New possibilities for hydrogen-producing algae

Photosynthesis produces the food that we eat and the oxygen that we breathe ― could it also help satisfy our future energy needs by producing clean-burning hydrogen? Researchers studying a hydrogen-producing, single-celled green alga,Chlamydomonas reinhardtii, have unmasked a previously unknown fermentation pathway that may open up possibilities for increasing hydrogen production.

C. reinhartii, a common inhabitant of soils, naturally produces small quantities of hydrogen when deprived of oxygen. Like yeast and other microbes, under anaerobic conditions this alga generates its energy from fermentation. During fermentation, hydrogen is released though the action of an enzyme called hydrogenase, powered by electrons generated by either the breakdown of organic compounds or the splitting of water by photosynthesis. Normally, only a small fraction of the electrons go into generating hydrogen. However, a major research goal has been to develop ways to increase this fraction, which would raise the potential yield of hydrogen.

In the new study by Dubini et al*, published in the Journal of Biological Chemistry, researchers at the Carnegie Institution's Department of Plant Biology, the National Renewable Energy Laboratory (NREL), and the Colorado School of Mines (CSM), examined metabolic processes in a mutant strain that was unable to assemble an active hydrogenase enzyme. The researchers, who include Alexandra Dubini (NREL), Florence Mus (Carnegie), Michael Seibert (NREL), Matthew Posewitz (CSM), and Arthur Grossman (Carnegie), expected the cell's metabolism to compensate by increasing metabolite flow along other known fermentation pathways, such as those producing formate and ethanol as end products. Instead, the algae activated a pathway leading to the production of succinate, which was previously not associated with fermentation metabolism in C. reinhardtii. Notably, succinate, a widely used industrial chemical normally synthesized from petroleum, is included in the Department of Energy's list of the top 12 value added chemicals from biomass.

"We actually didn't know that this particular pathway for fermentation metabolism existed in the alga until we generated the mutant," says Carnegie's Arthur Grossman. "This finding suggests that there is significant flexibility in the ways that soil-dwelling green algae can metabolize carbon under anaerobic conditions. By blocking and modifying some of these metabolic pathways, we may be able to augment the donation of electrons to hydrogenase under anaerobic conditions and produce elevated levels of hydrogen."

Grossman points out that it makes evolutionary sense that a soil organism such as Chlamydomonas would have a variety of metabolic pathways at its disposal. Oxygen levels, nutrient availability, and levels of metals and toxins can be extremely variable in soils, over both the short and long term. "In such an environment", Grossman says, "these organisms must evolve flexible metabolic circuits; the variety of conditions to which the organisms are exposed might favor one pathway for energy metabolism over another, which would help the organism compete in the soil environment over evolutionary time."

Grossman led the effort to generate a fully sequenced Chlamydomonas genome, which has allowed researchers to identify key genes encoding proteins involved in both fermentation and hydrogen production. Grossman feels that it is of immediate importance to generate new mutant strains to help us understand how we may be able to alter fermentation metabolism and the production of hydrogen. NREL's Michael Seibert, the project's Principal Investigator, observed that "the overarching goal of the work is to gain a fundamental understanding of the total suite of metabolic processes occurring in Chlamydomonas and how they interact; this discovery effort will lead to the development of novel ways to produce renewable hydrogen and other biofuels, which will benefit all of us".

"These are really exciting times in the field," says Matthew Posewitz. "The tools developed at Carnegie and by other groups in the field are presenting unprecedented opportunities for scientists to make important advances in our understanding of the basic biology of organisms such as Chlamydomonas."

As an energy source to potentially replace fossil fuels, hydrogen would greatly reduce the emission of greenhouse gases. Proponents of algal-based hydrogen production point out that, unlike ethanol produced from crops, it would not compete with food production for agricultural land.

Implants mimic infection to rally immune system against tumors

Bioengineers at Harvard University have shown that small plastic disks impregnated with tumor-specific antigens and implanted under the skin can reprogram the mammalian immune system to attack tumors.

The research -- which ridded 90 percent of mice of an aggressive form of melanoma that would usually kill the rodents within 25 days -- represents the most effective demonstration to date of a cancer vaccine.

Harvard's David J. Mooney and colleagues describe the research in the current issue of the journal Nature Materials.

