Optimal receptor-cluster size determined by intrinsic and extrinsic noise

Biological cells sense external chemical stimuli in their environment using cell-surface receptors. To increase the sensitivity of sensing, receptors often cluster, most noticeably in bacterial chemotaxis, a paradigm for signaling and sensing in general. While amplification of weak stimuli is useful in absence of noise, its usefulness is less clear in presence of extrinsic input noise and intrinsic signaling noise. Here, exemplified on bacterial chemotaxis, we combine the allosteric Monod-Wyman- Changeux model for signal amplification by receptor complexes with calculations of noise to study their interconnectedness. Importantly, we calculate the signal-to-noise ratio, describing the balance of beneficial and detrimental effects of clustering for the cell. Interestingly, we find that there is no advantage for the cell to build receptor complexes for noisy input stimuli in absence of intrinsic signaling noise. However, with intrinsic noise, an optimal complex size arises in line with estimates of the sizes of chemoreceptor complexes in bacteria and protein aggregates in lipid rafts of eukaryotic cells.Comment: 15 pages, 12 figures,accepted for publication on Physical Review

Unique Features of Odorant-Binding Proteins of the Parasitoid Wasp Nasonia vitripennis Revealed by Genome Annotation and Comparative Analyses

Insects are the most diverse group of animals on the planet, comprising over 90% of all metazoan life forms, and have adapted to a wide diversity of ecosystems in nearly all environments. They have evolved highly sensitive chemical senses that are central to their interaction with their environment and to communication between individuals. Understanding the molecular bases of insect olfaction is therefore of great importance from both a basic and applied perspective. Odorant binding proteins (OBPs) are some of most abundant proteins found in insect olfactory organs, where they are the first component of the olfactory transduction cascade, carrying odorant molecules to the olfactory receptors. We carried out a search for OBPs in the genome of the parasitoid wasp Nasonia vitripennis and identified 90 sequences encoding putative OBPs. This is the largest OBP family so far reported in insects. We report unique features of the N. vitripennis OBPs, including the presence and evolutionary origin of a new subfamily of double-domain OBPs (consisting of two concatenated OBP domains), the loss of conserved cysteine residues and the expression of pseudogenes. This study also demonstrates the extremely dynamic evolution of the insect OBP family: (i) the number of different OBPs can vary greatly between species; (ii) the sequences are highly diverse, sometimes as a result of positive selection pressure with even the canonical cysteines being lost; (iii) new lineage specific domain arrangements can arise, such as the double domain OBP subfamily of wasps and mosquitoes.Rothamsted Research receives grant-aided support from the BBSRC of the UK. The authors thank Prof. David M. Shuker, University of Edinburgh, UK, who provided us with N. vitripennis. FGV was supported by a predoctoral fellowship SFRH/BD/22360/2005 from the ‘Fundac¸a˜o para a Cieˆncia e a Tecnologı´a’ (Portugal). This work was funded by grants BFU2007-62927 and BFU2010-15484 from the ‘Direccio´n General de Investigacio´n Cientı´fica y Te´cnica’ (Spain) to JR. JR was partially supported by ICREA Academia (Generalitat de Catalunya). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Outflows in Infrared-Luminous Starbursts at z < 0.5. I. Sample, NaI D Spectra, and Profile Fitting

We have conducted a spectroscopic survey of 78 starbursting infrared-luminous galaxies at redshifts up to z = 0.5. We use moderate-resolution spectroscopy of the NaI D interstellar absorption feature to directly probe the neutral phase of outflowing gas in these galaxies. Over half of our sample are ultraluminous infrared galaxies that are classified as starbursts; the rest have infrared luminosities in the range log(L_IR/L_sun) = 10.2 - 12.0. The sample selection, observations, and data reduction are described here. The absorption-line spectra of each galaxy are presented. We also discuss the theory behind absorption-line fitting in the case of a partially-covered, blended absorption doublet observed at moderate-to-high resolution, a topic neglected in the literature. A detailed analysis of these data is presented in a companion paper.Comment: 59 pages, 18 figures in AASTeX preprint style; to appear in September issue of ApJ

Some algebraic properties of differential operators

First, we study the subskewfield of rational pseudodifferential operators over a differential field K generated in the skewfield of pseudodifferential operators over K by the subalgebra of all differential operators. Second, we show that the Dieudonne' determinant of a matrix pseudodifferential operator with coefficients in a differential subring A of K lies in the integral closure of A in K, and we give an example of a 2x2 matrix differential operator with coefficients in A whose Dieudonne' determiant does not lie in A.Comment: 15 page

