DNA sequenced in space for first time

Nasa astronaut Kate Rubins carried out the test on the International Space Station (ISS) at the weekend.

She was using a compact DNA sequencing device called Minion, which was developed in the UK.

The device, which was sent up to the space station in July, could help astronauts diagnose illness in space and allow them to identify disease-causing microbes on the ISS.

DNA sequencing is the process used to determine the order of the four chemical building blocks that make up the genetic information from a given living organism.

While Dr Rubins carried out her work on the orbiting outpost, researchers were simultaneously sequencing identical test samples on the ground.

The experiment was set up to attempt to make spaceflight conditions, particularly microgravity, the only variables that could account for differences in the results.

Using the Minion in a weightless environment introduces several challenges including the formation of air bubbles in fluid used in the test.

Bubbles rise to the top of a liquid solution and can be removed by centrifuge. But in space, bubbles are less predictable.

Sarah Castro-Wallace, project manager for the experiment, said: "Onboard sequencing makes it possible for the crew to know what is in their environment at any time.

"That allows us on the ground to take appropriate action - do we need to clean this up right away, or will taking antibiotics help or not?

"We can resupply the station with disinfectants and antibiotics now, but once crews move beyond the station's low Earth orbit, we need to know when to save those precious resources and when to use them."

Researchers find way to boost CRISPR-Cas9 efficiency

SAN FRANCISCO, Aug. 28 -- Researchers at the University of California, Berkeley, have found a way to boost the efficiency of a gene-editing tool, known as clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9), so that it cuts and disables genes up to fivefold in most types of human cells. While the key to figuring out the role of genes or the proteins they code for in the human body or in disease is disabling the gene to see what happens when it is removed, CRISPR-Cas9 is the go-to technique for knocking out genes in human cell lines to discover what the genes do and holds the promise of accelerating the process of making knockout cell lines. However, researchers must sometimes make and screen many variations of the genetic scissors to find one that works well. In the new study, published in a the journal Nature Communications, the UC Berkeley researchers found that this process can be made more efficient by introducing into the cell, along with the CRISPR-Cas9 protein, short pieces of deoxyribonucleic acid (DNA) that do not match any DNA sequences in the human genome. The short pieces of DNA, called oligonucleotides, seem to interfere with the DNA repair mechanisms in the cell to boost the editing performance of even mediocre CRISPR-Cas9s between 2½ and 5 times. "It turns out that if you do something really simple - just feed cells inexpensive synthetic oligonucleotides that have no homology anywhere in the human genome - the rates of editing go up as much as five times," said lead researcher Jacob Corn, the scientific director of UC Bekeley's Innovative Genomics Initiative and an assistant adjunct professor of molecular and cell biology. The technique boosts the efficiency of all CRISPR-Cas9s, even those that initially failed to work at all. Corn portrays CRISPR-Cas9 gene editing as a competition between cutting and DNA repair: once Cas9 cuts, the cell exactly replaces the cut DNA, which Cas9 cuts again, in an endless cycle of cut and repair until the repair enzymes make a mistake and the gene ends up disfunctional. Perhaps, he said, the oligonucleotides decrease the fidelity of the repair process, or make the cell switch to a more error-prone repair that allows Cas9 to more readily break the gene. The next frontier, he was quoted as saying in a UC Berkeley news release, is trying to take advantage of the peculiarities of DNA repair to improve sequence insertion, in order to replace a defective gene with a normal gene and possibly cure a genetic disease.

Study identifies gene related to coffee urge

LONDON, Aug. 26 -- An international team of researchers has discovered a gene that is linked to the regulations of our coffee consumption, a study says.Previous studies have investigated the biological mechanisms of caffeine metabolism. The new findings suggest that the gene reduces the ability of cells to breakdown caffeine, causing it to stay in the body for longer.

According to the study published Friday by the University of Edinburgh, the team analyzed genetic information from 370 people living in a small village in south Italy and 843 people from six villages in northeast Italy.

They found that people with a DNA variation in a gene called PDSS2 tended to consume fewer cups of coffee than people without the variation. The effect was equivalent to around one fewer cup of coffee per day on average, according to the study.

