A comparison of methods for determining ploidy in white sturgeon (Acipenser transmontanus)

Release of sturgeon with abnormal ploidy into the wild may result in reduced fitness due to lowered fertility in the F2 and subsequent generations. Further, there is evidence that ploidy affects reproductive development and caviar yield. Therefore, the ability to accurately characterize the ploidy of white sturgeon (Acipenser transmontanus)is essential for both commercial and conservation aquaculture. This study compares nuclear volume and whole erythrocyte long-axis lengths obtained using Coulter counter and blood smears, respectively, from captive white sturgeon from populations originating in California and Idaho. We examine which method provides the most accurate, time efficient and cost-effective characterization of ploidy in this species. Results from Coulter counter and blood smears were compared to results from flow cytometry, the gold standard for genome size analysis. Previous work suggests that blood smears can distinguish between 8N (diploid)and 12N (triploid)sturgeon, but further analysis is required to see if this method can also be used to identify 10N fish and to provide robust evidence of its utility in 8N and 12N fish across populations. In this study, we demonstrated that the Coulter counter had 100% agreement with flow cytometry in ploidy assignment, while blood smears vary in their accuracy based on population. Blood smears showed a high degree of overlap in erythrocyte long-axis length between 8N and 10N individuals as well as some overlap between 10N and 12N individuals in the California fish, and a high degree of overlap between 8N and 12N individuals in the Idaho fish. Although blood smears are time-intensive and vary in their ploidy assignment accuracy, they are a low-cost technique and as such may have some utility for caviar farms attempting to identify 12N individuals in a small number of broodstock. By comparing the accuracy, efficiency and cost of these three methods, sturgeon farmers and conservation hatcheries will be able to choose the best method for their needs in determining the ploidy of their fish. We determined that Coulter counter is equally accurate to flow cytometry and is also the most time efficient method for ploidy determination in white sturgeon

Single-shot qubit readout in circuit Quantum Electrodynamics

The future development of quantum information using superconducting circuits requires Josephson qubits [1] with long coherence times combined to a high-fidelity readout. Major progress in the control of coherence has recently been achieved using circuit quantum electrodynamics (cQED) architectures [2, 3], where the qubit is embedded in a coplanar waveguide resonator (CPWR) which both provides a well controlled electromagnetic environment and serves as qubit readout. In particular a new qubit design, the transmon, yields reproducibly long coherence times [4, 5]. However, a high-fidelity single-shot readout of the transmon, highly desirable for running simple quantum algorithms or measur- ing quantum correlations in multi-qubit experiments, is still lacking. In this work, we demonstrate a new transmon circuit where the CPWR is turned into a sample-and-hold detector, namely a Josephson Bifurcation Amplifer (JBA) [6, 7], which allows both fast measurement and single-shot discrimination of the qubit states. We report Rabi oscillations with a high visibility of 94% together with dephasing and relaxation times longer than 0:5 \mu\s. By performing two subsequent measurements, we also demonstrate that this new readout does not induce extra qubit relaxation.Comment: 14 pages including 4 figures, preprint forma

Quantum Non-demolition Detection of Single Microwave Photons in a Circuit

Thorough control of quantum measurement is key to the development of quantum information technologies. Many measurements are destructive, removing more information from the system than they obtain. Quantum non-demolition (QND) measurements allow repeated measurements that give the same eigenvalue. They could be used for several quantum information processing tasks such as error correction, preparation by measurement, and one-way quantum computing. Achieving QND measurements of photons is especially challenging because the detector must be completely transparent to the photons while still acquiring information about them. Recent progress in manipulating microwave photons in superconducting circuits has increased demand for a QND detector which operates in the gigahertz frequency range. Here we demonstrate a QND detection scheme which measures the number of photons inside a high quality-factor microwave cavity on a chip. This scheme maps a photon number onto a qubit state in a single-shot via qubit-photon logic gates. We verify the operation of the device by analyzing the average correlations of repeated measurements, and show that it is 90% QND. It differs from previously reported detectors because its sensitivity is strongly selective to chosen photon number states. This scheme could be used to monitor the state of a photon-based memory in a quantum computer.Comment: 5 pages, 4 figures, includes supplementary materia

