Vaccination with DNA encoding the encephalitogenic autoantigen myelin oligodendrocyte glycoprotein (MOG), pMOG91-108, induce a protective immunity against experimental autoimmune encephalomyelitis (EAE), an animal model of human multiple sclerosis. By injection of a DNA vaccine that contains a DNA region encoding short interfering RNA specific for IFNβ (pMOG-IFNβ) the protective effect of the DNA vaccination is totally inhibited. This demonstrates that IFN-β is directly involved in the protective mechanism against EAE. The objective of this project was to study how molecules involved in the inflammatory process in EAE are regulated by suppressive DNA vaccination. mRNA expression of IL-1β, TGF β, IL-23p40 and Axl receptor tyrosine kinas did not show any significant differences between the groups vaccinated with these DNA vaccines. IL-6 and IFNγ mRNA expression after MOG stimulation in rats treated with pCI, a control vaccine was significantly higher compared to the group vaccinated with vaccine containing pMOG-IFNβ. IL-17 m RNA expression after MOG stimulation in pCl-treated rats was significantly higher compared to the group vaccinated with vaccine containing pMOG-91-108. Of these results the mRNA expression of IL-17 and IL-6 were of interest for the project. The immune system normally protects the body against infections and T-cells have an important role in this defence system. In MS and EAE, the immune system attacks the myelin and this process is caused by a dysregulation of the T-cells. IL-17-producing Th17 cells mediate EAE. Naïve CD4 T-cells in the presence of IL-6 and TGFβ are differentiated to Th17 cells instead of differentiating into T-helper or regulatory T-cells. These IL-17-producing T-cells are highly pathogenic and essential for the development of EAE. The results showed that pMOG IFNβ vaccine had an effect at the immune response, which resulted in an inhibition of the IL-6 production and that vaccination with pMOG91-108 impairs differentiation of IL-17-producing T-cells.

Over 500 million people worldwide suffer from disease associated with intestinal inflammation, including gastric cancer, inflammatory bowel disease, h. pylori infections, and numerous viral and bacterial infections. Although potentially effective therapeutics exist for many of these pathologies, delivery challenges thwart their clinical viability. The objective of this work was to develop drug delivery platforms that could target toxic immunomodulatory therapeutics to diseased intestinal tissues. To meet this objective, we developed an oral delivery vehicle for siRNA and an NF-κB inhibiting nanoparticle that reduces drug-resistance. Small interfering RNA (siRNA) represents a promising treatment strategy for numerous gastrointestinal (GI) diseases; however, the oral delivery of siRNA to inflamed intestinal tissues remains a major challenge. In this presentation, we describe a delivery vehicle for siRNA, termed thioketal nanoparticles (TKNs), that can orally deliver siRNA to sites of intestinal inflammation, and thus inhibit gene expression in diseased intestinal tissue. Using a murine model of ulcerative colitis, we demonstrate that orally administered TKNs loaded with TNFα-siRNA (TNFα-TKNs) diminish TNFα messenger RNA (mRNA) levels in the colon and protect mice from intestinal inflammation. Activation of nuclear factor-κB (NF-κB) results in the expression of numerous prosurvival genes that block apoptosis, thus mitigating the efficacy of chemotherapeutics. Paradoxically, all conventional therapeutics for cancer activate NF-κB, and in doing so initiate drug resistance. Although adjuvant strategies that block NF-κB activation could potentiate the activity of chemotherapeutics in drug resistant tumors, clinical evidence suggests that current adjuvant strategies also increase apoptosis in non-malignant cells. In this presentation, we present a nanoparticle, formulated from a polymeric NF-κB-inhibiting prodrug, that target the chemotherapeutic irinotecan (CPT-11) to solid tumors, and thus abrogates CPT-11-mediated drug resistance and inhibits tumor growth. In order to maximize the amount of NF-κB inhibitor delivered to tumors, we synthesized a novel polymeric prodrug, termed PCAPE, that releases the NF-κB inhibitor caffeic acid phenethyl ester (CAPE) as its major degradation product. Using a murine model of colitis-associated cancer, we demonstrate that when administered systemically, CPT-11-loaded PCAPE-nanoparticles (CCNPs) are three time more effective than a cocktail of the free drugs at reducing both tumor multiplicity and tumor size.

