Limits and tradeoffs in the control of autocatalytic systems

Despite the complexity of biological networks, we find that certain common architectures govern network structures. These architectures impose fundamental constraints on system performance and create tradeoffs that the system must balance in the face of uncertainty in the environment. This means that while a system may be optimized for a specific function through evolution, the optimal achievable state must follow these constraints. One such constraining architecture is autocatalysis, as seen in many biological networks including glycolysis and ribosomal protein synthesis. Using a minimal model, we show that ATP autocatalysis in glycolysis imposes stability and performance constraints and that the experimentally well-studied glycolytic oscillations are in fact a consequence of a tradeoff between error minimization and stability. We also show that additional complexity in the network results in increased robustness. Ribosome synthesis is also autocatalytic where ribosomes must be used to make more ribosomal proteins. When ribosomes have higher protein content, the autocatalysis is increased. We show that this autocatalysis destabilizes the system, slows down response, and also constrains the system’s performance. On a larger scale, transcriptional regulation of whole organisms also follows architectural constraints and this can be seen in the differences between bacterial and yeast transcription networks. We show that the degree distributions of bacterial transcription network follow a power law distribution while the yeast network follows an exponential distribution. We then explored the evolutionary models that have previously been proposed and show that neither the preferential linking model nor the duplication-divergence model of network evolution generates the power-law, hierarchical structure found in bacteria. However, in real biological systems, the generation of new nodes occurs through both duplication and horizontal gene transfers, and we show that a biologically reasonable combination of the two mechanisms generates the desired network.

The Flocculation of E. coli with Polyethyleneimine

A comprehensive study was made of the flocculation of dispersed E. coli bacterial cells by the cationic polymer polyethyleneimine (PEI). The three objectives of this study were to determine the primary mechanism involved in the flocculation of a colloid with an oppositely charged polymer, to determine quantitative correlations between four commonly-used measurements of the extent of flocculation, and to record the effect of varying selected system parameters on the degree of flocculation. The quantitative relationships derived for the four measurements of the extent of flocculation should be of direct assistance to the sanitary engineer in evaluating the effectiveness of specific coagulation processes.

A review of prior statistical mechanical treatments of absorbed polymer configuration revealed that at low degrees of surface site coverage, an oppositely- charged polymer molecule is strongly adsorbed to the colloidal surface, with only short loops or end sequences extending into the solution phase. Even for high molecular weight PEI species, these extensions from the surface are theorized to be less than 50 Å in length. Although the radii of gyration of the five PEI species investigated were found to be large enough to form interparticle bridges, the low surface site coverage at optimum flocculation doses indicates that the predominant mechanism of flocculation is adsorption coagulation.

The effectiveness of the high-molecular weight PEI species 1n producing rapid flocculation at small doses is attributed to the formation of a charge mosaic on the oppositely-charged E. coli surfaces. The large adsorbed PEI molecules not only neutralize the surface charge at the adsorption sites, but also cause charge reversal with excess cationic segments. The alignment of these positive surface patches with negative patches on approaching cells results in strong electrostatic attraction in addition to a reduction of the double-layer interaction energies. The comparative ineffectiveness of low-molecular weight PEI species in producing E. coli flocculation is caused by the size of the individual molecules, which is insufficient to both neutralize and reverse the negative E.coli surface charge. Consequently, coagulation produced by low molecular weight species is attributed solely to the reduction of double-layer interaction energies via adsorption.

Electrophoretic mobility experiments supported the above conclusions, since only the high-molecular weight species were able to reverse the mobility of the E. coli cells. In addition, electron microscope examination of the seam of agglutination between E. coli cells flocculation by PEI revealed tightly- bound cells, with intercellular separation distances of less than 100-200 Å in most instances. This intercellular separation is partially due to cell shrinkage in preparation of the electron micrographs.

The extent of flocculation was measured as a function of PEl molecular weight, PEl dose, and the intensity of reactor chamber mixing. Neither the intensity of mixing, within the common treatment practice limits, nor the time of mixing for up to four hours appeared to play any significant role in either the size or number of E.coli aggregates formed. The extent of flocculation was highly molecular weight dependent: the high-molecular-weight PEl species produce the larger aggregates, the greater turbidity reductions, and the higher filtration flow rates. The PEl dose required for optimum flocculation decreased as the species molecular weight increased. At large doses of high-molecular-weight species, redispersion of the macroflocs occurred, caused by excess adsorption of cationic molecules. The excess adsorption reversed the surface charge on the E.coli cells, as recorded by electrophoretic mobility measurements.

