Showing papers by "Jožef Stefan Institute published in 1996"

The evaluation of waste, surface and ground water quality using the Allium test procedure.

Abstract: The bulbs of Allium cepa were grown in test liquids of various pollution levels as follows: undiluted industrial and municipal waste water; biological treatment plant output water; water from the Drava river upstream and downstream of the city of Maribor; and non-chlorinated drinking water as a negative control test. The paper presents the response of the Allium cepa genetic material to the presence of potential cytotoxic and genotoxic substances in test liquids and the suitability of the Allium cepa testing procedure as a method for short-term determination of water pollution level. The suitability of the Allium test procedure as a system for environmental monitoring is presented. The influence of water pollution on macroscopic and cytologic parameters of the common onion by application of the biological testing method was examined. The macroscopic parameter was inhibition of root growth. The cytological parameters were: aberrant cells in metaphase and anaphase, index of micronuclei appearance and inhibition of cell division. The possibility of categorization the different polluted test liquids into quality classes is presented according to the influence of the test liquids on macroscopic and cytologic parameters. Test liquids are divided into 8 quality classes: the first class is the least polluted surface waters, the second and the third classes are more polluted surface water, the fourth and the fifth classes are biological treatment plant output waters, the sixth till the eighth quality classes are untreated waste waters. The most polluted test liquids (untreated industrial and municipal waste waters) caused sublethal and even lethal effects. The most polluted tested liquids cause the inhibition of root growth over 50% (even up to 74%), decrease of mitotic index over 36% (even up to 66%), increase of presence of interphase cells with micronuclei over 3% and increase of presence of aberrant cells for more than 10 times in comparison to control test.

Performance of the DELPHI detector

Abstract: DELPHI (DEtector with Lepton, Photon and Hadron Identification) is a detector for e^+e^- physics, designed to provide high granularity over a 4\pi solid angle, allowing an effective particle identification. It has been operating at the LEP (Large Electron-Positron) collider at CERN since 1989. This article reviews its performance.

Major histocompatibility complex class II-associated p41 invariant chain fragment is a strong inhibitor of lysosomal cathepsin L.

Abstract: The invariant chain (Ii) is associated with major histocompatibility complex class II molecules during early stages of their intracellular transport. In an acidic endosomal/lysosomal compartment, it is proteolytically cleaved and removed from class II heterodimers. Participation of aspartic and cysteine proteases has been observed in in vitro degradation of Ii, but the specific enzymes responsible for its in vivo processing are as yet undefined. We have previously isolated a noncovalent complex of the lysosomal cysteine protease cathepsin L with a peptide fragment derived from the p41 form of Ii from human kidney. Here we show that this Ii fragment, which is identical to the alternatively spliced segment of p41, is a very potent competitive inhibitor of cathepsin L (equilibrium inhibition constant Ki = 1.7 X 10(-12) M). It inhibits two other cysteine proteases, cathepsin H and papain, but to much lesser extent. Cysteine proteases cathepsins B, C, and S, as well as representatives of serine, aspartic, and metalloproteases, are not inhibited at all. These findings suggest a novel role for p41 in the regulation of various proteolytic activities during antigen processing and presentation. The Ii inhibitory fragment shows no sequence homology with the known cysteine protease inhibitors, and may, therefore, represent a new class.

Ca2+/S100 regulation of giant protein kinases.

Abstract: PROTEIN phosphorylation by protein kinases plays a central regulatory role in cellular processes and these kinases are themselves tightly regulated1. One common mechanism of regulation involves Ca2+-binding proteins (CaBP) such as calmodu-lin (CaM)2. Here we report a Ca2+-effector mechanism for protein kinase activation by demonstrating the specific and > 1,000-fold activation of the myosin-associated giant protein kinase twitchin by Ca2+/S100Al2. S100A12 is a member of a large CaBP family that is implicated in various cellular processes, including cell growth, differentiation and motility, but whose molecular actions are largely unknown3. The S100Al2-binding site is a part of the autoregulatory sequence positioned in the active site that is responsible for intrasteric autoinhibition of twitchin kinase; the mechanism of autoinhibition based on the crystal structures of two twitchin kinase fragments is described elsewhere4. Ca2+/S100 represents a likely physiological activator for the entire family of giant protein kinases involved in muscle contractions and cyto-skeletal structure2,5–9.

