Scientists Identify Antivirus System in Host Cells

Scientists Identify Antivirus System in Host Cells

  10:13:00 AM    Science Lover

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Viruses have led scientists at Washington University School of Medicine in St. Louis to the discovery of a security system in host cells. Viruses that cause disease in animals beat the security system millennia ago. But now that researchers are aware of it, they can explore the possibility of bringing the system back into play in the fight against diseases such as sudden acute respiratory syndrome (SARS), West Nile virus, dengue and yellow fever.

West Nile virus (brown) infects neurons, whose nuclei 
are the round purple-blue spots. Scientists have 
discovered a new anti-virus system in host cells by 
studying how viruses like West Nile defeated the system. 
It may one day be possible to use pharmaceuticals
to bring this security system back online in the fight 
against diseases such as West Nile, sudden acute 
respiratory syndrome (SARS), dengue and yellow 
fever. (Credit: Michael Diamond, MD, PhD)

The findings, published in Nature, solve a 35-year-old mystery that began when National Institutes of Health researcher Bernard Moss, MD, PhD, noticed that poxviruses put chemical "caps" on particular spots in every piece of genetic material transcribed from their DNA. That transcribed material is RNA; to reproduce, viruses need to trick the host cell into making viral proteins from this RNA.

Noting evidence that the host cell puts caps on its own RNA in identical positions, Moss theorized that the caps might be a way for cells to distinguish between their RNA and that of an invader. He guessed the caps might serve as a sort of fake identification badge for the virus' RNA, allowing it to bypass host cell security systems primed to attack any RNA lacking the caps.

Since Moss's study, scientists have learned that some viruses have strategies for stealing RNA caps from host cells and putting them on their own RNA. Several disease-causing viruses have to make their own caps, including:

* poxviruses, which cause smallpox

* flaviviruses, which cause West Nile encephalitis, yellow fever and dengue;

* rhabdoviruses, which cause rabies;

* coronaviruses, which cause SARS;

* reoviruses, which cause mild respiratory distress or diarrhea.

Scientists also learned that one of the chemical caps added to RNA helps stabilize it, preventing the RNA from breaking down. However, despite years of research, the purpose of another cap, added near the beginning of every RNA strand in a position scientists refer to as 2' (two prime), was a persistent mystery.

The new paper from the laboratory of senior author Michael S. Diamond, MD, PhD, solves that puzzle and confirms Moss' speculation. The study used a mutant form of the West Nile virus created by Pei-Yong Shi, PhD, now a researcher at the Novartis Institute for Tropical Diseases. The mutant strain can attach the cap that keeps RNA stable but is unable to add the 2' cap. When Diamond, professor of medicine, pathology and immunology, and molecular microbiology at Washington University School of Medicine, infected mice with this mutant virus, it could not cause disease.

Next, scientists injected the mutant virus into mice lacking the receptors for interferons. These proteins are important players in defensive reactions to invading viruses within the cell, a branch of the immune system known as intrinsic immunity. The mutant virus made these mice sick, suggesting that intrinsic immunity stops the mutant viruses in normal mice, and that the 2' cap was helping normal viruses evade this part of the immune system.

Researchers recently identified a gene, IFIT2, that is activated by interferons, has mild antiviral effects against West Nile virus and seems to have potential connections to translation of RNA into proteins. When Diamond turned IFIT2 levels up in cell culture and exposed it to the mutant West Nile virus, the mutant virus could barely replicate. Tests of a mutant poxvirus and a mutant coronavirus that could not attach the 2' cap produced similar results. Knocking out a related gene in mice, IFIT1, allowed the mutant virus to evade intrinsic immunity and cause infection when it was injected into the brain.

"Now that we know what this cap is used for, we can look at the question of whether the human and viral enzymes that put the cap on are sufficiently different," says Diamond. "If they are, we may be able to design inhibitors that prevent viruses from capping their RNA and make it much harder for them to replicate once the intrinsic immune system is activated."

Special Note: This article is not intended to provide medical advice, diagnosis or treatment.

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Microscope 'Sees' Atoms for First Time

Microscope 'Sees' Atoms for First Time

  9:16:00 PM    Science Lover

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UCLA researchers report in the April 30 edition of the journal Cell that they have imaged a virus structure at a resolution high enough to effectively "see" atoms, the first published instance of imaging biological complexes at such a resolution.

Cover of the journal Cell showing an artistic 
representation of a Cryo-EM 3-D reconstruction 
of an aquareovirus, the colors are added to show 
contrast between various structures in the virus. 
(Credit: Image courtesy of UCLA)

The research team, led by Hong Zhou, UCLA professor of microbiology, immunology and molecular genetics, used cryo-electron microscopy to image the structure at 3.3 angstroms. An angstrom is the smallest recognized division of a chemical element and is about the distance between the two hydrogen atoms in a water molecule.

The study, the researchers say, demonstrates the great potential of cryo-electron microscopy, or Cryo-EM, for producing extremely high-resolution images of biological samples in their native environment.

"This is the first study to determine an atomic resolution structure through Cryo-EM alone," said Xing Zhang, a postdoctoral candidate in Zhou's group and lead author of the Cell paper. "By proving the effectiveness of this microscopy technique, we have opened the door to a wide variety of biological studies."

With traditional light microscopy, a magnified image of a sample is viewed through a lens. Some samples, however, are too small to diffract visible light (in the 500 to 800 nm range, or 5,000 to 8,000 angstroms) and therefore cannot be seen. To image objects at the sub-500 nm scale, scientists must turn to other tools, such as atomic force microscopes, which use an atomically thin tip to generate an image by probing a surface, in much the same way a blind person reads by touching Braille lettering.

