The H5N1 virus, or Bird Flu, was easily transmissible between birds but not humans. Two scientists have changed that and are publishing how they did it.

The emergence of the avian flu in 2003 caused alarm around the world as it spread through countries in Asia, leaving victims in its wake. While largely contained to the bird population, for the relatively few humans unlucky enough to catch it the flu proved deadly. Now, two groups of perhaps seemingly mad scientists have successfully modified the H5N1 virus so that it could be passed easily between humans. One of them has already published the work for all the world to see, and the second is soon to follow. What kind of dangers will materialize in a world where the laboratory formulas for superflus and other potential bioweapons are out in the open?

Of the 603 people infected since the 2003 H5N1 outbreak, 356 have died – a 59 percent mortality rate (by comparison, the Great Flu Pandemic of 1918 that claimed the lives of over 50 million had a mortality rate of just 2 percent). Still, people could take solace in the fact that the flu, luckily, while very well suited to being passed between birds, was not effective at passing from human to human.

Until now.

Yoshihiro Kawaoka at the University of Wisconsin-Madison and Ron Fouchier at Erasmus University in the Netherlands have both been able to modify the virus so that it now is easily transmitted between humans.

Understandably, some are none too happy.

The wisdom of making the DNA sequence of a potentially very deadly virus public was discussed extensively in the media and behind closed public health office doors in the months prior to publication. The University of Pittsburgh’s D. A. Henderson, who helped eradicate smallpox, issued an editorial last December in response to the “ominous news,” arguing that “the benefits of this work do not outweigh the risks.” That same month the World Health Organization expressed “deep concern” about the “possible risks and misuses associated with this research” and about “the potential negative consequences.” Also in December, US Secretary of State Hillary Clinton provoked concerns further by being clear that we’re all talking about terrorists, citing “evidence in Afghanistan that…al Qaeda…made a call to arms for – and I quote – ‘brothers with degrees in microbiology or chemistry to develop a weapon of mass destruction.’”

The growing concern and condemnation seemed justified when the December tumult concluded with a ruling by the National Science Advisory Board for Biosecurity (NSABB) that Kawaoka’s paper and Fouchier’s paper that was also in the works, be censored – that the mutations shouldn’t be published lest terrorist groups be given the secret formula for a superflu.

Now the debates raged within the scientific community, with one side rejecting the censoring of science in any form, the other side echoed D. A. Henderson’s doubt that the research was even merited in the first place. Long story short, the advisory board reversed their ruling in March after receiving ‘revised’ versions of Kawaoka and Fouchier’s papers. I use that term lightly, as all the mutation data is still there.

The key to Kawaoka’s (controversial yet FBI-approved) breakthrough was a viral protein called hemagglutinin that affects the ability of a virus to bind host cells. The hemagglutinin in H5N1 was well-suited to promote transmission of the virus between birds but not between humans. Kawaoka produced millions of H5N1 variants in which the hemagglutinin was mutated in different ways. When they screened the variants they found a version that, unlike its naturally-occurring counterpart, was very good at infecting human cells in a Petri dish.

The hemagglutinin of the human-targeting H5N1 virus showed four new mutations. Three of the mutations changed the shape of the protein from its normal shape and the fourth changed the pH level at which the virus attaches to cells and injects their genetic material. Sifting through the millions of mutations revealed a secret molecular formula for gaining deadly entry into human cells. To maximize the lethality of their creation, the team combined the mutated gene with the seven remaining genes – flu viruses have a total of eight genes – of a particularly transmittable flu virus; specifically, from the 2009 H1N1 pandemic virus.

And then they gave the modified viruses to ferrets. The new virus worked ‘beautifully,’ rapidly infecting ferrets separately housed in different cages. Assuming ferrets are a good model for viral transmission among other mammals, like humans, the scientists would have taken a virus that was relatively harmless to humans and turned it into a Franken-flu with a monstrous potential for harm were it ever to get out.

The paper, detailing what mutations went where, was published May 2nd in the journal Nature.

Only four or five mutations were needed to turn the relatively harmless bird flu into a potential nightmare.

So should we be concerned about the world knowing that switching asparagine-224 to a lysine and a few other like changes turns a relatively harmless bird disease into a superbug threat for humans? A couple months ago during one of our Google+ Hangouts we brought up the debate to New York Times science columnist and writer of The Loom Carl Zimmer who’d last year wrote a book about viruses.

