Derivado cinamoílico com atividade no reparo de DNA e outras substâncias de Cinnamomum australe (Lauraceae)

The bioactive compound trans-3'-methylsulphonylallyl trans-cinnamate (1) along with the inactives iryelliptin (2) and (7R,8S,1'S)-delta8'-3',5'-dimethoxy-1',4'-dihydro-4'-oxo-7.0.2',8.1'-neolignan (3) were isolated from the leaves of Cinnamomum australe. The structures of these compounds were assigned by analysis of 1D and 2D NMR data and comparison with data registered in the literature for these compounds. The DNA-damaging activity of 1 is being described for the first time.

Câncer e agentes antineoplásicos ciclo-celular específicos e ciclo-celular não específicos que interagem com o DNA: uma introdução

The chemotherapy agents against cancer may be classified as "cell cycle-specific" or "cell cycle-nonspecific". Nevertheless, several of them have their biological activity related to any kind of action on DNA such as: antimetabolic agents (DNA synthesis inhibition), inherently reactive agents (DNA alkylating electrophilic traps for macromolecular nucleophiles from DNA through inter-strand cross-linking - ISC - alkylation) and intercalating agents (drug-DNA interactions inherent to the binding made due to the agent penetration in to the minor groove of the double helix). The earliest and perhaps most extensively studied and most heavily employed clinical anticancer agents in use today are the DNA inter-strand cross-linking agents.

The maximum voltage drop in an on-chip power distribution network: analysis of square, triangular and hexagonal power pad arrangements

A mathematical model of the voltage drop which arises in on-chip power distribution networks is used to compare the maximum voltage drop in the case of different geometric arrangements of the pads supplying power to the chip. These include the square or Manhattan power pad arrangement, which currently predominates, as well as equilateral triangular and hexagonal arrangements. In agreement with the findings in the literature and with physical and SPICE models, the equilateral triangular power pad arrangement is found to minimize the maximum voltage drop. This headline finding is a consequence of relatively simple formulas for the voltage drop, with explicit error bounds, which are established using complex analysis techniques, and elliptic functions in particular.

Lesões em DNA induzidas pela autoxidação de S(IV) na presença de íons metálicos de transição

The oxidation of sulfite catalyzed by transition metal ions produces reactive oxysulfur species that can damage plasmid and isolated DNA in vitro. Among the four DNA bases, guanine is the most sensitive to one-electron oxidation promoted by the species formed in the autoxidation of sulfite (HSO5-, HO•, SO3•-, SO4•- and SO5•-) due to its low reduction potential and ability to bind transition metal ions capable to catalyze oxidative processes. Some oxidative DNA lesions are promutagenic and oxidative DNA damage is proposed to play a crucial role in certain human pathologies, including cancer.

Reactions of Chlorambucil and its main metabolite, Phenylacetic Acid Mustard, with 2’-deoxyribonucleosides and Calf Thymus DNA

Chlorambucil is an anticancer agent used in the treatment of a variety of cancers, especially in chronic lymphocytic leukemia, and autoimmune diseases. Nevertheless, chlorambucil is potentially mutagenic, teratogenic and carcinogenic. The high antitumor activity and high toxicity of chlorambucil and its main metabolite, phenylacetic acid mustard, to normal tissues have been known for a long time. Despite this, no detailed chemical data on their reactions with biomolecules in aqueous media have been available. The aim of the work described in this thesis was to analyze reactions of chlorambucil with 2’-deoxyribonucleosides and calf thymus DNA in aqueous buffered solution, at physiological pH, and to identify and characterize all adducts by using modern analyzing methods. Our research was also focused on the reactions of phenylacetic acid mustard with 2’-deoxynucleosides under similar conditions. A review of the literature consisting of general background of nucleic acids, alkylating agents and ultraviolet spectroscopy used to identify the purine and pyrimidine nucleosides, as well as the results from experimental work are presented and discussed in this doctoral thesis.

