Up until now DNA sequencing has been done using many copies of each section of DNA. The older style sequencing machines do not have the sensitivity needed to measure the results from reading a single DNA strand. So many strands are used to boost the signal that comes from reading DNA letters. This use of many strands requires bigger and more expensive instruments with more reagents. Now Helicos Biosciences has demonstrated the sequencing of a genome using single DNA strand sequencing.
The latest revolution in the rapidly moving field of genome sequencing is upon us--single-molecule sequencing. Last week, Helicos Biosciences, a genomics company based in Cambridge, MA, published the first scientific paper to describe the sequencing of a whole genome using this approach. Experts say single-molecule sequencing, which reads the sequence of a single fragment of DNA, will ultimately simplify and speed the sequencing process, which could in turn enable the advance of personalized medicine. "The bottom line is, if at the end of day if you can just put a single strand of DNA onto a platform and sequence it directly, it's a huge advantage," says Elaine R. Mardis, co-director of the genome center at Washington University in St. Louis.
This is another step on the road to $1000 genome sequencing. Their machine is too expensive and this is not yet a step forward in cost. But if they can find ways to cut big costs out of their design it might turn into a useful way to lower the cost of DNA sequencing. Lots of other companies are chasing this same goal and costs are already falling quite rapidly without using single strand reading. But the development of cheaper ways to build small scale sequencers seems inevitable.
Thanks for the heads up Brock who draws attention to the fact that Helicos already has an even cheaper design than what they used in this paper.
A cheap small scale cell sorter for disease diagnosis might be 5 years away from clinical use.
CAMBRIDGE, Mass. — Capitalizing on a cell’s ability to roll along a surface, MIT researchers have developed a simple, inexpensive system to sort different kinds of cells — a process that could result in low-cost tools to test for diseases such as cancer, even in remote locations.
A cheap, small, and easy-to-operate device for detecting cancers would allow more frequent, cheaper, and earlier stage cancer detection. One can imagine such devices available in supermarkets or drug stores. A small blood sample could tell you pretty quickly whether to seek out a doctor. The resulting earlier stage diagnoses will substantially up cure rates.
Notice this result was published in Nano Letters. Advances in biotechnology are increasingly coming from working with very small scale materials and devices. Smaller devices can be orders of magnitude cheaper, faster, reliable, and sensitive.
Rohit Karnik, an MIT assistant professor of mechanical engineering and lead author of a paper on the new finding appearing this week in the journal Nano Letters, said the cell-sorting method was minimally invasive and highly innovative.
“It’s a new discovery,” Karnik said. “Nobody has ever done anything like this before.”
The method relies on the way cells sometimes interact with a surface (such as the wall of a blood vessel) by rolling along it. In the new device, a surface is coated with lines of a material that interacts with the cells, making it seem sticky to specific types of cells. The sticky lines are oriented diagonally to the flow of cell-containing fluid passing over the surface, so as certain kinds of cells respond to the coating they are nudged to one side, allowing them to be separated out.
The device will take 2 years to become usable as a lab research tool and 5 years before use in clinical tests.
Now that the basic principle has been harnessed in the lab, Karnik estimates it may take up to two years to develop into a standard device that could be used for laboratory research purposes. Because of the need for extensive testing, development of a device for clinical use could take about five years, he estimates.
At least the upper class can now get their full genomes sequenced.
CAMBRIDGE, Massachusetts — Nov. 29, 2007 — Knome, a personal genomics company, today announced the launch of the first commercial whole-genome sequencing and analysis service for individuals.
Knome does genetic sequencing and not just genetic testing. The latter usually involves testing a number of predetermined locations in genes where genes are known to vary between individuals and groups. The former, what Knome is offering, involves the much harder task of going through and reading every letter in your genome. When done well full genetic sequencing can identify rarer single letter differences that the cheaper genetic testing techniques won't identify. Also, full sequencing can measure what are called copy variations where the number of copies of each gene gets measured.
Whole-genome sequencing decodes the 6 billion bits of information that make up an individual’s genome. Unlike existing genome scanning or “SNP chip” technologies that provide useful but limited information on approximately 20 conditions, whole-genome sequencing allows for the analysis of up to 2,000 common and rare conditions, and over 20,000 genes – numbers that are rapidly growing.
“Whole-genome sequencing is the endgame,” according to Mr. Conde. “It will enable us to look at nearly 100% of your genetic code compared to the less than 0.02% currently available on SNP chips. This is the approach that most fully reveals what our genomes can tell us about ourselves.”
Pricing for Knome’s service will start at $350,000, including whole-genome sequencing and a comprehensive analysis from a team of leading geneticists, clinicians and bioinformaticians. This team will also provide continued support and counseling.
But if you don't have a spare $350k but can scrape up a thousand or two you can still get fairly cheap genetic testing of some large subset of known genetic differences.
Two rival firms have just unveiled services that will allow people to scrutinize their own genomes for $1,000.
The first was deCODE genetics, an Icelandic firm that has already developed genetic tests for several diseases. On Nov. 16 it announced an Internet-based service, called deCODEme.
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Then, on Nov. 19, 23andMe, a start-up based in California's Silicon Valley, announced a similar service.
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Navigenics, another Californian firm, says it will unveil a more medically oriented service, priced at around $2,500, in January.
The X Prize Foundation has an Archon prize to encourage the development of faster full genome sequencing technology.
If the X Prize Foundation has its way, it will soon be possible to sequence a genome in hours. To make that happen, the foundation, perhaps better known for its spaceflight prize, is offering the Archon genomics prize. This will be worth $10m to the first team able to sequence 100 human genomes accurately in ten days or less. (The prize is sponsored by Stewart Blusson, a philanthropist who is president of Archon Minerals, a mining company based in Vancouver.)
Faster sequencing is usually cheaper sequencing. So the effect of this prize is to create incentives to develop cheaper DNA sequencing technologies.
Expect to see huge price drops for DNA sequencing and testing services. Also, as the underlying technologies become cheaper the resulting flood of genetic information will allow scientists to discover orders of magnitude more information about what each genetic difference means. So genetic test results will tell us far more useful information than the results can tell us do today.
I expect the biggest impact of genetic testing to occur with mating practices. People will use genetic testing to select suitable partners (or donors) for reproduction. Also, they will use gene testing to select among embryos with in vitro fertilization. They will choose among embryos based on what genetic test results indicate about looks, intelligence, personality qualities, athletic abilities, health risks, and other qualities. These genetic testing companies are going to usher in huge shifts in the directions of human evolution.
Faster and cheaper continues to be the story for genetic sequencing technology.
BRANFORD, Conn., Sept. 27, 2007 – 454 Life Sciences, a Roche company, in collaboration with Yale University researchers today announced that they have developed a method, using the company’s Genome Sequencer system, to identify significant human genetic variability with an unprecedented level of detail. The new method enables researchers to analyze genome-wide structural variations (SV), the gross changes to the genetic code much faster and economically than existing techniques. The study, entitled "Paired-End Mapping Reveals Extensive Genomic Structural Variation in Humans," appears online (ahead of print) today in the journal Science.
