Asia to North America: Eat My Dust!

North Americans breathe dust, pollutants, and microbial spores that cross oceans and mountain ranges without difficulty. University of Washington researchers describe the phenomenon in a recent issue of Applied and Environmental Microbiology.

Plumes of Dust & Microbial Spores

For the first time researchers have been able to gather enough biomass in the form of DNA to apply molecular methods to samples from two large dust plumes originating in Asia in the spring of 2011. The scientists detected more than 2,100 unique species compared to only 18 found in the very same plumes using traditional methods of culturing, results they published in July.

“It’s a small world. Global wind circulation can move Earth’s smallest types of life to just about anywhere,” Smith said.

It’s been estimated that about 7.1 million tons (64 teragrams) of aerosols – dust, pollutants and other atmospheric particles, including microorganisms – cross the Pacific each year. The aerosols are carried by wind storms into the upper reaches of the troposphere. The troposphere, the layer of air closest to earth up to about 11 miles (18 kilometers), is where almost all our weather occurs. _University of Washington

The Earth's biosphere is interconnected by sea, air, and land. When volcanic islands erupt from the sea -- barren and lifeless -- it does not take long before life springs up on the mass of lava rock.

Update: Apparently someone notified the UW news site of their author's error, described below. The UW site has now corrected its error, but a number of other "science news" sites continue to repeat the mistake. How can they call themselves "science news outlets" when they mindlessly propagate such a basic error?

The paragraphs below were written in response to the original version of the news release, which contained the error described:

The UW newsrelease describes the increase in numbers detected in the most recent study as "99% more than reported in findings published just 4 months ago." But if 2100 unique species are detected now compared with only 18 unique species in findings published 4 months ago, the increase is much more than 99%. A 99% increase is almost 1 doubling, or roughly twice as many. 2100 is more than 100X 18, or over 10,000% more.

Such a mistake on the part of the news release author reflects a basic lack of mathematical understanding -- which reflects badly on the institution and on any news outlets which unwittingly repeat the mistake. This is particularly true for a science news article.

This is just one small example of a general dumbing down taking place in schools, popular culture, and the news media.

Examples of error propagation across the web:

A surprising number of microorganisms -- 99 percent more kinds than had been reported in findings published just four months ago -- are leaping the biggest gap on the planet. Hitching rides in the upper troposphere, they're making their way from Asia across the Pacific Ocean and landing in North America. _Sciencedaily

A surprising number of microorganisms – 99 percent more kinds than had been reported in findings published just four months ago – are leaping the biggest gap on the planet. Hitching rides in the upper troposphere, they’re making their way from Asia across the Pacific Ocean and landing in North America. _Newswise

A surprising number of microorganisms – 99 percent more kinds than had been reported in findings published just four months ago – are leaping the biggest gap on the planet. Hitching rides in the upper troposphere, they’re making their way from Asia across the Pacific Ocean and landing in North America. _RedOrbit

There is no telling how long it will take these websites to correct the mistake -- if they ever do. Just take it as fair warning when reading such sites, that they often unwittingly repeat significant errors that an intelligent 4th grader would have detected.

Keep that in mind as these "science journalists" tell you what you should think about climate change, gun control, resource scarcity, overpopulation, or any number of other complex concepts. Pity the poor school child who is at the mercy of teachers who themselves are incapable of catching basic science and maths errors in their teaching materials and other sources from which they draw.

New Magic Bullets Against Emerging and Chronic Infections?

Emerging infections -- both human engineered and naturally evolved -- present a difficult challenge for modern and future medicine. Recent scares from SARS and Bird Flu have sent journalists and health watchers into a frenzy, although fortunately neither outbreak proved as rapidly contagious and broadly lethal as anticipated -- so far.

A "magic bullet" that could provide resistance against a wide array of new viral, bacterial, and fungal infections would give medical practitioners and public health officials new confidence for a healthier human future.

Two potential "magic bullets" have been recently developed. The first is an artificial protein -- EP67 -- which appears to boost mammalian immune systems -- even when given alone without other drugs or vaccines.

Mice treated with EP67 within a twenty-four hour window of non-lethal infection were significantly protected from influenza-induced weight loss. Furthermore, EP67 delivered twenty-four hours after lethal infection completely blocked influenza-induced mortality (0% vs. 100% survival). Since protection based on innate immune induction is not restricted to any specific pathogen, EP67 may well prove equally efficacious against a wide variety of possible viral, bacterial, and fungal pathogens. Such a strategy could be used to stop the worldwide spread of emergent respiratory diseases, including but not limited to novel strains of influenza.

...In summary, this report shows that the C5a agonist peptide EP67 provides both prophylactic and therapeutic protection against influenza infection. Protection results from the rapid induction of a robust innate immune response that includes high local concentrations of anti-viral cytokines and the influx of several populations of innate immune effector cell types. These results have profound implications for influenza therapeutic development and, ultimately, for broad-spectrum emergency therapy against unidentified respiratory pathogens. _PLoS

Medical Express News Release on EP67

Another potential "magic bullet" approach to both new and old infectious diseases, is the T Cell vaccine.

For some infectious diseases, traditional vaccines just don't cut it. Microbes that hide inside human cells and cause chronic illness aren't stymied by the antibody response generated by the kind of vaccine available at the doctor's office. T-cell vaccines, which activate a different type of immune response, could, in theory, better prevent or control such chronic infections, but so far nobody has been successful at transitioning T-cell vaccines from the lab bench to the clinic.


A Cambridge, Massachusetts, biotech company called Genocea thinks its high-throughput method could change that. The company will begin its first clinical trial later this year, when its experimental herpes vaccine will be the first test of its claims.


All existing vaccines rouse the body into creating antibodies that attach to the surface of infecting microbes and flag them for destruction. But pathogens that live inside our cells, such as the viruses, bacteria, and other microbes that cause AIDS, malaria, herpes, and chlamydia, can evade this surveillance. "In order to deal with those types of pathogens, oftentimes we have to stimulate what we call cellular immunity. Unlike antibody immunity, which recognizes pathogens directly, cellular immunity has to recognize the infected cell and get rid of your own infected cells," says Darren Higgins, a biologist at Harvard Medical School who studies the interaction between hosts and pathogens and is a cofounder of Genocea.


... our understanding of how T cells control infection is still developing. The challenge is to identify the right protein—or antigen—from a pathogen that will grab a T cell's attention and signal that a human cell harbors an infectious agent. "If you can figure out what those protein pieces are, then you can use those proteins as a vaccine to sort of educate your immune system on what to respond to," says Higgins, who is now a consultant and scientific advisor for Genocea.


...Genocea plans to enter clinical trials with its genital herpes vaccine later this year. If successful, Genocea's herpes simplex 2 vaccine would be the first to combat the disease, which affects one out of every six people aged 15 to 49. Currently, patients can take antiviral drugs as a treatment, but there is no cure. Genocea's candidate vaccine would be used as a therapeutic treatment for patients who already have the disease.


Genocea's herpes vaccine program is moving faster than typical vaccine research, which can take 10 years to go from discovery to proof-of-concept and 20 years to reach the market, says Higgins. "Now you can screen very rapidly what is going to be the optimal vaccine component that allows you to get into clinical trials at a rapid rate." _TechnologyReview

These two distinct approaches to triggering immune system activity work on different parts of the immune system. EP67 protein induces an immediate immune response against acute threats. T Cell vaccines induce cellular immunity to destroy cells which are already infected, often chronically.

