Signal transduction, regulation, and developmental logic of EGFR signalling in C. elegans

RTKs-mediated signaling systems and the pathways with which they interact (e.g., those initiated by G protein-mediated signaling) involve a highly cooperative network that sense a large number of cellular inputs and then integrate, amplify, and process this information to orchestrate an appropriate set of cellular responses. The responses include virtually all aspects of cell function, from the most fundamental (proliferation, differentiation) to the most specialized (movement, metabolism, chemosensation). The basic tenets of RTK signaling system seem rather well established. Yet, new pathways and even new molecular players continue to be discovered. Although we believe that many of the essential modules of RTK signaling system are rather well understood, we have relatively little knowledge of the extent of interaction among these modules and their overall quantitative importance.

My research has encompassed the study of both positive and negative signaling by RTKs in C. elegans. I identified the C. elegans S0S-1 gene and showed that it is necessary for multiple RAS-mediated developmental signals. In addition, I demonstrated that there is a SOS-1-independent signaling during RAS-mediated vulval differentiation. By assessing signal outputs from various triple mutants, I have concluded that this SOS-1-independent signaling is not mediated by PTP-2/SHP-2 or the removal of inhibition by GAP-1/ RasGAP and it is not under regulation by SLI-1/Cb1. I speculate that there is either another exchange factor for RASor an as yet unidentified signaling pathway operating during RAS-mediated vulval induction in C. elegans.

In an attempt to uncover the molecular mechanisms of negative regulation of EGFR signaling by SLI-1/Cb1, I and two other colleagues codiscovered that RING finger domain of SLI-1 is partially dispensable for activity. This structure-function analysis shows that there is an ubiquitin protein ligase-independent activity for SLI-1 in regulating EGFR signaling. Further, we identified an inhibitory tyrosine of LET-23/ EGFR requiring sli-1(+)for its effects: removal of this tyrosine closely mimics loss of sli-1 but not loss of other negative regulator function.

By comparative analysis of two RTK pathways with similar signaling mechanisms, I have found that clr-1, a previously identified negative regulator of egl-15 mediated FGFR signaling, is also involved in let-23 EGFR signaling. The success of this approach promises a similar reciprocal test and could potentially extend to the study of other signaling pathways with similar signaling logic.

Finally, by correlating the developmental expression of lin-3 EGF to let-23 EGFR signaling activity, I demonstrated the existence of reciprocal EGF signaling in coordinating the morphogenesis of epithelia. This developmental logic of EGF signaling could provide a basis to understand a universal mechanism for organogenesis.

The logic of receptor-ligand interactions in the Notch signaling pathway

The Notch signaling pathway enables neighboring cells to coordinate developmental fates in diverse processes such as angiogenesis, neuronal differentiation, and immune system development. Although key components and interactions in the Notch pathway are known, it remains unclear how they work together to determine a cell's signaling state, defined as its quantitative ability to send and receive signals using particular Notch receptors and ligands. Recent work suggests that several aspects of the system can lead to complex signaling behaviors: First, receptors and ligands interact in two distinct ways, inhibiting each other in the same cell (in cis) while productively interacting between cells (in trans) to signal. The ability of a cell to send or receive signals depends strongly on both types of interactions. Second, mammals have multiple types of receptors and ligands, which interact with different strengths, and are frequently co-expressed in natural systems. Third, the three mammalian Fringe proteins can modify receptor-ligand interaction strengths in distinct and ligand-specific ways. Consequently, cells can exhibit non-intuitive signaling states even with relatively few components.

In order to understand what signaling states occur in natural processes, and what types of signaling behaviors they enable, this thesis puts forward a quantitative and predictive model of how the Notch signaling state is determined by the expression levels of receptors, ligands, and Fringe proteins. To specify the parameters of the model, we constructed a set of cell lines that allow control of ligand and Fringe expression level, and readout of the resulting Notch activity. We subjected these cell lines to an assay to quantitatively assess the levels of Notch ligands and receptors on the surface of individual cells. We further analyzed the dependence of these interactions on the level and type of Fringe expression. We developed a mathematical modeling framework that uses these data to predict the signaling states of individual cells from component expression levels. These methods allow us to reconstitute and analyze a diverse set of Notch signaling configurations from the bottom up, and provide a comprehensive view of the signaling repertoire of this major signaling pathway.

