2012 October 14 Sunday
Star Trek Tricorder Too Big

The first device that is like the Star Trek tricorder medical monitoring device (as used by Dr. McCoy) will probably be much smaller than a tricorder.

UNIVERSITY PARK, Pa. -- A technique that uses acoustic waves to sort cells on a chip may create miniature medical analytic devices that could make Star Trek's tricorder seem a bit bulky in comparison, according to a team of researchers.

Think about McCoy or Spock staring into some scientific instrument on a bench. In all likelihood humans won't stare at cells under a microscope when instead microfluidic devices with lots of built-in sensors will do all the data collection.

The device uses two beams of acoustic -- or sound -- waves to act as acoustic tweezers and sort a continuous flow of cells on a dime-sized chip, said Tony Jun Huang, associate professor of engineering science and mechanics, Penn State. By changing the frequency of the acoustic waves, researchers can easily alter the paths of the cells.

Huang said that since the device can sort cells into five or more channels, it will allow more cell types to be analyzed simultaneously, which paves the way for smaller, more efficient and less expensive analytic devices.

"Eventually, you could do analysis on a device about the size of a cell phone," said Huang. "It's very doable and we're making in-roads to that right now."

An increasing portion of all medical testing won't be done in labs. It will be done by a handheld device that either the doctor or patient uses. The device will upload collected data wirelessly to a web server that will run medical diagnostic logic and offer treatment recommendations. We will have all this long before humans colonize Mars, let alone travel between the stars.

Miniaturization is the key enabling trend in technology. Without miniaturization of factories, lab tests, and computing migration of humans to other planets would be too hard.

Update: Cell phones and web servers will monitor for changes in your habits to detect mental and physical health problems. Add some sensors embedded into your body (or even worn like a watch or pendant) that the cell phones can interrogate and then the constant monitoring will be able to detect many more problems and much more quickly. Some of those sensors embedded in your body will dissolve after collecting needed data.

By Randall Parker    2012 October 14 10:04 AM   Entry Permalink | Comments (2)
2012 June 04 Monday
3-Million-Fold Improvement In Immunoassay Sensitivity

Why make small steps forward when really big steps are possible? Princeton researchers have developed a way to make immunoassays for biomarkers (e.g. blood proteins for cancer or Alzheimer's) 3 million times for sensitive. So far fewer molecules need be present to detect a medical condition. Earlier detection becomes possible.

The breakthrough involves a common biological test called an immunoassay, which mimics the action of the immune system to detect the presence of biomarkers – the chemicals associated with diseases. When biomarkers are present in samples, such as those taken from humans, the immunoassay test produces a fluorescent glow (light) that can be measured in a laboratory. The greater the glow, the more of the biomarker is present. However, if the amount of biomarker is too small, the fluorescent light is too faint to be detected, setting the limit of detection. A major goal in immunoassay research is to improve the detection limit.

The Princeton researchers tackled this limitation by using nanotechnology to greatly amplify the faint fluorescence from a sample. By fashioning glass and gold structures so small they could only be seen with a powerful electron microscope, the scientists were able to drastically increase the fluorescence signal compared to conventional immunoassays, leading to a 3-million-fold improvement in the limit of detection. That is, the enhanced immunoassay would require 3 million times fewer biomarkers to be present compared to a conventional immunoassay. (In technical terms, the researchers measured an improvement in the detection limit from 0.9 nanomolars to 300 attomolars.)

This technique doesn't just enable earlier detection. It also enables detection of compounds that never reach high concentrations. So expect more biomarkers to be found with this technique and for .

These researchers are now going to compare the sensitivity of this approach for cancers and Alzheimer's in hopes of earlier stage detection.

As next steps in his research, Chou said he is conducting tests to compare the sensitivity of the D2PA-enhanced immunoassay to a conventional immunoassay in detecting breast and prostate cancers. In addition he is collaborating with researchers at Memorial Sloan-Kettering Cancer Center in New York to develop tests to detect proteins associated with Alzheimer's disease at a very early stage.

"You can have very early detection with our approach," he said.

The scaling of biotechnology to work at very small scales is yielding rapid advances just as scaling down of semiconductor devices enabled computers to become both cheaper and more powerful at the same time. It is this trend toward smaller scale devices that gives me the most optimism about how soon we will get advances in biotechnology that will enable the development of rejuvenation therapies.

By Randall Parker    2012 June 04 08:50 PM   Entry Permalink | Comments (5)
2011 October 17 Monday
Car Measures Blood Sugar

Your car as a doctor.

Your car may soon be able to warn you if your blood sugar dips, alert you to high pollen counts, and remind you to take your medication. Ford demonstrated the new in-car technology—currently a research project—this week at the Wireless Health 2011 conference in La Jolla, California.

Cars, homes, cell phones, office chairs, clothing should all measure us and report to a medical diagnostic server that tracks our health and runs expert systems diagnostic apps to detect problems. Also, embedded sensors should test our blood continuously.

We need a different economic model for medicine so that mobile medical technology and the home as a medical lab (get diagnosed while you sleep - why not?) become a reality.

One of the easiest things to predict about the future: more data will flow. But how soon will we make it useful for things that matter like our own health? It is all well and good to be able to use your cell phone to check your email. But remember my motto: First, don't die.

By Randall Parker    2011 October 17 09:02 PM   Entry Permalink | Comments (4)
2011 August 01 Monday
Microfluidic Chip For Medical Testing In Remote Regions

Of course it will work in a suburban tract home too.

New York, NY—July 31, 2011—Samuel K. Sia, assistant professor of biomedical engineering at Columbia Engineering, has developed an innovative strategy for an integrated microfluidic-based diagnostic device—in effect, a lab-on-a-chip—that can perform complex laboratory assays, and do so with such simplicity that these tests can be carried out in the most remote regions of the world. In a paper published in Nature Medicine online on July 31, Sia presents the first published field results on how microfluidics—the manipulation of small amounts of fluids—and nanoparticles can be successfully leveraged to produce a functional low-cost diagnostic device in extreme resource-limited settings.

Sia and his team performed testing in Rwanda over the last four years in partnership with Columbia's Mailman School of Public Health and three local non-government organizations in Rwanda, targeting hundreds of patients. His device, known as mChip (mobile microfluidic chip), requires only a tiny finger prick of blood, effective even for a newborn, and gives—in less than 15 minutes—quantitative objective results that are not subject to user interpretation. This new technology significantly reduces the time between testing patients and treating them, providing medical workers in the field results that are much easier to read at a much lower cost. New low-cost diagnostics like the mChip could revolutionize medical care around the world.

The chip is expected to cost $1 and the reader device $100. Imagine the ability to plug the chip into a future generation smart phone and test yourself to find out whether you have a bacterial or viral infection. Or test yourself to find out whether your diet of late has done bad things to your blood lipids and blood sugar.

30 years from now (if not much sooner) most medical testing will be done before you show up in a doctor's office. Your data will get uploaded to a expert system diagnostic server. You will show up for a doctor's appointment for treatment when necessary. I expect in the longer run most doctors will shift their attention to delivering rejuvenation therapies rather than diagnosing common illnesses. Diagnostics expert systems running in cloud computers will do most of the work for illnesses unrelated to aging.

By Randall Parker    2011 August 01 08:05 AM   Entry Permalink | Comments (4)
2011 July 21 Thursday
Smart Phone And Tattoo Dye To Read Blood Chemicals

A fluorescent dye injected into the skin will change its fluorescence based on concentrations of a target chemical in the blood (e.g. sodium or sugar) and then a smart phone add-on can read the dye to measure blood levels of a the chemical of interest.

Using a nanosensor "tattoo" and a modified iPhone, cyclists could closely monitor sodium levels to prevent dehydration, and anemic patients could track their blood oxygen levels.

