bluuebunny/crossref_metadata_2025 huggingface dataset:
How accurate is the fundamental parameter approach? XRF analysis of bulk and multilayer samples
Authors: De Boer D. K. G. , Borstrok J. J. M. , Leenaers A. J. G. , Van Sprang H. A. , Brouwer P. N.
Published: May 2005

The accuracy of Fundamental Parameter‐based XRF quantification is investigated for both bulk and multilayer analysis. It is found that for bulk materials the relative accuracy is of the order of 1% and for multilayers a few percent. The method can be set up in such a way that it contains an inherent validity check. Further possibilities of the Fundamental Parameter method are discussed.
A low dilution fusion technique for the analysis of geological samples. 2—major and minor element analysis and the use of influence/alpha coefficients
Authors: Eastell J. , Willis J. P.
Published: May 2005

A previously described low‐dilution fusion technique has been used successfully for the accurate determination of major and minor elements in geological samples. Three methods of calculating appropriate α coefficients have been investigated, namely (1) multiple regression analysis, (2) the Norrish and Hutton method and (3) a computer program, NBSGSC, involving fundamental parameters and the COLA equation. Methods (1) and (2) gave poor results for rock types of widely varying composition. The third method requires that the variation of α coefficients with varying weight fraction of the analyte element be taken into account when calculating such coefficients.
The fundamental parameter method for energy‐dispersive x‐ray fluorescence analysis of intermediate thickness samples with the use of monochromatic excitation
Authors: Wȩegrzynek Dariusz , Holyńnska Barbara , Pilarski Tomasz
Published: May 2005

The fundamental parameter method for correction for enhancement and absorption effects in the energy‐dispersive x‐ray fluorescence analysis of intermediate thickness samples using monochromatic excitation was evaluated. A simple means for the calculation of the concentration of an element in an unknown sample without using the iterative approach is proposed. Based on the derived equation, the influence of the higher Z sample components and their concentration levels on the enhancement correction factor was examined theoretically and tested experimentally. The concentration of an interfering element was found to have a stronger influence on the enhancement correction factor than the concentration level of the determined element. The method was tested experimentally using various two‐element standard samples and reference materials. The calculated concentrations were in good agreement with the known values.
X‐ray absorption near‐edge study of some rare earth complexes
Authors: Shrivastava B. D. , Katre S. S. , Srinivasulu K. , Joshi S. K.
Published: May 2005

The x‐ray L3 absorption edges of all cis‐1,2,3,4‐cyclopentanetetracarboxylic acid complexes of Gd, Tb, Dy and Ho were recorded with the help of a 400 mm Cauchois‐type bent crystal x‐ray spectrograph. The behaviour of the four lanthanide cations in the environment of the same complexing ligand was investigated. The chemical shifts were correlated with IR studies. Information regarding bonding in these complexes was obtained from the observed chemical shifts. A regular decrease was observed in the average metal—ligand bond distances with increasing atomic number of the metal ion in these complexes and this is interpreted in terms of metal—oxygen interaction.
EDXRF analysis of trace elements in Nerium oleander for pollution monitoring
Authors: Marques M. I. , Carvalho M. L. , Öblad M. , Amorim P. , Ramos M. T.
Published: May 2005

Biomonitoring studies of elements (Ti, Mn, Fe, Cu, Zn, Br, Sr and Pb) in leaves of Nerium oleander were performed using energy‐dispersive x‐ray fluorescence spectrometry. The samples were collected at different locations in Lisbon, some with light and others with heavy traffic. The results were compared with those obtained for samples from the same species collected in an unpolluted region. Significant differences in the concentrations of some elements, particularly iron, titanium, zinc, strontium and lead, were found for samples from different locations. Titanium and iron concentrations had similar variations from one site to another with an almost constant ratio (Ti/Fe ≈︁ 0.2). The concentrations of lead were, as expected, higher at locations with heavier traffic.
A simple, inexpensive gas proportional scintillation counter for x‐ray fluorescence analysis
Authors: Dos Santos J. M. F. , Bento A. C. S. S. , Conde C. A. N.
Published: May 2005

A simple, inexpensive, high‐performance gas proportional scintillation counter for x‐ray spectrometry is described. Energy resolutions below 9% are obtained with detector window diameters of less than 22 mm, for 5.9 keV Mn fluorescent x‐rays, even for a small window‐to‐sample distance where beam collimation is not effective. X‐ray fluorescence spectra are presented for biotite, pyrite/chalcopyrite and stainless‐steel samples.
EDXRF study of the effects of Cr on the growth of barley seedlings
Authors: Calliari I. , Concheri G. , Nardi S.
Published: May 2005

Energy‐dispersive x‐ray fluorescence spectrometry was used to determine Cr and bioessential trace elements (Fe, Zn, Cu, Mn) in the leaves and roots of barley seedlings. The thin‐film approach, secondary target excitation and microwave acid digestion were applied. The effects of Cr and other microelements on the growth of barley seedlings are discussed.
Differential scattering cross‐sections for 8 keV photons in kapton and crystalline targets
Authors: Karydas A. G. , Potiriadis C. , Paradellis T.
Published: May 2005

