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Archive for April, 2006

Virus reproduction and spread are studied

Posted by tumicrobiology on April 7, 2006

Wake Forest University scientists have made a surprising discovery about a powerful virus — a discovery that may lead to better vaccines and medications.

The biochemists have identified a protein that plays an important role in the ability of the vesicular stomatitis virus to invade healthy cells and reproduce.

Although VSV infects animals, it is not a human pathogen. Nevertheless, scientists study it because of its similarity to the Ebola, rabies and Marburg hemorrhagic fever viruses.

“VSV is a good model of a variety of other viruses,” said John Connor, an assistant professor of biochemistry. “Our research has given us a better understanding of how viruses like these are able to do the nasty things they do.”

Normally, VSV is extremely powerful, with the ability to shut down a cell’s system for making proteins. VSV then controls the cell’s protein-making machinery, making its own proteins so it can replicate and spread. The scientists were able to weaken that power by altering the matrix protein, so VSV cannot make as much protein and does not reproduce.

The study is reported in the April issue of the Journal of Virology.

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DNA links abductees from Japan, S.Korea

Posted by tumicrobiology on April 7, 2006

TOKYO, April 7 (UPI) — A DNA test has shown the husband of a Japanese woman kidnapped by North Korea in the 1970s is a South Korean who also was abducted by the North.

North Korea had insisted that Megumi Yokota, a Japanese national kidnapped by North Korean agents in 1977 at age 13, married North Korean agent Kim Chol Jun in 1986 but committed suicide in 1994.

However, Japan has concluded that Kim is not North Korean, as claimed by Pyongyang, but an abducted South Korean, the JoongAng Ilbo reported Friday.

"After conducting DNA tests on family members of five abducted South Koreans, one matched the DNA of the daughter of Mr. Kim," Japanese officials said Thursday.

The Japanese government obtained DNA samples from Kim Hye Gyong, the daughter of Kim and Yokota, in 2002 during an interview in Pyongyang. Japan also collected DNA samples from the relatives of five South Korean men allegedly abducted by North Korea to see if any of them matched the DNA of Yokota's daughter.

The Japanese government reportedly is discussing with South Korea when they will make a formal announcement of their findings.

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Saliva might become common diagnostic tool

Posted by tumicrobiology on April 7, 2006

A University of Kentucky research study suggests the use of saliva might help change the diagnosis and treatment methods for periodontal disease.

Scientists wanted to determine if saliva could be tested for signs of periodontal disease, a chronic bacterial infection affecting millions of Americans. The study's results showed it could.

"Our research team has been working on methods and point-of-care devices that could allow saliva to be used as a diagnostic fluid," said Craig Miller, primary investigator and professor of oral medicine. "This could impact the practice of dentistry and medicine in the very near future, as healthcare practitioners use saliva, possibly instead of blood, to diagnose and monitor oral and systemic health."

He said eventually portable devices might be created to diagnose a wide variety of disease conditions using saliva.

The research appears in the March issue of the Journal of American Dental Association.

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African Sleeping Sickness Breakthrough

Posted by tumicrobiology on April 7, 2006

Researchers have made a crucial breakthrough in the journey towards finding a treatment for African Sleeping Sickness.

The team of researchers from Lancaster, Oxford and Manchester Universities have discovered a weakness in the parasite that causes the disease – it cannot survive in the human bloodstream without the use of its flagellum, a protein 'tail' that allows it to swim.

This unexpected discovery offers up a valuable lead in the search for new drugs to control the killer disease.

The study is published this week (March 9) in the leading scientific journal Nature.

The sleeping sickness parasite, Trypanosoma brucei, is a single-celled organism equipped with a whip-like tail or flagellum. The parasite initially lives in the bloodstream of the human host causing fever and headaches, but eventually crosses into the brain where it causes irreversible neurological damage. Without treatment, the disease is fatal.

According to the latest figures from the World Health Organisation (WHO), African Sleeping sickness threatens over 60 million people in 36 countries of sub-Saharan Africa. The number of new cases per year is estimated to be between 300,000 to 500,000 with at least 60,000 people dying annually from the disease.

