Immunity all in a flap

The identification of a protein flap—a loop of just eight amino acids—could lead to novel approaches to treat a variety of immune disorders, according to researchers at the National Jewish Medical and Research Center (Denver, CO) and Rockefeller Center (New York). Gongyi Zhang and colleagues determined the crystal structure of soluble Tall-1 protein (also known as BLyS and BAFF), a member of the tumor necrosis factor (TNF) ligand family (Cell, 108, 383–394, 2002). Tall-1 triggers the proliferation of B cells, which are the primary source of antibodies and key to healthy immune systems. The crystal structure revealed that the Tall-1 protein was distinct from other TNF family members; it possesses an eight-amino-acid side loop and forms oligomers comprising 60 subunits. When the researchers deleted the “flap”, Tall-1 failed to oligomerize and no longer activated B cells, despite its continued ability to bind to its receptor. The researchers view the flap region as the potential Achilles' heal of the protein, providing a target for small molecule intervention. The study will be of interest to several biotechnology companies, including Human Genome Sciences (Rockville, MD), which has BLyS in clinical trials. LF

Ever decreasing circles

Nanocircles—tiny circles of single-stranded DNA—can act as promoters for bacterial RNA polymerases, thereby generating thousands of copies of encoded transcripts through a process called rolling circle amplification. Now, Eric Kool and colleagues at Stanford University (Stanford, CA) have optimized the technology, showing, for the first time, that a nanocircle-encoded ribozyme can cleave a gene—in this instance, the drug-resistance gene marA—in living bacteria (Proc. Natl. Acad. Sci. USA 99, 54–59, 2002). Kool et al. first generated a library of nanocircles, allowing the bacterial RNA polymerase to amplify the nanocircles with highest affinity, and then selected out these species. Further cycles of amplification and selection ultimately identified a high-affinity nanocircle. When bacteria were “treated" with this nanocircle, almost 90% of the marA-encoded protein was eliminated in cultures of Escherichia coli. Kool says, “Nanocircle vector with optimized single-stranded promoters is by far the most efficient way to make large quantities of RNAs, either in vitro or in [living] cells.” Nanocircles could be used as “Trojan horses” to sneak millions of copies of therapeutic RNAs, such as antisense molecules, into cells. LF

Highly charged mud

Microbial slime could, literally, light up your life, say Derek Lovely and colleagues from the University of Amherst (Boston, MA). Organic matter found in anoxic environments, such as that on the ocean floor, represents a large source of potential energy. Although some of the organic matter (for example, petroleum) is available in a ready-to-use form, there is no practical means of harvesting the remainder. Lovley's team devised a simple battery to harvest sufficient energy from marine sediment to power a light bulb (Science, 295, 483–485, 2002). The team constructed “sediment batteries” by placing a graphite electrode in the anoxic sediment and connecting this to a cathode in the overlying water. Further studies suggested that microorganisms, notably those of the Geobacteraceae family, played a key role in the conversion of slime to electricity. The microorganisms grow by oxidizing organic compounds (using iron rather than oxygen) in the sludge, transferring electrons in the process to the graphite electrode. Not only did this create an electrical current, it stimulated a surge in the population of the microbes, enriching their presence in the slime. Microbial communities containing Geobacteraceae may also detoxify organic waste, thereby helping to clean up the ocean's subsurface. CM

All in the blood

Finding a safe, specific, and effective means of delivering genes as therapeutic agents remains a challenge. Now, researchers at the John Hopkins Cancer Center (Baltimore, MD) have developed a way to direct the expression of genes to a highly specific subset of blood cells—antigen-presenting cells (APCs)—by targeting stem cells (Blood, 99, 399–408, 2002). Hematopoietic stem cells are attractive targets for gene therapy because they replicate throughout life and can differentiate into all subtypes of blood cells. However, existing gene therapy techniques indiscriminately incorporate the transgene into all stem cells and their progeny, whereas common blood disorders result from anomalies in more restricted populations of cells. To overcome this problem, Linzhao Cheng and colleagues used a lentiviral vector to load hematopoietic stem cells with a “test” gene encoding green fluorescent protein (GFP). The lentivirus was engineered so that it could not replicate and the encoded GFP could be transcribed only in APCs. In confirmation, the researchers found that GFP was expressed in APCs both in vitro and in immune-deficient mice in vivo. In the future, the team intends to use the technique to modify various subsets of APCs and study the nature of the resulting immune reactions in vivo. LF

Chaos in motion

So-called “lab-on-a-chip” microfluidic devices could function more efficiently if the networks of channels had grooved floors instead of flat ones, say engineers at Harvard University (Cambridge, MA), the University of California (Santa Barbara, CA), and the Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris (France). In existing microfluidic devices, the channels are so narrow that liquids pumped through the chip are forced to flow in smooth currents. This phenomenon, which physicists call “Poiseuille flow”, prevents mixing of the sample and reagent solutions, thereby impairing the assay process. Therefore, the researchers modified the microfluidic channels, etching a series of diagonal ridges into the channel floors (Science 295, 647–650, 2002). The “staggered herringbone” pattern caused the fluid to flow in a turbulent or “chaotic” manner, mixing it thoroughly within a distance of 1–1.5 cm. The simple design can be readily incorporated into microfluidic devices constructed using standard techniques. PM

Research News Briefs written by Liz Fletcher, Christopher Martino, and Peter Mitchell.