RNA interference (RNAi) in the nematode Caenorhabditis elegans is a type of homology-dependent post-transcriptional gene silencing induced by dsRNA. This dissertation describes the genetic analysis of the RNA interference pathway and inheritance properties associated with this phenomenon. We demonstrate that the RNAi effect can be observed in the progeny of the injected animal for at least two generations. Transmission of the interference effect occurs through a dominant extragenic agent. The wild-type activities of the RNAi pathway genes rde-l and rde-4 are required for the formation of this interfering agent but are not needed for interference thereafter. In contrast, the rde-2 and mut-7 genes are required downstream for interference. These findings provide evidence for germline transmission of an extragenic sequence-specific silencing factor and implicate rde-l and rde-4in the formation of the inherited agent. Other forms of homology-dependent silencing in C. elegansinclude co-suppression and transcriptional silencing of transgenes in the germline. We demonstrate that silencing of a germline transgene can be initiated by injected dsRNA, via the RNAi pathway, and then maintained on a different level. This observation indicates that post-transcriptional and transcriptional silencing of homologous genes could be connected. This dissertation also describes the connection between RNAi and developmental pathways of gene regulation in C. elegans. We show that inactivation of genes related to RNAi pathway genes, a homolog of Drosophila Dicer (dcr-l), and two homologs of rde-1 (alg-l and alg-2) cause heterochronic phenotypes similar to lin-4 and let-7 mutations. Further we show that dcr-l, alg-l, and alg-2 are necessary for the maturation and activity of the lin-4 and let-7small temporal RNAs that regulate stage-specific development. Our findings suggest that a common processing machinery generates guide RNAs that mediate both RNAi and endogenous gene regulation. Finally, this study illustrates the detection of small interfering RNAs (siRNAs), intermediates in the RNAi process, and describes requirements for their accumulation. We show that, in the course of RNAi induced by feeding dsRNA, C. elegans accumulate only siRNAs complementary to the target gene. This accumulation depends on the presence of the target sequence and requires activities of several RNAi-pathway genes. We show that selective retention or amplification of RNAi-active molecules can create a reservoir of memory antisense siRNAs that prevent future expression of the genes with complementary sequence. This suggests a parallel at the molecular level with the clonal selection of antibody forming cells and in the vertebrate immune system.

abstract: This research by studies the computational performance of four different mixed integer programming (MIP) formulations for single machine scheduling problems with varying complexity. These formulations are based on (1) start and completion time variables, (2) time index variables, (3) linear ordering variables and (4) assignment and positional date variables. The objective functions that are studied in this paper are total weighted completion time, maximum lateness, number of tardy jobs and total weighted tardiness. Based on the computational results, discussion and recommendations are made on which MIP formulation might work best for these problems. The performances of these formulations very much depend on the objective function, number of jobs and the sum of the processing times of all the jobs. Two sets of inequalities are presented that can be used to improve the performance of the formulation with assignment and positional date variables. Further, this research is extend to single machine bicriteria scheduling problems in which jobs belong to either of two different disjoint sets, each set having its own performance measure. These problems have been referred to as interfering job sets in the scheduling literature and also been called multi-agent scheduling where each agent's objective function is to be minimized. In the first single machine interfering problem (P1), the criteria of minimizing total completion time and number of tardy jobs for the two sets of jobs is studied. A Forward SPT-EDD heuristic is presented that attempts to generate set of non-dominated solutions. The complexity of this specific problem is NP-hard. The computational efficiency of the heuristic is compared against the pseudo-polynomial algorithm proposed by Ng et al. [2006]. In the second single machine interfering job sets problem (P2), the criteria of minimizing total weighted completion time and maximum lateness is studied. This is an established NP-hard problem for which a Forward WSPT-EDD heuristic is presented that attempts to generate set of supported points and the solution quality is compared with MIP formulations. For both of these problems, all jobs are available at time zero and the jobs are not allowed to be preempted. / Dissertation/Thesis / Ph.D. Industrial Engineering 2012

No description available.

