Protein mirrors

Credit: Courtesy M.J. McFall-Ngai

Tissues that reflect light are found throughout the animal kingdom and are especially common in ocean creatures. Squid use reflective tissue for camouflage: their light organ, containing symbiotic luminescent bacteria and a layer of reflector platelets, directs light downwards, making the squid less visible to predators in the sand. Investigating the molecular basis of reflector activity in the squid Euprymna scolopes, McFall-Ngai and colleagues discovered a novel class of proteins, which they named 'reflectins.' Reflectins have an unusual amino acid composition: 57% of the molecule consists of four relatively rare residues (tyrosine, methionine, arginine and tryptophan), and four residues common in proteins (alanine, isoleucine, leucine and lysine) are absent. The proteinaceous nature of squid reflector platelets is itself unusual, as most reflective tissues characterized so far are made of purine crystals. The authors suggest that reflectins could be incorporated into a variety of nanoscale optical devices. (Science 303, 235–238, 2004) KA

T-cell identification on the spot

Identification and characterization of antigen-specific T cells is crucial for investigating the immune response in health and disease. These cells recognize a particular peptide bound to a major histocompatibility complex (MHC) molecule on a host cell. Now, Soen et al. have used arrays of peptide-MHC complexes for the simultaneous identification, isolation and characterization of multiple antigen-specific populations of T cells. Currently, antigen-specific T cells labeled with fluorescently tagged tetrameric MHC-peptide complexes have provided an approach to characterize the immune response. However, detection using flow cytometry is technically difficult, expensive and limited to only one or a few antigen specificities at a time. Using the new screening approach, multiple antigen-specific cells can be captured onto an array of individual spots of peptide-MHC complexes, with cell capture dependent on T-cell specificity. The approach can detect rare T-cell specificities in a complex cell population and even weak immune responses after vaccination. The arrays of peptide-MHC complexes should be useful for epitope discovery, as well as for the analysis of T-cell populations during immune responses related to vaccination, infection and cancer. (PloS 1, 429–438, 2004) MS

SOS for antibiotics

Concern is growing about the transfer of antibiotic resistance among different bacterial populations. A paper by Beaber et al. sets even more alarm bells ringing: they observe that certain antibiotics, such as ciprofloxacin and mitomycin C, can promote the spread of antibiotic resistance genes. They found that antibiotics that induce an 'SOS response' (activation of genes that promote cell survival) increase the rate of conjugative transfer of antibiotic resistance genes in Escherichia coli and Vibrio cholerae. These bacteria contain SXT, a conjugative element, normally repressed, that encodes resistance to several antibacterial agents. The authors found that SetR, an SXT-encoded repressor, represses the expression of activators of SXT transfer. However, induction of the SOS response alleviates this repression. The results indicate that the use of antibiotics could promote dissemination of antibiotic resistance genes to a wide variety of bacteria. (Nature 427, 72–74, 2004) MZ

Mass production of shRNAs

RNA interference (RNAi) has become one of the approaches of choice for studying gene function in eukaryotic systems, but no efficient systems exist to economically generate and screen libraries of possible double-stranded RNA (dsRNA) molecules. Two groups now report on the rapid and efficient generation of small-interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) from cDNA using a series of enzymatic steps. Sen et al. devised a stepwise procedure for producing siRNAs to target genes; after an initial digestion of the cDNA with a combination of restriction enzymes, the DNA fragments are ligated to hairpin DNA oligonucleotides, and the constructs cloned and finally amplified. Shirane et al. generated a library of shRNAs from a cDNA library by first randomly fragmenting the cDNA with DNaseI and then producing stable RNA expression vectors (an approach similar to that of Sen et al.). Both approaches yield dsRNA libraries that can be effectively screened to identify those molecules that most efficiently silence the activity of a gene of interest. These technologies provide the basis for genome-wide determination of gene function using RNAi. (Sen et al. Nat. Genet. 36, 183–189, 2004; Shirane et al. Nat. Genet. 36, 190–196, 2004) GTO

Scab-resistant apples

To control apple scab disease, farmers currently apply fungicides dozens of times in a growing season. What's more, although wild cultivars resistant to the etiologic agent (Venturia inaequalis) are available, attempts to breed resistance into commercial apple varieties have thus far had only limited success. Now, Sansavini and colleagues have engineered scab-resistant apples using a wild apple (Malus floribunda) gene identified on the basis of its homology to a tomato gene that confers resistance to the tomato leaf mold fungus Cladosporium fulvum. Using Agrobacterium tumefaciens–mediated transformation, they transferred HcfVf (homologous to Cladosporium fulvum resistance genes of the Vf region) into Gala apples and confirmed its integration and expression in four out of five independent lines of transgenic plants. (The fifth contained only the selectable marker used to isolate transgenic plants.) Transformed plants showed a high level of resistance compared with controls, although there was some variation thought to be due to differing sites of integration. All plants containing HcfVf displayed greater resistance than naturally resistant cultivars. (Proc. Natl. Acad. Sci. USA 101, 886–890, 2004) LD

Research Notes written by Kathy Aschheim, Laura DeFrancesco, Meeghan Sinclair, Gaspar Taroncher-Oldenburg and Mark Zipkin.