Temporal and molecular characteristics of lacZ mutations in somatic tissues of transgenic mice

In order to help establish criteria for optimizing protocols for in vivo mutation studies, lacZ transgenic mice (Muta mouse) were treated with five consecutive daily doses of ethylnitrosourea (50 mg/kg), sampled at times up to 55 days after treatment, and mutant frequencies and DNA sequences determined for liver and bone marrow. In the bone marrow, the mutant frequency rose very rapidly in the first 5 days after treatment to 34 times the control frequency. Subsequently, there was a brood peak where the mutant frequency did not vary significantly, although it did appear to begin to decline after 45 days. In contrast, in the liver, the peak mutant frequency (11 times the control frequency) was not achieved until 35 days, after which there appeared to be a slow decline up to 55 days, which was not statistically significant. Once the maximum mutant frequency was reached, the mutation spectra in the two tissues were indistinguishable. In contrast to the G:C-->A:T transitions in 5'-CpG sites characteristic of untreated mice, A:T-->T:A transversions and A:T-->G:C transitions were prominent in both liver and bone marrow of ENU-treated mice, suggesting the involvement of unrepaired O2- and O4-ethylthymine adducts. In addition, G:C-->T:A transversions were induced in liver. This study demonstrates the possibility that although tissues may have different mutation fixation times, a single mutation fixation time equal to the longest time may be appropriate for in vivo mutation studies, provided that the mutation frequency does not decline appreciably after the peak is reached. This study also illustrates the necessity of ensuring that mutation characteristics are determined after optimal fixation has occurred.     

Role of the modular domains of SR proteins in subnuclear localization and alternative splicing specificity

SR proteins are required for constitutive pre-mRNA splicing and also regulate alternative splice site selection in a concentration-dependent manner. They have a modular structure that consists of one or two RNA-recognition motifs (RRMs) and a COOH-terminal arginine/serine-rich domain (RS domain). We have analyzed the role of the individual domains of these closely related proteins in cellular distribution, subnuclear localization, and regulation of alternative splicing in vivo. We observed striking differences in the localization signals present in several human SR proteins. In contrast to earlier studies of RS domains in the Drosophila suppressor-of-white-apricot (SWAP) and Transformer (Tra) alternative splicing factors, we found that the RS domain of SF2/ASF is neither necessary nor sufficient for targeting to the nuclear speckles. Although this RS domain is a nuclear localization signal, subnuclear targeting to the speckles requires at least two of the three constituent domains of SF2/ASF, which contain additive and redundant signals. In contrast, in two SR proteins that have a single RRM (SC35 and SRp20), the RS domain is both necessary and sufficient as a targeting signal to the speckles. We also show that RRM2 of SF2/ASF plays an important role in alternative splicing specificity: deletion of this domain results in a protein that, although active in alternative splicing, has altered specificity in 5' splice site selection. These results demonstrate the modularity of SR proteins and the importance of individual domains for their cellular localization and alternative splicing function in vivo.     

A clustering method to distribute a database on a grid

Clusters and grids of workstations provide available resources for data mining processes. To exploit these resources, new distributed algorithms are necessary, particularly concerning the way to distribute data and to use this partition. We present a clustering algorithm dubbed Progressive Clustering that provides an “intelligent” distribution of data on grids. The usefulness of this algorithm is shown for several distributed datamining tasks.     

Theoretical analysis of a fractal surface radiation

We compare, in this paper, the far field radiated by two fractal distributions of current. The first one is obtained by a fractal cut following the Cantor arrangement, the second one keeps the length of each previous current element, but modifies the distance between the elements which is now taken as a constant. We establish the analytical formulations of the far field at any step n of the Cantor set. Then, we extract the array factor and we analyse and compare the following properties : convergence of the radiation pattern, wide of the main lobe, side lobes level and directivity.     

Nonlinear black-box modeling in system identification: a unified overview

A nonlinear black-box structure for a dynamical system is a model structure that is prepared to describe virtually any nonlinear dynamics. There has been considerable recent interest in this area, with structures based on neural networks, radial basis networks, wavelet networks and hinging hyperplanes, as well as wavelet-transform-based methods and models based on fuzzy sets and fuzzy rules. This paper describes all these approaches in a common framework, from a user's perspective. It focuses on what are the common features in the different approaches, the choices that have to be made and what considerations are relevant for a successful system-identification application of these techniques. It is pointed out that the nonlinear structures can be seen as a concatenation of a mapping form observed data to a regression vector and a nonlinear mapping from the regressor space to the output space. These mappings are discussed separately. The latter mapping is usually formed as a basis function expansion. The basis functions are typically formed from one simple scalar function, which is modified in terms of scale and location. The expansion from the scalar argument to the regressor space is achieved by a radial- or a ridge-type approach. Basic techniques for estimating the parameters in the structures are criterion minimization, as well as two-step procedures, where first the relevant basis functions are determined, using data, and then a linear least-squares step to determine the coordinates of the function approximation. A particular problem is to deal with the large number of potentially necessary parameters. This is handled by making the number of ‘used’ parameters considerably less than the number of ‘offered’ parameters, by regularization, shrinking, pruning or regressor selection.     

Human chromosome 5 sequence primer amplifies Alu polymorphisms on chromosomes 2 and 17

Members of the Alu family of repetitive elements occur frequently in the human genome and are often polymorphic. Techniques involving Alu element mediated polymerase chain reactions (Alu PCR) allow the isolation of region-specific human DNA fragments from mixed DNA sources. Such fragments are a source of region-specific Alu elements useful for the detection of Alu-related polymorphisms. A clone from human chromosome 5, corresponding to locus D5F40S1, was isolated using Alu PCR differential hybridization. Alu elements within this clone were investigated for the presence of potentially polymorphic 3' polyA tails. Primers were devised to amplify the 3' polyA tail of an Alu element present within the clone. One primer, D5F40S1-T, was specific to the DNA flanking the 3' end of the Alu element, and the other primer was homologous to sequences within the element. When these primers were used in PCR reactions, products from chromosomes 2 and 17 (loci D2F40S2 and D17F40S3) were amplified in addition to the expected product from chromosome 5. The most likely explanation for this nonspecific amplification is that the D5F40S1-T primer is located within a low-copy repetitive element that is 3' of the Alu element. This phenomenon presents a potential problem for the identification of region-specific Alu polymorphisms.     

Absorbing surface impedances of lossy layers in the finite difference time-domain method

In this paper the time-domain surface impedances of an homogeneous absorber layer, are given for the vertical and horizontal polarizations, or respectively for the electric field perpendicular or parallel to the incidence plane. It turns out that the application of the concept in finite difference time-domain (FDTD) in absorbing surface impedances boundary conditions, gives results in good agreement with analytical Fresnel reflection coefficients.