Integral finite surgeries on knots in S^3

Using the correction terms in Heegaard Floer homology, we prove that if a knot in S³ admits a positive integral T-, O-, or I-type surgery, it must have the same knot Floer homology as one of the knots given in our complete list, and the resulting manifold is orientation-preservingly homeomorphic to the p-surgery on the corresponding knot.

1. Ultrasonic studies of binary liquid structure in the critical region. Theory and experiment for the 2,6-lutidine/water system. 2. Hartree-Fock calculations of electric polarizabilities of some simple atoms and molecules, and their practicality. 3. Calculation of vibrational transition probabilities in collinear atom-diatom and diatom-diatom collisions with Lennard-Jones interaction

Part 1. Many interesting visual and mechanical phenomena occur in the critical region of fluids, both for the gas-liquid and liquid-liquid transitions. The precise thermodynamic and transport behavior here has some broad consequences for the molecular theory of liquids. Previous studies in this laboratory on a liquid-liquid critical mixture via ultrasonics supported a basically classical analysis of fluid behavior by M. Fixman (e. g., the free energy is assumed analytic in intensive variables in the thermodynamics)--at least when the fluid is not too close to critical. A breakdown in classical concepts is evidenced close to critical, in some well-defined ways. We have studied herein a liquid-liquid critical system of complementary nature (possessing a lower critical mixing or consolute temperature) to all previous mixtures, to look for new qualitative critical behavior. We did not find such new behavior in the ultrasonic absorption ascribable to the critical fluctuations, but we did find extra absorption due to chemical processes (yet these are related to the mixing behavior generating the lower consolute point). We rederived, corrected, and extended Fixman's analysis to interpret our experimental results in these more complex circumstances. The entire account of theory and experiment is prefaced by an extensive introduction recounting the general status of liquid state theory. The introduction provides a context for our present work, and also points out problems deserving attention. Interest in these problems was stimulated by this work but also by work in Part 3.

Part 2. Among variational theories of electronic structure, the Hartree-Fock theory has proved particularly valuable for a practical understanding of such properties as chemical binding, electric multipole moments, and X-ray scattering intensity. It also provides the most tractable method of calculating first-order properties under external or internal one-electron perturbations, either developed explicitly in orders of perturbation theory or in the fully self-consistent method. The accuracy and consistency of first-order properties are poorer than those of zero-order properties, but this is most often due to the use of explicit approximations in solving the perturbed equations, or to inadequacy of the variational basis in size or composition. We have calculated the electric polarizabilities of H₂, He, Li, Be, LiH, and N₂ by Hartree-Fock theory, using exact perturbation theory or the fully self-consistent method, as dictated by convenience. By careful studies on total basis set composition, we obtained good approximations to limiting Hartree-Fock values of polarizabilities with bases of reasonable size. The values for all species, and for each direction in the molecular cases, are within 8% of experiment, or of best theoretical values in the absence of the former. Our results support the use of unadorned Hartree-Pock theory for static polarizabilities needed in interpreting electron-molecule scattering data, collision-induced light scattering experiments, and other phenomena involving experimentally inaccessible polarizabilities.

Part 3. Numerical integration of the close-coupled scattering equations has been carried out to obtain vibrational transition probabilities for some models of the electronically adiabatic H₂-H₂ collision. All the models use a Lennard-Jones interaction potential between nearest atoms in the collision partners. We have analyzed the results for some insight into the vibrational excitation process in its dependence on the energy of collision, the nature of the vibrational binding potential, and other factors. We conclude also that replacement of earlier, simpler models of the interaction potential by the Lennard-Jones form adds very little realism for all the complication it introduces. A brief introduction precedes the presentation of our work and places it in the context of attempts to understand the collisional activation process in chemical reactions as well as some other chemical dynamics.

2,4-dimethylene-1,3-cyclobutanediyl and 2,4-dimethylenebicyclobutane. Synthesis, spectroscopy, and reactivity of a triplet biradical and its covalent isomer

The preparation and direct observation of triplet 2,4-dimethylene-1,3- cyclobutanediyl (1), the non-Kekule isomer of benzene, is described. The biradical was generated by photolysis of 5,6-dimethylene-2,3- diazabicyclo[2.1.1]hex-2-ene (2) (which was synthesized in several steps from benzvalene) under cryogenic, matrix-isolation conditions. Biradical 1 was characterized by EPR spectroscopy (‌‌‌‌‌│D/hc│ =0.0204 cm^(-1), │E/hc│ =0.0028 cm^(-1)) and found to have a triplet ground state. The Δm_s= 2 transition displays hyperfine splitting attributed to a 7.3-G coupling to the ring methine and a 5.9-G coupling to the exocyclic methylene protons. Several experiments, including application of the magnetophotoselection (mps) technique in the generation of biradical 1, have allowed a determination of the zero-field triplet sublevels as x = -0.0040, y = +0.0136, and z = -0.0096 cm^(-1), where x and y are respectively the long and short in-plane axes and z the out-of-plane axis of 1.

