Brain development and function depend on intrinsic and extrinsic factors. In particular, the proper functioning of sensory systems can be altered according to the quality of extrinsic sensory information received during life. In this context, questions concerning neuroplasticity take on special relevance when considering that sensory experience has a big impact on the degree of plasticity of the brain. In this thesis, we have sought to understand how visual deprivation affects the development and maintenance of visual centers in the brain and the role of visual deprivation on plasticity throughout life. We have addressed this question by studying the retinocollicular projection, which is the neuronal pathway that connects the retina with a visual input processing center, the superior colliculus (SC). Unexpectedly, we found that in Syrian hamsters (Mesocricetus auratus) the size of receptive fields (RFs) of neurons in the SC is plastic in adult animals if they have been deprived of a minimum of visual experience when juveniles. Specifically, dark-reared (DR) hamsters refine SC RFs as do their normally-reared counterparts, but they lose RF refinement if they remain in the dark after their RFs get refined. We found that a well defined period and duration of visual experience can stabilize RF size in adulthood. Furthermore, we sought to investigate the mechanisms by which RF size is increased in adult DR hamsters. By testing the strength of intracollicular inhibition using electrophysiological and molecular techniques, we have found that visually-deprived animals have weaker inhibitory circuitry in their SC than normal animals. The quantity of GABA receptors and GABA containing neurons is decreased in the SC of adult DR animals. We propose that these results explain at least in part the RF enlargement we find in visually-deprived animals. Knowledge from this study provides general insight into sensory system plasticity in adulthood and new information about visual system development that is relevant for treatments of diseases.

Fusarium solani is a soil-borne pathogen devastating agricultural crops throughout the world. While most pathogens are host specific, the fusaria are able to infect both plants and animals. In 2004, an outbreak of Fusarium occurred in association with contact lens wear. Several species of Fusarium were involved but F. solani and F. oxysporum were most prominent. In this work, we have identified a MAP kinase (MAPK), highly similar to fmk1 in F. oxysporum, belonging to the YERK1 subfamily of extracellular regulated kinases. Directed disruption of fmk1 in F. solani AFR4 (FSSC 1) affected several aspects of fungal growth and pathogenicity. Colonies of AFR4„½fmk1 displayed pigmented colony-like formation as opposed to the cottony-white diffuse growth observed with the wild-type strain. Mutants displayed changes in morphology and conidiation patterns with AFR4„½fmk1 mutants producing increased amounts of macroconidia vs. microconidia. AFR4„½fmk1 germ tube emergence was similar to that of wild-type AFR4 and wet weight growth was equivalent but germinules were not able to sense nutrient in chemotropic assays. The disruption of fmk1 increased spore surface hydrophobicity leading to a decrease in association with commercially available hydrogel contact lenses. FMK1 did not affect unworn lens penetration in phosphate buffered saline as both wild-type and mutant strains were able to penetrate commercially available silicone hydrogel contact lenses. AFR4 displayed increased penetration of silicone lenses and this is likely due to: increased spore/lens association, and the inability of AFR4„½fmk1 macroconidia to germinate in phosphate buffered saline. Diminished invasive growth was also noted with disruption of fmk1. Wild-type AFR4 was detected throughout the eye after conidial microinjection while AFR4„½fmk1 was limited to the vitreous fluid. The reduced invasive growth seen is attributed to the loss of chemotropism. The ability to sense and respond to the environment is essential for pathogenicity. MAPK has been deemed essential for plant pathogenicity and now, with its affect on chemotropism, appears to be necessary for animal pathogenicity. FMK1 plays a conserved role in the pathogenicity of Fusarium.

The Australian zebra finch (Taeniopygia guttata) serves as an excellent model organism for studying the mechanisms that influence brain sexual differentiation. The brain and behavior of the zebra finch are sexually dimorphic. The regions of the brain that control the learning and production of song (song control nuclei) are significantly larger in the male brain than in the female brain and only males sing courtship songs, thus the majority of past research has focused on the development of these sex differences. In the majority of mammals, brain sexual differentiation occurs because hormones secreted from the gonads act to initiate male or female brain development. In zebra finches, estradiol is sufficient to masculinize the male brain, however manipulations of developmental hormone exposure fail to fully reverse the sex differences in song nuclei size. Furthermore, genetic females induced to develop functional testicular tissue do not develop a completely masculinized song system and castration has no effect on development of the song system in males. The source of the increased estrogenic signal in male zebra finch brain has yet to be identified, but data suggest that other neuronal factors play a role in development of the song control nuclei. Coregulators, such as coactivators and corepressors, are proteins and RNA activators that work by enhancing or depressing transcriptional activity of the nuclear steroid receptor with which they associate. Coregulators also modulate the development of sex-specific brain morphology and behavior in rodents and birds and may help to explain the difficulties observed in altering song nuclei development via castration and gonadal hormone replacement. As an estrogen receptor-α coactivator, ribosomal protein L7 (RPL7) is able to make the brain more sensitive to estradiol by enhancing the effects of steroid receptor action. Therefore, this dissertation addressed the following questions regarding RPL7: (1) is RPL7 expression sexually dimorphic in the song nuclei of the zebra finch brain?; (2) is RPL7 protein expression regulated by steroid hormones?; and (3) does decreasing RPL7 protein expression with antisense oligonucleotides alter neuronal survival in vivo and song nuclei size and neuron number in vitro? Collectively, these studies will provide valuable information about the role of steroid receptor coactivators in development of the zebra finch song system and on the role of coactivators on sexual differentiation of the brain.

Nitrogen is known to be a limiting factor in polluted environments, however many studies overlook the potential role for nitrogen to significantly influence the removal rate and efficiency with which microorganisms can degrade aromatic hydrocarbons. In this study, inoculated and uninoculated aerated soil microcosms containing different s-triazines were examined for their ability to efficiently and rapidly treat contaminated soils containing naphthalene, nitrobenzene, and toluene (NNT), via a microbial consortium consisting of Pseudomonas, Rhodococcus, and Aeromonas. After an experimental period of 14 days, greater than 90% degradation of NNT supplemented with different s-triazines, at concentrations of 1000-3000 ppm was observed. A difference in the degradation of NNT was seen in inoculated box reactors supplemented with cyanuric acid, melamine, and atrazine in comparison to uninoculated box reactors. Combined usage of 16s rDNA and 16s rRNA analysis was then applied to study the bacterial communities, and determine the abundance and survival of inoculated strains within box reactors contaminated with NNT. The bacterial diversity within clone libraries obtained illustrated a dominance of proteobacteria and gram positive bacteria. Analysis from clone libraries also showed that inoculated strains did survive within each condition, but were not the most predominant members present in the communities. This research shows that significant removal of NNT can be achieved in two weeks with the supplementation of one of the s-triazines. However, differences in degradation and the microbial populations present within contaminated communities will be seen depending on which nitrogen sources are used and whether or not environments are bioaugmented or not.

The DrrAB proteins of Streptomyces peucetius belong to the ABC family of ubiquitous membrane transporters. The DrrA and DrrB proteins together form a drug efflux pump that carries out the transport of the anticancer drug doxorubicin by carrying out ATP hydrolysis. The present study is the first where the intrinsic factors involved in the assembly of the DrrAB functional complex have been elucidated. The drrA and drrB genes in the wild type operon have overlapping stop and start codons (ATGA) which indicates translational coupling between the two genes. On insertion of a fortuitous stop codon in DrrA it was shown that the expression of DrrB is coupled to that of the upstream gene drrA. Furthermore, it was observed that a functional complex could be achieved only when the genes were maintained in cis in a translationally coupled manner. Translational regulation in DrrA was found to be involved in the control of optimal levels of DrrB. Inhibitory interactions within drrA sequence were speculated to cause translational arrest at the C terminus of DrrA. A novel assembly domain that forms the interface between DrrA containing the Nucleotide Binding Domain (NBD) and DrrB comprising the TransMembrane Domain (TMD) was found. Based on the data presented in this study a model is proposed for the biogenesis of the DrrAB drug pump. The model suggests that translational coupling between DrrA and DrrB is crucial for functional complex formation. Further, there is evidence of regulation of translation by attenuation in the intergenic region of drrA and drrB. The regulation seems to involve the last 30 nucleotides of the mRNA of drrA and some upstream sequences within drrA that cause translational arrest within the C terminus of DrrA. Since DrrB is translationally coupled to drrA, this translational arrest in conjunction with coupling causes lowering in the levels of DrrB. Finally, since the DrrA-DrrB interaction domain lies in the C terminus of DrrA, only the fully translated DrrA product will be competent to form a complex with DrrB. This interaction between the C terminus of DrrA and the N terminus of DrrB may be crucial for initial targeting of the complex to the membrane. The model is expected to serve as primer and open up an interesting yet insufficiently understood subject of membrane protein biogenesis.