On time optimal path control of manipulators with bounded joint velocities and torques

Abstract: In the paper we present a solution to the optimal trajectory planning problem subject to constraints given by joint torques and velocities, and the task. The main result is a trajectory planning algorithm which enables the calculation of the optimal motion due to the given requirements and taking into account the dynamics of the manipulator. First, the dynamic model of the manipulator in the parametric form (as a function of the scalar path parameter) is given. Next, the constraints on torques and velocities are converted to those on the path parameter. Using these, the task and joint trajectories are calculated. In the end, some examples are given to illustrate the capabilities of the given trajectory planning algorithm.

Atmospheric heavy metal pollution in Slovenia derived from results for epiphytic lichens.

Abstract: In 1992, a monitoring survey has been started on the national scale in Slovenia using the epiphytic lichen Hypogymnia physodes (L.) Nyl. The primary aim has been to analyse lichens using the k0-based INAA method to obtain information about the levels of elements in the atmosphere and to identify significant pollution sources. Monte Carlo-Assisted Factor Analysis was applied to a data set of the 28 elements As, Ag, Ba, Br, Ce, Cd, Co, Cr, Cs, Fe, Ga, Hf, Hg, K, La, Mo, Na, Rb, Sb, Sc, Se, Sr, Sm, Tb, Th, U, W and Zn, which have been selected from the elements determined as the most important ones for the identification of pollution sources. A Monte Carlo approach has been used to give more insight into the uncertainties and significance levels of the factor analysis results. It has been found that concentration patterns in lichens yielded 9 factors (source types) which are presented and discussed in detail. The geographical patterns of the contributions of all factors are also shown.

Nonuniversal Scaling Behavior of Barkhausen Noise.

Abstract: We simulate Barkhausen avalanches on fractal clusters in a two-dimensional diluted Ising ferromagnet with an effective Gaussian random field We vary the concentration of defect sites $c$ and find a scaling region for moderate disorder, where the distribution of avalanche sizes has the form $D(s,c,L) = s^{-(1+\tau (c))}{\cal{D}}(sL^{-D_s(c)})$ The exponents $\tau (c)$ for size and $\alpha (c)$ for length distribution, and the fractal dimension of avalanches $D_s(c)$ satisfy the scaling relation $D_s(c)\tau (c) =\alpha (c)$ For fixed disorder the exponents vary with driving rate in agreement with experiments on amorphous Si-Fe alloys

Electrochemical Oxidation of ZrN Hard (PVD) Coatings Studied by XPS

Abstract: Zirconium nitride (ZrN) belongs to the group of technologically important materials, namely hard tribological coatings. X-ray photoelectron spectroscopy (XPS) in combination with polarization experiments and electrochemical a.c. impedance spectroscopy has been used to study the composition, structure, thickness and electronic properties of layers formed by electrochemical oxidation of ZrN in phthalate buffer (pH 5.0). Results are compared to those obtained for layers formed by thermal oxidation at elevated temperature, i.e. ZrO2 , as well as by air oxidation at room temperature. Electrochemical oxidation of ZrN to ZrO2 proceeds via the formation of a mixed oxynitride/oxide layer, which then transforms into oxide at sufficiently positive potentials. Angle-resolved XPS measurements contribute to a better understanding of the in-depth layer structure. Exposure of ZrN to air at room temperature results in the formation of a thin oxynitride/oxide layer. The layer exhibits a gradually changing in-depth distribution of various species, i.e. nitride, oxynitride and oxide. Analysis of XPS valence band spectra offers valuable information concerning the electronic properties of investigated materials. The experimental valence band spectrum for ZrN correlates well with a theoretically calculated density-of-states diagram from the literature. In contrast to ZrN, which is a metallic conductor, layers formed by electrochemical oxidation, as well as by air oxidation, exhibit insulating properties. The insulating character of the formed layers is supported also by a decreased current density in subsequent cycles in cyclic voltammograms, as well as by the resistivity value (∽1012 Ω · cm) calculated from a.c. impedance measurements. Therefore, the oxide layer formed on ZrN is stable and prevents further oxidation of the ZrN substrate.

