Showing papers by "University of Ljubljana published in 2009"

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Abstract: mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

The Seventh Data Release of the Sloan Digital Sky Survey

Abstract: This paper describes the Seventh Data Release of the Sloan Digital Sky Survey (SDSS), marking the completion of the original goals of the SDSS and the end of the phase known as SDSS-II. It includes 11,663 deg^2 of imaging data, with most of the ~2000 deg^2 increment over the previous data release lying in regions of low Galactic latitude. The catalog contains five-band photometry for 357 million distinct objects. The survey also includes repeat photometry on a 120° long, 2°.5 wide stripe along the celestial equator in the Southern Galactic Cap, with some regions covered by as many as 90 individual imaging runs. We include a co-addition of the best of these data, going roughly 2 mag fainter than the main survey over 250 deg^2. The survey has completed spectroscopy over 9380 deg^2; the spectroscopy is now complete over a large contiguous area of the Northern Galactic Cap, closing the gap that was present in previous data releases. There are over 1.6 million spectra in total, including 930,000 galaxies, 120,000 quasars, and 460,000 stars. The data release includes improved stellar photometry at low Galactic latitude. The astrometry has all been recalibrated with the second version of the USNO CCD Astrograph Catalog, reducing the rms statistical errors at the bright end to 45 milliarcseconds per coordinate. We further quantify a systematic error in bright galaxy photometry due to poor sky determination; this problem is less severe than previously reported for the majority of galaxies. Finally, we describe a series of improvements to the spectroscopic reductions, including better flat fielding and improved wavelength calibration at the blue end, better processing of objects with extremely strong narrow emission lines, and an improved determination of stellar metallicities.

The nature and experience of entrepreneurial passion

Abstract: Entrepreneurial passion plays an important role in entrepreneurship, but theoretical understanding of what it is and what it does is lacking. We build on fragmented and disparate extant work to conceptualize the nature of entrepreneurial passion associated with salient entrepreneurial role identities. We also theorize the mechanisms of the experience of entrepreneurial passion that provide coherence to goal-directed cognitions and behaviors during the pursuit of entrepreneurial effectiveness.

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

Abstract: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

SEGUE: A SPECTROSCOPIC SURVEY OF 240,000 STARS WITH g = 14-20

Abstract: The Sloan Extension for Galactic Understanding and Exploration (SEGUE) Survey obtained {approx}240,000 moderate-resolution (R {approx} 1800) spectra from 3900 {angstrom} to 9000 {angstrom} of fainter Milky Way stars (14.0 10 per resolution element, stellar atmospheric parameters are estimated, including metallicity, surface gravity, and effective temperature. SEGUE obtained 3500 deg{sup 2} of additional ugriz imaging (primarily at low Galactic latitudes) providing precise multicolor photometry ({sigma}(g, r, i) {approx} 2%), ({sigma}(u, z) {approx} 3%) and astrometry ({approx}0.1) for spectroscopic target selection. The stellar spectra, imaging data, and derived parameter catalogs for this survey are publicly available as part of Sloan Digital Sky Survey Data Release 7.

