Electron flow through cytochrome P450

The cytochromes P450 (P450s) are a remarkable class of heme enzymes that catalyze the metabolism of xenobiotics and the biosynthesis of signaling molecules. Controlled electron flow into the thiolate-ligated heme active site allows P450s to activate molecular oxygen and hydroxylate aliphatic C–H bonds via the formation of high-valent metal-oxo intermediates (compounds I and II). Due to the reactive nature and short lifetimes of these intermediates, many of the fundamental steps in catalysis have not been observed directly. The Gray group and others have developed photochemical methods, known as “flash-quench,” for triggering electron transfer (ET) and generating redox intermediates in proteins in the absence of native ET partners. Photo-triggering affords a high degree of temporal precision for the gating of an ET event; the initial ET and subsequent reactions can be monitored on the nanosecond-to-second timescale using transient absorption (TA) spectroscopies. Chapter 1 catalogues critical aspects of P450 structure and mechanism, including the native pathway for formation of compound I, and outlines the development of photochemical processes that can be used to artificially trigger ET in proteins. Chapters 2 and 3 describe the development of these photochemical methods to establish electronic communication between a photosensitizer and the buried P450 heme. Chapter 2 describes the design and characterization of a Ru-P450-BM3 conjugate containing a ruthenium photosensitizer covalently tethered to the P450 surface, and nanosecond-to-second kinetics of the photo-triggered ET event are presented. By analyzing data at multiple wavelengths, we have identified the formation of multiple ET intermediates, including the catalytically relevant compound II; this intermediate is generated by oxidation of a bound water molecule in the ferric resting state enzyme. The work in Chapter 3 probes the role of a tryptophan residue situated between the photosensitizer and heme in the aforementioned Ru-P450 BM3 conjugate. Replacement of this tryptophan with histidine does not perturb the P450 structure, yet it completely eliminates the ET reactivity described in Chapter 2. The presence of an analogous tryptophan in Ru-P450 CYP119 conjugates also is necessary for observing oxidative ET, but the yield of heme oxidation is lower. Chapter 4 offers a basic description of the theoretical underpinnings required to analyze ET. Single-step ET theory is first presented, followed by extensions to multistep ET: electron “hopping.” The generation of “hopping maps” and use of a hopping map program to analyze the rate advantage of hopping over single-step ET is described, beginning with an established rhenium-tryptophan-azurin hopping system. This ET analysis is then applied to the Ru-tryptophan-P450 systems described in Chapter 2; this strongly supports the presence of hopping in Ru-P450 conjugates. Chapter 5 explores the implementation of flash-quench and other phototriggered methods to examine the native reductive ET and gas binding events that activate molecular oxygen. In particular, TA kinetics that demonstrate heme reduction on the microsecond timescale for four Ru-P450 conjugates are presented. In addition, we implement laser flash-photolysis of P450 ferrous–CO to study the rates of CO rebinding in the thermophilic P450 CYP119 at variable temperature. Chapter 6 describes the development and implementation of air-sensitive potentiometric redox titrations to determine the solution reduction potentials of a series of P450 BM3 mutants, which were designed for non-native cyclopropanation of styrene in vivo. An important conclusion from this work is that substitution of the axial cysteine for serine shifts the wild type reduction potential positive by 130 mV, facilitating reduction by biological redox cofactors in the presence of poorly-bound substrates. While this mutation abolishes oxygenation activity, these mutants are capable of catalyzing the cyclopropanation of styrene, even within the confines of an E. coli cell. Four appendices are also provided, including photochemical heme oxidation in ruthenium-modified nitric oxide synthase (Appendix A), general protocols (Appendix B), Chapter-specific notes (Appendix C) and Matlab scripts used for data analysis (Appendix D).

Seismic structure above and below the core-mantle boundary

Seismic structure above and below the core-mantle boundary (CMB) has been studied through use of travel time and waveform analyses of several different seismic wave groups. Anomalous systematic trends in observables document mantle heterogeneity on both large and small scales. Analog and digital data has been utilized, and in many cases the analog data has been optically scanned and digitized prior to analysis.

