Coupling light into optical fibres near the diffraction limit

The burgeoning field of astrophotonics explores the interface between astronomy and photonics. Important applications include photonic OH suppression at near-infrared wavelengths, and integrated photonic spectroscopy. These new photonic mechanisms are not well matched to conventional multi-mode fibres and are best fed with single or few-mode fibres. We envisage the largest gains in astrophotonics will come from instruments that operate with single or few-mode fibres in the diffraction limited or near diffraction limited regimes. While astronomical instruments have largely solved the problem of coupling light into multi-mode fibres this is largely unexplored territory for few-mode and single-mode fibres. Here we describe a project to explore this topic in detail, and present initial results on coupling light into single and few-mode fibres at the diffraction limit. We find that fibres with as few as ~5 guided modes have qualitatively different behaviour to single-mode fibres and share a number of the beneficial characteristics of multi-mode fibres.Comment: 11 pages, 5 figures, to be published in Proc. SPIE 6269 Ground-based and Airborne Instrumentation for Astronom

Luminescent 1,8-Naphthalimide-Derived ReI Complexes: syntheses, spectroscopy, X-ray structure and preliminary bioimaging in fission yeast cells

A series of picolyl-functionalised, fluorescent 1,8-naphthalimide ligands (L) have been synthesised and coordi-nated to ReI to form luminescent cationic complexes of the general form fac-[Re(phen)(CO)3(L)]BF4. The complexes were characterised by using a range of spectroscopic and analytical techniques. One example of a complex was also characterised in the solid-state by using single-crystal X-ray diffraction, reveal-ing a distorted octahedral coordination sphere at ReI and Re– C/Re–N bond lengths within the expected ranges. All ligands were shown to be fluorescent, with the 4-amino derivatives showing intramolecular charge transfer in the visible region (511–534 nm). The complexes generally showed a mixture of ligand-centred and/or 3MLCT emission depending upon the na-ture of the coordinated 1,8-naphthalimide ligand. For selected complexes, confocal fluorescence microscopy was undertaken by using fission yeast cells (Schizosaccharomyces pombe) and showed that the structure of the 1,8-naphthalimide ligand influ-ences the uptake and localisation of the rhenium complex

Identification of three single nucleotide polymorphisms in Anopheles gambiae immune signaling genes that are associated with natural Plasmodium falciparum infection

<p>Abstract</p> <p>Background</p> <p>Laboratory studies have demonstrated that a variety of immune signaling pathways regulate malaria parasite infection in <it>Anopheles gambiae</it>, the primary vector species in Africa.</p> <p>Methods</p> <p>To begin to understand the importance of these associations under natural conditions, an association mapping approach was adopted to determine whether single nucleotide polymorphisms (SNPs) in selected immune signaling genes in <it>A. gambiae </it>collected in Mali were associated with the phenotype of <it>Plasmodium falciparum </it>infection.</p> <p>Results</p> <p>Three SNPs were identified in field-collected mosquitoes that were associated with parasite infection in molecular form-dependent patterns: two were detected in the <it>Toll5B </it>gene and one was detected in the gene encoding insulin-like peptide 3 precursor. In addition, one infection-associated <it>Toll5B </it>SNP was in linkage disequilibrium with a SNP in sequence encoding a mitogen-activated protein kinase that has been associated with Toll signaling in mammalian cells. Both <it>Toll5B </it>SNPs showed divergence from Hardy-Weinberg equilibrium, suggesting that selection pressure(s) are acting on these loci.</p> <p>Conclusions</p> <p>Seven of these eight infection-associated and linked SNPs alter codon frequency or introduce non-synonymous changes that would be predicted to alter protein structure and, hence, function, suggesting that these SNPs could alter immune signaling and responsiveness to parasite infection.</p

Antigenic and genetic characterization of a divergent African virus, Ikoma lyssavirus

In 2009, a novel lyssavirus (subsequently named Ikoma lyssavirus, IKOV) was detected in the brain of an African civet (Civettictis civetta) with clinical rabies in the Serengeti National Park of Tanzania. The degree of nucleotide divergence between the genome of IKOV and those of other lyssaviruses predicted antigenic distinction from, and lack of protection provided by, available rabies vaccines. In addition, the index case was considered likely to be an incidental spillover event, and therefore the true reservoir of IKOV remained to be identified. The advent of sensitive molecular techniques has led to a rapid increase in the discovery of novel viruses. Detecting viral sequence alone, however, only allows for prediction of phenotypic characteristics and not their measurement. In the present study we describe the in vitro and in vivo characterization of IKOV, demonstrating that it is (1) pathogenic by peripheral inoculation in an animal model, (2) antigenically distinct from current rabies vaccine strains and (3) poorly neutralized by sera from humans and animals immunized against rabies. In a laboratory mouse model, no protection was elicited by a licensed rabies vaccine. We also investigated the role of bats as reservoirs of IKOV. We found no evidence for infection among 483 individuals of at least 13 bat species sampled across sites in the Serengeti and Southern Kenya

