In a Lab, an Ever-Growing Database of DNA Profiles
New York Times (05/12/09) P. D3 ; Moore, Solomon

The FBI's DNA laboratory has helped identify thousands of suspects and exonerate hundreds of wrongfully convicted people, but the expansion of DNA databases has provided major challenges to the agency. As of 2007, the Justice Department estimates that the FBI had a backlog of 600,000 to 700,000 samples, but technological advances have helped to speed up the process. In 2002, the FBI processed about 5,000 DNA samples annually, but analysts hope that new robotic systems will allow them to process 90,000 samples a month by 2010. The FBI's new automated system can process up to 2,000 samples per day for each machine, using polymerase chain reaction to clean, dry, and replicate each sample. This system also helps avoid mistakes such as contamination and mislabeling.
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Do-It-Yourself Genetic Sleuthing
Boston Globe (05/11/09) Johnson, Carolyn Y.

Many people tinker with electronics in their homes or garages, but some amateur scientists conduct do-it-yourself genetic experiments in a similar environment. MIT graduate Katherine Aull has used a vintage thermal cycler, a high-voltage power supply from eBay, chemicals, and kitchen equipment to test her own DNA for a genetic mutation that may cause hemochromatosis. After swabbing her cheek for cells and adding compounds that isolate the relevant DNA fragments, Aull places the samples into a thermal cycler to create copies. She then places the samples into a box of gel, which the DNA moves across to create bands that reveal which gene mutations exist in the DNA. Home experiments such as Aull's have led to a variety of questions regarding safety and how amateur science can coexist with more professional efforts. Such experimentation may cause people to become overly anxious about the results, concerned that they have a disease, and patients are advised not act on the results of their genetic experiments without discussing them with a physician.
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Students Secure Funding to Develop Solar-Powered Pasteurization System in Peru
Rensselaer Polytechnic Institute (05/13/09)

A team of students from Rensselaer Polytechnic Institute in New York will spend part of the summer building solar-powered pasteurization systems in southern Peru. The group of engineers has received a Summer Engineering Experience in Development grant from the nonprofit volunteer organization Engineers for a Sustainable World. The new, solar-powered systems will allow families in the Langui and Canas communities to pasteurize milk, yogurt, and cheeses produced by their dairy cows, meeting government regulations to sell these products for added income.
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Simple Blood Test Proves Powerful Ally in the Fight Against Malaria
Science Centric (04/28/2009)

Rapid diagnostic tests (RDT) may help low- and mid-income countries fight malaria, according to a study at the Karolinska Institute's research center in Zanzibar, Tanzania. Malaria RDT measures the presence of a protein produced by the parasite Plasmodium falciparum in a blood sample taken from the patient's finger, and requires no advanced lab equipment or training. Study leader Dr. Anders Bjoerkman said, Since the existing test methods are too complicated and expensive for most primary health care clinics in Africa, people are prescribed malaria treatment based on presence of fever only. With an improved diagnostic tool, treatment can be targeted to patients with confirmed malaria. The study involved 1,887 adults and children who had a fever within 48 hours of enrollment and were divided into two groups: one of which was given a regular medical examination and diagnosed based only on symptoms, and the other tested with RDT. Two weeks after treatment, the researchers noted that 36 percent of patients tested with RDT had received artemisinin-based combination therapy (ACT), compared to 85 percent of the control group. The RDT group received more antibiotics, however. The number of patient revisits made because of perceived ineffectiveness of the prescribed ACT malaria treatment was also lower in the RDT group. Bjoerkman noted that this testing method may also help track the spread of the disease, allowing for improved control.
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Sequencing on Target
The Scientist (05/09) Vol. 23 , No. 5 , P. 57 ; Perkel, Jeffrey M.

Innovative techniques are being used to make polymerase chain reaction (PCR) more scalable. These processes are often referred to as targeted resequencing or genomic partitioning. Elaine Mardis at Washington University in Missouri uses Raindance Technologies' RDT-1000 system, which features millions of separate reaction chambers. Primer pairs must first be designed for each targeted genomic segment and shipped to Raindance. The company encapsulates each pair into 8-pL microdroplets to create multiple aqueous micelles in oil, which are returned to the lab. The micelles, genomic DNA, and other PCR reagents are mixed together and placed in individual reaction vessels that can be amplified. Meanwhile, Hanlee Ji at Stanford University uses selector probes, or 80-nucleotide-long double stranded oligos. They feature a central 40-base generic vector sequence and two target-specific overhanging terminals. The selector probe is used to incubate the genomic DNA after it has been broken down with a restriction enzyme and denatured. A partially double-stranded circle emerges when the ends of the probe locate their target sequences, enabling amplification and sequencing.
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State Lab Working on H1N1 Flu Test
Salt Lake Tribune (05/05/09) Maffly, Brian

