Day: 01/13/2011

enjoy chocolate and strawberry together

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Drafts of cacao and strawberry sequences unveiled.


Strawberries and chocolate anyone?Strawberries and chocolate anyone?P. LEFEVRE/ISTOCKPHOTO

Genome gastronomes rejoice! Today sees the publication of genome sequences behind two of the tastiest treats: the cacao tree, whose beans yield chocolate, and the woodland strawberry.

Earlier this year, a team backed by food giant Mars unveiled a preliminary sequence of the cacao tree Theobroma cacao. Now a team partly supported by rival chocolate company Hershey has become the first to get a genome of the valuable plant into a peer-reviewed journal1.

Led by researchers at the Agricultural Research for Development (CIRAD) centre in Montpellier, France, the genome, published in Nature Genetics, looks at the Belizean Criollo variety of the crop. “The Criollo is one of the two varieties that provide fine favour chocolate,” says Claire Lanaud, a geneticist at CIRAD and last author on the paper. “We chose this variety also because we are very interested in the genes involved in quality traits.”

Criollo is also extremely homozygous — it has matching copies of most of its genes on each pair of chromosomes. This is an important factor in producing a high quality genome sequence.

Flavour saver

Although fine cocoa commands a high price, Criollo is not a great crop for farmers; it is susceptible to disease and its yields are not the best.

“In plantations, people are using a hybrid between this Criollo variety and other cocoa genotypes,” says Lanaud. This hybrid is called Trinitario, created by crossing Criollo crossed with the more common Forastero variety. But the hybridization reduces “the high flavour quality of this ancestral Criollo variety”, she says. Consequently, “it is very important to try to have a better knowledge of the genetic determinants of the quality traits of the cocoa”.

Lanaud’s team found scores of genes potentially involved in the production of lipids, flavonoids and terpenoids, responsible for much of the taste of chocolate. T. cacao had some 84 candidate genes involved in lipid biosynthesis, compared with 71 in the well-studied but less flavoursome plant thale cress (Arabidopsis thaliana), and 96 involved in flavonoid biosynthesis, versus just 36 in Arabidopsis.

The paper also highlights genes potentially involved in disease resistance. These may eventually allow breeders to improve the quality and yields of the cocoa varieties.

In contrast to the French-led team, the Mars-backed researchers, who were also supported by the US Department of Agriculture, chose a more widely-farmed hybrid variety of Forastero, known as Matina 1-6, for their sequence (online at www.cacaogenomedb.org).

Having two cacao genomes will be “particularly valuable” and should provide additional candidate genes for important traits, says Brian Scheffler, research leader of the Stoneville, Mississippi-based Genomics and Bioinformatics Research Unit at the US Department of Agriculture’s Agricultural Research Service, who worked on that effot.

“Breeding disease-resistant varieties is one of the major goals of our group’s breeding team. They are already making significant progress in attaining this goal,” he says. “With genomic information from two divergent varieties, they should be able to proceed more rapidly.”

An initial draft of his team’s sequence was unveiled in September this year, although Lanaud says that it has not been possible to directly compare the two versions, as the Mars-sequence appears to have a number of fragments that were inverted when the genome was assembled.

“There indeed might be chromosomal inversions distinguishing these varieties, because they are distantly related,” responds Scheffler. “But determining that will probably require refinements to the assemblies of both genomes, and additional data.”

Strawberry genomes forever

The genome of the woodland strawberry, also known as the wild or alpine strawberry, is also published today in Nature Genetics2. Fragaria vesca — the fleshy shoot tips of which are technically neither fruit nor berry — has a relatively small genome. The authors of the new paper on its genome note that it takes up very little space, potentially making it a good candidate for further study in the lab.

This could open the way to studies on flavour and disease resistance in the cultivated strawberry Fragaria x ananassa, and even in other relatives of the plant such as apples and peaches, all members of the Rosaceae family.

source: nature

Amygdala at the centre of your social network

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A larger emotion-processing brain centre is linked to a bigger circle of friends.

 

AmygdalaThe size of your amygdala (circled) indicates the extent of your social network.Brad Dickerson

How many friends do you have? A rough answer can be predicted by the size of a small, almond-shaped brain structure that is present in a wide range of vertebrates, scientists report today in Nature Neuroscience.

The researchers studied the amygdala, which is involved in inter-personal functions such as interpreting emotional facial expressions, reacting to visual threats and trusting strangers. Inter-species comparisons in non-human primates have previously shown that amygdala volume is associated with troop size, suggesting that the brain region supports skills necessary for a complex social life1.

On the basis of these past findings, psychologist Lisa Feldman Barrett of Northeastern University in Boston, Massachusetts, wondered whether a larger amygdala size allows some humans to build a richer social world.

Barrett’s team measured the amygdala volume in 58 healthy adults using brain images gathered during magnetic resonance imaging sessions. To construct social networks, the researchers asked the volunteers how many people they kept in regular contact with, and how many groups those individuals belonged to.

They found that participants who had bigger and more complex social networks had larger amygdala volumes. This effect did not depend on the age of the volunteers or their own perceived social support or life satisfaction, suggesting that happiness is not the underlying causal factor that links the size of this brain structure in an individual to their number of friends2.

“We’d all predict this relationship should be found, but [the authors] did it in a very smart way by ruling out other variables,” says cognitive neuroscientist Kevin Ochsner of Columbia University in New York City. “That’s why I think this paper is going to end up being a citation classic, because it demonstrates the relationship in a way that gives you confidence that it’s real,” he adds.