"Our immune systems work by recognizing and attacking foreign invaders, allowing most cancer cells -- which originate inside the body -- to escape detection," says Mooney, Gordon McKay Professor of Bioengineering in Harvard's School of Engineering and Applied Sciences. "This technique, which redirects the immune system from inside the body, appears to be easier and more effective than other approaches to cancer vaccination."

Most previous work on cancer vaccines has focused on removing immune cells from the body and reprogramming them to attack malignant tissues. The altered cells are then reinjected back into the body. While Mooney says ample theoretical work suggests this approach should work, in experiments more than 90 percent of the reinjected cells have died before having any effect.

The implants developed by Mooney and colleagues are slender disks measuring 8.5 millimeters across. Made of an FDA-approved biodegradable polymer, they can be inserted subcutaneously, much like the implantable contraceptives that can be placed in a woman's arm.

The disks are 90 percent air, making them highly permeable to immune cells. They release cytokines, powerful attractants of immune-system messengers called dendritic cells.

These cells enter an implant's pores, where they are exposed to antigens specific to the type of tumor being targeted. The dendritic cells then report to nearby lymph nodes, where they activate the immune system's T cells to hunt down and kill tumor cells throughout the body.

"Much as an immune response to a bacterium or virus generates long-term resistance to that particular strain, we anticipate our materials will generate permanent and body-wide resistance against cancerous cells, providing durable protection against relapse," says Mooney, a core member of the recently established Wyss Institute for Biologically Inspired Engineering at Harvard.

The implants could also be loaded with bacterial or viral antigens to safeguard against an array of infectious diseases. They could even redirect the immune system to combat autoimmune diseases such as type 1 diabetes, which occurs when immune cells attack insulin-producing pancreatic cells.

"This study demonstrated a powerful new application for polymeric biomaterials that may potentially be used to treat a variety of diseases by programming or reprogramming host cells," Mooney and his co-authors write in Nature Materials. "The system may be applicable to other situations in which it is desirable to promote a destructive immune response (for example, eradicate infectious diseases) or to promote tolerance (for example, subvert autoimmune disease)."

Topical treatment wipes out herpes with RNAi

Whether condoms or abstinence, most efforts to prevent sexually transmitted diseases have a common logic: keep the pathogen out of your body altogether. While this approach is certainly reasonable enough, it doesn't help the countless people worldwide who, for a number of reasons, are not in a position to control their sexual circumstances.

Now, Harvard Medical School professor of pediatrics Judy Lieberman, who is also a senior investigator at the Immune Disease Institute, has overseen the development of a topical treatment that, in mice, disables key genes necessary for herpesvirus transmission. Using a laboratory method called RNA interference, or RNAi, the treatment cripples the virus in a molecular two-punch knockout, simultaneously disabling its ability to replicate, as well as the host cell's ability to take up the virus.

What's more, the treatment is just as effective when applied anywhere from one week prior to a few hours after exposure to the virus. In that sense, the basic biology of this prophylactic enables a real-world utility.

"People have been trying to make a topical agent that can prevent transmission, a microbicide, for many years," says Lieberman. "But one of the main obstacles for this is compliance. One of the attractive features of the compound we developed is that it creates in the tissue a state that's resistant to infection, even if applied up to a week before sexual exposure. This aspect has a real practicality to it. If we can reproduce these results in people, this could have a powerful impact on preventing transmission."

These findings will be published in the January 22 issue of Cell Host and Microbe.

The World Health Organization estimates that approximately 536 million people worldwide are infected with herpes simplex virus type 2 (HSV-2), the most common strain of this sexually transmitted disease. Women are disproportionately affected. This is especially serious, since the virus can easily be passed from mother to child during birth, and untreated infants face risks of brain damage and death. While HSV-2 alone isn't life-threatening in adults, infection does increase a person's vulnerability to other viruses such as HIV.

In order for the herpesvirus to infect the host, two conditions must be met. First, the virus must be able to enter and take over host cells. Second, the virus must then reproduce itself. Lieberman's topical treatment uses RNAi to foil both these events.

RNAi, a biological process that was identified barely a decade ago, has transformed the field of biological research. A breakthrough that earned the Nobel Prize in 2006, RNAi is a natural cellular process that occurs in all cells of all multicellular organisms to regulate the translation of genetic information into proteins. This natural process can be manipulated by researchers to switch off specific genes, and there is much research and development work to harness RNAi for therapeutics.

Many in the field think RNAi-based drugs may be the next important new class of drugs.

