Tag: dna

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

Immortality Inc: Regrowing Body Parts

https://i0.wp.com/images.gizmag.com/hero/lizardtails-2.jpgAnyone who has ever observed a lizard must not have failed to notice that they are capable of detaching their tails, and then regenerating them from scratch. This propensity for “spontaneous regeneration” is something that few organisms possess, and mammals are sadly not one of them. But thanks to a team of Arizona State University scientists, the genetic recipe behind this ability has finally been unlocked.

This breakthrough is a small part of a growing field of biomedicine that seeks to improve human health by tampering with the basic components (i.e. our DNA). The research, which was funded by grants from the National Institutes of Health and Arizona Biomedical Research Commission, also involved scientists from the University of Arizona College of Medicine, Translational Genomic Research Institute, and Michigan State University.

dna_cancerAccording to Prof. Kenro Kusumi, lead author of a paper on the genetic study, lizards are the most closely-related animals to humans that can regenerate entire appendages. They also share the same genetic language as us, so it’s theoretically possible that we could do what they do, if only we knew which genes to use and in what amounts. As Kusumi explains in the paper, which was published Aug. 20 in the journal PLOS ONE. :

Lizards basically share the same toolbox of genes as humans. We discovered that they turn on at least 326 genes in specific regions of the regenerating tail, including genes involved in embryonic development, response to hormonal signals, and wound healing.

Other animals, such as salamanders, frog tadpoles, and fish, can also regenerate their tails. During tail regeneration, they all turn on genes in what is called the ‘Wnt pathway’ — a process that is required to control stem cells in many organs such as the brain, hair follicles and blood vessel. However, lizards have a unique pattern of tissue growth that is distributed throughout the tail.

calico-header-640x353 It takes lizards more than 60 days to regenerate a functional tail — forming a complex regenerating structure with cells growing into different tissues at a number of sites along the tail. According to Katsumi, harnessing this would be a boon for medicine for obvious reasons:

Using next-generation technologies to sequence all the genes expressed during regeneration, we have unlocked the mystery of what genes are needed to regrow the lizard tail. By following the genetic recipe for regeneration that is found in lizards, and then harnessing those same genes in human cells, it may be possible to regrow new cartilage, muscle or even spinal cord in the future.

The researchers also hope their findings will also help repairing birth defects and treating diseases such as arthritis. Given time, and enough positive results, I think it would be fair to expect that Google’s Clinical Immortality subsidiary – known as Calico – will buy up all the necessary rights. Then, it shouldn’t be more than a decade before a gene treatments is produced that will allow for spontaneous regeneration and the elimination of degenerative diseases.

The age of post-mortal is looming people. Be scared/enthused!

Sources: kurzweil.net, gizmag.com

An End to HIV: HIV Remove from Cultured Cells

https://i0.wp.com/292fc373eb1b8428f75b-7f75e5eb51943043279413a54aaa858a.r38.cf3.rackcdn.com/health-fitness_01_temp-1357384489-50e80b29-620x348.jpgAt the closing ceremony of the AIDS 2014 conference a few weeks ago in Melbourne, Australia, many of the speakers – including longtime AIDS researcher and International AIDS Society Presidential Award winner Eric Goosby – told of how utterly terrifying the disease seemed 30 years ago. And while that fear is not gone, it has since diminished, replaced by and large with a sense of hope that the disease will be eradicated.

According to UNAIDS – the Joint United Nations Programme on HIV/AIDS, which is dedicated to destroying the disease by 2030 – the medical community has learned much in the past few years and stands a good chance at accomplishing this goal. And with new advances being announced every few months, hopes for a world in which this terrible disease no longer exists all seem firmly on track.

UNAIDSConsider this latest development, which comes from the Temple University School of Medicine in Philadelphia. Here, researchers have discovered how to permanently extricate HIV-1 from human cells, effectively curing a patient of the disease. Combined with new vaccines that have shown the ability to block infection (and in some cases, even reverse it), this news may yet be reason for even greater hope.

