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The left-handed double helical nucleic acids.: Acta Biochim Pol, Vol. 48, No. 2. (2001), pp. 295-312.The conversion of right-handed dsDNA and dsRNA to the left-handed Z-conformation involves a reorganization of the nucleotides relative to each other. This conversion can be facilitated by the tight binding of a Z-conformation -specific protein domain from the editing enzyme dsRNA adenosine deaminase. This may influence the modification of both pre-mRNAs as well as some replicating RNA viruses.BA Brown, A Rich

Source: Acta Biochim Pol, Vol. 48, No. 2. (2001), pp. 295-312.
Object-oriente d real-time systems using a hybrid distributed model of Ada 95's built-in DSA capability (Distributed Systems Annex-E) and CORBA: ACM SIGADA Ada Letters, Vol. 17, No. 5. (to possibly already existing implementation code. The GARLIC system does away with this because the communication code is generated every time changes are made. This is possible since the distribution specification is Ada and not in a neutral language like IDL. 5.4 Seamless Hybrid Integration with CORBA Should automatic tools be developed to ease the creation of CORBA IDL specifications from already existing Ada distributed capabilities? The reverse already occurs with existing products - but ...SA Moody

Source: ACM SIGADA Ada Letters, Vol. 17, No. 5. (
Hardware compilation of sequential ada: (2001), pp. 99-107.M Ward, NC Audsley

Source: (2001), pp. 99-107.
Critical residues for histone acetylation by Gcn5, functioning in Ada and SAGA complexes, are also required for transcriptiona l function in vivo.: Genes Dev, Vol. 12, No. 5. (1 March 1998), pp. 640-653.Severa l previously known transcription cofactors have been demonstrated in vitro recently to be histone acetyltransfer ases and deacetyltransf erases, suggesting that remodeling of chromatin through histone acetylation plays a fundamental role in gene regulation. Clear evidence has not yet been obtained, however, to demonstrate that histone acetylation is required for gene activation in vivo. In this study we performed an alanine-scan mutagenesis through the HAT (histone acetyltransfer ase) domain identified previously by deletion mapping in recombinant yeast Gcn5. We identified multiple substitution mutations that eliminated completely Gcn5's ability to potentiate transcriptiona l activation in vivo. Strikingly, each of these mutations was also critical for free and nucleosomal histone acetylation by Gcn5 functioning within the native yeast HAT complexes, Ada, and SAGA. Moreover, the growth phenotypes of these mutations as measured by colony size and liquid growth assay closely tracked transcription and HAT activities. In contrast, mutations that did not affect in vivo function of Gcn5 were able to acetylate histones. These data argue strongly that acetylation is required for gene regulation by Gcn5 in vivo, and support previous arguments that nucleosomal histones are among the physiological substrates of acetylation by Gcn5.L Wang, L Liu, SL Berger

Source: Genes Dev, Vol. 12, No. 5. (1 March 1998), pp. 640-653.
The Gcn4p activation domain interacts specifically in vitro with RNA polymerase II holoenzyme, TFIID, and the Adap-Gcn5p coactivator complex.: Mol Cell Biol, Vol. 18, No. 3. (March 1998), pp. 1711-1724.The Gcn4p activation domain contains seven clusters of hydrophobic residues that make additive contributions to transcriptiona l activation in vivo. We observed efficient binding of a glutathione S-transferase (GST)-Gcn4p fusion protein to components of three different coactivator complexes in Saccharomyces cerevisiae cell extracts, including subunits of transcription factor IID (TFIID) (yeast TAFII20 [yTAFII20], yTAFII60, and yTAFII90), the holoenzyme mediator (Srb2p, Srb4p, and Srb7p), and the Adap-Gcn5p complex (Ada2p and Ada3p). The binding to these coactivator subunits was completely dependent on the hydrophobic clusters in the Gcn4p activation domain. Alanine substitutions in single clusters led to moderate reductions in binding, double-cluster substitutions generally led to greater reductions in binding than the corresponding single-cluster mutations, and mutations in four or more clusters reduced binding to all of the coactivator proteins to background levels. The additive effects of these mutations on binding of coactivator proteins correlated with their cumulative effects on transcriptiona l activation by Gcn4p in vivo, particularly with Ada3p, suggesting that recruitment of these coactivator complexes to the promoter is a cardinal function of the Gcn4p activation domain. As judged by immunoprecipit ation analysis, components of the mediator were not associated with constituents of TFIID and Adap-Gcn5p in the extracts, implying that GST-Gcn4p interacted with the mediator independently of these other coactivators. Unexpectedly, a proportion of Ada2p coimmunoprecip itated with yTAFII90, and the yTAFII20, -60, and -90 proteins were coimmunoprecip itated with Ada3p, revealing a stable interaction between components of TFIID and the Adap-Gcn5p complex. Because GST-Gcn4p did not bind specifically to highly purified TFIID, Gcn4p may interact with TFIID via the Adap-Gcn5p complex or some other adapter proteins. The ability of Gcn4p to interact with several distinct coactivator complexes that are physically and genetically linked to TATA box-binding protein can provide an explanation for the observation that yTAFII proteins are dispensable for activation by Gcn4p in vivo.CM Drysdale, BM Jackson, R McVeigh, ER Klebanow, Y Bai, T Kokubo, M Swanson, Y Nakatani, PA Weil, AG Hinnebusch