Successful quantitative comparisons were made between changes in suspension turbidity with flocculation and corresponding changes in aggregate size distribution. E. coli aggregates were treated as coalesced spheres, with Mie scattering coefficients determined for spheres in the anomalous diffraction regime. Good quantitative comparisons were also found to exist between the reduction in refiltration time and the reduction of the total colloid surface area caused by flocculation. As with turbidity measurements, a coalesced sphere model was used since the equivalent spherical volume is the only information available from the Coulter particle counter. However, the coalesced sphere model was not applicable to electrophoretic mobility measurements. The aggregates produced at each PEl dose moved at approximately the same vlocity, almost independently of particle size.

PEl was found to be an effective flocculant of E. coli cells at weight ratios of 1 mg PEl: 100 mg E. coli. While PEl itself is toxic to E.coli at these levels, similar cationic polymers could be effectively applied to water and wastewater treatment facilities to enhance sedimentation and filtration characteristics.

Macroscopically Dissipative Systems with Underlying Microscopic Dynamics : Properties and Limits of Measurement

While some of the deepest results in nature are those that give explicit bounds between important physical quantities, some of the most intriguing and celebrated of such bounds come from fields where there is still a great deal of disagreement and confusion regarding even the most fundamental aspects of the theories. For example, in quantum mechanics, there is still no complete consensus as to whether the limitations associated with Heisenberg's Uncertainty Principle derive from an inherent randomness in physics, or rather from limitations in the measurement process itself, resulting from phenomena like back action. Likewise, the second law of thermodynamics makes a statement regarding the increase in entropy of closed systems, yet the theory itself has neither a universally-accepted definition of equilibrium, nor an adequate explanation of how a system with underlying microscopically Hamiltonian dynamics (reversible) settles into a fixed distribution.

Motivated by these physical theories, and perhaps their inconsistencies, in this thesis we use dynamical systems theory to investigate how the very simplest of systems, even with no physical constraints, are characterized by bounds that give limits to the ability to make measurements on them. Using an existing interpretation, we start by examining how dissipative systems can be viewed as high-dimensional lossless systems, and how taking this view necessarily implies the existence of a noise process that results from the uncertainty in the initial system state. This fluctuation-dissipation result plays a central role in a measurement model that we examine, in particular describing how noise is inevitably injected into a system during a measurement, noise that can be viewed as originating either from the randomness of the many degrees of freedom of the measurement device, or of the environment. This noise constitutes one component of measurement back action, and ultimately imposes limits on measurement uncertainty. Depending on the assumptions we make about active devices, and their limitations, this back action can be offset to varying degrees via control. It turns out that using active devices to reduce measurement back action leads to estimation problems that have non-zero uncertainty lower bounds, the most interesting of which arise when the observed system is lossless. One such lower bound, a main contribution of this work, can be viewed as a classical version of a Heisenberg uncertainty relation between the system's position and momentum. We finally also revisit the murky question of how macroscopic dissipation appears from lossless dynamics, and propose alternative approaches for framing the question using existing systematic methods of model reduction.

As sentenças aditivas na jurisdição constitucional

Como o título deixa ver, o trabalho tem como objeto as sentenças aditivas, alvos de uma análise crítica, à luz de pressupostos filosóficos, sociais, políticos e jurídicos. Para isso, fez-se uma visitação à doutrina, nacional e estrangeira, em torno do tema, além de proceder à coleta posicionamentos, emanados das cortes supremas de alguns países expoentes, acerca da matéria em foco. O Supremo Tribunal Federal não poderia ficar como não ficou fora desse universo de pesquisa. O primeiro capítulo trata dos tópicos relativos ao Estado e à Jurisdição, contemplando as relações entre eles para focalizar, com propriedade, a Jurisdição Constitucional. O segundo capítulo traz à discussão a criação judicial do direito e o ativismo judicial, temas correlatos e imprescindíveis ao estudo proposto, porque a sentença aditiva tem, entranhada, uma dose de ativismo judicial. Tem-se, pois, que o criacionismo judicial insere-se nesse contexto e, por isso, carece de uma abordagem descritiva e crítica. O terceiro capítulo versa sobre as cortes constitucionais e o Supremo Tribunal Federal, móveis principais das sentenças aditivas, e que devem ser bem conhecidos para facilitar a digressão do tema-base. O quarto capítulo aborda as decisões no controle de constitucionalidade das normas e seus efeitos, de fundamental importância porque se conectam diretamente com as aditivas. Finalmente, a quinta parte centra-se, no núcleo do tema-objeto da dissertação, contemplando minudências referentes ao assunto, bastante conflituoso ressalte-se , no limite que separa as atribuições de dois Poderes do Estado, o Judiciário e o Legislativo.

