Validation of a mutant of the pore-forming toxin sticholysin-I for the construction of proteinase-activated immunotoxins

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

Thermal behavior of residues (sludge) originated from Araraquara water and sewage treatment station

The number of the cities with canalized water and sewage treatment stations has increased lately and consequently having in mind the great concern on environment preservation and the quality of the water used by society. However, these stations are nowadays causing another kind of problem: a huge quantity of sludge as residue. Due to the implication of the residue on the environment and, consequently, to human life quality, performing of an accurate investigation about the components of such sludge, as well as the thermal stability of this residue in the environment become necessary. This paper presents a study on sludge from water and sewage treatment station, as well as the thermal characterization of residue. Such study was performed through FTIR, atomic absorption, thermoanalytical (TG/DTG, DTA) techniques, that made it possible to observe that the main components of the sludge are clay, carbonates and organic substance, presenting a low rate of metals and a unique thermal behavior since the sludge from the treatment station has a higher thermal stability.

Reuse of sand, crushed sugarcane and peanut hull-based substrates for cherry tomato cultivation

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Use of chemically modified silica with beta-diketoamine groups for separation of alpha-lactoalbumin from bovine milk whey by affinity chromatography

Silica gel surface was chemically modified with beta-diketoamine groups by reacting the silanol from the silica surface with 3-aminopropyl-triethoxysilane and 3-bromopentanedione, With this material, copper ions were adsorbed from aqueous solutions, the chemical analysis of the silica-gel-immobilized acetylacetone provided a quantity of 0.67 mmol g(-1) of organic groups attached to the support and 0.63 mmol g(-1) of copper, This material was used as a stationary phase in IMAC (immobilized metal affinity chromatography), to separate alpha-lactoalbumin from bovine milk whey, the results showed an efficient separation in the chromatographic column, the possibility of reutilization of the stationary phase was also investigated. (C) 1997 Academic Press

Fate of Some New Fungicides (Cyprodinil, Fludioxonil, Pyrimethanil, and Tebuconazole) from Vine to Wine

The fate of four new fungicides (cyprodinil, fludioxonil, pyrimethanil, and tebuconazole) from the treatment on vine to the production of wine was studied. The influence of clarifying agents (bentonite, charcoal, potassium caseinate, gelatin, and polyvinylpolypyrrolidone) on residue concentrations in wine was also studied. The fungicide residues on grapes showed different decay rates after treatment, with first-order kinetics and half-lives ranging from 8 to 57 days. Grape processing into wine caused considerable residue reduction with cyprodinil (ca. 80%), fludioxonil (ca. 70%), and tebuconazole (ca. 50%) and no reduction with pyrimethanil. The two wine-making techniques employed (with and without maceration) had the same influence on the residue concentrations in wine, except for fludioxonil which showed maximum residue reduction with vinification with maceration. Among the clarifying agents tested, only charcoal showed effective action on the elimination of residue content in wine, proving complete elimination, or almost, of fungicide residues.

Inhibitory effects of jackbean (Canavalia ensiformis L.) leaf residues on germination and vigour of crops and weeds

The effects of jackbean leaf residues incorporated in the soil on germination and seedlings growth of cucumber, radish and some weeds was examined. Trials were carried out under greenhouse conditions to (a) determine the amount of incorporated residue that is inhibitory to two test plants, (b) to determine if decomposition time changes the inhibitory levels of jackbean residues on test plants and (c) to determine the amount of residue that is inhibitory to the weed species. Jackbean leaf residues incorporated in soil at concentration of 2% or higher and allowed to decompose for a period of 0 to 2 weeks before sowing, reduced the initial growth of cucumber and radish and at different concentrations, reduced germination and growth of three weed species. These results suggest the presence of allelopathic components in Jackbean leaves that could affect seed germination and seedling development.