Rhodococcus is an important industrial organism that possesses diverse metabolic capabilities, it also has a unique cell envelope, composed of an outer layer of mycolic acids and glycolipids (free or bound lipids generally linked to the sugar trehalose). Rhodococcus is able to transform nitriles to the corresponding amide by the enzyme Nitrile Hydratase (NHase), therefore rhodococcal cells can be utilized as biocatalysts in the detoxification of nitrile waste water or in the production of industrially important amides such as acrylamide. However, the NHase within the native cells must be stable with high activity. This research examined how NHase activity and stability can be increased in native cells by changing growth media composition, the impact on the rhodococcal cell envelope was also studied. Growth media composition was altered by supplementing different sugars such as fructose, maltose or maltodextrin to replace glucose in rich solid media containing cobalt and urea for induction of NHase. The supplementation of maltose or maltodextrin resulted in significantly higher NHase activities and greater NHase stability at 55„aC. The supplementation of these different sugars was shown to alter cellular and lipid bound trehalose levels, a sugar known to stabilize proteins and a component of the rhodococcal cell envelope. Cells that had higher levels of cellular trehalose had significantly greater NHase stability at 55„aC. The effect of the different sugar supplements and inducers of NHase, such as cobalt, on cell envelope components such as mycolic acids and glycolipids were examined by High Performance Liquid Chromatography (HPLC) and Thin Layer Chromatography (TLC). The results showed that changes in mycolic acids and glycolipids occurred when the cells were grown in the presence of different sugar supplements and when the cells were induced for NHase. Susceptibility of Rhodococcus sp DAP 96253 to different antibiotics was examined to indicate if changes were occurring in the cell envelope. Differences in antibiotic susceptibility were observed when the cells were grown on media with different sugar supplements and when the cells were induced for NHase. In the presence of cobalt Rhodococcus sp DAP 96253 showed a significant increase in sensitivity to antibiotics. Changes in growth media composition influences the cell envelope of Rhodococcus sp DAP 96253 and also affects NHase activity and stability. Therefore, achieving increased enzyme activity and stability is not entirely dependent on the actual enzyme, but is related to other aspects of the cell, such as the cell envelope and metabolites of the cell.

The nervous systems of animals evolved to exert dynamic control of behavior in response to the needs of the animal and changing signals from the environment. To understand the mechanisms of dynamic control, we need a means of predicting how individual neural and body elements will interact to produce the performance of the entire system. We have developed a neuromechanical application named AnimatLab that addresses this problem through simulation. A computational model of a body and nervous system can be constructed from simple components and situated in a virtual world for testing. Simulations and live experiments were used to investigate questions about locust jumping. The neural circuitry and biomechanics of kicking in locusts have been extensively studied. It has been hypothesized that the same neural circuit and biomechanics governed both behaviors, but this hypothesis was not testable with current technology. We built a neuromechanical model to test this and to gain a better understanding of the role of the semi-lunar process (SLP) in jump dynamics. The SLP are bands of cuticle that store energy for use during jumping. The results of the model were compared to a variety of published data and were similar. The SLP significantly increased jump distance, power, total energy, and duration of the jump impulse. Locust can jump precisely to a target, but also exhibit tumbling. We proposed two mechanisms for controlling tumbling during the jump. The first was that locusts adjust the pitch of their body prior to the jump to move the center of mass closer to the thrust vector. The second was that contraction of the abdominal muscles during the jump produced torques that countered the torque due to thrust. There was a strong correlation relating increased pitch and takeoff angle. In simulations there was an optimal pitch-takeoff combination that minimized tumbling that was similar to the live data. The direction and magnitude of tumbling could be controlled by adjusting abdominal tension. Tumbling also influenced jump elevation. Neuromechanical simulation addressed problems that would be difficult to examine using traditional physiological approaches. It is a powerful tool for understanding the neural basis of behavior.

