA at the University of Adelaide.
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       "It lets us travel back in time - days, years or hundreds of thousands of years - to study extinct species, to re-create past environments and to identify the remains of, and relationships between, peoples or animal populations who have been long dead," he says.
That is why Austin and his colleague, Professor Alan Cooper, were keen to fly to hot, sticky Jakarta after the discovery of the hobbits, Homo floresiensis, to examine the few precious remains of the tiny people that are kept there.
         The ancient DNA specialists took their own mini sterile lab, the size of tiny table. "And they used a dental drill to drill in to the teeth," recalls Austin of their 2006 trip.
Regrettably, although lots of human DNA was obtained from the teeth, none of it was indisputably hobbit DNA.
"The main issue was that all the skeletal material had been handled by limitless people," says Austin.
This issue of contamination of ancient bones with modern human DNA has also been a giant hurdle for scientists studying our closest relatives - the Neanderthals. But earlier this month an international team made an weird announcement: that they had not only obtained DNA from the squat, thick-browed humans who went extinct over 30,000 years ago, but also sequenced most of their genetic code.
Dr Mike Bunce, of Murdoch University's Ancient DNA Research Laboratory in Perth, says this feat would have been unimaginable even years ago.
"It's an brilliant accomplishment." The team, led by Professor Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, France, could work out the order of over two billion letters in the DNA code, most of it from a 38,000-year-old male Neanderthal present in a Croatian cave.
Analysis of all this information will reveal a lot about our own evolutionary history as well as what Neanderthals were like, such as whether they could talk and all had red hair. Already the DNA proof shows there was tiny, if any, breeding between Neanderthals and the modern humans who lived in Europe simultaneously as them.
Mammoths were the first extinct animals to have their genome sequenced, with the results published last November. Clumps of hair from carcasses frozen in the permafrost were used as the source of the DNA.
Hair is a nice alternative to bone and teeth because it does not attract as much bacteria or fungi that complicate the analysis, says Bunce. "It is naturally waterproof."
The mammoth researchers have discovered that the giant woolly elephants split in to genetically distinct populations six million years ago, of which became extinct about 45,000 years ago, the other about ten,000 years ago.
In 2007 Bunce was part of an international team that studied a quantity of the most ancient DNA on earth - genetic material up to 600,000 years elderly that was collected from under a kilometre of ice in Greenland. It showed that half a million years ago, the frozen island was green, covered by a lush forest filled with butterflies, moths and the ancestors of beetles, flies and spiders.
The colder northern hemisphere has proved the best source so far of ancient DNA because the creatures and plants have been stored in a natural refrigerator, the permafrost. In Australia the oldest DNA that has been collected is about 15,000 to twenty,000 years elderly. But it is hoped that Antarctica and caves in Tasmania will offer up even more well-preserved ancient samples.
The holy grail on our continent is to receive DNA that is older than 40,000 years - the time when Australia's giant kangaroos, wombats and other megafauna went extinct.
The query of their demise is contentious: whether they disappeared in a blitzkrieg soon after Aborigines arrived here, hunting and lighting fires, or whether the giant animals were already in genetic decline and climate alter dealt a deadly blow.
In the quest to find megafauna DNA, Bunce has found himself squeezing through underground caves, where unintentional creatures had become trapped and died long ago.
At site, Tight Entrance Cave - which was true to its name - he had to climb down a long narrow shaft before being able to remove bones under sterile conditions.
"Not being a caver, it was fascinating fieldwork," he recalls.
Even dirt can contain DNA if an animal has been rolling around in it. And the ancient DNA specialists would be happy in the event that they could find DNA in droppings left behind by ancient megafauna. Tiny marsupials called stick nest rats that lived in Australia's arid zone up to 4000 years ago have also provided DNA hunters with a rich source of ancient material.
The stick nest rats built nests or middens from any bones or sticks or other materials they found and then urinated on them.
"It's unusual behaviour, but nice from a molecular point of view," says Bunce.
From these ancient nests, DNA from wallabies, insects, possums and plants has been identified, providing a one-of-a-kind insight in to what the environment was like thousands of years ago.
Austin says New Zealand, with its cooler climate, is a source of well-preserved specimens of ancient birds including the extinct giant moa, which weighed up to 250 kilograms. He recalls running in to caves thick with ancient moa remains perhaps twenty,000 years elderly. "Yet they looked fresh, like the moa died there only twenty years ago." of his former students, Dr Jamie Wood, has collected over 1500 moa droppings from across NZ - a quantity of them up to 15 centimetres in length - with surprising results. Although the birds stood up to metres tall, the plants they had eaten were under 30 centimetres in height. "This suggests that some moa grazed on small herbs, in contrast to the current view of them as chiefly shrub and tree browsers," says Wood, of the University of Otago.
               The Adelaide researchers and their NZ colleagues also got another surprise when they studied of the world's rarest penguins, the yellow-eyed penguin. Tests on DNA from ancient penguin bones in NZ showed they belonged to a different species known as the Waitaha that had gone extinct by 500 years ago.
Austin says it had been thought the endangered yellow-eyed penguins were the remnants of a once-thriving population in NZ. But now it looks as in the event that they only arrived there from islands further south historicallyin the past 500 years, after the demise of the Waitaha.
"That was an brilliant find. You go looking for thing and find something different."
Clues point to viking plundering
FROM out of the north they swept, like an chilled wind, raiding villages and plundering the ladies of the British Isles. The exploits of the Vikings are legendary. But now there is also proof from ancient DNA to back up this picture.
             Tests on people from Iceland, including on 68 skeletal remains of those who died there about 1000 years ago, show that the country was settled by men from Scandinavia. But most of the original female inhabitants were from the coastal regions of Scotland and Ireland, areas that regularly suffered raids from Vikings. Scientists at an Icelandic company, deCODE genetics, analysed the DNA that is passed from sister to children, known as mitochondrial DNA, to see how the current Icelandic population differed from the ancestors who came to the remote island about 1100 years ago. The results were published last month in the journal PLoS Genetics.
"This study is a major contribution to the use of ancient DNA studies in tracing the history not of single populations, but of our species and how they spread from Africa to every corner of the globe," said deCode chief executive, Kari Stefansson.

