Diversity and prevalence of type VI secretion system effectors in clinical Pseudomonas aeruginosa isolates

Pseudomonas aeruginosa is an opportunistic pathogen and a major driver of morbidity and mortality in people with Cystic Fibrosis (CF). The Type VI secretion system (T6SS) is a molecular nanomachine that translocates effectors across the bacterial membrane into target cells or the extracellular environment enabling intermicrobial interaction. P. aeruginosa encodes three T6SS clusters, the H1-, H2- and H3-T6SS, and numerous orphan islands. Genetic diversity of T6SS-associated effectors in P. aeruginosa has been noted in reference strains but has yet to be explored in clinical isolates. Here, we perform a comprehensive bioinformatic analysis of the pangenome and T6SS effector genes in 52 high-quality clinical P. aeruginosa genomes isolated from CF patients and housed in the Personalised Approach to P. aeruginosa strain repository. We confirm that the clinical CF isolate pangenome is open and principally made up of accessory and unique genes that may provide strain-specific advantages. We observed genetic variability in some effector/immunity encoding genes and show that several well-characterised vgrG and PAAR islands are absent from numerous isolates. Our analysis shows clear evidence of disruption to T6SS genomic loci through transposon, prophage, and mobile genetic element insertions. We identified an orphan vgrG island in P. aeruginosa strain PAK and five clinical isolates using in silico analysis which we denote vgrG7, predicting a gene within this cluster to encode a Tle2 lipase family effector. Close comparison of T6SS loci in clinical isolates compared to reference P. aeruginosa strain PAO1 revealed the presence of genes encoding eight new T6SS effectors with the following putative functions: cytidine deaminase, lipase, metallopeptidase, NADase, and pyocin. Finally, the prevalence of characterised and putative T6SS effectors were assessed in 532 publicly available P. aeruginosa genomes, which suggests the existence of accessory effectors. Our in silico study of the P. aeruginosa T6SS exposes a level of genetic diversity at T6SS genomic loci not seen to date within P. aeruginosa, particularly in CF isolates. As understanding the effector repertoire is key to identifying the targets of T6SSs and its efficacy, this comprehensive analysis provides a path for future experimental characterisation of these mediators of intermicrobial competition and host manipulation

Towards a Holistic Migration Research Strategic Agenda: Integration, Partnerships, and Impact

The London International Development Centre Migration Leadership Team (LIDC-MLT) was commissioned by the UK Economic and Social Research Council (ESRC) and the Arts and Humanities Research Council (AHRC), which are part of UK Research and Innovation (UKRI), to develop a shared interdisciplinary and participatory strategic agenda for supporting migration research. This document sets out proposals for ESRC/AHRC and wider UKRI-funded migration research for the next five years (2020-2025) making clear recommendations about future agenda-setting and work prioritie

Telomerase Activation and Rejuvenation of Telomere Length in Stimulated T Cells Derived from Serially Transplanted Hematopoietic Stem Cells

Telomeres shorten in hematopoietic cells, including hematopoietic stem cells (HSCs), during aging and after transplantation, despite the presence of readily detectable levels of telomerase in these cells. In T cells, antigenic stimulation has been shown to result in a marked increase in the level of telomerase activity. We now show that stimulation of T cells derived from serially transplanted HSC results in a telomerase-dependent elongation of telomere length to a size similar to that observed in T cells isolated directly from young mice. Southern analysis of telomere length in resting and anti-CD3/CD28 stimulated donor-derived splenic T cells revealed an increase in telomere size by ∼7 kb for the population as a whole. Stimulation of donor-derived T cells from recipients of HSCs from telomerase-deficient mice did not result in regeneration of telomere length, demonstrating a dependence on telomerase. Furthermore, clonal anti-CD3/CD28 stimulation of donor-derived T cells followed by fluorescent in situ hybridization (FISH) analysis of telomeric signal intensity showed that telomeres had increased in size by ∼50% for all clonal expansions. Together, these results imply that one role for telomerase in T cells may be to renew or extend replicative potential via the rejuvenation of telomere length

"Endomicrobia" and Other Bacteria Associated with the Hindgut of Dermolepida albohirtum Larvae

Symbiotic bacteria residing in the hindgut chambers of scarab beetle larvae may be useful in paratransgenic approaches to reduce larval root-feeding activities on agricultural crops. We compared the bacterial community profiles associated with the hindgut walls of individual Dermolepida albohirtum third-instar larvae over 2 years and those associated with their plant root food source among different geographic regions. Denaturing gradient gel electrophoresis analysis was used with universal and Actinobacteria-specific 16S rRNA primers to reveal a number of taxa that were found consistently in all D. albohirtum larvae but not in samples from their food source, sugarcane roots. These taxa included representatives from the "Endomicrobia," Firmicutes, Proteobacteria, and Actinobacteria and were related to previously described bacteria from the intestines of other scarab larvae and termites. These universally distributed taxa have the potential to form vertically transmitted symbiotic associations with these insects