It is evident that components of the 26S proteasome function beyond protein degradation in the regulation of transcription. Studies in yeast implicate the 26S proteasome, specifically the 19S cap, in the epigenetic regulation of transcription. Saccharomyces cerevisiae 19S ATPases remodel chromatin by facilitating histone acetylation and methylation. However, it is unclear if the 19S ATPases play similar roles in mammalian cells. We previously found that the 19S ATPase Sug1 positively regulates transcription of the critical inflammatory gene MHC-II and that the MHC-II promoter fails to efficiently bind transcription factors upon Sug1 knockdown. MHC-II transcription is regulated by the critical coactivator CIITA. We now find that Sug1 is crucial for regulating histone H3 acetylation at the cytokine inducible MHC-II and CIITA promoters. Histone H3 acetylation is dramatically decreased upon Sug1 knockdown with a preferential loss occurring at lysine 18. Research in yeast indicates that the ortholog of Sug1, Rpt6, acts as a mediator between the activating modifications of histone H2B ubiquitination and H3 methylation. Therefore, we characterized the role the 19S proteasome plays in regulating additional activating modifications. As with acetylation, Sug1 is necessary for proper histone H3K4 and H3R17 methylation at cytokine inducible promoters. In the absence of Sug1, histone H3K4me3 and H3R17me2 are substantially inhibited. Our observation that the loss of Sug1 has no significant effect on H3K36me3 implies that Sug1’s regulation of histone modifications is localized to promoter regions as H3K4me3 but not H3K36me3 is clustered around gene promoters. Here we show that multiple H3K4 histone methyltransferase subunits bind constitutively to the inducible MHC-II and CIITA promoters and that over-expressing one subunit significantly enhances promoter activity. Furthermore, we identified a critical subunit of the H3K4 methyltransferase complex that binds multiple histone modifying enzymes, but fails to bind the CIITA promoter in the absence of Sug1, implicating Sug1 in recruiting multi-enzyme complexes responsible for initiating transcription. Finally, Sug1 knockdown maintains gene silencing as elevated levels of H3K27 trimethylation are observed upon Sug1 knockdown. Together these studies strongly implicate the 19S proteasome in mediating the initial reorganization events to relax the repressive chromatin structure surrounding inducible genes.

P68 is a prototypical member of the DEAD box RNA helicase family. Implicated in numerous functions such as cell proliferation, cancer metastasis, transcription regulation and pre-mRNA spllicing, p68 is a multifunctional protein whose roles are still not completely understood. In the studies presented, we found that p68 was an important regulator of numerous cancer related genes. This study focuses on the cancer related genes Snail and hTERT. We show that p68 binds to the promoter and a downstream region within each gene, suggesting that p68 operates via the same mechanism with both genes. We also show that tyrosine phosphorylated p68 is the major player in transcription regulation. p68 was also discovered to recruit CREB-binding protein to the promoters of these genes as well as aid in the removal of HDAC1 from the promoters; these findings are consistent with chromatin remodeling and active transcription. Also, we found that p68 phosphorylation level correlates with the expression level of these genes. Finally, we describe other genes that are potentially regulated by p68 in the same manner, through the use of ChiP-on-chip technology.

Host defense against infection and disease relies on the reciprocal communication between the immune and neuroendocrine systems where sex hormones exert negative and positive feedback actions on immune functions. Indeed, sex hormones have been implicated in gender dimorphic immune response and in the potentiation of immune-related disorders. The female hormone estrogen plays a role as an immunomodulator and may exert immunosuppressive and immunostimulatory effects. Though many studies focus on estrogen’s role in immunity within the female reproductive tract and autoimmunity, the modulatory effects of estrogen on vaccine responses are largely unexplored. The insufficient efficacy of some vaccines in certain target populations, as for example the elderly population, is well recognized. Hormones fluctuate throughout an individual’s life, and females in particular undergo several necessary reproductive (pregnancy and menopause) and lifestyle (oral contraceptive use) changes which involve sex hormones. Vaccine efficacy might be influenced by endogenous estrogen levels or by exogenous estrogen administration. Therefore, in the pursuit of improved vaccine efficacy, it is necessary to consider such hormonal factors and their contribution to immune status. We have studied estrogen’s role in modulation of vaccine responses using a mouse ovariectomy model where exogenous estrogen delivery can be controlled. Our studies included two different types of vaccines, a bacterial toxoid formulation and a bacterial secreted protein formulation. Results from these studies indicate that estrogen enhances vaccine-specific antibody production by likely supporting a general TH2 pathway and also modulates expression of genes encoding molecules critical in innate immune signaling and required for development of proper adaptive immune responses and antigen clearance through antibody-mediated mechanisms. The level at which estrogen modulates antibody responses appears to be dependent on the route of vaccine administration. The enhancement of specific humoral responses may involve mechanisms involving TLR2 and antibody Fc receptor expression on macrophages, cells that link innate and adaptive immune responses. Advances in our understanding of the relationship between sex hormones and the immune system may provide new insights into the mechanisms by which hormones act and thus may be exploited to guide the design of future vaccine strategies.