Interaction of non-histone chromosomal proteins HMG1 and HMG2 with DNA

Interaction between non-histone protein HMG1 or HMG2 and DNA has been studied by using thermal denaturation and circular dichroism (CD) spectroscopy. We have made the following observations. 1. The binding of each of these two proteins to DNA stabilizes the latter, as shown by an increase in melting temperature of 20 degrees C (from 45 degrees C to about 65 degrees C). 2. There are 6.0 amino acids/nucleotide in HMG1-bound DNA and 5.0 in HMGI-bound DNA which suggests that each HMB1 moleculae would cover about 20 base pairs of DNA and each HMG2 molecule would cover about 25 base pairs. 3. The alpha-helical content of these two non-histone proteins in the complexes, estimated from the CD value at 220 nm, is about one third to one half that of total proteins in calf thymus chromatin. 4. DNA conformation is distorted only slightly by the binding of protein HMG1 or HMG2. 5. Neither the melting nor the CD properties of HMG1-DNA or HMG2-DNA complexes differ substantially whether they are prepared by NaCl-gradient dialysis in urea or by direct mixing of protein and DNA at 0.15 M NaCl, followed by dialysis against the same buffer i.e. 0.25 mM EDTA (pH 8.0).     

Characterization of the evaporation rates of complex hydrocarbon mixtures under environmental conditions

The characterization of the evaporation rate of complex hydrocarbon mixtures, such as commercial oil fractions, under environmental conditions is discussed. It is shown that the relevant thermodynamic quantity is the total volume of vapour (per unit of initial oil mass) removed under isothermal differential distillation conditions (V m³/kg) as a function of the mass fraction of the oil remaining (F). Plots of F versus V for various isothermal conditions can be used to estimate evaporation rates since it is shown that V is equivalent to the group K_sA_sτ_s/Ms where K_s is the evaporation mass transfer coefficient (m/s), A_s is the spill area (m²), τ_s is the evaporation time (s) and M_s is the spill mass (kg). The basis of a methodology for estimating environmental evaporation rates is thus outlined. Methods of obtaining V versus F data are discussed, with calibrated wind tunnel evaporations being preferred. The estimation of evaporation rates under spreading and non-isothermal conditions and the analogous dissolution process are discussed briefly.     

Effect of Cobalt Precursors on the Dispersion of Cobalt on MCM-41

The photocatalytic activity of titanium dioxide supported on zeolites HZSM-5, HY and H was evaluated for a novel intermolecular cyclization of ethylenediamine with propylene glycol leading to dihydropyrazine. Titanium dioxide supported on zeolites has been prepared with 2 and 5 wt% of TiO₂ by solid-state reaction, impregnation and sol impregnation methods. From the characterization by XRD, BET, EDAX and TPD of NH₃, it is deduced that in all cases titanium dioxide is in small particles of anatase on zeolites. The highest photocatalytic activity was obtained with 2 wt% TiO₂/H prepared by solid-state reaction. The acidity determined by TPD of NH₃ was found to be lower for TiO₂/H than for TiO₂/HZSM-5 and TiO₂/HY. From the above observations, it can be concluded that adsorption, acidity and structure of zeolites have an influence on the activity of supported TiO₂.     

A simple quenching method for fluorescence background reduction and its application to the direct, quantitative detection of specific mRNA

New genome sequence information is rapidly increasing the number of nucleic acid (NA) targets of use for characterizing and treating diseases. Detection of these targets by fluorescence-based assays is often limited by fluorescence background from unincorporated or unbound probes that are present in large excess over the target. To solve this problem, energy transfer-based probes have been developed and used to reduce the fluorescence from unbound probes. Although these probes have revolutionized NA target detection, their use requires scrupulous attention to design constraints, extensive probe quality control, and individually optimized experimental conditions. Here, we describe a simpler background reduction approach using singly labeled quencher oligomers to suppress excess unbound probe fluorescence following probe-target hybridization. A second limitation of most fluorescence-based NA target detection and quantification assays is the requirement for enzymatic amplification of target or signal for sensitivity. Amplification steps make quantification of original target copy number problematic because of variations in amplification efficiencies between the sequence targets and the experimental conditions. To avoid amplification, we coupled our quenching approach to a two-color NA assay with correlated, two-color, single-molecule fluorescence detection. We demonstrate a >100-fold background reduction and detection of targets present at concentrations as low as 100 fM using the two-color assay. The application of this technique to the detection and quantification of specific mRNA sequences enabled us to estimate beta-actin copy numbers in cell-derived total RNA without an amplification step.     