Human knowledge of the immune system was advanced significantly by the $billions spent on HIV / AIDS since the 1980s. Research tools and computational power have advanced along with this growing knowledge. Understanding the immune system better is one of the most important keys to effective treatment of a wide range of cancers, as well as to the development of effective anti-aging treatments.

Brian Wang looks at T Cell vaccines

IBM's Nano Approach to Killing Drug Resistant Bacteria

Chemists at IBM Research have been working to create "ninja polymers" that can target MRSA-infected cells in the human body and destroy their harmful payload.

Bacteria such as methicillin-resistant staphylococcus aureus (MRSA) are resistant to commonly-used antibiotics. IBM has drawing upon its experiences with semiconductor technology to create antibiotic-free bacteria killers. While they were researching ways to etch silicon wafers at a smaller scale than currently possible, they found some materials that could produce an electrostatic charge when chained together to form a polymer.

When these "ninja polymers" are introduced to the bloodstream, they self-assemble into biocompatible nanostructures that are electrostatically drawn to infected cells while not affecting healthy ones. When the reach those cells, they destroy the bacteria and then biodegrade with no side effects or accumulation within the body. Because the attack is physical, rather than chemical, the bacteria are les likely to be able to build up resistance to it.

These sticky nanostructures work in a very different way to antibiotics, according topolymer chemist Jim Hedrick. "They try to mimic what the immune system does: the polymer attaches to the bacteria's membrane and then facilitates destabilisation of the membrane. It falls apart, everything falls out and there's little opportunity for it to develop resistance to these polymers."

In addition to being useful vehicles for the delivery of drugs, these polymers could also be added to every day cleaning solutions. The research team believes that they could be used to replace the widespread distribution of antimicrobial agents found in hand gels, antibacterial wipes, toothpaste and even socks. _Wired

An earlier description of this research

There are a number of physical approaches to attacking drug-resistant bacteria, which are less likely to induce bacterial resistance -- including metal ions such as silver and titanium.

Nanotechnological materials research is likely to discover large numbers of other physical approaches to destroying drug resistant bacteria before they can spread.

The Rise of the Zombie Empire: Resistance is Futile

They walk freely among us, unheeded. Infected by brain parasites, behaviours subtly altered. Two billion infected, and counting.
Zombies are popular fictional examples of brain alteration that is usually caused by a biological agent. But inside every fiction is the kernel of truth. Zombies are so popular in part because they are uncomfortably familiar.

LaughingSquid

At least two billion people worldwide are infected by the protozoan, many from eating infected meat. Initial symptoms are mild flu, after which the parasite forms cysts that lodge in the brain. There they remain for decades... _NYT

Two recent studies reveal how microbes can alter normal brain functioning. Researchers from California and Singapore detailed how the protozoan Toxoplasma Gondii is capable of blunting normal fear responses to threat in animals. Canadian and Irish researchers have discovered a mind-altering effect from probiotic bacteria -- specifically, a species of lactobacillus. The lactobacillus was found to lower stress, anxiety, and depression related behaviours in mice.

Microbes can change our brains, and make us somehow different. In extreme cases -- as in brain-eating amoeba or fatal encephalitis and meningitis -- they can kill our brains outright. But sometimes they kill or disable only a portion of our brains, and leave us alive, but altered. And sometimes they live inside of us, changing us chemically by their metabolic excreta.

These are not the "borg" of fiction. There are no brain implants or electrodes controlling us. But biology is much stranger than we understand. We can go to Robert Heinlein's "The Puppet Masters," for a vivid fictional account of extraterrestrial invaders able to attach to humans, growing tentacles into human brains and spinal cords. That would be an extreme example of biological control of humans by "the other."

Far more subtle, and easier to bring about, would be genetically controlled microbes able to insert themselves into particular parts of the brain, to bring about neurochemical alterations -- either temporary or permanent. By targeting the brain region of choice, behaviours could be manipulated according to an overall plan or scheme.

Even easier, would be normal body flora genetically altered to secrete brain-altering chemicals, such as benzodiazepine or amphetamine. Something a little extra in your yogurt or your moisturizing cream. Schools, prisons, and armies should take special note.

We are far beyond the skills needed for such simple manipulations. And given the apparent state control of modern popular media and scientific publishing, who would know -- or be able to say anything about it?

Here is how to make your own yogurt. Just in case. Some of us may not be infected yet. There may be safe retreats left, far from the teeming mobs. It may not be too late......Heh.

MIT Scientists Unleash DRACO: Viral Genocide Imminent

We have developed a new broad-spectrum antiviral approach, dubbed Double-stranded RNA (dsRNA) Activated Caspase Oligomerizer (DRACO) that selectively induces apoptosis in cells containing viral dsRNA, rapidly killing infected cells without harming uninfected cells. We have created DRACOs and shown that they are nontoxic in 11 mammalian cell types and effective against 15 different viruses, including dengue flavivirus, Amapari and Tacaribe arenaviruses, Guama bunyavirus, and H1N1 influenza. _PLoS

PLoS One: Broad Spectrum Anti-viral
The DRACO antiviral approach created by MIT researchers has the potential to develop into an all-purpose antiviral prophylactic and early-stage treatment. This development is a timely reminder that while microbes can be shifty and clever in avoiding antimicrobial medicines, humans have incredibly creative and resourceful brains -- if they would only use them.

Now, in a development that could transform how viral infections are treated, a team of researchers at MIT’s Lincoln Laboratory has designed a drug that can identify cells that have been infected by any type of virus, then kill those cells to terminate the infection.

In a paper published July 27 in the journal PLoS One, the researchers tested their drug against 15 viruses, and found it was effective against all of them — including rhinoviruses that cause the common cold, H1N1 influenza, a stomach virus, a polio virus, dengue fever and several other types of hemorrhagic fever.

The drug works by targeting a type of RNA produced only in cells that have been infected by viruses. “In theory, it should work against all viruses,” says Todd Rider, a senior staff scientist in Lincoln Laboratory’s Chemical, Biological, and Nanoscale Technologies Group who invented the new technology.

Because the technology is so broad-spectrum, it could potentially also be used to combat outbreaks of new viruses, such as the 2003 SARS (severe acute respiratory syndrome) outbreak, Rider says.

...When viruses infect a cell, they take over its cellular machinery for their own purpose — that is, creating more copies of the virus. During this process, the viruses create long strings of double-stranded RNA (dsRNA), which is not found in human or other animal cells.

As part of their natural defenses against viral infection, human cells have proteins that latch onto dsRNA, setting off a cascade of reactions that prevents the virus from replicating itself. However, many viruses can outsmart that system by blocking one of the steps further down the cascade.

Rider had the idea to combine a dsRNA-binding protein with another protein that induces cells to undergo apoptosis (programmed cell suicide) — launched, for example, when a cell determines it is en route to becoming cancerous. Therefore, when one end of the DRACO binds to dsRNA, it signals the other end of the DRACO to initiate cell suicide.

