Full-Potential LMTO: Total Energy and Force Calculations

The essential features of a full potential electronic structure method using Linear Muffin-Tin Orbitals (LMTOs) are presented. The electron density and potential in the this method are represented with no inherent geometrical approximation. This method allows the calculation of total energies and forces with arbitrary accuracy while sacrificing much of the efficiency and physical content of approximate methods such as the LMTO-ASA method.Comment: 25 pages, 2 figures, Workshop on the TB-LMTO method, Monastery of Mont St. Odile, October 4-5, 199

Theory of quasiparticle spectra for Fe, Co, and Ni: bulk and surface

The correlated electronic structure of iron, cobalt and nickel is investigated within the dynamical mean-field theory formalism, using the newly developed full-potential LMTO-based LDA+DMFT code. Detailed analysis of the calculated electron self-energy, density of states and the spectral density are presented for these metals. It has been found that all these elements show strong correlation effects for majority spin electrons, such as strong damping of quasiparticles and formation of a density of states satellite at about -7 eV below the Fermi level. The LDA+DMFT data for fcc nickel and cobalt (111) surfaces and bcc iron (001) surface is also presented. The electron self energy is found to depend strongly on the number of nearest neighbors, and it practically reaches the bulk value already in the second layer from the surface. The dependence of correlation effects on the dimensionality of the problem is also discussed.Comment: 15 pages, 24 figure

Magnetic instability with increasing hybridization in cerium compounds

A synthesis of a phenomenological theory of orbitally driven magnetic ordering of moderately delocalized light rare-earth systems and ab initio electronic structure calculations has been applied to investigate the change in magnetic behavior on going from CeSb to CeTe, both of which have rocksalt structure with a small decrease in lattice parameter. The hybridization-potential matrix elements and the band energies entering the Anderson-lattice Hamiltonian are obtained from linear-muffin-tin-orbital (LMTO) electronic-structure calculations with the Ce 4f states treated as core states. The position of the Ce 4f energy level relative to the Fermi energy and the intra-atomic Coulomb energy U are obtained by use of a sequence of three total-energy supercell calculations with one out of four Ce sites constrained to f occupation with n=0, 1,2, successively. The calculations elucidate the origins, in the electronic structure, of the variation of the f-state resonance width and hybridization potential on going from Cesb to CeTe, and the resultant sensitivity of the hybridization dressing of the crystal-field splitting and the hybridization-induced exchange interactions to chemical environment. The effect of opening up successive angular momentum scattering channels of the ab initio calculated two-ion exchange-interaction matrix on the nature of the magnetic ordering is examined. The calculated magnitude and range dependence of the two-ion exchange interactions changes sharply from CeSb to CeTe, yielding a change in magnetic behavior in qualitative agreement with experiment. The nonlinear hybridization effects on the hybridization dressing of the crystal-field splitting have been examined. These effects, which are associated with the self-consistent determination of both the band states and f states in the presence of band-f hybridization, are found to be small in both systems

Transcriptional frameshifting rescues Citrobacter rodentium Type VI secretion by the production of two length variants from the prematurely interrupted tssM gene

The Type VI secretion system (T6SS) mediates toxin delivery into both eukaryotic and prokaryotic cells. It is composed of a cytoplasmic structure resembling the tail of contractile bacteriophages anchored to the cell envelope through a membrane complex composed of the TssL and TssM inner membrane proteins and of the TssJ outer membrane lipoprotein. The C-terminal domain of TssM is required for its interaction with TssJ, and for the function of the T6SS. In Citrobacter rodentium, the tssM1 gene does not encode the C-terminal domain. However, the stop codon is preceded by a run of 11 consecutive adenosines. In this study, we demonstrate that this poly-A tract is a transcriptional slippery site that induces the incorporation of additional adenosines, leading to frameshifting, and hence the production of two TssM1 variants, including a full-length canonical protein. We show that both forms of TssM1, and the ratio between these two forms, are required for the function of the T6SS in C. rodentium. Finally, we demonstrate that the tssM gene associated with the Yersinia pseudotuberculosis T6SS-3 gene cluster is also subjected to transcriptional frameshifting

Poisson-event-based analysis of cell proliferation.

A protocol for the assessment of cell proliferation dynamics is presented. This is based on the measurement of cell division events and their subsequent analysis using Poisson probability statistics. Detailed analysis of proliferation dynamics in heterogeneous populations requires single cell resolution within a time series analysis and so is technically demanding to implement. Here, we show that by focusing on the events during which cells undergo division rather than directly on the cells themselves a simplified image acquisition and analysis protocol can be followed, which maintains single cell resolution and reports on the key metrics of cell proliferation. The technique is demonstrated using a microscope with 1.3 μm spatial resolution to track mitotic events within A549 and BEAS-2B cell lines, over a period of up to 48 h. Automated image processing of the bright field images using standard algorithms within the ImageJ software toolkit yielded 87% accurate recording of the manually identified, temporal, and spatial positions of the mitotic event series. Analysis of the statistics of the interevent times (i.e., times between observed mitoses in a field of view) showed that cell division conformed to a nonhomogeneous Poisson process in which the rate of occurrence of mitotic events, λ exponentially increased over time and provided values of the mean inter mitotic time of 21.1 ± 1.2 hours for the A549 cells and 25.0 ± 1.1 h for the BEAS-2B cells. Comparison of the mitotic event series for the BEAS-2B cell line to that predicted by random Poisson statistics indicated that temporal synchronisation of the cell division process was occurring within 70% of the population and that this could be increased to 85% through serum starvation of the cell culture

