Josef Stefan Institute

Ljubljana, Slovenia

Josef Stefan Institute

Ljubljana, Slovenia
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Zupunski V.,University of Ljubljana | Kordis D.,Josef Stefan Institute
Scientific Reports | Year: 2016

S1 family of serine peptidases is the largest family of peptidases. They are specifically inhibited by the Kunitz/BPTI inhibitors. Kunitz domain is characterized by the compact 3D structure with the most important inhibitory loops for the inhibition of S1 peptidases. In the present study we analysed the action of site-specific positive selection and its impact on the structurally and functionally important parts of the snake venom Kunitz/BPTI family of proteins. By using numerous models we demonstrated the presence of large numbers of site-specific positively selected sites that can reach between 30-50% of the Kunitz domain. The mapping of the positively selected sites on the 3D model of Kunitz/BPTI inhibitors has shown that these sites are located in the inhibitory loops 1 and 2, but also in the Kunitz scaffold. Amino acid replacements have been found exclusively on the surface, and the vast majority of replacements are causing the change of the charge. The consequence of these replacements is the change in the electrostatic potential on the surface of the Kunitz/BPTI proteins that may play an important role in the precise targeting of these inhibitors into the active site of S1 family of serine peptidases. © The Author(s) 2016.

Ligeti Z.,Lawrence Berkeley National Laboratory | Papucci M.,Institute for Advanced Study | Perez G.,Weizmann Institute of Science | Zupan J.,University of Ljubljana | And 2 more authors.
Physical Review Letters | Year: 2010

The D0 Collaboration reported a 3.2σ deviation from the standard model (SM) prediction in the like-sign dimuon asymmetry. Assuming that new physics contributes only to Bd,s mixing, we show that the data can be analyzed without using the theoretical calculation of ΔΓs, allowing for robust interpretations. We find that this framework gives a good fit to all measurements, including the recent CDF Collaboration Sψ result. The data allow universal new physics with similar contributions relative to the SM in the Bd and Bs systems, but favors a larger deviation in Bs than in Bd mixing. The general minimal flavor violation framework with flavor diagonal CP violating phases can account for the former case and remarkably even for the latter case. This observation makes it simpler to speculate about which extensions with general flavor structure may also fit the data. © 2010 The American Physical Society.

Drobnak J.,Josef Stefan Institute | Kamenik J.F.,Josef Stefan Institute | Kamenik J.F.,University of Ljubljana | Zupan J.,University of Cincinnati
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

We show that the charge asymmetry in tt̄ production at the LHC, A C, and the forward-backward asymmetry at the Tevatron, A FB, are in general not tightly correlated. They can even have opposite signs if the underlying new physics (NP) model is general enough. We demonstrate this using two examples of NP: a light axigluon, and a vector that is a color octet and electroweak triplet. The small value of A C measured at the LHC is thus shown not to exclude a NP interpretation of the anomalously large A FB at the Tevatron. We identify two observables where significant NP effects are still expected at the Tevatron and the LHC, the bb̄ production forward-backward asymmetry and spin polarizations of the pair-produced tops and antitops. © 2012 American Physical Society.

Kopp J.,Fermi National Accelerator Laboratory | Schwetz T.,Max Planck Institute for Nuclear Physics | Zupan J.,University of Ljubljana | Zupan J.,Josef Stefan Institute
Journal of Cosmology and Astroparticle Physics | Year: 2010

We perform a global fit to data from Dark Matter (DM) direct detection experiments, including the recent CDMS-II results. We discuss possible interpretations of the DAMA annual modulation signal in terms of spin-independent and spin-dependent DM-nucleus interactions, both for elastic and inelastic scattering. We find that for the spin-dependent inelastic scattering off protons a good fit to all data is obtained. We present a simple toy model realizing such a scenario. In all the remaining cases the DAMA allowed regions are disfavored by other experiments or suffer from severe fine tuning of DM parameters with respect to the galactic escape velocity. Finally, we also entertain the possibility that the two events observed in CDMS-II are an actual signal of elastic DM scattering, and we compare the resulting CDMS-II allowed regions to the exclusion limits from other experiments. © 2010 IOP Publishing Ltd and SISSA.

SelectfluorTM F-TEDA-BF4 (1-chloromethyl-4-fluoro-1, 4-diazoniabicyclo [2.2.2]octane bis(tetrafluoroborate) is not only one of the most efficient and popular reagents for electrophilic fluorination, but as a strong oxidant is also a convenient mediator or catalyst of several "fluorine-free" functionalizations of organic compounds. Its applications as a mediator in transformations of oxidizable functional groups or gold-catalyzed C-C and C-heteroatom oxidative coupling reactions, a catalyst in formation of various heterocyclic rings, a reagent or catalyst of various functionalizations of electron-rich organic compounds (iodination, bromination, chlorination, nitration, thiocyanation, sulfenylation, alkylation, alkoxylation), a catalyst of one-pot-multicomponent coupling reactions, a catalyst of regioselective ring opening of epoxides, a deprotection reagent for various protecting groups, and a mediator for stereoselective rearrangement processes of bicyclic compounds are reviewed and discussed.

