Immigration, Social Disadvantage and Urban Youth Gangs: Results of a Toronto-Area Survey

Both media coverage and public opinion suggest that immigrants are responsible for a high proportion of youth gang activity in Canada. Unfortunately, very little academic research has actually examined the extent and nature of youth gang activity in this country. Our paper attempts to address this gap in the literature through an analysis of data from a survey of Toronto high school students and street youth. Our results suggest that: 1) immigrant youth are less likely to report gang affiliation than their Canadian born counterparts; 2) although Black and Hispanic youth are more likely to report gang activity than youth from all other racial backgrounds, the majority of gang members in Toronto are Canadian-born whites; and 3) racial differences in gang involvement can be explained by racial differences in economic and social marginalization. The policy implications of these findings are discussed

Subspecies typing of Streptococcus agalactiae based on ribosomal subunit protein mass variation by MALDI-TOF MS

Background: A ribosomal subunit protein (rsp)-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method was developed for fast subspecies-level typing of Streptococcus agalactiae (Group B Streptococcus, GBS), a major cause of neonatal sepsis and meningitis. Methods: A total of 796 GBS whole genome sequences, covering the genetic diversity of the global GBS population, were used to in silico predict molecular mass variability of 28 rsp and to identify unique rsp mass combinations, termed “rsp-profiles”. The in silico established GBS typing scheme was validated by MALDI-TOF MS analysis of GBS isolates at two independent research sites in Europe and South East Asia. Results: We identified in silico 62 rsp-profiles, with the majority (>80%) of the 796 GBS isolates displaying one of the six rsp-profiles 1-6. These dominant rsp-profiles classify GBS strains in high concordance with the core-genome based phylogenetic clustering. Validation of our approach by in-house MALDI-TOF MS analysis of 248 GBS isolates and external analysis of 8 GBS isolates showed that across different laboratories and MALDI-TOF MS platforms, the 28 rsp were detected reliably in the mass spectra, allowing assignment of clinical isolates to rsp-profiles at high sensitivity (99%) and specificity (97%). Our approach distinguishes the major phylogenetic GBS genotypes, identifies hyper-virulent strains, predicts the probable capsular serotype and surface protein variants and distinguishes between GBS genotypes of human and animal origin. Conclusion: We combine the information depth of whole genome sequences with the highly cost efficient, rapid and robust MALDI-TOF MS approach facilitating high-throughput, inter-laboratory, large-scale GBS epidemiological and clinical studies based on pre-defined rsp-profiles

Production of glycoprotein vaccines in Escherichia coli

<p>Abstract</p> <p>Background</p> <p>Conjugate vaccines in which polysaccharide antigens are covalently linked to carrier proteins belong to the most effective and safest vaccines against bacterial pathogens. State-of-the art production of conjugate vaccines using chemical methods is a laborious, multi-step process. <it>In vivo </it>enzymatic coupling using the general glycosylation pathway of <it>Campylobacter jejuni </it>in recombinant <it>Escherichia coli </it>has been suggested as a simpler method for producing conjugate vaccines. In this study we describe the <it>in vivo </it>biosynthesis of two novel conjugate vaccine candidates against <it>Shigella dysenteriae </it>type 1, an important bacterial pathogen causing severe gastro-intestinal disease states mainly in developing countries.</p> <p>Results</p> <p>Two different periplasmic carrier proteins, AcrA from <it>C. jejuni </it>and a toxoid form of <it>Pseudomonas aeruginosa </it>exotoxin were glycosylated with <it>Shigella </it>O antigens in <it>E. coli</it>. Starting from shake flask cultivation in standard complex medium a lab-scale fed-batch process was developed for glycoconjugate production. It was found that efficiency of glycosylation but not carrier protein expression was highly susceptible to the physiological state at induction. After induction glycoconjugates generally appeared later than unglycosylated carrier protein, suggesting that glycosylation was the rate-limiting step for synthesis of conjugate vaccines in <it>E. coli</it>. Glycoconjugate synthesis, in particular expression of oligosaccharyltransferase PglB, strongly inhibited growth of <it>E. coli </it>cells after induction, making it necessary to separate biomass growth and recombinant protein expression phases. With a simple pulse and linear feed strategy and the use of semi-defined glycerol medium, volumetric glycoconjugate yield was increased 30 to 50-fold.</p> <p>Conclusions</p> <p>The presented data demonstrate that glycosylated proteins can be produced in recombinant <it>E. coli </it>at a larger scale. The described methodologies constitute an important step towards cost-effective <it>in vivo </it>production of conjugate vaccines, which in future may be used for combating severe infectious diseases, particularly in developing countries.</p

Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment

BACKGROUND: Charging of transfer-RNA with cognate amino acid is accomplished by the aminoacyl-tRNA synthetases, and proceeds through an aminoacyl adenylate intermediate. The lysyl-tRNA synthetase has evolved an active site that specifically binds lysine and ATP. Previous molecular dynamics simulations of the heat-inducible Escherichia coli lysyl-tRNA synthetase, LysU, have revealed differences in the binding of ATP and aspects of asymmetry between the nominally equivalent active sites of this dimeric enzyme. The possibility that this asymmetry results in different binding affinities for the ligands is addressed here by a parallel computational and biochemical study. RESULTS: Biochemical experiments employing isothermal calorimetry, steady-state fluorescence and circular dichroism are used to determine the order and stoichiometries of the lysine and nucleotide binding events, and the associated thermodynamic parameters. An ordered mechanism of substrate addition is found, with lysine having to bind prior to the nucleotide in a magnesium dependent process. Two lysines are found to bind per dimer, and trigger a large conformational change. Subsequent nucleotide binding causes little structural rearrangement and crucially only occurs at a single catalytic site, in accord with the simulations. Molecular dynamics based free energy calculations of the ATP binding process are used to determine the binding affinities of each site. Significant differences in ATP binding affinities are observed, with only one active site capable of realizing the experimental binding free energy. Half-of-the-sites models in which the nucleotide is only present at one active site achieve their full binding potential irrespective of the subunit choice. This strongly suggests the involvement of an anti-cooperative mechanism. Pathways for relaying information between the two active sites are proposed. CONCLUSIONS: The asymmetry uncovered here appears to be a common feature of oligomeric aminoacyl-tRNA synthetases, and may play an important functional role. We suggest a manner in which catalytic efficiency could be improved by LysU operating in an alternating sites mechanism

Distinct Transcriptional and Anti-Mycobacterial Profiles of Peripheral Blood Monocytes Dependent on the Ratio of Monocytes: Lymphocytes.

The ratio of monocytes and lymphocytes (ML ratio) in peripheral blood is associated with tuberculosis and malaria disease risk and cancer and cardiovascular disease outcomes. We studied anti-mycobacterial function and the transcriptome of monocytes in relation to the ML ratio. Mycobacterial growth inhibition assays of whole or sorted blood were performed and mycobacteria were enumerated by liquid culture. Transcriptomes of unstimulated CD14 + monocytes isolated by magnetic bead sorting were characterised by microarray. Transcript expression was tested for association with ML ratio calculated from leucocyte differential counts by linear regression. The ML ratio was associated with mycobacterial growth in vitro (β = 2.23, SE 0.91, p = 0.02). Using sorted monocytes and lymphocytes, in vivo ML ratio (% variance explained R(2) = 11%, p = 0.02) dominated over in vitro ratios (R(2) = 5%, p = 0.10) in explaining mycobacterial growth. Expression of 906 genes was associated with the ML ratio and 53 with monocyte count alone. ML-ratio associated genes were enriched for type-I and -II interferon signalling (p = 1.2 × 10(− 8)), and for genes under transcriptional control of IRF1, IRF2, RUNX1, RELA and ESRRB. The ML-ratio-associated gene set was enriched in TB disease (3.11-fold, 95% CI: 2.28-4.19, p = 5.7 × 10(− 12)) and other inflammatory diseases including atopy, HIV, IBD and SLE. The ML ratio is associated with distinct transcriptional and anti-mycobacterial profiles of monocytes that may explain the disease associations of the ML ratio

TRAPPC9 Mediates the Interaction between p150Glued and COPII Vesicles at the Target Membrane

