Observations of nitrogen and oxygen isotopes in the low energy cosmic rays

The isotopic composition of the enhanced low energy nitrogen and oxygen cosmic rays can provide information regarding the source of these particles. Using the Caltech Electron/Isotope Spectrometer aboard the IMP-7 satellite, a measurement of this isotopic composition was made. To determine the isotope response of the instrument, a calibration was performed, and it was determined that the standard range-energy tables were inadequate to calculate the isotope response. From the calibration, corrections to the standard range-energy tables were obtained which can be used to calculate the isotope response of this and similar instruments.

The low energy nitrogen and oxygen cosmic rays were determined to be primarily ^(14)N and ^(16)O. Upper limits were obtained for the abundances of the other stable nitrogen and oxygen isotopes. To the 84% confidence level the isotopic abundances are: ^(15)N/N ≤ 0.26 (5.6- 12.7 MeV/nucleon), ^(17)0/0 ≤ 0.13 (7.0- 11.8 MeV/nucleon), (18)0/0 ≤ 0.12 (7.0 - 11.2 MeV/nucleon). The nitrogen composition differs from higher energy measurements which indicate that ^(15)N, which is thought to be secondary, is the dominant isotope. This implies that the low energy enhanced cosmic rays are not part of the same population as the higher energy cosmic rays and that they have not passed through enough material to produce a large fraction of ^(15)N. The isotopic composition of the low energy enhanced nitrogen and oxygen is consistent with the local acceleration theory of Fisk, Kozlovsky, and Ramaty, in which interstellar material is accelerated to several MeV/nucleon. If, on the other hand, the low energy nitrogen and oxygen result from nucleosynthesis in a galactic source, then the nucleosynthesis processes which produce an enhancement of nitrogen and oxygen and a depletion of carbon are restricted to producing predominantly ^(14)N and ^(16)O.

Acceleration Sensing, Feedback Cooling, and Nonlinear Dynamics with Nanoscale Cavity-Optomechanical Devices

Light has long been used for the precise measurement of moving bodies, but the burgeoning field of optomechanics is concerned with the interaction of light and matter in a regime where the typically weak radiation pressure force of light is able to push back on the moving object. This field began with the realization in the late 1960's that the momentum imparted by a recoiling photon on a mirror would place fundamental limits on the smallest measurable displacement of that mirror. This coupling between the frequency of light and the motion of a mechanical object does much more than simply add noise, however. It has been used to cool objects to their quantum ground state, demonstrate electromagnetically-induced-transparency, and modify the damping and spring constant of the resonator. Amazingly, these radiation pressure effects have now been demonstrated in systems ranging 18 orders of magnitude in mass (kg to fg).

In this work we will focus on three diverse experiments in three different optomechanical devices which span the fields of inertial sensors, closed-loop feedback, and nonlinear dynamics. The mechanical elements presented cover 6 orders of magnitude in mass (ng to fg), but they all employ nano-scale photonic crystals to trap light and resonantly enhance the light-matter interaction. In the first experiment we take advantage of the sub-femtometer displacement resolution of our photonic crystals to demonstrate a sensitive chip-scale optical accelerometer with a kHz-frequency mechanical resonator. This sensor has a noise density of approximately 10 micro-g/rt-Hz over a useable bandwidth of approximately 20 kHz and we demonstrate at least 50 dB of linear dynamic sensor range. We also discuss methods to further improve performance of this device by a factor of 10.

In the second experiment, we used a closed-loop measurement and feedback system to damp and cool a room-temperature MHz-frequency mechanical oscillator from a phonon occupation of 6.5 million down to just 66. At the time of the experiment, this represented a world-record result for the laser cooling of a macroscopic mechanical element without the aid of cryogenic pre-cooling. Furthermore, this closed-loop damping yields a high-resolution force sensor with a practical bandwidth of 200 kHZ and the method has applications to other optomechanical sensors.

The final experiment contains results from a GHz-frequency mechanical resonator in a regime where the nonlinearity of the radiation-pressure interaction dominates the system dynamics. In this device we show self-oscillations of the mechanical element that are driven by multi-photon-phonon scattering. Control of the system allows us to initialize the mechanical oscillator into a stable high-amplitude attractor which would otherwise be inaccessible. To provide context, we begin this work by first presenting an intuitive overview of optomechanical systems and then providing an extended discussion of the principles underlying the design and fabrication of our optomechanical devices.

