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EmmmEmiima Hollow core fiber What could be better than a conventional opticalfiberfor transmitting and guiding light? In theory, afiberwith a hollow core filled with air. But that is not possible because there is no solid cladding material with a refractive index lower than air. That problem exists as long as the optical fiber relies on the principle of total internal reflection to transmit light. So, P. St. J. Russell and colleagues at the University of Bath (U.K.), the Defence Evaluation and Research Agency (U.K.), and Corning exploit a different phenomenon—twodimensional photonic band gap (PBG)—to confine light within the hollow core of a specially designed silica-air fiber. PBG requires afibercladding with a near-perfect periodic array of air holes (the photonic crystal), a high air-filling fraction, and a small distance between adjacent holes in the lattice. In this study, the appropriatefibers,known as photonic crystalfibers,were constructed by bundling together capillary canes with external diameters of ~ 1 mm, and then the canes were drawn down into afiberwith a diameter of 40-100 um and fused to-
Left: Scanning electron micrograph of a photonic crystal fiber. Right: White light in one end yields colored light at the other end. (Adapted with permission. Copyright 1999 American Association for the Advancement of Science.)
gether. The result is a honeycomb arrangement with about 30% of the volumefilledby air. A "large" air hole is in the center. The authors investigated a seven-unit-cell air core fiber. When white light from a tungsten halogen lamp is introduced into the fiber, the central core transmits and guides only certain wavelength bands (following PBG principles), emitting a colored light in many cases. The light transmitted depends on the overallfiberlength and the drawing
defined by an automated scanning technology that uses fluorescence microscopy. The technique has been previously applied, The traditional tools of genome mapping are but obtaining and mapping extremely large (0.4-2.4 megabases [Mb]), randomly DNA libraries, PCR, and electrophoresis. sheared DNA molecules are new. The reBut researchers no longer need them to searchers achieve that with a semiautomap a genome, according to Jieyi Lin; J. mated image acquisition system to collect Craig Venter; David C. Schwartz; and colleagues at New York University, The Insti- successive images and assemble them into tute for Genomic Research, Uniformed Ser- a single superimage, maintaining pixel alignment in the process. vices University of the Health Sciences, and Celera Genomics. The researchers describe A new image analysis system also was the construction of a whole-genome restricdeveloped. Using bacteriophage X DNA as tion map of the radiation-resistant bacterium a standard, the size of each genomic fragDeionococcus radiodurans using shotgun ment was calculated by dividing the fluooptical mapping. Whole-genome restriction rescence intensity of that fragment by the maps are not detailed maps. Instead, they average fluorescence intensity of the stanprovide a scaffold for the verification and dards in the image. That quotient was mulhigh-resolution alignment of sequence astiplied by the size of the standard. The raw semblies called "contigs". maps were then assembled into a complete In shotgun optical mapping, the DNA is genome-wide map using a specialized algorithm called Gentig. The researchers restraightened and then cut with restriction port that this process, which used to be enzymes. Each fragment is measured and
Genome mapping goes light
conditions. Light losses for these wavelengths are very small, even over fiber lengths of several centimeters. Similar results are seen with laser light. The authors say that these fibers could have many applications, including supporting extremely high power densities without breakdown and greatly increasing the threshold intensities for stimulated Raman scattering. (Science 1999, 285, 1537-39) measured in months, now can be measured in minutes. Before sequencing D. radiodurans, the researchers tested the optical mapping system on a previously sequenced bacteria, Escherichia coli K12 substrain MG1665, and found