One of the main issues in the treatment of HIV-1 is not simply that it is expensive, but that antiretroviral therapy have terrible side effects that can speed up diseases more commonly associated with aging or can cause co-infections, such as Hepatitis C, to become worse.  Added to this is that HIV is a tricky and tenacious disease that becomes part of a patient’s DNA, making it virtually impossible to eradicate.

https://i0.wp.com/images.gizmag.com/gallery_lrg/scientistseliminatehivfromhumancells.jpgHowever, researchers from Temple University School of Medicine have found a way to cut the infected genes out, potentially eradicating the virus for good and negating the need for lifelong ARV treatment. The technique uses a DNA-snipping enzyme, a nuclease, and a targeting RNA strand to hunt down the genome and cuts the HIV-1 DNA from it. The cell is able to repair its own genomes, essentially sewing itself together again, only now HIV-free.

This treatment will work in varied cell types such as the T-cells and monocytic cells that harbor HIV. In designing the molecular tools, researchers chose nucleotide sequences that do not appear in any coding sequences of human DNA to avoid what they call off-target effects, where patient’s cells or own DNA might be damaged. The technique may also be applicable against many other viruses.

There are still serious hurdles, like how to get the treatment into each, individual cell. Also, HIV-1 is known for mutations, and every patient has their own viral sequence. This means that there can be no single, prescriptive treatment for it. However, another potential upside is that there is the chance this may be used not simply as a treatment but also a vaccine as cells containing the nuclease-RNA combination do not acquire the HIV infection.

https://i0.wp.com/www.templehealth.org/AssetMgmt/getImage.aspxDr. Kamel Khalili, Professor and Chair of the Department of Neuroscience at Temple, calls it an “important step” towards the eradication of AIDS, though it is still years away from the clinical stage. As he put it:

We want to eradicate every single copy of HIV-1 from the patient. That will cure AIDS. I think this technology is the way we can do it.

Though it is not the one-shot breakthrough many have been hoping for, this enzyme-based treatment is another step along the long road towards the end of HIV and another nail in its coffin. As long as treatments exist that are not only able to treat and block, but also fight the disease, there is much reason for hope.

And be sure to check out this video from Temple University, where Dr. Khalili explains the medical breakthrough:


Sources: gizmag.com, templehealth.org

Biomedical Breakthroughs: Vascular Network Bioprinting

bioprintingThe ability to generate biological tissues using 3-D printing methods – aka. “bioprinting” – may one day help medical researchers and hospitals to create artificial, on-demand custom body parts and organs for patients. And numerous recent advancements – such as the creation of miniature kidneys, livers, and stem cell structures – are bringing that possibility closer to reality.

And now, according to a new study produced by researchers from the University of Sydney, it is now possible to bioprint artificial vascular networks that mimic the body’s circulatory system. Being able to bio-print an artificial vascular network would give us the ability to keep tissue and organs alive where previously it would not have been possible. The body’s vascular network enables it to transport blood and, therefore, oxygen and nutrients, to tissues and organs.

vascularIt also provides a means of transporting waste materials away from tissues and organs. Dr. Luiz Bertassoni. the lead author of the study explained:

Cells die without an adequate blood supply because blood supplies oxygen that’s necessary for cells to grow and perform a range of functions in the body. To illustrate the scale and complexity of the bio-engineering challenge we face, consider that every cell in the body is just a hair’s width from a supply of oxygenated blood. Replicating the complexity of these networks has been a stumbling block preventing tissue engineering from becoming a real world clinical application.

In order to solve this problem, the researchers used a bioprinter to create a framework of tiny interconnected fibers to serve as a mold. The structure was then covered with a “cell-rich protein-based material” and solidified using light. The fibers were removed to leave a network of tiny channels that formed into stable human blood-capillaries within just a week’s time.

stem_cells3According to the University of Sydney study, the technique demonstrated better cell survival, differentiation and proliferation compared to cells that received no nutrient supply. In addition, it provides the ability to create large, life-supporting three-dimensional, micro-vascular channels quickly and with the precision required for application to different individuals.

This is a major step forward for the bioprinting industry, according to Bertassoni:

While recreating little parts of tissues in the lab is something that we have already been able to do, the possibility of printing three-dimensional tissues with functional blood capillaries in the blink of an eye is a game changer.

bioprinter1In addition, Bertassoni claims that the ultimate aim of the research is for patients to be able to walk into a hospital and have a full organ printed with all the cells, proteins and blood vessels in the right place:

We are still far away from that, but our research is addressing exactly that. Our finding is an important new step towards achieving these goals. At the moment, we are pretty much printing ‘prototypes’ that, as we improve, will eventually be used to change the way we treat patients worldwide.

