Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple ‘omic’ strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53 and 74 % of the Sodalis transcriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or that Sodalis is a recent introduction across the genus Glossina as a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host–microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches

Congregational bonding social capital and psychological type : an empirical enquiry among Australian churchgoers

This study explores the variation in levels of bonding social capital experienced by individual churchgoers, drawing on data generated by the Australian National Church Life Survey, and employing a five-item measure of church-related bonding social capital. Data provided by 2065 Australian churchgoers are used to test the thesis that individual differences in bonding social capital are related to a psychological model of psychological types (employing the Jungian distinctions). The data demonstrated that higher levels of bonding social capital were found among extraverts (compared with introverts), among intuitive types (compared with sensing types) and among feeling types (compared with thinking types), but no significant differences were found between judging types and perceiving types

Probing quantum phases of ultracold atoms in optical lattices by transmission spectra in cavity QED

Studies of ultracold atoms in optical lattices link various disciplines, providing a playground where fundamental quantum many-body concepts, formulated in condensed-matter physics, can be tested in much better controllable atomic systems, e.g., strongly correlated phases, quantum information processing. Standard methods to measure quantum properties of Bose-Einstein condensates (BECs) are based on matter-wave interference between atoms released from traps which destroys the system. Here we propose a nondestructive method based on optical measurements, and prove that atomic statistics can be mapped on transmission spectra of a high-Q cavity. This can be extremely useful for studying phase transitions between Mott insulator and superfluid states, since various phases show qualitatively distinct light scattering. Joining the paradigms of cavity quantum electrodynamics (QED) and ultracold gases will enable conceptually new investigations of both light and matter at ultimate quantum levels, which only recently became experimentally possible. Here we predict effects accessible in such novel setups.Comment: 6 pages, 3 figure

Centre-of-mass separation in quantum mechanics: Implications for the many-body treatment in quantum chemistry and solid state physics

We address the question to what extent the centre-of-mass (COM) separation can change our view of the many-body problem in quantum chemistry and solid state physics. It was shown that the many-body treatment based on the electron-vibrational Hamiltonian is fundamentally inconsistent with the Born-Handy ansatz so that such a treatment can never respect the COM problem. Born-Oppenheimer (B-O) approximation reveals some secret: it is a limit case where the degrees of freedom can be treated in a classical way. Beyond the B-O approximation they are inseparable in principle. The unique covariant description of all equations with respect to individual degrees of freedom leads to new types of interaction: besides the known vibronic (electron-phonon) one the rotonic (electron-roton) and translonic (electron-translon) interactions arise. We have proved that due to the COM problem only the hypervibrations (hyperphonons, i.e. phonons + rotons + translons) have true physical meaning in molecules and crystals; nevertheless, the use of pure vibrations (phonons) is justified only in the adiabatic systems. This fact calls for the total revision of our contemporary knowledge of all non-adiabatic effects, especially the Jahn-Teller effect and superconductivity. The vibronic coupling is responsible only for removing of electron (quasi)degeneracies but for the explanation of symmetry breaking and forming of structure the rotonic and translonic coupling is necessary.Comment: 39 pages, 11 sections, 3 appendice

Exciton Condensation and Perfect Coulomb Drag

Coulomb drag is a process whereby the repulsive interactions between electrons in spatially separated conductors enable a current flowing in one of the conductors to induce a voltage drop in the other. If the second conductor is part of a closed circuit, a net current will flow in that circuit. The drag current is typically much smaller than the drive current owing to the heavy screening of the Coulomb interaction. There are, however, rare situations in which strong electronic correlations exist between the two conductors. For example, bilayer two-dimensional electron systems can support an exciton condensate consisting of electrons in one layer tightly bound to holes in the other. One thus expects "perfect" drag; a transport current of electrons driven through one layer is accompanied by an equal one of holes in the other. (The electrical currents are therefore opposite in sign.) Here we demonstrate just this effect, taking care to ensure that the electron-hole pairs dominate the transport and that tunneling of charge between the layers is negligible.Comment: 12 pages, 4 figure

Controlling Chaos through Compactification in Cosmological Models with a Collapsing Phase

We consider the effect of compactification of extra dimensions on the onset of classical chaotic "Mixmaster" behavior during cosmic contraction. Assuming a universe that is well-approximated as a four-dimensional Friedmann-Robertson--Walker model (with negligible Kaluza-Klein excitations) when the contraction phase begins, we identify compactifications that allow a smooth contraction and delay the onset of chaos until arbitrarily close the big crunch. These compactifications are defined by the de Rham cohomology (Betti numbers) and Killing vectors of the compactification manifold. We find compactifications that control chaos in vacuum Einstein gravity, as well as in string theories with N = 1 supersymmetry and M-theory. In models where chaos is controlled in this way, the universe can remain homogeneous and flat until it enters the quantum gravity regime. At this point, the classical equations leading to chaotic behavior can no longer be trusted, and quantum effects may allow a smooth approach to the big crunch and transition into a subsequent expanding phase. Our results may be useful for constructing cosmological models with contracting phases, such as the ekpyrotic/cyclic and pre-big bang models.Comment: 1 figure. v2/v3: minor typos correcte

The psychological-type profile of lay church leaders in Australia

A sample of 845 lay church leaders (444 women and 401 men) from a range of 24 different denominations and movements (including house churches and independent churches) completed the Francis Psychological-Type Scales within the context of the 2006 Australian National Church Life Survey. The psychological-type profiles of these lay church leaders were almost identical to the type profiles of 1527 Australian churchgoers (936 women and 591 men) published in an earlier study by Robbins and Francis. The predominant types among female lay church leaders were ISFJ (21%), ESFJ (21%), and ISTJ (18%). The predominant types among male lay church leaders were ISTJ (28%), ISFJ (17%), ESTJ (13%), and ESFJ (12%). The SJ temperament accounted for 67% of the female lay church leaders and for 70% of the male lay church leaders. The strengths and weaknesses of the SJ leadership style are discussed

Search for electric dipole moments at storage rings

Permanent electric dipole moments (EDMs) violate parity and time reversal symmetry. Within the Standard Model (SM) they are many orders of magnitude below present experimental sensitivity. Many extensions of the SM predict much larger EDMs, which are therefore an excellent probe for the existence of "new physics". Until recently it was believed that only electrically neutral systems could be used for sensitive searches of EDMs. With the introduction of a novel experimental method, high precision for charged systems will be within reach as well. The features of this method and its possibilities are discussed.Comment: Proc. EXA2011, 6 pages; http://www.springerlink.com/content/45l35376832vhrg0

Anomalous Transport in Conical Granular Piles

Experiments on 2+1-dimensional piles of elongated particles are performed. Comparison with previous experiments in 1+1 dimensions shows that the addition of one extra dimension to the dynamics changes completely the avalanche properties, appearing a characteristic avalanche size. Nevertheless, the time single grains need to cross the whole pile varies smoothly between several orders of magnitude, from a few seconds to more than 100 hours. This behavior is described by a power-law distribution, signaling the existence of scale invariance in the transport process.Comment: Accepted in PR