Structural variations in chromosomes are things like variable number of repeats of whole genes. We do not all have equal numbers of copies of each gene. People who have more copies of a gene can get more proteins and other pieces made from their greater number of copies. The ability to detect more structural variations and to do so more cheaply and rapidly will speed up the identification and characterization of structural variations in the genome.
Previous studies of human genomic variation tended to look at changes called single nucleotide polymorphism, variations that involve just one nucleotide, commonly referred to as SNP. However, the study published today suggests that structural variation is responsible for a larger number of differences between the genomes of two individuals than SNPs. Furthermore, structural variation may have notable physical effects on an individual. The role that SV plays in human variability has not been well understood because of cost-prohibitive and imprecise technology used in previous research. The novel approach described today in Science, called Paired End Mapping (PEM), used 454 Sequencing to comprehensively study SV at an unmatched level of precision, detecting most of the structural variation in the human genome.
“454 Sequencing enabled us to efficiently identify over 1000 structural variations in two individuals. Our study demonstrates that a large number of SVs are present in the human population and that SV plays a greater role in genetic diversity than SNP,” explained Michael Snyder, PhD., senior author and Lewis B. Cullman Professor of Molecular, Cellular and Developmental Biology and Professor of Molecular Biophysics and Biochemistry; Director of the Yale Center for Genomics and Proteomics. “The widespread occurrence of structural variation and the observation that many genes are affected, suggests that SV is likely to be a major form of human variation. It will be essential to incorporate SV detection in human genome sequencing projects.”
Advances in technologies for genetic sequencing and genetic testing are more important than any of the discoveries that these advances enable. The discoveries become increasingly easier to make as the genetic sequencing equipment becomes increasingly powerful. As the sequencing devices become more powerful we are going to reach a point where the rate of discovery per day will exceed the rate of discovery of the previous decade.
The Cheap DNA sequencing technology we will have 10 to 20 years hence will enable us each to have detailed profiles of all of our individual genetic variations. The low cost and exhaustive identification of genetic differences between humans will allow scientists to do massive comparisons between millions of people of genetic differences, health histories, personalities, cognitive abilities, and other characteristics. Those comparisons will allow us to learn the significance of most genetic differences.
Knowledge about the meaning of genetic differences will lead to widespread use of sperm, egg, and embryo screening when starting pregnancies. People will want to choose which genes they pass on to their offspring. The ability to knowledgeably make such choices will accelerate the rate of human evolution by orders of magnitude. Humans born 50 years from now (assuming the Singularity does not put a stop to human reproduction) will differ greatly from humans today. Future humans (transhumans?) will be far smarter, mentally healthier, better looking, healthier, stronger, and less susceptible to death from accidents or suicide.
Dr Peter Mazzone and colleagues at the Cleveland Clinic have developed a small device that can detect cancer in breath. Cheap miniature cancer detectors will allow more frequent testing and earlier detection.
A breath test can successfully pick up lung cancer with "moderate accuracy" even in the early stages, reveals research published ahead of print in Thorax.
It could revolutionise the way cancer is detected and potentially save lives, say the authors.
The test comprises a chemical colour sensor, which detects tiny changes in the unique chemical signature of the breath of people with lung cancer.
Metabolic changes in lung cancer cells cause changes in the production and processing of volatile organic compounds, which are then breathed out
This sensor detected 3 out of 4 cases in people known to have lung cancer.
The test device is the size of a large coin.
The concept of a "gas fingerprint" for lung cancer is not new, but the kit is.
The sensor, which is slightly bigger than a quarter dollar or a two pound coin, is inexpensive and easy to use.
The small size argues for an eventual low manufacturing cost. But see the picture the previous. It looks like it gets used once. In the longer run microfluidic devices and other silicon-based miniature devices will allow continuous monitoring with electronic connections to a personal health computer. Just lying in bed your bedstand will contain sensors that'll detect a large assortment of diseases while you sleep.
Diagnosis by doctors will become the exception rather than the rule as miniature sensors embedded in bathrooms, bedrooms, cars, workplaces, and in our bodies detect and diagnose diseases automatically. Early diagnosis will enable earlier treatments and better outcomes. Also, the automated nature of diagnosis will cut the cost of diagnosis by reducing the need for human labor.
Will the net result of early diagnosis cut or increases the percentage of the time people spend knowing they are sick? It depends on how much early diagnosis enables effective treatments and cures. If early diagnosis just lets you know further in advance that you have a fatal disease then people will spend more time pondering their coming death. But for cancer I'm hoping early diagnosis will increase cure rates as more cancers get caught and removed before metastasis.
Want an example of yet another orders of magnitude improvement in what bioscientists and biotechnologists can do? Blood tests will be able to detect diseases at much earlier stages when the FACTT assay reaches the market.
(Philadelphia, PA) - Researchers at the University of Pennsylvania School of Medicine have developed a paradigm-shifting method for detecting small amounts of proteins in the blood. Applications of this method will make discerning low-abundance molecules associated with cancers (such as breast cancer), Alzheimer's disease, prion diseases, and possibly psychiatric diseases relatively easy and more accurate compared with the current methodology, including the widely used ELISA (enzyme-linked immunoadsorbent assay).
ELISA is a common immune-system-based assay that uses enzymes linked to an antibody or antigen as a marker for picking out specific proteins. For example, it is used as a diagnostic test to determine exposure to infectious agents, such as HIV, by identifying antibodies present in a blood sample.
The sensitivity of detecting molecules by the new method, called FACTT, short for Florescent Amplification Catalyzed by T7-polymerase Technique, is five orders of magnitude (100,000 times) greater than that of ELISA, the Penn researchers found.
Senior author Mark I. Greene MD, PhD, the John Eckman Professor of Medical Science, Hongtao Zhang, PhD research specialist; Xin Cheng, PhD, research investigator, and Mark Richter, a research technician in Greene's lab, report their findings in the advanced online publication of Nature Medicine.
"The current ELISA tests can only detect proteins when they are in high abundance," says Zhang. "But the problem is that many of the functional proteins - those that have a role in determining your health - exist in very low amounts until diseases are apparent and cannot be detected or measured at early stages of medical pathology. It was important to develop a technique that can detect these rare molecules to detect abnormalities at an early stage."
One problem that'll arise as a result of more sensitive blood and saliva assays is finding very early stage cancers. Okay, you'll know you have cancer. But it is incredibly small and your body is big. How to find it? As things stand now in spite of advanced CAT scanners and MRI machines surgeons sometimes have to cut into people to poke around to find something oncologists can't localize even at an advanced state of illness.
Imagine a cancer about the size of a needle tip. You have lots of little cancers in your body that are stuck at a small size because they haven't mutated the ability to grow blood vessels (they do not yet secrete angiogenesis factors). How to find just the right cancer to remove that has just crossed that threshold? Seems hard to me.
An article in The Scientist surveys the growing use of genetic testing target drug use and dosages based on genetic profiles.
Richard Hockett, medical fellow, department of diagnostic and experimental medicine at Eli Lilly, says as many as 180 genes could affect drug metabolism, including metabolic enzymes, transporters, and other proteins. By his count those genes contain at least 2,000 different variants, and a truly comprehensive metabolic genotyping panel, he says, would have to test for all of them. In March, Eli Lilly and ParAllele BioScience of South San Francisco announced the development of just such a chip. Starting this summer, the MegAllele D-MET chip will be used to screen patients in Lilly's Phase I trials. ParAllele plans to file for FDA approval of the chip later this year.
