Model of Transcriptional Activation by MarA in Escherichia coli

We have developed a mathematical model of transcriptional activation by MarA in Escherichia coli, and used the model to analyze measurements of MarA-dependent activity of the marRAB, sodA, and micF promoters in mar-rob- cells. The model rationalizes an unexpected poor correlation between the mid-point of in vivo promoter activity profiles and in vitro equilibrium constants for MarA binding to promoter sequences. Analysis of the promoter activity data using the model yielded the following predictions regarding activation mechanisms: (1) MarA activation of the marRAB, sodA, and micF promoters involves a net acceleration of the kinetics of transitions after RNA polymerase binding, up to and including promoter escape and message elongation; (2) RNA polymerase binds to these promoters with nearly unit occupancy in the absence of MarA, making recruitment of polymerase an insignificant factor in activation of these promoters; and (3) instead of recruitment, activation of the micF promoter might involve a repulsion of polymerase combined with a large acceleration of the kinetics of polymerase activity. These predictions are consistent with published chromatin immunoprecipitation assays of interactions between polymerase and the E. coli chromosome. A lack of recruitment in transcriptional activation represents an exception to the textbook description of activation of bacterial sigma-70 promoters. However, use of accelerated polymerase kinetics instead of recruitment might confer a competitive advantage to E. coli by decreasing latency in gene regulation.Comment: 30 pages, 2 figure

Advancing Knowledge on Situation Comprehension in Dynamic Traffic Situations by Studying Eye Movements to Empty Spatial Locations

Objective: This study used the looking-at-nothing phenomenon to explore situation awareness (SA) and the effects of working memory (WM) load in driving situations. Background: While driving, people develop a mental representation of the environment. Since errors in retrieving information from this representation can have fatal consequences, it is essential for road safety to investigate this process. During retrieval, people tend to fixate spatial positions of visually encoded information, even if it is no longer available at that location. Previous research has shown that this "looking-at-nothing" behavior can be used to trace retrieval processes. Method: In a video-based laboratory experiment with 2 (WM) x 3 (SA level) within-subjects design, participants (N = 33) viewed a reduced screen and evaluated auditory statements relating to different SA levels on previously seen dynamic traffic scenarios while eye movements were recorded. Results: When retrieving information, subjects more frequently fixated emptied spatial locations associated with the information relevant for the probed SA level. The retrieval of anticipations (SA level 3) in contrast to the other SA level information resulted in more frequent gaze transitions that corresponded to the spatial dynamics of future driving behavior. Conclusion: The results support the idea that people build a visual-spatial mental image of a driving situation. Different gaze patterns when retrieving level-specific information indicate divergent retrieval processes. Application: Potential applications include developing new methodologies to assess the mental representation and SA of drivers objectively

Radiative D∗D^* Decay Using Heavy Quark and Chiral Symmetry

The implications of chiral $SU(3)_L \times SU(3)_R$ symmetry and heavy quark symmetry for the radiative decays $D^{*0}\to D^0\gamma$, $D^{*+}\to D^+\gamma$, and $D_s^*\to D_s\gamma$ are discussed. Particular attention is paid to $SU(3)$ violating contributions of order $m_q^{1/2}$. Experimental data on these radiative decays provide constraints on the $D^* D\pi$ coupling.Comment: 9 pages plus 3 pages of figures in POSTSCRIPT file appended to TeX file (uses harvmac.tex and tables.tex), UCSD/PTH 92-31, CALT-68-1816, EFI-92-45, CERN-TH.6650/9

Boron Isotope Fractionation in Bell Pepper

Various plant compartments of a single bell pepper plant were studied to verify the variability of boron isotope composition in plants and to identify possible intra-plant isotope fractionation. Boron mass fractions varied from 9.8 mg/kg in the fruits to 70.0 mg/kg in the leaves. Boron (B) isotope ratios reported as δ11B ranged from -11.0‰ to +16.0‰ (U ≤ 1.9‰, k=2) and showed a distinct trend to heavier δ11B values the higher the plant compartments were located in the plant. A fractionation of Δ11Bleaf-roots = 27‰ existed in the studied bell pepper plant, which represents about 1/3 of the overall natural boron isotope variation (ca. 80‰). Two simultaneous operating processes are a possible explanation for the observed systematic intra-plant δ11B variation: 1) B is fixed in cell walls in its tetrahedral form (borate), which preferentially incorporates the light B isotope and the remaining xylem sap gets enriched in the heavy B isotope and 2) certain transporter preferentially transport the trigonal 11B-enriched boric acid molecule and thereby the heavy 11B towards young plant compartments which were situated distal of the roots and typically high in the plant. Consequently, an enrichment of the heavy 11B isotope in the upper young plant parts located at the top of the plant could explain the observed isotope systematic. The identification and understanding of the processes generating systematic intra-plant δ11B variations will potentially enable the use of B isotope for plant metabolism studies

