Prediction of operons in microbial genomes

Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons. This study describes a computational method to estimate the likelihood that such conserved gene sets form operons. The method was used to analyze 34 bacterial and archaeal genomes, and yielded more than 7600 pairs of genes that are highly likely (P ≥ 0.98) to belong to the same operon. The sensitivity of our method is 30–50% for the Escherichia coli genome. The predicted gene pairs are available from our World Wide Web site http://www.tigr.org/tigr-scripts/operons/operons.cgi.

Recent improvements in prediction of protein structure by global optimization of a potential energy function

Recent improvements of a hierarchical ab initio or de novo approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic α-helical protein of 70 residues was predicted to within 4.3 Å α-carbon (Cα) rms deviation (rmsd) whereas, for other α-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 Å Cα rmsd. Whereas β structures can now be predicted with the new procedure, the success rate for α/β- and β-proteins is lower than that for α-proteins at present. For the β portions of α/β structures, the Cα rmsd's are less than 6.0 Å for contiguous fragments of 30–40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a Cα rmsd less than 6.0 Å. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence.

Prediction of protein deamidation rates from primary and three-dimensional structure

A method for the quantitative estimation of instability with respect to deamidation of the asparaginyl (Asn) residues in proteins is described. The procedure involves the observation of several simple aspects of the three-dimensional environment of each Asn residue in the protein and a calculation that includes these observations, the primary amino acid residue sequence, and the previously reported complete set of sequence-dependent rates of deamidation for Asn pentapeptides. This method is demonstrated and evaluated for 23 proteins in which 31 unstable and 167 stable Asn residues have been reported and for 7 unstable and 63 stable Asn residues that have been reported in 61 human hemoglobin variants. The relative importance of primary structure and three-dimensional structure in Asn deamidation is estimated.

A three-hybrid system to detect RNA-protein interactions in vivo.

RNA-protein interactions are pivotal in fundamental cellular processes such as translation, mRNA processing, early development, and infection by RNA viruses. However, in spite of the central importance of these interactions, few approaches are available to analyze them rapidly in vivo. We describe a yeast genetic method to detect and analyze RNA-protein interactions in which the binding of a bifunctional RNA to each of two hybrid proteins activates transcription of a reporter gene in vivo. We demonstrate that this three-hybrid system enables the rapid, phenotypic detection of specific RNA-protein interactions. As examples, we use the binding of the iron regulatory protein 1 (IRP1) to the iron response element (IRE), and of HIV trans-activator protein (Tat) to the HIV trans-activation response element (TAR) RNA sequence. The three-hybrid assay we describe relies only on the physical properties of the RNA and protein, and not on their natural biological activities; as a result, it may have broad application in the identification of RNA-binding proteins and RNAs, as well as in the detailed analysis of their interactions.

Theoretical prediction of a crystal structure.

The diffusion equation method of global minimization is applied to compute the crystal structure of S6, with no a priori knowledge about the system. The experimental lattice parameters and positions and orientations of the molecules in the unit cell are predicted correctly.

Prediction of protein folding class using global description of amino acid sequence.

We present a method for predicting protein folding class based on global protein chain description and a voting process. Selection of the best descriptors was achieved by a computer-simulated neural network trained on a data base consisting of 83 folding classes. Protein-chain descriptors include overall composition, transition, and distribution of amino acid attributes, such as relative hydrophobicity, predicted secondary structure, and predicted solvent exposure. Cross-validation testing was performed on 15 of the largest classes. The test shows that proteins were assigned to the correct class (correct positive prediction) with an average accuracy of 71.7%, whereas the inverse prediction of proteins as not belonging to a particular class (correct negative prediction) was 90-95% accurate. When tested on 254 structures used in this study, the top two predictions contained the correct class in 91% of the cases.

Repacking protein cores with backbone freedom: structure prediction for coiled coils.

Progress in homology modeling and protein design has generated considerable interest in methods for predicting side-chain packing in the hydrophobic cores of proteins. Present techniques are not practically useful, however, because they are unable to model protein main-chain flexibility. Parameterization of backbone motions may represent a general and efficient method to incorporate backbone relaxation into such fixed main-chain models. To test this notion, we introduce a method for treating explicitly the backbone motions of alpha-helical bundles based on an algebraic parameterization proposed by Francis Crick in 1953 [Crick, F. H. C. (1953) Acta Crystallogr. 6, 685-689]. Given only the core amino acid sequence, a simple calculation can rapidly reproduce the crystallographic main-chain and core side-chain structures of three coiled coils (one dimer, one trimer, and one tetramer) to within 0.6-A root-mean-square deviations. The speed of the predictive method [approximately 3 min per rotamer choice on a Silicon Graphics (Mountain View, CA) 4D/35 computer] permits it to be used as a design tool.

A novel hybrid simulation-optimization approach for the optimal design of multicomponent distillation columns

Póster presentado en Escape 22, European Symposium on Computer Aided Process Engineering, University College London, UK, 17-20 June 2012.

