Simulations of knotting in confined circular DNA.

The packing of DNA inside bacteriophages arguably yields the simplest example of genome organization in living organisms. As an assay of packing geometry, the DNA knot spectrum produced upon release of viral DNA from the P4 phage capsid has been analyzed, and compared to results of simulation of knots in confined volumes. We present new results from extensive stochastic sampling of confined self-avoiding and semiflexible circular chains with volume exclusion. The physical parameters of the chains (contour length, cross section, and bending rigidity) have been set to match those of P4 bacteriophage DNA. By using advanced sampling techniques, involving multiple Markov chain pressure-driven confinement combined with a thermodynamic reweighting technique, we establish the knot spectrum of the circular chains for increasing confinement up to the highest densities for which available algorithms can exactly classify the knots. Compactified configurations have an enclosing hull diameter approximately 2.5 times larger than the P4 caliper size. The results are discussed in relation to the recent experiments on DNA knotting inside the capsid of a P4 tailless mutant. Our investigation indicates that confinement favors chiral knots over achiral ones, as found in the experiments. However, no significant bias of torus over twist knots is found, contrary to the P4 results. The result poses a crucial question for future studies of DNA packaging in P4: is the discrepancy due to the insufficient confinement of the equilibrium simulation or does it indicate that out-of-equilibrium mechanisms (such as rotation by packaging motors) affect the genome organization, hence its knot spectrum in P4?

Knotting of random ring polymers in confined spaces.

Stochastic simulations are used to characterize the knotting distributions of random ring polymers confined in spheres of various radii. The approach is based on the use of multiple Markov chains and reweighting techniques, combined with effective strategies for simplifying the geometrical complexity of ring conformations without altering their knot type. By these means we extend previous studies and characterize in detail how the probability to form a given prime or composite knot behaves in terms of the number of ring segments N and confining radius R. For 50 < or =N < or =450 we show that the probability of forming a composite knot rises significantly with the confinement, while the occurrence probability of prime knots are, in general, nonmonotonic functions of 1R. The dependence of other geometrical indicators, such as writhe and chirality, in terms of R and N is also characterized. It is found that the writhe distribution broadens as the confining sphere narrows.

Novel display of knotted DNA molecules by two-dimensional gel electrophoresis.

We describe a two-dimensional agarose gel electrophoresis procedure that improves the resolution of knotted DNA molecules. The first gel dimension is run at low voltage, and DNA knots migrate according to their compactness. The second gel dimension is run at high voltage, and DNA knots migrate according to other physical parameters such as shape and flexibility. In comparison with one-dimensional gel electrophoresis, this procedure segregates the knotted DNA molecules from other unknotted forms of DNA, and partially resolves populations of knots that have the same number of crossings. The two-dimensional display may allow quantitative and qualitative characterization of different types of DNA knots simply by gel velocity.

Analyzing functional brain images in a probabilistic atlas: a validation of subvolume thresholding.

PURPOSE: The development of structural probabilistic brain atlases provides the framework for new analytic methods capable of combining anatomic information with the statistical mapping of functional brain data. Approaches for statistical mapping that utilize information about the anatomic variability and registration errors of a population within the Talairach atlas space will enhance our understanding of the interplay between human brain structure and function. METHOD: We present a subvolume thresholding (SVT) method for analyzing positron emission tomography (PET) and single photon emission CT data and determining separately the statistical significance of the effects of motor stimulation on brain perfusion. Incorporation of a priori anatomical information into the functional SVT model is achieved by selecting a proper anatomically partitioned probabilistic atlas for the data. We use a general Gaussian random field model to account for the intrinsic differences in intensity distribution across brain regions related to the physiology of brain activation, attenuation effects, dead time, and other corrections in PET imaging and data reconstruction. RESULTS: H2(15)O PET scans were acquired from six normal subjects under two different activation paradigms: left-hand and right-hand finger-tracking task with visual stimulus. Regional region-of-interest and local (voxel) group differences between the left and right motor tasks were obtained using nonparametric stochastic variance estimates. As expected from our simple finger movement paradigm, significant activation (z = 6.7) was identified in the left motor cortex for the right movement task and significant activation (z = 6.3) for the left movement task in the right motor cortex. CONCLUSION: We propose, test, and validate a probabilistic SVT method for mapping statistical variability between groups in subtraction paradigm studies of functional brain data. This method incorporates knowledge of, and controls for, anatomic variability contained in modern human brain probabilistic atlases in functional statistical mapping of the brain.

The topological mechanism of phage lambda integrase.

Bacteriophage lambda integrase (Int) is a versatile site-specific recombinase. In concert with other proteins, it mediates phage integration into and excision out of the bacterial chromosome. Int recombines intramolecular sites in inverse or direct orientation or sites on separate DNA molecules. This wide spectrum of Int-mediated reactions has, however, hindered our understanding of the topology of Int recombination. By systematically analyzing the topology of Int reaction products and using a mathematical method called tangles, we deduce a unified model for Int recombination. We find that, even in the absence of (-) supercoiling, all Int reactions are chiral, producing one of two possible enantiomers of each product. We propose that this chirality reflects a right-handed DNA crossing within or between recombination sites in the synaptic complex that favors formation of right-handed Holliday junction intermediates. We demonstrate that the change in linking number associated with excisive inversion with relaxed DNA is equally +2 and -2, reflecting two different substrates with different topology but the same chirality. Additionally, we deduce that integrative Int recombination differs from excisive recombination only by additional plectonemic (-) DNA crossings in the synaptic complex: two with supercoiled substrates and one with relaxed substrates. The generality of our results is indicated by our finding that two other members of the integrase superfamily of recombinases, Flp of yeast and Cre of phage P1, show the same intrinsic chirality as lambda Int.

A symbolic environment for visualizing activated foci in functional neuroimaging datasets.

This paper presents a symbolic visualization environment known as the Corner Cube environment, which was developed to facilitate rapid examination and comparison of activated foci defined by analyses of functional neuroimaging datasets. We have performed a comparative evaluation of this environment against maximum-intensity projection and 'gallery of slices' displays, and the results suggest that the Corner Cube environment has definite advantages over both conventional display techniques. We conclude that the Corner Cube is an effective tool for summarizing the spatial characteristics of activated foci within an easily understood visual context and is especially useful for displaying the similarities and differences in functional neuroimaging datasets.