Thursday, November 19, 2009
Enigma ML System for Quick and Easy PCR
This week at MEDICA2009 in Düsseldorf, Enigma Diagnostics out of Wiltshire, UK is unveiling its new polymerase chain reaction (PCR) apparatus. The Enigma ML provides almost fool proof testing using single disposable reagent cartridges, and can be expanded to run multiple PCR tests in parallel using one control unit.
The Enigma ML has a modular, easily scalable architecture providing flexibility and choice in different healthcare settings. At entry level with a single processing module it is a compact, portable, inexpensive instrument ideally suited to settings where usage is lower and space is a premium e.g. in the doctor's office, pharmacy or intensive care unit. At the other end of the scale, multiple processing modules can be controlled by a single master unit allowing random-access, parallel running of different samples and tests.It incorporates a clever, disposable cartridge which can accommodate either liquid or swab samples without any requirements for manual processing. All reagents and sample preparation tools are held on the self-contained cartridge and all steps are automated, minimising the risk of human error. The instrument also has a simple to use touch-screen for data entry and result reporting, plus an integrated label printer.
The system can perform multiplex, real-time PCR assays for both DNA and RNA targets.
Key features:
Fully automated real-time PCR system
rapid test (30 ~ 45 minutes to result)
multi-sample and scalable
accepts swabs and liquids (e.g. urine, blood plasma)
integrated sample preparation and analysis
low system price
small footprint (no specialist skills or cold storage requirements)
Product page: Enigma ML ...
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Tuesday, November 17, 2009
Ultrafast Lab-on-a-Chip for Detection of Disease Biomarkers
Researchers from IBM Research in Zurich and the University Hospital of Basel in Switzerland developed a microfluidic device that uses capillary action to detect the presence of protein biomarkers for various disease types. The five square centimeter silicon-based lab-on-a-chip takes only fifteen seconds to perform its analysis.
Here are the five functional stages of the device:
Stage 1: A one microliter sample, 50 times smaller than a tear drop, is pipetted onto the chip, where the capillary forces begin to take effect.
Stage 2: These forces push the sample through an intricate series of mesh structures, which prevent clogging and air bubbles from forming.
Stage 3: The sample then passes into a region where microscopically small amounts of the detection antibody have been deposited. These antibodies have a fluorescent tag and similar to the antibodies within our body, they recognize the disease marker and attach to it within the sample. Only seventy picoliters (a volume one million times smaller than a tear) of these antibodies are used, making their dissolution in the passing sample extremely fast and efficient.
Stage 4: The most critical stage is called the "reaction chamber" and it measures 30 micrometers in width and 20 micrometers in depth, roughly the diameter of a strand of human hair. Similar to a common pregnancy test, in this stage the disease marker that was previously tagged is captured on the surface of the chamber. By shining a focused beam of red light, the tagged disease markers can be viewed using a portable sensor device that contains a chip similar to those used by digital cameras, albeit this one being much more sensitive. Based on the amount of light detected, medical professionals can visually confirm the strength of the disease marker in the sample to determine the next course of treatment.
Stage 5: Less a stage and more a part of the entire process is the capillary pump. The capillary pump, which has a depth of 180 micrometers, contains an intricate set of microstructures, the job of which is to pump the sample through the device for as long as needed and at a regular flow rate, just like the human heart. This pump makes the test accurate, portable and simple to use. IBM scientists have developed a library of capillary pumps so that tests needing a variety of sample
More from IBM Research: IBM Scientists Reinvent Medical Diagnostic Testing ...
Abstract in Lab on a Chip: Toward one-step point-of-care immunodiagnostics using capillary-driven microfluidics and PDMS substrates
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Monday, October 12, 2009
World's First Bioreactor Monitoring System for iPhone
If you're a lab tech who oversees cell culture growth in DASGIP bioreactor, you'll be happy to know that the firm has released an iPhone app to monitor the device. Perhaps now you can sit down to a round of Halo without too much anxiety about what's going on with your cultures.
Features from the product page:
Monitoring of device and alarm states by colored icons Read and optional write access to process values and set- points Online charts Monitoring of all available reactors from multiple parallel systems Supports network encryption and authentification Supports DASGIP Control user levels and passwords. Uses Microsoft Silverlight or Apple Software technology DASGIP Remote Control meets IT security standards and can be configured according to various IT requirements. Depending on additional services provided at site, extended access may be possible:
Mobile access using iPhone and UMTS
Home access from Windows PC or Mac using a VPN connection
Product page: Remote Access from iPod and Webbrowser to DASGIP Control...
Press release: DASGIP Bioreactor System on the iPhone...
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Thursday, October 8, 2009
IBM's "DNA Transistor" May Lead to Cheap, Rapid DNA Sequencing
Cheap DNA sequencing is a holy grail for geneticists and advocates of personalized medicine. IBM has embarked on its own search for a technology, capable of bringing down personalized genome sequencing to $1,000. The technique they're currently pursuing involves running a DNA thread through a nanopore three nanometers wide. Inside would be an electrical sensor that can distinguish which of the four DNA bases is in proximity. If the DNA can be moved through the nanopore quickly enough with short pauses for base readings, the project researchers believe this approach will make genome sequencing common for clinical applications.
IBM Research is working to optimize a process for controlling the rate at which a DNA strand moves through a nano-scale aperture on a thin membrane during analysis for DNA sequencing. While scientists around the world have been working on using nanopore technology to read DNA, nobody has been able to figure out how to have complete control of a DNA strand as it travels through the nanopore. Slowing the speed is critical to being able to read the DNA strand. IBM scientists believe they have a unique approach that could tackle this challenge.To control the speed at which the DNA flows through the microprocessor nanopore, IBM researchers have developed a device consisting of a multilayer metal/dielectric nano-structure that contains the nanopore. Voltage biases between the electrically addressable metal layers will modulate the electric field inside the nanopore. This device utilizes the interaction of discrete charges along the backbone of a DNA molecule with the modulated electric field to trap DNA in the nanopore. By cyclically turning on and off these gate voltages, scientists showed theoretically and computationally, and expect to be able prove experimentally, the plausibility of moving DNA through the nanopore at a rate of one nucleotide per cycle - a rate that IBM scientists believe would make DNA readable.
