Daily Archives: January 16, 2015

A pair of giant kangaroos that died about 45,000 years ago have had their DNA extracted by scientists from the University of Adelaide in Australia.

A giant short-faced kangaroo (Simosthenurus occidentalis) and a giant wallaby (Protemnodon anak) were the sample donators. They were found in a cave in Tasmania, and thanks to the cold, dry conditions there, short pieces of DNA were able to be retrieved from their remains.

The material shed some new light on the ancient, huge creatures (the short-faced kangaroo weighed about 260 pounds; the giant wallaby more than 240) and gave the extinct giant wallaby a promotion of sorts.

"The ancient DNA reveals that extinct giant wallabies are very close relatives of large living kangaroos, such as the red and western grey kangaroos," said lead author Dr. Bastien Llamas, senior researcher for the university's Australian Centre for Ancient DNA, in a statement.

"Their skeletons had suggested they were quite primitive macropods -- a group that includes kangaroos, wallabies, pademelons and quokkas -- but now we can place giant wallaby much higher up the kangaroo family tree," Llamas said.

The DNA extraction is welcome news to scientists interested in decoding the evolutionary tangle of Australian megafauna. Poor preservation conditions and the sheer age of remains have most often meant DNA was unobtainable, leaving scientists just bones for analysis.

"In addition to poor DNA preservation, most of the extinct Australian megafauna do not have very close relatives roaming around today, which makes it more difficult to retrieve and interpret the genetic data," said Llamas. "We had to think hard about experimental and bioinformatics approaches to overcome more than 10 million years of divergent evolution between the extinct and living species."

Another happy note concerned family matters. While the short-faced kangaroo does not have any modern descendants, the team was able to report that it does at least have a cousin, in the form of the banded hare-wallaby (Lagostrophus fasciatus). Today, that endangered creature lives only on small, isolated islands off Australia's western coast.

"Our results suggest the banded hare-wallaby is the last living representative of a previously diverse lineage of kangaroos," said co-author Mike Lee, of the South Australian Museum and a professor in the universitys School of Biological Sciences. "It will hopefully further encourage and justify conservation efforts for this endangered species."

Read more from the original source:
DNA Extracted from Extinct Giant Kangaroo

A man accused of following a woman to her apartment, forcing his way into her home and raping her in May pleaded not guilty Friday to felony rape and burglary charges.

Investigators used DNA evidence and surveillance footage to link David Glenn Chandler to the crimes, charging documents say.

Chandler, 29, appeared in Yellowstone County District Court by video from jail Friday morning and denied the charges before Judge Ingrid Gustafson, who set his bond at $70,000 and ordered him to pay for and wear a GPS monitor if he bails out of custody.

Billings police started investigating the case on May 24, when a woman at Billings Clinic reported she had been sexually assaulted by a stranger, records say.

The woman reported that she had gone to a convenience store on South 27th Street and then gone back to her apartment. She reported that a man, later identified as Chandler, followed her to the apartment complex.

While they were in the elevator, he groped her, she said. She told him to stop. When she got off the elevator and went to her apartment, he followed her and forced his way into her apartment, she said.

Inside the apartment, he raped her, stole cash and cigarettes and then left, charging documents say.

The woman told police that she didnt know the man, but thought that his name was David.

The woman completed a sexual assault examination, from which samples were sent to the Montana State Crime Lab. Police also obtained video surveillance from both the convenience store and the womans apartment complex. Using that footage, they were able to identify Chandler.

When interviewed, he insisted that he didnt rape the woman and that no DNA evidence would be found linking him to the rape, court documents say.

More here:
DNA evidence links man to rape of woman at her South Side apartment

This news release is available in German.

In the majority of cases, the onset of cancer is characterised by a minor change in a person's genetic material. A cell's DNA mutates in a particular area to the extent that the cell no longer divides in a controlled manner, but begins to grow uncontrollably. In many cases, this type of genetic mutation involves chemical changes to individual building blocks of DNA. These changes are induced by smoking tobacco and consuming foods such as cured meats. This is because the contents of these materials can chemically react with and change building blocks of cellular DNA, thereby creating DNA adducts. Up to now, scientists have been able to determine whether gene samples contain adducts and if so, how many. However, the procedure is laborious and finding out exactly where a building block in the genetic code has been altered into an adduct has not been possible.

