Scientists Identify Key Factor That Controls HIV Latency

SOURCE

ScienceDaily (June 27, 2009) — Scientists at the Gladstone Institutes of Virology and Immunology (GIVI) have found another clue that may lead to eradication of HIV from infected patients who have been on antiretroviral therapy. A real cure for HIV has been elusive because the virus can "hide" in a latent form in resting CD4-T cells. By understanding this "latency" effect, researchers can identify ways to reactivate the virus and enable complete clearance by current or future therapies.

Researchers in the laboratory of GIVI Associate Director Eric Verdin, MD have found that methylation of cytosine in the DNA of infected cells is associated with HIV latency and that inhibition of DNA methylation causes the reactivation of latent HIV. These observations offer a potential new strategy for inhibiting HIV latency and reactivating the virus. The discovery was reported in the current edition of PLoS Pathogens.
"While HIV-1 latency is likely to be a multifactorial process, we have shown that inhibiting the methylation of the provirus contributes to an almost complete reactivation of latent HIV-1," said lead author Steven E. Kauder.
The research team, which also included scientists from the University of Utah and Stockholm's Karolinska Institute, developed in vitro models of HIV-1 latency in T cells that harbor a full-length HIV genome. The provirus in the cell lines also encoded a fluorescent marker to illuminate HIV-1 transcriptional activity.
In addition to finding that DNA methylation is a mechanism of latency, the scientists also discovered that a host protein, called methlyl-CpG binding domain protein 2 (MBD2) binds to the methylated HIV DNA and is an important mediator of latency.
"Interfering with methylation greatly potentiates the reactivation of HIV," Kauder said. In this study, the researchers found that the drug 5-aza-2'deoxycytidine (aza-CdR) can inhibit HIV methylation and cause the virus to reactivate.
"Combined with other areas of our investigation into HIV latency, this research provides important new knowledge about the process and opens many new pathways for future study," said Dr. Verdin, senior author of the study.
The research team included Alberto Bosque and Vicente Planelles of the University of Utah and Annica Lindqvist of Karolinska University. The study was supported by the National Institutes of Health
Eric Verdin's primary affiliation is with the Gladstone Institute of Virology and Immunology, where his laboratory is located and all his research is conducted. He is also professor of medicine at the University of California, San Francisco.
Adapted from materials provided by Gladstone Institutes, via EurekAlert!, a service of AAAS.

Artificial Liver For Drug Tests.

SOURCE

ScienceDaily (June 25, 2009) — If you have hay fever, headaches or a cold, it’s only a short way to the nearest chemist. The drugs, on the other hand, can take eight to ten years to develop. Until now animal experiments have been an essential step, yet they continue to raise ethical issues. “Our artificial organ systems are aimed at offering an alternative to animal experiments,” says Professor Heike Mertsching of the Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB in Stuttgart.

“Particularly as humans and animals have different metabolisms. 30 per cent of all side effects come to light in clinical trials.” The test system, which Professor Mertsching has developed jointly with Dr. Johanna Schanz, should in future give pharmaceutical companies greater security and shorten the path to new drugs. Both researchers received the “Human-centered Technology” prize for their work.
“The special feature, in our liver model for example, is a functioning system of blood vessels,” says Dr. Schanz. “This creates a natural environment for cells.” Traditional models do not have this, and the cells become inactive. “We don’t build artificial blood vessels for this, but use existing ones – from a piece of pig’s intestine.” All of the pig cells are removed, but the blood vessels are preserved. Human cells are then seeded onto this structure – hepatocytes, which, as in the body, are responsible for transforming and breaking down drugs, and endothelial cells, which act as a barrier between blood and tissue cells.
In order to simulate blood and circulation, the researchers put the model into a computer-controlled bioreactor with flexible tube pump, developed by the IGB. This enables the nutrient solution to be fed in and carried away in the same way as in veins and arteries in humans. “The cells were active for up to three weeks,” says Dr. Schanz. “This time was sufficient to analyze and evaluate the functions. A longer period of activity is possible, however.”
The researchers established that the cells work in a similar way to those in the body. They detoxify, break down drugs and build up proteins. These are important pre-conditions for drug tests or transplants, as the effect of a substance can change when transformed or broken down – many drugs are only metabolized into their therapeutic active form in the liver, while others can develop poisonous substances. The researchers have demonstrated the basic possibilities for use of the tissue models – liver, skin, intestine and windpipe. At the moment, the test system is being examined. Within two years it could provide a safer alternative to animal experiments.
Adapted from materials provided by Fraunhofer-Gesellschaft.

