Preimplantation genetic diagnosis: Analysis of gene expression, nuclear DNA and cytoplasmic DNA

Preimplantation genetic diagnosis (PGD) following in vitro fertilization (IVF) offers couples at risk for transmitting genetic disorders the opportunity to identify affected embryos prior to replacement. In particular, embryo gender determination permits screening for X-linked diseases of unknown etiology. Analysis of embryos can be performed by polymerase chain reaction (PCR) amplification of material obtained by micromanipulation. This approach provides an alternative to the termination of an established pregnancy following chorionic villi sampling or amniocentesis. ^ Lately, the focus of preimplantation diagnosis and intervention has been shifting toward an attempt to correct cytoplasmic deficiencies. Accordingly, it is the aim of this investigation to develop methods to permit the examination of single cells or components thereof for clinical evaluation. In an attempt to lay the groundwork for precise therapeutic intervention for age related aneuploidy, transcripts encoding proteins believed to be involved in the proper segregation of chromosomes during human oocyte maturation were examined and quantified. Following fluorescent rapid cycle RT-PCR analysis it was determined that the concentration of cell cycle checkpoint gene transcripts decreases significantly as maternal age increases. Given the well established link between increasing maternal age and the incidence of aneuploidy, these results suggest that the degradation of these messages in aging oocytes may be involved with inappropriate chromosome separation during meiosis. ^ In order to investigate the cause of embryonic rescue observed following clinical cytoplasmic transfer procedures and with the objective of developing a diagnostic tool, mtDNA concentrations in polar bodies and subcellular components were evaluated. First, the typical concentration of mtDNA in human and mouse oocytes was determined by fluorescent rapid cycle PCR. Some disparity was noted between the copy numbers of individual cytoplasmic samples which may limit the use of the current methodology for the clinical assessment of the corresponding oocyte. ^

Mechanistic studies on the degradation of gasoline oxygenates by advanced oxidation technologies and the reaction of 4-methyl-1,2,4-triazoline-3,5-dione with tetracyclopropylethylene

Gasoline oxygenates (MTBE, methyl tert-butyl ether; DIPE, di-isopropyl ether; ETBE, ethyl tert-butyl ether; TAME, tert-amyl ether) are added to gasoline to boost octane and enhance combustion. The combination of large scale use, high water solubility and only minor biodegradability has now resulted in a significant gasoline oxygenate contamination occurring in surface, ground, and drinking water systems. Combination of hydroxyl radical formation and the pyrolytic environment generated by ultrasonic irradiation (665 kHz) leads to the rapid degradation of MTBE and other gasoline oxygenates in aqueous media. ^ The presence of oxygen promotes the degradation processes by rapid reaction with carbon centered radicals indicating radical processes involving O 2 are significant pathways. A number of the oxidation products were identified. The formation of products (alcohols, ketones, aldehydes, esters, peroxides, etc) could be rationalized by mechanisms which involve hydrogen abstraction by OH radical and/or pyrolysis to form carboncentered radicals which react with oxygen and follow standard oxidation chain processes. ^ The reactions of N-substituted R-triazolinediones (RTAD; R = CH 3 or phenyl) have attracted considerable interest because they exhibit a number of unusual mechanistic characteristics that are analogous to the reactions of singlet oxygen (1O2) and offer an easy way to provide C-N bond(s) formation. The reactions of triazolinedione with olefins have been widely studied and aziridinium imides are generally accepted to be the reactive intermediates. ^ We observed the rapid formation of an unusual intermediate upon mixing tetracyclopropylethylene with 4-methyl-1,2,4-triazoline-3,5-dione in CDCl 3. Detailed characterization by NMR (proton, 13C, 2-D NMRs) indicates the intermediate is 5,5,6,6-tetracyclopropyl-3-methyl-5,6-dihydro-oxazolo[3,2- b][1,2,4]-triazolium-2-olate. Such products are extremely rare and have not been studied. Upon warming the intermediate is converted to 2 + 2 diazetidine (major) and ene product (minor). ^ To further explore the kinetics and dynamics of the reaction activation energies were obtained using Arrhenius plots. Activation energies for the formation of the intermediate from reactants, and 2+2 adduct from the intermediate were determined as 7.48 kcal moll and 19.8 kcal mol−1 with their pre-exponential values of 2.24 × 105 dm 3 mol−1 sec−1 and 2.75 × 108 sec−1, respectively, meaning net slow reactions because of low pre-exponential values caused by steric hindrance. ^

