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Where a galaxy is located has a strong effect on its properties. The dense cluster environment is home to a large population of red, quiescent elliptical galaxies, whereas blue, star-forming, spiral galaxies are common in lower-density environments. This difference is intricately linked to the ability of the galaxy to form new stars and therefore ultimately to the fuel for star formation, the atomic and molecular gas. In this thesis, I use two large JCMT surveys to explore the effects of environment on the atomic gas, molecular gas, and star formation properties of a large sample of nearby gas-rich galaxies. From the NGLS and follow-up studies, I select a sub-sample of 98 HI-flux selected spiral galaxies. I measure their total molecular gas mass using the CO J=3-2 line and combine this data with measurements of their total atomic gas mass using the 21-cm line and star formation rate using attenuation-corrected H-alpha luminosity. I find an enhancement in the mean H2 mass and a higher H2-to-HI ratio for the Virgo Cluster sample. Virgo Cluster galaxies also have longer molecular gas depletion times (H2/SFR), which suggests that they are forming stars at a lower rate relative to their molecular gas reservoirs than non-Virgo galaxies. Next, I collect VLA 21 cm line maps from the VIVA survey and follow-up VLA studies of selected galaxies in the NGLS. I measure the surface density maps of the atomic gas, molecular gas, and star formation rate in order to determine radial trends. I find that the H2 distribution is enhanced near the centre for Virgo Cluster galaxies, along with a steeper total gas (HI + H2) radial profile. I suggest that this is due to the effects of moderate ram pressure stripping, which would strip away low-density gas in the outskirts while enhancing high-density gas near the centre. There are no trends with radius for the molecular gas depletion times, but the longer depletion times for the Virgo Cluster sample is still present. Finally, I use 850 micron continuum observations for 105 star-forming galaxies and CO J=2-1 line observations for 35 galaxies in the initial data release (DR1) of the JINGLE survey. I match the JINGLE galaxies to a SDSS group catalogue and measure environmental parameters such as the host halo mass, environment density, and location in phase space. I find that the molecular gas masses estimated from the 850 μm and CO J=2-1 line observations are well-correlated. The H2-to-HI ratio and the molecular gas depletion times do not appear to vary with stellar mass. I did not find any significant variation with environment in the DR1 sample, but I will apply this framework to the full JINGLE sample once the complete dataset is available. / Thesis / Doctor of Philosophy (PhD)

Iron-sulfur [Fe-S] clusters are protein cofactors that facilitate various life-sustaining biological processes. Their in vivo assembly is accomplished by three different systems known to date. These are: the NIF system which provides [Fe-S] clusters for nitrogenase and other nitrogen-fixing proteins, the SUF system which is induced during conditions of oxidative stress and iron starvation in E. coli, and the ISC system which serves as the housekeeping assembly apparatus. The latter is the focus of this dissertation and includes the proteins IscR, IscS, IscU, IscA, HscB, HscA, Fdx, and IscX. IscU is purified in its cluster-less (apo) form, but can serve as a scaffold to assemble [Fe-S] clusters in vitro in the presence of excess iron and sulfide. To test the scaffold hypothesis and gain insight into the events that occur during [Fe-S] cluster assembly and delivery, we developed two methods that allow the isolation of IscU and other ISC proteins in vivo. In the first method, Azotobacter vinelandii IscU is isolated from its native host, whereas in the second, it is isolated recombinantly from E. coli using a vector that allows expression of the entire isc operon. We found that IscU exists in vivo in two forms: apo-IscU and [2Fe-2S]2+ cluster-loaded IscU which are believed to be conformationally distinct. Both transient and stable IscU-IscS complexes were identified, indicating that the two proteins interact in vivo in a manner that involves their association and dissociation. The [2Fe-2S]2+-IscU species was present as a single entity, whereas significant amounts of apo-IscU were found associated with IscS, suggesting that IscU-IscS dissociation is triggered by the completion of [2Fe-2S] clusters. Both apo and [2Fe-2S]2+-IscU were predominantly monomeric whereas IscU-IscS complexes were determined to have an α2β2 composition. IscU was purified in the absence of the chaperones HscA and HscB and was also shown to accommodate a [2Fe-2S]2+ cluster similar to the one bound to IscU isolated from wild type cells. The findings suggest that [2Fe-2S]2+-IscU exists in one conformation in vivo and that any conformational changes on IscU are exerted after [2Fe-2S] cluster formation. In silico studies showed that a flexible loop containing the conserved LPPVK motif, which is responsible for interactions with HscA, may facilitate cluster exposure to either mediate its delivery to acceptor proteins or participation in the construction of [4Fe-4S] clusters. Experiments with NfuA, a protein similar to the C-terminal domain of NifU, demonstrated that NfuA and similar proteins might serve as [Fe-S] cluster carriers to accomplish the efficient delivery of nascent cofactors to the various recipient proteins. / Ph. D.