“I can sleep at night knowing that that’s going on but I don’t rule out the danger of it. On the other hand I do think there’s a danger in totally stifling this type of research. If somebody did release some sort of horrible bioweapon we would probably find a vaccine or cure if this information was available to people as easily and quickly as possible so that you’re essentially crowdsourcing a solution as opposed to, say, if anybody wants this data you’re going to have to fill out three thousand pages of paperwork and then we’ll get back to you, and in the meanwhile another thousand people have died.”

The practicalities of a quick and effective response aside, Zimmer isn’t too alarmed by the threat of a superbug let loose in the first place.

“I think an argument could be made that [a virus] is a pretty lousy bioweapon. There’s good chance that if you were…trying to make a very virulent kind of flu you might very well be the first person to die. But let’s imagine you were able to transport it to some other country and unleash it. Take a look at what happened in 2009 with the Swine Flu. It was first noticed in Mexico, and by the time scientists really had a good handle on it in Mexico, we now know that it was already all over the world, because people have been getting on planes and going all over the place. So, if some horrible person unleashed a very virulent flu in New York, a lot of people would get on planes and go back to that terrorist’s home country trying to escape the flu.”

Of course, anyone willing to unleash a virulent flu in New York might not have cared to think these matters through.

And the second recipe, Fouchier’s, which will be published shortly in Science, is rumored to formulate an H5N1 virus even more lethal than Kawaoka’s. Fouchier’s group took a slightly different strategy by jumpstarting it with mutations that fostered its transmission from birds to ferrets, but then instead of screening for mutations that made the virus transmissible between ferrets, they took viruses from sick ferrets and injected them into healthy ferrets. Mimicking the way the viruses adapt in nature the viruses mutated as they were artificially transmitted from ferret to ferret, until they began transmitting on their own. As Fouchier told the New Scientist, his flu “is transmitted as efficiently as seasonal flu.” With a near 60 percent mortality, let’s hope his observation is never confirmed. The seasonal flu already leaves between 250,000 and 500,000 around the world dead each year.

But the method by which Fouchier’s bird flu was created could be considered an argument for creating superflus in the lab in the first place. Injecting viruses from sick ferrets into healthy ones until they adapted simulates the worst case scenario for humans. Conceivably, all it would take for the bird-to-human H5N1 to become a human-to-human H5N1 would be a finite number of transmissions between humans. As with the ferrets, the virus would adapt. How many direct contact transmissions would it need before it became airborne? The virus passed between Fouchier’s ferrets need just ten transmissions.

Ten transmissions and five mutations – one more than Kawaoka’s virus needed. Either way, it’s a very short jaunt along evolution’s path to go from a relatively benign bird flu to the potentially most destructive infectious agent ever to face humanity. So if similar mutations are needed to make the virus airborne between humans, knowing ahead of time what those mutations are, as Zimmer pointed out, gives us a head start in creating a vaccine.

A good enough reason? You tell me. But in the end it doesn’t really matter which side of the issue you’re on because the superflu recipe is already out there. We know it’s the first of two, and we can bet that other publications will follow that are potential bioweapon cheat sheets for “horrible persons.” Surely the debate will rage on as these papers come out, with one side saying benefits don’t outweigh risk, the other side saying we can’t afford to not be prepared.

[image credits: Wall Street Journal, International Business Times, and Nature]
images: China, China2, Paper

Incapsula's report finds that 51 percent of traffic to their customers' websites is generated by software, most of which is harmful.

It probably is no surprise to most that much of online traffic isn’t human. Hacker software, spam, or innocuous data collection from search engines all get their slice of the bandwidth pie. But what might surprise you is exactly how much bandwidth is consumed by humans versus non-humans. It’s pretty much an even split.

Actually, a slight lead goes to the non-human, web-surfing robots.

According to a report by Internet security company Incapsula, 51 percent of total online traffic is non-human. There’s more bad news. Of the 51 percent, 20 percent of the traffic is accounted for by search engines, the other 31 percent are the bad bots.

Here’s the breakdown:

- 49 percent human traffic, 51 percent non-human traffic

Non-human traffic:
- 5 percent hacking tools
- 5 percent “scrapers,” software that posts the contents of your website to other websites, steals email addresses for spamming, or reverse engineers your website’s pricing and business models
- 2 percent comment spammers
- 19 percent other sorts of spies that are competitive analyzers, sifting your website for keyword and SEO (search engine optimization) data to help give them a competitive edge in climbing the search engine ladder
- 20 percent search engines and other benevolent bot traffic

The report was based on data compiled from 1,000 of Incapsula customer websites.