Heather Clark, a professor in the Department of Pharmaceutical Sciences at Northeastern University, is leading a team working to make this possible. The team begins by injecting a solution containing carefully chosen nanoparticles into the skin.

You can imagine a series of small bars of dyes added to the skin to measure different chemicals. Reading it would be akin to doing bar code reading except each bar could indicate levels of a different blood chemical: sodium, potassium, glucose, etc.

This is part of a larger trend: direct consumer measurement of one's own body. Some of that measuring is going to be embedded in your environment. Imagine a toilet and sink that measure your excretions and logs them either to a home or cloud medical diagnostics server. Your bed stand will monitor your gases for signs of poor cardiovascular performance or sleep apnea. Will pillows monitor brain waves for sleep quality?

Update: Similar work has been done on glucose monitoring.

By Randall Parker    2011 July 21 07:47 AM   Entry Permalink | Comments (2)
2011 March 22 Tuesday
Biochip Does Blood Sample Analysis

The field of microfluidics holds the promise of orders of magnitude cheaper biological assays of blood and other samples. Plus, it will enable fast testing without sending off to a lab. Well, an international group of researchers has developed an autonomous lab-on-a-chip.

BERKELEY — A major milestone in microfluidics could soon lead to stand-alone, self-powered chips that can diagnose diseases within minutes. The device, developed by an international team of researchers from the University of California, Berkeley, Dublin City University in Ireland and Universidad de Valparaíso Chile, is able to process whole blood samples without the use of external tubing and extra components.

The researchers have dubbed the device SIMBAS, which stands for Self-powered Integrated Microfluidic Blood Analysis System. SIMBAS appeared as the cover story March 7 in the peer-reviewed journal Lab on a Chip.

“The dream of a true lab-on-a-chip has been around for a while, but most systems developed thus far have not been truly autonomous,” said Ivan Dimov, UC Berkeley post-doctoral researcher in bioengineering and co-lead author of the study. “By the time you add tubing and sample prep setup components required to make previous chips function, they lose their characteristic of being small, portable and cheap. In our device, there are no external connections or tubing required, so this can truly become a point-of-care system.”

The FDA and AMA line up to restrict your freedom to get personal genetic testing. Yet the technological trends are running very rapidly toward the development of very powerful hand-held medical testing devices. You can already buy home triglycerides and cholesterol test kits. I do not want to see governments restrict their availability. Rather, we should some day be able to each individually check a very large list of chemicals in our blood by pulling out a little medical testing lab from a pants pocket.

Instant real-time medical testing any time of the day anywhere you are can revolutionize medicine and medical research. The number of people generating their own personal medical records can explode with cheap lab-on-a-chip devices. These gadgets will some day take your medical test results, send them to a medical expert system web server, and report back to you about whether you have any looming or current problems.

By Randall Parker    2011 March 22 12:11 AM   Entry Permalink | Comments (5)
2011 January 31 Monday
Labrador Retriever Detects Bowel Cancer

Have you gone too long since you last saw a dog for a check-up? Don't worry, he'll still be happy to see you.

A specially trained Labrador retriever completed 74 sniff tests, each comprising five breath (100 to 200 ml) or stool samples (50 ml) at a time, only one of which was cancerous, over a period of several months.

The samples came from 48 people with confirmed bowel cancer and 258 volunteers with no bowel cancer or who had had cancer in the past.

Around half of the volunteer samples came from people with bowel polyps, which although benign, are considered to be a precursor of bowel cancer. And 6% of the breath samples and one in 10 of the stool samples from this group came from those with other gut problems, such as inflammatory bowel disease, ulcers, diverticulitis, and appendicitis.

The bowel cancer samples came from patients with varying stages of disease, including early stage.

I read about dogs being trained to detect cancer years ago and have been disappointed that they have not become widely used for this purpose. Does the medical profession have a hard time taking dogs seriously? Or are regulatory agencies the problem?

What I wonder: How fast does the dog's nose fatigue at this job? How many samples could a trained dog test per day?

This lab produces accurate results. The especially accurate results at early stage are ideal really. The sooner the cancer is removed the lower the chance it has metastasized.

The dog successfully identified which samples were cancerous, and which were not, in 33 out of 36 breath tests and in 37 out of 38 stool tests, with the highest detection rates among those samples taken from people with early stage disease.

This equates to 95% accuracy, overall, for the breath test and 98% accuracy for the stool test, compared with conventional colonoscopy - a procedure involving a tube with a camera on the end inserted through the back passage.

The LA Times has a good picture of this good black lab. Here is the research paper by the Japanese researchers who trained the dog. Her name is Marine and she is 8 years old. She is more accurate than other dogs trained for this task.

By Randall Parker    2011 January 31 09:00 PM   Entry Permalink | Comments (7)
2011 January 27 Thursday
Paper Strips To Do More Medical Tests

Paper strips will perform a wider variety of medical tests.

WEST LAFAYETTE, Ind. - Researchers have invented a technique that uses inexpensive paper to make "microfluidic" devices for rapid medical diagnostics and chemical analysis.

The innovation represents a way to enhance commercially available diagnostic devices that use paper-strip assays like those that test for diabetes and pregnancy.

Advances that lower medical testing costs while also provide immediate results without a big lab will accelerate the trend direct-to-consumer medical testing. People will do medical testing at home and more frequently. They'll upload their test results to servers running medical expert systems that will provide diagnostic results and monitor your conditions.

Paper test strips will do more complex chemical assays at lower cost.

"With current systems that use paper test strips you can measure things like pH or blood sugar, but you can't perform more complex chemical assays," said Babak Ziaie, a Purdue University professor of electrical and computer engineering and biomedical engineering. "This new approach offers the potential to extend the inexpensive paper-based systems so that they are able to do more complicated multiple analyses on the same piece of paper. It's a generic platform that can be used for a variety of applications.”

By Randall Parker    2011 January 27 12:06 AM   Entry Permalink | Comments (7)
2011 January 10 Monday
Medical Test Results In 30 Minutes With Microfluidic Chips

Microfluidic devices will eliminate the need to return to a doctor's office to get test results. The testing will be done while you wait.

KINGSTON, R.I. – January 10, 2011 -- While most blood tests require shipping a vial of blood to a laboratory for analysis and waiting several days for the results, a new device invented by a team of engineers and students at the University of Rhode Island uses just a pinprick of blood in a portable device that provides results in less than 30 minutes.

Microfluidic devices will enable point-of-care diagnostics. But they will also enable drug stores to offer a wide range of blood testing services at a lower cost, at more convenient locations, and over a much wider range of hours and days. Why make an appointment during your work day to go to a doctor's office when you can get tested at a drug store you already shop at after work? Government regulators might block this sort of thing. Otherwise the convenience and lower costs will be a boon.

"This development is a big step in point-of-care diagnostics, where testing can be performed in a clinic, in a doctor's office, or right at home," said Mohammad Faghri, URI professor of mechanical engineering and the lead researcher on the project. "No longer will patients have to wait anxiously for several days for their test results. They can have their blood tested when they walk into the doctor's office and the results will be ready before they leave."

With the new lab-on-a-chip technology, a drop of blood is placed on a plastic polymer cartridge smaller than a credit card and inserted into a shoebox-sized biosensor containing a miniature spectrometer and piezoelectric micro-pump. The blood travels through the cartridge in tiny channels 500 microns wide to a detection site where it reacts with preloaded reagents enabling the sensor to detect certain biomarkers of disease.

Several patents are pending on the invention.

The first test checks levels of C-reactive proteins (CRP) in the blood. But their approach can be used to test other blood components.

Cheap.

Compared to similar devices in development elsewhere, the URI system is much smaller, more portable, requires a smaller blood sample, and is less expensive. While the sensor costs about $3,200, each test costs just $1.50, which is the cost for the plastic cartridge and reagents.