Combining those two elements is a “great idea” and a very novel approach, says Karla Kirkegaard, professor of microbiology and immunology at Stanford University. “Viruses are pretty good at developing resistance to things we try against them, but in this case, it’s hard to think of a simple pathway to drug resistance,” she says.

Each DRACO also includes a “delivery tag,” taken from naturally occurring proteins, that allows it to cross cell membranes and enter any human or animal cell. However, if no dsRNA is present, DRACO leaves the cell unharmed.

Most of the tests reported in this study were done in human and animal cells cultured in the lab, but the researchers also tested DRACO in mice infected with the H1N1 influenza virus. When mice were treated with DRACO, they were completely cured of the infection. The tests also showed that DRACO itself is not toxic to mice. _Physorg

So far, the treatment appears safe and non-toxic, and fairly effective when used pre-infection, and in the early stages of infection, for the viruses tested. Whether this general approach will lead to successful treatments for herpes viruses or HIV and other retroviruses, remains to be studied.

Since DRACO leads to the death of viral-infected cells, the potential exists that this approach might lead to eradication of "stealth viruses" which hide in particular cell types for a person's entire lifetime.

As for other stealth viruses living inside human cells which have not been discovered by human science, presumably some of these would also be killed by a DRACO-like approach. No one knows what the result of such a broad-spectrum clearance of body viruses might be, because no one knows what these undiscovered stealth viruses are doing in the first place. Assuming they are there, which is quite probable, according to Al Fin system biologists.

Algae are Optimistic about the Future

More: A study from the Pacific Northwest National Lab outlines how the US could replace 17% of its petroleum imports with homegrown algal fuels.
Abstract from study

NewScientist
While human academics and analysts are all too quick to write off algae as serious contenders in the energy race, the algae themselves are completely optimistic about their own futures. Perhaps the algae know something that we do not know? Well, for one thing, algae is already a big business. For another, algae has a lot of potential for productive yield -- and is just getting started.

ALGAE are being put to work performing a unique double duty: cleaning up sewage waste while simultaneously producing biofuel.

All algae feast on phosphates and nitrogen-containing compounds, converting them to lipids. Some of these oils can be converted to biofuel, but only a few algal species produce lipids of the right type and quantity to be easily converted to fuel. In theory, though, algae are a perfect renewable fuel source. The main obstacle is that brewing the right nutrient mix can be prohibitively expensive.

Now, in work for a master's thesis, Eric Lannan, a mechanical engineer at Rochester Institute of Technology (RIT) in New York and colleagues have identified three types of microalgae - Scenedesmus, Chlorella and Chlamydomonas - that efficiently convert nutrients to fuel on a diet of municipal waste water, while happily living in its harsh, salty environment. In a lab test, it took just three days for the algae to gobble up 99 per cent of the ammonia, 88 per cent of the nitrate and 99 per cent of the phosphates in a broth resembling that from a domestic sewage treatment plant, turning themselves into rich sources of fuel even as they purified the water.

"People had looked at algae to clean waste water, others to make biodiesel," Lannan says. "We're putting those ideas together." _NewScientist

The idea to use waste feedstocks for boosting algal production is not especially new, but it still needs to be demonstrated on a large scale. And the demonstration must show that the resulting algae can be used to produce valuable products to make the entire process self-sustaining and profitable.

Besides using wastewater, the use of high CO2 effluent from power plants and cement factories etc. would provide the carbon boost for rapid growth, which algae crave.

Algae do not need too much sunlight -- in fact too much sunlight can reduce yields for valuable algal products. Solazyme, for example, grows its algae in the dark by feeding them sugars from biomass for fuel. They claim an 80% lipid yield, which is quite high.

Artificially inflated prices for crude oil are driving a multitude of approaches to the production of alternative liquid fuels. Fuel from algae is but one of many alternative approaches to liquid fuels, and algal researchers are taking dozens of divergent approaches to create algal fuels. Other microbial fuels approaches appear equally promising at this time.

A lot of money is going into the effort to create microbial fuels and fuels from biomass. But the key discoveries will not necessarily come from the best-financed research labs. Time will tell.

Those who think "biofuel" means only maize ethanol, are going to be very surprised when they discover what is really happening.

Beware the Plastic Apocalypse!!!

Enviros See Armageddon In Every Plastic Bag
We are told the oceans are covered with floating plastic debris, clogging the ocean food chains and destroying free-swimming wildlife. But solid evidence of this eco-catastrophe is quite thin. And ever since a Canadian high-schooler (and another in Taiwan) in 2009 discovered species of microbes that thrive on eating plastic, most informed observers have been somewhat less concerned.

Since then, scientists in Ireland have begun to put microbes to work digesting waste plastics, and UK scientists have discovered plastic-eating microbes in ocean waters.

Sargasso SeaThe latest story in the long-running ocean apocalypse saga, involves scientists from the Woods Hole Oceanographic Institute in Massachusetts. Woods Hole scientists explored the Sargasso Sea, in search of plastic-eating bacteria.

Mincer and his colleagues examined bits of fishing line, a plastic bag and a plastic nurdle (a pre-production plastic pellet) fished out of the Sargasso Sea, an area of the North Atlantic where currents cause debris to accumulate. The region as a whole contains more than 1,100 tonnes of plastic1.

...Plastic-eating bacteria might help explain why the amount of debris in the ocean has levelled off, despite continued pollution. But researchers don't yet know whether the digestion produces harmless by-products, or whether it might introduce toxins into the food chain.

...Genetic analysis shows that the bacteria on the plastic differ from those in the surrounding seawater or on nearby seaweed, says microbiologist Linda Amaral-Zettler of the Marine Biological Laboratory, Woods Hole. So far, the DNA sequences obtained by her lab show that almost 25% of the bacteria on one polyethylene surface were vibrios, bacteria from the same group as the cholera bacterium.

...Amaral-Zettler and Mincer also found genetic and microscope evidence of eukaryotes — organisms with more complicated cells than bacteria — on the plastic. What she calls the "plastisphere" might contain complex living communities. "It may be a little world that we've created, for better or worse." _Nature_via_Impactlab

It is fascinating that particular ocean bacteria have adapted to using plastics as a food source. This is all quite reminiscent of the bacteria that have adapted to eating crude oil and methane gas around oil spills and and natural hydrocarbon seeps in the ocean floor.

To the bacteria, our discarded plastics are a feast and a windfall, allowing them to feed and reproduce to their microbial hearts' content. Of course the same phenomena occurs on land, except with a much wider range of microbes -- both prokaryotic and eukaryotic -- partaking of the cornucopian repast.

Environmentalists are concerned that the microbes may be releasing toxins into the seawater which will pollute larger sea creatures and perhaps get into the human food chain. A plastic apocalypse on the prowl, don't you see? And yet, in the middle of the ocean, nothing is wasted. If something can be seen as food, it will be used as food by something. That includes anything which humans may perceive as toxic.

Here is the amusing thing in all this: Waste plastics are increasingly being seen as valuable feedstocks in the production of synthetic fuels, chemicals, and other high-value substances. Gasification of solid wastes for production of power, process heat, and chemical/fuel feedstock is just getting started in the developed world. In the future, the only plastic wastes the oceans will see will be coming from places too primitive to know how to unlock their intrinsic value.