Chemists see first building blocks to life on Earth

SOURCE

British scientists said on Wednesday that they had figured out key steps in the process by which life on Earth may have emerged from a seething soup of simple chemicals.

Genetic information in living organisms today is held in deoxyribonucleic acid (DNA), the famous "double helix" molecule of sugar, phosphate and a base.
But DNA is too sophisticated to have popped up in an instant, and one avenue of thought says its single-stranded cousin, ribonucleic acid, or RNA, came first.
RNA plays a key role in making proteins and, in viruses, is used to store genetic code.
It is chemically similar to DNA but is simpler and tougher in structure, and thus looks like a good candidate for Earth's first information-coding nucleic acid.
But for all its allure, the "RNA first" theory has run into practical problems.
Its three ingredients -- the base, ribose sugar and phosphate -- must have formed separately and then combined to form the molecule, according to conventional thinking.
Critics, though, say that RNA, while somewhat simpler than DNA, is still a complex molecule and could not have been assembled spontaneously.
These doubters have been comforted by the failure to find any feasible chain of chemical events to explain how the three components all came together.
But a paper published in the British journal Nature by University of Manchester chemists puts forward a different explanation.
The team, led by Professor John Sutherland, venture that an RNA-like synthesis took place through a series of chemical reactions and an important intermediate substance.
Their lab model uses starting materials and environmental conditions that are believed to have been around in early Earth and are also used in the standard "RNA first" scenario.
Their theory starts with a simple sugar called glycolaldehyde, which reacts with cyanmide (a compound of cyanide and ammonia) and phosphate to produce an intermediate compound called 2-aminooxazole.
Gentle warming from the Sun and cooling at night help purify the 2-aminooxazole, turning it into a plentiful precursor which contributes the sugar and base portions of the new ribonucleotide molecule.
The presence of phosphate and ultraviolet light from the Sun complete the synthesis.
In a commentary also published by Nature, US molecular biologist Jack Szostak hailed the research as an elegant explanation as to why the sugar and base would not have to form separately before forming the new molecule.
"It will stand for years as one of the great advances in prebiotic chemistry," the term for the study of the chemical processes that led to life on Earth, he enthused.
Opinions vary as to when the first organisms appeared on Earth.
One estimate, based on fossilised mats of bacteria found in Australia, is that this happened around 3.8 billion years ago, around 700 million years after the planet was formed.
(c) 2009 AFP

Breakthrough in the treatment of bacterial meningitis

SOURCE

It can take just hours after the symptoms appear for someone to die from bacterial meningitis. Now, after years of research, experts at The University of Nottingham have finally discovered how the deadly meningococcal bacteria is able to break through the body's natural defence mechanism and attack the brain.

The discovery could lead to better treatment and vaccines for meningitis and could save the lives of hundreds of children.
Bacterial meningitis in childhood is almost exclusively caused by the respiratory tract pathogens Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae. The mechanism used by these lethal germs to break through the blood brain barrier (BBB) has, until now, been unknown.
The team led by Dlawer Ala'Aldeen, Professor of Clinical Microbiology and Head of the Molecular Bacteriology and Immunology Group at the Centre for Biomolecular Sciences, recently discovered that all three pathogens target the same receptor on human cerebrovascular endothelial cells — the specialised filtering system that protects our brain from disease — enabling the organisms to cross the blood-brain barrier.
Their findings, published today in The Journal of Clinical Investigation, suggest that disruption or modulation of this interaction of bacterial adhesins with the receptor might offer unexpectedly broad protection against bacterial meningitis and may provide a therapeutic target for the prevention and treatment of disease.
Professor Ala'Aldeen, who has been studying meningitis and its causes for over 20 years, said: "This is a significant breakthrough which will help us design novel strategies for the prevention and treatment of bacterial meningitis. Identification of the human receptor and bacterial ligands is like identifying a mysterious key and its lock, which will open new doors and pave the way for new discoveries."
The research, carried out in collaboration with the Department of Infectious Diseases at St. Jude Children's Research Hospital in Memphis Tennessee, also involved students from the University who have been regular and willing volunteers in the research programme.
Professor Ala'Aldeen said: "The ultimate aim is to save lives by protecting the healthy and curing the sick. We are one step closer to new breakthroughs that would prevent disease or its complications. There still is a long way to go before we have the ultimate vaccine and the ultimate treatment of bacterial meningitis."
Source: University of Nottingham (news : web)

Developed a human monoclonal antibody that neutralizes the Hepatitis C virus (HCV).

