Patients with Rett Syndrome (RTT) show severe breathing disorders in addition to other neuropathological features, contributing to the high incidence of sudden unexplained death and abnormal brain development. However, the molecular and cellular mechanisms underlying the breathing disorders are still unknown. Recent studies indicate that the dysfunction of brainstem norepinephrine (NE) systems are closely associated with breathing disorders in RTT patients as well as its mice model, the Mecp2-null (Mecp2─/Y) mice. This as well as the fact the major group of NE-ergic neurons in the locus coeruleus (LC) is CO2 chemosensitive suggests that the breathing disorders in RTT may be related these LC neurons. To test this hypothesis, we took a multidisciplinary approach and systematically studied these neurons using molecular biology, in-vitro brain slices, acutely dissociated neurons, immunocytochemistry, and whole-body plethysmograph. To facilitate the electrophysiological studies, we developed a new strain of transgenic mice with GFP expression selectively in the LC neurons of both WT and Mecp2─/Y mice. Breathing activity of the Mecp2─/Y mice showed selective disruptions in responses to mild hypercapnia. The defect was alleviated with the NE uptake blocker desipramine, suggesting the involvement of NE in central CO2 chemosensitivity. In the LC region, the expressions of tyrosine hydroxylase (TH) and dopamine beta-hydroxylase (DBH) at both protein and mRNA levels reduced by ~50% in Mecp2─/Y mice. No evidence was found for selective deficiency in TH- or DBH-containing neurons in Mecp2─/Y mice, and no major loss of NE-ergic LC cells were found, indicating that the NE defect is likely to result from deficient expression of biosynthetic enzymes rather than a loss of neurons in the LC. Several intrinsic membrane properties were abnormal in Mecp2─/Y LC neurons in comparison to wild type cells, including stronger inward rectification, shorter time constant, extended action potential duration, smaller amplitude of medium afterhyperpolarization (AHP) and over-expression of fast AHP. These abnormalities seem to be associated with the altered K+ and Na+ currents. Most importantly, Mecp2─/Y LC neurons displayed defective CO2 chemosensitivity in agreement of in vivo CO2 response, likely due to excessive expression of the homomeric Kir4.1 channel. Thus, it seems that the global effect of MeCP2 on the A6 NE system contributes to the impaired systemic CO2 response as well as the breathing irregularities in Mecp2─/Y mice. Such an alteration allowed CO2 to be detected only when hypercapnia became severe, leading to periodical hyper- and hypoventilation. These findings not only provide a novel etiology for the breathing disturbances of Mecp2─/Y mice but also show direct evidence for the first time on a molecular mechanism for the central CO2 chemosensitivity.

Social status influences reproductive physiology in many species, and sex change in marine teleost fishes provides an excellent model to understand how an organism can modulate its reproductive system in response to social stimuli. The series of experiments presented in this dissertation has focused on the proximate mechanisms underlying sex change and, in particular, the neuroendocrine factors that might translate social information into physiological changes. The bluebanded goby (Lythrypnus dalli) is a sexually plastic fish, and the dominant female typically changes sex when the male is removed from the social group. The direct physical interactions between the male and the females were found to be the main sensory cues that inhibit sex change. Sex steroids can both modulate and be modulated by behavior, and as a result they have been the most obvious candidates for a key role in the regulation of sex change. Males and females showed similar diurnal patterns for steroid hormones, but females had significantly higher water-borne estrogen levels. Concentrations of estradiol, testosterone and 11-ketotestosterone presented sex and tissue differences in brain, gonad and muscle, and they varied in complex ways in different tissues during sex change. The neurotransmitter serotonin (5-HT) has been suggested to be involved in the inhibition of socially regulated sex change because of its role in the modulation of both reproductive and aggressive behavior. None of the pharmacological manipulations performed in L. dalli to alter serotonergic activity was able to overcome the input from the social environment and affect sex change. Neither monoamine levels nor the area or number of 5-HT immunoreactive neurons were different between males, females and sex changers or between dominant and subordinate females. The results do not support the hypothesis of a serotonergic inhibition on sex change in L. dalli, but show that rapid changes in brain androgen levels might be implicated in inducing behavioral or morphological changes associated with sex reversal. Also, steroids respond to changes in the social environment in different ways in different tissues so local steroid synthesis should receive greater attention, and caution is required when using circulating levels to understand behavioral regulation.

