Function of microRNA-146a and NF-κB in physiologic and pathologic hematopoiesis

During inflammation and infection, hematopoietic stem and progenitor cells (HSPCs) are stimulated to proliferate and differentiate into mature immune cells, especially of the myeloid lineage. MicroRNA-146a (miR-146a) is a critical negative regulator of inflammation. Deletion of the gene encoding miR-146a—expressed in all blood cell types—produces effects that appear as dysregulated inflammatory hematopoiesis, leading to a decline in the number and quality of hematopoietic stem cells (HSCs), excessive myeloproliferation, and, ultimately, to exhaustion of the HSCs and hematopoietic neoplasms. Six-week-old deleted mice are normal, with no effect on cell numbers, but by 4 months bone marrow hypercellularity can be seen, and by 8 months marrow exhaustion is becoming evident. The ability of HSCs to replenish the entire hematopoietic repertoire in a myelo-ablated mouse also declines precipitously as miR-146a-deficient mice age. In the absence of miR-146a, LPS-mediated serial inflammatory stimulation accelerates the effects of aging. This chronic inflammatory stress on HSCs in deleted mice involves a molecular axis consisting of upregulation of the signaling protein TRAF6 leading to excessive activity of the transcription factor NF-κB and overproduction of the cytokine IL-6. At the cellular level, transplant studies show that the defects are attributable to both an intrinsic problem in the miR-146a-deficient HSCs and extrinsic effects of miR-146a-deficient lymphocytes and non-hematopoietic cells. This study has identified a microRNA, miR-146a, to be a critical regulator of HSC homeostasis during chronic inflammatory challenge in mice and has provided a molecular connection between chronic inflammation and the development of bone marrow failure and myeloproliferative neoplasms. This may have implications for human hematopoietic malignancies, such as myelodysplastic syndrome, which frequently displays downregulated miR-146a expression.

Measurement of the direct CP asymmetry in b-->s+gamma via sum of exclusive B Meson decays using the BABAR detector

We perform a measurement of direct CP violation in b to s+gamma Acp, and the measurement of a difference between Acp for neutral B and charged B mesons, Delta A_{X_s\gamma}, using 429 inverse femtobarn of data recorded at the Upsilon(4S) resonance with the BABAR detector. B mesons are reconstructed from 16 exclusive final states. Particle identification is done using an algorithm based on Error Correcting Output Code with an exhaustive matrix. Background rejection and best candidate selection are done using two decision tree-based classifiers. We found $\acp = 1.73%+-1.93%+-1.02% and Delta A_X_sgamma = 4.97%+-3.90%+-1.45% where the uncertainties are statistical and systematic respectively. Based on the measured value of Delta A_X_sgamma, we determine a 90% confidence interval for Im C_8g/C_7gamma, where C_7gamma and C_8g are Wilson coefficients for New Physics amplitudes, at -1.64 < Im C_8g/C_7gamma < 6.52.

Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

The intramolecular Buchner reaction of α-diazo-β-ketonitriles : development and application to the total synthesis of (+)-Salvileucalin B

Since its discovery in 1896, the Buchner reaction has fascinated chemists for more than a century. The highly reactive nature of the carbene intermediates allows for facile dearomatization of stable aromatic rings, and provides access to a diverse array of cyclopropane and seven-membered ring architectures. The power inherent in this transformation has been exploited in the context of a natural product total synthesis and methodology studies.

The total synthesis work details efforts employed in the enantioselective total synthesis of (+)-salvileucalin B. The fully-substituted cyclopropane within the core of the molecule arises from an unprecedented intramolecular Buchner reaction involving a highly functionalized arene and an α-diazo-β-ketonitrile. An unusual retro-Claisen rearrangement of a complex late-stage intermediate was discovered on route to the natural product.

The unique reactivity of α-diazo-β-ketonitriles toward arene cyclopropanation was then investigated in a broader methodological study. This specific di-substituted diazo moiety possesses hitherto unreported selectivity in intramolecular Buchner reactions. This technology was enables the preparation of highly functionalized norcaradienes and cyclopropanes, which themselves undergo various ring opening transformations to afford complex polycyclic structures.