Nonlinear response of the vacuum Rabi resonance

On the level of single atoms and photons, the coupling between atoms and the electromagnetic field is typically very weak. By employing a cavity to confine the field, the strength of this interaction can be increased many orders of magnitude to a point where it dominates over any dissipative process. This strong-coupling regime of cavity quantum electrodynamics has been reached for real atoms in optical cavities, and for artificial atoms in circuit QED and quantum-dot systems. A signature of strong coupling is the splitting of the cavity transmission peak into a pair of resolvable peaks when a single resonant atom is placed inside the cavity - an effect known as vacuum Rabi splitting. The circuit QED architecture is ideally suited for going beyond this linear response effect. Here, we show that increasing the drive power results in two unique nonlinear features in the transmitted heterodyne signal: the supersplitting of each vacuum Rabi peak into a doublet, and the appearance of additional peaks with the characteristic sqrt(n) spacing of the Jaynes-Cummings ladder. These constitute direct evidence for the coupling between the quantized microwave field and the anharmonic spectrum of a superconducting qubit acting as an artificial atom.Comment: 6 pages, 4 figures. Supplementary Material and Supplementary Movies are available at http://www.eng.yale.edu/rslab/publications.htm

Experimental violation of a Bell's inequality in time with weak measurement

The violation of J. Bell's inequality with two entangled and spatially separated quantum two- level systems (TLS) is often considered as the most prominent demonstration that nature does not obey ?local realism?. Under different but related assumptions of "macrorealism", plausible for macroscopic systems, Leggett and Garg derived a similar inequality for a single degree of freedom undergoing coherent oscillations and being measured at successive times. Such a "Bell's inequality in time", which should be violated by a quantum TLS, is tested here. In this work, the TLS is a superconducting quantum circuit whose Rabi oscillations are continuously driven while it is continuously and weakly measured. The time correlations present at the detector output agree with quantum-mechanical predictions and violate the inequality by 5 standard deviations.Comment: 26 pages including 10 figures, preprint forma

Climbing the Jaynes-Cummings Ladder and Observing its Sqrt(n) Nonlinearity in a Cavity QED System

The already very active field of cavity quantum electrodynamics (QED), traditionally studied in atomic systems, has recently gained additional momentum by the advent of experiments with semiconducting and superconducting systems. In these solid state implementations, novel quantum optics experiments are enabled by the possibility to engineer many of the characteristic parameters at will. In cavity QED, the observation of the vacuum Rabi mode splitting is a hallmark experiment aimed at probing the nature of matter-light interaction on the level of a single quantum. However, this effect can, at least in principle, be explained classically as the normal mode splitting of two coupled linear oscillators. It has been suggested that an observation of the scaling of the resonant atom-photon coupling strength in the Jaynes-Cummings energy ladder with the square root of photon number n is sufficient to prove that the system is quantum mechanical in nature. Here we report a direct spectroscopic observation of this characteristic quantum nonlinearity. Measuring the photonic degree of freedom of the coupled system, our measurements provide unambiguous, long sought for spectroscopic evidence for the quantum nature of the resonant atom-field interaction in cavity QED. We explore atom-photon superposition states involving up to two photons, using a spectroscopic pump and probe technique. The experiments have been performed in a circuit QED setup, in which ultra strong coupling is realized by the large dipole coupling strength and the long coherence time of a superconducting qubit embedded in a high quality on-chip microwave cavity.Comment: ArXiv version of manuscript published in Nature in July 2008, 5 pages, 5 figures, hi-res version at http://www.finkjohannes.com/SqrtNArxivPreprint.pd

Preparation and Measurement of Three-Qubit Entanglement in a Superconducting Circuit

