bluuebunny/crossref_metadata_2025 huggingface dataset:
Progress in X‐ray microbeam spectroscopy
Authors: Rindby A.
Published: May 2005

X‐ray spectroscopy has been widely used for chemical analysis since its discovery in 1895. X‐ray fluorescence (XRF) has been used for over 60 years for identifying the elemental composition in most kinds of samples and in combination with modern semiconductor detector technology XRF has developed into a versatile, multi‐element method. With the high X‐ray flux attainable from the synchrotron source, new spectroscopic techniques have become available, such as extended x‐ray absorption fine structure (EXAFS) and x‐ray absorption near‐edge spectroscopy (XANES), for studying the chemical states of the different elements. With the use of high‐intensity x‐ray microbeams all of these different analytical methods can be performed on a microscopic level. By scanning the microbeam over a sample, the distribution of different elements can be determined. A description of the basic principles of x‐ray microbeam spectroscopy, and the historical background, is given and comparisons with other techniques are discussed. Different techniques for focusing of x‐rays, detection and image reconstruction are described. Examples of applications and future perspectives are discussed with particular emphasis on capillary optical systems.
EDXRS study of aerosol composition variations in air masses crossing the North Sea
Authors: Injuk J. , Van Malderen H. , Van Grieken R. , Swietlicki E. , Knox J. M. , Schofield R.
Published: May 2005

X‐ray emission techniques for bulk and individual particle analysis (EDXRF, EPXMA, micro‐PIXE) were combined and applied in atmospheric research on the North Sea area as part of a field‐study on air‐sea exchange processes of particulate matter. The atmospheric loading for a number of elements was determined by EDXRF, yielding bulk concentrations for Mg, Al, Si, S, Cl, K, Ca, Cr, Mn, Fe, Ni, Cu, Zn, Br and Sr. From these EDXRF data, deposition rates were derived and, based on a classical multivariate statistical approach, different aerosol sources were identified. Complementary to this work, EPXMA combined with automated image analysis was applied to individual size‐segregated aerosol particles to determine their inorganic composition, physical size and shape. Also, the first results of micro‐PIXE analyses on individual North Sea aerosol particles, particularly their large‐size fraction, are discussed and compared with the corresponding EPXMA results. In summary, such a joint approach with the use of different x‐ray emission techniques contributed to the resolution of the mixed structure of the lower North Sea troposphere and to the determination of the atmospheric supply of material to the North Sea environment.
Synchrotron x‐ray fluorescence analysis of heavy trace elements in light silicate minerals
Authors: Figueiredo M. O. , Basto M. J. , Abbas K. , Chevallier P. , Melo Z. , Ramos M. T.
Published: May 2005

A description is presented of fluorescence spectrometric experiments using synchrotron radiation and an energydispersive detection system performed at the LURE (DCI storage ring) where a study of geological materials is under development. Early results obtained for natural lithium aluminosilicates (lepidolites) from pegmatite formations in northern Portugal are discused. Data handling and processing (deconvolution of the complex spectral lines, deduction of continuous background and peak area calculation) are briefly described. Some heavy trace elements previously unreported for these lepidolites (TI, W, Ta, Nb) and one geochemically relevant sub‐trace metal (Au) were detected. The analytical efficiencies of three excitation energies (6, 13 and 19 keV) are compared. The difficulities and drawbacks versus advantages of this techique for the assessment of trace and sub‐trace elements in geological samples are discussed.
Proton‐induced monochromatie x‐ray beams
Authors: Karydas A. G. , Paradellis T.
Published: May 2005

The bombardment of thick pure targets by protons produces intense monochromatic x‐ray beams which can be used for x‐ray fluorescence analysis. An experimental arrangement suitable for sample irradiation and detection of the fluorescent x‐rays in vacuum was constructed and was attached to the accelerator leg. The general characteristics of the method are described and some examples from the use of Cu, Fe and Ti as primary targets are presented.
A fast convergence procedure for a direct determination method in XRF
Authors: Wang Yongzhong
Published: May 2005

A comparison among current methods in x‐ray spectrometry showed that it is possible to abandon the traditional concept of comparing unknown samples with standards if it is expected that unknown samples with a rough surface can be determined directly without sample preparation. The error caused by the uncertainties of the fundamental parameters can be reduced and the effect of the attenuation in the x‐ray path on the intensities of the characteristic fluorescent x‐rays can also be accounted for by the introduction of the instrumental factors Pik which are initially determined. In order to speed up the calculation, a new iterative equation is presented in the direct determination method. In addition, a new way to select the starting values in the iteration and a simplified way to iterate the calculation are presented. With these improvements, the convergence in iteration is faster than before.
Intensities of individual L x‐ray spectra calculated using the TEREN program
Authors: Verkhovodov Peter A.
Published: May 2005

In characteristic x‐ray intensity calculations, the total L spectrum can be represented by separate spectra from L1, L2 and L3 subshell transitions. The expressions presented here take into account the ionization not only of the L1, L2 and L3 subshells but also of the K shell. The approximating polynomials for the calculation of the radiative transition probability and the Koster‐Kroning transition probability are derived. Examples are presented of intensity calculations in multi‐component systems using the TEREN program.
Anomalous X‐ray absorption of the Mα lines in the rare earth elements
Authors: Lábár János L.
Published: May 2005