Until now doctors have struggled to treat the disease as most of the drugs currently used to combat this disease have undesirable side-effects and parasites are beginning to show evidence of increasing drug resistance. Furthermore there is little hope of a vaccine.

Lancaster University Biologist Dr Paul McKean said: “In this study we describe, for the first time, a full catalogue of the proteins required to build the trypanosome flagellum (the sleeping sickness parasite’s tail).

“We also show that many of these proteins are specific to the trypanosome flagellum. This latter finding is of critical importance since we also show that flagellum function is essential to the survival of bloodstream trypanosomes. These two observations raise the possibility that the flagellum may represent a novel target for the development of new drugs against this important medical pathogen.”

Source: Lancaster University

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Oxidation Defense In Mosquitoes Benefits Malaria Parasite

Posted by tumicrobiology on April 7, 2006

Scientists from two universities in Italy and Virginia Tech in the United States have determined the structure of a protein that is responsible for the production xanthurenic acid (XA) in Anopheles gambiae, the malaria carrying mosquitoes. XA plays a key role in the sexual reproduction of the malaria parasite (Plasmodium falciparum) in A. gambiae mosquitoes. Interfering with the formation of XA could be an avenue for development of drugs and insecticides to block malaria transmission. Millions of people worldwide are infected with malaria.

The research will be presented in the Proceedings of the National Academy of Science (PNAS) on-line as early as April 3 and in print April 11, 2006 ("Crystal structure of the Anopheles gambiae 3-hydroxykynurenine transaminase" by Franca Rossi, Silvia Garavaglia, and Giovanni Battista Giovenzana, of the DiSCAFF-Drug and Food Biotechnology Center at the University of Piemonte Orientale 'Amedeo Avogadro'; Bruno Arca' of the Department of Biological Structure and Function at the University of Napoli 'Federico II'; Jianyong Li of the Department of Biochemistry at Virginia Tech, and Menico Rizzi, also of the University of Piemonte Orientale).

The synthesis of XA is one of the biochemical defenses against oxidative stress resulting from 3-hydroxykynurenine (3-HK) accumulation in mosquitoes and possibly other species as well. "3-HK is oxidized easily under physiological condition, stimulating the production of reactive oxygen species, which can damage cells," said Li.

Mammals have various biochemical pathways of disposing of 3-HK, which mosquitoes lack. Research by Li's group at Virginia Tech on Aedes aegypti mosquitoes determined that "mosquitoes have developed an efficient strategy to prevent the accumulation of 3-HK by converting the chemically reactive 3-HK to the chemically stable XA via transaminase-mediated reactions," said Li.

The protein described in the PNAS article is responsible for this transforming of 3-HK into XA in the malaria vector Anopheles gambiae, where XA also helps the malarial parasite reproduce. So stopping the oxidative defense could stop the parasite as well as make the insect a victim of oxidative stress.

Rizzi's group at the University of Piemonte Orientale focuses on the structural characterization of enzymes involved in tryptophan degradation in mosquitoes, which results in the synthesis of XA. "Deciphering the molecular architecture of each enzyme in this pathway will be used for the structure-based rational design of potent and highly selective inhibitors of potential interest as innovative antimalarial agents," said Rizzi

Li's group at Virginia Tech biochemically characterizes enzymes involved in conversion to XA, including trptophan, the initial precursor of the process.

The researchers have collaborated since 2003.

"The use of protein crystallography in combination with biochemical studies and medicinal chemistry, represents a highly multidisciplinary approach that could lead to the identification of novel agents for the treatment of malaria," said Rizzi.

The PNAS article describes what an International team of scientists learned about the structure of Anopheles gambiae 3-HK transaminase. The research will continue on the rational design of a small molecule that could be synthesized, and that would allow the malaria cycle to be interrupted, therefore representing a novel avenue for the treatment of malaria.