Image: A membrane containing the nanopore, funtionalized with metal contacts (orange) separated by dielectric materials (lime), devides a reservoir into a top part containing an ionic solution with a high concentration of single stranded DNA, and a bottom part, where the DNA will be translocated to. The DNA on the top reservoir is induced to go to the bottom reservoir by the action of a biasing voltage. In the absence of anything else, the DNA would translocate through the pore at a speed of several million bases per second. To control the passage of DNA trhough the nano-hole, voltages of appropriate polarity (not shown) are applied to the metal contacts inside the pore, which create an internal electric field that trap the DNA. By alternating the trapping voltages applied to the metal contacts, the DNA can be made ratchet from the top to the bottom reservoirs in a controlled way.
(hat tip: Engadget)
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Philips' New Digital Photomultipliers May Replace Large, Imprecise, Power Hungry Tubes
Scientists at Philips have developed a new fully digital silicon photomultipliers (SiMP's) that may replace detectors within PET scanners as well as open up possibilities for other ultra-sensitive detectors for DNA sequencing and protein/DNA microarrays.
By integrating low-power CMOS electronics into the silicon photomultiplier chip, the team at Philips has developed a digital silicon photomultiplier in which each photon detection is converted directly into an ultra high speed digital pulse that can be directly counted by on-chip counter circuitry. In contrast to conventional silicon photomultipliers, the Philips digital silicon photomultiplier is therefore an all-digital (digital-in/digital-out) device. As a result, it produces faster and more accurate photon counts with extremely well defined timing of the first photon detection, both of which are important factors in applications such as medical imaging scanners and high-energy nuclear particle detectors.The PET system detects pairs of gamma rays (high energy electromagnetic radiation) originating from a radioactive tracer, a small amount of which is injected into the patient prior to the scan. To image metabolic activity, PET typically uses a radioactive derivative of glucose called fluorodeoxyglucose (FDG). This compound mimics the behavior of glucose in the body and can be detected by the PET system.
For so-called ‘time-of-flight’ PET scanners, accurately determining the time at which the first photon arrives at the detector is extremely important. Philips’ digital silicon photomultiplier prototypes achieve a timing accuracy for the detection of the first photon of around 190 ps (full-width, half-maximum using a standard scintillator crystal (LYSO) at 511 keV for two detectors in coincidence).
Conventional silicon photomultipliers (SiPMs) consist of a two-dimensional array of avalanche photodiodes (APDs) each of which is connected in series with its own polysilicon ‘quenching’ resistor. All of these diode/resistor ‘microcells’ are then connected in parallel and the entire microcell array is reverse-biased to a voltage above the diodes’ normal breakdown voltage – typically in the range 30V to 70V. Operating in this so-called ‘Geiger mode’, the diodes are ultra-sensitive to single electron-hole pairs that result in individual diodes experiencing avalanche breakdown. These electron-hole pairs can be generated either by the absorption of a photon (the desired signal), or by thermal energy or electron tunneling (unwanted background noise). The unwanted background noise produced by thermally generated electron-hole pairs and/or electron tunneling, together with false counts due to defective microcells, are collectively referred to as the SiPM’s ‘dark count’.
To eliminate a conventional SiPM’s need for an external digitizing ASIC, the digital silicon photomultiplier developed by Philips equips each individual avalanche photodiode with its own 1-bit on-chip ADC (Analog to Digital Converter) in the form of a CMOS inverter. Each microcell that experiences avalanche breakdown therefore produces its own digital output that is captured, along with the digital outputs from all other triggered microcells, by an on-chip counter. The Philips digital SiPM therefore converts digital events (photon detections) directly into a digital photon count. As a result, it is capable of achieving significantly better resolution than conventional SiPMs.
To overcome the ‘dark count’ problem associated with conventional SiPMs, each microcell in the Philips digital SiPM is also equipped with an addressable static memory cell that can be used to disable or enable the microcell. Microcells that show high dark count levels can therefore be prevented from contributing false counts to the SiPM’s output. This facility allows the Philips’ digital SiPM to achieve better signal-to-noise ratios than conventional devices. Because defective microcells in the array can be disabled, it also helps to improve production yield.
Press release: Philips announces breakthrough in fully digital light detection technology...
Technology backgrounder: PHILIPS' FULLY DIGITAL LIGHT DETECTION TECHNOLOGY (.pdf)...
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Tuesday, September 29, 2009
Cancer Diagnosis Via Semiconductor
Researchers at the University of Toronto, led by Dr. Shana Kelly and Dr. Ted Sargent, are reporting in Nature that they have used a combination of nanoparticles and a microchip to determine the type and severity of a patient's cancer based on the signature of biomarkers that indicate the presence of cancer at the cellular level.
>Dr. Kelly's work demonstrates that the cells can be differentiated with these biomarkers because of the cellular genes that indicate aggressive or benign forms. The scanning electron micrograph illustrates the eight variable structures that the system can repeatably track with less than 5% variation. Analysis time is reported to be 30 minutes as compared with contemporary diagnostics tests which can take days.
The researchers' new device can easily sense the signature biomarkers that indicate the presence of cancer at the cellular level, even though these biomolecules - genes that indicate aggressive or benign forms of the disease and differentiate subtypes of the cancer - are generally present only at low levels in biological samples. Analysis can be completed in 30 minutes, a vast improvement over the existing diagnostic procedures that generally take days."Today, it takes a room filled with computers to evaluate a clinically relevant sample of cancer biomarkers and the results aren't quickly available," said Shana Kelley, a professor in the Leslie Dan Faculty of Pharmacy and the Faculty of Medicine, who was a lead investigator on the project and a co-author on the publication.
"Our team was able to measure biomolecules on an electronic chip the size of your fingertip and analyse the sample within half an hour. The instrumentation required for this analysis can be contained within a unit the size of a BlackBerry."
Press release: U of T researchers create microchip that can detect type and severity of cancer...