Selective gas-phase dissociation strategies have been developed for the characterization of cross-linked peptides and proteins in quadrupole ion trap mass spectrometers. An infrared chromogenic cross-linker (IRCX) containing a phosphotriester afforded rapid differentiation of cross-linked peptides from unmodified ones in proteolytic digests of cross-linked proteins by selective infrared multiphoton dissociation (IRMPD). Only the cross-linked peptides containing the chromogenic phosphate underwent IRMPD and unmodified peptides were not affected by IR irradiation. IRMPD of IRCX-cross-linked peptides yielded uncross-linked y-ion sequence tags of the constituent peptides due to secondary dissociation of all primary product ions which contained the chromophore, thus allowing successful de novo sequencing of the cross-linked peptides. Peptides cross-linked via a two-step conjugation strategy through the formation of a bis-arylhydrazone (BAH) bond were selectively dissociated by ultraviolet radiation at 355 nm. The BAH-cross-linked peptides could be distinguished from not only unmodified peptides but also dead-end modified peptides based on the selectivity of ultraviolet photodissociation. In a complementary approach, electron transfer dissociation of BAH-cross-linked peptides resulted in preferential cleavage of the hydrazone bond which produced two modified peptides. These modified peptides were subsequently interrogated by CID which allowed for the original site of cross-linking to be pinpointed. IRMPD was implemented in a dual pressure linear ion trap to demonstrate successful photodissociation of peptides having modest absorptivities. Peptides were observed to efficiently dissociation by IR irradiation exclusively in the low pressure cell whereas no dissociation was observed in the high pressure cell due to extensive collisional cooling. IRMPD provided greater sequence coverage of the peptides than CID and yielded product ion mass spectra which were predominantly composed of singly charged product ions which simplified spectral interpretation. IRMPD was further applied for the sequencing of small-interfering RNA. Complete sequence coverage was obtained and the results were compared to CID. / text

A ativação neutrônica é uma técnica analítica para determinação da composição química elementar. Através da irradiação com nêutrons, é induzida a radioatividade artificial na amostra. Esta radiação é medida usualmente por espectrometria gama. Suas características de sensibilidade elevada (μg.g-1 ng.g-1), exatidão e precisão, capacidade multielementar, limites de detecção da ordem de μg.g-1 a ng.g-1 e natureza não destrutiva, isto é, permite que a amostra seja analisada sem preparo químico prévio, classificam a técnica como muito poderosa na análise de traços. Apesar de ser uma técnica versátil, apresenta limitações. Uma delas é relacionada com as interferências primárias que ocorrem durante a irradiação. Usualmente, o cálculo de concentração se baseia na reação principal sob nêutrons térmicos nX(nt, )n+1X, mas, sob nêutrons rápidos, podem ocorrer as reações interferentes n+1Y(nr, p)n+1X e n+4Y(nr, a)n+1X. A conseqüência disso, é que a concentração final deverá ser a soma dos resultados das reações e não será possível distinguir a concentração real da concentração gerada pelo interferente. Assim, o impacto da interferência dependerá da contribuição do fluxo de nêutrons rápidos no fluxo total de nêutrons no local da irradiação. Isto significa que a interferência dependerá do quanto o canal de irradiação é termalizado e isso é uma característica do reator. Nesta pesquisa, diversas reações de interferência foram estudadas: 28Si(nr,p)28Al na determinação de alumínio; 27Al(nr, p)27Mg na determinação de magnésio; 27Al(nr,a)24Na na determinação de sódio e 56Fe (nr, p)56Mn na determinação de manganês. Duas metodologias foram seguidas: Procedimento I, no qual foram utilizados padrões puros dos elementos. Nesta etapa foram calculadas as massas aparentes de Al, Mg, Mn e Na provenientes das reações interferentes. A razão entre o elemento interferente e o de interesse foi determinada para cada elemento em estudo. No Procedimento II, a contribuição de Fe na determinação de Mn foi estudada em detalhes, analisando diversos materiais de referência de solo e sedimento. Nesta etapa foi desenvolvido um método de correção irradiando as amostras com e sem filtro de cádmio. O mesmo procedimento foi aplicado em amostras de solo coletadas no Quadrilátero Ferrífero, Minas Gerais, com concentração de ferro de 19 a 40%. O Procedimento II confirmou os resultados do Procedimento I, provando que nas condições de trabalho da aplicação da AAN no Centro de Desenvolvimento da Tecnologia Nuclear/Comissão Nacional de Energia Nuclear, (CDTN/CNEN), apenas para razão de concentração Fe/Mn igual ou maior do que 50.000 0.002% de Mn em ferro - é que será necessário corrigir os valores de manganês. Desta pesquisa sugere-se que as correções devem ser aplicadas somente em ligas de ferro, quando a presença de manganês for considerada impureza. Esta pesquisa também sugere que, nas mesmas condições de análise, correções devem ser aplicadas quando as razões de Si/Al, Al/Mg and Al/Na forem iguais ou maiores do que 420, 82 and 2.500, respectivamente. / The neutron activation (NAA) is an analytical technique for the determination of the elementary chemical composition. It is based on the induction of artificial radioactivity in a sample by neutrons and the resulting activity is usually measured, by gamma spectrometry. Its more relevant characteristics are the high sensibility (μg.g-1 ng.g-1), accuracy and precision, capability of multielementary analysis, low detection limits and its non destructive nature. These properties classify NAA as a very powerful analytical technique. In spite of being a versatile technique, the NAA presents limitations, one of them is related to the primary interference reactions that occur during the irradiation. The calculation of the concentration is usually based on the main reaction under thermal neutrons nX(nth, )n+1X but under fast flux, the reactions n+1Y(nr, p)n+1X e n+4Y(nr, a)n+1X can take place. The consequence of this interference is that the final elemental concentration will be the sum of results of the reactions and it is not possible to distinguish the real concentration. Therefore, the impact of this interference depends on the contribution of the fast neutron flux on the total neutron flux in the local irradiation channel. It means that the interference depends on how much the irradiation channel is thermalized and it is a characteristic of the reactor. In this research, several interference reactions were studied: 28Si(nf, p)28Al on the aluminium determination; 27Al(nf, p)27Mg, on the determination of magnesium; 27Al(nf, a)24Na, on the determination of sodium and 56Fe(nf, p)56Mn on the determination of manganese. Two procedures were adopted: Method I, in which using pure standards of the elements, the apparent masses of Al, Mg, Mn and Na from interfering reactions were evaluated and a ratio between the interference of the element to the interested element was determined for each studied element. In Method II, the contribution of Fe on Mn determination was studied in detail using several soil and sediment reference materials. In Method II, a correction method was developed irradiating bare and Cd covered samples. The same procedure was applied to soil samples from the Iron Quadrangle, Minas Gerais, with 19 to 40% of iron content. Method II confirmed the results of Method I, proving that in the technical conditions of the application of the NAA at Centro de Desenvolvimento da Tecnologia Nuclear/Comissão Nacional de Energia Nuclear, CDTN/CNEN, only for ratio Fe/Mn equal or higher than 50,000 0.002% of Mn in Iron - it will be necessary to correct the values of Mn. It is suggested that the correction should be applied only in Fe alloys when the presence of Mn is considered impurity. This research also suggests that in the same conditions, the corrections should be applied when the ratios Si/Al, Al/Mg and Al/Na, are equal or higher than 420, 82 and 2,500, respectively.