The researchers carried out the same study in a group of 1,731 people from the Netherlands. The result was similar but the effect of the gene on the number of cups of coffee consumed was slightly lower.

One explanation is that the different styles of coffee that are drunk in the two countries lead to the difference, says the researchers.

In Italy, people tend to drink smaller cups such as espresso while people in the Netherlands prefer larger cups that contain more caffeine overall.

The results of this study add to existing research suggesting that our drive to drink coffee may be embedded in our genes, said Dr Nicola Pirastu, Chancellor's Fellow at the University of Edinburgh's Usher Institute.

Pirastu is one of the authors of the study.

However, larger studies are needed to confirm the discovery and also to clarify the biological link between PDSS2 and coffee consumption, says Pirastu.

The study has been published in the journal Scientific Reports.

Chinese scientists map genome sequence of mustard

Chinese scientists have mapped the genome sequence of allopolyploid Brassica juncea, or mustard, a vegetable commonly used in Chinese cooking.

Zhejiang University's Zhang Mingfang, who is a member of the research program, said Tuesday that the sequencing would help scientists understand and improve the agriculturally important vegetable.

The research paper was published in the Nature Genetics journal.

Brassica juncea, known as "jei cai" in its native China, contains a diverse range of oilseed and vegetable corps important for human nutrition. It mainly grows south of the Yangtze River.

Zhang said under the program, the team has, for the first time, analyzed the cause of mustard's different genetic expressions.

He said mustard used for pickling and oil can bring great economic and social benefits. China has 133,000 hectares of mustard for pickling.

Pickled mustard uses a variant of Brassica juncea. Once processed, the stem retains its crisp texture.

Yang Jinghua, one of the authors of the paper, said scientists had previously published the genome maps of Chinese cabbage and kale. The genome of jei cai has more flexible phenotypes and a complex evolutionary process, which made it harder to decode, he said. The vegetable has double genomes after its natural hybridization between Chinese cabbage and black mustard.

For future application, Yang said they aim to develop a more hardy variant of the plant, which will result in larger yields.

"Some of the Brassica juncea are better at resisting disease, but others are the complete opposite. We can improve it through molecular breeding if we find the genes which determine the strength of disease resistance," he said.

Stress gene linked to heart attacks

By Helen BriggsBBC News

A stress gene has been linked to having a higher risk of dying from a heart attack or heart disease.

Heart patients with the genetic change had a 38% increased risk of heart attack or death, say US researchers.

Personalised medicine may lead to better targeting of psychological or drug treatment to those most at risk, they report in PLOS ONE.

The study adds to evidence stress may directly increase heart disease risk, says the British Heart Foundation.

A team at Duke University School of Medicine studied a single DNA letter change in the human genome, which has been linked to being more vulnerable to the effects of stress.

They found heart patients with the genetic change had a 38% increased risk of heart attack or death from heart disease after seven years of follow up compared with those without, even after taking into account factors like age, obesity and smoking.

This suggests that stress management techniques and drug therapies could reduce deaths and disability from heart attacks, they say.

Dr Redford Williams, director of the Behavioural Medicine Research Center at Duke University School of Medicine, said the work is the first step towards finding genetic variants that identify people at higher risk of cardiovascular disease.

"This is one step towards the day when we will be able to identify people on the basis of this genotype who are at higher risk of developing heart disease in the first place," he told BBC News.

"That's a step in the direction of personalised medicine for cardiovascular disease."

Identifying people with the genetic change could lead to early interventions for heart patients who are at high risk of dying or having a heart attack, say the researchers.

About one in 10 of men and 3% of women in the group of 6,000 heart patients studied had the genetic change associated with handling emotional stress badly.

Commenting on the study, Prof Jeremy Pearson, associate medical director at the British Heart Foundation, said the results provided further evidence that stress may directly increase heart disease risk.

"By finding a possible mechanism behind this relationship, these researchers have suggested tackling the problem either by changing behaviour or, if needed, with existing medicines," he said.

"There are positive lifestyle changes you can make to help you cope with stress. A balanced diet and regular physical activity will help you feel better able to cope with life's demands.

"If you often feel anxious and you're worried about your stress levels, make an appointment to talk it through with your doctor."

