It’s Monday, and there’s plenty of catching up to do around the world of genetics. This week month -

The Broad Institute received an astonishing $400 million endowment from the donors that bear its name. The Institute helped mapped the full complement of the human genes. This record-setting gift will fund genomics research.

A melanoma cell line mistakenly identified as breast cancer cell line was used in more than 650 published breast cancer studies. The mistake happened 25 years ago, and could have implications for the cancer studies the cell line was used in.

The NIH awarded $138M to 47 scientists for “deep innovation” in genomics proteomics and other molecular biology research efforts.

Your genes can map your ancestry to your home country.

Joseph Vanden Plas takes a hard look at the hype of stem cell research.

Who owns the genetic data for the avian influenza virus? WHO, Indonesia and other developing nations want a say. Pharmaceuticals use the viral data for vaccine research, so whoever owns the intellectual property right gets a share of the cash.

image: sxc

Closely related species of Pairie dog don’t live together (Photo credit Imperial College) Ever wondered why family feuds result in fighting relatives keeping their distance … often for a very long time? Well, reseachers at Imperial College, UK have observed that steering clear of your rels may have evolutionary beginnings. Mammals cannot share their habitat with closely related species because the need for the same kind of food and shelter would lead them to compete to the death. This idea that closely related species would be unlikely to be found together because they compete ferociously was first put forward by Charles Darwin in 1859. This study provides the most evidence so far for Darwin’s prediction, thanks to the new complete ‘family tree’ for mammals, developed by Imperial biologists last year, and new comprehensive data on the location and make-up of different mammal communities worldwide. The new research focused on communities of three different types of mammals: new world monkeys (including marmosets, tamarins and spider monkeys), possums, and ground squirrels (including marmots, prairie dogs and chipmunks). For further information, click on: http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_28-5-2008-10-20-29?newsid=37114 Elaine Warburton  www.geneticsandhealth.com

(Photo credit: www.marinebio.org) 

At the Convention on Biological Diversity meeting in Bonn nearly 200 countries agreed on measures to protect the world’s most threatened wildlife.  They pledged:

1. To set up a deep-sea nature reserve and increase by tens of millions of hectares the area of land protected (the resulting protected area would be twice the size of Germany).

2. To ban experiments to boost plankton growth to reverse climate change, because of the potential risks to other animals.

3. To set global standards for developing biofuels, a renewable energy that has been blamed for deforestation.

But environmentalists said the progress achieved at the conference was still failing the UN Millennium Development Goal, which aims to “substantially reduce” biodiversity loss by 2010.

Elaine Warburton  www.geneticsandhealth.com

Stonehenge, UK 

(Photo credit: www.activemind.com)

A topical article for me as I will be passing Stonehenge today.  It is an amazing feat of 4,500 year old primitive engineering and still provokes feelings of wonder and awe everytime I pass by, especially on solstice and equinox days.

Stonehenge served as a burial ground for much longer than had previously been believed, new research suggests. The site was used as a cemetery for 500 years, from the point of its inception.

Archaeologists have said the cremation burials found at the site might represent a single elite family and its descendents - perhaps a ruling dynasty.

Professor Mike Parker Pearson, from the department of archaeology at the University of Sheffield, and his colleagues have now carried out radiocarbon dating of burials excavated in the 1950s that were kept at the nearby Salisbury Museum. Their results suggest burials took place at the site from the initiation of Stonehenge, just after 3,000 BC, until the time the large stones appear at about 2,500 BC.

However, two other Stonehenge experts, Professor Tim Darvill, from the University of Bournemouth, and Professor Geoff Wainwright, from the Society of Antiquaries, have a different theory about the monument.

They are convinced that the dominating feature on Salisbury Plain in Wiltshire, UK was akin to a “Neolithic Lourdes” - a place where people went on a pilgrimage to get cured.

They recently carried out a two-week excavation at the site to search for clues to why the 4,500-year-old landmark was erected.

Elaine Warburton  www.geneticsandhealth.com

King Akhenaten (photo credit www.usu.edu) 

The feminine features and elongated head of ancient Egypt’s King Akhenaten may be attributed to two genetic defects called aromatose excess syndrome and craniosynostosis, reports Yale School of Medicine dermatology Professor Irwin Braverman, M.D.

Akhenaten, a pharaoh during Egypt’s 18th Dynasty credited with starting the practice of worshipping one God, fathered six children. He was often portrayed in sculptures and carvings with a thin neck, elongated head, large buttocks, breasts, and even a prominent belly, suggesting pregnancy.

Aromatose excess syndrome can lead to feminine features in men and advanced sexual development in girls. Akhenaten’s daughters are depicted with breasts at age three and seven in some carvings.

It may be possible to confirm his diagnoses, Braverman said, by conducting genetic tests on the five relevant mummies of Akhenaten’s relatives. “DNA taken from the bone marrow could reveal the presence of the gene defects,” he said.

Braverman explains that Akhenaten’s elongated head could be due to the gene defect causing craniosynostosis, in which the fibrous joints of the head fuse at an early age and disrupt the process of skull formation. Braverman said that a number of Akhenaten’s relatives-including his daughters, and two other 18th-Dynasty rulers, Queen Hatshepsut and King Tut-all had cranial abnormalities that mimicked craniosynostosis.

Elaine Warburton  www.geneticsandhealth.com

 (Tasmanian Tiger - photo credit www.bbc.co.uk/news)

Using transgenic mice, Australian and American researchers have shown that they can “resurrect” a snippet of DNA from the genome of an extinct animal — the Tasmanian tiger — and test its biological function in a living animal.   The last Tasmanian Tiger died in an Australian zoo in 1936 having been hunted to extinction.