Characterization of Plum Procyanidins by Thiolytic Depolymerization

The phenolic compounds of ?Green Gage? (GG) plums (Prunus domestica L.), ?Rainha Cla?udia Verde?, from a ?protected designation of origin? (PDO), in Portugal, were quantified in both flesh and skin tissues of plums collected in two different orchards (GG-V and GG-C). Analyzes of phenolic compounds were also performed on another GG European plum obtained in France (GG-F) and two other French plums, ?Mirabelle? (M) and ?Golden Japan? (GJ). Thiolysis was used for the first time in the analysis of plum phenolic compounds. This methodology showed that the flesh and skin contain a large proportion of flavan-3-ols, which account, respectively, for 92 and 85% in GJ, 61 and 44% in GG-V, 62 and 48% in GG-C, 54 and 27% in M, and 45 and 37% in GG-F. Terminal units of procyanidins observed in plums are mainly (+)-catechin (54?77% of all terminal units in flesh and 57?81% in skin). The GJ plums showed a phenolic composition different from all of the others, with a lower content of chlorogenic acid isomers and the presence of A-type procyanidins as dimers and terminal residues of polymerized forms. The average degree of polymerization (DPn) of plum procyanidins was higher in the flesh (5?9 units) than in the skin (4?6 units). Procyanidin B7 was observed in the flesh of all GG plums and in the skin of the Portuguese ones. Principal component analysis of the phenolic composition of the flesh and skin of these plums obtained after thiolysis allowed their distinction according to the variety and origin, opening the possibility of the use of phenolic composition for variety/origin identification

An Upper Limit on the Reflected Light from the Planet Orbiting the Star tau Bootis

The planet orbiting tau Boo at a separation of 0.046 AU could produce a reflected light flux as bright as 1e-4 relative to that of the star. A spectrum of the system will contain a reflected light component which varies in amplitude and Doppler-shift as the planet orbits the star. Assuming the secondary spectrum is primarily the reflected stellar spectrum, we can limit the relative reflected light flux to be less than 5e-5. This implies an upper limit of 0.3 for the planetary geometric albedo near 480 nm, assuming a planetary radius of 1.2 R_Jup. This albedo is significantly less than that of any of the giant planets of the solar system, and is not consistent with certain published theoretical predictions.Comment: 5 pages, 1 figure, accepted by ApJ Letter

The One-dimensional KPZ Equation and the Airy Process

Our previous work on the one-dimensional KPZ equation with sharp wedge initial data is extended to the case of the joint height statistics at n spatial points for some common fixed time. Assuming a particular factorization, we compute an n-point generating function and write it in terms of a Fredholm determinant. For long times the generating function converges to a limit, which is established to be equivalent to the standard expression of the n-point distribution of the Airy process.Comment: 15 page

Floods in the Pampas : Insights from over a decade of satellite observations

Non peer reviewedPublisher PD

An Explicit Framework for Interaction Nets

Interaction nets are a graphical formalism inspired by Linear Logic proof-nets often used for studying higher order rewriting e.g. \Beta-reduction. Traditional presentations of interaction nets are based on graph theory and rely on elementary properties of graph theory. We give here a more explicit presentation based on notions borrowed from Girard's Geometry of Interaction: interaction nets are presented as partial permutations and a composition of nets, the gluing, is derived from the execution formula. We then define contexts and reduction as the context closure of rules. We prove strong confluence of the reduction within our framework and show how interaction nets can be viewed as the quotient of some generalized proof-nets

A High-Eccentricity Low-Mass Companion to HD 89744

HD 89744 is an F7 V star with mass 1.4 M, effective temperature 6166 K, age 2.0 Gy and metallicity [Fe/H]= 0.18. The radial velocity of the star has been monitored with the AFOE spectrograph at the Whipple Observatory since 1996, and evidence has been found for a low mass companion. The data were complemented by additional data from the Hamilton spectrograph at Lick Observatory during the companion's periastron passage in fall 1999. As a result, we have determined the star's orbital wobble to have period P = 256 d, orbital amplitude K = 257 m/s, and eccentricity e = 0.7. From the stellar mass we infer that the companion has minimum mass m2 sin i = 7.2 MJup in an orbit with semi-major axis a2 = 0.88 AU. The eccentricity of the orbit, among the highest known for extra-solar planets, continues the trend that extra-solar planets with semi-major axes greater than about 0.15 AU tend to have much higher eccentricities than are found in our solar system. The high metallicity of the parent star reinforces the trend that parent stars of extra-solar planets tend to have high metallicityComment: AASTEX-LateX v5.0, 7 pages w/ 3 figures, to be published in ApJ