In the meantime, the mortality rate of this flu, while initially high in the Mexico City area, has fallen overall to around 2% or less, in line with annual deaths during flu season. Those who contract the virus are still those generally considered to be in the healthiest range of the population. On the vaccine development front there have been several developments since the 2009 Swine Flu epidemic began:

On April 29 vaccine researchers at St. Louis University announced that they’d accomplished the first step in developing a universal vaccine against pandemic influenza. To accomplish this the researchers used proteins (engineered a ‘bug’ that produced said proteins from genetic sequences coding for them) from both A and B influenza strains. The vaccine introduces those proteins so the body can engineer antibodies specific to them. More testing is needed, they say, before the vaccine is ready for prime time.

On May 1 Juergen A. Richt, a pathobiologist at Kansas State University’s college of veterinary medicine released findings that the current lineage of H1N1 Swine Flu is a descendant of the 1918 strain that killed more than 20 million people worldwide. For the study Richt and colleagues from Canada, USDA and Mount Sinai engineered their ‘bug’ in a biosafety-level-4 lab (like the one at UT-Austin) at the National Centre for Foreign Animal Disease in Canada using elements from both the 1918 virus and a 1930 descendent of that virus.

On May 22 researchers at the University of Pittsburgh’s Center for Vaccine Research announced that they’d evoked a robust immune response with a vaccine made of virus-like particles [VLPs], which are just the protein coats of actual viruses without any genes inside. This approach, which like other approaches involves genetic manipulation to produce the “hollow” virus shells, may work better than attenuated virus vaccines. The new vaccine for Human Papilloma Virus is a VLP.

And finally, on June 4 Genetic Engineering and Biotechnology News reported that scientists around the world are accelerating efforts to develop an effective vaccine against the current Chimera strain. This is ‘news’ in the GE/biotech community because genetic manipulation is standard operating procedure in the development of influenza vaccines, of any type – live, attenuated, killed and dissociated or VLP. Step #1 is to engineer your Chimera.

No matter how the Chimera came to be, Bellerophon is engineered very much on purpose. I personally like the idea of the VLP vaccine, as it ONLY has coat proteins and it excites a more robust immune response to those than to dissociated coat proteins. The robust response is to the form of the viral shell. Even better, if these beasties get out in an ‘oops’ it won’t kill anybody – it’ll just immunize ‘em. Let’s all hope one of these is available come September.

Well, I’ve got to admit this much-touted development in the world of medical research took me somewhat by surprise. Mostly because it caused me to stop eating my grilled cheese sandwich mid-bite to wonder “Huh? Why in the world would they do that?”

Seems this week’s Nature is reporting that researchers in Japan have managed to genetically engineer the green fluorescent protein gene into primates – specifically marmosets. Yes, these endearingly cute little monkeys have been engineered to express the gene in their hair roots, skin and blood, all of which glow green under UV light sources.

Now, I can understand why tropical fish aficionados might want several tetras of each color (they’ve got several now) in their aquarium to impress friends, neighbors and potential mates, but glowing green marmosets? You’ve got to have a primate license to own any kind of monkey or ape! The researchers responsible for this development say that this feat of genetic engineering could lead to monkeys being bred with genetic changes that would make them good animal models of human diseases.

Researchers have been breeding genetically engineered mice for decades to exhibit specific genetically influenced disease conditions so they can work on treatments and cures, but rodents aren’t close enough to humans on the evolutionary tree to be all that useful for the purpose. Primates would, they contend, be much better models because they actually are close to humans genomically speaking. If a team believes it has discovered a particular gene that causes something like Parkinson’s Disease or Alzheimers or ALS or such, they could engineer a line of monkeys that carry the defect – thus suffer the disease – so researchers can play with various methods of treatment that might someday be effective for people who suffer the disease.

Transgenic primates have been created before, but have never managed to pass the engineering on to their offspring. This means “lines” of, say, Parkinson’s monkeys haven’t proved out.

The development is causing some concern among animal rights activists and anti-vivisectionists who object to creating populations of genetically diseased primates exclusively so they can serve as the subjects for painful (and often fatal) experiments. The new development will open the ethical debates that must accompany animal-based research, so perhaps will be a good thing.

And what of these glow in the dark marmosets? Well, humans that glow in the dark generally don’t get that trait from jellyfish genes, so these little monkeys aren’t actually useful for medical research beyond ‘the usual’ medical research performed on little monkeys. I figure they’ll start showing up at high end pet shops along with those multi-colored glow in the dark fish, a curiosity for the rich and bored. Those clever Japanese!

