Category Archives: Genome

There's more to Darwin's finches than meets the eye. Famously, the 14 species found on the Galapagos islands are distinguished from one another largely by differences in beak shape. But the first full genome analysis of the birds shows the approach isn't foolproof, because some characteristic beak shapes appear to have evolved on two or three separate occasions.

The finches are named in Darwin's honour because he was the first to collect them during his time on the Beagle and later referred to them when he was formulating his theory of natural selection.

The Galapagos islands owe their reputation as a hotbed of adaptation to their geographical isolation and to the considerable changes in their climate and environments over the last few million years. The finches that inhabit the islands and which featured in Darwin's writings are generally distinguished from one another by the size and beak shape. Some species, for instance, have deep and blunt beaks for cracking nuts while others have long and pointed beaks for feeding on nectar.

Leif Andersson at Uppsala University, Sweden, and his colleagues, have now sequenced the full genomes of 120 birds, representing all 14 established species of Galapagos finch, a 15th species that lives on nearby Cocos Island, and two closely related species that live in the Caribbean. Theirs is the most comprehensive genetic analysis of the famous birds to date, says Andersson. Earlier studies have examined just the bird's mitochondrial DNA or small regions of the genome.

When comparing the full genetic sequences to build an evolutionary tree, the researchers found that what ornithologists going back to Darwin's time thought were just two species, based on their beak shape, may in fact be five separate species, based on their genomes.

One species of finch Geospiza difficilis pops up in three completely different branches of the family tree, so it should be counted as three separate species. Another species Geospiza conirostris sits on two separate evolutionary branches, so should be treated as two species.

That means there are 17 not 14 species of finch living on the Galapagos, says Andersson. "We hope that taxonomists will accept our suggestions."

The genetic evidence revealed something else. A single gene, ALX1, has played a vital role in shaping the evolution of beak shape in the finches in particular, whether they are long and pointed or deep and blunt, says Andersson. The find is remarkable because more often than not, important traits are encoded by hundreds of genes, each playing such a small role that linking single genes to a particular trait is very difficult.

"For instance, if you consider stature in humans, genetic studies have shown that there are hundreds of genes that each explain a very small part of the population variance," says Andersson.

So why was it easy to link ALX1 to beak shape? It may be down to the fact that the finch beak has been the focus of exceptionally strong natural selection during the evolutionary radiation of the finches, says Andersson. This means that any genes that are particularly important in its development will have evolved substantially, making them easier to spot in genetic studies.

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Genome reveals three more species of Darwin's finches

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Newswise ANN ARBOR, Mich. There are many reasons why people gain different amounts of weight and why fat becomes stored in different parts of their bodies. Now researchers are homing in on genetic reasons. Their findings, part of the largest genome-wide study to date, were published in two companion papers today in the journal Nature.

By analyzing genetic samples from more than 300,000 individuals to study obesity and body fat distribution, researchers in the international Genetic Investigation of Anthropometric Traits (GIANT) Consortium completed the largest study of genetic variation to date, and found over 140 locations across the genome that play roles in various obesity traits.

By applying novel computational methods to the genetic results, they discovered new biological pathways that are important in controlling body weight and fat distribution.

This work is the first step toward finding individual genes that play key roles in body shape and size. The proteins these genes help produce could become targets for future drug development.

Obesity is a global public health burden that affects millions of people. Yet, there are no long-term treatments.

Waist-to-hip ratios key for health risk One paper focused on where fat is stored in the body, one determinant of health risk. One of the observable traits linked to the genetic locations was waist-to-hip circumference ratio. People with waistlines larger than hip circumferences have more belly fat surrounding their abdominal organs. This makes them more likely to have metabolic conditions, such as type-2 diabetes, and cardiovascular problems than do people with body fat concentrated more in the hip area or distributed equally throughout the body.

We need to know these genetic locations because different fat depots pose different health risks, says Karen Mohlke, Ph.D., professor of genetics at the University of North Carolina School of Medicine and senior author of the paper that examined waist-to-hip ratio of fat distribution. If we can figure out which genes influence where fat is deposited, it could help us understand the biology that leads to various health conditions, such as insulin resistance/diabetes, metabolic syndrome, and heart disease.