Just as computers have dropped in cost so will the costs of lab-on-a-chip devices. Once they get cheap enough they'll make sense as home testing devices that allow us to monitor ourselves more frequently and easily for early signs of disease.

By Randall Parker    2011 January 10 09:47 PM   Entry Permalink | Comments (5)
2011 January 04 Tuesday
Cheap DNA Sequencer Size Of A Printer

Smaller and cheaper.

Dr. Rothberg is the founder of Ion Torrent, which last month began selling a sequencer it calls the Personal Genome Machine. While most sequencers cost hundreds of thousands of dollars and are at least the size of small refrigerators, this machine sells for just under $50,000 and is the size of a largish desktop printer.

While not intended for the general public, the machine could expand the use of DNA sequencing from specialized centers to smaller university and industrial labs, and into hospitals and doctors’ offices, helping make DNA sequencing a standard part of medical practice.

It is not as cheap as it sounds because it sequences only smaller genomes and consumes a $250 chip for each genome. But its cost, as well as the costs for competitors such as Illumina, will surely fall. We are definitely on course for the $1000 genome some time in the next 5 years.

What is interesting about it is the size of the machine and the promise of even smaller and cheaper machines in the future. The researchers in the article are intrigued by the idea of doing sequencing in a doctor's office. I suppose that will help in diagnosing infections. Certainly it will be done very widely to identify mutations in cancers and the best methods for treating each cancer. But leaving aside cancer most full genome DNA sequencing will not be done to diagnose a disease. Sequencing will be done to people who are perfectly healthy who just want to understand their metabolisms, disease risks, best diets, their genealogies, and other aspects of who they are.

Initially adults will get sequenced. But (again leaving aside cancer patients) once all adults have been sequenced only babies or candidate embryos from in vitro fertilization (IVF) will be sequenced. Future generations won't go to a doctor's office to get sequenced because they'll be born with known DNA sequences.

I can see one other reason adults will continue to be sequenced aside from cancer patients: surreptitious tissue samples will be stolen from people (or from their hair left on a hair brush or in other ways) to get their DNA sequence. Imagine the equivalent of Brad Pitt or Lady Gaga 20 or 30 years hence. Paparazzi might refrain from DNA sample stealing due to laws against it. But crazed fans will want to do it if they can secretly get DNA sequencing done. Well, if DNA sequencing machines continue to fall in price by orders of magnitude while becoming far more automated and easy to use then individuals will be able to buy DNA sequencing machines. Or they'll send DNA samples offshore to labs in countries with little regulation of the DNA sequencing business.

You can imagine how fans will be able to secretly publish DNA sequences by uploading DNA sequence data files from internet cafes with clues as to which celebrity they are for. Then what happens? Well, web servers with DNA modeling software will allow people to take an uploaded genome sequence and run algorithms to find out what the person looks like.

Recently 13 genetic variants that contribute to hair color were published. Genetic variants for height and eye color have been identified as well. Many thousands more genes for appearance and other attributes will be identified. So it will become relatively easy to take a genetic sequence and figure out whether it might be for a President, singer, politician, or assorted friends, enemies, or love interests.

Go even further into the future and I wonder whether stolen DNA sequences will be used to make babies.

By Randall Parker    2011 January 04 08:16 PM   Entry Permalink | Comments (6)
2010 November 30 Tuesday
Universal Microfluidics Connector For Portable Labs

20 years from now microfluidic chips will plug into our smart phones (or maybe into our virtual reality goggles). When we need to do a fast genetic test (either in a bar with a potential mate or at the pound when choosing a dog to adopt) pluggable microfluidic chips will come in handy.

Biomedical engineers at UC Davis have developed a plug-in interface for the microfluidic chips that will form the basis of the next generation of compact medical devices. They hope that the "fit to flow" interface will become as ubiquitous as the USB interface for computer peripherals.

UC Davis filed a provisional patent on the invention Nov. 1. A paper describing the devices was published online Nov. 25 by the journal Lab on a Chip.

"We think there is a huge need for an interface to bridge microfluidics to electronic devices," said Tingrui Pan, assistant professor of biomedical engineering at UC Davis. Pan and graduate student Arnold Chen - invented the chip and co-authored the paper.

Or maybe a microfluidic chip will come in handy at a picnic where each person brings a dish. Does that casserole have a bad case of salmonella or another pathogen that risks trashing your intestines? A quick test of a sample could come in handy.

Or how about testing your own blood for micronutrient deficiencies or signs that you really are as behind in your sleep as you feel?

If you could do fast biological tests in the course of your day what would you test for?

By Randall Parker    2010 November 30 09:59 PM   Entry Permalink | Comments (3)
2010 October 03 Sunday
MicroRNA Testing For Early Bladder Cancer Diagnosis

DENVER — Scientists may have discovered a way to diagnose bladder cancer at its earliest and, therefore, most treatable stages by measuring the presence or absence of microRNA using already available laboratory tests.

They found these microRNA fingerprints for bladder cancer in blood, not urine. This suggests the same can be done for other cancers. If so, early stage cancer diagnosis for just about all cancers could some day be done with blood tests for patterns of microRNAs. To state the obvious: The earlier the diagnosis the easier a cancer is to cure. Get it before it metastasizes, remove it, and then avoid losing your hair, pucking up your guts, becoming extremely emaciated, and dying with cancer in your bones that makes the end of your existence total agony.

"Measuring expressions of microRNA in bodily fluid represents a very promising tool with widespread implications for screening," said Liana Adam, M.D., Ph.D., assistant professor in urology at The University of Texas MD Anderson Cancer Center.

Only frequent and cheap testing can catch all cancers at an early enough stages. This has important implications for policies governing medical device regulation. In a nutshell: We need to allow the masses to test themselves (a.k.a. Direct To Consumer - DTC).

At an intermediate stage of expense and complexity it should be possible to get your secretions extensively tested at a drug store with sample drop-off at any time the store is open. We need a suite of fairly cheap tests of microRNA and other molecules that are reliable indicators for all the cancers as well as some other diseases.

As medical testing devices get shrunken down into mass produced microfluidic devices and costs drop by orders of magnitude much of that testing capability should move into the home. The goal should be to move toward constant home monitoring. All secretions should be testable once a week or even daily. We need to move beyond the model of visits to doctors' offices for medical testing.

The testing that saves your life has to happen much more often than doctor's office visits would make practical. So we need medical testing to become far more accessible. Plus, in order for it to be done monthly, weekly, or even daily for a large number of cancers and other diseases it has to become orders of magnitude cheaper. Microfluidics and a favorable (i.e. much different) regulatory environment are key to making this happen.

By Randall Parker    2010 October 03 09:03 PM   Entry Permalink | Comments (3)
2010 August 18 Wednesday
Breath Alcohol Analyzer Devices Compared

One breath alcohol analyzer company takes a critical look at its competition.

DENVER – August 18, 2010 – Lifeloc Technologies, Inc., a leading manufacturer of professional breathalyzers has released the industry's first independent report on the accuracy and reliability of popular semiconductor (silicone oxide) breath testers sold in mass retail, pharmacy, specialty stores and on the Internet.

"Anecdotal reports and experiences of consumers, law enforcement and other industry players have centered on the inaccuracy of semiconductor alcohol testers," said Barry Knott, president of Lifeloc. "New third party research has confirmed that popular semiconductor personal breathalyzers are notoriously inaccurate and should not be trusted for accurate BAC measurement. What we didn't know, until the test results came in, was just how inaccurate these devices are."

We are better off if the free flow of information regulates the market for sensor devices because we'll benefit by low barriers to entry and the rapid innovation that those low barriers foster. Competitive pressures are enough to get breathalyzers compared for performance.

I want less regulation of sensor devices we can use on ourselves because I see the rapid development of better sensor devices as helpful toward slowing and reversing the aging process. Increasingly powerful monitoring sensors will inevitably get enhanced to begin intervening in our metabolism. If human body sensor systems become heavily regulated then only highly capitalized companies will be able to enter the market and their high costs will translate into orders of magnitude higher product costs.