My guess is that the 180 gene count is too low a figure. As our knowledge of the human genome increases many more genes with variants which affect drug metabolism will be found.
Eli Lilly's use of genetic testing of drugs entering phase I trials will not produce useful information for doctors and patients right away. Drugs spend years going through phases I, II, and III before being approved for sale. Testing started at the level of phase I trials means that only new drugs hitting the market 5 or 10 years from now will have the clinical trials data on their genetic profiles. The existing drugs already on the market will not have as much genetic profiling information available.
Worse yet, drug companies lack economic incentives to run expensive clinical trials for existing drugs that are off-patent or nearing patent expiration. This lack of economic incentive to do research on older drugs also translates into a lack of clinical trials to test old drugs for safety problems that have surfaced in similar newer drugs. For example, experts at the FDA suspect some of the older non-steroidal anti-inflammatory drugs (NSAIDs) might pose similar heart health risks as those found in Cox2 inhihitors such as Vioxx.
The National Institutes of Health has a program called the Pharmacogenetics Research Network (PGRN) which collects information about differences in drug reactions which are a product of genetic differences. One of the researchers involved in the PRGN argues that all NIH trials should have tissue samples collected on all trial participants for later genetic testing to compare clinical outcomes and adverse reactions against DNA sequences.
"We think every publicly funded clinical trial should contain pharmacogenetics," says Mary Relling, a PGRN member who chairs the department of pharmaceutical sciences at St. Jude Children's Research Hospital, Memphis, Tenn. "We should be getting DNA and appropriate consent from patients on every trial that's supported by tax dollars," says Relling. "Otherwise, 20 years from now we will have made very little progress."
I think Relling is absolutely correct and would even expand on this to argue that big expensive social science research studies should have DNA samples collected on their participants for testing years from now when DNA testing costs have fallen by orders of magnitude.
Wider spread adoption of electronic medical records systems will eventually reduce the costs of comparing patient populations for drug reactions and also for differences in health outcomes due to genetic differences. However, DNA sequencing and DNA testing may well become cheap years before electronic medical records systems become widespread and mature. Therefore the collection of DNA samples from clinical trials participants should be treated as an urgent priority that has the potential to pay rich dividends when DNA testing becomes very cheap.
An electronic sniffing sensor can detect lung cancer.
The electronic nose, a device long used for safety and quality control in the food, wine and perfume industries, also can be used to detect early evidence of lung cancer, according to research conducted at The Cleveland Clinic.
Known as the Cyranose, the electronic nose is a hand-sized device that uses biosensor technology to produce a “smellprint” of the volatile organic compounds that comprise human breath and other scents.
Led by Serpil Erzurum, M.D., chairman of the Department of Pathobiology at the Cleveland Clinic Lerner Research Institute, researchers speculated the electronic nose could be used to detect and distinguish between lung diseases, particularly lung cancer. Testing their theory, they found the exhaled breath of lung cancer patients had specific characteristics that, in fact, could be detected with the device. Their findings will be published in the American Journal of Respiratory Medicine later this spring.
“Our work indicates that the electronic nose can be used as a non-invasive tool for the early diagnosis of lung cancer and to monitor the effectiveness of treatment on lung cancer patients,” Dr. Erzurum said. “Use of the electronic nose could enable physicians to determine the appropriate course for a lung cancer patient’s treatment at an earlier stage, rather than after the cancer has spread to other parts of the body and is more difficult to treat. The small, portable nature of the electronic nose also makes it easy to use in physician offices and outpatient settings.”
Breath of lung cancer patients is detectably different than breath of healthy patients.
In their study, Cleveland Clinic researchers examined the exhaled breath of 14 lung cancer patients and 45 healthy patients. The electronic nose was programmed to detect certain characteristics in breath and used algorithms to create patterns viewable on a computer screen. Researchers found the pattern characterizing the breath of lung cancer patients was distinctly different from that of healthy patients and of people with other lung diseases.
Breath is not the only promising target for the development of fast and less invasive methods for detecting diseases. Back in December 2004 David Wong and colleagues at UCLA found human messenger RNA (mRNA which is made from DNA to be translated into proteins) in saliva. Wong has been able to show that salivary mRNA can be used to detect some types of cancer.
The UCLA team collected saliva and blood from 32 patients with primary oral squamous cell carcinoma and 40 breast cancer patients, and matched each with saliva and blood from otherwise normal subjects. New techniques were developed to halt RNA degradation so the scientists could recover as much mRNA as possible for their samples. In all, the new techniques allowed the scientists to harvest up to 10,000 types of human mRNA from saliva, setting up a comparison test between cancer patients and the normal subjects based on analysis of their genetic "profiles."
"Both serum and saliva exhibited unique genetic profiles," said Wong. "The risk model yielded a predictive power of 95 percent by using only the salivary transcriptome samples and 88 percent by using only serum transcriptome samples for oral squamous cell carcinomas," said Wong. "For oral cancer, salivary transcriptome has a slight edge of that of serum transcriptome analysis."
Messenger RNA can be tested for using chips designed to bind with minute quantities of different mRNA sequences. A single chip can be made to test for the presence of many different mRNA sequences in parallel. Results from such tests will form patterns akin to fingerprints with different diseases having different patterns of mRNAs present.
Wong is director of the UCLA Human Salivary Proteome Project which has as its goal to identify and characterize all the proteins in saliva. But Wong is also working on development of tests for salivary mRNA to detect pathogens, cancers, and other diseases. My guess: mRNA patterns in saliva will become far more important than protein patterns because the mRNA patterns will be much easier to test for.
Watch for a gradual partial replacement of blood tests by breath and saliva tests that will be performed in doctors' offices while you wait. Then watch for the introduction of home saliva and breath tests that can be done cheaply and more often. Expect the mRNA saliva tests to hit the market in this decade. Ditto for breath tests.
Why get a CAT scan when you can get a HUTT scan instead?
Researchers at the USC Viterbi School of Engineering have successfully demonstrated a novel “High-resolution Ultrasonic Transmission Tomography” (HUTT) system that offers 3-D images of soft tissue that are superior to those produced by existing commercial X-ray, ultrasound or MRI units.
Vasilis Marmarelis, professor of biomedical engineering in the USC Viterbi School, presented HUTT images of animal organ tissue at the 28th International Acoustical Imaging Symposium recently held in San Diego.
According to Marmarelis, HUTT offers nearly order-of-magnitude improvement in resolution of structures in soft tissue (i.e., 0.4 mm, compared to 2 mm for the best alternatives).
HUTT supplies high resolution images while simultaneously avoiding the use of ionizing radiation
• Robust algorithmic tools enable HUTT to differentiate separate types of tissue based on their distinctive “frequency-dependent attenuation” profiles that should allow clinicians to distinguish malignant lesions from benign growths in a non-invasive and highly reliable manner.
• In addition to improved resolution, the system can locate tissue features with extreme precision in an objective, fixed-coordinate 3-D grid, crucial for guiding surgical procedures.