The model adopted for the calculation of the atomic scattering (Rayleigh or Compton) cross‐section in a material assumes that each atom scatters independently of the others (isolated or independent atomic model approximation). An investigation of the accuracy of this model was performed by measuring differential scattering (Rayleigh plus Compton) cross‐sections for 8 keV photons in a medium of low atomic number (Kapton) and in two crystalline targets (silicon and copper). The results for Kapton are in good agreement with theory but for the two crystalline targets there is a large discrepancy owing to diffraction phenomena. For this case, the influence of the crystal perfection of the target on the experimental scattered yield is discussed.
Determination of selected trace elements in silicates by electron and proton probe microanalysis
Authors: Sweeney R. J. , Jablonski W. , Sie S. H.
Published: May 2005

The elements Nb, Zr, Ta, Y, Ce, Nd, Lu, Ba and Sr were calibrated on a wavelength‐dispersive spectrometerequipped electron probe microanalyser (EPMA) using existing standards and a Ta‐bearing primary glass standard manufactured for Ta calibration. These calibrations were tested using a manufactured secondary glass standard doped with 600‐1800 ppm of these elements. The EPMA calibrations reproduced the glass secondary standard concentrations to within ±10% relative (except for Y) with detection limits of 40‒100 ppm. The accuracy of this technique was compared with that of proton‐induced x‐ray emission (PIXE) determinations on the secondary standard.
EXFIT—a computer code for processing energy‐dispersive X‐ray fluorescence spectra of environmental thin samples
Authors: Stoev Krassimir N. , Dlouhy Joseph F.
Published: May 2005

Problems in the development and application of software for processing of environmental energy‐dispersive x‐ray fluorescence spectra of thin samples are reviewed. The main principles and requirements for the software are discussed. A new program, EXFIT‐8.10, was created to meet these requirements and is described in detail. It is capable of analyzing up to 50 elements simultaneously by combining results from up to 3 different excitation conditions. A set of supporting and post‐processing programs is also included. The main specifications of the software and possible ways for improvement are discussed.
Chlorine determination in photographic developer solutions using wavelength‐dispersive X‐ray fluorescence
Authors: Morse Mark A.
Published: May 2005

A wavelength‐dispersive x‐ray fluorescence method is described for the determination of total chlorine in fresh and seasoned photographic developer solutions. The method uses a cadmium internal standard to correct for slight changes in the solution matrix and covers a concentration range of 15–500 mg l‒1 chlorine. Precision studies using the method resulted in a relative standard deviation (RSD) of 0.41% (1s) at the 200 mg l‒1 chlorine level and a RSD of 1.13% (1s) at the 50 mg l‒1 level. The limit of detection for chlorine was found to be 5 mg l‒1 and the limit of quantification was calculated as 15 mg l‒1.
Calculation of photo‐ and auger electron contribution to X‐ray fluorescence excitation of elements with low atomic number
Authors: Pavlinsky G. V. , Dukhanin A. Yu.
Published: May 2005

The contribution of photo‐ and Auger electrons generated in analyte material to the x‐ray fluorescence of elements with atomic numbers from Z = 5 (boron) to 9 (fluorine) was evaluated. The calculations were performed for different x‐ray tube anodes, window thicknesses and working regimes. This contribution to x‐ray fluorescence excitation increases rapidly with decreasing atomic number of the measured element and depends greatly on the sample composition and experimental conditions. In some cases the contribution may exceed 90%. This high value results from the absorption in the window and in the x‐ray anode tube material of the long‐wavelength component of primary radiation which is most effective in photoionization of element atoms. It follows from the calculations that at shorter wavelengths, e.g. for Na and Cu, the contribution of photo‐ and Auger electrons to the excitation of their fluorescence seems to be much less significant than that obtained in other work.
Study on journal distribution of publications in the field of X‐ray fluorescence analysis
Authors: Stoev K. N.
Published: May 2005

The distribution of the publications on x‐ray fluorescence analysis among different journals is discussed on the basis of frequency of citation in major review articles. Differentiation among major sub‐fields such as particle induced X‐ray emission, total‐reflection x‐ray fluorescence and synchrotron radiation induced X‐ray fluorescence is studied. A comparison with the results from a computer search in the Science Citation Index and INSPEC databases is presented. Important sources of new information in x‐ray fluorescence analysis are identified and discussed.
Analysis of X‐ray spectra by iterative least squares (AXIL): New developments
Authors: Vekemans B. , Janssens K. , Vincze L. , Adams F. , Van Espen P.
Published: May 2005

The functionality of the computer package AXIL (Analysis of X‐ray spectra by Iterative Least squares), suitable for the evaluation of energy‐dispersive X‐ray spectra, has been extended in a number of ways. First, a background modelling algorithm, based on the use of mutually orthogonal polynomials was introduced to replace the linear or exponential polynomials employed previously. Second, the Gaussian photopeak model employed in previous versions of the program was extended to include the non‐Gaussian parts of the characteristic peaks and related background contributions. Both innovations are shown to improve the performance of the spectrum evaluation procedure. Third, the user‐friendliness of the evaluation program was enhanced (a) by allowing a PC plug‐in MCA card to be directly controlled from within the program and (b) by extending the command‐interface to allow for repeated execution of series of commands by means of control loops. A brief description of these changes is given; as an application, the accurate evaluation of micro‐XRF images is discussed.
Near room temperature energy‐dispersive detectors processed on high‐purity silicon
Authors: Jalas P. , Sipilä H. , Eränen S. , Leinonen K.
Published: May 2005

