Showing posts with label DNA. Show all posts

Saturday 7 December 2013

ancient humans

Saturday, 7 December 2013

Neanderthal sex boosted immunity in modern humans

Labels: evolve

Neanderthal sex boosted immunity in modern humans

By Matt McGrathScience reporter, BBC World Service Infographic

Human leucocyte antigen (mauve) is expressed on the outside of white blood cells

Sexual relations between ancient humans and their evolutionary cousins are critical for our modern immune systems,researchers report in Science journal.

Mating with Neanderthals and another ancient group called Denisovans introduced genes that help us cope with viruses to this day, they conclude.

Previous research had indicated that prehistoric interbreeding led to up to 4% of the modern human genome.

The new work identifies stretches of DNA derived from our distant relatives.

In the human immune system, the HLA (human leucocyte antigen) family of genes plays an important role in defending against foreign invaders such as viruses.

The authors say that the origins of some HLA class 1 genes are proof that our ancient relatives interbred with Neanderthals and Denisovans for a period.

“Start Quote

Getting these genes by mating would have given an advantage to populations that acquired them”

Peter Parham

At least one variety of HLA gene occurs frequently in present day populations from West Asia, but is rare in Africans.

The researchers say that is because after ancient humans left Africa some 65,000 years ago, they started breeding with their more primitive relations in Europe, while those who stayed in Africa did not.

"The HLA genes that the Neanderthals and Denisovans had, had been adapted to life in Europe and Asia for several hundred thousand years, whereas the recent migrants from Africa wouldn't have had these genes," said study leader Peter Parham from Stanford University School of Medicine in California.

"So getting these genes by mating would have given an advantage to populations that acquired them." Meet the Denisovans

When the team looked at a variant of HLA called HLA-B*73 found in modern humans, they found evidence that it came from cross-breeding with Denisovans.

Scanty remains

While Neanderthal remains have been found in many sites across Europe and Asia, Denisovans are known from only a finger and a tooth unearthed at a single site in Russia, though genetic evidence suggests they ranged further afield.

"Our analysis is all done from one individual, and what's remarkable is how informative that has been and how our data looking at these selected genes is very consistent and complementary with the whole genome-wide analysis that was previously published," said Professor Parham.

A similar scenario was found with HLA gene types in the Neanderthal genome.

"We are finding frequencies in Asia and Europe that are far greater than the whole genome estimates of archaic DNA in modern humans, which is 1-6%," said Professor Parham.

The scientists estimate that Europeans owe more than half their variants of one class of HLA gene to interbreeding with Neanderthals and Denisovans.

Asians owe up to 80%, and Papua New Guineans up to 95%.

Uneven exchange

Other scientists, while agreeing that humans and other ancients interbred, are less certain about the evidence of impacts on our immune system.

"I'm cautious about the conclusions because the HLA system is so variable in living people," commented John Hawks, assistant professor of anthropology at the University of Wisconsin-Madison, US.

DNA from a tooth (pictured) and a finger bone show the Denisovans were a distinct group

"It is difficult to align ancient genes in this part of the genome.

"Also, we don't know what the value of these genes really was, although we can hypothesise that they are related to the disease environment in some way."

While the genes we received might be helping us stay a step ahead of viruses to this day, the Neanderthals did not do so well out of their encounters with modern human ancestors, disappearing completely some 30,000 years ago.

Peter Parham suggested a parallel could be drawn between the events of this period and the European conquest of the Americas.

"Initially you have small bands of Europeans exploring, having a difficult time and making friends with the natives; but as they establish themselves, they become less friendly and more likely to take over their resources and eliminate them.

"Modern experiences reflect the past, and vice versa."

DNA: the 'smartest' molecule in existence

DNA: the 'smartest' molecule in existence?

By Jennifer Green and Dhruti ShahBBC Science

Composite image of zip, ladder, DNA strand, Morse code (courtesy Porthcurno Telegraph Museum) and telephone coil. Other images via Getty

DNA is structured like a ladder, opens and closes like a zip, codes data like Morse code and coils tightly

DNA is the molecule that contains and passes on our genetic information. The publication of its structure on the 25th of April 1953 was vital to understanding how it achieves this task with such startling efficiency.

