Bacteria Are Smartphones and Mobile Genes Are Apps

Bacterial core and accessory genome components are analogous to the operating system and applications of smartphones. The core genome provides stable taxonomy and species lists, but phenotypes reflect the mobile pool of accessory genes. This suggests changes to the ways we define bacterial species and describe bacterial communities

Orientation-sensitivity to facial features explains the Thatcher illusion

The Thatcher illusion provides a compelling example of the perceptual cost of face inversion. The Thatcher illusion is often thought to result from a disruption to the processing of spatial relations between face features. Here, we show the limitations of this account and instead demonstrate that the effect of inversion in the Thatcher illusion is better explained by a disruption to the processing of purely local facial features. Using a matching task, we found that participants were able to discriminate normal and Thatcherized versions of the same face when they were presented in an upright orientation, but not when the images were inverted. Next, we showed that the effect of inversion was also apparent when only the eye region or only the mouth region was visible. These results demonstrate that a key component of the Thatcher illusion is to be found in orientation-specific encoding of the expressive features (eyes and mouth) of the face

Imaging Polarimeter Arrays for Near-Millimeter Waves

An integrated-circuit antenna array has been developed that images both polarization and intensity. The array consists of a row of antennas that lean alternately left and right, creating two interlaced sub-arrays that respond to different polarizations. The arrays and the bismuth bolometer detectors are made by a photoresist shadowing technique that requires only one photolithographic mask. The array has measured polarization at a wavelength of 800 µm with an absolute accuracy of 0.8° and a relative precision of 7 arc min. and has demonstrated nearly diffraction-Iimited resolutiort of a 20° step in polarization

The performance of the quantum adiabatic algorithm on random instances of two optimization problems on regular hypergraphs

In this paper we study the performance of the quantum adiabatic algorithm on random instances of two combinatorial optimization problems, 3-regular 3-XORSAT and 3-regular Max-Cut. The cost functions associated with these two clause-based optimization problems are similar as they are both defined on 3-regular hypergraphs. For 3-regular 3-XORSAT the clauses contain three variables and for 3-regular Max-Cut the clauses contain two variables. The quantum adiabatic algorithms we study for these two problems use interpolating Hamiltonians which are stoquastic and therefore amenable to sign-problem free quantum Monte Carlo and quantum cavity methods. Using these techniques we find that the quantum adiabatic algorithm fails to solve either of these problems efficiently, although for different reasons.Comment: 20 pages, 15 figure

Slipins: ancient origin, duplication and diversification of the stomatin protein family

<p>Abstract</p> <p>Background</p> <p>Stomatin is a membrane protein that was first isolated from human red blood cells. Since then, a number of stomatin-like proteins have been identified in all three domains of life. The conservation among these proteins is remarkable, with bacterial and human homologs sharing 50 % identity. Despite being associated with a variety of diseases such as cancer, kidney failure and anaemia, precise functions of these proteins remain unclear.</p> <p>Results</p> <p>We have constructed a comprehensive phylogeny of all 'stomatin-like' sequences that share a 150 amino acid domain. We show these proteins comprise an ancient family that arose early in prokaryotic evolution, and we propose a new nomenclature that reflects their phylogeny, based on the name "slipin" (stomatin-like protein). Within prokaryotes there are two distinct subfamilies that account for the two different origins of the eight eukaryotic stomatin subfamilies, one of which gave rise to eukaryotic SLP-2, renamed here "paraslipin". This was apparently acquired through the mitochondrial endosymbiosis and is widely distributed amongst the major kingdoms. The other prokaryotic subfamily gave rise to the ancestor of the remaining seven eukaryotic subfamilies. The highly diverged "alloslipin" subfamily is represented only by fungal, viral and ciliate sequences. The remaining six subfamilies, collectively termed "slipins", are confined to metazoa. Protostome stomatin, as well as a newly reported arthropod subfamily slipin-4, are restricted to invertebrate groups, whilst slipin-1 (previously SLP-1) is present in nematodes and higher metazoa. In vertebrates, the stomatin family expanded considerably, with at least two duplication events giving rise to podocin and slipin-3 subfamilies (previously SLP-3), with the retained ancestral sequence giving rise to vertebrate stomatin.</p> <p>Conclusion</p> <p>Stomatin-like proteins have their origin in an ancient duplication event that occurred early on in the evolution of prokaryotes. By constructing a phylogeny of this family, we have identified and named a number of orthologous groups: these can now be used to infer function of stomatin subfamilies in a meaningful way.</p

Accurate prediction of gene feedback circuit behavior from component properties

A basic assumption underlying synthetic biology is that analysis of genetic circuit elements, such as regulatory proteins and promoters, can be used to understand and predict the behavior of circuits containing those elements. To test this assumption, we used time‐lapse fluorescence microscopy to quantitatively analyze two autoregulatory negative feedback circuits. By measuring the gene regulation functions of the corresponding repressor–promoter interactions, we accurately predicted the expression level of the autoregulatory feedback loops, in molecular units. This demonstration that quantitative characterization of regulatory elements can predict the behavior of genetic circuits supports a fundamental requirement of synthetic biology

Extending Bauer's corollary to fractional derivatives

We comment on the method of Dreisigmeyer and Young [D. W. Dreisigmeyer and P. M. Young, J. Phys. A \textbf{36}, 8297, (2003)] to model nonconservative systems with fractional derivatives. It was previously hoped that using fractional derivatives in an action would allow us to derive a single retarded equation of motion using a variational principle. It is proven that, under certain reasonable assumptions, the method of Dreisigmeyer and Young fails.Comment: Accepted Journal of Physics A at www.iop.org/EJ/journal/JPhys