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We demonstrate an optical waveguide device capable of supporting the optical power necessary for trapping a single atom or a cold-atom ensemble with evanescent fields. Our photonic integrated platform successfully manages optical powers of ~30mW.

We demonstrate ultrafast (

Kainate and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are two major, closely related receptor subtypes in the glutamate ion channel family. Excessive activities of these receptors have been implicated in a number of central nervous system diseases. Designing potent and selective antagonists of these receptors, especially of kainate receptors, is useful for developing potential treatment strategies for these neurological diseases. Here, we report on two RNA aptamers designed to individually inhibit kainate and AMPA receptors. To improve the biostability of these aptamers, we also chemically modified these aptamers by substituting their 2′-OH group with 2′-fluorine. These 2′-fluoro aptamers, FB9s-b and FB9s-r, were markedly resistant to RNase-catalyzed degradation, with a half-life of ∼5 days in rat cerebrospinal fluid or serum-containing medium. Furthermore, FB9s-r blocked AMPA receptor activity. Aptamer FB9s-b selectively inhibited GluK1 and GluK2 kainate receptor subunits, and also GluK1/GluK5 and GluK2/GluK5 heteromeric kainate receptors with equal potency. This inhibitory profile makes FB9s-b a powerful template for developing tool molecules and drug candidates for treatment of neurological diseases involving excessive activities of the GluK1 and GluK2 subunits.

Lodgepole pine (Pinus contorta Dougl. ex. Loud.) is an important tree species in British Columbia, Canada, both commercially and ecologically. Much of the seed used for reforestation after harvesting and wildfires is produced by seed orchards that rely on an extensive breeding program. Tree breeders require tools to adjust quickly to unforeseen challenges exacerbated by a changing climate and two approaches were examined: mulit-environment trial (MET) analyses and genomic selection. A MET dataset was used to analyse height growth data across five breeding zones using a factor analytic model for estimating additive (co)variance among test sites and the use of molecular markers to predict breeding values for height growth and wood quality traits (average wood density, earlywood density, latewood density, latewood proportion and microfibril angle) was assessed for a subsample of 1,569 trees from four progeny test sites using 19,584 single-nucleotide polymorphism markers. Test sites were clustered into four main breeding zones based on genetic correlations between sites. Climate change projections were applied to the four new zones which suggested that southern zones will expand. Predicted breeding values from Bayesian models (Bayes B and C) and best linear unbiased prediction (BLUP) using a hybrid matrix (H-matrix) were compared to models that used an average relationship matrix (ABLUP) and a realized relationship matrix (GBLUP). Bayesian models had similar prediction accuracies compared to ABLUP and GBLUP when models were confined to a closed population (> 0.74), but accuracy decreased substantially when relatedness was controlled between the training and validation populations (> 0.25). The models also worked well across environments and test cycles and were similar to GBLUP for ranking trees within families. HBLUP was equivalent to ABLUP and GBLUP models for genetic parameters and prediction accuracy, but had very low within-family rank correlations (0.08 average Spearman rank correlation across traits). Bayesian models can be used to predict breeding values and rank trees that have no phenotypic data. In contrast, HBLUP should not be used for ranking trees within families in the absence of phenotypic data, but can effectively improve estimates of variance components and breeding value estimates.

Iron nanoparticles are a promising new technology to treat contaminated groundwater, particularly as they can be engineered to optimise their transport properties. Technetium is a common contaminant at nuclear sites and can be reductively scavenged from groundwater by iron(II). Here we investigated the potential for a range of optimised iron nanoparticles to remove technetium from contaminated groundwater, and groundwater/sediment systems. Nano zero-valent iron and Carbo-iron stimulated the development of anoxic conditions while generating Fe(II) which reduced soluble Tc(VII) to sparingly soluble Tc(IV). Similar results were observed for Fe(II)-bearing biomagnetite, albeit at a slower rate. Tc(VII) remained in solution in the presence of the Fe(III) mineral nano-goethite, until acetate was added to stimulate microbial Fe(III)-reduction after which Tc(VII) concentrations decreased concomitant with Fe(II) ingrowth. The addition of iron nanoparticles to sediment microcosms caused an increase in the relative abundance of Firmicutes, consistent with fermentative/anoxic metabolisms. Residual bacteria from the synthesis of the biomagnetite nanoparticles were out-competed by the sediment microbial community. Overall the results showed that iron nanoparticles were highly effective in removing Tc(VII) from groundwater in sediment systems, and generated sustained anoxic conditions via the stimulation of beneficial microbial processes including Fe(III)-reduction and sulfate reduction.