In fact, it's hard to think of another molecule that performs so many intelligent functions so effortlessly. So what is it that makes DNA so smart?

Multi-millennial survivor

For such a huge molecule, DNA is very stable so if it's kept in cold, dry and dark conditions, it can last for a very, very long time. This is why we have been able to extract and analyse DNA taken from species that have been extinct for thousands of years.

Scientists have 'resurrected' blood protein from preserved mammoths after harvesting their DNA

It's the double-stranded, double-helix structure of DNA that stops it falling apart.

DNA's structure is a bit like a twisted ladder. The twisted 'rails' are made of sugar-phosphate, which give DNA its shape and protect the information carrying 'rungs' inside. Each sugar-phosphate unit is joined to the next by a tough covalent bond, which needs a lot of energy to break.

In between the 'rails', weaker hydrogen bonds link the two halves of the rungs together. Individually each hydrogen bond is weak - but there are thousands of hydrogen bonds within a single DNA molecule, so the combined effect is an extremely powerful stabilising force.

It's this collective strength of DNA that has allowed biologists to study genes of ancient species like the woolly mammoth - extinct but preserved in the permafrost.

This short animation explains everything else you need to know about DNA.

Clever facsimile machine

Our cells need to divide so we can grow and re-build, but every cell needs to have the instructions to know 'how to be' a cell.

Intelligent error correction

The consequences of wrongly read or copied information can be disastrous and cause deformities in the proteins.

So as DNA replicates, enzymes carry out a proof-reading job and fix any rare errors.

They tend to repair about 99% of these types of errors, with further checks taking place later.

Can the Human Genome project help spot common genetic mutations?

DNA provides those instructions - so a new copy of itself must be made before a cell divides.

It's the super-smart structure that makes this easy. The 'rungs' of the DNA ladder are made from one of four nitrogen-based molecules, commonly known as A, T, G and C. These form complementary pairs - A always joins with T and G always joins with C.

So one side of the double-stranded DNA helix can be used as a template to produce a new side that perfectly complements it. A bit like making a new coat zip, but by using half of the old zip as a template.

The original side and the new one combine together to form a new DNA double helix, which is identical to the original.

Cleverly, human DNA can unzip and 'replicate' at hundreds of places along the structure at the same time - speeding up the process for a very long molecule.

Molecular contortionist

Two metres of DNA coils like a telephone cord to fit into each cell

DNA is one of the longest molecules in the natural world. You possess enough DNA, stretched out in a line, to reach from here to the sun and back more than 300 times.

Yet each cell nucleus must contain two metres of DNA, so it has to be very flexible. It coils - much like a telephone cord - into tight complex structures called chromatins without corrupting the vital information within.

DNA bases - vital rungs in the ladder

There are four different nucleotide bases in each DNA molecule:

Adenine (A)
Thymine (T)
Guanine (G)
Cytosine (C)

These small molecules join DNA together and encode our genetic information.

And despite being packed in so tightly, the genetic material can still be accessed to create new copies and proteins as required.

Human cells contain 23 pairs of chromosomes, with each containing one long DNA molecule as well as the proteins which package it. It's no wonder DNA needs to be extremely supple.

Amazingly, this folded and packed form of DNA is approximately 10,000 times shorter than the linear DNA strand would be if it was pulled taut.

This is why we have the 'luxury' of having the plans for our entire body in nearly every cell.

Biological database

DNA storage

A research team has encoded data in artificially produced segments of DNA, including:

A 26-second snippet of Martin Luther King's classic anti-racism address from 1963
A .pdf" of the seminal 1953 paper by Crick and Watson describing DNA' structure

The total data package was equivalent to 760 kilobytes on a computer drive. Physically, the DNA carrying all that information is no bigger than a speck of dust.

Genes are made up of stretches of the DNA molecule which contain information about how to build proteins - the building blocks of life which make up everything about us.

Different sequences of the four types of DNA bases make 'codes' which can be translated into the components of proteins, called amino acids. These amino acids, in different combinations can produce at least 20,000 different proteins in the human body.

