Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: A possible advantage of DNA over RNA as genomic material

Heteroduplex joints are general intermediates of homologous genetic recombination in DNA genomes. A heteroduplex joint is formed between a single-stranded region (or tail), derived from a cleaved parental double-stranded DNA, and homologous regions in another parental double-stranded DNA, in a reaction mediated by the RecA/Rad51-family of proteins. In this reaction, a RecA/Rad51-family protein first forms a filamentous complex with the single-stranded DNA, and then interacts with the double-stranded DNA in a search for homology. Studies of the three-dimensional structures of single-stranded DNA bound either to Escherichia coli RecA or Saccharomyces cerevisiae Rad51 have revealed a novel extended DNA structure. This structure contains a hydrophobic interaction between the 2′ methylene moiety of each deoxyribose and the aromatic ring of the following base, which allows bases to rotate horizontally through the interconversion of sugar puckers. This base rotation explains the mechanism of the homology search and base-pair switch between double-stranded and single-stranded DNA during the formation of heteroduplex joints. The pivotal role of the 2′ methylene-base interaction in the heteroduplex joint formation is supported by comparing the recombination of RNA genomes with that of DNA genomes. Some simple organisms with DNA genomes induce homologous recombination when they encounter conditions that are unfavorable for their survival. The extended DNA structure confers a dynamic property on the otherwise chemically and genetically stable double-stranded DNA, enabling gene segment rearrangements without disturbing the coding frame (i.e., protein-segment shuffling). These properties may give an extensive evolutionary advantage to DNA.

Large-scale dynamic hydrofracturing, healing and fracture network characterization

Permeability of a rock is a dynamic property that varies spatially and temporally. Fractures provide the most efficient channels for fluid flow and thus directly contribute to the permeability of the system. Fractures usually form as a result of a combination of tectonic stresses, gravity (i.e. lithostatic pressure) and fluid pressures. High pressure gradients alone can cause fracturing, the process which is termed as hydrofracturing that can determine caprock (seal) stability or reservoir integrity. Fluids also transport mass and heat, and are responsible for the formation of veins by precipitating minerals within open fractures. Veining (healing) thus directly influences the rock’s permeability. Upon deformation these closed factures (veins) can refracture and the cycle starts again. This fracturing-healing-refacturing cycle is a fundamental part in studying the deformation dynamics and permeability evolution of rock systems. This is generally accompanied by fracture network characterization focusing on network topology that determines network connectivity. Fracture characterization allows to acquire quantitative and qualitative data on fractures and forms an important part of reservoir modeling. This thesis highlights the importance of fracture-healing and veins’ mechanical properties on the deformation dynamics. It shows that permeability varies spatially and temporally, and that healed systems (veined rocks) should not be treated as fractured systems (rocks without veins). Field observations also demonstrate the influence of contrasting mechanical properties, in addition to the complexities of vein microstructures that can form in low-porosity and permeability layered sequences. The thesis also presents graph theory as a characterization method to obtain statistical measures on evolving network connectivity. It also proposes what measures a good reservoir should have to exhibit potentially large permeability and robustness against healing. The results presented in the thesis can have applications for hydrocarbon and geothermal reservoir exploration, mining industry, underground waste disposal, CO2 injection or groundwater modeling.

Resistência ao Cisalhamento de um Latossolo sob Diferentes uso e Manejo

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Experimental damage detection using system norms

Nowadays there is great interest in structural damage detection in systems using nondestructive tests. Once the failure is detected, as for instance a crack, it is possible to take providences. There are several different approaches that can be used to obtain information about the existence, location and extension of the fault in the system by non-destructive tests. Among these methodologies, one can mention different optimization techniques, as for instance classical methods, genetic algorithms, neural networks, etc. Most of these techniques, which are based on element-byelement adjustments of a finite element (FE) model, take advantage of the dynamic behavior of the model. However, in practical situations, usually, is almost impossible to obtain an accuracy model. In this paper, it is proposed an experimental technique for damage location. This technique is based on H: norm to obtain the damage location. The dynamic properties of the structure were identified using experimental data by eigensystem realization algorithm (ERA). The experimental test was carried out in a beam structure through varying the mass of an element. For the output signal was used a piezoelectric sensor. The signal of input of sine form was generated through SignalCalc® software.