By introducing tiny RNA molecules into cells, researchers can target a gene of interest and, in effect, throw a wrench into that gene's ability to build protein molecules. For all intents and purposes, that gene is now disabled.

While RNAi has profoundly accelerated the ability of scientists to probe and interrogate cells in the Petri dish, therapeutic breakthroughs have proved far more problematic. Researchers have had a difficult time delivering these tiny RNA molecules and ensuring that they actually penetrate the desired cells and tissues in a living organism.

Modifying a delivery technique that Lieberman developed in 2005, she and postdoctoral fellow Yichao Wu and junior researcher Deborah Palliser (who now heads her own laboratory at Albert Einstein College of Medicine) treated mice with strands of RNA that were fused to cholesterol molecules, which made it possible for the molecules to pass through the cell membranes. When applied in the form of a topical solution, these RNA molecules could then be fully absorbed into the vaginal tissue, protecting the mice against a lethal dose of administered virus.

One RNA molecule in the topical solution targeted a herpes gene called UL29, which the virus needs to replicate. Knocking out UL29 inactivates the virus.

Another RNA molecule targeted Nectin-1, a surface protein found on cells in the vaginal tissue. Nectin-1 acts as a kind of host gatekeeper to which the virus binds to pass into the cell. Without Nectin-1, the virus simply can't infect cells.

Either RNA molecule delivered by itself would be sufficient to block the virus, but together in this RNAi cocktail, the host tissue becomes like a fortress that pulls up the drawbridge to block the enemy's entrance, and also has a full-fledged battle plan to slaughter the enemy if they make it through.

"As far as we could tell, the treatment caused no adverse effects, such as inflammation or any kind of autoimmune response," says Lieberman. "And while knocking out a host gene can certainly be risky, we didn't see any indication that temporarily disabling Nectin-1 interfered with normal cellular function."

New sperm shaker to improve IVF success

Scientists have developed a ground-breaking method for testing the quality of a sperm before it is used in IVF and increase the chances of conception.

Researchers at the University of Edinburgh, funded by the EPSRC (Engineering and Physical Sciences Research Council), have created a way of chemically 'fingerprinting' individual sperm to give an indication of quality. Scientists can then consider whether the sperm is healthy enough to be used to fertilise an egg as part of an IVF treatment.

The sperm are captured in two highly focussed beams of laser light. Trapped in what are essentially 'optical tweezers', an individual sperm's DNA properties are identified by the pattern of the vibrations they emit in a process known as Raman spectroscopy. This is the first time this process has been used to evaluate DNA damage in sperm.

Dr Alistair Elfick, lead scientist on the project, said: "In natural conception the fittest and healthiest sperm are positively selected by the arduous journey they make to the egg. What our technology does is to replace natural selection with a DNA based 'quality score'. But this is not about designer babies. We can only tell if the sperm is strong and healthy not if it will produce a baby with blue eyes."

In the past quality tests of sperm have mostly been carried out on the basis of shape and activity. While these do give some indication of health of the sperm they do not give its DNA status.

There are established tests for sperm DNA quality but they work by cutting the cells in half and tagging them with fluorescent dye – a process that kills the sperm and renders it useless. This new process does not destroy the sperm, so if it is found to have good DNA quality, it can still be used in IVF treatment.

Conception rates in both IVF treatment and intercourse are at around one in four. By selecting the best quality sperm it is hoped this new process could both increase a couple's chances of conception and give the child the best potential start in life.

The research is currently in a pre-clinical phase, and if successful could be available to patients in the next five to ten years.

Cell-building discovery could reduce need for some animal research

Brown University biomedical engineers can now grow and assemble living microtissues into complex three-dimensional structures in a way that will advance the field of tissue engineering and may eventually reduce the need for certain kinds of animal research.

The team, led by Brown professor Jeffrey Morgan, successfully used clusters of cells grown in a 3-D Petri dish also invented by the group, in order to build microtissues of more complex shapes.

Such a finding, detailed in the March 1 issue of Biotechnology and Bioengineering and posted at the end of January on the journal's Web site, has enormous implications for basic cell biology, drug discovery and tissue research, Morgan said.

Because the tissues Morgan's team created in the lab are more like natural tissue, they can be constructed to have complex lace-like patterns similar to a vasculature, the arrangement of blood vessels in the body or in an organ. Morgan said that added complexity could eventually reduce the need to use animals in certain kinds of research. The National Science Foundation and the International Foundation for Ethical Research funded the study, with the latter group's mission focused in part on reducing the use of animals in research.

