Loss of PopZ At activity in Agrobacterium tumefaciens by Deletion or Depletion Leads to Multiple Growth Poles, Minicells, and Growth Defects.

Agrobacterium tumefaciens grows by addition of peptidoglycan (PG) at one pole of the bacterium. During the cell cycle, the cell needs to maintain two different developmental programs, one at the growth pole and another at the inert old pole. Proteins involved in this process are not yet well characterized. To further characterize the role of pole-organizing protein A. tumefaciens PopZ (PopZ At ), we created deletions of the five PopZ At domains and assayed their localization. In addition, we created a popZAt deletion strain (ΔpopZAt ) that exhibited growth and cell division defects with ectopic growth poles and minicells, but the strain is unstable. To overcome the genetic instability, we created an inducible PopZ At strain by replacing the native ribosome binding site with a riboswitch. Cultivated in a medium without the inducer theophylline, the cells look like ΔpopZAt cells, with a branching and minicell phenotype. Adding theophylline restores the wild-type (WT) cell shape. Localization experiments in the depleted strain showed that the domain enriched in proline, aspartate, and glutamate likely functions in growth pole targeting. Helical domains H3 and H4 together also mediate polar localization, but only in the presence of the WT protein, suggesting that the H3 and H4 domains multimerize with WT PopZ At , to stabilize growth pole accumulation of PopZ AtIMPORTANCEAgrobacterium tumefaciens is a rod-shaped bacterium that grows by addition of PG at only one pole. The factors involved in maintaining cell asymmetry during the cell cycle with an inert old pole and a growing new pole are not well understood. Here we investigate the role of PopZ At , a homologue of Caulobacter crescentus PopZ (PopZ Cc ), a protein essential in many aspects of pole identity in C. crescentus We report that the loss of PopZ At leads to the appearance of branching cells, minicells, and overall growth defects. As many plant and animal pathogens also employ polar growth, understanding this process in A. tumefaciens may lead to the development of new strategies to prevent the proliferation of these pathogens. In addition, studies of A. tumefaciens will provide new insights into the evolution of the genetic networks that regulate bacterial polar growth and cell division

GenePath: a System for Automated Construction of Genetic Networks from Mutant Data

Motivation: Genetic pathways are often used in the analysis of biological phenomena. In classical genetics, they are constructed manually from experimental data on mutants. The field lacks formalism to guide such analysis, and accounting for all the data becomes complicated when large amounts of data are considered. Results: We have developed GenePath, an intelligent assistant that mimics expert geneticists in the analysis of genetic data. GenePath employs expert-defined patterns to uncover gene relations from the data, and uses these relations as constraints that guide the search for a plausible genetic network. GenePath provides formalism to genetic data analysis, facilitates the consideration of all the available data in a consistent and systematic manner, and aids in the examination of the large number of possible consequences of a planned experiment. It also provides an explanation mechanism that traces back every finding to the pertinent data. GenePath was successfully tested on several genetic problems. Availability: GenePath can be accessed at http://genepath.org. Supplementary information: Supplementary material is available at http://genepath.org/bi-supp

Web-enabled knowledge-based analysis of genetic data

We present a web-based implementation of GenePath, an intelligent assistant tool for data analysis in functional genomics. GenePath considers mutant data and uses expert-defined patterns to find gene-to-gene or gene-to-outcome relations. It presents the results of analysis as genetic networks, wherein a set of genes has various influence on one another and on a biological outcome. In the paper, we particularly focus on its web-based interface and explanation mechanisms

Computational Design Optimization of a Smart Material Shape Changing Building Skin Tile

The development and evaluation of a computational approach for optimal design of a smart material shape changing building skin is presented and numerically evaluated. Specifically, a unique shape-based approach is utilized to create an optimization approach to identify the activation and actuation mechanisms to minimize the difference between a desired shape and the estimated morphed shape. Three potential metrics of shape difference are considered and their capability to facilitate an efficient optimization process leading to accurate shape matching is evaluated. Details of the optimal design framework are presented, particularly focusing on the shape difference metrics as well as the strategy to parameterize the activation of the smart material. In particular, the parameterization strategy is a unique approach to easily integrate controllable localized activation within a smart material structure in a generally applicable way that does not limit the design search space. A series of numerical design examples are presented based on the concept of a smart material (e.g., shape memory polymer) shape changing tile that can be activated and actuated in a variety of ways to achieve desirable surface wrinkle patterns. These numerical design examples are applied to both 2D and 3D problems and consider a variety of parameterizations and target shapes. Results indicate that the shape-based approach can consistently determine the mechanisms of morphing needed to accurately match a target shape. Furthermore, it is shown that localized material activation can lead to not only a more accurate shape but also requires less energy and actuation devices to do so