Updated clinical diagnostic criteria for sporadic Creutzfeldt-Jakob disease

Abstract: Several molecular subtypes of sporadic Creutzfeldt–Jakob disease have been identified and electroencephalogram and cerebrospinal fluid biomarkers have been reported to support clinical diagnosis but with variable utility according to subtype. In recent years, a series of publications have demonstrated a potentially important role for magnetic resonance imaging in the pre-mortem diagnosis of sporadic Creutzfeldt–Jakob disease. Magnetic resonance imaging signal alterations correlate with distinct sporadic Creutzfeldt–Jakob disease molecular subtypes and thus might contribute to the earlier identification of the whole spectrum of sporadic Creutzfeldt–Jakob disease cases. This multi-centre international study aimed to provide a rationale for the amendment of the clinical diagnostic criteria for sporadic Creutzfeldt–Jakob disease. Patients with sporadic Creutzfeldt–Jakob disease and fluid attenuated inversion recovery or diffusion-weight imaging were recruited from 12 countries. Patients referred as ‘suspected sporadic Creutzfeldt–Jakob disease’ but with an alternative diagnosis after thorough follow up, were analysed as controls. All magnetic resonance imaging scans were assessed for signal changes according to a standard protocol encompassing seven cortical regions, basal ganglia, thalamus and cerebellum. Magnetic resonance imaging scans were evaluated in 436 sporadic Creutzfeldt–Jakob disease patients and 141 controls. The pattern of high signal intensity with the best sensitivity and specificity in the differential diagnosis of sporadic Creutzfeldt–Jakob disease was identified. The optimum diagnostic accuracy in the differential diagnosis of rapid progressive dementia was obtained when either at least two cortical regions (temporal, parietal or occipital) or both caudate nucleus and putamen displayed a high signal in fluid attenuated inversion recovery or diffusion-weight imaging magnetic resonance imaging. Based on our analyses, magnetic resonance imaging was positive in 83% of cases. In all definite cases, the amended criteria would cover the vast majority of suspected cases, being positive in 98%. Cerebral cortical signal increase and high signal in caudate nucleus and putamen on fluid attenuated inversion recovery or diffusion-weight imaging magnetic resonance imaging are useful in the diagnosis of sporadic Creutzfeldt–Jakob disease. We propose an amendment to the clinical diagnostic criteria for sporadic Creutzfeldt–Jakob disease to include findings from magnetic resonance imaging scans.

Frequency and Evolution of Azole Resistance in Aspergillus fumigatus Associated with Treatment Failure

Abstract: Azoles are the mainstay of oral therapy for aspergillosis. Azole resistance in Aspergillus has been reported infrequently. The first resistant isolate was detected in 1999 in Manchester, UK. In a clinical collection of 519 A. fumigatus isolates, the frequency of itraconazole resistance was 5%, a significant increase since 2004 (p<0.001). Of the 34 itraconazole-resistant isolates we studied, 65% (22) were cross-resistant to voriconazole and 74% (25) were cross-resistant to posaconazole. Thirteen of 14 evaluable patients in our study had prior azole exposure; 8 infections failed therapy (progressed), and 5 failed to improve (remained stable). Eighteen amino acid alterations were found in the target enzyme, Cyp51A, 4 of which were novel. A population genetic analysis of microsatellites showed the existence of resistant mutants that evolved from originally susceptible strains, different cyp51A mutations in the same strain, and microalterations in microsatellite repeat number. Azole resistance in A. fumigatus is an emerging problem and may develop during azole therapy.

Explaining microbial population genomics through phage predation

Abstract: Not all isolates of a species contain the same set of genes. In this Opinion article, Rodriguez-Valera and colleagues propose the constant-diversity model to account for these differences. In this model, predation by phages promotes bacterial diversity and allows more efficient use of the nutrients in the environment. The remarkable differences that have been detected by metagenomics in the genomes of strains of the same bacterial species are difficult to reconcile with the widely accepted paradigm that periodic selection within bacterial populations will regularly purge genomic diversity by clonal replacement. We have found that many of the genes that differ between strains affect regions that are potential phage recognition targets. We therefore propose the constant-diversity dynamics model, in which the diversity of prokaryotic populations is preserved by phage predation. We provide supporting evidence for this model from metagenomics, mathematical analysis and computer simulations. Periodic selection and phage predation dynamics are not mutually exclusive; we compare their predictions to shed light on the ecological circumstances under which each type of dynamics could predominate.

Measurement of the differential branching fraction and forward-backward asymmetry for B --> K(*)l+l-.

