One benefit of this technology as reported in the letter is the flexibility of the cell culture medium. Current products available use a fixed chemical environment in their scaffolding to support three dimensional growth of cells. Because certain cell populations have specific metabolic requirements which must be met by the culture medium, the fixed chemical environment of existing 3-D culture techniques may preclude specific cell populations from being used. However, because this technology does not rely on a chemical environment, cell lines are not limited by the medium they grow in but rather the ability to take in the iron laced hydrogel.

The researchers state the potential applications of their work include “biotechnology, drug discovery, stem cell research, or regenerative medicine.” They go on to say, “Indeed, a potential long-term goal is the possibility of accomplishing the ‘engineering’ of normal tissues or complex organs.” The technology has been licensed to n3D Biosciences out of Houston, Texas.

M. D. Anderson press release: 3-D Cell Culture: Making Cells Feel Right at Home

Abstract in Nature Nanotechnology: Three-dimensional tissue culture based on magnetic cell levitation

Link: n3D Biosciences...

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.

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 were quite surprised about binding to bare electrodes because, like many physicists, we had always assumed that the bases would just tumble through. But actually, any surface chemist will tell you that the bases have weak chemical interactions with metal surfaces."

Next, Lindsay's group is hard at work trying to adapt the reader to work in water-based solutions, a critically practical step for DNA sequencing applications. Also, the team would like to combine the reader capabilities with the carbon nanotube technology to work on reading short stretches of DNA.

Universal DNA reader expedites code sequencing ...

Article in Nano Letters: Electronic Signatures of all Four DNA Nucleosides in a Tunneling Gap

Zhang's [Miqin Zhang, UW professor of materials science and engineering] cylindrical scaffold is made of chitosan, found in the shells of crustaceans, and alginate, a gelatinous substance found in algae. Chitosan and alginate have a structure similar to the matrix that surrounds cells in the body, to which cells can attach. Different processing techniques can make the scaffold out of interconnected pores of almost any size, Zhang said.

Researchers first seeded the scaffold with 500,000 embryonic stem cells, and after 21 days the scaffold was completely saturated. The cells infiltrated the structure, Zhang added, unlike other materials where cells often grow only on the surface.

To retrieve the cells, researchers immersed the scaffold in a mild solution. The structure is biodegradable and so dissolved to release the stem cells. One also could implant the stem cell-covered scaffold directly into the body.

Analysis of gene activity and testing in the lab and in mice showed that the new stem cells retained the same properties as their predecessors.

Other researcher groups are also looking for alternatives to feeder layers. The leading contenders are scaffolds coated with custom proteins designed to mimic the key properties of the animal cells in the feeder layer. Such products are expensive and difficult to produce in a consistent manner, Zhang said. The proteins also get used up in a few days and have to be replaced, making them costly and time-consuming for everyday use.

"Our scaffold is made of natural materials that are already FDA-approved for food and biomedical applications. Also, these materials are unlimited, and the cost is cheap," she said.

Press release: 3-D scaffold provides clean, biodegradable structure for stem cell growth ...

Abstract in Biomaterials: Feeder-free self-renewal of human embryonic stemnext term cells in 3D porous natural polymer scaffolds

Images: Top: The UW's biodegradable scaffold was built as a cylinder which was then cut into dime-sized slices. Bottom: A magnified view of the scaffold shows the pores, each about a tenth of a millimeter wide, where stem cells can grow.

The company introduced the Applied Biosystems SOLiD(TM) 4 Sequencing System, the most advanced next-generation genomic analysis sequencing system on the market, generating up to 100 gigabases of mappable sequence data per run at a cost of $6,000 per genome. The system, which leverages proprietary advances in sequencing chemistry, will be available as an upgrade for all SOLiD installations in the first quarter of 2010. The company also announced that in the second half of the year, the SOLiD 4 System can be upgraded with the SOLiD 4hq package, which will generate up to 300 gigabases of mappable sequence data per run and deliver unprecedented accuracy of 99.99 percent, enabling customers to sequence the highest quality whole genome for a cost of $3,000.

