Pistil transcriptome analysis to disclose genes and gene products related to aposporous apomixis in Hypericum perforatum L.

Unlike sexual reproduction, apomixis encompasses a number of reproductive strategies,which permit maternal genome inheritance without genetic recombination and syngamy. The key biological features of apomixis are the circumvention of meiosis (i.e., apomeiosis),the differentiation of unreduced embryo sacs and egg cells, and their autonomous development in functional embryos through parthenogenesis, and the formation of viable endosperm either via fertilization-independent means or following fertilization with a sperm cell. Despite the importance of apomixis for breeding of crop plants and although much research has been conducted to study this process, the genetic control of apomixis is still not well understood. Hypericum perforatum is becoming an attractive model system for the study of aposporous apomixis. Here we report results from a global gene expression analysis of H. perforatum pistils collected from sexual and aposporous plant accessions for the purpose of identifying genes, biological processes and molecular functions associated with the aposporous apomixis pathway. Across two developmental stages corresponding to the expression of aposporous apomeiosis and parthenogenesis in ovules, a total of 224 and 973 unigenes were found to be significantly up- and down-regulated with a fold change >= 2 in at least one comparison, respectively.Differentially expressed genes were enriched for multiple gene ontology (GO) terms,including cell cycle, DNA metabolic process, and single-organism cellular process. For molecular functions, the highest scores were recorded for GO terms associated withDNA binding, DNA (cytosine-5-)-methyltransferase activity and heterocyclic compound binding. As deregulation of single components of the sexual developmental pathway is believed to be a trigger of the apomictic reproductive program, all genes involved in sporogenesis, gametogenesis and response to hormonal stimuli were analyzed in great detail. Overall, our data suggest that phenotypic expression of apospory is concomitant with the modulation of key genes involved in the sexual reproductive pathway. Furthermore, based on gene annotation and co-expression, we underline a putative role of hormones and key actors playing in the RNA-directed DNA methylation pathway in regulating the developmental changes occurring during aposporous apomixis in H. perforatum

Stellar populations in the dwarf spheroidal galaxy Leo I

We present a detailed study of the color magnitude diagram (CMD) of the dwarf spheroidal galaxy Leo I, based on archival Hubble Space Telescope data. Our photometric analysis, confirming previous results on the brighter portion of the CMD, allow us to obtain an accurate sampling of the stellar populations also at the faint magnitudes corresponding to the Main Sequence. By adopting a homogeneous and consistent theoretical scenario for both hydrogen and central helium-burning evolutionary phases, the various features observed in the CMD are interpreted and reliable estimations for both the distance modulus and the age(s) for the main stellar components of Leo I are derived. More in details, from the upper luminosity of the Red Giant Branch and the lower luminosity of the Subgiant Branch we simultaneously constrain the galaxy distance and the age of the oldest stellar population in Leo I. In this way we obtain a distance modulus (m-M)_V=22.00$\pm$0.15 mag and an age of 10--15 Gyr or 9--13 Gyr, adopting a metallicity Z=0.0001 and 0.0004, respectively. The reliability of this distance modulus has been tested by comparing the observed distribution of the Leo I anomalous Cepheids in the period-magnitude diagram with the predicted boundaries of the instability strip, as given by convective pulsating models.Comment: 19 pages, 3 tables, 14 figures To be published in A

Engineering exotic phases for topologically-protected quantum computation by emulating quantum dimer models

We use a nonperturbative extended contractor renormalization (ENCORE) method for engineering quantum devices for the implementation of topologically protected quantum bits described by an effective quantum dimer model on the triangular lattice. By tuning the couplings of the device, topological protection might be achieved if the ratio between effective two-dimer interactions and flip amplitudes lies in the liquid phase of the phase diagram of the quantum dimer model. For a proposal based on a quantum Josephson junction array [L. B. Ioffe {\it et al.}, Nature (London) {\bf 415}, 503 (2002)] our results show that optimal operational temperatures below 1 mK can only be obtained if extra interactions and dimer flips, which are not present in the standard quantum dimer model and involve three or four dimers, are included. It is unclear if these extra terms in the quantum dimer Hamiltonian destroy the liquid phase needed for quantum computation. Minimizing the effects of multi-dimer terms would require energy scales in the nano-Kelvin regime. An alternative implementation based on cold atomic or molecular gases loaded into optical lattices is also discussed, and it is shown that the small energy scales involved--implying long operational times--make such a device impractical. Given the many orders of magnitude between bare couplings in devices, and the topological gap, the realization of topological phases in quantum devices requires careful engineering and large bare interaction scales.Comment: 12 pages, 10 figure

Finding 16S rRNA gene-based SNPs for the genetic traceability of commercial species belonging to Gadiformes

A SNPs (Single Nucleotide Polymorphism) based analysis was developed to differentiate four economically important species belonging to the Gadiformes order: Pacific cod Gadus macrocephalus, Atlantic cod Gadus morhua, Haddock Melanogrammus aeglefinus and Ling Molva molva. A 430bp fragment of the 16s rRNA gene was amplified using interspecific conserved primer and sequenced. The sequences were aligned and analyzed for the presence of SNPs; three SNPs (MerSNP1, MerSNP7 and MerSNP9) were identified and selected to allow discrimination between the four species. Aplotypes were TCC, CCC, CAT and CAC for Pacific cod, Atlantic cod, Haddock and Ling respectively. Confirmation of results was achieved by sequencing 16s rRNA gene fragments of 16 G. morhua, 7 G. macrocephalus, 15 M. aeglefinus and 5 M. molva samples collected at different fish catching campaign. Nucleotide sequence of 16s rRNA mitochondial gene has been shown to be a useful tool to allow rapid reliable and fully automatable for discrimination of 4 economically important species in fisheries industry

Demonstration of binding induced structural plasticity in a SH2 domain

SH2 domains are common protein interaction domains able to recognize short aminoacidic sequences presenting a phosphorylated tyrosine (pY). In spite of their fundamental importance for cell physiology there is a lack of information about the mechanism by which these domains recognize and bind their natural ligands. The N-terminal SH2 (N-SH2) domain of PI3K mediates the interaction with different scaffolding proteins and is known to recognize a specific pY-X-X-M consensus sequence. These interactions are at the cross roads of different molecular pathways and play a key role for cell development and division. By combining mutagenesis, chemical kinetics and NMR, here we provide a complete characterization of the interaction between N-SH2 and a peptide mimicking the scaffolding protein Gab2. Our results highlight that N-SH2 is characterized by a remarkable structural plasticity, with the binding reaction being mediated by a diffused structural region and not solely by the residues located in the binding pocket. Furthermore, the analysis of kinetic data allow us to pinpoint an allosteric network involving residues far from the binding pocket involved in specificity. Results are discussed on the light of previous works on the binding properties of SH2 domains