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)

Biotechnology: Engineered Moss Can Produce Human Proteins

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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.

Sexually Transmitted Infections: Transistors Used To Detect Fungus Candida Albicans

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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.

Battling Bacteria: Antimicrobial 'Hole Puncher' Mechanism Described

Source:

http://www.sciencedaily.com/releases/2007/09/070920111411.htm

Science Daily — In the battle against bacteria, researchers have scored a direct hit. They have made a discovery that could shorten the road to new and more potent antibiotics.

The rapid development of bacterial resistance to conventional antibiotics (such as penicillin or vancomycin) has become a major public health concern. Because resistant strains of bacteria can arise faster than drug companies can create antibiotics, understanding how these molecules function could help companies narrow their focus on potential antibiotics and bring them to market sooner.
As reported in a paper accepted for publication in the Journal of the American Chemical Society and posted on its Web site, researchers have now deciphered the molecular mechanism behind selective antimicrobial activity for a prototypical class of synthetic compounds.
The compounds, which mimic antimicrobial peptides found in biological immune systems, "function as molecular 'hole punchers,' punching holes in the membranes of bacteria," said Gerard Wong, a professor of materials science and engineering, physics, and bioengineering at the U. of I., and a corresponding author of the paper. "It's a little like shooting them with a hail of nanometer-sized bullets -- the perforated membranes leak and the bacteria consequently die."
The researchers also determined why some compounds punch holes only in bacteria, while others kill everything within reach, including human cells.
"We can use this as a kind of Rosetta stone to decipher the mechanisms of much more complicated antimicrobial molecules," said Wong, who also is a researcher at the university's Beckman Institute.
"If we can understand the design rules of how these molecules work, then we can assemble an arsenal of killer molecules with small variations, and no longer worry about antimicrobial resistance."
In a collaboration between the U. of I. and the University of Massachusetts at Amherst, the researchers first synthesized a prototypical class of antimicrobial compounds, then used synchrotron small-angle X-ray scattering to examine the structures made by the synthetic compounds and cell membranes.
Composed of variously shaped lipids, including some that resemble traffic cones, the cell membrane regulates the passage of materials in and out of the cell. In the presence of the researchers' antimicrobial molecules, the cone-shaped lipids gather together and curl into barrel-shaped openings that puncture the membrane. Cell death soon follows.
The effectiveness of an antimicrobial molecule depends on both the concentration of cone-shaped lipids in the cell membrane, and on the shape of the antimicrobial molecule, Wong said. For example, by slightly changing their synthetic molecule's length, the researchers created antimicrobial molecules that would either kill nothing, kill only bacteria, or kill everything within reach.
"By understanding how these molecules kill bacteria, and how we can prevent them from harming human cells, we can provide a more direct and rational route for the design of future antibiotics," Wong said.
This work was supported by the National Science Foundation, the National Institutes of Health and the Office of Naval Research.
Note: This story has been adapted from a news release issued by University of Illinois at Urbana-Champaign.

Fausto Intilla

www.oloscience.com

Spaceflight Can Change Bacteria Into More Infectious Pathogens

Source:

http://www.sciencedaily.com/releases/2007/09/070924151126.htm

Science Daily — Space flight has been shown to have a profound impact on human physiology as the body adapts to zero gravity environments.