"There is a need for … tissue models that more closely mimic natural tissue already inside the body in terms of function and architecture," said Morgan, a Brown professor of medical science and engineering. "This shows we can control the size, shape and position of cells within these 3-D structures."

But Morgan said the finding also makes an important contribution to the field of tissue engineering and regenerative medicine.

"We think this is one step toward using building blocks to build complex-shaped tissues that might one day be transplanted," he said.

The new finding builds on earlier work by Morgan and a team of Brown students, which appeared in September 2007 in the journal Tissue Engineering. The earlier study highlighted the invention of a 3-D Petri dish about the size of a peanut-butter cup and made of agarose, a complex carbohydrate derived from seaweed with the consistency of Jell-O. Morgan and students in his lab developed the dish, creating a product where cells do not stick to the surface. Instead, the cells self-assemble naturally and form "microtissues."

For the new research, Morgan, with students including Adam Rago and Dylan Dean, made 3-D microtissues in one 3-D Petri dish, harvested these living building blocks and then added them to more complex 3-D molds shaped either like a honeycomb, with holes, or a donut with a hole in the middle.

Those skin cells fused with liver cells in the more complex molds and formed even larger microstructures. Researchers found that the molds helped control the shape of the final microtissue.

They also found that they could control the rate of fusion of the cells by aging them for a longer or shorter time before they were harvested. The longer the wait, Morgan found, the slower the process.

Rago has since graduated from Brown, and Dean, an M.D.-Ph.D. student, has moved on from the Morgan lab to pursue his surgical rotations.

Technique tricks bacteria into generating their own vaccine

Scientists have developed a way to manipulate bacteria so they will grow mutant sugar molecules on their cell surfaces that could be used against them as the key component in potent vaccines.

Any resulting vaccines, if proven safe, could be developed more quickly, easily and cheaply than many currently available vaccines used to prevent bacterial illnesses.

Most vaccines against bacteria are created with polysaccharides, or long strings of sugars found on the surface of bacterial cells. The most common way to develop these vaccines is to remove sugars from the cell surface and link them to proteins to give them more power to kill bacteria.

Polysaccharides alone typically do not generate a strong enough antibody response needed to kill bacteria. But this new technique would provide an easy approach to make a small alteration to the sugar structure and produce the polysaccharide by simple fermentation.

"We are showing for the first time that you don't have to use complicated chemical reactions to make the alteration to the polysaccharide," said Peng George Wang, Ohio Eminent Scholar and professor of biochemistry and chemistry at Ohio State University and senior author of the study. "All we need to do is ferment the bacteria, and then the polysaccharides that grow on the surface of the cell already incorporate the modification."

The research is scheduled to appear in the online early edition of the Proceedings of the National Academy of Sciences.

In vaccines, polysaccharides linked with carrier proteins are injected into the body. That sets off a process that causes the release of antibodies that recognize the sugars as an unwanted foreign body. The antibodies then remain dormant but ready to attack if they ever see the same polysaccharides again – which would be a signal that bacteria have infected the body.

Polysaccharides are chains of sugars, or monosaccharides, and they are targeted for vaccine development because they are the portion of bacterial cells that interact with the rest of the body.

Escherichia coli was used as a model for the study. Wang and colleagues used one of the existing monosaccharides present on the E. coli cell surface polysaccharides, called fucose, to generate this new modification. They manipulated the structure of the fucose to create 10 different analogs, or forms of the sugar in which just one small component is changed.

The scientists then manually introduced these altered forms of fucose to a solution in which bacterial cells were growing, and the bacterial cells absorbed the altered fucose as they would normal forms of the sugar. The presence of these altered forms of fucose then altered the properties of the polysaccharides that grew on the surface of the cells.

"This way, we don't have to do anything to modify the polysaccharides. We let bacteria do it for us," Wang said.

"Bacteria grow lots of polysaccharides – it's similar to the way humans grow hair. But for a vaccine, you need to make the molecules more active, or energetic," he said. "In our method, we feed the bacteria these chemicals while they are growing, and those chemicals end up in the polysaccharides and that makes them more immunogenic. That's the technology."

Wang said the approach is likely to be applicable to many different kinds of bacteria. But each type of pathogen must be tested individually with the alteration of sugars unique to its surface.