Mother Nature's DNA


                  It may appear as if J. Craig Venter is on an extended holiday as he sails his 95-ft. luxury yacht on a 25,000-mile voyage around the globe. But the iconoclastic scientist who took on a consortium of national governments in a race to map the human genome--and fought them to a picture finish years ago--is actually hard at work. He is prospecting--not for gold but for DNA, applying the same techniques developed to decode human genes to the genes of microbes scooped from the ocean and out of the air. On a pilot voyage, through the Sargasso Sea in the North Atlantic, he found over one,800 new species of bacteria and viruses--a surprise, since he had always thought of the Sargasso as a biological desert, comparatively devoid of life.
                   Indeed, half a decade after Venter and his archrival, Francis Collins, director of the National Human Genome Research Institute, stood together at the White House to announce that the human genome had been sequenced, biologists have come to re-evaluate what that milestone meant. Back then, it was widely assumed that the emerging science of human genomics would quickly lead to spectacular cures for cancer and other diseases and even permit couples to have "designer" children with desirable traits plucked from a catalog.
                   Although researchers around the globe have made solid progress in understanding the genetic basis of disease--and the pharmaceutical industry now depends on gene sequencing in its search for new drugs--revolutionary new treatments have yet to emerge. "It's actually very fascinating," says Collins. "But we are still probably a decade or possibly 15 years away from the actual revolution in medicine that genomics promises."
                   Simultaneously, however, scientists have come to appreciate what can be gained from decoding other genomes, from modern chimps and ancient cave bears to microscopic bacteria and viruses. As the cost of sequencing each base pair has dropped, from $10 in 1990 to less than 9¢ in 2002 to 1/10 of 1¢ today, researchers are doing more on a regular basis. Although 99% of the planet's genomes have yet to be decoded, researchers have identified hundreds of thousands if not millions of genes, dwarfing the trifling 24,000 or so they carryover in our DNA.
                  Additionally, scientists are getting a much better understanding of what individual genes do, no matter where they are from. The challenge, explains Venter, is to identify the genes that permit some microbes to change sunlight in to sugars, others to absorb carbon dioxide from the air and still others to transform dead plant matter in to clean-burning hydrogen.
                  So researchers have set out to look for those genes--and not in the ocean. Venter is also sampling the air over New York City, and other scientists are looking in to hot springs, digging in to the ground and even testing toxic-waste sites. "You can pick up a gram of soil," says Aristides Patrinos, who oversees the Department of Energy's genome program, "and there is DNA in it. By sequencing that DNA, you can conclude what is there in terms of diversity." As a rule, the more diverse a given ecosystem--the more genes present, even at the microbial level--the more resistant it is to destroy.

Difference between DNA and RNA


                DNA is a term that they use & listen to often. Be it for chemistry or forensic inquiry, DNA has not only played an important role, but a popular . RNA on the other hand has been a silent (& for plenty of years, invisible) hero, for the same fields. Definitively, RNA & DNA are proteins. DNA has less OH than the RNA. This, makes their structure a tiny bit different .

Technically, ribonucleic acid & deoxyribonucleic acid definite sound similar. But lets face it, in the human body, redundancy does not exist. Check out this article to understand the differentiation in DNA & RNA.