A incidência de melanomas tem crescido mundialmente. Apesar de representar um potencial problema de saúde pública pela sua incidência crescente, melanomas ainda se apresentam como tumores de difícil tratamento, especialmente quando diagnosticados em estadios avançados. A taxa de resposta a quimioterapia não ultrapassa 30% de resposta clínica objetiva nestes casos. As bases moleculares da quimiorresistência não são ainda completamente esclarecidas e seu conhecimento será útil para o delineamento de estratégias de quimiossensibilização. Em estudos anteriores, observamos que o tratamento de linhagem de células de melanoma metastático humano com o quimioterápico cisplatina induz o acúmulo de proibitina nas células sobreviventes. Proibitina é uma molécula expressa ubiquamente na maioria das células. Há evidências de que a forma nuclear esteja envolvida com o processo de morte celular e inibição de E2F1 enquanto a forma citoplasmática parece atuar como chaperona mitocondrial, garantindo sua homeostasia. O objetivo deste projeto foi avaliar a compartimentalização subcelular e a expressão de proibitina, após tratamento com 25 M de cisplatina por 24 horas em diferentes linhagens de melanoma metastático humano; e, o efeito de sua subexpressão, usando-se small interference (si) RNA. Nós mostramos que nas linhagens de melanoma humano LB373Mel, SKMel 37 e Mel 85, a proibitina foi encontrada predominantemente no citoplasma, associada, pelo menos em parte, com a mitocôndria. Após tratamento com cisplatina, uma porção da proibitina também foi encontrada no núcleo, como pode ser detectado utilizando-se anticorpo monoclonal (clone II-14-1). Experimentos de knockdown de proibitina por siRNA obtiveram sucesso em duas de três linhagens. Nessas duas linhagens (LB373Mel e Mel 85), o bloqueio do acúmulo de proibitina após tratamento com cisplatina levou à quimiossensibilização. A quimiossensibilização à cisplatina não foi observada na linhagem SKMel 37, que foi capaz de acumular proibitina mesmo quando tratada com siRNA específico para proibitina. A conclusão deste projeto é que a expressão de proibitina é parte da resposta celular que leva a sobrevivência de células de melanoma expostas à cisplatina / The incidence of melanomas has grown world-wide. Besides representing a potential problem of public health for its increasing incidence, melanomas are tumors of difficult treatment, especially when diagnosed in advanced phases. The clinical objective response rate does not exceed 30% in these cases. The molecular bases of chemoresistance are not completely clarified and their understanding will be useful for the delineation of chemosensitization strategies. In previous studies, we observed that the treatment of a human metastatic melanoma cell line with the chemotherapeutic agent cisplatin induced the accumulation of prohibitin in the surviving cells. Prohibitin is ubiquitously expressed molecule in most cells. There is evidence that the nuclear form is involved with the process of cell death and inhibition of E2F1, while the cytoplasmic form seems to act as mitochondrial chaperone, guaranteeing its homeostasis. The aim of this project was to evaluate the subcellular compartmentalization and protein expression profile of prohibitin, after treatment with 25M of cisplatin for 24 hours in different human metastatic melanoma cell line, and the effect of its underexpression, using siRNA. We showed that, in human melanoma cell lines, LB373Mel, SKMel 37 and Mel 85, prohibitin was found predominantly in the cytoplasm, associated at least in part with the mitochondria. Upon cisplatin treatment, a fraction of prohibitin was also found in the nucleus, as detected by using a monoclonal antibody (clone II-14-10). Knockdown experiments were successful in two out of three cell lines. In these two cell lines (LB373Mel and Mel 85) blockage of the accumulation of prohibitin upon cisplatin treatment led to chemosensitization. Chemosensitization to cisplatin was not observed for SKMel 37 cells, which accumulated prohibitin even when treated with prohibitin specific siRNA oligonucleotides. Altogether, we concluded that expression of prohibitin is part of the cellular response that leads to cell survival in melanoma cells exposed to cisplatin