Analysis of a transcriptional network involving PU.1, Notch, and Gata3 in the lymphomyeloid lineage decision during early T-cell development

Hematopoiesis is a well-established system used to study developmental choices amongst cells with multiple lineage potentials, as well as the transcription factor network interactions that drive these developmental paths. Multipotent progenitors travel from the bone marrow to the thymus where T-cell development is initiated and these early T-cell precursors retain lineage plasticity even after initiating a T-cell program. The development of these early cells is driven by Notch signaling and the combinatorial expression of many transcription factors, several of which are also involved in the development of other cell lineages. The ETS family transcription factor PU.1 is involved in the development of progenitor, myeloid, and lymphoid cells, and can divert progenitor T-cells from the T-lineage to a myeloid lineage. This diversion of early T-cells by PU.1 can be blocked by Notch signaling. The PU.1 and Notch interaction creates a switch wherein PU.1 in the presence of Notch promotes T-cell identity and PU.1 in the absence of Notch signaling promotes a myeloid identity. Here we characterized an early T-cell cell line, Scid.adh.2c2, as a good model system for studying the myeloid vs. lymphoid developmental choice dependent on PU.1 and Notch signaling. We then used the Scid.adh.2c2 system to identify mechanisms mediating PU.1 and Notch signaling interactions during early T-cell development. We show that the mechanism by which Notch signaling is protecting pro-T cells is neither degradation nor modification of the PU.1 protein. Instead we give evidence that Notch signaling is blocking the PU.1-driven inhibition of a key set of T-regulatory genes including Myb, Tcf7, and Gata3. We show that the protection of Gata3 from PU.1-mediated inhibition, by Notch signaling and Myb, is important for retaining a T-lineage identity. We also discuss a PU.1-driven mechanism involving E-protein inhibition that leads to the inhibition of Notch target genes. This is mechanism may be used as a lockdown mechanism in pro-T-cells that have made the decision to divert to the myeloid pathway.

Engineering nucleic acid mechanisms for regulation and readout of gene expression : conditional Dicer substrate formation and sensitive multiplexed northern blots

Nucleic acids are most commonly associated with the genetic code, transcription and gene expression. Recently, interest has grown in engineering nucleic acids for biological applications such as controlling or detecting gene expression. The natural presence and functionality of nucleic acids within living organisms coupled with their thermodynamic properties of base-pairing make them ideal for interfacing (and possibly altering) biological systems. We use engineered small conditional RNA or DNA (scRNA, scDNA, respectively) molecules to control and detect gene expression. Three novel systems are presented: two for conditional down-regulation of gene expression via RNA interference (RNAi) and a third system for simultaneous sensitive detection of multiple RNAs using labeled scRNAs.

RNAi is a powerful tool to study genetic circuits by knocking down a gene of interest. RNAi executes the logic: If gene Y is detected, silence gene Y. The fact that detection and silencing are restricted to the same gene means that RNAi is constitutively on. This poses a significant limitation when spatiotemporal control is needed. In this work, we engineered small nucleic acid molecules that execute the logic: If mRNA X is detected, form a Dicer substrate that targets independent mRNA Y for silencing. This is a step towards implementing the logic of conditional RNAi: If gene X is detected, silence gene Y. We use scRNAs and scDNAs to engineer signal transduction cascades that produce an RNAi effector molecule in response to hybridization to a nucleic acid target X. The first mechanism is solely based on hybridization cascades and uses scRNAs to produce a double-stranded RNA (dsRNA) Dicer substrate against target gene Y. The second mechanism is based on hybridization of scDNAs to detect a nucleic acid target and produce a template for transcription of a short hairpin RNA (shRNA) Dicer substrate against target gene Y. Test-tube studies for both mechanisms demonstrate that the output Dicer substrate is produced predominantly in the presence of a correct input target and is cleaved by Dicer to produce a small interfering RNA (siRNA). Both output products can lead to gene knockdown in tissue culture. To date, signal transduction is not observed in cells; possible reasons are explored.