Folding and Activation of Human Procathepsin S from Inclusion Bodies Produced in Escherichia coli

Abstract: Human procathepsin S was produced in the form of insoluble inclusion bodies in Escherichia coli using an inducible T7-based expression system. After cell disruption, the dissolved inclusion body proteins were S-sulphonated with 2-nitro-5-thiosulphobenzoate and purified by gel filtration. Recombinant procathepsin S was renatured at pH 7.6 by a two-step dilution which significantly increased the yield of production compared to single-step dilution. The proenzyme was autocatalytically processed to active cathepsin S at pH 4.5 in the presence of an excess of cysteine and catalytic amounts of dextran sulphate. Most of the loss of procathepsin S occurred during folding, probably because of aggregation. Concentrations lower than 20 microgram/ml of procathepsin S were necessary to minimise such aggregation. The recombinant cathepsin S was catalytically active on fluorogenic substrates and had kinetic properties similar to those of recombinant enzyme produced in yeast. The expression, renaturation, and activation procedures used enable the production of up to 2 mg of catalytically active recombinant human cathepsin S/l fermentation broth.

Determining the CD spectrum of a protein.

Abstract: This unit describes the theory behind circular dichroism (CD) and deals with considerations regarding instrumentation and reagents for CD spectrometry. A protocol is provided that outlines the steps in recording a CD spectrum and two support protocols explain the interpretation of near-UV and far-UV CD spectra.

Ammodytoxin C Gene Helps to Elucidate the Irregular Structure of Crotalinae Group II Phospholipase A2 Genes

Abstract: Ammodytoxin C is a presynaptically neurotoxic phospholipase A2 (PLA2) expressed in the venom glands of Vipera ammodytes (subfamily Viperinae) The gene spans more than 4 kb and consists of five exons and four introns characteristic of group II phospholipase A2 genes The first exon encodes the 5′ untranslated region, the second exon encodes most of the signal peptide, while exons 3–5 encode three parts of the mature protein Comparison of the Crotalinae and Viperinae PLA2 genes has shown that Crotalinae PLA2 retain the first intron in their mRNAs The apparent cause of this retention is a deletion of 40 bp in the first exon of PLA2 genes of the subfamily Crotalinae, which prevents splicing of the first intron Analysis of the secondary structure of the pre-mRNA of the ammodytoxin C gene has shown that the first exon is able to form an intra-exon hairpin which is absent in Crotalinae PLA2 pre-mRNAs Our results indicate that this intra-exon hairpin structure is essential for the splicing of the retained first intron Contrary to the predictions of the neutral theory of molecular evolution, the introns of all known snake venom PLA2 genes are conserved up to 90%, that is considerably more than the exons Consequently it is proposed that highly conserved introns, in imiltigene families, which evolve under positive Darwinian selection, may have an important role in enabling homologous recombination

The rate‐limiting step in the folding of the cis‐Pro 167Thr mutant of TEM‐1 β‐lactamase is the trans to cis isomerization of a non‐proline peptide bond

Abstract: The stability and kinetics of unfolding and refolding of the P167T mutant of the TEM-1 β-lactamase have been investigated as a function of guanidine hydrochloride concentration. The activity of the mutant enzyme was not significantly modified, which strongly suggests that the Glu166–Thr167 peptide bond, like the Glu166–Pro167, is cis. The mutation, however, led to a significant decrease in the stability of the native state relative to both the thermodynamically stable intermediate and the fully unfolded state of the protein. In contrast to the two slower phases seen in the refolding of the wild-type enzyme, only one phase was detected in the refolding of the mutant, indicating a determining role of proline 167 in the kinetics of folding of the wild-type enzyme. The former phases are replaced by rapid refolding when the enzyme is unfolded for short periods of time, but the latter is independent of the time of unfolding. The monophasic refolding reaction of the mutant is proposed to reflect mainly the trans→cis isomerization of the Glu166–Thr167 peptide bond. © 1996 John Wiley & Sons, Inc.

Low-energy electron beam induced regrowth of isolated amorphous zones in Si and Ge

Abstract: Spatially isolated amorphous regions in Si and Ge have been regrown at room temperature by using an electron beam with an energy less than that required to cause displacement damage in crystalline material. The rate at which the zones regrow is a function of the energy of the electron beam. As the electron energy is increased from 25 keV (lowest energy employed), the regrowth rate decreases and reaches a minimum below the threshold displacement voltage. With further increases in the electron energy, the rate again increases. It is suggested that at the lower electron energies this room temperature regrowth process is stimulated by electronic excitation rather than by displacive-type processes.