The presence of an unfilled inner electron shell in the rare earth elements is manifested in x‐ray absorption effects that are unique to the energy region including the Mα and Mβ lines of these elements. In contrast to the normal edge‐type absorption, this anomalous absorption appears as an absorption line. A method is presented here for the quantitative determination of the extent of this anomalous absorption. Solid bulk metal samples, excited with a monoenergetic electron beam, were examined with a wavelength‐dispersive x‐ray spectrometer. The discussed method makes the experimentally determined absorption independent of both the detection efficiency and atomic data such as the fluorescence yield and transition probabilities. A simple empirical model is proposed to explain the dependence of the absorption of the Mα line on the absorption path length, which was varied by the primary beam energy. Normal and anomalous absorption are treated as independent and competing processes in this model. Atomic data such as the mass absorption coefficients pertinent to the anomalous absorption of the Mα lines were also determined and are presented.
X‐Ray fluorescence analysis with elements having overlapped lines
Authors: Mainardi Raúl T. , Barrea Raúl A.
Published: May 2005

The overlapping of characteristic spectral lines of two or more elemental constituents of a sample has always been a drawback in x‐ray fluorescence analysis. A new approach to solve this problem is presented, based in the excitation at two different energies. The results show that it is possible to calculate the concentration of elements with overlapped lines with high accuracy. We thus avoid the use of other means to obtain the needed number of spectral lines, such as secondary characteristic lines, which usually have a low peak to background ratio, or to recur to the line fraction (i.e. Kβ/Kα), which is matrix dependent.
Energy‐dispersive XRF analysis of pure element intensities from their oxides using a Cd‐109 source
Authors: Hua Younan , Yap C. T.
Published: May 2005

The relationship between the fluorescent intensity ratio of analyte to pure analyte/concentration of analyte and the fluorescent energy can be expressed as In(Ii/Ii0ci) = a In Ei + b, where a and b are constants for a given matrix. This relationship depends on the pure element intensity Ii0. Experimental pure element intensities can be obtained in a number of ways. Although the use of thick pure metal foils is perhaps the simplest, there are many elements for which pure metal foils are not available. This paper discusses the determination of experimental values of pure element intensities from their oxides and shows that their values are in good agreement with those obtained from pure metal foils.
Effect of features of inner atomic shells excitation by accelerated ions on the shape of the emitted X‐ray lines
Authors: Altynov V. A. , Blokhin S. M.
Published: May 2005

A study of the effects of various factors in forming the structure of the characteristic x‐ray spectrum of atoms excited by heavy ions with an energy of ca. 1 MeV u−1 is reported. In particular, the structure of multiple ionization satellites was analysed and also the effect of the bombarding ion field and the reflection in the emitted spectrum of the Doppler‐shaped lines connected with the presence of the emitting atom recoil velocity. It is shown that the experimental shape of the corresponding x‐ray lines is satisfactorily reproduced if the contribution of the effects under investigation is taken into account.
Efficiency calibration of a Ge(In) semiconductor detector by thin‐ and thick‐arget PIXE
Authors: Kallithrakas‐Kontos N. , Katsanos A. A.
Published: May 2005

The efficiency of a Ge(In) semiconductor x‐ray detector was measured in the energy region 1‒25 keV using proton‐induced x‐rays from thick targets and from thin targets of standard thickness, and the results of the two calibration methods were compared. A proton energy of 2.00 MeV was used in an external beam facility. A model based on fundamental parameters (mass absorption coefficients, fluorescence yields and relative x‐ray emission rates) was used to reproduce the experimental results.
Method for quantitative electron microprobe EDS X‐ray analysis of small incluasions in matrices with similar composition
Authors: Stoyanchev R. , Iliev Tz. , Recalov K.
Published: May 2005

A method is proposed for the quantitative elemental analysis of small inclusions in matrices with similar composition. The method is applicable provided that the difference between the matrix and the inclusion is at least one x‐ray‐detectable element. The approach is based on a technique for the determination of phase fractions by scanning the surface of the sample by the electron beam and recording the x‐ray intensities with an energy‐dispersive x‐ray spectrometer. By using the phase fraction of the matrix as a multiplier–coefficient, the contribution of the matrix to the overall area‐scanned spectrum around the inclusion is determined. Then the contribution of the matrix in the same spectrum is subtracted from the overall area‐scanned spectrum. The elemental composition of the remaining spectrum is analysed by the standardless ZAF method. The new method was tested experimentally with different sulphide inclusions within sulphide matrices.
Kinetic equation‐based calculation of the electron distribution in the target exposed to the electron beam
Authors: Bakaleinikov L. A. , Tropp E. A.
Published: May 2005

Singular perturbation methods were used to investigate the kinetic equation for electron distribution in targets. This approach permits the determination of the domains of applicability of kinetic equation approximations and the establishment of the connections between them. The analytical solution of the approximate kinetic equation in some of these domains was obtained and numerical calculations were performed in the others. On the basis of these solutions, the energy spectrum of backscattered electrons and the x‐ray depth distribution were found.
Quantitative analysis of some elements of aydin basin soils by X‐ray fluorescence spectrometry
Authors: Bassari Asiye , Kumru Mehmet
Published: May 2005