Source: Virginia Tech

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Scientists Elucidate The Kinome Of Key Model Organism

Posted by tumicrobiology on April 3, 2006

The journal PLoS Genetics has published the findings of a team of scientists at the nonprofit Boston Biomedical Research Institute that provides a whole genome analysis of the protein kinases from a scientifically valuable model organism known as Dictyostelium.Led by Dr. Janet Smith, this study offers important insights into the evolution of kinases, which are enzymes involved in cell communication pathways. Approximately 2.5% of human genes code for protein kinases, and mutations in many of these genes are at the root of a range of human diseases. Dictyostelium is a widely used model organism for scientific study, as it is remarkably similar to mammalian cells, and it is amenable to a range of laboratory techniques.
To solve the kinome of Dictyostelium, Dr. Smith and her colleagues at Boston Biomedical utilized the power of bioinformatics, a cutting edge scientific technique which employs databases and computer algorithms to allow researchers to gain information and compile data about genes and kinases in a fast and efficient way, which can be very useful for drug discovery and development.

According to Dr. Smith, Dictyostelium provides a simple model in which to study conserved cellular processes, and illuminates a period in the evolutionary history of the metazoa after the divergence of the plants but before that of the fungi. "Our findings document the impressive evolutionary creativity of the Dictyostelium kinome- a large portion of the kinases are unique to Dictyostelium, and are probably involved in unique aspects of this organism's biology," said Dr. Smith.

But conservation is also a major theme. By comparing the Dictyostelium kinome with those of other organisms, the authors find 46 types of kinases that appear to be conserved in all organisms, and are likely to be involved in fundamental cellular processes. "We believe this study will be very useful to researchers who are studying cell communication pathways in other organisms, including vertebrates, by demonstrating what aspects of signaling are conserved, and revealing opportunities to use Dictyostelium to understand important human proteins."

Boston Biomedical Research Institute is a not-for-profit institution dedicated to the understanding, treatment and prevention of specific human diseases including cancer, Alzheimer's disease, muscular dystrophy, diabetes and conditions such as obesity and reproductive health problems. For more information visit www.bbri.org.

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Posted by tumicrobiology on April 3, 2006

Scientists Elucidate The Kinome Of Key Model Organism

The journal PLoS Genetics has published the findings of a team of scientists at the nonprofit Boston Biomedical Research Institute that provides a whole genome analysis of the protein kinases from a scientifically valuable model organism known as Dictyostelium.

Led by Dr. Janet Smith, this study offers important insights into the evolution of kinases, which are enzymes involved in cell communication pathways. Approximately 2.5% of human genes code for protein kinases, and mutations in many of these genes are at the root of a range of human diseases. Dictyostelium is a widely used model organism for scientific study, as it is remarkably similar to mammalian cells, and it is amenable to a range of laboratory techniques.

To solve the kinome of Dictyostelium, Dr. Smith and her colleagues at Boston Biomedical utilized the power of bioinformatics, a cutting edge scientific technique which employs databases and computer algorithms to allow researchers to gain information and compile data about genes and kinases in a fast and efficient way, which can be very useful for drug discovery and development.

According to Dr. Smith, Dictyostelium provides a simple model in which to study conserved cellular processes, and illuminates a period in the evolutionary history of the metazoa after the divergence of the plants but before that of the fungi. "Our findings document the impressive evolutionary creativity of the Dictyostelium kinome- a large portion of the kinases are unique to Dictyostelium, and are probably involved in unique aspects of this organism's biology," said Dr. Smith.

But conservation is also a major theme. By comparing the Dictyostelium kinome with those of other organisms, the authors find 46 types of kinases that appear to be conserved in all organisms, and are likely to be involved in fundamental cellular processes. "We believe this study will be very useful to researchers who are studying cell communication pathways in other organisms, including vertebrates, by demonstrating what aspects of signaling are conserved, and revealing opportunities to use Dictyostelium to understand important human proteins."

Boston Biomedical Research Institute is a not-for-profit institution dedicated to the understanding, treatment and prevention of specific human diseases including cancer, Alzheimer's disease, muscular dystrophy, diabetes and conditions such as obesity and reproductive health problems. For more information visit www.bbri.org.

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Posted by tumicrobiology on April 3, 2006

Melanoma Vaccine Strategy Shows Promise In Laboratory Experiments
A novel approach to creating a vaccine to treat melanoma has demonstrated promising effectiveness in a new laboratory study led by researchers at The Wistar Institute. About a third of melanoma patients might benefit from such a vaccine. The study appears in the current issue of Cancer Research.

