Structure-Based, Rational Design of T Cell Receptors.

Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce T cell receptor (TCR) modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction with peptides (p) bound to major histocompatibility complexes (MHC). Using the well-characterized 2C TCR/SIYR/H-2K(b) structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157-165 cancer-testis epitope. Fifty-four percent of the designed sequence replacements exhibited improved pMHC binding as compared to the native TCR, with up to 150-fold increase in affinity, while preserving specificity. Genetically engineered CD8(+) T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity, K D = ∼1 - 5 μM. Beyond the affinity threshold at K D < 1 μM we observed an attenuation in cellular function, in line with the "half-life" model of T cell activation. Our computer-aided protein-engineering approach requires the 3D-structure of the TCR-pMHC complex of interest, which can be obtained from X-ray crystallography. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes when experimental data is not available. Since the accuracy of the models depends on the prediction of the TCR orientation over pMHC, we have complemented the approach with a simplified rigid method to predict this orientation and successfully assessed it using all non-redundant TCR-pMHC crystal structures available. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of stage IV melanoma.

Speciation and Bioavailability Measurements of Environmental Plutonium Using Diffusion in Thin Films.

The biological uptake of plutonium (Pu) in aquatic ecosystems is of particular concern since it is an alpha-particle emitter with long half-life which can potentially contribute to the exposure of biota and humans. The diffusive gradients in thin films technique is introduced here for in-situ measurements of Pu bioavailability and speciation. A diffusion cell constructed for laboratory experiments with Pu and the newly developed protocol make it possible to simulate the environmental behavior of Pu in model solutions of various chemical compositions. Adjustment of the oxidation states to Pu(IV) and Pu(V) described in this protocol is essential in order to investigate the complex redox chemistry of plutonium in the environment. The calibration of this technique and the results obtained in the laboratory experiments enable to develop a specific DGT device for in-situ Pu measurements in freshwaters. Accelerator-based mass-spectrometry measurements of Pu accumulated by DGTs in a karst spring allowed determining the bioavailability of Pu in a mineral freshwater environment. Application of this protocol for Pu measurements using DGT devices has a large potential to improve our understanding of the speciation and the biological transfer of Pu in aquatic ecosystems.

Método Melhorado para Calcular a Leitura Infinita de Cinéticas de Primeira Ordem

Infinity readings for first order kinetics can be calculated from any three measurements (triads) of a physical property l at three equallyspaced times. Accurate results can be obtained from time intervals aslow as 0.4 half-life. Calculation of infinity readings l¥ from severaltriads at increasing values of time gives an insight into the deviation of the first order kinetics when parallel, consecutive or other spurious reactions occur along with the main first order reaction, not allowing direct measurements or calculation of l¥. The proposed method is more sensitive in distinguishing between first and second order kinetics than the Guggenheim and Kezdy-Swinbourne methods.

A contaminação dos oceanos por radionuclídeos antropogênicos

Several hundreds of artificial radionuclides are produced as the result of human activities, such as the applications of nuclear reactors and particle accelerators, testing of nuclear weapons and nuclear accidents. Many of these radionuclides are short-lived and decay quickly after their production, but some of them are longer-lived and are released into the environment. From the radiological point of view the most important radionuclides are cesium-137, strontium-90 and plutonium-239, due to their chemical and nuclear characteristics. The two first radioisotopes present long half life (30 and 28 years), high fission yields and chemical behaviour similar to potassium and calcium, respectively. No stable element exists for plutonium-239, that presents high radiotoxicity, long half-life (24000 years) and some marine organisms accumulate plutonium at high levels. The radionuclides introduced into marine environment undergo various physical, chemical and biological processes taking place in the sea. These processes may be due to physical dispersion or complicated chemical and biological interactions of the radionuclides with inorganic and organic suspend matter, variety of living organisms, bottom sediments, etc. The behaviour of radionuclides in the sea depends primarily on their chemical properties, but it may also be influenced by properties of interacting matrices and other environmental factors. The major route of radiation exposure of man to artificial radionuclides occuring in the marine environment is through ingestion of radiologically contamined marine organisms. This paper summarizes the main sources of contamination in the marine environment and presents an overview covering the oceanic distribution of anthropogenic radionuclides in the FAO regions. A great number of measurements of artificial radionuclides have been carried out on various marine environmental samples in different oceans over the world, being cesium-137 the most widely measured radionuclide. Radionuclide concentrations vary from region to region, according to the specific sources of contamination. In some regions, such as the Irish Sea, the Baltic Sea and the Black Sea, the concentrations depend on the inputs due to discharges from reprocessing facilities and from Chernobyl accident. In Brazil, the artificial radioactivity is low and corresponds to typical deposition values due to fallout for the Southern Hemisphere.