The genetic locations associated with fat depots are associated with genes previously identified as being important for the creation of adipose tissue. Researchers also determined that 19 of the fat distribution genetic locations had a stronger effect in women; one had a stronger effect in men.

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Largest Ever Genome-Wide Study Strengthens Genetic Link to Obesity

GBS: genome-wide association analysis (GWAS)
Workshop on Marine Evolutionary Genomics and Proteomics - GBS: genome-wide association analysis (GWAS) Video available at: http://tv.campusdomar.es/en/video/...

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CRISPR technology for genome editing - Spanish
CRISPR, a pioneering genome-editing technique, technology will allow AstraZeneca to identify and validate new drug targets in preclinical models that closely...

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CRISPR technology for genome editing - Spanish - Video

The Human Genome Unlocked
The Aspen Health Forum, 2009. With the mapping of the human genome complete, scientists are hoping to use stem cell therapy and related interventions to alleviate or even cure diseases. What...

By: The Aspen Institute

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Bradley Malin and Jacques Fellay on Whole Genome Sequencing
Guest editor Alf Weaver interviews Bradley Malin and Jacques Fellay about the possibilities and challenges of whole genome sequencing. From Computer #39;s Februa...

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Britain #39;s parliament takes unprecedented step and allows human genome manipulation to prevent
Mother #39;s day may be about to get more complicated in the UK after parliament voted to allow a three-parent IVF technique. It is designed to eliminate the pos...

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Britain's parliament takes unprecedented step and allows human genome manipulation to prevent - Video

MELBOURNE: Decoding the letters of the human genome revolutionised scientists understanding of the role of genetic mutations in many diseases, including about one in every five cancers.

Now a team of Australian scientists have gone a step further, inventing a way to decipher another layer of information that garnishes genes, called methyl groups, which may explain the cause of many more cancers, The Age reported. Methyl groups hang off sections of DNA like Christmas lights and act like a switch, affecting how genes are expressed in different cell types.

Collectively called the methylome, they can also switch off tumour suppressor genes and switch on cancer promoting genes. Professor Susan Clark from the Garvan Institute of Medical Research and her team have for first the first time translated the methylome of breast cancer, finding distinct patterns associated with different types of breast cancer.

They have also found a way to classify women with the worst type of breast cancer, triple-negative, into two groups; those with a highly aggressive form and those with a lower-risk variety with a longer survival time. At present there is no reliable way to divide triple-negative cancers, which do not respond to targeted treatment, into these sub-groups. With further testing, methylation signatures may be used as predictive biomarkers that doctors use to prescribe more appropriate treatments for women diagnosed with breast cancer in the future.

Clarks team are the first in the world to sequence large chunks of the methylome from samples of cancer tissue that had been archived for up to two decades. Using historical samples meant they could trace which methylation patterns were linked to patient survival times. Cancer specialist Dr Paul Mainwaring, who was not involved in the research, said Clarks new technique to decode the entire methylome will have significant implications for cancer research in general.

The power of this technology is that its allowing us to get a much sharper view on how cancer starts, progresses, metastasises, behaves and a new avenue of treatment, said Dr Mainwaring from Icon Cancer Care in Brisbane. Well still be talking about this paper in 20 years, he said.

While specific faults in a persons DNA sequence have been shown to increase their risk of certain cancers the BRCA 2 mutation which significantly increases a womans chance of developing breast tumours in about two-thirds of cancers there are no changes to the DNA code.

In many of these cases scientists are finding changes to the genome that do not affect the underlying code, principally through DNA methylation. Every cancer has some sort of mutational profile, but there are multiple layers of where those abnormalities can occur. This is a giving us the ability to read one of those layers, he said.

Dr Mainwaring said the exciting part about identifying methylation patterns was that they are potentially reversible. Its the bit of the genome we may be able to influence most, certain regions can be changed either by diet, exercise or drugs, he said. Clark and teams research was funded by the National Breast Cancer Foundation and has been published in the leading scientific journal Nature Communications.

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The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions. TAIR also provides extensive linkouts from our data pages to other Arabidopsis resources.

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