Analysis of large-scale sequencing of small RNAs

The advent of large-scale sequencing has opened up new areas of research, such as the study of Piwi-interacting small RNAs (piRNAs). piRNAs are longer than miRNAs, close to 30 nucleotides in length, involved in various functions, such as the suppression of transposons in germline. Since a large number of them (many tens of thousands) are generated from a wide range of positions in the genome, large-scale sequencing is the only way to study them. The key to understanding their genesis and biological roles is efficient analysis, which is complicated by the large volumes of sequence data. Taking account of the underlying biology is also important. We describe here novel analyses techniques and tools applied to small RNAs from germ cells in D. melanogaster, that allowed us to infer mechanism and biological function

An epigenetic role for maternally inherited piRNAs in transposon silencing

In plants and mammals, small RNAs indirectly mediate epigenetic inheritance by specifying cytosine methylation. We found that small RNAs themselves serve as vectors for epigenetic information. Crosses between Drosophila strains that differ in the presence of a particular transposon can produce sterile progeny, a phenomenon called hybrid dysgenesis. This phenotype manifests itself only if the transposon is paternally inherited, suggesting maternal transmission of a factor that maintains fertility. In both P- and I-element-mediated hybrid dysgenesis models, daughters show a markedly different content of Piwi-interacting RNAs (piRNAs) targeting each element, depending on their parents of origin. Such differences persist from fertilization through adulthood. This indicates that maternally deposited piRNAs are important for mounting an effective silencing response and that a lack of maternal piRNA inheritance underlies hybrid dysgenesis

Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform

Drosophila melanogaster expresses three classes of small RNAs, which are classified according to their mechanisms of biogenesis. MicroRNAs are ∼22-23 nucleotides (nt), ubiquitously expressed small RNAs that are sequentially processed from hairpin-like precursors by Drosha/Pasha and Dcr-1/Loquacious complexes. MicroRNAs usually associate with AGO1 and regulate the expression of protein-coding genes. Piwi-interacting RNAs (piRNAs) of ∼24-28 nt associate with Piwi-family proteins and can arise from single-stranded precursors. piRNAs function in transposon silencing and are mainly restricted to gonadal tissues. Endo-siRNAs are found in both germline and somatic tissues. These ∼21-nt RNAs are produced by a distinct Dicer, Dcr-2, and do not depend on Drosha/Pasha complexes. They predominantly bind to AGO2 and target both mobile elements and protein-coding genes. Surprisingly, a subset of endo-siRNAs strongly depend for their production on the dsRNA-binding protein Loquacious (Loqs), thought generally to be a partner for Dcr-1 and a cofactor for miRNA biogenesis. Endo-siRNA production depends on a specific Loqs isoform, Loqs-PD, which is distinct from the one, Loqs-PB, required for the production of microRNAs. Paralleling their roles in the biogenesis of distinct small RNA classes, Loqs-PD and Loqs-PB bind to different Dicer proteins, with Dcr-1/Loqs-PB complexes and Dcr-2/Loqs-PD complexes driving microRNA and endo-siRNA biogenesis, respectively. Copyright © 2009 RNA Society

Collapse and revival of oscillations in a parametrically excited Bose-Einstein condensate in combined harmonic and optical lattice trap

In this work, we study parametric resonances in an elongated cigar-shaped BEC in a combined harmonic trap and a time dependent optical lattice by using numerical and analytical techniques. We show that there exists a relative competition between the harmonic trap which tries to spatially localize the BEC and the time varying optical lattice which tries to delocalize the BEC. This competition gives rise to parametric resonances (collapse and revival of the oscillations of the BEC width). Parametric resonances disappear when one of the competing factors i.e strength of harmonic trap or the strength of optical lattice dominates. Parametric instabilities (exponential growth of Bogoliubov modes) arise for large variations in the strength of the optical lattice.Comment: 9 pages, 20 figure

Generalised quantum weakest preconditions

Generalisation of the quantum weakest precondition result of D'Hondt and Panangaden is presented. In particular the most general notion of quantum predicate as positive operator valued measure (POVM) is introduced. The previously known quantum weakest precondition result has been extended to cover the case of POVM playing the role of a quantum predicate. Additionally, our result is valid in infinite dimension case and also holds for a quantum programs defined as a positive but not necessary completely positive transformations of a quantum states.Comment: 7 pages, no figures, added references, changed conten

