Fluorescence in situ hybridization of YAC clones after Alu-PCR amplification

Alu-PCR protocols were optimized for the generation of human DNA probes from yeast strains containing yeast artificial chromosomes (YACs) with human inserts between 100 and 800 kb in size. The resulting DNA probes were used in chromosome in situ suppression (CISS) hybridization experiments. Strong fluorescent signals on both chromatids indicated the localization of specific YAC clones, while two clearly distinguishable signals were observed in ≥90% of diploid nuclei Signal intensities were generally comparable to those observed using chromosome-specific alphoid DNA probes. This approach will facilitate the rapid mapping of YAC clones and their use in chromosome analysis at all stages of the cell cycle

Generating cryptographically-strong random lattice bases and recognizing rotations of Zn\mathbb{Z}^n

Lattice-based cryptography relies on generating random bases which are difficult to fully reduce. Given a lattice basis (such as the private basis for a cryptosystem), all other bases are related by multiplication by matrices in $GL(n,\mathbb{Z})$. How can one sample random elements from $GL(n,\mathbb{Z})$? We consider various methods, finding some are stronger than others with respect to the problem of recognizing rotations of the $\mathbb{Z}^n$ lattice. In particular, the standard algorithm of multiplying unipotent generators together (as implemented in Magma's RandomSLnZ command) generates instances of this last problem which can be efficiently broken, even in dimensions nearing 1,500. Similar weaknesses for this problem are found with the random basis generation method in one of the NIST Post-Quantum Cryptography competition submissions (DRS). Other algorithms are described which appear to be much stronger.Comment: 24 pages, 2 figure

Generalized monotonic functional mixed models with application to modelling normal tissue complications

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73586/1/j.1467-9876.2007.00606.x.pd

Quaternary structure change as a mechanism for the regulation of thymidine kinase 1-like enzymes

SummaryThe human cytosolic thymidine kinase (TK) and structurally related TKs in prokaryotes play a crucial role in the synthesis and regulation of the cellular thymidine triphosphate pool. We report the crystal structures of the TK homotetramer from Thermotoga maritima in four different states: its apo-form, a binary complex with thymidine, as well as the ternary structures with the two substrates (thymidine/AppNHp) and the reaction products (TMP/ADP). In combination with fluorescence spectroscopy and mutagenesis experiments, our results demonstrate that ATP binding is linked to a substantial reorganization of the enzyme quaternary structure, leading to a transition from a closed, inactive conformation to an open, catalytic state. We hypothesize that these structural changes are relevant to enzyme function in situ as part of the catalytic cycle and serve an important role in regulating enzyme activity by amplifying the effects of feedback inhibitor binding

Shape, motion, and inertial parameter estimation of space objects using teams of cooperative vision sensors

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2005."February 2005."Includes bibliographical references (leaves 133-140).Future space missions are expected to use autonomous robotic systems to carry out a growing number of tasks. These tasks may include the assembly, inspection, and maintenance of large space structures; the capture and servicing of satellites; and the redirection of space debris that threatens valuable spacecraft. Autonomous robotic systems will require substantial information about the targets with which they interact, including their motions, dynamic model parameters, and shape. However, this information is often not available a priori, and therefore must be estimated in orbit. This thesis develops a method for simultaneously estimating dynamic state, model parameters, and geometric shape of arbitrary space targets, using information gathered from range imaging sensors. The method exploits two key features of this application: (1) the dynamics of targets in space are highly deterministic and can be accurately modeled; and (2) several sensors will be available to provide information from multiple viewpoints. These features enable an estimator design that is not reliant on feature detection, model matching, optical flow, or other computation-intensive pixel-level calculations. It is therefore robust to the harsh lighting and sensing conditions found in space. Further, these features enable an estimator design that can be implemented in real- time on space-qualified hardware. The general solution approach consists of three parts that effectively decouple spatial- and time-domain estimations. The first part, referred to as kinematic data fusion, condenses detailed range images into coarse estimates of the target's high-level kinematics (position, attitude, etc.).(cont.) A Kalman filter uses the high-fidelity dynamic model to refine these estimates and extract the full dynamic state and model parameters of the target. With an accurate understanding of target motions, shape estimation reduces to the stochastic mapping of a static scene. This thesis develops the estimation architecture in the context of both rigid and flexible space targets. Simulations and experiments demonstrate the potential of the approach and its feasibility in practical systems.by Matthew D. Lichter.Ph.D