In recent years, electro-optic polymers have been used to make various optical devices in the telecommunication field due to several advantages, such as large and fast electro-optic (EO) response. Semiconductor nano-crystals promise even higher response speed due to the unique quantum confinement mechanism, and they also show very high EO response because of surface and quantum size effects. Many investigative efforts have been made in the area of semiconductor nano-clusters. These efforts mainly focus on synthesizing high quality particles, and their physical and chemistry properties (luminescence spectra, nonlinear optical, and other effects), but their electro-optic properties and potential uses in devices have not been fully investigated, so there is still much work to do in this aspect. For application of electro-optic polymers in electro-optic devices, the challenges are to develop more stable electro-optic polymers with higher electro-optic coefficients. The electrostatic self-assembly (ESA) technique has many advantages over traditional polymer electro-optic film synthesis processes, such as spin coating. For ESA-generated EO films, no poling field is needed, high orientation of the EO polymer can be obtained which does not degrade with time, so the films can be very stable, and this processing is easily compatible with semiconductor VLSI technology. This is a very attractive technique. The goal of this research is to develop new electro-optic materials by means of ESA techniques and to use them to form improved performance next generation electro-optic devices, with emphasis on two kinds of electro-optic materials: nano-sized II-VI semiconductors (CdS, CdSe), and electro-optic active polymers (chromophores), and their potential use in electro-optic devices. In this research work, II-VI semiconductor nano-clusters have been synthesized, with particle diameters ranging from 4 nm to several tens of nanometers. There is a difference in peak positions of absorption and photo luminescence spectra, related to defects in nano-crystals. Larger CdS particles have larger differences than small CdSe particles. Particle sizes measured by absorption spectrum and by HRTEM methods are very close. Based on quantum mechanical theory, peak spectral shifts as a function of particle size can be predicted, but the theoretical results are typically far from the experimental results, because many complicating factors should be considered. Films fabricated by ESA have much stronger absorption than spin coated films, and exhibit a slight blue shift in peak position wavelength. Photo luminescence spectra also show a blue shift for ESA films with respect to spun films. Polymeric electro-optic films were also fabricated by the ESA technique. Effects due to applying an external electrical field during the ESA process on film growth and properties have also been investigated. Peak position, optical density and wavelength at maximum absorption, all increase with the number of bilayers, and films made under external fields have lower absorption and peak wavelength than those of films fabricated without an external field. These results are related to the order parameter, and indicate that molecule alignment can be improved by the application of an external field during the process of ESA film growth. CdSe nano-clusters have a much higher electro-optic coefficient than their bulk crystal counterparts. In comparison with polymers, they have totally different origins in their electro-optic effects. For both nano-cluster-and chromophore based ESA films, electro-optic coefficients are hi gher than those of spin-coated films, and no poling voltage is needed. The reasons have been fully discussed. This result means that the ESA technique is effective to align and hold the dipoles in films and to intensify the electro-optic effect. CdSe quantum dots need 17. 5 ms to complete their physical orientation due to a rotation of the permanent dipole moment. Therefore, at lower frequencies (<100Hz), electro-optic modulation mainly stems from the orientation of the permanent dipole moment. At frequencies higher than 100 Hz, the electro-optic modulation mainly arises from the induced dipole moment orientation and pure electron movement. The ratio of the electro-optic coefficients r333/r113 > 3. This means that ESA films cannot be treated as an ideal isotropic system with the C v symmetry, and interactions should be considered. Quadratic Kerr electro-optic coefficients have a similar frequency dependence to that of the linear electro-optic coefficients r333 and r113. This indicates that the orientational distribution of the CdSe quantum dots particularly