Calling behavior and parasite intensity in Treefrogs, Hypsiboas prasinus

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Desenvolvimento e avaliação de equipamentos e metodologia para determinação de parâmetros físicos do solo relacionados a dias trabalháveis com máquinas agrícolas

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Análise dinâmica em vigas compostas com amortecimento utilizando o método dos elementos espectrais e elementos finitos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

COMPRESSION BEHAVIOR AT HIGH STRAIN RATE FOR AN ULTRA HIGH PERFORMANCE CONCRETE

The need for a stronger and more durable building material is becoming more important as the structural engineering field expands and challenges the behavioral limits of current materials. One of the demands for stronger material is rooted in the effects that dynamic loading has on a structure. High strain rates on the order of 101 s-1 to 103 s-1, though a small part of the overall types of loading that occur anywhere between 10-8 s-1 to 104 s-1 and at any point in a structures life, have very important effects when considering dynamic loading on a structure. High strain rates such as these can cause the material and structure to behave differently than at slower strain rates, which necessitates the need for the testing of materials under such loading to understand its behavior. Ultra high performance concrete (UHPC), a relatively new material in the U.S. construction industry, exhibits many enhanced strength and durability properties compared to the standard normal strength concrete. However, the use of this material for high strain rate applications requires an understanding of UHPC’s dynamic properties under corresponding loads. One such dynamic property is the increase in compressive strength under high strain rate load conditions, quantified as the dynamic increase factor (DIF). This factor allows a designer to relate the dynamic compressive strength back to the static compressive strength, which generally is a well-established property. Previous research establishes the relationships for the concept of DIF in design. The generally accepted methodology for obtaining high strain rates to study the enhanced behavior of compressive material strength is the split Hopkinson pressure bar (SHPB). In this research, 83 Cor-Tuf UHPC specimens were tested in dynamic compression using a SHPB at Michigan Technological University. The specimens were separated into two categories: ambient cured and thermally treated, with aspect ratios of 0.5:1, 1:1, and 2:1 within each category. There was statistically no significant difference in mean DIF for the aspect ratios and cure regimes that were considered in this study. DIF’s ranged from 1.85 to 2.09. Failure modes were observed to be mostly Type 2, Type 4, or combinations thereof for all specimen aspect ratios when classified according to ASTM C39 fracture pattern guidelines. The Comite Euro-International du Beton (CEB) model for DIF versus strain rate does not accurately predict the DIF for UHPC data gathered in this study. Additionally, a measurement system analysis was conducted to observe variance within the measurement system and a general linear model analysis was performed to examine the interaction and main effects that aspect ratio, cannon pressure, and cure method have on the maximum dynamic stress.

Occurrence and Function of Hoogsteen Base Pairs in Nucleic Acids

Nucleic acids (DNA and RNA) play essential roles in the central dogma of biology for the storage and transfer of genetic information. The unique chemical and conformational structures of nucleic acids – the double helix composed of complementary Watson-Crick base pairs, provide the structural basis to carry out their biological functions. DNA double helix can dynamically accommodate Watson-Crick and Hoogsteen base-pairing, in which the purine base is flipped by ~180° degrees to adopt syn rather than anti conformation as in Watson-Crick base pairs. There is growing evidence that Hoogsteen base pairs play important roles in DNA replication, recognition, damage or mispair accommodation and repair. Here, we constructed a database for existing Hoogsteen base pairs in DNA duplexes by a structure-based survey from the Protein Data Bank, and structural analyses based on the resulted Hoogsteen structures revealed that Hoogsteen base pairs occur in a wide variety of biological contexts and can induce DNA kinking towards the major groove. As there were documented difficulties in modeling Hoogsteen or Watson-Crick by crystallography, we collaborated with the Richardsons’ lab and identified potential Hoogsteen base pairs that were mis-modeled as Watson-Crick base pairs which suggested that Hoogsteen can be more prevalent than it was thought to be. We developed solution NMR method combined with the site-specific isotope labeling to characterize the formation of, or conformational exchange with Hoogsteen base pairs in large DNA-protein complexes under solution conditions, in the absence of the crystal packing force. We showed that there are enhanced chemical exchange, potentially between Watson-Crick and Hoogsteen, at a sharp kink site in the complex formed by DNA and the Integration Host Factor protein. In stark contrast to B-form DNA, we found that Hoogsteen base pairs are strongly disfavored in A-form RNA duplex. Chemical modifications N1-methyl adenosine and N1-methyl guanosine that block Watson-Crick base-pairing, can be absorbed as Hoogsteen base pairs in DNA, but rather potently destabilized A-form RNA and caused helix melting. The intrinsic instability of Hoogsteen base pairs in A-form RNA endows the N1-methylation as a functioning post-transcriptional modification that was known to facilitate RNA folding, translation and potentially play roles in the epitranscriptome. On the other hand, the dynamic property of DNA that can accommodate Hoogsteen base pairs could be critical to maintaining the genome stability.