We always knew it was us against the machines. But until now the arms race had generally referred to virus versus anti-virus, malware versus anti-malware. Symantec wasn’t warning us about the perils of non-human traffic. For web-based business owners though, that extra traffic can turn into lost business. Tagman recently reported that a delay of just one second in webpage load time decreases page views by 11 percent, customer satisfaction by 16 percent, and conversions – the number of people who buy something divided by the number of visits – by 6.7 percent. Incapsula says it’s easy enough to get around the hacker, scraper, and spam software, but that most website owners aren’t equipped to spot the infiltrators.

Extra traffic, longer loading times, less customers.

We already knew that robots did some amazing things, now we learn that they’re doing things we’re not even aware of – at least not the extent. They’re not alive, yet they’re surfing the web more than we are. So who will win in the end, human or machine? Better monitoring tools – for free – would help. You can’t get rid of the critters if you don’t know they’re there in the first place.

[image credits: Incapsula, Tagman, and Average Bro]
image 1: graph
image 2: tagman
image 3: spambot

Oral Polio vaccines have been around for a while, but their versatility is about to increase dramatically.

Researchers in India and Switzerland have found that a relatively new vaccine may hold the key to eradicating Polio from the face of the Earth. Bivalent oral poliovirus vaccine (bOPV) not only performs as well as traditional vaccines, it does so against a wider range of virus types. It may allow children in Polio hotspots to develop resistance to more strains of the virus quicker, cutting down on infections, and stopping pandemics from growing. According to Reuters, 55 million children in Africa will receive bOPV starting this week, and the vaccine is already in wide use in Afghanistan. Thank goodness because Polio is a nasty little bug. One in two hundred infected will develop paralysis and between 5-10% of those will die from inability to breathe. For much of the world, the threat of Polio is only a frightening bit of history, but as long as any child has the disease, the risk of global infection remains. bOPV not only gives hope for the eradication of Polio, but may serve as a model for eliminating other viruses from our world as well.

Since 1988, the prevalence of Polio has been curtailed dramatically. According to the World Health Organization we’ve gone from around 350,000 cases in ’88 to less than 2000 cases reported in 2006. However, just because Polio has been on the decline in the past decades doesn’t mean it is gone. In fact, between 2003 and 2005, 25 countries that were previously Polio free were reinfected. In the modern age of high speed travel the only true protection a nation has against a Polio pandemic spreading to their borders is eliminating the disease from the Earth entirely.

To that end, bOPV is a godsend. It’s oral, allowing for easier, faster dosing, and it provides great resistance to two strains of the virus (type 1 and type 3). As discussed in the Lancet, researchers in India, with guidance from Roland Sutter (Switzerland) from the WHO, compared bOPV to triple and single strain versions of polio vaccines. bOPV clearly outperformed the triple vaccine, and came very close to matching the single strain vaccines. In other words, bOPV isn’t the absolute best, but it hits two strains at once while still being very effective. That means it could be the perfect tool for immunizations in remote locations.

Which is exactly what’s happening. The four countries in the world with major Polio problems are Afghanistan, Nigeria, Pakistan, and India. bOPV has been in wide use in Afghanistan since late last year, and is working it’s way through northern India now. bOPV is generated by GSK in Britain and Panacea Biotec in India, the latter of which helped fund the Lancet study. According to comments about that study in the Lancet, cases in India have dropped from 260 in 2009 to just 32 in 2010. The 55 million children slated to receive bOPV in Africa will hopefully reduce rates there as well. According to Reuters, however, that funding for 2010-2012 vaccinations is only at 50% of what it needs to be.

Clearly the fight against Polio isn’t over. If the world focuses on it now, while the problem is shrinking, we could consign the disease to history. If we grow lackluster in our efforts because we think the virus is less threatening now than before, we open ourselves to reinfection and increased global danger. I am reminded of a game of Risk, where a pesky opponent has retreated to Australia and bunkered down for a long siege (apologies to the Aussies, but their nation is probably the most infuriating place in the world in that game for this reason alone). We just need to push a little harder and we can knock Polio off the map. Until we do, we’re still at war.

As critical as this situation may be, I hope that it is one that we will face repeatedly in the future…only for different viruses. Let’s eradicate Polio now, and then work to do the same for other contagious diseases. Polio, with its global history of destruction, is a great place for us to gather worldwide support and momentum. Kill Polio, then move on to the rest. Vaccines may not always be the solution, either. We’ve discussed how other virus treatments, based on protein disruption, could also work to treat and reduce infection. It doesn’t matter what tool we use, we just need to have complete victory as often as possible. Not every pathogen can be destroyed in this way, flus and colds will probably always be with us, but some of the worst can be. A future with fewer deadly epidemics is possible, we just need to fight for it.