contributes to the quadratic electro-optic modulation. From the FT-IR measurement of the films, proton irradiation can break the N=N double bonding in pi-conjugated bridges, leading to damage of the conjugating structure, so causing a decrease of the EO coefficient. But the thermal and temporal stability of ESA films are much better than those of spin coated films; this is a significant feature of ESA technique. The effect of an external field and film thickness on the optical and electro-optic properties of ESA films has been investigated. Electro-optic coefficient decreases with thickness. Electrical field influences the electronic states of the chromophores. Based on the properties of electro-optic films, the applications of polymer and nano-cluster electro-optic films are discussed. A nano-cluster CdSe electro-optic film has a higher refractive index than the PS-119 polymer film, and these values they are much lower than that of semiconductor wafers, but slightly higher than optical silica glasses. Accordingly optical silica glasses are the ideal substrates for those films. By analysis, the cutoff thickness was determined, which defines the minimum film thickness required for light propagation. For channel waveguides, the aspect ratio w/t, w, and t are determined versus the refractive index of the electro-optic films. Modulator beam length and modulation index were discussed, for high speed operation. Modulator beam length should be carefully chosen to obtain high modulation index; similarly important is the refractive index match between core, substrate, and cladding layers. For high speed operation, traveling wave electrode designs were considered, based on effective refractive index and impedance matching. The effective dielectric constant and characteristic impedance as a function of electrode configuration (sizes) were diagramed, and this served as a basic design suggestion for traveling wave electrodes. / Ph. D.

Iron-sulfur clusters are simple inorganic cofactors that are ubiquitous in living systems. The assembly of iron sulfur clusters is an essential process and must be carefully controlled in order to limit the release of toxic free iron or sulfide. Thus far there are three known protein systems for iron sulfur cluster assembly including the <i>nif, suf,</i> and <i>isc</i> systems. The <i>nif</i> system makes iron-sulfur clusters for nitrogenase production, while both the <i>suf</i> and <i>isc</i> systems provide iron-sulfur clusters for general cellular use. In <i>Azotobacter vinelandii</i> the isc operon contains eight genes which are transcribed together as a single operon: <i>iscR iscS iscU iscA hscB hscA fdx iscX</i>. The two central <i>isc</i> players include IscS, a cysteine desulfurase, and IscU the proposed site of iron-sulfur cluster assembly. Using <i>A. vinelandii</i> as a model organism, we have sought to better understand the mechanism of <i>in vivo isc</i> cluster assembly. In order test the scaffold hypothesis, we constructed strains that allowed for quick and rapid isolation of IscU. The purification of IscU with a bound [2Fe-2S] cluster strongly supports the model that IscU serves as the site of cluster synthesis <i>in vivo</i>. Additionally, using this same genetic system we isolated an IscU39DA variant with an oxygen stable bound [2Fe-2S] cluster. The IscU39^DA scaffold came in tight α₂β₂ complex with IscS and was not separated by high salt, size exclusion, or reducing conditions. On the other hand, wild-type IscU also associated with IscS in a α₂β₂ complex, but readily dissociated upon increased salt concentration. The tight association of IscU39^DA and IscS was found to occur regardless of the presence of a bound [Fe-S] cluster. We conclude that the IscU Asp-39 residue is essential for mediating the dissociation of IscU and IscS. In addition to studying IscS and IscU, we were interested to further understand how the isc system is regulated in response to external factors. Previous work has demonstrated that IscR controls expression of the isc operon in <i>Escherichia coli</i>. When IscR is holo this protein represses <i>isc</i> expression, while in its apo-form it allows <i>isc</i> expression. In <i>A. vinelandii</i> we found that ∆<i>iscR</i> strains exhibit in a 5 – 7 fold elevation of isc expression. Additionally, ∆<i>iscR</> strains reveal a small growth phenotype on plates, and a tendency to form spontaneous suppressor mutations allowing reversion to wild-type growth. Loss of apo-IscR function was found to cause a more severe effect on growth than the loss of holo-IscR function, suggesting IscR has cellular roles in addition to the regulation of the <i>isc</i> operon. / Ph. D.