"If you want to prevent one type of bacteria, you have to find something very unique for this bacteria because different microbes have different characteristics," he said. "You have to find the oddest thing on the cell surface. It has to be on surface because what the body sees first is the surface."

His lab will next be testing the method's effectiveness on the pneumococcus bacteria under an exploratory $100,000 grant from the Bill & Melinda Gates Foundation. The current vaccine to prevent pneumonia in babies and the elderly combines 23 strains of bacteria, making it complex and expensive to produce. Each injection costs about $50 in the United States. A less expensive way to develop the vaccine would increase its availability in the developing world, Wang said.

Protein structure determined in living cells

The function of a protein is determined both by its structure and by its interaction partners in the cell. Until now, proteins had to be isolated for analyzing them. An international team of researchers from Tokyo Metropolitan University, Goethe University, and the Frankfurt Institute for Advanced Studies (FIAS) has, for the first time, determined the structure of a protein in its natural environment, the living cell. Using nuclear magnetic resonance (NMR) spectroscopy, the researchers solved the structure of a protein within the bacterium Escherichia coli. "We have reached an important goal of molecular biology", says Prof. Peter Güntert from the Goethe University's Biomolecular Magnetic Resonance Center. (BMRZ) of The research results will be published by the scientific journal Nature on March 5, 2009.

Conventionally, proteins are extracted from the cell, purified, and analyzed in single crystals or in solution. NMR spectroscopy detects signals from the nuclei of hydrogen atoms that are ubiquitous in organic molecules. Measurements in the living cell are challenging because it is difficult to distinguish between the protein of interest and the many other proteins in the cytoplasm. The Japanese researchers around Prof. Yutaka Ito solved this problem by introducing the gene of a putative heavy-metal-binding protein into the model system Escherichia coli, where the protein was in high concentration.

The success of the measurements relies on the method of "in-cell" NMR spectroscopy that was developed a few years ago by Prof. Volker Dötsch from BMRZ at Goethe University. Dötsch was able to attribute signals from living cells to specific proteins that he had labeled with the stable nitrogen isotope N-15. However, it was not possible to calculate a three-dimensional structure. "About two days of measurement time are required to measure a multidimensional NMR spectrum", says Peter Güntert. "Unfortunately, the cells survive for only a 5-6 hours without supply of oxygen and nutrients. Güntert and his colleagues compensated for the concomitant drastic reduction of the measurement time by computational reconstruction of the complete spectrum. Then, they calculated a detailed three-dimensional structure of the protein within E. coli cells using software that was developed in their research group.

The structure determination of proteins by in-cell NMR spectroscopy opens new avenues to investigate at atomic resolution how proteins participate in biological processes in living systems. In-cell NMR spectroscopy advances our understanding of the molecular basis of life, and can contribute to the development of new, better targeted pharmaceuticals.

DNA-based assembly line for precision nano-cluster construction

Building on the idea of using DNA to link up nanoparticles - particles measuring mere billionths of a meter - scientists at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory have designed a molecular assembly line for predictable, high-precision nano-construction. Such reliable, reproducible nanofabrication is essential for exploiting the unique properties of nanoparticles in applications such as biological sensors and devices for converting sunlight to electricity. The work will be published online March 29, 2009, by Nature Materials.

The Brookhaven team has previously used DNA, the molecule that carries life's genetic code, to link up nanoparticles in various arrangements, including 3-D nano-crystals. The idea is that nanoparticles coated with complementary strands of DNA - segments of genetic code sequence that bind only with one another like highly specific Velcro - help the nanoparticles find and stick to one another in highly specific ways. By varying the use of complementary DNA and strands that don't match, scientists can exert precision control over the attractive and repulsive forces between the nanoparticles to achieve the desired construction. Note that the short DNA linker strands used in these studies were constructed artificially in the laboratory and don't "code" for any proteins, as genes do.

The latest advance has been to use the DNA linkers to attach some of the DNA-coated nanoparticles to a solid surface to further constrain and control how the nanoparticles can link up. This yields even greater precision, and therefore a more predictable, reproducible high-throughput construction technique for building clusters from nanoparticles.

"When a particle is attached to a support surface, it cannot react with other molecules or particles in the same way as a free-floating particle," explained Brookhaven physicist Oleg Gang, who led the research at the Lab's Center for Functional Nanomaterials. This is because the support surface blocks about half of the particle's reactive surface. Attaching a DNA linker or other particle that specifically interacts with the bound particle then allows for the rational assembly of desired particle clusters.