GNOSIS: the first instrument to use fibre Bragg gratings for OH suppression

GNOSIS is a prototype astrophotonic instrument that utilizes OH suppression fibres consisting of fibre Bragg gratings and photonic lanterns to suppress the 103 brightest atmospheric emission doublets between 1.47-1.7 microns. GNOSIS was commissioned at the 3.9-meter Anglo-Australian Telescope with the IRIS2 spectrograph to demonstrate the potential of OH suppression fibres, but may be potentially used with any telescope and spectrograph combination. Unlike previous atmospheric suppression techniques GNOSIS suppresses the lines before dispersion and in a manner that depends purely on wavelength. We present the instrument design and report the results of laboratory and on-sky tests from commissioning. While these tests demonstrated high throughput and excellent suppression of the skylines by the OH suppression fibres, surprisingly GNOSIS produced no significant reduction in the interline background and the sensitivity of GNOSIS and IRIS2 is about the same as IRIS2. It is unclear whether the lack of reduction in the interline background is due to physical sources or systematic errors as the observations are detector noise-dominated. OH suppression fibres could potentially impact ground-based astronomy at the level of adaptive optics or greater. However, until a clear reduction in the interline background and the corresponding increasing in sensitivity is demonstrated optimized OH suppression fibres paired with a fibre-fed spectrograph will at least provide a real benefits at low resolving powers.Comment: 15 pages, 13 figures, accepted to A

Achieving population-level immunity to rabies in free-roaming dogs in Africa and Asia.

Canine rabies can be effectively controlled by vaccination with readily available, high-quality vaccines. These vaccines should provide protection from challenge in healthy dogs, for the claimed period, for duration of immunity, which is often two or three years. It has been suggested that, in free-roaming dog populations where rabies is endemic, vaccine-induced protection may be compromised by immuno-suppression through malnutrition, infection and other stressors. This may reduce the proportion of dogs that seroconvert to the vaccine during vaccination campaigns and the duration of immunity of those dogs that seroconvert. Vaccination coverage may also be limited through insufficient vaccine delivery during vaccination campaigns and the loss of vaccinated individuals from populations through demographic processes. This is the first longitudinal study to evaluate temporal variations in rabies vaccine-induced serological responses, and factors associated with these variations, at the individual level in previously unvaccinated free-roaming dog populations. Individual-level serological and health-based data were collected from three cohorts of dogs in regions where rabies is endemic, one in South Africa and two in Indonesia. We found that the vast majority of dogs seroconverted to the vaccine; however, there was considerable variation in titres, partly attributable to illness and lactation at the time of vaccination. Furthermore, >70% of the dogs were vaccinated through community engagement and door-to-door vaccine delivery, even in Indonesia where the majority of the dogs needed to be caught by net on successive occasions for repeat blood sampling and vaccination. This demonstrates the feasibility of achieving population-level immunity in free-roaming dog populations in rabies-endemic regions. However, attrition of immune individuals through demographic processes and waning immunity necessitates repeat vaccination of populations within at least two years to ensure communities are protected from rabies. These findings support annual mass vaccination campaigns as the most effective means to control canine rabies.This study was funded by the International Fund for Animal Welfare (IFAW) http://www.ifaw.org/united-kingdom and the World Society for the Protection of Animals (WSPA) http://www.wspa.org.uk/, with support from the Charles Slater Fund and Jowett Fund. OR is supported by the Royal Society, and JLNW the Alborada Trust. JLNW, OR and ARF receive support from the Research and Policy for Infectious Disease Dynamics Program of the Science and Technology Directorate, Department of Homeland Security, Fogarty International Centre, National Institute of Health. DLH and ARF are supported by the U.K. Department for the Environment, Food and Rural Affairs project number SEV3500. TJM is supported by Biotechnology and Biological Sciences Research Council grant number BB/I012192/1.This is the final version. It was first published by PLOS in PLOS Neglected Tropical Diseases at http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003160

The Sydney-AAO Multi-object Integral field spectrograph (SAMI)

We demonstrate a novel technology that combines the power of the multi-object spectrograph with the spatial multiplex advantage of an integral field spectrograph (IFS). The Sydney-AAO Multi-object IFS (SAMI) is a prototype wide-field system at the Anglo-Australian Telescope (AAT) that allows 13 imaging fibre bundles ("hexabundles") to be deployed over a 1-degree diameter field of view. Each hexabundle comprises 61 lightly-fused multimode fibres with reduced cladding and yields a 75 percent filling factor. Each fibre core diameter subtends 1.6 arcseconds on the sky and each hexabundle has a field of view of 15 arcseconds diameter. The fibres are fed to the flexible AAOmega double-beam spectrograph, which can be used at a range of spectral resolutions (R=lambda/delta(lambda) ~ 1700-13000) over the optical spectrum (3700-9500A). We present the first spectroscopic results obtained with SAMI for a sample of galaxies at z~0.05. We discuss the prospects of implementing hexabundles at a much higher multiplex over wider fields of view in order to carry out spatially--resolved spectroscopic surveys of 10^4 to 10^5 galaxies.Comment: 24 pages, 16 figures. Accepted by MNRA

Achieving population-level immunity to rabies in free-roaming dogs in Africa and Asia