• Scans can be performed in a matter of a few minutes and because they are ultrasonic, they do not use potentially harmful ionizing radiation.
• The system requires a minimum of special pre-scan procedures and appears likely, in clinical use, to be more comfortable for patients than alternatives.
While conventional ultrasound works by recording echoes that bounce back from tissues HUTT works by recording the sound that passes all the way through tissue. Since 2000 times more sound passes through than echoes the amount of sound signal that can be recorded using HUTT is much greater.
HUTT also allows very selective scanning for details of specific tissue types.
The technology could also be used to isolate one type of tissue, allowing, for example, all the blood vessel structures to be displayed alone and studied.
Medical imaging technology keeps getting better.
Sophisticated brain imaging techniques show that when storing and accessing memories, individuals who carry a genetic variant linked to a heightened risk of Alzheimer Disease "activate" brain functions differently than do non-carriers, even when no outward signs of disease are present, according to a study reported in the November-December issue of the American Journal of Geriatric Psychiatry (AJGP).
The study by investigators at Columbia University is one of two in the current issue of the journal offering new evidence that brain imaging technology known as positron-emission tomography or PET scans has the potential to play an increasingly prominent role in the study and treatment of Alzheimer Disease (AD).
The second report, from researchers at Baycrest Centre for Geriatric Care, the Centre for Addiction and Mental Health PET Center and the University of Toronto, describes an advance in using PET scans to detect the presence of brain deposits known as beta-amyloid plaques, which are believed to be a telltale sign of the disease.
While it is interesting to know that there is a difference in brain function of elderly people who have a genetic variant for Alzheimer's it is the second report that is especially interesting. The ability to detect beta amyloid plaque build-up before Alzheimer's Disease symptoms become noticeable has a couple of uses. First of all, the ability to study the progression of plaque build-up will make it easier to measure the effectiveness of intervention therapies aimed at removing or stopping the build-up of plaque.
Scarmeas said the above conundrum could be solved if the PET scans could be paired with tests that would offer some biological evidence of the disease. That's why he's intrigued by another study in this same AJGP issue in which a team headed by Nicolaas Verhoeff, M.D., Ph.D., from the Kunin-Lunenfeld Applied Research Unit at Baycrest Centre for Geriatric Care, the PET Centre at the Centre for Addiction and Mental health, and the University of Toronto, reports that it successfully used a novel PET scan technique to detect beta-amyloid plaques, one of the brain lesions linked to AD. Thus, now we may be able to explore which are the earliest changes that could be detected in AD: changed brain functions during "active" memory processing or deposition of brain chemicals linked to AD.
As it now stands, doctors have no laboratory tests they can use for confirming the existence of AD or for monitoring its progression. Diagnosis is confirmed only after a relatively clear set of symptoms appears. However, autopsies of AD victims have revealed abnormally high levels of what are known as beta-amyloid plaques. Some scientists believe beta-amyloid plays a central role in AD-related brain damage. They also suspect that abnormally high levels of the substance begin accumulating in the brains of AD patients long before symptoms appear. But they have lacked a reliable test for detecting amyloid build-up.
Verhoeff and his colleagues recruited five AD patients and six healthy volunteers. All were injected with a new compound designed to cross from the bloodstream into the brain, attach itself to amyloid deposits and then send out harmless radioactive signals that can be detected with a PET scan. This new compound, which had been originally developed at the University of Pennsylvania in collaboration with the Centre for Addiction and Mental Health PET Centre in Toronto, was compared to another compound that had been developed independently at the University of Pittsburgh. What the study found is preliminary evidence that the new compound or "tracer" may also be effective at allowing the researchers to use PET scans to discriminate between amyloid levels one would expect to see in AD versus non-AD patients.
Currently if a doctor could tell you that you have beta amyloid plaque build-up there is probably not much you could do in response except perhaps to follow any dietary advice gleaned from population studies of Alzheimer's Disease risk. However, eventually effective treatments will be developed to reverse beta amyloid plaque build-up. If the treatments have no side-effects and are easy to deliver then everyone may decide to get treated periodically as they get older. However, if the treatments are difficult to administer (e.g. injection of antibodies into the brain) or carry some risk (e.g, a vaccine that occasionally causes brain inflammation) it would be better to get a PET scan to test for the presence of plaque build-up. Then only those with plaque build-up could get treated.
In the short to medium term a PET scan technique that can detect beta amyloid plaque build-up is going accelerate scientific research. For scientists trying to understand AD progression and testing methods of intervention against it the ability to measure plaque levels will be quite valuable. Every advance in the ability to watch internal biological processes whether normal processes or disease processes, makes it easier to understand and manipulate those processes.
A fairly small device is able to quickly and accurately diagnose pneumonia and may be able to diagnose a large number of other diseases including cancers. (same article here and here)
(Philadelphia, PA) – Researchers at the University of Pennsylvania School of Medicine have recently completed three studies – the most comprehensive and largest to date – that demonstrate the effectiveness of an electronic nose device for diagnosing common respiratory infections, specifically pneumonia and sinusitis. Doctors hope that the device – called the Cyranose 320, or e-nose – will provide a faster, more cost-effective and easier-to-use method for accurately diagnosing pneumonia and, as a result, help reduce over-prescription of antibiotics. Their initial findings will be presented at the combined annual meetings of otorhinolaryngology (ear, nose and throat) experts – the Triologic Society and the American Broncho-Esophagological Association – on April 30th, 2004, in Phoenix, Arizona.
“Pneumonia is a serious bacterial infection that can cause serious injury or even death; indeed, it remains a leading cause of death in intensive care units (ICUs),” said lead author of the first study, C. William Hanson III, MD, Professor of Anesthesia and board-certified expert in critical care medicine. “Treating this illness is complicated because there are many kinds of pneumonia, and it can be commonly misdiagnosed in the ICU and confused with other diseases which cannot be treated using antibiotics. This is a leading cause of the overuse – through over-prescription – of antibiotics for false cases of pneumonia.”
The first two studies looked at pneumonia cases among patients who are on ventilators in the surgical intensive care unit (SICU). Here, diagnosis is made difficult by the patients’ limited ability to move, and they are vulnerable to infections from other compounding injuries. In the first study, researchers found that the e-nose effectively diagnosed 92 percent of pneumonia cases among 25 patients, as confirmed by computed tomography (CT) scans of the lungs. It successfully distinguished 13 positive cases from 12 other patients who did not have pneumonia. Similarly, in the second study, researchers found the e-nose effective in providing accurate diagnoses of pneumonia in 31 of 44 SICU patients (70 percent).
One quarter of ventilated SICU patients develop pneumonia – a serious complication that can threaten the patient’s life, requires immediate treatment with antibiotics, and also increases their hospital stay three-fold, with average additional hospital costs of $11,000 per patient.
The third study looked at sinusitis, the most common diagnosis from respiratory complaints by patients in outpatient clinics. The e-nose was effective at diagnosing 82 percent of sinusitis cases among 22 patients, one half infected and the other half not so.
