Tag: proteins

News from Space: “Life” Molecules Detected in Space!

SagitariusB2The secret to the creation to life in our universe appears to be seeding – the proper elements in the right mix in the right places to form the right kind of molecules. Only then can these molecules evolve chemically into more and more complex structures, thus following a general pathway toward biology. The pathway for life as we know it starts with carbon, but one which is specific organized and structured.

Recently, a team of astronomers  at the ALMA Observatory reported the discovery of this very element while probing distant galaxies. What they found was not just interstellar carbon, but a form of carbon with a branched structure. The discovery was made in the gaseous-star forming region known as Sagittarius B2 – a giant molecular cloud of gas and dust that is located about 390 light years from the center of the Milky Way.

radio-wave-dishesSimple carbon chains aren’t particularly unusual in the cosmos, but complex carbon is a different matter. It is what the researchers, based at Cornell University and the Max Planck Institute, describe as finding a molecular needle in a cosmic haystack. The actual molecule in question is isopropyl cyanide, and it was discerned thanks to the miracle known as radio astronomy.

Within clouds of interstellar dust and gas, elements find themselves shielded from the harsh radiation of open space and are, thus, free to form into more complex arrangements. These molecules don’t just sit there, but instead move around within their cloud-homes and bump into each other. The result of this activity are radio signals which can be detected light-years away – in this case, by radio telescopes here on Earth.

MaxPlanckIns_radiowavepulseEvery molecule has a different radio signal, so it’s possible to pick apart the contents of interstellar junk by examining a cloud’s frequency spectra. NASA, via the Ames Research Center, even maintains a radio-emission frequency database to aid in the tracking of polycyclic aromatic hydrocarbons, a form of molecule thought to contain much of the universe’s carbon stockpiles.

The branching carbon structure of isopropyle cyanide is of particular interest because it’s thought that this arrangement is a step on the way to the production of amino acids, the building blocks of proteins, and hence organic life. The discovery gives weight to the increasingly popular notion that life, or at least many of the key steps leading toward life, actually occurs off-planet.

alien-worldLife on Earth may have been well on its way while the planet was still just space dust waiting to come together into our rock-home. What’s more, the molecules discovered by the ALMA team probably aren’t alone.  As the authors, led by astronomer Arnaud Belloche, wrote:

[Isopropyle cyanide’s] detection therefore bodes well for the presence in the [interstellar medium] (ISM) of amino acids, for which such side-chain structure is a key characteristic… This detection suggests that branched carbon-chain molecules may be generally abundant in the [interstellar medium].

The discovery follows a general progression in recent years adding more and more life-ingredients to our picture of the ISM. A 2011 study revealed that complex organic matter should be created in large volumes from stars, while a 2012 report study found that conditions within the ISM are uniquely suited to the creation of increasingly complex molecules, “step[s] along the path toward amino acids and nucleotides, the raw materials of proteins and DNA, respectively.”

sugar-in-space-molecules_58724_990x742Also in 2012, astronomers working for ALMA found basic sugar molecules hanging out in the gas cloud around IRAS 16293-2422 – a young star located some 400 light-years from Earth. The particular form, glycoaldehyde, is thought to be a key component of the reaction behind the creation of DNA. Indeed, more and more, the universe is looking less and less like a harsh environment in which life must struggle to emerge, to a life factory.

Source: motherboard.vice.com

First Ever Organism with “Alien” DNA

alien-dna-640x353Normal DNA, which is characterized by the double helix and its the four bases that bond it together – known as T, G, A, and C – is at the heart of all living organisms. While permutations and differences exist between species, this basic structure has existed unchanged for billions of years. That is, until now. This past May, researchers announced that they had created the first ever organism with synthetic DNA that has two new bases – X and Y. Mary Shelley and H.G. Wells must be turning over in their graves, as scientists are officially playing God now!

This landmark study, 15 years in the making, was carried out by scientists at the Scripps Research Institute and published in Nature today under the title “A semi-synthetic organism with an expanded genetic alphabet”. In normal DNA, the four bases combine in predictable ways. A always bonds with T, and C always bonds with G, creating a fairly simple “language” of base pairs — ATCGAAATGCC, etc. Combine a few dozen base pairs together in a long strand of DNA and you then have a gene, which tells the organism how to produce a certain protein.

DNA-MicroarrayIf you know the sequence of letters down one strand of the helix, you always know what other letter is. This “complementarity” is the fundamental reason why a DNA helix can be split down the middle, and then have the other half perfectly recreated. In this new study, the Scripps scientists found a method of inserting a new base pair into the DNA of an e. coli bacterium. These two new bases are represented by the letters X and Y, but the actual chemicals are described as “d5SICS” and “dNaM.”

A previous in vitro (test tube) study had shown that these two chemicals were compatible with the enzymes that split and copy DNA. For the purposes of this study, the scientists began by genetically engineering an e. coli bacterium to allow the new chemicals (d5SICS and dNaM) through the cell membrane. Then they inserted a DNA plasmid (a small loop of DNA) that contained a single XY base pair into the bacterium.

dnaheadAs long as the new chemicals were available, the bacterium continued to reproduce normally, copying and passing on the new DNA, alien plasmid and all, and continued to carry on flawlessly for almost a week. For now, the XY base pair does nothing; it just sits there in the DNA, waiting to be copied. In this form, it could be used as biological data storage which, as a new form of biocomputing, could result in hundreds of terabytes of data being stored in a single gram of synthetic, alien DNA. 