With electron microscopy, another sub-500 nm technology, a beam of electrons is fired at a sample, passing through empty areas and bouncing off dense areas. A digital camera reads the path of the electrons passing through the sample to create a two-dimensional projection image of the sample. By repeating this process at hundreds of different angles, a computer can construct a three-dimensional image of the sample at a very high resolution.

Zhou is faculty director of the Electron Imaging Center for Nanomachines (EICN) at UCLA's California NanoSystems Institute, which is using cryo-electron microscopy to create 3-D reconstructions of nano-machineries, nano-devices and biological nano-structures, such as viruses.

Structurally accurate 3-D reconstructions of biological complexes are possible with cryo-electron microscopy because the samples are flash frozen, which allows them to be imaged in their native environment, and the microscope operates in a vacuum, because electrons travel better in that environment. The Cell paper focused on a structural study of the aquareovirus, a non-envelope virus that causes disease in fish and shellfish, in an effort to better understand how non-envelope viruses infect host cells.

"We are extremely excited about the recent breakthrough achieved by Hong Zhou and his team at the EICN lab," said Leonard H. Rome, senior associate dean for research at the David Geffen School of Medicine at UCLA and associate director of the California NanoSystems Institute. "The ability to understand the structure of viruses at an atomic level will open avenues for manipulating them for use in drug delivery and propel numerous innovations in treatments of diseases. UCLA is fortunate to have such specialized instrumentation and the expertise of Professor Zhou and his team to take advantage of these marvelous microscopes."

Viruses can be classed into two types: envelope and non-envelope. Envelope viruses, which include influenza and HIV, are surrounded by an envelope-like membrane which the virus uses to fuse with and infect a host cell. Non-envelope viruses lack this membrane and instead use a protein to fuse with and infect cells. This process was poorly understood until Zhou's study.

"Through better knowledge of virus structures, we hope to engineer medications in three ways," Zhou said. "If we understand how viruses work, first we can identify small molecules or drugs that block their infection; second, we can engineer ultra-stable and non-infectious virus-like particles as optimal vaccines; and third, we can alter their characteristics so that instead of delivering a disease, viruses could deliver medications.

"Indeed, we are working with UCLA physicians and engineers to engineer viruses for gene therapy and drug delivery," he said. "In essence, we hope to take advantage of millions of years of evolution that have made viruses incredibly effective delivery platforms."

From the high-resolution 3-D images produced with the cryo-electron microscopy, Zhou's group was able to determine that the aquareovirus employs a priming stage to accomplish cell infection. In its dormant state, the virus has a protective protein covering, which it sheds during priming. Once the outer shell has been shed, the virus is in a primed state and is ready to use a protein called an "insertion finger" to infect a cell.

The team's study ushers in a new era of structural biology for understanding important biological processes. The group was able to discover this functionality because of the accurate structural model produced through cryo-electron microscopy. In addition to producing a high-resolution 3-D image of samples, the technology allows samples to be imaged in their native environment, so the structural model is faithful to the original sample. From a technical point of view, this work also demonstrates the power of cryo-electron microscopy in obtaining 3-D structures of biological complexes without needing to grow a crystal.

The California NanoSystems Institute at UCLA is an integrated research center operating jointly at UCLA and UC Santa Barbara whose mission is to foster interdisciplinary collaborations for discoveries in nanosystems and nanotechnology; train the next generation of scientists, educators and technology leaders; and facilitate partnerships with industry, fueling economic development and the social well-being of California, the United States and the world. The CNSI was established in 2000 with $100 million from the state of California and an additional $250 million in federal research grants and industry funding. At the institute, scientists in the areas of biology, chemistry, biochemistry, physics, mathematics, computational science and engineering are measuring, modifying and manipulating the building blocks of our world -- atoms and molecules. These scientists benefit from an integrated laboratory culture enabling them to conduct dynamic research at the nanoscale, leading to significant breakthroughs in the areas of health, energy, the environment and information technology.

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Solar Power Goes Viral: Researchers Use Virus to Improve Solar-Cell Efficiency

Solar Power Goes Viral: Researchers Use Virus to Improve Solar-Cell Efficiency

  10:02:00 AM    Science Lover

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Researchers at MIT have found a way to make significant improvements to the power-conversion efficiency of solar cells by enlisting the services of tiny viruses to perform detailed assembly work at the microscopic level.

In this diagram, the M13 virus consists of a strand 
of DNA (the figure-8 coil on the right) attached to a 
bundle of proteins called peptides -- the virus coat 
proteins (the corkscrew shapes in the center) which 
attach to the carbon nanotubes (gray cylinders) 
and hold them in place. A coating of titanium 
dioxide (yellow spheres) attached to dye molecules 
(pink spheres) surrounds the bundle. More of the 
viruses with their coatings are scattered across the 
background. (Credit: Matt Klug, Biomolecular 
Materials Group)

In a solar cell, sunlight hits a light-harvesting material, causing it to release electrons that can be harnessed to produce an electric current. The new MIT research, published online in the journal Nature Nanotechnology, is based on findings that carbon nanotubes -- microscopic, hollow cylinders of pure carbon -- can enhance the efficiency of electron collection from a solar cell's surface.