Triplet 1 is yellow-orange and displays highly structured absorption (λ_(max)= 506 nm) and fluorescence (λ_(max) = 510 nm) spectra, with vibronic spacings of 1520 and 620 cm^(-1) for absorption and 1570 and 620 cm^(-1) for emission. The spectra were unequivocally assigned to triplet 1 by the use of a novel technique that takes advantage of the biradical's photolability. The absorption є = 7200 M^(-1) cm^(-1) and f = 0.022, establishing that the transition is spin-allowed. Further use of the mps technique has demonstrated that the transition is x-polarized, and the excited state 1s therefore of B_(1g) symmetry, in accord with theoretical predictions.

Thermolysis or direct photolysis of diazene 2 in fluid solution produces 2,4- dimethylenebicyclo[l.l.0]butane (3), whose ^(l)H NMR spectrum (-80°C, CD_(2)Cl_(2)) consists of singlets at δ 4.22 and 3.18 in a 2:1 ratio. Compound 3 is thermally unstable and dimerizes with second-order kinetics between -80 and -25°C (∆H^(‡) = 6.8 kcal mol^(-1), (∆s^(‡) = -28 eu) by a mechanism involving direct combination of two molecules of 3 in the rate-determining step. This singlet-manifold reaction ultimately produces a mixture of two dimers, 3,8,9- trimethylenetricyclo[5.1.1.0^(2,5)]non-4-ene (75) and trans-3,10-dimethylenetricyclo[6.2.0.0^(2,5)]deca-4,8-diene (76t), with the former predominating. In contrast, triplet-sensitized photolysis of 2, which leads to triplet 1, provides, in addition to 75 and 76t, a substantial amount of trans-5,10- dimethylenetricyclo[6.2.0.0^(3,6)]deca-3,8-diene (77t) and small amounts of two unidentified dimers.

In addition, triplet biradical 1 ring-closes to 3 in rigid media both thermally (77-140 K) and photochemically. In solution 3 forms triplet 1 upon energy transfer from sensitizers having relatively low triplet energies. The implications of the thermal chemistry for the energy surfaces of the system are discussed.

Studies in vortex motion

This thesis covers four different problems in the understanding of vortex sheets, and these are presented in four chapters.

In Chapter 1, free streamline theory is used to determine the steady solutions of an array of identical, hollow or stagnant core vortices in an inviscid, incompressible fluid. Assuming the array is symmetric to rotation through π radians about an axis through any vortex centre, there are two solutions or no solutions depending on whether A^(1/2)/L is less than or greater than 0.38 where A is the area of the vortex and L is the separation distance. Stability analysis shows that the more deformed shape is unstable to infinitesimal symmetric disturbances which leave the centres of the vortices undisplaced.

Chapter 2 is concerned with the roll-up of vortex sheets in homogeneous fluid. The flow over conventional and ring wings is used to test the method of Fink and Soh (1974). Despite modifications which improve the accuracy of the method, unphysical results occur. A possible explanation for this is that small scales are important and an alternate method based on "Cloud-in-Cell" techniques is introduced. The results show small scale growth and amalgamation into larger structures.

The motion of a buoyant pair of line vortices of opposite circulation is considered in Chapter 3. The density difference between the fluid carried by the vortices and the fluid outside is considered small, so that the Boussinesq approximation may be used. A macroscopic model is developed which shows the formation of a detrainment filament and this is included as a modification to the model. The results agree well with the numerical solution as developed by Hill (1975b) and show that after an initial slowdown, the vortices begin to accelerate downwards.

Chapter 4 reproduces completely a paper that has already been published (Baker, Barker, Bofah and Saffman (1974)) on the effect of "vortex wandering" on the measurement of velocity profiles of the trailing vortices behind a wing.

Anatomical and developmental patterns of interleukin-2 gene expression in the mouse: analysis of IL-2 expressing cells and partial characterization of interactions involved in mediating IL-2 gene expression in vivo

Interleukin-2 (IL-2) is an important mediator in the vertebrate immune system. IL-2 is a potent growth factor that mature T lymphocytes use as a proliferation signal and the production of IL-2 is crucial for the clonal expansion of antigen-specific T cells in the primary immune response. IL-2 driven proliferation is dependent on the interaction of the lymphokine with its cognate multichain receptor. IL-2 expression is induced only upon stimulation and transcriptional activation of the IL-2 gene relies extensively on the coordinate interaction of numerous inducible and constitutive trans-acting factors. Over the past several years, thousands of papers have been published regarding molecular and cellular aspects of IL-2 gene expression and IL-2 function. The vast majority of these reports describe work that has been carried out in vitro. However, considerably less is known about control of IL-2 gene expression and IL-2 function in vivo.

To gain new insight into the regulation of IL-2 gene expression in vivo, anatomical and developmental patterns of IL-2 gene expression in the mouse were established by employing in situ hybridization and immunohistochemical staining methodologies to tissue sections generated from normal mice and mutant animals in which T -cell development was perturbed. Results from these studies revealed several interesting aspects of IL-2 gene expression, such as (1) induction of IL-2 gene expression and protein synthesis in the thymus, the primary site of T-cell development in the body, (2) cell-type specificity of IL-2 gene expression in vivo, (3) participation of IL-2 in the extrathymic expansion of mature T cells in particular tissues, independent of an acute immune response to foreign antigen, (4) involvement of IL-2 in maintaining immunologic balance in the mucosal immune system, and (5) potential function of IL-2 in early events associated with hematopoiesis.