Differential travel times of S - SKS are shown to be an excellent diagnostic of anomalous lower mantle shear velocity (V s) structure. Wavepath geometries beneath the central Pacific exhibit large S- SKS travel time residuals (up to 10 sec), and are consistent with a large scale 0(1000 km) slower than average V_s region (≥3%). S - SKS times for paths traversing this region exhibit smaller scale patterns and trends 0(100 km) indicating V_s perturbations on many scale lengths. These times are compared to predictions of three tomographically derived aspherical models: MDLSH of Tanimoto [1990], model SH12_WM13 of Suet al. [1992], and model SH.10c.17 of Masters et al. [1992]. Qualitative agreement between the tomographic model predictions and observations is encouraging, varying from fair to good. However, inconsistencies are present and suggest anomalies in the lower mantle of scale length smaller than the present 2000+ km scale resolution of tomographic models. 2-D wave propagation experiments show the importance of inhomogeneous raypaths when considering lateral heterogeneities in the lowermost mantle.

A dataset of waveforms and differential travel times of S, ScS, and the arrival from the D" layer, Scd, provides evidence for a laterally varying V_s velocity discontinuity at the base of the mantle. Two different localized D" regions beneath the central Pacific have been investigated. Predictions from a model having a V_s discontinuity 180 km above the CMB agree well with observations for an eastern mid-Pacific CMB region. This thickness differs from V_s discontinuity thicknesses found in other regions, such as a localized region beneath the western Pacific, which average near 280 km. The "sharpness" of the V_s jump at the top of D", i.e., the depth range over which the V_s increase occurs, is not resolved by our data, and our data can in fact may be modeled equally well by a lower mantle with the increase in V_s at the top of D" occurring over a 100 krn depth range. It is difficult at present to correlate D" thicknesses from this study to overall lower mantle heterogeneity, due to uncertainties in the 3-D models, as well as poor coverage in maps of D" discontinuity thicknesses.

P-wave velocity structure (V_p) at the base of the mantle is explored using the seismic phases SKS and SPdKS. SPdKS is formed when SKS waves at distances around 107° are incident upon the CMB with a slowness that allows for coupling with diffracted P-waves at the base of the mantle. The P-wave diffraction occurs at both the SKS entrance and exit locations of the outer core. SP_dKS arrives slightly later in time than SKS, having a wave path through the mantle and core very close to SKS. The difference time between SKS and SP_dKS strongly depends on V_p at the base of the mantle near SK Score entrance and exit points. Observations from deep focus Fiji-Tonga events recorded by North American stations, and South American events recorded by European and Eurasian stations exhibit anomalously large SP_dKS - SKS difference times. SKS and the later arriving SP_dKS phase are separated by several seconds more than predictions made by 1-D reference models, such as the global average PREM [Dziewonski and Anderson, 1981] model. Models having a pronounced low-velocity zone (5%) in V_p in the bottom 50-100 km of the mantle predict the size of the observed SP_dK S-SKS anomalies. Raypath perturbations from lower mantle V_s structure may also be contributing to the observed anomalies.

Outer core structure is investigated using the family of SmKS (m=2,3,4) seismic waves. SmKS are waves that travel as S-waves in the mantle, P-waves in the core, and reflect (m-1) times on the underside of the CMB, and are well-suited for constraining outermost core V_p structure. This is due to closeness of the mantle paths and also the shallow depth range these waves travel in the outermost core. S3KS - S2KS and S4KS - S3KS differential travel times were measured using the cross-correlation method and compared to those from reflectivity synthetics created from core models of past studies. High quality recordings from a deep focus Java Sea event which sample the outer core beneath the northern Pacific, the Arctic, and northwestern North America (spanning 1/8th of the core's surface area), have SmKS wavepaths that traverse regions where lower mantle heterogeneity is pre- dieted small, and are well-modeled by the PREM core model, with possibly a small V_p decrease (1.5%) in the outermost 50 km of the core. Such a reduction implies chemical stratification in this 50 km zone, though this model feature is not uniquely resolved. Data having wave paths through areas of known D" heterogeneity (±2% and greater), such as the source-side of SmKS lower mantle paths from Fiji-Tonga to Eurasia and Africa, exhibit systematic SmKS differential time anomalies of up to several seconds. 2-D wave propagation experiments demonstrate how large scale lower mantle velocity perturbations can explain long wavelength behavior of such anomalous SmKS times. When improperly accounted for, lower mantle heterogeneity maps directly into core structure. Raypaths departing from homogeneity play an important role in producing SmKS anomalies. The existence of outermost core heterogeneity is difficult to resolve at present due to uncertainties in global lower mantle structure. Resolving a one-dimensional chemically stratified outermost core also remains difficult due to the same uncertainties. Restricting study to higher multiples of SmKS (m=2,3,4) can help reduce the affect of mantle heterogeneity due to the closeness of the mantle legs of the wavepaths. SmKS waves are ideal in providing additional information on the details of lower mantle heterogeneity.