A hybrid simulation-optimization approach for the design of internally heat-integrated distillation columns

Paper submitted to AIChE 2012 Annual Meeting: Energy Efficiency by Process Intensification, Pittsburgh, PA, October 28-November 2, 2012.

Evaluation of hybrid and distance education learning environments in Spain

This article describes the adaptation and validation of the Distance Education Learning Environments Survey (DELES) for use in investigating the qualities found in distance and hybrid education psycho-social learning environments in Spain. As Europe moves toward post-secondary student mobility, equanimity in access to higher education, and more standardised degree programs across the European Higher Education Area (EHEA) the need for a high quality method for continually assessing the excellence of distance and hybrid learning environments has arisen. This study outlines how the English language DELES was adapted into the new Spanish-Distance Education Learning Environments Survey (S-DELES) for use with a Bachelor of Psychology and Criminology degree program offering both distance and hybrid education classes. We present the relationships between psycho-social learning environment perceptions and those of student affect. We also present the asynchronous aspects of the environment, scale means, and a comparison between the perceptions of distance education students and their hybrid education counterparts that inform the university about the baseline health of the information and communication technologies (ICT) environment within which the study was conducted.

Event-based visual servoing with features’ prediction

Event-based visual servoing is a recently presented approach that performs the positioning of a robot using visual information only when it is required. From the basis of the classical image-based visual servoing control law, the scheme proposed in this paper can reduce the processing time at each loop iteration in some specific conditions. The proposed control method enters in action when an event deactivates the classical image-based controller (i.e. when there is no image available to perform the tracking of the visual features). A virtual camera is then moved through a straight line path towards the desired position. The virtual path used to guide the robot improves the behavior of the previous event-based visual servoing proposal.

Hybrid simulation-optimization based approach for the optimal design of single-product biotechnological processes

In this work, we present a systematic method for the optimal development of bioprocesses that relies on the combined use of simulation packages and optimization tools. One of the main advantages of our method is that it allows for the simultaneous optimization of all the individual components of a bioprocess, including the main upstream and downstream units. The design task is mathematically formulated as a mixed-integer dynamic optimization (MIDO) problem, which is solved by a decomposition method that iterates between primal and master sub-problems. The primal dynamic optimization problem optimizes the operating conditions, bioreactor kinetics and equipment sizes, whereas the master levels entails the solution of a tailored mixed-integer linear programming (MILP) model that decides on the values of the integer variables (i.e., number of equipments in parallel and topological decisions). The dynamic optimization primal sub-problems are solved via a sequential approach that integrates the process simulator SuperPro Designer® with an external NLP solver implemented in Matlab®. The capabilities of the proposed methodology are illustrated through its application to a typical fermentation process and to the production of the amino acid L-lysine.

Reflections on the institutional balance, the Community Method and the interplay between jurisdictions after Lisbon. Research Papers in Law, 04/2012

[Introduction.] Over the last two years, not only inside but also outside the framework of the EU treaties, far reaching measures have been taken at the highest political level in order to address the financial and economic crisis in Europe and in particular the sovereign debt crisis in the Euro area. This has triggered debates forecasting the “renationalisation of European politics.” Herman Van Rompuy, the President of the European Council, countered the prediction that Europe is doomed because of such a renationalisation: “If national politics have a prominent place in our Union, why would this not strengthen it?” He took the view that not a renationalisation of European politics was at stake, but an Europeanization of national politics emphasising that post war Europe was never developed in contradiction with nation states.1 Indeed, the European project is based on a mobilisation of bundled, national forces which are of vital importance to a democratically structured and robust Union that is capable of acting in a globalised world. To that end, the Treaty of Lisbon created a legal basis. The new legal framework redefines the balance between the Union institutions and confirms the central role of the Community method in the EU legislative and judiciary process. This contribution critically discusses the development of the EU's institutional balance after the entry into force of the Treaty of Lisbon, with a particular emphasis on the use of the Community Method and the current interplay between national constitutional courts and the Court of Justice. This interplay has to date been characterised by suspicion and mistrust, rather than by a genuine dialogue between the pertinent judicial actors.

Application of Monte Carlo techniques to insolation characterization and prediction : status report, October 1, 1978-June 1, 1979 /

"July 1979."

Structural basis and prediction of substrate specificity in protein serine/threonine kinases

The large number of protein kinases makes it impractical to determine their specificities and substrates experimentally. Using the available crystal structures, molecular modeling, and sequence analyses of kinases and substrates, we developed a set of rules governing the binding of a heptapeptide substrate motif (surrounding the phosphorylation site) to the kinase and implemented these rules in a web-interfaced program for automated prediction of optimal substrate peptides, taking only the amino acid sequence of a protein kinase as input. We show the utility of the method by analyzing yeast cell cycle control and DNA damage checkpoint pathways. Our method is the only available predictive method generally applicable for identifying possible substrate proteins for protein serine/threonine kinases and helps in silico construction of signaling pathways. The accuracy of prediction is comparable to the accuracy of data from systematic large-scale experimental approaches.