Regulation of gene expression using small interfering RNA (siRNA) is a promising strategy for research and treatment of numerous diseases. However, siRNA cannot easily cross the cell membrane due to its inherent instability, large molecular weight and anionic nature. For this reason, a carrier that protects, delivers and unloads siRNA is required for successful gene silencing. The goal of this research was to develop a potential siRNA delivery system for in vitro and in vivo applications using cationic polymers, chitosan and polyethylenimine (PEI), poly(ethylene glycol) (PEG), mannose, and poly(D,L-lactic-co-glycolic acid) (PLGA). Furthermore, the delivery system was constructed in two different ways to explore the effect of mannose location in the structure. In the first approach, mannose and PEG were directly conjugated to the chitosan/PEI backbone, while mannose was connected to the chitosan/PEI backbone through PEG spacer in the second approach. First, the ability of modified chitosan polymers to complex and deliver siRNA for gene silencing was investigated. Despite the modified chitosan polymers successfully formed nanoplexes with siRNA, entered target cells and reduced cytotoxicity of unmodified chitosan, they showed limited gene silencing efficiency. For this reason, modified PEIs were examined to improve in vitro gene knockdown. The modified PEI polymers also complexed with siRNA and facilitated endocytosis of the nanoplexes. In addition, the modifications reduced inherent cytotoxicity of unmodified PEI without compromising the gene silencing efficiency on both mRNA and protein levels. Interestingly, we found that complexation of siRNA with PEI-PEG-mannose resulted in higher cell uptake and gene silencing than complexes made with mannose-PEI-PEG. Finally, the effect of sustained release of the mannosylated pegylated PEI/siRNA nanoplexes on gene silencing was tested by encapsulating the nanoplexes within PLGA microparticles. The modified PEIs enhanced the entrapment efficiency of siRNA into the particles and resulted in reduced initial burst followed by sustained release. Incorporating the modified PEIs increased cellular uptake of siRNA, whereas it did not enhance in vitro gene knockdown efficiency due to the sustained release properties. The modified PEIs reduced the in vitro cytotoxicity and in vivo hepatotoxicity of the PLGA microparticles. In addition, encapsulating the nanoplexes into PLGA microparticles further reduced the cytotoxicity of PEI. Throughout the study, the second structure was proven more efficacious than the first structure in cellular uptake, gene silencing, siRNA encapsulation, and sustained release. We have developed novel polymeric siRNA delivery systems that enhance delivery efficiency and cellular uptake of siRNA. They have great potential for utility as a long-acting siRNA delivery system in biomedical research.

Dissertation (Ph.D.)--University of South Florida, 2009. / Title from PDF of title page. Document formatted into pages; contains 86 pages. Includes vita. Includes bibliographical references.