Estimating column density from ammonia (1,1) emission in star-forming regions

We present a new, approximate method of calculating the column density of ammonia in mapping observations of the 23 GHz inversion lines. The temperature regime typically found in star forming regions allows for the assumption of a slowly varying partition function for ammonia. It is therefore possible to determine the column density using only the (J=1,K=1) inversion transition rather than the typical combination of the (1,1) and (2,2) transitions, with additional uncertainties comparable to or less than typical observational error. The proposed method allows column density and mass estimates to be extended into areas of lower signal to noise ratio. We show examples of column density maps around a number of cores in the W3 and Perseus star-forming regions made using this approximation, along with a comparison to the corresponding results obtained using the full two-transition approach. We suggest that this method is a useful tool in studying the distribution of mass around YSOs, particularly in the outskirts of the protostellar envelope where the (2,2) ammonia line is often undetectable on the short timescales necessary for large area mapping.Comment: 6 pages, 6 figures, accepted by MNRA

Strain evolution in GaN Nanowires: from free-surface objects to coalesced templates

Top-down fabricated GaN nanowires, 250 nm in diameter and with various heights, have been used to experimentally determine the evolution of strain along the vertical direction of 1-dimensional objects. X-ray diffraction and photoluminescence techniques have been used to obtain the strain profile inside the nanowires from their base to their top facet for both initial compressive and tensile strains. The relaxation behaviors derived from optical and structural characterizations perfectly match the numerical results of calculations based on a continuous media approach. By monitoring the elastic relaxation enabled by the lateral free-surfaces, the height from which the nanowires can be considered strain-free has been estimated. Based on this result, NWs sufficiently high to be strain-free have been coalesced to form a continuous GaN layer. X-ray diffraction, photoluminescence and cathodoluminescence clearly show that despite the initial strain-free nanowires template, the final GaN layer is strained

The Interaction between the ISM and Star Formation in the Dwarf Starburst Galaxy NGC 4214

We present the first interferometric study of the molecular gas in the metal-poor dwarf starburst galaxy NGC 4214. Our map of the 12CO(1-0) emission, obtained at the OVRO millimeter array, reveals an unexpected structural wealth. We detected three regions of molecular emission in the north-west (NW), south-east (SE) and centre of NGC 4214 which are in very different and distinct evolutionary stages (total molecular mass: 5.1 x 10^6 M_sun). These differences are apparent most dramatically when the CO morphologies are compared to optical ground based and HST imaging: massive star formation has not started yet in the NW region; the well-known starburst in the centre is the most evolved and star formation in the SE complex started more recently. We derive a star formation efficiency of 8% for the SE complex. Using high--resolution VLA observations of neutral hydrogen HI and our CO data we generated a total gas column density map for NGC 4214 (HI + H_2). No clear correlation is seen between the peaks of HI, CO and the sites of ongoing star formation. This emphasizes the irregular nature of dwarf galaxies. The HI and CO velocities agree well, so do the H-alpha velocities. In total, we cataloged 14 molecular clumps in NGC 4214. Our results from a virial mass analysis are compatible with a Galactic CO-to-H_2 conversion factor for NGC 4214 (lower than what is usually found in metal-poor dwarf galaxies).Comment: accepted for publication in the AJ (February 2001), full ps file at: ftp://ftp.astro.caltech.edu/users/fw/ngc4214/walter_prep.p

Genetic differentiation of Glossina morsitans centralis populations

Variation at mitochondrial and microsatellite loci was used to study the breeding and dispersal structure of Glossina morsitans centralis, in six natural populations from Botswana, the Caprivi Strip (Namibia), Zambia, and in a laboratory culture derived from Singida, Tanzania. Only seven mitochondrial haplotypes were found. Mean diversity averaged over the six natural populations was 0.216 ± 0.085. The fixation index FST = 0.866 indicated a high degree of genetic differentiation among populations. Fifty-three alleles were detected among six microsatellite loci and six natural populations. Mean microsatellite diversity was 0.702 ± 0.091. Depending on the estimating model used, fixation indices varied from 0.15 to 0.225 confirming that G. m. centralis populations are strongly subdivided. For all FST estimates, positive correlations were detected between pair-wise genetic distance measures and geographical distances. The difference in fixation indices estimated from mitochondrial or nuclear loci was explained by the greater sensitivity of mitochondrial genomes to genetic drift. Population differentiation can be explained by genetic drift and the subsequent recovery of extant populations from small, discontinuous populations. These data confirm genetically the collapse and retreat of G. m. centralis populations caused by the rinderpest epizootic of the late 19th and early 20th centuries

Giant Conductance Oscillations In Mesoscopic Andreev Interferometers

We analyze the electrical conductance $G(\phi)$ of a two-dimensional, phase coherent structure in contact with two superconductors, which is known to be an oscillatory function of the phase difference $\phi$ between the superconductors. It is predicted that for a metallic sample, the amplitude of oscillation is enhanced by placing a normal barrier at the interface and that, by tuning the strength of the barrier, can be orders of magnitude greater than values observed in recent experiments. Giant oscillations can also be obtained without a barrier, provided a crucial sum rule is broken. This can be achieved by disorder induced normal scattering. In the absence of zero phase inter-channel scattering, the conductance possesses a zero phase minimum.Comment: 4 pages of Revtex, 6 figures available on reques