[image credit: WikiCommons]
[sources: Sutter et al 2010 Lancet, WHO, Reuters]

The MicroKit (seen at left) was developed by this team at IBN. It can screen for viruses in a few hours.

The Institute of Bioengineering and Nanotechnology (IBN) in Singapore has developed an automated testing device that could enable mass screening for viruses in airports and other public places. The MicroKit requires a minimum of training to use: the operator simply pipettes a blood sample into a disposable cartridge and the machine does the rest. According to results recently published in the journal Lab on a Chip, the MicroKit can detect H1N1 (swine flu) as accurately as traditional lab techniques but in only two and half hours. This would make it possible to routinely test travelers in airports and customs stations to prevent epidemic outbreaks. IBN partnered with SG Molecular Diagnostics to develop the MicroKit for commercial sales back in 2009 and hoped to have launched the product some time this year. Whenever it arrives the MicroKit promises to bring new opportunities and concerns in the fight to stop the spread of diseases like influenza, dengue fever, and HIV/AIDS.

Most laboratory testing to detect disease takes hours and the work of highly trained technicians. The MicroKit cuts the time required for these tests down drastically (less than an hour in some cases), is designed to be easy for the novice to use, and is portable. That’s a magic formula. And it gets better. The disposable cartridges used in the MicroKit contain all of the needed reagents in the right amounts, but they don’t have movable parts, making them easy to mass produce. This means the MicroKit won’t only be faster than normal lab work, but probably cheaper as well.

The disposable polymer catridge used in the MicroKit can be manufactured easily using ejection molding.

How will we use this new technology? IBN seems focused on the mass screenings of travelers, but there are equally important applications for third world testing. We could have custom agents collecting blood samples to stop the spread of H1N1 or the next scary flu virus, but that’s going to be a privacy nightmare. Voluntary screenings are much more appealing to me. A single person with a MicroKit could test remote villages on their own – which could help with the HIV pandemic, as well as with Malaria and other diseases.

If the MicroKit becomes cheap enough we could use them to routinely screen the people in population centers that are most at risk for flu epidemics, such as nursing homes and schools. Neither doctors nor lab technicians would be needed to quickly screen patients and stop the spread of disease. Who knows, one day such kits could even be cheap enough for people to own in their homes. If they were made very very simple, we could screen ourselves and avoid others if contagious.

The catridge fits into the MicroKit where DNA/RNA extraction and RRT-PCR is automatically performed.

For those interested in its inner workings, the MicroKit contains a minithermal cycler, a single color 3-chamber fluorescence detector, pneumatic fluidic delivery system. The MicroKit can perform DNA/RNA extraction/purification very quickly (reportedly less than 6 minutes in some cases) and combines this with real time reverse transcription polymerase chain reaction (RRT-PCR) to detect viral loads.

The MicroKit is still under development, but its current capabilities are impressive. It can detect viral loads as low as 100 copies per microliter – not as sensitive as the most advanced manual lab techniques, but good enough for many applications. Current cartridge design would allow for the screening of up to three diseases at the same time. Dr. Mo-Huang Li, who lead the development team, hopes that the next phase of the MicroKit will be able to screen for 25 using just one cartridge. As the MicroKit continues to improve it has the potential to become an ‘all in one’ testing device. A single sample of blood, a single machine, and a few hours could tell you whether you have any number of diseases. That’s damn cool.

[image credits: IBN]
[source: IBN Press Release (PDF), Xu et al Lab on a Chip 2010, A-Star Press Release]

Zirus' approach to fighting viruses could work against strains as different as the HIV and Rhinovirus (common cold) shown here.

Zirus isn’t making medicine directly, they’re researching the way viruses exploit cells. But what kind of medications might Zirus’ research make possible? Well, treatments for the common cold for starters. Herpes, SARS, Hepatitis C, those could all be medicated. How about a single drug that could help you fight off Ebola, HIV, or the Flu. Yep, Zirus technology could be used to target not just one virus, but a whole family of viruses.

When you can target entire families of viruses, you can prepare for diseases that haven’t even developed yet. Vaccines and standard anti-viral meds can’t do that. As Perryman says, “There’s no way you can vaccinate against the unknown.” In this way, Zirus based meds are superior to vaccines. So now we may have a pro-active response to the threats of bio-terrorism. And in-vitro experiments show that the techniques developed by Zirus can prevent viral caused cell destruction with every virus tested to date. That’s right, these medications could be nearly universal in their application.