Finally, an enantioselective variant of the intramolecular Buchner reaction is described. Various chiral copper and dirhodium catalysts afforded moderate stereoinduction in the cyclization event.

Morphometric, meristics and comparative studies of Chrysichthys nigrodigititus (Lacepede) from Lagos Lekki and Badagry Lagoons, Lagos State, south west Nigeria

Morphometric measurements, meristic counts and comparative studies of Chrysicthys nigrodigitatus samples from Lagos, Lekki, and Badagry Lagoons was carried out to determine the amount of variation among the species from the different locations using seven meristic and two morphometric characters. Significant differences were observed only between the headlength (F==14.02; P<00.05), number of anal rays (F=19.9; P<0.05) and of gill raker counts (F=142.0, 160.94; P<0.05). The differences observed in the meristic characters could be attributed to environmental and climatic differences of the three isolated sites and therefore phenotypic rather than genetic. This study is valuable for the selection of quality strains of fish species for aquaculture production

Experimente über die Wirkung von UV-B auf pelagische Fischembryonen in einem Sonnenscheinsimulator

One of the supposed effects of the observed ozone depletion is the increase of solar UV-B irradiation at the seasurface. This will cause an impact on certain compartments of marine ecosystems. Especially, sensitive developmental stages of pelagic fish embryos might be affected. Embryos of dab (Limanda limanda) and plaice (Pleuronectes plalessa) were experimentally exposed 10 different amounts of UVB irradiation in a sunshine simulator. This programmable device allows the dosage of realistic solar irradiation in quality and guantity. Experiments were carried out in March 1995 and February 1996. Either artificially inserninated and reared emhryos of dab and plaice or embryos caught in the German Bight were exposed to simulated solar irradiation. The 1995 experiments served to identify the effective irradiation dosages. For the 1996 experiments irradiation applied was much lower, being dose to realistic valucs expected over the North Sea as a consequence of ozone depletion. The following end points were studied: 1. Mortality, 2. sublethal morphological effects (malformations), 3. DNA damage, 4. changes in buoyancy of embryos measured as changes in osmolarity of the perivitelline fluid. Conditions for the simulation of daylight were a c1oudless sky with a solar zenith distance of 34 % (air mass 1.2). The adopted ozone depletion was 40 % corresponding to 180 DU (Dobson Units) instead of 300 DU. In the 1995 experiments time and dosage dependent influenccs on mortality and buoyancy of embryos of dab and plaice were found. Even in those embryos which were protected from the UV-B spectral range a loss of buoyancy was registered after 12 hours in the simulator. No diffcrences in DNA integrity as determined by DNA unwinding of exposed and control embryos were found. Also with lower amounts of irradiation in the 1996 experiments dosage dependent acute mortality, malformations, and impact on the buoyancy of the emhryos was registered. Sublethal effects occurred as well in embryos protected against UV-B in the exposure chambers, but were not found in the dark controls. The impact of low dosages of UV-B on the buoyancy of pelagic fish embryos might indicate an important ecological threat and deserves further studies.

Application of microwave diagnostics to copper chloride and carbon dioxide lasers

Part A

A problem restricting the development of the CuCl laser has been the decrease in output power with increases of tube temperature above 400°C. At that temperature the CuCl vapor pressure is about .1 torr. This is a small fraction of the buffer gas pressure (He at 10 torr).

The aim of the project was to measure the peak radiation temperature (assumed related to the mean energy of electrons) in the laser discharge as a function of the tube temperature. A 24 gHz gated microwave radiometer was used.

It was found that at the tube temperatures at which the output power began to deteriorate, the electron radiation temperature showed a sharp increase (compared with radiation temperature in pure buffer).

Using the above result, we have postulated that this sudden increase is a result of Penning ionization of the Cu atoms. As a consequence of this process the number of Cu atoms available for lasing decrease.

PART B

The aim of the project was to study the dissociation of CO₂ in the glow discharge of flowing CO₂ lasers.