Another Look at the Null of Stationary Real Exchange Rates: Panel Data with Structural Breaks and Cross-section Dependence

This paper re-examines the null of stationary of real exchange rate for a panel of seventeen OECD developed countries during the post-Bretton Woods era. Our analysis simultaneously considers both the presence of cross-section dependence and multiple structural breaks that have not received much attention in previous panel methods of long-run PPP. Empirical results indicate that there is little evidence in favor of PPP hypothesis when the analysis does not account for structural breaks. This conclusion is reversed when structural breaks are considered in computation of the panel statistics. We also compute point estimates of half-life separately for idiosyncratic and common factor components and find that it is always below one year.

Efeito do polietilenoglicol e da albumina na imobilização de lipase microbiana e na catálise em meio orgânico

Poly (ethylene) glycol (PEG) and bovine serum albumin (BSA), as additive agents, were used to enhance the activity of immobilized microbial lipase in organic solvent. Controlled pore silica (CPS) was selected as matrix and different immobilization procedures were evaluated: directly lipase binding on CPS and simultaneous addition of lipase and additive agent on the same support. The highest coupling yield (59.6%) was attained when the immobilization procedure was performed at lipase loading of 150 U/g support in the presence of PEG-1.500. This immobilized system was used in esterification reactions under repeated batch cycles and the biocatalyst half-life was found to increase 2.7 times when compared with the control.

Sorção e persistência da sorgoleona em um Latossolo Vermelho-Amarelo

The root exudates produced by sorghum contain a biologically active constituent known as sorgoleone. The behavior of sorgoleone in a Red-Yellow Latosol was studied. The sorption model of sorgoleone in soil was better adjusted to the Freundlich equation, through the coefficients Kf (capacity of sorption) and 1/n (linearity of the isotherm). The persistence of sorgoleone in soil and its possible degradation were also evaluated by monitoring their residues in the soil along the time. Recovery rate of sorgoleone from the soil reached 93% after 24h. It was verified that sorgoleone is strongly sorbed in the soil and its half-life is 10 days, under the experimental conditions. The presence of sorgoleone or its metabolites was not detected in the soil after 60 days.

Comparação do desempenho da lipase de candida rugosa imobilizada em suporte híbrido de polissiloxano-polivinilálcool empregando diferentes metodologias

The efficiency for immobilizing microbial Candida rugosa lipase on a hybrid matrix of polysiloxane polyvinyl alcohol, by adsorption, covalent coupling and encapsulation was compared. The activities of immobilized derivatives were evaluated using p-nitrophenylpalmitate (hydrolysis) and butyric acid and butanol (esterification) as substrates. Operational stability and storage tests were also performed. Among the procedures tested, the proposed matrix was efficient for immobilizing C. rugosa lipase by adsorption and covalent coupling techniques and unsuitable for encapsulation purposes. The results reveal that better catalytic properties in both aqueous and organic media were demonstrated by the covalent coupling POS-PVA immobilized lipase, including also satisfactory half-life and good storage stability.

Differential Regulation of c-FLIP Isoforms Through Post-translational Modifications

Cells are constantly responding to signals from the surrounding tissues and the environment. To dispose of infected and potentially dangerous cells, to ensure the optimal execution of developmental processes and to maintain tissue homeostasis, a multicellular organism needs to tightly control both the number and the quality of its cells. Apoptosis is a form of active cellular self-destruction that enables an organism to regulate its cell number by deleting damaged or potentially dangerous cells. Apoptosis can be induced by death ligands, which bind to death receptors on the cell surface. Ligation of the receptors leads to the formation of an intracellular death inducing signaling complex (DISC). One of the DISC components is caspase-8, a protease that triggers the caspase cascade and is thereby a key initiator of programmed cell death. The activation of caspase-8 is controlled by the cellular FLICE-inhibitory proteins (c-FLIPs). Consequently, sensitivity towards receptor-mediated apoptosis is determined by the amount of c-FLIP, and the c-FLIP levels are actively regulated for example during erythroid differentiation of K562 erythroleukemia cells and by hyperthermia in Jurkat leukemia cells. The aim of my thesis was to investigate how c-FLIP is regulated during these processes. We found that c-FLIP isoforms are short-lived proteins, although c-FLIPS had an even shorter half-life than c-FLIPL. In both experimental models, increased death receptor sensitivity correlated with induced ubiquitylation and consequent proteasomal degradation of c-FLIP. Furthermore, we elucidated how phosphorylation regulates the biological functions and the turnover of c-FLIP, thereby contributing to death receptor sensitivity. We mapped the first phosphorylation sites on c-FLIP and dissected how their phosphorylation affects c-FLIP. Moreover, we demonstrated that phosphorylation of serine 193, a phosphorylated residue common to all c-FLIPs, is primarily mediated by the classical PKC. Furthermore, we discovered a novel connection between the phosphorylation and ubiquitylation of c-FLIP: phosphorylation of S193 protects c-FLIP from ubiquitylation. Surprisingly, although all c-FLIP isoforms are phosphorylated on this conserved residue, the biological outcome is different for the long and short isoforms, since S193 specifically prolongs the half-lives of the short c-FLIP isoforms, but not c-FLIPL. To summarize, we show that c-FLIP proteins are modified by ubiquitylation and phosphorylation, and that the biological outcomes of these modifications are isoform-specifically determined.