"By controlling the number of DNA linkers and their length, we can regulate interparticle distances and a cluster's architecture," said Gang. "Together with the high specificity of DNA interactions, this surface-anchored technique permits precise assembly of nano-objects into more complex structures."

Instead of assembling millions and millions of nanoparticles into 3-D nanocrystals, as was done in the previous work, this technique allows the assembly of much smaller structures from individual particles. In the Nature Materials paper, the scientists describe the details for producing symmetrical, two-particle linkages, known as dimers, as well as small, asymmetrical clusters of particles - both with high yields and low levels of other, unwanted assemblies.

"When we arrange a few nanoparticles in a particular structure, new properties can emerge," Gang emphasized. "Nanoparticles in this case are analogous to atoms, which, when connected in a molecule, often exhibit properties not found in the individual atoms. Our approach allows for rational and efficient assembly of nano-'molecules.' The properties of these new materials may be advantageous for many potential applications."

For example, in the paper, the scientists describe an optical effect that occurs when nanoparticles are linked as dimer clusters. When an electromagnetic field interacts with the metallic particles, it induces a collective oscillation of the material's conductive electrons. This phenomenon, known as a plasmon resonance, leads to strong absorption of light at a specific wavelength.

"The size and distance between the linked particles affect the plasmonic behavior," said Gang. By adjusting these parameters, scientists might engineer clusters for absorbing a range of wavelengths in solar-energy conversion devices. Modulations in the plasmonic response could also be useful as a new means for transferring data, or as a signal for a new class of highly specific biosensors.

Asymmetric clusters, which were also assembled by the Brookhaven team, allow an even higher level of control, and therefore open new ways to design and engineer functional nanomaterials.

MIT virus battery could power cars, electronic devices

For the first time, MIT researchers have shown they can genetically engineer viruses to build both the positively and negatively charged ends of a lithium-ion battery.

The new virus-produced batteries have the same energy capacity and power performance as state-of-the-art rechargeable batteries being considered to power plug-in hybrid cars, and they could also be used to power a range of personal electronic devices, said Angela Belcher, the MIT materials scientist who led the research team.

The new batteries, described in the April 2 online edition ofScience, could be manufactured with a cheap and environmentally benign process: The synthesis takes place at and below room temperature and requires no harmful organic solvents, and the materials that go into the battery are non-toxic.

In a traditional lithium-ion battery, lithium ions flow between a negatively charged anode, usually graphite, and the positively charged cathode, usually cobalt oxide or lithium iron phosphate. Three years ago, an MIT team led by Belcher reported that it had engineered viruses that could build an anode by coating themselves with cobalt oxide and gold and self-assembling to form a nanowire.

In the latest work, the team focused on building a highly powerful cathode to pair up with the anode, said Belcher, the Germeshausen Professor of Materials Science and Engineering and Biological Engineering. Cathodes are more difficult to build than anodes because they must be highly conducting to be a fast electrode, however, most candidate materials for cathodes are highly insulating (non-conductive).

To achieve that, the researchers, including MIT Professor Gerbrand Ceder of materials science and Associate Professor Michael Strano of chemical engineering, genetically engineered viruses that first coat themselves with iron phosphate, then grab hold of carbon nanotubes to create a network of highly conductive material.

Because the viruses recognize and bind specifically to certain materials (carbon nanotubes in this case), each iron phosphate nanowire can be electrically "wired" to conducting carbon nanotube networks. Electrons can travel along the carbon nanotube networks, percolating throughout the electrodes to the iron phosphate and transferring energy in a very short time.

The viruses are a common bacteriophage, which infect bacteria but are harmless to humans.

The team found that incorporating carbon nanotubes increases the cathode's conductivity without adding too much weight to the battery. In lab tests, batteries with the new cathode material could be charged and discharged at least 100 times without losing any capacitance. That is fewer charge cycles than currently available lithium-ion batteries, but "we expect them to be able to go much longer," Belcher said.

The prototype is packaged as a typical coin cell battery, but the technology allows for the assembly of very lightweight, flexible and conformable batteries that can take the shape of their container.

Last week, MIT President Susan Hockfield took the prototype battery to a press briefing at the White House where she and U.S. President Barack Obama spoke about the need for federal funding to advance new clean-energy technologies.