And no doubt there will be plenty of plastic-eating ocean microbes to take care of those remnants. Otherwise we will need to raise our seawalls quite high, to avoid the ocean plastic tsunamis that may come from Neptune, with a crashing vengeance.

Beware the plastic apocalypse.

More on plastic apocalypse 31March11: The death of the environment by plastic bags may have been exaggerated. (via Daily Bayonet)

That Feeling in Your Gut? Intestinal Flora

"As animals ourselves, we have more than 1000 different kinds of microorganisms living in our guts ...._abcnet

Intestinal microbes can determine the quality of your life, and your perception of it. Your guts are the repository of the majority of your microbial complement. Life without "normal flora" would be a different animal.

Professor Petterson and his colleagues bred a number of mice under normal and germ-free conditions. In stantardised tests of activity, the germ-free mice explored more of an "open-field activity box", rearing up on their hind legs more often, and showed less of the signs associated with anxiety.

In studies of the animals' brains, they showed higher levels of a number of hormones, and even differences in the expression of over 170 genes.

The result does not paint a clear picture of whether the development of the germ-free mice is specifically "better" or "worse" for the animals, Professor Pettersson explained, but is a "very, very interesting" first demonstration that the bugs can have such profound effects even within the brain.

It follows a long line of studies that suggest the bugs are far more involved in mammalian function than just in their digestion. _BBC

Very interesting. The germ-free animals lived longer and seemed more curious, but they were very fragile to stress and various types of injury, compared to animals with normal bacterial and skin flora.

If we are to swim in a sea of bacteria -- as it seems we are destined to do -- it is best that our bacterial partners be sympatico with us. If we wish to avoid chronic intestinal inflammation, fatty liver, obesity, and a wide range of other pathologies and malaise, we need to pay attention to our bacterial friends.

Gut inflammation allows the intrusion of large numbers of various protein intruders which are better kept out of the blood and lymph systems. Yes, we can eat more yoghurt, or take probiotic capsules or powders. Not a bad idea, actually. We may even want to begin to gene-engineer our probiotics for maximal benefit against these ailments. In situations of grave extremis, we may be forced into fecal transplants -- as a last resort.

Al Fin clinical and synth-bio microbiologists recommend genetically engineered probiotics out of all the choices mentioned above: from germ-free environments to fecal transplants. But different situations call for different remedies. Consider each case individually.

Researchers looked in detail at the molecular effects of the engineered bacteria and found that the production of regulatory immune cells, rather than of inflammatory immune cells, was enhanced. "When we treat mice with the new strain, we see more accumulation and generation of cells that produce regulatory proteins, which lure and generate regulatory T cells," says Mohamadzadeh. The regulatory T cells, a type of immune cell, counteract the effects of harmful immune cells that attack the cells lining the gut, he says.

...Mohamadzadeh's team is also exploring engineered probiotics as a treatment for colon cancer. In preliminary studies in mice designed to mimic colon cancer, treatment with the modified bacteria reduced the number of polyps the animals developed by 90 percent. "We observed an average of just three small polyps in treated mice, compared to about 35 to 50," he says.

He adds that the bacteria's ability to reduce inflammation isn't limited to the gut; the regulatory cells migrate throughout the body. That means the microbes may also be able to help treat other diseases linked to inflammation, such as rheumatoid arthritis and psoriasis. _TechnologyReview

Of course, once you start introducing targeted gene-engineered microbes into the gut, the possibilities for treatments and specific optimisations multiply rapidly.

You may be aware that peptic ulcers and gastric cancer are tied to a gastric microbe, helicobacter pylori. The development of counter-bacteria to H. Pylori would allow simple, food-assisted treatment for a number of illnesses specific to that microbe.

The same arguments could be applied to skin bacteria and other parts of the body where normal bacterial flora reside. There are plenty of diseases of multiple systems which are caused or made worse by absent or insufficient symbiotic bacteria.

But once we start applying, ingesting, and inserting engineered microbes for treatment and prophylaxis, we are likely to begin thinking about optimisation. Why take nutritional supplements, for example, when microbes can produce the needed substance just as well? The same applies to particular medications, enzymes, or hormones. And so on...

Now go eat your yoghurt.

Lipid Fermentation via Engineered Microbes for Bio-Jet Fuel

GCC
The US military's DARPA has awarded Logos technology with a $17.5 million phase 2 award to produce jet fuel from biomass, using microbial lipid fermentation.

This contract is to demonstrate an end-to-end Lipid Fermentation Process (LFP) at scale for the commercially viable production, from cellulosic biomass, of Hydrotreated Renewable Jet (HRJ) spec jet fuel—a near term surrogate for JP-8 that can be readily commercialized.

HRJ is produced from renewable oils (lipids) by methods common in petroleum refining. Fatty acids and triglycerides are hydrotreated to remove oxygen, and the resulting paraffinic hydrocarbons are processed to yield a mixture of straight-chain, branched-chain, and cyclic paraffinic hydrocarbons with collective properties that are similar to those of conventional jet fuel.

Oleaginous yeast can produce lipids from the sugars resulting from the pretreatment and hydrolysis of biomass; certain fungi can also produce lipids, either via solid-state fermentation of biomass or from the biomass hydrolyzate.

This primary program effort is to consist of optimized process development and engineering along with regionally specific economic modeling to produce fuel, demonstrate process energy efficiency and support commercialization.

...This phase of the BioJET program requires the delivery of larger quantities of jet fuel with a projected cost of production of JP-8 at commercial scale implementation (50Mgal/yr) at less than $3.00 per gallon. _GCC

Al Fin bio-synthesists believe that the greatest value of current advanced biofuels research is to put a rough ceiling on future prices of hydrocarbon fuels. Peak oil doomsayers claim that liquid fuels will have no price ceilings when "peak oil" truly hits the fan.

But that claim has already been falsified by the fact that shale gas cost per BTU is well less than half the cost of crude oil per BTU. As efficiencies of conversion from gas to liquids improve, we will see the "price ceiling" effect of shale gas begin to affect markets. Something similar will begin to happen in about ten years, as more efficient biomass to liquids processes begin to scale up.

Like everything associated with energy these days, oil futures markets are heavily politicised, and infiltrated by persons whose behaviour is -- shall we say -- somewhat less than ethical. The fluctuations of oil markets are highly profitable to those who know how to put their fingers on the scale in a reasonably surreptitious manner. But the conversion of alternative and unconventional fuels to liquid hydrocarbons: GTL, CTL, BTL, kerogensTL, BitumensTL, etc etc, provides a multiple bypass to the oil commodities markets. Such alternative routes to fuel makes the work of the energy mafias and faux environmentalists much harder -- unless they can use bribed politicians to stop the alternatives and unconventionals.

Cross-posted to Al Fin Energy

Craig Venter Aims to Replace the Entire Petrochemical Industry

“Designing and building synthetic cells will be the basis of a new industrial revolution,” Dr. Venter says. “The goal is to replace the entire petrochemical industry.” _NYT

NYT

Peak Oil will occur when humans no longer want to bother drilling into the ground to extract dark, gooey, messy liquids to turn into fuels. Instead, humans are slowly but surely developing other, more reliable and sustainable ways to fuel their industrial base and somewhat affluent lifestyles. Dieoff.orgiasts and other members of the Voluntary Human Extinction Movement hate to see any alternatives to Peak Oil Doom, or any skepticism to the orthodoxy of Catastrophic Anthropogenic Global Warming. But humans are innately a problem-solving and skeptical lot.