Biodegradation studies of selected hydrocarbons from diesel oil

Abstract: In-vitro biodegradation of aliphatic and aromatic hydrocarbons present in diesel oil by Pseudomonas fluorescens, Texaco was studied in an aqueous medium. Small aliquots of diesel oil and its aromatic fraction were incubated aerobically for periods of up to seven months and analysed by GC–MS. Biotic losses proved to be greater for aliphatic than aromatic compounds. Most biodegradation occurred within the first 20 d of incubation. The most rapid biodegradation, up to 65% in 8 d, was observed for n-alkanes (C14–C18). The same compounds were also shown to be less affected by abiotic losses. Biodegradation of n-alkanes from diesel oil and diesel oil itself showed first order kinetics for the initial incubation period. Aromatic compounds proved to be resistant to biodegradation and only phenanthrene had been degraded (30%) within 6 months.

A method for generating magnetic resonance microimaging T2 maps with low sensitivity to diffusion.

Abstract: Generating T2 maps in magnetic resonance microimaging is often complicated by the self-diffusion of water molecules. A modification of the standard spin-echo pulse sequence is proposed which minimizes this effect. Experiments with doped water confirmed that the T2 values obtained with the modified sequence were equal within the experimental error to the value obtained by the spectroscopic Carr-Purcell-Meiboom-Gill method. The applicability of the technique is demonstrated by generating T2 maps of porcine articular cartilage. Key words: MR microimaging; relaxation; diffusion; cartilage.

Transmission electron microscopy studies of nanophase TiO2

Abstract: The chemical and microstructural properties of nanosized TiO 2 , obtained by sol—gel procedure, were investigated. The samples were characterized by analytical electron microscopy combining electron diffraction, high resolution electron microscopy and atomic force microscopy. These methods were supported by X-ray diffraction and thermal analysis. The chemical and structural properties, as well as the size of grains, depended on the temperature of TiO 2 preparation. In the temperature range between 293 and 820 K the TiO 2 grains consisted of anatase, as the dominant phase, and brookite. High resolution electron microscopy showed that the sample heated at 573 K had grain sizes from 2 to 10 nm, the average being (5 ± 1) nm, and the pore sizes from 4.5 to 12 nm. The sample heated at820 K revealed larger grain sizes, from 7 to 12 nm, the average being (9 ± 1) nm, and the pore sizes from 6 to 10 nm. These values were confirmed by X-ray diffraction broadening.

Interplay between antiferromagnetic and ferromagnetic phases of TDAE-C60: An ESR study of high-temperature annealed samples.

Abstract: The low-temperature magnetic properties of annealed TDAE-${\mathrm{C}}_{60}$ single crystals are studied with electron spin resonance. Whereas freshly grown single crystals are found to order antiferromagnetically at low temperature, annealing at room temperature and above results in an enhanced ferromagnetic ordering and three separate magnetic phases can be identified below 25 K, below 16 K, and below 10 K. The orientational ordering transition temperature ${T}_{0}$ is found to be correlated with the annealing temperature ${T}_{a}$ and the drop in susceptibility which is systematically observed below 100 K is interpreted as the onset of antiferromagnetic correlations.

Fluorinated γ-alumina aerogels and xerogels: characterisation and catalytic behaviour

Abstract: The porosity of γ-alumina-based materials is an important parameter affecting the extent of fluorination (aerogels > commercial γ-Al2O3 > xerogels) and, consequently, also the textural, acidic and catalytic properties of the final fluorinated materials. Only the highly fiuorinated aluminas having strong Lewis acidic sites catalyse the isomerisation of CHF2CHF2 to CF3CH2F.

Optimization of fermentation medium by a modified method of genetic algorithms

Abstract: During the study of mevinolin biosynthesis by Aspergillus terreus ATCC 20542, 10 different medium components were selected for medium optimization. A new optimization method based on genetic algorithms and inductive learning was used for experimental design. For better efficiency the method was supported by a model, constructed with machine learning method, to predict the productivity. In four generations of fermentation experiments the productivity increased nearly three times.