The 2HA line of Medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive

BACKGROUND The Medicago truncatula 2HA seed line is highly embryogenic while the parental line Jemalong rarely produces embryos. The 2HA line was developed from one of the rare Jemalong regenerates and this method for obtaining a highly regenerable genotype in M. truncatula is readily reproducible suggesting an epigenetic mechanism. Microarray transcriptomic analysis showed down regulation of an ETHYLENE INSENSITIVE 3-like gene in 2HA callus which provided an approach to investigating epigenetic regulation of genes related to ethylene signalling and the 2HA phenotype. Ethylene is involved in many developmental processes including somatic embryogenesis (SE) and is associated with stress responses. RESULTS Microarray transcriptomic analysis showed a significant number of up-regulated transcripts in 2HA tissue culture, including nodule and embryo specific genes and transposon-like genes, while only a few genes were down-regulated, including an EIN3-like gene we called MtEIL1. This reduced expression was associated with ethylene insensitivity of 2HA plants that was further investigated. The weak ethylene insensitivity affected root and nodule development. Sequencing of MtEIL1 found no difference between 2HA and wild-type plants. DNA methylation analysis of MtEIL1 revealed significant difference between 2HA and wild-type plants. Tiling arrays demonstrated an elevated level of miRNA in 2HA plants that hybridised to the antisense strand of the MtEIL1 gene. AFLP-like methylation profiling revealed more differences in DNA methylation between 2HA and wild-type. Segregation analysis demonstrated the recessive nature of the eil1 phenotype and the dominant nature of the SE trait. CONCLUSIONS We have demonstrated that EIL1 of Medicago truncatula (MtEIL1) is epigenetically silenced in the 2HA seed line. The possible cause is an elevated level of miRNA that targets its 3'UTR and is also associated with DNA methylation of MtEIL1. Down regulation of MtEIL1 makes it possible to form nodules in the presence of ethylene and affects root growth under normal conditions. Segregation analysis showed no association between MtEIL1 expression and SE in culture but the role and mechanism of ethylene signalling in the process of plant regeneration through SE requires further investigation. The work also suggests that epigenetic changes to a particular gene induced in culture can be fixed in regenerated plants.This work was funded by the Australian Research Council (CEO348212) through the ARC Centre of Excellence for Integrative Legume Research (CILR)

Characterisation of the legume SERK-NIK gene superfamily including splice variants: Implications for development and defence

<p>Abstract</p> <p>Background</p> <p><it>SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE </it>(<it>SERK</it>) genes are part of the regulation of diverse signalling events in plants. Current evidence shows SERK proteins function both in developmental and defence signalling pathways, which occur in response to both peptide and steroid ligands. <it>SERKs </it>are generally present as small gene families in plants, with five <it>SERK </it>genes in Arabidopsis. Knowledge gained primarily through work on Arabidopsis SERKs indicates that these proteins probably interact with a wide range of other receptor kinases and form a fundamental part of many essential signalling pathways. The <it>SERK1 </it>gene of the model legume, <it>Medicago truncatula </it>functions in somatic and zygotic embryogenesis, and during many phases of plant development, including nodule and lateral root formation. However, other <it>SERK </it>genes in <it>M. truncatula </it>and other legumes are largely unidentified and their functions unknown.</p> <p>Results</p> <p>To aid the understanding of signalling pathways in <it>M. truncatula</it>, we have identified and annotated the <it>SERK </it>genes in this species. Using degenerate PCR and database mining, eight more <it>SERK</it>-like genes have been identified and these have been shown to be expressed. The amplification and sequencing of several different PCR products from one of these genes is consistent with the presence of splice variants. Four of the eight additional genes identified are upregulated in cultured leaf tissue grown on embryogenic medium. The sequence information obtained from <it>M. truncatula </it>was used to identify <it>SERK </it>family genes in the recently sequenced soybean (<it>Glycine max</it>) genome.</p> <p>Conclusions</p> <p>A total of nine <it>SERK </it>or <it>SERK-like </it>genes have been identified in <it>M. truncatula </it>and potentially 17 in soybean. Five <it>M. truncatula SERK </it>genes arose from duplication events not evident in soybean and Lotus. The presence of splice variants has not been previously reported in a <it>SERK </it>gene. Upregulation of four newly identified <it>SERK </it>genes (in addition to the previously described <it>MtSERK1</it>) in embryogenic tissue cultures suggests these genes also play a role in the process of somatic embryogenesis. The phylogenetic relationship of members of the <it>SERK </it>gene family to closely related genes, and to development and defence function is discussed.</p