Links:

Glowing green monkeys set ‘dangerous precedent’
‘Glowing’ Transgenic Monkeys Carry Green Fluorescent Protein Gene

Please go to the ScienceDebate 2008 website, take a hard look at Obama’s answers for our future, and don’t forget to drop the crew a dime (or ten) on your way out. These folks have been hard at it since November of last year, and have gathered some very impressive institutional support. The future is important to all of us – and our children – and the future needs the very best science we can possibly field to meet it head-on.

When I started college in the late 1960s in Oklahoma, I could buy gas for my Volkswagon Bug for 19.9¢ a gallon. That’s 5 gallons for a dollar, enough to drive home to visit the folks, drive around town to see friends, and get back to college without having to stop at a gas station. This past weekend I drove our little pickup to Gatlinburg, Tennessee to see an old Navy buddy, a round trip equivalent to that past Oklahoma weekend trek. Gas for the journey cost us right around $50. A dollar’s worth won’t get me to the grocery store and back any more, and it doesn’t look like the price is ever going to come down.

The going price per barrel of petroleum is pushing $150 hard and will probably go over $200 before the end of the year. Diesel fuel is a dollar more expensive than gasoline, and the price of everything grown on a farm and transported by ship, train or truck must go up accordingly.

The good news – or, at least the hopeful news is that progress is being made in deciding what replacement fuels we should be developing. Most people are skeptical of corn-based ethanol and the diversion of food crops as well as crop land to biofuels. And while new techniques can make biofuels from native vegetation like switchgrass or even algae, the fact is that plants aren’t very efficient at converting solar energy into the biomass required.

Biotech researchers are now turning to engineered microorganisms as both helpers in turning biomass into fuels and as fuel themselves – photosynthetic bacteria that can capture sunlight energy 100 times more efficiently than plants – that can be grown in massive amounts without competing for cropland.

It does appear that the time has finally come when human civilization must change its ways, the only questions being how much it’s going to hurt regular people and which nations and/or multinational corporations will corner the markets. Perhaps biotechnology can be put to good use creating new fuel sources instead of turning staple foods into pesticides. That would be a positive change of focus, help get the tarnish of public resistance off the biotech bus, and maybe even save the planet.

But you and I will probably be paying at least $5 a gallon to fill our tanks, no matter what kind of fuels are developed. Just something we’ll have to get used to.

Links:

New Source for Biofuels Discovered
Harnessing Microbes to Meet Future Energy Needs
Are microbes the answer to the energy crisis?

In its mad bid to privatize and control the world’s agriculture and food supply with its patented biotech seeds and cushy revolving door within governmental regulatory agencies, Monsanto cannot be very happy with a recent Soil Association report that shows GM crops decrease yields, whether it’s cotton or soybeans or corn.

As reported in The Washington Post, the biotech industry immediately released yet another bought-and-paid-for report claiming totally opposite conclusions (some things don’t change just because the science is against you). The Soil Association report took a serious look at reality, something quite refreshing in this field. The material included among other citations:

• a 2007 study from Kansas State University that showed Roundup Ready soy has suffered “yield drag” since it was introduced, producing an average of 9-25% less per acre than conventional soy.

• a rigorous independent US study under controlled conditions demonstrating that Bt corn yields up to 12% less than conventional corn.

• an article in Nature Biotechnology reporting that Bt cotton doesn’t even express the engineered pesticide in 25% of some varieties sold under exclusive license.

The crop failures and their tragic effects on farmers in poorer nations may be a product of the technology itself according to some analysts.

US scientists have finally called for more access to biotech crop data so they can perform studies to assess environmental impacts of the technology as well. Indications are that herbicide resistance has increased herbicide usage (polluting land and water), led to pest immunity (with increased crop losses), creates “superweeds” from wild relatives that are hard to eradicate, and may even have something to do with massive die-offs of bees in recent years.

A quote from Michelle Marvier of Santa Clara University in the ag-dependent state of California pretty much sums up the situation -

“Since 1996 more than a billion acres have been planted with biotech crops in the U.S. We don’t really know what are the pros and cons of this important new agricultural technology.”