Soil samples from 40 different sampling points in the Aydin Basin were analysed and the distributions of Ti, Cr, Mn, Cu, Zn, Sr, Zr, Rb, Ba and Ce were investigated by energy‐dispersive x‐ray fluorescence spectrometry. Two annular sources, 238Pu (10 mCi) and 241Am (30 mCi) and two detectors, Si(Li) and HPGe, were used. The fundamental parameter technique was adopted for quantitative analysis of elements. The concentrations of Cr, Zr, Zn and Ce were found to be higher than those corresponding to the mean chemical composition of the lithosphere.
A novel method to ascertain sample mass thickness and matrix effects for X‐ray fluorescence element determinations
Authors: Giauque Robert D.
Published: May 2005

An x‐ray fluorescence method was developed for the determination of both trace and major elements in environmental samples that are primarily of geochemical origin. For analysis, unweighed finely pulverized sample material is lightly compressed to a mass thickness between 0.1 and 0.4 g cm−2. The method utilizes the relative intensities of two incoherent and one coherent scattered excitation radiation to ascertain the sample mass thickness and the photoelectric cross‐section of the sample for the excitation radiation. This information is employed to calculate matrix absorption and enhancement effect corrections required for the individual element determinations. The intensity of one of the incoherently scattered radiations serves as an internal standard for all of the element determinations. The capability of the method has been demonstrated with three US National Institute of Standards and Technology reference materials. The concentrations of sixteen trace elements (Mn, Ni, Cu, Zn, Ga, As, Se, Br, Rb, Sr, Y, Zr, Nb, Ba, Pb, and Th) and four major elements (K, Ca, Ti, and Fe) were determined from one x‐ray spectrum which was acquired over a 1000 s counting interval.
An analytical algorithm for correction of edge effects in X‐ray microfluorescence analysis of geological samples
Authors: Lankosz Marek , Pella Peter A.
Published: May 2005

Geometrical effects occur when primary x‐rays irradiate a mineral inclusion which lies close to the boundary between it and a surrounding mineral having a different chemical composition. An investigation of two types of near‐edge effects was performed in the case when x‐ray microfluorescence is applied for analysis. For zinc sulfide in calcium carbonate and for arsenopyrite in serpentine, the increase in measured characteristic x‐ray intensity near the boundary is 15‒25%. Analytical mathematical expressions were developed to correct for such effects and the calculated results are in good agreement with measured values.
Quantitative total reflection X‐ray fluorescence analysis with monoenergetic excitation
Authors: Ladisich Wolfgang , Rieder Robert , Wobrauschek Peter
Published: May 2005

By applying monoenergetic excitation in total reflection x‐ray fluorescence analysis, the quantitative analysis can be further simplified since fundamental parameters from tables can be used for the calculation of elemental sensitivities. Establishing calibration graphs experimentally by measuring multielement standards is no longer necessary. Advantages of monoenergetic excitation are discussed.
Electronic structure and L X‐ray emission spectra of molybdenum carbide, boride, nitride, silicide and silicocarbide
Authors: Acharya B. S. , Sakthivel R.
Published: May 2005

K and L emission spectra of the carbide, boride, nitride, silicide and silicocarbide of molybdenum were studied using x‐ray spectrometry method. It was observed that satellite lines influence the K and L spectra in these molybdenum compounds. From the chemical shift of these lines, the nature of the bonding is found to be covalent in these compounds. Further, hybridization of both p‐d and s‐p orbitals plays a major role in shifting these lines and high asymmetry indices. In MoSi2 and MoSi3 C a quasi‐gap is found to be present. The abnormally high value of the I/I ratio was explained on the basis of multi‐hole configuration, shake‐off and Coster‐Kronig processes taking place in these compunds.
Tunable exciting energies for total reflection X‐ray fluorescence spectrometry using a tungsten anode and bandpass filtering
Authors: Knoth Joachim , Schneider Harald , Schwenke Heinrich
Published: May 2005

The applicability of crystal monochromators, X‐ray mirrors and multilayer configurations as filter elements in the primary beam of a total reflection X‐ray fluorescence spectrometer is discussed. The best compromise between detection limits and multielement capability was found to be a double multilayer arrangement with variable distance between the multilayer mirrors. Two multilayers in combination with the respective control units for multilayer distance, tube height and sample positioning provide a free choice of isolated X‐ray lines and narrow energy bands of the bremsstrahlung continuum. This permits optional excitation energies in one instrument. Using a tungsten anode at 60 kV, three arbitrarily selected energies of 9.7, 20 and 40 keV were applied. The effect of tunable exciting energies was demonstrated by means of a standard multielement solution.
L‐subshell fluorescence yields measured with synchrotron radiation
Authors: Sáanchez Héctor J. , Rubio Marcelo , Pérez Roberto D. , Burattini Emilio
Published: May 2005

The synchrotron photoionization method was applied to measure L‐subshell fluorescence yields. This method is based on the capability of tuning the energy of the synchrotron photons producing a selective subshell ionization. Three foil samples of Tb, Ho and Yb were irradiated and their characteristic spectra were recorded. Although it was not possible to obtain absolute results for the three ω, ω and ω fluorescence yields, the poorly known ω and ω coefficients were calculated using theoretical values for the well known ω yield. The results are very reliable and agree with reported theoretical and experimental data. These coefficients are valuable information for spectroscopists considering the lack of data for L1‐ and L2‐subshell parameters. Finally, synchrotron radiation has proved to be a useful tool for fundamental parameter determinations.
Determination of the copper oxidation state in a zeolite catalyst through the X‐ray absorption edge/self‐absorption effect by electron probe microanalysis
Authors: Wang Frank Cheng‐Yu
Published: May 2005

