Multilayer parking with screening on a random tree

In this paper we present a multilayer particle deposition model on a random tree. We derive the time dependent densities of the first and second layer analytically and show that in all trees the limiting density of the first layer exceeds the density in the second layer. We also provide a procedure to calculate higher layer densities and prove that random trees have a higher limiting density in the first layer than regular trees. Finally, we compare densities between the first and second layer and between regular and random trees.Comment: 15 pages, 2 figure

Absorption of a pulse by an optically dense medium: An argument for field quantization

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98713/1/AJP000527.pd

Raman scheme for adjustable bandwidth quantum memory

We propose a scenario of quantum memory for light based on Raman scattering. The storage medium is a vapor and the different spectral components of the incoming signal are stored in different atomic velocity classes. One uses appropriate pulses to reverse the resulting Doppler phase shift and to regenerate the signal, without distortion, in the backward direction. The different stages of the protocol are detailed and the recovery efficiency is calculated in the semi-classical picture. Since the memory bandwidth is determined by the Raman transition Doppler width, it can be adjusted by changing the angle of the signal and control beams. The optical depth also depends on the beam angle. As a consequence the available optical depth can be optimized, depending on the needed bandwidth. The predicted recovery efficiency is close to 100% for large optical depth.Comment: 21 pages, 3 figure

A second row Parking Paradox

We consider two variations of the discrete car parking problem where at every vertex of the integers a car arrives with rate one, now allowing for parking in two lines. a) The car parks in the first line whenever the vertex and all of its nearest neighbors are not occupied yet. It can reach the first line if it is not obstructed by cars already parked in the second line (screening). b) The car parks according to the same rules, but parking in the first line can not be obstructed by parked cars in the second line (no screening). In both models, a car that can not park in the first line will attempt to park in the second line. If it is obstructed in the second line as well, the attempt is discarded. We show that both models are solvable in terms of finite-dimensional ODEs. We compare numerically the limits of first and second line densities, with time going to infinity. While it is not surprising that model a) exhibits an increase of the density in the second line from the first line, more remarkably this is also true for model b), albeit in a less pronounced way.Comment: 11 pages, 4 figure

Spectral hole burning for stopping light

We propose a novel protocol for storage and retrieval of photon wave packets in a $\Lambda$-type atomic medium. This protocol derives from spectral hole burning and takes advantages of the specific properties of solid state systems at low temperature, such as rare earth ion doped crystals. The signal pulse is tuned to the center of the hole that has been burnt previously within the inhomogeneously broadened absorption band. The group velocity is strongly reduced, being proportional to the hole width. This way the optically carried information and energy is carried over to the off-resonance optical dipoles. Storage and retrieval are performed by conversion to and from ground state Raman coherence by using brief $\pi$-pulses. The protocol exhibits some resemblance with the well known electromagnetically induced transparency process. It also presents distinctive features such as the absence of coupling beam. In this paper we detail the various steps of the protocol, summarize the critical parameters and theoretically examine the recovery efficiency.Comment: 17 pages, 6 figures, submitted to Phys. Rev.

Sequential precedence tests

In this paper we introduce the sequential precedence test (SPT) for testing the equality of two continuous distribution functions, against the stochastically ordered alternative. This procedure replaces the classical precedence test (PT), used in life-testing experiments, by a sequence of tests which are applied at the failure times of one of the samples. This allows the possibility of stopping the experiment earlier than the PT. By means of extensive Monte Carlo simulations and real data, we show that the proposed methodology results in substantial saving of experimental time and cost, without compromising in power. Algorithms for the implementation of the SPT are included

X-ray diffraction reveals the intrinsic difference in the physical properties of membrane and soluble proteins.

Membrane proteins are distinguished from soluble proteins by their insertion into biological membranes. This insertion is achieved via a noticeable arrangement of hydrophobic amino acids that are exposed at the surface of the protein, and renders the interaction with the aliphatic tails of lipids more energetically favorable. This important difference between these two categories of proteins is the source of the need for a specific handling of membrane proteins, which transpired in the creation of new tools for their recombinant expression, purification and even crystallization. Following this line, we show here that crystals of membrane proteins display systematically higher diffraction anisotropy than those of soluble proteins. This phenomenon dramatically hampers structure solution and refinement, and has a strong impact on the quality of electron-density maps. A farther search for origins of this phenomenon showed that the type of crystallization, and thus the crystal packing, has no impact on anisotropy, nor does the nature or function of the membrane protein. Membrane proteins fully embedded within the membrane display equal anisotropy compared to the ones with extra membranous domains or fusions with soluble proteins. Overall, these results overturn common beliefs and call for a specific handling of their diffraction data