Comportamento do herbicida hexazinone em área de recarga do aqüífero Guarani cultivada com cana-de-açúcar

São Paulo state (Brazil) has an important area of sugarcane production, mainly for obtaining alcohol and sugar, where there is an intensive use of pesticides. An important recharge zone of Guarani aquifer, with supplies water for the local population, is located at Ribeirão Preto city, so the local behavior of pesticides must be investigated. The GUS index was obtained by using the paramenters Koc and half-life for hezazinone herbicide, determinated in representative soil of this region. This study has demonstrated that there is potential risks of hexazinone leaching to ground water, indicating that this herbicide must be monitored in ground water.

Perfil espacial e temporal de poluentes nas águas da represa municipal de São José do Rio Preto, São Paulo, Brasil

In this manuscript, seasonal and spatial trends of water collected from two sampling places in the Preto River in the Turvo-Grande watershed were evaluated. Water samples were collected during June/07 to July/08 and parameters sulphate, total organic carbon, ammonia, conductivity, dissolved oxygen, temperature, dissolved total solids and nitrate were quantified. Seasonal trend indicated sanitary effluents as a point source of contamination in both sampling points. Vertical trends demonstrated that the Municipal Dam was not stratified and received a diffuse source of pollutants from flooding and agriculture runoffs. It was also verified that there is relatively fast ammonia consumption kinetics having a half-life time of 1.43 h which can explain the low ammonia concentrations found in these aquatic bodies.

Imobilização de lipase por encapsulação em sílica aerogel

Lipase from Burkholderia cepacia was immobilized in a silica matrix and dried in high pressure carbon dioxide media (aerogel). The protic ionic liquid (PIL) was used in the immobilization process by encapsulation. The objective of this work was to evaluate the influence of the drying technique using supercritical carbon dioxide in biocatalysts obtained through the sol-gel technique by evaluating temperature and pressure and, after selecting the best drying conditions, to investigate the application of the technique for the biocatalyst using ionic liquid as an additive in the immobilization process. The results for immobilized biocatalysts showed that the best conditions of pressure and temperature were 100 bar and 25 ºC, respectively, giving a total activity recovery yield of 37.27% without PIL (EN) and 44.23% with PIL (ENLI). The operational stability of the biocatalysts showed a half-life of 11.4 h for ENLI and 6 h for EN. Therefore, solvent extraction using supercritical CO2, besides shortening drying time, offers little resistance to the immobilization of lipases, since their macropores provide ample room for their molecules. The use of the ionic liquid as an additive in the process studied for the immobilization of enzymes produced attractive yields for immobilization and therefore has potential for industrial applications in the hydrolysis of vegetable oils.

The Role of Cytochrome P450 3A Inducers and Inhibitors in the Metabolism and the Effects of Oxycodone