SOURCE

ScienceDaily (May 11, 2009) — aking aim at a leading cause of liver failure in the United States, a team of scientists at the Massachusetts Biologic Laboratories (MBL) of the University of Massachusetts Medical School (UMMS) has developed a human monoclonal antibody that neutralizes the Hepatitis C virus (HCV). The new antibody effectively neutralized the virus in culture, and then prevented infection by the virus in a pre-clinical animal model of the disease.

Details of the research were presented April 23 in Copenhagen, Denmark at the 44th Annual Meeting of the European Association for the Study of the Liver (EASL). "We are pleased with the progress of this program," said Donna Ambrosino, MD, executive director of the MBL and a professor of pediatrics at the Medical School. "This antibody shows significant efficacy against the virus."
In the current study, MBL scientists injected transgenic mice (HuMAb Mouse® technology, Medarex, Inc.) with elements of HCV and then painstakingly searched for individual human antibodies produced in the mice that would recognize and bind to the HCV's outer coat, known as the glycoprotein. Once they found human antibodies that looked promising, they evaluated in vitro the ability of those antibodies to neutralize the virus and selected a lead candidate antibody for further characterization. Collaborative work with clinical researchers from the Department of Medicine at the Medical School's Worcester campus demonstrated that this antibody, now known as MBL-HCV1, was able to bind tightly with all genotypes of HCV tested from infected patient samples.
MBL-HCV1 was then tested off-site on three non-human primates. In that study, one animal received no antibody, one a low dose of the new antibody, and one a higher dose. Then all three animals were exposed to HCV. The animals with low or no antibody dosages developed HCV infections, but the animal with the higher dose was protected. Subsequently, researchers gave the high-dose of the antibody to the animal that originally received no antibody, and in that case the HCV was cleared from that animal's system. "These results are encouraging as a possible treatment for HCV infected patients, but more work needs to be done before we know how effective it will be in people," Dr. Ambrosino noted.
HCV attacks the liver and can eventually lead to liver failure. According to the U.S. Centers for Disease Control and Prevention, 3.2 million Americans are chronically infected with HCV and some 10,000 die annually of the disease. Globally, as many as 170 million people are estimated to suffer from HCV infection. For the most serious cases of HCV that do not respond to antiviral drugs, liver transplantation is the only option.
Typically 2,000 to 4,000 liver transplants are done each year in the United States (far less than the number of people on the waiting list for available organs). Transplantation can be a life saving treatment; however, in nearly all cases the patient's new liver is eventually infected by HCV because the virus remains in the patient's bloodstream during surgery. The powerful antiviral drugs now used to attack HCV prior to end-stage liver failure are not routinely used during surgery due to the patients' weakened condition and because of the strong medication used to avoid rejection of the new liver. After re-infection with HCV, nearly 40 percent of patients suffer rapid liver failure.
To close that clinical gap, the new antibody developed at MBL is designed to be a therapy shortly before and after transplant surgery. By giving a patient the new antibody before and during the time when the donor liver is implanted, researchers hope the HCV virus left in the bloodstream will be neutralized and rendered unable to infect the new liver. Then, because monoclonal antibodies are highly specific and typically have little or no side-effects, additional dosages of the new antibody could, theoretically, be given immediately after transplant surgery to continue neutralizing any remaining virus.
It is also possible, researchers theorize, that the antibody could be used in combination with new antiviral drugs for treatment in patients with newly diagnosed HCV infection. Use of the new antibody for both liver transplant patients and in newly diagnosed HCV patients will now be further evaluated. A Phase 1 human clinical trial of MBL-HCV1 in healthy subjects is expected to begin later this year.
Adapted from materials provided by University of Massachusetts Medical School, via EurekAlert!, a service of AAAS.

Biotechnology: Engineered Moss Can Produce Human Proteins

SOURCE

ScienceDaily (May 11, 2009) — ETH Zurich researchers have shown that mosses and humans share unexpected common characteristics. These evolutionary relics could be useful in the production of therapeutic proteins.