Dr Andrew Pask, of the Department of Zoology at Melbourne University, who led the research, said it was the first time that DNA from an extinct species had been used to carry out a function in a living organism.

“As more and more species of animals become extinct, we are continuing to lose critical knowledge of gene function and its potential,” he said.  “Up until now we have only been able to examine gene sequences from extinct animals. This research was developed to go one step further to examine extinct gene function in a whole organism.”

The team extracted DNA from some of these specimens, and injected a gene involved in cartilage formation into developing mouse embryos.  The DNA functioned in a similar way to the equivalent gene in mice, giving information about the genetic make-up of the extinct marsupial.

“At a time when extinction rates are increasing at an alarming rate, especially of mammals, this research discovery is critical,”said Professor Marilyn Renfree, also of the University of Melbourne’s Department of Zoology.

“For those species that have already become extinct, our method shows that access to their genetic biodiversity may not be completely lost.”

Elaine Warburton  www.geneticsandhealth.com

A nationwide team of researchers, funded in part by the National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), has produced the first sequence-based map of large-scale structural variation across the human genome.

Recently created maps such as the HapMap have catalogued the patterns of small-scale variations in the genome that involve single DNA letters, or bases.  A sequence-based map provides much finer resolution and location information.

Researchers constructed the structural variation map by partially sequencing the genomes of eight people: four people of African descent, two of Asian descent and two of European descent. Sequence data were collected from each end of roughly 1 million random small pieces of DNA from each individual’s genome.

These end sequences were compared to the reference sequence of the human genome completed in 2003. Where precise matches did not occur, the scientists inferred that there was a structural difference between the volunteer’s sample and the reference sequence of the human genome.

In addition to revealing new variations, the map also provides a more detailed look at the locations of nearly 1,700 structural variations - half of which had not been previously described . About half of the structural variations were found in at least two of the eight genomes analyzed. The work also uncovered 525 new regions of large-scale structural variation in the human genome. The large-scale differences came in many forms, including deletions and out-of-place insertions of long stretches of DNA. Almost half of the new variations consist of differences in how many copies individuals have of a certain gene, which researchers refer to as a copy number variant.

“The structural variation map will give us a much better picture of genetic variation between each individual, and help us better understand these areas of the genome that are prone to large-scale changes over time,”said Evan Eichler, Ph.D., of the University of Washington, who led the research.

Sequence data from the structural variation map are publicly available through the NIH’s National Center for Biotechnology Information Trace Archive, www.ncbi.nlm.nih.gov/Traces. Mapping data are also freely available from the University of Washington, http://hgsv.washington.edu.

Elaine Warburton  www.geneticsandhealth.com

KQED Public Broadcasting in San Francisco recently did a radio story about the UC San Francisco Canine Behavioral Genetics Project run in collaboration with the University of Pennsylvania. The aims of the project are:

1. To explore the relationship between genes and behavior, both normal and abnormal, in domestic dogs.

2. To assess the amount and nature of genetic diversity in domestic dogs, both within and between breeds. 

Melanie Chang of the CBG project

Anyone wishing to send in their dog’s DNA can visit the site:

http://www.k9behavioralgenetics.com/ 

Dog DNA samples waiting to be processed at the CBG project 

However, it is often said dogs and their owners resemble each other. Now, researchers within this project are looking for those connections on a whole new level. They’re searching for the genes that cause common psychiatric problems in humans - by looking at the DNA of dogs. Have a listen to this very interesting broadcast:

http://www.kqed.org/quest/radio/view/836

Elaine Warburton  www.geneticsandhealth.com

(Picture courtesy of BBC News)

Scientists have discovered the oldest human remains in western Europe.

A jawbone and teeth discovered at the famous Atapuerca site in northern Spain have been dated between 1.1 and 1.2 million years old.

Scientists also found stone tools and animal bones with tell-tale cut marks from butchering by humans.

Its small size suggests it could have belonged to a female.

The finds provide further evidence for the great antiquity of human occupation on the continent, the researchers write in the journal Nature.

Elaine Warburton  www.geneticsandhealth.com

‘Clover structure’ of Transfer RNA 

Transfer RNA (tRNA) is ancient. It is the most direct intermediary between genes and proteins. Like many other RNAs (ribonucleic acids), tRNA aids in translating genes into the chains of amino acids that make up proteins. The fact that tRNA is so central to the task of building proteins probably means that it has been around for a long time.

Professor Gustavo Caetano-Anollés and Feng-Jie Sung of Univeristy of Illinois-Urbana Champaigne had a hunch that understanding the structural properties of tRNA would shed light on how organisms and viruses evolved.

All tRNAs assemble themselves into a shape that, if flattened, resembles a cloverleaf. The team began by looking for patterns in this cloverleaf structure, using detailed data from hundreds of molecules representing virusesand each of the three superkingdoms of life: archaea (microbes that can survive in boiling acid, near sulfurous ocean vents or in other extreme environments), bacteria and eukarya.

“Perhaps in evolution there are things that are so fundamental that they are kept, held onto, for millions or even billions of years,”Caetano-Anollés said. “Those are the fossils, the molecular fossils, that tell us about the past. Therefore, studying these molecules can address fundamental questions in biology and evolution”.

They conducted the same analysis on the tRNAs of each of the superkingdoms, to see how far these groupings diverged from the overall tree. This comparison allowed them to determine the order in which viruses and each of the superkingdoms diverged.

The new analysis supports an earlier study that suggested that the archaea were the first to arise as an evolutionarily distinguishable group. The research also indicated that viruses emerged not long after the archaea, with the superkingdoms eukarya and bacteria following much later - and in that order.

This finding may influence the ongoing debate over whether viruses existed prior to, or after, the emergence of living cells, Caetano-Anollés said.

Elaine Warburton  www.geneticsandhealth.com