Now, a new study led by researchers from the Biodesign Institute at Arizona State University has shown that the tiniest passengers flown in space -- microbes -- can be equally affected by space flight, making them more infectious pathogens.
"Space flight alters cellular and physiological responses in astronauts including the immune response," said Nickerson, who led a project aboard NASA's space shuttle mission STS-115 (September 2006) involving a large, international collaboration between NASA, ASU and 12 other research institutions. "However, relatively little was known about microbial changes to infectious disease risk in response to space flight."
Cheryl Nickerson and lead author James Wilson, both professors in ASU's School of Life Sciences, have performed the first study of its kind to investigate the effect of space flight on the genetic responses and disease-causing potential, or virulence, of Salmonella typhimurium, the main bacterial culprit of food poisoning.
Their results, published in the journal Proceedings of the National Academy of Sciences, reveal a key role for a master regulator, called Hfq, in triggering the genetic changes that show an increase in the virulence of Salmonella as a result of spaceflight. The results of these studies hold potential to greatly advance infectious disease research in space and here on Earth, and may lead to the development of new therapeutics to treat and prevent infectious disease.
To study the effects of space flight, Nickerson and colleagues sent specially contained tubes of Salmonella in an experimental payload aboard the Space Shuttle Atlantis. The tubes of bacteria were placed in triple containment for safety and posed no threat to the health and safety of the crew during or after the mission.
During the flight, astronaut Heidemarie M. Stefanyshyn-Piper activated growth of the bacteria in sealed hardware and 'fixed' the cultures after a day of growth to determine changes in gene and protein expression levels.
"The bacterial cultures were taken up into space and activated to grow in a separate compartment of the tubes called the growth chamber," said Nickerson. "The bacteria didn't have access to the growth chamber until Heide pushed down on a plunger which introduced the bacteria into the growth media. Then they were grown for 24 hours, and at the end of 24 hours, Heide pushed down on the plunger again, which either "fixed" the bacteria with chemicals that preserved the gene expression message, or else introduced fresh media to keep the bacteria growing to perform the virulence studies."
As a synchronous control experiment back on Earth, Nickerson's team grew an identical set of bacteria in the same type of tubes used for flight and incubated them in a special room at the NASA Kennedy Space Center called the orbital environmental simulator.
"This simulator is linked in real-time to the shuttle, and duplicates the exact temperature, humidity and growth conditions of the shuttle, with the exception that they are not flying in space," said Nickerson. "In addition, we were also linked via real-time telecommunications with the shuttle crew when they were activating and terminating our experiments in flight, and we did the exact same things at the same time to the ground samples that the astronauts did to the flight samples -- thus we had perfectly matched synchronous ground controls."
After the bacteria returned to Earth, the group performed the first global analysis of Salmonella to measure the effect of space flight on gene and protein expression and virulence. By measuring the gene and protein patterns, the researchers could hone in on the key molecular players necessary for virulence from among thousands of potential candidates.
"We chose to measure gene expression at the mRNA level since the technique to do this, called microarray analysis, is a highly advanced and convenient way to quantitatively measure the expression of every gene in a single experiment," said Wilson, who coordinated the team's molecular profiling efforts for the Nickerson lab, and played a central role in the performance of these experiments, including data analysis. "It is a very powerful technique that was very applicable to the spaceflight experiment. The isolation of mRNA poses particular challenges since it is very sensitive to degradation, but we designed the experiment using a fixative that preserved the mRNA very well."
After logging in millions of miles in space, the invaluable and well-traveled bacterial samples were analyzed back on Earth, and for the protein profiling studies, were taken to the University of Arizona's core proteomics facility at its Center for Toxicology to measure the level of every protein that had been subjected to space flight.
"Working with the UA group was great and we obtained very nice data that complemented the microarray analysis very well," said Wilson. "Keep in mind also that our body of mRNA and protein expression data from this experiment is precious, since comprehensive analysis of an organism's molecular genetic response to space flight is very rare."
Compared to bacteria that remained on earth, the space-traveling Salmonella had changed expression of 167 genes. After the flight, animal virulence studies showed that bacteria that were flown in space were almost three times as likely to cause disease when compared with control bacteria grown on the ground.
The study discovered that an important regulatory protein, Hfq, may be a key molecule responsible for the increased virulence due to space flight. "Hfq is a protein that binds to and regulates a number of regulatory RNAs, which in turn, control gene expression," said Nickerson. "Our studies suggest that there may be a role for these regulatory RNAs in the cellular response to the physical and mechanical forces found in spaceflight, which are relevant to conditions that cells encounter here on Earth during the normal course of their lifecycles."
These results have important implications for human health since Salmonella (and other gut-related bacterial pathogens) are a leading cause of food-borne illness and infectious disease, especially in the developing world. Nickerson's group further highlights Hfq as a potential therapeutic target, since no vaccine currently exists for Salmonella food-borne infections in humans. In addition, the space flight studies may shed new light on why Salmonella has become increasingly resistant to antibiotic treatment.
"We also studied the morphology of the bacteria in response to space flight, and the change that we observed is consistent with what looks like formation of a biofilm. The ground grown samples did not show biofilm formation. Biofilms are associated with increased pathogenicity because the immune system can't clear the bacteria effectively and antibiotics don't treat them effectively."
The group will embark on another space shuttle mission likely next year to further understand the risks and mechanisms of infectious disease agents during space flight and how microbes cause infections on Earth.
Note: This story has been adapted from a news release issued by Arizona State University.