Bioprinting that uses a patient’s own DNA to generate custom-made organs and tissues offers a world of medical possibilities in which organ donors are no longer necessary, and the risk of rejection and incompatibility is negligible. Not only that, it will usher in a world where no injury is permanent and prosthetics are a thins of the past.

Sources: gizmag.com, sydney.edu.au

Immortality Inc: Google’s Kurzweil Talks Life Extension

calico-header-640x353Human life expectancy has been gradually getting longer and longer over the past century, keeping pace with advances made in health and medical technologies. And in the next 20 years, as the pace of technological change accelerates significantly, we can expect life-expectancy to undergo a similarly accelerated increase. So its only natural that one of the worlds biggest tech giants (Google) would decide to becoming invested in the business of post-mortality.

As part of this initiative, Google has been seeking to build a computer that can think like a human brain. They even hired renowed futurist and AI expert Ray Kurzweil last year to act as the director of engineering on this project. Speaking at Google’s I/O conference late last month, he detailed his prediction that our ability to improve human health is beginning to move up an “exponential” growth curve, similar to the law of accelerating returns that governs the information technology and communications sectors today.

raykurzweilThe capacity to sequence DNA, which is dropping rapidly in cost and ease, is the most obvious example. At one time, it took about seven years to sequence 1% of the first human genome. But now, it can be done in a matter of hours. And thanks to initiatives like the Human Genome Project and ENCODE, we have not only successfully mapped every inch of the human genome, we’ve also identified the function of every gene within.

But as Kurzweil said in the course of his presentation – entitled “Biologically Inspired Models of Intelligence” – simply reading DNA is only the beginning:

Our ability to reprogram this outdated software is growing exponentially. Somewhere between that 10- and 20-year mark, we’ll see see significant differences in life expectancy–not just infant life expectancy, but your remaining life expectancy. The models that are used by life insurance companies sort of continue the linear progress we’ve made before health and medicine was an information technology… This is going to go into high gear.

immortality_dnaKurzweil cited several examples of our increasing ability to “reprogram this outdated data” – technologies like RNA interference that can turn genes on and off, or doctors’ ability to now add a missing gene to patients with a terminal disease called pulmonary hypertension. He cited the case of a girl whose life was threatened by a damaged wind pipe, who had a new pipe designed and 3-D printed for her using her own stem cells.

In other countries, he notes, heart attack survivors who have lasting heart damage can now get a rejuvenated heart from reprogrammed stem cells. And while this procedure awaits approval from the FDA in the US, it has already been demonstrated to be both safe and effective. Beyond tweaking human biology through DNA/RNA reprogramming, there are also countless initiatives aimed at creating biomonitoring patches that will improve the functionality and longevity of human organs.

avatar_imageAnd in addition to building computer brains, Google itself is also in the business of extending human life. This project, called Calico, hopes to slow the process of natural aging, a related though different goal than extending life expectancy with treatment for disease. Though of course, the term “immortality” is perhaps a bit of misnomer, hence why it is amended with the word “clinical”. While the natural effects of aging are something that can be addressed, there will still be countless ways to die.

As Kurzweil himself put it:

Life expectancy is a statistical phenomenon. You could still be hit by the proverbial bus tomorrow. Of course, we’re working on that here at Google also, with self-driving cars.

Good one, Kurzweil! Of course, there are plenty of skeptics who question the validity of these assertions, and challenge the notion of clinical immortality on ethical grounds. After all, our planet currently plays host to some 7 billion people, and another 2 to 3 billion are expected to be added before we reach the halfway mark of this century. And with cures for diseases like HIV and cancer already showing promise, we may already be looking at a severe drop in mortality in the coming decades.

calico1Combined with an extension in life-expectancy, who knows how this will effect life and society as we know it? But one thing is for certain: the study of life has become tantamount to a study of information. And much like computational technology, this information can be manipulated, resulting in greater performance and returns. So at this point, regardless of whether or not it should be done, it’s an almost foregone conclusion that it will be done.

After all? While very few people would dare to live forever, there is virtually no one who wouldn’t want to live a little longer. And in the meantime, if you’ve got the time and feel like some “light veiwing”, be sure to check out Kurzweil’s full Google I/O 2014 speech in which he addresses the topics of computing, artificial intelligence, biology and clinical immortality:


Sources: fastcoexist.com, kurzweilai.net

Looking Forward: 10 Breakthroughs by 2025

BrightFutureWorld-changing scientific discoveries are emerging all the time; from drugs and vaccines that are making incurable diseases curable, to inventions that are making renewable energies cheaper and more efficient. But how will these develops truly shape the world of tomorrow? How will the combination of advancements being made in the fields of medical, digital and industrial technology come together to change things by 2025?