Oxycodone is an opioid used in the treatment of moderate or severe pain. It is principally metabolized in the liver by cytochrome P450 3A (CYP3A) enzymes whereas approximately 10% is metabolized by CYP2D6. Little is known about the interactions between oxycodone and other drugs, herbals and nutritional substances. In this work the effects of CYP3A inducers rifampicin and St. John’s wort and CYP3A inhibitors voriconazole, grapefruit juice, ritonavir and lopinavir/ritonavir were investigated on the pharmacokinetics and pharmacodynamics of oxycodone. All studies were randomized, balanced, placebo-controlled crossover clinical studies in healthy volunteers. The plasma concentrations of oxycodone and its metabolites were determined for 48 hours and pharmacodynamic parameters were recorded for 12 hours in each study. Pharmacokinetic parameters were calculated by noncompartmental methods. Rifampicin decreased the plasma concentrations, analgesic effects, and oral bioavailability of oral oxycodone. St. John’s wort reduced the concentrations of oxycodone and diminished the self-reported drug effect. Voriconazole increased the exposure to oral oxycodone by 3.6-fold whereas grapefruit juice, which inhibits predominantly the intestinal CYP3A, elevated the mean concentrations of oxycodone by 1.7-fold. Ritonavir and lopinavir/ritonavir increased the mean AUC of oxycodone by 3.0- and 2.6-fold, respectively, and prolonged its elimination half-life. In spite of increased oxycodone plasma concentrations during concomitant administration of CYP3A inhibitors, the analgesic effects were not increased. These studies show that the induction or inhibition of CYP3A alters the pharmacokinetics and pharmacologic effects of oxycodone. The exposure to oxycodone decreased after induction and increased after inhibition of CYP3A. As a conclusion, the clinicians should avoid concomitant administration of CYP3A inducers or inhibitors and oral oxycodone. If this is not possible, they should be prepared to interactions leading to impaired analgesia after CYP3A inducers or increased adverse effects after CYP3A inhibitors and oral oxycodone.

Observations on the Pharmacokinetics and Pharmacodynamics of Dexmedetomidine. Clinical Studies on Healthy Volunteers and Intensive Care Patients

Patients treated in intensive care units require sedation and analgesia. However, sedative drugs also have potential adverse effects, and there is no single ideal sedativeanalgesic drug for these patients. Dexmedetomidine is an apha2-adrenoceptor agonist licenced for sedation of intensive care patients and patients undergoing surgery and other invasive procedures. Several routes of parenteral administration (intravenous, intramuscular, subcutaneous and intranasal) have been utilized. In the present series of studies, the pharmacokinetics and pharmacodynamics of intranasally administered dexmedetomidine as well as the gastrointestinal effects of intravenous dexmedetomidine were determined in healthy volunteers. Pharmacokinetics of dexmedetomidine during long lasting, high-dose infusions were characterized in intensive care patients. The bioavailability of intranasal dexmedetomidine was relatively good (65%), but interindividual variation was large. Dexmedetomidine significantly inhibited gastric emptying and gastrointestinal transit. In intensive care patients, the elimination half-life of dexmedetomidine was somewhat longer than reported for infusions of shorter duration and in less ill patients or healthy volunteers. Dexmedetomidine appeared to have linear pharmacokinetics up to the studied dose rate of 2.5 μg/kg/h. Dexmedetomidine clearance was decreasing with age and its volume of distribution was increased in hypoalbuminaemic patients, resulting in a longer elimination half-life and context-sensitive half-time. Intranasally administered dexmedetomidine was efficacious and well tolerated, making it appropriate for clinical situations requiring light sedation. The clinical significance of the gastrointestinal inhibitory effects of dexmedetomidine should be further evaluated in intensive care patients. The possibility of potentially altered potency and effect duration should be taken into account when administering dexmedetomidine to elderly or hypoalbuminaemic patients.

Decomposition kinetics of gaseous ozone in peanuts

This study was conducted to evaluate the decomposition kinetics of gaseous ozone in peanut grains. This evaluation was made with 1-kg peanut samples, moisture contents being 7.1 and 10.5% wet basis (w.b.), placed in 3-liter glass containers. The peanut grains were ozonated at the concentration of 450 µg L-1, at 25 and 35 ºC, with gas flow rates of 1.0 and 3.0 L min-1. Time of saturation was determined by quantifying the residual concentration of ozone after the gas passed through the grains to constant mass. The decomposition kinetics of ozone was evaluated after the grain mass was ozone-saturated. For the peanut grains whose moisture content was 7.1% (w.b.), at 25 and 35ºC and with flow rates of 1.0 and 3.0 L min-1, the values obtained for time of saturation of gaseous ozone ranged between 173 and 192 min; the concentration of saturation was approximately 260 µg L-1. For the grains whose moisture content was 10.5% (w.b.), a higher residual concentration of gaseous ozone was obtained at 25 ºC, that of 190 µg L-1. As regards the half-life of ozone, the highest value obtained was equivalent to 7.7 min for grains ozonated at 25 ºC, while for those with moisture content of 10.5% at 35 ºC, half-life was 3.2 min. In the process of ozone decomposition in peanut grains, temperature was concluded to be the key factor. An increase of 10 ºC in the temperature of the grains results in a decrease of at least 43% in the half-life of ozone.