Nature: Programming nucleic acids detection sensitivity using controlled nanostructuring
University of Toronto: Shana Kelly Lab
(hat tip: Next Big Future)
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Friday, August 28, 2009
Leica Unveils New Single Cell Imaging Product Line
Leica has just announced a new confocal microscope system that provides one platform for performing common single cell imaging techniques like FLIM (fluorescence lifetime imaging) and FCS (fluorescence correlation spectroscopy). Additionally, the same system allows to use the newer, more precise confirmation methods like FCCS (fluorescence cross-correlation spectroscopy) and FLCS (fluorescence lifetime correlation spectroscopy).
The Leica TCS SMD Series integrates hardware and software from PicoQuant with the high-end confocal system Leica TCS SP5 II. Researchers can now control a complete SMD experiment via one interface, the LAS AF software from Leica Microsystems. The coordination of different hardware and software components for one SMD experiment is now a thing of the past.Complex SMD technologies are no longer complicated due to the user-friendly design of the system series. Quick and easy operation is ensured by dedicated application wizards. They guide the user step-by-step through SMD experiments and significantly maximize the reproducibility of data. With the universal SMD raw data format, one and the same data file can be analyzed in various ways and leads to quantification with maximum content.
Press release: All in One: A Single Platform to Study the Dynamics of Cellular Processes ...
Product pages: Leica TCS SMD FCS, TCS SMD FLIM, TCS SMD FLCS
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Wednesday, August 19, 2009
Stem Cell Concentrator from ThermoGenesis Going to Market
ThermoGenesis out of Rancho Cordova, California is releasing a point-of-care device for concentrating stem cells derived from patients' bone marrow. The company promises a 15 minute processing time and consistently high yields of viable mononuclear cells.
Here's how you operate the Res-Q:
STEP 1 Fill the Res-Q™60 BMC with bone marrow aspirate using a syringe and the supplied clot filter. The needleless port protects the sample from contamination.STEP 2 Place the Res-Q™60 BMC into a benchtop centrifuge and spin at 3200 rpm for 12 minutes to allow for the separation of the bone marrow components and capturing of the buffy coat into the collection chamber.
STEP 3 Remove device from centrifuge and place on processing tray to re-suspend the buffy coat.
STEP 4 Harvest 6-10 mL of a stem cell rich buffy coat. A 12" sterile line is provided to facilitate transfer of sample back into the surgical field if required.
Press release: THERMOGENESIS ANNOUNCES LAUNCH OF RES-Q SYSTEM...
Product page: Res-Q™60 BMC ...
Res-Q™60 BMC product brochure...
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Thursday, August 13, 2009
Systems Biology Graphical Notation: A Visual Language for Biology
Shown above is a summary of the physiology of a neuro-muscular junction in a newly introduced visual language called Systems Biology Graphical Notation (SBGN). Developed to standardize and simplify a knowledge database in an exploding field of Systems Biology, the language is touted to represent "networks of biochemical interactions in a standard, unambiguous way" in order to "foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling."
Caltech has released the following statement about SBGN:
SBGN will make it easier for biologists to understand each other's models and share network diagrams more easily, which, Hucka says, has never been more important than in today's era of high-throughput technologies and large-scale network reconstruction efforts. [Michael Hucka is a senior research fellow and codirector of the Biological Network Modeling Center at Caltech's Beckman Institute --ed.] A standard graphical notation will help researchers share this mass of data more efficiently and accurately, which will benefit systems biologists working on a variety of biochemical processes, including gene regulation, metabolism, and cellular signaling."Finally, and perhaps most excitingly," adds Hucka, "I believe that, just as happened with the engineering fields, SBGN will act as an enabler for the emergence of new industries devoted to the creation of software tools for working with SBGN, as well as its teaching and publication."
Previous graphical notations in biology have tended to be ambiguous, used in different ways by different researchers, and only suited to specific needs--for example, to represent metabolic networks or signaling pathways. Past efforts to create a more rigid notation failed to become accepted as a standard by the community. Hucka and his collaborators believe that SBGN should be more successful because it represents a more concerted effort to establish a standard by engaging many biologists, modelers, and software-tool developers. In fact, many of those involved in the SBGN effort are the same pioneers who proposed previous notations, demonstrating the degree to which they endorse SBGN as a new standard.
To ensure that this new visual language does not become too vast and complicated, the researchers decided to define three separate types of diagram, which describe molecular process, relationships between entities, and links among biochemical activities. These different types of diagrams complement each other by representing different "views" of the same information, presented in different ways for different purposes, but reusing most of the same graphical symbols. This approach reduces the complexity of any one type of diagram while broadening the range of what can be expressed about a given biological system.
To learn more about SBGN, follow these links:
Abstract in Nature Biotechnology: The Systems Biology Graphical Notation Nature Biotechnology 27, 735 - 741 (2009)
Press release: Caltech Scientists Help Launch the First Standard Graphical Notation for Biology...
Flashback: BioModels: a Computational Systems Biology Database
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Tuesday, August 11, 2009
Single Molecule Sequencer Reads Human DNA in Four Weeks
As we've reported in the last few years, Helicos BioSciences out of Cambridge, MA has been working on a revolutionary new method of sequencing DNA molecules. The technique does not require any cloning, amplification or ligation to be performed, but uses a novel combination of physics, chemistry, and computer vision to identify base pairs at an unprecedented speed. This week researchers from Stanford University and Howard Hughes Medical Institute are reporting the sequencing of an entire human genome using a Helicos machine within four weeks at a cheap cost of only $50,000.
The basics of the technology from Helicos BioSciences:
Within two flow cells, billions of single molecules of sample DNA are captured on an application-specific proprietary surface. These captured strands serve as templates for the sequencing-by-synthesis process:Polymerase and one fluorescently labeled nucleotide (C, G, A or T) are added.
* The polymerase catalyzes the sequence-specific incorporation of fluorescent nucleotides into nascent complementary strands on all the templates.
* After a wash step, which removes all free nucleotides, the incorporated nucleotides are imaged and their positions recorded.
* The fluorescent group is removed in a highly efficient cleavage process, leaving behind the incorporated nucleotide.