Kamenik J.F.,Josef Stefan Institute | Kamenik J.F.,University of Ljubljana | Zupan J.,Josef Stefan Institute | Zupan J.,University of Ljubljana | Zupan J.,University of Cincinnati
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2011

We show that the discovery channel for dark matter (DM) production at colliders can be through flavor violating interactions resulting in a novel signature of a single top and large missing transverse energy. We discuss several examples where the production of DM is dominated by flavor violating couplings: minimal flavor violating models with a large bottom Yukawa, models with horizontal symmetries, and DM in nontrivial flavor group representations. Discovery at the 7 TeV LHC with a few fb -1 may already be possible. © 2011 American Physical Society.

Kokosar J.,Josef Stefan Institute | Kordis D.,Josef Stefan Institute
Molecular Biology and Evolution | Year: 2013

Molecular domestications of transposable elements have occurred repeatedly during the evolution of eukaryotes. Vertebrates, especially mammals, possess numerous single copy domesticated genes (DGs) that have originated from the intronless multicopy transposable elements. However, the origin and evolution of the retroelement-derived DGs (RDDGs) that originated from Metaviridae has been only partially elucidated, due to absence of genome data or to limited analysis of a single family of DGs. We traced the genesis and regulatory wiring of the Metaviridae-derived DGs through phylogenomic analysis, using whole-genome information from more than 90 chordate genomes. Phylogenomic analysis of these DGs in chordate genomes provided direct evidence that major diversification has occurred in the ancestor of placental mammals. Mammalian RDDGs have been shown to originate in several steps by independent domestication events and to diversify later by gene duplications. Analysis of syntenic loci has shown that diverse RDDGs and their chromosomal positions were fully established in the ancestor of placental mammals. By analysis of active Metaviridae lineages in amniotes, we have demonstrated that RDDGs originated from retroelement remains. The chromosomal gene movements of RDDGs were highly dynamic only in the ancestor of placental mammals. During the domestication process, de novo acquisition of regulatory regions is shown to be a prerequisite for the survival of the DGs. The origin and evolution of de novo acquired promoters and untranslated regions in diverse mammalian RDDGs have been explained by comparative analysis of orthologous gene loci. The origin of placental mammal-specific innovations and adaptations, such as placenta and newly evolved brain functions, was most probably connected to the regulatory wiring of DGs and their rapid fixation in the ancestor of placental mammals. © 2013 The Author.

Alexandrov A.S.,Loughborough University | Alexandrov A.S.,Josef Stefan Institute | Kabanov V.V.,Loughborough University
Physical Review Letters | Year: 2011

Unconventional symmetries of the order parameter allowed some researchers to maintain that a purely repulsive interaction between electrons provides superconductivity without phonons in a number of high-temperature superconductors. It is shown that the Cooper pairing in p and d states is not possible with the realistic Coulomb repulsion between fermions at relevant temperatures in any dimension. © 2011 American Physical Society.

Alexandrov A.S.,Josef Stefan Institute | Alexandrov A.S.,Loughborough University | Alexandrov A.S.,University of Campinas | Dediu V.A.,CNR Institute of Nanostructured Materials | Kabanov V.V.,Josef Stefan Institute
Physical Review Letters | Year: 2012

In hopping magnetoresistance of doped insulators, an applied magnetic field shrinks the electron (hole) s-wave function of a donor or an acceptor and this reduces the overlap between hopping sites resulting in the positive magnetoresistance quadratic in a weak magnetic field, B. We extend the theory of hopping magnetoresistance to states with nonzero orbital momenta. Different from s states, a weak magnetic field expands the electron (hole) wave functions with positive magnetic quantum numbers, m>0, and shrinks the states with negative m in a wide region outside the point defect. This together with a magnetic-field dependence of injection/ionization rates results in a negative weak-field magnetoresistance, which is linear in B when the orbital degeneracy is lifted. The theory provides a possible explanation of a large low-field magnetoresistance in disordered π-conjugated organic materials. © 2012 American Physical Society.

Kordis D.,Josef Stefan Institute
Biology Direct | Year: 2011

Background: Genome-wide studies of intron dynamics in mammalian orthologous genes have found convincing evidence for loss of introns but very little for intron turnover. Similarly, large-scale analysis of intron dynamics in a few vertebrate genomes has identified only intron losses and no gains, indicating that intron gain is an extremely rare event in vertebrate evolution. These studies suggest that the intron-rich genomes of vertebrates do not allow intron gain. The aim of this study was to search for evidence of de novo intron gain in domesticated genes from an analysis of their exon/intron structures.Results: A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. Gain of introns in domesticated genes has been reconstructed on well established mammalian, vertebrate and chordate phylogenies, and examined as to where and when the gain events occurred. The locations, sizes and amounts of de novo introns gained in the domesticated genes during the evolution of mammals and chordates has been analyzed. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5' UTR and coding regions, while 3' UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Intron densities in Eutheria-specific domesticated genes and in older domesticated genes that originated early in vertebrates are lower than those for normal mammalian and vertebrate genes. Surprisingly, the majority of intron gains have occurred in the ancestor of placentals.Conclusions: This study provides the first evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for reconstructing intron evolution. The findings of this comprehensive study slightly challenge the current view on the evolutionary stasis in intron dynamics during the last 100 - 200 My. Domesticated genes could constitute an excellent system on which to analyse the mechanisms of intron gain in placental mammals.Reviewers: this article was reviewed by Dan Graur, Eugene V. Koonin and Jürgen Brosius. © 2011 Kordiš; licensee BioMed Central Ltd.

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