Well, according to the Thomson Reuters IP & Science unit – a leading intellectual property and collaboration platform – has made a list of the top 10 breakthroughs likely to change the world. To make these predictions, they  looked at two sorts of data – current scientific journal literature and patent applications. Counting citations and other measures of buzz, they identified 10 major fields of development, then made specific forecasts for each.

As Basil Moftah, president of the IP & Science business (which sells scientific database products) said:

A powerful outcome of studying scientific literature and patent data is that it gives you a window into the future–insight that isn’t always found in the public domain. We estimate that these will be in effect in another 11 years.

In short, they predict that people living in 2025 will have access to far more in the way of medical treatments and cures, food will be more plentiful (surprisingly enough), renewable energy sources and applications will be more available, the internet of things will become a reality, and quantum and medical science will be doing some very interesting thins.

1. Dementia Declines:
geneticsPrevailing opinion says dementia could be one of our most serious future health challenges, thanks in no small part to increased life expectancy. In fact, the World Health Organization expects the number of cases to triple by 2050. The Thomson Reuters report is far more optimistic though, claiming that a focus on the pathogenic chromosomes that cause neuro-degenerative disease will result in more timely diagnosis, and earlier, more effective treatment:

In 2025, the studies of genetic mutations causing dementia, coupled with improved detection and onset-prevention methods, will result in far fewer people suffering from this disease.

2. Solar Power Everywhere:
solarpowergeWith the conjunction of increased efficiencies, dropping prices and improved storage methods, solar power will be the world’s largest single source of energy by 2025. And while issues such as weather-dependence will not yet be fully resolved, the expansion in panel use and the incorporation of thin photovoltaic cells into just about every surface imaginable (from buildings to roadways to clothing) will means that solar will finally outstrip fossil fuels as coal as the predominant means of getting power.

As the authors of the report write:

Solar thermal and solar photovoltaic energy (from new dye-sensitized and thin-film materials) will heat buildings, water, and provide energy for devices in the home and office, as well as in retail buildings and manufacturing facilities.

3. Type 1 Diabetes Prevention:
diabetes_worldwideType 1 diabetes strikes at an early age and isn’t as prevalent as Type 2 diabetes, which comes on in middle age. But cases have been rising fast nonetheless, and explanations range from nutritional causes to contaminants and fungi. But the report gives hope that kids of the future won’t have to give themselves daily insulin shots, thanks to “genomic-editing-and-repairing” that it expects will fix the problem before it sets in. As it specifies:

The human genome engineering platform will pave the way for the modification of disease-causing genes in humans, leading to the prevention of type I diabetes, among other ailments.

4. No More Food Shortages:
GMO_seedsContrary to what many speculative reports and futurists anticipate, the report indicates that by the year 2025, there will be no more food shortages in the world. Thanks to a combination of lighting and genetically-modified crops, it will be possible to grow food quickly and easily in a plethora of different environments. As it says in the report:

In 2025, genetically modified crops will be grown rapidly and safely indoors, with round-the-clock light, using low energy LEDs that emit specific wavelengths to enhance growth by matching the crop to growth receptors added to the food’s DNA. Crops will also be bred to be disease resistant. And, they will be bred for high yield at specified wavelengths.

5. Simple Electric Flight:
Solar Impulse HB-SIA prototype airplane attends his first flight over PayerneThe explosion in the use of electric aircraft (be they solar-powered or hydrogen fueled) in the past few decades has led to predictions that by 2025, small electric aircraft will offset commercial flight using gas-powered, heavy jets. The report says advances in lithium-ion batteries and hydrogen storage will make electric transport a reality:

These aircraft will also utilize new materials that bring down the weight of the vehicle and have motors with superconducting technology. Micro-commercial aircraft will fly the skies for short-hop journeys.

6. The Internet of Things:
internet-of-things-2By 2025, the internet is likely to expand into every corner of life, with growing wifi networks connecting more people all across the world. At the same time, more and more in the way of devices and personal possessions are likely to become “smart” – meaning that they will can be accessed digitally and networked to other things. In short, the internet of things will become a reality. And the speed at which things move will vastly increase due to proposed solutions to the computing bottleneck.