Effect of intercropping on yields of corn with different relative maturities and Palisadegrass

Intercropping corn (Zea mays L.) with palisadegrass [Brachiaria brizantha (Hochst. ex A. Rich) Stapf] can result in high amounts of residue and improve nutrient cycling. Long-season corn hybrids will live longer, competing with palisadegrass, which may reduce both corn and forage biomass yields. This study, conducted in the state of São Paulo, Brazil, had the objective of evaluating nutrient concentration and yield of corn hybrids with different maturity ratings as affected by intercropped palisadegrass as well as forage dry matter production. Te experimental design was randomized blocks with a factorial arrangement of eight treatments consisting of two cropping systems (corn alone and intercropped with palisadegrass) and four corn hybrids (105-, 121-, 132, and 144-d relative maturity). Compared with corn grown alone, intercropping treatments resulted in corn grain yields of 107% (105-d hybrid) to 71.7% (144-d hybrid). In the corn-alone system, the 132- and 144-d corn hybrids provided the highest corn yields (9581 and 9606 kg ha-1, respectively). Corn yield was similar between the single-crop and intercrop systems when using 105-, 121-, and 132-d hybrids. Intercropping with the 144-d hybrid reduced forage production (6619 kg ha-1) and quality of palisadegrass (86 g kg-1 of crude protein) compared with the other hybrids. Te intercropping system with the 132-d hybrid allowed both the highest corn grain (8860 kg ha-1) and palisadegrass (8256 kg ha-1) yields. Therefore, intercropping palisadegrass with the earlier (105-, 121-, and 132-d) corn hybrids is a viable option for crop-livestock integration because it did not affect either corn or palisadegrass yield. © 2013 by the American Society of Agronomy, 5585 Guilford Road, Madison, WI 53711. All rights reserved.

Processamento de farinha de resíduo de polpa de amora-preta (Rubus sp.) e avaliação de biocompostos

Pós-graduação em Biociências - FCLAS

Effectiveness of several solutions to prevent the formation of precipitate due to the interaction between sodium hypochlorite and chlorhexidine and its effect on bond strength of an epoxy-based sealer

To evaluate the effectiveness of isopropyl alcohol, saline or distilled water to prevent the precipitate formed between sodium hypochlorite (NaOCl) and chlorhexidine (CHX) and its effect on the bond strength of an epoxy-based sealer in radicular dentine. Methodology The root canals of 50 extracted human canines (n = 10) were instrumented. In G1, root canals were irrigated with 17% EDTA and 2.5% NaOCl; G2, as G1, except that 2% CHX was used as the final irrigant. In the other groups, intermediate flushes with isopropyl alcohol (G3), saline (G4) or distilled water (G5) were used between NaOCl and CHX. The specimens were submitted to SEM analysis to evaluate the presence of debris and smear layer, in the apical and cervical segments. In sequence, fifty extracted human canines were distributed into five groups (n = 10), similar to the SEM study. After root filling, the roots were sectioned transversally to obtain dentine slices, in the cervical, middle and apical thirds. The root filling was submitted to a push-out bond strength test using an electromechanical testing machine. Statistical analysis was performed using Kruskal–Wallis and Dunn's tests (α = 5%). Results All groups had similar amounts of residue precipitated on the canal walls (P > 0.05). The push-out bond strength values were similar for all groups, independently of the root third evaluated (P > 0.05). Conclusions Isopropyl alcohol, saline and distilled water failed to prevent the precipitation of residues on canal walls following the use of NaOCl and CHX. The residues did not interfere with the push-out bond strength of the root filling.

Pré-tratamento e hidrólise da casca de uva para liberação de açúcares fermentescíveis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Successful Careers in Football – Findings of a Person-Oriented Study

A successful career in football is the result of the appropriate interaction between different aspects of an individual’s life, since the various areas and phases of one’s life depend on each other. An endogenous causal relationship exists throughout a person’s entire history (Mayer, 1990). In particular, their family, work and sports career must be tuned to each other. The transition from the initial stages of education (compulsory schooling) to vocational training, which coincides with the beginning of the selection for the national youth teams, is a particularly critical phase (Wylleman, Theeboom, & Lavallee, 2004). In order to do justice to the overall life situation of a young sports talent during this transition phase, we have adopted a holistic perspective and follow Bergman, Magnusson and El-Khouri (2003) in using a person-oriented and systemic approach. In doing so, our main focus lies on the person-environment system. This overall system is made up of various subsystems, consisting of several operating factors which interact with one another. The different levels to which these operating factors are expressed lead to observable patterns, which can be summarised in the form of types. Particularly promising types can therefore be identified and the developmental process can be described. Former players on the Swiss U16 to U21 national football teams, born between 1981 and 1987 (n=159), were interviewed concerning their careers, and the operating factors school/vocational training, family support and sports environment were examined. With the help of the LICUR method (Linking of Clusters after removal of Residue) (Bergman et al., 2003), developmental types were identified which were promising in terms of achieving top performance in adulthood. A range of developmental types and anti-types emerge for the transition from the under-15 phase to the over-16 phase. One particularly promising type is observed in the over-16 phase, for which the operating factors education, family support and participation in national U16 to U18 teams have slightly above-average scores, with scores that are well above average in the sports environment.