At first glance, mosses and human beings have little in common. The moss Physcomitrella patens is small, pale green, immobile, and uses sunlight as its energy source. Humans are large, mobile, and need to obtain energy by eating vegetable or animal foods.
Transferring mammalian genes into moss
This made the result of the experiments carried out by researchers in the group led by Martin Fussenegger, Professor of Chemical and Bioengineering at ETH Zurich, all the more astonishing. In collaboration with researchers at the University of Freiburg im Breisgau, the PhD student Marc Gitzinger carried out tests to see what happens when unmodified human or mammalian genes are inserted into the moss genome. They transferred the foreign, unmodified genes into the moss and discovered that the moss was easily able to manufacture the proteins encoded therein.
This cannot be taken for granted, since the same process does not work when a mammalian gene is implanted into what are known as “higher” flowering plants. The reason is that sections of the start and finish sequences of the genes of animals, plants, fungi and bacteria are considerably different. They are responsible for ensuring that a gene in the organism is recognized as such, and the proteins encoded by it are produced in the correct amount and are released from the cell. The more remote the relationship between living organisms, the greater the difference between these sequences. This is why biotechnologists must normally adapt them to a foreign organism before transplanting a gene into it. The researchers were astonished to find that this was not necessary in the case of the moss.
Moss as a generalist
The explanation given for this by Ralf Reski, Professor of Plant Biotechnology at the University of Freiburg im Breisgau, is that the moss has remained a generalist. It underwent the last major modification about 450 million years ago when it changed from living in water to a life on land, adapting to the new living conditions and then remaining unaltered for millions of years, both in its appearance and at a genetic level.
The process used by the moss to produce its proteins is less sophisticated than in “higher” organisms. In contrast to the moss, these latter organisms underwent major further developments and specializations over the course of 450 million years. On the other hand, the moss clearly retained – for millions of years – the ability to read foreign genes such as those from mammals and thus also from humans, and to translate them into proteins, probably without ever having made any use of this capability during these 450 million years.
A cost-effective alternative to mammalian cells
Today, the moss Physcomitrella patens and its ability to manufacture mammalian proteins could help to satisfy the large worldwide demand for therapeutic proteins. One well-known example is insulin, which enables diabetics to control their blood sugar level.
Nowadays, therapeutic proteins are mainly manufactured in mammalian cells, which are very expensive to culture. They need to be maintained at body temperature with a continuous supply of nutrients and oxygen, and the production process is costly. At present, global production capacity cannot match the demand. Because of the difficulties involved in handling them, production is possible only in industrialized countries.
In contrast, the moss Physcomitrella patens is comparatively undemanding. It needs water, a couple of nutrient salts and some light to allow it to flourish and produce proteins. This makes it convenient and simple to handle in a bioreactor, and, in the future, it might enable even less developed nations to satisfy their requirement for therapeutic proteins. However, further research will be needed before the moss can be used to produce therapeutic proteins on an industrial scale.
Journal reference:
Gitzinger et al. Functional cross-kingdom conservation of mammalian and moss (Physcomitrella patens) transcription, translation and secretion machineries. Plant Biotechnology Journal, 2009; 7 (1): 73 DOI: 10.1111/j.1467-7652.2008.00376.x
Adapted from materials provided by ETH Zurich.

How Cells Move: Cooperative Forces Boost Collective Mobility Of Cells

SOURCE

ScienceDaily (May 11, 2009) — Research by scientists in Spain and their colleagues offers for the first time an experimental answer to the question of how cells move during biological processes as diverse as the development, metastasis, or regeneration of tissues.

The work addresses the issue of collective mobility of cells, that is to say, how cells are moved within tissues, and what is the prevalent form of movement inside living organisms.
"Research into collective cell mobility is very active due to the direct implications it has on fields such as embryologic development, organ regeneration, and cancer. For example, if we could find a way to control cell mobility during metastasis, cancer would be a curable disease in the majority of cases," says Dr. Xavier Trepat, senior researcher of the cellular and respiratory biomechanics group and researcher in the Department of Physiological Sciences at the University of Barcelona, and in the Networking Biomedical Research Centre for respiratory diseases (CIBER).
Up until now, scientists had proposed various mechanisms to explain collective cell migration. One hypothesis for example, suggests that the cells move collectively due to the existence of “leader” cells, which stretch out in the rest of the group, like a train pulls carriages behind it. Another hypothesis suggests that each cell moves independently to those around it, like cars on the motorway during a traffic jam, or like soldiers in a military parade. “We have rejected both these possibilities,” says Trepat.
According to his research, collective cell mobility is the result of a cooperative process in which each cell contributes to the movement of the group, stretching to those around it. “It is a mechanism similar to a tug-of-war game, in which two teams pull a rope by its extremes and the team that pulls the hardest wins. During the game, each player generates force and transmits it to the rope, so that the tension in the rope is the sum of the forces generated by each member of the team. Cells do the same. Each cell generates force to stretch to its neighbours in the direction of the movement» explains the researcher.
Journal reference:
Xavier Trepat, Michael R. Wasserman, Thomas E. Angelini, Emil Millet, David A. Weitz, James P. Butler & Jeffrey J. Fredberg. Physical forces during collective cell migration. Nature Physics, 2009; DOI: 10.1038/nphys1269
Adapted from materials provided by Universidad de Barcelona, via AlphaGalileo.

Sexually Transmitted Infections: Transistors Used To Detect Fungus Candida Albicans

SOURCE

ScienceDaily (May 11, 2009) — The Nanosensors group from the Universidad Rovira i Virgili has created a biosensor, an electrical and biological device, which is able to selectively detect the Candida albicans yeast in very small quantities of only 50 cfu/ml (colony-forming units per millilitre).

"The technique uses field-effect transistors (electronic devices that contain an electrode source and a draining electrode connected to a transducer) based on carbon nanotubes and with Candida albicans-specific antibodies", Raquel A. Villamizar, lead author of the study said.
The Candida samples, which can be obtained from blood, serum or vaginal secretions, are placed directly on the biosensor, where the interaction between antigens and antibodies changes the electric current of the devices. This change is recorded and makes it possible to measure the amount of yeast present in a sample.
"Thanks to the extraordinary charge transference properties of the carbon nanotubes, the fungus detection process is direct, fast, and does not require the use of any marker", remarks Villamizar, who is co-author of a study that provides details of the biosensor and was published recently in the journal Sensors and Actuators B: Chemical.
To date, conventional diagnosis of Candida has been carried out using microbial cultures, serological tests, PCR molecular biology techniques (polymerase chain reactions used to amplify DNA), or immunoassays such as ELISA (Enzyme Linked Inmunoabsorbent Assay).
These techniques require long analysis times and sometimes give rise to false positives and negatives. ELISA also requires the use of markers (compounds that must be added to detect the presence of yeast by fluorescence and other techniques).
The new carbon nanotubes biosensor, however, "makes it possible to improve some of the quality parameters of the traditional methods, for example the speed and simplicity of measurements, and it is an alternative tool that could be used in routine sample analysis", explains Villamizar.
The researcher adds that by using this biosensor "it will be possible in future to obtain a rapid diagnosis of infection with this pathogen, which will help to ensure administration of the correct prophylactic treatments".
The Candida albicans fungus exists naturally in the skin, mouth, the mucous membranes lining the digestive tract, and the respiratory and genitourinary systems. This yeast can cause anything from simple mycosis of the skin to complicated cases of candidiasis. It is much more commonly found in patients suffering from immunodeficiency, tumours, diabetes and lymphomas, among other diseases.
Journal reference:
Villamizar et al. Improved detection of Candida albicans with carbon nanotube field-effect transistors. Sensors and Actuators B Chemical, 2009; 136 (2): 451 DOI: 10.1016/j.snb.2008.10.013
Adapted from materials provided by Plataforma SINC.

Deep in the Red: Using Infrared to Watch What Goes On in a Living Body

SOURCE

An infrared version of the Nobel Prize-winning green fluorescent protein could make the technique even more powerful.

