One goal of computational anatomy (CA) is to develop tools to accurately segment brain structures in healthy and diseased subjects. In this paper, we examine the performance and complexity of such segmentation in the framework of the large deformation diffeomorphic metric mapping (LDDMM) registration method with reference to atlases and parameters. First we report the application of a multi-atlas segmentation approach to define basal ganglia structures in healthy and diseased kids' brains. The segmentation accuracy of the multi-atlas approach is compared with the single atlas LDDMM implementation and two state-of-the-art segmentation algorithms—Freesurfer and FSL—by computing the overlap errors between automatic and manual segmentations of the six basal ganglia nuclei in healthy subjects as well as subjects with diseases including ADHD and Autism. The high accuracy of multi-atlas segmentation is obtained at the cost of increasing the computational complexity because of the calculations necessary between the atlases and a subject. Second, we examine the effect of parameters on total LDDMM computation time and segmentation accuracy for basal ganglia structures. Single atlas LDDMM method is used to automatically segment the structures in a population of 16 subjects using different sets of parameters. The results show that a cascade approach and using fewer time steps can reduce computational complexity as much as five times while maintaining reliable segmentations.

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Several mutant Escherichia coli aspartate aminotransferases (eAATases) have been characterized in the attempt to evolve or rationally redesign the substrate specificity of eAATase into that of E. coli tyrosine aminotransferase (eTATase). These include HEX (designed), HEX + A293D (design followed by directed evolution), and SRHEPT (directed evolution). The A293D mutation realized from directed evolution of HEX is here imported into the SRHEPT platform by site-directed mutagenesis, resulting in an enzyme (SRHEPT + A293D) with nearly the same ratio of k(cat)/K(m)(Phe) to k(cat)/K(m)(Asp) as that of wild-type eTATase. The A293D substitution is an important specificity determinant; it selectively disfavors interactions with dicarboxylic substrates and inhibitors compared to aromatic ones. Context dependence analysis is generalized to provide quantitative comparisons of a common substitution in two or more different protein scaffolds. High-resolution crystal structures of ligand complexes of HEX + A293D, SRHEPT, and SRHEPT + A293D were determined. We find that in both SRHEPT + A293D and HEX + A293D, the additional mutation holds the Arg 292 side chain away from the active site to allow increased specificity for phenylalanine over aspartate. The resulting movement of Arg 292 allows greater flexibility of the small domain in HEX + A293D. While HEX is always in the closed conformation, HEX + A293D is observed in both the closed and a novel open conformation, allowing for more rapid product release.

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Homopolar doublets of syngen 1, T. pyriformis, may be induced by treatment of conjugating pairs with immobilizing antiserum. These doublets have geometric properties and basal body populations generally indicative of separate autonomous integrative systems in the two halves. The duplex system, though metastable, is transformed through a process of "simplification" back to the simplex state. The transformation is not a single event, but a series involving changes at different times for different structures and processes; for the micronuclei and the macronuclei; for the capacity to generate two oral apparatuses through stomatogenesis and the capacity to develop them through oral replacement; for the structures at the anterior and posterior ends of the cell; for the numbers of ciliary rows and for the numbers of basal bodies which make up the rows. Although the two semicells composing a doublet are in important respects independent of each other, they are coordinated in significant ways. The positions of the contractile vacuole pores and their numbers depend not only on the number of ciliary rows in a semicell, but also on the number of ciliary rows in the opposing twin. Most notably, the probability for dual stomatogenesis, and hence the perpetuation of the doubled oral apparatus, depends on the symmetry of the semicells. The cell as a whole is maintained as an integrated unit over a prolonged interval as various aspects of duplex structure and function are progressively consolidated.