Nuclear relaxation contribution to static and dynamic (infinite frequency approximation) nonlinear optical properties by means of electrical property expansions: Application to HF, CH4, CF4, and SF6

Electrical property derivative expressions are presented for the nuclear relaxation contribution to static and dynamic (infinite frequency approximation) nonlinear optical properties. For CF4 and SF6, as opposed to HF and CH4, a term that is quadratic in the vibrational anharmonicity (and not previously evaluated for any molecule) makes an important contribution to the static second vibrational hyperpolarizability of CF4 and SF6. A comparison between calculated and experimental values for the difference between the (anisotropic) Kerr effect and electric field induced second-harmonic generation shows that, at the Hartree-Fock level, the nuclear relaxation/infinite frequency approximation gives the correct trend (in the series CH4, CF4, SF6) but is of the order of 50% too small

Nuclear relaxation contribution to static and dynamic (infinite frequency approximation) nonlinear optical properties by means of electrical property expansions: Application to HF, CH4, CF4, and SF6

Electrical property derivative expressions are presented for the nuclear relaxation contribution to static and dynamic (infinite frequency approximation) nonlinear optical properties. For CF4 and SF6, as opposed to HF and CH4, a term that is quadratic in the vibrational anharmonicity (and not previously evaluated for any molecule) makes an important contribution to the static second vibrational hyperpolarizability of CF4 and SF6. A comparison between calculated and experimental values for the difference between the (anisotropic) Kerr effect and electric field induced second-harmonic generation shows that, at the Hartree-Fock level, the nuclear relaxation/infinite frequency approximation gives the correct trend (in the series CH4, CF4, SF6) but is of the order of 50% too small

Constructing good deals in discrete time arbitrage-free dynamic pricing models

Recent literature has proved that many classical pricing models (Black and Scholes, Heston, etc.) and risk measures (V aR, CV aR, etc.) may lead to “pathological meaningless situations”, since traders can build sequences of portfolios whose risk leveltends to −infinity and whose expected return tends to +infinity, i.e., (risk = −infinity, return = +infinity). Such a sequence of strategies may be called “good deal”. This paper focuses on the risk measures V aR and CV aR and analyzes this caveat in a discrete time complete pricing model. Under quite general conditions the explicit expression of a good deal is given, and its sensitivity with respect to some possible measurement errors is provided too. We point out that a critical property is the absence of short sales. In such a case we first construct a “shadow riskless asset” (SRA) without short sales and then the good deal is given by borrowing more and more money so as to invest in the SRA. It is also shown that the SRA is interested by itself, even if there are short selling restrictions.

Residential property loans and performance during property price booms: evidence from European banks

Understanding the performance of banks is of the utmost relevance, because of the impact of this sector on economic growth and financial stability. Of all the different assets that make up a bank portfolio, the residential mortgage loans constitute one of its main. Using the dynamic panel data method, we analyse the influence of residential mortgage loans on bank profitability and risk, using a sample of 555 banks in the European Union (EU-15), over the period from 1995 to 2008. We find that banks with larger weights of residential mortgage loans show lower credit risk in good times. This result explains why banks rush to lend on property during booms due to the positive effects it has on credit risk. The results show further that credit risk and profitability are lower during the upturn in the residential property price cycle. The results also reveal the existence of a non-linear relationship (U-shaped marginal effect), as a function of bank’s risk, between profitability and the residential mortgage loans exposure. For those banks that have high credit risk, a large exposure of residential mortgage loans is associated with higher risk-adjusted profitability, through lower risk. For banks with a moderate/low credit risk, the effects of higher residential mortgage loan exposure on its risk-adjusted profitability are also positive or marginally positive.

Residential property loans and performance during property price booms: evidence from European

Understanding the performance of banks is of the u tmost importance due to the impact the sector may have on economic growth and financial stability. Residential mortgage loans constitute a large proportion of the portfolio of many banks and are one of the key assets in the determination of performance. Using a dynamic panel model , we analyse the impact of res idential mortgage loans on bank profitability and risk , based on a sample of 555 banks in the European Union ( EU - 15 ) , over the period from 1995 to 2008. We find that banks with larger weight s in residential mortgage loans display lower credit risk in good market conditions . This result may explain why banks rush to lend on property during b ooms due to the positive effect it has on credit risk . The results also show that credit risk and profitability are lower during the upturn in the residential property cy cle. Furthermore, t he results reveal the existence of a non - linear relationship ( U - shaped marginal effect), as a function of bank’s risk, between profitability and residential mortgage exposure . For those banks that have high er credit risk, a large exposur e to residential loans is associated with increased risk - adjusted profitability, through a reduction in risk. For banks with a moderate to low credit risk, the impact of higher exposure are also positive on risk - adjusted profitability.