Shrimp MultiPath™ multiplexed PCR white spot syndrome virus detection in penaeid shrimp.

White spot syndrome virus (WSSV), which causes white spot disease, is one of the notoriously feared infectious agents in the shrimp industry, inflicting estimated production losses world-wide of up to US$1 billion annually. Cost-effective accessible surveillance testing and targeted diagnosis are key to alerting shrimp industries and authorities worldwide early about WSSV carrier status in targeted shrimp populations. Here we present key validation pathway metrics for the Shrimp MultiPathTM (SMP) WSSV assay as part of the multi-pathogen detection platform. With superior throughput, fast turn-around time, and extremely low cost per test, the SMP WSSV assay achieves a high level of analytical sensitivity (~2.9 copies), perfect analytical specificity (~100%), and good intra- and inter-run repeatability (coefficient of variation <5%). The diagnostic metrics were estimated using Bayesian latent class analysis on data from 3 experimental shrimp populations from Latin America with distinct WSSV prevalence and yielded a diagnostic sensitivity of 95% and diagnostic specificity of 99% for SMP WSSV, which was higher than these parameters for the TaqMan quantitative PCR (qPCR) assays currently recommended by the World Organisation for Animal Health and the Commonwealth Scientific and Industrial Research Organisation. This paper additionally presents compelling data for the use of synthetic double-stranded DNA analyte spiked into pathogen-naïve shrimp tissue homogenate as a means to substitute clinical samples for assay validation pathways targeting rare pathogens. SMP WSSV shows analytical and diagnostic metrics comparable to qPCR-based assays and demonstrates fit-for-purpose performance for detection of WSSV in clinically diseased and apparently healthy animals.

Detection and genetic diversity of porcine rotavirus A, B and C in eastern Australian piggeries.

Rotaviruses (RV) have a high prevalence in piggeries worldwide and are one of the major pathogens causing severe diarrhoea in young pigs. RV species A, B, and C have been linked to piglet diarrhoea in Australian pig herds, but their genetic diversity has not been studied in detail. Based on sequencing of the structural viral protein 7 (VP7) RVA G genotypes G3, G4 and G5, and RVC types G1, G3, G5, and G6 have been identified in Australian piggeries in previous studies. Although occurrence of RVB was reported in Australia in 1988, no further genetic analysis has been conducted. To improve health management decisions in Australian pig herds, more information on RV prevalence and genetic diversity is needed. Here, 243 enteric samples collected from 20 pig farms within Eastern Australia were analysed for the presence of RV in different age groups using a novel PCR-based multiplex assay (Pork MultiPath™ enteric panel). RVA, RVB, and RVC were detected in 10, 14, and 14 farms, respectively. Further sequencing of VP7 in selected RV-positive samples revealed G genotypes G2, G5, G9 (RVA), G6, G8, G14, G16, G20 (RVB), and G1, G3, G5, G6 (RVC) present. RVA was only detected in young (<10 weeks old) pigs whereas RVB and RVC were also detected in older animals (>11 weeks old). Interestingly, RVB and RVC G-type occurrence differed between age groups. In conclusion, this study provides new insights on the prevalence and diversity of different RV species in pig herds of Eastern Australia whilst demonstrating the ability of the Pork MultiPath™ technology to accurately differentiate between these RV species.

Enterocytozoon hepatopenaei real-time and Shrimp MultiPathTM PCR assay validation for South-East Asian and Latin American strains of Penaeid shrimp.