Abstract: We study B -> Kd(*)l(+)l(-) decays (l = e,u) based on a data sample of 657 x 10(6) B (B) over bar pairs collected with the Belle detector at the KEKB e(+)e(-) collider. We report the differential branching fraction, isospin asymmetry, K* polarization, and the forward-backward asymmetry (A(FB)) as functions of q(2) = M(ll)(2)c(2). The fitted A(FB) spectrum exceeds the standard model expectation by 2.7 standard deviations. The measured branching fractions are B(B -> K*l(+)l(-)) = (10: 7(-1.0)(+1.1)) x 10(-7) and B(B -> Kl(+)l(-)) = (4.8 (+0.5)(-0.4) +/- 0.3) x 10(-7), where the first errors are statistical and the second are systematic, with the muon to electron ratios R-K* = 0.83 +/- 0: 17 +/- 0.08 and R-K = 1.03 +/- 0.19 +/- 0.06.

Electrically tunable liquid crystal optical microresonators

Abstract: Whispering-gallery-mode resonators made of nematic liquid-crystal droplets offer a wavelength tunability approximately two orders of magnitude larger than that of conventional solid-state microresonators.

Multi-attribute Decision Analysis in GIS: Weighted Linear Combination and Ordered Weighted Averaging

Abstract: Multi-attribute Decision Analysis in GIS: Weighted Linear Combination and Ordered Weighted Averaging

Substructure revealed by RR Lyraes in SDSS Stripe 82

Abstract: We present an analysis of the substructure revealed by RR Lyraes in Sloan Digital Sky Survey Stripe 82, which covers 2°5 in declination on the celestial equator over the right ascension range α = 20 h 7 to 3 h 3 We use the new public archive of light-motion curves in Stripe 82, published by Bramich et al in 2008, to identify a set of high-quality RR Lyrae candidates Period estimates are determined to high accuracy using a string-length method A subset of 178 RR Lyraes with spectrally derived metallicities are employed to derive metallicity-period-amplitude relations, which are then used, together with archive magnitude data and light-curve Fourier decomposition, to estimate metallicities and hence distances for the entire sample The RR Lyraes lie 5-115 kpc from the Galactic Centre, with distance estimates accurate to ∼8 per cent The RR Lyraes are further divided into subsets of 316 RRab types and 91 RRc types based on their period, colour and metallicity We fit a smooth density law to the distribution as a simple representation of the data For Galactocentric radii 5-25 kpc the number density of RR Lyraes falls as r ―2,4 , but beyond 25 kpc, the number density falls much more steeply, as r ―45 However, we stress that in practice the density distribution is not smooth, but dominated by clumps and substructure Samples of 55 and 237 RR Lyraes associated with the Sagittarius Stream and the Hercules-Aquila Cloud, respectively, are identified Hence, ∼70 per cent of the RR Lyraes in Stripe 82 belong to known substructure, and the sharp break in the density law reflects the fact that the dominant substructure in Stripe 82 - the Hercules-Aquila Cloud and the Sagittarius Stream -lie within 40 kpc In fact, almost 60 per cent of all the RR Lyraes in Stripe 82 are associated with the Hercules-Aquila Cloud alone, which emphasizes the cloud's pre-eminence Additionally, evidence of a new and distant substructure - the Pisces Overdensity ― is found, consisting of 28 faint RRLyraes centred on Galactic coordinates (l ≈ 80°, b ≈ -55°), with distances of ∼80 kpc The total stellar mass in the Pisces Overdensity is ∼10 4 M ⊙ and its metallicity is [Fe/H]∼ ―15

Comet Assay measurements: a perspective

Abstract: The Comet Assay or single cell gel electrophoresis assay is one of the very widely used assays to microscopically detect DNA damage at the level of a single cell. The determination of damage is carried out either through visual scoring of cells (after classification into different categories on the basis of tail length and shape) or by using different commercially available or public domain software (which automatically recognise the extent of damage). In this assay, the shape, size and amount of DNA within the ‘comet’ play important roles in the determination of the level of damage. The use of a software in particular also provides a range of different parameters, many of which might not be relevant in determining the extent of DNA damage. As a large number of factors could influence the shape, size, identification and determination of induced damage, which includes the scoring criteria, staining techniques, selection of parameters (whilst using the software packages) and appearance of ‘hedgehog’ or ‘clouds’, this article aims (a) to provide an overview of evolution of measurements of DNA damage using the Comet Assay and (b) to summarise and critically analyse the advantages and disadvantages of different approaches currently being adopted whilst using this assay. It is suggested that judicious selection of different parameters, staining methods along with inter-laboratory validation and harmonisation of methodologies will further help in making this assay more robust and widely acceptable for scientific as well as regulatory studies.