Think of it like Morse Code. It too uses only four symbols (dot, dash, short spaces and long spaces), but it's possible to spell out entire encyclopaedias with that simple code.

Just one gram of DNA can hold about two petabytes of data - the equivalent of about three million CDs.

That's pretty smart, especially when you compare it to other information-storing molecules. Using the same amount of space, DNA can store 140,000 times more data than iron (III) oxide molecules, which stores information on computer hard drives.

DNA may be tiny but with properties including stability, flexibility, replication and the ability to store vast amounts of data, there's a reason why it must be one of the smartest known molecules.

With huge quantities of data being produced by ever-growing computer systems, traditional data storage solutions, like magnetic hard drives are becoming bulky and cumbersome. Researchers have now used DNA to store artificially-produced information, but could this be the future of data storage?

Find out how all DNA's qualities could lead to extinct animals being resurrected

Friday 25 January 2013

Quadruple helix' DNA seen in human cells

'Quadruple helix' DNA seen in human cells

By Jonathan Amos Science correspondent, BBC News

A representation of the four-stranded structure (L) and fluorescent markers reveal its presence inside cells (R)

A representation of the four-stranded structure (L) with fluorescent markers revealing its presence inside cells (R)

Cambridge University scientists say they have seen four-stranded DNA at work in human cells for the first time.

The famous "molecule of life", which carries our genetic code, is more familiar to us as a double helix.
But researchers tell the journal Nature Chemistry that the "quadruple helix" is also present in our cells, and in ways that might possibly relate to cancer.
They suggest that control of the structures could provide novel ways to fight the disease.
"The existence of these structures may be loaded when the cell has a certain genotype or a certain dysfunctional state," said Prof Shankar Balasubramanian from Cambridge's department of chemistry.
"We need to prove that; but if that is the case, targeting them with synthetic molecules could be an interesting way of selectively targeting those cells that have this dysfunction," he told BBC News.
Tag and track It will be exactly 60 years ago in February that James Watson and Francis Crick famously burst into the pub next to their Cambridge laboratory to announce the discovery of the "secret of life".
What they had actually done was describe the way in which two long chemical chains wound up around each other to encode the information cells need to build and maintain our bodies.
Today, the pair's modern counterparts in the university city continue to work on DNA's complexities.
Balasubramanian's group has been pursuing a four-stranded version of the molecule that scientists have produced in the test tube now for a number of years.
It is called the G-quadruplex. The "G" refers to guanine, one of the four chemical groups, or "bases", that hold DNA together and which encode our genetic information (the others being adenine, cytosine, and thymine).
The G-quadruplex seems to form in DNA where guanine exists in substantial quantities.
And although ciliates, relatively simple microscopic organisms, have displayed evidence for the incidence of such DNA, the new research is said to be the first to firmly pinpoint the quadruple helix in human cells.
'Funny target' The team, led by Giulia Biffi, a researcher in Balasubramaninan's lab, produced antibody proteins that were designed specifically to track down and bind to regions of human DNA that were rich in the quadruplex structure. The antibodies were tagged with a fluorescence marker so that the time and place of the structures' emergence in the cell cycle could be noted and imaged.
This revealed the four-stranded DNA arose most frequently during the so-called "s-phase" when a cell copies its DNA just prior to dividing.
Prof Balasubramaninan said that was of key interest in the study of cancers, which were usually driven by genes, or oncogenes, that had mutated to increase DNA replication.
If the G-quadruplex could be implicated in the development of some cancers, it might be possible, he said, to make synthetic molecules that contained the structure and blocked the runaway cell proliferation at the root of tumours.
"We've come a long way in 10 years, from simple ideas to really seeing some substance in the existence and tractability of targeting these funny structures," he told the BBC.
"I'm hoping now that the pharmaceutical companies will bring this on to their radar and we can perhaps take a more serious look at whether quadruplexes are indeed therapeutically viable targets."

Prof Shankar Balasubramanian in front of a painting by artist Annie Newman that represents quadruplex DNA

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Saturday 7 December 2013

ancient humans

Saturday, 7 December 2013