O papel do óleo de peixe na via L-arginina-óxido nítrico e no estresse oxidativo em eritrócitos: um estudo dose-resposta

Os ácidos graxos poli-insaturados n-3 derivados do óleo de peixe estão associados a benefícios cardiovasculares, que podem ser decorrentes da ativação da óxido nítrico sintase (NOS). Assim como as células endoteliais, os eritrócitos possuem NOS endotelial (eNOS) e induzível (iNOS) e, portanto, são capazes de sintetizar óxido nítrico (NO). O presente estudo testou a capacidade que diferentes concentrações de óleo de peixe tem de ativar a via L-arginina-NO e, em seguida, alterar os níveis de guanosina monofosfato cíclica (GMPc) em eritrócitos de camundongos alimentados com dieta hiperlipídica. Além disso, foram analisados os marcadores de estresse oxidativo nos eritrócitos, objetivando investigar a biodisponibilidade do NO. O transporte de L-arginina, avaliado através da incubação com L-[3H]-arginina, mostrou-se ativado quando da administração de dietas contendo elevadas concentrações de óleo de peixe, em comparação com as dietas contendo baixas concentrações e controle. A atividade da NOS, medida pela conversão de L-[3H]-arginina em L-[3H]-citrulina, e a expressão da eNOS também aumentaram nos animais que se alimentaram com dietas ricas em óleo de peixe. Apesar da ativação da via L-arginina-óxido nítrico observada em nossos experimentos, os níveis de GMPc intraeritrocitário não foram afetados. O dano oxidativo nos eritrócitos aumentou linearmente conforme o óleo de peixe era acrescido na dieta, sem afetar a atividade das enzimas antioxidantes. Além do endotélio, os eritrócitos contribuem para o metabolismo do NO. Desta forma, a ativação da via L-arginina-NO nessas células pode ser benéfica para saúde cardiovascular. Estudos futuros poderão investigar outros marcadores de estresse oxidativo durante o consumo de óleo de peixe para assegurar que o seu uso não resulta em efeitos prejudiciais secundários e para garantir a biodisponibilidade de NO.

Efeito do treinamento físico intenso e da dose única de polifenóis sobre indicadores cardiometabólicos em militares fisicamente condicionados

O exercício físico pode promover o desequilíbrio oxidativo e na secreção e ação das adipocinas, leptina e adiponectina, que desempenham papel fundamental no desenvolvimento de doenças cardiometabólicas, incluindo a síndrome metabólica, disfunção endotelial, desordens inflamatórias e vasculares. Militares são submetidos a exercícios físicos intensos e podem apresentar maior risco de doenças cardiovasculares. A identificação de parâmetros capazes de detectar o risco cardiovascular precoce em grupos muito ativos fisicamente é complexa. A razão leptina/adiponectina (L/A) e a concentração de LDL eletronegativa (LDL (-)) vem sendo considerados bons indicadores de risco cardiovascular precoce porém não há estudos que investiguem a utilidade destes marcadores em militares. Os polifenóis, presentes na uva (Vitis vinífera), apresentam efeitos cardioprotetores como inibição da oxidação das lipoproteínas e controle glicêmico. Na presente tese objetivou-se identificar o risco cardiovascular em jovens militares altamente treinados, utilizando diferentes parâmetros, incluindo a razão L/A e investigar a influência do exercício militar e do uso de dose única de Vitis vinifera sobre parâmetros cardiometabólicos de militares fisicamente treinados. O primeiro estudo contou com a participação de 54 militares d gênero masculino, condicionados fisicamente, após descanso de 24h. No segundo estudo, participaram 54 militares do gênero masculino distribuídos aleatoriamente, de forma duplo-cego, para receber única dose contendo 200 mg de extrato seco de Vitis vinifera (GS, n = 27) ou 200 mg de placebo (amido) (GP, n = 27). Considerados em conjunto, os resultados sugerem que militares treinados poderiam ser classificados como limítrofes quanto ao risco cardiovascular, quando somente o perfil lipídico é empregado como marcador. As medidas de CC e CC/E são parâmetros de fácil obtenção e podem ser empregados na identificação do potencial risco cardiovascular, enquanto outros estudos não confirmam a eficácia da razão L/A para este fim. A comparação das concentrações plasmáticas de adiponectina e leptina apresentou diferença significativa apenas intragrupo para ambos os grupos. As concentrações plasmáticas das adipocinas foram influenciadas pelo treinamento. Os indicadores de homeostase glicêmica, glicemia de jejum e insulina plasmática, foram semelhantes entre os grupos, não sendo sendo influenciada pelo treinamento ou suplementação. A suplementação de polifenóis reduziu as concentrações de LDL(-) do GS em relação ao GP em T24h e T48h (p<0,05). Estes achados sugerem que o treinamento físico afeta a secreção das adipocinas independentemente do uso da Vitis vinífera. Entretanto, a dose única de polifenóis pode reduzir o risco cardiometabólico proveniente da oxidação da LDL (-)