It is not known whether biosynthesis of [Fe-S] clusters occurs through a spontaneous self-assembly process or an enzymatic process. However, in the <I>Azotobacter</I> <I>vinelandii</I> nitrogenase system, it has been proposed that NifS and NifU are involved in the mobilization of sulfur and iron necessary for nitrogenase-specific [Fe-S] cluster assembly. The NifS protein has been shown to have cysteine desulfurase activity and can be used to supply sulfur for the <I>in</I> <I>vitro</I> catalytic formation of [Fe-S] clusters. The activity of the NifU protein has not yet been established, but NifU could have functions complementary to NifS by mobilizing iron or serving as an intermediate site necessary for nitrogenase-specific [Fe-S] cluster assembly. A second iron-binding site within NifU was predicted to serve these functions because two identical [2Fe-2S] clusters that had previously been identified within the homodimeric NifU are tightly bound, and the NifU primary sequence is rich in cysteine residues. In this dissertation, I examined the possibility that NifU might mobilize iron or serve as an intermediate site for [Fe-S] cluster assembly, as well as the possibility that NifU could work in concert with NifS. Primary sequence comparisons, amino acid substitution experiments, and biophysical characterization of recombinantly-produced NifU fragments were used to show that NifU has a modular structure. One module is contained in approximately the C-terminal half of NifU and provides the binding site for the [2Fe-2S] cluster previously identified (the permanent [2Fe-2S] cluster). Cysteine residues Cys¹³⁷, Cys¹³⁹, Cys¹⁷⁵, and Cys¹⁷⁵ serve as ligands to the [2Fe-2S] cluster. Another module (referred to as NifU-1) is contained in approximately the N-terminal third of NifU and provides a second iron-binding site (rubredoxin-like Fe(III)-binding site). Cysteine residues Cys³⁵, Cys⁶², Cys¹⁰⁶>, and a putative non-cysteine ligand of unknown origin provide coordination to the iron at this site. The significance of these iron-binding sites was also accessed by showing that cysteine residues involved in providing the rubredoxin-like Fe(III)-binding site and those that provide the [2Fe-2S] cluster binding site are all required for the full physiological function of NifU. The two other cysteine residues contained within NifU, Cys²⁷² and Cys²⁷⁵, are neither necessary for binding iron at either site nor are they required for the full physiological function of NifU. These results provide the basis for a model where iron bound at the rubredoxin-like sites within NifU-1 (one iron per monomer) is proposed to be destined for [Fe-S] cluster formation. It was possible to find in vitro evidence supporting this idea. First, it was demonstrated that NifU and NifS are able to form a transient complex. Second, in the presence of NifS as well as L-cysteine and a reducing agent, the Fe(III) contained at the rubredoxin-like sites within the NifU-1 or NifU homodimer can rearrange to form a transient [2Fe-2S] cluster between the two subunits. Finally, a mutant form of NifU-1 was isolated that appears to be trapped in the [2Fe-2S] cluster-containing form, and this [2Fe-2S] cluster (the transient [2Fe-2S] cluster) can be released from the polypeptide matrix upon reduction with dithionite. Previous work has shown that the permanent [2Fe-2S] clusters of as-isolated NifU are in the oxidized form but can be reduced chemically. The transient [2Fe-2S] cluster formed between rubredoxin-like sites, in contrast, is reductively labile. If the transient cluster serves as an intermediate [Fe-S] cluster to be destined for [Fe-S] cluster assembly, I propose that the permanent [2Fe-2S] clusters could have redox roles participating in either one or all of the following events. The permanent [2Fe-2S] clusters could have a redox function in the acquisition of iron for initial binding at the mononuclear sites. They could also provide reducing equivalents for releasing the transient [2Fe-2S] cluster. In addition, upon releasing the transient [2Fe-2S] cluster, the permanent [2Fe-2S] clusters could provide the appropriate oxidation state of the irons to be destined to nitrogenase metallocluster core formation. Finally, because proteins homologous to NifU and NifS are widely distributed in nature, it is suggested that the mechanism for NifU and NifS in the formation of nitrogenase-specific [Fe-S] clusters could represent a general mechanism for [Fe-S] cluster synthesis in other systems. / Ph. D.