Catechol 2,3-dioxygenase-assisted cleavage of aromatics by “anaerobic” termite gut spirochetes and genomic evidence of a complete meta-pathway

The termite hindgut microbial ecosystem functions like a miniature lignocellulose-metabolizing natural bioreactor, has significant implications to nutrient cycling in the terrestrial environment, and represents an array of microbial metabolic diversity. Deciphering the intricacies of this microbial community to obtain as complete a picture as possible of how it functions as a whole, requires a combination of various traditional and cutting-edge bioinformatic, molecular, physiological, and culturing approaches. Isolates from this ecosystem, including Treponema primitia str. ZAS-1 and ZAS-2 as well as T. azotonutricium str. ZAS-9, have been significant resources for better understanding the termite system. While not all functions predicted by the genomes of these three isolates are demonstrated in vitro, these isolates do have the capacity for several metabolisms unique to spirochetes and critical to the termite system’s reliance upon lignocellulose. In this thesis, work culturing, enriching for, and isolating diverse microorganisms from the termite hindgut is discussed. Additionally, strategies of members of the termite hindgut microbial community to defend against O₂-stress and to generate acetate, the “biofuel” of the termite system, are proposed. In particular, catechol 2,3-dioxygenase and other meta-cleavage catabolic pathway genes are described in the “anaerobic” termite hindgut spirochetes T. primitia str. ZAS-1 and ZAS-2, and the first evidence for aromatic ring cleavage in the phylum (division) Spirochetes is also presented. These results suggest that the potential for O₂-dependent, yet nonrespiratory, metabolisms of plant-derived aromatics should be re-evaluated in termite hindgut communities. Potential future work is also illustrated.

Application of microwave diagnostics to copper chloride and carbon dioxide lasers

Part A

A problem restricting the development of the CuCl laser has been the decrease in output power with increases of tube temperature above 400°C. At that temperature the CuCl vapor pressure is about .1 torr. This is a small fraction of the buffer gas pressure (He at 10 torr).

The aim of the project was to measure the peak radiation temperature (assumed related to the mean energy of electrons) in the laser discharge as a function of the tube temperature. A 24 gHz gated microwave radiometer was used.

It was found that at the tube temperatures at which the output power began to deteriorate, the electron radiation temperature showed a sharp increase (compared with radiation temperature in pure buffer).

Using the above result, we have postulated that this sudden increase is a result of Penning ionization of the Cu atoms. As a consequence of this process the number of Cu atoms available for lasing decrease.

PART B

The aim of the project was to study the dissociation of CO₂ in the glow discharge of flowing CO₂ lasers.

A TM₀₁₁ microwave (3 gHz) cavity was used to measure the radially averaged electron density n_e and the electron-neutral collision frequency in the laser discharge. An estimate of the electric field is made from these two measurements. A gas chromatograph was used to measure the chemical composition of the gases after going through the discharge. This instrument was checked against a mass spectrometer for accuracy and sensitivity.

Several typical laser mixtures were .used: CO₂-N₂-He (1,3,16), (1,3,0), (1,0,16), (1,2,10), (1,2,0), (1,0,10), (2,3,15), (2,3,0), (2,0,15), (1,3,16)+ H₂O and pure CO₂. Results show that for the conditions studied the dissociation as a function of the electron density is uniquely determined by the STP partial flow rate of CO₂, regardless of the amount of N₂ and/or He present. The presence of water vapor in the discharge decreased the degree of dissociation.

A simple theoretical model was developed using thermodynamic equilibrium. The electrons were replaced in the calculations by a distributed heat source.

The results are analyzed with a simple kinetic model.

Microwave absorption and emission from magnetized afterglow plasmas

The microwave scattering properties of an axially magnetized afterglow plasma column in an S-band waveguide have been investigated experimentally. The column axis is perpendicular to the electric field and the direction of wave propagation in the H_(10)-mode waveguide. Strong absorption is found in the range of upper hybrid frequencies, ω_c ≤ ω ≤ [ω^2_c + ω^2_p(r,t)]^(1/2) where ω_c is the electron cyclotron frequency and ω_p is the locally and temporally varying electron plasma frequency. With the high absorption the noise emission approaches the blackbody limit. A microwave radiometer has been used to measure the noise power and with a comparison and null-technique the electron temperature. As emission and absorption are largely confined to a resonant layer, spatially resolved temperature data are obtained. Time resolution is obtained by gating the radiometer. The peak electron density is derived from the emission or absorption onset at the maximum upper hybrid frequency and confirmed by independent measurements. With this diagnostic technique the electron density and temperature decay has been studied under a variety of experimental conditions. Ambipolar diffusion and collisional cooling essentially account for the plasma decay, but impurities and metastable ions play an important role. The diagnostic method is successfully applied in a microwave heating experiment. The existence of absorbing resonant layers is shown by a peak in the radial temperature profile where the local upper hybrid frequency equals the heating frequency. The knowledge of the plasma parameters is important in the study of hot plasma effects. Buchsbaum-Hasegawa modes are investigated in a wide range of magnetic fields (.5 < ω_c/ω < .985).