Nucleic acids are macromolecules in cells for storing and transferring genetic information. Moreover, nucleic acids, especially RNAs, can fold into well-defined 3D structures and catalyze biochemical reactions. As ubiquitous biological molecules in all living systems, nucleic acids are important drug targets, and they can also be used in diagnostics and therapeutics. Structural information of nucleic acids provides the foundation for DNA and RNA function studies. X-ray crystallography has been a useful tool for structural studies of bio-macromolecules at atomic level. There are two major problems in macromolecular crystal structure determination: phasing and crystallization. Although selenium derivatization is routinely used for solving novel protein structures through the MAD phasing technique, the phase problem is still a critical issue in nucleic acid crystallography. The covalent selenium-derivatization of nucleic acids has been proven to be a useful strategy for solving the phase problem in nucleic acid X-ray crystallography. Besides the facilitation of nucleic acid crystallography, there is also a wide range of other applications for selenium-derivatized nucleic acids (SeNA). The investigation presented in this dissertation mainly focuses on the following research subjects (1) Synthesis and characterization of selenium-derivatized nucleic acids for X-ray crystallography, especially phosphoroselenoate RNAs. They are generated and used for crystallization. (2) Application of selenium-derivatized RNA for RNA interference. Phosphoroselenoate RNAs are tested for RNAi activities. (3) Synthesis and characterization of the uridine 5’-triphosphate modified with selenium at position 4. (4) Facile synthesis and antitumor activities of selenium modified deoxyribonucleosides. MeSe-thymidine nucleosides have shown antitumor activity in cell assays.

Rubella virus (RUBV) is a positive-strand RNA virus and the causative agent of rubella and congenital rubella syndrome in humans. To replicate its RNA, RUBV forms membrane-associated spherules, called replication complexes (RCs), the induction of which requires the two virus nonstructural proteins (NSPs), P150 and P90. Interestingly, late in infection the NSPs form a unique cytoplasmic fiber network, similar in appearance to microtubules, the function of which is unknown. Little is known about the roles of the RUBV NSPs in forming these structures and, to this end, we scrutinized the behavior and biochemical properties of the NSPs, both after expression from plasmids and during RUBV infection, using mutagenic, biochemical and pharmacological approaches. The following findings were made: First, the precursor from which P150 and P90 are produced via an embedded protease at the C-terminus of P150, called P200, was required for initial targeting to cytoplasmic foci. P150 was the determinant of fiber formation and while P90 had no specific targeting sequences on its own, P90 sequences within P200 were required for correct targeting of P200. An alpha-helix at the N-terminus of P150 was also important for correct targeting of P200, putatively by mediating the interaction between P150 and P90 within the precursor. Second, the membrane binding domain within the NSPs was within the N-terminal ~450 amino acids of P150. P150 is in an exceptionally tight association with membranes. Third, both the N- and C-terminal regions of P150, and specifically long alpha-helices within these regions, are necessary for fiber formation. Fiber formation relied on an intact microtubule network, but neither microtubule repositioning nor dynamic movement along microtubules was required. Additionally, it was shown that microtubules were not necessary in RUBV replication. Finally, P150 fibers were not required for RUBV replication; however, it was shown that the fibers are likely important in formation of cytoplasmic extensions through which a novel system of cell-to-cell transport of viral RNA in the absence of virus particles appears to occur.

Heavy metals, such as copper and cadmium have been linked to a number of cellular dysfunctions in single and multicellular organisms that are associated with apoptosis. The yeast, Saccharomyces cerevisiae, provides a valuable model for elucidating apoptosis mechanisms, and this study extends that capability to Cu and Cd-induced apoptosis. We demonstrate that S. cerevisiae undergoes a glucose-dependent, programmed cell death in response to low cadmium concentrations, which is initiated within the first hour of Cd exposure. The response was associated with induction of the yeast caspase, Yca1p, and was abolished in YCA1∆ mutant. Other apoptotic markers, including sub-G1 DNA fragmentation and hyper-polarization of mitochondrial membranes, were also evident among Cd-exposed cells. We also show that low levels of copper can induce a similar apoptotic response in yeast within the first hour of exposure. Such cellular responses were verified by analyzing mitochondrial perturbation, generation of superoxide ions, activation of the yeast caspase1, and the eventual fragmentation of nuclear DNA (through TUNEL). In analyzing the response of yeast to the different metals, we also demonstrated that the metal-induced PCD is instigated through the sequential activity of at least two caspase-like proteins (i.e., Yca1 and Atg4), both of which appear to be in involved in the process of inducing mitochondrial stress. The additional caspase-like activity is shown to be derived from an enzyme involved in the latter stages of autophagy (Atg4), and provides an intriguing association of apoptosis with autophagy. Here we also demonstrate that metals such as copper and cadmium causes oxidative damage to mitochondrial proteins. Such oxidative attack is targeted and we show that oxidation of certain crucial proteins is required for apoptosis upon metal exposure. By showing that such targeted protein oxidation is dependent on YCA1 and ATG, we also confirm the finding that in yeast that have been exposed to a heavy metal, YCA1 and ATG are essential for damaging mitochondria and to initiate apoptosis. These novel findings highlight several new perspectives about the mechanism of metal-dependent apoptosis, while opening up future analyses to the power of the yeast model system.