Diode detectors and silicon drift chambers were processed on TOPSIL high‐purity silicon of resistivity 7 kΩ cm. Their suitability for XRF spectroscopy, when cooled to −30°C, was evaluated. The efficiency for different x‐ray energies was calculated starting from the processing parameters used in manufacturing. Spectrum measurements were made in order to establish the mechanisms causing electrical noise and charge trapping. With an 18 mm2 active area detector it was possible to achieve an FWHM of 385 eV for the 55Fe source 5.89 keV peak and better than 300 eV with detectors of 1 mm2 area. Incomplete charge collection was found to be due to effects on the edge of the detector active area or in the implanted surface facing the radiation.
Application of partial least‐squares calibration methods in low‐resolution EDXRS
Authors: Urbański Piotr , Kowalska Ewa
Published: May 2005

The partial least‐squares calibration method was studied on some examples of EDXRS applications: determination of strontium and iron in samples of rock, determination of tin in plated deposits, measurements of ash and sulphur in powdered samples of coal and coating thickness gauging. The spectra of the PLS predictors and the scatter plots of the load and score vectors are presented and an analysis of their interpretation is made. A non‐linearity problem which appeared in some cases was approached either by pretreatment of the entry data or modification of the latent variable. Application of this calibration technique in EXDRS gives two main advantages: (i) it allows systematic factors influencing the final results to be included in the calculated model and (ii) it can provide a new insight into some aspects of the measurement methodology since the data in the following steps of the calibration procedure can be studied and analysed.
Glancing‐incidence x‐ray analysis of thin‐layered materials: A review
Authors: de Boer D. K. G. , Leenaers A. J. G. , van den Hoogenhof W. W.
Published: May 2005

Glancing‐incidence x‐rays provide a wealth of possibilities for the analysis of thin layers and multilayers. This paper discusses reflectometry under both specular and non‐specular conditions, and also the combination with angle‐dependent x‐ray fluorescence. From these measurements information can be obtained on layer thickness, interface quality and compositional depth profile. First the historical development of glancing‐incidence x‐ray analysis is sketched. Then the physical principles of the interaction of glancing‐incidence x‐rays with samples which may contain rough interfaces are discussed. The equipment, which allows for both x‐ray fluorescence and reflectivity measurements, is also described. The possibilities are illustrated with a number of examples from the literature.
Total reflection x‐ray fluorescence analysis of light elements under various excitation conditions
Authors: Streli C. , Wobrauschek P. , Ladisch W. , Rieder R. , Aiginger H.
Published: May 2005

Total reflction x‐ray fluorescence (TXRF) analysis was tested for its suitability for the photon‐induced energy dispersiver analysis of light elements such as B, C, N, O, F, Na and Mg using a special spectrometer meeting the requirements for the detection of low‐energy fluorescence radiation. The influence of different spectral modification devices such as a high‐energy cut‐off reflector and a multilayer monochromator were compared using excitation by a Cr tube and also synchrotron radiation. The effects on intensity, background and detection lilmits are compared and discussed. A new method of monitoring the x‐ray beam to adjust total reflection by a CCD camera is introduced. Considerations on the penetration depth and information depth of light elements are presented.
Calculation of the x‐ray fluorescence intensity from heterogeneous substances by the Monte Carlo method
Authors: Gunicheva T. N. , Kalughin A. G. , Afonin V. P.
Published: May 2005

A Monte Carlo simulation model for the computation of the x‐ray fluorescence intensity from heterogeneous substances is proposed. The geometric presentation used and its simulation provide an adequate description of the experimental data for slurries, alloys and powders with the same and different particle sizes for the fluorescent phase and the matrix. The total fluorescence flux is considered to consist of the first‐, second‐ and third‐order fluorescence. The adequacy of the model was estimated by comparison of the computational results with the experimental data and with calculation results from the analytical equations. The model made possible the evaluation of the magnitude of the enhancement and scattering effect contributions for different substances.
Non‐destructive x‐ray fluorescence analysis of soils and friable and marine sediments
Authors: Gunicheva T. N. , Aisueva T. S. , Afonin V. P.
Published: May 2005

A procedure for the non‐destructive x‐ray fluorescence (XRF) spectrometric determination of major and some minor elements in soils, marine sediments and friable deposits is proposed. It does not require any preliminary treatment of the sample except for its drying at 105°C. The matrix correction procedure used is based on α‐ coefficients which are simulated for maximum possible variations of interfering element concentrations in the matrix and are calculated on the assumption that the sample is homogeneous. The achieved agreement between the XRF results and the certified values is satisfactory. The paper discusses why the above material cannot be homogenized by fusion and the effect of this on the XRF results.
White line in L absorption spectra of rare earths in their oxides and cuprates
Authors: Moghe Nitin V. , Sapre V. B.
Published: May 2005

A method for curve fitting was used to study and compare the variation in the density of state responsible for the occurrence of the white line associated with the LII and LIII absorption discontinuities of rare earths in their oxides and cuprates. It is observed that the increased covalent character of the rare earth–oxygen bond in rare earth cuprate results in a decrease in the density of the final energy state responsible for the white line.
L x‐ray fluorescence cross‐sections in the atomic region 62 ⩽ Z ⩽ 70 excited by 15.20, 17.80, 23.62 and 24.68 keV photons
Authors: Rao D. V. , Cesareo R. , Gigante G. E.
Published: May 2005

