Photon-photon gates in Bose-Einstein condensates

It has recently been shown that light can be stored in Bose-Einstein condensates for over a second. Here we propose a method for realizing a controlled phase gate between two stored photons. The photons are both stored in the ground state of the effective trapping potential inside the condensate. The collision-induced interaction is enhanced by adiabatically increasing the trapping frequency and by using a Feshbach resonance. A controlled phase shift of $\pi$ can be achieved in one second.Comment: 4 pages, 3 figure

Secretory RING finger proteins function as effectors in a grapevine galling insect.

BackgroundAll eukaryotes share a conserved network of processes regulated by the proteasome and fundamental to growth, development, or perception of the environment, leading to complex but often predictable responses to stress. As a specialized component of the ubiquitin-proteasome system (UPS), the RING finger domain mediates protein-protein interactions and displays considerable versatility in regulating many physiological processes in plants. Many pathogenic organisms co-opt the UPS through RING-type E3 ligases, but little is known about how insects modify these integral networks to generate novel plant phenotypes.ResultsUsing a combination of transcriptome sequencing and genome annotation of a grapevine galling species, Daktulosphaira vitifoliae, we identified 138 putatively secretory protein RING-type (SPRINGs) E3 ligases that showed structure and evolutionary signatures of genes under rapid evolution. Moreover, the majority of the SPRINGs were more expressed in the feeding stage than the non-feeding egg stage, in contrast to the non-secretory RING genes. Phylogenetic analyses indicated that the SPRINGs formed clusters, likely resulting from species-specific gene duplication and conforming to features of arthropod host-manipulating (effector) genes. To test the hypothesis that these SPRINGs evolved to manipulate cellular processes within the plant host, we examined SPRING interactions with grapevine proteins using the yeast two-hybrid assay. An insect SPRING interacted with two plant proteins, a cellulose synthase, CSLD5, and a ribosomal protein, RPS4B suggesting secretion reprograms host immune signaling, cell division, and stress response in favor of the insect. Plant UPS gene expression during gall development linked numerous processes to novel organogenesis.ConclusionsTaken together, D. vitifoliae SPRINGs represent a novel gene expansion that evolved to interact with Vitis hosts. Thus, a pattern is emerging for gall forming insects to manipulate plant development through UPS targeting

Controllable-dipole quantum memory

We present a quantum memory protocol for photons that is based on the direct control of the transition dipole moment. We focus on the case where the light-matter interaction is enhanced by a cavity. We show that the optimal write process (maximizing the storage efficiency) is related to the optimal read process by a reversal of the {\it effective time} $\tau=\int dt g^2(t)/\kappa$, where $g(t)$ is the time-dependent coupling and $\kappa$ is the cavity decay rate. We discuss the implementation of the protocol in a rare-earth ion doped crystal, where an optical transition can be turned on and off by switching a magnetic field.Comment: 7 pages, 6 figure

Tempo and mode of early gene loss in endosymbiotic bacteria from insects

BACKGROUND: Understanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode (size and types of deletions) of gene losses. In this study, we analysed five endosymbiotic genome sequences of the gamma-proteobacteria (three different Buchnera aphidicola strains, Wigglesworthia glossinidia, Blochmannia floridanus) to test if gene loss could be driven by the selective importance of genes. We used a parsimony method to reconstruct a minimal ancestral genome of insect endosymbionts and quantified gene loss along the branches of the phylogenetic tree. To evaluate the selective or functional importance of genes, we used a parameter that measures the level of adaptive codon bias in E. coli (i.e. codon adaptive index, or CAI), and also estimates of evolutionary rates (Ka) between pairs of orthologs either in free-living bacteria or in pairs of symbionts. RESULTS: Our results demonstrate that genes lost in the early stages of symbiosis were on average less selectively constrained than genes conserved in any of the extant symbiotic strains studied. These results also extend to more recent events of gene losses (i.e. among Buchnera strains) that still tend to concentrate on genes with low adaptive bias in E. coli and high evolutionary rates both in free-living and in symbiotic lineages. In addition, we analyzed the physical organization of gene losses for early steps of symbiosis acquisition under the hypothesis of a common origin of different symbioses. In contrast with previous findings we show that gene losses mostly occurred through loss of rather small blocks and mostly in syntenic regions between at least one of the symbionts and present-day E. coli. CONCLUSION: At both ancient and recent stages of symbiosis evolution, gene loss was at least partially influenced by selection, highly conserved genes being retained more readily than lowly conserved genes: although losses might result from drift due to the bottlenecking of endosymbiontic populations, we demonstrated that purifying selection also acted by retaining genes of greater selective importance

Quantum Memory with a controlled homogeneous splitting

We propose a quantum memory protocol where a input light field can be stored onto and released from a single ground state atomic ensemble by controlling dynamically the strength of an external static and homogeneous field. The technique relies on the adiabatic following of a polaritonic excitation onto a state for which the forward collective radiative emission is forbidden. The resemblance with the archetypal Electromagnetically-Induced-Transparency (EIT) is only formal because no ground state coherence based slow-light propagation is considered here. As compared to the other grand category of protocols derived from the photon-echo technique, our approach only involves a homogeneous static field. We discuss two physical situations where the effect can be observed, and show that in the limit where the excited state lifetime is longer than the storage time, the protocols are perfectly efficient and noise-free. We compare the technique to other quantum memories, and propose atomic systems where the experiment can be realized.Comment: submitted to New Journal of Physics, Focus on Quantum Memor