Fluorescent proteins, which are compounds that can absorb and then emit light, have become a powerful instrument in the cell biologist's toolkit—so powerful, in fact, that the discovery and development of green fluorescent proteins from jellyfish earned the 2008 Nobel Prize in Chemistry. (Here's a Q&A with one of the winners, Columbia University's Martin Chalfie, about his work.) These proteins have limitations, however: They need to be excited with the blue to orange part of the visible spectrum, at wavelengths of 495 to 570 nanometers. These wavelengths of light are too short to penetrate tissue very well, and so green fluorescent proteins are mainly used in test tube studies to watch cell division or to label certain cell types.
But one of the 2008 Nobelists, Roger Y. Tsien of the University of California, San Diego, and his U.C.S.D. colleagues report in today's issue of Science that they have developed a new fluorescent protein that could enable scientists to tag and visualize cellular activity as it happens inside a live animal. The protein, after absorbing light from the far-red part of the spectrum, shines in the near-infrared, at wavelengths of around 700 nanometers.
These longer wavelengths can penetrate mammalian tissue and even pass through bone. "Say you label a tumor with a green fluorescent protein, and if this labeled tumor is buried inside the animal, then you barely can get green fluorescence out," says lead researcher Xiaokun Shu. "But if you label this deeply buried tumor by infrared fluorescent proteins, you will get a stronger signal because infrared penetrates tissue more efficiently."
Tsien's group derived the infrared fluorescent protein from a hardy bacterium called Deinococcus radiodurans, famous for its ability to survive extreme environments. Bacteria do not actually use this class of proteins, called bacteriophytochromes, to emit light. "They use these bacteriophytochromes to control gene expression,” Shu says—the proteins convert absorbed light into energy to signal certain genes to turn on or off.
The initial challenge for researchers was to re-engineer the protein so that absorbed light would be re-emitted instead of being used as a source of power. They accomplished the feat by deleting the part of the protein that converts the absorbed light into chemical energy; as a result, this truncated and mutant form gave up its absorbed energy as an infrared glow. The scientists incorporated the engineered bacterial protein into mammalian cells—specifically, into the liver of a live mouse, which lit up with infrared light.
The finding paves the way for in vivo visualization of a wide range of biochemical processes and internal organs in animals. (Its use in humans is unlikely, as it would require gene therapy and the ethically dubious transplantation of bacterial genes into humans.)
“This is so important," comments David James, a cell biologist from Australia's Garvan Institute in Sydney, "because a lot of knowledge at the moment is confined to individual cells grown on a glass coverslip," leaving open the question of whether that knowledge "is transferable to an animal." The infrared version could also solve the problem of naturally occuring fluorescence from other biological molecules, which tend to glow at wavelengths similar to conventional fluorescent protein markers and thereby create a lot of “background noise," James says.

But even greater potential lies in harnessing the bacteriophytochrome's original function, namely, powering gene expression. It should be feasible, Tsien thinks, to put back in the signal-controlling properties of the phytochrome. Then it could be possible with animals to “switch on genes and control biochemistry" with light, he says.
For example, you want to explore the effects on mouse behavior of switching on a particular gene that controls some aspect of brain function, but, thankfully for the mouse, you do not want to open up its skull or stick a needle in its brain. "If the infrared fluorescent protein can be made to turn back into an infrared phytochrome, you could have the switch all ready and just waiting for enough infrared light," Tsien speculates. Because infrared light can penetrate the skull, it can reach the phytochrome and remotely switch the gene on, resulting in observable changes in the mouse's behavior.
It's the next evolutionary step for fluorescent proteins, remarks Tsien, who believes that phytochromes represent a class of proteins with enormous potential. If he's correct, then in the coming years, expect more scientists to see the (infrared) light.

By Bianca Nogrady

Parasitic Battles Can Involve Gene Transfer That Aids Evolution

Source:

http://www.sciencedaily.com/releases/2007/09/070905134534.htm

Science Daily — Scientists at MIT's Department of Civil and Environmental Engineering and the Technion Israel Institute of Technology have for the first time recorded the entire genomic expression of both a host bacterium and an infecting virus over the eight-hour course of infection.