All bacteria, as living organisms, produce unique arrays or mixtures of exhaled gases. The e-nose works by comparing “smellprints” from a patient’s breath sample to standardized, or known, readings stored on a computer chip. These “smellprints” are created from both electro-chemical and mathematical analysis of exhaled gases contained in a breath sample. Upon analysis, identifiable patterns emerge, and a patient’s “smellprint” can tell a physician whether or not bacteria are present and, if so, what kind. This can aid not just in the accuracy of diagnosis, but can also help physicians select the most effective antibiotic for treatment.
“The results confirm that exhaled breath can be analyzed for pneumonia and sinusitis using a commercially available e-nose device,” said lead investigator for the sinusitis study and co-investigator for the pneumonia studies, Erica Thaler, MD, an Associate Professor of Otorhinolaryngology: Head and Neck Surgery at Penn. “There is the potential with this device to radically change and improve the way we diagnose and treat both conditions – for which there is no gold-standard test. And, given that we can apply this sensory analysis to the detection of pneumonia and sinusitis, then, hopefully, it can be applied to common bacterial infections of the upper respiratory tract.”
The e-nose is also being studied for its possible use in diagnosing many other illnesses, including: lung cancer, kidney disease and cirrhosis of the liver, otitis media (middle ear infections) in children, or even detection of chemicals and biological agents. Manufactured by Smiths Detection of Pasadena, CA, the machines cost approximately $8,000 USD, and still require approval from the federal Food and Drug Administration before they can be widely used. Breath samples are taken with a hand-held sensor – about the size of child’s video game player – connected to a standard oxygen mask with cup, as the patient breathes normally. Readings are displayed by connecting the device to a laptop computer.
"Flexibility and ease-of-use are the greatest advantages of the e-nose," said lead researcher Neil Hockstein, MD, a clinical instructor and Penn otorhinolaryngologist. "They are miniaturized devices, provide quick results, are relatively inexpensive, non-invasive, safe for patients and they could be used in a doctor's office - or, potentially, even at home."
One big advantage of devices that can rapidly diagnose infectious diseases is that they can cut antibiotic overuse and therefore reduce the rate at which pathogens develop resistance to antibiotics. Another advantage is the more rapid diagnosis and treatment of infections. More generally the use of devices of this type will accelerate the speed of diagnosis of diseases of all types.
In the longer run automated diagnosis devices are going to drop in cost by orders of magnitude. The sensor systems are mostly electronics and the electronics will drop in price as the sensors become more powerful and automated. Check out the size of the Cyranose 320 e-nose. I bet the vast bulk of their costs are development costs (especially regulatory approval but clinical testing is expensive regardless of regulatory requirements) and that their manufacturing costs are a small fraction of product price. So in the long run this device and future devices like it will become much cheaper.
Many diagnostic devices will become so easy to use and widely available and cheap that it will become very common to do self-diagnosis for a large assortment of diseases. This will cause a radical change in how medical care is delivered. Most people will test themselves at home using cheap home diagnostic sensor kits and show up at a doctor's office already diagnosed. Also, the increasing power of over-the-counter (OTC) drugs will reduce the need to go to a doctor's office to seek treatment in the first place. Even when a doctor does choose the course of treatment in many cases there will be no need for an office visit as the diagnostic information will be passed to the doctor's computer for review with the doctor then electronically passing the chosen treatment information to a pharmacy.
Further in the future even the trip to the pharmacy will become unnecessary for some treatments. Cheap microfluidic devices available in many homes will be able to synthesis some drugs and some types of gene therapy. Just as an upscale home is not complete without a high tech home entertainment center and an assortment of other home appliances it will become common to have home medical appliances for testing, treatment synthesis, and treatment delivery.
Expect to see diagnostic devices embedded into houses. Chemical testers for toilets are an obvious possibility. Expect parents to eagerly buy such testers when the testers get the ability to instantly spot junior's illicit drug use. Also, sensors embedded in bathtub drains and kitchen sinks could check for patterns of secretions which indicate disease. Sensors at the head of a bed and in couches and chairs could check exhaled gasses for signs of disease.
Diagnostic and treatment appliances embedded in the human body will also become common. A person will be able to wear a watch that sounds an alarm if internal body sensors report something amiss. A watch or some other worn device could even make a cellular phone call to a medical facility with GPS information to warn of an especially urgent medical condition.
Advances in basic instrumentation and in techniques for characterizing the structure of biological molecules enable many other advances to be made that produce results that are more directly usable in medicine and in other fields. While people who produce medical treatments tend to get most of the glory the scientists who make advances in instrumentation and in biological assays create the tools that make possible the many advances which are of more direct benefit.
With this thought in mind you might therefore be mildly excited to learn that some researchers at UC San Diego have developed a new method to determine the structure of proteins whose structures could not be determined by existing methods.
An innovative method that allows increased success and speed of protein crystallization – a crucial step in the laborious, often unsuccessful process to determine the 3-dimensional structure unique to each of the body’s tens of thousands of folded proteins – has been developed by researchers at the University of California, San Diego (UCSD) School of Medicine and verified in tests with the Joint Center for Structural Genomics (JCSG) at The Scripps Research Institute (TSRI) and the Genomics Institute of the Novartis Research Foundation in La Jolla, California.
Described in the Jan. 20, 2004 issue of the journal Proceedings of the National Academy of Sciences (PNAS)*, the method, which employs a UCSD invention called enhanced amide hydrogen/deuterium-exchange mass spectrometry, or DXMS, rapidly identifies small regions within proteins that interfere with their ability to crystallize, or form a compact, folded state. The investigators demonstrate that once these regions are removed by what amounts to “molecular surgery”, the proteins then crystallize very well.
“Although the sequencing of the human genome gave us the code for genes that are the recipes for proteins, we need to see and understand the folded shape taken by proteins to determine how they work as the fundamental components of all living cells,” said UCSD’s Virgil Woods, Jr., M.D., the inventor of DXMS, senior author of the PNAS article and an associate professor of medicine. “Definition of a protein folded structure is of great use in the discovery of disease-targeting drugs. Furthermore, when we’re able to identify incorrectly folded proteins in disease states, such as Alzheimer’s, cystic fibrosis and many cancers, we may then be able to design drugs that encourage proper folding or block the misshapen protein.”
The 3-dimensional structure of a protein is a useful piece of knowledge for drug developers. Detailed knowledge of a protein structure is a useful starting point to suggest what types of chemical compounds to build to test against a protein for binding affinity. Better protein structure determination tools will therefore speed drug development.
X-rays are used to gather information used to discover 3-dimensional structures of proteins. The problem is that x-ray crystallography requires that a protein first be induced to form crystalline structures and not all proteins can be made to do so.
Unfortunately, many proteins do not naturally form a single, compact state in solution and hence, they are often highly resistant to crystallization, which is required for the x-ray crystallographic process that determines their shape. X-ray crystallography works by bombarding x-rays off crystals of a protein that contain a 3-dimensional lattice, or array of the individual protein or of a protein complex. The scattered, or diffracted pattern of the x-ray beams is used to calculate a s-dimensional structure of the protein.
Out of 24 proteins used to test this technique, including 18 which existing techniques had failed to crystallize, the researchers were able to determine the structures of the 6 easy ones and 15 of the hard ones. Then with some genetic manipulation the researchers were able to determine the structures of 2 of the 3 remaining proteins.