The bacterial LexA transcriptional repressor.

Abstract: Bacteria respond to DNA damage by mounting a coordinated cellular response, governed by the RecA and LexA proteins. In Escherichia coli, RecA stimulates cleavage of the LexA repressor, inducing more than 40 genes that comprise the SOS global regulatory network. The SOS response is widespread among bacteria and exhibits considerable variation in its composition and regulation. In some well-characterised pathogens, induction of the SOS response modulates the evolution and dissemination of drug resistance, as well as synthesis, secretion and dissemination of the virulence. In this review, we discuss the structure of LexA protein, particularly with respect to distinct conformations that enable repression of SOS genes via specific DNA binding or repressor cleavage during the response to DNA damage. These may provide new starting points in the battle against the emergence of bacterial pathogens and the spread of drug resistance among them.

Incremental dynamic analysis with consideration of modeling uncertainties

Abstract: Incremental dynamic analysis (IDA) has been extended by introducing a set of structural models in addition to the set of ground motion records which is employed in IDA analysis in order to capture record-to-record variability. The set of structural models reflects epistemic (modeling) uncertainties, and is determined by utilizing the latin hypercube sampling (LHS) method. The effects of both aleatory and epistemic uncertainty on seismic response parameters are therefore considered in extended IDA analysis. The proposed method has been applied to an example of the four-storey-reinforced concrete frame, for which pseudo-dynamic tests were performed at the ELSA Laboratory, Ispra. The influence of epistemic uncertainty on the seismic response parameters is presented in terms of summarized IDA curves and dispersion measures. The results of extended IDA analysis are compared with the results of IDA analysis, and the sensitivity of the seismic response parameters to the input random variable using the LHS method is discussed. It is shown that epistemic uncertainty does not have significant influence on the seismic response parameters in the range far from collapse, but could have a significant influence on collapse capacity.

Landau–de Gennes modelling of nematic liquid crystal colloids

Abstract: Phenomenological Landau–de Gennes modelling based on the free energy of nematic liquid crystal colloids is reviewed. Nematic phase, gradient of order, and surface anchoring contributions to the total free energy are used. The numerical finite difference relaxation technique is explained as an efficient tool for the minimisation of the free energy. Effects of the mesh and mesh allocation are discussed. Various conceptually different colloidal structures are calculated to show the universality of the model. Single particles, dipolar–quadrupolar dimers, entangled dimers, dimers bound by escaped hyperbolic rings, and hierarchically patterned Saturn-ring colloidal superstructures are presented.

Transmission of Drug-Resistant HIV-1 Is Stabilizing in Europe

Abstract: The SPREAD Programme investigated prospectively the time trend from September 2002 through December 2005 of trans- mitted drug resistance (TDR) among 2793 patients in 20 European countries and in Israel with newly diagnosed human immunodeficiency virus type 1 (HIV-1) infection. The overall prevalence of TDR was 8.4% (225 of 2687 patients; 95% confidence interval [CI], 7.4%-9.5%), the prevalence of nucleoside reverse-transcriptase inhibitor (NRTI) resistance was 4.7% (125 of 2687 patients; 95% CI, 3.9%-5.5%), the prevalence of nonucleoside reverse-transcriptase inhibitor (NNRTI) resistance was 2.3% (62 of 2687 patients; 95% CI, 1.8%-2.9%), and the prevalence of protease inhibitor (PI) resistance was 2.9% (79 of 2687 patients; 95% CI, 2.4%-3.6%). There was no time trend in the overall TDR or in NRTI resistance, but there was a statistically significant decrease in PI resistance (P = .04) and in NNRTI resistance after an initial increase (P = .02). We found that TDR appears to be stabilizing in Europe, consistent with recent reports of decreasing drug resistance and improved viral sup- pression in patients treated for HIV-1 infection.