Source: Mol Cell Biol, Vol. 18, No. 3. (March 1998), pp. 1711-1724.
Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterizati on of an Ada complex and the SAGA (Spt/Ada) complex.: Genes Dev, Vol. 11, No. 13. (1 July 1997), pp. 1640-1650.The transcriptiona l adaptor protein Gcn5 has been identified as a nuclear histone acetyltransfer ase (HAT). Although recombinant yeast Gcn5 efficiently acetylates free histones, it fails to acetylate histones contained in nucleosomes, indicating that additional components are required for acetylation of chromosomal histones. We report here that Gcn5 functions as a catalytic subunit in two high-molecular -mass native HAT complexes, with apparent molecular masses of 0.8 and 1.8 megadalton (MD), respectively, which acetylate nucleosomal histones. Both the 0.8- and 1.8-MD Gcn5-containin g complexes cofractionate with Ada2 and are lost in gcn5delta, ada2delta, or ada3delta yeast strains, illustrating that these HAT complexes are bona fide native Ada-transcript ional adaptor complexes. Importantly, the 1.8-MD adaptor/HAT complex also contains Spt gene products that are linked to TATA-binding protein (TBP) function. This complex is lost in spt20/ada5delt a and spt7delta strains and Spt3, Spt7, Spt20/Ada5, Ada2, and Gcn5 all copurify with this nucleosomal HAT complex. Therefore, the 1.8-MD adaptor/HAT complex illustrates an interaction between Ada and Spt gene products and confirms the existence of a complex containing the TBP group of Spt proteins as demonstrated by genetic and biochemical studies. We have named this novel transcription regulatory complex SAGA (Spt-Ada-Gcn5- Acetyltransfer ase). The function of Gcn5 as a histone acetyltransfer ase within the Ada and SAGA adaptor complexes indicates the importance of histone acetylation during steps in transcription activation mediated by interactions with transcription activators and general transcription factors (i.e., TBP).PA Grant, L Duggan, J Côté, SM Roberts, JE Brownell, R Candau, R Ohba, T Owen-Hughes, CD Allis, F Winston, SL Berger, JL Workman

Source: Genes Dev, Vol. 11, No. 13. (1 July 1997), pp. 1640-1650.
Distributed control systems simulation using high level Petri nets: Mathematics and Computers in Simulation, Vol. 46, No. 1. (01 April 1998), pp. 47-55.To deal with the complexity of the implementation of control systems for flexible manufacturing systems, formal methods of design are needed. In this work the modeling and validation tool selected is high level Petri nets. Based on this approach we have studied the problems that a distributed implementation can introduce. For the evaluation of different strategies of the model implementation and the scheduling of production tasks a simulator has been constructed. This simulator has been written in Ada language.Ferna ndo Tricas, Javier Martinez