Signal transduction cascades are composed of multiple scRNAs (or scDNAs). The need to study multiple molecules simultaneously has motivated the development of a highly sensitive method for multiplexed northern blots. The core technology of our system is the utilization of a hybridization chain reaction (HCR) of scRNAs as the detection signal for a northern blot. To achieve multiplexing (simultaneous detection of multiple genes), we use fluorescently tagged scRNAs. Moreover, by using radioactive labeling of scRNAs, the system exhibits a five-fold increase, compared to the literature, in detection sensitivity. Sensitive multiplexed northern blot detection provides an avenue for exploring the fate of scRNAs and scDNAs in tissue culture.

Investigation of hypervelocity impact phenomena using real-time concurrent diagnostics

Hypervelocity impact of meteoroids and orbital debris poses a serious and growing threat to spacecraft. To study hypervelocity impact phenomena, a comprehensive ensemble of real-time concurrently operated diagnostics has been developed and implemented in the Small Particle Hypervelocity Impact Range (SPHIR) facility. This suite of simultaneously operated instrumentation provides multiple complementary measurements that facilitate the characterization of many impact phenomena in a single experiment. The investigation of hypervelocity impact phenomena described in this work focuses on normal impacts of 1.8 mm nylon 6/6 cylinder projectiles and variable thickness aluminum targets. The SPHIR facility two-stage light-gas gun is capable of routinely launching 5.5 mg nylon impactors to speeds of 5 to 7 km/s. Refinement of legacy SPHIR operation procedures and the investigation of first-stage pressure have improved the velocity performance of the facility, resulting in an increase in average impact velocity of at least 0.57 km/s. Results for the perforation area indicate the considered range of target thicknesses represent multiple regimes describing the non-monotonic scaling of target perforation with decreasing target thickness. The laser side-lighting (LSL) system has been developed to provide ultra-high-speed shadowgraph images of the impact event. This novel optical technique is demonstrated to characterize the propagation velocity and two-dimensional optical density of impact-generated debris clouds. Additionally, a debris capture system is located behind the target during every experiment to provide complementary information regarding the trajectory distribution and penetration depth of individual debris particles. The utilization of a coherent, collimated illumination source in the LSL system facilitates the simultaneous measurement of impact phenomena with near-IR and UV-vis spectrograph systems. Comparison of LSL images to concurrent IR results indicates two distinctly different phenomena. A high-speed, pressure-dependent IR-emitting cloud is observed in experiments to expand at velocities much higher than the debris and ejecta phenomena observed using the LSL system. In double-plate target configurations, this phenomena is observed to interact with the rear-wall several micro-seconds before the subsequent arrival of the debris cloud. Additionally, dimensional analysis presented by Whitham for blast waves is shown to describe the pressure-dependent radial expansion of the observed IR-emitting phenomena. Although this work focuses on a single hypervelocity impact configuration, the diagnostic capabilities and techniques described can be used with a wide variety of impactors, materials, and geometries to investigate any number of engineering and scientific problems.

Synthetic, kinetic and mechanistic studies in early transition metal systems. I. α- and β-hydrogen elimination reactions in derivatives of permethyltitanocene, -zirconocene, and -hafnocene. II. The reactions of aluminum alkyls with derivatives of permethylniobocene

The thermal decomposition of Cp*Ti(CH_3)_2 (Cp*≡ ƞ^5-C_5Me_5) toluene solution follows cleanly first-order kinetics and produces a single titanium product Cp*(C_5Me_4CH_2)Ti(CH_3) concurrent with the evolution of one equivalent of methane. Labeling studies using Cp*_2Ti- (CD_3)_2 and (Cp*-d_(15))_2Ti(CH_3)_2 show the decomposition to be intramolecular and the methane to be produced by the coupling of a methyl group with a hydrogen from the other TiCH_3 group. Activation parameters, ΔH^‡ and ΔS^‡, and kinetic deuterium isotope effects have been measured. The alternative decomposition pathways of α-hydrogen abstraction and a-hydrogen elimination, both leading to a titanium-methylidene intermediate, are discussed.