Electronic structures of La3_3S4_4 and Ce3_3S4_4

We have investigated electronic structures of La$_3$S$_4$ and Ce$_3$S$_4$ using the LSDA and LSDA+$U$ methods. Calculated density of states (DOS) are compared with the experimental DOS obtained by the valence band photoemission spectroscopy. The DOS at $E_{\rm{F}}$ indicates the 5$d$ character in La$_3$S$_4$ and 4$f$ character in Ce$_3$S$_4$. It is found to be nearly half metallic in the ferromagnetic ground state of Ce$_3$S$_4$. %Ce$_3$S$_4$ has ferromagnetic ground states with spin and orbital magnetic %moments of 1.27 $\mu_{\rm{B}}$ and $-$2.81 $\mu_{\rm{B}}$ per Ce, respectively, %and shows nearly half metallic ground state. We discuss the superconductivity and structural transition in La$_3$S$_4$, and the absence of structural transition in Ce$_3$S$_4$.Comment: Transport and Thermal Properties of Advanced Materials(Aug. 2002; Hiroshima, Japan

Tensor hierarchies, Borcherds algebras and E11

Gauge deformations of maximal supergravity in D=11-n dimensions generically give rise to a tensor hierarchy of p-form fields that transform in specific representations of the global symmetry group E(n). We derive the formulas defining the hierarchy from a Borcherds superalgebra corresponding to E(n). This explains why the E(n) representations in the tensor hierarchies also appear in the level decomposition of the Borcherds superalgebra. We show that the indefinite Kac-Moody algebra E(11) can be used equivalently to determine these representations, up to p=D, and for arbitrarily large p if E(11) is replaced by E(r) with sufficiently large rank r.Comment: 22 pages. v2: Published version (except for a few minor typos detected after the proofreading, which are now corrected

Classification of a supersolid: Trial wavefunctions, Symmetry breakings and Excitation spectra

A state of matter is characterized by its symmetry breaking and elementary excitations. A supersolid is a state which breaks both translational symmetry and internal $U(1)$ symmetry. Here, we review some past and recent works in phenomenological Ginsburg-Landau theories, ground state trial wavefunctions and microscopic numerical calculations. We also write down a new effective supersolid Hamiltonian on a lattice. The eigenstates of the Hamiltonian contains both the ground state wavefunction and all the excited states (supersolidon) wavefunctions. We contrast various kinds of supersolids in both continuous systems and on lattices, both condensed matter and cold atom systems. We provide additional new insights in studying their order parameters, symmetry breaking patterns, the excitation spectra and detection methods.Comment: REVTEX4, 19 pages, 3 figure

Glide and Superclimb of Dislocations in Solid 4^4He

Glide and climb of quantum dislocations under finite external stress, variation of chemical potential and bias (geometrical slanting) in Peierls potential are studied by Monte Carlo simulations of the effective string model. We treat on unified ground quantum effects at finite temperatures $T$. Climb at low $T$ is assisted by superflow along dislocation core -- {\it superclimb}. Above some critical stress avalanche-type creation of kinks is found. It is characterized by hysteretic behavior at low $T$. At finite biases gliding dislocation remains rough even at lowest $T$ -- the behavior opposite to non-slanted dislocations. In contrast to glide, superclimb is characterized by quantum smooth state at low temperatures even for finite bias. In some intermediate $T$-range giant values of the compressibility as well as non-Luttinger type behavior of the core superfluid are observed.Comment: Updated version submitted to JLTP as QFS2010 proceedings; 11 pages, 6 figure

Squeezed States of the Generalized Minimum Uncertainty State for the Caldirola-Kanai Hamiltonian

We show that the ground state of the well-known pseudo-stationary states for the Caldirola-Kanai Hamiltonian is a generalized minimum uncertainty state, which has the minimum allowed uncertainty $\Delta q \Delta p = \hbar \sigma_0/2$, where $\sigma_0 (\geq 1)$ is a constant depending on the damping factor and natural frequency. The most general symmetric Gaussian states are obtained as the one-parameter squeezed states of the pseudo-stationary ground state. It is further shown that the coherent states of the pseudo-stationary ground state constitute another class of the generalized minimum uncertainty states.Comment: RevTex4, 9 pages, no fingure; to be published in Journal of Physics

A glassy contribution to the heat capacity of hcp 4^4He solids

We model the low-temperature specific heat of solid $^4$He in the hexagonal closed packed structure by invoking two-level tunneling states in addition to the usual phonon contribution of a Debye crystal for temperatures far below the Debye temperature, $T < \Theta_D/50$. By introducing a cutoff energy in the two-level tunneling density of states, we can describe the excess specific heat observed in solid hcp $^4$He, as well as the low-temperature linear term in the specific heat. Agreement is found with recent measurements of the temperature behavior of both specific heat and pressure. These results suggest the presence of a very small fraction, at the parts-per-million (ppm) level, of two-level tunneling systems in solid $^4$He, irrespective of the existence of supersolidity.Comment: 11 pages, 4 figure