Previous attempts to use the nanotubes, however, had been thwarted by two problems. First, the making of carbon nanotubes generally produces a mix of two types, some of which act as semiconductors (sometimes allowing an electric current to flow, sometimes not) or metals (which act like wires, allowing current to flow easily). The new research, for the first time, showed that the effects of these two types tend to be different, because the semiconducting nanotubes can enhance the performance of solar cells, but the metallic ones have the opposite effect. Second, nanotubes tend to clump together, which reduces their effectiveness.

And that's where viruses come to the rescue. Graduate students Xiangnan Dang and Hyunjung Yi -- working with Angela Belcher, the W. M. Keck Professor of Energy, and several other researchers -- found that a genetically engineered version of a virus called M13, which normally infects bacteria, can be used to control the arrangement of the nanotubes on a surface, keeping the tubes separate so they can't short out the circuits, and keeping the tubes apart so they don't clump.

The system the researchers tested used a type of solar cell known as dye-sensitized solar cells, a lightweight and inexpensive type where the active layer is composed of titanium dioxide, rather than the silicon used in conventional solar cells. But the same technique could be applied to other types as well, including quantum-dot and organic solar cells, the researchers say. In their tests, adding the virus-built structures enhanced the power conversion efficiency to 10.6 percent from 8 percent -- almost a one-third improvement.

This dramatic improvement takes place even though the viruses and the nanotubes make up only 0.1 percent by weight of the finished cell. "A little biology goes a long way," Belcher says. With further work, the researchers think they can ramp up the efficiency even further.

The viruses are used to help improve one particular step in the process of converting sunlight to electricity. In a solar cell, the first step is for the energy of the light to knock electrons loose from the solar-cell material (usually silicon); then, those electrons need to be funneled toward a collector, from which they can form a current that flows to charge a battery or power a device. After that, they return to the original material, where the cycle can start again. The new system is intended to enhance the efficiency of the second step, helping the electrons find their way: Adding the carbon nanotubes to the cell "provides a more direct path to the current collector," Belcher says.

The viruses actually perform two different functions in this process. First, they possess short proteins called peptides that can bind tightly to the carbon nanotubes, holding them in place and keeping them separated from each other. Each virus can hold five to 10 nanotubes, each of which is held firmly in place by about 300 of the virus's peptide molecules. In addition, the virus was engineered to produce a coating of titanium dioxide (TiO2), a key ingredient for dye-sensitized solar cells, over each of the nanotubes, putting the titanium dioxide in close proximity to the wire-like nanotubes that carry the electrons.

The two functions are carried out in succession by the same virus, whose activity is "switched" from one function to the next by changing the acidity of its environment. This switching feature is an important new capability that has been demonstrated for the first time in this research, Belcher says.

In addition, the viruses make the nanotubes soluble in water, which makes it possible to incorporate the nanotubes into the solar cell using a water-based process that works at room temperature.

Prashant Kamat, a professor of chemistry and biochemistry at Notre Dame University who has done extensive work on dye-sensitized solar cells, says that while others have attempted to use carbon nanotubes to improve solar cell efficiency, "the improvements observed in earlier studies were marginal," while the improvements by the MIT team using the virus assembly method are "impressive."

"It is likely that the virus template assembly has enabled the researchers to establish a better contact between the TiO2 nanoparticles and carbon nanotubes. Such close contact with TiO2 nanoparticles is essential to drive away the photo-generated electrons quickly and transport it efficiently to the collecting electrode surface."

Kamat thinks the process could well lead to a viable commercial product: "Dye-sensitized solar cells have already been commercialized in Japan, Korea and Taiwan," he says. If the addition of carbon nanotubes via the virus process can improve their efficiency, "the industry is likely to adopt such processes."

Belcher and her colleagues have previously used differently engineered versions of the same virus to enhance the performance of batteries and other devices, but the method used to enhance solar cell performance is quite different, she says.

Because the process would just add one simple step to a standard solar-cell manufacturing process, it should be quite easy to adapt existing production facilities and thus should be possible to implement relatively rapidly, Belcher says.

The research team also included Paula Hammond, the Bayer Professor of Chemical Engineering; Michael Strano, the Charles (1951) and Hilda Roddey Career Development Associate Professor of Chemical Engineering; and four other graduate students and postdoctoral researchers. The work was funded by the Italian company Eni, through the MIT Energy Initiative's Solar Futures Program.

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Swine Flu Outbreak Illuminated By Avian Flu Research

Swine Flu Outbreak Illuminated By Avian Flu Research

  9:15:00 PM    Science Lover

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A new study by University of Maryland researchers suggests that the potential for an avian influenza virus to cause a human flu pandemic is greater than previously thought. Results also illustrate how the current swine flu outbreak likely came about.

This graphic shows why the Type A virus can't be eradicated.
(Credit: Image courtesy of University of Maryland)

As of now, avian flu viruses can infect humans who have contact with birds, but these viruses tend not to transmit easily between humans. However, in research recently published in the Proceedings of the National Academy of Sciences, Associate Professor Daniel Perez from the University of Maryland showed that after reassortment with a human influenza virus, a process that usually takes place in intermediary species like pigs, an avian flu virus requires relatively few mutations to spread rapidly between mammals by respiratory droplets.

"This is similar to the method by which the current swine influenza strain likely formed," said Perez, program director of the University of Maryland-based Prevention and Control of Avian Influenza Coordinated Agricultural Project, AICAP. "The virus formed when avian, swine, and human-like viruses combined in a pig to make a new virus. After mutating to be able to spread by respiratory droplets and infect humans, it is now spreading between humans by sneezing and coughing."