Oxygen isotope ratios in coexisting minerals of regionally metamorphosed rocks

The O¹⁸/O¹⁶ ratios of coexisting minerals from a number of regionally metamorphosed rocks have been measured, using a bromine pentafluoride extraction-technique. Listed in order of their increasing tendency to concentrate O¹⁸, the minerals analyzed are magnetite, ilmenite, chlorite, biotite, garnet, hornblende, kyanite, muscovite, feldspar, and quartz. The only anomalous sequence detected occurs in a xenolith of schist, in which quartz, muscovite, biotite, and ilmenite, but not garnet, have undergone isotopic exchange with surrounding trondjemite.

With few exceptions, quartz-magnetite and quartz-ilmenite fractionations decrease with increasing metamorphic grade determined by mineral paragenesis and spatial distribution. This consistency does not apply to quartz-magnetite and quartz-ilmenite fractionations obtained from rocks in which petrographic evidence of retrogradation is present.

Whereas measured isotopic fractionations among quartz, garnet, ilmenite, and magnetite are approximately related to metamorphic grade, fractionations between these minerals and biotite or muscovite show poor correlation with grade. Variations in muscovite-biotite fractionations are relatively small. These observations are interpreted to mean that muscovite and biotite are affected by retrograde re-equilibration to a greater extent than the anhydrous minerals analyzed.

Measured quartz-ilmenite fractionations range from 12 permil in the biotite zone of central Vermont to 6.5 permil in the sillimanite-orthoclase zone of southeastern Connecticut. Analyses of natural assemblages from the kyanite and sillimanite zones suggest that equilibrium quartz-ilmenite fractionations are approximately 8 percent smaller than corresponding quartz-magnetite fractionations. Employing the quartz-magnetite geothermometer calibrated by O'Neil and Clayton (1964), a temperature of 560°C was obtained for kyanite-bearing schists from Addison County, Vermont. Extending the calibration to quartz-ilmenite fractionations, a temperature of 600°C was obtained for kyanite-schists from Shoshone County, Idaho. At these temperatures kyanite is stable only at pressures exceeding 11 kbars (Bell, 1963), corresponding to lithostatic loads of over 40 km.

Mechanisms of Transposable Element Repression by Piwi Proteins in the piRNA Pathway of Drosophila Germ Cells

The ability to reproduce is a defining characteristic of all living organisms. During reproduction, the integrity of genetic material transferred from one generation to the next is of utmost importance. Organisms have diverse strategies to ensure the fidelity of genomic information inherited between generations of individuals. In sexually reproducing animals, the piRNA pathway is an RNA-interference (RNAi) mechanism that protects the genomes of germ cells from the replication of ‘selfish’ genetic sequences called transposable elements (TE). When left unabated, the replication of TE sequences can cause gene disruption, double-stranded DNA breaks, and germ cell death that results in sterility of the organism. In Drosophila, the piRNA pathway is divided into a cytoplasmic and nuclear branch that involves the functions of three Piwi-clade Argonaute proteins—Piwi, Aubergine (Aub) and Argonaute-3 (Ago3)—which bind piwi-interacting RNA (piRNA) to form the effector complexes that represses deleterious TE sequences.

The work presented in this thesis examines the function and regulation of Piwi proteins in Drosophila germ cells. Chapter 1 presents an introduction to piRNA biogenesis and to the essential roles occupied by each Piwi protein in the repression of TE. We discuss the architecture and function of germ granules as the cellular compartments where much of the piRNA pathway operates. In Chapter 2, we present how Piwi in the nucleus co-transcriptionally targets genomic loci expressing TE sequences to direct the deposition of repressive chromatin marks. Chapter 3 examines the cytoplasmic function of the piRNA pathway, where we find that the protein Krimper coordinates Aub and Ago3 in the piRNA ping-pong pathway to adaptively target and destroy TE transcripts. Chapter 4 explores how interactions of Piwis with associated proteins are modulated by arginine methylation modifications. Lastly, in Chapter 5 I present evidence that the cytoplasmic branch of the piRNA pathway can potentially ‘cross-talk’ with the nuclear branch to transfer sequence information to better target and co-transcriptionally silence the genomic loci coding active TE sequences. Overall, the work presented in this thesis constitutes a part of the first steps in understanding the molecular mechanisms that protect germ cells from invasion by TE sequences.