Brain teaser

But it’s still a mystery how the amygdala contributes to social networks. Perhaps the structure’s response to faces, emotions or emotional memories influences whether someone decides to develop and maintain relationships, says Brad Dickerson, a cognitive neuroscientist at Massachusetts General Hospital in Boston, who helped lead the study.

It’s likely that social behaviour relies on a much broader set of brain regions, Dickerson says. In the future, the team will use functional neuroimaging approaches to determine the relationship between patterns of brain activity in an individual and the size of social groups to which they belong.

Another important question is whether a big amygdala is a cause or a consequence of having a large social network. “In the end, it’s probably some of both,” Ochsner says. “But you first had to establish that the relationship really exists before you could address those critical questions.”

source:nature

ASPIRIN:the wonder drug

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Effect of Daily Aspirin on Long-Term Risk of Death Due to Cancer: Analysis of Individual Patient Data From Randomised Trials

Results of this analysis of individual patient data from all randomised trials of long-term daily aspirin use were the first to provide proof in man that aspirin reduces deaths due to several common c…

Background: Treatment with daily aspirin for 5 years or longer reduces subsequent risk of colorectal cancer. Several lines of evidence suggest that aspirin might also reduce risk of other cancers, particularly of the gastrointestinal tract, but proof in man is lacking. We studied deaths due to cancer during and after randomised trials of daily aspirin versus control done originally for prevention of vascular events.

Methods: We used individual patient data from all randomised trials of daily aspirin versus no aspirin with mean duration of scheduled trial treatment of 4 years or longer to determine the effect of allocation to aspirin on risk of cancer death in relation to scheduled duration of trial treatment for gastrointestinal and non-gastrointestinal cancers. In three large UK trials, long-term post-trial follow-up of individual patients was obtained from death certificates and cancer registries.

Results: In eight eligible trials (25 570 patients, 674 cancer deaths), allocation to aspirin reduced death due to cancer (pooled odds ratio [OR] 0•79, 95% CI 0•68—0•92, p=0•003). On analysis of individual patient data, which were available from seven trials (23 535 patients, 657 cancer deaths), benefit was apparent only after 5 years’ follow-up (all cancers, hazard ratio [HR] 0•66, 0•50—0•87; gastrointestinal cancers, 0•46, 0•27—0•77; both p=0•003). The 20-year risk of cancer death (1634 deaths in 12 659 patients in three trials) remained lower in the aspirin groups than in the control groups (all solid cancers, HR 0•80, 0•72—0•88, p<0•0001; gastrointestinal cancers, 0•65, 0•54—0•78, p<0•0001), and benefit increased (interaction p=0•01) with scheduled duration of trial treatment (≥7•5 years: all solid cancers, 0•69, 0•54—0•88, p=0•003; gastrointestinal cancers, 0•41, 0•26—0•66, p=0•0001). The latent period before an effect on deaths was about 5 years for oesophageal, pancreatic, brain, and lung cancer, but was more delayed for stomach, colorectal, and prostate cancer. For lung and oesophageal cancer, benefit was confined to adenocarcinomas, and the overall effect on 20-year risk of cancer death was greatest for adenocarcinomas (HR 0•66, 0•56—0•77, p<0•0001). Benefit was unrelated to aspirin dose (75 mg upwards), sex, or smoking, but increased with age—the absolute reduction in 20-year risk of cancer death reaching 7•08% (2•42—11•74) at age 65 years and older.

Interpretation: Daily aspirin reduced deaths due to several common cancers during and after the trials. Benefit increased with duration of treatment and was consistent across the different study populations. These findings have implications for guidelines on use of aspirin and for understanding of carcinogenesis and its susceptibility to drug intervention.

source:Lancet

Retrovirus XMRV

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Early Events in Retrovirus XMRV Infection of the Wild-Derived Mouse Mus pahari{triangledown} ,{dagger}

A novel gammaretrovirus, xenotropic murine leukemia virus-related virus (XMRV), has been identified in patients with prostate cancer and in patients with chronic fatigue syndromes. Standard Mus musculus laboratory mice lack a functional XPR1 receptor for XMRV and are therefore not a suitable model for the virus. In contrast, Gairdner’s shrew-mice (Mus pahari) do express functional XPR1. To determine whether Mus pahari could serve as a model for XMRV, primary Mus pahari fibroblasts and mice were infected with cell-free XMRV. Infection of cells in vitro resulted in XMRV Gag expression and the production of XMRV virions. After intraperitoneal injection of XMRV into Mus pahari mice, XMRV proviral DNA could be detected in spleen, blood, and brain. Intravenous administration of a green fluorescent protein (GFP) vector pseudotyped with XMRV produced GFP+ CD4+ T cells and CD19+ B cells. Mice mounted adaptive immune responses against XMRV, as evidenced by the production of neutralizing and Env- and Gag-specific antibodies. Prominent G-to-A hypermutations were also found in viral genomes isolated from the spleen, suggesting intracellular restriction of XMRV infection by APOBEC3 in vivo. These data demonstrate infection of Mus pahari by XMRV, potential cell tropism of the virus, and immunological and intracellular restriction of virus infection in vivo. These data support the use of Mus pahari as a model for XMRV pathogenesis and as a platform for vaccine and drug development against this potential human pathogen.

source: international journal of virology