Image via Wikipedia

In his study, Perez used the avian H9N2 influenza virus, one that is on the list of candidates for human pandemic potential. Using reverse genetics, a technique whereby individual genes from viruses are separated, selected, and put back together, Perez and his team created a hybrid human-avian virus. Their research hybrid has internal human flu genes and surface avian flu genes from the H9N2 virus. Though it comes from a different strain of avian flu than the one that contributed to the hybrid virus now causing the swine flu outbreak, Perez's research virus is similar in origin to the swine flu virus, in that both involved a combination of avian and human influenza viruses.

Perez infected ferrets (considered a good model for human influenza transmission) with the virus he created, and allowed the virus to mutate in the species. Before long, healthy ferrets that shared air space but not physical space with the infected ferret had the virus, showing that the virus had mutated to spread by respiratory droplets.

When the genetic sequences of the mutant virus and original hybrid virus were compared, the only differences were five amino acid mutations, three on the surface, and two internally. Two of the surface mutations were determined to be solely responsible for supporting respiratory droplet transmission. Because so few mutations were necessary to make the hybrid H9N2 transmissible this way, they concluded that after an animal-human hybrid influenza virus forms in nature, a human pandemic of this virus is potentially just a few mutations away.

"We do not know if the mutations we saw in the lab are the same that have made the H1N1 swine flu transmissible by respiratory droplets," Perez said. "We will be doing more research on the current swine flu strain to study its specific genetic mutations."

Perez found that one of the two of the genetic mutations in his lab strain that enabled respiratory transmission between mammals was on the tip of the HA surface protein, one of the sites where human antibodies created in response to current vaccines would bind.

"Because the binding site of the mutant virus is different from the virus upon which the vaccine is modeled, it may mean that current vaccine stocks would not be as effective against the H9N2 mutant strain as previously anticipated," said Perez. "We should keep this in mind when designing vaccines for an avian flu pandemic in humans."

However, scientists cannot predict what the actual mutations will look like if and when they occur in nature, or even which strain of avian influenza will mutate to infect mammals.

"This is just the tip of the iceberg," said Perez. "Many more studies have to be done to see which combinations of mutations cause this type of transmission before we can design the appropriate vaccines."

Perez will be talking this week with the NIH and the CDC to discuss his team's role in researching the current swine flu virus strain. Perez will likely do studies related to vaccine development, virus transmission between humans and animals, and the pathogenesis of the virus.

A virus vaccine is derived from the virus itself. The vaccine consists of virus components or killed viruses that mimic the presence of the virus without causing disease. These prime the body's immune system to recognize and fight against the virus. The immune system produces antibodies against the vaccine that remain in the system until they are needed. If that virus, or in some cases a closely similar one is later introduced into the system, those antibodies attach to viral particles and remove them before they have time to replicate, preventing or lessening symptoms of the virus.

The immune system also retains antibodies to a virus after being infected with it, so humans have general immunity to human strains of avian influenza strains. But humans do not generally have immunity to avian flu strains because they have not been infected by them before. The surface proteins are sufficiently different to escape the human immune response. Avian flu strains are therefore more dangerous for humans because the human immune system cannot recognize the virus or protect against it.

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Virus-built Battery Could Power Cars, Electronic Devices

Virus-built Battery Could Power Cars, Electronic Devices

  9:11:00 PM    Science Lover

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Angela Belcher holds a display of the virus-built battery she helped engineer. The battery -- the silver-colored disc -- is being used to power an LED. (Credit: Photo by Donna Coveney)

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 of Science, 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.

Lead authors of the Science paper are Yun Jung Lee and Hyunjung Yi, graduate students in materials science and engineering. Other authors are Woo-Jae Kim, postdoctoral fellow in chemical engineering; Kisuk Kang, recent MIT PhD recipient in materials science and engineering; and Dong Soo Yun, research engineer in materials science and engineering.

The research was funded by the Army Research Office Institute of the Institute of Collaborative Technologies, and the National Science Foundation through the Materials Research Science and Engineering Centers program.

==================================================================

Journal reference:

1. Yun Jung Lee, Hyunjung Yi, Woo-Jae Kim, Kisuk Kang, Dong Soo Yun, Michael S. Strano, Gerbrand Ceder, and Angela M. Belcher. Fabricating Genetically Engineered High-Power Lithium Ion Batteries Using Multiple Virus Genes. Science, 2009; DOI: 10.1126/science.1171541

Adapted from materials provided by Massachusetts Institute of Technology.

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Evolutionary Surprise: Eight Percent of Human Genetic Material Comes from a Virus

Evolutionary Surprise: Eight Percent of Human Genetic Material Comes from a Virus

  10:15:00 PM    Science Lover

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About eight percent of human genetic material comes from a virus and not from our ancestors, according to researchers in Japan and the U.S.

A new study shows that the genomes of humans and other mammals contain DNA derived from the insertion of bornaviruses, RNA viruses whose replication and transcription takes place in the nucleus. (Credit: iStockphoto)

The study, and an accompanying News & Views article by University of Texas at Arlington biology professor Cédric Feschotte, is published in the journal Nature.

The research showed that the genomes of humans and other mammals contain DNA derived from the insertion of bornaviruses, RNA viruses whose replication and transcription takes place in the nucleus. Feschotte wrote on recent research led by Professor Keizo Tomonaga at Osaka University in Japan. Feschotte said this virally transmitted DNA may be a cause of mutation and psychiatric disorders such as schizophrenia and mood disorders.