In the study, the scientists used a small protein called a peptide found in approximately 70 percent of melanomas, but not in normal cells, to stimulate immune cells called killer T cells to attack the melanoma cells. Another type of immune cell called a monocyte was used to present the peptide, BRAFV600E, to the killer T cells to trigger their attack on the melanoma cells.

“In our experiments, we saw a strong cancer-killing immune response when killer T cells are stimulated with this peptide,” says Dorothee Herlyn, D.V.M., senior author on the study and a professor in the Immunology Program and Molecular and Cellular Oncogenesis Program at Wistar. “The results emphasize the potential of this approach for creating an effective melanoma vaccine, and we hope to move toward human clinical trials as soon as possible.”

A substantial proportion of melanoma patients, about 50 percent, have killer T cells able to recognize the BRAFV600E peptide. Combining the prevalence of the peptide among melanoma patients – about 70 percent – with the number of patients whose immune cells are able to respond to the peptide suggests that a vaccine based on BRAFV600E could treat approximately a third of all melanoma patients.

Herlyn adds that the specificity of the peptide – the fact that it is found only in melanoma cells, not normal cells – suggests that the toxicity of any vaccine based on the peptide would be minimal. Killer T cells sparked into action by the vaccine would target only the cancer cells, sparing healthy cells entirely.

Looking ahead to possible human clinical trials, another member of the scientific team, University of Pennsylvania assistant professor Brian Czerniecki, M.D., Ph.D., is working to prepare yet another type of immune cell, called a dendritic cell, to present the BRAFV600E peptide to killer T cells. Dendritic cells have as their primary job the presentation of foreign materials to the immune system, and the expectation is that dendritic cells presenting the BRAFV600E peptide would trigger the killer T cells even more effectively than the monocyte cells used in the current study. Indeed, such prepared dendritic cells might serve as the basis for a treatment vaccine that could be taken into human clinical trials.

Herlyn is senior author on the Cancer Research study. The lead author is Rajasekharan Somasundaram, also at Wistar. The additional Wistar coauthors are Rolf Swoboda, Laura Caputo, and Laszlo Otvos (now at Temple University). The remaining coauthors are Barbara Weber, Patricia Volpe, Patricia van Belle, Susan Hotz, David E. Elder, Lynn Schuchter, DuPont Guerry, and Brian J. Czerniecki of the University of Pennsylvania, and Francesco M. Marincola with the National Institutes of Health.

Support for the research was provided by the National Institutes of Health and the Commonwealth Universal Research Enhancement Program of the Pennsylvania Department of Health.

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DNA Gene Vaccine Protects Against Harmful Protein Of Alzheimer’s Disease

Posted by tumicrobiology on April 3, 2006

Doses of DNA-gene-coated gold particles protect mice against a protein implicated in Alzheimer's disease, researchers at UT Southwestern Medical Center have found
By pressure-injecting the gene responsible for producing the specific protein — called amyloid-beta 42 — the researchers caused the mice to make antibodies and greatly reduce the protein's build-up in the brain. Accumulation of amyloid-beta 42 in humans is a hallmark of Alzheimer's disease.

"The whole point of the study is to determine whether the antibody is therapeutically effective as a means to inhibit the formation of amyloid-beta storage in the brain, and it is," said Dr. Roger Rosenberg, the study's senior author and director of the Alzheimer's Disease Center at UT Southwestern.

The gene injection avoids a serious side-effect that caused the cancellation of a previous multi-center human trial with amyloid-beta 42, researchers said. UT Southwestern did not participate in that trial. In that earlier study, people received injections of the protein itself and some developed dangerous brain inflammation.

The new study is available online and appears in an upcoming issue of the Journal of the Neurological Sciences.

The researchers used mutant mice with two defective human genes associated with Alzheimer's, genes that produce amyloid-beta 42. "By seven months, the mice are storing abundant amounts of amyloid-beta 42," said Dr. Rosenberg, who holds the Abe (Brunky), Morris and William Zale Distinguished Chair in Neurology.