Some of the most interesting product innovation for human sensor systems will happen at price points so low that product manufacturers can not afford to go thru regulatory approval processes to get their devices to market. Imagine a plug-in cable for iPhones Android phones that lets you measure your heart rate or skin temperature. You aren't going to see that sort of product on sale if the product makers have to pay to go thru testing for regulatory approval.

Smart phones give us the compute power in our pockets that we need to monitor and analyze our bodies. Now all we need are the sensors to plug into the phones. THen we can start learning useful information our metabolisms.

By Randall Parker    2010 August 18 11:16 PM   Entry Permalink | Comments (6)
2010 March 30 Tuesday
Lab Tests Coming To MD Offices And Worn On Body

Having your blood sent to a lab for testing is so 20th century.

In an office park in Woburn, MA, a volunteer presents his fingertip for a quick finger stick. A phlebotomist wicks up the small drop of blood with a specially made square of plastic, then snaps the plastic into a credit-card sized microfluidics cartridge and feeds it into a special reader. Fifteen minutes later, the device spits out the volunteer's prostate specific antigen (PSA) level, a protein used to monitor the return of prostate cancer after treatment.

Microfluidics will move many lab tests to doctors' offices.

The rapid results are possible because of a novel microfluidics technology developed by startup Claros Diagnostics, which hopes to make quick PSA screening in the doctor's office a reality.

In the longer run microfluidic testing will move to the home and office. Why have to go anywhere to get tested? I see a future where your own house will have biomedical sensors embedded in it that do continuous monitoring for early indicators of health problems.

How big of a regulatory obstacle stands in the way of drug stores providing walk-in blood testing and other testing services? One shouldn't have to see a doctor in order to get screened for cholesterol, blood sugar, and other commonly used tests.

We will wear some types of medical testing devices including contact lenses that monitor existing glaucoma to detect worsening symptoms.

Glaucoma is the second most common cause of blindness, and without constant vigilance it can prove a very difficult disease to manage. But a Swiss biotech company has developed a monitoring system that allows physicians to keep track of their patients' symptoms over 24 hours. Sensimed's "Triggerfish" system consists of a contact lens with embedded sensors that can pick up subtle physical changes in a patient's eye, and then wirelessly transmit that data to a receiver worn around his neck.

Imagine a watch or perhaps your cell phone alerting you when an embedded miniature blood sensor reports you've eaten too much junk food. Worn, surgically embedded, and injected sensors will become very popular due to their ability to provide lab test results at a moment's notice.

By Randall Parker    2010 March 30 11:21 PM   Entry Permalink | Comments (0)
2010 March 20 Saturday
Mini Laboratory For MD Offices

Why make a second visit to your doctor to discuss test results when the tests can be completed during your first visit?

In a joint project, researchers from seven Fraunhofer institutes have developed a modular platform for in vitro diagnosis which enables various types of bioanalysis – of blood and saliva for example – to be conducted in the doctor’s surgery. Thanks to its modular design our IVD platform is so flexible that it can be used for all possible bioanalytical tasks, states Dr. Eva Ehrentreich-Förster from the Fraunhofer Institute for Biomedical Engineering (IBMT) in Potsdam-Golm. The core element of the mini-laboratory is a disposable cartridge made of plastic which can be fitted with various types of sensor. For an analysis the doctor fills the cartridge with reagents – binding agents which indicate the presence of certain substances such as antigens in the specimen material. Various tests or assays are available for different types of analysis. To perform an assay, the doctor only has to place the relevant substances in the cartridge and the test then takes place automatically. »We have optimized the assays so that up to 500 assay reactions can be conducted in parallel in a single analysis step, explains Dr. Ehrentreich-Förster. Even in the case of complex analyses the doctor obtains a result within about 30 minutes. A new module on the reverse side of the cartridge also makes it possible to analyze the specimen material at DNA level.

Of course one logical future step is to make miniature test labs so cheap and easy to use that you can do your own testing at home. Beyond that comes embeddable devices that will monitor your blood chemistry from within your body. Then your cell phone will query the embedded sensor devices, pass up the results to a medical diagnostic server somewhere on the web, and then pass back down to you the news that you need to stop at a drug store to pick up a drug that is waiting for you.

Even without home medical testing it should become possible to avoid going to a doctor's office. Just as some drug stores have automated blood pressure testing devices they could also have miniature automated medical testing labs. The test results could be used by expert system software to recommend over-the-counter treatments or refer you to a doctor's office if the test results suggest a prescription-only drug is needed as a treatment.

By Randall Parker    2010 March 20 12:45 PM   Entry Permalink | Comments (8)
2010 February 15 Monday
Progress On Nanotech For DNA Sequencing

The ultimate DNA sequencing devices will process individual strands of DNA, one letter at a time, thru measuring gates. Arizona State University researcher Stuart Lindsay leads a team using nanotech to read strands of DNA.

Lindsay's team relies on the eyes of nanotechnology, scanning tunneling- (STM) and atomic force- (ATM) microscopes, to make their measurements. The microscopes have a delicate electrode tip that is held very close to the DNA sample. In their latest innovation, Lindsay's team made two electrodes, one on the end of microscope probe, and another on the surface, that had their tiny ends chemically modified to attract and catch the DNA between a gap like a pair of chemical tweezers. The gap between these functionalized electrodes had to be adjusted to find the chemical bonding sweet spot, so that when a single chemical base of DNA passed through a tiny, 2.5 nanometer gap between two gold electrodes, it momentarily sticks to the electrodes and a small increase in the current is detected. Any smaller, and the molecules would be able to bind in many configurations, confusing the readout, any bigger and smaller bases would not be detected.

"What we did was to narrow the number of types of bound configurations to just one per DNA base," said Lindsay. "The beauty of the approach is that all the four bases just fit the 2.5 nanometer gap, so it is one size fits all, but only just so!"

At this scale, which is just a few atomic diameters wide, quantum phenomena are at play where the electrons can actually leak from one electrode to the other, tunneling through the DNA bases in the process. Each of the chemical bases of the DNA genetic code, abbreviated A, C, T or G, gives a unique electrical signature as they pass between the gap in the electrodes. By trial and error, and a bit of serendipity, they discovered that just a single chemical modification to both electrodes could distinguish between all 4 DNA bases.

"We've now made a generic DNA sequence reader and are the first group to report the detection of all 4 DNA bases in one tunnel gap," said Lindsay. "Also, the control experiments show that there is a certain (poor) level of discrimination with even bare electrodes (the control experiments) and this is in itself, a first too."

The computer revolution has been driven by rapidly making devices of ever smaller sizes. Smaller is cheaper and faster. The same drive to smaller scale in biotechnology makes the rate of advance in biotech look more like the very fast rate of advance in computing. I am optimistic about the prospects for developing rejuvenation therapies mainly because of this drive to attack biological problems at much smaller scale which enables greater precision, finer control, more automation, and therefore much lower costs.

By Randall Parker    2010 February 15 05:37 PM   Entry Permalink | Comments (1)
2010 January 03 Sunday
New Technique Sequences Old DNA

Caveman DNA to reveal all.

DNA that is left in the remains of long-dead plants, animals, or humans allows a direct look into the history of evolution. So far, studies of this kind on ancestral members of our own species have been hampered by scientists' inability to distinguish the ancient DNA from modern-day human DNA contamination. Now, research by Svante Pääbo from The Max-Planck Institute for Evolutionary Anthropology in Leipzig, published online on December 31st in Current Biology — a Cell Press publication — overcomes this hurdle and shows how it is possible to directly analyze DNA from a member of our own species who lived around 30,000 years ago.

The ability to sequence individual DNA strands allows the scientists to recognize which pieces of DNA really are ancient. So 30,000 year old DNA can be sequenced.