A TM₀₁₁ microwave (3 gHz) cavity was used to measure the radially averaged electron density n_e and the electron-neutral collision frequency in the laser discharge. An estimate of the electric field is made from these two measurements. A gas chromatograph was used to measure the chemical composition of the gases after going through the discharge. This instrument was checked against a mass spectrometer for accuracy and sensitivity.

Several typical laser mixtures were .used: CO₂-N₂-He (1,3,16), (1,3,0), (1,0,16), (1,2,10), (1,2,0), (1,0,10), (2,3,15), (2,3,0), (2,0,15), (1,3,16)+ H₂O and pure CO₂. Results show that for the conditions studied the dissociation as a function of the electron density is uniquely determined by the STP partial flow rate of CO₂, regardless of the amount of N₂ and/or He present. The presence of water vapor in the discharge decreased the degree of dissociation.

A simple theoretical model was developed using thermodynamic equilibrium. The electrons were replaced in the calculations by a distributed heat source.

The results are analyzed with a simple kinetic model.

Short-pulse laser absorption via J x B heating in ultrahigh intensity laser plasma interaction

An analytical fluid model for JxB heating during the normal incidence by a short ultraintense linearly polarized laser on a solid-density plasma is proposed. The steepening of an originally smooth electron density profile as the electrons are pushed inward by the laser is included self-consistently. It is shown that the JxB heating includes two distinct coupling processes depending on the initial laser and plasma conditions: for a moderate intensity (a <= 1), the ponderomotive force of the laser light can drive a large plasma wave at the point n(e)=4 gamma(0)n(c) resonantly. When this plasma wave is damped, the energy is transferred to the plasma. At higher intensity, the electron density is steepened to a high level by the time-independent ponderomotive force, n(e)> 4 gamma(0)n(c), so that no 2 omega resonance will occur, but the longitudinal component of the oscillating ponderomotive field can lead to an absorption mechanism similar to "vacuum heating." (c) 2006 American Institute of Physics.

Studies toward the total synthesis of ritterazine B : the investigation of alkynylation reactions for use in the synthesis of the western fragment

The ritterazine and cephalostatin natural products have biological activities and structures that are interesting to synthetic organic chemists. These products have been found to exhibit significant cytotoxicity against P388 murine leukemia cells, and therefore have the potential to be used as anticancer drugs. The ritterazines and cephalostatins are steroidal dimers joined by a central pyrazine ring. Given that the steroid halves are unsymmetrical and highly oxygenated, there are several challenges in synthesizing these compounds in an organic laboratory.

Ritterazine B is the most potent derivative in the ritterazine family. Its biological activity is comparable to drugs that are being used to treat cancer today. For this reason, and the fact that there are no reported syntheses of ritterazine B to date, our lab set out to synthesize this natural product.

Herein, efforts toward the synthesis of the western fragment of ritterazine B are described. Two different routes are explored to access a common intermediate. An alkyne conjugate addition reaction was initially investigated due to the success of this key reaction in the synthesis of the eastern fragment. However, it has been found that a propargylation reaction has greater reactivity and yields, and has the potential to reduce the step count of the synthesis of the western fragment of ritterazine B.

Aderência, invasão e persistência intracelular de estreptococos do grupo B em células epiteliais respiratórias A549

