A scalable method for automatically measuring pharyngeal pumping in C. elegans

Background: The nematode Caenorhabditis elegans is widely used for studying small neural circuits underlying behavior. In particular, the rhythmic feeding motions collectively termed pharyngeal pumping are regulated by a nearly autonomous network of 20 neurons of 14 types. Despite much progress achieved through laser ablation, genetics, electrophysiology, and optogenetics, key questions regarding the regulation of pumping remain open. New method: We describe the implementation and application of a scalable automated method for measuring pumping in controlled environments. Our implementation is affordable and flexible: key hardware and software elements can be modified to accommodate different requirements. Results: We demonstrate prolonged measurements under controlled conditions and the resulting high quality data. We show the scalability of our method, enabling high throughput, and its suitability for maintaining static and dynamic conditions. When food availability was oscillated, pumping rates were low as compared to steady conditions and pumping activity was not reliably modulated in response to changes in food concentration. Comparison with existing method: The prevailing method for measuring rates of pumping relies on scoring by visual inspection of short recordings. Our automated method compares well with manual scoring. It enables detailed statistical characterization under experimental conditions not previously accessible and minimizes unintentional bias. Conclusions: Our approach adds a powerful tool for studying pharyngeal pumping. It enhances the experimental versatility of assaying genetic and pharmacological manipulations and the ability to characterize the resulting behavior. Both the experimental setup and the analysis can be readily adapted to additional challenging motion detection problems

Algebraic analysis of quantum search with pure and mixed states

An algebraic analysis of Grover's quantum search algorithm is presented for the case in which the initial state is an arbitrary pure quantum state of n qubits. This approach reveals the geometrical structure of the quantum search process, which turns out to be confined to a four-dimensional subspace of the Hilbert space. This work unifies and generalizes earlier results on the time evolution of the amplitudes during the quantum search, the optimal number of iterations and the success probability. Furthermore, it enables a direct generalization to the case in which the initial state is a mixed state, providing an exact formula for the success probability.Comment: 13 page

Theory of Initialization-Free Decoherence-Free Subspaces and Subsystems

We introduce a generalized theory of decoherence-free subspaces and subsystems (DFSs), which do not require accurate initialization. We derive a new set of conditions for the existence of DFSs within this generalized framework. By relaxing the initialization requirement we show that a DFS can tolerate arbitrarily large preparation errors. This has potentially significant implications for experiments involving DFSs, in particular for the experimental implementation, over DFSs, of the large class of quantum algorithms which can function with arbitrary input states

Nested quantum search and NP-complete problems

A quantum algorithm is known that solves an unstructured search problem in a number of iterations of order $\sqrt{d}$, where $d$ is the dimension of the search space, whereas any classical algorithm necessarily scales as $O(d)$. It is shown here that an improved quantum search algorithm can be devised that exploits the structure of a tree search problem by nesting this standard search algorithm. The number of iterations required to find the solution of an average instance of a constraint satisfaction problem scales as $\sqrt{d^\alpha}$, with a constant $\alpha<1$ depending on the nesting depth and the problem considered. When applying a single nesting level to a problem with constraints of size 2 such as the graph coloring problem, this constant $\alpha$ is estimated to be around 0.62 for average instances of maximum difficulty. This corresponds to a square-root speedup over a classical nested search algorithm, of which our presented algorithm is the quantum counterpart.Comment: 18 pages RevTeX, 3 Postscript figure

Inhibition of Epstein-Barr Virus Replication by a Benzimidazole l-Riboside: Novel Antiviral Mechanism of 5,6-Dichloro-2-(Isopropylamino)-1-β-l-Ribofuranosyl-1H-Benzimidazole