Source: Mathematics and Computers in Simulation, Vol. 46, No. 1. (01 April 1998), pp. 47-55.
Well-adapted adolescent ethnic German immigrants in spite of adversity: The protective effects of human, social, and financial capital: European Journal of Developmental Psychology, Vol. 5, No. 2. (2008), pp. 186-209.About 10% of 1081 adolescent ethnic German immigrants aged between 10 and 20 from Russia and Kazakhstan experienced severe difficulties during acculturation. They felt discriminated against in various domains of their lives and failed at school. Not surprisingly, this group at risk also reported higher rates of delinquent activities than the others. Yet, there were a few young people who seemed to function well even under such bad conditions. The present paper aims at shedding light on the processes behind such positive developmental outcomes in spite of discrimination and school failure. We computed logistic regressions (1 = delinquen t, 0 = not delinquent) separately for the risk group and the normative group, with protective factors (personal and family assets) as predictors. Financial assets, language competence, or shorter residence predicted membership in the non-delinquent group for those at risk and not at risk alike. Educational attainment of the father, however, worked differently for the two groups, but opposite to what was expected: Among those at risk, a higher education of the father posed an additional problem, whereas those whose fathers had a lower education often showed less problematic outcomes. Given that there is ample evidence that high parental educational levels relate to positive adolescent outcomes in non-immigrant groups, it seems that intergeneratio nal transmission does not work under conditions of a glass ceiling, which may be particularly problematic for immigrant families from higher educational backgrounds.Ev a Schmitt-Roderm und, Rainer Silbereisen

Source: European Journal of Developmental Psychology, Vol. 5, No. 2. (2008), pp. 186-209.
Automatic Ada Code Generation Using a Model-Driven Engineering Approach: Vol. 4498 (2007), pp. 168-179.Curren tly, Model-Driven Engineering (MDE) is considered one of the most promising approaches for software development. In this paper, a simple but complete example based on state-machines will be used to demonstrate the benefits of this approach. After defining a modelling language (meta-model) for statemachines, a graphical tool will be presented which is aimed at easing the description and validation of state-machine models. These models will then be used as inputs for another tool which will automatically generate the corresponding Ada code, including a simulation program to test the correctness and performance of the implemented application.Di ego Alonso, Cristina Vicente-Chicot e, Pedro Sánchez, Bárbara Álvarez, Fernando Losilla

Source: Vol. 4498 (2007), pp. 168-179.
Termination of cardiac Ca(2+) sparks: an investigative mathematical model of calcium-induce d calcium release.: Biophys J, Vol. 83, No. 1. (July 2002), pp. 59-78.A Ca(2+) spark arises when a cluster of sarcoplasmic reticulum (SR) channels (ryanodine receptors or RyRs) opens to release calcium in a locally regenerative manner. Normally triggered by Ca(2+) influx across the sarcolemmal or transverse tubule membrane neighboring the cluster, the Ca(2+) spark has been shown to be the elementary Ca(2+) signaling event of excitation-con traction coupling in heart muscle. However, the question of how the Ca(2+) spark terminates remains a central, unresolved issue. Here we present a new model, "sticky cluster," of SR Ca(2+) release that simulates Ca(2+) spark behavior and enables robust Ca(2+) spark termination. Two newly documented features of RyR behavior have been incorporated in this otherwise simple model: "coupled gating" and an opening rate that depends on SR lumenal [Ca(2+)]. Using a Monte Carlo method, local Ca(2+)-induced Ca(2+) release from clusters containing between 10 and 100 RyRs is modeled. After release is triggered, Ca(2+) flux from RyRs diffuses into the cytosol and binds to intracellular buffers and the fluorescent Ca(2+) indicator fluo-3 to produce the model Ca(2+) spark. Ca(2+) sparks generated by the sticky cluster model resemble those observed experimentally , and Ca(2+) spark duration and amplitude are largely insensitive to the number of RyRs in a cluster. As expected from heart cell investigation, the spontaneous Ca(2+) spark rate in the model increases with elevated cytosolic or SR lumenal [Ca(2+)]. Furthermore, reduction of RyR coupling leads to prolonged model Ca(2+) sparks just as treatment with FK506 lengthens Ca(2+) sparks in heart cells. This new model of Ca(2+) spark behavior provides a "proof of principle" test of a new hypothesis for Ca(2+) spark termination and reproduces critical features of Ca(2+) sparks observed experimentally .EA Sobie, KW Dilly, J dos Santos Cruz, WJ Lederer, MS Jafri

Source: Biophys J, Vol. 83, No. 1. (July 2002), pp. 59-78.

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