AP-UV-MALDI mit flüssigen Matrizes: stabile Ionenausbeuten von mehrfach geladenen Peptid- und Proteinionen für die empfindliche Massenspektrometrie

In der biologischen Massenspektrometrie (MS) werden überwiegend zwei Ionisationstechniken für die Analyse von grçßeren Biomolekfürlen wie Polypeptiden eingesetzt. Dies sind die Nano-Elektrospray-Ionisation[1,2] (nanoESI) und die matrixunterstfürtzte Laserdesorption/-ionisation[3, 4] (MALDI). Beide Techniken werden als „sanft“ bezeichnet, weil sie die Desorption und Ionisation von intakten Analytmolekfürlen und damit ihre erfolgreiche massenspektrometrische Analyse erlauben. Einer der wichtigsten Unterschiede zwischen diesen beiden Ionisationstechniken liegt in ihrer F�higkeit, mehrfach geladene Ionen zu erzeugen. MALDI erzeugt typischerweise einfach geladene Peptidionen, w�hrend nano- ESI leicht mehrfach geladene Ionen produziert, sogar für Peptide mit einer Masse von weniger als 1000 Da. Die Erzeugung von hoch geladenen Ionen ist wünschenswert, da dies die Verwendung von Massenanalysatoren wie Ionenfallen (inkl. Orbitraps) und Hybrid-Quadrupolinstrumenten ermçglicht, die typischerweise nur einen begrenzten m/z- Bereich (<2000–4000) bieten. Hohe Ladungszust�nde ermçglichen auch die Aufnahme von informativeren Fragmentionenspektren, wenn Methoden wie die kollisionsinduzierte Dissoziation (CID), die Elektroneneinfang-Dissoziation (ECD) und die Elektronentransfer-Dissoziation (ETD) in Kombination mit der Tandem-MS (MS/MS) verwendet werden.

Investigation and optimization of parameters affecting the multiply charged ion yield in AP-MALDI MS

Liquid matrix-assisted laser desorption/ionization (MALDI) allows the generation of predominantly multiply charged ions in atmospheric pressure (AP) MALDI ion sources for mass spectrometry (MS) analysis. The charge state distribution of the generated ions and the efficiency of the ion source in generating such ions crucially depend on the desolvation regime of the MALDI plume after desorption in the AP-tovacuum inlet. Both high temperature and a flow regime with increased residence time of the desorbed plume in the desolvation region promote the generation of multiply charged ions. Without such measures the application of an electric ion extraction field significantly increases the ion signal intensity of singly charged species while the detection of multiply charged species is less dependent on the extraction field. In general, optimization of high temperature application facilitates the predominant formation and detection of multiply charged compared to singly charged ion species. In this study an experimental setup and optimization strategy is described for liquid AP-MALDI MS which improves the ionization effi- ciency of selected ion species up to 14 times. In combination with ion mobility separation, the method allows the detection of multiply charged peptide and protein ions for analyte solution concentrations as low as 2 fmol/lL (0.5 lL, i.e. 1 fmol, deposited on the target) with very low sample consumption in the low nL-range.

Effect of arsenic on transcription factor AP-1 and NF-kB DNA binding activity and related gene expression

Both acute (24 h) and chronic (10–20 week) exposure of human fibroblast cells to low dose sodium arsenite (As(III)) significantly affects activating protein-1 (AP-1) and nuclear factor kappa B (NF-&kappa;B) DNA binding activity. Short-term treatment with 0.1–5 μM As(III) up-regulates expression of c-Fos and c-Jun and the redox regulators, thioredoxin (Trx) and Redox factor-1 (Ref-1) and activates both AP-1 and NF-&kappa;B binding. Chronic exposure to 0.1 or 0.5 μM As(III) decreased c-Jun, c-Fos and Ref-1 protein levels and AP-1 and NF-&kappa;B binding activity, but increased Trx expression. Short term exposure to phorbol 12-myristate 13-acetate (TPA), a phorbol ester tumour promoter, or hydrogen peroxide (H₂O₂) also activates AP-1 and NF-&kappa;B binding. However, pre-treatment with As(III) prevents this increase. These results suggest that As(III) may alter AP-1 and NF-&kappa;B activity, in part, by up-regulating Trx and Ref-1. The different effects of short- versus long-term As(III) treatment on acute-phase response to oxidative stress reflect changes in the expression of Ref-1, c-Fos and c-Jun, but not Trx.