Although a number of antiviral drugs inhibit replication of Epstein-Barr virus (EBV) in cell culture, and acyclovir (ACV) suppresses replication in vivo, currently available drugs have not proven effective for treatment of EBV-associated diseases other than oral hairy leukoplakia. Benzimidazole riboside compounds represent a new class of antiviral compounds that are potent inhibitors of human cytomegalovirus (HCMV) replication but not of other herpesviruses. Here we characterize the effects of two compounds in this class against lytic replication of EBV induced in a Burkitt lymphoma cell line latently infected with EBV. We analyzed linear forms of EBV genomes, indicative of lytic replication, and episomal forms present in latently infected cells by terminal probe analysis followed by Southern blot hybridization as well as the high-molecular-weight unprocessed viral DNA by pulsed-field gel electrophoresis. d-Ribofuranosyl benzimidazole compounds that act as inhibitors of HCMV DNA maturation, including BDCRB (5,6-dichloro-2-bromo-1-β-d-ribofuranosyl-1H-benzimidazole), did not affect the accumulation of high-molecular-weight or monomeric forms of EBV DNA in the induced cells. In contrast, the generation of linear EBV DNA as well as precursor viral DNA was sensitive to the l-riboside 1263W94 [5,6-dichloro-2-(isopropylamino)-1-β-l-ribofuranosyl-1H-benzimidazole]. The 50% inhibitory concentration range for 1263W94 was 0.15 to 1.1 μM, compared with 10 μM for ACV. Thus, 1263W94 is a potent inhibitor of EBV. In addition, 1263W94 inhibited the phosphorylation and the accumulation of the essential EBV replicative cofactor, early antigen D

Anti-human immunodeficiency virus agent 3'-azido-3'-deoxythymidine inhibits replication of Epstein-Barr virus.

We show that the anti-human immunodeficiency virus agent, 3'-azido-3'-deoxythymidine (AZT), which suppresses infectivity and cytopathic effects of human immunodeficiency virus, also effectively inhibits Epstein-Barr virus (EBV) DNA replication. However, AZT has no effect on four other human herpesviruses: cytomegalovirus, varicella-zoster virus, and herpes simplex virus types 1 and 2. The combination of acyclovir and AZT, while it is not synergistic, has an additive effect against EBV replication. AZT may prove to be a useful drug for treatment of coinfections with human immunodeficiency virus and EBV

Stress Generation and Filament Turnover during Actin Ring Constriction

We present a physical analysis of the dynamics and mechanics of contractile actin rings. In particular, we analyze the dynamics of ring contraction during cytokinesis in the Caenorhabditis elegans embryo. We present a general analysis of force balances and material exchange and estimate the relevant parameter values. We show that on a microscopic level contractile stresses can result from both the action of motor proteins, which cross-link filaments, and from the polymerization and depolymerization of filaments in the presence of end-tracking cross-linkers

Chemo- and Thermosensory Responsiveness of Grueneberg Ganglion Neurons Relies on Cyclic Guanosine Monophosphate Signaling Elements

Neurons of the Grueneberg ganglion (GG) in the anterior nasal region of mouse pups respond to cool temperatures and to a small set of odorants. While the thermosensory reactivity appears to be mediated by elements of a cyclic guanosine monophosphate (cGMP) cascade, the molecular mechanisms underlying the odor-induced responses are unclear. Since odor-responsive GG cells are endowed with elements of a cGMP pathway, specifically the transmembrane guanylyl cyclase subtype GC-G and the cyclic nucleotide-gated ion channel CNGA3, the possibility was explored whether these cGMP signaling elements may also be involved in chemosensory GG responses. Experiments with transgenic mice deficient for GC-G or CNGA3 revealed that GG responsiveness to given odorants was significantly diminished in these knockout animals. These findings suggest that a cGMP cascade may be important for both olfactory and thermosensory signaling in the GG. However, in contrast to the thermosensory reactivity, which did not decline over time, the chemosensory response underwent adaptation upon extended stimulation, suggesting that the two transduction processes only partially overlap. Copyright (C) 2011 S. Karger AG, Base