Let's start with the brass tacks. Several factors differentiate DNA from RNA.

Definitively speaking :
~~>  DNA is a nucleic acid, that contains the genetic instructions used in the development & functioning of all known living organisms. RNA is a nucleic acid polymer, that plays an important role in the method that translates genetic information from deoxyribonucleic acid (DNA) in to protein products.

Physique & structure :
~~> DNA is a double - strand molecule. It's a long chain of nucleotides. RNA is a single stranded molecule that has comparatively shorter chains of nucleotides.

Job role & profile :
~~> DNA is a medium of storing & transferring genetic information. RNA facilitates the transfer of messages from the DNA to the ribosomes (they are protein synthesis complex).

Base formation :
~~> DNA is paired as A-T (Adenine-Thymine ) & G-C (Guanine-Cytosine). RNA is paired as A-U (Adenine-Uracil) & G-C (Guanine-Cytosine).

Location, location, location :
~~> DNA is present in the nucleus, the genetic material & as sugar in the deoxiribose. RNA can be tracked in the nucleus & cytoplasm.

Stability factors :
~~> Deoxyribose sugar in DNA is less reactive because they are ruled by the C-H bonds. They are stable in alkaline conditions. They have smaller grooves where the damaging enzyme can attach itself. This makes it harder for the enzyme to assault DNA. Ribose sugar in RNA is more reactive, thanks to the C-OH (hydroxyl) bonds. They are absolutely not stable in alkaline conditions. RNA has larger grooves which makes it simpler to be attacked by enzymes (it is the weak-link!).

Geometric facts :
~~> DNA has helix geometry of the B-form. RNA has helix geometry of the A-form.

USP's :
~~> The body destroys enzymes that cleave DNA. Ultra-violet rays can severely destroy the DNA. RNA strands are made, broken down & reused repeatedly. RNA is more resistant to destroy by ultra-violet rays (alright, here RNA is not the weak-link!).

1.  The characteristic difference in the is the difference in the sugar present in both of them. DNA has deoxysibose sugar and RNA has ribose sugar. The of them differ on single point that ribose sugar has more OH as compared to deoxyribose sugar.

2.  RNA & DNA are different from each other. Nevertheless, each is important for the smooth functioning of the other. Whatever characteristics an individual has, are because of the composition of the storage in the DNA & the functioning of the RNA.

My basic attempt in this article was to give a generic understanding of these complex elements, so that further research (if intended) is simpler. Hopefully, by the finish of the article the terms didn't appear to be in Greek & Latin!!

Mitochondrial DNA and Human Evolution


              The evolution of man has always been a matter of great interest & a widely debated topic in recent times. DNA is present in each cell of the human body. The DNA of  mitochondria in the cell, can be used to reconstruct the evolutionary history of the human species.

              The origin of humans has always been a subject of great interest. Perhaps you might be the descendant of a relatives line, surviving in Africa & the other maintaining the lineage in deep pockets of Europe. Perhaps, the mitochondrial DNA may establish a clear link between a definite descendant & the parent group. Scientists analyze morphological & anatomical evidences that support the theory of evolution of life. Human DNA from diverse cultures is being compared to trace the origins of a specific lineage. There is every possibility that people living in Asia may share their ancestral origins with Americans. The reasons for choosing mitochondrial DNA as the means to study human evolutionary principles are listed below.
It avoids recombination, although, research suggests that it can merge with the nuclear DNA. The mixing of already mixed sections from the father & the brother creates a garbled genetic history.

               There's several thousand copies of mitochondrial DNA as compared to only versions of the nuclear.
Mitochondrial DNA is inherited maternally. Therefore, the tracking of the genetic line becomes simple. The traits are passed on from a great grandmother to the grandmother to her daughter & so on.
Its rate of mutation is much faster than nuclear DNA.
                 Mitochondrial DNA remains fossilized due to the sheer giant numbers.
There's conditions that select what amount or type of mitochondria enters the egg in the work of fertilization. In all the cases, homoplasmic or single type of mitochondrial DNA enters the egg indicating a slow technique of female gamete development. One time the fertilization technique gets over, the coding region of mitochondrial DNA mutates at the rate of about 0.017x10-6/site/year. The hypervariable region is the with no coding where the rate of mutation is 0.47x10-6. The rate of mutation of the whole genome is thought about to select the ancestry, while the descendants analysis reveals the changes in the mitochondrial genome. This technique of determining the evolution through mutation of mitochondrial DNA is called the 'phylogenetic technique.'

Why is DNA Important in Biology?