Gene knockdown by RNAi in the pea aphid Acyrthosiphon pisum

<p>Abstract</p> <p>Background</p> <p>RNA interference (RNAi) is a powerful method to inhibit gene expression in a sequence specific manner.</p> <p>Results</p> <p>Here, we described the development of RNAi by micro-injection of double-stranded RNA (dsRNA) in the pea aphid <it>Acyrthosiphon pisum</it>. Injection of dsRNA into whole aphid body induced the silencing of two marker genes with different expression patterns: the ubiquitously expressed <it>Ap-crt </it>genes encoding a calreticulin and the gut specific <it>Ap-cath-L </it>gene encoding a cathepsin-L. Time-course analysis of the silencing showed similar temporal patterns for both genes: inhibition started at 1 day after injection, reached its maximum at 5 days and stopped at 7 days. A comparable 40% decrease of gene expression was observed for <it>Ap-crt </it>and <it>Ap-cath-L</it>.</p> <p>Conclusion</p> <p>The pea aphid is the first Hemipteran insect for which genome sequence will be available soon. The gene knockdown technique developed in this study will be an essential post-genomic tool for further investigations in aphidology.</p

Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)

Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.Beatriz Sabater-Muñoz... et al

Comparison of Gene Repertoires and Patterns of Evolutionary Rates in Eight Aphid Species That Differ by Reproductive Mode

In theory, the loss of sexual reproduction is expected to result in the accumulation of deleterious mutations. In aphids, two main types of life cycle, cyclic and obligate parthenogenesis, represent respectively “sexual” and “asexual” reproductive modes. We used the complete pea aphid genome and previously published expressed sequence tags (ESTs) from two other aphid species. In addition, we obtained 100,000 new ESTs from five more species. The final set comprised four sexual and four asexual aphid species and served to test the influence of the reproductive mode on the evolutionary rates of genes. We reconstructed coding sequences from ESTs and annotated these genes, discovering a novel peptide gene family that appears to be among the most highly expressed transcripts from several aphid species. From 203 genes found to be 1:1 orthologs among the eight species considered, we established a species tree that partly conflicted with taxonomy (for Myzus ascalonicus). We then used this topology to evaluate the dynamics of evolutionary rates and mutation accumulation in the four sexual and four asexual taxa. No significant increase of the nonsynonymous to synonymous ratio or of nonsynonymous mutation numbers was found in any of the four branches for asexual taxa. We however found a significant increase of the synonymous rate in the branch leading to the asexual species Rhopalosiphum maidis, which could be due to a change in the mutation rate or to an increased number of generations implied by its change of life cycle

An AT Mutational Bias in the Tiny GC-Rich Endosymbiont Genome of Hodgkinia

The fractional guanine + cytosine (GC) contents of sequenced bacterial genomes range from 13% to 75%. Despite several decades of research aimed at understanding this wide variation, the forces controlling GC content are not well understood. Recent work has suggested that a universal adenine + thymine (AT) mutational bias exists in all bacteria and that the elevated GC contents found in some bacterial genomes is due to genome-wide selection for increased GC content. These results are generally consistent with the low GC contents observed in most strict endosymbiotic bacterial genomes, where the loss of DNA repair mechanisms combined with the population genetic effects of small effective population sizes and decreased recombination should lower the efficacy of selection and shift the equilibrium GC content in the mutationally favored AT direction. Surprisingly, the two smallest bacterial genomes, Candidatus Hodgkinia cicadicola (144 kb) and Candidatus Tremblaya princeps (139 kb), have the unusual combination of highly reduced genomes and elevated GC contents, raising the possibility that these bacteria may be exceptions to the otherwise apparent universal bacterial AT mutational bias. Here, using population genomic data generated from the Hodgkinia genome project, we show that Hodgkinia has a clear AT mutational bias. These results provide further evidence that an AT mutational bias is universal in bacteria, even in strict endosymbionts with elevated genomic GC contents

Masculinization of the X Chromosome in the Pea Aphid

International audienceEvolutionary theory predicts that sexually antagonistic mutations accumulate differentially on the X chromosome and autosomes in species with an XY sex-determination system, with effects (masculinization or feminization of the X) depending on the dominance of mutations. Organisms with alternative modes of inheritance of sex chromosomes offer interesting opportunities for studying sexual conflicts and their resolution, because expectations for the preferred genomic location of sexually antagonistic alleles may differ from standard systems. Aphids display an XX/X0 system and combine an unusual inheritance of the X chromosome with the alternation of sexual and asexual reproduction. In this study, we first investigated theoretically the accumulation of sexually antagonistic mutations on the aphid X chromosome. Our results show that i) the X is always more favourable to the spread of male-beneficial alleles than autosomes, and should thus be enriched in sexually antagonistic alleles beneficial for males, ii) sexually antagonistic mutations beneficial for asexual females accumulate preferentially on autosomes, iii) in contrast to predictions for standard systems, these qualitative results are not affected by the dominance of mutations. Under the assumption that sex-biased gene expression evolves to solve conflicts raised by the spread of sexually antagonistic alleles, one expects that male-biased genes should be enriched on the X while asexual female-biased genes should be enriched on autosomes. Using gene expression data (RNA-Seq) in males, sexual females and asexual females of the pea aphid, we confirm these theoretical predictions. Although other mechanisms than the resolution of sexual antagonism may lead to sex-biased gene expression, we argue that they could hardly explain the observed difference between X and autosomes. On top of reporting a strong masculinization of the aphid X chromosome, our study highlights the relevance of organisms displaying an alternative mode of sex chromosome inheritance to understanding the forces shaping chromosome evolution