Constraining the interpretation of 2-methylhopanoids through genetic and phylogenetic methods

Hopanoids are a class of sterol-like lipids produced by select bacteria. Their preservation in the rock record for billions of years as fossilized hopanes lends them geological significance. Much of the structural diversity present in this class of molecules, which likely underpins important biological functions, is lost during fossilization. Yet, one type of modification that persists during preservation is methylation at C-2. The resulting 2-methylhopanoids are prominent molecular fossils and have an intriguing pattern over time, exhibiting increases in abundance associated with Ocean Anoxic Events during the Phanerozoic. This thesis uses diverse methods to address what the presence of 2-methylhopanes tells us about the microbial life and environmental conditions of their ancient depositional settings. Through an environmental survey of hpnP, the gene encoding the C-2 hopanoid methylase, we found that many different taxa are capable of producing 2-methylhopanoids in more diverse modern environments than expected. This study also revealed that hpnP is significantly overrepresented in organisms that are plant symbionts, in environments associated with plants, and with metabolisms that support plant-microbe interactions; collectively, these correlations provide a clue about the biological importance of 2-methylhopanoids. Phylogenetic reconstruction of the evolutionary history of hpnP revealed that 2-methylhopanoid production arose in the Alphaproteobacteria, indicating that the origin of these molecules is younger than originally thought. Additionally, we took genetic approach to understand the role of 2-methylhopanoids in Cyanobacteria using the filamentous symbiotic Nostoc punctiforme. We found that hopanoids likely aid in rigidifying the cell membrane but do not appear to provide resistance to osmotic or outer membrane stressors, as has been shown in other organisms. The work presented in this thesis supports previous findings that 2-methylhopanoids are not biomarkers for oxygenic photosynthesis and provides new insights by defining their distribution in modern environments, identifying their evolutionary origin, and investigating their role in Cyanobacteria. These efforts in modern settings aid the formation of a robust interpretation of 2-methylhopanes in the rock record.

A search for fractionally charged particles in cosmic rays and a theoretical interpretation of the results

An array of two spark chambers and six trays of plastic scintillation counters was used to search for unaccompanied fractionally charged particles in cosmic rays near sea level. No acceptable events were found with energy losses by ionization between 0.04 and 0.7 that of unit-charged minimum-ionizing particles. New 90%-confidence upper limits were thereby established for the fluxes of fractionally charged particles in cosmic rays, namely, (1.04 ± 0.07)x10^-10 and (2.03 ± 0.16)x10^-10 cm^-2sr^-1sec^-1 for minimum-ionizing particles with charges 1/3 and 2/3, respectively.

In order to be certain that the spark chambers could have functioned for the low levels of ionization expected from particles with small fractional charges, tests were conducted to estimate the efficiency of the chambers as they had been used in this experiment. These tests showed that the spark-chamber system with the track-selection criteria used might have been over 99% efficient for the entire range of energy losses considered.

Lower limits were then obtained for the mass of a quark by considering the above flux limits and a particular model for the production of quarks in cosmic rays. In this model, which is one involving the multi-peripheral Regge hypothesis, the production cross section and a corresponding mass limit are critically dependent on the Regge trajectory assigned to a quark. If quarks are "elementary'' with a flat trajectory, the mass of a quark can be expected to be at least 6 ± 2 BeV/c². If quarks have a trajectory with unit slope, just as the existing hadrons do, the mass of a quark might be as small as 1.3 ± 0.2 BeV/c². For a trajectory with unit slope and a mass larger than a couple of BeV/c², the production cross section may be so low that quarks might never be observed in nature.

Observation and interpretation of tectonic strain release mechanisms

In four chapters various aspects of earthquake source are studied.

Chapter I

Surface displacements that followed the Parkfield, 1966, earthquakes were measured for two years with six small-scale geodetic networks straddling the fault trace. The logarithmic rate and the periodic nature of the creep displacement recorded on a strain meter made it possible to predict creep episodes on the San Andreas fault. Some individual earthquakes were related directly to surface displacement, while in general, slow creep and aftershock activity were found to occur independently. The Parkfield earthquake is interpreted as a buried dislocation.

Chapter II

The source parameters of earthquakes between magnitude 1 and 6 were studied using field observations, fault plane solutions, and surface wave and S-wave spectral analysis. The seismic moment, M_O, was found to be related to local magnitude, M_L, by log M_O = 1.7 M_L + 15.1. The source length vs magnitude relation for the San Andreas system found to be: M_L = 1.9 log L - 6.7. The surface wave envelope parameter AR gives the moment according to log M_O = log AR₃₀₀ + 30.1, and the stress drop, τ, was found to be related to the magnitude by τ = 0.54 M - 2.58. The relation between surface wave magnitude M_S and M_L is proposed to be M_S = 1.7 M_L - 4.1. It is proposed to estimate the relative stress level (and possibly the strength) of a source-region by the amplitude ratio of high-frequency to low-frequency waves. An apparent stress map for Southern California is presented.

