Classical analogs for Rabi-oscillations, Ramsey-fringes, and spin-echo in Josephson junctions

We investigate the results of recently published experiments on the quantum behavior of Josephson circuits in terms of the classical modelling based on the resistively and capacitively-shunted (RCSJ) junction model. Our analysis shows evidence for a close analogy between the nonlinear behavior of a pulsed microwave-driven Josephson junction at low temperature and low dissipation and the experimental observations reported for the Josephson circuits. Specifically, we demonstrate that Rabi-oscillations, Ramsey-fringes, and spin-echo observations are not phenomena with a unique quantum interpretation. In fact, they are natural consequences of transients to phase-locking in classical nonlinear dynamics and can be observed in a purely classical model of a Josephson junction when the experimental recipe for the application of microwaves is followed and the experimental detection scheme followed. We therefore conclude that classical nonlinear dynamics can contribute to the understanding of relevant experimental observations of Josephson response to various microwave perturbations at very low temperature and low dissipation.Comment: 16 pages, 7 figure

Antibacterial Activity of Dipeptide Constructions of Acetylsalicylic Acid and Nicotinic Acid

Two dipeptide drugs are synthesized utilizing an acetylsalicylic acid or nicotinic acid molecule for the framework. A D-alanine-D-alanine dipeptide moiety is attached to the carbonyl carbon of acetylsalicylic acid (I) and nicotinic acid (II). Dipeptide derivatives (I) and (II) showed significant reduction of Escherichia coli (E. coli) bacterial growth and colony-forming units. A mixture of (I) and (II) induced growth inhibition of 8%, 17.5%, 28%, and 42.5% at concentrations of 100, 200, 300, and 400 μg/mL, respectively. Ampicillin demonstrated much less growth inhibition of this penicillin-resistant E. coli bacteria. Derivatives (I) and (II) showed significant reduction of colony-forming units at concentrations higher than 200 μg/mL, whereas ampicillin showed no significant affect on colony-forming units. Both (I) and (II) produced no violations of the Rule of 5, indicating favorable characteristics for bioavailability. Molecular properties were determined and showed (I) to have a Log Kow of −0.22 with aqueous solubility of 683.8 mg/L, whereas (II) had a Log Kow of −1.00 and aqueous solubility of 6859 mg/L. A mixture of the parent compounds acetyl salicylic acid and nicotinic acid demonstrated some antibacterial activity

Novel Tuberculostatic Agents Suitable for Treatment of Mycobacterium tuberculosis Infections of the Central Nervous System

Aims: To demonstrate the efficacy of five small molecule compounds for inhibiting the growth of Mycobacterium tuberculosis. To present evidence that these compounds will penetrate into the central nervous system. Study Design: Five small molecule compounds bearing a hydrazide group were synthesized utilizing microwave excitation. These compounds were then placed into tissue culture with Mycobacterium tuberculosis at various concentrations for evaluation of bacterial growth inhibition. Place and Duration of Study: The compounds to be tested were prepared at the University of Nebraska Chemistry Department August 2013. The evaluation of antibacterial activity was determined at the Texas A&M Health Science Center during October to December of 2013. Methodology: Applying microwave excitation for generation of hydrazide groups within the structure of small molecule carboxylic acids, five agents were prepared for evaluation of bacterial growth inhibition. These agents were dissolved into tissue culture media at various concentrations. Having various levels of tuberculostatic agents, then tuberculosis bacteria were added to determine level of growth inhibition. Growth inhibition of the bacteria was achieved and measured by compound concentration for comparison and evaluation. Results: Five compounds having a hydrazide functional group greatly inhibited the growth of Mycobacterium tuberculosis. All five agents had molecular weight less than 215 grams/mole and polar surface area of less than 70 Angstroms2. Values of Log P ranged from -0.226 to 0.998. Values of Log BB (Log [Cbrain/Cblood]) ranged from -0.711 to - 0.525, with a range in central nervous system penetration Cbrain/Cblood of 0.195 to 0.299. All compounds showed zero violations of the Rule of 5. Substantial inhibition of bacterial growth was observed at concentrations as low as 30 micrograms/mL, as measured by optical density and colony forming units. Conclusion: These five hydrazide compounds substantially decreased the proliferation of tuberculosis bacteria at concentrations as low as 30 micrograms/mL. In addition, their physicochemical properties are shown to allow high levels of penetration into the central nervous system

The Mycobacterium marinum mel2 locus displays similarity to bacterial bioluminescence systems and plays a role in defense against reactive oxygen and nitrogen species

BACKGROUND: Mycobacteria have developed a number of pathways that provide partial protection against both reactive oxygen species (ROS) and reactive nitrogen species (RNS). We recently identified a locus in Mycobacterium marinum, mel2, that plays a role during infection of macrophages. The molecular mechanism of mel2 action is not well understood. RESULTS: To better understand the role of the M. marinum mel2 locus, we examined these genes for conserved motifs in silico. Striking similarities were observed between the mel2 locus and loci that encode bioluminescence in other bacterial species. Since bioluminescence systems can play a role in resistance to oxidative stress, we postulated that the mel2 locus might be important for mycobacterial resistance to ROS and RNS. We found that an M. marinum mutant in the first gene in this putative operon, melF, confers increased susceptibility to both ROS and RNS. This mutant is more susceptible to ROS and RNS together than either reactive species alone. CONCLUSION: These observations support a role for the M. marinum mel2 locus in resistance to oxidative stress and provide additional evidence that bioluminescence systems may have evolved from oxidative defense mechanisms