Extensive analysis of IL-2 mRNA accumulation and protein production in the murine thymus at various stages of development established the existence of two classes of intrathymic IL-2 producing cells. One class of intrathymic IL-2 producers was found exclusively in the fetal thymus. Cells belonging to this subset were restricted to the outermost region of the thymus. IL-2 expression in the fetal thymus was highly transient; a dramatic peak ofiL-2 mRNA accumulation was identified at day 14.5 of gestation and maximal IL-2 protein production was observed 12 hours later, after which both IL-2 mRNA and protein levels rapidly decreased. Significantly, the presence of IL-2 expressing cells in the day 14-15 fetal thymus was not contingent on the generation of T-cell receptor (TcR) positive cells. The second class of IL-2 producing cells was also detectable in the fetal thymus (cells found in this class represented a minority subset of IL-2 producers in the fetal thymus) but persist in the thymus during later stages of development and after birth. Intrathymic IL-2 producers in postnatal animals were located in the subcapsular region and cortex, indicating that these cells reside in the same areas where immature T cells are consigned. The frequency of IL-2 expressing cells in the postnatal thymus was extremely low, indicating that induction of IL-2 expression and protein synthesis are indicative of a rare activation event. Unlike the fetal class of intrathymic IL-2 producers, the presence of IL-2 producing cells in the postnatal thymus was dependent on to the generation of TcR+ cells. Subsequent examination of intrathymic IL-2 production in mutant postnatal mice unable to produce either αβ or γδ T cells showed that postnatal IL-2 producers in the thymus belong to both αβ and γδ lineages. Additionally, further studies indicated that IL-2 synthesis by immature αβ -T cells depends on the expression of bonafide TcR αβ-heterodimers. Taken altogether, IL-2 production in the postnatal thymus relies on the generation of αβ or γδ-TcR^+ cells and induction of IL-2 protein synthesis can be linked to an activation event mediated via the TcR.

With regard to tissue specificity of IL-2 gene expression in vivo, analysis of whole body sections obtained from normal neonatal mouse pups by in situ hybridization demonstrated that IL-2 mRNA^+ cells were found in both lymphoid and nonlymphoid tissues with which T cells are associated, such as the thymus (as described above), dermis and gut. Tissues devoid of IL-2 mRNA^+ cells included brain, heart, lung, liver, stomach, spine, spinal cord, kidney, and bladder. Additional analysis of isolated tissues taken from older animals revealed that IL-2 expression was undetectable in bone marrow and in nonactivated spleen and lymph nodes. Thus, it appears that extrathymic IL-2 expressing cells in nonimmunologically challenged animals are relegated to particular epidermal and epithelial tissues in which characterized subsets of T cells reside and thatinduction of IL-2 gene expression associated with these tissues may be a result of T-cell activation therein.

Based on the neonatal in situ hybridization results, a detailed investigation into possible induction of IL-2 expression resulting in IL-2 protein synthesis in the skin and gut revealed that IL-2 expression is induced in the epidermis and intestine and IL-2 protein is available to drive cell proliferation of resident cells and/or participate in immune function in these tissues. Pertaining to IL-2 expression in the skin, maximal IL-2 mRNA accumulation and protein production were observed when resident Vγ_3^+ T-cell populations were expanding. At this age, both IL-2 mRNA^+ cells and IL-2 protein production were intimately associated with hair follicles. Likewise, at this age a significant number of CD3ε^+ cells were also found in association with follicles. The colocalization of IL-2 expression and CD3ε^+ cells suggests that IL-2 expression is induced when T cells are in contact with hair follicles. In contrast, neither IL-2 mRNA nor IL-2 protein were readily detected once T-cell density in the skin reached steady-state proportions. At this point, T cells were no longer found associated with hair follicles but were evenly distributed throughout the epidermis. In addition, IL-2 expression in the skin was contingent upon the presence of mature T cells therein and induction of IL-2 protein synthesis in the skin did not depend on the expression of a specific TcR on resident T cells. These newly disclosed properties of IL-2 expression in the skin indicate that IL-2 may play an additional role in controlling mature T-cell proliferation by participating in the extrathymic expansion of T cells, particularly those associated with the epidermis.

Finally, regarding IL-2 expression and protein synthesis in the gut, IL-2 producing cells were found associated with the lamina propria of neonatal animals and gut-associated IL-2 production persisted throughout life. In older animals, the frequency of IL-2 producing cells in the small intestine was not identical to that in the large intestine and this difference may reflect regional specialization of the mucosal immune system in response to enteric antigen. Similar to other instances of IL-2 gene expression in vivo, a failure to generate mature T cells also led to an abrogation of IL-2 protein production in the gut. The presence of IL-2 producing cells in the neonatal gut suggested that these cells may be generated during fetal development. Examination of the fetal gut to determine the distribution of IL-2 producing cells therein indicated that there was a tenfold increase in the number of gut-associated IL-2 producers at day 20 of gestation compared to that observed four days earlier and there was little difference between the frequency of IL-2 producing cells in prenatal versus neonatal gut. The origin of these fetally-derived IL-2 producing cells is unclear. Prior to the immigration of IL-2 inducible cells to the fetal gut and/or induction of IL-2 expression therein, IL-2 protein was observed in the fetal liver and fetal omentum, as well as the fetal thymus. Considering that induction of IL-2 protein synthesis may be an indication of future functional capability, detection of IL-2 producing cells in the fetal liver and fetal omentum raises the possibility that IL-2 producing cells in the fetal gut may be extrathymic in origin and IL-2 producing cells in these fetal tissues may not belong solely to the T lineage. Overall, these results provide increased understanding of the nature of IL-2 producing cells in the gut and how the absence of IL-2 production therein and in fetal hematopoietic tissues can result in the acute pathology observed in IL-2 deficient animals.