Using the remains of humans that lived in Russia about 30,000 years ago, Pääbo and his colleagues now make use of the latest DNA sequencing (i.e., reading the sequence of bases that make up the DNA strands) techniques to overcome this problem. These techniques, known as "second-generation sequencing," enable the researchers to "read" directly from ancient DNA molecules, without having to use probes to multiply the DNA. Moreover, they can read from very short sequence fragments that are typical of DNA ancient remains because over time the DNA strands tend to break up. By contrast, DNA that is younger and only recently came in contact with the sample would consist of much longer fragments. This and other features, such as the chemical damage incurred by ancient as opposed to modern DNA, effectively enabled the researchers to distinguish between genuine ancient DNA molecules and modern contamination. "We can now do what I thought was impossible just a year ago – determine reliable DNA sequences from modern humans - but this is still possible only from very well-preserved specimens," says Pääbo.

I expect these 30,000 year old humans to be genetically different than us in important ways. For an argument on why that should be so see an excellent book by Greg Cochran and Henry Harpending entitled The 10,000 Year Explosion: How Civilization Accelerated Human Evolution.

By Randall Parker    2010 January 03 11:45 PM   Entry Permalink | Comments (1)
Carbon Nanotubes For DNA Sequencing

Carbon nanotubes can measure electrical fields of individual DNA letters.

Faster sequencing of DNA holds enormous potential for biology and medicine, particularly for personalized diagnosis and customized treatment based on each individual's genomic makeup. At present however, sequencing technology remains cumbersome and cost prohibitive for most clinical applications, though this may be changing, thanks to a range of innovative new techniques.

In the current issue of Science, Stuart Lindsay, director of Arizona State University's Center for Single Molecule Biophysics at the Biodesign Institute, along with his colleagues, demonstrates the potential of one such method in which a single-stranded ribbon of DNA is threaded through a carbon nanotube, producing voltage spikes that provide information about the passage of DNA bases as they pass through the tube—a process known as translocation.

This technique is nowhere near ready for production use. But it illustrates where biology is going: manipulate individual molecules using nanotechnology. As computer chip manufacturing advances have shown, the smaller things can be made the lower costs can drop. Carbon nanotubes and other nano components will be used to make nanodevices for doing biological assays and manipulations. DNA will be sequenced and synthesized by cheap small devices. DNA sequencing machines will some day be hand held.

Miniaturization of computing and communication technologies led to the cell phone and texting. The resulting reshaping of personal interactions illustrates how technology that each person can hold will change how we relate to each other. I argue that something similar will happen with personal DNA sequencers. People will check out each others' DNA sequences in mating situations such as in bars and night clubs. In some cases the DNA samples will be gotten surreptitiously (e.g. kiss someone while running fingers thru their hair to get hair ends with cells on them). In other cases potential mates will simply demand some spit to check out. People will choose others based on odds of personality traits and other characteristics at least partially controlled by genes.

By Randall Parker    2010 January 03 10:40 PM   Entry Permalink | Comments (0)
2009 December 02 Wednesday
Desktop Drug Gene Tester For Hospitals

A start-up is aiming a genetic testing machine at hospitals and doctors offices.

A desktop instrument recently approved by the U.S. Food and Drug Administration might finally bring pharmacogenomic testing--the use of a patient's genetic information for drug prescription decisions--to the mainstream. The device, made by Nanosphere, a startup based in Northbrook, IL, can, in a matter of hours, detect genetic variations in blood that modulate the effectiveness of some drugs. Dubbed Verigene, the technology employs a combination of microfluidics and nanotechnology, housed in a single plastic cartridge, to pull DNA from a blood sample and then screen it for the relevant sequences.

Microfluidics and nanotechnology moving into the marketplace.

Genetic variations affect how we respond to drugs in a number of ways. For example, genetic variants in liver enzymes determine the rate at which the liver will break down drugs and even how drugs will get broken down. Still more genetic variants influence whether the drugs will cause harmful side effects and how well or poorly drugs will work. The ability to test a patient in a matter of hours will allow a hospital's staff to decide which drugs to use, at which doses, and whether additional precautions are needed such as aggressive monitoring of heart, liver, and other organ functionality.

The value of genetic testing for drug compatibility is going to rise due to the torrent of genetic testing data getting generated by researchers who suddenly have much cheaper ways to do genetic testing and DNA sequencing.

In a way this is a transitional technology. In a few decades (if not sooner) most people will get their DNA sequenced at birth. Then either a big internet server databases will hold each person's DNA sequence for emergency hospital use or each person will have an implanted machine-readable record of their DNA sequence for fast scanning in an emergency ward.

But desktop DNA testing is also a step down the road toward personal surreptitious DNA testing and DNA sequencing. Bars, clubs, and other mating scenes will some day be big locations for stealing saliva and tissue samples to test someone's DNA to decide whether to pursue a relationship or steal some sperm in a one night stand for single motherhood.

By Randall Parker    2009 December 02 03:25 PM   Entry Permalink | Comments (3)
2009 September 01 Tuesday
More Sensitive Cancer Breathalyzer Developed

Higher levels of volatile organic compounds in the breath serve as markers for lung cancer.

Lung cancer is a brutal disease, often not caught until it's too late for treatment to do much good. Now researchers are building an electronic nose that could help physicians detect the disease during its initial stages. Using gold nanoparticles, scientists at the Israel Institute of Technology in Haifa have created sensors with an unprecedented sensitivity for sniffing out compounds present in the breath of lung-cancer patients.

Many of the highly sensitive disease detector assay devices will end up portable for use at home or work. People will test themselves every day or week as they are inclined. For some tests there won't even be need for a person to initiate testing. One's bed stand or sink or toilet will have sensors built in that constantly scan for tell tale signs.

What I want: something that tells me when my sleep deficit is getting too big. Though such a device would probably have the effect of prodding me to go to sleep rather than write that last blog post of the day.

By Randall Parker    2009 September 01 10:42 PM   Entry Permalink | Comments (1)
2009 April 21 Tuesday
Cell Phones Display Ultrasound Images

Another step closer to the medical tricorder.

Computer engineers at Washington University in St. Louis are bringing the minimalist approach to medical care and computing by coupling USB-based ultrasound probe technology with a smartphone, enabling a compact, mobile computational platform and a medical imaging device that fits in the palm of a hand.

I see this as part of a trend that amounts to a sort of democratization of medical testing. While this instrument at its current stage of development still requires an expert to wield it that won't always be the case. Small stuff costs less. It just has to become more powerful and more able to analyze images to discern what they mean without human expertise.

One way ultrasound for the masses could work is for the images to be sent via 4G and other faster wireless networks to a server. Then the server could do the computational heavy lifting to explain the medical significance of the stream of images.

William D. Richard, Ph.D., WUSTL associate professor of computer science and engineering, and David Zar, research associate in computer science and engineering, have made commercial USB ultrasound probes compatible with Microsoft Windows mobile-based smartphones, thanks to a $100,000 grant Microsoft awarded the two in 2008. In order to make commercial USB ultrasound probes work with smartphones, the researchers had to optimize every aspect of probe design and operation, from power consumption and data transfer rate to image formation algorithms. As a result, it is now possible to build smartphone-compatible USB ultrasound probes for imaging the kidney, liver, bladder and eyes, endocavity probes for prostate and uterine screenings and biopsies, and vascular probes for imaging veins and arteries for starting IVs and central lines. Both medicine and global computer use will never be the same.

In the future our houses, cars, and offices will contain embedded medical instruments that watch us during our daily tasks and let us know when we are developing medical conditions. Oh, and our bodies will contain embedded miniaturized medical testing devices that'll let our smart phones know when we have a problem. At least this will happen unless the robots take over first.