AMPA and kainate receptors, along with NMDA receptors, are distinct subtypes of glutamate ion channels. Excessive activity of AMPA and kainate receptors has been implicated in neurological diseases, such as epilepsy and neuropathic pain. Antagonists that block their activities are therefore potential drug candidates. In a recent article in the Journal of Biological Chemistry by Jaremko et al. 2017, we have reported on the discovery and molecular characterization of an RNA aptamer of a dual functionality: the full-length RNA (101 nucleotide) inhibits AMPA receptors while the truncated or the short (55 nucleotide) RNA inhibits both the AMPA and kainate receptors. The full-length RNA aptamer was isolated through a specially designed, systematic evolution of ligands by exponential enrichment (SELEX) using only a single type of AMPA receptors expressed in HEK-293 cells. The design feature and the results of our recent article are highlighted here, as they demonstrate the utility of the SELEX approach and the potential of using a single AMPA receptor type to develop potent, novel RNA aptamers targeting multiple subunits and AMPA/kainate receptor subtypes with length-dependent functionalities.

AMPA and kainate receptors, along with NMDA receptors, represent different subtypes of glutamate ion channels. AMPA and kainate receptors share a high degree of sequence and structural similarities, and excessive activity of these receptors has been implicated in neurological diseases such as epilepsy. Therefore, blocking detrimental activity of both receptor types could be therapeutically beneficial. Here, we report the use of an in vitro evolution approach involving systematic evolution of ligands by exponential enrichment with a single AMPA receptor target (i.e. GluA1/2R) to isolate RNA aptamers that can potentially inhibit both AMPA and kainate receptors. A full-length or 101-nucleotide (nt) aptamer selectively inhibited GluA1/2R with a KI of ∼5 μm, along with GluA1 and GluA2 AMPA receptor subunits. Of note, its shorter version (55 nt) inhibited both AMPA and kainate receptors. In particular, this shorter aptamer blocked equally potently the activity of both the GluK1 and GluK2 kainate receptors. Using homologous binding and whole-cell recording assays, we found that an RNA aptamer most likely binds to the receptor's regulatory site and inhibits it noncompetitively. Our results suggest the potential of using a single receptor target to develop RNA aptamers with dual activity for effectively blocking both AMPA and kainate receptors.

Subsurface contamination is common at nuclear sites and it is likely that radioactive wastes will be managed in the long-term via burial in a deep Geological Disposal Facility (GDF). The migration of radionuclides in the geosphere from such sites is a major societal concern. In particular, long-lived, redox-active radionuclides (in the case of this thesis: 99Tc and Np) can migrate over large distances due to their high solubility under oxic conditions. Bioremediation has been proposed as a mechanism to limit the migration of 99Tc and Np in the environment. Here, an electron donor is supplied to the subsurface and soluble Tc(VII) and Np(V) are reduced to poorly soluble Tc(IV) and Np(IV), respectively. Reduction occurs via direct microbial action (termed bioreduction) or through radionuclide reaction with the by-products of microbial metabolism (primarily Fe(II)). Given the ubiquity of microorganisms and Fe in the geosphere, similar reactions can be expected in the deep subsurface surrounding a GDF. Once reduced, the long-term stability of the Tc(IV) and Np(IV) phases will significantly impact migration rates. Oxidative dissolution of Tc(IV)- and Np(IV)-bearing solids has been demonstrated in the literature and can be pervasive, thus questioning the efficacy of bioreduction. However, these studies have been conducted over short time-scales and during a single period of oxidation.Given the long half-life of 99Tc and Np and the ephemeral nature of redox conditions in the subsurface, there is a need to better understand 99Tc and Np biogeochemistry during longer time-scales and across multiple redox cycles. In this thesis, microcosm experiments have been used to address this knowledge gap. Sediment and groundwater used in the microcosms were representative of the Sellafield Ltd. nuclear site. For Tc, three successive redox cycles (reduction followed by oxidation with O2) over 2 years, gradually reduced the extent of Tc remobilisation during oxidation, and molecular scale characterisation of solids revealed that sediment associated Tc was always present as Tc(IV). Further, over time sequential extractions and EXAFS revealed an increased significance of Tc-Fe bonding in the sediment at the expense of TcO2. Despite this, a small but significant fraction of Tc(IV) was also found to be stable in solution during the experiments and XAS and TEM analysis suggested this was Tc(IV) associated with magnetite colloids. In other experiments completed with higher concentrations of bioavailable Fe (added as ferrihydrite to sediments, and in pure culture experiments with Geobacter sulfurreducens), the significance of Tc-Fe bonding was again highlighted, and potential Tc(IV) incorporation into biogenic magnetite was also documented. In experiments with Np, virtually all of the Np(V) added to oxic groundwater was removed to the sediment commensurate with microbially mediated Fe(III) reduction. Further, in systems with elevated bioavailable Fe, Np removal from solution was more extensive. Taken together, the data for Tc and Np reveals critical links between redox-active radionuclides and Fe cycling in sediments over periods of years and across multiple redox cycles. Furthermore, these processes help to predict the long-term fate of radioactive contamination at the Sellafield Ltd. nuclear site and have implications for contaminated land worldwide.