Using Process Tailoring to Manage Software Development Challenges

To ensure high-quality software processes and leverage best practices, project managers strive to tailor standard processes such as the rational unified process or those developed within their own organizations. Software process tailoring is the activity of tuning a process to meet the needs of a specific project. Despite the critical role that tailoring software processes plays in ensuring project success, few guidelines on it are available for practitioners. The authors conducted an empirical study in two organizations and developed a framework to guide process tailoring.     

Induced fit of a peptide loop of methionyl-tRNA formyltransferase triggered by the initiator tRNA substrate

A 16-aa insertion loop present in eubacterial methionyl-tRNA formyltransferases (MTF) is critical for specific recognition of the initiator tRNA in Escherichia coli. We have studied the interactions between this region of the E. coli enzyme and initiator methionyl-tRNA (Met-tRNA) by using two complementary protection experiments: protection of MTF against proteolytic cleavage by tRNA and protection of tRNA against nucleolytic cleavage by MTF. The insertion loop in MTF is uniquely sensitive to cleavage by trypsin. We show that the substrate initiator Met-tRNA protects MTF against trypsin cleavage, whereas a formylation-defective mutant initiator Met-tRNA, which binds to MTF with approximately the same affinity, does not. Also, mutants of MTF within the insertion loop (which are defective in formylation) are not protected by the initiator Met-tRNA. Thus, a functional enzyme-substrate complex is necessary for protection of MTF against trypsin cleavage. Along with other data, these results strongly suggest that a segment of the insertion loop, which is exposed and unstructured in MTF, undergoes an induced fit in the functional MTF.Met-tRNA complex but not in the nonfunctional one. Footprinting experiments show that MTF specifically protects the acceptor stem and the 3'-end region of the initiator Met-tRNA against cleavage by double and single strand-specific nucleases. This protection also depends on formation of a functional MTF.Met-tRNA complex. Thus, the insertion loop interacts mostly with the acceptor stem of the initiator Met-tRNA, which contains the critical determinants for formylation.     

Dielectric nanocomposites for integral thin film capacitors: materials design, fabrication and integration issues

Nanocomposites of organically modified barium titanate (BTO) nanoparticles in an epoxy matrix have been synthesized and evaluated as dielectrics for the fabrication of integral thin film capacitor arrays. Organic modification of the polymer inorganic interface has been used as a design tool to control the cross link density of the polymeric matrix and the interfacial interactions. Impedance spectra generated with model networks has been employed to analyze the experimental data and to model the role of the ceramic core, interface and the polymer matrix in determining the dielectric behavior of the nanocomposites. Stealth decoupling capacitor arrays were fabricated employing BTO-Epoxy nanocomposite thin films as dielectric layer. Capacitor arrays were fabricated by patterning the top electrode in the glass/Al/BTO-epoxy/spl bsol/Al heterostructures employing a photolithographic process and their electrical performance characterized. The role of an organically modified interface in limiting the thermal diffusion of copper metal in the composite thin film has been investigated employing Rutherford backscattering spectroscopy.     

Automated Path Planning of Cooperative Crane Lifts Using Heuristic Search

The use of cooperative cranes can improve the cost effectiveness of heavy lift operations. However, the complexity in developing a reliable lift plan prevents the widespread use of cooperative crane lifts. The availability of a computer-aided planning system can improve planning efficiency and reliability. Path planning is an important subtask of the lift planning process. This paper presents work done to develop a computer aided path planner for two crane lifts. Two heuristic search methods, hill climbing and A?, were implemented for automating the path-planning task. Search space was represented using the concept of configuration space. The effectiveness of the search methods was evaluated by solving three problems with increasing levels of complexity. The formulation of these problems was based on the type of movement of cooperative cranes (in synchronous or asynchronous manner) and the presence of trapping space. It was found that while the hill climbing approach found feasible paths in a few seconds or minutes, these paths were far from optimal in situations containing trapping space. In contrast, the A? search resulted in near optimal paths, but the execution time was of the order of hours.     

Conformational changes in a mammalian voltage-dependent potassium channel inactivation peptide

Fast inactivation is restored in inactivation deletion mutant voltage-gated potassium (Kv) channels by application of synthetic inactivation 'ball' peptide. Using Fourier transform infrared and circular dichroism spectroscopy, we have investigated the structure of synthetic Kv3.4 channel ball peptide, in a range of environments relevant to the function of the ball domain. The ball peptide contains no alpha-helix or beta-sheet in reducing conditions in aqueous solution, but when cosolubilized with anionic lipid or detergent in order to mimic the environment which the ball domain encounters during channel inactivation, the ball peptide adopts a partial beta-sheet structure. Oxidation of the Kv3.4 ball peptide facilitates formation of a disulfide bond between Cys6 and Cys24 and adoption of a partial beta-sheet structure in aqueous solution; the tendency of the oxidized ball peptide to adopt beta-sheet is generally greater than that of the reduced ball peptide in a given environment. THREADER modeling of the Kv3.4 ball peptide structure predicts a beta-hairpin-like conformation which corresponds well to the structure suggested by spectroscopic analysis of the ball peptide in its cyclic arrangement. A V7E mutant Kv3.4 ball peptide analogue of the noninactivating Shaker B L7E mutant ball peptide cannot adopt beta-structure whatever the environment, and regardless of oxidation state. The results suggest that the Kv3.4 ball domain undergoes a conformational change during channel inactivation and may implicate a novel regulatory role for intramolecular disulfide bond formation in the Kv3.4 ball domain in vivo.     

Functional interaction of an arginine conserved in the sixteen amino acid insertion module of Escherichia coli methionyl-tRNA formyltransferase with determinants for formylation in the initiator tRNA

Formylation of initiator methionyl-tRNA by methionyl-tRNA formyltransferase (MTF) is important for initiation of protein synthesis in eubacteria. The determinants for formylation are clustered mostly in the acceptor stem of the initiator tRNA. Previous studies suggested that a 16 amino acid insertion loop, present in all eubacterial MTF's (residues 34-49 in the E. coli enzyme), plays an important role in specific recognition of the initiator tRNA. Here, we have analyzed the effect of site-specific mutations of amino acids within this region. We show that an invariant arginine at position 42 within the loop plays a very important role both in the steps of substrate binding and in catalysis. The kinetic parameters of the R42K and R42L mutant enzymes using acceptor stem mutant initiator tRNAs as substrates suggest that arginine 42 makes functional contacts with the determinants at the 3:70 and possibly also the 2:71 base pairs in the acceptor stem of the initiator tRNA. The kinetic parameters of the G41R/R42L double mutant enzyme are essentially the same as those of R42L mutant, suggesting that the requirement for arginine at position 42 cannot be fulfilled by an arginine at position 41. Along with other data, this result suggests that the insertion loop, which is normally unstructured and flexible, adopts a defined conformation upon binding to the tRNA.