Fossil of "most successful mammal" on Earth unearthed in China

A nearly complete skeleton that belongs to the oldest ancestor of "the most evolutionarily successful and long-lived mammal lineage" on Earth has been unearthed in northeastern China, researchers from China and the United States said Thursday.

Dubbed Rugosodon eurasiaticus, the newly discovered species looked a bit like a small rat or a chipmunk. It lived 160 million years ago and was an early member of the group of mammals known as multituberculates, which flourished across the planet from about 170 million to 35 million years ago.

"The new mammal is called Rugosodon after the rugose teeth ornamented by numerous tiny ridges and grooves and pits, indicating that it was an omnivore that fed on leaves and seeds of ferns and gymnosperm plants, plus worms and insects," an international team of scientists from Chinese Academy of Geological Sciences, Beijing Museum of Natural History and the University of Chicago said in a statement.

The researchers described in the U.S. journal Science Rugosodon 's ankle bones as being "surprisingly mobile and flexible," a feature that suggests Rugosodon was a fast-running and agile mammal.

"The later multituberculates of the Cretaceous era and the Paleocene epoch are extremely functionally diverse: Some could jump, some could burrow, others could climb trees and many more lived on the ground. The tree-climbing multituberculates and the jumping multituberculates had the most interesting ankle bones, capable of 'hyper-back-rotation' of the hind feet," said ZheXi Luo, professor at the University of Chicago and co-author of the study. "What is surprising about this discovery is that these ankle features were already present in Rugosodon."

The researchers also said Rugosodon was a nocturnal mammal and lived in a temperate climate in lakeshores of what is now known as Jianchang County of Liaoning province in northeastern China. At that time, the creature shared the land with the feathered dinosaur Anchiornis, the pterosaur Darwinipterus, and abundant arthropods, several other mammals.

The discovery of Rugosodon extends the distribution of certain multituberculates from Europe to Asia during the Late Jurassic period, the researchers said.

"This new fossil from eastern China is very similar to the Late Jurassic fossil teeth of multituberculates from Portugal in western Europe," explained Luo. "This suggests that Rugosodon and its closely related multituberculates had a broad paleogreographic distribution and dispersals back-and-forth across the entire Eurasian continent."

Multituberculates arose in the Jurassic period and went extinct in the Oligocene epoch, occupying a diverse range of habitats for more than 100 million years before they were out-competed by more modern rodents.

Scientists believed that by the end of their run on the planet, multituberculates had evolved complex teeth that allowed them to enjoy vegetarian diets and unique locomotive skills that enabled them to traverse treetops. Both adaptations helped them thrive in the shadows of dinosaurs and survive through their mass extinction 65 million years ago. They became the most abundant mammals of the Mesozoic Era and constitute almost half of all mammal species that lived in the Jurassic and Cretaceous.

Nanoparticles could help sperm defects probe

A way of using nanoparticles to investigate the mechanisms underlying infertility has been developed by British scientists, according to a new report published in a scientific journal on Friday.

The technique, published in Nanomedicine: Nanotechnology, Biology and Medicine, could help researchers discover the causes behind cases of unexplained infertility, and develop treatments for affected couples.

The method involves loading porous silica nanoparticle "envelopes" with compounds to identify, diagnose or treat the causes of infertility. Researchers demonstrated that the nanoparticles could be attached to boar sperm with no detrimental effects on their function.

"An attractive feature of nanoparticles is that they are like an empty envelope that can be loaded with a variety of compounds and inserted into cells," Natalia Barkalina, lead author of the study from Oxford University, said.

"The nanoparticles we use don't appear to interfere with the sperm, making them a perfect delivery vessel."

According to researchers, sperm are difficult to study due to their small size, unusual shape and short lifetime outside of the body, yet this is a vital part of infertility research. Previous methods involved complicated procedures in animals and introduced months of delays before the sperm could be used.

The new technique enabled researchers to expose sperm to nanoparticles in a petri dish, which can all be done quickly enough for the sperm to survive perfectly unharmed.

"We will start with compounds to investigate the biology of infertility, and within a few years may be able to explain or even diagnose rare cases in patients. In future we could even deliver treatments in a similar way," study co-author Celine Jones said.