Estreptococos do grupo B (EGB) comumente colonizam adultos saudáveis, sem sintomas, mas sob certas circunstâncias possui a capacidade de invadir tecidos do hospedeiro, evadir da detecção imunológica e causar doenças invasivas graves. Por conseguinte, os EGB continuam sendo uma das principais causas de mortalidade neonatal, pneumonia, sepse e meningite. Contudo, a patogênese desta infecção ainda está pouco elucidada. O sorotipo V é freqüentemente associado à doença invasiva em mulheres adultas não gestantes e o segundo mais prevalente em mulheres grávidas. O principal objetivo deste trabalho foi estudar a aderência, invasão e persistência intracelular de amostras pertencentes ao sorotipo V (88641-vagina/portador e 90186-sangue/paciente) usando as células epiteliais respiratórias A549. As amostras de EGB demonstraram capacidade de aderir e invadir as células epiteliais A549, mas somente a amostra 90186-sangue apresentou maior invasão quando comparada com a de vagina (P <0.001). Ambas as amostras demonstraram persistência intracelular sem replicação no interior das células A549. Apenas o isolado 90186-sangue sobreviveu dentro das células epiteliais até 24h de incubação (P <0,05). A fusão dos lisossomas das células epiteliais com vacúolos contendo bactérias foi observada em células A549 tratadas com Lyso Tracker Grenn DND-26 para todas as amostras testadas. Nossos dados indicam pela primeira vez que as amostras viáveis do sorotipo V permanecem dentro de vacúolos ácidos epiteliais. Curiosamente, a amostra 90186- sangue induziu vacuolização celular e a amostra 88641-vagina promoveu a morte celular após 7h de incubação. Finalmente, nossos resultados aumentam o nosso conhecimento sobre eventos celulares da fagocitose e da patogênese das doenças invasivas promovidas pelos EGB.

A. An investigation of the relation between the tensile strength and (Brinell) hardness of non-ferrous alloys. B. A design of a fatigue testing machine for a college laboratory

[no abstract]

Flavor SU(3) predictions for charmed baryon and B-meson decays

The predictions of the SU(3) flavor symmetry of the strong interactions for the weak decay of charmed baryons and B-mesons are detailed. It is hoped that comparison between these predictions and experiment will shed some light on the underlying dynamics involved in these weak decays. Although only a few decay modes of the charmed baryons and B-mesons have been studied experimentally it is hoped that the next generation of B-factories and even Z-decays at LEP will provide enough events to test these predictions.

Avaliação das propriedades de barreira a gases de membranas obtidas a partir de dispersões aquosas à base de poliuretanos e argila

Materiais nanoestruturados têm recebido destaque na comunidade científica, destacando-se, dentre eles, os nanocompósitos à base de polímeros e argila. Quando esses materiais são obtidos no estado líquido, ressalta-se também o uso de água em substituição a solventes orgânicos, devido a questões ambientais. Neste trabalho foram sintetizadas dispersões aquosas à base de poliuretanos (WPUs) e argila hidrofílica do tipo montimorilonita (MMT) de natureza sódica, com o objetivo de avaliar as propriedades de barreira a gases conferidas pela presença de argila e pela variação nas proporções entre os segmentos flexíveis poli(glicol propilênico) (PPG) e o copolímero em bloco à base de poli(glicol etilênico) e poli(glicol propilênico) (EG-b-PG). Os monômeros empregados na síntese foram: poli(glicol propilênico) (PPG); copolímero em bloco à base de poli(glicol etilênico) e poli(glicol propilênico) (EG-b-PG), com teor de 7% de EG; ácido dimetilolpropiônico (DMPA), diisocianato de isoforona (IPDI) e etilenodiamina (EDA), como extensor de cadeia. Foram sintetizadas dispersões aquosas com e sem a presença de argila, fixando-se a razão entre o número de equivalentes-grama de grupos diisocianato e hidroxila (razão NCO/OH) em 1,5. Nas formulações foi variado também o teor de argila em relação à massa de prepolímero em 0,5% e 1%. Foi adicionada uma etapa de agitação adicional com dispersor Turrax em algumas formulações. A argila foi previamente deslaminada em água deionizada e incorporada à formulação na etapa da dispersão do prepolímero. As dispersões foram avaliadas, quanto ao teor de sólidos totais, tamanho médio de partícula e viscosidade aparente. Os filmes vazados a partir das dispersões foram caracterizados por espectrometria na região do infravermelho (FTIR) e permeabilidade ao CO2. A resistência térmica dos filmes foi determinada por termogravimetria (TG). Foram observadas modificações nas propriedades dos filmes obtidos com a inserção da argila e com a variação no teor de segmentos à base de poli(glicol etilênico). A inserção da argila promoveu uma melhoria na resistência térmica das membranas bem como uma redução na permeabilidade das mesmas. Foi observado um aumento na permeabilidade das membranas obtidas a partir das formulações com maior percentual de copolímero (EG-b-PG), com e sem argila.