Owing to improvements in impregnation techniques, the impregnation of copper compounds into a zeolite framework to form copper zeolite catalysts results in more uniformly distributed and finer (nanoscale size) copper‐containing particles. In order to determine the oxidation state of copper in a copper zeolite catalyst, a method utilizing the X‐ray absorption‐induced (absorption edge/self‐absorption) effect was developed using electron probe microanalysis. This method can provide oxidation state information that is not possible with traditional quantitative microanalysis owing to the electron beam and specimen interaction volume. The advantages and limitations of this method are discussed.
Tree sub‐ring structure analyses by x‐ray microprobe analysis
Authors: Kuczumow Andrzej , Rindby Anders , Larsson Sture
Published: May 2005

An X‐ray capillary microprobe was applied to the investigation of Pinus silvestris wood from Polish forests. The micrometre range of the microprobe gave an insight into the wood sub‐ring structure. The use of transmitted and scattered radiation permitted the detailed tracing of the subtle changes in the density of the wood. The changes in density were connected with the changes in temperature during the growth period. It was established that some kinds of biological activity in the case of Polish conifers covered the whole year, including winter. Samples of wood from the northern Swedish Picea Abies showed totally different mechanisms of winter behaviour.
Experimental investigation of heterogeneity effects in x‐ray fluorescence analysis of hair
Authors: Bacsó József , Uzonyi Imre
Published: May 2005

The effect of heterogeneity on the accuracy of analytical results was experimentally investigated for some biologically important elements in hair, viz. S, Cl, K and Ca. Measurements were carried out by energy‐dispersive x‐ray fluorescence spectrometry using annular 55Fe radioisotope source excitation. The differences between the concentration values from direct hair analysis, using bunches of hair strands for the measurements, and those from ground and pelletized hair samples were compared. On average, the discrepancy in the measured concentrations was ca. 5% for Ca, whereas for S, Cl and K it was higher at ca. 10–15%. Good agreement was found between the experimental values and the theoretical predictions of other workers.
Total reflection PIXE (TPIXE) and RBS for surface analysis
Authors: van Kan J. A. , Vis R. D.
Published: May 2005

Proton beams with an energy of 2.5 MeV and α beams with an energy of 4.8 MeV at small incident angles (0–35 mrad) were used to analyse surfaces by detecting x‐rays (PIXE) and backscattered protons (RBS). The specimens consisted of a flat substrate, such as Si wafers or quartz, with a thin evaporated coating. PIXE detection limits were investigated as a function of angle. A minimum detection limit for Au, using L x‐rays, was found to be 15% of an atomic layer using an incident angle of 16 mrad and 2.5 MeV protons. For angles between 4 and 20 mrad, both the PIXE and RBS yields drop drastically owing to reflection of the incoming ions. This was confirmed by ion trajectory calculations. At very small angles of a few mrad, was observed that the RBS yield drops faster than the x‐ray yield, which indicates surface channelling.
Application of EDXRF in a survey of concentrations of lead, zinc and arsenic in soil from selected areas in Krakow, Poland
Authors: Ostachowicz Jerzy , Ostachowicz Beata , Hołyńska Barbara , Baran Władysław
Published: May 2005

An investigation on the contamination by heavy metals of the surface layer of soil in the area around steelworks located in an industrial quarter of Krakow and in several locations in the city centre was carried out. Particular attention was paid to soil contamination by Pb, Zn and As. The EDXRF technique with radioisotope excitation was applied with the emission‐transmission method for matrix correction. Analyses of over 140 samples of soil were performed. The concentrations obtained of Pb and Zn were 15–200 and 40–650 μg g−1, respectively, whereas that of As was 0–30 μg g−1. The distributions of Pb contents in two regions of Krakow were similar whereas the distributions of Zn contents were different. Higher concentrations of Zn were observed in the industrial area. Such results suggest that there are different sources of contamination of the soil: the Pb content is from transportation and Zn is mainly from industry.
A novel process of x‐ray excitation
Authors: Pillay A. E. , Peisach M.
Published: May 2005

A new mechanism of x‐ray excitation is proposed. Possible applications in physics and chemistry are discussed.
Analysis of pressed pellets of geological samples using wavelength‐dispersive x‐ray fluorescence spectrometry
Authors: Longerich Henry P.
Published: May 2005

The analysis of silicate geological reference materials for 30 elements (Na, Mg, Al, Si, P, S, Cl, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Ni, Cu, Zn, Ga, As, Rb, Sr, Y, Zr, Nb, Ba, Ce, Pb, Th and U) is reported. Samples were prepared as pressed pellets using a phenolic resin. Matrix was uncorrected (NaCl), Lachance–Traill corrected (KFe, Ba and Ce) or Compton corrected (NiNb, Pb, Th and U).
Novel applications of topological indices. I—correlation of edge shifts in x‐ray absorption with wiener indices
Authors: Khadikar Padmakar V. , Joshi Shobha
Published: May 2005

A novel application of Wiener indices in estimating edge shifts is described. It is demonstrated that edge shifts in x‐ray K absorption are linearly correlated with Wiener indices. Copper and cobalt complexes were used to establish this linearity. A novel technique of data reduction using topological indices was employed for the first time for correlation purposes in x‐ray absorption studies.
Simple approach to the analysis of oxides, silicates and carbonates using x‐ray fluorescence spectrometry
Authors: Giles H. L. , Hurley P. W. , Webster H. W. M.
Published: May 2005