By Randall Parker    2009 April 21 11:25 PM   Entry Permalink | Comments (6)
2009 March 05 Thursday
$100 Genome Sequencing In 5 Years?

Will we be able to get our complete genome sequenced for $100 by 2014?

Despite many experts' doubt that whole-genome sequencing could be done for $1,000, let alone a 10th that much, BioNanomatrix believes it can reach the $100 target in five years. The reason for its optimism: company founder Han Cao has created a chip that uses nanofluidics and a series of branching, ever-narrowin­g channels to allow researchers, for the first time, to isolate and image very long strands of individual DNA molecules.

Nanofluidic devices are going to revolutionize biomedical research and medical treatment by lowering testing costs by orders of magnitude. These devices won't just make DNA sequencing cheap. They will make many types of biological testing very cheap, highly automated, and portable. We won't need to go to a doctor's office for most blood tests because blood testers with embedded microfluidic devices will let us test ourselves quickly and cheaply at home.

Cheap portable DNA sequencers will also lead to surreptitious DNA sequencing of people without their awareness. I expect to see this on the dating and bar scene. I also expect to see it in job interview and business negotiation situations. Check to see if your potential employee or business partner has genes that give them cognitive traits to avoid or embrace.

By Randall Parker    2009 March 05 12:12 AM   Entry Permalink | Comments (2)
2008 December 29 Monday
Cell Phones To Become Star Trek Medical Tricorders

Cell phones are already absorbing the functions of handheld games and MP3 music players and look set to replace laptop computers for many functions. Well, the idea of a separate handheld device for medical scanning turns out to be so 1960s. Cell phones will eventually scan blood and saliva.

Cell phones have already revolutionized the way people around the world communicate and do business. Thanks to advances being made at UCLA, they are about to do the same thing for medicine.

In the lab of UCLA electrical engineering professor Aydogan Ozcan, a prototype cell phone has been constructed that is capable of monitoring the condition of HIV and malaria patients, as well as testing water quality in undeveloped areas or disaster sites. The innovative imaging technology was invented by Ozcan, a member of the California NanoSystems Institute at UCLA, and has been miniaturized by researchers in his lab to the point that it can fit in standard cell phones.

The imaging platform, known as LUCAS (Lensless Ultra-wide-field Cell monitoring Array platform based on Shadow imaging), has now been successfully installed in both a cell phone and a webcam. Both devices acquire an image in the same way, using a short wavelength blue light to illuminate a blood, saliva or other fluid sample. LUCAS captures an image of the microparticles in the solution using a sensor array.

So you will feel lousy, point your cell phone at your mouth as you stick out your tongue, and the cell phone will tell you what ails you. Beyond what is getting reported here I also expect eventually cell phones will either contain microfluidic devices (i.e. lab-on-a-chip) or will provide a UI into microfluidic devices. The cell phone will report the test results to an A.I. running on a server and will direct you to a local drug store to pick up a treatment.

Dr. McCoy won't even enter into it.

By Randall Parker    2008 December 29 08:43 PM   Entry Permalink | Comments (0)
2008 November 23 Sunday
Microfluidic Chip Tests For Cancer In 10 Minutes

Microfluidic chips will get more powerful every year just like computer processors and will drive down the cost of medical testing by orders of magnitude.

Measuring proteins in the blood can help doctors determine patients' cancer risk and monitor the health of the elderly and people with chronic diseases. But current methods for testing these proteins are too expensive and require too much blood to be performed regularly. A microfluidic chip in clinical trials does on a single chip in 10 minutes what normally takes multiple technicians hours to do--and with just a single drop of blood. Researchers hope to make bedside diagnostics based on blood proteins a reality by bringing down the cost of such tests by at least an order of magnitude.

The diagnostic chip is being developed by Caltech chemistry professor James Heath and by Leroy Hood, the president and founder of the Institute for Systems Biology, in Seattle. Heath and Hood have founded a company called Integrated Diagnostics to commercialize the blood chip.

Microfluidic chips will eventually show up at home and people will test themselves using a home lab kit at very low cost. A laptop or smart phone will display the test results. The number of diseases these chips can detect will grow enormously and the chips will allow diagnosis at much earlier stages of disease development. This will of course help cure cancer before it metastasizes. But it will also enable much earlier and successful intervention in many other disease processes.

Home testing will lead to computer expert systems for home diagnosis. The data will be at home. Why not upload the daily test results to a web site that monitors for trends and detects bad test results? This will tend to decrease the role of doctors as diagnosticians and leave them more in the role of treatment deliverers. Though eventually automated systems for preparation of stem cell and gene therapies will cut back the need for doctors to deliver treatments.

Rejuvenation therapies and therapies that boost the immune system will cut the incidence of disease. In the long run doctors will spend almost all their time delivering rejuvenation therapies, enhancement therapies (including for appearances, athletics, and even cognitive function), and emergency treatments for accidents and assaults.

Update: The researchers expect their chip design will be far more powerful in another year.

The chip offers a significant improvement over the cost and speed of standard laboratory tests to analyze proteins in the blood. In traditional tests, one or more vials of blood are removed from a patient's arm and taken to a laboratory, where the blood is centrifuged to separate whole blood cells from the plasma. The plasma is then assayed for specific proteins. "The process is labor intensive, and even if the person doing the testing hurries, the tests will still take a few hours to complete," says Heath. A kit to test for a single diagnostic protein costs about $50.

"We wanted to dramatically lower the cost of such measurements, by orders of magnitude," he says. "We measure many proteins for the cost of one. Furthermore, if you reduce the time it takes for the test, the test is cheaper, since time is money. With our barcode chip, we can go from pinprick to results in less than 10 minutes."

A single chip can simultaneously test the blood from eight patients, and each test measures many proteins at once. The researchers reported on devices that could measure a dozen proteins from a fingerprick of blood, and their current assays are designed for significantly more proteins. "We are aiming to measure 100 proteins per fingerprick within a year or so. It's a pretty enabling technology," Heath says.

Microfluidic chip power will continue to increase rapidly. More tests will be done in a doctor's office while you wait. Further out more tests will be done routinely at home at much more frequent intervals. Costs will plummet by orders of magnitude and the tests will become far more sensitive.

By Randall Parker    2008 November 23 09:50 PM   Entry Permalink | Comments (1)
2008 October 26 Sunday
Assay Tools Watch Gene Expression During Common Cold Infection

Here's an example of scientific questions biologists can now ask due to advances in assaying tools. Scientists can watch the effects of a rhinovirus (one of the several families of viruses that cause the common cold) on human gene expression in the nasal passages. This will help guide development of treatments to reduce the symptoms and spread of viruses that cause the common cold.

"Advances in genomics technology now allow us to analyze tens of thousands of genes in the same amount of time required to analyze just a handful of genes just a decade ago," said Jay Tiesman, P&G Genomics Group Leader and study author.

Forty-eight hours after inoculation, the expression of 6,530 genes in infected volunteers were significantly either up-regulated or down-regulated compared to the same genes in the control group. In other words, rhinovirus infection triggered a massive immune response in the nasal mucosa. Because rhinovirus is not as destructive as other more serious viral infections, this response appears to be disproportionate to the threat.

Gene expression testing and gene sequencing tools have become so powerful so quickly that we aren't yet seeing the results at the clinical level of treatments. Advanced assaying tools are enabling the asking and answering of questions which couldn't be approached a decade ago. Because of the continuing big increases in ability to measure gene expression I expect many heretofore incurable diseases to finally become curable. Even the common cold will meet its defeat.

The cold causes an excess of inflammation.

The researchers classified the active genes according to function, and found many involved in a process known as chemotaxis, which recruits various immune cells to the site of infection. These particular genes have been correlated with symptoms such as inflammation, congestion and runny nose. Other groups of active genes have also been classified; among them are genes which make antiviral compounds thought to help thwart infections.