How does it all work?

Vaccines prepare your immune system, and traditional anti-viral meds attack the virion directly. Zirus discovered a third avenue of approach: make the host-cell construction and assembly mechanisms impossible for viruses to break-into and corrupt. How? The key is cell proteins.

Viruses use proteins in host cells to reproduce. They’re the microscopic version of James Bond. Break in, hijack and destroy, then skip town and do it again. But what if the virion couldn’t break into a cell? What if there wasn’t a sexy protein for our James Bond virus to corrupt? That’s the whole concept behind Zirus: find the ways that viruses enter and hijack cells, and then remove those elements so that there’s no pathway for the virus to reproduce. Derail the reproduction process and a virus (or James Bond) is basically powerless.

The gene-trap retrovirus infects cells so that Zirus can find ways to prevent other viruses from doing the same.

Zirus has a new application of a proprietary technology called gene trap. Gene trap is actually a retrovirus, genetically designed to enter into test cells and change just one single gene. Apply it to enough cells and you’ll have one cell for each gene in the human genome. Every cell has a different gene that’s been messed with. Many of these cells will die (random changes to the genome tend to have that effect), but some will live.

So what does the genetic change do? Well, many will alter the proteins in a cell. Zirus exposes each of these living cells to a virus that is typically 100% lethal. A few select cells survive the viral exposure. These remaining cells had a genetic change that altered proteins and kept the virus from killing them. If you’ve tested the whole genome, you have found all such possible proteins.

“Can I tell you [something] really cool about gene trap…it’s a small retrovirus. The trap itself is a modified virus…So it’s really virus versus virus to provide us with this information…That sort of cleverness [engineered by our founding scientist Don Rubin] blows me away.” —David Perryman, 2009

You could, theoretically, alter someone’s DNA so that they never produce these virus-friendly proteins, but who knows the long term effects or dangers of that. Instead of genetic doping, we’re going to see doctors affect those proteins in a temporary way through drugs. The medications that scientists would develop will target those proteins and the genes encoding the proteins and either suppress their production (called down-regulating) or disrupt their use (through small molecule sized inhibitors). According to Perryman, ” …Making drugs that inhibit the protein’s functions are the nearest term, most durable, most likely drugs.”

The Long Term Stability of a Three-Legged Stool

No matter what anti-viral treatment you use, some of the work will have to be done by the body itself.

David Perryman is quick to point out the benefits and limits of Zirus’ discoveries. Medications that target host cell proteins are less likely to be defeated by viral mutations. They can target wide ranges of viruses all at once to create broad spectrum antiviral drugs. They may work against viruses that haven’t even been seen yet. These advantages place protein-inhibiting medications above the other two common treatments: vaccines and anti-viral drugs. Perryman, however, likens the three options as legs of a stool. Some may be stronger choices than others, but you need all three to keep things stable.

That’s because there are some drawbacks to protein-inhibiting meds. First, toxicity. Messing with cellular proteins, even temporarily, isn’t always healthy for a cell. While the most disruptive changes were eliminated during the gene trap (remember all those cells that died in the beginning?) other problems could still arise. The second major drawback: research time. Finding a protein is not the same thing as finding the drug that will affect that protein. Finally, no matter how wonderful gene trap directed medication could be, viruses are likely to eventually find a way around them.

“There’s always a concern with any drug about toxicity. When you think about the drugs you already take…they’re affecting our proteins and [cell] processes in some way. So what we’re doing is making [anti]viral drugs that are more like all other drugs.” —David Perryman, 2009

Zirus isn’t too concerned about toxicity, however. With a whole genome of proteins to test, there’s bound to be several options for each virus. You can target the protein whose temporary inhibition will have the least toxic effect on a cell. In fact, Zirus is confident that the proteins they help choose will result in effective new drugs that have relatively low toxicity.

As for research time, there is a huge host of medications that are already approved by the FDA, such as some for high blood pressure. Some, if not many, of these may be effecting proteins that Zirus could point out as virally important. Already, Zirus has worked with its partners to develop one such medication as a treatment against influenza. Because it’s already FDA approved, the medicine just has to be shown to be effective in this new use. Perryman thinks we may see re-purposing of existing medications in the next few years.