Craig Venter is one example of an unlikely problem solver. He was a poor student in his youth, and only after living through some harrowing experiences in Vietnam as a military medic was young Venter able to get his head on straight, and decide to do something with his life.

...Dr. Venter has a history of defying skeptics, and many people are betting that he will succeed this time as well. Dr. Walton, in fact, invested personally in Synthetic Genomics, and his venture firm, Oxford Bioscience Partners, recently wanted to sink a hefty sum into the company but was turned down when Dr. Venter found other investors offering better terms.

Exxon Mobil is giving Synthetic Genomics $300 million in research financing to design algae that could be used to produce gasoline and diesel fuel. (The new greenhouse will be used for that research.)

BP has invested in the company itself, turning to Synthetic Genomics to study microbes that might help turn coal deposits into cleaner-burning natural gas. Another investor, the Malaysian conglomerate Genting, wants to improve oil output from its palm tree plantations, working toward what its chief executive calls a “gasoline tree.”

...In the approach toward which Dr. Venter is driving, engineers would specify the entire genetic code of a cell — essentially the software that runs the cell — on computers, making design changes as if on a word processor. They would then press the “print” button, so to speak, and the DNA would be manufactured from its chemical components. The synthetic DNA would then be transplanted into an existing cell, where it would “boot up” and take control of the cell’s operations.

...Synthetic Genomics has about 130 employees. But much of its research, including the development of the synthetic cell, is done at the J. Craig Venter Institute. Synthetic Genomics pays for about 25 of the institute’s roughly 300 researchers, and has rights to their results. The rest of the institute’s funding comes mainly from federal grants and its endowment.... _NYT

Venter seems to love challenges and competitions. He lives to defy skeptics and to defeat rivals. And do you know the odd thing? The world is full of young Venters who have not yet -- and may never -- figured out what they want to do with their lives.

Pelted mercilessly with nightmarish predictions of doom and gloom, and instilled by governmenbt schools and indoctrinating universities with the futility of trying to fight their fate, hundreds of thousands of young Venters never amount to much -- when they might have done, given the right experiences in early life.

From an article published at Al Fin Energy

Bioremediation of Hydrocarbon Polluted Soil

There are several approaches being promoted for bioremediation of the water, sand, and soil impacted by the Macondo oil spill in the Gulf of Mexico. Some companies are promoting bacterial remediation, some are promoting enzymatic remediation, and some are promoting fungal remediation.

The video above looks at an experiment conducted on six mounds of diesel-contaminated soil, using 6 different approaches to bioremediation.

According to the narrator, the fungal approach was the only type of remediation that restored the badly contaminated soil fully to a thriving micro ecosystem. Who knew that oyster mushrooms love diesel and other hydrocarbons?

Of course you can't grow oyster mushrooms in seawater, where bacterial approaches make more sense. In fact, bacteria that naturally break down oil are contained within the oil itself, and in the seawater of the Gulf of Mexico and other naturally oil-rich waters. Nature has dealt with hydrocarbon contamination for billions of years, and has learned how to recover from an oil spill.

We just need to learn the best way of giving nature a hand.

Update on LS9, "Green Chemicals"

The technology is pretty straightforward. LS9 uses any sugar source (though initially it will use sugar cane due to the favorable economics and logistics of sugarcane compared to cellulosic sugars) and feeds genetically modified E. coli bacteria (the same kind found in our guts that helps digest sugars into energy) a combination of sugar, nutrients, methanol, and enzymes in a low-heat environment _Greentechmedia

LS9 is the south San Francisco bioenergy company that produces ASTM quality diesel from E. Coli. The company has made some progress in 2010 already that is worth looking at.

1. It closed a $25 million equity round with investor Chevron Ventures

2. It signed a memorandum of understanding with Proctor & Gamble to produce green surfactant chemicals

3. In February LS9 purchased a 10 acre demo production plant in Florida that is capable of producing  50,000 to 100,000 gallons of diesel (a year?) for a mere $2 million in a bankruptcy sale

4.  The demo plant is due to be up and running by mid 2010, and the company will be working to try to convert the plant to commercial scale by 2011, if feasible.

5.  There is a possibility that the company can scale up to a production of 10 to 12 million gallons of diesel per year by 2012, tentatively.

Source _ Greentechmedia

In summary, LS9 is hoping to reach commercial production levels within 2 years -- about 8 years sooner than Al Fin predicts that microbial fuels will begin to make an impact on energy markets.  Can  they do it?

LS9 is only one of dozens of well financed microbial fuels companies, racing to supply global fuel markets with commercial micro-biofuels.

LS9's foray into "green chemicals" may actually bring it its first real profits.  In fact, the green chemistry arena is receiving considerable interest and investment.

Genomatica, a company that scuttled biofuel ambitions in favor of full-time chemical production, has just raised $15 million in a third round of funding (PDF) to make the industrial chemical business at large more sustainable. It says this financing should be enough to build its own demonstration plant before breaking into full-scale commercial production.

Much like LS9, Synthetic Genomics, and Codexis — companies pursuing biofuel strategies in addition to chemicals — Genomatica’s core business is the microbe it engineered to convert sustainable feedstocks (corn, switchgrass, sugar cane, biomass) into fuels and chemicals. The company, which uses sugar as its primary feedstock, says its strain of e.coli has reached a level of efficiency and speed that makes production of green products cost competitive with petroleum.

Genomatica’s number one product, 1,4-butanediol (BDO), is incredibly versatile — a key ingredient in durable polymers used in clothing, cars and electronics, as well as solvents. The global BDO market, which hit 1.25 million tons last year, represents a $4 billion opportunity, the company says. Until now, all of this BDO has been produced using petroleum. It’s a ripe area for change. _GreenVentureBeat

The name of the game in business is making a profit. It you find that your first product is taking longer to get to market than you thought, try to find another product that you can get up and running sooner -- perhaps even at a greater profit than your first idea.

The Obama Pelosi regime is making the US a bad place to start a new business -- or to keep a pre-existing business running and employing people. Unless US voters start to wake up very soon, expect more of the "enterprises of the future" to begin sprouting up overseas.

Solazyme Wins Gold Medal In Amsterdam

This weeks World Biofuels Market in Amsterdam has gotten a lot of people thinking about microbial biofuels -- including algal fuels. US company Solazyme won the gold prize for Sustainable Biofuels Technology at the WBF this year, so we will take a closer look at Solazyme.

Solazyme, a private company based in South San Francisco, stands out from the algae crowd, for a number of reasons.

First, there’s the sheer variety of its products. Solazyme makes fuel for the U.S. Navy. It makes a heart-healthy, vegetarian, protein-rich microalgae power that goes into Garden of Life supplements and vitamins sold at stores like Whole Foods. And it recently announced a deal with Unilever to use algal oil in renewable, sustainable personal care products like soap. Its algae are multi-talented.