Investigation of Mantle Dynamics from Platinum Group Elements and Rhenium-Osmium Isotope Systematics of Mantle Xenoliths from Oahu, Hawaii

Intraplate volcanism that has created the Hawaiian-Emperor seamount chain is generally thought to be formed by a deep-seated mantle plume. While the idea of a Hawaiian plume has not met with substantial opposition, whether or not the Hawaiian plume shows any geochemical signal of receiving materials from the Earth’s Outer Core and how the plume may or may not be reacting with the overriding lithosphere remain debatable issues. In an effort to understand how the Hawaiian plume works I report on the first in-situ sulfides and bulk rock Platinum Group Element (PGE) concentrations, together with Os isotope ratios on well-characterized garnet pyroxenite xenoliths from the island of Oahu in Hawaii. The sulfides are Fe-Ni Monosulfide Solid Solution and show fractionated PGE patterns. Based on the major elements, Platinum Group Elements and experimental data I interpret the Hawaiian sulfides as an immiscible melt that separated from a melt similar to the Honolulu Volcanics (HV) alkali lavas at a pressure-temperature condition of 1530 ± 100OC and 3.1±0.6 GPa., i.e. near the base or slightly below the Pacific lithosphere. The 187Os/188Os ratios of the bulk rock vary from subchondritic to suprachondritic (0.123-0.164); and the 187Os/188Os ratio strongly correlates with major element, High Field Strength Element (HFSE), Rare Earth Element (REE) and PGE abundances. These correlations strongly suggest that PGE concentrations and Os isotope ratios reflect primary mantle processes. I interpret these correlations as the result of melt-mantle reaction at the base of the lithosphere: I suggest that the parental melt that crystallized the pyroxenites selectively picked up radiogenic Os from the grain boundary sulfides, while percolating through the Pacific lithosphere. Thus the sampled pyroxenites essentially represent crystallized melts from different stages of this melt-mantle reaction process at the base of the lithosphere. I further show that the relatively low Pt/Re ratios of the Hawaiian sulfides and the bulk rock pyroxenites suggest that, upon ageing, such pyroxenites plus their sulfides cannot generate the coupled 186Os- 187Os isotope enrichments observed in Hawaiian lavas. Therefore, recycling of mantle sulfides of pyroxenitic parentage is unlikely to explain the enriched Pt-Re-Os isotope systematics of plume-derived lavas.

QCD structure of nuclear interactions

The research presented in this dissertation investigated selected processes involving baryons and nuclei in hard scattering reactions. These processes are characterized by the production of particles with large energies and transverse momenta. Through these processes, this work explored both, the constituent (quark) structure of baryons (specifically nucleons and Δ-Isobars), and the mechanisms through which the interactions between these constituents ultimately control the selected reactions. The first of such reactions is the hard nucleon-nucleon elastic scattering, which was studied here considering the quark exchange between the nucleons to be the dominant mechanism of interaction in the constituent picture. In particular, it was found that an angular asymmetry exhibited by proton-neutron elastic scattering data is explained within this framework if a quark-diquark picture dominates the nucleon’s structure instead of a more traditional SU(6) three quarks picture. The latter yields an asymmetry around 90o center of mass scattering with a sign opposite to what is experimentally observed. The second process is the hard breakup by a photon of a nucleon-nucleon system in light nuclei. Proton-proton (pp) and proton-neutron (pn) breakup in 3He, and ΔΔ-isobars production in deuteron breakup were analyzed in the hard rescattering model (HRM), which in conjunction with the quark interchange mechanism provides a Quantum Chromodynamics (QCD) description of the reaction. Through the HRM, cross sections for both channels in 3He photodisintegration were computed without the need of a fitting parameter. The results presented here for pp breakup show excellent agreement with recent experimental data. In ΔΔ-isobars production in deuteron breakup, HRM angular distributions for the two ΔΔ channels were compared to the pn channel and to each other. An important prediction fromthis study is that the Δ++Δ- channel consistently dominates Δ+Δ0, which is in contrast with models that unlike the HRM consider a ΔΔ system in the initial state of the interaction. For such models both channels should have the same strength. These results are important in developing a QCD description of the atomic nucleus.