             A simple answer to the query introduced above is that DNA is necessary for the beginning of life. Main tasks carried out by deoxyribonucleic acid (DNA) are the transfer of hereditary information from generation to the next & controlling production of proteins. DNA also plays an important part in determining the structure & functionality of cells. DNA is known to store information coded in the type of biological molecules. The amount of information stored in DNA is massive. A simple E. coli bacteria has a DNA with nucleotides that are about two million in number. can therefore, get an idea about how much information is present in DNAs of different organisms present in this world. Unveiling the information that lies in these DNA sequences proves to be helpful for scientists.


Forensic Science

  • The use of DNA tests in forensic science has helped in solving lots of criminal cases. In this field, samples of DNA collected from the crime scene are used in verifying the identity of a person. The police and judiciary method as a whole is thus, relying on the credibility of DNA fingerprinting and other such tests to catch criminals.


Applications in Agriculture

  • The use of DNA is being made for genetically modifying important crop varieties. Genetic manipulation of crops can be carried out to make them strong to fight diseases, to increase crop yield and for lots of such purposes. Not only plants, but animal breeds have also been improved with the help of genetic engineering techniques.

RFLP EXPLAINED IN EASY TERMS


             RFLP has been  entirely replaced by PCR-based testing. The following description of RFLP is included here primarily for historic reasons (more current formats see below).
RFLP DNA testing has basic steps:
        The DNA from crime-scene facts or from a reference sample is cut with something called a restriction enzyme. The restriction enzyme recognizes a specific short sequence such as AATT that occurs lots of times in a given cell's DNA. enzyme often used is called Hae III (pronounced: Hay) but the choice of enzyme varies.  For RFLP to work, the analyst needs thousands of cells. If thousands of cells are present from a single individual, they will all be cut in same place along their DNA by the enzyme because each cells DNA is identical to every other cell of that person.

         The cut DNA pieces are now sorted according to size by a gizmo called a gel. The DNA is placed at finish of a slab of gelatin & it is drawn through the gel by an electric current. The gel acts like a sieve allowing tiny DNA fragments to move more quickly than larger ones.

          The size or sizes of the target DNA fragments recognized by the probe are measured. Using the same probe & enzyme, the check lab will perform these same steps for lots of people. These sizes & how they distribute among massive groups of people form a database. From the database a rough idea of how common a given DNA size measured by a given probe is found. The commonness of a given size of DNA fragment is called a population frequency.

           After the gel has separated the DNA pieces according to size, a blot or replica of the gel is made to trap the DNA in the positions that they finish up in, with tiny DNA fragments near finish of the blot & massive ones near the other finish. The blot is now treated with a piece of DNA called a probe. The probe is basically a piece of DNA that binds to the DNA on the blot in the position were a similar sequence (the target sequence) is located.

For RFLP analysis to be reliable, all complex steps of the analysis must be carefully controlled. Databases must be massive meaning they include lots of people; they must be representative of the potential check subjects. Because of the complexities of populations, databases must be interpreted with extreme care. For example, DNA fragment sizes rare in population may be common in other populations. Further, sub-populations or populations within populations must be thought about.

 The restriction enzyme cuts the DNA in to thousands of fragments of  all feasible sizes. The sample is then electrophoretically separated. The DNA at this point is invisible in the gel unless the DNA is stained with a dye. A replica of the gel's DNA is made on something called a blot (also called a Southern blot) or membrane. The blot is then probed (mixed with) a special preparation of DNA that recognizes a specific DNA sequence or locus. Often, the probe is a radioactively labelled DNA sequence (represented by * labelled object in the figure above). Excess probe is washed off the blot, then the blot is laid onto X-ray film. Development reveals bands indicating the sizes of the alleles for the locus within each sample. The film is now called an "autorad." The band sizes are measured by comparing them with a "ladder" of known DNA sizes that is run next to the sample. A match may be declared if samples have RFLP band sizes that are all within 5% of another in size.

FORENSIC DNA TESTING


  • There have been main types of forensic DNA testing. They are often called, RFLP and PCR based testing, although these terms are not very descriptive. Usually, RFLP testing requires larger amounts of DNA and the DNA must be undegraded. Crime-scene facts that is elderly or that is present in tiny amounts is often unsuitable for RFLP testing. Warm damp conditions may speed up DNA degradation rendering it unsuitable for RFLP in a comparatively short time period. 
  • PCR-based testing often requires less DNA than RFLP testing and the DNA may be partially degraded, more so than is the case with RFLP. However, PCR still has sample size and degradation limitations that sometimes may be under-appreciated. PCR-based tests are also very sensitive to contaminating DNA at the crime scene and within the check laboratory. In the work of PCR, contaminants may be amplified up to a billion times their original concentration. Contamination can influence PCR results, without proper handling techniques and proper controls for contamination.

  • PCR is less direct and more liable to error than RFLP. However, PCR has tended to replace RFLP in forensic testing primarily because PCR based tests are faster and more sensitive.