Chapter III

Seismic triggering and seismic shaking are proposed as two closely related mechanisms of strain release which explain observations of the character of the P wave generated by the Alaskan earthquake of 1964, and distant fault slippage observed after the Borrego Mountain, California earthquake of 1968. The Alaska, 1964, earthquake is shown to be adequately described as a series of individual rupture events. The first of these events had a body wave magnitude of 6.6 and is considered to have initiated or triggered the whole sequence. The propagation velocity of the disturbance is estimated to be 3.5 km/sec. On the basis of circumstantial evidence it is proposed that the Borrego Mountain, 1968, earthquake caused release of tectonic strain along three active faults at distances of 45 to 75 km from the epicenter. It is suggested that this mechanism of strain release is best described as "seismic shaking."

Chapter IV

The changes of apparent stress with depth are studied in the South American deep seismic zone. For shallow earthquakes the apparent stress is 20 bars on the average, the same as for earthquakes in the Aleutians and on Oceanic Ridges. At depths between 50 and 150 km the apparent stresses are relatively high, approximately 380 bars, and around 600 km depth they are again near 20 bars. The seismic efficiency is estimated to be 0.1. This suggests that the true stress is obtained by multiplying the apparent stress by ten. The variation of apparent stress with depth is explained in terms of the hypothesis of ocean floor consumption.

Probability in Quantum Mechanics: The Everett Interpretation and the Decision-Theoretic Program

The Everett interpretation of quantum mechanics is an increasingly popular alternative to the traditional Copenhagen interpretation, but there are a few major issues that prevent the widespread adoption. One of these issues is the origin of probabilities in the Everett interpretation, which this thesis will attempt to survey. The most successful resolution of the probability problem thus far is the decision-theoretic program, which attempts to frame probabilities as outcomes of rational decision making. This marks a departure from orthodox interpretations of probabilities in the physical sciences, where probabilities are thought to be objective, stemming from symmetry considerations. This thesis will attempt to offer evaluations on the decision-theoretic program.

Phase interpretation for polarization-dependent near-field images of high-density gratings

It has been described that the near-field images of a high-density grating at the half self-imaging distance could be different for TE and TM polarization states. We propose that the phases of the diffraction orders play an important role in such polarization dependence. The view is verified through the coincidence of the numerical result of finite-difference time-domain method and the reconstructed results from the rigorous coupled-wave analysis. Field distributions of TE and TM polarizations are given numerically for a grating with period d = 2.3 lambda, which are verified through experiments with the scanning near-field optical microscopy technique. The concept of phase interpretation not only explains the polarization dependence at the half self-imaging distance of gratings with a physical view, but also, it could be widely used to describe the near-field diffraction of a variety of periodic diffractive optical elements whose feature size comparable to the wavelength. (C) 2008 Elsevier B.V. All rights reserved.

Thermal analyses, spectral characterization and structural interpretation of Yb3+ doped TeO2-ZnO-ZnCl2 glasses

Bulk-lasses have been prepared in the TeO2-ZnO-ZnCl2 systems. Their characteristic temperatures were determined and analyzed. Raman and FT-IR spectra were used to analyze the effect of ZnCl2 on the structure and spectral properties of tellurite glasses and OH- groups in this glass system. The spectroscopic properties including absorption spectra, emission cross-sections and fluorescence lifetimes of Yb3+ in TeO2-ZnO-ZnCl2 were measured and calculated. It is demonstrated that the progressive replacement less than 20 mol% of TeO2 by ZnCl2 improves the thermal stability, removes the OH- groups, turns TeO4 bipyramidal arrangement into TeO3 (and/or TeO3+1) trigonal pyramids structures and results in the decrease of the symmetry of the structure, which increases the emission cross-sections and lifetimes. But when the content of ZnCl2 up to 30 mol%, the glass system becomes more hygroscopic and introduces more OH- groups, which decrease the emission cross-sections and shorten the lifetimes. The results show that the glass system with (TeO2)-Te-69-(ZnO)-Zn-10-20ZnCl(2)-1Yb(2)O(3) is a desirable component for active laser media for high power generation. (c) 2005 Elsevier B.V. All rights reserved.

Fisheries statutory instruments 1950-93 [collection of salmon and fisheries legislation with special respect to Cumbria]

This document is a collection of legislative documents relating to fisheries, especially Statutory Instruments, with special regards to the county Cumbria in the north of England. This includes Orders on salmon and trout spanning the years 1950-1993.

Zonation of submerged vegetation in Lake Kariba, Zimbabwe and its ecological interpretation

The submerged vegetation of Lake Kariba is described in relation to degree of slope (lake morphometry), depth and light transparency. The direct gradient analysis technique - canonical correspondence analysis and the TWINSPAN classification programs were used to analyse the data set. The western end of the lake with low transparency has a low species diversity (with Vallisneria aethiopica dominating). Species diversity increases with increased transparency in the other parts of the lake. The classification revealed monospecific communities for all species as well as mixed communities with Lagarosiphon as the associate species with the broadest distribution. The ordination revealed a first axis strongly related to the depth and transparency gradients and the second axis related to slope.

A guide to the interpretation of sea trout scales

The overall purpose of this guide is to provide a manual for the collection and interpretation of sea trout scales. A brief introduction considers the advantages and disadvantages of using scales to determine age and growth. To ensure that scales are interpreted in a consistent manner, all major terms are defined and a standard system for age notation is proposed. The methodology for the collection, mounting and interpretation of scales is described in detail, and this is followed by a section on the back-calculation of lengths at different ages. Each topic is discussed critically. The final part of this guide is an atlas illustrating scales from a wide range of sea trout and including not only excellent "type-scales" but also difficult and impossible scales.