L x‐ray fluorescence cross‐sections were measured for the elements Sm, Ho and Yb using photon energies of 15.20, 17.80, 23.62 and 24.68 keV. Measurements were performed using an x‐ray tube with a modified exciter system as the excitation source. In order to improve the efficiency of the detection system, the excitation source, the sample and the detector assembly were placed in a vacuum chamber and a pressure of 10−2 mbar was maintained through‐out the measurements. The present system considerably reduced the scattering and background effects and improved the monochromaticity. The x‐ray transitions were chosen on the basis of experimentally observed spectra and a particular goup of x‐rays are included in the calculation of fractional x‐ray emission rates. The experimental results were in excellent agreement with theoretical values.
Description of x‐ray beams using the fluorescence yields of a set of thick targets
Authors: Martínez C. , Delgado V.
Published: May 2005

Quantitative methods in x‐ray fluorescence analysis require a knowledge of the spectral distribution of the fluorescence‐exciting beam. The use of XRF yield measurements of a set of thick pure element targets is proposed for the description of a fluorescence‐exciting x‐ray beam, without the need to obtain its spectral distribution. This new approach is derived theoretically and verified by comparing thin‐target yields calculated from XRF yield measurements of thick pure element specimens with those obtained from a calculated spectral distribution. The difference between the two methods of obtaining the thin‐target yields is within 9% relative error.
Preparation of quartz fibre filter standards for x‐ray fluorescence analysis of aerosol samples
Authors: Haupt O. , Klaue B. , Schaefer C. , Dannecker W.
Published: May 2005

Results are presented for an intercomparison of two different techniques to produce standard filter materials for the energy‐dispersive x‐ray analysis of aerosol filter samples. In one, multi‐element standard solutions were dropped on to Munktell quartz‐fibre filters and air dried. The other technique utilized an aerosol generator. The dried aerosol was deposited on the filter surface. Extensive calibration procedures were performed with both types of standards. The data were applied to the analysis of urban aerosol filter samples. The results indicated that the aerosol technique provides good accuracy even for elements of atomic numbers below 30. The dropping technique is not applicable for fibre filters and the calibration of light elements (atomic number < 30) and achieves lower accuracy. Therefore, the aerosol technique should be applied generally to the preparation of standard filters. This method provides small particles and homogeneous coatings of the multi‐element standards.
Studies of uranium—cerium admixture solutions by EDXRF spectroscopy
Authors: Hanif Imtiaz , Hanif J. , Hasany S. M. , Iqbal M. Zafar
Published: May 2005

Uranium and cerium were studied in nitric acid solutions after presentation to an energy‐dispersive x‐ray fluorescence (EDXRF) spectrometer on filter‐paper fixed on Scotch tape. Ce Lα and U Lα peaks were used as analyte lines after excitation with a tungsten tube target at low potential (20 kV). These non‐conventional excitation conditions were considered to be suitable for low contents of cerium strongly but high contents of uranium weakly in a nuclear fuel. Lower net integrated line intensities observed in an actinide as compared with a lanthanide are discussed along with the scattered, Auger and Coster–Kronig intensities responsible for the production of back‐ground before calibrations with known concentrations. Difficulties in establishing an explicit relationship between these with change in matrix composition are discussed. The known concentrations of the mixed solutions when compared with the results from various computer programs using regression analysis showed that the algorithm developed by Plesch and Thiele for Siemens is better than the others. An accuracy of <2% was achieved. The importance of certified, standard or simulated reference materials is realized for quality analysis of occasional samples.
Overexpression of the RAD2 gene of S. cerevisiae: Identification and preliminary characterization of Rad2 protein
Authors: Nicolet Charles M. , Friedberg Errol C.
Published: May 2005

The cloned RAD2 gene of S. cerevisiae was tailored into regulatable expression vectors for overexpression of Rad2 protein in E. coli and in yeast. In E. coli both Rad2/β‐galactosidase fusion protein and native Rad2 protein are insoluble, but are extractable with 1% Sarkosyl. In yeast some of the overexpressed native Rad2 protein is also insoluble; however, soluble protein is readily detected by immunoblotting with Rad2‐specific antibodies. All forms of the protein detected in transformed or untransformed yeast cells and the insoluble species in E. coli migrate in denaturing polyacrylamide gels with an apparent molecular weight considerably larger than the size predicted from the sequence of the RAD2 coding region. This property is not the result of post‐translational glycosylation detectable by binding of concanavalin A, or of phosphorylation of the protein. Overexpression of the RAD2 gene is toxic to yeast. Transformed yeast cells grow much more slowly than untransformed controls and when yeast transformants are serially propagated cultures show considerable colony heterogeneity and concomitant selection for rapidly growing variants which express less Rad2 protein. Antisera raised against Rad2/β‐galactosidase fusion protein expressed in E. coli do not cross‐react with Rad1, Rad3 or Rad10 protein in crude extracts of yeast, nor with purified E. coli UvrA, UvrB or UvrC proteins.
Expression of env sequences of the bovine leukemia virus (BLV) in the yeast Saccharomyces cerevisiae
Authors: Brantl S. , Eldarov M. A. , Rößler H. , Drescher B. , Lang H. , Rosenthal S. , Skryabin K. G.
Published: May 2005

DNA sequences of the envelop (env) gene of the bovine leukemia virus (BLV) were expressed in the yeast saccharomyces cerevisiae. Two yeast promoters, the responsible PH05 promoter and the constitutive PGK promoter, were used to construct four expression plasmids either a sequence of the surface antigen gp51 or a (gp51 + gp30) sequence.

The expressed hetrologous gene products were characterized by Western blot analysis and competitive radio‐immunoassay. By means of Northern blot analysis the steady‐state level of env‐specific mRNA was analysed.