Measurement of the Polarization of the Cosmic Microwave Background with the BICEP2 and Keck Array Telescopes

Precision polarimetry of the cosmic microwave background (CMB) has become a mainstay of observational cosmology. The ΛCDM model predicts a polarization of the CMB at the level of a few μK, with a characteristic E-mode pattern. On small angular scales, a B-mode pattern arises from the gravitational lensing of E-mode power by the large scale structure of the universe. Inflationary gravitational waves (IGW) may be a source of B-mode power on large angular scales, and their relative contribution to primordial fluctuations is parameterized by a tensor-to-scalar ratio r. BICEP2 and Keck Array are a pair of CMB polarimeters at the South Pole designed and built for optimal sensitivity to the primordial B-mode peak around multipole l ~ 100. The BICEP2/Keck Array program intends to achieve a sensitivity to r ≥ 0.02. Auxiliary science goals include the study of gravitational lensing of E-mode into B-mode signal at medium angular scales and a high precision survey of Galactic polarization. These goals require low noise and tight control of systematics. We describe the design and calibration of the instrument. We also describe the analysis of the first three years of science data. BICEP2 observes a significant B-mode signal at 150 GHz in excess of the level predicted by the lensed-ΛCDM model, and Keck Array confirms the excess signal at > 5σ. We combine the maps from the two experiments to produce 150 GHz Q and U maps which have a depth of 57 nK deg (3.4 μK arcmin) over an effective area of 400 deg² for an equivalent survey weight of 248000 μK². We also show preliminary Keck Array 95 GHz maps. A joint analysis with the Planck collaboration reveals that much of BICEP2/Keck Array's observed 150 GHz signal at low l is more likely a Galactic dust foreground than a measurement of r. Marginalizing over dust and r, lensing B-modes are detected at 7.0σ significance.

Microwave dynamics of quasiparticles and critical fields in superconducting films

The microwave response of the superconducting state in equilibrium and non-equilibrium configurations was examined experimentally and analytically. Thin film superconductors were mostly studied in order to explore spatial effects. The response parameter measured was the surface impedance.

For small microwave intensity the surface impedance at 10 GHz was measured for a variety of samples (mostly Sn) over a wide range of sample thickness and temperature. A detailed analysis based on the BCS theory was developed for calculating the surface impedance for general thickness and other experimental parameters. Experiment and theory agreed with each other to within the experimental accuracy. Thus it was established that the samples, thin films as well as bulk, were well characterised at low microwave powers (near equilibrium).

Thin films were perturbed by a small dc supercurrent and the effect on the superconducting order parameter and the quasiparticle response determined by measuring changes in the surface resistance (still at low microwave intensity and independent of it) due to the induced current. The use of fully superconducting resonators enabled the measurement of very small changes in the surface resistance (< 10^-9 Ω/sq.). These experiments yield information regarding the dynamics of the order parameter and quasiparticle systems. For all the films studied the results could be described at temperatures near T_c by the thermodynamic depression of the order parameter due to the static current leading to a quadratic increase of the surface resistance with current.

For the thinnest films the low temperature results were surprising in that the surface resistance decreased with increasing current. An explanation is proposed according to which this decrease occurs due to an additional high frequency quasiparticle current caused by the combined presence of both static and high frequency fields. For frequencies larger than the inverse of the quasiparticle relaxation time this additional current is out of phase (by π) with the microwave electric field and is observed as a decrease of surface resistance. Calculations agree quantitatively with experimental results. This is the first observation and explanation of this non-equilibrium quasiparticle effect.

For thicker films of Sn, the low temperature surface resistance was found to increase with applied static current. It is proposed that due to the spatial non-uniformity of the induced current distribution across the thicker films, the above purely temporal analysis of the local quasiparticle response needs to be generalised to include space and time non-equilibrium effects.

The nonlinear interaction of microwaves arid superconducting films was also examined in a third set of experiments. The surface impedance of thin films was measured as a function of the incident microwave magnetic field. The experiments exploit the ability to measure the absorbed microwave power and applied microwave magnetic field absolutely. It was found that the applied surface microwave field could not be raised above a certain threshold level at which the absorption increased abruptly. This critical field level represents a dynamic critical field and was found to be associated with the penetration of the app1ied field into the film at values well below the thermodynamic critical field for the configuration of a field applied to one side of the film. The penetration occurs despite the thermal stability of the film which was unequivocally demonstrated by experiment. A new mechanism for such penetration via the formation of a vortex-antivortex pair is proposed. The experimental results for the thinnest films agreed with the calculated values of this pair generation field. The observations of increased transmission at the critical field level and suppression of the process by a metallic ground plane further support the proposed model.