Topics in gravitational-wave science : macroscopic quantum mechanics and black hole physics

The theories of relativity and quantum mechanics, the two most important physics discoveries of the 20th century, not only revolutionized our understanding of the nature of space-time and the way matter exists and interacts, but also became the building blocks of what we currently know as modern physics. My thesis studies both subjects in great depths --- this intersection takes place in gravitational-wave physics.

Gravitational waves are "ripples of space-time", long predicted by general relativity. Although indirect evidence of gravitational waves has been discovered from observations of binary pulsars, direct detection of these waves is still actively being pursued. An international array of laser interferometer gravitational-wave detectors has been constructed in the past decade, and a first generation of these detectors has taken several years of data without a discovery. At this moment, these detectors are being upgraded into second-generation configurations, which will have ten times better sensitivity. Kilogram-scale test masses of these detectors, highly isolated from the environment, are probed continuously by photons. The sensitivity of such a quantum measurement can often be limited by the Heisenberg Uncertainty Principle, and during such a measurement, the test masses can be viewed as evolving through a sequence of nearly pure quantum states.

The first part of this thesis (Chapter 2) concerns how to minimize the adverse effect of thermal fluctuations on the sensitivity of advanced gravitational detectors, thereby making them closer to being quantum-limited. My colleagues and I present a detailed analysis of coating thermal noise in advanced gravitational-wave detectors, which is the dominant noise source of Advanced LIGO in the middle of the detection frequency band. We identified the two elastic loss angles, clarified the different components of the coating Brownian noise, and obtained their cross spectral densities.

The second part of this thesis (Chapters 3-7) concerns formulating experimental concepts and analyzing experimental results that demonstrate the quantum mechanical behavior of macroscopic objects - as well as developing theoretical tools for analyzing quantum measurement processes. In Chapter 3, we study the open quantum dynamics of optomechanical experiments in which a single photon strongly influences the quantum state of a mechanical object. We also explain how to engineer the mechanical oscillator's quantum state by modifying the single photon's wave function.

In Chapters 4-5, we build theoretical tools for analyzing the so-called "non-Markovian" quantum measurement processes. Chapter 4 establishes a mathematical formalism that describes the evolution of a quantum system (the plant), which is coupled to a non-Markovian bath (i.e., one with a memory) while at the same time being under continuous quantum measurement (by the probe field). This aims at providing a general framework for analyzing a large class of non-Markovian measurement processes. Chapter 5 develops a way of characterizing the non-Markovianity of a bath (i.e.,whether and to what extent the bath remembers information about the plant) by perturbing the plant and watching for changes in the its subsequent evolution. Chapter 6 re-analyzes a recent measurement of a mechanical oscillator's zero-point fluctuations, revealing nontrivial correlation between the measurement device's sensing noise and the quantum rack-action noise.

Chapter 7 describes a model in which gravity is classical and matter motions are quantized, elaborating how the quantum motions of matter are affected by the fact that gravity is classical. It offers an experimentally plausible way to test this model (hence the nature of gravity) by measuring the center-of-mass motion of a macroscopic object.

The most promising gravitational waves for direct detection are those emitted from highly energetic astrophysical processes, sometimes involving black holes - a type of object predicted by general relativity whose properties depend highly on the strong-field regime of the theory. Although black holes have been inferred to exist at centers of galaxies and in certain so-called X-ray binary objects, detecting gravitational waves emitted by systems containing black holes will offer a much more direct way of observing black holes, providing unprecedented details of space-time geometry in the black-holes' strong-field region.

The third part of this thesis (Chapters 8-11) studies black-hole physics in connection with gravitational-wave detection.

Chapter 8 applies black hole perturbation theory to model the dynamics of a light compact object orbiting around a massive central Schwarzschild black hole. In this chapter, we present a Hamiltonian formalism in which the low-mass object and the metric perturbations of the background spacetime are jointly evolved. Chapter 9 uses WKB techniques to analyze oscillation modes (quasi-normal modes or QNMs) of spinning black holes. We obtain analytical approximations to the spectrum of the weakly-damped QNMs, with relative error O(1/L^2), and connect these frequencies to geometrical features of spherical photon orbits in Kerr spacetime. Chapter 11 focuses mainly on near-extremal Kerr black holes, we discuss a bifurcation in their QNM spectra for certain ranges of (l,m) (the angular quantum numbers) as a/M → 1. With tools prepared in Chapter 9 and 10, in Chapter 11 we obtain an analytical approximate for the scalar Green function in Kerr spacetime.