Numerical Investigation of Capabilities for Dynamic Self-Shading through Shape Changing Building Surface Tiles

A concept for a smart material morphing building surface tile that would utilize adaptive surface wrinkle patterns to improve solar interaction is explored. The effect of the wrinkle patterns is numerically investigated in the context of an objective to reduce solar irradiance entering buildings by changing the shape of the surface (i.e., surface topography) so that the facade is self-shading, thereby reducing energy costs of the building for temperature control. A generally applicable algorithm was utilized and is presented to quantify the area of an arbitrarily shaped/oriented surface that is in shade for any given date/time and geographic location. Numerical case studies are shown that utilize the surface shading algorithm to evaluate the capabilities of various basic wrinkle patterns, both static and dynamically changing, to self-shade a building surface over the course of a day. The results indicate that a morphing wrinkle pattern can substantially increase the amount and duration of surface area in shade over time in comparison to any of the static (non-morphing) patterns, although it is noted that there is an expected tradeoff in the energy cost to change the surface pattern. Furthermore, it is shown that as the location of the proposed tile on the building facade changes, the optimal wrinkle pattern changes as well

Study of Tau-pair Production in Photon-Photon Collisions at LEP and Limits on the Anomalous Electromagnetic Moments of the Tau Lepton

Tau-pair production in the process e+e- -> e+e-tau+tau- was studied using data collected by the DELPHI experiment at LEP2 during the years 1997 - 2000. The corresponding integrated luminosity is 650 pb^{-1}. The values of the cross-section obtained are found to be in agreement with QED predictions. Limits on the anomalous magnetic and electric dipole moments of the tau lepton are deduced.Comment: 20 pages, 9 figures, Accepted by Eur. Phys. J.

CP asymmetry in B→ϕKSB \to \phi K_S in a general two-Higgs-doublet model with fourth-generation quarks

We discuss the time-dependent CP asymmetry of decay $B \to \phi K_S$ in an extension of the Standard Model with both two Higgs doublets and additional fourth-generation quarks. We show that although the Standard Model with two-Higgs-doublet and the Standard model with fourth generation quarks alone are not likely to largely change the effective $\sin 2 \beta$ from the decay of $B \to \phi K_S$, the model with both additional Higgs doublet and fourth-generation quarks can easily account for the possible large negative value of $\sin 2 \beta$ without conflicting with other experimental constraints. In this model, additional large CP violating effects may arise from the flavor changing Yukawa interactions between neutral Higgs bosons and the heavy fourth generation down type quark, which can modify the QCD penguin contributions. With the constraints obtained from $b \to s \bar{s} s$ processes such as $B \to X_s \gamma$ and $\Delta m_{B_s^0}$, this model can lead to the effective $\sin 2 \beta$ to be as large as $- 0.4$ in the CP asymmetry of $B \to \phi K_S$.Comment: 13 pages, 5 figures, references added, to appear in Eur.Phys.J.

Energy dependence of Cronin momentum in saturation model for p+Ap+A and A+AA+A collisions

We calculate $\sqrt{s}$ dependence of Cronin momentum for $p+A$ and $A+A$ collisions in saturation model. We show that this dependence is consistent with expectation from formula which was obtained using simple dimentional consideration. This can be used to test validity of saturation model (and distinguish among its variants) and measure $x$ dependence of saturation momentum from experimental data.Comment: LaTeX2e, 12 pages, 8 figure

A Precise Measurement of the Tau Lifetime

The tau lepton lifetime has been measured with the e+e- -> tau+tau- events collected by the DELPHI detector at LEP in the years 1991-1995. Three different methods have been exploited, using both one-prong and three-prong tau decay channels. Two measurements have been made using events in which both taus decay to a single charged particle. Combining these measurements gave tau_tau (1 prong) = 291.8 +/- 2.3 (stat) +/- 1.5 (sys) fs. A third measurement using taus which decayed to three charged particles yielded tau_tau (3 prong) = 288.6 +/- 2.4 (stat) +/- 1.3 (sys) fs. These were combined with previous DELPHI results to measure the tau lifetime, using the full LEP1 data sample, to be tau_tau = 290.9 +/- 1.4 (stat) +/- 1.0 (sys) fs.Comment: 27 pages, 7 figure