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Biologists Wake Dormant Viruses and Uncover Mechanism for Survival

Biologists Wake Dormant Viruses and Uncover Mechanism for Survival

  9:44:00 PM    Science Lover

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It is known that viral "squatters" comprise nearly half of our genetic code. These genomic invaders inserted their DNA into our own millions of years ago when they infected our ancestors. But just how we keep them quiet and prevent them from attack was more of a mystery until EPFL researchers revived them.

This shows the functioning of Kap1 protein in mouse embrocation cells. (Credit: Pascal Coderay, pascal@salut.ch)

The reason we survive the presence of these endogenous retroviruses -- viruses that attack and are passed on through germ cells, the cells that give rise to eggs and sperm -- is because something keeps the killers silent. Now, publishing in the journal Nature, Didier Trono and his team from EPFL, in Switzerland, describe the mechanism. Their results provide insights into evolution and suggest potential new therapies in fighting another retrovirus -- HIV.

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Ancient Viral Invasion Shaped Human Genome

Ancient Viral Invasion Shaped Human Genome

  2:14:00 AM    Science Lover

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Scientists at the Genome Institute of Singapore (GIS), a biomedical research institute of the Agency for Science, Technology and Research (A*STAR), and their colleagues from the National University of Singapore, Nanyang Technological University, Duke-NUS Graduate Medical School and Princeton University have recently discovered that viruses that 'invaded' the human genome millions of years ago have changed the way genes get turned on and off in human embryonic stem (ES) cells.

Scientists have discovered that viruses that "invaded" 
the human genome millions of years ago have changed the 
way genes get turned on and off in human embryonic
stem cells. (Credit: iStockphoto/Martin McCarthy)

The study provides definitive proof of a theory that was first proposed in the 1950s by Nobel Laureate in physiology and medicine, Barbara McClintock, who hypothesized that transposable elements, mobile pieces of the genetic material (DNA), such as viral sequences, could be "control elements" that affect gene regulation once inserted in the genome.

This finding is an important contribution to the advancement of stem cell research and to its potential for regenerative medicine. Led by GIS Senior Group Leader Dr Guillaume Bourque, the study was published in Nature Genetics on June 6, 2010.

Through the use of new sequencing technologies, the scientists studied the genomic locations of three regulatory proteins (OCT4, NANOG and CTCF) in human and mouse embryonic stem (ES) cells. Interestingly, while the scientists found a lot of similarities, they also found many differences in the methods and the types of genes that are being regulated in humans. In particular, it was discovered that specific types of viruses that inserted themselves in the human genomes millions of years ago have dramatically changed the gene regulatory network in human stem cells.

"This study is a computational and experimental tour de force. It provides undeniable evidence that some transposable elements, which are too often dismissed as merely junk DNA, are key components of a regulatory code underlying human development," said Dr Cedric Feschotte, Associate Professor of the University of Texas Arlington.

The comparisons between the human and mouse model system in the study of gene regulatory networks help to advance the understanding of how stem cells differentiate into various cell types of the body. "This understanding is crucial in the improved development of regenerative medicine for diseases such as Parkinson's disease and leukaemia," said Dr Bourque. "Despite the advantages of using mouse ES cells in the study of gene regulatory networks, further research must focus more directly on human stem cells. This is due to the inherent challenges of converting the results of studies done from one species to that of the next. More research will need to be done in both human and non-human primate stem cells for findings on stem cells to be used in clinical application."

Prof Raymond L. White, PhD, Rudi Schmid Distinguished Professor of Neurology, University of California said, "The paper reports very exciting new findings that establish a new and fundamentally distinct mechanism for the regulation of gene expression. By comparing the genomes of mouse with human, the scientists were able to show that the binding sites for gene regulatory factors are very often not in the same place between the two species. This by itself would be very surprising, but the investigators go further and demonstrate that many of the sites are imbedded within a class of DNA sequences called "transposable" elements because of their ability to move to new places in the genome. There are a number of such elements believed to be the evolutionary remnants of viral genomes, but it was very surprising to learn that they were carrying binding sites for regulatory elements to new locations. These changes in regulation would be expected to create major changes in the organisms which carry them. Indeed, many think that regulatory changes are at the heart of speciation and may have played a large role in the evolution of humans from their predecessors. This is likely to be a landmark paper in the field."

Dr Eddy Rubin, Director of the U.S. Department of Energy Joint Genome Institute and Director of the Genomics Division at Lawrence Berkeley National Laboratory in Berkeley added, "This study using a comparative genomics strategy discovered important human specific properties of the regulatory network in human ES cells. This information is significant and should contribute to helping move the regenerative medicine field forward."

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New Visible Light Photocatalyst Kills Bacteria, Even After Light Turned Off

New Visible Light Photocatalyst Kills Bacteria, Even After Light Turned Off

  12:34:00 AM    Science Lover

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In the battle against bacteria, researchers at the University of Illinois have developed a powerful new weapon -- an enhanced photocatalytic disinfection process that uses visible light to destroy harmful bacteria and viruses, even in the dark.

Jian Ku Shang, a professor of materials science and engineering, holds a sample of a new photocatalytic material that uses visible light to destroy harmful bacteria and viruses, even in the dark.

Based upon a new catalyst, the disinfection process can be used to purify drinking water, sanitize surgical instruments and remove unwanted fingerprints from delicate electrical and optical components.

"The new catalyst also has a unique catalytic memory effect that continues to kill deadly pathogens for up to 24 hours after the light is turned off," said Jian Ku Shang, a professor of materials science and engineering at the U. of I.

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A New Way to Make Stem Cells Using RNA instead of DNA could avoid the health risks--and the political pitfalls--of stem-cell treatments.