The results of this research likely will encourage scientists in several fields to rethink their approach to the study of host-virus systems, which are believed to play a key evolutionary role by facilitating the transfer of genes between species.
Professors Debbie Lindell of the Technion and Sallie Chisholm of MIT and co-authors report in the Sept. 6 issue of Nature that their study of a system involving the marine bacteria, Prochlorococcus, leads them to speculate that viral infection may play a role in shaping the genetic repertoire of families of bacteria, even though individual infected bacteria die.
This could indicate that the meeting between a marine bacterial host and its virus may not be just a battle between two individuals, but an evolutionarily significant exchange that helps both species become more fit for life in the ocean environment.
"The current status of host-virus relations has been influenced by a rich history of interactions," said Lindell. "While we can't definitively pin down the sequence of past co-evolutionary events, our findings suggest a novel means through which the exchange of beneficial genes between host and virus have been triggered."
And, because the pattern of genomic expression in this host-virus system differed significantly from that in the more commonly studied system of intestinal bacteria such as E. coli and a virus called T7, the research will likely lead to increased appreciation for the need to study diverse types of marine bacteria, rather than relying on a single system as a broad model.
"We hope this work will encourage scientists to explore a wide range of host-pathogen systems and thus lead to a significant broadening of our understanding of the diversity of the host-pathogen interactions existing in nature," said Chisholm, one of the discoverers of Prochlo-rococcus in 1985. "More importantly, these studies will help us understand the role these interactions play in shaping microbial ecosystems."
Researchers have only in the past few decades begun discovering and studying ecologically relevant ocean bacteria, such as Prochlorococcus, which play a very important role in our lives. These single-celled photosynthetic bacteria use light energy to produce oxygen and organic carbon --supplying a significant portion of the oxygen we breathe--and forming the basis for the ocean food chain.
In previously studied host-virus systems, a virus hijacks the bacterial host cell and shuts down genome expression immediately, preventing the bacterium from conducting its own metabolic processes. The attacking virus redirects expression to its own genome and activates the genes beneficial for its activity, which is to replicate itself quickly at the cost of the host.
But uncharacteristically, in the system of Prochlorococcus and virus P-SSP7, an unprecedented 41 of the bacteria's 1,717 genes were upregulated. That is, the researchers detected increased quantities of the messenger RNA encoded by these genes in the cell during the infection process. The upregulation of so many host genes during infection is a phenomenon unseen before in the world of bacteriology.
Moreover, many of the host genes upregulated during infection are among those that are found in genomic islands in the host, variable regions that appear to be hot-spots for genetic exchange between bacterial hosts and viruses. In this case, some of the genes that have been transferred back and forth encode for proteins that affect the bacteria's ability to adapt to changes in environmental factors, such as nutrient deprivation and light stress. The scientists hypothesize that modifications made to the bacterial genes when they were in the virus led to new versions of the proteins that may provide the bacteria with an increased ability to withstand environmental changes. It is also possible that multiple copies of a gene provide some benefit.
Another unusual occurrence is that the viral genome contains genes transferred from bacterial hosts that encode energy-producing proteins, including photosynthesis genes that cyanobacteria need for metabolism and DNA replication. Although these genes are positioned far apart in the viral genome, they are transcribed at the same time during infection rather than in the usual left-to-right order. This leads the researchers to surmise that the virus is trying to keep its host alive longer so that the host continues to provide the energy needed for the virus's own DNA replication.
Lindell and Chisholm believe the most plausible scenario to explain the gene upregulation and gene trading is that the bacterium activates certain genes in response to infection as a means of self-protection. The virus has "learned" to use those genes to its own advantage and so incorporates them into its own genome. Later, when infecting another bacterium, the virus upregulates those genes itself to facilitate its own reproduction within the host bacterium. When a bacterium survives an infection, those viral modified genes are incorporated back into the bacterial DNA in genome islands, making that bacterium and its descendants more likely to survive in the harsh ocean environment.
"These viral parasites cooperate with their hosts during infection, providing proteins that probably function within host metabolic pathways, to squeeze every bit of energy out them before killing them off," said Lindell. "Yet on evolutionary scales, such host-pathogen interactions are influencing the evolution of gene content in both host and virus, which in turn is likely impacting their ability to colonize new niches."
Next steps in the research are to see if the host-like genes in the virus really do confer a fitness advantage to the virus and then to the host bacterium when transferred back.
Funding for this research came from the Department of Energy's GTL Program, the Gordon and Betty Moore Foundation, and the National Science Foundation.
Lindell performed the research as a postdoctoral associate in Chisholm's lab before joining the Technion faculty in the Department of Biology in October 2006. It builds on previous work in Chisholm's lab at MIT, including research by Lindell and co-author Matthew Sullivan, who in 2004 noted the presence of host genes in the viruses and their transfer back to the host, and by Maureen Coleman, who in 2006 found genomic islands in the host that had most likely come from viruses.
Other authors are MIT graduate students Gregory Kettler and Coleman; MIT postdoctoral associate Sullivan; Jacob Jaffe of the Broad Institute; Matthias Futschik and Ilka Axmann of Humboldt University; Trent Rector, Robert Steen and George Church of Harvard Medical School; and Wolfgang Hess of the University of Freiburg.
Note: This story has been adapted from a news release issued by Massachusetts Institute of Technology.

Fausto Intilla

www.oloscience.com