Contribution of the temporoammonic pathway to hippocampal processing

The temporoammonic (TA) pathway is the direct, monosynaptic projection from layer III of entorhinal cortex to the distal dendritic region of area CA1 of the hippo­ campus. Although this pathway has been implicated in various functions, such as memory encoding and retrieval, spatial navigation, generation of oscillatory activity, and control of hippocampal excitability, the details of its physiology are not well understood. In this thesis, I examine the contribution of the TA pathway to hippocampal processing. I find that, as has been previously reported, the TA pathway includes both excitatory, glutamatergic components and inhibitory, GABAergic components. Several new discoveries are reported in this thesis. I show that the TA pathway is subject to forms of short-term activity-dependent regulation, including paired-pulse and frequency­ dependent plasticity, similar to other hippocampal pathways such as the Schaffer collateral (SC) input from CA3 to CA1. The TA pathway provides a strongly excitatory input to stratum radiatum giant cells of CA1. The excitatory component of the TA pathway undergoes a long-lasting decrease in synaptic strength following low-frequency stimulation in a manner partially dependent on the activation of NMDA receptors. High­ frequency activation of the TA pathway recruits a feedforward inhibition that can prevent CA1 pyramidal cells from spiking in response to SC input; this spike-blocking effect shows that the TA pathway can act to regulate information flow through the hippocampal trisynaptic pathway.

Investigation of Fundamental Processes Governing Secondary Organic Aerosol Formation in Laboratory Chambers

Our understanding of the processes and mechanisms by which secondary organic aerosol (SOA) is formed is derived from laboratory chamber studies. In the atmosphere, SOA formation is primarily driven by progressive photooxidation of SOA precursors, coupled with their gas-particle partitioning. In the chamber environment, SOA-forming vapors undergo multiple chemical and physical processes that involve production and removal via gas-phase reactions; partitioning onto suspended particles vs. particles deposited on the chamber wall; and direct deposition on the chamber wall. The main focus of this dissertation is to characterize the interactions of organic vapors with suspended particles and the chamber wall and explore how these intertwined processes in laboratory chambers govern SOA formation and evolution.

A Functional Group Oxidation Model (FGOM) that represents SOA formation and evolution in terms of the competition between functionalization and fragmentation, the extent of oxygen atom addition, and the change of volatility, is developed. The FGOM contains a set of parameters that are to be determined by fitting of the model to laboratory chamber data. The sensitivity of the model prediction to variation of the adjustable parameters allows one to assess the relative importance of various pathways involved in SOA formation.

A critical aspect of the environmental chamber is the presence of the wall, which can induce deposition of SOA-forming vapors and promote heterogeneous reactions. An experimental protocol and model framework are first developed to constrain the vapor-wall interactions. By optimal fitting the model predictions to the observed wall-induced decay profiles of 25 oxidized organic compounds, the dominant parameter governing the extent of wall deposition of a compound is identified, i.e., wall accommodation coefficient. By correlating this parameter with the molecular properties of a compound via its volatility, the wall-induced deposition rate of an organic compound can be predicted based on its carbon and oxygen numbers in the molecule.

Heterogeneous transformation of δ-hydroxycarbonyl, a major first-generation product from long-chain alkane photochemistry, is observed on the surface of particles and walls. The uniqueness of this reaction scheme is the production of substituted dihydrofuran, which is highly reactive towards ozone, OH, and NO3, thereby opening a reaction pathway that is not usually accessible to alkanes. A spectrum of highly-oxygenated products with carboxylic acid, ester, and ether functional groups is produced from the substituted dihydrofuran chemistry, thereby affecting the average oxidation state of the alkane-derived SOA.

The vapor wall loss correction is applied to several chamber-derived SOA systems generated from both anthropogenic and biogenic sources. Experimental and modeling approaches are employed to constrain the partitioning behavior of SOA-forming vapors onto suspended particles vs. chamber walls. It is demonstrated that deposition of SOA-forming vapors to the chamber wall during photooxidation experiments can lead to substantial and systematic underestimation of SOA. Therefore, it is likely that a lack of proper accounting for vapor wall losses that suppress chamber-derived SOA yields contribute substantially to the underprediction of ambient SOA concentrations in atmospheric models.