Which is a good thing, because developing entirely new medications may take 10 to 15 years. That’s all part of the plan, though. Current medications, vaccinations and anti-viral cocktails are working well enough to hopefully see us through as Zirus builds that third leg of the stool. Once the leg is in place, a combination of vaccines, anti-virals, and human protein inhibitors will allow us to combat viruses in a holistic way

Ziruses and Viruses of the Future

“When you think about antibiotics, …it’s sort of similar. We started with penicillin and we’ve evolved to all these…broad spectrum antibiotics…Now [we] basically have the same kind of technology [platform] with viruses.” —David Perryman, 2009

While the gene trap technology is an amazing tool for learning more about combating viruses, Zirus isn’t a traditional pharmaceutical company. They aren’t going to be making medications themselves. Instead, Perryman sees Zirus as becoming a hub for viral research. The company will point the way to promising new proteins and existing drugs that could be used in viral medications. It already works with several major universities, the CDC, NIH, and the biodefense part of the NIADA. In the future, Zirus will help combat not just the commercially important viruses like the flu and HIV, but all viruses that have the potential to harm us.

Here at the Hub, we like ideas that attack a problem from a completely new angle: computers built like brains, building materials that can think, or fuel from poop. Zirus is one of those kinds of ideas. With a whole new method to combat viruses, the gene trap technology will radically improve our response to viral illness whether natural or lab manufactured. Proactive research, finding ways to combat viruses before they are even discovered, further insulates us against global catastrophe. No viral treatment is perfect, but Zirus provides a great line of defense. You almost feel sorry for the bad guys.

“There’s no limits because all viruses…need to exploit our cells, our factories, to reproduce themselves…We can affect any virus. It’s doable.” —David Perryman, 2009

[All photos provided courtesy of Zirus]

Light and Channels and Receptors, Oh My!

This device could be tremendously useful when an epidemic breaks out.  There would be no need for guesswork in outbreaks like the recent swine flu.  Once the disease itself is isolated and added to the database, patients could be told in mere minutes whether they are affected and quarantined so as not to spread the disease.  If these devices disseminated into home use, the results could be even more effective.  Parents would know immediately what their children are suffering from and could respond accordingly.  The entire family could be treated before symptoms are even seen.

Conversely, this system could also help to save money in the already bloated healthcare system.  Patients could test themselves at home for a disease and, if it just turns out to be the common cold, they would not need to go in and see their primary care physician.  There would be no need for extraneous visits to the doctor to run tests that will simply come back negative.  This device could be the biggest breakthrough since thermometers went from rectal to oral.

The device works on the fairly simple concept of light refraction.  If there is something (on the molecular scale) in the way of a beam of light, that beam will be scattered ever so slightly.  It’s a bit like a fingerprint, where no two molecules scatter light in the same manner.  A detector determines exactly how the light was scattered and checks the patterns against a database of known patterns that can positively identify the mystery molecule.  For this to work effectively, the molecule, bacterium or virus needs to be held directly in the path of the light.

To do that, a special microchip of sorts was created with channels for the light to pass through.  Molecular receptors were placed on the chip in such a way that when it binds to a target, it is held in the beam.  On the chip are many types of molecular receptors, with at least one capable of attaching to each species in the database.  As a sample of the patient’s saliva or blood is spread on the chip, the receptors bind the malady in place.

This device is still in its prototype stage, so it will be a few years before “say ahhh” disappears from the doctor’s office altogether.  But the sheer excitement generated by the prospect of this absolutely remarkable machine should be enough to warrant a trip to the clinic or at least a new pair of pants.  The journey from prototype to product is perilous, arduous and time consuming, but hopefully we’ll be seeing this device hitting hospitals in the near future.

Microscopic workers of the world unite! There’s a trend floating around laboratories: designing tiny mechanisms that can build other devices from the atomic level up. The concept isn’t new, but we’re finally seeing some real progress in the field. When most people think of these tiny workers, there’s just one word on their mind: nanobots. But we’re here to tell you that the playing field is much wider than that. Biology is getting into the micro-worker game.

Virus-Built Batteries from MIT

Some could give you a cold, the Swine Flu, or Ebola, but viruses may just end up being humanity’s best tool. Researchers at MIT have created the next generation of battery assembled using special genetically engineered viruses. These batteries are close to out-performing the lithium-ion standards used today, and will soon exceed them in scale and power. Better yet, the virus built batteries are green-energy — constructed without hazardous chemicals or waste. Who knew that viruses could help save our environment?

Of course, no virus comes out of the wild willing to make batteries. You have to rewire the little guys to become happy workers.