A New Way to Make Stem Cells Using RNA instead of DNA could avoid the health risks--and the political pitfalls--of stem-cell treatments.

  1:27:00 AM    Science Lover

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A Harvard researcher has developed a way to make pluripotent stem cells that solves several of the major impediments to using them to treat human diseases.

New cell: This microscope image shows neurons
(colored green) created from pluripotent stem
cells using modified RNA.
Credit: Phil Manos, Cell Press

Derrick Rossi, an assistant professor at Harvard Medical School, created pluripotent stem cells--which can turn into virtually any other type of cell in the body--from non-stem cells without using viruses to tinker with a cell's genome, as conventional methods do. This means that Rossi's method could be substantially safer for treating disease. The work is published today in the journal Cell Stem Cell.

"Rossi has figured out how to turn a skin cell into a stem cell without genetic modifications, and to do it efficiently," said Doug Melton, codirector of the Harvard Stem Cell Institute, where Rossi is a principal faculty member, at a press conference.

Rossi's innovation, which has not yet been tested in people, was to use messenger RNA instead of DNA to produce the four proteins needed to reprogram the cell. He has started a company called ModeRNA to commercialize this use of messenger RNA. He said the approach may also have potential in gene therapy, which also relies on viruses to deliver treatment, but he declined to talk further about the company or possible gene therapy applications because the work is at such an early stage.

Improving the usability of man-made stem cells is key to helping patients and ending the political morass that has slowed stem-cell research. On Tuesday, a U.S. federal appeals court allowed federal funding of embryonic stem-cell research to continue while a legal case against such funding proceeds.

The human embryonic stem cells used in research were mostly derived from embryonic tissue grown a decade ago. These are the most versatile cells in the body, and the gold standard by which man-made cells are judged.

Four years ago, Japanese researcher Shinya Yamanaka showed that regular cells could be turned into embryonic-like stem cells--called induced pluripotent stem (iPS) cells--through the introduction of four specific proteins. Theoretically, this meant that doctors could take skin cells from a sick or disabled person, transform them into stem cells, and then into a specialized cell to treat them--an insulin-producing islet cell for someone with diabetes or a nerve cell for someone who is paralyzed, for instance. Using iPS cells avoids the need to destroy embryos and, because they can be derived from the patient's own cells, means less risk of rejection.

But only one in 1,000 or one in 10,000 skin cells could be transformed into a stem cell using Yamanaka's method. It also changes a cell's genes in ways that might trigger cancer or other problems.

Rossi 's idea was to produce Yamanaka's four proteins in a different way. Instead of using the DNA that holds the instructions for making proteins, he wanted to use RNA, which carries those instructions to the place in a cell where proteins are made.

His first several attempts were miserable failures. When he tried to change the messages the RNA carried, he triggered a serious immune response and most of the cells shut down or self-destructed. Rossi then tried modifying the RNA chemically and eventually figured out a way to allow his changes to escape immune detection while delivering the message. "This was key to our success," said Rossi, who is also a researcher at Children's Hospital Boston. "We could encode RNA for any protein we wanted to express and insert it into a cell."

Rossi said it was a happy coincidence that using RNA instead of changing the DNA was as much as 100-fold more efficient. He said the effect was possibly because the process more closely reflects how cells themselves transform.

Rossi successfully differentiated his stem cells into muscle cells using RNA, a process that may offer promise in gene therapy and other treatments. His method does not alter the cell's underlying genome, though Rossi admits that he does not yet understand what it does to the cell's epigenome, which controls expression of genes.

Rossi said that his cells, which he's named RiPS, for "RNA induced Pluripotent Stem" cells, are more like embryonic stem cells than traditional iPS cells because they have not been genetically altered.

Melton said the Harvard Stem Cell Institute, which includes several hundred stem-cell researchers from across Harvard University and its affiliated hospitals, will now be making its standard iPS cells with Rossi's method.

In a prepared statement, Yamanaka, now at the University of California, San Francisco, said Rossi's approach to generating stem cells seems promising, and he would like to have someone in his lab try it.

"The quality of the induced pluripotent stem cells generated by this method should be carefully examined because their characteristics vary depending on the induction methods and the origins of the resulting cells," he said. "The standard method to generate iPSCs for clinical applications has yet to be established. I think this method has the potential for it."

Jacob Hanna, a postdoctoral fellow at the Whitehead Institute for Biomedical Research in Cambridge, said he's also eager to begin working with the cells.

"I think it's a very exciting paper with a very promising method," said Hanna, who was not involved in the research. When asked if he was jealous that Rossi had developed the method first, Hanna said, "Yes, of course! It's a very nice paper," quickly adding, "Jealous in a very positive and supporting way."

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Scientists Create Nanoscale Window to Biological World

Scientists Create Nanoscale Window to Biological World

  9:13:00 AM    Science Lover

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If the key to winning battles is knowing both your enemy and yourself, then scientists are now well on their way toward becoming the Sun Tzus of medicine by taking a giant step toward a priceless advantage -- the ability to see the soldiers in action on the battlefield.

A novel microfluidics platform allowed viewing of structural 
details of rotavirus double-layered particles; the 3-D graphic 
of the virus, in purple, was reconstructed from data gathered by 
the new technique. (Credit: Virginia Tech)

Investigators at the Virginia Tech Carilion Research Institute have invented a way to directly image biological structures at their most fundamental level and in their natural habitats. The technique is a major advancement toward the ultimate goal of imaging biological processes in action at the atomic level.