The insertion of unactivated acetylenes into the metal-hydride bonds of Cp*_2MH_2 (M = Zr, Hf) proceeds rapidly at low temperature to form monoand/ or bisinsertion products, dependent upon the steric bulk of the acetylene substituents. Cp*_2M(H)(C(Me)=CHMe), Cp*_2M(H)(CH=CHCMe_3), Cp*_2M(H)-(CH=CHPh), Cp*_2M(CH=CHPh)_2, Cp*_2M(CH=CHCH_3)_2 and Cp*_2Zr- (CH=CHCH_2CH_3)_2 have been isolated and characterized. To extend the study of unsaturated-carbon ligands, Cp*_2M(C≡CCH_3)_2 have been prepared by treating Cp*_2MCl_2 with LiC≡CCH_3. The reactivity of many of these complexes with carbon monoxide and dihydrogen is surveyed. The mono(2- butenyl) complexes Cp*_2M(H)(C(Me)=CHMe) rearrange at room temperature, forming the crotyl-hydride species Cp*_2M(H)(ƞ^3-C_4H_7). The bis(propenyl) and bis(l-butenyl) zirconium complexes Cp*_2Zr(CH=CHR)_2 (R = CH_3, CH_2CH_3) also rearrange, forming zirconacyclopentenes. Labeling studies, reaction chemistry, and kinetic measurements, including deuterium isotope effects, demonstrate that the unusual 6-hydrogen elimination from an sp^2-hybridized carbon is the first step in these latter rearrangements but is not observed in the former. Details of these mechanisms and the differences in reactivity of the zirconium and hafnium complexes are discussed.

The reactions of hydride- and alkyl-carbonyl derivatives of permethylniobocene with equimolar amounts of trialkylaluminum reagents occur rapidly producing the carbonyl adducts Cp*_2Nb(R)(COAlR'_3) (R = H, CH_3, CH_2CH_3, CH_2CH_2Ph, C(Me)=CHMe; R' = Me, Et). The hydride adduct Cp*_2NbH_3•AlEt_3 has also been formed. In solution, each of these compounds exists in equilibrium with the uncomplexed species. The formation constants for Cp*_2Nb(H)(COA1R'_R) have been measured. They indicate the steric bulk of the Cp* ligands plays a deciding factor in the isolation of the first example of an aluminum Lewis acid bound to a carbonyl-oxygen in preference to a metalhydride. Reactions of Cp*_2Nb(H)CO with other Lewis acids and of the one:one adducts with H_2, CO and C_2H_4 are also discussed.

Cp*_2Nb(H)(C_2H_4) also reacts with equimolar amounts of trialkylaluminum reagents, forming a one:one complex that ^1H NMR spectroscopy indicates contains a Nb-CH_2CH_2-Al bridge. This adduct also exists in equilibrium with the uncomplexed species in solution. The formation constant for Cp*_2N+/b(H)(CH_2CH_2ĀlEt_3) has been measured. Reactions of Cp*_2Nb(H)(C_2H_4) with other Lewis acids and the reactions of Cp*_2N+b(H)- (CH_2CH_2ĀlEt_3) with CO and C_2H_4 are described, as are the reactions of Cp_*2Nb(H)(CH_2=CHR) (R = Me, Ph), Cp*_2Nb(H)(CH_3C≡CCH_3) and Cp*_2Ti-(C_2H_4) with AlEt_3.

Transition metal clusters supported by multinucleating ligand frameworks as models of biological active sites

This dissertation describes efforts to model biological active sites with small molecule clusters. The approach used took advantage of a multinucleating ligand to control the structure and nuclearity of the product complexes, allowing the study of many different homo- and heterometallic clusters. Chapter 2 describes the synthesis of the multinucleating hexapyridyl trialkoxy ligand used throughout this thesis and the synthesis of trinuclear first row transition metal complexes supported by this framework, with an emphasis on tricopper systems as models of biological multicopper oxidases. The magnetic susceptibility of these complexes were studied, and a linear relation was found between the Cu-O(alkoxide)-Cu angles and the antiferromagnetic coupling between copper centers. The triiron(II) and trizinc(II) complexes of the ligand were also isolated and structurally characterized.

Chapter 3 describes the synthesis of a series of heterometallic tetranuclear manganese dioxido complexes with various incorporated apical redox-inactive metal cations (M = Na⁺, Ca²⁺, Sr²⁺, Zn²⁺, Y³⁺). Chapter 4 presents the synthesis of heterometallic trimanganese(IV) tetraoxido complexes structurally related to the CaMn₃ subsite of the oxygen-evolving complex (OEC) of Photosystem II. The reduction potentials of these complexes were studied, and it was found that each isostructural series displays a linear correlation between the reduction potentials and the Lewis acidities of the incorporated redox-inactive metals. The slopes of the plotted lines for both the dioxido and tetraoxido clusters are the same, suggesting a more general relationship between the electrochemical potentials of heterometallic manganese oxido clusters and their “spectator” cations. Additionally, these studies suggest that Ca²⁺ plays a role in modulating the redox potential of the OEC for water oxidation.

Chapter 5 presents studies of the effects of the redox-inactive metals on the reactivities of the heterometallic manganese complexes discussed in Chapters 3 and 4. Oxygen atom transfer from the clusters to phosphines is studied; although the reactivity is kinetically controlled in the tetraoxido clusters, the dioxido clusters with more Lewis acidic metal ions (Y³⁺ vs. Ca²⁺) appear to be more reactive. Investigations of hydrogen atom transfer and electron transfer rates are also discussed.

Appendix A describes the synthesis, and metallation reactions of a new dinucleating bis(N-heterocyclic carbene)ligand framework. Dicopper(I) and dicobalt(II) complexes of this ligand were prepared and structurally characterized. A dinickel(I) dichloride complex was synthesized, reduced, and found to activate carbon dioxide. Appendix B describes preliminary efforts to desymmetrize the manganese oxido clusters via functionalization of the basal multinucleating ligand used in the preceding sections of this dissertation. Finally, Appendix C presents some partially characterized side products and unexpected structures that were isolated throughout the course of these studies.

Studies of phonon anharmonicity in solids

Today our understanding of the vibrational thermodynamics of materials at low temperatures is emerging nicely, based on the harmonic model in which phonons are independent. At high temperatures, however, this understanding must accommodate how phonons interact with other phonons or with other excitations. We shall see that the phonon-phonon interactions give rise to interesting coupling problems, and essentially modify the equilibrium and non-equilibrium properties of materials, e.g., thermodynamic stability, heat capacity, optical properties and thermal transport of materials. Despite its great importance, to date the anharmonic lattice dynamics is poorly understood and most studies on lattice dynamics still rely on the harmonic or quasiharmonic models. There have been very few studies on the pure phonon anharmonicity and phonon-phonon interactions. The work presented in this thesis is devoted to the development of experimental and computational methods on this subject.

Modern inelastic scattering techniques with neutrons or photons are ideal for sorting out the anharmonic contribution. Analysis of the experimental data can generate vibrational spectra of the materials, i.e., their phonon densities of states or phonon dispersion relations. We obtained high quality data from laser Raman spectrometer, Fourier transform infrared spectrometer and inelastic neutron spectrometer. With accurate phonon spectra data, we obtained the energy shifts and lifetime broadenings of the interacting phonons, and the vibrational entropies of different materials. The understanding of them then relies on the development of the fundamental theories and the computational methods.

We developed an efficient post-processor for analyzing the anharmonic vibrations from the molecular dynamics (MD) calculations. Currently, most first principles methods are not capable of dealing with strong anharmonicity, because the interactions of phonons are ignored at finite temperatures. Our method adopts the Fourier transformed velocity autocorrelation method to handle the big data of time-dependent atomic velocities from MD calculations, and efficiently reconstructs the phonon DOS and phonon dispersion relations. Our calculations can reproduce the phonon frequency shifts and lifetime broadenings very well at various temperatures.

To understand non-harmonic interactions in a microscopic way, we have developed a numerical fitting method to analyze the decay channels of phonon-phonon interactions. Based on the quantum perturbation theory of many-body interactions, this method is used to calculate the three-phonon and four-phonon kinematics subject to the conservation of energy and momentum, taking into account the weight of phonon couplings. We can assess the strengths of phonon-phonon interactions of different channels and anharmonic orders with the calculated two-phonon DOS. This method, with high computational efficiency, is a promising direction to advance our understandings of non-harmonic lattice dynamics and thermal transport properties.

These experimental techniques and theoretical methods have been successfully performed in the study of anharmonic behaviors of metal oxides, including rutile and cuprite stuctures, and will be discussed in detail in Chapters 4 to 6. For example, for rutile titanium dioxide (TiO₂), we found that the anomalous anharmonic behavior of the B_1g mode can be explained by the volume effects on quasiharmonic force constants, and by the explicit cubic and quartic anharmonicity. For rutile tin dioxide (SnO₂), the broadening of the B_2g mode with temperature showed an unusual concave downwards curvature. This curvature was caused by a change with temperature in the number of down-conversion decay channels, originating with the wide band gap in the phonon dispersions. For silver oxide (Ag₂O), strong anharmonic effects were found for both phonons and for the negative thermal expansion.

Luminescence properties of electron-hole-droplets in pure and doped germanium

This work contains 4 topics dealing with the properties of the luminescence from Ge.

The temperature, pump-power and time dependences of the photoluminescence spectra of Li-, As-, Ga-, and Sb-doped Ge crystals were studied. For impurity concentrations less than about 10¹⁵cm^-3, emissions due to electron-hole droplets can clearly be identified. For impurity concentrations on the order of 10¹⁶cm^-3, the broad lines in the spectra, which have previously been attributed to the emission from the electron-hole-droplet, were found to possess pump-power and time dependent line shape. These properties show that these broad lines cannot be due to emission of electron-hole-droplets alone. We interpret these lines to be due to a combination of emissions from (1) electron-hole- droplets, (2) broadened multiexciton complexes, (3) broadened bound-exciton, and (4) plasma of electrons and holes. The properties of the electron-hole-droplet in As-doped Ge were shown to agree with theoretical predictions.

The time dependences of the luminescence intensities of the electron-hole-droplet in pure and doped Ge were investigated at 2 and 4.2°K. The decay of the electron-hole-droplet in pure Ge at 4.2°K was found to be pump-power dependent and too slow to be explained by the widely accepted model due to Pokrovskii and Hensel et al. Detailed study of the decay of the electron-hole-droplets in doped Ge were carried out for the first time, and we find no evidence of evaporation of excitons by electron-hole-droplets at 4.2°K. This doped Ge result is unexplained by the model of Pokrovskii and Hensel et al. It is shown that a model based on a cloud of electron-hole-droplets generated in the crystal and incorporating (1) exciton flow among electron-hole-droplets in the cloud and (2) exciton diffusion away from the cloud is capable of explaining the observed results.

It is shown that impurities, introduced during device fabrication, can lead to the previously reported differences of the spectra of laser-excited high-purity Ge and electrically excited Ge double injection devices. By properly choosing the device geometry so as to minimize this Li contamination, it is shown that the Li concentration in double injection devices may be reduced to less than about 10¹⁵cm^-3 and electrically excited luminescence spectra similar to the photoluminescence spectra of pure Ge may be produced. This proves conclusively that electron-hole-droplets may be created in double injection devices by electrical excitation.

The ratio of the LA- to TO-phonon-assisted luminescence intensities of the electron-hole-droplet is demonstrated to be equal to the high temperature limit of the same ratio of the exciton for Ge. This result gives one confidence to determine similar ratios for the electron-hole-droplet from the corresponding exciton ratio in semiconductors in which the ratio for the electron-hole-droplet cannot be determined (e.g., Si and GaP). Knowing the value of this ratio for the electron-hole-droplet, one can obtain accurate values of many parameters of the electron-hole-droplet in these semiconductors spectroscopically.

Proteolytic processing of the nonstructural proteins of dengue 2 virus

The genomes of many positive stranded RNA viruses and of all retroviruses are translated as large polyproteins which are proteolytically processed by cellular and viral proteases. Viral proteases are structurally related to two families of cellular proteases, the pepsin-like and trypsin-like proteases. This thesis describes the proteolytic processing of several nonstructural proteins of dengue 2 virus, a representative member of the Flaviviridae, and describes methods for transcribing full-length genomic RNA of dengue 2 virus. Chapter 1 describes the in vitro processing of the nonstructural proteins NS2A, NS2B and NS3. Chapter 2 describes a system that allows identification of residues within the protease that are directly or indirectly involved with substrate recognition. Chapter 3 describes methods to produce genome length dengue 2 RNA from cDNA templates.