Here’s how the report puts it:

Thanks to the prevalence of improved semiconductors, graphene-carbon nanotube capacitators, cell-free networks of service antenna, and 5G technology, wireless communications will dominate everything, everywhere.

7. No More Plastic Garbage:
110315-N-IC111-592Ever heard of the Great Pacific Garbage Patch (aka. the Pacific Trash Vortex), the mass of plastic debris in the Pacific Ocean that measures somewhere between 700,000 and 15,000,000 square kilometres (270,000 – 5,800,000 sq mi)? Well, according to the report, such things will become a thing of the past. By 2025, it claims, the “glucose economy” will lead to the predominance of packaging made from plant-derived cellulose (aka. bioplastics).

Because of this influx of biodegradable plastics, there will be no more permanent deposits of plastic garbage filling our oceans, landfills, and streets. As it says:

Toxic plastic-petroleum packaging that litters cities, fields, beaches, and oceans, and which isn’t biodegradable, will be nearing extinction in another decade. Thanks to advancements in the technology related to and use of these bio-nano materials, petroleum-based packaging products will be history.

8. More Precise Drugs:
drugsBy 2025, we’ll have sophisticated, personalized medicine, thanks to improved production methods, biomedical research, and the growth of up-to-the-minute health data being provided by wearable medical sensors and patches. The report also offers specific examples:

Drugs in development are becoming so targeted that they can bind to specific proteins and use antibodies to give precise mechanisms of action. Knowledge of specific gene mutations will be so much more advanced that scientists and physicians can treat those specific mutations. Examples of this include HER2 (breast cancer), BRAF V600 (melanoma), and ROS1 (lung cancer), among many others.

9. DNA Mapping Formalized:
DNA-1Recent explosions in genetic research – which include the Genome Project and ENCODE – are leading to a world where personal genetic information will become the norm. As a result, kids born in 2025 will be tested at the DNA level, and not just once or twice, but continually using nano-probes inserted in the body. The result will be a boon for anticipating genetic diseases, but could also raise various privacy-related issues. As it states:

In 2025, humans will have their DNA mapped at birth and checked annually to identify any changes that could point to the onset of autoimmune diseases.

10. Teleportation Tested:
quantum-entanglement1Last, but certainly not least, the report says research into teleportation will be underway. Between the confirmation of the Higgs Boson (and by extension, the Standard Model of particle physics), recent revelations about quantum entanglements and wormholes, and the discovery of the Amplituhedron, the field of teleportation is likely to produce some serious breakthroughs. No telling what these will be – be it the ability to teleport simple photons or something larger – but the fact that the research will be happening seems a foregone conclusion:

We are on the precipice of this field’s explosion; it is truly an emerging research front. Early indicators point to a rapid acceleration of research leading to the testing of quantum teleportation in 2025.

Summary:
Will all of these changes come to pass? Who knows? If history has taught us anything, it’s that predictions are often wrong and much in the way of exciting research doesn’t always make it to the market. And as always, various factors – such as politics, money, public resistance, private interests – have a way of complicating things. However, there is reason to believe that the aforementioned 10 things will become a viable reality. And Moftah believes we should be positive about the future:

[The predictions] are positive in nature because they are solutions researchers and scientists are working on to address challenges we face in the world today. There will always be obstacles and issues to overcome, but science and innovation give us hope for how we will address them.

I, for one, am happy and intrigued to see certain items making this list. The explosion in solar usage, bioplastics, and the elimination of food scarcity are all very encouraging. If there was one thing I was anticipating by 2025, it was increased drought and food shortages. But as the saying goes, “necessity is the mother of invention”. And as someone who has had two grandmothers who lived into their nineties and have both suffered from the scourges of dementia, it is good to know that this disease will be on the wane for future generations.

It is also encouraging to know that there will be better treatments for diseases like cancer, HIV, and diabetes. While the idea of a world in which all diseases are preventable and/or treatable worries some (on a count of how it might stoke overpopulation), no one who has ever lived with this disease, or known someone who has, would think twice if presented with a cure. And hardship, hunger, a lack of education, resources and health services are some of the main reasons for population explosions.

And, let’s face it, its good to live in an age where the future looks bright for a change. After a good century of total war, totalitarianism, atomic diplomacy, terrorism, and oh so much existential angst and dystopian fiction, it’s nice to think that the coming age will turn out alright after all.