While the mice were young, the scientists coated microscopically small gold particles with human amyloid-beta 42 genes attached to other genes that program cells to make the protein. The particles were then injected with a gene gun into the skin cells of the mice's ears using a blast of helium.

After receiving 11 injections over several months, the mice showed a high level of antibodies to amyloid-beta 42, and a 60 percent to 77.5 percent reduction of plaques in their brains.

As controls, the researchers also either injected mutant mice with the gene for a related but harmless protein, amyloid-beta 16, or with a gene vaccine that lacked any amyloid genes. These treatments did not cause antibody production, and the mice showed the large amounts of amyloid-beta 42 brain plaques normally seen in animals with these mutations.

The gene injection showed superior results compared to a previous human study in which amyloid-beta 42 protein itself was injected into muscle, Dr. Rosenberg said. That study was halted when a small percentage of participants developed inflammation of the brain and spinal cord.

Injecting the gene, in contrast, caused no brain inflammation in the mice.

Dr. Rosenberg said the difference was partly because in the human trial, the protein was injected along with a substance called an adjuvant, which increased the immune response to abnormal excessive levels, causing the dangerous brain inflammation. In addition, the immune response in humans may have involved antibodies called Th1, which were probably partly responsible for the inflammation. The gene injection in the mouse study produced Th2 antibodies, which have a low probability of causing brain inflammation. Furthermore, no adjuvant was needed for antibody production.

The gene immunization is now undergoing further animal studies, with the ultimate goal being a clinical trial in humans. The researchers also plan to see if it can reverse the size of established plaques in the brains of mice.

Other UT Southwestern researchers involved in the study were Drs. Bao-Xi Qu, assistant professor of neurology, Philip Boyer, assistant professor of pathology, and Linda Hynan, associate professor of clinical sciences and psychiatry. Dr. Stephen Johnston, formerly with UT Southwestern and now at Arizona State University, also participated.

The work was supported by the National Institute on Aging, the National Alzheimer's Coordinating Center, the Rudman Foundation, the Luttrell Foundation, and UT Southwestern's Winspear Family Special Center for Research on the Neuropathy of Alzheimer's Disease.

Source: UT Southwestern Medical Center

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Paper Reports Discovery Of Virus Implicated In Genetics Of Prostate Cancer

Posted by tumicrobiology on April 3, 2006

The Open Access journal PLoS Pathogens has published an article detailing research that identifies a new retrovirus in the tissue of human prostate tumors.

The research was first announced at an American Society of Clinical Oncology Meeting, but only now is the full, peer-reviewed report available.

The paper, entitled "Identification of a Novel Gammaretrovirus in Prostate Tumors of Patients Homozygous for R462Q RNASEL Variant," reports that the researchers detected the new virus more frequently in men with mutations in both their copies of RNASEL than in those with at least one normal copy.

Scientists have long speculated about a connection between cancer and infectious diseases. The possible connection has been especially true in the case of prostate cancer because a variant on the viral-defense gene, RNASEL, has been implicated in 15% of prostate cancer cases. The newly discovered virus is closely related to virus associated with leukemia in mice.

"We have made a very fascinating discovery never before seen in humans that is very similar to one found in a mammal that causes cancer," said Dr. Eric Klein of the Cleveland Clinic. "But we have not proven this virus causes prostate cancer."

Klein was a coauthor on the paper, along with Joe Derisi, the lead author, and other scientists at the University of California San Francisco.

The paper's observations raise a large number of questions for future experimentation, including whether there is any relationship between the virus and the disease, what cells are infected, and the epidemiology of infection.

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Bacteria Aid In Clean-Up Of Uranium Contamination

Posted by tumicrobiology on April 3, 2006

In research that could help control contamination from the radioactive element uranium, scientists have discovered that some bacteria found in the soil and subsurface can release phosphate that converts uranium contamination into an insoluble and immobile form.
Based on laboratory studies, Georgia Institute of Technology researchers report promising results using bacterial species from three genera isolated from subsurface soils collected at a U.S. Department of Energy (DOE) Field Research Center site in Oak Ridge, Tenn. Researchers conducted preliminary screenings of many bacterial isolates and found several candidate strains that released inorganic phosphate after hydrolyzing an organo-phosphate source the researchers provided.