Enterocytozoon hepatopenaei (EHP) infections are a global challenge for the Penaeid shrimp industry with a sharp rise in prevalence over the last 10 yr. EHP is known to cause sub-optimal growth, large size variation and reduced survival of shrimp. Molecular methods development has mainly focussed on 18S rRNA or spore wall protein 1 (SWP1). Due to the specificity and sensitivity issues with previously designed assays for both targets, new molecular assays are needed by the global shrimp industry and regulators to help manage the risks posed by EHP. This paper describes new real-time PCR (qPCR) methods developed for the novel EHP gene targets polar tube protein 2 (PTP2) and spore wall protein 26 (SWP26), whilst also presenting performance metrics of the new Shrimp MultiPathTM technology EHP assay. qPCR assays PTP2G and SWP26G show high amplification efficiency, a limit of detection (LOD) of between 1 and 4 copies, low assay variation and high diagnostic sensitivity (DSe) and specificity (DSp) compared to imperfect reference assays. Similar performance is seen with Shrimp MultiPathTM EHP showing an LOD of 8 copies, low assay variation and high DSe and DSp. These novel molecular targets for EHP and Shrimp MultiPathTM EHP strengthen global efforts to monitor and mitigate risks of EHP infections and outbreaks. Moreover, this study presents novel data on distribution of EHP in shrimp populations from South-East Asia and Latin America, and how sequence variations need to be considered when monitoring EHP in different geographies.

Ultranarrow Optical Inhomogeneous Linewidth in a Stoichiometric Rare-Earth Crystal.

We obtain a low optical inhomogeneous linewidth of 25 MHz in the stoichiometric rare-earth crystal EuCl_{3}·6H_{2}O by isotopically purifying the crystal in ^{35}Cl. With this linewidth, an important limit for stoichiometric rare-earth crystals is surpassed: the hyperfine structure of ^{153}Eu is spectrally resolved, allowing the whole population of ^{153}Eu^{3+} ions to be prepared in the same hyperfine state using hole-burning techniques. This material also has a very high optical density, and can have long coherence times when deuterated. This combination of properties offers new prospects for quantum information applications. We consider two of these: quantum memories and quantum many-body studies. We detail the improvements in the performance of current memory protocols possible in these high optical depth crystals, and describe how certain memory protocols, such as off-resonant Raman memories, can be implemented for the first time in a solid-state system. We explain how the strong excitation-induced interactions observed in this material resemble those seen in Rydberg systems, and describe how these interactions can lead to quantum many-body states that could be observed using standard optical spectroscopy techniques.

Storage and retrieval of collective excitations on a long-lived spin transition in a rare-earth ion-doped crystal.

Robust, long-lived optical quantum memories are important components of many quantum information and communication protocols. We demonstrate coherent generation, storage, and retrieval of excitations on a long-lived spin transition via spontaneous Raman scattering in a rare-earth ion-doped crystal. We further study the time dynamics of the optical correlations in this system. This is the first demonstration of its kind in a solid and an enabling step toward realizing a solid-state quantum repeater.

Ultrastructure of putative germ granules in the penaeid shrimp Marsupenaeus japonicus.

Knowledge about the specification of the germ line in penaeid shrimp would allow development of techniques to control germ cell formation and/or fate to produce reproductively sterile shrimp for genetic copyright purposes. Recent studies have traced the localization of an RNA-enriched intracellular body (ICB) in the putative germ line of four penaeid shrimp species. It is hypothesized that the ICB may serve as a putative germ granule and marker of germ line fate. In this study semi-thin and ultra-thin sections of Marsupenaeus japonicus embryos were prepared, and the dimensions and ultrastructure of the ICB was examined at different stages of embryogenesis. The ICB was an aggregation of electron dense granules, small vesicles and multi-vesicular bodies (MVBs), similar to germ granules from other species. Lamellar membranes and mitochondria were localized at the periphery of the ICB. Using fluorescence microscopy, microtubules were also observed between the centrosome and the ICB. The localization of the ICB in the D lineage and putative germ cell line, the enrichment of RNA in the ICB, and the ultrastructural similarities to other germ granules characterized in this study support the hypothesis that the ICB contains germ granules.

Precision measurement of electronic ion-ion interactions between neighboring Eu3+ optical centers.