Sources: fastcoexist.com, ip-science.thomsonreuters.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

Happy DNA Day!

dna_cancerThough I am a week late in expressing this sentiment, I feel I must acknowledge this rather interesting of events. As it stands, this past April 22nd was the sixty-first anniversary of the molecular structure of DNA being revealed to the world. What began as a publication in the magazine Nature has now become emblematic of the programming language of life, and our understanding of DNA has grown by leaps and bounds over the past six decades.

To commemorate such an important landmark in the history of humanity, a look back at some of the more recent developments in the field of genetic research would seem to be in order. For example, it was on April 22nd of this year that a rather interesting study was published in the Proceedings of the National Academy of Sciences. The lead on this study was none other than Svante Pääbo – the world’s foremost expert in Neanderthal genetics.

humanEvolutionBased on the genomes of three neanderthals that were found in disparate locations in Eurasia, Pääbo and his colleagues have concluded that the genetic diversity in Neanderthals is significantly less when compared to present-day Homo sapiens. It also appears as if the Neanderthal populations were relatively isolated and tiny, so gene flow was extremely limited for these groups. In short, our homonid cousins didn’t get around and interbreed quite as much as we’ve done, which may shed some light on their disappearance.

On the very same day, an article was published in the Proceedings of the Royal Society B that proposed that skin cancer from the sun’s damaging UV rays was actually a driving force in the national selection for dark skin in early humans. In the article, Mel Greaves delivers a compelling argument that the deadliness of skin cancer in young albino children in Africa and Central America demonstrates just how vital it was for early humans to develop dark skin.

GenoChipAnd on April 25th, National Geographic and Family Tree DNA teamed up to announce the release of a brand new version of the human Y-DNA tree. This new tree of Y chromosome mutations has over 1,200 branches — almost double the number of branches that the Genographic Project was displaying before. With this much refinement, it’s now even easier to track the historical migrations of your distant ancestors.

To celebrate this monumental roll-out, Family Tree DNA offered a 20% discount on the 37-marker Y-DNA test and all individual Y-DNA SNP (single-nucleotide polymorphism) tests, an offer which sadly expired on April 27th. However, interested parties can still have this cutting-edge anthropological genetic test performed for $200. And it’s something to keep in mind for next year certainly. What better way to celebrate DNA day than to have a full genetic profile of yourself made?

encodeAnd let’s not forget, 2012 was also the year that the Encyclopedia of DNA Elements (ENCODE) Consortium – an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI) – released the world’s most complete report on the human genome to date. Unlike the Human Genome Project, which released the first catalog of human DNA back in 2003, ENCODE was not only able to catalog the human genome’s various parts, but also what those components actually do.

Among the initiative’s many findings was that so-called “junk DNA” – outlier DNA sequences that do not encode for protein sequences – are not junk at all, and are in fact responsible for such things as gene regulation, disease onset, and even human height. As I’ve said before, these findings will go a long way towards developing gene therapy, biotechnology that seeks to create artificial DNA and self-assembling structures, and even cloning.

Tree-600x405Yes, it’s an exciting time for the field of DNA research, and not just because of the many doors its likely to open. Beyond medical and bioresearch, it helps us to understand of ourselves as a species, our collective origins, and may perhaps help us to see just how interconnected we all truly are. For centuries now, a great many evils and prejudices have been committed in the name of “racial superiority” or racial differences.

Armed with this new knowledge, we might just come to realize that this great organism known as humanity is all fruit of the same tree.

Sources: extremetech.com, genome.ucsc.edu, newswatch.nationalgeographic.com

The Future of Medicine: Replacement Ears and “Mini Hearts”

biomedicineBiomedicine is doing some amazing things these days, so much so that I can hardly keep up with the rate of developments. Just last month, two amazing ones were made, offering new solutions for replacing human tissue and treating chronic conditions. The first has to do with a new method of growing human using a patients own DNA, while the second involves using a patient’s own heart tissue to create “mini hearts” to aid in circulation.

The first comes from London’s Great Ormond Street Hospital, where researchers are working on a process that will grow human ears using genetic material taken from a patient’s own fat tissue. Building upon recent strides made in the field of bioprinting, this process will revolution reconstructive surgery as we know it. It also seeks to bring change to an area of medicine which, despite being essential for accident victims, has been sadly lacking in development.

replacement_earCurrently, the procedure to repair damaged or non-existent cartilage in the ear involves an operation that is usually carried out when the patient is a child. For the sake of this procedure, cartilage is extracted from the patient’s ribs and painstakingly crafted into the form of an ear before being grafted back onto the individual. Whilst this method of reconstruction achieves good results, it also comes with its share of unpleasant side effects.