On Fault Tolerance Methods for Networks-on-Chip

Technology scaling has proceeded into dimensions in which the reliability of manufactured devices is becoming endangered. The reliability decrease is a consequence of physical limitations, relative increase of variations, and decreasing noise margins, among others. A promising solution for bringing the reliability of circuits back to a desired level is the use of design methods which introduce tolerance against possible faults in an integrated circuit. This thesis studies and presents fault tolerance methods for network-onchip (NoC) which is a design paradigm targeted for very large systems-onchip. In a NoC resources, such as processors and memories, are connected to a communication network; comparable to the Internet. Fault tolerance in such a system can be achieved at many abstraction levels. The thesis studies the origin of faults in modern technologies and explains the classification to transient, intermittent and permanent faults. A survey of fault tolerance methods is presented to demonstrate the diversity of available methods. Networks-on-chip are approached by exploring their main design choices: the selection of a topology, routing protocol, and flow control method. Fault tolerance methods for NoCs are studied at different layers of the OSI reference model. The data link layer provides a reliable communication link over a physical channel. Error control coding is an efficient fault tolerance method especially against transient faults at this abstraction level. Error control coding methods suitable for on-chip communication are studied and their implementations presented. Error control coding loses its effectiveness in the presence of intermittent and permanent faults. Therefore, other solutions against them are presented. The introduction of spare wires and split transmissions are shown to provide good tolerance against intermittent and permanent errors and their combination to error control coding is illustrated. At the network layer positioned above the data link layer, fault tolerance can be achieved with the design of fault tolerant network topologies and routing algorithms. Both of these approaches are presented in the thesis together with realizations in the both categories. The thesis concludes that an optimal fault tolerance solution contains carefully co-designed elements from different abstraction levels

A monolithic glass chip for active single-cell sorting based on mechanical phenotyping

The mechanical properties of biological cells have long been considered as inherent markers of biological function and disease. However, the screening and active sorting of heterogeneous populations based on serial single-cell mechanical measurements has not been demonstrated. Here we present a novel monolithic glass chip for combined fluorescence detection and mechanical phenotyping using an optical stretcher. A new design and manufacturing process, involving the bonding of two asymmetrically etched glass plates, combines exact optical fiber alignment, low laser damage threshold and high imaging quality with the possibility of several microfluidic inlet and outlet channels. We show the utility of such a custombuilt optical stretcher glass chip by measuring and sorting single cells in a heterogeneous population based on their different mechanical properties and verify sorting accuracy by simultaneous fluorescence detection. This offers new possibilities of exact characterization and sorting of small populations based on rheological properties for biological and biomedical applications.

Formal Power Analysis of Systems-on-Chip

The design methods and languages targeted to modern System-on-Chip designs are facing tremendous pressure of the ever-increasing complexity, power, and speed requirements. To estimate any of these three metrics, there is a trade-off between accuracy and abstraction level of detail in which a system under design is analyzed. The more detailed the description, the more accurate the simulation will be, but, on the other hand, the more time consuming it will be. Moreover, a designer wants to make decisions as early as possible in the design flow to avoid costly design backtracking. To answer the challenges posed upon System-on-chip designs, this thesis introduces a formal, power aware framework, its development methods, and methods to constraint and analyze power consumption of the system under design. This thesis discusses on power analysis of synchronous and asynchronous systems not forgetting the communication aspects of these systems. The presented framework is built upon the Timed Action System formalism, which offer an environment to analyze and constraint the functional and temporal behavior of the system at high abstraction level. Furthermore, due to the complexity of System-on-Chip designs, the possibility to abstract unnecessary implementation details at higher abstraction levels is an essential part of the introduced design framework. With the encapsulation and abstraction techniques incorporated with the procedure based communication allows a designer to use the presented power aware framework in modeling these large scale systems. The introduced techniques also enable one to subdivide the development of communication and computation into own tasks. This property is taken into account in the power analysis part as well. Furthermore, the presented framework is developed in a way that it can be used throughout the design project. In other words, a designer is able to model and analyze systems from an abstract specification down to an implementable specification.

Combined dielectrophoretic and impedance system for on-chip controlled bacteria concentration: Application to Escherichia coli

The present paper reports a bacteria autonomous controlled concentrator prototype with a user-friendly interface for bench-top applications. It is based on a micro-fluidic lab-on-a-chip and its associated custom instrumentation, which consists in a dielectrophoretic actuator, to pre-concentrate the sample, and an impedance analyser, to measure concentrated bacteria levels. The system is composed by a single micro-fluidic chamber with interdigitated electrodes and a instrumentation with custom electronics. The prototype is supported by a real-time platform connected to a remote computer, which automatically controls the system and displays impedance data used to monitor the status of bacteria accumulation on-chip. The system automates the whole concentrating operation. Performance has been studied for controlled volumes of Escherichia coli (E. coli) samples injected into the micro-fluidic chip at constant flow rate of 10 μL/min. A media conductivity correcting protocol has been developed, as the preliminary results showed distortion of the impedance analyser measurement produced by bacterial media conductivity variations through time. With the correcting protocol, the measured impedance values were related to the quantity of bacteria concentrated with a correlation of 0.988 and a coefficient of variation of 3.1%. Feasibility of E. coli on-chip automated concentration, using the miniaturized system, has been demonstrated. Furthermore, the impedance monitoring protocol had been adjusted and optimized, to handle changes in the electrical properties of the bacteria media over time.