* The process continues through each of the other three bases.
* Multiple four-base cycles result in complementary strands greater than 25 bases in length synthesized on billions of templates—providing a greater than 25-base read from each of those individual templates.
More about the announcement from Ars Technica...
Stanford press release: Professor sequences his entire genome at low cost, with small team...
Article in Nature Biotechnology: Single-molecule sequencing of an individual human genome
Product page: HeliScope™ Single Molecule Sequencer
Flashbacks: Helicos BioSciences Sequences Entire Genome from a Single Molecule of DNA; High Speed Sequencing of Single DNA
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Thursday, August 6, 2009
Philips Bids on Ultrasound Guided Gene Therapy
Delivering DNA sequences to cells for gene therapy is already being investigated, with the current approaches relying on viruses and smart nanoparticles as vectors for gene transfers. But Philips and GlyGenix Therapeutics, out of Woodbridge, CT, plan on taking another approach, hoping that the large molecules can be pushed to their destination using ultrasound. Specifically, the pre-clinical trials will study the technology, known as ultrasound-mediated plasmid DNA (pDNA) delivery, on Glycogen Storage Disease Type 1a (GSD-1a) that exhibits a defective G6Pase gene.
Current gene therapies that rely solely on the bloodstream to deliver corrective gene molecules typically fail to deliver sufficient quantities to the target organs. However, by directing focused ultrasound to target organs following DNA delivery, an increase in uptake via a process known as sonoporation has been successfully demonstrated in pre-clinical studies. Sonoporation increases the permeability of cell walls to allow the uptake of large molecules, thereby enabling the delivery of therapeutic genes.Compared to current gene therapies that use viral vectors to infect cells, this ultrasound-mediated technique carries no risk of an anti-viral immune or inflammatory response. In addition, this targeted approach could reduce side effects.
The proposed treatment is known as ultrasound-mediated plasmid DNA (pDNA) delivery. The research program into it will specifically target the expression of a functional human G6Pase therapeutic pDNA to the liver, the primary organ responsible for glycogen storage and glucose release. Pre-clinical studies to investigate the feasibility of the technique will be carried out by Philips Research and GlyGenix Therapeutics in collaboration with the Duke University School of Medicine’s Division of Medical Genetics (Durham, North Carolina, USA) – a recognized leader in GSD-1a diagnosis, managed care, pediatric genetics and experimental models.
Press release: Philips and GlyGenix Therapeutics team up to research ultrasound-mediated gene therapy...
Link: GlyGenix Therapeutics...
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Wednesday, July 22, 2009
Stem Cell Modulators Technology: Drugs That Turn On/Off Stem Cell Activity As Needed
By using induced pluripotent stem (iPS) cells as a discovery tool, Fate Therapeutics, a La Jolla, California company, is trying to develop drugs that would activate resident stem cells in the body for specific clinical purposes. This proprietary Stem Cell Modulators (SCMs) technology is already showing promise, as the company currently conducts a Phase 1b clinical trial of FT1050, "a small molecule SCM designed to increase hematopoietic stem cell number and function in dual umbilical cord blood transplant recipients with hematologic malignancies."
The MIT Technology Review reports:
Fate's first clinical trial focuses on a molecule known as FT1050. The molecule appears to stimulate proliferation of hematopoietic stem cells--which give rise to blood and immune cells--and helps guide them to the bone marrow. If successful, the drug could become an invaluable companion treatment to bone-marrow transplants and cord-blood transfusions used to treat cancer and blood diseases.In an early-stage clinical trial, Fate Therapeutics is testing FT1050 in 12 patients who've undergone chemotherapy for lymphoma. The patients will each receive two units of cord blood: one that's been treated with the stem-cell-modulating drug, and another that's been left alone. The trial is primarily a safety study, but because the two units were harvested from two different newborns, researchers can use the genetic differences to track the cells and determine if FT1050-treated stem cells can more efficiently take hold and prosper in bone marrow.
More from MIT Technology Review...
Company technology page: Fate Therapeutics...
Fate Therapeutics' recent press releases...
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Monday, July 20, 2009
Holographic Microscope Reveals Workings of Biochemical Reactions
A new method to record biological events at the molecular level, using holographic technology, has been developed at New York University. The technology uses a microscope that illuminates targets with a collimated laser beam, and that results in a diffraction pattern, which is reinterpreted by the system as a hologram so it can be viewed by the researchers:
NYU press office explains:
The scattered light overlaps with the original beam to create an interference pattern reminiscent of overlapping ripples in a pool of water. The microscope then magnifies the resulting pattern of light and dark and records it with a conventional digital video recorder (DVR). Each snapshot in the resulting video stream is a hologram of the original object. Unlike a conventional photograph, each holographic snapshot stores information about the three-dimensional structure and composition of the object that created the scattered light field.The recorded holograms appear as a pattern of concentric light and dark rings. This resulting pattern contains a wealth of information about the material that originally scattered the light-where it was and what it was comprised of.
Analyzing the images provided a different set of challenges. To do so, the researchers based their work on a quantitative theory explaining the pattern of light that objects scatter. The theory, Lorenz-Mie theory, maintains that the way light is scattered can reveal the size and composition of the object that is scattering it.
“We use that theory to analyze the hologram of each object in the snapshots of our video recording,” explained [David] Grier, who is part of NYU’s Center for Soft Matter Research. “Fitting the theory to the hologram of a sphere reveals the three-dimensional position of the sphere’s center with remarkable resolution. It allows us to view particles a micrometer in size and with nanometric precision-that is, it captures their traits to within one billionth of a meter.”
“That’s a tremendous amount of information to obtain about a micrometer-scale object, particularly when you consider that you get all of that information in each snapshot,” Grier added. “It exceeds other existing technology in terms of tracking particles and characterizing their make-up-and the holographic microscope can do both simultaneously.”
Because the analysis is computationally intensive, the researchers employ the number-crunching power of the graphical processing unit (GPU) used in high-end computer video cards. Originally intended to provide high-resolution video performance for computer games, these cards possess capabilities ideal for the holographic microscope.
Press release: NYU Physicists Find Way to Explore Microscopic Systems Through Holographic Video...