We report measurements of discrete excitation-induced frequency shifts on the 7F0→5D0 transition of the Eu+ center in La:Lu:EuCl3·6D2O resulting from the optical excitation of neighboring Eu3+ ions. Shifts of up to 46.081±0.005 MHz were observed. The magnitude of the interaction between neighboring ions was found to be significantly larger than expected from the electric dipole-dipole mechanism often observed in rare earth systems. We show that a large network of interacting and individually addressable centers can be created by lightly doping crystals otherwise stoichiometric in the optically active rare earth ion, and that this network could be used to implement a quantum processor with more than ten qubits.

Triploidy induction in the Pacific white shrimp Litopenaeus vannamei: an assessment of induction agents and parameters, embryo viability, and early larval survival.

In this study, we trialed 6-dimethylaminopurine (6-DMAP) chemical shocks to induce meiosis I or meiosis II Pacific White shrimp, Litopenaeus vannamei, triploids for the first time, and cold temperature shocks to induce meiosis II L. vannamei triploids as done previously. Inductions were performed on 37 spawnings in total with experiments being progressively designed in a factorial manner to allow optimization of induction parameters. Treatment with a 200-µm 6-DMAP final concentration at 1 min post-spawning detection for a 6 to 8 min duration resulted in the most consistent induction of chemically induced meiosis I triploids while treatment at 7 min 30 s post-spawning detection for a 10-min duration resulted in the most consistent induction of chemically induced meiosis II triploids. A cold temperature shock of 11.7°C to 13.25°C (final treatment temperature; spawning water temperature 28.5°C) applied at 8 min post-spawning detection for a 4 to 10 min duration resulted in the most consistent induction of cold-temperature-induced meiosis II triploids. 6-DMAP shocks resulted in meiosis I induction rates from 29% to 100% in unhatched embryos and 50% in nauplii, and meiosis II induction rates from 65% to 100% in unhatched embryos and 52% to 100% in nauplii. Cold shocks resulted in induction rates from 5% to 100% in unhatched embryos and nauplii. Confocal microscopy analysis of embryos revealed that there are major developmental abnormalities in a large proportion of later stage triploid L. vannamei embryos compared to their diploid sibling controls. Despite this, however, some triploid embryos did appear normal and both shock agents induced small numbers of viable triploid L. vannamei nauplii which were successfully reared to protozoeal stage 3 as confirmed by flow cytometry. Triploids beyond this life-history stage were not observed in the present study as confirmed by flow cytometry at mysis stages. This study adds to our knowledge base of triploid induction in L. vannamei and further highlights the inherent difficulties with triploid embryonic and larval viability in this species.

Observation and control of blinking nitrogen-vacancy centres in discrete nanodiamonds.

Nitrogen-vacancy colour centres in diamond can undergo strong, spin-sensitive optical transitions under ambient conditions, which makes them attractive for applications in quantum optics, nanoscale magnetometry and biolabelling. Although nitrogen-vacancy centres have been observed in aggregated detonation nanodiamonds and milled nanodiamonds, they have not been observed in very small isolated nanodiamonds. Here, we report the first direct observation of nitrogen-vacancy centres in discrete 5-nm nanodiamonds at room temperature, including evidence for intermittency in the luminescence (blinking) from the nanodiamonds. We also show that it is possible to control this blinking by modifying the surface of the nanodiamonds.

Multimodal properties and dynamics of gradient echo quantum memory.

We investigate the properties of a recently proposed gradient echo memory (GEM) scheme for information mapping between optical and atomic systems. We show that GEM can be described by the dynamic formation of polaritons in k space. This picture highlights the flexibility and robustness with regards to the external control of the storage process. Our results also show that, as GEM is a frequency-encoding memory, it can accurately preserve the shape of signals that have large time-bandwidth products, even at moderate optical depths. At higher optical depths, we show that GEM is a high fidelity multimode quantum memory.

Electro-optic quantum memory for light using two-level atoms.