Now that the researchers have demonstrated they can wire virus batteries at the nanoscale, they intend to pursue even better batteries using materials with higher voltage and capacitance, such as manganese phosphate and nickel phosphate, said Belcher. Once that next generation is ready, the technology could go into commercial production, she said.

Researchers develop new way to see single RNA molecules inside living cells

Biomedical engineers have developed a new type of probe that allows them to visualize single ribonucleic acid (RNA) molecules within live cells more easily than existing methods. The tool will help scientists learn more about how RNA operates within living cells.

Techniques scientists currently use to image these transporters of genetic information within cells have several drawbacks, including the need for synthetic RNA or a large number of fluorescent molecules. The fluorescent probes developed at the Georgia Institute of Technology circumvent these issues.

"The probes we designed shine bright, are small and easy to assemble, bind rapidly to their targets, and can be imaged for hours. These characteristics make them a great choice for studying the movement and location of RNA inside a single cell and the interaction between RNA and binding proteins," said Philip Santangelo, an assistant professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University.

Details of the probe production process and RNA imaging strategy were published online in the journal Nature Methods on April 6. In addition to Santangelo, Georgia Tech graduate student Aaron Lifland, Emory University associate professor Gary Bassell and Vanderbilt University professor James Crowe Jr. also contributed to this research. This research was funded by new faculty support from Georgia Tech.

In the study, the probes – produced by attaching a few small fluorescent molecules called fluorophores to a modified nucleic acid sequence and combining the sequences with a protein – exhibited single-molecule sensitivity and allowed the researchers to target and follow native RNA and non-engineered viral RNA in living cells.

"The great thing about these probes is that they recognize RNA sequences and bind to them using the same base pairing most people are familiar with in regards to DNA," explained Santangelo. "By adding only a few probes that would bind to a region of RNA, we gained the ability to distinguish a targeted RNA molecule from a single unbound probe because the former lit up two or three times brighter."

For their experiments, the team used a bacterial toxin to transport the probes into living cells – a delivery technique that when combined with the high affinity of the probes for their targets, required significantly fewer probes than existing techniques. The toxin created several tiny holes in the cell membrane that allowed the probes to enter the cell's cytoplasm.

The researchers tested the sensitivity of conventional fluorescence microscopy to image individual probes inside a cell. Previous studies showed that these techniques were able to image an accumulation of probes inside a cell, but the current study demonstrated that individual probes without cellular targets could be observed homogenously distributed in the cytoplasm with no localization or aggregation.

With single-molecule sensitivity accomplished, the researchers investigated whether they could visualize individual RNA molecules using the probes. To do this, they simultaneously delivered probes designed to target a human messenger RNA (mRNA) sequence region and a probe designed with no target in the human genome. They were able to image unbound probes of both types as well as individual RNA molecules that had attached to the former probes.

The imaging technique also allowed the researchers to observe a process called dynamic RNA-protein co-localization, which is the joining of RNA molecules and RNA binding proteins in a single cell.

"We observed substantial transient interactions between proteins and viral RNA molecules that I don't think had ever been seen before with non-engineered RNA," noted Santangelo. "We saw one of the proteins move into a viral RNA granule and reside within it for over a minute before it was released, and we also saw another protein that appeared to dock with a viral RNA granule."

Santangelo is currently trying to improve the probes by making them smaller and brighter, while also using them to investigate viral pathogenesis and other biological phenomena.

"We are excited to use this imaging strategy to study how single viral RNAs travel from the nucleus of a cell to a virus assembly site, how mRNAs are regulated by location and time, and RNA trafficking in neurons," added Santangelo.

Scientists develop method for comprehensive proteome analysis

Investigators at Burnham Institute for Medical Research (Burnham) have deciphered a large percentage of the total protein complement (proteome) in Schizosaccharomyces pombe (S. pombe) fission yeast.

Laurence Brill, Khatereh Motamedchaboki, Ph.D. and lead investigator Dieter Wolf, Ph.D., developed the novel method, used to identify 4,600 proteins in the organism, using an array of sophisticated techniques. The research was published online on March 9 in the journal Methods.

"Analysis of the proteome of an organism tells us so much more than simple DNA sequence analysis," said Dr. Wolf. "Proteome analysis gives us a snapshot of what proteins are being expressed in the cell at any given point in time. This can tell us how protein expression changes in response to certain stimuli and in disease states, which may help identify new biomarkers for diseases. We are now applying the methodology to protein profiling of human stem cells in collaboration with Burnham's stem cell program director, Evan Snyder."