On erasure coding for distributed storage and streaming communications

The work presented in this thesis revolves around erasure correction coding, as applied to distributed data storage and real-time streaming communications.

First, we examine the problem of allocating a given storage budget over a set of nodes for maximum reliability. The objective is to find an allocation of the budget that maximizes the probability of successful recovery by a data collector accessing a random subset of the nodes. This optimization problem is challenging in general because of its combinatorial nature, despite its simple formulation. We study several variations of the problem, assuming different allocation models and access models, and determine the optimal allocation and the optimal symmetric allocation (in which all nonempty nodes store the same amount of data) for a variety of cases. Although the optimal allocation can have nonintuitive structure and can be difficult to find in general, our results suggest that, as a simple heuristic, reliable storage can be achieved by spreading the budget maximally over all nodes when the budget is large, and spreading it minimally over a few nodes when it is small. Coding would therefore be beneficial in the former case, while uncoded replication would suffice in the latter case.

Second, we study how distributed storage allocations affect the recovery delay in a mobile setting. Specifically, two recovery delay optimization problems are considered for a network of mobile storage nodes: the maximization of the probability of successful recovery by a given deadline, and the minimization of the expected recovery delay. We show that the first problem is closely related to the earlier allocation problem, and solve the second problem completely for the case of symmetric allocations. It turns out that the optimal allocations for the two problems can be quite different. In a simulation study, we evaluated the performance of a simple data dissemination and storage protocol for mobile delay-tolerant networks, and observed that the choice of allocation can have a significant impact on the recovery delay under a variety of scenarios.

Third, we consider a real-time streaming system where messages created at regular time intervals at a source are encoded for transmission to a receiver over a packet erasure link; the receiver must subsequently decode each message within a given delay from its creation time. For erasure models containing a limited number of erasures per coding window, per sliding window, and containing erasure bursts whose maximum length is sufficiently short or long, we show that a time-invariant intrasession code asymptotically achieves the maximum message size among all codes that allow decoding under all admissible erasure patterns. For the bursty erasure model, we also show that diagonally interleaved codes derived from specific systematic block codes are asymptotically optimal over all codes in certain cases. We also study an i.i.d. erasure model in which each transmitted packet is erased independently with the same probability; the objective is to maximize the decoding probability for a given message size. We derive an upper bound on the decoding probability for any time-invariant code, and show that the gap between this bound and the performance of a family of time-invariant intrasession codes is small when the message size and packet erasure probability are small. In a simulation study, these codes performed well against a family of random time-invariant convolutional codes under a number of scenarios.

Finally, we consider the joint problems of routing and caching for named data networking. We propose a backpressure-based policy that employs virtual interest packets to make routing and caching decisions. In a packet-level simulation, the proposed policy outperformed a basic protocol that combines shortest-path routing with least-recently-used (LRU) cache replacement.

Origin of Th/U variations in chondritic meteorites

Isotope dilution thorium and uranium analyses of the Harleton chondrite show a larger scatter than previously observed in equilibrated ordinary chondrites (EOC). The linear correlation of Th/U with 1/U in Harleton (and all EOC data) is produced by variation in the chlorapatite to merrillite mixing ratio. Apatite variations control the U concentrations. Phosphorus variations are compensated by inverse variations in U to preserve the Th/U vs. 1/U correlation. Because the Th/U variations reflect phosphate ampling, a weighted Th/U average should converge to an improved solar system Th/U. We obtain Th/U=3.53 (1_-mean=0.10), significantly lower and more precise than previous estimates.

To test whether apatite also produces Th/U variation in CI and CM chondrites, we performed P analyses on the solutions from leaching experiments of Orgueil and Murchison meteorites.

A linear Th/U vs. 1/U correlation in CI can be explained by redistribution of hexavalent U by aqueous fluids into carbonates and sulfates.