X‐ray fluorescence spectrometry has always been considered to be a comparative method of analysis requiring chemically analysed samples or reference materials for calibration. The fusion technique, which is widely used as the method of sample preparation to eliminate particle size and mineralogical effects, allows the use of synthetic ‘standards’ as the means of calibration, but most laboratories use large numbers to establish the primary calibration line and calculate empirical interelement correction coefficients. In the 1970s, de Jongh proposed the use of theoretically based correction coefficients, and his concept of ‘apparent concentration,’ which is related linearly to the measured intensity, means that in principle only two samples are necessary to define the primary calibration line. This paper describes the use of this principle to calibrate a spectrometer for the 13 most commonly occurring oxides, plus six others, over wide composition ranges. Each calibration line requires one sample, which is made from a commercially available source of the element, a blank or zero sample, which is used for all calibration lines, and a set of theoretical α coefficients calculated using de Jongh's program. Sample preparation is by fusion in Li2B4O7. The calibration was tested using reference materials and was found to be accurate for every element except sulphur.
Analyse spatiale d'une source X à l'aide d'un spectromètre à cristal convexe
Authors: Barré C. , André J.‐M. , Jonnard P. , Bonnelle C.
Published: May 2005

Utilisant un spectromètre à cristal convexe, une méthode numérique à été mise au point qui permet de déterminer la taille linéaire d'une source x à partir de la mesure des largeurs spectrales des raies x. Cette méthode à été appliquée à la détermination de la taille d'une étincelle très brève, produite par décharge haute tension au voisinage de pointes de tungstène et de fer. On montre que, dans les conditions d'expérience, l'effet d'élargissement géométrique lié à la taille prédomine sur tous les autres effets d'élargissement.
Polarization effects and photon transport in x‐ray spectrometry
Authors: Fernández J. E.
Published: May 2005

The nature of the scattering interactions in the x‐ray energy regime makes the effect of polarization extremely important, mainly when the incident beam is partially or totally polarized. The effects of the source polarization on the x‐ray spectrum are analysed, stressing the points of interest in each case of unpolarized, linearly polarized and circularly polarized excitation.
Quantitative analysis of individual particles by x‐ray microfluorescence spectrometry
Authors: Lankosz M. , Pella P. A.
Published: May 2005

A fundamental parameters method using polychromatic x‐ray microbeam excitation was developed and applied to the quantitative analysis of individual particles from 50–160 μm. From the ratio of the projected area of a particle to the cross‐sectional area of the microbeam, an effective portion of the microbeam irradiating the particle can be determined and used to correct the measured x‐ray intensities. Because particles in this size range may not be infinitely thick and may contain unmeasurable elements such as C and O, calculation of the average mass thickness of the particle allows complete matrix absorption corrections to be made. For this purpose, the ratio of coherent to incoherent x‐ray tube target lines scattered from the particle was used to calculate the average atomic number of the particle, and its mass thickness was determined from incoherent scatter. A parametric equation was derived and tested. In addition, irregularly shaped particles were analyzed using a well known equation usually applied to flat samples having intermediate thickness. Both models were tested with homogeneous glass particles of known composition and size.
Isolation and characterization of a phosphoprotein phosphatase‐deficient mutant in yeast
Authors: Matsumoto Kunihiro , Uno Isao , Kato Kayoko , Ishikawa Tatsuo
Published: May 2005

The ppd1 mutant of yeast, Saccharomyces cerevisiae, was isolated as a suppressor of the cyr2 mutation which caused alteration of the catalytic subunit of cAMP‐dependent protein kinase. Three peaks of phosphoprotein phosphatase activity (peak I, II and III) were identified by DEAE‐Sephacel chromatography of crude extracts of the wild‐type strain. The ppd1 mutant was deficient in peak III phosphoprotein phosphatase activity. The peak III enzyme efficiently utilized the phosphorylated forms of NAD‐dependent glutamate dehydrogenase and trehalase as substrate. The ppd1 mutation did not suppress the cyr1, CYR3 or ras1 ras2 mutations. The ppd1 locus was located on chromosome II and had identical characteristcs with glc1. The ppd1 mutation suppressed the G1 arrest caused by nutritional limitation, but maintained sensitivity to mating pheromone. In diploids homozygous for the ppd1 mutation, no premeiotic DNA replication and commitment to intragenic recombination occurred and no spores were formed, suggesting that the accumulation of phosphorylated proteins in the absence of one of the phosphoprotein phosphatases is required for mitosis but not for the initiation of meiosis.
The PET18 locus of Saccharomyces cerevisiae: A complex locus containing multiple genes
Authors: Toh‐e Akio , Sahashi Yuko
Published: May 2005

The basis of pleiotropy shown by the pet18 mutants of Saccharomyces cerevisiae (rho‐0, KIL‐0 and temperature sensitive growth) was examined by cloning the fragment which complements the defect in growth at 37°C of the pet18 mutants. the cloned DNA could complement the defect in the maintenance of the killer plasmid but did not give the cell the ability to maintain mitochondrial DNA. Sequence analysis of the cloned DNA revealed the presence of four open reading frames, at least two of which are necessary for the complementation activity. By using the cloned DNA as a probe, we found that two independent pet18 mutants have a deletion covering the entire sequence contained in the probe. From these results we predict that the traits of the pet18 mutants that concern temperature sensitivity and killer of the pet18 mutants are controlled by a separate gene(s) from that which participates in the maintenance of mitochondrial DNA.
Identification of polypeptides of the carbon metabolism machinery on the two‐dimensional protein map of Saccharomyces cerevisiae. Location of 23 additional polypeptides
Authors: Bataillé Nelly , Peypouquet Marie‐France , Boucherie Hélian
Published: May 2005

