Strong Coupling Solver for the Quantum Impurity Model

We propose a fast impurity solver for the general quantum impurity model based on the perturbation theory around the atomic limit, which can be used in combination with the local density approximation (LDA) and the dynamical mean field theory (DMFT). We benchmark the solver in the two band Hubbard model within DMFT against quantum Monte Carlo (QMC) and numerical renormalization group (NRG) results. We find that the solver works very well in the paramagnetic Mott insulator phase. We also apply this impurity solver to the DMFT study of the anti-ferromagnetic phase transition in the unfrustrated Bethe lattice. The Neel temperature obtained by the fast impurity solver agrees very well with the QMC results in the large Hubbard U limit. The method is a promising tool to be used in combination with the LDA+DMFT to study Mott insulators starting from first principles.Comment: 5 pages, 5 figures. to be published in Physical Review

Decoupling method for dynamical mean field theory calculations

In this paper we explore the use of an equation of motion decoupling method as an impurity solver to be used in conjunction with the dynamical mean field self-consistency condition for the solution of lattice models. We benchmark the impurity solver against exact diagonalization, and apply the method to study the infinite $U$ Hubbard model, the periodic Anderson model and the $pd$ model. This simple and numerically efficient approach yields the spectra expected for strongly correlated materials, with a quasiparticle peak and a Hubbard band. It works in a large range of parameters, and therefore can be used for the exploration of real materials using LDA+DMFT.Comment: 30 pages, 7 figure

Computational biology applied to genomic analyses of two tomato elite cultivars (Solanum lycopersicum: Heinz & M82) and a wild species (Solanum pennellii: LA0716)

Mediante la aplicación de diferentes enfoques de Biología Computacional, en esta Tesis se abordaron tres proyectos genoma de tomate: i) el genoma mitocondrialdel cultivar élite Heinz se secuenció, ensambló y anotó; ii) se ancló la secuenciacompleta del genoma de la especie silvestre de tomate Solanum pennellii, el padredonante de la conocida población de líneas de introgresión (IL), al mapa genéticoy iii) mediante genómica comparativa y análisis de QTL (loci de caracterescuantitativos) se identificaron genes candidatos asociados a variaciones en lafotosíntesis y en caracteres relacionados con el crecimiento de las plantas. Losresultados del ensamblado del genoma mitocondrial del tomate mostraron que lasinserciones nucleares de origen mitocondrial (del inglés, numts: nuclearmitochondrial DNA segments) están presentes aún en los tomatescontemporáneos. Este hallazgo fue validado por hibridación fluorescente in situ lacual mostró un número particularmente elevado de numts en el cromosoma 11 delcultivar Heinz. En la segunda parte de esta Tesis se presenta la secuencia completadel genoma de S. pennellii la cual fue ensamblada de novo en 4.591 scaffolds, de loscuales, el 97,1% fueron anclados (mediante una base de datos interna de 16.940marcadores moleculares) al mapa genético del tomate. Por último, en el capítulofinal de esta Tesis, el potencial como herramientas para la investigación y elmejoramiento de cultivos de las secuencias genómicas aquí presentadas, sedemostró por el genoma del cultivar S. lycopersicum M82, ensamblado porreferencia. En esta parte, se identificaron 87 genes candidatos involucrados en ladeterminación de loci de caracteres cuantitativos responsables de variaciones en lafotosíntesis y en caracteres relacionados con el crecimiento de la planta presentesen 11 regiones (BINs) de las líneas de introgresión de tomate.By the application of different Computational Biology approaches, in this Thesis,three tomato genome projects were boarded and analyzed: i) the mitochondrialgenome from the elite Heinz cultivar was sequenced, assembled and annotated; ii)the genome sequence of Solanum pennellii, the donor parent of the well-knowntomato introgression lines population (IL), was studied and anchored to a tomatogenetic map to construct high-quality pseudo-chromosomes; and lastly iii) by acomparative genomics approach the assembled-by-reference genome of the M82elite cultivar and recurrent IL parent was contrasted to the donor parental genome. In this regard, quantitative trait loci (QTL) containing candidate genes whereselected for a comparative analysis of chromosomic regions (BINs) linked tovariations in photosynthesis- and plant growth-related traits. In the first chapterof this Thesis, an in-depth analysis of the tomato mitochondrial genome showedthat nuclear DNA segments of mitochondrial origin (numts) are still present in thecontemporary tomatoes. This in silico discovery was further cross-validated byfluorescence in situ hybridization (FISH) which confirmed a particularly highnumber of numts in Heinz cultivar chromosome 11. In the following chapter, thecomplete de novo genome sequence of S. pennellii is presented with a total of 4,591scaffolds of which 97.1% were anchored (with an in-house database of 16,940molecular markers) to the tomato genetic map. Indeed, the use of these genomesas tools for research and crop improvement was showcased by the assembled-byreference M82 genome introduced in the last chapter of this Thesis. On thissubject, structural and functional annotated loci distributed over 11 BINs werecompared and evaluated: 4,916 and 5,886 loci in M82 and LA0716, respectively. Thisstudy resulted in the selection of 87 candidate genes underpinning the geneticbases of QTL for variations in tomato photosynthesis and plant growth.Fil: Lichtenstein, Gabriel. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina

A note on cluster methods for strongly correlated electron systems

We develop, clarify and test various aspects of cluster methods dynamical mean field methods using a soluble toy model as a benchmark. We find that the Cellular Dynamical Mean Field Theory (C-DMFT) converges very rapidly and compare its convergence properties with those of the Dynamical Cluster Approximation (DCA). We propose and test improved estimators for the lattice self energy within C-DMFT.Comment: 5 pages, 3 figures; major change

Semiclassical Analysis of Extended Dynamical Mean Field Equations

The extended Dynamical Mean Field Equations (EDMFT) are analyzed using semiclassical methods for a model describing an interacting fermi-bose system. We compare the semiclassical approach with the exact QMC (Quantum Montecarlo) method. We found the transition to an ordered state to be of the first order for any dimension below four.Comment: RevTex, 39 pages, 16 figures; Appendix C added, typos correcte

Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds

Nunes Nesi, Adriano. Universidade Federal de Viçosa. Departamento de Biologia Vegetal. Viçosa, Minas Gerais, Brazil.Alseekh, Saleh. Max - Planck- Institute of Molecular Plant Physiology. Potsdam, Germany.Oliveira Silva, Franklin Magnum de. Universidade Federal de Viçosa. Departamento de Biologia Vegetal. Viçosa, Minas Gerais, Brazil.Omranian, Nooshin. Max - Planck- Institute of Molecular Plant Physiology. Potsdam, Germany.Lichtenstein, Gabriel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología. Castelar, Buenos Aires, Argentina.Mirnezhad, Mohammad. Leiden University. Plant Ecology, Institute of Biology. The Netherlands.Romero González, Roman R. Leiden University. Plant Ecology. Institute of Biology. The Netherlands.Carrari, Fernando. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología. Castelar, Buenos Aires, Argentina.1-13Introduction To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. Objective This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. Methods The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses. Results Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism. Conclusions Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits

Extracellular non-coding rna signatures of the metacestode stage of echinococcus multilocularis