Huh. I thought these are just the sort of things USDA and the FDA were supposed to find out before the technology was deployed on such a massive scale. Who could have guessed that allowing corporate control of law, policy and regulatory oversight might lead to bad law, policy and regulatory oversight? Oops…

The US Centers for Disease Control and Prevention is reporting this week that researchers from the US and Canada have successfully tested several vaccines for Ebola in primates, and are now seeking to modify them for human use.

This is a significant development not because Ebola in its natural habitat is such a grave danger to humanity, but because it’s got a 90% fatality rate and thus represents a threat to humanity as a bioweapon. While Ebola is not easily spread (direct contact with bodily fluids of an infected person or animal is required), officials have long been concerned that it could be “weaponized” – as has been done with anthrax, for instance – into a form that will be easily infective. There have been just over 1500 documented cases of Ebola in humans, and so far it does not seem to have been used as a bioweapon.

The Federation of American Scientists maintains an Ebola Fact Sheet indicating that the Soviet Union probably investigated weaponizing Ebola. There have been three reported incidents of researchers being infected after being stuck with contaminated syringes. Those in England and the U.S. recovered, one in Russia died. There is no effective treatment for the disease, and while the current research is hopeful, there is no vaccine to prevent it.

The biosafety threat level for Ebola is 4, a rating it shares with the 18 other hemorrhagic fevers it is akin to. Because the dead virus does not produce an effective immune response, researchers have been trying several different recombinant DNA techniques. The latest, most effective candidates are soon to be tested on humans. It is hoped that if the testing proves successful, the techniques will be as useful in developing vaccines for other hemorrhagic fever viruses, HIV and avian influenza.

Links:

Vaccine for Ebola Virus Successful in Primates
Ebola Fact Sheet

Bloomberg reported today that whatever killed the bees last year is back again this year, threatening some $15 billion worth of crops that depend on bees for pollination.

Honeybee Deaths Resume in U.S. Hives cites the USDA’s top honeybee researcher as saying that the effects of continuing Colony Collapse Disorder should become apparent by the end of the month, when growers will see how effective the pollination of California’s huge almond crop has been.

“Colony Collapse Disorder” is a fancy name for an unknown entity, since no one has been able to figure out what’s killing the bees. The bees that have been found (most just disappear) have devastated immune systems, but still no one knows what, exactly, they’re dying of. The US lost a quarter of all hives in 2006 and 2007, and may lose that much or more this year despite the importation of Australian bees to replenish the supply.

Some experts think a virus is responsible, others say that any illness could easily kill bees whose immune systems have been seriously compromised, so it’s whatever is attacking immune systems that is the real killer. Dead bees that remain in the hives are infected with a host of pathogens – “every known bee virus” according to UK’s The Independent newspaper – not just one. Some bees were carrying five or six viruses at the same time, along with fungal infections. That is more likely to be a pesticide or herbicide being used on the crops or on neighboring crops, though others claim it’s just stress.

Some experts in Europe, where Colony Collapse Disorder is hitting Germany hard, are concerned about pollen from genetically modified crops, many of which contain microbial toxins – pesticide – in every cell. If that turns out to be the issue, farmers may end up with restrictions on growing genetically engineered crops in regions where bee pollinated crops are also grown. Research demonstrating that the transgenes in GE crops have migrated to wild plants may make restrictions a moot point, however, and we’ll just have to come up with another way to pollinate crops.

Links:

Honeybee Deaths Resume in U.S. Hives

NRDC: The Bees’ Needs

The Silence of the Bees

European Bees Also Taking a Nosedive – Perhaps GM Crops?

The Chicago Tribune reports this week that scientists at Loyola University have established that the pollen, leaves and other plant parts of corn engineered to kill the European corn borer with Bt toxins could endanger the American midwest’s aquatic ecosystems when washed into nearby streams.

When eaten by aquatic insects called caddisflies, the Bt toxin stunts growth and increases mortality. These insects are food for fish and amphibians in the ecosystem. The scientists reportedly ‘feel’ that such unanticipated effects of GE technology need to be investigated, but of course the EPA and USDA (and Monsanto) don’t feel that way at all.

It might be difficult to separate the effects of GE plant wastes from the general toxic overload caused by modern agribusiness mega-farming practices, which also cause death and deformity among aquatic life forms and amphibians in midwestern ecosystems. And while consumers at home and abroad have made it known that they do not wish to consume genetically engineered pesticides disguised as food, the new market for corn as ethanol fodder makes it unlikely that GM corn is going to be phased out any time soon.