Classical analysis of phase-locking transients and Rabi-type oscillations in microwave-driven Josephson junctions

We present a classical analysis of the transient response of Josephson junctions perturbed by microwaves and thermal fluctuations. The results include a specific low frequency modulation in phase and amplitude behavior of a junction in its zero-voltage state. This transient modulation frequency is linked directly to an observed variation in the probability for the system to switch to its non-zero voltage state. Complementing previous work on linking classical analysis to the experimental observations of Rabi-oscillations, this expanded perturbation method also provides closed form analytical results for attenuation of the modulations and the Rabi-type oscillation frequency. Results of perturbation analysis are compared directly (and quantitatively) to numerical simulations of the classical model as well as published experimental data, suggesting that transients to phase-locking are closely related to the observed oscillations.Comment: 18 pages total, 8 figures (typos corrected; minor revisions to figures and equations

Aromatic Hydrazide Compounds that Inhibit the Growth of Mycobacterium Tuberculosis

Aims: To demonstrate the efficacy of aromatic hydrazide compounds to inhibit growth of Mycobacterium tuberculosis. Study Design: To synthesize tuberculostats and test their antibacterial activity in-vitro. Place and Duration of Study: University of Nebraska, Durham Science Center, 6001 Dodge Street, Omaha NE 68182, and Texas A&M Health Science Center, Department of Microbial Pathogenesis and Immunology, 8447 State Hwy 47, Medical Research and Education Building, Room #3012, Bryan, TX 7780. From March 2019 to October 2019. Methodology: Hydrazide functional groups were formed by covalently bonding hydrazine onto a carbonyl carbon that is a substituent of a single aromatic ring. Microwave excitation was utilized for synthesis, followed by evaluation of antibacterial activity. These compounds were placed into tissue culture media at various concentrations and then Mycobacterium tuberculosis bacteria was added, in order to determine the level of growth inhibition. Growth inhibition of the bacteria was measured as a function of compound concentration versus growth inhibition. Results: Compounds A, B, C, and D carry hydrazide groups as a substituent to a single aromatic ring. All four compounds show zero violations of Rule of 5, indicating favorable drug-likeness. All four compounds showed greater than 50% growth inhibition of bacteria at concentrations below 50 micrograms per milliliter. Growth inhibition was measured by colony forming units and luminescence. Polar surface area, Log P, molecular volume, and other molecular properties were determined for these four compounds. Conclusion: These four hydrazide compounds induced substantial inhibition of bacterial growth. Microwave excitation for the synthesis of hydrazide compounds is effective. These compounds have favorable drug-likeness properties and are highly effective inhibiting the growth of Mycobacterium tuberculosis

Four Compounds Suppressing Growth of Mycobacterium tuberculosis

Aims: To demonstrate the efficacy of several small molecular weight compounds having hydrazide groups, for inhibiting the growth of Mycobacterium tuberculosis. To show these same compounds have favorable drug-likeness properties. Study Design: To synthesize tuberculostats and test their antibacterial activity in-vitro. Place and Duration of Study: University of Nebraska, Durham Science Center, 6001 Dodge Street, Omaha NE 68182, and Texas A&M Health Science Center, Department of Microbial Pathogenesis and Immunology, 8447 State Hwy 47, Medical Research and Education Building, Room #3012, Bryan, TX 7780. From January 2015 to June 2015. Methodology: Hydrazide groups were formed by covalently bonding hydrazine onto small molecules having a single aromatic ring by utilizing microwave excitation and evaluating for antibacterial activity. These compounds were placed into tissue culture media at various concentrations and then tuberculosis bacteria were added to determine the level of growth inhibition. Growth inhibition of the bacteria was measured as a function of compound concentration for assessment and comparison. Results: Compounds A, B, C, and D carry hydrazide groups with various substituents that are bonded to a single aromatic ring. All four compounds show zero violations of Rule of 5, indicating favorable absorption and membrane permeation. All four compounds showed greater than 85% growth inhibition of bacteria at concentrations below 50 micrograms per milliliter, while assayed by colony forming units and luminescence. Values of Log BB suggests compounds A and C will have greater penetration into the central nervous system than isoniazid. Conclusion: These four hydrazide compounds induced substantial inhibition of bacterial growth. Microwave excitation for the synthesis of hydrazide compounds is effective. These compounds have favorable drug-likeness properties and are highly effective inhibiting growth of Mycobacterium tuberculosis

Real-Time Bioluminescence Imaging of Mixed Mycobacterial Infections

Molecular analysis of infectious processes in bacteria normally involves construction of isogenic mutants that can then be compared to wild type in an animal model. Pathogenesis and antimicrobial studies are complicated by variability between animals and the need to sacrifice individual animals at specific time points. Live animal imaging allows real-time analysis of infections without the need to sacrifice animals, allowing quantitative data to be collected at multiple time points in all organs simultaneously. However, imaging has not previously allowed simultaneous imaging of both mutant and wild type strains of mycobacteria in the same animal. We address this problem by using both firefly (Photinus pyralis) and click beetle (Pyrophorus plagiophthalamus) red luciferases, which emit distinct bioluminescent spectra, allowing simultaneous imaging of two different mycobacterial strains during infection. We also demonstrate that these same bioluminescence reporters can be used to evaluate therapeutic efficacy in real-time, greatly facilitating our ability to screen novel antibiotics as they are developed. Due to the slow growth rate of mycobacteria, novel imaging technologies are a pressing need, since they can they can impact the rate of development of new therapeutics as well as improving our understanding of virulence mechanisms and the evaluation of novel vaccine candidates