Of the 24 proteins provided by JCSG for DXMS analysis, six had already been crystallized and their structures determined. The results provided by DXMS matched the information on those six proteins, correctly identifying even small unfolded regions. The remaining 18 proteins provided by JCSG had all failed extensive prior crystallization attempts. In the new experiments, DXMS technology rapidly determined the unstructured regions in 15 of these proteins.
Two of the previously failed proteins were then subjected to “molecular surgery”, in which the DXMS-identified unstructured regions were selectively removed from the DNA that coded for the proteins. DXMS study of the resulting modified proteins demonstrated that the surgery had removed the unstructured regions without otherwise altering the shape of the originally well-folded regions. Each of the two resulting DXMS stabilized forms of the proteins were then found to crystallize well, while the original, unmodified proteins again failed to crystallize.
JCSG investigators were subsequently able to determine the 3-dimensional structures of these two proteins by x-ray analysis of the crystals resulting from DXMS-guided stabilization. One of the proteins that was successfully crystallized was found to have a unique shape or “fold”, not previously seen in proteins.
So now a technique has been found that can determine the 3-dimensional structures of proteins which were previously beyond the reach of researchers. Science marches on.
New ways to identify cells in a precancerous state well before they become numerous and metastasize hold the potential to prevent many cases of cancer which now are not discovered until they reach a fatal state of development. Researchers at MIT's George R. Harrison Spectroscopy Laboratory in the School of Science have just received a $7.2 million dollar grant from the National Institutes of Health (NIH) to develop a method using optical fibers to detect precancerous lesions more accurately, cheaply, quickly, and easily.
Clinical screening for cervical and oral precancer are multibillion-dollar industries which currently rely on visual detection of suspicious areas followed by invasive biopsy and microscopic examination. Given that visually identified suspicious areas do not always correspond to clinically significant lesions, spectroscopic imaging and diagnosis could prevent unnecessary invasive biopsies and potential delays in diagnosis.
Furthermore, real-time detection and diagnosis of lesions could pave the way for combined diagnosis and treatment sessions, thus preventing unnecessary follow-up visits.
Michael S. Feld, professor of physics and director of the Spectroscopy Lab, says the laboratory has developed a portable instrument that delivers weak pulses of laser light and ordinary white light from a thin optical fiber probe onto the patient’s tissue through an endoscope. This device analyzes tissue over a region around 1 millimeter in diameter and has shown promising results in clinical studies. It accurately identified invisible precancerous changes in the colon, bladder and esophagus, as well as the cervix and oral cavity.
The second device, which has not yet been tested on patients, can image precancerous features over areas of tissue up to a few centimeters in diameter.
The researchers hope that these new methods, which can provide accurate results in a fraction of a second, may one day replace tissue biopsies in diagnosing certain types of cancers.
Feld predicted that in a couple of years, these devices will lead to a new class of endoscopes and other diagnostic instruments that will allow physicians to obtain high-resolution images. These easy-to-read images will map out normal, precancerous and cancerous tissue the way a contour map highlights elevations in reds, yellows and greens.
The optical fiber probe instrument employs a method called trimodal spectroscopy, in which three diagnostic techniques—light-scattering spectroscopy (LSS), diffuse reflectance spectroscopy (DRS) and intrinsic fluorescence spectroscopy (IFS)—are combined.
IFS provides chemical information about the tissue, LSS provides information about the cell nuclei near the tissue surface and DRS provides structural information about the underlying tissue. The information provided by the three techniques is complementary and leads to a combined diagnosis, though the imaging technique is based on LSS alone.
This brings to mind a different effort aimed at making cancer cells show up with greater contrast versus normal cells. Shuming Nie at Georgia Tech is doing work to develop quantum dot labelling techniques for cancer cells.
Cancer cells have certain characteristics or markers. After targeting and labeling these markers with color-coded quantum dots, Nie's computer-based algorithm converts the optical information into biological data. He then knows which markers are present, as well as their distribution over the surface of a cell. The patterns formed by the optical information may indicate the presence of cancer.
One can imagine how a liquid or paste containing quantum dots could be spread on a target tissue surface such as a cervix as a preparation to enhance the contrast for the spectroscopic device being developed by MIT.
Scientists at the University of California at San Diego have adapted an inkjet printer and a CD player to make a scientific instrument that detects types of proteins molecules present in a solution by measuring where they bind on the surface of a specially prepared CD.
To do molecular screening, the researchers took a CD encoded with digital data, and enhanced the chemical reactivity of the plastic on the readable surface. They then added molecules they wanted to attach to this surface to the empty ink wells of an inkjet printer cartridge and used the printer to “print” the molecules onto the CD. This resulted in a CD with molecules bound to its readable surface in specific locations relative to the pits in the metal layer of the CD encoding the digital information. When the CD with these molecules attached is placed in a CD player, the laser detects a small error in the digital code relative to what is read from the CD without the molecules attached.
To detect proteins or other large molecules in a solution like a blood sample, the modified CD is allowed to react with the sample solution. Like a key that only fits in a certain lock, some proteins bind to specific target molecules. Thus, specific molecules on the surface of a CD can be used to “go fishing” for certain proteins in a sample. The attachment of these proteins will introduce further errors into the reading of the CD. Furthermore, since the molecules on the surface of the CD are at known locations relative to the bits of encoded information, the errors tell the researchers what molecules have attached to their target protein and, thus, whether or not that protein is present in the sample.
“James has even done this using CDs with music, like Beethoven’s Fifth Symphony,” says Burkart. “And you can actually hear the errors.”
“How many people on this planet can actually hear a molecule attached to another molecule?” asks La Clair.
While a few bugs need to be ironed out before the technique can be used to accurately quantify the amount of a given protein in solution, Burkart plans to apply it immediately to help him screen for new compounds in his natural products chemistry research laboratory. Compared to the $100,000 price tag for a fluorescent protein chip reader, he points out, a CD player costs as little as $25.
The researchers envision many other potential applications for this technology outside the laboratory, particularly in the development of inexpensive medical diagnostic tests, now beyond the means of many people around the world, particularly in developing countries.
“In theory, anyone who has a computer with a CD drive could do medical tests in their own home,” says La Clair.
Basically, they use an inkjet printer cartridge to put different kinds of molecules at differnet locations on the CD. Each kind of molecule has affinity for a different type of target protein molecule. Then they expose the CD to a solution that has unknown assortment of proteins. Those proteins with affinity for specific places on the CD bind in those places and then when the CD is read the signal in those areas is changed by the addition of the larger proteins that have bound to the molecules which have been anchored to the CD.
This work demonstrates how advances in electronic technology are helping to lower the cost and increasing the speed of doing biomedical research and clinical testing. This is not the first use of inkjet printer technology as tools for doing biomedical research. See Modified Printers Used For Tissue Engineering and STMicro Releases Silicon DNA Analysis Chip for other examples.
Diagnoses of cancers and neurodegenerative diseases, such as Alzheimer's disease, are two applications suggested by the researchers in their report in Proceedings of the National Academy of Sciences (PNAS , June 10, 2003), "Live tissue intrinsic emission microscopy using multiphoton-excited native fluorescence and second harmonic generation." The researchers predict that it should be possible to obtain endoscopic and laparoscopic images of tissues at the cellular level from deep within living animals, or even human patients, thus enabling a new form of optical biopsy.