Basically, the patient is left with a permanent defect around the area from where the cells were harvested, as the cartilage between the ribs does not regenerate. In this new technique, the cartilage cells are engineered from mesenchymal stem cells, extracted from the child’s abdominal adipose (fat) tissue. The benefit of this new system is that unlike the cartilage in the ribs, the adipose tissue regenerates, therefore leaving no long-term defect to the host.

stem_cells1There is also the potential to begin reconstructive treatment with stem cells derived from adipose tissue earlier than previously possible, as it takes time for the ribs to grow enough cartilage to undergo the procedure. As Dr. Patrizia Ferretti, a researcher working on the project, said in a recent interview:

One of the main benefits in using the patient’s own stem cells is that there is no need for immune suppression which would not be desirable for a sick child, and would reduce the number of severe procedures a child needs to undergo.

To create the form of the ear, a porous polymer nano-scaffold is placed in with the stem cells. The cells are then chemically induced to become chondrocytes (aka. cartilage cells) while growing into the holes in the scaffold to create the shape of the ear. According to Dr. Ferretti, cellularized scaffolds – themselves a recent medical breakthrough – are much better at integrating than fully-synthetic implants, which are more prone to extrusion and infection.

cartilage2Dr. Ferretti continued that:

While we are developing this approach with children with ear defects in mind, it could ultimately be utilized in other types of reconstructive surgery both in children and adults.

Basically, this new, and potentially more advantageous technique would replace the current set of procedures in the treatment of defects in cartilage in children such as microtia, a condition which prevents the ear from forming correctly. At the same time, the reconstructive technology also has the potential to be invaluable in improving the quality of life of those who have been involved in a disfiguring accident or even those injured in the line of service.

mini_hearts`Next up, there is the “mini heart” created by Dr. Narine Sarvazyan of George Washington University in Washington D.C.. Designed to be wrapped around individual veins, these cuffs of rhythmically-contracting heart tissue are a proposed solution to the problem of chronic venous insufficiency – a condition where leg veins suffer from faulty valves, which prevents oxygen-poor blood from being pumped back to the heart.

Much like process for creating replacement ears, the mini hearts are grown  by coaxing a patient’s own adult stem cells into becoming cardiac cells. When one of those cuffs is placed around a vein, its contractions aid in the unidirectional flow of blood, plus it helps keep the vein from becoming distended. Additionally, because it’s grown from the patient’s own cells, there’s little chance of rejection. So far, the cuffs have been grown in the lab, where they’ve also been tested. But soon, Sarvazyan hopes to conduct animal trials.

mini_hearts2As Sarvazyan explained, the applications here far beyond treating venous insufficiency. In addition, there are the long-range possibilities for organ replacement:

We are suggesting, for the first time, to use stem cells to create, rather than just repair damaged organs. We can make a new heart outside of one’s own heart, and by placing it in the lower extremities, significantly improve venous blood flow.

One of the greatest advantages of the coming age of biomedicine is the ability to replace human limbs, organs and tissue using organic substitutions. And the ability to grow these from the patient’s own tissue is a major plus, in that it cuts down on the development process and ensures a minimal risk of rejection. On top of all that, the ability to create replacement organs would also significantly cut down on the costs of replacement tissue, as well as the long waiting periods associated with donor lists.

Imagine that, if you will. A future where a patient suffering from liver, kidney, circulatory, or heart problems is able to simply visit their local hospital or clinic, donate a meager supply of tissue, and receive a healthy, fully-compatible replacement after an intervening period (days or maybe even hours). The words “healthy living” will achieve new meaning!

 

Sources: gizmag.com, (2), nanomedjournal.com

The Future of Medicine: Elastic Superglue and DNA Clamps

nanomachineryIf there’s one thing medical science is looking to achieve, it’s ways of dealing with sickness and injuries that are less invasive. And now more than ever, researchers are looking to the natural world for solutions. Whether it is working with the bodies own components to promote healing, or using technologies that imitate living organism, the future of medicine is all about engineered-natural solutions.