Proteomic analysis of the Cdc48/Ubx network identifies a role for Ubx2 in the regulation of lipid biosynthesis

Cdc48/p97 is an essential, highly abundant hexameric member of the AAA (ATPase associated with various cellular activities) family. It has been linked to a variety of processes throughout the cell but it is best known for its role in the ubiquitin proteasome pathway. In this system it is believed that Cdc48 behaves as a segregase, transducing the chemical energy of ATP hydrolysis into mechanical force to separate ubiquitin-conjugated proteins from their tightly-bound partners.

Current models posit that Cdc48 is linked to its substrates through a variety of adaptor proteins, including a family of seven proteins (13 in humans) that contain a Cdc48-binding UBX domain. As such, due to the complexity of the network of adaptor proteins for which it serves as the hub, Cdc48/p97 has the potential to exert a profound influence on the ubiquitin proteasome pathway. However, the number of known substrates of Cdc48/p97 remains relatively small, and smaller still is the number of substrates that have been linked to a specific UBX domain protein. As such, the goal of this dissertation research has been to discover new substrates and better understand the functions of the Cdc48 network. With this objective in mind, we established a proteomic screen to assemble a catalog of candidate substrate/targets of the Ubx adaptor system.

Here we describe the implementation and optimization of a cutting-edge quantitative mass spectrometry method to measure relative changes in the Saccharomyces cerevisiae proteome. Utilizing this technology, and in order to better understand the breadth of function of Cdc48 and its adaptors, we then performed a global screen to identify accumulating ubiquitin conjugates in cdc48-3 and ubxΔ mutants. In this screen different ubx mutants exhibited reproducible patterns of conjugate accumulation that differed greatly from each other, pointing to various unexpected functional specializations of the individual Ubx proteins.

As validation of our mass spectrometry findings, we then examined in detail the endoplasmic-reticulum bound transcription factor Spt23, which we identified as a putative Ubx2 substrate. In these studies ubx2Δ cells were deficient in processing of Spt23 to its active p90 form, and in localizing p90 to the nucleus. Additionally, consistent with reduced processing of Spt23, ubx2Δ cells demonstrated a defect in expression of their target gene OLE1, a fatty acid desaturase. Overall, this work demonstrates the power of proteomics as a tool to identify new targets of various pathways and reveals Ubx2 as a key regulator lipid membrane biosynthesis.

Complex behavior and perception in Drosophila emerges from iterative feedback-regulated reflexes

For a hungry fruit fly, locating and landing on a fermenting fruit where it can feed, find mates, and lay eggs, is an essential and difficult task requiring the integration of both olfactory and visual cues. Understanding how flies accomplish this will help provide a comprehensive ethological context for the expanding knowledge of their neural circuits involved in processing olfaction and vision, as well as inspire novel engineering solutions for control and estimation in computationally limited robotic applications. In this thesis, I use novel high throughput methods to develop a detailed overview of how flies track odor plumes, land, and regulate flight speed. Finally, I provide an example of how these insights can be applied to robotic applications to simplify complicated estimation problems. To localize an odor source, flies exhibit three iterative, reflex-driven behaviors. Upon encountering an attractive plume, flies increase their flight speed and turn upwind using visual cues. After losing the plume, flies begin zigzagging crosswind, again using visual cues to control their heading. After sensing an attractive odor, flies become more attracted to small visual features, which increases their chances of finding the plume source. Their changes in heading are largely controlled by open-loop maneuvers called saccades, which they direct towards and away from visual features. If a fly decides to land on an object, it begins to decelerate so as to maintain a stereotypical ratio of expansion to retinal size. Once they reach a stereotypical distance from the target, flies extend their legs in preparation for touchdown. Although it is unclear what cues they use to trigger this behavior, previous studies have indicated that it is likely under visual control. In Chapter 3, I use a nonlinear control theoretic analysis and robotic testbed to propose a novel and putative mechanism for how a fly might visually estimate distance by actively decelerating according to a visual control law. Throughout these behaviors, a common theme is the visual control of flight speed. Using genetic tools I show that the neuromodulator octopamine plays an important role in regulating flight speed, and propose a neural circuit for how this controller might be implemented in the flies brain. Two general biological and engineering principles are evident across my experiments: (1) complex behaviors, such as foraging, can emerge from the interactions of simple independent sensory-motor modules; (2) flies control their behavior in such a way that simplifies complex estimation problems.

Temporal and spacial control of RNA stability in the early embryo of Drosophila melanogaster

Early embryogenesis in metazoa is controlled by maternally synthesized products. Among these products, the mature egg is loaded with transcripts representing approximately two thirds of the genome. A subset of this maternal RNA pool is degraded prior to the transition to zygotic control of development. This transfer of control of development from maternal to zygotic products is referred to as the midblastula transition (or MBT). It is believed that the degradation of maternal transcripts is required to terminate maternal control of development and to allow zygotic control of development to begin. Until now this process of maternal transcript degradation and the subsequent timing of the MBT has been poorly understood. I have demonstrated that in the early embryo there are two independent RNA degradation pathways, either of which is sufficient for transcript elimination. However, only the concerted action of both pathways leads to elimination of transcripts with the correct timing, at the MBT. The first pathway is maternally encoded, is triggered by egg activation, and is targeted to specific classes of mRNAs through cis-acting elements in the 3' untranslated region (UTR}. The second pathway is activated 2 hr after fertilization and functions together with the maternal pathway to ensure that transcripts are degraded by the MBT. In addition, some transcripts fail to degrade at select subcellular locations adding an element of spatial control to RNA degradation. The spatial control of RNA degradation is achieved by protecting, or masking, transcripts from the degradation machinery. The RNA degradation and protection events are regulated by distinct cis-elements in the 3' untranslated region (UTR). These results provide the first systematic dissection of this highly conserved process in development and demonstrate that RNA degradation is a novel mechanism used for both temporal and spatial control of development.