The researchers have demonstrated the new imaging technique by making live-tissue intrinsic fluorescence scans of autopsy samples from the brains of patients with Alzheimer's disease and by imaging mammary gland tumors in mice that serve as models of human cancer. Side-by-side comparison with conventional medical biopsy images of thin embalmed sections of the same organs reveals that the new method provides at least equal information, and in some cases contains additional diagnostic details not found in the conventional biopsies, which require invasive surgery.
Another advantage of live-tissue intrinsic emission imaging, the researchers say, is that the scans can be made through the surface of intact organs or body systems. By comparison, histopathology studies generally are performed on biopsy samples removed from subjects, then "fixed" or embalmed and stained with labeling chemicals, which involves extended time delays.The Cornell-Harvard team incorporated a technology into the new imaging procedure called multiphoton microscopy, invented in 1989 by Watt W. Webb, Cornell's S.B. Eckert Professor of Engineering and professor of applied physics, and Winfried Denk, now director of the Max-Planck-Institut für Medizinische Forschung Biomedizinische Optik, Germany.
Biological imaging technology has already gone thru dramatic advances with the development of CAT scanners, MRI scanners, and other scanning technologies. The general trend toward easier and more detailed 3 dimensional imaging of living biological tissue shows no sign of stopping.
The use of multiphoton microscopy can be enhanced by use of quantum dots. The use of shock waves in photonic crystals to shift light frequencies may provide a useful method to produce the light needed for this kind of imaging.
What I think is kinda funny about these advances is that they are starting to make science fiction TV shows set a few centuries into the future look backward in comparison. Dr. McCoy's medical tricorder has not yet been equalled. But can anyone doubt that within a few decades real medical science will be far more advanced than 22nd, 23rd, and 24th century fictional Star Trek Federation technology?
If you are under the impression that the use of individual DNA profiles for making personalized choices for medical treatments lay many years into the science fiction future then it is time to think again. The Roche CYP450 Amplichip will hit the market shortly and will be enhanced over the next 18 months to test for an increasing number of human genetic variations that relate to disease and disease treatment and even to detect viruses.
BASEL, Switzerland, May 7 (Reuters) - Roche Holding AG
intends to roll out six "gene chip" tests over the next 18 months that can help diagnose how patients respond to certain drugs, detect viruses or expose a risk of developing cancer, the company said on Wednesday.
Roche is testing for a large variety of types of genetic variations in the genes coding for cytochrome P450 enzymes.
A microarray-based genotyping assay will be described that detects over two dozen allelic variants affecting CYP450 enzyme activity, including those caused by SNPs, frame shifts, multiple base repeats, and even complete gene deletion or duplication.
Individual variations in those enzymes will affect how quickly the liver breaks down drugs. Because of those individual variations there are enormous variation between individuals as to the best dose of a drug to take and even whether a particular drug will work. A person whose body breaks down a particular drug incredibly rapidly may not be able to derive any therapeutic benefit from taking it. Therefore they may benefit more from taking a different drug which they can not break down as easily.
The Roche product will be also be improved by automation so that it can be used in clinics and other point-of-care locations.
The product will include both a set of reagents and a microarray, and will be released in the second quarter of 2003. Initially, the technology will be restricted to use in reference laboratories, to which it will be marketed as an analyte-specific reagent (ASR) set. However, Roche expects that within the next 3–5 years, it will develop the technology into a fully automated system that can be marketed as a certified in vitro diagnostic. The company hopes to eventually bring the test closer to the patient for use in clinical laboratories or even at the point of care.
Jonathan Knowles, head of Roche research, promotes the use of the AmpliChip to reduce the guesswork involved in choosing which anti-depressant will treat an individual case of depression.
"There is a whole series of existing antidepressants," said Knowles. "The probability of anyone responding to any particular medicine is around 50% or even less. The only way to find out is to give someone a particular medicine for a couple of months and see if they feel better. If they don't feel better, then you try another one, and you keep going. There are all sorts of risks and emotional cost to the individual, an emotional cost to their family."
The test checks for genetic variations in genes that code for enzymes in the cytochrome P450 group of enzymes which are involved in breaking down toxic compounds and drugs in the liver and elsewhere in the body.
The new chip from Roche and Affymetrix will test for the most common variations in two genes, CYP2D6 and CYP2C19, which play roles in the way the body handles about 45 percent of the prescription drugs on the market,
This first generation AmpliChip surprisingly does not test the enzyme CYP3A which is the biggest metabolizer of drugs. But looked at from the standpoint of human genetic diversity it makes sense that Roche attached a greater importance to testing CYP2D6 because CYP2D6 is missing in 7% of caucasians and 2% of non-caucasians. CYP2D6 is also hyperactive in 30% of East Africans. Therefore what makes CYP2D6 testing more important than CYP3A testing is that CYP2D6 expression varies more from one person to the next.
This new test kit represents just the tip of the iceberg for the future use of knowledge of personal DNA sequence variations to choose medical treatments.
The testing of DNA sequence variations is not the only way to measure differences between people in gene function. Another way is to test methylation patterns on DNA that the cell uses to control gene expression.
Molecular Diagnostics’ in vitro diagnostics business grew by 14%. However, Molecular Diagnostics’ sales were down 1% overall and thus slightly below expectations as a result of the sharp downturn in sales to the biotech industry (-58%). By signing a licensing agreement at the beginning of the year with Affymetrix on the use of its GeneChip technology, Roche has laid the foundation for future growth in this newly created market. The AmpliChip P450, scheduled for launch in the second quarter of 2003, will be the first DNA chip-based diagnostic test that provides information on patients’ metabolic status. Roche also signed an agreement with the German-based company Epigenomics to codevelop a range of diagnostic tests for the early detection of cancers, their characterisation and prediction of treatment response.
"We are very enthusiastic about this collaboration. Roche is already the world leader in cancer therapies and with this alliance we will complement our position in the diagnostics field. The products that are being developed as part of this collaboration address the urgent need for earlier detection of cancer in bodily fluids by more accurate screening tests, as well as identifying those patients who need chemotherapy and most likely respond to particular cancer therapies," says Heino von Prondzynski, Head of Roche Diagnostics and member of Roche's Corporate Executive Committee. "As the worldwide leader in in vitro Diagnostics we are committed to identify diseases early in order to improve treatment and enhance patients' quality of life. The alliance with Epigenomics will help us to remain at the forefront of the molecular diagnostics market and support our activities to pursue a market that could be greater than 3 billion Swiss francs ten years from now for our divisional cancer care program."
Alexander Olek, CEO of Epigenomics, adds: "This collaboration validates Epigenomics' DNA methylation technology and product development approach. By underlining the synergy between our in-house units, Diagnostics and Pharma Technology businesses, it allows us to pursue our vision of personalizing medicine. With the emerging trend of the pharmaceutical industry moving towards administering therapy only with a specific diagnostic test, we feel that the partnership with Roche Diagnostics solidifies Epigenomics' position as a leader in this field."
DNA testing is no longer just a research tool or a tool to test for rare inherited genetic diseases. It is moving very rapidly into widespread use to allow doctors to make more optimal decisions when choosing treatments for major diseases which have millions of sufferers.