"It's sort of like the difference between seeing Han Solo frozen in carbonite and watching him walk around blasting stormtroopers," said Deborah Kelly, an assistant professor at the VTC Research Institute and a lead author on the paper describing the first successful test of the new technique. "Seeing viruses, for example, in action in their natural environment is invaluable."

The technique involves taking two silicon-nitride microchips with windows etched in their centers and pressing them together until only a 150-nanometer space between them remains. The researchers then fill this pocket with a liquid resembling the natural environment of the biological structure to be imaged, creating a microfluidic chamber.

Then, because free-floating structures yield images with poor resolution, the researchers coat the microchip's interior surface with a layer of natural biological tethers, such as antibodies, which naturally grab onto a virus and hold it in place.

In a recent study in Lab on a Chip, Kelly joined Sarah McDonald, also an assistant professor at the VTC Research Institute, to prove that the technique works. McDonald provided a pure sample of rotavirus double-layered particles for the study.

"What's missing in the field of structural biology right now is dynamics -- how things move in time," said McDonald. "Debbie is developing technologies to bridge that gap, because that's clearly the next big breakthrough that structural biology needs."

Rotavirus is the most common cause of severe diarrhea among infants and children. By the age of 5, nearly every child in the world has been infected at least once. And although the disease tends to be easily managed in the developed world, in developing countries rotavirus kills more than 450,000 children a year.

At the second step in the pathogen's life cycle, rotavirus sheds its outer layer, which allows it to enter a cell, and becomes what is called a double-layered particle. Once its second layer is exposed, the virus is ready to begin using the cell's own infrastructure to produce more viruses. It was the viral structure at this stage that the researchers imaged in the new study.

Kelly and McDonald coated the interior window of the microchip with antibodies to the virus. The antibodies, in turn, latched onto the rotaviruses that were injected into the microfluidic chamber and held them in place. The researchers then used a transmission electron microscope to image the prepared slide.

The technique worked perfectly.

The experiment gave results that resembled those achieved using traditional freezing methods to prepare rotavirus for electron microscopy, proving that the new technique can deliver accurate results.

"It's the first time scientists have imaged anything on this scale in liquid," said Kelly.

The next step is to continue to develop the technique with an eye toward imaging biological structures dynamically in action. Specifically, McDonald is looking to understand how rotavirus assembles, so as to better know and develop tools to combat this particular enemy of children's health.

The researchers said their ongoing collaboration is an example of the cross-disciplinary work that is becoming a hallmark of the VTC Research Institute.

"It's an ideal collaboration because Sarah provides a phenomenal model system by which we can develop new technologies to move the field of microstructural biology forward," said Kelly.

"It's very win-win," McDonald added. "While the virus is a great tool for Debbie to develop her techniques, her technology is critical for allowing me to understand how this deadly virus assembles and changes dynamically over time."

The paper "Visualizing viral assemblies in a nanoscale biosphere" was published online and will appear in a 2013 edition of Lab on a Chip.

The authors are Brian Gilmore, a research associate at the VTC Research Institute; Shannon Showalter, a research assistant at the VTC Research Institute; Madeline Dukes, an applications scientist at Protochips; Justin Tanner, a postdoctoral associate at the VTC Research Institute; Andrew Demmert, a student at the Virginia Tech Carilion School of Medicine; McDonald, in addition to her position at the VTC Research Institute, is an assistant professor of biomedical sciences and pathobiology in the Virginia-Maryland Regional College of Veterinary Medicine; and Kelly, in addition to her position at the VTC Research Institute, is an assistant professor of biological sciences in Virginia Tech's College of Science.

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Editing the Genome: Scientists Unveil New Tools for Rewriting the Code of Life

Editing the Genome: Scientists Unveil New Tools for Rewriting the Code of Life

  2:50:00 AM    Science Lover

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The power to edit genes is as revolutionary, immediately useful and unlimited in its potential as was Johannes Gutenberg's printing press. And like Gutenberg's invention, most DNA editing tools are slow, expensive, and hard to use -- a brilliant technology in its infancy. Now, Harvard researchers developing genome-scale editing tools as fast and easy as word processing have rewritten the genome of living cells using the genetic equivalent of search and replace -- and combined those rewrites in novel cell strains, strikingly different from their forebears.

Researchers have unveiled genome-engineering technologies capable of fundamentally re-engineering genomes from the nucleotide to the megabase scale. Treating the chromosome as both an editable and an evolvable template, the researchers have demonstrated methods to rewrite a cell's genome through powerful new tools for biotechnology, energy and agriculture. (Credit: iStockphoto/Zmeel Photography)

"The payoff doesn't really come from making a copy of something that already exists," said George Church, a professor of genetics at Harvard Medical School who led the research effort in collaboration with Joe Jacobson, an associate professor at the Media Lab at the Massachusetts Institute of Technology. "You have to change it -- functionally and radically."

Such change, Church said, serves three goals. The first is to add functionality to a cell by encoding for useful new amino acids. The second is to introduce safeguards that prevent cross-contamination between modified organisms and the wild. A third, related aim, is to establish multi-viral resistance by rewriting code hijacked by viruses. In industries that cultivate bacteria, including pharmaceuticals and energy, such viruses affect up to 20 percent of cultures. A notable example afflicted the biotech company Genzyme, where estimates of losses due to viral contamination range from a few hundred million dollars to more than $1 billion.