Development of a simulation model to predict LiDAR interception in forested environments

Airborne scanning LiDAR systems are used to predict a range of forest attributes. However, the accuracy with which this can be achieved is highly dependent on the sensor configuration and the structural characteristics of the forest examined. As a result, there is a need to understand laser light interactions with forest canopies so that LiDAR sensor configurations can be optimised to assess particular forest types. Such optimisation will not only ensure the targeted forest attributes can be accurately and consistently quantified, but may also minimise the cost of data acquisition and indicate when a survey configuration will not deliver information needs.In this paper, we detail the development and application of a model to simulate laser interactions within forested environments. The developed model, known as the LiDAR Interception and Tree Environment (LITE) model, utilises a range of structural configurations to simulate trees with variable heights, crown dimensions and foliage clumping. We developed and validated the LITE model using field data obtained from three forested sites covering a range of structural classes. Model simulations were then compared to coincident airborne LiDAR data collected over the same sites. Results indicate that the LITE model can be used to produce comparable estimates of maximum height of trees within plots (differences < 2.42 m), mean heights of first return data (differences < 2.27 m), and canopy height percentiles (r² = 0.94, p < 0.001) when compared to airborne LiDAR data. In addition, the distribution of airborne LiDAR hits through the canopy profile was closely matched by model predictions across the range of sites. Importantly, this demonstrates that the structural differences between forest stands can be characterised by LITE. Models that are capable of interpreting the response of small-footprint LiDAR waveforms can facilitate algorithm development, the generation of corrections for actual LiDAR data, and the optimisation of sensor configurations for differing forest types, benefiting a range of experimental and commercial LiDAR applications. As a result, we also performed a scenario analysis to demonstrate how differences in forest structure, terrain, and sensor configuration can influence the interception of LiDAR beams.     

Robust optimal experiment design for system identification

This paper develops the idea of min-max robust experiment design for dynamic system identification. The idea of min-max experiment design has been explored in the statistics literature. However, the technique is virtually unknown by the engineering community and, accordingly, there has been little prior work on examining its properties when applied to dynamic system identification. This paper initiates an exploration of these ideas. The paper considers linear systems with energy (or power) bounded inputs. We assume that the parameters lie in a given compact set and optimise the worst case over this set. We also provide a detailed analysis of the solution for an illustrative one parameter example and propose a convex optimisation algorithm that can be applied more generally to a discretised approximation to the design problem. We also examine the role played by different design criteria and present a simulation example illustrating the merits of the proposed approach.     

Curve fitting of time-series Landsat imagery for characterizing a mountain pine beetle infestation

In this technical note we present a new technique using mixed linear models for characterizing a mountain pine beetle (Dendroctonus ponderosae Hopkins) infestation from multiyear satellite imagery. The main benefit of our approach is an ability to determine the statistical significance of each annual spectral change. Knowledge of the annual spectral change characteristics can then be used to statistically determine if a disturbance event has occurred, the timing of a given disturbance event, as well as to provide information for clustering fitted multitemporal reflectance curves (i.e. spectral trajectories) with a common shape. The spatial clustering of spectral trajectories provides insights into the nature of the disturbance and recovery imposed by infestation over a 14-year period.     

An algebraic approach to decoupling in linear multivariable systems

This paper examines the problem of decoupling designs for linear multivariable systems. Both partial and diagonal decoupling designs are considered. The development is based on an algebraic approach and the use of coprime factorizations, which provide a mechanism to account for key system properties including internal stability and decoupling invariants. The results obtained include necessary and sufficient conditions for decoupling and a parametrization of all decoupling controllers.     

Frequency domain design trade-offs for linear periodic feedback systems*

The purpose of this paper is to analyse inherent design limitations associated with systems that are linear and periodically time-varying. The contributions of the paper are (i) to relate frequency domain raising methods from signal processing literature to time-domain lifting used in control literature, and (ii) to develop extensions of the Poisson sensitivity and complementary sensitivity integral constraints. In particular, it is shown that there is generally an additional cost associated with having a time invariant target closed loop for a periodic open loop plant. It is also shown that design limitations due to unstable poles and/or non-minimum phase zeros of a discrete linear time-invariant plant remain even if a periodic time-varying controller is used. As a consequence, the utility of periodic control in circumventing design limitations is questioned.