Multiple-complete-digest restriction fragment mapping: Generating sequence-ready maps for large-scale DNA sequencing

Multiple-complete-digest mapping is a DNA mapping technique based on complete-restriction-digest fingerprints of a set of clones that provides highly redundant coverage of the mapping target. The maps assembled from these fingerprints order both the clones and the restriction fragments. Maps are coordinated across three enzymes in the examples presented. Starting with yeast artificial chromosome contigs from the 7q31.3 and 7p14 regions of the human genome, we have produced cosmid-based maps spanning more than one million base pairs. Each yeast artificial chromosome is first subcloned into cosmids at a redundancy of ×15–30. Complete-digest fragments are electrophoresed on agarose gels, poststained, and imaged on a fluorescent scanner. Aberrant clones that are not representative of the underlying genome are rejected in the map construction process. Almost every restriction fragment is ordered, allowing selection of minimal tiling paths with clone-to-clone overlaps of only a few thousand base pairs. These maps demonstrate the practicality of applying the experimental and software-based steps in multiple-complete-digest mapping to a target of significant size and complexity. We present evidence that the maps are sufficiently accurate to validate both the clones selected for sequencing and the sequence assemblies obtained once these clones have been sequenced by a “shotgun” method.

New perspectives on forbidden symmetries, quasicrystals, and Penrose tilings

Quasicrystals are solids with quasiperiodic atomic structures and symmetries forbidden to ordinary periodic crystals—e.g., 5-fold symmetry axes. A powerful model for understanding their structure and properties has been the two-dimensional Penrose tiling. Recently discovered properties of Penrose tilings suggest a simple picture of the structure of quasicrystals and shed new light on why they form. The results show that quasicrystals can be constructed from a single repeating cluster of atoms and that the rigid matching rules of Penrose tilings can be replaced by more physically plausible cluster energetics. The new concepts make the conditions for forming quasicrystals appear to be closely related to the conditions for forming periodic crystals.

Spatial organization of retinal information about the direction of image motion.

The visual stimuli that elicit neural activity differ for different retinal ganglion cells and these cells have been categorized by the visual information that they transmit. If specific visual information is conveyed exclusively or primarily by a particular set of ganglion cells, one might expect the cells to be organized spatially so that their sampling of information from the visual field is complete but not redundant. In other words, the laterally spreading dendrites of the ganglion cells should completely cover the retinal plane without gaps or significant overlap. The first evidence for this sort of arrangement, which has been called a tiling or tessellation, was for the two types of "alpha" ganglion cells in cat retina. Other reports of tiling by ganglion cells have been made subsequently. We have found evidence of a particularly rigorous tiling for the four types of ganglion cells in rabbit retina that convey information about the direction of retinal image motion (the ON-OFF direction-selective cells). Although individual cells in the four groups are morphologically indistinguishable, they are organized as four overlaid tilings, each tiling consisting of like-type cells that respond preferentially to a particular direction of retinal image motion. These observations lend support to the hypothesis that tiling is a general feature of the organization of information outflow from the retina and clearly implicate mechanisms for recognition of like-type cells and establishment of mutually acceptable territories during retinal development.