That’s where Dr. Angela Belcher comes in. She’s the head of MIT’s Biomolecular Materials Group and the genius behind the virus-built batteries. Belcher added two genes into a virus called M13. These genes caused two changes: the virus built amorphous iron phosphate (a-FePO4) into its shell and the virus started hunting down and attaching to single-walled nanotubes (SWNTs).

For those of you who know your chemistry (no, not the relationship kind), you’ll recognize these materials as key ingredients in building better conductors. The mixed structure of SWNTs and amorphous iron phosphate creates a great cathode (negative end) of a battery. By using these materials, the viruses create a battery that has lower toxicity, lower cost (based on materials), and is more stable than current lithium-ion technology. In short, these viruses kick the Energizer Bunny’s® butt.

And the viruses work for free. Once you get the genetic modifications correct, they just need materials. You place them in water with some ions and they build a battery the same way that other organisms build shells. As Belcher points out, that’s one of the big benefits of using biological tools: they follow their genetic instructions and work on their own. Another benefit is that selection and evolution help you improve your tiny workers again and again.

A genetically engineered virus (yellow and red) attaches to a carbon nanotube to help form the next generation of compact and powerful batteries.

Viruses: powered by fear?

But wait, you say, you’re afraid of what these viruses might do if unleashed on the world. Can’t they mutate into a terrible disease? Might they stop building batteries and start building weapons of mass destruction? Couldn’t these little electronic-minded viruses one day develop into *gasp* Decepticons™?

Let’s get the facts straight. These viruses are bacteriaphages, meaning they hunt down and eat bacteria, not humans. Second, Belcher and her cautious colleagues have only adapted two genes. Just two, so there is little chance of rampant mutation. Last, the viruses are relatively fragile things, that’s why the process to make the batteries has to be so environmentally friendly. The little guys would die off otherwise. In short, there’s no reason to be afraid of these engineered viruses, they just want to build you batteries. Won’t you let them try?

Right now the batteries can only handle being charged and discharged about 100 times, and there’s just enough power for a LED. Belcher thinks that once she and the rest of her crew can get the batteries working on a larger scale, however, we will see virus-built batteries powering laptops, cell phones, possibly even electric cars. It’s for potential like this that Dr. Belcher was named one of Rolling Stone’s 100 People Who are Changing America, and why she’s been featured on NPR and the BBC. In the end, it’s not just the viruses who are doing all the work.

Influenza, commonly called “the flu,” is a virus that infects the respiratory tract.  Worldwide, the flu is responsible for up to 500,000 deaths annually and hospitalizes millions more, according to the World Health Organization.  Each year, the virus mutates into new forms resistant to flu vaccines and natural antibodies, making it extremely difficult to treat.  This is why vaccines must be re-engineered and re-administered for each yearly flu season, and even this strategy shows limited effectiveness.  But soon, a single shot could make you immune to the virus for the rest of your life.

A team led by researchers at Dana-Farber Cancer Institute developed the new antibody treatment by drawing on a library of 27 billion human antibodies.  They injected one of several antibodies being studied into mice that had been infected with the H5N1 strain – the deadly bird flu – three days earlier.  Not only did the mice recover, but the antibody protected the mice from more than just that single strain.  “What surprised us is that the same antibody protected mice from a lethal infection with a very different virus such as the H1N1 subtype that causes seasonal human infections; this is really remarkable,” said Ruben Donis, chief of the Molecular Virology and Vaccines Branch at the Center for Disease Control.

Most flu vaccines are specific to a particular strain, and must be re-engineered every year in response to new mutations in the virus.  This new antibody treatment from the Dana Farber Cancer Institute is unique because it attacks a non-mutating section of the virus, preventing it from deploying the genetic material that infects the body’s cells and spreads the virus.  This provides the immune system with the weapons to target multiple strains of influenza, and to protect against newly mutated strains – including strains that haven’t even evolved yet.  Researchers say human testing of the drug could begin in time for the 2011-2012 flu season.

After an individual breathes in influenza, a protein called hemagglutinin on the surface of the virus help it to bind to target cells along the respiratory tract.  Once the protein binds to the cell, the membranes of the virus and the cell fuse together.  This creates a bridge that allows viral RNA to enter the cell and find the nucleus, where the cell’s genetic code is stored.  In the cell’s nucleus, the viral RNA is copied along with the cell’s own genome.  This allows a virus to spread quickly, using the body’s own cellular mechanisms to make more copies of itself.