Extracellular RNAs (ex-RNAs) are secreted by cells through different means that may involve association with proteins, lipoproteins or extracellular vesicles (EV). In the context of parasitism, ex-RNAs represent new and exciting communication intermediaries with promis-ing potential as novel biomarkers. In the last years, it was shown that helminth parasites secrete ex-RNAs, however, most work mainly focused on RNA secretion mediated by EV. Ex-RNA study is of special interest in those helminth infections that still lack biomarkers for early and/or follow-up diagnosis, such as echinococcosis, a neglected zoonotic disease caused by cestodes of the genus Echinococcus. In this work, we have characterised the ex-RNA profile secreted by in vitro grown metacestodes of Echinococcus multilocularis, the casuative agent of alveolar echinococcosis. We have used high throughput RNA-sequencing together with RT-qPCR to characterise the ex-RNA profile secreted towards the extra-and intra-parasite milieus in EV-enriched and EV-depleted fractions. We show that a polarized secretion of small RNAs takes place, with microRNAs mainly secreted to the extra-parasite milieu and rRNA-and tRNA-derived sequences mostly secreted to the intra-parasite milieu. In addition, we show by nanoparticle tracking analyses that viable metacestodes secrete EV mainly into the metacestode inner vesicular fluid (MVF); however, the number of nanoparticles in culture medium and MVF increases > 10-fold when metacestodes show signs of tegument impairment. Interestingly, we confirm the presence of host miRNAs in the intra-parasite milieu, implying their internali-zation and transport through the tegument towards the MVF. Finally, our assessment of the detection of Echinococcus miRNAs in patient samples by RT-qPCR yielded negative results suggesting the tested miRNAs may not be good biomarkers for this disease. A comprehensive study of the secretion mechanisms throughout the life cycle of these parasites will help to understand parasite interaction with the host and also, improve current diagnostic tools.Fil: Ancarola, María Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Lichtenstein, Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Herbig, Johannes. Universität Würzburg; AlemaniaFil: Holroyd, Nancy. No especifíca;Fil: Mariconti, Mara. San Matteo Hospital Foundation; ItaliaFil: Brunetti, Enrico. San Matteo Hospital Foundation; ItaliaFil: Berriman, Matthew. No especifíca;Fil: Albrecht, Krystyna. Universität Würzburg; AlemaniaFil: Marcilla, Antonio. Universidad de Valencia; EspañaFil: Rosenzvit, Mara Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Kamenetzky, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Brehm, Klaus. Universität Würzburg; AlemaniaFil: Cucher, Marcela Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentin

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

As researchers begin probing deep coverage sequencing data for increasingly rare mutations and subclonal events, the fidelity of next generation sequencing (NGS) laboratory methods will become increasingly critical. Although error rates for sequencing and polymerase chain reaction (PCR) are well documented, the effects that DNA extraction and other library preparation steps could have on downstream sequence integrity have not been thoroughly evaluated. Here, we describe the discovery of novel C > A/G > T transversion artifacts found at low allelic fractions in targeted capture data. Characteristics such as sequencer read orientation and presence in both tumor and normal samples strongly indicated a non-biological mechanism. We identified the source as oxidation of DNA during acoustic shearing in samples containing reactive contaminants from the extraction process. We show generation of 8-oxoguanine (8-oxoG) lesions during DNA shearing, present analysis tools to detect oxidation in sequencing data and suggest methods to reduce DNA oxidation through the introduction of antioxidants. Further, informatics methods are presented to confidently filter these artifacts from sequencing data sets. Though only seen in a low percentage of reads in affected samples, such artifacts could have profoundly deleterious effects on the ability to confidently call rare mutations, and eliminating other possible sources of artifacts should become a priority for the research community.National Human Genome Research Institute (U.S.) (HG03067-05

Single nucleotide polymorphisms and breast cancer: not yet a success story

Numerous studies have examined low penetrance susceptibility polymorphisms in candidate genes, with some reporting significant findings. However, for the most part these associations could not be replicated in subsequent studies, suggesting that the original observations were due to chance. The failure to identify meaningful common genetic variation in relation to breast cancer should give us pause for thought and make us reconsider our current research strategies. The most recent directions of pooling samples to increase statistical power and pursuing whole genome screens may overcome some obstacles while also creating new challenges. Future studies should perhaps also consider alternative designs such as using surrogate (preferably continuous) markers of breast cancer, focusing on high-risk populations, and defining pathologically distinct outcomes

Single nucleotide polymorphisms and breast cancer: not yet a success story

Numerous studies have examined low penetrance susceptibility polymorphisms in candidate genes, with some reporting significant findings. However, for the most part these associations could not be replicated in subsequent studies, suggesting that the original observations were due to chance. The failure to identify meaningful common genetic variation in relation to breast cancer should give us pause for thought and make us reconsider our current research strategies. The most recent directions of pooling samples to increase statistical power and pursuing whole genome screens may overcome some obstacles while also creating new challenges. Future studies should perhaps also consider alternative designs such as using surrogate (preferably continuous) markers of breast cancer, focusing on high-risk populations, and defining pathologically distinct outcomes