In a paper scheduled for publication July 15 in Science, the researchers describe how they replaced instances of a codon -- a DNA "word" of three nucleotide letters -- in 32 strains of E. coli, and then coaxed those partially-edited strains along an evolutionary path toward a single cell line in which all 314 instances of the codon had been replaced. That many edits surpasses current methods by two orders of magnitude, said Harris Wang, a research fellow in Church's lab at the Wyss Institute for Biologically Inspired Engineering who shares lead-author credit on the paper with Farren Isaacs, an assistant professor of molecular, cellular and developmental biology at Yale University and former Harvard research fellow, and Peter Carr, a research scientist at the MIT Media Lab.



In the genetic code, most codons specify an amino acid, a protein building block. But a few codons tell the cell when to stop adding amino acids to a protein chain, and it was one of these "stop" codons that the Harvard researchers targeted. With just 314 occurrences, the TAG stop codon is the rarest word in the E. coli genome, making it a prime target for replacement. Using a platform called multiplex automated genome engineering, or MAGE, the team replaced instances of the TAG codon with another stop codon, TAA, in living E. coli cells. (Unveiled by the team in 2009, the MAGE process has been called an evolution machine for its ability to accelerate targeted genetic change in living cells.)

While MAGE, a small-scale engineering process, yielded cells in which TAA codons replaced some but not all TAG codons, the team constructed 32 strains that, taken together, included every possible TAA replacement. Then, using bacteria's innate ability to trade genes through a process called conjugation, the researchers induced the cells to transfer genes containing TAA codons at increasingly larger scales. The new method, called conjugative assembly genome engineering, or CAGE, resembles a playoff bracket -- a hierarchy that winnows 16 pairs to eight to four to two to one -- with each round's winner possessing more TAA codons and fewer TAG, explains Isaacs, who invokes "March Madness."

"We're testing decades-old theories on the conservation of the genetic code," Isaacs said. "And we're showing on a genome-wide scale that we're able to make these changes."

Eager to share their enabling technology, the team published their results as CAGE reached the semifinal round. Results suggested that the final four strains were healthy, even as the team assembled four groups of 80 engineered alterations into stretches of the chromosome surpassing 1 million DNA base pairs. "We encountered a great deal of skepticism early on that we could make so many changes and preserve the health of these cells," Carr said. "But that's what we've seen."

The researchers are confident that they will create a single strain in which TAG codons are completely eliminated. The next step, they say, is to delete the cell's machinery that reads the TAG gene -- freeing up the codon for a completely new purpose, such as encoding a novel amino acid.

"We're trying to challenge people," Wang said, "to think about the genome as something that's highly malleable, highly editable."

This research was funded by U.S. Department of Energy and the National Science Foundation.

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New Laser Technology Could Kill Viruses and Improve DVDs

New Laser Technology Could Kill Viruses and Improve DVDs

  10:16:00 AM    Science Lover

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A team led by a professor at the University of California, Riverside Bourns College of Engineering has made a discovery in semiconductor nanowire laser technology that could potentially do everything from kill viruses to increase storage capacity of DVDs.

From left, Guoping Wang, a graduate student, Jianlin Liu, a professor of electrical engineering, and Sheng Chu, a graduate student. (Credit: Image courtesy of University of California - Riverside)

Ultraviolet semiconductor diode lasers are widely used in data processing, information storage and biology. Their applications have been limited, however, by size, cost and power. The current generation of ultraviolet lasers is based on a material called gallium nitride, but Jianlin Liu, a professor of electrical engineering, and his colleagues have made a breakthrough in zinc oxide nanowire waveguide lasers, which can offer smaller sizes, lower costs, higher powers and shorter wavelengths.

Until now, zinc oxide nanowires couldn't be used in real world light emission applications because of the lack of p-type, or positive type, material needed by all semiconductors. Liu solved that problem by doping the zinc oxide nanowires with antimony, a metalloid element, to create the p-type material.

The p-type zinc oxide nanowires were connected with n-type, or negative type, zinc oxide material to form a device called p-n junction diode. Powered by a battery, highly directional laser light emits only from the ends of the nanowires.

"People in the zinc oxide research community throughout the world have been trying hard to achieve this for the past decade," Liu said. "This discovery is likely to stimulate the whole field to push the technology further."

Liu's findings have been published in the July issue of Nature Nanotechnology. Co-authors are: Sheng Chu, Guoping Wang, Jieying Kong, Lin Li and Jingjian Ren, all graduate students at UC Riverside; Weihang Zhou, a student at Fudan University in China; Leonid Chernyak, a professor of physics at the University of Central Florida; Yuqing Lin, a graduate student at the University of Central Florida; and Jianze Zhao, a visiting student from Dalian University of Technology in China.

The discovery could have a wide-range of impacts.



For information storage, the zinc oxide nanowire lasers could be used to read and process much denser data on storage media such as DVDs because the ultraviolet has shorter wavelength than other lights, such as red. For example, a DVD that would store two hours of music could store four or six hours using the new type of laser.

For biology and medical therapeutics, the ultra-small laser light beam from a nanowire laser can penetrate a living cell, or excite or change its function from a bad cell to a good cell. The light could also be used to purify drinking water.

For photonics, the ultraviolet light could provide superfast data processing and transmission. Reliable small ultraviolet semiconductor diode lasers may help develop ultraviolet wireless communication technology, which is potentially better than state-of-the-art infrared communication technologies used in various electronic information systems.

While Liu and the students in his laboratory have demonstrated the p-type doping of zinc oxide and electrically powered nanowire waveguide lasing in the ultraviolet range, he said more work still needs to be done with the stability and reliability of the p-type material.

The work on the ZnO device was in part supported by Army Research Office Young Investigator Program and the National Science Foundation. The work on p-type ZnO was supported by the Department of Energy.

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