Then, there’s the fact that Solazyme, unlike other startups, is “producing large volumes of oils and fuels, and we have been for a while,” says its CEO, Jonathan Wolfson. What’s large volumes? An annual rate of tens of thousands of gallons, including a little over 20,000 gallons of shipboard fuel during the first half of this year for the Navy, part of an $8.5 million contract signed last year...

... They got off on what they now say was the wrong track, growing algae in ponds, as most algal fuel companies do. A couple of years and a few million dollars later, they told their investors that it wasn’t working. Instead of growing algae in ponds using sunlight as an input, they decided to feed biomass such as sugar cane or switchgrass to their algae and grow them in tanks. This gives the company more control over the production process.

Wolfson says:

Pretty much everyone in the space disagrees, but the conclusion that we drew is is that…algae is by far the best thing on the planet at making oil but it’s far less economically efficient at capturing photons than higher plants.

We take algae, we put them in a tank, we feed them biomass, they make oil and we take the oil out. There’s a lot of technology in the process, but that’s basically what’s happening.

By genetically modifying the algae, Solazyme can produce a range of products, much as a standard oil refinery can make fuels and chemicals by refining crude oil. The company is exploring three distinct market segments: fuel oils, nutritionals (human and animal nutrition) and health sciences (cosmetics and nutraceuticals). “You have the whole world of chemistry at your fingertrips,” Wolfson says. _EnergyCollective

Solazyme is pursuing 1. algal fuels, 2. algal foods for humans -- including cooking oils -- and animal feeds, and 3. algal cosmetics and nutraceuticals.  Whether the Solazyme approach of growing algae in the dark by feeding it sugars is the most economical approach to algal fuels or not, Solazyme does appear to be learning a lot about different phases and types of algal production.

Petroleum, natural gas, and coal were all made by microbes over geological time scales.  But modern microbes are getting a boost from genetic engineering and advanced industrial engineering.  Right now, the race to microbial fuels is happening in laboratories and small pilot plants.  Within ten years, the race will move to larger scale pilot and production plants.  That is when things will get interesting on the commercial and financial scale.

Do Not Bet Against Craig Venter

Craig Venter has true grit. He came by it honestly over his lifetime, and continues to display true grit in all of his ventures.

Since mapping the human genome 10 years ago, J. Craig Venter has found plenty of work. The biologist now is burrowing into DNA in as many forms as he can discover, in organisms from the sea and deep underground. His goal: to use the building blocks found in naturally occurring DNA to make synthetic cells. He and his partners at Exxon Mobil Corp. and BP PLC believe genetically engineered life forms hold great promise for energy and other industries. _WallStreetJournal

Fuels-from-microbes is a topic of interest to scientists, venture capitalists, and technologists around the world. It is no wonder that Craig Venter finds himself at the center of the cyclone that involves finding the replacement for fossil fuels and finding the keys to biological magic both at the same time.

In July of last year, Synthetic Genomics announced a $300 million agreement with Exxon to research and develop next generation biofuels using photosynthetic algae. That investment will occur over a number of years -- but that's still a lot of cash. It's more than the total amount of venture capital invested in algae startups since 2005. A drop in the bucket for Exxon but still, big money.

Here's what Venter had to say: "We are at the early stages of seeing what biology can do."

Venter has come up an idea to trick algae into pumping more lipids out. He also claims to have "engineered algae to continuously pump out hydrocarbons," which eliminates much of the cost and energy-intensity of conventional algae oil farming. If that can be done, economically and at scale -- it is absolutely disruptive.

...Venter speaks in a matter-of-fact manner about his activities but beneath that calm tone are mind-bending ideas straight out of science-fiction novels. Venter has already created the first cell with a synthetic DNA gene. If not exactly creating life, Venter is bending the genetic code to do his bidding. He said that he is "going from the four-letter genetic code of A, C, G and T to the binary codes of ones and zeros."

He is "amassing a genetic database...continually learning to write the genetic code" and "treating the genetic code as a raw material." By "changing the DNA software in the cell, the cell converts to a new species." In Venter's words, "The concept of life is changing."

In Venter's "optimistic" estimation, it will take roughly a decade to get to scale on CO2 to fuel. But "once the proof of concept is done, this will move rapidly."

There remain many problems with algae -- it's not just a matter of tricking the algae to pump more lipids out or to secrete hydrocarbons. There's an entire process chain in algae farming that needs to be optimized -- algae growth, water issues, nutrient issues and more.

But Venter is a man of action and it's not a good bet to wager against him. _BiofuelsDigest

Venter is the Vietnam war veteran who beat the Human Genome Project to the human genome. Venter understands the stakes that are involved in learning the secrets of the gene -- whether for humans or for algae. Once these secrets are out of the box, there is no replacing them.

Programming algae to replace fossil fuels will be a trivial achievement in comparison to finding the genetic keys to nurturing smarter humans. Whatever Venter may say, there is little doubt that he would like to be at the center of that cyclone as well.

Venter is a man of grit, accomplishment, and great ambition. Such men aim high, and once they reach great heights of achievement, they tend to aim even higher.

Genetics Magic: Two Examples of a Startling Future

Here are two fascinating examples of genetics magic:

Brain cells from skin cells

Skin cells called fibroblasts can be transformed into neurons quickly and efficiently with just a few genetic tweaks, according to new research. The surprisingly simple conversion, which doesn't require the cells to be returned to an embryonic state, suggests that differentiated adult cells are much more flexible than previously thought.

If the research, published in the journal Nature yesterday, can be repeated in human cells, it would provide an easier method for generating replacement neurons from individual patients. Brain cells derived from a skin graft would be genetically identical to the patient and therefore remove the risk of immune rejection--such an approach might one day be used to treat Parkinson's or other neurodegenerative diseases.

"It's almost scary to see how flexible these cell fates are," says Marius Wernig, a biologist at the Institute for Stem Cell Biology and Regenerative Medicine at Stanford, who led the research. "You just need a few factors, and within four to five days you see signs of neuronal properties in these cells." _TechnologyReview

Humans will soon be living longer, but in order for those longer lives to be meaningful, humans must have ways to keep their brains and other organs young and fully functional. Using common skin fibroblasts to provide replacement cells for aging brains would be the bare beginning steps to the regenerative society.



Diesel from bacteria

Jay Keasling, professor of chemical engineering and bioengineering at UC Berkeley and one of LS9's founders, and scientists at LS9 report engineering E. coli bacteria to synthesize and excrete the enzyme hemicellulase, which breaks down cellulose into sugars. The bacteria can then convert those sugars into a variety of chemicals--diesel fuel among them. The final products are excreted by the bacteria and then float to the top of the fermentation vat before being siphoned off.

Using these methods, it's possible to create a range of fuels from biomass, but LS9 is focusing on diesel rather than fuels similar to gasoline for the time being, says Stephen del Cardayre, the company's vice president of research and development. Diesel specifications are easier to meet and the market for diesel is growing by 2 to 4 percent a year, while that for gasoline is flat. Last May, LS9 partnered with Procter & Gamble to develop fuels as well as commodity chemicals. _TechnologyReview

Biomass can be grown in the oceans, in the deserts, on land, and in all ranges of climate. If a microbe can easily convert biomass to fuels on a large enough scale, you can say goodbye to fears of energy depletion.