"This study shows that after rhinovirus infection, cold symptoms develop because parts of our immune system are in overdrive," said Lynn Jump, Principal Researcher at P&G and study author. "The findings are important because they provide us a blueprint for developing the ideal cold treatment: one that maintains the body's natural antiviral response while normalizing the inflammatory response."

I would say the ideal cold treatment would be a vaccine that vaccinates against a large variety of cold viruses.

By Randall Parker    2008 October 26 11:20 PM   Entry Permalink | Comments (0)
2008 September 20 Saturday
Handheld DNA Testers On Horizon

Microfluidic lab-on-a-chip technology brings within sight hand-held field deployable DNA testers.

September 18, 2008 — Using new "lab on a chip" technology, James Landers hopes to create a hand-held device that may eventually allow physicians, crime scene investigators, pharmacists, even the general public, to quickly and inexpensively conduct DNA tests from almost anywhere, without need for a complex and expensive central laboratory.

"We are simplifying and miniaturizing the analytical processes so we can do this work in the field, away from traditional laboratories, with very fast analysis times, and at a greatly reduced cost," said Landers, a University of Virginia professor of chemistry and mechanical engineering and associate professor of pathology.

Crime scene testing has obvious value. But that won't be the biggest application. Guess what will be? Bar and club testing of prospective mates. Qualify prospective mates for likely personality characteristics. Looking for good material for a longer term relationship? Check their genetic profile. I figure women will find this especially useful. Guys who are looking for one night stands won't care as much.

This group does not have a chip ready for field deployment. But Landers says something important here: the micro-chip field has matured to the point where such a field-deployable handheld DNA tester is now within technological reach.

"This area of research has matured enough during the last five years to allow us to seriously consider future possibilities for devices that would allow sample-in, answer-out capabilities from almost anywhere," he said.

Landers and a team of researchers at U.Va., including mechanical and electrical engineers, with input from pathologists and physicians, are designing a hand-held device — based on a unit the size of a microscope slide — that houses many of the analytical tools of an entire laboratory, in extreme miniature. The unit can test, for example, a pin-prick-size droplet of blood, and within an hour provide a DNA analysis.

A device that can work from saliva or skin flakes will allow more surreptitious testing.

Women determined to have a kid but who have given up on finding a guy to help raise a child (or who simply don't want a guy around) will find this technology useful. A woman who has decided to get pregnant from a one night stand (and I know a woman who did this) could use a handheld DNA tester to decide whether a candidate in a bar has the right stuff to contribute to her baby's DNA.

European researchers think they can develop credit card sized disposable microfluidic testers for less than 50 euros.

Researchers in the European SEMOFS (Surface Enhanced Micro Optical Fluidic Systems) team knew that, to reach their goal of disposable cartridges capable of performing complex medical diagnostic tests quickly and at low cost, they would have to push existing technology to the limit.

“We are targeting state-of-the-art sensitivities or better,” says Jerôme Gavillet, the dissemination coordinator of SEMOFS, “in a system that could be available anywhere for less than €50.”

The team’s goal is a polymer-based device the size of a credit card that would incorporate sophisticated technologies to control the movement of biological fluids, detect the presence of specific proteins, for example early signs of cancer, and analyse the results.

“For each patient, a physician would open the package, put some blood or serum on the card, let it work, and then connect it to a card reader,” says Gavillet.

The relatively inexpensive card reader would display and record what the card had measured.

DNA testing in club and bar scenes wouldn't even have to be surreptitious in many cases. So a woman goes to a club. Some guy hits on her and tries to get her to go home with him. She demands a DNA sample. What's he going to do? Say no? He doesn't have much downside from saying yes. She pulls out a card. Scraps some skin off his inner cheek. Puts sample material into the end of the card. It processes. Then she pulls out a PDA which has a slot to insert the card. She slides in the card and the PDA runs an analysis program she previously downloaded. It tells her the red and green flags based on an ideal profile she previously chose. To get to her desired profile she might have hired a genetic counselor a few months before that bar encounter.

Now, if she likes his qualities but he's short of ideal maybe she takes a pill to prevent pregnancy but goes home with him anyhow.

By Randall Parker    2008 September 20 10:21 PM   Entry Permalink | Comments (3)
2008 September 06 Saturday
MicroRNAs In Blood Show Patterns For Cancer And Pregnancy

A group of researchers in Nanjing China have demonstrated that each type of cancer shows a unique fingerprint of types of microRNA in the blood. This opens up the possibility of cheap screening for cancer detection.

Serum microRNAs (miRNAs) can serve as biomarkers for the detection of diseases including cancer and diabetes, according to research published online this week in Cell Research. The findings pave the way for a revolutionary non-invasive diagnostic tool.

“Nowadays, almost all of the routinely used serum markers are proteins and the conventional methodologies used to measure them remain labor-intensive. No serum-based test is currently suitable for widespread use in diseases diagnosis, particularly in early tumor detection,” said Chen-Yu Zhang of School of Life Sciences, Nanjing University. “Our goal therefore was to discover a novel class of serum biomarkers for clinic uses, even for drug screening and personalized medicine.”

miRNAs are a class of naturally occurring small non-coding RNAs that have been linked with cancer development. Recent studies reporting individual miRNAs as diagnostic biomarkers of specific cancers were unable to rule out the possibility that these miRNAs appeared as a result of contamination.

Chen-Yu Zhang and colleagues are the first to comprehensively characterize entire blood miRNA profiles of healthy subjects and patients with lung cancer, colorectal cancer and diabetes, ruling out contamination. They propose that the specific serum miRNA expression profiles they identified constitute ‘fingerprints’ for cancer and disease.

But will diagnosis using microRNAs lead to cancer cures? Detection at early stage is key. Longitudinal studies that watch the same subjects from healthy starting points until disease diagnosis are probably needed in order determine whether microRNAs will allow early detection of cancer. Early stages of these studies could probably be conducted first in mice and other species with shorter lives where the time between healthy to cancerous is shorter.

Separately an Israeli group has just published a paper in Plos One where they demonstrate that circulating microRNA show distinct patterns between pregnant and non-pregnant women.

Finally, as a proof of concept, we investigated whether circulating microRNAs can be used to identify clinical conditions. It has been established that circulating maternal RNA contains placental embryonic RNA [2]. Therefore, we chose to compare the serum microRNA abundance profiles of non pregnant versus pregnant women, the latter in either their first or third trimester. We measured the serum levels of 28 microRNAs, including microRNAs reported to be placenta-specific [10], [20] as well as broadly expressed microRNAs. Box plots show relative microRNA levels in the sera of 10 non pregnant women, 10 women in the first trimester and 10 women in the third trimester (Figure 4A). The median fold changes in microRNA levels comparing third trimester pregnant women to non pregnant women are detailed in Table 1. MicroRNAs expressed equivalently across all samples were used for normalization. All of the placental microRNAs are found at higher levels in the sera from pregnant women, their levels rising with gestational age, and the levels of 12 microRNAs increased by more than 5-fold. Specifically, amounts of hsa-miR-526a and hsa-miR-527 are dramatically higher in the sera of third trimester pregnant women (elevated by more than 600 fold). Indeed, we found that the levels of three placental microRNAs (hsa-miR-526a, hsa-miR-527 and hsa-miR-520d-5p) could be used to accurately distinguish pregnant from non pregnant women (Figure 5).

This seems like a technology that could be commercialized pretty quickly. If microRNAs can detect cancers at early stages then going to the doctor a few times a year for periodic microRNA tests might replace many uses of colonoscopy, mammography, pap smears, and other early stage cancer tests.

I expect that microRNA expression patterns change with age and at different rates for different people. This might lead to more accurate ways to predict life expectancy. But will that allow extension of life expectancies? Or will it just give people a better idea of how much to save for retirement?

