We discuss the role of symmetries in the dissociative recombinations (DR) of three polyatomic ions, namely the linear HCO+ (formyl) ion and the two highly symmetric H+3 and H3O+ (hydronium) molecular ions. Regarding the HCO+ ion, we apply a quantum mechanical treatment using the Multi-channel Quantum Defect Theory (MQDT) formalism to describe the ion-electron scattering process. Our study takes into account the Renner-Teller effect in order to model the non Born-Oppenheimer vibronic coupling in linear polyatomic ions. The coupling has shown to represent the main mechanism responsible for electronic capturing in highly excited Rydberg states associated with excited vibrational levels of the ionic core. We consider all internal degrees of freedom of HCO+ and obtain the dissociative cross section as a function of the incident electron kinetic energy. We have also improved the theoretical approach by including the large permanent dipole moment of HCO+ using a generalization of the MQDT formalism. To our knowledge, this is the rst time the permanent dipole moment of an ion is included in a DR study. The obtained results are in good agreement with experimental data. We also study the DR of H+3 and H3O+ symmetric ions using a simpli ed theoretical treatment, which focuses on the key ingredient of the DR process, the electron capture in the rst excited degenerate vibrational normal mode of the ions through non Born-Oppenheimer Jahn-Teller coupling. For both ions the obtained cross sections are in very good agreement with the available experimental data. Moreover, in the case of H+3 , the results reproduce previous calculations from two independent theoretical studies. Finally, we investigate the role of symmetries in few body ultra-cold collisions by considering both three and four identical atoms systems. We derive allowed rearrangements of different fragments of the system, satisfying the complete symmetry of the molecular Hamiltonian. For that purpose we establish a correspondence between constants of motion of the system in di erent large-distance con gurations and irreducible representations of the total symmetry group. Selection rules (forbidden transitions) and allowed states, which depend on the fermionic or bosonic nature of the atoms, can be derived from these results.

This dissertation will investigate electron beam induced current (EBIC) for determining semiconductor material and device parameters. While previous experimental work on PN junction delineation using EBIC with the scanning electron microscope has resulted in resolution to approximately 10 nm, theoretical study shows the potential use of EBIC for higher resolution (nanometer) PN junction and FET channel length delineation using the transmission electron microscope. Theoretical arguments using computer simulations of electron beam generation volume, collection probability and EBIC were performed and are presented for the purpose of determining EBIC use in a 300 keV transmission electron microscope (TEM) for PN junction depth determination. Measured results indicate that by measuring thin semiconductor samples with high surface recombination velocity and by using a narrow, high-energy electron beam in the STEM mode of a transmission electron microscope, nanometer resolution may be possible. The practical and experimental limits of beam energy and semiconducting material thermal damage will be discussed.

Meiosis is a specialized type of cell division characterized by a single round of DNA replication and two rounds of chromosome segregation, ultimately resulting in four haploid cells. During meiosis I, chromosomes align and reciprocal recombination results in the formation of a crossover, creating the tension required to properly segregate homologs during the first round of meiosis. Two mechanisms involved in regulating the occurrence of crossing over are assurance and interference. Crossover assurance describes the phenomenon that at least one crossover will form between each pair of homologous chromosomes during prophase I. Crossover interference, on the other hand, describes the nonrandom placement of crossovers between homologs, increasing the probability that a second crossover will occur at a discrete distance away from the first one. In addition to assurance and interference, chromosome size may play a role in the rate of meiotic recombination during prophase I. As a result of crossover assurance, small chromosomes receive a minimum of one crossover, the obligate crossover. Assuming chromosome size does not influence the rate of recombination, pairs of large chromosomes should experience the same number of crossovers per base pair as small chromosomes. Previous studies have been inconsistent: Kaback et al. (1999) saw decreased rates of crossing over between large chromosomes relative to small ones, suggesting that crossover interference acts across a larger distance on large chromosomes. Turney et al. (2004), however, saw no such effect, suggesting that these findings may be site- or sequence-specific. The current study used the Cre-loxP system to create translocated chromosomes, decreasing the size of chromosome VIII from 562 kb to 125 kb. The rate of crossing over was evaluated using nutrient marker genes that were inserted on the left arm of chromosome VIII to facilitate phenotypic detection of crossing over between homologous translocated chromosomes in comparison to crossing over between homologous nontranslocated chromosomes. Translocated strains were attempted, though further testing suggests that the translocation itself may be lethal. In the future, we plan to further investigate the potential lethal nature of the translocation. We also experienced difficulty in curing yeast cells of the Cre expression plasmid: as pSH47 was removed, translocated chromosomes reverted to nontranslocated chromosomes. In addition, crossing over in nontranslocated yeast, along with subsequent molecular analysis, revealed that one of the marker genes presumed to be on the left arm of chromosome VIII is, in fact, located on a different chromosome, preventing analysis of crossing over in this region. As a result, we were unable to proceed with current experimentation.

<p> The phenomenon of genetic recombination is of fundamental importance to the evolution and adaptation of species, and is a valuable laboratory aid to the biological scientist. Probable mechanisms of control of recombination are largely unknown, due partly to the difficulty of obtaining artificial mutants affecting the process. The studies reported here avoid this difficulty by the use of different factors controlling recombination which occur naturally in the species Neurospora crassa and N. sitophila. Studies of hybrid N. crassa strains carrying factors from N. sitophila are described, and some models for the control of genetic recombination are discussed. </p> / Thesis / Master of Science (MSc)

atfish production is the largest aquaculture industry in the United States and infectious agents are responsible for 45% of all economic losses. Ictalurid herpesvirus 1 or Channel catfish virus (CCV) has a great economic impact on channel catfish aquaculture; yet it also has the potential for becoming a highly efficient vaccine vector eliciting long-lived immune responses against itself and, as a recombinant, other important catfish pathogens (bacteria, myxosporean, and fungi). However, little is known about CCV’s genome, its gene functions or genetic interactions with its host. Better understanding of CCV biology and pathogenesis could enable more rational vaccine design and other control strategies for CCV. My thesis is that “systems biology” can enable much more rapid understanding of CCV biology and pathogenesis. To test this thesis I needed to first more fully annotate the CCV genome, then construct a rapid system for generating CCV mutants and recombinants for systems biology research and then apply these tools in a systems biology experiment. I experimentally annotated the CCV proteome by proteogenomic mapping followed by real-time PCR and confirmed the expression of 37 of the 76 previously predicted ORFs (25 for the first time) as well as 17 novel ORFs. I next constructed two different infectious clones of CCV: one as three overlapping bacterial artificial chromosomes (BACs) and the other as a full length CCV BAC. These CCV BACs facilitate CCV mutant and recombinant production and I regenerated a genotypically wild-type and an attenuated virus. To further simplify CCV mutant production, I next adapted the CCV infectious clone for lambda phage crossover recombination cloning to enable sequence transfer into a specific CCV locus by a simple one-step in-vitro reaction. Finally, I used the CCV infectious clone, in combination with affinity purification, to identify interacting partners of the CCV zinc RING finger proteins ORF9, ORF11 and ORF12 to provide insight into the topology of one presumptive CCV-channel catfish molecular interaction network module. The work in this dissertation supports my thesis and the CCV BAC tools were patented; together these provide tools to facilitate and accelerate the development and testing of better CCV vaccines.

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