The highest expression rate was obtained from recombinant plasmid YEpSG 94 comprising a gp51 sequence—a 630 base pair fragment containing 70% of the gp51 but lacking the N terminus—as well as the PH05 promoter including PH05 signal sequence and the PH05 terminator. The recombinant gp51 was partially lycosylated but the PH05 signal peptide did not seem to be cleaved off. No immunoreactive material could be found in the periplasm or in the culture medium.

By means of monoclonal antibodies directed against eight different epitopes of viral gp51, all for sequential antigenic determinants were detected in the AH 216(YEpSG 94) expression product.
Properties of enzymes which reduce dihydroxyacetone and related compounds in hansenula polymorpha CBS 4732
Authors: Verduyn Cornelis , Breedveld Guido J. , Schreuder Henk , Scheffers W. Alexander , Van Dijken Johannes P.
Published: May 2005

Hansenula polymorpha CBS 4732 grown on a variety of substrates contained very high activities of enzymes catalyzing the NADH‐linked reduction of dihydroxyacetone, acetoin, diacetyl, acetol, methylglyoxal and acetone. The enzymes catalyzing these reductions have been purified and their kinetic properties are described. Three different enzymes were found responsible for the above‐mentioned activities, namely: (1) dihydroxyacetone reductase; (2) acetone reductase; and (3) alcohol dehydrogenase.

So far, the physiological function of dihydroxyacetone reductase and acetone reductase is obscure. The kinetic properties of dihydroxyacetone reductase and the regulation of the synthesis of this enzyme suggest that it does not function as a glycerol dehydrogenase.
The influence of oxygen and organic hydrogen acceotors on glycolytic dioxide production in Brettanomyces anomalus
Authors: Gaunt Davis M. , Degn Hans , Lloyd David
Published: May 2005

The yeast Brettanomyces anomalus showed the Custers effect in that under strictly anaerobic conditions, in the presence of glucose, CO2 production was negligble. CO2 production was stimulated by mixing anaerobic cell suspensions with an aerated glucose solution in astopped‐flow cell. Glycolytic CO2 production continued even after oxygen exhaustion. Studies using an open reaction vessel showed that the rate of glycolytic CO2 production could be increased to a maximum level by exposing the anaerobic cell suspension to brief pulses of O2. A cell suspension CO2 at a maximal rate demonstrated the Pasteur effect on switching the mobile gas to a mixture conatining oxygen (5.05 KPa). In contrast to glycolytic CO2 production in vivo nicotinamide pool responded rapidly to changes in oxygen concentration. The addition of acetaldehyde, acetone, or 3‐hydroxy‐butan‐2‐one led to a temprorary production of CO2 at an initial rate depending on the concentration of substance added according to the Michaelis–Menten equation. The maximal rates were equal with all three substances, whereas tha apparent Km values were different. The total amount of CO2 produced was 22‐fold greater than the amount of acetaldehyde added. Added organic hydrogen acceptors modulated the intracellular reedox balance of B. anomalus under conditions. These results are discussed in relation to the current hypothesis of the Custers effect.
High level of expression of a protective antigen of schistosomes in Saccharomyces cerevisiae
Authors: Loison G. , Vidal A. , Findeli A. , Roitsch C. , Balloul J. M. , Lemoine Y.
Published: May 2005

Strains of Saccharomyces cerevisiae expressing P28‐I, an antigen inducing protection against schistosomiasis, have been constructed. Transformants containing a very high copy number of a P28‐I expression vector were selected by genetic complementation involving deficient LEU2 or URA3 alleles carried by plasmids. Using the ura3 fur1 auto‐selection system, constitutive and stable expression of P28‐I could be obtained in cultures grown in rich medium.

The accumulation of the foreign protein exceeds 25% of total yeast proteins when estimated by Coomassie Brilliant Blue staining of SDS‐PAGE. Moreover, P28‐I which was located intracellularly was soluble and biologically active.
Classical transketolase functions as the formaldehyde‐assimilating enzyme during growth of a dihydroxyacetone synthase‐negative mutant of the methylotrophic yeast Hansenula polymorpha on mixtures of xylose and methanol in continuous cultures
Authors: De Koning W. , Bonting K. , Harder W. , Dijkhuizen L.
Published: May 2005

Contrary to expectation, a mutant of Hansenula polymorpha blocked in dihydroxyacetone (DHA) synthase was able to assimilate methanol‐carbon when grown in chemostat culture on mixtures of xylose and methanol. Incubation of a DHA synthase‐ and DHA kinase‐negative double mutant resulted in DHA accumulation, indicating that a DHA synthase‐type of reaction was involved. Low residual DHA synthase activity subsequently was shown to be present when using an assay with improved sensitivity. This activity was not associated with the (mutated) DHA synthase protein, which was still present in the peroxisomes, but with the enzyme transketolase. Transketolase from methanol grown cells was purified (525‐fold) to homogeneity in 9% yield. The native enzyme was dimeric, as has been reported fro other transketolases, with a subunit molecular weight of 74000. The affinity of the purified enzyme for formaldehyde was low (Km = 5 mM), but high for xylulose‐5‐phosphate (ca. 10 μM). The in vivo functioning of transketolase in formaldehyde assimilation, and the influence of the hydration state of formaldehyde is discussed.
DNA relatedness among species of the genus Zygosaccharomyces
Authors: Kurtzman C. P.
Published: May 2005