The reprogramming of cellular genetic mechanisms allows humans to use living cells as molecular manufacturing plants, and as cell replication factories.   Programmed replacement brain cells can perform their normal functions plus secrete neuroprotective molecules to preserve their neighbors.  Re-programmed probiotics in the gut can provide a full range of nutrients and supplementary molecules to promote full body regeneration.  Programmed cells in the skin can use sunlight to synthesise a wide range of energy-providing molecules to power the body and brain.   Programmed biomass can turn itself into gasoline, diesel, jet fuel, etc. with a minimum of post-harvest processing.



When you look at all of the phantom fears held over our heads by the zombies in government, the UN, the media, and the rest of our fearful culture,  you need to understand that there are solutions to virtually every problem.  More importantly, you need to learn to distinguish problems that are fabricated to control your behaviour from problems that desperately require your attention to be solved.

Magic Helical Bullets to Kill Cancer and Bacteria?

The compound [Fe2L3]4+ is an iron triple helicate with three organic strands wrapped around two iron centres to give a helix which looks cylindrical in shape and neatly fits within the major groove of a DNA helix. It is about the same size as the parts of a protein that recognise and bind with particular sequences of DNA. The high positive charge of the compound enhances its ability to bind to DNA which is negatively charged.

When the iron-helicate binds to the major groove of DNA it coils the DNA so that it is no longer available to bind to anything else and is not able to drive biological or chemical processes. _PO

The interesting structure known as [Fe(2)L(3)](4+) was first researched as a treatment for cancer. But University of Warwick researchers have discovered that the metallomolecule is a particularly potent killer of bacteria -- even bacteria that are resistant to conventional antibiotics.

Initially the researchers focused on the application of this useful property for targeting the DNA of cancer cells as it could bind to, coil up and shut down the cancer cell's DNA either killing the cell or stopping it replicate. However the team quickly realised that it might also be a very clever way of targeting drug-resistant bacteria.

New research at the University of Warwick, led by Dr Adair Richards and Dr Albert Bolhuis, has now found that the [Fe2L3]4+ does indeed have a powerful effect on bacteria. When introduced to two test bacteria Bacillus subtilis and E. coli they found that it quickly bound to the bacteria's DNA and killed virtually every cell within two minutes of being introduced - though the concentration required for this is high. _PO

It will be important for the researchers to learn ways that the compound can be preferentially transported across bacterial membranes, to bacterial DNA. By reducing the necessary concentrations needed to kill the bacteria, and by making the construct preferentially attracted to pathological bacteria rather than to normal human cells, the safety and the efficacy of any possible future treatment using this compound will be enhanced.

The prevalence of antibiotic resistance has resulted in the need for new approaches to be developed to combat previously easily treatable infections. Here we investigated the potential of the synthetic metallomolecules [Fe(2)L(3)](4+) and [Cu(2)(L')(2)](2+) as antibacterial agents.... [Fe(2)L(3)](4+) binds in the major groove and causes DNA coiling... The work described here shows that ... [Fe(2)L(3)](4+) is bactericidal for Bacillus subtilis and Escherichia coli. We demonstrate that [Fe(2)L(3)](4+) binds bacterial DNA in vivo and, strikingly, that it kills B. subtilis cells very rapidly. _IntJnlAntimicrobialAgents

Cytocidal approaches are valuable medically to the extent they can be targeted and controlled -- with only limited damage to normal cells and tissues.

One of the main pillars of the SENS anti-aging approach is the elimination of superfluous and dangerous cells that have outlived their usefulness. The more precisely that one can target cytotoxic molecules, the more useful they will be for anti-aging therapies in addition to more conventional medical disciplines such as oncology and infectious disease.

Fast Forward Evolution: Advanced Microbe Fab

LS9 biofuels company aims to create "magic microbes" to solve the world's energy problems, and other problems besides. To that end, they have developed a machine to create rapid multiple changes in a bacterial genome. They have put evolution on "fast forward" in the hope of riding the magic microbes into the future.

"What once took months now takes days," says Stephen del Cardayré, vice president of research and development at LS9, a biofuels company based in South San Francisco of which Church is a founder. LS9 soon plans to use the technology--called multiplex-automated genomic engineering, or MAGE--to accelerate development of bacterial cells that can produce low-cost renewable fuels and chemicals.

...Church and his collaborators attack the genome on a broad scale. They design numerous genetic changes targeting genes throughout the genome, and then implement them all at once, looking for the resulting bacterial strain that can best produce the desired product. "It allows you to make modifications to the genome much more rapidly than the traditional one-step processes we have," says Kristala Jones-Prather, a metabolic engineer at MIT who was not directly involved in the research.

...As a test run of the device, Church and his team created bacteria that could more efficiently produce lycopene, an antioxidant abundant in tomatoes. They designed DNA strands targeting genes known to be involved in lycopene production, and then monitored multiple tubes of engineered bacteria for production of the bright-red compound. In just three days, they had generated a strain that could produce five times more lycopene, according to findings presented at a conference at Harvard this month. The best lycopene producer had 24 genetic changes--four that completed blocked production of the gene's protein, and 20 that resulted in small or large changes in the expression of that gene.

Church and his collaborators, who ultimately plan on making a commercial version of the device, are now working on creating different types of chemicals, including biofuels and drug precursors. _TechnologyReview

Biofuels from microbes will not take up croplands, will not destroy rainforests, will not produce pollutants -- but count on faux environmentalists to dream up some reason that abundant microbial biofuels will destroy the planet. In the meantime--before they dash our childish hopes-- let us cultivate our simple-minded optimistic belief that humans can somehow find a way to live in the world without destroying it.

Ancient Sponges May Help Humans Survive

Researchers led by Moeller, of Hollings Marine Laboratory in Charleston, found a sponge thriving in the midst of dead organisms. This anomalous life amidst death raised an obvious question, says Moeller: “How is this thing surviving when everything else is dead?”

Chemical analyses of the sponge’s chemical defense factory pointed to a compound called algeferin. Biofilms, communities of bacteria notoriously resistant to antibiotics, dissolved when treated with fragments of the algeferin molecule. And new biofilms did not form. _ScienceNews

Sea sponges live in a very tough neighborhood, microbially speaking. The billion-year arms race between competing organisms, and between predator and prey, has left a long trail of failed survival strategies in its wake. But the strategies that have worked, time and time again, can prove extremely potent.

Humans have their own arms race against bacteria, involving human manufactured antibiotics vs. some very clever strategies developed by bacteria over a billion year span or so. On the front lines of this battle, inside most of the hospitals of the world, bacteria are winning. Humans have been forced to come up with ever more expensive strategies to combat multiply resistant bacteria. What if we could borrow powerful strategies from other, more "street savvy" organisms? More of us might survive longer.

The compound is able to reprogram antibiotic-resistant bacteria that don’t form biofilms. When bacteria are treated with the compound, antibiotics that usually have no effect are once again lethal. This substance may be the first one that can restore bacterial resistance, Moeller says. “This resensitization is brand new.”

And the problem of perpetuating a bacterial-resistance arms race, in which bacteria rapidly develop countermeasures against new antibiotics, may be avoided entirely with the new compound. “Since the substance is nontoxic to the bacterium, it’s not throwing up any red flags,” says Moeller.