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Friday, July 17, 2009
MarrowMiner Digs Out More Marrow Using Fewer Holes
Daniel Kraft from the Stanford Institute for Stem Cell Biology and Regenerative Medicine invented a device to make bone marrow harvesting in donors a less invasive and less stressful process on the body. The idea is to drill one hole into the pelvis and then to approach the bone marrow from different angles, thus widening the harvesting region.
Here's a TED talk of Kraft presenting the MarrowMiner device:
More from TED: Daniel Kraft invents a better way to harvest bone marrow
Product page: MarrowMiner...
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Friday, July 10, 2009
Hand Powered DNA Separation System for Remote Point of Care
In order to aid with disease diagnosis in remote places, researchers at Boston University have built a prototype pump device to separate DNA out of a sample of blood. The SNAP (System for Nucleic Acid Preparation) is powered by a bicycle-like pump and may one day make it easy for local clinicians to separate, bottle, and ship a sample to a clinic with sequencing technology for analysis.
The conventional method of extracting DNA from blood involves a number of instruments: researchers first break open blood cell walls, either with chemicals or by shaking the blood, in order to get at genetic material inside cells. They then add a detergent to wash away the fatty cell walls, and spin the DNA out of solution with a centrifuge. The SNAP prototype performs a similar series of events with a bicycle pump, some simple chemicals, and a specialized straw lined with a polymer designed to attract and bind DNA.A clinician first takes a fluid sample, such as blood or saliva from a patient, and injects it into the disposable straw within the device. A large cap on the device contains two small packets: a lysis buffer and an ethanol wash. Pressure from the pump releases the lysis buffer, which breaks open cells in the fluid, releasing DNA. A second pump of air releases ethanol, which washes out everything but the DNA.
More from MIT Technology Review...
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Thursday, July 9, 2009
Faster PCR Technology Developed
Researchers from Japan's National Institute of Advanced Industrial Science and Technology are reporting on the development of a new polymerase chain reaction (PCR) technique that promises to be considerably faster than current methods. The new technology is meant to replace multiple fluorescent probes with a single multi-targeting one, resulting in improved throughput and higher precision.
From the study abstract:
In this technique, a quenching probe (QProbe) and a nonfluorescent 3′-tailed probe are used. The QProbe is a singly labeled oligonucleotide bearing a fluorescent dye that is quenched via electron transfer between the dye and a guanine base at a particular position. The nonfluorescent 3′-tailed probe consists of two parts: one is the target-specific sequence on the 5′ side, and the other is complementary to the QProbe on the 3′ side. When the QProbe/nonfluorescent 3′-tailed probe complex hybridizes with the target in PCR, the fluorescence of the dye is quenched. Fluorescence quenching efficiency is proportional to the amount of the target. We called this method the universal QProbe system. This method substantially reduces the cost of real-time PCR setup because the same QProbe can be used for different target sequences. Moreover, this method allows accurate quantification even in the presence of nonspecific PCR products because the use of nonfluorescent 3′-tailed probe significantly increases specificity. Our results demonstrate that this method can accurately and reproducibly quantify specific nucleic acid sequences in crude samples, comparable with conventional TaqMan chemistry. Furthermore, this method is also applicable to single-nucleotide polymorphism (SNP) genotyping.
Article in Analytical Chemistry: Universal Quenching Probe System: Flexible, Specific, and Cost-Effective Real-Time Polymerase Chain Reaction Method
Image: Epicatt
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Faster PCR Technology Developed
Researchers from Japan's National Institute of Advanced Industrial Science and Technology are reporting on the development of a new polymerase chain reaction (PCR) technique that promises to be considerably faster than current methods. The new technology is meant to replace multiple fluorescent probes with a single multi-targeting one, resulting in improved throughput and higher precision.
From the study abstract:
In this technique, a quenching probe (QProbe) and a nonfluorescent 3′-tailed probe are used. The QProbe is a singly labeled oligonucleotide bearing a fluorescent dye that is quenched via electron transfer between the dye and a guanine base at a particular position. The nonfluorescent 3′-tailed probe consists of two parts: one is the target-specific sequence on the 5′ side, and the other is complementary to the QProbe on the 3′ side. When the QProbe/nonfluorescent 3′-tailed probe complex hybridizes with the target in PCR, the fluorescence of the dye is quenched. Fluorescence quenching efficiency is proportional to the amount of the target. We called this method the universal QProbe system. This method substantially reduces the cost of real-time PCR setup because the same QProbe can be used for different target sequences. Moreover, this method allows accurate quantification even in the presence of nonspecific PCR products because the use of nonfluorescent 3′-tailed probe significantly increases specificity. Our results demonstrate that this method can accurately and reproducibly quantify specific nucleic acid sequences in crude samples, comparable with conventional TaqMan chemistry. Furthermore, this method is also applicable to single-nucleotide polymorphism (SNP) genotyping.
Article in Analytical Chemistry: Universal Quenching Probe System: Flexible, Specific, and Cost-Effective Real-Time Polymerase Chain Reaction Method
Image: Epicatt
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Thursday, March 26, 2009
BioTrove Wins Frost & Sullivan Award
Frost & Sullivan awarded BioTrove, a Woburn, Massachusetts developer of mass spectrometry and qPCR (quantitative real time polymerase chain reaction) technology, with the 2009 North American Award for Growth Strategy Leadership of the Year. F&S bases the prize on an "analysis of the most significant drug-discovery innovations and acknowledgments by life sciences category leaders."
Here's a bit about the company's technology:
The OpenArray® technology enables researchers to perform large-volume nanoliter arrays, conducting up to 3,000 assays simultaneously, while the RapidFire® Mass Spectrometry (RF-MS) technology uses microfluidics to conduct sample analysis 10-to-100 times faster than conventional liquid chromatography-mass spectrometry (LC-MS) technologies.“These solid technologies facilitate faster, higher-throughput and ultimately more efficient research and drug discovery,” said Frost & Sullivan Research Analyst Christi Bird. “In addition to directly distributing these products to end-users, BioTrove has also collaborated with several top life sciences tool and services providers to develop optimized products, services and workflows utilizing OpenArray® or RapidFire® technologies.”