Taenia solium is a cestode that has a two-hosts life cycle. The adult tapeworm causes an asymptomatic disease known as taeniasis whereas the larval stage causes a disease called cysticercosis. In humans, the most common localization for the larvae is the central nervous system where it produces the neurological disorder neurocysticerco-sis. Previous works by several research groups around the world have shown that T. so-lium is a potentially eradicable parasite. Control programs have included treatment of human and pig populations with antihelmintics in conjunction with health education and are now considering vaccination of naïve piglets. The potential of a live vector vaccine system to deliver Taenia solium Tsol18, a proven protective antigen, to prevent transmission of cysticercosis was investigated. An attenuated strain of Salmonella enterica serovar Typhimurium χ9402 was used to develop an oral delivery system. Tsol18 gene was cloned downstream from the β-lactamase signal sequence in a multicopy asd + plasmid vector pYA3620 to yield plasmid pYA3620/Tsol18 and then transformed into the vaccine strain. The recombinant atte-nuated salmonella vaccine construct was stable for 50 generations and expressed rTsol18. Immunization of mice either with one or two doses of 109 CFU of the recombi-nant vaccine strain carrying plasmid pYA3620/Tsol18 elicited specific antibody response to Salmonella self antigens and to rTsol18. Moreover, oral immunization of piglets with 1012 CFU of the vaccine construction significantly reduced the numbers of viable cysts after challenged. The development of a quantitative assay to detect specific antibodies against Tsol18 is also presented here. The Falcon assay screening test –enzyme linked immu-noabsorbant assay (FAST-ELISA) format was used to develop a quantitative antibody detection assay. We have cloned, expressed and purified rTsol18. With purified porcine IgGs we constructed a standard curve that can be used to quantify the immune re-sponse. Our Fast-ELISA was able to follow the kinetics of the immune response in vac-cinated pigs from an experimental trial. The data we present here provides the basis for a safe, affordable and easy vaccine delivery system that can be used as an adjunct in control programs.

Cancer cells take more glucose to provide energy and phosphoryl intermediates for cancer progression. Meanwhile, energy-provider function of mitochondria in cancer cells is disrupted. This phenomenon is so-called Warburg effect, which is discovered over eighty years ago. The detail mechanisms for Warburg effect are not well defined. How glycolytic enzymes contribute to cancer progression is not well known. PKM2 is a glycolytic enzyme dominantly localized in the cytosol, catalyzing the production of ATP from PEP. In this study, we discovered that there were more nuclear PKM2 expressed in highly proliferative cancer cells. The nuclear PKM2 levels are correlated with cell proliferation rates. According to our microarry analyses, MEK5 gene was upregulated in PKM2 overexpression cells. Our studies showed that PKM2 regulated MEK5 gene transcription to promote cell proliferation. Moreover, nuclear PKM2 phosphorylated Stat3 at Y705 site using PEP as a phosphoryl group donor to regulate MEK5 gene transcription. Our study also showed that double phosphorylated p68 RNA helicase at Y593/595 interacted with PKM2 at its FBP binding site. Under the stimulation of growth factors, p68 interacted with PKM2 to promote the conversion from tetrameraic to dimeric form so as to regulate its protein kinase activity. Overexpression PKM2 in less aggressive cancer cells induced the formation of multinuclei by regulating Cdc14A gene transcription. Overall, this study presents a step forward in understanding the Warburg effect.