Disentangling global warming, multi-decadal variability, and El Niño in Pacific temperatures

A key challenge in climate science is to separate observed temperature changes into components due to internal variability and responses to external forcing. Extended integrations of forced and unforced climate models are often used for this purpose. Here we demonstrate a novel method to separate modes of internal variability from global warming based on differences in time scale and spatial pattern, without relying on climate models. We identify uncorrelated components of Pacific sea surface temperature variability due to global warming, the Pacific Decadal Oscillation (PDO), and the El Niño–Southern Oscillation (ENSO). Our results give statistical representations of PDO and ENSO that are consistent with their being separate processes, operating on different time scales, but are otherwise consistent with canonical definitions. We isolate the multidecadal variability of the PDO and find that it is confined to midlatitudes; tropical sea surface temperatures and their teleconnections mix in higher‐frequency variability. This implies that midlatitude PDO anomalies are more persistent than previously thought

Human cytomegalovirus latency-associated proteins elicit immune-suppressive IL-10 producing CD4⁺ T cells.

Human cytomegalovirus (HCMV) is a widely prevalent human herpesvirus, which, after primary infection, persists in the host for life. In healthy individuals, the virus is well controlled by the HCMV-specific T cell response. A key feature of this persistence, in the face of a normally robust host immune response, is the establishment of viral latency. In contrast to lytic infection, which is characterised by extensive viral gene expression and virus production, long-term latency in cells of the myeloid lineage is characterised by highly restricted expression of viral genes, including UL138 and LUNA. Here we report that both UL138 and LUNA-specific T cells were detectable directly ex vivo in healthy HCMV seropositive subjects and that this response is principally CD4⁺ T cell mediated. These UL138-specific CD4⁺ T cells are able to mediate MHC class II restricted cytotoxicity and, importantly, show IFNγ effector function in the context of both lytic and latent infection. Furthermore, in contrast to CDCD4⁺ T cells specific to antigens expressed solely during lytic infection, both the UL138 and LUNA-specific CD4⁺ T cell responses included CD4⁺ T cells that secreted the immunosuppressive cytokine cIL-10. We also show that cIL-10 expressing CD4⁺ T-cells are directed against latently expressed US28 and UL111A. Taken together, our data show that latency-associated gene products of HCMV generate CD4⁺ T cell responses in vivo, which are able to elicit effector function in response to both lytic and latently infected cells. Importantly and in contrast to CD4⁺ T cell populations, which recognise antigens solely expressed during lytic infection, include a subset of cells that secrete the immunosuppressive cytokine cIL-10. This suggests that HCMV skews the T cell responses to latency-associated antigens to one that is overall suppressive in order to sustain latent carriage in vivo

Interactive effect of STAT6 and IL13 gene polymorphisms on eczema status: results from a longitudinal and a cross-sectional study

BACKGROUND: Eczema is a prevalent skin disease that is mainly characterized by systemic deviation of immune response and defective epidermal barrier. Th2 cytokines, such as IL-13, and transcription factor STAT6 are key elements in the inflammatory response that characterize allergic disorders, including eczema. Previous genetic association studies showed inconsistent results for the association of single nucleotide polymorphisms (SNPs) with eczema. Our aim was to investigate whether SNPs in IL13 and STAT6 genes, which share a biological pathway, have an interactive effect on eczema risk.METHODS: Data from two independent population-based studies were analyzed, namely the Isle of Wight birth cohort study (IOW; n = 1,456) and for the purpose of replication the Swansea PAPA (Poblogaeth Asthma Prifysgol Abertawe; n = 1,445) cross-sectional study. Log-binomial regressions were applied to (i) account for the interaction between IL13 (rs20541) and STAT6 (rs1059513) polymorphisms and (ii) estimate the combined effect, in terms of risk ratios (RRs), of both risk factors on the risk of eczema.RESULTS: Under a dominant genetic model, the interaction term [IL13 (rs20541) x STAT6 (rs1059513)] was statistically significant in both studies (IOW: adjusted Pinteraction = 0.046; PAPA: Pinteraction = 0.037). The assessment of the combined effect associated with having risk genotypes in both SNPs yielded a 1.52-fold increased risk of eczema in the IOW study (95% confidence interval (CI): 1.05 -- 2.20; P = 0.028) and a 2.01-fold higher risk of eczema (95% CI: 1.29 -- 3.12; P = 0.002) in the PAPA study population.CONCLUSIONS: Our study adds to the current knowledge of genetic susceptibility by demonstrating for the first time an interactive effect between SNPs in IL13 (rs20541) and STAT6 (rs1059513) on the occurrence of eczema in two independent samples. Findings of this report further support the emerging evidence that points toward the existence of genetic effects that occur via complex networks involving gene-gene interactions (epistasis)