Binding site size limitations of imidazole-pyrrole polyamides for recognition in the minor groove of DNA

The discovery that the three ring polyamide Im-Py-Py-Dp containing imidazole (Im) and pyrrole (Py) carboxamides binds the DNA sequence 5'-(A,T)G(A,T)C(A,T)-3' as an antiparallel dimer offers a new model for the design of ligands for specific recognition of sequences in the minor groove containing both G,C and A,T base pairs. In Chapter 2, experiments are described in which the sequential addition of five N- methylpyrrolecarboxamides to the imidazole-pyrrole polyamide Im-Py-Py-Dp affords a series of six homologous polyamides, Im-(Py)_2-7-Dp, that differ in the size of their binding site, apparent first order binding affinity, and sequence specificity. These results demonstrate that DNA sequences up to nine base pairs in length can be specifically recognized by imidazole-pyrrole polyamides containing three to seven rings by 2:1 polyamide-DNA complex formation in the minor groove. Recognition of a nine base pair site defines the new lower limit of the binding site size that can be recognized by polyamides containing exclusively imidazole and pyrrolecarboxamides. The results of this study should provide useful guidelines for the design of new polyamides that bind longer DNA sites with enhanced affinity and specificity.

In Chapter 3 the design and synthesis of the hairpin polyamide Im-Py-Im-Py-γ-Im- Py-Im-Py-Dp is described. Quantitative DNase I footprint titration experiments reveal that Im-Py-Im-Py-γ-Im-Py-Im-Py-Dp binds six base pair 5'-(A,T)GCGC(A,T)-3' sequences with 30-fold higher affinity than the unlinked polyamide Im-Py-Im-Py-Dp. The hairpin polyamide does not discriminate between A•T and T•A at the first and sixth positions of the binding site as three sites 5'-TGCGCT-3', 5'-TGCGCA-3', and 5 'AGCGCT- 3' are bound with similar affinity. However, Im-Py-Im-Py-γ-Im-Py-Im-PyDp is specific for and discriminates between G•C and C•G base pairs in the 5'-GCGC-3' core as evidenced by lower affinities for the mismatched sites 5'-AACGCA-3', 5'- TGCGTT-3', 5'-TGCGGT-3', and 5'-ACCGCT-3'.

In Chapter 4, experiments are described in which a kinetically stable hexa-aza Schiff base La³⁺ complex is covalently attached to a Tat(49-72) peptide which has been shown to bind the HIV-1 TAR RNA sequence. Although these metallo-peptides cleave TAR site-specifically in the hexanucleotide loop to afford products consistent with hydrolysis, a series of control experiments suggests that the observed cleavage is not caused by a sequence-specifically bound Tat(49-72)-La(L)³⁺ peptide.

Developmentally regulated transcription factors in Drosophila melanogaster

During early stages of Drosophila development the heat shock response cannot be induced. It is reasoned that the adverse effects on cell cycle and cell growth brought about by Hsp70 induction must outweigh the beneficial aspects of Hsp70 induction in the early embryo. Although the Drosophila heat shock transcription factor (dHSF) is abundant in the early embryo, it does not enter the nucleus in response to heat shock. In older embryos and in cultured cells the factor is localized within the nucleus in an apparent trimeric structure that binds DNA with high affinity. The domain responsible for nuclear localization upon stress resides between residues 390 and 420 of the dHSF. Using that domain as bait in a yeast two-hybrid system we now report the identification and cloning of a nuclear transport protein Drosophila karyopherin-α3(dKap- α3). Biochemical methods demonstrate that the dKap-α3 protein binds specifically to the dHSF's nuclear localization sequence (NLS). Furthermore, the dKap-α3 protein does not associate with NLSs that contain point mutations which are not transported in vivo. Nuclear docking studies also demonstrate specific nuclear targeting of the NLS substrate by dKap-α3.Consistant with previous studies demonstrating that early Drosophila embryos are refractory to heat shock as a result of dHSF nuclear exclusion, we demonstrate that the early embryo is deficient in dKap-α3 protein through cycle 12. From cycle 13 onward the transport factor is present and the dHSF is localized within the nucleus thus allowing the embryo to respond to heat shock.

