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

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

Structure of HrcQ(B)-C, a conserved component of the bacterial type III secretion systems

Type III secretion systems enable plant and animal bacterial pathogens to deliver virulence proteins into the cytosol of eukaryotic host cells, causing a broad spectrum of diseases including bacteremia, septicemia, typhoid fever, and bubonic plague in mammals, and localized lesions, systemic wilting, and blights in plants. In addition, type III secretion systems are also required for biogenesis of the bacterial flagellum. The HrcQ(B) protein, a component of the secretion apparatus of Pseudomonas syringae with homologues in all type III systems, has a variable N-terminal and a conserved C-terminal domain (HrcQ(B)-C). Here, we report the crystal structure of HrcQ(B)-C and show that this domain retains the ability of the full-length protein to interact with other type III components. A 3D analysis of sequence conservation patterns reveals two clusters of residues potentially involved in protein–protein interactions. Based on the analogies between HrcQ(B) and its flagellum homologues, we propose that HrcQ(B)-C participates in the formation of a C-ring-like assembly

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

An extracellular steric seeding mechanism for Eph-ephrin signaling platform assembly

Erythropoetin-producing hepatoma (Eph) receptors are cell-surface protein tyrosine kinases mediating cell-cell communication. Upon activation, they form signaling clusters. We report crystal structures of the full ectodomain of human EphA2 (eEphA2) both alone and in complex with the receptor-binding domain of the ligand ephrinA5 (ephrinA5 RBD). Unliganded eEphA2 forms linear arrays of staggered parallel receptors involving two patches of residues conserved across A-class Ephs. eEphA2-ephrinA5 RBD forms a more elaborate assembly, whose interfaces include the same conserved regions on eEphA2, but rearranged to accommodate ephrinA5 RBD. Cell-surface expression of mutant EphA2s showed that these interfaces are critical for localization at cell-cell contacts and activation-dependent degradation. Our results suggest a 'nucleation' mechanism whereby a limited number of ligand-receptor interactions 'seed' an arrangement of receptors which can propagate into extended signaling arrays

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

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

Effect of different weaning age (21, 28 or 35 days) on production, growth and certain parameters of the digestive tract in rabbits

The effect of different weaning ages, that is, 21 (G21), 28 (G28) or 35 (G35) days, on growth and certain parameters of the digestive tract was examined in rabbits to assess the risk of early weaning attributable to the less-developed digestive system. On days 35 and 42, G35 rabbits had 10% to 14% and 10% higher BW, respectively ( P,0.05), than those weaned at days 21 and 28. In the 4th week of life, early weaned animals had 75% higher feed intake than G28 and G35 rabbits ( P,0.05). The relative weight of the liver increased by 62% between 21 and 28 days of age, and thereafter it decreased by 76% between 35 and 42 days of age ( P,0.05), with G21 rabbits having 29% higher weight compared with G35 animals on day 35 ( P,0.05). The relative weight of the whole gastrointestinal (GI) tract increased by 49% and 22% after weaning in G21 and G28 rabbits, respectively ( P,0.05). On day 28, the relative weight of the GI tract was 19% higher in G21 than in G28 rabbits, whereas on day 35 G21 and G28 animals had a 12% heavier GI tract compared with G35 rabbits ( P,0.05). Age influenced the ratio of stomach, small intestine and caecum within the GI tract; however, no effect of different weaning age was demonstrated. The pH value of the stomach and caecum decreased from 5.7 to 1.6 and from 7.1 to 6.3, respectively, whereas that of the small intestine increased from 6.8 to 8.4 ( P,0.05); the differences between groups were not statistically significant. Strictly anaerobic culturable bacteria were present in the caecum in high amounts (108), already at 14 days of age; no significant difference attributable to weaning age was demonstrable. The concentration of total volatile fatty acids (tVFA) was higher in G21 than in G28 and G35 throughout the experimental period ( P,0.05). The proportion of acetic and butyric acid within tVFA increased, whereas that of propionic acid decreased, resulting in a C3 : C4 ratio decreasing with age. Early weaning (G21) resulted in higher butyric acid and lower propionic acid proportions on day 28 ( P,0.05). No interaction between age and treatment was found, except in relative weight of the GI tract and caecal content. In conclusion, early weaning did not cause considerable changes in the digestive physiological parameters measured, but it resulted in 10% lower growth in rabbits

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