The extent of nuclear DNA complementarity was determined for members of the genus Zygosaccharomyces. From these comparisons, nine species have been identified: Z. baillii, Z. bisporus, Z. cidri, Z. fermentati, Z. florentinus, Z. mellis, Z. microellipsoides, Z. mrakii, and Z. riuxii. Candida mogii, the proposed anamorph of Z. rouxii, showed low relatedness to all nine species. The recently described Saccharomyces astigiensis and S. albasitensis were conspecific with Z. fermentati, and S. placentae showed high relatedness with Z. rouxii. Growth tests were defined that allow recognition of all Zygosaccharomyces species.
The start gene CDC28 and the genetic stability of yeast
Authors: Devin A. B. , Prosvirova T. Yu. , Peshekhonov V. T. , Chepurnaya O. V. , Smirnova M. E. , Koltovaya N. A. , Troitskaya E. N. , Arman I. P.
Published: May 2005

The cdc28‐srm mutation in Saccheromyces cerevisiae decreases spontaneous and induced mitochondrial rhomutability and the mitotic stability of native chromosomes and recombinant circular minichromosomes. The effects of cdc28‐srm on the genetic stability of cells support the hypothesis that links cell cycle regulation in yeast to changes in chromatin organization dependent on the start gene CDC28 (Hayles and Nurse, 1986).
Dekkera, Brettanomyces and Eeniella: Electrophoretic comparison of enzymes and DNA–DNA homology
Authors: Smith Maudy Th. , Yamazaki M. , Poot G. A.
Published: May 2005

The taxonomic status of various species of Dekkera, Brettanomyces and Eeniella was examined by electrophoretic comparison of enzymes, by deoxyribonucleic acid homology and by physiological characterization. These studies demonstrated that two teleomorphic Dekkera species, D. anomala and D. bruxellensis (Synonym. D. intermedia), and four anamorphic Brettanomyces species, B. anomalus (synonym B. claussenii), B. bruxellensis (synonym B. abstinens, B. custersii, B. Intermedius, B. lambicus), B. custersianus and B. naardenesis, can be recognized. The anamorphic genus Eeniella remained as a separate, monotypic taxon.
Increase of anion and proton permeability of Saccharomyces carlsbergensis plasmalemma by n‐alcohols as a possible cause of its de‐energization
Authors: Petrov Valery V , Okorokov Lev A.
Published: May 2005

The effect on n‐alcohols on ATP‐dependent generation of ΔpH and Em across the plasma membrane vesicles of the yeast Saccharomyces carlsbergenesis was investigated. The alcohols were shown to collapse ΔpH and Em in the order C2<C3<C4C8>C11, the dissipation of Em being more pronounced. Inhibition of the plasmalemma H+‐ATPase was insignificannt: at low alcohol concentrations its activity even increased. The basic reason for the toxic effect of the alcohols on the yeast cells was suggested to be due to the increase in the anion and proton permeability of the plasma membrane. Mg2+ partially prevented the increase in the plasmalemma ion permeability by the alcohols investigated.
Purification of δ‐aminolevulinate dehydratase from genetically engineered yeast
Authors: Borralho Leda M. , Ortiz Claudio H. D. , Panek Anita D. , Mattoon James R.
Published: May 2005

Saccharomyces cerevisiae transformed with a multicopy plasmid carrying the yeast structural gene HEM2, which codes for δ‐aminolevulinate dehydratase, was enriched 20‐fold in the enzyme. Beginning with cell‐free extracts of transformed cells, the dehydratase was purified 193‐fold to near‐homogeneity. This represents a 3900‐fold purification relative to the enzyme activity in normal, untransformed yeast cells. The specific activity of the purified enzyme was 16·2 μmol h−1 per mg protein at pH 9·4 and 37·5°C. In most respects the yeast enzyme resembles mammalian enzymes. It is a homo‐octamer with an apparent Mr, of 275 000, as determined by centrifugation in glycerol density gradients, and under denaturing conditions behaved as a single subunit of Mr ≃ 37 000. The enzyme requires reduced thiol compounds to maintain full activity, and maximum activity was obtained in the presence of 1·0 mM‐Zn2+. It is sensitive to inhibition by the heavy metal ions Pb2+ and Cu2+. The enzyme exhibits Michaelis‐Menten kinetics and has an apparent Km of 0·359 mM. Like dehydratases from animal tissues, the yeast enzyme is rather thermostable. During the purification process an enhancement in total δ‐aminolevulinate dehydratase activity suggested the possibility that removal of an inhibitor of the enzyme could be occurring.
Chromosome III of Saccharomyces cerevisiae: An ordered clone bank, a detailed restriction map and analysis of transcripts suggest the presence of 160 genes
Authors: Yoshikawa Akikazu , Isono Katsumi
Published: May 2005

Using λ phage vector EMBL4, we isolated 344 clones containing segments of chromosome III of Saccharomyces cerevisiae, analysed their physical structure with eight restriction enzymes and sorted the data in contiguous groups with computer programmes. Furthermore, we performed Southern hybridizations between the sorted contiguous clone groups and interrelated them into larger groups. In this way, we constructed an ordered clone bank that covers almost the whole of chromosome III with a single gap of several kilobases in length. The consensus physical map thus obtained totals 334·6 kb, which is in good agreement with the size of this chromosome estimated by pulsed‐field gel electrophoresis. Southern hybridization analysis with the DNA probes containing telomere‐specific sequences showed that the bank contained a telomere at a position corresponding to the right arm terminus of chromosome III. Also, five Ty elements were found to be present. To estimate the number of genes on this chromosome and to analyse their levels of expression, we performed a series of Northern hybridization experiments using total poly(A)+ RNA from vegetatively growing cells and appropriate restriction enzyme fragments from the bank. Thus, we identified a total of 156 transcripts on chromosome III, indicating, on an average, one gene in every 2 kb on this chromosome. The transcripts were visually categorized into five groups according to their apparent levels of expression. It was found that the genes located near both termini are expressed only at low levels and that highly expressed genes are rather scattered over the chromosome.
Nucleotide sequence of the cytochrome oxidase subunit 2 and val‐tRNA genes and surrounding sequences from Kluyveromyces lactis K8 mitochondrial DNA
Authors: Hardy Chris M. , Clark‐Walker G. D.
Published: May 2005