Using a modification of the basic two‐dimensional polyacrylamide gel electrophoresis technique, we have undertaken a systematic identification of the polypeptides of the protein map of Saccharomyces cerevisiae corresponding to components of the carbon metabolism machinery. To the previous location of nine glycolytic enzyme polypeptides on the yeast protein map we add the location of 23 polypeptides. Ten of them were identified as corresponding to cytoplasmic enzymes of the carbon metabolism machinery and 13 were characterized as mitochondrial proteins. The criteria used to establish the identification of these polypeptides spots include migration with purified proteins, immunodetection, overproduction by plasmid–carrying strains and physiological behaviour.
Effects of weak acids and external pH on the intracellular pH of Zygosaccharomyces bailii, and its implications in weak‐acid resistance
Authors: Cole Martin B. , Keenan Michael H. J.
Published: May 2005

Weak acids and hydrogen ions in different concentration combinations affect the intracellular pH value (pHi) of Zygosaccharomyces bailii. The lowest pHi value measured was not at the most extreme, but at intermediate conditions of inhibition. Proton and organic‐acid ejection, on a cell volume basis, is greater in cells grown under inhibitory conditions and is stimulated by weak acids, whilst in cells not grown under inhibitory conditions acid efflux is lower and is depressed by weak acids; this may be important in the maintenance of tolerable pHi values in the presence of weak acids. The concentration of benzoic acid measured internally is identical to the value expected from its pK, external pH and pHi. Addition of fructose to starved cells causes both a decreased pHi and a concomitant efflux of previously loaded benzoic acid, quantitatively in accord with the shift in equilibrium of the freely permeable undissociated acid. There is no evidence that weak acids are actively extruded. Protoplast volume also varies with hydrogen‐ion and weak‐acid concentration and this too may play a role in intracellular pH maintenace.
Proliferation of microbodies in Saccharomyces cerevisiae
Authors: Veenhuis M. , Mateblowski M. , Kunau W. H. , Harder W.
Published: May 2005

The development of microbodies in the yeast Saccharomyces cerevisiae was studied in response to different conditions of growth. Various strains of S. cerevisiae were investigated, using cells from the exponential growth phase on glucose as an inocullum in all transfer experiments. Electron microscopy, including serial sectioning, revealed that these cells generally contained one to four small microbodies which were localized in the vicinity of the cell wall and characterized by the presence of catalase. Transfer of these glucose‐grown cells into media supplemented with various compounds known to induce microbody proliferation in other yeasts—i.e. uric acid, alkylated amines, amino acids, C2‐compounds such as ethanol or acetate, in the presence or absence of compounds that induce oxygen radical formation—did not result in a significant change in the number of microbody profiles observed. Marked microbody proliferation was, however, observed after a shift of cells into media containing oleic acid and was associated with the induction of activities of β‐oxidation enzymes. In addition, catalase and isocitrate lyase were present in enhanced levels. Kinetic experiments suggested that these microbodies developed from those originally present in the inoculum cells. In thin sections up to 14 microbody profiles were occasionally observed, often present in small clusters. Their ultimate volume fraction amounted to 8–10% of the cytoplasmic volume.
Cyclic AMP controls the switch between division cycle and resting state programs in response to ammonium availability in Saccharomyces cerevisiae
Authors: Boy‐Marcotte Emmanuelle , Garreau Hervé , Jacquet Michel
Published: May 2005

We have identified a mutation called rcal (for rescue by cAMP) which allows adenylate cyclase‐deficient mutants to divide in the presence of cAMP. We took advantage of this rcal mutation to study the effect of externally added cAMP on the onset of the resting state when cells are starved for ammonium. We measured the resistance of the cells to zymolyase treatment as a parameter of the resting state. We observed that the onset of the resting state is reversibly blocked by cAMP. This inhibitory effect of cAMP is discussed together with the cAMP control of the start. This leads us to propose a model in which the cAMP level, controlled by the availability of nutrients, should trigger the choice between the entry of the cell into the resting state and the initiation of a new division cycle.
Protein phosphorylation in yeast mitochondria: cAMP‐Dependence, submitochondrial localization and substrates of mitochondrial protein kinases
Authors: Müller Günter , Bandlow Wolfhard
Published: May 2005

We describe the identification and submitochondrial localization of four protein kinases and of their target proteins in derepressed yeast mitochondria. The activity of one of the kinases depends on the presence of cyclic AMP (cAMP). It is soluble and localized in the mitochondrial intermembrane space. Its natural target is a polypeptide of 40 kDa molecular mass, which is bound to the inner membrane. Besides this natural target this kinase phosphorylates acidic heterologous proteins, like casein, with high efficiency. The other protein kinases identified so far are cAMP‐independent. At least one is localized in the matrix having its natural substrates (49 and 24 kDa) in the same compartment. Two others are firmly bound to the inner membrane phosphorylating target proteins in the inner membrane (52·5 kDa) and in the intermembrane space (17·5 kDa), respectively.
A nuclear gene required for the expression of the linear DNA‐asociated killer system in the yeast Kluyveromyces lactis
Authors: Wesolowski‐Louvel Micheline , Tanguy‐Rougeau Christine , Fukuhara Hiroshi
Published: May 2005

