Spin-flip effects on the current-in-plane magnetotransport in magnetic multilayers with arbitrary magnetization alignments

An extended Boltzmann equation approach, with nondiagonal components of the electron distribution, function taken into account, is proposed to study spin-flip effects on the magnetoresistance (MR) in magnetic inhomogeneous systems with arbitrary magnetization alignments. The presence of spin-flip scattering is found to reduce the MR and to decrease deviation of the MR from linear dependence on sin 2(θ/2) where θ is the angle between the magnetizations of successive magnetic films.published_or_final_versio

Spin and orbital excitations in undoped manganites

We develop a theory for spin and orbital excitations in undoped manganites to account for the spin and orbital orderings observed experimentally. It is found that the anisotropy of the magnetic structure is closely related to the orbital ordering, and the Jahn-Teller effect stabilizes the orbital ordering. The phase diagram and the low-energy excitation spectra for both spin and orbital orderings are obtained. The calculated critical temperatures can be quantitatively comparable to the experimental data. © 2000 American Institute of Physics.published_or_final_versio

Theory of electric-field-induced metal-insulator transition in doped manganites

The insulator to metal transition (IMT) induced by the application of an electric field in doped manganites is investigated theoretically. Starting from the double-exchange mechanism with the long-range Coulomb interaction included, we find that the electric field may suppress the charge ordering and drive the system from the antiferromagnetic and charge-ordered state with an energy gap at the Fermi level to the ferromagnetic and gapless state, resulting in the IMT. A numerical simulation is performed for manganite films with intrinsic inhomogeneities, and an important impact of the inhomogeneities on this electric-field-induced transition is obtained. Our results can naturally account for the recently observed electric-filed-induced IMT phenomenon in manganites.published_or_final_versio

Macroscopic theory of giant magnetoresistance in magnetic granular metals

A macroscopic theory of giant magnetoresistance in granular magnetic materials is developed to improve on that of Rubinstein [Phys. Rev. B 50, 3830 (1994)]. By using a self-consistent method and introducing a useful parametrization, we show the magnetotransport in granular systems to be between those for currents in the plane of layers and currents perpendicular to the plane of the layers in multilayers. The theoretical result in the local limit is found to be in agreement with the observed singular dependence of the giant magnetoresistance on annealing temperature.published_or_final_versio

Phase diagram of an extended Kondo lattice model for manganites: The Schwinger-boson mean-field approach

We investigate the phase diagram of an extended Kondo lattice model for doped manganese oxides in the presence of strong but finite Hund's coupling and on-site Coulomb interaction. By means of the Schwinger-boson mean-field approach, it is found that, besides magnetic ordering, there will be nonuniform charge distributions, such as charge ordering and phase separation, if the interaction between electrons prevails over the hybridization. Which of the charge ordering and phase separation appears is determined by a competition between effective repulsive and attractive interactions due to virtual processes of electron hopping. Calculated results show that strong electron correlations caused by the on-site Coulomb interaction as well as the finite Hund's coupling play an important role in the magnetic ordering and charge distribution at low temperatures. ©2000 The American Physical Society.published_or_final_versio

Orbital ordering and two ferromagnetic phases in low-doped La 1-xSr xMnO 3

We present a theory for the transition between two ferromagnetic phases observed experimentally in lightly doped La 1-xSr xMnO 3. Starting from an electronic model, the instabilities to various types of orbital orderings are studied within the random-phase approximation. In most cases, the instabilities occur in the region of strong correlations. A phase diagram is calculated in the case of strong correlation by means of the projected perturbation technique and the Schwinger boson technique. A phase transition between two types of orbital ordering occurs at a low doping, which may be closely relevant to recent experimental observations.published_or_final_versio

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression

Defending the genome from the enemy within:mechanisms of retrotransposon suppression in the mouse germline

The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable genetic elements, particularly retrotransposons. There are many different types of retrotransposon in mammalian genomes, and these target different points in germline development to amplify and integrate into new genomic locations. Germ cells, and their pluripotent developmental precursors, have evolved a variety of genome defence mechanisms that suppress retrotransposon activity and maintain genome stability across the generations. Here, we review recent advances in understanding how retrotransposon activity is suppressed in the mammalian germline, how genes involved in germline genome defence mechanisms are regulated, and the consequences of mutating these genome defence genes for the developing germline

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

August 1, 2010Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. Here, we optimize bisulfite sequencing for genome-scale analysis of clinical samples. Specifically, we outline how restriction digestion targets bisulfite sequencing to hotspots of epigenetic regulation; we show that 30ng of DNA are sufficient for genome-scale analysis; we demonstrate that our protocol works well on formalinfixed, paraffin-embedded (FFPE) samples; and we describe a statistical method for assessing significance of altered DNA methylation patterns.National Institutes of Health (U.S.) (Grant R01HG004401)National Institutes of Health (U.S.) (Grant U54HG03067)National Institutes of Health (U.S.) (Grant U01ES017155

Complementary intestinal mucosa and microbiota responses to caloric restriction

The intestine is key for nutrient absorption and for interactions between the microbiota and its host. Therefore, the intestinal response to caloric restriction (CR) is thought to be more complex than that of any other organ. Submitting mice to 25% CR during 14 days induced a polarization of duodenum mucosa cell gene expression characterised by upregulation, and downregulation of the metabolic and immune/inflammatory pathways, respectively. The HNF, PPAR, STAT, and IRF families of transcription factors, particularly the Pparα and Isgf3 genes, were identified as potentially critical players in these processes. The impact of CR on metabolic genes in intestinal mucosa was mimicked by inhibition of the mTOR pathway. Furthermore, multiple duodenum and faecal metabolites were altered in CR mice. These changes were dependent on microbiota and their magnitude corresponded to microbial density. Further experiments using mice with depleted gut bacteria and CR-specific microbiota transfer showed that the gene expression polarization observed in the mucosa of CR mice is independent of the microbiota and its metabolites. The holistic interdisciplinary approach that we applied allowed us to characterize various regulatory aspects of the host and microbiota response to CR