Floyd Romesberg, who led the research, has much grander plans:

If you read a book that was written with four letters, you’re not going to be able to tell many interesting stories. If you’re given more letters, you can invent new words, you can find new ways to use those words and you can probably tell more interesting stories.

Now his target is to find a way of getting the alien DNA to actually do something, such as producing amino acids (and thus proteins) that aren’t found in nature. If Romesberg and his colleagues can crack that nut, then it will suddenly become possible to engineer cells that produce proteins that target cancer cells, or special amino acids that help with fluorescent microscopy, or new drugs/gene therapies that do weird and wonderful things.

dna_cancerUltimately it may even be possible to create a wholly synthetic organism with DNA that contains dozens (or hundreds) of different base pairs that can produce an almost infinitely complex library of amino acids and proteins. At that point, we’d basically be rewriting some four billion years of evolution. The organisms and creatures that would arise would be unrecognizable, and be capable of just about anything that a researcher (or mad scientist) could dream up.

In the future, this breakthrough should allow for the creation of highly customized organisms – bacteria, animals, humans – that behave in weird and wonderful ways that mundane four-base DNA would never allow. At the same time, it raises ethical dilemmas and fears that may be well founded. But such is the nature of breakthroughs. The potential for harm and good are always presumably equal when they are firts conceived.

Source: extremetech.com

Coming Soon: A Universal Flu Vaccine?

flu_vaccineScientists have been making great strides in coming up with treatments and cures for illnesses that were previously thought to be incurable. While some of these are aimed at eliminating pandemics that have taken millions of lives worldwide (such as HIV/AIDS) others are aimed at treating the more common – but no less infectious – viruses, like the common flu.

When it comes to the latter, the difficulty is not so much in creating a cure, as it is a cure all. The flu is a virus that is constantly evolving, changing with the seasons and with each host. This requires medical researchers to constantly develop new vaccines year after year to address the latest strain, as well as specialized vaccines to address different  types – i.e. H1N1, swine, avian bird.

flu_vaccine1Luckily, a research team at Imperial College London say they have made a “blueprint” for a universal flu vaccine. Their report appeared in a recent issue of Nature Medicine. In their report, they specified that the key to creating a universal vaccine lies in targeting the core of the virus, rather than its ever-evolving DNA.

Just last year, researchers at the Friedrich-Loeffler Institute in Riems Island, Germany sought to create a similar vaccine that would target the virus’ RNA structure rather than the key proteins found in the DNA. By contrast, the Imperial researchers set about looking into T-cells, the crucial part of the immune system that is thought to be able to recognize proteins in the core.

2009_world_subdivisions_flu_pandemicTheir research began with a series of clinical examinations of the 2009 swine flu pandemic, which was produced by the combining of earlier strains of pig and bird flu. The team then compared levels of one kind of T-cells at the start of the pandemic with symptoms of flu in 342 staff and students at the university. They showed that the higher the levels of the T-cells a patient had, the milder their symptoms were.

Researchers then teased out the specific part of the immune system that offered some pandemic flu protection and which part of the virus it was attacking. from there, They began developing a vaccine that would trigger the production of these cells – known as CD8 T cells. These cells would attack the invading flu virus, ignoring the outer protein structure and focusing on the core which it had encountered before.

Influenza_virus_2008765Prof Ajit Lalvani, who led the study, told the BBC:

It’s a blueprint for a vaccine. We know the exact subgroup of the immune system and we’ve identified the key fragments in the internal core of the virus. These should be included in a vaccine. In truth, in this case it is about five years [away from a vaccine]. We have the know-how, we know what needs to be in the vaccine and we can just get on and do it.

The benefits of such a vaccine would be profound and obvious. While many of us consider the seasonal flu to be an inconvenience, it is important to note that it kills between 250,000 and 500,000 people worldwide each year. While this is a fraction of the total number of deaths attributed to AIDS (1.6 to 1.9 million in 2010, it is still a significant toll. What’s more, new pandemics have the potential to take doctors by surprise and kill large numbers of people.
t-cellHowever, the Imperial College researchers admit that it is generally harder to develop a T-cell vaccine than a traditional one designed to provoke an antibody response. The challenge will be to get a big enough of a T-cell response to offer protection and a response that will last. So while the blueprint is in place, medical researchers still have a long road ahead of them.

Prof John Oxford, of Queen Mary University of London, put it this way:

This sort of effect can’t be that powerful or we’d never have pandemics. It’s not going to solve all the problems of influenza, but could add to the range of vaccines. It’s going to be a long journey from this sort of paper to translating it into a vaccine that works.

AI-fightingfluWhat’s more, there are concerns that a T-cell vaccine would be limited when it comes to certain age groups. Jenner Institute at Oxford University, explains:

Live attenuated influenza vaccines which are given by nasal spray and will be used in children in the UK from this autumn are much better at increasing the number of influenza-specific T cells, but these vaccines only work in young children who haven’t yet had much exposure to influenza virus, so we need an alternative approach for adults.

Interestingly enough, this approach of stimulating the production of T-cells bears a striking resemblance to the work being done at the Vaccine and Gene Therapy Institute at OHSU, where researchers are working towards a vaccine that could also cure HIV. This research also appeared in Nature Medicine last month.

So not only could we be looking at a cure for both HIV and the flu in the near future, we could be looking at the containment of infectious viruses all over the world. As these two cases demonstrate, advances in medical science towards antivirals appear to be tied at the hip.

Sources: bbc.co.uk, gizmodo.com, nature.com