Detection of low-level promoter activity within open reading frame sequences of Escherichia coli

The search for promoters has largely been confined to sequences upstream of open reading frames (ORFs) or stable RNA genes. Here we used a cloning approach to discover other potential promoters in Escherichia coli. Chromosomal fragments of ∼160 bp were fused to a promoterless lacZ reporter gene on a multi-copy plasmid. Eight clones were deliberately selected for high activity and 105 clones were selected at random. All eight of the high-activity clones carried promoters that were located upstream of an ORF. Among the randomly-selected clones, 56 had significantly elevated activity. Of these, 7 had inserts which also mapped upstream of an ORF, while 49 mapped within or downstream of ORFs. Surprisingly, the eight promoters selected for high activity matched the canonical σ(70) −35 and −10 sequences no better than sequences from the randomly-selected clones. For six of the nine most active sequences with orientations opposite to that of the ORF, chromosomal expression was detected by RT–PCR, but defined transcripts were not detected by northern analysis. Our results indicate that the E.coli chromosome carries numerous −35 and −10 sequences with weak promoter activity but that most are not productively expressed because other features needed to enhance promoter activity and transcript stability are absent

Within-ring movement of free water in dehydrating Norway spruce sapwood visualized by neutron radiography

This study is a first approach to visualize moisture distribution and movement between annual rings during sapwood drying by neutron imaging (NI). While Norway spruce [Picea abies (L.) Karst.] sapwood beams were allowed to dehydrate on a balance at ambient conditions, NI was performed in 1-10 min time steps. From NI raw files, radial dimensional changes were calculated during dehydration and transmission profiles were drawn for different relative moisture content (MC) steps from full saturation until equilibrium moisture content. The NI technique proved to be a useful tool to visualize the movement of free water within, and between, annual rings. Removal of free water in the middle part of the wood beam did not proceed continuously from the surface to the central part, but was strongly influenced by wood anatomy. Water is removed from earlywood during early stages of dehydration and later, at higher moisture loss (<50% MC), from the main latewood parts. It is therefore concluded that the radial dimensional changes measured at moderate moisture loss are not only caused by cell wall shrinkage of the outer wood parts located beneath the wood surface, but a result of elastic deformation of earlywood tracheids under the influence of negative hydrostatic pressure

TSIL: a program for the calculation of two-loop self-energy integrals

TSIL is a library of utilities for the numerical calculation of dimensionally regularized two-loop self-energy integrals. A convenient basis for these functions is given by the integrals obtained at the end of O.V. Tarasov's recurrence relation algorithm. The program computes the values of all of these basis functions, for arbitrary input masses and external momentum. When analytical expressions in terms of polylogarithms are available, they are used. Otherwise, the evaluation proceeds by a Runge-Kutta integration of the coupled first-order differential equations for the basis integrals, using the external momentum invariant as the independent variable. The starting point of the integration is provided by known analytic expressions at (or near) zero external momentum. The code is written in C, and may be linked from C, C++, or Fortran. A Fortran interface is provided. We describe the structure and usage of the program, and provide a simple example application. We also compute two new cases analytically, and compare all of our notations and conventions for the two-loop self-energy integrals to those used by several other groups.Comment: 31 pages. Updated to reflect new functionality through v1.4 May 2016 and new information about use with C++. Source code and documentation are available at http://www.niu.edu/spmartin/TSIL or http://faculty.otterbein.edu/DRobertson/tsil

Identification of Neutral B Mesons Using Correlated Hadrons

The identification of the flavor of a neutral $B$ meson can make use of hadrons produced nearby in phase space. Examples include the decay of ``$B^{**}$'' resonances or the production of hadrons as a result of the fragmentation process. Some aspects of this method are discussed, including time-dependent effects in neutral $B$ decays to flavor states, to eigenstates of CP and to other states, and the effects of possible coherence between $B^0$ and $\overline{B}^0$ in the initial state. We study the behavior of the leading hadrons in $b$-quark jets and the expected properties of $B^{**}$ resonances. These are extrapolated from the corresponding $D^{**}$ resonances, of whose properties we suggest further studies.Comment: To be submitted to Phys. Rev. D. 26 pages, LaTeX, figures not included (available upon request). Technion-PH-93-32 / EFI 93-4