Molecular mechanisms of protein kinase-mediated desensitization and internalization of the $\beta$-adrenergic receptor

The $\beta$-adrenergic receptor ($\beta$AR), which couples to G$\sb{\rm s}$ and activates adenylylcyclase, has been a prototype for studying the activation and desensitization of G-protein-coupled receptors. The main objective of the present study is to elucidate the molecular mechanisms of protein kinase-mediated desensitization and internalization of the $\beta$AR.^ Activation of cAPK or PKC causes a rapid desensitization of $\beta$AR stimulation of adenylylcyclase in L cells, which previous studies suggest involves the cAPK/PKC consensus phosphorylation site in the third intracellular loop of the $\beta$AR, RRSSK$\sp{263}$. To determine the role of the individual serines in the cAPK- and PKC-meditated desensitizations, wild type (WT) and mutant $\beta$ARs containing the substitutions, Ser$\sp{261} \to$ A, Ser$\sp{262} \to$ A, Ser$\sp{262} \to$ D, and Ser$\sp{261/262} \to$ A, were constructed and stably transfected into L cells. The cAPK-mediated desensitization was decreased 70-80% by the Ser$\sp{262} \to$ A, Ser$\sp{262} \to$ D, and the Ser$\sp{261/262} \to$ A mutations, but was not altered by the Ser$\sp{261} \to$ A substitution, demonstrating that Ser$\sp{262}$ was the primary site of the cAPK-induced desensitization. The PMA/PKC-induced desensitization was unaffected by either of the single serine to alanine substitutions, but was reduced 80% by the double serine to alanine substitution, suggesting that either serine was sufficient to confer the PKC-mediated desensitization. Coincident stimulation of cAPK and PKC caused an additive desensitization which was significantly reduced (80%) only by the double substitution mutation. Quantitative evaluation of the coupling efficiencies and the GTP-shift of the WT and mutant receptors demonstrated that only one of the mutants, Ser$\sp{262} \to$ A, was partially uncoupled. The Ser$\sp{262} \to$ D mutation did not significantly uncouple, demonstrating that introducing a negative charge did not appear to mimic the desensitized state of the receptor.^ To accomplish the in vivo phosphorylation of the $\beta$AR, we used two epitope-modified $\beta$ARs, hemagglutinin-tagged $\beta$AR (HA-$\beta$AR) and 6 histidine-tagged $\beta$AR (6His-$\beta$AR), for a high efficiency purification of the $\beta$AR. Neither HA-$\beta$AR nor 6His-$\beta$AR altered activation and desensitization of the $\beta$AR significantly as compared to unmodified wild type $\beta$AR. 61% recovery of ICYP-labeled $\beta$AR was obtained with Ni-NTA column chromatography.^ The truncation 354 mutant $\beta$AR(T354), lacking putative $\beta$ARK site(s), displayed a normal epinephrine stimulation of adenylylcyclase. Although 1.0 $\mu$M epinephrine induced 60% less desensitization in T354 as compared to wild type $\beta$AR, 1.0 $\mu$M epinephrine-mediated desensitization in T354 was 35% greater than PGE$\sb1$-mediated desensitization, which is essentially identical in both WT and T354. These results suggested that sequences downstream of residue 354 may play a role in homologous desensitization and that internalization may be attributed to the additional desensitization besides the cAMP mechanism in T354 $\beta$AR. (Abstract shortened by UMI.) ^