The nucleotide sequence of the cytochrome oxidase subunit 2 (cox2) and val‐tRNA genes and surrounding regions from Kluyveromyces lactis mitochondrial DNA is reported. Analysis of the coding regions shows that the codons CUN (Thr), CGN (Arg) and AUA (Met) are absent in this gene. A single sequence, ATATAAGTAA, identical to the baker's yeast mtRNA polymerase recognition site, was detected upstream of val‐tRNA. This sequence is absent from regions between val‐tRNA‐cox2 and cox2‐cox1. In addition a sequence AATAATATTCTT, identical to the mRNA processing site in other yeast mitochondrial genomes is present 32–43 bp downstream to the TAA stop codon for the cox‐2 gene. Another short conserved sequence of 5 bp, TCTAA, is present upstream of the coding regions of cox2 genes in several yeasts, including K. lactis, but is not present upstream of other genes. Comparison of cox2 sequences from other organisms indicates that the mitochondrial DNA of K. lactis. is closely related to that of Saccharomyces cerevisiae.
An assay of relative cell wall porosity in Saccharomyces cerevisiae, Kluyveromyces lactis and Schizosaccharomyces pombe
Authors: De Nobel Johannes G. , Klis Frans M. , Munnik Teun , Priem Jan , Van Den Ende Herman
Published: May 2005

We have developed a new assay to determine relative cell wall porosity in yeasts, which is based on polycation‐induced leakage of UV‐absorbing compounds. Polycations with a small hydrodynamic radius as measured by gel filtration (poly‐L‐lysine) caused cell leakage independent of cell wall porosity whereas polycations with a large hydrodynamic radius (DEAE‐dextrans) caused only limited cell leakage due to limited passage through the cell wall. This allowed the ratio between DEAE‐dextran‐ and poly‐L‐lysine‐induced cell leakage to be used as a measure of cell wall porosity in Saccharomyces cerevisiae, Kluyveromyces lactis and Schizosaccharomyces pombe. Using this assay, we found that the composition of the growth medium affected cell wall porosity in S. cerevisiae. In addition, we could show that cell wall porosity is limited by the number of disulphide bridges in the wall and is dependent on cell turgor. It is argued that earlier methods to estimate cell wall porosity in S. cerevisiae resulted in large underestimations.
The glucanase‐soluble mannoproteins limit cell wall porosity in Saccharomyces cerevisiae
Authors: De Nobel Johannes G. , Klis Frans M. , Priem Jan , Munnik Teun , Van Den Ende Herman
Published: May 2005

The cell porosity of batch‐grown Saccharomyces cerevisiae was maximal in the early exponential phase and fell off rapidly to lower levels in later growth phases.

Treatment of stationary‐phase cells with alpha‐mannosidase restored wall porosity to the level of cells in early exponential phase. When cells in the early exponential phase were treated with alpha‐mannosidase, or tunicamycin, an inhibitor of N‐glycosylation, even higher porosities were obtained. Mutants with truncated mannan side‐chains in their wall proteins also had very porous walls. The importance of the mannan side‐chains for wall porosity was also seen during sexual induction. Treatment with alpha pheromone, which leads to the formation of wall proteins with shorter mannan side‐chains, enhanced wall porosity.

Disulphide bridges also affect cell wall porosity. They were predominantly found in the glucanase‐soluble wall proteins. Because the main part of the mannan side‐chains is also found in this family of wall proteins, our results demonstrate that the glucanase‐soluble mannoproteins limit cell wall porosity in yeast.
The complete sequence of the 8·2 kb segment left of MAT on chromosome III reveals five ORFs, including a gene for a yeast ribokinase
Authors: Thierry Agnès , Fairhead Cécile , Dujon Bernard
Published: May 2005

We report here the DNA sequence of a segment of chromosome III extending over 8·2 kb. The sequence was determined using the random clone strategy followed by oligonucleotide‐directed sequencing. The segments contains five long open reading frames, YCR521, 522, 523, 524 and 526, with only short distances between them. YCR523 (333 codons) endodes a ribokinase, a new function for yeast. YCR526 originates inside the MAT cassette, which is in continuity with the present segment, and extends over 358 codons outside of MAT. YCR524 (923 codons) codes for a putative membrane protein. YCR521, 522 and 524, have each been disrupted by insertion of a URA3 cassette and are non‐essential genes. An active ARS element is located within YCR523 or its vicinity.
RCS1, a gene involved in controlling cell size in Saccharomyces cerevisiae
Authors: Gil Rosario , Zueco Jesús , Sentandreu Rafael , Herrero Enrique
Published: May 2005