By Randall Parker    2008 September 06 08:14 PM   Entry Permalink | Comments (0)
2008 August 20 Wednesday
Skin Cancer Detected As Airborne Chemical Profile

Here's a capability needed for Dr. McCoy's medical tricorder.

PHILADELPHIA, Aug. 20, 2008 — Chemists today described the first identification of a specific "odor profile" for skin cancer, a discovery that could form the basis of a rapid, non-invasive test for diagnosing the most common type of cancer in the United States. The findings may enable doctors in the future to diagnose skin cancer quickly and accurately by waving a handheld scanner or sensor above the skin, they reported today at the 236th national meeting of the American Chemical Society.

Note how they refer to doctors of the future using scanners to detect skin cancer. But once the technology becomes cheap enough it would make much more sense to embed cancer detection sensors in bathrooms, living rooms, and bed rooms. Scanning for cancer should become a daily practice in order to allow cancer to get detected at the earliest possible stage in development.

The researchers have found distinct patterns in the airborne chemicals that evaporate off of the surface of normal and cancerous skin cells. They expect nano-sensors to eventually allow the development of compact sensing equipment.

To examine whether skin odors change in people with skin cancer, Gallagher and colleagues used advanced chromatography techniques to sample and analyze the air above tumor sites in 11 patients diagnosed with basal cell carcinoma, the most common type of skin cancer with more than one million new cases every year. They compared the profile of chemicals detected above the tumor sites to profiles obtained from skin of 11 individuals without cancer.

"We found a different profile of chemicals above tumor sites relative to healthy skin," says Gallagher. "The same chemicals are present, but at skin cancer sites some chemicals are increased, while others are decreased compared to healthy individuals." She declined to give specific details about the chemicals found, noting that the researchers had applied for a patent on their technique.

The scientists eventually plan to identify a reliable "odor profile" of all three forms of skin cancer, including squamous cell cancer and melanoma, the deadliest form. If successful, the researchers hope to combine their method with emerging nano-sensor "electronic nose" technology designed to identify odorous chemicals. Gallagher envisions a wand-like "E-nose" that can be moved across the skin and will set off an alarm or beep when cancer is detected, similar to the fictional medical "tricorder" from Star Trek.

One can imagine beds, sinks, toilets, and other locations in a house will all some day have sensors embedded in them that detect a large assortment of diseases at very early stages. Early detection will reduce the total amount of accumulated damage and will make cures much easier for some diseases like cancer.

By Randall Parker    2008 August 20 10:48 PM   Entry Permalink | Comments (3)
2008 July 29 Tuesday
$10 Microscope On A Chip

Smaller and cheaper is the future of biotechnology.

PASADENA, Calif.--Researchers at the California Institute of Technology have turned science fiction into reality with their development of a super-compact high-resolution microscope, small enough to fit on a finger tip. This "microscopic microscope" operates without lenses but has the magnifying power of a top-quality optical microscope, can be used in the field to analyze blood samples for malaria or check water supplies for giardia and other pathogens, and can be mass-produced for around $10.

"The whole thing is truly compact--it could be put in a cell phone--and it can use just sunlight for illumination, which makes it very appealing for Third-World applications," says Changhuei Yang, assistant professor of electrical engineering and bioengineering at Caltech, who developed the device, dubbed an optofluidic microscope, along with his colleagues at Caltech.

The new instrument combines traditional computer-chip technology with microfluidics--the channeling of fluid flow at incredibly small scales. An entire optofluidic microscope chip is about the size of a quarter, although the part of the device that images objects is only the size of Washington's nose on that quarter.

We will someday have cheap automated medical instrumentation installed in our bathroom sinks, toilets, and bed stands, watches, glasses, and other things in our environment so that we get constantly, rapidly, but unobtrusively tested far more extensively than a hospital can today. Our home computers will let us know when we have a medical problem that needs attention.

By Randall Parker    2008 July 29 11:54 PM   Entry Permalink | Comments (6)
2008 April 08 Tuesday
First Single Strand DNA Sequencing Demonstrated

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.

By Randall Parker    2008 April 08 11:21 PM   Entry Permalink | Comments (0)
2008 March 09 Sunday
Miniature Cell Sorter For Cancer Detection 5 Years Away?

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.

By Randall Parker    2008 March 09 03:02 PM   Entry Permalink | Comments (6)
2007 December 22 Saturday
$350,000 Full Personal Genome Sequencing Service

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.

...

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 they can so far 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.

By Randall Parker    2007 December 22 10:48 PM   Entry Permalink | Comments (8)
2007 September 28 Friday
New Technology Detects Human Genetic Structural Variations Faster

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.

By Randall Parker    2007 September 28 10:32 AM   Entry Permalink | Comments (5)
2007 February 26 Monday
Mini Lung Cancer Sensor Detects Most Cases

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.

By Randall Parker    2007 February 26 12:10 AM   Entry Permalink | Comments (4)
2006 March 14 Tuesday
Blood Protein Test Orders Of Magnitude More Sensitive

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.

By Randall Parker    2006 March 14 10:41 PM   Entry Permalink | Comments (3)
2005 May 08 Sunday
Growing Use Of DNA Testing Seen In Drug Development

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.

By Randall Parker    2005 May 08 12:05 PM   Entry Permalink | Comments (2)
2005 April 27 Wednesday
Electronic Nose Can Detect Lung Cancer

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.

By Randall Parker    2005 April 27 02:06 AM   Entry Permalink | Comments (4)
USC Scientists Develop HUTT 3-D Ultrasound Imaging Scanner

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.

By Randall Parker    2005 April 27 01:17 AM   Entry Permalink | Comments (8)
2004 November 10 Wednesday
New PET Brain Scan Method Detects Early Alzheimer's Plaque Build-Up

Two PET scanning techniques promise to provide a way to detect early Alzheimer's Disease beta amyloid plaque build-up.

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.

By Randall Parker    2004 November 10 06:53 PM   Entry Permalink | Comments (1)
2004 May 24 Monday
Handheld Nose Odor Sensor Diagnoses Pneuomia

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.

By Randall Parker    2004 May 24 01:15 PM   Entry Permalink | Comments (3)
2004 January 23 Friday
UCSD Researchers Develop New Way To Look At 3-D Protein Structures

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.

By Randall Parker    2004 January 23 01:29 PM   Entry Permalink | Comments (0)
2003 September 24 Wednesday
Optical Fibers To Be Used To Catch Pre-Cancerous Lesions

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.

By Randall Parker    2003 September 24 12:06 PM   Entry Permalink | Comments (0)
2003 August 21 Thursday
CD Player Turned Into Bioassay Molecule Detection Instrument

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.

By Randall Parker    2003 August 21 03:00 PM   Entry Permalink | Comments (6)
2003 June 12 Thursday
Multiphoton Microscopy Allows 3-D Live Tissue Imaging

Optical biopsies on horizon using noninvasive biomedical imaging technique developed by Cornell-Harvard group.

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?

By Randall Parker    2003 June 12 03:44 PM   Entry Permalink | Comments (0)
2003 May 24 Saturday
Roche AmpliChip To Test Genes For Personalized Drug Selection

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.

Roche and Epigenomics are working on a three year collaboration to bring DNA methylation tests to market for use in making more personalized choices of best cancer treatments.

"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.

By Randall Parker    2003 May 24 05:47 PM   Entry Permalink | Comments (3)
2003 April 19 Saturday
Contact Lens Color To Show Diabetic Blood Sugar Level

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.

By Randall Parker    2003 April 19 01:57 AM   Entry Permalink | Comments (6)
2003 January 19 Sunday
Easier DNA Sequence Detection Method Developed

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.

By Randall Parker    2003 January 19 04:21 PM   Entry Permalink | Comments (1)
2002 November 05 Tuesday
In Vivo Bioluminescence Used To Track Virus Infection

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.

By Randall Parker    2002 November 05 02:10 PM   Entry Permalink | Comments (1)
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