Press release: Frost & Sullivan Lauds BioTrove for Providing Research-Enabling Life Sciences and Drug Discovery Technologies
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Friday, March 20, 2009
Laboratory Evolution Sped Up With a New Machine
Genetic bioengineering can be a slow process, as forcing evolution onto organisms typically requires splicing and dicing of individual genes. Now George Church of Harvard and colleagues developed a system to rapidly speed up the process using a parallel approach.
MIT Tech Review explains the technology:
Under the MAGE technology, scientists first generate 50 short strands of DNA, each containing a sequence similar to a gene or gene regulatory sequence in the target bacterial genome, but that has been updated in some way--incorporating a change that might make an enzyme more efficient, or boost production of a particular protein.The DNA is mixed into a vial of bacteria, which is then put into a custom-made machine designed in Church's lab. In the machine, the mixture is subjected to a precisely choreographed routine of temperature and chemical cycles that encourage the bacterial cells to take up the foreign DNA, swapping it into their genomes in place of the native piece it resembles. The single-stranded pieces of DNA are thought to "fake out the cell's DNA replication machinery, sneaking in and filling a gap" during the replication process, says Church. Each generation of the rapidly reproducing bacteria takes up more of the foreign DNA, ultimately producing a population that has all the desired genetic changes.
More from MIT Tech Review...
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» Topographical Method to Analyze DNA Molecules (March 16, 2009)
» Genetic Test for Finasteride Response (March 10, 2009)
» World's Smallest Periscope Looks at Cells from All Angles (March 6, 2009)
» Cell-CT, a 3-D Single Cell Microscopy Might Become a New Tool for Cancer Diagnosis (February 10, 2009)
» Leica Introduces New Laser Microdissection Technology (February 9, 2009)
» New Imaging Technique Helps Visualize Biomolecular Structures (February 4, 2009)
» Microgrippers That Perform Cell Biopsies (January 26, 2009)
» Umbilical Cord Blood Processor Given US Approval (January 15, 2009)
» Scientists Develop Microfluidic Method of Cell Fusion (January 5, 2009)
» New Dyes Point to Presence of Reactive Oxygen (December 17, 2008)
» Photonic Syringe for Inracellular Injections (December 10, 2008)
» New Fluorescent Imaging Compound Lights Up When Inside Viable Cells (December 8, 2008)
» DNA Microarrays for Prenatal Identification of Genetic Disease (December 2, 2008)
» SMRT: New High Speed DNA Sequencing Technology Promises Cheaper Genetic Testing (November 26, 2008)
» Nanomovies Reveal Events at Tiny Scales (November 25, 2008)
» Cool Light Microscopy with Leica DM IL LED (November 10, 2008)
» Computer Model of Intracellular Failure Cascade and the Future of Chemotherapy? (October 20, 2008)
» Stem Cells From Skin Cells...Phew! (October 14, 2008)
» New Blood Test for Down Syndrome (October 7, 2008)
» High Resolution Massively Parallel Holography to Peer Inside The Cell (September 17, 2008)
» Gene Chips Help Uncover Causes of Genetic Disorders (September 17, 2008)
» UMass Stem Cell Registry Going Online (September 15, 2008)
» Large Scale Single Cell Biochemical Monitoring (September 8, 2008)
» Dead-Cert Nanoparticles Use Magnets to Pull Dead Cells from Healthy Ones (August 27, 2008)
» Thoughts on The Stem Cell Future (August 27, 2008)
» DNA Sequencing Technology from Oxford Nanopore (August 22, 2008)
» Panasonic Develops A Novel Way to Sequence SNPs (August 21, 2008)
» Scientists Develop Compact On-chip Microscope (July 30, 2008)
» Neuron Membrane Model to Study Alzheimer's (July 24, 2008)
» Innocent Dating, or Eugenics for 21st Century? (July 22, 2008)
» Mouse Spinal Cord Gene Map Goes Online (July 21, 2008)
» The Ergopip: Pipette Remixed (July 18, 2008)
» MarrowXpress Gets Green Light in US (July 15, 2008)
» Novel Molecular Probes Detect Protein-Protein Interaction (July 2, 2008)
» BioTime Begins First Complete Database of Human Stem Cell Differentiations (June 30, 2008)
» Zinc Finger DNA-Binding Protein Technology Gives T-Cells Shield Against HIV (June 30, 2008)
» Genetic Silencing Technology Improves With Help From Quantum Dots (June 24, 2008)
» OMX, World's Highest Resolution Wide-field Light Microscope Goes Live (June 20, 2008)
» MarrowXpress Stem Cell Processing System Gets CE Mark (June 19, 2008)
» X-Ray Linear Accelerator, A New Ultra-Microscope Into Life (June 13, 2008)
» A Single Cell Pedometer Developed (June 12, 2008)
» DNA Sequencing Through Imaging of Base Pairs (May 19, 2008)
» Probing Protein-Membrane Interaction by Single Plasmonic Nanoparticles (May 16, 2008)
» Leica Introduces New Stereomicroscopes M205 FA and M165 FC (May 16, 2008)
» Scientists Create Cardiac Cells From Stem Cells (April 25, 2008)
» The $100 Genome (April 22, 2008)
» Single Cell Tweezers Developed (April 18, 2008)
» The Latest on Genetically Created Pacemaker Cells (April 18, 2008)
» Capturing Biochem Terahertz Radiation (April 16, 2008)
» Scientists Create Biomolecular Movies (April 16, 2008)
» Spiegelmer Technology (April 14, 2008)
