‘Alien’ life form is grown in a lab: Scientists add unnatural DNA strands to the genetic code of bacteria to create a new strain

 

  • Researchers at the Scripps Research Institute in La Jolla, California, introduced DNA molecules not found in nature to a common bacterium
  • The E. coli bugs are able to grow and reproduce as normal despite containing two extra letters in their genetic code
  • Research involved overcoming a billion years of evolution to get the expanded genetic alphabet into living bacteria
  • In the future the research could lead to creation of microbes capable of manufacturing entirely new proteins that could be used in medicine
  • Some people are worried that the rapid advance of ‘synthetic biology’ could lead to the worrying prospect of new life-forms escaping from labs

 

From left to right, the structures of A-, B- a...

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Scripps Research Institute scientists describe elusive replication machinery of flu viruses

Contact: Jann Coury
jcoury@scripps.edu
858-784-8245
Scripps Research Institute

IMAGE:The new Scripps Research Institute study shows flu virus proteins in the act of self-replication. Shown here is the influenza virus, which encapsidates its RNA genome (green) with a viral…

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LA JOLLA, CA – November 22, 2012 – Scientists at The Scripps Research Institute (TSRI) have made a major advance in understanding how flu viruses replicate within infected cells. The researchers used cutting-edge molecular biology and electron-microscopy techniques to “see” one of influenza’s essential protein complexes in unprecedented detail. The images generated in the study show flu virus proteins in the act of self-replication, highlighting the virus’s vulnerabilities that are sure to be of interest to drug developers.

The report, which appears online in Science Express on November 22, 2012, focuses on influenza’s ribonucleoprotein (RNP). RNPs contain the virus’s genetic material plus the special enzyme that the virus needs to make copies of itself.

“Structural studies in this area had stalled because of the technical obstacles involved, and so this is a welcome advance,” said Ian A. Wilson, the Hansen Professor of Structural Biology at TSRI and senior author of the report with TSRI Professors of Cell Biology Bridget Carragher and Clint Potter. “The data from this study give us a much clearer picture of the flu virus replication machinery.”

Unveiling the Mystery of RNPs

At the core of any influenza virus lie eight RNPs, tiny molecular machines that are vital to the virus’s ability to survive and spread in its hosts. Each RNP contains a segment—usually a single protein-coding gene—of the RNA-based viral genome. This viral RNA segment is coated with protective viral nucleoproteins and has a structure that resembles a twisted loop of chain. The free ends of this twisted loop are held by a flu-virus polymerase enzyme, which handles the two central tasks of viral reproduction: making new viral genomic RNA, and making the RNA gene-transcripts that will become new viral proteins.

Aside from its importance in ordinary infections, the flu polymerase contains some of the key “species barriers” that keep, for example, avian flu viruses from infecting mammals. Mutations at key points on the enzyme have enabled the virus to infect new species in the past. Thus researchers are eager to know the precise details of how the flu polymerase and the rest of the RNP interact.

Getting those details has been a real challenge. One reason is that flu RNPs are complex assemblies that are hard to produce efficiently in the lab. Flu polymerase genes are particularly resistant to being expressed in test cells, and their protein products exist in three separate pieces, or subunits, that have to somehow self-assemble. Until now, the only flu RNPs that have been reproduced in the laboratory are shortened versions whose structures aren’t quite the same as those of native flu RNPs. Researchers also are limited in how much virus they can use for such studies.

The team nevertheless managed to develop a test-cell expression system that produced all of the protein and RNA components needed to make full-length flu RNPs. “We were able to get the cells to assemble these components properly so that we had working, self-replicating RNPs,” said Robert N. Kirchdoerfer, a first author of the study. Kirchdoerfer was a PhD candidate in the Wilson laboratory during the study, and is now a postdoctoral research associate in the laboratory of TSRI Professor Erica Ollmann Saphire.

Kirchdoerfer eventually purified enough of these flu RNPs for electron microscope analysis at TSRI’s Automated Molecular Imaging Group, which is run jointly by Carragher and Potter.