Background: The transport of endoplasmic reticulum (ER)-derived COPII vesicles toward the ER-Golgi intermediate compartment (ERGIC) requires cytoplasmic dynein and is dependent on microtubules. p150Glued, a subunit of dynactin, has been implicated in the transport of COPII vesicles via its interaction with COPII coat components Sec23 and Sec24. However, whether and how COPII vesicle tether, TRAPP (Transport protein particle), plays a role in the interaction between COPII vesicles and microtubules is currently unknown. Principle Findings: We address the functional relationship between COPII tether TRAPP and dynactin. Overexpressed TRAPP subunits interfered with microtubule architecture by competing p150Glued away from the MTOC. TRAPP subunit TRAPPC9 bound directly to p150Glued via the same carboxyl terminal domain of p150Glued that binds Sec23 and Sec24. TRAPPC9 also inhibited the interaction between p150Glued and Sec23/Sec24 both in vitro and in vivo, suggesting that TRAPPC9 serves to uncouple p150Glued from the COPII coat, and to relay the vesicle-dynactin interaction at the target membrane. Conclusions: These findings provide a new perspective on the function of TRAPP as an adaptor between the ERGIC membrane and dynactin. By preserving the connection between dynactin and the tethered and/or fused vesicles, TRAPP allows nascent ERGIC to continue the movement along the microtubules as they mature into the cis-Golgi

Microwave experiments simulating quantum search and directed transport in artificial graphene

A series of quantum search algorithms have been proposed recently providing an algebraic speedup compared to classical search algorithms from N to \sqrt{N}, where N is the number of items in the search space. In particular, devising searches on regular lattices has become popular in extending Grover’s original algorithm to spatial searching. Working in a tight-binding setup, it could be demonstrated, theoretically, that a search is possible in the physically relevant dimensions 2 and 3 if the lattice spectrum possesses Dirac points. We present here a proof of principle experiment implementing wave search algorithms and directed wave transport in a graphene lattice arrangement. The idea is based on bringing localized search states into resonance with an extended lattice state in an energy region of low spectral density—namely, at or near the Dirac point. The experiment is implemented using classical waves in a microwave setup containing weakly coupled dielectric resonators placed in a honeycomb arrangement, i.e., artificial graphene. Furthermore, we investigate the scaling behavior experimentally using linear chains

FroDO: From Detections to 3D Objects

Object-oriented maps are important for scene understanding since they jointly capture geometry and semantics, allow individual instantiation and meaningful reasoning about objects. We introduce FroDO, a method for accurate 3D reconstruction of object instances from RGB video that infers object location, pose and shape in a coarse-to-fine manner. Key to FroDO is to embed object shapes in a novel learnt space that allows seamless switching between sparse point cloud and dense DeepSDF decoding. Given an input sequence of localized RGB frames, FroDO first aggregates 2D detections to instantiate a category-aware 3D bounding box per object. A shape code is regressed using an encoder network before optimizing shape and pose further under the learnt shape priors using sparse and dense shape representations. The optimization uses multi-view geometric, photometric and silhouette losses. We evaluate on real-world datasets, including Pix3D, Redwood-OS, and ScanNet, for single-view, multi-view, and multi-object reconstruction.Comment: To be published in CVPR 2020. The first two authors contributed equall

Climate policy meets national development contexts: Insights from Kenya and Mozambique

Despite the growth in work linking climate change and national level development agendas, there has been limited attention to their political economy. These processes mediate the winners, losers and potential trade-offs between different goals, and the political and institutional factors which enable or inhibit integration across different policy areas. This paper applies a political economy analysis to case studies on low carbon energy in Kenya and carbon forestry in Mozambique. In examining the intersection of climate and development policy, we demonstrate the critical importance of politics, power and interests when climate-motivated initiatives encounter wider and more complex national policy contexts, which strongly influence the prospects of achieving integrated climate policy and development goals in practice. We advance the following arguments: First, understanding both the informal nature and historical embeddedness of decision making around key issue areas and resource sectors of relevance to climate change policy is vital to engaging actually existing politics; why actors hold the positions they do and how they make decisions in practice. Second, we need to understand and engage with the interests, power relations and policy networks that will shape the prospects of realising climate policy goals; acting as barriers in some cases and as vehicles for change in others. Third, by looking at the ways in which common global drivers have very different impacts upon climate change policy once refracted through national levels institutions and policy processes, it is easier to understand the potential and limits of translating global policy into local practice. And fourth, climate change and development outcomes, and the associated trade-offs, look very different depending on how they are framed, who frames them and in which actor coalitions. Understanding these can inform the levers of change and power to be navigated, and with whom to engage in order to address climate change and development goals