Sensing and Actuation from Biology to Electronics

We introduce an in vitro diagnostic magnetic biosensing platform for immunoassay and nucleic acid detection. The platform has key characteristics for a point-of-use (POU) diagnostic: portability, low-power consumption, low cost, and multiplexing capability. As a demonstration of capabilities, we use this platform for the room temperature, amplification-free detection of a 31 bp DNA oligomer and interferon-gamma (a protein relevant for tuberculosis diagnosis). Reliable assay measurements down to 100 pM for the DNA and 1 pM for the protein are demonstrated. We introduce a novel "magnetic freezing" technique for baseline measurement elimination and to enable spatial multiplexing. We have created a general protocol for adapting integrated circuit (IC) sensors to any of hundreds of commercially available immunoassay kits and custom designed DNA sequences.

We also introduce a method for immunotherapy treatment of malignant gliomas. We utilize leukocytes internalized with immunostimulatory nanoparticle-oligonucleotide conjugates to localize and retain immune cells near the tumor site. As a proof-of-principle, we develop a novel cell imaging and incubation chamber for in vitro magnetic motility experiments. We use the apparatus to demonstrate the controlled movement of magnetically loaded THP-1 leukocytes.

Finally, we introduce an IC transmitter and power ampli er (PA) that utilizes electronic digital infrastructure, sensors, and actuators to self-heal and adapt to process, dynamic, and environmental variation. Traditional IC design has achieved incredible degrees of reliability by ensuring that billions of transistors on a single IC die are all simultaneously functional. Reliability becomes increasingly difficult as the size of a transistor shrinks. Self-healing can mitigate these variations.

Cavity-enhanced spectroscopies for applications of remote sensing, chemical kinetics and detection of radical species

This thesis describes applications of cavity enhanced spectroscopy towards applications of remote sensing, chemical kinetics and detection of transient radical molecular species. Both direct absorption spectroscopy and cavity ring-down spectroscopy are used in this work. Frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) was utilized for measurements of spectral lineshapes of O₂ and CO₂ for obtaining laboratory reference data in support of NASA’s OCO-2 mission. FS-CRDS is highly sensitive (> 10 km absorption path length) and precise (> 10000:1 SNR), making it ideal to study subtle non-Voigt lineshape effects. In addition, these advantages of FS-CRDS were further extended for measuring kinetic isotope effects: A dual-wavelength variation of FS-CRDS was used for measuring precise D/H and ¹³C/¹²C methane isotope ratios (sigma>0.026%) for the purpose of measuring the temperature dependent kinetic isotope effects of methane oxidation with O(¹D) and OH radicals. Finally, direct absorption spectroscopic detection of the trans-DOCO radical via a frequency combs spectrometer was conducted in collaboration with professor Jun Ye at JILA/University of Colorado.

Investigations of DNA-mediated protein oxidation

DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt π-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA π-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]^3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.

Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.

Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)₂, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)₂ is substituted with poly(dAdT)₂, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.

We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.

DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.

While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]^3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]³⁺ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.

In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.

Design of an oxygen flow meter for hospital application

A general description of the need for hospital flow meters is given along with an analysis of some common flow measurement methods.

The design criteria, establishment of the basic configuration of the instrument, and the evolution of the final design are presented in detail. The ability of the magnetic crossover mechanism to extract the square root of an input is explained, and design curves are presented. The action of the flow totalizer is described in relation to the rest of the instrument. A complete set of manufacturing drawings for the instrument and its tooling is included in the thesis.

In conclusion, an evaluation of the completed instrument is made, and improvements and modifications are indicated. Mention is made of the adaptability of the magnetic crossover mechanism to other instrumentation.

Oxygen relationships in intermittent sand filtration of wastewaters

A model for some of the many physical-chemical and biological processes in intermittent sand filtration of wastewaters is described and an expression for oxygen transfer is formulated.

The model assumes that aerobic bacterial activity within the sand or soil matrix is limited, mostly by oxygen deficiency, while the surface is ponded with wastewater. Atmospheric oxygen reenters into the soil after infiltration ends. Aerobic activity is resumed, but the extent of penetration of oxygen is limited and some depths may be always anaerobic. These assumptions lead to the conclusion that the percolate shows large variations with respect to the concentration of certain contaminants, with some portions showing little change in a specific contaminant. Analyses of soil moisture in field studies and of effluent from laboratory sand columns substantiated the model.

The oxygen content of the system at sufficiently long times after addition of wastes can be described by a quasi-steady-state diffusion equation including a term for an oxygen sink. Measurements of oxygen content during laboratory and field studies show that the oxygen profile changes only slightly up to two days after the quasi-steady state is attained.

Results of these hypotheses and experimental verification can be applied in the operation of existing facilities and in the interpretation of data from pilot plant-studies.