A Computational Approach to Estimating Nondisjunction Frequency in Saccharomyces cerevisiae.

Errors segregating homologous chromosomes during meiosis result in aneuploid gametes and are the largest contributing factor to birth defects and spontaneous abortions in humans. Saccharomyces cerevisiae has long served as a model organism for studying the gene network supporting normal chromosome segregation. Measuring homolog nondisjunction frequencies is laborious, and involves dissecting thousands of tetrads to detect missegregation of individually marked chromosomes. Here we describe a computational method (TetFit) to estimate the relative contributions of meiosis I nondisjunction and random-spore death to spore inviability in wild type and mutant strains. These values are based on finding the best-fit distribution of 4, 3, 2, 1, and 0 viable-spore tetrads to an observed distribution. Using TetFit, we found that meiosis I nondisjunction is an intrinsic component of spore inviability in wild-type strains. We show proof-of-principle that the calculated average meiosis I nondisjunction frequency determined by TetFit closely matches empirically determined values in mutant strains. Using these published data sets, TetFit uncovered two classes of mutants: Class A mutants skew toward increased nondisjunction death, and include those with known defects in establishing pairing, recombination, and/or synapsis of homologous chromosomes. Class B mutants skew toward random spore death, and include those with defects in sister-chromatid cohesion and centromere function. Epistasis analysis using TetFit is facilitated by the low numbers of tetrads (as few as 200) required to compare the contributions to spore death in different mutant backgrounds. TetFit analysis does not require any special strain construction, and can be applied to previously observed tetrad distributions

Transition Events in Butane Simulations: Similarities Across Models

From a variety of long simulations of all-atom butane using both stochastic and fully-solved molecular dynamics, we have uncovered striking generic behavior which also occurs in one-dimensional systems. We find an apparently universal distribution of transition event durations, as well as a characteristic speed profile along the reaction coordinate. An approximate analytic distribution of event durations, derived from a one-dimensional model, correctly predicts the asymptotic behavior of the universal distribution for both short and long durations.Comment: 18 pages, 6 figure

Data types

A Mathematical interpretation is given to the notion of a data type. The main novelty is in the generality of the mathematical treatment which allows procedural data types and circularly defined data types. What is meant by data type is pretty close to what any computer scientist would understand by this term or by data structure, type, mode, cluster, class. The mathematical treatment is the conjunction of the ideas of D. Scott on the solution of domain equations (Scott (71), (72) and (76)) and the initiality property noticed by the ADJ group (ADJ (75), ADJ (77)). The present work adds operations to the data types proposed by Scott and generalizes the data types of ADJ to procedural types and arbitrary circular type definitions. The advantages of a mathematical interpretation of data types are those of mathematical semantics in general : throwing light on some ill-understood constructs in high-level programming languages, easing the task of writing correct programs and making possible proofs of correctness for programs or implementations"

MMT Survey for Intervening MgII Absorption

We present the results from a spectroscopic survey for intervening MgII absorption in the spectra of 381 background QSOs conducted at the Multiple Mirror Telescope. This survey complements our earlier SDSS EDR MgII survey, extending our results to lower redshift ($z \simeq 0.15$) and weaker MgII $\lambda2796$ rest equivalent width ($W_0^{\lambda2796} \simeq 0.1$\AA). We confirm two major results from that survey: the transition in the $W_0^{\lambda2796}$ distribution at $W_0^{\lambda2796} \approx 0.3$\AA, and the $W_0^{\lambda2796}$-dependent evolution of the incidence of systems. The nature of $\partial^2N/\partial z \partial W_0^{\lambda2796}$ is consistent with the idea that multiple physically-distinct components/processes contribute to the incidence of MgII absorption systems in a $W_0$-dependent manner and evolve at different rates. A significant decrease in the total proper absorption cross section is detected in our MMT data for systems as weak as 1.0 \AA $\le W_0^{\lambda2796} < 1.5$\AA at $z\lesssim 0.4$. We discuss this $W_0$-dependent evolution in the context of the evolution of galaxy structures, processes including superwinds and interactions, and damped-Ly$\alpha$ absorbers. We also consider the possibility that the observed redshift and $W_0^{\lambda2796}$ dependence of the incidence of absorption in spectroscopic surveys for low-ion/neutral gas results from the effects of dust-induced extinction.Comment: 16 pages, 7 figures, accepted for publication in The Astrophysical Journa