Studies on the role of BCR in Philadelphia chromosome-positive leukemias

It is well established that the chimeric Bcr-Abl oncoprotein resulting from fusing 3$\sp\prime$ ABL sequences on chromosome 9 to 5$\sp\prime$ BCR sequences on chromosome 22 is the primary cause of Philadelphia chromosome-positive (Ph$\sp1$) leukemias. Although it is clear that the cis-Bcr sequence present within Bcr-Abl is able to activate the tyrosine kinase activity and F-actin binding capacity of Bcr-Abl which is critical for the transforming ability of BCR-ABL, the biological role of normal BCR gene product (P160 BCR) remains largely unknown. The previous finding by our lab that P160 BCR forms stable complexes with Bcr-Abl oncoprotein in Ph$\sp1$-positive leukemic cells implicated P160 BCR in the pathogenesis of Ph$\sp1$-positive leukemias. Here, we demonstrated that P160 BCR physically interacts with P210 BCR-ABL and become tyrosine phosphorylated when co-expressed with P210 BCR-ABL in COS1 cells while no tyrosine phosphorylation of P160 BCR can be detected when it is expressed alone. The results suggest that P160 BCR is a target for the Bcr-Abl tyrosine kinase. Although we were unable to detect stable physical interaction between P160 BCR and P145 c-ABL (Ib) in COS1 cells overexpressing both proteins, P160 BCR was phosphorylated on tyrosine residues when co-expressed with activated tyrosine kinase of P145 c-ABL (Ib). In addition, studies of tyrosine phosphorylation of BCR deletion mutants and 2-dimensional tryptic mapping of in vitro phosphorylated wild type and mutant (tyrosine to phenylalanine) Bcr-Abl indicated that tyrosine 177, 283 and 360 of Bcr represent some of the phosphorylation sites. Even though the significance of tyrosine phosphorylation of residues 283 and 360 of Bcr has not been determined, tyrosine phosphorylation of residue 177 within Bcr-Abl has been reported to be critical for its interaction with Grb2 molecule and subsequent activation of Ras signaling pathway. Here, we further demonstrated that tyrosine 177 phosphorylated P160 BCR is also able to bind to Grb2 molecule suggesting the role of P160 BCR in the Ras signaling pathway.^ Surprisingly, using 3$\sp\prime$ BCR antisense oligonucleotide to reduce the expression of P160 BCR without interfering with the expression of BCR-ABL resulted in increased growth or survival of B15 cells and M3.16 cells expressing either P185 BCR-ABL or P210 BCR-ABL respectively. The results provided strong arguments that P160 BCR may function as a negative regulator for cell growth.^ Considering all these results, we hypothesize that P160 BCR negatively regulate cell growth and tyrosine phosphorylation of P160 BCR turns off its growth suppressor function and turns on its growth stimulatory function. We further speculate that Bcr-Abl oncoprotein in leukemia cells stably interacts with and constitutively phosphorylates portions of P160 BCR converting it into a growth stimulatory state. In normal cells, the growth suppressor effects of P160 BCR could only be transiently and conditionally switched to growth stimulatory action by a strictly regulated cellular tyrosine kinase such as c-ABL. The model will be further discussed in the text. ^

Atomic mutagenesis of the ribosomal Sarcin-Ricin-Loop to study EF-G GTPase activation

Translocation factor EF-G, possesses a low basal GTPase activity, which is stimulated by the ribosome. One potential region of the ribosome that triggers GTPase activity of EF-G is the Sarcin-Ricin-Loop (SRL) (helix 95) in domain VI of the 23S rRNA. Structural data showed that the tip of the SRL closely approaches GTP in the active center of EF-G, structural probing data confirmed that EF-G interacts with nucleotides G2655, A2660, G2661 and A2662.1-3 The exocyclic group of adenine at A2660 is required for stimulation of EF-G GTPase activity by the ribosome as demonstrated using atomic mutagenesis.4 Recent crystal structures of EF-G on the ribosome, gave more insights into the molecular mechanism of EF-G GTPase activity.5 Based on the structure of EF-Tu on the ribosome1, the following mechanism of GTPase activation was proposed: upon binding of EF-G to the ribosome, the conserved His92 (E.coli) changes its position, pointing to the γ-phosphate of GTP. In this activated state, the phosphate of residue A2662 of the SRL positions the catalytic His in its active conformation. It was further proposed that the phosphate oxygen of A2662 is involved in a charge-relay system, enabling GTP hydrolysis. In order to test this mechanism, we use the atomic mutagenesis approach, which allows introducing non-natural modifications in the SRL, in the context of the complete 70S ribosome. Therefore, we replaced one of the non-bridging oxygens of A2662 by a methyl group. A methylphosphonat is not able to position or activate a histidine, as it has no free electrons and therefore no proton acceptor function. These modified ribosomes were then tested for stimulation of EF-G GTPase activity. First experiments show that one of the two stereoisomers incorporated into ribosomes does not stimulate GTPase activity of EF-G, whereas the other is active. From this we conclude that indeed the non-bridging phosphate oxygen of A2662 is involved in EF-G GTPase activation by the ribosome. Ongoing experiments aim at revealing the contribution of this non-bridging oxygen at A2662 to the mechanism of EF-G GTPase activation at the atomic level.