Never Seen Before

The imaging group’s innovations enable researchers to analyze molecular samples more easily, in less time, and often with less starting material. “We were able, for example, to automatically collect data for several days in a row, which is unusual in electron microscopy work,” said Arne Moeller, a postdoctoral research associate at the imaging group who was the other first author of the study.

Electron microscopes make high-resolution images of their tiny targets by hitting them with electrons rather than photons of light. The images revealed numerous well-defined RNP complexes. To Moeller and his colleagues’ surprise, many of these appeared to have new, partial RNPs growing out of them. “They were branching—this was very exciting,” he said.

“Essentially these were snapshots of flu RNPs being replicated, which had never been seen before,” said Kirchdoerfer. These and other data, built up from images of tens of thousands of individual RNPs, allowed the team to put together the most complete model yet for flu-RNP structure and functions. The model includes details of how the viral polymerase binds to its RNA, how it accomplishes the tricky task of viral gene transcription, and how a separate copy of the viral polymerase assists in carrying out RNP replication. “We’re now able to take a lot of what we knew before about flu virus RNP and map it onto specific parts of the RNP structure,” said Kirchdoerfer.

The new flu RNP model highlights some viral weak points. One is a shape-change that a polymerase subunit—which grabs viral RNA and feeds it to the polymerase’s active site on a second subunit—has to undergo during viral gene transcription. Another is key interaction between the polymerase and viral nucleoproteins. Flu RNPs are long and flexible, curving and bending in electron microscope images; and thus the structural model remains only modestly fine-grained. “You wouldn’t be able to design drugs based on this model alone,” said Kirchdoerfer, “but we now have a much better idea of how flu RNPs work, and that does suggest some possibilities for better flu drugs.”

 

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The study, “Organization of the Influenza Virus Replication Machinery,” was funded in part by grants from the National Institutes of Health (AI058113, GM095573) and the Joint Center for Innovation in Membrane Protein Production for Structure Determination (P50GM073197). TSRI’s Automated Molecular Imaging Group includes the National Resource for Automated Molecular Microscopy, which is supported by the National Institutes of Health’s National Center for Research Resources (2P41RR017573-11) and the National Institute of General Medical Sciences Biomedical Technology Resource Centers (9 P41 GM103310-11).

Macular Degeneration drugs may do More harm than good ( anti-VEGF drugs )

Scripps Research Institute Study Suggests Caution and Further Studies on Drugs Used to Treat Macular Degeneration

LA JOLLA, CA – October 24, 2012 – Millions of people with “wet” macular degeneration are prescribed a class of medication known as anti-VEGF drugs. But now scientists at The Scripps Research Institute (TSRI) have found that a drastic reduction of VEGF activity may do more harm than good.

In the new study, the researchers deleted the gene for the blood-vessel growth factor VEGF, which has been implicated in stimulating abnormal blood vessel growth in a range of cancers and eye diseases, from cells in the retinas of adult mice. The results showed that without VEGF a large subset of light-sensing cells lost their main blood supply and shut down, causing severe vision loss.

“It’s becoming clear that VEGF has a critical function in maintaining the health of the retina, and we need to preserve that critical function when we treat VEGF-related conditions,” said TSRI Professor Martin Friedlander, MD, PhD, senior author of the new study, which appears in the November 2012 issue of the Journal of Clinical Investigation.

Major Target for Drug Developers

VEGF (vascular endothelial growth factor) has long been a major target for drug developers. Tumors often overproduce VEGF to stimulate local blood vessel growth and thus keep their fast-dividing cells well supplied with oxygen and nutrients. Low-oxygen conditions in the eyes of elderly or diabetic individuals also can trigger the overproduction of VEGF, resulting in a vision-destroying bloom of abnormal, leaky retinal blood vessels.

Several anti-VEGF drugs (such as Lucentis® (ranibizumab), Macugen (pegaptanib), Eylea® (aflibercept) and Avastin® (bevacizumab)) are already in use, and dozens more are in clinical trials against cancers and common eye disorders such as wet macular degeneration.