History and evolutionary trajectory of the Iranian nuclear program

What actors and processes at what levels of analysis and through what mechanisms have pushed Iran's nuclear program (INP) towards being designated as a proliferation threat (securitization)? What actors and processes at what levels of analysis and through what mechanisms have pushed Iran's nuclear program away from being designated as an existential threat (de-securitization)? What has been the overall balance of power and interaction dynamics of these opposing forces over the last half-century and what is their most likely future trajectory? ^ Iran's nuclear story can be told as the unfolding of constant interaction between state and non-state forces of "nuclear securitization" and "nuclear de-securitization." Tracking the crisscrossing interaction between these different securitizing and de-securitizing actors in a historical context constitutes the central task of this project. ^ A careful tracing of "security events" on different analytical levels reveals the broad contours of the evolutionary trajectory of INP and its possible future path(s). Out of this theoretically conscious historical narrative, one can make informed observations about the overall thrust of INP along the securitization - de-securitization continuum. ^ The main contributions of this work are three fold: First, it brings a fresh theoretical perspective on Iran's proliferation behavior by utilizing the "securitization" theory tracing the initial indications of the threat designation of INP all the way back to the mid 1970s. Second, it gives a solid and thematically grounded historical texture to INP by providing an intimate engagement with the persons, processes, and events of Tehran's nuclear pursuit over half a century. Third, it demonstrates how INP has interacted with and even at times transformed the NPT as the keystone of the non-proliferation regime, and how it has affected and injected urgency to the international discourse on nuclear proliferation specifically in the Middle East.^

Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients

Chronic bronchopulmonary bacterial infections remain the most common cause of morbidity and mortality among patients with cystic fibrosis (CF). Recent community sequencing work has now shown that the bacterial community in the CF lung is polymicrobial. Identifying bacteria in the CF lung through sequencing can be costly and is not practical for many laboratories. Molecular techniques such as terminal restriction fragment length polymorphism or amplicon length heterogeneity-polymerase chain reaction (LH-PCR) can provide many laboratories with the ability to study CF bacterial communities without costly sequencing. The aim of this study was to determine if the use of LH-PCR with multiple hypervariable regions of the 16S rRNA gene could be used to identify organisms found in sputum DNA. This work also determined if LH-PCR could be used to observe the dynamics of lung infections over a period of time. Nineteen samples were analysed with the V1 and the V1_V2 region of the 16S rRNA gene. Based on the amplicon size present in the V1_V2 region, Pseudomonas aeruginosa was confirmed to be in all 19 samples obtained from the patients. The V1 region provided a higher power of discrimination between bacterial profiles of patients. Both regions were able to identify trends in the bacterial population over a period of time. LH profiles showed that the CF lung community is dynamic and that changes in the community may in part be driven by the patient's antibiotic treatment. LH-PCR is a tool that is well suited for studying bacterial communities and their dynamics.

Weak electron scattering for the 3He-3H transition and the weak nuclear form factors

We calculate the differential cross section for weak electron scattering reaction, e + 3He-' 3H + ve, for energies from 100 MeV to 6 GeV as a function of outgoing nucleus angle from 0 to n/2 radians. We find that the differential cross section at low [q2] increases with electron energy from 0.1 GeV to 6.0 GeV, such that the peak value at 6.0 GeV is approximately 3.2 x 10-40 cm 2 / ster, a factor of 10 larger than the peak value at 0.1 GeV. We also find that the width of the peak falls very rapidly with increasing electron energy. At high [q2] we find that the differential cross section falls by approximately three orders of magnitude making experimental observation at this time unlikely. The contributions of the individual form factors are obtained for electron energies of 0.5GeV and 2.0 GeV. It is found that at low [q2] the form factors, FA(q2) and Fv(q2), make contributions of similar size to the differential cross section and might be simultaneously determined , but for the case of FM(q2) we find that the contribution is too small to determine. It is also found that at large [q2] values, the contribution of FM(q2) is substantially enhanced , but that the cross section is probably too small to enable a direct determination of FM(q2).

Exclusive electrodisintegration of three-nucleon systems

The purpose of this research was to develop a theory of high-energy exclusive electrodisintegration of three-nucleon systems on the example of 3He(e, e'NN)N reaction with knocked-out nucleon in the final state. The scattering amplitudes and differential cross section of the reaction were calculated in details within the Generalized Eikonal Approximation(GEA). The manifestly covariant nature of Feynman diagrams derived in GEA allowed us to preserve both the relativistic dynamics and kinematics of the scattering while identifying the low momentum nuclear part of the amplitude with a nonrelativistic nuclear wave function. Numerical calculations of the residual system's total and relative momentum distribution were performed which show reasonable agreement with available experimental data. The theoretical framework of GEA, which was applied previously only for the case of two-body (deuteron) high energy break up reactions, has been practically implemented and shown to provide a valid description for more complex A = 3 systems.