Fausto Intilla

www.oloscience.com

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

First Diploid Human Genome Sequence Shows We're Surprisingly Different

Source:

http://www.sciencedaily.com/releases/2007/09/070904072204.htm

Science Daily — Researchers at the J. Craig Venter Institute (JCVI), along with collaborators at The Hospital for Sick Children (Sick Kids) in Toronto and the University of California, San Diego (UCSD), have published a genome sequence of an individual, J. Craig Venter, Ph.D., that covers both of his chromosome pairs (or diploid genome), one set being inherited from each of his parents.

Two other versions of the human genome currently exist—one published in 2001 by Dr. Venter and colleagues at Celera Genomics, and another at the same time by a consortium of government and foundation-funded researchers. These genomes were not of any single individual, but rather were a mosaic of DNA sequences from various donors. In the case of Celera it was a consensus assembly from five individuals, while the publicly-funded version was based on patching together sequences from over 100 anonymous human sources. Both versions greatly underestimated human genetic diversity.
This new genome (called “HuRef”) represents the first time a true diploid genome from one individual—Dr. Venter, has been published. The research is available in the open access public journal, PLoS Biology.
Researchers at the JCVI have been sequencing and analyzing this version of Dr. Venter’s genome since 2003. Building on reanalyzed data from Dr. Venter’s genome that constituted 60% of the previously published Celera genome, the team had the goal of constructing a definitive reference human genome based on one individual. Using whole genome shotgun sequencing and highly accurate DNA sequencing using Sanger-based chemistry, the team produced additional data which constitutes the final 32 million sequence reads.
From the combined data of more than 20 billion base pairs of DNA, the team was able to assemble the majority of Dr. Venter's genome. Since this genome assembly uniquely catalogues the contributions of each of the parental chromosomes, for the first time the amount of variation existing between the two could be determined. Surprisingly, a higher than expected amount of genetic variation was found to exist between the two human chromosomes.
“Each time we peer deeper into the human genome we uncover more valuable insight into our intricate biology,” said Dr. Venter. “With this publication we have shown that human to human variation is five to seven-fold greater than earlier estimates proving that we are in fact more unique at the individual genetic level than we thought.” He added, “It is clear however that we are still at the earliest stages of discovery about ourselves and only with additional sequencing of more individual genomes will we garner a full understanding of how our genes influence our lives.”
Within the human genome there are several different kinds of DNA variants. The most studied type is single nucleotide polymorphisms or SNPs, which are thought to be the essential variants implicated in human traits and disease susceptibility. A total of 4.1 million variants covering 12.3 million base pairs of DNA were uncovered in this analysis of Dr. Venter’s genome. Of the 4.1 million variations between chromosome sets, 3.2 million were SNPs. This is a typical number expected to be found in any other human genome, but there were at least 1.2 million variants that had not been described before. Surprisingly, nearly one million were different kinds of variants including: insertion/deletions (“indels”), copy number variants, block substitutions and segmental duplications.
While the SNP events outnumbered the non-SNP variants, the latter class involved a larger portion (74%) of the variable component of Dr. Venter's genome. This data suggests that human-to-human variation is much greater than the 0.1% difference found in earlier genome sequencing projects. The new estimate based on this data is that genomes between individuals have at least 0.5% total genetic variation (or are 99.5% similar) The researchers suggest that much more research needs to be done on these non-SNP variants to better understand their role in individual genomics.
According to Samuel Levy, Ph.D., lead author and senior scientist at JCVI, “The ability to use unbiased, high throughput, sequencing methods coupled with advance computational analytic methods, enables us to characterize more comprehensively the wide variety of individual genetic variation. This offers us an unprecedented opportunity to study the prevalence and impact of these DNA variants on traits and diseases in human populations.”