Unlike CI and EOC, whole rock Th/U variations in CMs are mostly due to Th variations. A Th/U vs. 1/U linear correlation suggested by previous data for CMs is not real. We distinguish 4 components responsible for the whole rock Th/U variations: (1) P and actinide-depleted matrix containing small amounts of U-rich carbonate/sulfate phases (similar to CIs); (2) CAIs and (3) chondrules are major reservoirs for actinides, (4) an easily leachable phase of high Th/U. likely carbonate produced by CAI alteration. Phosphates play a minor role as actinide and P carrier phases in CM chondrites.

Using our Th/U and minimum galactic ages from halo globular clusters, we calculate relative supernovae production rates for ²³²Th/²³⁸U and ²³⁵U/²³⁸U for different models of r-process nucleosynthesis. For uniform galactic production, the beginning of the r-process nucleosynthesis must be less than 13 Gyr. Exponentially decreasing production is also consistent with a 13 Gyr age, but very slow decay times are required (less than 35 Gyr), approaching the uniform production. The 15 Gyr Galaxy requires either a fast initial production growth (infall time constant less than 0.5 Gyr) followed by very low decrease (decay time constant greater than 100 Gyr), or the fastest possible decrease (≈8 Gyr) preceded by slow in fall (≈7.5 Gyr).

Extractive institutions in colonial Africa

A common explanation for African current underdevelopment is the extractive character of institutions established during the colonial period. Yet, since colonial extraction is hard to quantify and its exact mechanisms are not well understood, we still do not know precisely how colonial institutions affect economic growth today. In this project, I study this issue by focusing on the peculiar structure of trade and labor policies employed by the French colonizers.

First, I analyze how trade monopsonies and coercive labor institutions reduced African gains from trade during the colonial period. By using new data on prices to agricultural producers and labor institutions in French Africa, I show that (1) the monopsonistic character of colonial trade implied a reduction in prices to producers far below world market prices; (2) coercive labor institutions allowed the colonizers to reduce prices even further; (3) as a consequence, colonial extraction cut African gains from trade by over 60%.

Given the importance of labor institutions, I then focus on their origin by analyzing the colonial governments' incentives to choose between coerced and free labor. I argue that the choice of institutions was affected more by the properties of exported commodities, such as prices and economies of scale, than by the characteristics of colonies, such indigenous population density and ease of settlement for the colonizers.

Finally, I study the long-term effects of colonial trade monopsonies and coercive labor institutions. By combining archival data on prices in the French colonies with maps of crop suitability, I show that the extent to which prices to agricultural producers were reduced with respect to world market prices is strongly negatively correlated with current regional development, as proxied by luminosity data from satellite images. The evidence suggests that colonial extraction affected subsequent growth by reducing development in rural areas in favor of a urban elite. The differential impact in rural and urban areas can be the reason why trade monopsonies and extractive institutions persisted long after independence.

A Detailed Analysis of Transcriptional Regulators Affecting the Saccharomyces cerevisiae Heat-shock Gene SSA1

The yeast Saccharomyces cerevisiae contains a family of hsp70 related genes. One member of this family, SSA1, encodes a 70kD heat-shock protein which in addition to its heat inducible expression has a significant basal level of expression. The first 500 bp upstream of the SSA1 start point of transcription was examined by DNAse I protection analysis. The results reveal the presence of at least 14 factor binding sites throughout the upstream promoter region. The function of these binding sites has been examined using a series of 5' promoter deletions fused to the recorder gene lacZ in a centromere-containing yeast shuttle vector. The following sites have been identified in the promoter and their activity in yeast determined individually with a centromere-based recorder plasmid containing a truncated CYC1 /lacZ fusion: a heat-shock element or HSE which is sufficient to convey heat-shock response on the recorder plasmid; a homology to the SV40 'core' sequence which can repress the GCN4 recognition element (GCRE) and the yAP1 recognition element (ARE), and has been designated a upstream repression element or URE; a 'G'-rich region named G-box which can also convey heatshock response on the recorder plasmid; and a purine-pyrimidine alternating sequence name GT-box which is an activator of transcription. A series of fusion constructs were made to identify a putative silencer-like element upstream of SSA1. This element is position dependent and has been localized to a region containing both an ABF1 binding site and a RAP1 binding site. Five site-specific DNA-binding factors are identified and their purification is presented: the heat-shock transcription factor or HSTF, which recognizes the HSE; the G-box binding factor or GBF; the URE recognition factor or URF; the GT-box binding factor; and the GC-box binding factor or yeast Sp1.