General minimal flavor violation

Abstract: A model independent study of the minimal flavor violation (MFV) framework is presented, where the only sources of flavor breaking at low energy are the up and down Yukawa matrices. Two limits are identified for the Yukawa coupling expansion: linear MFV, where it is truncated at the leading terms, and nonlinear MFV, where such a truncation is not possible due to large third generation Yukawa couplings. These are then resummed to all orders using nonlinear $\ensuremath{\sigma}$-model techniques familiar from models of collective breaking. Generically, flavor-diagonal $CP$ violating (CPV) sources in the UV can induce $O(1)$ CPV in processes involving third generation quarks. Because of a residual $U(2)$ symmetry, the extra CPV in ${B}_{d}\ensuremath{-}{\overline{B}}_{d}$ mixing is bounded by CPV in ${B}_{s}\ensuremath{-}{\overline{B}}_{s}$ mixing. If operators with right-handed light quarks are subdominant, the extra CPV is equal in the two systems, and is negligible in processes involving only the first two generations. We find large enhancements in the up-type sector, both in CPV in $D\ensuremath{-}\overline{D}$ mixing and in top flavor violation.

Rhodanine as a privileged scaffold in drug discovery.

Abstract: Rhodanines, thiazolidine-2,4-diones and pseudothiohydantoins have become a very interesting class of heterocyclic compounds since the introduction of various glitazones and epalrestat into clinical use for the treatment of type II diabetes mellitus and diabetic complications, respectively. Chemical modifications of these heterocycles constantly result in compounds with a wide spectrum of pharmacological activities. 5-Arylidenerhodanines are frequently identified as potent hits in high throughput screening against various prokaryotic and eukaryotic targets. Synthesis of substituted rhodanines, based on high throughput screening hits, often leads to potent and selective modulators of targeted enzymes or receptors, which exert their pharmacological activities through different mechanisms of action. Due to various possibilities of chemical derivatization of the rhodanine ring, rhodanine-based compounds will probably remain a privileged scaffold in drug discovery. We have therefore reviewed their biological activities, mechanism of action, structure activity relationship and selectivity against other targets.

Database of cattle candidate genes and genetic markers for milk production and mastitis.

Abstract: Summary A cattle database of candidate genes and genetic markers for milk production and mastitis has been developed to provide an integrated research tool incorporating different types of information supporting a genomic approach to study lactation, udder development and health. The database contains 943 genes and genetic markers involved in mammary gland development and function, representing candidates for further functional studies. The candidate loci were drawn on a genetic map to reveal positional overlaps. For identification of candidate loci, data from seven different research approaches were exploited: (i) gene knockouts or transgenes in mice that result in specific phenotypes associated with mammary gland (143 loci); (ii) cattle QTL for milk production (344) and mastitis related traits (71); (iii) loci with sequence variations that show specific allele-phenotype interactions associated with milk production (24) or mastitis (10) in cattle; (iv) genes with expression profiles associated with milk production (207) or mastitis (107) in cattle or mouse; (v) cattle milk protein genes that exist in different genetic variants (9); (vi) miRNAs expressed in bovine mammary gland (32) and (vii) epigenetically regulated cattle genes associated with mammary gland function (1). Fourty-four genes found by multiple independent analyses were suggested as the most promising candidates and were further in silico analysed for expression levels in lactating mammary gland, genetic variability and top biological functions in functional networks. A miRNA target search for mammary gland expressed miRNAs identified 359 putative binding sites in 3¢UTRs of candidate genes.