The state health department in Utah has received about 500 H1N1 test kits from the Centers for Disease Control and Prevention (CDC) to help identify the swine flu virus. In an effort to speed detection of the virus, the Food and Drug Administration has approved the distribution of the test kits to public health labs around the United States. The kits are packaged in cardboard boxes about the size of two soap bars and contain chemical reagents that react with genetic material from the H1N1 flu strain. Lab technicians extract RNA from the flu samples and then conduct an initial screening to see if it is a probable case of swine flu. Combining the RNA with the reagents, the technicians amplify its genetic fingerprint with cycles of heating and cooling. The genetic profile is analyzed in a computer program, which displays any positive results. The lab can confirm a suspected case of swine flu in as little as six hours, though it takes additional time to match the samples with actual patients and to check the results against those of the CDC.
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Outbreaks and Recalls Put Worry on the Table
New York Times (05/11/09) Martin, Andrew ; Harris, Gardiner

Fewer people are getting sick from contaminated food, but large outbreaks and recalls, such as the melamine in infant formula and salmonella in peanut butter, keep emerging. Newer foods such as bagged salads require additional handling, using foods from multiple sources, and more food products are being imported from abroad, increasing risk of contact with contaminants. Food recalls are more common in recent decades, because investigators can now employ modern genetic techniques to identify the source of tainted foods. In the case of salmonella-tainted peanut butter, authorities were able to track the salmonella to an open jar of peanut butter in Minnesota, identify victims in 46 states, and discover the plant that the peanut butter had come from.
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Mobile Units Get FDA up to Speed
USA Today (05/04/09) P. 1D ; Weise, Elizabeth

In the past, produce traveling from Mexico to the United States via the border crossing at Nogales, Ariz., was tested for contaminants by 13 Food and Drug Administration (FDA) inspectors assigned to the area, who would then ship samples to one of the agency's 13 labs. Produce that was tagged as being potentially contaminated with bacteria such as E. coli or salmonella was either shipped or impounded at an FDA warehouse and was prohibited from being put on the market until test results came back negative. This process often resulted in food being destroyed because it got to be too old, said Chris Ciruli of Ciruli Brothers, which imports peppers and tomatoes from the Mexican state of Sonora. But now the FDA has a mobile lab that can be deployed to any location where there is the risk of naturally-occurring food contamination or contamination caused by terrorists. The lab--which consists of three trailers, each with a different function--were recently deployed to Nogales at the request of the Fresh Produce Association of the Americas, which was concerned about the amount of time it took some Mexican produce to make it across the border and into U.S. grocery stores. During the three weeks the lab was in Nogales, hold-and-test times were reduced for some Mexican produce coming into the country. For one load of peppers, the hold-and-test time was a little less than 36 hours--which was far shorter than the week it could have taken, said Jim Cathey, the general manager of the shipper Del Campo Supreme. Mexican growers are hoping that the lab will eventually return to Nogales to speed the movement of produce through the border during peak growing times. However, the lab has been criticized by some in Congress, including Rep. Rosa DeLauro (D-Conn.), who said the facility is just a Band-Aid for the problem of moving items through the U.S.-Mexican border.
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Scientists Create Liquid Lens on a Chip
The Post Chronicle (05/11/09)

Research engineers from the Pennsylvania State University have developed tunable fluidic micro lenses that can change focal length or direction in less than a second while remaining stationary. These lenses, as reported in the journal Lab on a Chip, can be fabricated on a chip. The researchers note that such lenses can be used for counting cells, evaluating molecules, creating on-chip optical tweezers, or to provide imaging in medical devices.
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Sustainable Nanotech
Chemical & Engineering News (04/13/09) Vol. 87 , No. 15 , P. 37 ; Erickson, Britt E.

Although more consumer products are being created with nanotechnology, it is still largely unknown how nanoparticles act when they are disposed of in soil, water, and air. A two-day workshop in March sponsored by the International Council on Nanotechnology (ICON) at Rice University addressed the progress of safe design and disposal of nanomaterials. Kristen Kulinowski, director of ICON, said that safe nanomaterial design depends on identifying what it is about a nanomaterial that gives it an interesting property or makes it interact with the environment in a certain way. The great number of different nanomaterials in existence, however, makes this identification more difficult, and it is still unknown if minimizing the biological effects of nanomaterials will affect their performance characteristics. Workshop participants were also concerned with the lack of requirements for manufacturers in reporting the concentrations of nanomaterials in their products. Others in the workshop discussed minimizing waste by designing the nanomaterials to be recycled, through safe disposal, and the potential environmental effects, would remain an issue for nanomaterials that could not be reused. The nanomaterial industry must continue to study the management of its nanomaterial waste stream, currently without guidance from regulatory agencies.
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FDA Authorizes Emergency Use of Influenza Medicines, Diagnostic Test in Response to Swine Flu Outbreak in Humans
FDA.gov (04/27/09)