ATP Binding Cassette (ABC) transporters are trans-membrane proteins that exist in all phyla. Mutations in this family of proteins can cause inherited diseases like Cystic Fibrosis. ABC transporters consist of dimers of nucleotide binding domains (NBDs) and transmembrane domains (TMDs). NBDs regulate ABC transporters by binding to and hydrolyzing ATP. Although NBD-ATP interactions, NBD-TMD interactions and NBD-water interactions are known to be crucial to the function of these proteins, it is still not clear what structural and energetic factors are involved in the NBD-NTP interactions, how NBD and TMD interact with each other, how water is involved in the functions of ABC transporters and what are the structures and energetics of protein bound water. Molecular modeling and molecular dynamics (MD) simulations were conducted to interpret and predict the structural and energetic factors in control and action of two ABC transporters, CvaB and SUR2B. Water is essential for ABC transporters to carry out their functions, to increase the accuracy of simulations. Therefore, water potentials in molecular modeling and dynamics simulations were improved based on the calculation of water structures from protein surface. Previous study showed the NBDs of ABC transporter CvaB bind tighter to GTP than to ATP at lower temperature but not at high temperature. The MD simulations in this study suggested the velocity of water molecules initiates the temperature dependent functional change of proteins. Previous study found that Ser1387 in the NBD of SUR2B, an ABC transporter in vascular smooth muscles, is critical to Kir6.1/SUR2B channel. The molecular modeling and dynamics simulation conducted on SUR2B showed that Ser1387 is located at a region that contacts a TMD. Upon the phosphorylation, the interaction between the NBD and TMD was enhanced which led to an inter domain movement. Water is essential for ABC transporters to carry out their functions, to increase the accuracy of simulations, and, therefore, the structures and energetics of protein bound water were studied. The water radial distribution function for protein bound water was calculated from 105 atomic resolution protein crystal structures and was found to be sharper than that observed for bulk water.

Nosocomial infections associated with implanted medical- devices are on the rise due to a growing immunocompromised patient population. The organisms of interest in this study are Pseudomonas aeruginosa and Candida albicans. These organisms are opportunistic pathogens and are frequently implicated as the cause of infection and colonization of medical devices. P. aeruginosa is a motile gram-negative bacterium that is able to suppress the growth of C. albicans. Quourm sensing mimicry and biofilm formation on the hyphal surface of C. albicans by P. aeruginosa aids in suppression. C. albicans is a dimorphic fungus capable of quorum sensing with E,E-farnesol and is a central focus in this work. The goal of this project is to determine changes in protein expression when P. aeruginosa is exposed to E,E,-farnesol using 2D DIGE®. Changes in the cytosolic proteome of P. aeruginosa expose metabolic shifts that result in suppression of C. albicans. This work summarizes the effect of growth phase and concentration of E,E-farnesol on P. aeruginosa PAO1 and GSU3. Preliminary results reveal a general response of P. aeruginosa to C. albicans as changes in relevant metabolic nodes that affect pyocyanin production and the induction of virulence factors that lead to the killing of C. albicans. The overall goal of this study was to generate a profile of protein expression where a variety of conditions to further characterize the response could be easily assayed.

B. henselae, B. bacilliformis and B. quintana are capable of causing vasoproliferative diseases in humans by modulating apoptosis and proliferation of endothelial cells. Bartonella clarridgeiae, a close relative of the pathogenic Bartonellae, has been implicated in human disease but has not yet been isolated from a human patient. Both B. bacilliformis and B. clarridgeiae have flagella and a flagellar type 3 secretion system, while B. henselae and B. quintana do not. We created 2 non-motile mutants of B. clarridgeiae by interrupting the flagellin gene, flaA, or the flagellar motor genes, motBC. We investigated whether B. clarridgeiae could invade human endothelial cells (HMECs) and if functional flagella were important for invasion. The non-motile mutants and the wild-type strain were capable of entering HMECs in vitro. The flaA mutant was deficient in attachment, but the HMECs in culture with the flaA mutant demonstrated increased proliferation. The motBC mutant showed enhanced invasion. Differential secretion of proteins was revealed by 2-D electrophoresis and MALDI-TOF analysis of secretomes from the co-cultures compared to uninfected HMECs. HMECS infected with wild-type B. clarridgeiae secreted proteins indicative of proliferation. The flaA mutant induced the secretion of proteins involved in cytoskeletal rearrangement, cell migration, and proliferation. The motBC-infected HMECs showed signs of hypoxia. The co-chaperonin GroES was found in higher concentration in the supernatant of the hyper-invasive motBC strain/HMEC co-culture than the wild-type co-culture and was found at a very low concentration in the flaA culture supernatant. Cross-talk between secretion systems is suggested.