Related Links:

Older farmers less likely to plant Bt corn

GM corn might affect ecosystems

Eat to Live: 1 million against GM food

Eat to Live: Agriculture inspectors chided

The dramatic breakup of the northern ice sheet has tended to confirm global warming, and there are other indications that things are worse than we thought. Turns out that North America’s Northernmost Lake is showing signs of climate change too.

An international research team reports that a core sample of lake bed sediment indicates a drastic change in algae and diatom concentrations in the lake over the last 200 years, but not in the 8,000 years prior – when the lake was permanently frozen. This tends to support the hypothesis that human industrialization has contributed to the warming.

Even if we stopped releasing greenhouse gases today we’d still have to deal with the effects of climate change, and this has been a concern for important ecosystems’ stability. Good news is that researchers have discovered Forests of Endangered Tropical Kelp surviving just fine in the deep waters off the Galapagos Islands.

According to the researchers, the discovery demonstrates a surprising resilience for tropical marine systems in response to climate change. Using a computer model designed to predict where kelp forests might survive despite warming waters, student divers explored the tropical reefs where the computer had predicted likely kelp habitat. They found the forests growing at depths from 40 to 200 feet below the surface, in the cool water layer. Their find may get this species of kelp removed from the World Conservation Union’s database of threatened species.

Meanwhile, in our struggle to develop alternatives to fossil fuels that contribute to greenhouse gases, the National Research Council has reported a serious effect of increased ethanol production from corn that may lead to changing policies on what biofuels we as a nation decide to develop.

Increase in Ethanol Production from Corn Could Harm Water Quality outlines how, if projected increases in corn production for conversion to ethanol occur, water quality could be significantly harmed. This has to do with agricultural practices and expansion of farmland for growing fuel crops, particularly into arid and semi-arid regions of the country.

Irrigation could divert water resources for drinking, industry and hydropower, fish habitat and recreation. In dry regions corn typically requires more water than soybeans or cotton. Native grasses and switchgrass are possible alternative choices for ethanol production that do not require massive irrigation or intense chemical additives, or new crops could be bioengineered that are more water efficient.

It’s good to see the NRC evaluating the relative wisdom of any dramatic change in agriculture to accommodate biofuels production, as factory farming practices already pose a significant threat to public health by pollution of land and water, and agriculture accounts for a hefty chunk of our fossil fuels use all by itself. But ethanol may not be the best choice anyway, if future cars used a different kind of engine. It turns out that just such engines are under development.

Focusing on biodiesel instead of ethanol may be a better policy. Trucks, trains, agricultural machinery and ships already run on petro-diesel, and could switch to 20-80 biodiesel blends immediately without altering the existing engines. New engines can be run on 80-20 biodiesel mixtures, thereby cutting the petroleum content by an additional 60%. GM could deploy its new passenger diesel engine for at least half its new cars and light trucks as soon as nationwide biodiesel distribution allows and the factories can be re-tooled. People would surely buy them, if the popularity of hybrids is any indication.

Production of biodiesel is more energy efficient and less polluting all the way down the line than production of ethanol, though new technologies are being developed to make ethanol production more efficient (and from more easily grown crops). Bioengineered oil crops that will grow in semi-arid climates could be deployed on land not suitable for growing food crops without intensive additions and irrigation, and the machinery that plants and harvests them can run on biodiesel. Researchers are also looking at algae as a source of oil for biodiesel.

As we plan for the future and attempt to wean ourselves from our addiction to fossil fuels, it helps to remember that Rudolf Diesel, inventor of the diesel engine, designed it to run on vegetable oil in the first place, though petroleum magnates in the early years of the 20th century ensured that only petroleum-based fuel would be used. 100 years later there is hope that his dream may finally come to fruition.

In the science news this week reports run the gambit of science and technology, including biofuels, nanotechnology, genes and genomes, evolution, and bizarre animal behavior.

Nanotechnology

Single-Atom Data Storage, Single-Molecule Switching
In the quest for ever smaller, ever more useful computers and other devices, IBM reported this week that its researchers have made significant progress in understanding the magnetic properties of atoms, which opens the door to computational and data storage devices that will have practical applications even beyond current AI dreams of quantum computers.