A novel mechanism of CD40-induced apoptosis of carcinoma cells involving TRAF3 and JNK/AP-1 activation

Membrane-presented CD40 agonists can induce apoptosis in carcinoma, but not normal homologous epithelial cells, whereas soluble agonists are growth inhibitory but not proapoptotic unless protein synthesis is blocked. Here we demonstrate that membrane-presented CD40 ligand (CD154) (mCD40L), but not soluble agonists, triggers cell death in malignant human urothelial cells via a direct mechanism involving rapid upregulation of TNFR-associated factor (TRAF)3 protein, without concomitant upregulation of TRAF3 mRNA, followed by activation of the c-Jun N-terminal kinase (JNK)/activator protein-1 (AP-1) pathway and induction of the caspase-9/caspase-3-associated intrinsic apoptotic machinery. TRAF3 knockdown abrogated JNK/AP-1 activation and prevented CD40-mediated apoptosis, whereas restoration of CD40 expression in CD40-negative carcinoma cells restored apoptotic susceptibility via the TRAF3/AP-1-dependent mechanism. In normal human urothelial cells, mCD40L did not trigger apoptosis, but induced rapid downregulation of TRAF2 and 3, thereby paralleling the situation in B-lymphocytes. Thus, TRAF3 stabilization, JNK activation and caspase-9 induction define a novel pathway of CD40-mediated apoptosis in carcinoma cells.

Separação caulinita-dióxido de titânio por floculação seletiva : mecanismo, seletividade e aplicação no cualim do Rio Jari (AP)

No presente trabalho, é investigado um método alternativo para remover as impurezas coloridas contidas no caulim ultrafino do Rio Jari (AP), mediante a adsorção seletiva com polímeros aquosolúveis. Apesar desse método (floculação seletiva) ser considerado inovador no tratamento de minérios ultrafinos, problemas como a alta sensibilidade do meio e o baixo rendimento, freqüentemente comprometem a sua aplicação em sistemas naturais. Nesse contexto, o presente trabalho enfatiza questões envolvendo a seletividade do processo, bem como os mecanismos e os fenômenos envolvidos na adsorção seletiva de uma das fases minerais, A caracterização do minério define o tipo de contaminante (anatásio) e as suas relações de contato com a caulinita (ausência de adesão física). Tal informação é útil na avaliação do rendimento ativo do processo. A eficiência na remoção do anatásio, frente ao ambiente específico do meio e em combinação com a intensidade de carga aniônica do polímero floculante, define a condição mais favorável em termos de adsorção e seletividade. Tal condição prevê a utilização de poliacrilamidas fracamente aniônicas em meio alcalino (pH = 10). o aumento da concentração de hexametafosfato-Na (dispersante de atividade eletrostática) provoca uma redução nos níveis de adsorção da caulinita, pelo aumento da sua carga superficial. A seletividade do processo atinge o seu nível máximo com a adição de poliacrilato-Na (dispersante que combina a atividade eletrostática com o efeito estérico). Nessas condições, remoções consideráveis de anatásio são obtidas, fazendo com que o teor de Ti02 contido no caulim caia de 1,3% para 0,2% e com que a recuperação permaneça em níveis satisfatórios (57%). o nível de adição química do meio também condiciona o grau de consistência dos flocos gerados, aumentando a cinética de sedimentação. Nos ambientes considerados altamente seletivos, a sedimentação dos flocos chega a atingir uma velocidade de 18 mm/minuto em polpa com 30% de sólidos.

