Recent progress in open quantum systems: Non-Gaussian noise and decoherence in fermionic systems

We review our recent contributions to two topics that have become of interest in the field of open, dissipative quantum systems: non-Gaussian noise and decoherence in fermionic systems. Decoherence by non-Gaussian noise, i.e. by an environment that cannot be approximated as a bath of harmonic oscillators, is important in nanostructures (e.g. qubits) where there might be strong coupling to a small number of fluctuators. We first revisit the pedagogical example of dephasing by classical telegraph noise. Then we address two models where the quantum nature of the noise becomes essential: "quantum telegraph noise" and dephasing by electronic shot noise. In fermionic systems, many-body aspects and the Pauli principle have to be taken care of when describing the loss of phase coherence. This is relevant in electronic quantum transport through metallic and semiconducting structures. Specifically, we recount our recent results regarding dephasing in a chiral interacting electron liquid, as it is realized in the electronic Mach-Zehnder interferometer. This model can be solved employing the technique of bosonization as well as a physically transparent semiclassical method.Comment: Proceedings of Ustron 2008 conference, 6 pages, 3 figure

Controlled Dephasing of Electrons by Non-Gaussian Shot Noise

In a 'controlled dephasing' experiment [1-3], an interferometer loses its coherence due to entanglement with a controlled quantum system ('which path' detector). In experiments that were conducted thus far in mesoscopic systems only partial dephasing was achieved. This was due to weak interactions between many detector electrons and the interfering electron, resulting in a Gaussian phase randomizing process [4-10]. Here, we report the opposite extreme: a complete destruction of the interference via strong phase randomization only by a few electrons in the detector. The realization was based on interfering edge channels (in the integer quantum Hall effect regime, filling factor 2) in a Mach-Zehnder electronic interferometer, with an inner edge channel serving as a detector. Unexpectedly, the visibility quenched in a periodic lobe-type form as the detector current increased; namely, it periodically decreased as the detector current, and thus the detector's efficiency, increased. Moreover, the visibility had a V-shape dependence on the partitioning of the detector current, and not the expected dependence on the second moment of the shot noise, T(1-T), with T the partitioning. We ascribe these unexpected features to the strong detector-interferometer coupling, allowing only 1-3 electrons in the detector to fully dephase the interfering electron. Consequently, in this work we explored the non-Gaussian nature of noise [11], namely, the direct effect of the shot noise full counting statistics [12-15].Comment: 14 pages, 4 figure

DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a key role in the emerging field, synthetic biology. Five years after we constructed DEG, a database of essential genes, DEG 5.0 has significant advances over the 2004 version in both the number of essential genes and the number of organisms in which these genes are determined. The number of prokaryotic essential genes in DEG has increased about 10-fold, mainly owing to genome-wide gene essentiality screens performed in a wide range of bacteria. The number of eukaryotic essential genes has increased more than 5-fold, because DEG 1.0 only had yeast ones, but DEG 5.0 also has those in humans, mice, worms, fruit flies, zebrafish and the plant Arabidopsis thaliana. These updates not only represent significant advances of DEG, but also represent the rapid progress of the essential-gene field. DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org

Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits

MrkH, a Novel c-di-GMP-Dependent Transcriptional Activator, Controls Klebsiella pneumoniae Biofilm Formation by Regulating Type 3 Fimbriae Expression

Klebsiella pneumoniae causes significant morbidity and mortality worldwide, particularly amongst hospitalized individuals. The principle mechanism for pathogenesis in hospital environments involves the formation of biofilms, primarily on implanted medical devices. In this study, we constructed a transposon mutant library in a clinical isolate, K. pneumoniae AJ218, to identify the genes and pathways implicated in biofilm formation. Three mutants severely defective in biofilm formation contained insertions within the mrkABCDF genes encoding the main structural subunit and assembly machinery for type 3 fimbriae. Two other mutants carried insertions within the yfiN and mrkJ genes, which encode GGDEF domain- and EAL domain-containing c-di-GMP turnover enzymes, respectively. The remaining two isolates contained insertions that inactivated the mrkH and mrkI genes, which encode for novel proteins with a c-di-GMP-binding PilZ domain and a LuxR-type transcriptional regulator, respectively. Biochemical and functional assays indicated that the effects of these factors on biofilm formation accompany concomitant changes in type 3 fimbriae expression. We mapped the transcriptional start site of mrkA, demonstrated that MrkH directly activates transcription of the mrkA promoter and showed that MrkH binds strongly to the mrkA regulatory region only in the presence of c-di-GMP. Furthermore, a point mutation in the putative c-di-GMP-binding domain of MrkH completely abolished its function as a transcriptional activator. In vivo analysis of the yfiN and mrkJ genes strongly indicated their c-di-GMP-specific function as diguanylate cyclase and phosphodiesterase, respectively. In addition, in vitro assays showed that purified MrkJ protein has strong c-di-GMP phosphodiesterase activity. These results demonstrate for the first time that c-di-GMP can function as an effector to stimulate the activity of a transcriptional activator, and explain how type 3 fimbriae expression is coordinated with other gene expression programs in K. pneumoniae to promote biofilm formation to implanted medical devices

Varieties of living things: Life at the intersection of lineage and metabolism

publication-status: Publishedtypes: Articl

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis