High-resolution high-frequency dynamic nuclear polarization for biomolecular solid state NMR

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, June 2011.Vita. Cataloged from PDF version of thesis.Includes bibliographical references.Dynamic Nuclear Polarization (DNP) has exploded in popularity over the last few years, finally realizing its potential to overcome the detrimental lack of sensitivity that has plagued performing NMR experiments. Applied to magic angle spinning (MAS) experiments, this renaissance of DNP has been primarily driven by the development of instrumentation; namely gyrotron oscillators as high-power stable microwave power sources and the NMR probes and associated equipment required to spin samples routinely below 100 Kelvin. The first three chapters of this thesis provide an overview of the theory, instrumentation, and applications of DNP. Chapter 1 introduces the magnetic resonance Hamiltonian with a focus on interactions that are necessary to control in order to obtain high-resolution DNP spectra. Chapters 2 and 3 are published reviews of DNP. Whereas Chapter 2 targets magnetic resonance spectroscopists, Chapter 3 is intended for an electric engineering audience. Both reviews are included as the associated depth and coverage of the topics are complementary and lead to a better understanding of DNP. The later chapters describe in detail advancements in probe, cryogenics, and gyrotron technology required to perform DNP MAS experiments, as well as the gains in sensitivity and resolution such instrumentation has permitted. Of particular importance is the development of a cryogenic sample ejection system that resulted in exquisite resolution of spectra recorded 10 W across the band, which results in substantially improved DNP performance.by Alexander B. Barnes.Ph.D

Combinations of isoform-targeted histone deacetylase inhibitors and bryostatin analogues display remarkable potency to activate latent HIV without global T-cell activation

AbstractCurrent antiretroviral therapy (ART) for HIV/AIDS slows disease progression by reducing viral loads and increasing CD4 counts. Yet ART is not curative due to the persistence of CD4+ T-cell proviral reservoirs that chronically resupply active virus. Elimination of these reservoirs through the administration of synergistic combinations of latency reversing agents (LRAs), such as histone deacetylase (HDAC) inhibitors and protein kinase C (PKC) modulators, provides a promising strategy to reduce if not eradicate the viral reservoir. Here, we demonstrate that largazole and its analogues are isoform-targeted histone deacetylase inhibitors and potent LRAs. Significantly, these isoform-targeted HDAC inhibitors synergize with PKC modulators, namely bryostatin-1 analogues (bryologs). Implementation of this unprecedented LRA combination induces HIV-1 reactivation to unparalleled levels and avoids global T-cell activation within resting CD4+ T-cells.</jats:p

A 250 GHz gyrotron with a 3 GHz tuning bandwidth for dynamic nuclear polarization

We describe the design and implementation of a novel tunable 250 GHz gyrotron oscillator with >10 W output power over most of a 3 GHz band and >35 W peak power. The tuning bandwidth and power are sufficient to generate a >1 MHz nutation frequency across the entire nitroxide EPR lineshape for cross effect DNP, as well as to excite solid effect transitions utilizing other radicals, without the need for sweeping the NMR magnetic field. Substantially improved tunability is achieved by implementing a long (23 mm) interaction cavity that can excite higher order axial modes by changing either the magnetic field of the gyrotron or the cathode potential. This interaction cavity excites the rotating TE[subscript 5,2,q] mode, and an internal mode converter outputs a high-quality microwave beam with >94% Gaussian content. The gyrotron was integrated into a DNP spectrometer, resulting in a measured DNP enhancement of 54 on the membrane protein bacteriorhodopsin.National Institutes of Health (U.S.) (Grant EB002804)National Institutes of Health (U.S.) (Grant EB003151)National Institutes of Health (U.S.) (Grant EB002026)National Institutes of Health (U.S.) (Grant EB001960)National Institutes of Health (U.S.) (Grant EB001035)National Institutes of Health (U.S.) (Grant EB001965)National Institutes of Health (U.S.) (Grant EB004866)National Science Foundation (U.S.). Graduate Research Fellowshi

Cosmogenic Nuclide Tracking of Sediment Recycling From a Frontal Siwalik Range in the Northwestern Himalaya

The Himalayan orogen exports millions of tons of sediment annually to the Indo-Gangetic foreland basin, derived from both hinterland and foreland fold-thrust belts (FTB). Although erosion rates in the hinterland are well-constrained, erosion rates in the foreland FTB and, by extension, the sediment flux have remained poorly constrained. Here, we quantified erosion rates and sediment flux from the Mohand Range in the northwestern Himalaya by modeling and measuring the cosmogenic radionuclide (CRN) 10Be and 26Al concentrations in modern fluvial sediments. Our model uses local geological and geophysical constraints and accounts for CRN inheritance and sediment recycling, which enables us to determine the relative contributions of the hinterland and foreland FTB sources to the CRN budget of the proximal foreland deposits. Our model predictions closely match measured concentrations for a crustal shortening rate across the Mohand Range of 8.0 +/- 0.5 mm yr-1 (i.e., approximately 50% of the total shortening across the Himalaya at this longitude) since 0.75-0.06+0.02 $0.7{5}_{-0.06}{+0.02}$ Ma. This shortening implies a spatial gradient in erosion rates ranging from 0.42 +/- 0.03 to 4.92 +/- 0.34 mm yr-1, controlled by the geometry of the underlying structure. This erosion pattern corresponds to an annual sediment recycling of similar to 2.0 megatons from the Mohand Range to the downstream Yamuna foreland. Converted to sediment fluxes per unit width along the Himalaya, the foreland FTB accounts for similar to 21% +/- 5% of the total flux entering the foreland. Because these sediments have lower 10Be concentrations than hinterland-derived sediment, they would lead to similar to 14% overestimation of 10Be-derived erosion rates, based on Yamuna sediments in the proximal foreland

Development of a Coherent Doppler Lidar for Precision Maneuvering and Landing of Space Vehicles

A coherent Doppler lidar has been developed to address NASAs need for a high-performance, compact, and cost-effective velocity and altitude sensor onboard its landing vehicles. Future robotic and manned missions to planetary bodies require precise ground-relative velocity vector and altitude data to execute complex descent maneuvers and safe, soft landing at a pre-designated site. This lidar sensor, referred to as a Navigation Doppler Lidar, meets the required performance of landing missions while complying with vehicle size, mass, and power constraints. Operating from over five kilometers altitude, the lidar obtains velocity and range precision measurements with 2 cm/sec and 2 meters, respectively, dominated by the vehicle motion. After a series of flight tests onboard helicopters and rocket-powered free-flyer vehicles, the Navigation Doppler Lidar is now being ruggedized for future missions to various destinations in the solar system

Genetic and Antigenic Analysis of the First A/New Caledonia/20/99-like H1N1 Influenza Isolates Reported in the Americas

From February through May of 1999, 13 cases of Influenza A virus (FLUAV), type H1N1 were reported at a Department of Defense influenza surveillance sentinel site in Lima, Peru. Genetic and antigenic analysis by hemagglutination inhibition and direct nucleotide sequencing of the HA1 region of the hemagglutinin gene were performed on two isolates, A/Peru/1641/99 and A/Peru/1798/99. Both isolates were distinct from the Bayern/7/95-like viruses circulating in the Americas and closely related to a Beijing/262/95-like variant, A/New Caledonia/20/99. With the exception of travel-related cases, the detection of these isolates represents the first appearance of New Caledonia/20/99-like viruses in the Americas. Since the characterization of these Peru isolates, a number of New Caledonia/20/99-like viruses have been reported worldwide. For the 2000/01 and 2001/02 influenza seasons, the World Health Organization (WHO) has recommended the inclusion of A/New Caledonia/20/99 as the H1N1 vaccine component for both the southern and northern hemispheres

Microwave field distribution in a magic angle spinning dynamic nuclear polarization NMR probe

We present a calculation of the microwave field distribution in a magic angle spinning (MAS) probe utilized in dynamic nuclear polarization (DNP) experiments. The microwave magnetic field (B[subscript 1S]) profile was obtained from simulations performed with the High Frequency Structure Simulator (HFSS) software suite, using a model that includes the launching antenna, the outer Kel-F stator housing coated with Ag, the RF coil, and the 4 mm diameter sapphire rotor containing the sample. The predicted average B[subscript 1S] field is 13 μT/W[superscript 1/2], where S denotes the electron spin. For a routinely achievable input power of 5 W the corresponding value is γ[subscript S]B[subscript 1S] = 0.84 MHz. The calculations provide insights into the coupling of the microwave power to the sample, including reflections from the RF coil and diffraction of the power transmitted through the coil. The variation of enhancement with rotor wall thickness was also successfully simulated. A second, simplified calculation was performed using a single pass model based on Gaussian beam propagation and Fresnel diffraction. This model provided additional physical insight and was in good agreement with the full HFSS simulation. These calculations indicate approaches to increasing the coupling of the microwave power to the sample, including the use of a converging lens and fine adjustment of the spacing of the windings of the RF coil. The present results should prove useful in optimizing the coupling of microwave power to the sample in future DNP experiments. Finally, the results of the simulation were used to predict the cross effect DNP enhancement (ϵ) vs. ω[subscript 1S]/(2π) for a sample of [superscript 13]C-urea dissolved in a 60:40 glycerol/water mixture containing the polarizing agent TOTAPOL; very good agreement was obtained between theory and experiment.National Institutes of Health (U.S.) (Grant EB002804)National Institutes of Health (U.S.) (Grant EB003151)National Institutes of Health (U.S.) (Grant EB002026)National Institutes of Health (U.S.) (Grant EB001960)National Institutes of Health (U.S.) (Grant EB001035)National Institutes of Health (U.S.) (Grant EB004866)National Science Foundation (U.S.). Graduate Research Fellowshi

A Sample of Intermediate-Mass Star-Forming Regions: Making Stars at Mass Column Densities <1 g/cm^2

In an effort to understand the factors that govern the transition from low- to high-mass star formation, we identify for the first time a sample of intermediate-mass star-forming regions (IM SFRs) where stars up to - but not exceeding - 8 solar masses are being produced. We use IRAS colors and Spitzer Space Telescope mid-IR images, in conjunction with millimeter continuum and CO maps, to compile a sample of 50 IM SFRs in the inner Galaxy. These are likely to be precursors to Herbig AeBe stars and their associated clusters of low-mass stars. IM SFRs constitute embedded clusters at an early evolutionary stage akin to compact HII regions, but they lack the massive ionizing central star(s). The photodissociation regions that demarcate IM SFRs have typical diameters of ~1 pc and luminosities of ~10^4 solar luminosities, making them an order of magnitude less luminous than (ultra)compact HII regions. IM SFRs coincide with molecular clumps of mass ~10^3 solar masses which, in turn, lie within larger molecular clouds spanning the lower end of the giant molecular cloud mass range, 10^4-10^5 solar masses. The IR luminosity and associated molecular mass of IM SFRs are correlated, consistent with the known luminosity-mass relationship of compact HII regions. Peak mass column densities within IM SFRs are ~0.1-0.5 g/cm^2, a factor of several lower than ultra-compact HII regions, supporting the proposition that there is a threshold for massive star formation at ~1 g/cm^2.Comment: 61 pages, 6 tables, 20 figures. Accepted for publication in the Astronomical Journa

Optimizing allocation of curricular content across the undergraduate & graduate medical education continuum

BACKGROUND: Medical educators struggle to incorporate socio-cultural topics into crowded curricula. The continuum of learning includes undergraduate and graduate medical education. Utilizing an exemplar socio-cultural topic, we studied the feasibility of achieving expert consensus among two groups of faculty (experts in medical education and experts in social determinants of health) on which aspects of the topic could be taught during undergraduate versus graduate medical education. METHODS: A modified Delphi method was used to generate expert consensus on which learning objectives of social determinants of health are best taught at each stage of medical education. Delphi respondents included experts in medical education or social determinants of health. A survey was created using nationally published criteria for social determinants of health learning objectives. Respondents were asked 1) which learning objectives were necessary for every physician (irrespective of specialty) to develop competence upon completion of medical training and 2) when the learning objective should be taught. Respondents were also asked an open-ended question on how they made the determination of when in the medical education continuum the learning objective should be taught. RESULTS: 26 out of 55 experts (13 social determinants of health and 13 education experts) responded to all 3 Delphi rounds. Experts evaluated a total of 49 learning objectives and were able to achieve consensus for at least one of the two research questions for 45 of 49 (92%) learning objectives. 50% more learning objectives reached consensus for inclusion in undergraduate (n = 21) versus graduate medical education (n = 14). CONCLUSIONS: A modified Delphi technique demonstrated that experts could identify key learning objectives of social determinants of health needed by all physicians and allocate content along the undergraduate and graduate medical education continuum. This approach could serve as a model for similar socio-cultural content. Future work should employ a qualitative approach to capture principles utilized by experts when making these decisions