Mês: Julho 2015

A cellular puzzle: The weird and wonderful architecture of RNA

Cells contain an ocean of twisting and turning RNA molecules. Now researchers are working out the structures — and how important they could be.

Sourced through Scoop.it from: www.nature.com

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Finding Hidden Messages in DNA (Bioinformatics I) – University of California, San Diego | Coursera

Finding Hidden Messages in DNA (Bioinformatics I) from University of California, San Diego. This course begins a series of classes illustrating the power of computing in modern biology. Please join us on the frontier of bioinformatics to look for hidden messages in DNA without ever needing to put on a lab coat. After warming up our algorithmic muscles, we will learn how randomized algorithms can be used to solve problems in bioinformatics. Take free online classes from 120+ top universities and

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Um curso engraçado do Coursera suportado pela Universidade da Califórnia (campus de San Diego) sob o título "Encontrando mensagens ocultas no DNA". Engraçado o tema escolhido para o video de apresentação: "A bioinformática tem crescido imenso mas continua a ser um campo inexplorado, ao estilo de um Western americano". Já um professor meu me dizia que a Bioinformática me dizia que a Bioinformática continua a ser um verdadeiro faroeste…

 

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Why is life left-handed? The answer is in the stars

Researchers have created a star-forming cloud in the laboratory to try to recreate the first-ever biological molecule. The study could explain why such molecules are left-handed.

 

While most humans are right-handed, our proteins are made up of lefty molecules. In the same way your left and right hands mirror one another, molecules can assemble in two reflected structures. Life prefers the left-handed version, which is puzzling since both mirrored types form equally in the laboratory. But a new study suggests that this may be because the star-forming cloud that created the first-ever biological molecule, before our sun was even born, made it left-handed.

In 2004, NASA’s Stardust spacecraft swept through the nebulous halo surrounding a comet. What it found was the simplest of life’s building blocks: the amino acid glycine. Comets are frozen remnants from the earliest days in our solar system. Their material is therefore not made in planets, but likely originates in the natal gas cloud that formed our sun.

A research team recently recreated the freezing conditions inside such a star-forming cloud. In apparatus sealed completely from the already crisp air in the laboratory, the temperature can be brought down to -263 degrees Celsius, just ten degrees above absolute zero where even molecules stop vibrating. They believed that on the surface of dust grains suspended in this chilly gas, glycine may have undergone a change that made it left-handed.

At the core of the glycine molecule is a carbon atom with four bonds. If two of these bonds attach to hydrogen atoms, then the molecule is symmetric and neither right nor left handed. However, swap a hydrogen for a heavier atom and this symmetry is broken. The molecule can then form two mirrored versions, giving it handedness or “chirality” as it is called in chemistry.

The experiments suggest that a glycine hydrogen atom could be displaced by an atom of deuterium, which is a heavier version of hydrogen that contains an extra neutron in its nucleus, doubling its weight. It is abundant inside star-forming clouds, which is why they create many deuterium-enriched compounds, including heavy water. Once a deuterium atom has replaced a hydrogen, it is very hard to dislodge. This means that the fraction of chiral glycine steadily increases, until the main species of glycine inside the cloud shows left or right handedness.

Chiral glycine is very similar to original glycine, but with an important extra property. Laboratory experiments have shown that chiral glycine is a catalyst for other chiral molecules. That is, it promotes the production of other species with the same handedness as itself. The result is that if glycine became a left-handed molecule, then future biological molecules would also be predominantly left-handed. When life developed on Earth, it would therefore build from a pool of left-handed molecules, giving it the bias we observe today.

 

Sourced through Scoop.it from: theconversation.com

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Decoding data-driven healthcare: an interview with European Bioinformatics Institute’s Steven Newhouse

Newhouse tells Computing how technologies including cloud computing and wearable devices are helping to bring about the consumerisation of genetic sequencing

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Os desafios actuais que se apresentam à instituição europeia que agrega toda a investigação no continente: evolução das plataformas da infraestrutura a caminho de se preparar para o objectivo da sequenciação por indivíduo.

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Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee : Nature Communications : Nature Publishing Group

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What lives here? DNA sequencing analysis shows what lives in a stream of water

Industry, agriculture and human settlement put a strain on bodies of water; some organisms cannot survive due to the changing conditions in streams and rivers. Accordingly, their existence sheds light on the quality of the habitat. However, the number of experts able to identify the small animals on the basis of their appearance is in decline; only a few junior researchers are active in this field. RUB researchers from the Department Animal Ecology, Evolution and Biodiversity help preserve expert knowledge.

Database with “DNA barcodes”

For this purpose, they are creating a database in collaboration with the “German Barcode of Life Project”: in the first step, qualified experts identify the water organisms based on their appearance. Subsequently, a short characteristic segment of the animals’ genome – i.e. the barcode – is decoded and fed into the database. Someone who wishes to find out which species are represented in a body of water, takes a water sample, sequences the DNA of the organisms contained therein and matches it against the database. Vasco Elbrecht and Dr Florian Leese have developed an innovative lab protocol which renders this so-called DNA barcoding much faster than hitherto. They are able to identify more than thousand animals within a week after taking the sample. Even now in the development stage, the method identifies more than 80 per cent of the species correctly. It is thus more reliable than species identification based on external characteristics, and the biologists from Bochum are convinced that they will optimise the quota in the near future.

Assessment systems have to be adjusted to the new method

In their study, the Bochum-based biologists have also demonstrated the limitations of DNA barcoding. Using this method, it cannot be determined how many individuals of a certain species can be found in a body of water. The established assessment criteria for water quality, on the other hand, do include such data. “This is a problem for available assessment systems,” says Florian Leese. “However, running waters are very dynamic; the frequency of species varies strongly for natural reasons over time. Therefore, it makes sense to record the quality based on conclusive species lists, without focusing too much on frequency.”

 

V. Elbrecht, F. Leese (2015): Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass – sequence relationships with an innovative metabarcoding protocol,

PLOS ONE, DOI: 10.1371/journal.pone.0130324, http://dx.plos.org/10.1371/journal.pone.0130324

Sourced through Scoop.it from: aktuell.ruhr-uni-bochum.de

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