O desenvolvimento da linguagem escrita em crianças consideradas "deficientes mentais", em Macapá

Com base na prática da Divisão de Educação Especial e do Sistema Educacional Público do Estado do Amapá em relaçao às crianças que anualmente ingressam neste sistema, iniciando seu processo de escolarização, procedemos a análise dos mecanismos de seleção, exclusão e permanência que se instalam, tomando como ponto de partida o sucesso ou fracasso da escola em compreender o desenvolvimento da linguagem escrita em criancas na 1a sérle do 1o grau e as consequentes implicações subjacentes às concepções adotadas sobre este processo. Fundamentando teoricamente tal análise, procede-se a discussão acerca do aparelho escolar enquanto instância de reprodução e manutenção do modo hierarquizado adotado pelo modelo capitalista de produção e a consequente aceitação desta condição como processo natural. Contrapondo o critério de legitimação da incapacidade ou "deficiência" de crianças e adolescentes das camadas populares em desenvolver de modo "regular" seu processo de construção da leitura e escrita, apresentamos as contribuições de Vygotsky, Luria e Ferreiro que tratam a questão com base na interação aluno X linguagem escrita enquanto sujeito X objeto cultural, apresentando niveis de desenvolvimento de escrita obtidos junto a crianças consideradas "normais". Partindo desta última concepção, realizou-se estudo com 16 sujeitos considerados "deficientes mentais", para obter dados a respeito dos niveis evolutivoe deste processo, a fim de identificar as possíveis semelhançase e diferenças entre os grupos "deficientes" e os realizados com " normais" . De acordo com dados obtidos observa-se que crianças consideradas "deficientes mentais, neste estudo, desenvolvem linguagem escrita em niveis semelhantes aos encontrados em crianças consideradas "normais " nos estudos realizados por Luria e Ferreiro. Os resultados servirão de suporte para repensar a proposta da Educação Eepecial em conceituar e atender "deficiência mental", bem como, da Secretaria de Educação acerca do significado de alfabetização.

Análise filogenética e funcional de dois genes de reparo homólogos a AP endonuclease em cana-de-açúcar: ScARP1 e ScARP3

The genome of all organisms constantly suffers the influence of mutagenic factors from endogenous and/or exogenous origin, which may result in damage for the genome. In order to keep the genome integrity there are different DNA repair pathway to detect and correct these lesions. In relation to the plants as being sessile organisms, they are exposed to this damage frequently. The Base Excision DNA Repair (BER) is responsible to detect and repair oxidative lesions. Previous work in sugarcane identified two sequences that were homologous to Arabidopsis thaliana: ScARP1 ScARP3. These two sequences were homologous to AP endonuclease from BER pathway. Then, the aim of this work was to characterize these two sequence using different approaches: phylogenetic analysis, in silico protein organelle localization and by Nicotiana tabacum transgenic plants with overexpression cassette. The in silico data obtained showed a duplication of this sequence in sugarcane and Poaceae probably by a WGD event. Furthermore, in silico analysis showed a new localization in nuclei for ScARP1 protein. The data obtained with transgenic plants showed a change in development and morphology. Transgenic plants had slow development when compared to plants not transformed. Then, these results allowed us to understand better the potential role of this sequence in sugarcane and in plants in general. More work is important to be done in order to confirm the protein localization and protein characterization for ScARP1 and ScARP3

STREAM-AP: um processo para sistematizar a escolha de padrões arquiteturais baseado em requisitos não-funcionais

The importance of non-functional requirements for computer systems is increasing. Satisfying these requirements requires special attention to the software architecture, since an unsuitable architecture introduces greater complexity in addition to the intrinsic complexity of the system. Some studies have shown that, despite requirements engineering and software architecture activities act on different aspects of development, they must be performed iteratively and intertwined to produce satisfactory software systems. The STREAM process presents a systematic approach to reduce the gap between requirements and architecture development, emphasizing the functional requirements, but using the non-functional requirements in an ad hoc way. However, non-functional requirements typically influence the system as a whole. Thus, the STREAM uses Architectural Patterns to refine the software architecture. These patterns are chosen by using non-functional requirements in an ad hoc way. This master thesis presents a process to improve STREAM in making the choice of architectural patterns systematic by using non-functional requirements, in order to guide the refinement of a software architecture