Published onlineJournal ArticleResearch Support, Non-U.S. Gov'tCanine rabies can be effectively controlled by vaccination with readily available, high-quality vaccines. These vaccines should provide protection from challenge in healthy dogs, for the claimed period, for duration of immunity, which is often two or three years. It has been suggested that, in free-roaming dog populations where rabies is endemic, vaccine-induced protection may be compromised by immuno-suppression through malnutrition, infection and other stressors. This may reduce the proportion of dogs that seroconvert to the vaccine during vaccination campaigns and the duration of immunity of those dogs that seroconvert. Vaccination coverage may also be limited through insufficient vaccine delivery during vaccination campaigns and the loss of vaccinated individuals from populations through demographic processes. This is the first longitudinal study to evaluate temporal variations in rabies vaccine-induced serological responses, and factors associated with these variations, at the individual level in previously unvaccinated free-roaming dog populations. Individual-level serological and health-based data were collected from three cohorts of dogs in regions where rabies is endemic, one in South Africa and two in Indonesia. We found that the vast majority of dogs seroconverted to the vaccine; however, there was considerable variation in titres, partly attributable to illness and lactation at the time of vaccination. Furthermore, >70% of the dogs were vaccinated through community engagement and door-to-door vaccine delivery, even in Indonesia where the majority of the dogs needed to be caught by net on successive occasions for repeat blood sampling and vaccination. This demonstrates the feasibility of achieving population-level immunity in free-roaming dog populations in rabies-endemic regions. However, attrition of immune individuals through demographic processes and waning immunity necessitates repeat vaccination of populations within at least two years to ensure communities are protected from rabies. These findings support annual mass vaccination campaigns as the most effective means to control canine rabies.This study was funded by the International Fund for Animal Welfare (IFAW) http://www.ifaw.org/united-kingdom and the World Society for the Protection of Animals (WSPA) http://www.wspa.org.uk/, with support from the Charles Slater Fund and Jowett Fund. OR is supported by the Royal Society, and JLNW the Alborada Trust. JLNW, OR and ARF receive support from the Research and Policy for Infectious Disease Dynamics Program of the Science and Technology Directorate, Department of Homeland Security, Fogarty International Centre, National Institute of Health. DLH and ARF are supported by the U.K. Department for the Environment, Food and Rural Affairs project number SEV3500. TJM is supported by Biotechnology and Biological Sciences Research Council grant number BB/I012192/1. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host

Host shift events play an important role in epizootics as adaptation to new hosts can profoundly affect the spread of the disease and the measures needed to control it. During the late 1990s, an epizootic in Turkey resulted in a sustained maintenance of rabies virus (RABV) within the fox population. We used Bayesian inferences to investigate whole genome sequences from fox and dog brain tissues from Turkey to demonstrate that the epizootic occurred in 1997 (±1 year). Furthermore, these data indicated that the epizootic was most likely due to a host shift from locally infected domestic dogs, rather than an incursion of a novel fox or dog RABV. No evidence was observed for genetic adaptation to foxes at consensus sequence level and dN/dS analysis suggested purifying selection. Therefore, the deep sequence data were analysed to investigate the sub-viral population during a host shift event. Viral heterogeneity was measured in all RABV samples; viruses from the early period after the host shift exhibited greater sequence variation in comparison to those from the later stage, and to those not involved in the host shift event, possibly indicating a role in establishing transmission within a new host. The transient increase in variation observed in the new host species may represent virus replication within a new environment, perhaps due to increased replication within the CNS, resulting in a larger population of viruses, or due to the lack of host constraints present in the new host reservoir

Flavivirus-induced antibody cross-reactivity

Dengue viruses (DENV) cause countless human deaths each year, whilst West Nile virus (WNV) has re-emerged as an important human pathogen. There are currently no WNV or DENV vaccines licensed for human use, yet vaccines exist against other flaviviruses. To investigate flavivirus cross-reactivity, sera from a human cohort with a history of vaccination against tick-borne encephalitis virus (TBEV), Japanese encephalitis virus (JEV) and yellow fever virus (YFV) were tested for antibodies by plaque reduction neutralization test. Neutralization of louping ill virus (LIV) occurred, but no significant neutralization of Murray Valley encephalitis virus was observed. Sera from some individuals vaccinated against TBEV and JEV neutralized WNV, which was enhanced by YFV vaccination in some recipients. Similarly, some individuals neutralized DENV-2, but this was not significantly influenced by YFV vaccination. Antigenic cartography techniques were used to generate a geometric illustration of the neutralization titres of selected sera against WNV, TBEV, JEV, LIV, YFV and DENV-2. This demonstrated the individual variation in antibody responses. Most sera had detectable titres against LIV and some had titres against WNV and DENV-2. Generally, LIV titres were similar to titres against TBEV, confirming the close antigenic relationship between TBEV and LIV. JEV was also antigenically closer to TBEV than WNV, using these sera. The use of sera from individuals vaccinated against multiple pathogens is unique relative to previous applications of antigenic cartography techniques. It is evident from these data that notable differences exist between amino acid sequence identity and mapped antigenic relationships within the family Flaviviridae