The nonstructural protein NS3 is structurally related to viral trypsinlike proteases from the alpha-, picorna-, poty-, and pestiviruses. The hypothesis that the flavivirus nonstructural protein NS3 is a viral proteinase that generates the termini of several nonstructural proteins was tested using an efficient in vitro expression system and antisera specific for the nonstructural proteins NS2B and NS3. A series of cDNA constructs was transcribed using T7 RNA polymerase and the RNA translated in reticulocyte lysates. Proteolytic processing occurred in vitro to generate NS2B and NS3. The amino termini of NS2B and NS3 produced in vitro were found to be the same as the termini of NS2B and NS3 isolated from infected cells. Deletion analysis of cDNA constructs localized the protease domain necessary and sufficient for correct cleavage to the first 184 amino acids of NS3. Kinetic analysis of processing events in vitro and experiments to examine the sensitivity of processing to dilution suggested that an intramolecular cleavage between NS2A and NS2B preceded an intramolecular cleavage between NS2B and NS3. The data from these expression experiments confirm that NS3 is the viral proteinase responsible for cleavage events generating the amino termini of NS2B and NS3 and presumably for cleavages generating the termini of NS4A and NS5 as well.

Biochemical and genetic experiments using viral proteinases have defined the sequence requirements for cleavage site recognition, but have not identified residues within proteinases that interact with substrates. A biochemical assay was developed that could identify residues which were important for substrate recognition. Chimeric proteases between yellow fever and dengue 2 were constructed that allowed mapping of regions involved in substrate recognition, and site directed mutagenesis was used to modulate processing efficiency.

Expression in vitro revealed that the dengue protease domain efficiently processes the yellow fever polyprotein between NS2A and NS2B and between NS2B and NS3, but that the reciprocal construct is inactive. The dengue protease processes yellow fever cleavage sites more efficiently than dengue cleavage sites, suggesting that suboptimal cleavage efficiency may be used to increase levels of processing intermediates in vivo. By mutagenizing the putative substrate binding pocket it was possible to change the substrate specificity of the yellow fever protease; changing a minimum of three amino acids in the yellow fever protease enabled it to recognize dengue cleavage sites. This system allows identification of residues which are directly or indirectly involved with enzyme-substrate interaction, does not require a crystal structure, and can define the substrate preferences of individual members of a viral proteinase family.

Full-length cDNA clones, from which infectious RNA can be transcribed, have been developed for a number of positive strand RNA viruses, including the flavivirus type virus, yellow fever. The technology necessary to transcribe genomic RNA of dengue 2 virus was developed in order to better understand the molecular biology of the dengue subgroup. A 5' structural region clone was engineered to transcribe authentic dengue RNA that contains an additional 1 or 2 residues at the 5' end. A 3' nonstructural region clone was engineered to allow production of run off transcripts, and to allow directional ligation with the 5' structural region clone. In vitro ligation and transcription produces full-length genomic RNA which is noninfectious when transfected into mammalian tissue culture cells. Alternative methods for constructing cDNA clones and recovering live dengue virus are discussed.

Radar methods for the exploration of glaciers

The problem of finding the depths of glaciers and the current methods are discussed briefly. Radar methods are suggested as a possible improvement for, or adjunct to, seismic and gravity survey methods. The feasibility of propagating electromagnetic waves in ice and the maximum range to be expected are then investigated theoretically with the aid of experimental data on the dielectric properties of ice. It is found that the maximum expected range is great enough to measure the depth of many glaciers at the lower radar frequencies if there is not too much liquid water present. Greater ranges can be attained by going to lower frequencies.

The results are given of two expeditions in two different years to the Seward Glacier in the Yukon Territory. Experiments were conducted on a small valley glacier whose depth was determined by seismic sounding. Many echoes were received but their identification was uncertain. Using the best echoes, a profile was obtained each year, but they were not in exact agreement with each other. It could not be definitely established that echoes had been received from bedrock. Agreement with seismic methods for a considerable number of glaciers would have to be obtained before radar methods could be relied upon. The presence of liquid water in the ice is believed to be one of the greatest obstacles. Besides increasing the attenuation and possibly reflecting energy, it makes it impossible to predict the velocity of propagation. The equipment used was far from adequate for such purposes, so many of the difficulties could be attributed to this. Partly because of this, and the fact that there are glaciers with very little liquid water present, radar methods are believed to be worthy of further research for the exploration of glaciers.