We present a simple quantum memory scheme that allows for the storage of a light field in an ensemble of two-level atoms. The technique is analogous to the NMR gradient echo for which the imprinting and recalling of the input field are performed by controlling a linearly varying broadening. Our protocol is perfectly efficient in the limit of high optical depths and the output pulse is emitted in the forward direction. We provide a numerical analysis of the protocol together with an experiment performed in a solid state system. In close agreement with our model, the experiment shows a total efficiency of up to 15%, and a recall efficiency of 26%. We suggest simple realizable improvements for the experiment to surpass the no-cloning limit.

Photon echoes produced by switching electric fields.

We demonstrate photon echoes in Eu3+:Y2SiO5 by controlling the inhomogeneous broadening of the Eu3+ 7F0<-->5D0 optical transition. This transition has a linear Stark shift, and we induce inhomogeneous broadening by applying an external electric field gradient. After optical excitation, reversing the polarity of the field rephases the ensemble, resulting in a photon echo. This is the first demonstration of such a photon echo, and its application as a quantum memory is discussed.

Dynamic decoherence control of a solid-state nuclear-quadrupole qubit.

We report on the application of a dynamic decoherence control pulse sequence on a nuclear-quadrupole transition in Pr3+:Y(2)SiO(5). Process tomography is used to analyze the effect of the pulse sequence. The pulse sequence was found to increase the decoherence time of the transition to over 30 seconds. Although the decoherence time was significantly increased, the population terms were found to rapidly decay on the application of the pulse sequence. The increase of this decay rate is attributed to inhomogeneity in the ensemble. Methods to circumvent this limit are discussed.

Stopped light with storage times greater than one second using electromagnetically induced transparency in a solid.

We report on the demonstration of light storage for times greater than a second in praseodymium doped Y2SiO5 using electromagnetically induced transparency. The long storage times were enabled by the long coherence times possible for the hyperfine transitions in this material. The use of a solid-state system also enabled operation with the probe and coupling beam counter-propagating, allowing easy separation of the two beams. The efficiency of the storage was low because of the low optical thickness of the sample; as is discussed, this deficiency should be easy to rectify.

Demonstration of conditional quantum phase shift between ions in a solid.

Because of their long coherence times, dopant ions have been considered promising candidates for scalable solid state quantum computing. Here we demonstrate a conditional phase shift between two qubits based on an optical transition of europium ions. The demonstration uses ensembles that have been selected from a randomly doped sample using spectral hole burning techniques. The electron dipole-dipole interaction between the ions that usually causes instantaneous spectral diffusion is used to generate the conditional phase shift.

Method of extending hyperfine coherence times in Pr3+:Y2SiO5.

In this Letter, we present a method for increasing the coherence time of praseodymium hyperfine ground state transitions in Pr(3+):Y(2)SiO5 by the application of a specific external magnetic field. The magnitude and angle of the external field is applied such that the Zeeman splitting of a hyperfine transition is at a critical point in three dimensions, making the first order Zeeman shift vanishingly small for the transition. This reduces the influence of the magnetic interactions between the praseodymium ions and the spins in the host lattice on the transition frequency. Using this method a phase memory time of 82 ms was observed, a value 2 orders of magnitude greater than previously reported. It is shown that the residual dephasing is amenable to quantum error correction.

Accurate measurement of the 12.6 GHz "clock" transition in trapped (171)Yb(+) ions.

We have measured the frequency of the (171)Yb(+) 12.6 GHz M(F)=0-->0 ground state hyperfine "clock" transition in buffer gas-cooled ion clouds confined in two similar, but not identical, linear Paul traps. After correction for the known differences between the two ion traps, including significantly different second-order Doppler shifts, the frequencies agree within an uncertainty of less than 2 parts in 10(13). Our best value, based on an analytic model for the second-order Doppler shift, for the frequency of the clock transition of an isolated ion at zero temperature, velocity, electric field and magnetic field, is 12642812118.466+0.002 Hz.