» Manacles for C. elegans (April 10, 2008)
» Protein-based Glycanantagonists from ProtAffin (April 8, 2008)
» Darwinian Evolution on a Chip (April 8, 2008)
» Helicos BioSciences Sequences Entire Genome from a Single Molecule of DNA (April 4, 2008)
» Artificial Membrane Sacks as Mini Stem Cell Labs (March 27, 2008)
» Home Bi-Polar Test Kits Cause Mixed Emotions (March 25, 2008)
» Genomics 3.0: Synthetic Functional Enzymes Created Online (March 21, 2008)
» Metabolic Intracellular Tug of War (March 19, 2008)
» Craig Venter on Creating Synthetic Life (March 18, 2008)
» STORM, A New 3D Super-Resolution Microscopy Technique (February 19, 2008)
» CellTraffix Aims to Cleanse Blood of CA, Collect Stem Cells (February 13, 2008)
» Lab-on-a-chip for Neuro Studies (February 13, 2008)
» Genetic Barcoding to Aid with Drug Cancer Targeting (February 1, 2008)
» "Unnatural Base Pairs" Added to DNA (January 30, 2008)
» Researchers Create DNA Walker for Biocomputational Devices (January 22, 2008)
» On the Dynamic Nature of Proteins (January 14, 2008)
» Stem Cell Sifting Machine Developed (December 21, 2007)
» An Automatic Cell Sorting Machine from MIT (December 12, 2007)
» Illuminating Prions (December 12, 2007)
» Zooming in on Cells (December 11, 2007)
» AlgRx™ Algal Protein Expression System (December 10, 2007)
» Lab Mice with Human Liver Cells (December 5, 2007)
» New Digital Camera from Leica for Live Cell Research (November 27, 2007)
» Seaweed-based Scaffold to Shelter Stem Cells (November 21, 2007)
» Put Your Menstrual Flow to Work with C'elle (November 12, 2007)
» Opto-Electronic Tweezers from MIT (November 2, 2007)
» A Hope in Virotherapeutic Agents from Jennerex (October 29, 2007)
» Rosetta@home Delivers Results (October 17, 2007)
» Microgrid to Aid in Imaging and Correlating Organic and Trace-Metal Compositions in Biological Cells and Tissues (October 10, 2007)
» Nanotomography Reviewed (October 3, 2007)
» X-ray Resolution at Nanometer (October 3, 2007)
» The Orion Helium Ion Microscope (September 28, 2007)
» New Carcinogenic Role of microRNAs Discovered (September 28, 2007)
» Portable Polymerase Chain Reaction Device for Forensics (September 26, 2007)
» New 3D Petri Dish from Brown (September 26, 2007)
» 3D Styrene Polymer Growth Medium for Human Cells (September 24, 2007)
» Verigene® Warfarin Metabolism Nucleic Acid Test (September 18, 2007)
» Take One: Scientists Capture DNA-Enzyme Interaction Movie (September 18, 2007)
» Polymers for Gene Delivery (September 13, 2007)
» First Fully Mapped Human (September 6, 2007)
» "Oxygen Sandwich" Offers Hope to Type I Diabetics (September 5, 2007)
» Parasitism Taken to New Levels (August 31, 2007)
» 'Lab on a Chip' for Whole-animal Studies (August 24, 2007)
» Tomographic Phase Microscopy: A New Imaging Modality for Cells (August 23, 2007)
» In Solution, Evolution Creates an Artificial Enzyme (August 23, 2007)
» Scientists Descibe Direct Pathways into Cell Nuclei (August 20, 2007)
» 11.7 Tesla Bruker BioSpin MRI (August 3, 2007)
» From UTIs to Brain: Scientists Discover Biochemical Model of Amyloid Formation (July 24, 2007)
» Novel Hydrogels for Tissue Repair, Regeneration (July 20, 2007)
» TED Talk: Why can't we grow new body parts? (July 6, 2007)
» Novel Fluorescent DNA Probes Could Shed New Light on Genetic Disorders (July 6, 2007)
» Synthetic Biologists Unleash Biofilm Destroying Viruses (July 3, 2007)
» Scientists Create Biomolecular Computing Device with Bacterial Phenotype Output (July 3, 2007)
» World's First X-ray Free Electron Laser Is a Biochem Tool (June 25, 2007)
» The Apoptosis Chip (June 21, 2007)
» Casting the Biochemical Net (June 19, 2007)
» GM Rice to Carry Cholera Vaccine (June 13, 2007)
» World's First Personal DNA Analyzer (June 12, 2007)
» Scientists Reprogram Mature Cells to Become Embryonic Stem Cells (June 8, 2007)
» Visualizing Viral DNA Packaging (June 7, 2007)
» Protein Informant Captured on Video (June 1, 2007)
» Seeing Proteins with a New Vision (May 25, 2007)
» A Protein Rhapsody (May 9, 2007)
» DNA Replication on the Cheap! (May 4, 2007)
» New Biotech Company Wants to Fix Your DNA (April 26, 2007)
» On Mice and Light (April 20, 2007)
» Factories Churning Out Made-to-Order DNA (April 9, 2007)
» Scientists Control Brain Cell Activity with Light (April 5, 2007)
» Boffins Pave the Way for DNA Photography (March 28, 2007)
» Scientists Genetically Engineer Mice with Better Vision (March 26, 2007)
» Forensics of the Immune System (March 13, 2007)
» MicroRNAs in Oncogenesis (March 6, 2007)
» Rapid-Sequencing the Superbug (March 2, 2007)
» Studying 3D Structure of Influenza Polymerase (February 26, 2007)
» Mouse Brain Proteomics in 3-D (February 15, 2007)
» New Microchip for Protein Sorting (February 6, 2007)
» Hope for Noninvasive Prenatal Test (February 5, 2007)
» Unravelling Genetics of Autoimmune Diseases (January 22, 2007)
» Another Genetic Clue for Alzheimer's (January 16, 2007)
» Chinese Scientists Develop Fish that Turn Green in Presence of Estrogen (January 15, 2007)
» Genetically Modified Skin Cells Designed to Fight Infection (January 8, 2007)
» REDRUM: DNA Sequences that Kill (January 5, 2007)
» 3D Stem Cell Cultures in Self-Assembling Peptide Nanofiber Scaffolds (December 29, 2006)