Researchers from the team led by Shana Sturla, professor of Food and Nutrition Toxicology, have succeeded for the first time in amplifying gene samples containing DNA adducts while retaining references to these adducts. This type of amplification is a prerequisite for the majority of technologies used by researchers to determine a gene's DNA sequence. In the future, it may therefore be possible to expand DNA sequencing from the four basic DNA building blocks to include adducts. "The scientific community would have an important tool for making a detailed analysis of the molecular mechanisms involved in the initiation of cancer and the corresponding risk factors," says Sturla.

Artificial counterpart found

The researchers focused their efforts on a specific, typical DNA adduct, an alkylguanine called O-6-benzylguanine. They recreated an enzyme reaction in a test tube to obtain a negative copy of the genetic material - analogous to how DNA is replicated naturally in cells. The scientists first had to find an artificial counterpart of the alkylguanine to be incorporated into the negative copy in its position - due to the fact that nature produces molecular counterparts to the basic DNA building blocks, but not to DNA adducts. This is why replicating genes usually leads to copy errors (or mutations) when adducts are present.

The ETH researchers produced several artificial derivatives of the basic DNA building blocks in the laboratory and tested them as potential counterparts to the alkylguanine. One proved particularly suitable. The researchers were then able to produce a negative copy of a gene containing the alkylguanine.

The aim of the work carried out by Sturla and her colleagues was to demonstrate that it is feasible to amplify genes even when adducts are present. It should now be possible for researchers to find artificial counterparts to other adducts using the same method. As the ETH Professor points out, this means that altered genes could be amplified in the future and their sequences more easily ascertained. In 2010, Shana Sturla was awarded a five-year ERC Starting Grant from the European Research Council. The current project was partly financed by this award.

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Literature reference

Wyss LA, Nilforoushan A, Eichenseher F, Suter U, Blatter N, Marx A, Sturla SJ: Specific incorporation of an artificial nucleotide opposite a mutagenic DNA adduct by a DNA polymerase. Journal of the American Chemical Society, 9 December 2014, doi: 10.1021/ja5100542

More:
Damaged DNA amplified

In the majority of cases, the onset of cancer is characterised by a minor change in a person's genetic material. A cell's DNA mutates in a particular area to the extent that the cell no longer divides in a controlled manner, but begins to grow uncontrollably. In many cases, this type of genetic mutation involves chemical changes to individual building blocks of DNA. These changes are induced by smoking tobacco and consuming foods such as cured meats. This is because the contents of these materials can chemically react with and change building blocks of cellular DNA, thereby creating DNA adducts. Up to now, scientists have been able to determine whether gene samples contain adducts and if so, how many. However, the procedure is laborious and finding out exactly where a building block in the genetic code has been altered into an adduct has not been possible.

Researchers from the team led by Shana Sturla, professor of Food and Nutrition Toxicology, have succeeded for the first time in amplifying gene samples containing DNA adducts while retaining references to these adducts. This type of amplification is a prerequisite for the majority of technologies used by researchers to determine a gene's DNA sequence. In the future, it may therefore be possible to expand DNA sequencing from the four basic DNA building blocks to include adducts. "The scientific community would have an important tool for making a detailed analysis of the molecular mechanisms involved in the initiation of cancer and the corresponding risk factors," says Sturla.

Artificial counterpart found

The researchers focused their efforts on a specific, typical DNA adduct, an alkylguanine called O-6-benzylguanine. They recreated an enzyme reaction in a test tube to obtain a negative copy of the genetic material -- analogous to how DNA is replicated naturally in cells. The scientists first had to find an artificial counterpart of the alkylguanine to be incorporated into the negative copy in its position -- due to the fact that nature produces molecular counterparts to the basic DNA building blocks, but not to DNA adducts. This is why replicating genes usually leads to copy errors (or mutations) when adducts are present.

The ETH researchers produced several artificial derivatives of the basic DNA building blocks in the laboratory and tested them as potential counterparts to the alkylguanine. One proved particularly suitable. The researchers were then able to produce a negative copy of a gene containing the alkylguanine.

The aim of the work carried out by Sturla and her colleagues was to demonstrate that it is feasible to amplify genes even when adducts are present. It should now be possible for researchers to find artificial counterparts to other adducts using the same method. As the ETH Professor points out, this means that altered genes could be amplified in the future and their sequences more easily ascertained. In 2010, Shana Sturla was awarded a five-year ERC Starting Grant from the European Research Council. The current project was partly financed by this award.

Story Source:

The above story is based on materials provided by ETH Zurich. The original article was written by Fabio Bergamin. Note: Materials may be edited for content and length.

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Damaged DNA amplified by activities such as smoking