Another important feature that is made possible by having an individual, diploid genome is the ability to generate more informed haplotype assemblies. Haplotypes are groups of linked variations along the chromosomes. Other studies have generated many common haplotypes, however these are based on averages of large populations rather than individuals. Individual haplotypes enable scientists to study rare or 'private' variants that might explain and help predict traits and diseases in that particular person—allowing an individualized approach in genomic applications.
In the HuRef analysis, the team used the heterozygous portion of the 4.1 million variant set and new algorithms to build haplotype assemblies. These haplotype assemblies were typically an order of magnitude larger than what can be achieved by genotyping a single individual, with over half the genome contained in segments greater than 200,000 base pairs in length. The JCVI researchers expect this number to improve significantly as additional sequence coverage is added to HuRef using a variety of new sequencing technologies.
"In the future it will be possible to know the parental origin of DNA that is contributing, either alone or in combination, to various traits or disease," said co-author Stephen Scherer, Ph.D., senior scientist in Genetics and Genomic Biology at SickKids and professor of Molecular and Medical Genetics at the University of Toronto. "This study discovered that in an individual genome upwards of 44% of genes were variable in sequence, a number that geneticists have wondered about for 50 years. With this type of knowledge now in hand, the stage is set for an era of personalized medicine where genome sequence information becomes a critical reference to assist with health-related decisions", concluded Scherer.
Background
The publication of Dr. Venter’s genome represents the first publication of an individual’s genome and the first human genome publication since the first sequence and analysis of the human genome published in Science in 2001 by Dr. Venter and colleagues at Celera Genomics. The publicly funded genome project also published their version of the human genome at the same time in the journal Nature. At Celera there were five individuals whose genomes were used for that consensus human genome assembly. One of those individuals was Dr. Venter whose DNA constituted the majority of the DNA for that genome. The publicly funded genome project used DNA from a variety of individuals and is a composite version.
The new HuRef version of the human genome is the sequence and assembly of one individual in which the person’s two sets of chromosomes (one inherited from the mother and one set from the father) are represented. It is this kind of genome sequencing and analysis that will usher in the true era of individualized medicine.
Dr. Venter and the team at JCVI have long been proponents of finding new and improved methods for sequencing genomes since it is only through cost-effective and accurate sequencing methods that millions of human genomes can be sequenced. In September 2003, the JCVI announced a $500,000 prize for advances leading to the sequencing of one genome for $1,000 or less. The JCVI prize was eventually joined with the $10 million Archon X Prize for Genomics.
For the HuRef project, the team at JCVI used a more traditional method of sequencing—whole genome shotgun assembly which is built upon Sanger dideoxy sequencing. Then, Applied Biosystems 3730xl high-throughput DNA sequencing machines were employed since these methods still produce the longest and most accurate lengths of DNA. This project was designed to produce an accurate and more complete version of a single individual’s genome rather than producing a fast and potentially less expensive version. From the HuRef genome however the researchers believe that newer methods for sequencing can be used to enable more people to have their genome’s sequenced and analyzed. It is clear that the HuRef version is likely the last time that these more traditional methods of sequencing will be employed.
Funding for the research on the new HuRef diploid genome was from the J. Craig Venter Institute.
Note: This story has been adapted from a news release issued by J. Craig Venter Institute.

Fausto Intilla

www.oloscience.com