» DNAPrint Genomics Offering Personal DNA Storage (December 20, 2006)
» ApoSense™ Technology (November 21, 2006)
» The Biopump Treatment (November 20, 2006)
» 15-Minute Biochip Assay (November 20, 2006)
» Transplanted Light-sensing Cells Restore Visual Fx in Mice (November 9, 2006)
» "Would E. coli, by any other name, smell as sweet?" (November 3, 2006)
» Hyperpolarized Xenon Makes MRI Hypersensitive (October 20, 2006)
» Custom-Designed Anti-Microbial Peptides (October 20, 2006)
» Titan™ 80-300 S/TEM Electron Microscope (October 19, 2006)
» Computer with DNA Circuits Plays Games; One Day to Go Diagnostic (October 16, 2006)
» A Powerful Genome ID Method (October 13, 2006)
» Multi-Isotope Imaging Mass Spectrometry (MIMS) (October 6, 2006)
» Treatment to Offer "Instant Flu Protection" (October 4, 2006)
» Milestone: Fully Differentiated Cells Yield Clones (October 4, 2006)
» Connectivity Map, a Novel Genomic Tool (September 29, 2006)
» Allen Brain Atlas Completed (September 26, 2006)
» Knotty Proteins (September 21, 2006)
» Nanobodies™ by Ablynx (September 18, 2006)
» The Molecular Sieve to Sort Proteins (September 12, 2006)
» Humanized Biochem Pathway Achieved (September 11, 2006)
» CollPlant's Tobacco (September 6, 2006)
» Nanoparticles and siRNA: A Perfect Marriage? (August 29, 2006)
» New Stem Cell Method Avoids Destroying Embryos (August 24, 2006)
» Nanoparticles Loaded with siRNA Show Cancer Promise (August 17, 2006)
» New Light Microscope with Insane Resolution (August 11, 2006)
» Sticky DNA for Cancer Diagnosis (August 7, 2006)
» DNA 2.0? (July 25, 2006)
» Engineered Heart Cells Conduct Electricity and Hope (June 20, 2006)
» Bacterial Factory to Offer a Novel Ways to Study Membrane Proteins (June 5, 2006)
» E. coli , the Tumor Killer (June 2, 2006)
» Microbubbles Offer Hope in Type I Diabetes (May 23, 2006)
» Virtual Histology: No Frozen Sections, No Wax, No Mess (May 23, 2006)
» Using Gold Nanoparticles to Develop Antisense Cancer Drugs (May 19, 2006)
» The Book of Life Completed (May 18, 2006)
» A Novel Algorithm for Detecting Cancer Genes (May 15, 2006)
» Spontaneous Regression of Advanced Cancer in Mice after White Blood Cell Transfer (May 10, 2006)
» The Pall Filter Harvest System (May 10, 2006)
» I-space Medical Imaging (April 25, 2006)
» Novel Method to Study 3-D Organization of Cells (April 25, 2006)
» Nanopore Method for DNA Sequencing (April 7, 2006)
» Lipid Coated Pipettes for Rupture-free Cell Injections (March 17, 2006)
» Novel PCR Device for Fast, Disposable DNA Testing (March 10, 2006)
» Peeking at Intranuclear Proteins and Seeing Early Cancer (March 8, 2006)
» Mouse as Medgadget (March 8, 2006)
» Enzo Biochem Gets Approval to Combat HIV to AIDS progression (March 1, 2006)
» The Celution™ System (February 3, 2006)
» Nano Method for Detecting Disease-Causing Mutations (January 30, 2006)
» Susceptible Diagnoses (January 10, 2006)
» Stem Cell Lines Derived from Exclusively Human Sources (January 4, 2006)
» Biotechnology's Newest Chemical Tool (November 29, 2005)
» New Microscope Allows Scientists to Watch a Functioning Protein (November 15, 2005)
» New Dyslexia Gene Identified (October 31, 2005)
» Tiny Worms Paving Way for Better Anesthetics (October 26, 2005)
» Stem Cells vs CA: The Fight Begins (October 12, 2005)
» Genetically Manipulated Mosquito Species To Fight Malaria (October 11, 2005)
» Bacteriophage That Can Produce 10 Trillion Varieties of a Single Protein (September 20, 2005)
» Y May Not Die (September 12, 2005)
» Synthetic Genomics (September 12, 2005)
» RNAi (September 9, 2005)
» RoboLase: Real-time Cell Surgery via Internet (August 2, 2005)
» RNA-interference Disrupts Hepatitis B Virus (August 1, 2005)
» Nanoparticles Deliver Genes to Brains of Living Mice (July 25, 2005)
» Chemical 'Band-Aid' for MD Hearts (July 19, 2005)
» "Laser Tweezers" to Study Blood Clots (June 28, 2005)
» Control of Protein Synthesis by Light Achieved (June 27, 2005)
» Electroporation Therapy by Inovio (June 13, 2005)
» Human Kidney Development and the Drosophila Eyes (June 10, 2005)
» AgentCell: Digital Bacteria (June 6, 2005)
» A Novel Way to Control Bacteria Developed (June 6, 2005)
» Celacade™ Immune Modulation Therapy (May 31, 2005)
» The Logic of Smell (May 31, 2005)
» Activation of Thermoreceptors Mediates Raw Garlic's Burning Pungency (May 27, 2005)
» Scientists Observe Infectious Prion Proteins Invade and Move Within Brain Cells (May 25, 2005)
» Stem Cell Trial in CHF Patients to Begin (May 13, 2005)
» Stem cell treatment improves mobility after spinal cord injury (May 11, 2005)
» Garage-based DNA Labs (May 10, 2005)
» Improving Gene Chips (May 5, 2005)
» Making Bacteria 'Talk' (May 4, 2005)
» Human Cells Filmed Signaling Each Other (April 22, 2005)
» High Speed Sequencing of Single DNA (April 21, 2005)
» Scientists Discover How Ebola Virus Infects Cells (April 19, 2005)
» First Real Time View of Developing Neurons Reveals Surpises (April 11, 2005)
» DNA Chip Goes Wireless (April 7, 2005)
» DNA Analysis Time Reduced with New Chip (April 6, 2005)
» Genetic patch treats 'bubble-boy' disease (April 5, 2005)
» Biolaser Illuminates Stem Cell Development (April 4, 2005)
» New method of gene delivery using lasers (January 31, 2005)