The U.S. Centers for Disease Control and Prevention can distribute the rRT-PCR Swine Flu Panel diagnostic test to public health and medical personnel from other qualified laboratories who are trained to administer the test and interpret the results. The U.S. Food and Drug Administration (FDA) has issued Emergency Use Authorizations (EUAs) for the swine flu test, as well as certain Relenza and Tamiflu antiviral products, to help identify and respond to the swine flu virus under certain circumstances. The EUA for the rRT-PCR Swine Flu Panel diagnostic test means the FDA considers the swine flu test effective in testing samples from individuals diagnosed with influenza A infections, whose virus subtypes can not be identified by existing tests. The swine flu test targets the viral genetic material from a nasal or nasopharyngeal swab. A patient would be presumed infected with the swine flu virus if the result is positive; however, the test would not indicate the stage of infection.
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Time to Sequence the 'Red and the Dead'
Nature (04/16/09) Vol. 458 , No. 7240 , P. 812 ; Nicholls, Henry

With the falling cost of genome sequencing, some molecular biologists and conservationists have suggested that researchers begin the process of sequencing several endangered and extinct species. Biologists could use samples from the same species spanning several hundred, or even thousands, of years to study the very process of extinction. New technology has made such an effort possible, with a suite of Illumina GAII instruments allowing data to be produced at 500 times the rate that it was produced in 2006. Roche's Titanium 454, a high-throughput platform, is suited for sequencing genomes from species that have not yet been sequenced and was used to sequence a woolly-mammoth genome in 2008. The genomic data may be difficult to obtain, however, as it requires a sliver of tissue to be removed from museum specimens.
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Ultrasound to Go
Technology Review (04/23/09) Gravitz, Lauren

Washington University in St. Louis computer engineers have developed an ultrasound device that can be plugged directly into a smartphone's USB port. The device enables smartphones to capture images and display them directly on the phone's screen. The phone also can be used to send the images to other users. Washington University researchers William Richard and David Zar created the smartphone device from an ultrasound probe they previously developed that can plug into a laptop's USB port. The researchers transferred all of the necessary computing power to the probe and decreased its power consumption to only half a watt. The image the device creates is smaller and of a lower quality than the laptop version, but the researchers believe that it is more than sufficient for many medical applications. The researchers say it could be used in remote rural communities and developing nations, as well as for emergency imaging of patients en route to a hospital. They also say it could be used for battlefield medicine and for home use by patients with chronic illnesses. Zar plans to have open source software available this summer.
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Evolution in a Bottle
Scientific American (04/01/09) Vol. 300 , No. 4 , P. 18 ; Gibbs, W. Wayt

Molecular chemist Gerald F. Joyce, along with his student Tracey Lincoln, has managed to create a test-tube system that displays the essential characteristics of Darwinian evolution. Mixing some short, powerful RNA sequences with simpler RNA building blocks will cause the more complex RNA sequences to replicate as long as they have the space and the raw material to do so. By mutating the samples and setting up survival of the fittest competitions, the researchers found that some variants reproduced faster than others, competing with each other for the common building blocks. None of the RNA recombinants, or mutations, could do anything new that their ancestors could not perform, however, a detail that continues to separate artificial evolution from Darwinian evolution. The discovery could still allow scientists to better understand the basics of biological evolution. Other researchers have experimented with the process' next step, to engineer a set of synthetic molecules that can replicate and perform metabolism. Harvard Medical School geneticist Jack W. Szostak has developed nonbiological proteins that bind ATP, and his lab is also attempting to create protocells that encase RNA within tiny spheres of fatty acids, or micelles, that can form, merge, and replicate spontaneously. The results of creating synthetic life in a laboratory may still be too complex to prove that natural life began the same way.
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No Needles in a Nano Universe
Brisbane Times (Australia) (04/23/09)

Australian scientists are developing a vaccine nanopatch that delivers immunization against diseases without the use of needles. These patches could be sent to remote areas that do not have refrigeration or disposable syringes used in traditional vaccines. The patches consist of a centimeter-square silicon device, with thousands of very sharp, microscopic spikes. These spikes are coated with dried vaccine and penetrate the skin less than a hair's thickness below the surface, causing no pain and delivering the vaccine close to the immune cells, called dendritic cells. Eliminating or controlling diseases that have haunted humans for millenia requies a quantum leap in vaccine technology, notes Prof. Peter Gray, director of the Australian Institute for Bioengineering and Nanotechnology at the University of Queensland.
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