Consider the elastic glue developed by associate professor Jeffrey Karp, a Canadian-born medical researcher working at Harvard University. Created for heart surgery, this medical adhesive is designed to replace sutures and staples as the principle means of sealing incisions and defects in heart tissue. But the real kicker? The glue was inspired by sticky natural secretions of slugs.

hlaa-4Officially known as hydrophobic light-activated adhesive (HLAA), the glue was developed in a collaboration between Boston Children’s Hospital, MIT, and Harvard-affiliated Brigham and Women’s Hospital. And in addition to being biocompatible and biodegradable (a major plus in surgery), it’s both water-resistant and elastic, allowing it to stretch as a beating heart expands and contracts.

All of this adds up to a medical invention that is far more user-friendly than stitches and staples, does not have to be removed, and will not cause complications. On top of all that, it won’t complicate healing by restricting the heart’s movements, and only becomes active when an ultraviolet light shines on it, so surgeons can more accurately bind the adhesive exactly where needed.

hlaa-3The technology could potentially be applied not just to congenital heart defects, but to a wide variety of organs and other body parts. In an recent interview with CBC Radio’s Quirks & Quarks, Karp explained the advantages of the glue:

Sutures and staples really are not mechanically similar to the tissues in the body, so they can induce stress on the tissue over time. This is a material that’s made from glycerol and sebacic acid, both of which exist in the body and can be readily metabolized. What happens over time is that this material will degrade. Cells will invade into it and on top of it, and ideally the hole will remain closed and the patient won’t require further operations.

In lab tests, biodegradable patches coated with HLAA were applied to holes in the hearts of live pigs. Despite the high pressure of the blood flowing through the organs, the patches maintained a leakproof seal for the 24-hour test period. HLAA is now being commercially developed by Paris-based start-up Gecko Biomedical, which hopes to have it on the market within two to three years.

dnaclampIn another recent development, scientists at the Université de Montréal have created a new DNA clamp capable of detecting the genetic mutations responsible for causing cancers, hemophilia, sickle cell anemia and other diseases. This clamp is not only able to detect mutations more efficiently than existing techniques, it could lead to more advanced screening tests and more efficient DNA-based nanomachines for targeted drug delivery.

To catch diseases at their earliest stages, researchers have begun looking into creating quick screening tests for specific genetic mutations that pose the greatest risk of developing into life-threatening illnesses. When the nucleotide sequence that makes up a DNA strand is altered, it is understood to be a mutation, which specific types of cancers can be caused by.

DNA-MicroarrayTo detect this type of mutation and others, researchers typically use molecular beacons or probes, which are DNA sequences that become fluorescent on detecting mutations in DNA strands. The team of international researchers that developed the DNA clamp state that their diagnostic nano machine allows them to more accurately differentiate between mutant and non-mutant DNA.

According to the research team, the DNA clamp is designed to recognize complementary DNA target sequences, binds with them, and form a stable triple helix structure, while fluorescing at the same time. Being able to identify single point mutations more easily this way is expected to help doctors identify different types of cancer risks and inform patients about the specific cancers they are likely to develop.

dna_cancerDiagnosing cancer at a genetic level could potentially help arrest the disease, before it even develops properly. Alexis Vallée-Bélisle, a Chemistry Professor at the Université de Montréal, explained the long-term benefits of this breakthrough in a recent interview:

Cancer is a very complex disease that is caused by many factors. However, most of these factors are written in DNA. We only envisage identifying the cancers or potential of cancer. As our understanding of the effect of mutations in various cancer will progress, early diagnosis of many forms of cancer will become more and more possible.

Currently the team has only tested the probe on artificial DNA, and plans are in the works to undertake testing on human samples. But the team also believes that the DNA clamp will have nanotechnological applications, specifically in the development of machines that can do targeted drug-delivery.

dna_nanomachineFor instance, in the future, DNA-based nanomachines could be assembled using many different small DNA sequences to create a 3D structure (like a box). When it encounters a disease marker, the box could then open up and deliver the anti-cancer drug, enabling smart drug delivery. What’s more, this new DNA clamp could prove intrinsic in that assembly process.

Professor Francesco Ricci of the University of Rome, who collaborated on the project, explained the potential in a recent interview:

The clamp switches that we have designed and optimized can recognize a DNA sequence with high precision and high affinity. This means that our clamp switches can be used, for example, as super-glue to assemble these nano machines and create a better and more precise 3D structure that can, for example, open in the presence of a disease marker and release a drug.

Hmm, glues inspired by mollusc secretions, machines made from DNA. Medical technology is looking less like technology and more like biology every day now!

Sources: cbc.ca, gizmag.com, (2)