The method developed by Burnham scientists involved digestion of the proteins into smaller peptides, then separation of the peptides based on electrostatic charge using strong anionic exchange chromatography. The peptides were further separated by molecular weight using high pressure liquid chromatography. Each of the individual peptides was detected and identified using mass spectrometry and database analysis. DNA analysis of the yeast's genome predicts 5027 proteins. The team identified 4,600 proteins, which is not quite the entire proteome. The remaining 400 are only expressed during S. pombe's mating state.

S. pombe is often used as a model organism to study DNA damage response and repair, cell division, stress responses and other aspects of cellular biology.

Mining and Waste Management

The impact of the new technology will not, however, be confined to bio-based industries. Genetically engineered microbes may become more widely used to extract oil from the ground and valuable metals from factory wastes. In short, the lives of every one of us will be influenced by biotechnology.

Medicine

In the medical field, considerable efforts will be devoted to the development of vaccines for killer diseases such as AIDS. Monoclonal antibodiess will be used to boost the body's defenses and guide anti-cancer drugs to their target sites. This technology may also help to rid the human and animal world of a range of parasitic diseases by producing specific antibodies to particular parasites. Synthesis of drugs, hormones, and animal health products, together with drug-delivery mechanisms, are all advancing rapidly. Enzyme replacement and gene replacement therapy are other areas where progress is anticipated. The next decade will see significant advances in medicine, agriculture, and animal health directly attributable to biotechnology.

Agricultural and Chemical Industries

The bio-revolution resulting from advances in molecular biosciences and biotechnology has already outstripped the advances of the "Green Revolution." In the early 1960s, the pioneering studies of Nobel prize winner Norman Borlaug, using cross-breeding techniques based on classical genetics, offered for the first time a weapon against hunger in the countries of Latin America, Asia, and Africa. As a direct result of the comprehensive studies of Borlaug and his contemporaries, new wheat hybrids began to transform the harvests of India and China, although they had a relatively minor influence on agriculture in more temperate climates. There is little doubt that genetic manipulation will open more new doors in this field, and will dramatically alter farming worldwide.
It does not require a crystal ball to imagine the potential of the immediate biotechnological future. From the advances in recent years, it is possible to extrapolate to a number of likely developments based on research now in progress. In the plant world, the 1978 development of the "pomato," a laboratory-generated combination of two members of the Solanaceae family (the potato and the tomato), was a significant advance. The Flavr Savrr tomato was reviewed by the FDA in the spring of 1994 and found to be as safe as conventionally produced tomatoes. This is the first time the FDA has evaluated a whole food produced by biotechnology.
Exciting prospects are likely to result from industrial-scale plant tissue culture. This may soon obviate the need for rearing whole plants in order to generate valuable commodities such as dyes, flavorings, drugs, and chemicals. Cloning techniques could prove to be the way to tackle some of the acute problems of reforesting in semi-desert areas. Seedlings grown from the cells of mature trees could greatly speed up the process. In the summer of 1987, a Belgian team introduced into crop plants a group of genes encoding for insect resistance and resistance to widely used herbicides. This combination of advantageous genes could bring about a new era in plant protection. The crop can be treated safely with more effective doses of weed killer, and it is also engineered to be less susceptible to insect damage.
Dairy farming is also benefiting from advances in biotechnology. Bovine somatotropin (growth hormone) will enhance milk yields, with no increase in feed costs. Embryo duplication methods mean that cows will bear more calves than in the past, and embryo transfer techniques are enabling cattle of indifferent quality to rear good quality stock, a potentially important development for nations with less advanced agriculture. Genetic manipulation of other stock, such as sheep and pigs, appears to be feasible, and work is in progress on new growth factors for poultry.
The outcome of this intense activity will be improvements in the texture, quality, variety, and availability of traditional farm products, as well as the emergence of newly engineered food sources. Such bioengineered super-foods will be welcomed, and will offer new varieties, and hence find new markets in the quality-conscious advanced countries. Despite the enormous potential gains, the economic consequences of possible overproduction in certain areas must also be faced. It will be essential for those concerned with making agricultural policies to keep abreast of the pace of modern biotechnology. Short-term benefits to the consumer of lower agricultural prices must be weighed against a long-term assessment of the impact of new discoveries on the farming industry.