The researchers unveiled the first single-molecule switch, which operates flawlessly and does not disrupt the molecule’s outer frame. They used IBM’s scanning tunneling microscope [STM] to manipulate single iron atoms, arranging them with precision on a prepared copper surface. Two papers on the subject have been published in the Sept. 5 issue of the journal Science.

Nanotech Biology

Blending DNA and Nanotechnology
DNA – it’s not just a template for life anymore. It was reported this week that researchers at a John Wiley & Sons, Inc., a corporate nanotech laboratory, have developed a method of using DNA molecules as pattern templates for high-aspect ratio trenches for nanochannels and nanowire deposition for nanocircuitry and other nanofabrications.

They call it “DNA shadow nanolithography” and takes us yet another step farther into the brave new nanoworld.

Genetics, DNA

Genetic Trigger for the Cambrian Explosion?
A Croatian research team reported that a novel methodology they developed for approaching evolutionary studies has allowed them to shed light on issues that have puzzled biologists since Darwin’s time.

Their approach doesn’t rely on fossilized remains, which display significant gaps in the evolutionary record. Instead, they suggest that the current genome of every species carries within it a “snapshot” of each evolutionary epoch that species went through in the deep past. The paper fully presenting their theory of genomic phylostratigraphy will be published in the November issue of the journal Trends in Genetics.

One might wonder about that theory, given the asserted mechanisms and predictions of the standard theory of evolution, the Neodarwinian Synthesis. Yet strangely enough, there is intriguing evidence that large, very ancient portions of genomes are perfectly conserved through eons of evolution (with zero mutations), even though these ultraconserved sequences apparently serve no purpose for the organism. Hmmm…

Mice Thrive Missing Ancient DNA Sequences
Scientists reporting in the September issue of the online open access journal PLoS Biology are trying to explain why ‘knockout’ mice missing 4 of the 481 “ultraconserved” genetic sequences that are shared exactly with humans have showed no signs of abnormalities. As team leader Nadav Ahituv explained,

The discovery that deletion of ultraconserved elements does not render mice inviable or infertile is a major challenge to our understanding of how highly conserved elements of the genome persist and what their functions are, [team leader Nadav Ahituv said]. He and his colleagues are pursuing research aimed at answering these compelling new questions.

First Diploid Human Genome Sequence Shows Surprising Difference
Human genome sequencing superstar Craig Venter of the J. Craig Venter Institute [JCVI] has once again sequenced his own genome, this time accounting for both chromosome pairs instead of just one – a full diploid genome.

With help from collaborators in Toronto and UCSD, the new diploid genome was dubbed “HuRef” and the research is to be available to the public and other researchers via the open access online journal, PLoS Biology. Venter’s HuRef genome demonstrates how greatly previous human genome sequences underestimated the genetic diversity among humans at least sevenfold.

Biofuels

‘Sweet’ Biofuels Research Goes Down on the Farm
Oklahoma State University’s sorghum biofuels researchers are working on methods for producing ethanol from easily grown, environmentally friendly sorghum right on the farm where its grown.

With the help of a sorghum field harvester invented by entreppreneur Lee McClune of Sorganol Production Co., Inc., the OSU Ag Sciences workers are hoping to develop a means to ferment the harvested sorghum juice (300-600 gallons per acre depending on efficiency) right on the farm, during harvest season when environmental temperatures make it feasible.

Will A Biofuel Economy Be Sustainable?
Farmers in the midwestern U.S. “Corn Belt” grow a lot of corn. And they are increasingly growing it for biomass and biofuels production rather than for human and animal food. Researchers in agriculture and biosystems engineering have been trying to answer some questions about how the U.S. agricultural economy will be changing as our demand for biofuels increases.

The article reports a paper published in Crop Science online, Potential for Enhanced Nutrient Cycling through Coupling of Agricultural and Bioenergy Systems.

Biology News of the Bizarre

Got Arachnophobia? Here’s Your Worst Nightmare
That picture doesn’t do it justice. This communal web covers 5 acres of the Lake Tawakoni State Park in Texas, and it hosts millions of spiders. They’re taking over an entire lakeside penninsula.

Biologists say this behavior is usually not seen outside the tropics, where a few species of ‘social’ spiders are known to build communal webs. Some are saying it could be the unusual amount of rain this part of Texas enjoyed this year, others suggest it might be a symptom of global warming, and still others think it’s just a fluke. Any way you slice it, the town of Wills Point, Texas is going to have a heck of a haunted hayride opportunity this Halloween!