Concurrent with the launch of the SOLiD 4 System, researchers will also be able to reduce overall sequencing costs by automating their workflow through the introduction of the Applied Biosystems EZ Bead(TM) System. The EZ Bead System dramatically improves the efficiency of sample preparation and reduces hands-on and turnaround time by as much as 90 percent.

Features from the SOLID 4 product page:

Scalable system - 100 GB today, extendable to 300 GB with the SOLiD™ 4hq System upgrade

Superior accuracy - More than 80% of the bases have quality values >30 for higher confidence in your results

Uniform coverage - Total Precision reagents improve coverage to enable the discovery of rare variants in difficult (GC/AT-rich) regions of the genome for fewer false negatives

Expanded application support - Barcoded paired-end sequencing that detects somatic mutations, novel splice variation, and fusion transcripts with less input material

Automated sample preparation - 80% reduction in hands-on time

Press releases: Life Technologies Brings Genomic Sequencing Closer to the Clinic...; Life Technologies and Ignite Institute Partner to Create Largest Next Generation Genomic Sequencing Facility in North America...

Product page: SOLiD™ 4 System...

From a LANL press release:

The Attune Acoustic Focusing Cytometer is based on a portfolio of intellectual property developed at Los Alamos National Laboratory (LANL), for which Life Technologies holds the exclusive commercial license rights. The field of flow cytometry was originally invented at LANL in the 1960s. The Bioscience Division at LANL currently is home to the National Flow Cytometry Resource (NFCR), a center for the development and application of flow cytometry technology.

From the product page:

With the Attune™ instrument, you can control your sample concentration, the flow rate, the number of photons you detect, the length of your experiment, the number of samples you run, and more.

Offers small footprint to fit in any lab and on all standard lab benches

Accommodates standard tissue culture hoods for convenient aseptic work

Provides a “greener” solution due to low sheath

Eliminates need for a separate fluidics cart with fluidics on-board

Includes change-it-yourself optical filters

Offers added convenience by locating filter holder under the lid

Provides violet and blue laser combination for choice of six analysis colors

Here's a company promo video for the Attune cytometer:

Press releases: Attune Acoustic Focusing Cytometer Brings Technology Developed at LANL to the Marketplace...; Applied Biosystems Debuts Industry's First Acoustic Flow Cytometer...

Product page: Attune Acoustic Focusing Cytometer...

Here are the new features of the software:

Imports SOLiD and Solexa sequences as well as 454 sequences. The new, fast de novo assembler is capable of assembling a 5 mb bacterial genome for half a million sequences generated by the Sanger and 454 high-throughput methods in under 30 minutes while maintaining the most user-friendly environment available for research in the life sciences. Other new features in Geneious Pro 4.8 include:

Ultra-fast de novo assembler

Primer extension support

Primer design on alignments and assemblies

Map primer to sequence

Trim by primers

Batch export

Import FastQ, CsFasta, Qual file formats

Add, remove and combine enzymes from lists

Find in translated sequence

Quality statistics on chromatograms

Statistics: read length and chromatogram quality

Bundled EMBOSS Tools

Product page: Geneious 4.8...

Press release: Geneious Pro 4.8 released - over 15 new features...

InformationWeek reports:

The technology works by using a robot to lay down cells in precise positions in three dimensions, accurate to within 20 microns. "It's similar to the way a laser printer prints by putting solid particles in place," [Organovo CEO Keith] Murphy, told InformationWeek. The 3D medical printer puts down objects on 2D layers, one on top of the other. The particles used in the construction are made up of stem cells, formed into tiny spheres and cylinders.

The stem cells are available for research purposes from companies including Life Technologies and Invitrogen. When the device is used for treatment, cells will come from the patient, such as bone marrow, or fatty adipose tissues, where stem cells can be harvested. "Because they come from the patient, there's no risk of having a rejection," Murphy said. These are adult stem cells, not the fetal stem cells that have been politically controversial.