The killer system of Kluveromyces lactis is associated with two linear DNA plasmids, pGKL1 and pGKL2. The killer toxin and the immunity determinant are coded for by pGKL1. Mutations which we have named KEX1. The KEX1 gene of K. lactis has been cloned by complementation of kex1 mutations by using a recombinant plasmid pool containing the entire Kluyveromyces lactis genome, on a multicopy plasmid KEp6, which contains the Saccharomyces cerevisiae URA3 gene as a marker. Genetic analyses of strains carrying a distrupted kex1 allele demonstrated that the cloned DNA corresponded to the KEX1 gene. The cloned KEX1 gene of K. lactis has low but significant sequence homology with the KEX2 gene of Saccharomyces cerevisiae. In vivo complementation of the kex1 mutations of K. lactis by the KEX2 gene of S. cerevisiae, and complementation of the kex2 mutations of S. Cerevisiae by the KEX1 gene of K. lactis, demonstrated that KEX1 of K. Lactis is functionally related to the KEX2 gene of S. cerevisiae. K. lactis diploids homozygous for kex1 are deficient for sporulation.
Substrate specificity of alcohol dehydrogenase from the yeast Hansenyls polymorpha CBS 4732 and Candida utilis CBS 621
Authors: Verduyn Cornelis , Breedveld Guido J. , Scheffers W. Alexander , Van Dijken Johnnes P.
Published: May 2005

The substrate specificity of alcohol dehydrogenase (ADH) from Hansenula polymorpha and Candida utilis has been compared with that of the classical ADH from baker's yeast. Cell‐free extracts of H. polymorpha and C. utilis exhibited a much higher ratio of butanol to ethanol oxidation than baker's yeast ADH. This was also observed with the purified enzymes. The ratio of activities with ethanol and butanol was pH‐dependent. With the baker's yeast enzyme the activity strongly decreased with increasing chain length, whereas the enzymes form H. polymorpha and C. utilis showed a high reactivity with long‐chain alcohols. In addition, the affinity constant for ethanol was more than tenfold lower than that of the baker's yeast enzyme. The purified preparation yielded several protein bands on polyacrylamide slab gels, each of which showed activity with both ethanol and butanol.
Extraction and rapid inactivation of proteins from Saccharomyces cerevisiae by trichloroacetic acid precipitation
Authors: Wright Anthony P. H. , Bruns Michael , Hartley Brian S.
Published: May 2005

Methods currently used for the extraction of proteins from yeast involve relatively long time periods between sampling cells from a culture and analysis of their proteins by polyacrylamide gel electrophoresis–sodium dodecylsulphate. Often it is desirable to inactivate cellular metabolism rapidly after sampling and here we show that trichloroacetic acid precipitation techniques, often used for rapid extraction and inactivation of proteins from higher eukaryotes, can be adapted for use with organisms which have cell walls.
Sequence and mutational analysis of ESS1, a gene essential for growth in Saccharomyces cerevisiae
Authors: Hanes Steven D. , Shank Peter R. , Bostian Keith A.
Published: May 2005

A newly isolated gene, ESS1, was shown to encode a protein required for vegetative growth in Saccharomyces cerevisiae. The nucleotide sequence of ESS1 revealed a 172 amino acid open reading frame predicting a highly basic, 19·5 kilodalton product. Although the gene was isolated by cross‐hybridization with the vertebrate v‐sis oncogene, the primary amino acid sequence bears only a slight resemblance to the p28sis protein. ESS1 was shown to be single copy in the yeast genome and transcriptionally active during logarithmic growth. It is located on the right arm of chromosome X, 6 centimorgans distal to ilv3. The genetic map location indicates it is not allelic to any previously characterized mutation in this organism. Both inactivation of ESS1 by gene disruption and overexpression by fusion to a heterologous promoter were detrimental to growth in both haploid and diploid cell types. Under non‐permissive conditions, the terminal phenotype of strains containing a suppressible amber mutation within ESS1 was one of aberrant multibudded structures. Examination of this morphology indicates that loss of ESS1 function may lead to a defect in cytokinesis or cell separation.
Size distribution and general structural features of N‐linked oligosaccharides from the methylotrophic yeast, Pichia pastoris
Authors: Grinna Lynn S. , Tschopp Juerg F.
Published: May 2005

The secreted glycoproteins of Pichia pastoris contain more than 35% of their N‐linked oligosaccharides as structures smaller than Man14GlcNAc2 (Man = mannose; GlcNAc = N‐acetylglucosamine). On heterologous invertase produced in P. pastoris, approximately 85% of the oligosaccharides are in the size range Man8–14GlcNAc2. The structures appear to contain α‐linked mannose. In addition, one‐third of the structures contain net negative charge and can be radio‐labelled in vivo with 32P. The largest oligosaccharides isolated from P. pastoris are significantly shorter than the hypermannosylated structures typical of S. cerevisiae, indicating that the factors which influence the processing of N‐linked oligosaccharides in P. pastoris are different from those which influence processing in S. cerevisiae. The smaller N‐linked oligosaccharides synthesized by P. pastoris resemble high‐mannose oligosaccharides synthesized by animal cells, and this finding increases the utility of P. pastoris as a host for the production of heterologous glycoproteins.
Two pathways of DNA double‐strand break repair in G1 cells of Saccharomyces cerevisiae
Authors: Glasunov Alexander V. , Glaser Vadim M. , Kapultsevich Yuri G.
Published: May 2005