However, to date there have not been extensive studies on the effects of such drugs on the normal role of VEGF, in part because it is hard to generate adult animals that lack the VEGF gene. When the gene is removed from the embryos of mice, in a standard“knockout” experiment, the mice fail to develop normally and die before birth.

New Insights

In the new study, Friedlander laboratory postdoctoral fellows Toshihide Kurihara, MD, PhD, and Peter D. Westenskow, PhD, found a way to delete the major VEGF gene from mice after the animals had grown to adulthood. To determine VEGF’s role in the retina, they confined the gene deletion to the animals’ retinal pigment epithelial cells, which nourish and repair the retina and are a major retinal source of VEGF. The result suggests that VEGF does have a crucial function in the adult retina.

“Only three days after we knocked down the gene, we observed the complete deterioration of the choriocapillaris, a layer of capillaries that is a major supplier of nutrients to the outer retina, the location of the rod and cone photoreceptors,”said Kurihara.

Nearby light-sensing cone cells, which are specialized for detecting color and fine detail in visual images, also rapidly lost their function, causing pronounced vision loss in the mice. Seven months after the knockdown of the VEGF gene, the retinal damage and vision loss were still evident. “The deterioration seems irreversible if VEGF is not present,” said Westenskow.

Rod cells, which support low-light and peripheral vision, were not affected by the VEGF-gene deletion. The researchers note that cone cells may be more vulnerable because they are unusually active metabolically and may be unable to withstand a significant decrease in blood supply. Cone cells also bear receptors for VEGF molecules and thus may require direct VEGF stimulation to remain healthy. In any case, even if only cone cells died and rod cells were spared, a patient would experience severe vision loss. “You’d be defeating your purpose if you dried up the abnormal blood vessel growth but at the same time killed off the cone cells,” said Friedlander.

Paths for Future Research

Whether such side effects are happening with existing anti-VEGF treatments is unclear. While these assessments are possible, but they have been considered prohibitively expensive and invasive.

Friedlander, however, now believes such studies are necessary and plans to conduct such assessments in eye-disorder patients—who typically receive direct injections of anti-VEGF drugs to their eyes—to determine whether the drugs are causing these adverse side effects. He notes that the evaluations may be particularly necessary for a new class of anti-VEGF drugs recently approved for use in the treatment of age-related macular degeneration—drugs that are much more potent and persistent than previous anti-VEGF agents.

Fortunately, anti-VEGF drugs are not the only possible strategy for treating pathological blood vessel growth, as the new study makes clear. VEGF-related tumors and eye conditions also involve the overproduction of low-oxygen signaling proteins known as HIFs. The team found that deleting the genes for these HIFs in retinal cells largely prevents blood vessel overgrowth in a standard mouse model—without affecting the normal-level production of retinal VEGF or causing eye damage.

“In light of the present findings, other strategies for treating these eye conditions could be a possibility,” Friedlander said. “Conceivably, an anti-HIF treatment could also be combined with an anti-VEGF treatment, allowing the dose of the latter to be lowered significantly.”

The Friedlander lab, in collaboration with the laboratories of David Cheresh, PhD, and Michael Sailor, PhD, of the University of California, San Diego, has also been exploring the potential utility of inhibiting microRNAs that regulate angiogenic genes further upstream to VEGF. This work is being supported by a $10 million grant from the National Eye Institute and could lead to the development of antagonists that avoid the off-target effects of VEGF inhibitors.

In addition to Friedlander, Kurihara and Westenskow, other contributors to the study, “Targeted deletion of Vegfa in adult mice induces vision loss,” were Stephen Bravo and Edith Aguilar, both of TSRI. For more information on the paper, see http://www.jci.org/articles/view/65157.

The study was supported in part by grants from the National Eye Institute of the National Institutes of Health (EY-11254, EY-021416), the Lowy Medical Research Institute, the Manpei Suzuki Diabetes Foundation and The Japan Society for the Promotion of Science.