The pair-rule gene fushi tarazu (ftz) is a well-studied zygotic segmentation gene that is necessary for the development of the even-numbered parasegments in Drosophila melanogastor. During early embryogenesis, ftz is expressed in a characteristic pattern of seven stripes, one in each of the even-numbered parasegments. With a view to understand how ftz is transcriptionally regulated, cDNAs that encode transcription factors that bind to the zebra element of the ftz promoter have been cloned. Chapter Ill reports the cloning and characterization of the eDNA encoding zeb-1 (zebra element binding protein), a novel steroid receptor-like molecule that specifically binds to a key regulatory element of the ftz promoter. In transient transfection assays employing Drosophila tissue culture cells, it has been shown that zeb-1 as well as a truncated zeb-1 polypeptide (zeb480) that lacks the putative ligand binding domain function as sequencespecific trans-activators of the ftz gene.

The Oct factors are members of the POU family of transcription factors that are shown to play important roles during development in mammals. Chapter IV reports the eDNA cloning and expression of a Drosophila Oct transcription factor. Whole mount in-situ hybridization experiments revealed that the spatial expression patterns of this gene during embryonic development have not yet been observed for any other gene. In early embryogenesis, its transcripts are transiently expressed as a wide uniform band from 20-40% of the egg length, very similar to that of gap genes. This pattern progressively resolves into a series of narrower stripes followed by expression in fourteen stripes. Subsequently, transcripts from this gene are expressed in the central nervous system and the brain. When expressed in the yeast Saccharomyces cerevisiae, this Drosophila factor functions as a strong, octamer-dependent activator of transcription. The data strongly suggest possible functions for the Oct factor in pattern formation in Drosophila that might transcend the boundaries of genetically defined segmentation genes.

New insights into the formation and modification of carbonate-bearing minerals and methane gas in geological systems using multiply substituted isotopologues

This thesis describes the use of multiply-substituted stable isotopologues of carbonate minerals and methane gas to better understand how these environmentally significant minerals and gases form and are modified throughout their geological histories. Stable isotopes have a long tradition in earth science as a tool for providing quantitative constraints on how molecules, in or on the earth, formed in both the present and past. Nearly all studies, until recently, have only measured the bulk concentrations of stable isotopes in a phase or species. However, the abundance of various isotopologues within a phase, for example the concentration of isotopologues with multiple rare isotopes (multiply substituted or 'clumped' isotopologues) also carries potentially useful information. Specifically, the abundances of clumped isotopologues in an equilibrated system are a function of temperature and thus knowledge of their abundances can be used to calculate a sample’s formation temperature. In this thesis, measurements of clumped isotopologues are made on both carbonate-bearing minerals and methane gas in order to better constrain the environmental and geological histories of various samples.

Clumped-isotope-based measurements of ancient carbonate-bearing minerals, including apatites, have opened up paleotemperature reconstructions to a variety of systems and time periods. However, a critical issue when using clumped-isotope based measurements to reconstruct ancient mineral formation temperatures is whether the samples being measured have faithfully recorded their original internal isotopic distributions. These original distributions can be altered, for example, by diffusion of atoms in the mineral lattice or through diagenetic reactions. Understanding these processes quantitatively is critical for the use of clumped isotopes to reconstruct past temperatures, quantify diagenesis, and calculate time-temperature burial histories of carbonate minerals. In order to help orient this part of the thesis, Chapter 2 provides a broad overview and history of clumped-isotope based measurements in carbonate minerals.

In Chapter 3, the effects of elevated temperatures on a sample’s clumped-isotope composition are probed in both natural and experimental apatites (which contain structural carbonate groups) and calcites. A quantitative model is created that is calibrated by the experiments and consistent with the natural samples. The model allows for calculations of the change in a sample’s clumped isotope abundances as a function of any time-temperature history.

In Chapter 4, the effects of diagenesis on the stable isotopic compositions of apatites are explored on samples from a variety of sedimentary phosphorite deposits. Clumped isotope temperatures and bulk isotopic measurements from carbonate and phosphate groups are compared for all samples. These results demonstrate that samples have experienced isotopic exchange of oxygen atoms in both the carbonate and phosphate groups. A kinetic model is developed that allows for the calculation of the amount of diagenesis each sample has experienced and yields insight into the physical and chemical processes of diagenesis.

The thesis then switches gear and turns its attention to clumped isotope measurements of methane. Methane is critical greenhouse gas, energy resource, and microbial metabolic product and substrate. Despite its importance both environmentally and economically, much about methane’s formational mechanisms and the relative sources of methane to various environments remains poorly constrained. In order to add new constraints to our understanding of the formation of methane in nature, I describe the development and application of methane clumped isotope measurements to environmental deposits of methane. To help orient the reader, a brief overview of the formation of methane in both high and low temperature settings is given in Chapter 5.

In Chapter 6, a method for the measurement of methane clumped isotopologues via mass spectrometry is described. This chapter demonstrates that the measurement is precise and accurate. Additionally, the measurement is calibrated experimentally such that measurements of methane clumped isotope abundances can be converted into equivalent formational temperatures. This study represents the first time that methane clumped isotope abundances have been measured at useful precisions.

In Chapter 7, the methane clumped isotope method is applied to natural samples from a variety of settings. These settings include thermogenic gases formed and reservoired in shales, migrated thermogenic gases, biogenic gases, mixed biogenic and thermogenic gas deposits, and experimentally generated gases. In all cases, calculated clumped isotope temperatures make geological sense as formation temperatures or mixtures of high and low temperature gases. Based on these observations, we propose that the clumped isotope temperature of an unmixed gas represents its formation temperature — this was neither an obvious nor expected result and has important implications for how methane forms in nature. Additionally, these results demonstrate that methane-clumped isotope compositions provided valuable additional constraints to studying natural methane deposits.