Caracterização de dois cDNAs homológos e uma AP endonuclease em cana-de-açúcar

The genome of all organisms is subject to injuries that can be caused by endogenous and environmental factors. If these lesions are not corrected, it can be fixed generating a mutation which can be lethal to the organisms. In order to prevent this, there are different DNA repair mechanisms. These mechanisms are well known in bacteria, yeast, human, but not in plants. Two plant models Oriza sativa and Arabidopsis thaliana had the genome sequenced and due to this some DNA repair genes have been characterized. The aim of this work is to characterized two sugarcane cDNAs that had homology to AP endonuclease: scARP1 and scARP3. In silico has been done with these two sequences and other from plants. It has been observed domain conservation on these sequences, but the cystein at 65 position that is a characteristic from the redox domain in APE1 protein was not so conservated in plants. Phylogenetic relationship showed two branches, one branch with dicots and monocots sequence and the other branch with only monocots sequences. Another approach in order to characterized these two cDNAs was to construct overexpression cassettes (sense and antisense orientation) using the 35S promoter. After that, these cassettes were transferred to the binary vector pPZP211. Furthermore, previously in the laboratory was obtained a plant from nicotiana tabacum containing the overexpression cassette in anti-sense orientation. It has been observed that this plant had a slow development and problems in setting seeds. After some manual crossing, some seeds were obtained (T2) and it was analyzed the T2 segregation. The third approach used in this work was to clone the promoter region from these two cDNAs by PCR walking. The sequences obtained were analyzed using the program PLANTCARE. It was observed in these sequences some motives that may be related to oxidative stress response

Produtividade em colônias de Polistes (Ap hanilopterus) vers icolor Olivier, 1791 (Hymenoptera: Vespidae, Polis tinae)

From August 2000 to December 2003, 185 colonies of Polistes versicolor were observed at the Bioterio of the Instituto de Biociencias, UNESP, Campus de Rio Claro, SP. In 144 colonies (77,84%) didn't emerge wasps, and of others 41 (22,16%), in 16 it was not possible to obtain the number of meconia, because they were attacked in several degrees of injury by natural enemies such as, ants, birds and parasitic wasps. The colonies productivity was measured through the meconia count in the cells of 25 colonies, which ranged from 1 to 6 meconia by cell.

THE USE OF AMPPD AS AN ALTERNATIVE SUBSTRATE FOR AP-MEDIATED DETECTION OF NONRADIOLABELED DNA PROBES IN EUCALYPTUS-SALIGNA

We present a non-radioactive alternative to Southern's (J. Mol. Biol. 98: 503-517, 1975) DNA-DNA hybridization technique. The use of AMPPD - Disodium 3-(4-Methoxyspiro {1,2-dioxetane-3,2'tricyclo[3.3.1.1(3,7)]decan}-4-yl)phyenyl phosphate as an alternative substrate for AP-mediated detection of digoxigenin-11 dUTP-labeled probes made possible the simple and nonhazardous reuse of blots. We used 0.8 % agarose gels containing 30 mug per lane of Eucalyptus saligna DNA, digested with Eco RI, electrophoresed and blotted on to nylon membranes (Hybond-N, Amersham, UK), using the Southern blotting procedure, and UV irradiated for one minute for DNA fixation. The hybridizations were carried out overnight with digoxigenin labeled random inserts of E. saligna DNA by using the Genius Kit (Boehringer Mannheim). Detection of the DNA-DNA hybrids was performed in the presence of 0.5% blocking agent and the substrates NBT/BCIP were replaced by 0.26 mM AMPPD in the final alkaline assay buffer (50 mul/cm2). After membrane incubation for five minutes at room temperature in a sealed plastic bag, the AMPPD solution was retrieved and stored at 4-degrees-C for reuse. A Kodak X-BRAF QA-S film was pressed firmly onto the bag containing the wet membrane, exposed for two to six hours and then developed. After use, the probes were stripped off and the blots reutilized, three times so far, with the same results.