About The Scripps Research Institute

The Scripps Research Institute is one of the world’s largest independent, not-for-profit organizations focusing on research in the biomedical sciences. Over the past decades, Scripps Research has developed a lengthy track record of major contributions to science and health, including laying the foundation for new treatments for cancer, rheumatoid arthritis, hemophilia, and other diseases. The institute employs about 3,000 people on its campuses in La Jolla, CA, and Jupiter, FL, where its renowned scientists—including three Nobel laureates—work toward their next discoveries. The institute’s graduate program, which awards Ph.D. degrees in biology and chemistry, ranks among the top ten of its kind in the nation. For more information, see www.scripps.edu.

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Survivors of 1918 flu pandemic protected with a lifetime immunity to virus

Contact: Mount Sinai Newsroom
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New research has discovered that infection and natural exposure to the 1918 influenza virus made survivors immune to the disease for the remaining of their lives. Antibodies produced by cells isolated from these survivors served as an effective therapy to protect mice from the highly lethal 1918 infection. The study entitled “Neutralizing antibodies derived from the B cells of 1918 influenza pandemic survivors,” was released for advanced online publication by the journal Nature. Researchers at Mount Sinai School of Medicine’s Department of Microbiology contributed to the research findings. An estimated 50 million people were killed by the 1918 flu pandemic worldwide.

“Ninety years after survivors encountered the 1918 pandemic influenza virus, we collected antibody-producing B cells from them, and successfully isolated B cells that produce antibodies that block the viral infection,” said contributing author Dr. Christopher Basler, PhD, Associate Professor of Microbiology at Mount Sinai School of Medicine. “The antibodies produced by these cells demonstrated remarkable power to block 1918 flu virus infection in mice, proving that, even nine decades after infection with this virus, survivors retain protection from it.”

“The fact that you can isolate these anti-1918 memory B cells so long after infection will hopefully provide the impetus to further study the mechanisms behind long lived immunity,” said Dr. Osvaldo Martinez, post-doctoral fellow at Mount Sinai School of Medicine.

For this study, 32 individuals who were born before 1918 and lived through the influenza pandemic were recruited by Dr. Eric Altschuler at the University of Medicine and Dentistry of New Jersey to donate blood which was tested by Dr. Basler’s lab for the presence of antibodies that recognize the 1918 virus. Dr. James Crowe and colleagues at Vanderbilt University produced antibodies from these individuals’ blood cells and provided these to Dr. Basler’s lab where the potent neutralizing activity against 1918 virus was demonstrated. Antibodies were also provided to Dr. Terrence Tumpey at the CDC to test in mice the strength of the antibodies derived from the 1918 survivors.

“Our findings show that survivors of the pandemic have highly effective, virus neutralizing antibodies to this powerful virus, and humans can sustain circulating B memory cells to viruses for up to 9 decades after exposure,” said Dr. Tshidi Tsibane, post-doctoral fellow, Department of Microbiology, Mount Sinai School of Medicine. “These findings could serve as potential therapy for another 1918-like virus.”

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Vanderbilt University, Mount Sinai School of Medicine, University of Medicine and Dentistry of New Jersey, Centers for Disease Control and Prevention and The Scripps Research Institute collaborated on this research study.

About The Mount Sinai Medical Center The Mount Sinai Medical Center encompasses The Mount Sinai Hospital and Mount Sinai School of Medicine. The Mount Sinai Hospital is one of the nation’s oldest, largest and most-respected voluntary hospitals. Founded in 1852, Mount Sinai today is a 1,171-bed tertiary-care teaching facility that is internationally acclaimed for excellence in clinical care. Last year, nearly 50,000 people were treated at Mount Sinai as inpatients, and there were nearly 450,000 outpatient visits to the Medical Center.

Mount Sinai School of Medicine is internationally recognized as a leader in groundbreaking clinical and basic-science research, as well as having an innovative approach to medical education. With a faculty of more than 3,400 in 38 clinical and basic science departments and centers, Mount Sinai ranks among the top 20 medical schools in receipt of National Institute of Health (NIH) grants