Investigations of noise and of quantum interference in proximity effect bridges

This work reports investigations upon weakly superconducting proximity effect bridges. These bridges, which exhibit the Josephson effects, are produced by bisecting a superconductor with a short (<1µ) region of material whose superconducting transition temperature is below that of the adjacent superconductors. These bridges are fabricated from layered refractory metal thin films whose transition temperature will depend upon the thickness ratio of the materials involved. The thickness ratio is changed in the area of the bridge to lower its transition temperature. This is done through novel photolithographic techniques described in the text, Chapter 2.

If two such proximity effect bridges are connected in parallel, they form a quantum interferometer. The maximum zero voltage current through this circuit is periodically modulated by the magnetic flux through the circuit. At a constant bias current, the modulation of the critical current produces a modulation in the dc voltage across the bridge. This change in dc voltage has been found to be the result of a change in the internal dissipation in the device. A simple model using lumped circuit theory and treating the bridges as quantum oscillators of frequency ω = 2eV/h, where V is the time average voltage across the device, has been found to adequately describe the observed voltage modulation.

The quantum interferometers have been converted to a galvanometer through the inclusion of an integral thin film current path which couples magnetic flux through the interferometer. Thus a change in signal current produces a change in the voltage across the interferometer at a constant bias current. This work is described in Chapter 3 of the text.

The sensitivity of any device incorporating proximity effect bridges will ultimately be determined by the fluctuations in their electrical parameters. He have measured the spectral power density of the voltage fluctuations in proximity effect bridges using a room temperature electronics and a liquid helium temperature transformer to match the very low (~ 0.1 Ω) impedances characteristic of these devices.

We find the voltage noise to agree quite well with that predicted by phonon noise in the normal conduction through the bridge plus a contribution from the superconducting pair current through the bridge which is proportional to the ratios of this current to the time average voltage across the bridge. The total voltage fluctuations are given by <V^2(f ) > = 4kTR^2_d I/V where R_d is the dynamic resistance, I the total current, and V the voltage across the bridge . An additional noise source appears with a strong 1/f^(n) dependence , 1.5 < n < 2, if the bridges are fabricated upon a glass substrate. This excess noise, attributed to thermodynamic temperature fluctuations in the volume of the bridge, increases dramatically on a glass substrate due to the greatly diminished thermal diffusivity of the glass as compared to sapphire.

Electron tunneling in proteins and water

The subject of this thesis is electronic coupling in donor-bridge-acceptor systems. In Chapter 2, ET properties of cyanide-bridged dinuclear ruthenium complexes were investigated. The strong interaction between the mixed-valent ruthenium centers leads to intense metal-to-metal charge transfer bands (MMCT). Hush analysis of the MMCT absorption bands yields the electronic-coupling strength between the metal centers (H_(AB)) and the total reorganization energy (λ). Comparison of ET kinetics to calculated rates shows that classical ET models fail to account for the observed kinetics and nuclear tunneling must be considered.

In Chapter 3, ET rates were measured in four ruthenium-modified highpotential iron-sulfur proteins (HiPIP), which were modified at position His50, His81, His42 and His18, respectively. ET kinetics for the His50 and His81 mutants are a factor of 300 different, while the donor-acceptor separation is nearly identical. PATHWAY calculations corroborate these measurements and highlight the importance of structural detail of the intervening protein matrix.

In Chapter 4, the distance dependence of ET through water bridges was measured. Photoinduced ET measurements in aqueous glasses at 77 K show that water is a poor medium for ET. Luminescence decay and quantum yield data were analyzed in the context of a quenching model that accounts for the exponential distance dependence of ET, the distance distribution of donors and acceptors embedded in the glass and the excluded volumes generated by the finite sizes of the donors and acceptors.

In Chapter 5, the pH-dependent excited state dynamics of ruthenium-modified amino acids were measured. The [Ru(bpy)_(3)] ^(2+) chromophore was linked to amino acids via an amide linkage. Protonation of the amide oxygen effectively quenches the excited state. In addition. time-resolved and steady-state luminescence data reveal that nonradiative rates are very sensitive to the protonation state and the structure of the amino acid moiety.

The Mechanical Genome in Regulation and Infection

Biological information storage and retrieval is a dynamic process that requires the genome to undergo dramatic structural rearrangements. Recent advances in single-molecule techniques have allowed precise quantification of the nano-mechanical properties of DNA [1, 2], and direct in vivo observation of molecules in action [3]. In this work, we will examine elasticity in protein-mediated DNA looping, whose structural rearrangement is essential for transcriptional regulation in both prokaryotes and eukaryotes. We will look at hydrodynamics in the process of viral DNA ejection, which mediates information transfer and exchange and has prominent implications in evolution. As in the case of Kepler's laws of planetary motion leading to Newton's gravitational theory, and the allometric scaling laws in biology revealing the organizing principles of complex networks [4], experimental data collapse in these biological phenomena has guided much of our studies and urged us to find the underlying physical principles.