MicroRNA-132 is a physiological regulator of hematopoietic stem cell function and B-cell development

MicroRNAs are a class of small non-coding RNAs that negatively regulate gene expression. Several microRNAs have been implicated in altering hematopoietic cell fate decisions. Importantly, deregulation of many microRNAs can lead to deleterious consequences in the hematopoietic system, including the onset of cancer, autoimmunity, or a failure to respond effectively to infection. As such, microRNAs fine-tune the balance between normal hematopoietic output and pathologic consequences. In this work, we explore the role of two microRNAs, miR-132 and miR-125b, in regulating hematopoietic stem cell (HSC) function and B cell development. In particular, we uncover the role of miR-132 in maintaining the appropriate balance between self-renewal, differentiation, and survival in aging HSCs by buffering the expression of a critical transcription factor, FOXO3. By maintain this balance, miR-132 may play a critical role in preventing aging-associated hematopoietic conditions such as autoimmune disease and cancer. We also find that miR-132 plays a critical role in B cell development by targeting a key transcription factor, Sox4, that is responsible for the differentiation of pro-B cells into pre-B cells. We find that miR-132 regulates B cell apoptosis, and by delivering miR-132 to mice that are predisposed to developing B cell cancers, we can inhibit the formation of these cancers and improve the survival of these mice. In addition to miR-132, we uncovered the role of another critical microRNA, miR-125b, that potentiates hematopoietic stem cell function. We found that enforced expression of miR-125b causes an aggressive myeloid leukemia by downregulation of its target Lin28a. Importantly, miR-125b also plays a critical role in inhibiting the formation of pro-B cells. Thus, we have discovered two microRNAs with important roles in regulating normal hematopoiesis, and whose dregulation can lead to deleterious consequences such as cancer in the aging hematopoietic system. Both miR-132 and miR-125b may therefore be targeted for therapeutics to inhibit age-related immune diseases associated with the loss of HSC function and cancer progression.

Design of antenna-coupled lumped-element titanium nitride KIDs for long-wavelength multi-band continuum imaging

Many applications in cosmology and astrophysics at millimeter wavelengths including CMB polarization, studies of galaxy clusters using the Sunyaev-Zeldovich effect (SZE), and studies of star formation at high redshift and in our local universe and our galaxy, require large-format arrays of millimeter-wave detectors. Feedhorn and phased-array antenna architectures for receiving mm-wave light present numerous advantages for control of systematics, for simultaneous coverage of both polarizations and/or multiple spectral bands, and for preserving the coherent nature of the incoming light. This enables the application of many traditional "RF" structures such as hybrids, switches, and lumped-element or microstrip band-defining filters.

Simultaneously, kinetic inductance detectors (KIDs) using high-resistivity materials like titanium nitride are an attractive sensor option for large-format arrays because they are highly multiplexable and because they can have sensitivities reaching the condition of background-limited detection. A KID is a LC resonator. Its inductance includes the geometric inductance and kinetic inductance of the inductor in the superconducting phase. A photon absorbed by the superconductor breaks a Cooper pair into normal-state electrons and perturbs its kinetic inductance, rendering it a detector of light. The responsivity of KID is given by the fractional frequency shift of the LC resonator per unit optical power.

However, coupling these types of optical reception elements to KIDs is a challenge because of the impedance mismatch between the microstrip transmission line exiting these architectures and the high resistivity of titanium nitride. Mitigating direct absorption of light through free space coupling to the inductor of KID is another challenge. We present a detailed titanium nitride KID design that addresses these challenges. The KID inductor is capacitively coupled to the microstrip in such a way as to form a lossy termination without creating an impedance mismatch. A parallel plate capacitor design mitigates direct absorption, uses hydrogenated amorphous silicon, and yields acceptable noise. We show that the optimized design can yield expected sensitivities very close to the fundamental limit for a long wavelength imager (LWCam) that covers six spectral bands from 90 to 400 GHz for SZE studies.

Excess phase (frequency) noise has been observed in KID and is very likely caused by two-level systems (TLS) in dielectric materials. The TLS hypothesis is supported by the measured dependence of the noise on resonator internal power and temperature. However, there is still a lack of a unified microscopic theory which can quantitatively model the properties of the TLS noise. In this thesis we derive the noise power spectral density due to the coupling of TLS with phonon bath based on an existing model and compare the theoretical predictions about power and temperature dependences with experimental data. We discuss the limitation of such a model and propose the direction for future study.