...The research is still in very early phases.

“Everyone would like to see this in antibiotic trials tomorrow,” Moeller says, but treatments for human infections are a long way off.

Sotka agrees. “Of course, we need clinical trials to take it to the next level,” she says. _ScienceNews

Scientists are sending out "scouts" to all the continents, oceans, seas, lakes, large islands, mountain peaks, and polar extremes of the world to find the winners of the ancient arms race between microbes, and between microbes and multi-cellular organisms. Improved mass screening technologies allow rapid throughput analyses of these organsims and their strategies, so that we can select the best in their class, for our purposes.

Under the Obama / Pelosi reich, the rich biomedical research community is likely to be starved for funds to conduct such research, since the new reich plans on diverting most of America's wealth -- including private sector wealth -- into government run human and social services.

Even so, the current momentum of research in university science labs, corporate labs, and other labs performing actual science, will persist for some years to come. It will take time for the reich's changed priorities to take over all the research funding agencies. Everything hinges upon the American voter, and whether they will wake up in time.

ATCC 51142 An Amazing Microbe Full of Promise

These tiny green cyanobacteria may not look like much, but Cyanothece sp. ATCC 51142 is incredibly versatile. In sunlight it uses photosynthesis to produce sugars for energy. At night it fixes nitrogen from the air for making proteins, nucleic acids, and other important molecules. Its genomic makeup is complex for such a simple organism, and Washington University researchers in St. Louis are learning a great deal from the unique organism--using a clever combination of proteomics and genomics.

Cyanobacteria are the only known bacteria to have a circadian clock. By day, Cyanothece cells increase gene expression for photosynthesis and sugar production; at night they moonlight, ramping up gene expression that governs energy metabolism, nitrogen fixation and respiration.

Pakrasi and his collaborators found the presence of a rare linear chromosome in the organism's genome, a first in cyanobacteria...Cyanothece 51142 has one large circular chromosome, a linear chromosome and four small plasmids.

"This is the first time anything like this has been found in photosynthetic bacteria. It's extremely rare for bacteria to have a linear chromosome," said Pakrasi. "Nearly 100 percent of them do not. Now, we have the genome of this organism, which gives us a complete picture of everything that can possibly happen in this cell...Now, we can go back to this complete picture and compare its brother and sister organisms to find their talents and deficiencies. That's comparative genomics," said Pakrasi. _Source

A clever combination of the use of proteomics with genomics allowed the researchers to find more genes than through use of gene sequencing alone.

Proteomics analysis examines almost the whole complement of proteins in a cell, but requires a gene sequence with which to pair up protein shards for identification. On the other hand, DNA sequencing can't always identify potential genes or unmask which of those really function, and could benefit from knowing which proteins the cell actually makes.

Instead of waiting on one analysis to do the other, the collaborators simultaneously sequenced the bacteria's DNA and determined proteins that the microbe produced at different times of its life cycle. They then compared the information to determine which of the DNA sequences that looked like genes actually made proteins. In this way, they could better determine where genes lie along the length of its genome, as well as find ones that might otherwise be missed.

"This was an excellent example of using proteomics to guide initial genomic annotation," said protein chemist Jon Jacobs of PNNL. "We're helping to set a precedent if we can do the proteomics work while they're doing the genomics work."

...In addition to the 2,700-plus real genes, the DNA sequence contained more than 2,500 would-be genes. These had architectural features common to genes but didn't look like recognized genes from other organisms. The team found about 500 of these that produced proteins, so the researchers re-classified these genes as functioning. Lastly, the scientists also found 38 proteins out of another 12,000 sequences that were gene longshots. _SD

In the dark, cyanobacteria can also act as fermenting organisms, producing acetate, ethanol, H2, lactate, etc.

This already impressive work will only grow more sophisticated and productive with time. Using this tiny bacteria as a model organism and comparing it with related strains will bring about an exquisitely fine knowledge of its dynamic function under all conditions of energy, nutrient, and other environmental conditions. Such knowledge will be pivotal in the quest to create better energy and food sources.

Microbes Rule the World, The Least They Could Do is Give Us All the Energy We Want

...historically, the study of microbes has focused on single species in pure culture, so understanding of these complex communities lags behind understanding of their individual members. NAS_New_Science_of_Metagenomics

Image Source

It is fortuitous that humans are finally learning the reality behind the community of microbes that rules the world, just at the time that we could use their help. Craig Venter and competitors are trying to create the perfect energy-making microbe. But growing single strains of microbes to make energy from sunlight, waste nutrients, and CO2 may not be the right approach. A community of microbes working together might do a better job. In fact, you might even say it takes a village of microbes to make a fuel.

Unlike the E. coli situation, using just one species may not work well for bioenergy, since, in nature, bacteria do not grow in isolation. In other words, no bacterium is an island. The very biodiversity that fills the Earth with bacteria and offers great bioenergy potential also presents a challenge for engineers. Even if one picks the ideal "bug," growing, maintaining, and optimizing conditions for its use in bioenergy applications remains a daunting challenge in terms of scalability and reliability.

"Microbial communities that are used to harvest energy must be resilient to fluctuations in environmental conditions, variations in nutrient and energy inputs and intrusion by microbial invaders that might consume the desired energy product," say the authors. The key to large-scale success in microbial bioenergy is managing the microbial community so that that the community delivers the desired bioenergy product reliably and at high rate.

In the absence of these molecular techniques, the authors state, our understanding of methanogenic communities progressed through slow, incremental advances over several decades. Today, society cannot wait decades for new bioenergy sources. Fortunately, an array of pre-genomic, genomic, and post-genomic tools is available to understand microorganisms involved in bioenergy production. Taking full advantage of these tools will greatly speed up scientific and technological advances, which is what society most needs.

Genomics provides the base sequence of the entire DNA in an organism, and the complete genome reveals all the possible biological reactions that a microorganism can carry out. In the past, complete genomes were only obtained for those microorganisms that could be isolated into pure culture, but it is now possible to sequence the genomes of uncultivated microorganisms using metagenomics.

To date, approximately 75 genomes are available from microorganisms that have a role in bioenergy production. These include 21 genomes from methane producing archaea, 24 genomes from bacteria that can produce hydrogen or electricity, and 30 genomes from cyanobacteria that are potential biodiesel producers. At least half of the completed microbial genomes that are relevant to bioenergy were released in the past 2 years, and more than 80 bioenergy-related genomes are currently being sequenced. __ScienceDaily_via_NextBigFuture

If you are not familiar with "metagenomics" you are not alone. It is less than a decade old, and like its siblings "synthetic biology" and "systems biology" it is still developing the new tools it will need to take off like a rocket.

The "community microbe" approach to bioenergy makes a lot of sense. One microbe can only carry so many tools to work with, and a robust approach to high-yield bioenergy will require several tools working simultaneously.

I once suggested using multiple microbes for biofuels production, grown individually in a series of bioreactors. I suspect that a combination of the two ideas may be most successful--a series of bioreactors, each containing specialised communities of microbes rather than single cultures. Working out the best ways of separating the desired product from each stage--for transfer to the next bioreactor -- may take some time.

Also, see Brian Wang's excellent overview of microbial approaches to bioenergy.