Hemagglutinin is composed of a head region and a stem region.  The head of the protein is capable of mutation; this allows the virus to evolve into new forms that the body cannot recognize through established antibodies.  In contrast, the stem of the protein doesn’t mutate; it undergoes structural changes to help deliver the viral RNA, and any mutations would interfere with that function.  The researchers’ new antibodies bind to the stem region of the hemagglutinin, interfering with the delivery system in a way that the virus cannot evolve around.

Flu pandemics arise when a new strain of virus evolves that our species have very little tolerance for.  The Spanish flu of 1918 – the H1N1 subtype – killed between 50 and 100 million people worldwide.  The avian influenza strain, or H5N1 subtype, has killed millions of birds throughout the world and aroused fears that it might mutate into a form easily transmittable to humans.  Neutralizing influenza without allowing it the ability to mutate would be our species’ first line of defense against possible flu pandemics of the future.

Before a single flu shot can offer protection for a lifetime, more antibodies must be produced to neutralize strains that haven’t been tested yet.  While the present research offers treatment for the H1 and H5 strains, there are sixteen types of hemagglutinin known (H1 through H16).  Already, researchers are applying their new technique to the remaining strains.   As they are, the antibodies that have been developed can act as a treatment for people already infected with the flu – pending FDA testing, of course.

It is unclear how effective the technique will be in treating other viruses, as there are multiple ways for a virus to infect a cell.  Still, the new technique – finding a nonmutating component of a virus and causing it to malfunction – seems promising as a theoretical approach to how we fight viral infection on a global scale.

The study was published in the journal Nature Structural and Molecular Biology.  The video below, released by the Dana Farber Cancer Institute, explains the how the antibody works on a molecular level.

image: source

The new microscope uses a technique called magnetic resonance force microscopy (MRFM) to achieve 100 million times the resolution of standard MRI.  Using this new device researchers were able to build a 3D image of the tobacco mosaic virus.  Although the current results are impressive, the researchers are confident that they can make the microscope a further 10 times more powerful in the coming years, allowing for resolution of 1 nanometer or less.

This microscope from IBM is an incredible scientific achievement that is poised to accelerate the ongoing revolution in the fields of biological research, new medical treatments, and nanotechnology.   3-Dimensional shape is crucial to the proper function of proteins, enzymes, and other molecules in the human body and thus several human diseases result from their malformation.  3-Dimensional shape is equally important in the manufacture and function of nanomachines and nanomaterials where atoms and molecules must be arranged in very specific locations. 

Below is a video of the microscope released by IBM, followed by further analysis:

Although this breakthrough is substantial, we should keep in mind that several other techniques (many that also came from IBM in fact) are available for viewing objects at the nanoscale.  X-ray Crystallography and cryo electron microscopes have long given us the ability to determine molecular structure, atomic distance, and even “view” individual atoms.  

What is important about this new microscope from IBM is that it will be able to step in where the other techniques have failed.  X-ray crystallography requires the structure being analyzed to be crystallized for analysis, a requirement that is not achievable for entire subclasses of proteins and other nano sized structures.  Cryo electron microscopy has its own limitations, most notably that the electron beam can destroy the specimen under examination.  This new MRFM microscope from IBM will overcome these problems as well as add more flexibility and options to complement the other techniques.

Below are some cool pics with descriptions from IBM media:

Animation How an MRFM works — The magnetic resonance force microscope (MRFM) uses an ultrathin silicon cantilever (yellow) with a nanometer size magnetic tip (blue) to detect the magnetic signal from an individual electron buried below the surface of the sample. Because the electron has a quantum mechanical property called “spin,” it acts like a tiny bar magnet and can either attract or repel the magnetic tip. The interaction between the spin and the tip is localized to the bowl-shaped region in the sample called the “resonant slice,” which moves as the cantilever vibrates. With the aid of a high-frequency magnetic field generated by a coil (right, background), the orientation of the electron (green arrow) flips as the resonant slice passes through. The magnetic force between the electron and magnetic tip alternates between attraction and repulsion every time the electron flips its orientation, causing the cantilever frequency to change slightly. A laser beam (left) is used to measure precisely the variations in cantilever vibration frequency.

IBM Almaden’s MRFM research team — Raffi Budakian, John Mamin and Dan Rugar (left to right) are three of the four members of the IBM Research team who developed and used this Magnetic Resonance Force Microscope to detect the magnetic signal from a single electron. Benjamin Chui is not shown.

The end of the cantilever arm, with virus particles attached.