Structural insights into Clostridium perfringens delta toxin pore formation

Clostridium perfringens Delta toxin is one of the three hemolysin-like proteins produced by C. perfringens type C and possibly type B strains. One of the others, NetB, has been shown to be the major cause of Avian Nectrotic Enteritis, which following the reduction in use of antibiotics as growth promoters, has become an emerging disease of industrial poultry. Delta toxin itself is cytotoxic to the wide range of human and animal macrophages and platelets that present GM2 ganglioside on their membranes. It has sequence similarity with Staphylococcus aureus β-pore forming toxins and is expected to heptamerize and form pores in the lipid bilayer of host cell membranes. Nevertheless, its exact mode of action remains undetermined. Here we report the 2.4 Å crystal structure of monomeric Delta toxin. The superposition of this structure with the structure of the phospholipid-bound F component of S. aureus leucocidin (LukF) revealed that the glycerol molecules bound to Delta toxin and the phospholipids in LukF are accommodated in the same hydrophobic clefts, corresponding to where the toxin is expected to latch onto the membrane, though the binding sites show significant differences. From structure-based sequence alignment with the known structure of staphylococcal α-hemolysin, a model of the Delta toxin pore form has been built. Using electron microscopy, we have validated our model and characterized the Delta toxin pore on liposomes. These results highlight both similarities and differences in the mechanism of Delta toxin (and by extension NetB) cytotoxicity from that of the staphylococcal pore-forming toxins

The C-Terminal Domain of the Arabinosyltransferase Mycobacterium tuberculosis EmbC Is a Lectin-Like Carbohydrate Binding Module

The D-arabinan-containing polymers arabinogalactan (AG) and lipoarabinomannan (LAM) are essential components of the unique cell envelope of the pathogen Mycobacterium tuberculosis. Biosynthesis of AG and LAM involves a series of membrane-embedded arabinofuranosyl (Araf) transferases whose structures are largely uncharacterised, despite the fact that several of them are pharmacological targets of ethambutol, a frontline drug in tuberculosis therapy. Herein, we present the crystal structure of the C-terminal hydrophilic domain of the ethambutol-sensitive Araf transferase M. tuberculosis EmbC, which is essential for LAM synthesis. The structure of the C-terminal domain of EmbC (EmbCCT) encompasses two sub-domains of different folds, of which subdomain II shows distinct similarity to lectin-like carbohydrate-binding modules (CBM). Co-crystallisation with a cell wall-derived di-arabinoside acceptor analogue and structural comparison with ligand-bound CBMs suggest that EmbCCT contains two separate carbohydrate binding sites, associated with subdomains I and II, respectively. Single-residue substitution of conserved tryptophan residues (Trp868, Trp985) at these respective sites inhibited EmbC-catalysed extension of LAM. The same substitutions differentially abrogated binding of di- and penta-arabinofuranoside acceptor analogues to EmbCCT, linking the loss of activity to compromised acceptor substrate binding, indicating the presence of two separate carbohydrate binding sites, and demonstrating that subdomain II indeed functions as a carbohydrate-binding module. This work provides the first step towards unravelling the structure and function of a GT-C-type glycosyltransferase that is essential in M. tuberculosis. Author Summary Top Tuberculosis (TB), an infectious disease caused by the bacillus Mycobacterium tuberculosis, burdens large swaths of the world population. Treatment of active TB typically requires administration of an antibiotic cocktail over several months that includes the drug ethambutol. This front line compound inhibits a set of arabinosyltransferase enzymes, called EmbA, EmbB and EmbC, which are critical for the synthesis of arabinan, a vital polysaccharide in the pathogen's unique cell envelope. How precisely ethambutol inhibits arabinosyltransferase activity is not clear, in part because structural information of its pharmacological targets has been elusive. Here, we report the high-resolution structure of the C-terminal domain of the ethambutol-target EmbC, a 390-amino acid fragment responsible for acceptor substrate recognition. Combining the X-ray crystallographic analysis with structural comparisons, site-directed mutagenesis, activity and ligand binding assays, we identified two regions in the C-terminal domain of EmbC that are capable of binding acceptor substrate mimics and are critical for activity of the full-length enzyme. Our results begin to define structure-function relationships in a family of structurally uncharacterised membrane-embedded glycosyltransferases, which are an important target for tuberculosis therapy

Identification and characterization of a novel non-structural protein of bluetongue virus

Bluetongue virus (BTV) is the causative agent of a major disease of livestock (bluetongue). For over two decades, it has been widely accepted that the 10 segments of the dsRNA genome of BTV encode for 7 structural and 3 non-structural proteins. The non-structural proteins (NS1, NS2, NS3/NS3a) play different key roles during the viral replication cycle. In this study we show that BTV expresses a fourth non-structural protein (that we designated NS4) encoded by an open reading frame in segment 9 overlapping the open reading frame encoding VP6. NS4 is 77–79 amino acid residues in length and highly conserved among several BTV serotypes/strains. NS4 was expressed early post-infection and localized in the nucleoli of BTV infected cells. By reverse genetics, we showed that NS4 is dispensable for BTV replication in vitro, both in mammalian and insect cells, and does not affect viral virulence in murine models of bluetongue infection. Interestingly, NS4 conferred a replication advantage to BTV-8, but not to BTV-1, in cells in an interferon (IFN)-induced antiviral state. However, the BTV-1 NS4 conferred a replication advantage both to a BTV-8 reassortant containing the entire segment 9 of BTV-1 and to a BTV-8 mutant with the NS4 identical to the homologous BTV-1 protein. Collectively, this study suggests that NS4 plays an important role in virus-host interaction and is one of the mechanisms played, at least by BTV-8, to counteract the antiviral response of the host. In addition, the distinct nucleolar localization of NS4, being expressed by a virus that replicates exclusively in the cytoplasm, offers new avenues to investigate the multiple roles played by the nucleolus in the biology of the cell