Traditionally, quantum entanglement has played a central role in foundational discussions of quantum mechanics. The measurement of correlations between entangled particles can exhibit results at odds with classical behavior. These discrepancies increase exponentially with the number of entangled particles. When entanglement is extended from just two quantum bits (qubits) to three, the incompatibilities between classical and quantum correlation properties can change from a violation of inequalities involving statistical averages to sign differences in deterministic observations. With the ample confirmation of quantum mechanical predictions by experiments, entanglement has evolved from a philosophical conundrum to a key resource for quantum-based technologies, like quantum cryptography and computation. In particular, maximal entanglement of more than two qubits is crucial to the implementation of quantum error correction protocols. While entanglement of up to 3, 5, and 8 qubits has been demonstrated among spins, photons, and ions, respectively, entanglement in engineered solid-state systems has been limited to two qubits. Here, we demonstrate three-qubit entanglement in a superconducting circuit, creating Greenberger-Horne-Zeilinger (GHZ) states with fidelity of 88%, measured with quantum state tomography. Several entanglement witnesses show violation of bi-separable bounds by 830\pm80%. Our entangling sequence realizes the first step of basic quantum error correction, namely the encoding of a logical qubit into a manifold of GHZ-like states using a repetition code. The integration of encoding, decoding and error-correcting steps in a feedback loop will be the next milestone for quantum computing with integrated circuits.Comment: 7 pages, 4 figures, and Supplementary Information (4 figures)

Stabilizing entanglement autonomously between two superconducting qubits

Quantum error-correction codes would protect an arbitrary state of a multi-qubit register against decoherence-induced errors, but their implementation is an outstanding challenge for the development of large-scale quantum computers. A first step is to stabilize a non-equilibrium state of a simple quantum system such as a qubit or a cavity mode in the presence of decoherence. Several groups have recently accomplished this goal using measurement-based feedback schemes. A next step is to prepare and stabilize a state of a composite system. Here we demonstrate the stabilization of an entangled Bell state of a quantum register of two superconducting qubits for an arbitrary time. Our result is achieved by an autonomous feedback scheme which combines continuous drives along with a specifically engineered coupling between the two-qubit register and a dissipative reservoir. Similar autonomous feedback techniques have recently been used for qubit reset and the stabilization of a single qubit state, as well as for creating and stabilizing states of multipartite quantum systems. Unlike conventional, measurement-based schemes, an autonomous approach counter-intuitively uses engineered dissipation to fight decoherence, obviating the need for a complicated external feedback loop to correct errors, simplifying implementation. Instead the feedback loop is built into the Hamiltonian such that the steady state of the system in the presence of drives and dissipation is a Bell state, an essential building-block state for quantum information processing. Such autonomous schemes, broadly applicable to a variety of physical systems as demonstrated by a concurrent publication with trapped ion qubits, will be an essential tool for the implementation of quantum-error correction.Comment: 39 pages, 7 figure

Detection of Norovirus genogroup I and II by multiplex real-time RT- PCR using a 3'-minor groove binder-DNA probe

BACKGROUND: Due to an increasing number of norovirus infections in the last years rapid, specific, and sensitive diagnostic tools are needed. Reverse transcriptase-polymerase chain reactions (RT-PCR) have become the methods of choice. To minimize the working time and the risk of carryover contamination during the multi-step procedure of PCR the multiplex real-time RT-PCR for the simultaneous detection of genogroup I (GI) and II (GII) offers advantages for the handling of large amounts of clinical specimens. METHODS: We have developed and evaluated a multiplex one-tube RT-PCR using a combination of optimized GI and GII specific primers located in the junction between ORF1 and ORF2 of the norovirus genome. For the detection of GI samples, a 3'- minor groove binder-DNA probe (GI-MGB-probe) were designed and used for the multiplex real-time PCR. RESULTS: Comparable results to those of our in-house nested PCR and monoplex real-time-PCR were only obtained using the GI specific MGB-probe. The MGB-probe forms extremely stable duplexes with single-stranded DNA targets, which enabled us to design a shorter probe (length 15 nucleotides) hybridizing to a more conserved part of the GI sequences. 97 % of 100 previously norovirus positive specimens (tested by nested PCR and/or monoplex real-time PCR) were detected by the multiplex real-time PCR. A broad dynamic range from 2 × 10^1 to 2 × 10^7 genomic equivalents per assay using plasmid DNA standards for GI and GII were obtained and viral loads between 2.5 × 10^2 and 2 × 10^12 copies per ml stool suspension were detected. CONCLUSION: The one-tube multiplex RT real-time PCR using a minor groove binder -DNA probe for GI is a fast, specific, sensitive and cost-effective tool for the detection of norovirus infections in both mass outbreaks and sporadic cases and may have also applications in food and environmental testing