Researchers take a cross-section picture of the object they want to build, such as an artery. "We use that as a map to paint by numbers," he said.

Objects take about an hour to build, and then the cells fuse together on their own in the course of 24-48 hours, locking the object in shape.

From the press release:

The printer, developed by Invetech, fits inside a standard biosafety cabinet for sterile use. It includes two print heads, one for placing human cells, and the other for placing a hydrogel, scaffold, or support matrix. One of the most complex challenges in the development of the printer was being able to repeatedly position the capillary tip, attached to the print head, to within microns. This was essential to ensure that the cells are placed in exactly the right position. Invetech developed a computer controlled, laser-based calibration system to achieve the required repeatability.

Invetech plan to ship a number of 3D bio-printers to Organovo during 2010 and 2011 as a part of the instrument development program. Organovo will be placing the printers globally with researchers in centers of excellence for medical research.

Read on at InformationWeek...

Organovo press release: Organovo Receives Delivery of First Commercial 3D Bioprinters...

Today, we learn that glorious future may come faster Genetic testing is already being used in clinical applications, specifically testing patients' sensitivity to medications that are known to be related to heredity. A big roadblock to screening more people is that blood has to be sent to the lab for testing, which often takes weeks while prescribing needs may not be able to wait that long. Nanosphere out of Northbrook, IL recently received FDA clearance for technology, called Verigene, that could soon be used in point-of-care applications to screen for certain genetic sequencing within a matter of a few hours.

A snippet from Technology Review:

A patient's blood is injected into a disposable cartridge, which holds a glass slide dotted with DNA. The plastic frame also houses a system of microfluidics chambers containing the reagents for a number of chemical reactions. When the cartridge is inserted into the Verigene instrument, mechanical valves and air pressure mix the reagents in different chambers, triggering a series of reactions.

Magnetic beads first pull out white blood cells, which are burst open using sonic energy, releasing fragments of DNA. Everything but the DNA is then washed away, and a solution of these DNA fragments flows over the glass slide. Target DNA binds to spots on the slide that have been printed with DNA sequences complementary to those of the target sequence. Gold nanoparticles, about 13 nanometers in diameter, then attach to the other end of captured DNA fragments, sandwiching the target. Each gold nanoparticle is coated with silver, expanding the diameter to half a micron, thus allowing it to be easily detected when hit with light.

Read on at Technology Review...

Product page: Verigene

...the new genetics will reveal much less than hoped about how to cure disease, and much more than feared about human evolution and inequality, including genetic differences between classes, ethnicities and races.

...In 2010, GWAS [Genome-Wide Association Studies] fever will reach its peak. Dozens of papers will report specific genes associated with almost every imaginable trait—intelligence, personality, religiosity, sexuality, longevity, economic risk-taking, consumer preferences, leisure interests and political attitudes....

GWAS researchers will, in public, continue trumpeting their successes to science journalists and Science magazine. They will reassure Big Pharma and the grant agencies that GWAS will identify the genes that explain most of the variation in heart disease, cancer, obesity, depression, schizophrenia, Alzheimer’s and ageing itself. Those genes will illuminate the biochemical pathways underlying disease, which will yield new genetic tests and blockbuster drugs. Keep holding your breath for a golden age of health, happiness and longevity.

In private, though, the more thoughtful GWAS researchers are troubled. They hold small, discreet conferences on the “missing heritability” problem: if all these human traits are heritable, why are GWAS studies failing so often? The DNA chips should already have identified some important genes behind physical and mental health. They simply have not been delivering the goods.

Our natural instinct is to reject this prediction -- but we suppose the trait for skepticism was inherited as well.

More from the Economist...

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)

Press release: ENIGMA DIAGNOSTICS SHOWCASES ITS UNIQUE FULLY AUTOMATED rtPCR BASED ML (MINI-LABORATORY) INSTRUMENT FOR POINT-OFCARE TESTING AT MEDICA 2009... (.pdf)

Product page: Enigma ML ...