Plasmid DNA damage induced by singlet molecular oxygen released from the naphthalene endoperoxide DHPNO2 and photoactivated methylene blue

To investigate oxidative lesions and strand breaks induction by singlet molecular oxygen (¹O2), supercoiled-DNA plasmid was treated with thermo-dissociated DHPNO2 and photoactivated-methylene blue. DNA lesions were detected by Fpg that cleaves DNA at certain oxidized bases, and T4-endoV, which cleaves DNA at cyclobutane pyrimidine dimers and apurinic/apyrimidinic (AP) sites. These cleavages form open relaxed-DNA structures, which are discriminated from supercoiled-DNA. DHPNO2 or photoactivated-MB treatments result in similar plasmid damage profile: low number of single-strand breaks or AP-sites and high frequency of Fpg-sensitive sites; confirming that base oxidation is the main product for both reactions and that ¹O2 might be the most likely intermediate that reacts with DNA.

Electrochemical and theoretical evaluation of the interaction between dna and amodiaquine: evidence of the guanine adduct formation

The electrochemical behavior of the interaction of amodiaquine with DNA on a carbon paste electrode was studied using voltametric techniques. In an acid medium, an electroactive adduct is formed when amodiaquine interacts with DNA. The anodic peak is dependent on pH, scan rate and the concentration of the pharmaceutical. Adduct formation is irreversible in nature, and preferentially occurs by interaction of the amodiaquine with the guanine group. Theoretical calculations for optimization of geometry, and DFT analyses and on the electrostatic potential map (EPM), were used in the investigation of adduct formation between amodiaquine and DNA.

Investigação eletroquímica e calorimétrica da interação de novos agentes antitumorais biscatiônicos com DNA

Biscationic amidines bind in the DNA minor groove and present biological activity against a range of infectious diseases. Two new biscationic compounds (bis-α,ω-S-thioureido, amino and sulfide analogues) were synthesized in good yields and fully characterized, and their interaction with DNA was also investigated. Isothermal titration calorimetry (ITC) was used to measure the thermodynamic properties of binding interactions between DNA and these ligands. A double stranded calf thymus DNA immobilized on an electrode surface was used to study the possible DNA-interacting abilities of these compounds towards dsDNA in situ. A remarkable interaction of these compounds with DNA was demonstrated and their potential application as anticancer agents was furthered.

Phaeophytins from Thyrsacanthus ramosissimus Moric. with inhibitory activity on human dna topoisomerase II-α

Our study reports the extraction and isolation of a new phaeophytin derivative 15¹-hydroxy-(15¹-S)-porphyrinolactone, designated anamariaine (1) herein, isolated from the chloroform fraction of aerial parts of Thyrsacanthus ramosissimus Moric. along with the known 15¹-ethoxy-(15¹-S)-porphyrinolactone (2). These compounds were identified by usual spectroscopic methods. Both compounds were subjected to in vitro (inhibitory activity) tests by means of supercoiled DNA relaxation techniques and were shown to display inhibitory activity against human DNA topoisomerase II-α at 50 µM. Interconversion of these two pigments under the mild conditions of the isolation techniques should be highly unlikely but cannot be entirely ruled out.

Neolignans from Licaria chrysophylla and Licaria aurea with DNA topoisomerase II-α inhibitory activity

Seven natural neolignans isolated from Licaria chrysophylla and Licaria aurea along with five semisynthetic derivatives were tested for their inhibitory action on DNA-topoisomerase by relaxation assays on pBR322 plasmid DNA. All compounds tested showed strong inhibition at a concentration of 100 µM, while none showed activity between 5 and 70 µM. These results indicate that no obvious correlation can be derived between the structure of these compounds and their inhibitory effect on the DNA relaxation activity of topoisomerase II. This is the first report on DNA topoisomerase II inhibitors from Licaria chrysophylla and Licaria aurea leading to the identification of lignoids as topoisomerase II-α inhibitors.