Direct measurement of DNA-mediated adhesion between lipid bilayers

Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous artificial materials have been synthesised by functionalising the outer surface of compliant Brownian units, for example emulsion droplets and lipid vesicles, with selective linkers, in particular short DNA sequences. This development extended the range of applicability of DNA as a selective glue, originally applied to solid nano and colloidal particles. On very deformable lipid vesicles, the coupling between statistical effects of multivalent interactions and mechanical deformation of the membranes gives rise to complex emergent behaviours, as we recently contributed to demonstrate [Parolini et al., Nature Communications, 2015, 6, 5948]. Several aspects of the complex phenomenology observed in these systems still lack a quantitative experimental characterisation and fundamental understanding. Here we focus on the DNA-mediated multivalent interactions of a single liposome adhering to a flat supported bilayer. This simplified geometry enables the estimate of the membrane tension induced by the DNA-mediated adhesive forces acting on the liposome. Our experimental investigation is completed by morphological measurements and the characterisation of the DNA-melting transition, probed by in-situ F\"{o}rster Resonant Energy Transfer spectroscopy. Experimental results are compared with the predictions of an analytical theory that couples the deformation of the vesicle to a full description of the statistical mechanics of mobile linkers. With at most one fitting parameter, our theory is capable of semi-quantitatively matching experimental data, confirming the quality of the underlying assumptions.Comment: 16 pages, 7 figure

Chemo-Archaeological Downsizing in a Hierarchical Universe: Impact of a Top Heavy IGIMF

We make use of a semi-analytical model of galaxy formation to investigate the origin of the observed correlation between [a/Fe] abundance ratios and stellar mass in elliptical galaxies. We implement a new galaxy-wide stellar initial mass function (Top Heavy Integrated Galaxy Initial Mass Function, TH-IGIMF) in the semi-analytic model SAG and evaluate its impact on the chemical evolution of galaxies. The SFR-dependence of the slope of the TH-IGIMF is found to be key to reproducing the correct [a/Fe]-stellar mass relation. Massive galaxies reach higher [a/Fe] abundance ratios because they are characterized by more top-heavy IMFs as a result of their higher SFR. As a consequence of our analysis, the value of the minimum embedded star cluster mass and of the slope of the embedded cluster mass function, which are free parameters involved in the TH-IGIMF theory, are found to be as low as 5 solar masses and 2, respectively. A mild downsizing trend is present for galaxies generated assuming either a universal IMF or a variable TH-IGIMF. We find that, regardless of galaxy mass, older galaxies (with formation redshifts > 2) are formed in shorter time-scales (< 2 Gyr), thus achieving larger [a/Fe] values. Hence, the time-scale of galaxy formation alone cannot explain the slope of the [a/Fe]-galaxy mass relation, but is responsible for the big dispersion of [a/Fe] abundance ratios at fixed stellar mass.We further test the hyphothesis of a TH-IGIMF in elliptical galaxies by looking into mass-to-light ratios, and luminosity functions. Models with a TH-IGIMF are also favoured by these constraints. In particular, mass-to-light ratios agree with observed values for massive galaxies while being overpredicted for less massive ones; this overprediction is present regardless of the IMF considered.Comment: 24 pages, 15 figures, 2 tables. (Comments most welcome). Summited to MNRA

Gene expression in the deep biosphere

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature 499 (2013): 205-208, doi:10.1038/nature12230.Scientific ocean drilling has revealed a deep biosphere of widespread microbial life in sub-seafloor sediment. Microbial metabolism in the marine subsurface likely plays an important role in global biogeochemical cycles1-3 but deep biosphere activities are not well understood1. Here, we describe and analyze the first subseafloor metatranscriptomes from anaerobic Peru Margin sediment up to 159 meters below seafloor (mbsf) represented by over 1 billion cDNA sequence reads. Anaerobic metabolism of amino acids, carbohydrates, and lipids appear to be dominant metabolic processes, and profiles of dissimilatory sulfite reductase (Dsr) transcripts are consistent with porewater sulfate concentration profiles1. Moreover, transcripts involved in cell division increase as a function of microbial cell concentration, indicating that increases in subseafloor microbial abundance are a function of cell division across all three domains of life. These data support calculations1 and models4 of subseafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.This work was fostered by a Center for Dark Energy Biosphere Investigations (CDEBI) grant OCE-0939564 to WO and a NSF IOS grant 1238801 to JFB.2013-12-1

Photon creation in a spherical oscillating cavity

We study the photon creation inside a perfectly conducting, spherical oscillating cavity. The electromagnetic field inside the cavity is described by means of two scalar fields which satisfy Dirichlet and (generalized) Neumann boundary conditions. As a preliminary step, we analyze the dynamical Casimir effect for both scalar fields. We then consider the full electromagnetic case. The conservation of angular momentum of the electromagnetic field is also discussed, showing that photons inside the cavity are created in singlet states.Comment: 14 pages, no figure

Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal (2019), doi:10.1038/s41396-019-0373-4.The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of “microbial dark matter”, validating hypotheses put forth by earlier metagenomic studies.This work was supported by a grant OR 417/1-1 from the Deutsche Forschungsgemeinschaft, and a Junior Researcher Fund grant from LMU Munich to WDO. This work was performed in part, through the Master’s Program in Geobiology and Paleontology (MGAP) at LMU Munich

A method to localize gamma-ray bursts using POLAR

The hard X-ray polarimeter POLAR aims to measure the linear polarization of the 50-500 keV photons arriving from the prompt emission of gamma-ray bursts (GRBs). The position in the sky of the detected GRBs is needed to determine their level of polarization. We present here a method by which, despite of the polarimeter incapability of taking images, GRBs can be roughly localized using POLAR alone. For this purpose scalers are attached to the output of the 25 multi-anode photomultipliers (MAPMs) that collect the light from the POLAR scintillator target. Each scaler measures how many GRB photons produce at least one energy deposition above 50 keV in the corresponding MAPM. Simulations show that the relative outputs of the 25 scalers depend on the GRB position. A database of very strong GRBs simulated at 10201 positions has been produced. When a GRB is detected, its location is calculated searching the minimum of the chi2 obtained in the comparison between the measured scaler pattern and the database. This GRB localization technique brings enough accuracy so that the error transmitted to the 100% modulation factor is kept below 10% for GRBs with fluence Ftot \geq 10^(-5) erg cm^(-2) . The POLAR localization capability will be useful for those cases where no other instruments are simultaneously observing the same field of view.Comment: 13 pages, 10 figure

Genealogical analyses of multiple loci of litostomatean ciliates (Protista, Ciliophora, Litostomatea)

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Phylogenetics and Evolution 66 (2012): 397-411, doi:10.1016/j.ympev.2012.06.024.The class Litostomatea is a highly diverse ciliate taxon comprising hundreds of free-living and endocommensal species. However, their traditional morphology-based classification conflicts with 18S rRNA gene phylogenies indicating (1) a deep bifurcation of the Litostomatea into Rhynchostomatia and Haptoria + Trichostomatia, and (2) body polarization and simplification of the oral apparatus as main evolutionary trends in the Litostomatea. To test whether 18S rRNA molecules provide a suitable proxy for litostomatean evolutionary history, we used eighteen new ITS1-5.8S rRNA-ITS2 region sequences from various free-living litostomatean orders. These single- and multiple-locus analyses are in agreement with previous 18S rRNA gene phylogenies, supporting that both 18S rRNA gene and ITS region sequences are effective tools for resolving phylogenetic relationships among the litostomateans. Despite insertions, deletions and mutational saturations in the ITS region, the present study shows that ITS1 and ITS2 molecules can be used to infer phylogenetic relationships not only at species level but also at higher taxonomic ranks when their secondary structure information is utilized to aid alignment.Financial support was provided by the Austrian Science Foundation (FWF Projects P-19699-B17 and P-20360-B17 to Wilhelm Foissner), the Slovak Scientific Grant Agency (VEGA Project 1/0600/11 to Peter Vd’ačný), and US NSF Grants (Projects MCB-0348341 and DEB-0816840 to Slava S. Epstein)

Calibration of semi-analytic models of galaxy formation using Particle Swarm Optimization

We present a fast and accurate method to select an optimal set of parameters in semi-analytic models of galaxy formation and evolution (SAMs). Our approach compares the results of a model against a set of observables applying a stochastic technique called Particle Swarm Optimization (PSO), a self-learning algorithm for localizing regions of maximum likelihood in multidimensional spaces that outperforms traditional sampling methods in terms of computational cost. We apply the PSO technique to the SAG semi-analytic model combined with merger trees extracted from a standard $\Lambda$CDM N-body simulation. The calibration is performed using a combination of observed galaxy properties as constraints, including the local stellar mass function and the black hole to bulge mass relation. We test the ability of the PSO algorithm to find the best set of free parameters of the model by comparing the results with those obtained using a MCMC exploration. Both methods find the same maximum likelihood region, however the PSO method requires one order of magnitude less evaluations. This new approach allows a fast estimation of the best-fitting parameter set in multidimensional spaces, providing a practical tool to test the consequences of including other astrophysical processes in SAMs.Comment: 11 pages, 4 figures, 1 table. Accepted for publication in ApJ. Comments are welcom

Circular polarization in n-type resonant tunneling diodes with Si delta-doping in the quantum well

In this work, we have investigated magneto-transport and polarization resolved photoluminescence of a GaAs/AlGaAs resonant tunneling diode with Si delta-doping at the center of the quantum well under a magnetic field parallel to the tunnel current. Three resonant peaks were observed in the current-voltage characteristics curve (J(V)) which were associated to donor-assisted resonant tunneling, electron resonant tunneling and to phonon-­assisted resonant tunneling. The optical emission from GaAs contact layers shows evidence of highly spin-polarized two-dimensional electron and hole gases which affect the spin-polarization of carriers in the well. The quantum well photoluminescence shows strong circular polarization degrees with values up to 85% under 15T at the donor assisted resonant tunneling peak voltage. Our results can be exploited for future development of voltage-controlled spintronics devices