The ability to conduct genetic tests in hospitals and clinics is going to become commonplace in the next few years. Therefore the biggest factor which will determine the rate at which genetic testing increases will be the rate at which the clinical significance is discovered for the hundreds of thousands of genetic variations that exist in the human population.
Some day in the future diabetics will be able to look at the color of their eye contact lenses in the mirror in order to detect their blood sugar level.
PITTSBURGH, April 14 – Millions of people suffering from diabetes mellitus may be spared the ordeal of pricking their fingers several times a day to test blood sugar levels, thanks to a breakthrough by University of Pittsburgh researchers who have developed a non-invasive method to measure the glucose level in bodily fluids.
Researchers Sanford A. Asher, Ph.D., professor of chemistry in the faculty and College of Arts and Sciences, and David Finegold, M.D., professor of pediatrics in the School of Medicine, created a thin plastic sensor that changes color based on the concentrations of glucose.
The sensor material, which would be worn like a contact lens, was described in a paper published in the online version of Analytical Chemistry on April 11. The paper is scheduled to be published in the print version of Analytical Chemistry, a publication of the American Chemical Society, on May 1.
"There has been a increasing demand for continuous, non-invasive glucose monitoring due to the increasing number of people diagnosed with diabetes mellitus and the recognition that the long-term outcome of these patients can be dramatically improved by careful glucose monitoring and control," said Dr. Asher.
"The current method of testing glucose in diabetes patients-by drawing blood from a finger prick-is uncomfortable and is dependent on patient skill and compliance for regular testing," said Dr. Finegold.
The researchers plan to embed the sensing material into contact lenses worn in the patients' eyes. Patients will determine their glucose levels by looking into a mirror-similar to women's makeup compact mirrors, but with a color chart to indicate glucose concentrations-to compare the color of the sensing material with the chart.
The sensor will change from red, which indicates dangerously low glucose concentrations, to violet, which will indicate dangerously high glucose concentrations. When the glucose level is normal, the sensor will be green. The researchers are still determining the number of detectable gradations, but expect that it may be as high as the finger stick meters currently provide.
The University of Pittsburgh, which owns this patented technology, has licensed this technology to a new startup company that will engineer the material and commercialize it. The researchers believe the product is at least a year from being tested in humans. The researchers expect that their technology would be able to be incorporated into currently available commercial contact lenses, which would be replaced weekly.
This seems like a pretty cool idea. While it is reasonable to expect that cell therapy or gene therapy will provide a cure for diabetes in 10 or 15 years the concept has other potential applications for measuring other body biochemical levels. Imagine a sensor keyed to measuring the severity of some other biochemical problem that could provide an indicator for when to take other drugs. Heck, sensors could be designed to measure the level of a specific drug and if one is taking that drug one could also wear a contact lens designed to detect it. Then one could glance in a mirror to see a color that indicates that one needs to take another pill.
Researchers at The Scripts Research Institute have developed a new method for detecting specific DNA sequences.
Now TSRI Ph.D. graduate and current research associate Alan Saghatelian, TSRI graduate student Desiree Thayer, research associate Kevin Guckian, and Professor Reza Ghadiri in the Department of Chemistry have designed a non-PCR method for detecting specific sequences of nucleic acid that may have advantages over PCR, especially in such situations as field work and point-of-care medicine where the technology could be used by non-specialists. The new method is exquisitely sensitive and quite fast, according to Ghadiri, detecting as minute a sample as 10 femtomoles of DNA in less than three minutes. The method makes use of a detection system based on an inhibitor–DNA–enzyme complex. Specifically, the complex is composed of an enzyme, a single-stranded piece of DNA covalently attached to the enzyme, and, at the end of this DNA strand, an "intramolecular" inhibitor. The complex is able to "detect" pieces of DNA that are complimentary to its single strand of DNA. When complimentary DNA is not present, the single strand of DNA in the complex is flexible enough that it can loop around, allowing the inhibitor to occupy the binding site of the enzyme. But when complimentary DNA is present, the complimentary DNA forms a duplex with the complex's single strand—straightening out the DNA—and the inhibitor at the end on this duplex can no longer occupy the enzyme's binding site, enabling the enzyme to cleave its substrate. Ghadiri and his colleagues selected a fluorophoric substrate so that this cleavage releases energy in the form of easily detected fluorescence, signaling the presence of complimentary DNA. The sensitivity of the method comes from the fact that the system is self-amplifying. Any one molecule of DNA that hybridizes to one complex turns on that one enzyme, which can then do multiple turnovers of the substrate.
This is not a general sequencing method. Its designed to detect specific sequences of DNA. Its advantage over the existing polymerase chain reaction method is the potential ability to build devices that use it that do not require a trained technician. This will lower costs and allow use in a larger range of settings.
Its not clear from the press release what this technique's limitations might be. Could a partially matching fragment cause the method to report a match? Is it sensitive down to the level of a single nucleotide polymorphism (SNP) difference? It would be a lot more useful medically if it was. Eventually specific SNPs will be linked to medically useful factors such as drug sensitivities and incompatibilities. At that point what would be needed is the ability of a doctor to test for a specific SNP in order to choose the best drug treatment.
Here is an advance in techniques for watching what goes on in cells during viral infection:
This new technology, an imaging method known as in vivo bioluminescence, enables investigators to track changes in the viral population in the same animal day after day. The device is located in the Molecular Imaging Center at the University's Mallinckrodt Institute of Radiology.
"This technology can be used to explore questions about this virus that are possible only by studying entire living animals over time," says Gary D. Luker, M.D., an assistant professor of radiology with the Molecular Imaging Center and first author of the paper.
"This is an excellent example of the unique information and new collaborations that are generated when we examine fundamental biological processes with molecular imaging tools," says David Piwnica-Worms, M.D., Ph.D., professor of radiology and of molecular biology and pharmacology and director of the Molecular Imaging Center.
The investigators first added a gene for luciferase, an enzyme produced by fireflies, to a strain of herpes simplex type 1 virus. After determining that the modified virus behaves in cells like the normal virus, they injected the modified virus into several locations in mice, including the brain and abdominal cavity.
Daily for nine days, the mice were injected with luciferin, a compound also produced by fireflies that emits light when exposed to luciferase. They then were anesthetized, placed in a light-free box and photographed using a charged-coupled device, or CCD camera. The camera captures light emitted through the tissues of the mouse by the actively replicating virus. The image produced by the camera shows the location and amount of virus in a mouse as areas of color, ranging from blue (low levels) to red (high levels), superimposed on a photograph of the anesthetized animal. Light produced by the luciferase-luciferin reaction is known as bioluminescence because it is generated by biological chemicals.
This imaging method enabled the investigators to monitor the infection as it spread and receded over nine days. In a second experiment, mice infected with the modified virus were treated with the antiviral drug valacyclovir. The investigators found that decreases in bioluminescence correlated with the decline in the amount of virus present.
The method works in part because bioluminescence produced by fireflies contains a significant amount of red light, which penetrates tissues more effectively than other wavelengths of light. This effect can be seen by shining a flashlight through a finger; it is red light that penetrates the finger.