G1 cells of the diploid yeast Saccharomyces cerevisiae are known to be capable of a slow repair of DNA double‐strand breaks (DSB) during holding the cells in a non‐nutrient medium (Luchnik et al., 1977; Frankenberg‐Schwager et al., 1980). In the present paper, S. cerevisiae cells γ‐irradiated in the G1 phase of the cell cycle are shown to be capable of fast repair of DNA DSB; this process is completed within 30‒40 min, of holding the cells in water at 28°C. For this reason, the kinetics of DNA DSB repair during holding the cells in a non‐nutrient medium are biphasic, i.e., the first ‘fast’ phase is completed within 30‒40 min, whereas the second, ‘slow’ phase is completed within 48 h. Mututions rad51, rad52, rad54 and rad55 inhibit the fast repair of DNA DSB, whereas mutations rad50, rad53 and rad57 do not significantly influence this process.

It has been shown that the observed fast and slow repair of DNA DSB in the G1 diploid cells of S. cerevisiae are separate pathways of DNA DSB repair in yeast.
5′‐Secondary structure formation, in constrast to a short string of non‐preferred codons, inhibits the translation of the pyruvate kinase mRNA in yeast
Authors: Bettany Andrew J. E. , Moore Paul A. , Cafferkey Robert , Bell Les D. , Goodey Andrew R. , Carter Bruce L. A. , Brown Alistair J. P.
Published: May 2005

The effects of poor codon bias and secondary structure formation upon the translation of the pyruvate kinase (PYK1) mRNA have been investigated in Saccharomyces cerevisiae. Following insertion mutagenesis at the 5′‐end of the PYK1 coding region, the gene was transformed into yeast, and translation assessed directly in vivo by determining the distribution of the modified PYK1 mRNAs across polysomes fractionated by sucrose density gradient centrifugation. The chromosomally‐encoded (wild‐type) PYK1 mRNA, and the actin, ribosomal protein L3 and glyceraldehyde‐3‐phosphate dehydrogenase mRNAs were used to control for minor differences between polysome preparations. An insertion containing 13 non‐preferred codons at the 5′‐end of the coding region was found to have no significant effect upon PYK1 mRNA translation. In contrast, translation was inhibited by an insertion which increased the formation of secondary structures at the 5′‐end of the mRNA (overall ΔG = −36·6 kcal/mol). Control insertions were also analysed to exclude the possibility that alterations to the amino acid sequence of pyruvate kinase affect the translation of its mRNA. These insertions, which introduced preferred codons or restored wild‐type levels of secondary structure formation, did not significantly influence PYK1 mRNA translation.
Cloning and sequencing of the gene for apocytochrome b of the yeast Kluyveromyces lactis strains WM27 (NRRL Y‐17066) and WM37 (NRRL Y‐1140)
Authors: Brunner Aurora , Coria Roberto
Published: May 2005

The apocytochrome b genes from two strains of the yeast Kluyveromyces lactis, have been isolated and sequenced. The coding sequences in strains WM27 (NRRL Y‐17066) and WM37 (NRRL Y‐1140) were identical but the upstream noncoding regions were slightly different. The sequences demonstrated the presence of a continuous open reading frame with no introns. The amino acid sequence, derived from the coding strand, showed 82% homology to the apocytochrome b of Saccharomyces cerevisiae strain D273–10B and only 58% homology to the protein from Schizosaccharomyces pombe strain 50. CUN and CGN codon families were absent from the K. lactis gene. Codon usage was very similar to that of other mitochondrial genomes with mostly U or A in the third position. There were two unusual features. All threonines were coded by ACA(U) and all arginines by AGA.
Characterization of the adr1‐1 nonsense mutation identifies the translational start of the yeast transcriptional activator ADR1
Authors: Bemis Lynne T. , Denis Clyde L.
Published: May 2005

We have characterized a nonsense mutation in the ADR1 gene that identifies the translational start of the ADR1 protein. The ADR1 gene of Saccharomyces cerevisiae is required for synthesis of the glucose‐repressible alcohol dehydrogenase (ADH2). The adr1‐1 mutation, which inhibits ADH2 expression, was identified as a C to G transversion at base pair +32. This alteration would result in a UGA nonsense codon in place of a serine codon that would lead to termination of the ADR1 polypeptide after the 10th amino acid. The effect of the adr1‐1 mutation was partially reversed by UGA‐tRNA suppressors, indicating that the adr1‐1 mutation affects ADR1 expression at the translational level. These observations establish that the first available AUG in the ADR1 sequence is used as the translational start site of ADR1. Tyrosine or leucine UGA‐tRNA‐suppressors resulted in levels of adr1‐1 activity similar to that found for a serine UGA‐tRNA‐suppressor, suggesting that serine residue‐11 is not essential to ADR1 function. Northern analyses showed that the 5·1 kb ADR1 mRNA was two‐ to three‐fold more abundant when isolated from a strain carrying the ADR1 allele than from an isogenic strain containing the adr1‐1 allele. These data confirm that the 5·1 kb mRNA is the ADR1 mRNA and suggest that inhibition of adr1‐1 mRNA translation results in more rapid degradation of the adr1‐1 mRNA.