Batalin-Vilkovisky formalism in perturbative algebraic quantum field theory

On the basis of a thorough discussion of the Batalin-Vilkovisky formalism for classical field theory presented in our previous publication, we construct in this paper the Batalin-Vilkovisky complex in perturbatively renormalized quantum field theory. The crucial technical ingredient is a proof that the renormalized time-ordered product is equivalent to the pointwise product of classical field theory. The renormalized Batalin-Vilkovisky algebra is then the classical algebra but written in terms of the time-ordered product, together with an operator which replaces the ill defined graded Laplacian of the unrenormalized theory. We identify it with the anomaly term of the anomalous Master Ward Identity of Brennecke and D\"utsch. Contrary to other approaches we do not refer to the path integral formalism and do not need to use regularizations in intermediate steps.Comment: 34 page

All orders renormalizability of a Lorentz and CPT violating quantum electrodynamics

Renormalizability of the (minimal) single-fermion QED extension is investigated at all orders of perturbation theory in the framework of algebraic renormalization, a regularization-independent method. Relative to the standard QED, new structures that could lead to gauge anomalies are identified. Nevertheless, even if the anomaly coefficients fail to vanish in the general case, they shall be absent provided we require invariance of the action under C and/or PT transformations. Stability is also verified in this case, hence full renormalizability is attained.Comment: 7 page

Self-organization of a Bose-Einstein condensate in an optical cavity

The spatial self-organization of a Bose-Einstein condensate (BEC) in a high-finesse linear optical cavity is discussed. The condensate atoms are laser-driven from the side and scatter photons into the cavity. Above a critical pump intensity the homogeneous condensate evolves into a stable pattern bound by the cavity field. The transition point is determined analytically from a mean-field theory. We calculate the lowest lying Bogoliubov excitations of the coupled BEC-cavity system and the quantum depletion due to the atom-field coupling.Comment: 11 pages, final version. Accepted for publication in EPJ

Classical dynamics of a two-species Bose-Einstein condensate in the presence of nonlinear maser processes

The stability analysis of a generalized Dicke model, in the semi-classical limit, describing the interaction of a two-species Bose-Einstein condensate driven by a quantized field in the presence of Kerr and spontaneous parametric processes is presented. The transitions from Rabi to Josephson dynamics are identified depending on the relative value of the involved parameters. Symmetry-breaking dynamics are shown for both types of coherent oscillations due to the quantized field and nonlinear optical processes.Comment: 12 pages, 5 figures. Accepted for publication as chapter in "Spontaneous Symmetry Breaking, Self-Trapping, and Josephson Oscillations in Nonlinear Systems

Characterization of Prion Disease Associated with a Two-Octapeptide Repeat Insertion

Genetic prion disease accounts for 10–15% of prion disease. While insertion of four or more octapeptide repeats are clearly pathogenic, smaller repeat insertions have an unclear pathogenicity. The goal of this case series was to provide an insight into the characteristics of the 2-octapeptide repeat genetic variant and to provide insight into the risk for Creutzfeldt–Jakob disease in asymptomatic carriers. 2-octapeptide repeat insertion prion disease cases were collected from the National Prion Disease Pathology Surveillance Center (US), the National Prion Clinic (UK), and the National Creutzfeldt–Jakob Disease Registry (Australia). Three largescale population genetic databases were queried for the 2-octapeptide repeat insertion allele. Eight cases of 2-octapeptide repeat insertion were identified. The cases were indistinguishable from the sporadic Creutzfeldt–Jakob cases of the same molecular subtype. Western blot characterization of the prion protein in the absence of enzymatic digestion with proteinase K revealed that 2-octapeptide repeat insertion and sporadic Creutzfeldt–Jakob disease have distinct prion protein profiles. Interrogation of large-scale population datasets suggested the variant is of very low penetrance. The 2-octapeptide repeat insertion is at most a low-risk genetic variant. Predictive genetic testing for asymptomatic blood relatives is not likely to be justified given the low risk