Cloning and sequencing of RCS1, a Saccharomyces cerevisiae gene whose product seems to be involved in timing the budding event of the cell cycle, is described. A haploid strain in which the 3′‐terminal region of the chromosomal copy of the gene has been disrupted produces cells that are, on average, twice the size of cells of the parental strain. The critical size for budding in the mutant is similarly increased, and the disruption mutation is dominant in a diploid heterozygous for the RCS1 gene. Spores from this diploid have a reduced ability to germinate, the effect being more pronounced in the spores carrying the disrupted copy of RCS1. However, disrupted cells recover from α‐factor treatment equally as well as wild‐type cells.
Scarcity of ars sequences isolated in a morphogenesis mutant of the yeast Yarrowia lipolytica
Authors: Fournier Ph. , Guyaneux L. , Chasles M. , Gaillardin C.
Published: May 2005

Previous attempts to isolate autonomously replicating sequences (ars) from the dimorphic yeast Yarrowia lipolytica have been unsuccessful. We isolated a Fil− mutant unable to produce hyphae and growing only in a yeast form to facilitate ars isolation. This mutant was transformed with a Y. lipolytica DNA bank and several unstable clones were obtained. Extrachromosomal plasmids were evidenced in yeast recovered in Escherichia coli and characterized by restriction mapping. They were able to retransform Fil− and Fil+ yeast strains at high frequency and transformants displayed a slightly unstable phenotype. The detailed analysis of the plasmids showed that only two different ars sequences had been isolated, each of them corresponding to a unique sequence in the Y. lipolytica genome. We concluded that functional ars sequences that can be cloned on plasmids are rare in this yeast.
On the dependence of spontaneous mutation rates on the functional state of genes
Authors: Korogodin V. I. , Korogodina V. L. , Fajszi Cs. , Chepurnoy A. I. , Mikhova‐Tsenova N. , Simonyan N. V.
Published: May 2005

Spontaneous mutation of some genes was studied in haploid adenine and leucine auxotrophic yeast Saccharomyces.

It was shown that a decrease in the amount of adenine (from 500 to 0 mgl−1) or leucine (from 300 to 0·3 mgl−1) in the medium, simultaneously with the transition from repression to derepression of the biosynthesis of these metabolites, resulted in a 15‐ to 150‐fold increase in the reversion rate of genes ade2 and leu2, respectively, for different strains. At the same time the mutation rate of suppressor genes varied relatively little (up to five‐fold), and that of gene lys1 did not change at all. It was also demonstrated (on gene leu2) that the mutation rate is determined by the composition of the nutrient medium at the time of the S‐phase of the cell cycle and it does not depend on the cultivation conditions during the presynthetic period.

We discuss the hypothesis that derepressed genes mutate with a significantly higher rate than genes in the repressed state.
Quantitation of readthrough of termination codons in yeast using a novel gene fusion assay
Authors: Firoozan Mandy , Grant Christopher M. , Duarte Julio A. B. , Tuite Mick F.
Published: May 2005

A simple quantitative in vivo assay has been developed for measuring the efficiency of translation of one or other of the three termination codons, UAA, UAG and UGA in Saccharomyces cerevisiae. The assay employs a 3‐phosphoglycerate kinase‐β‐galactosidase gene fusion, carried on a multicopy plasmid, in which the otherwise retained reading frame is distupted by one or other of the three termination codons. Termination readthrough is thus quantitated by measuring β‐galactosidase in transformed strains. Using these plasmids to quantitate the endogenous levels of termination readthrough we show that readthrough of all three codons can be detected in a non‐suppressor (sup+) strain of S. cerevisiae. The efficiency of this endogenous readthrough is much higher in a [psi+] strain than in a [psi−] strain with the UGA codon being the leakiest in the nucleotide context used. The utility of the assay plasmids for studying genetic modifiers of nonsense suppressors is also shown by their use to demonstrate that the cytoplasmic genetic determinant [pse+] broadens the decoding properties of a serine‐inserting UAA suppressor tRNA (SUQ5) to allow it to translate the other two termination codons in the order of efficiency UAA > UAG > UGA.
Calcium‐dependent secretory vesicle‐binding and lipid‐binding proteins of Saccharomyces cerevisiase
Authors: Creutz Carl E. , Snyder Sandara L. , Kambouris Nicholas G.
Published: May 2005

Yeast (Saccharomyces cerevisiae) cytosol was examined for the presence of calcium‐dependent membrane‐ or lipidbinding proteins that might paly fundamental roles in membrane‐associated phenomena in stimulated cells. A complex group of proteins was isolated from late log phase cultures of yeast strain YP3 on the basis of calcium‐dependent association with yeast secretory vesicles isolated from the temperature‐sensitive sec6‐4 secretory mutant. The masses of the major proteins in this group were 32, 35, 47, 51, 55, 60, and 120 kDa. A similar group of proteins was isolated by calcium‐dependent association with bovine brain lipids enriched in the predominant acidic phospholipids of the yeast secretory vesicles. The 47 kDa protein was highly purified when commerical yeast cake was used as the source of yeast cytosol. The 32 kDa and 60 kDa proteins were demonstrated to reassociate with lipids at calcium concentrations of 100 μM or higher, while no association was promoted by 2 mM‐magnesium. The 47 kDa protein could be removed from lipids by reducing the calcium concentration to between 1 and 32 μM. The sequences of peptides isolated from digests of several of these proteins indicate that they are novel proteins but are insufficient to judge the possible homology of these proteins with mammalian membrane‐binding proteins. The sequence data may be adequeate to permit isolation and modification of the corresponding genes in order to assess the possible funtion of this class of proteins in stimulated cells.