The bioremediation research project, funded for three years by DOE's Environmental Remediation Sciences Division, is in its early stages. Research team member Melanie Beazley, a Ph.D. student in the Georgia Tech School of Earth and Atmospheric Sciences, will present preliminary findings on March 30 at the 231st American Chemical Society National Meeting in Atlanta.

"These organisms release phosphate into the medium, but the precipitation (of uranium phosphate) occurs chemically," explained Assistant Professor of Earth and Atmospheric Sciences Martial Taillefert, co-director of the study. "That is the biomineralization of uranium and the novelty of this approach."

The process begins when the bacteria — from the genera Rhanella, Bacillus and possibly Arthrobacter — degrade an organo-phosphate compound such as glycerol-3-phosphate (G3P) or phytic acid (IP6), which can be present in subsurface soils.

"During their growth, the organisms liberate phosphate they derive from the organo-phosphate compound," said project co-director Patricia Sobecky, an associate professor of biology. "The free phosphate is released to the surrounding media, which is a solution in the lab. Then we conduct assays to see how much uranium is mineralized by the phosphate released by the bacteria." The bacteria's role is crucial in this process because uranium cannot dissociate the organo-phosphate compound chemically, Taillefert explained. So uranium in the presence of organo-phosphate alone does not result in significant uranium precipitation.

Sobecky and her Ph.D. student Robert Martinez are conducting the microbiological and physiological component of the research, while Taillefert and Beazley study the uranium chemistry and analyze distribution of different forms of uranium during incubation in the lab.

"The devil's in the details with the chemistry of uranium: There are numerous forms of uranium in the environment, which are all influenced by the natural properties of soils and groundwater," Taillefert said.

Sobecky added, "What we're doing now is optimizing the assay conditions and the techniques to analyze the distribution of uranium species in the lab."

Traditionally, DOE has funded research investigating the chemical reduction of uranium contamination. But there are two approaches to immobilizing uranium. One strategy reduces uranium (VI) to uranium (IV), which is, in principle, immobile. But the uranium can re-oxidize even with traces of oxygen from rainwater seeping into the groundwater. The Georgia Tech approach biomineralizes uranium (VI) into an insoluble form of uranium via phosphate precipitation.

As they work toward a bioremediation strategy that will work in the field, researchers must design a mechanism to deal with competing organisms in the soil that might sequester the free phosphate, Sobecky noted. Though their current grant does not cover the cost of a field study, researchers hope to obtain funds in the future to test their strategy at Oak Ridge and potentially other DOE sites. Uranium contamination is a concern at DOE sites because it can migrate to groundwater in surrounding areas, Taillefert noted.

"At this point, we know the organisms we're studying are active in precipitating uranium phosphate," he said. "Now we need to determine how chemically stable it is."

Researchers also have learned that when the bacteria are releasing phosphate from G3P, the bacteria can tolerate the toxic uranium and can continue to grow once the uranium is precipitated by the released phosphate.

"Our challenge now is fine-tuning the conditions around the bacterium so eventually it can thrive and work chemically in a natural setting," Taillefert said.

Source: Georgia Institute of Technology

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Cancer virus protein needed after all

Posted by tumicrobiology on April 3, 2006

March 31 (UPI)

A protein made by a cancer-causing virus that was thought to be unimportant is critically needed by the virus to initiate an infection, says a U.S. study.

Scientists at the Ohio State University Cancer Program and OSU College of Veterinary Medicine examined the human T lymphotropic virus type 1 — HTLV-1 — and a protein it makes called p13.

The protein is one of the virus' so-called accessory proteins, which earlier studies done in laboratory-grown cells suggested the virus could live without.

"This viral protein is also important to study because it travels to the mitochondria of infected cells," said Michael Lairmore, professor and chair of veterinary biosciences and a member of the OSU Comprehensive Cancer Center. "Our findings are the first to indicate that the HTLV-1 p13 protein plays an essential biological role during the early phase of virus infection in an animal model."

The findings are published in the Journal of Virology.

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