Molecular basis of sulfonylurea herbicide inhibition of acetohydroxyacid synthase

Acetohydroxyacid synthase (AHAS) (acetolactate synthase, EC 4.1.3.18) catalyzes the first step in branchedchain amino acid biosynthesis and is the target for sulfonylurea and imidazolinone herbicides. These compounds are potent and selective inhibitors, but their binding site on AHAS has not been elucidated. Here we report the 2.8 Angstrom resolution crystal structure of yeast AHAS in complex with a sulfonylurea herbicide, chlorimuron ethyl. The inhibitor, which has a K-i of 3.3 nM blocks access to the active site and contacts multiple residues where mutation results in herbicide resistance. The structure provides a starting point for the rational design of further herbicidal compounds.

A creative solution for rapid and inexpensive model-making in product design processes

Rapid prototyping (RP) is an approach for automatically building a physical object through solid freeform fabrication. Nowadays, RP has become a vital aspect of most product development processes, due to the significant competitive advantages it offers compared to traditional manual model making. Even in academic environments, it is important to be able to quickly create accurate physical representations of concept solutions. Some of these can be used for simple visual validation, while others can be employed for ergonomic assessment by potential users or even for physical testing. However, the cost of traditional RP methods prevents their use in most academic environments on a regular basis, and even for very preliminary prototypes in many small companies. That results in delaying the first physical prototypes to later stages, or creating very rough mock-ups which are not as useful as they could be. In this paper we propose an approach for rapid and inexpensive model-making, which was developed in an academic context, and which can be employed for a variety of objects.

Experimental design methodologies for the identification of Michaelis-Menten type kinetics

The main objective of this work was to investigate the application of experimental design techniques for the identification of Michaelis-Menten kinetic parameters. More specifically, this study attempts to elucidate the relative advantages/disadvantages of employing complex experimental design techniques in relation to equidistant sampling when applied to different reactor operation modes. All studies were supported by simulation data of a generic enzymatic process that obeys to the Michaelis-Menten kinetic equation. Different aspects were investigated, such as the influence of the reactor operation mode (batch, fed-batch with pulse wise feeding and fed-batch with continuous feeding) and the experimental design optimality criteria on the effectiveness of kinetic parameters identification. The following experimental design optimality criteria were investigated: 1) minimization of the sum of the diagonal of the Fisher information matrix (FIM) inverse (A-criterion), 2) maximization of the determinant of the FIM (D-criterion), 3) maximization of the smallest eigenvalue of the FIM (E-criterion) and 4) minimization of the quotient between the largest and the smallest eigenvalue (modified E-criterion). The comparison and assessment of the different methodologies was made on the basis of the Cramér-Rao lower bounds (CRLB) error in respect to the parameters vmax and Km of the Michaelis-Menten kinetic equation. In what concerns the reactor operation mode, it was concluded that fed-batch (pulses) is better than batch operation for parameter identification. When the former operation mode is adopted, the vmax CRLB error is lowered by 18.6 % while the Km CRLB error is lowered by 26.4 % when compared to the batch operation mode. Regarding the optimality criteria, the best method was the A-criterion, with an average vmax CRLB of 6.34 % and 5.27 %, for batch and fed-batch (pulses), respectively, while presenting a Km’s CRLB of 25.1 % and 18.1 %, for batch and fed-batch (pulses), respectively. As a general conclusion of the present study, it can be stated that experimental design is justified if the starting parameters CRLB errors are inferior to 19.5 % (vmax) and 45% (Km), for batch processes, and inferior to 42 % and to 50% for fed-batch (pulses) process. Otherwise equidistant sampling is a more rational decision. This conclusion clearly supports that, for fed-batch operation, the use of experimental design is likely to largely improve the identification of Michaelis-Menten kinetic parameters.

Analysis of support for modularity in object teams based on design patterns

Dissertação de Mestrado em Engenharia Informática

A qualitative assessment of modularity in CaesarJ components based on implementations of design patterns

Tese de Mestrado em Engenharia Informática

Participatory mapping in the design process of a spatial data infrastructure SDI: a case study in the Biosphere Reserve Rio Platano (Honduras)

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

An investigation of safety design practices of metal machines

BACKGROUND: Machinery safety issues are a challenge facing manufacturers who are supposed to create and provide products in a better and faster way. In spite of their construction and technological advance, they still contribute to many potential hazards for operators and those nearby. OBJECTIVE: The aim of this study is to investigate safety aspects of metal machinery offered for sale on Internet market according to compliance with minimum and fundamental requirements. METHODS: The study was carried out with the application of a checklist prepared on the basis of Directive 2006/42/EC and Directive 2009/104/EC and regulations enforcing them into Polish law. RESULTS: On the basis of the study it was possible to reveal the safety aspects that were not met in practice. It appeared that in the case of minimum requirements the most relevant problems concerned information, signal and control elements, technology and machinery operations, whereas as far as fundamental aspects are concerned it was hard to assure safe work process. CONCLUSIONS: In spite of the fact that more and more legal acts binding in the Member Countries of the European Union are being introduced to alleviate the phenomenon, these regulations are often not fulfilled.

A proteção cumulativa do design pelo Direito de Autor e pelo Direito da Propriedade Industrial: o caso especial do contrato de trabalho

Dissertação de mestrado em Direito dos Contratos e das Empresas

Internship report of blog translation at the company Menina Design Group

Dissertação de mestrado em Tradução e Comunicação Multilingue

Green furniture: sustainable design guidelines for the Irish furniture and wood products industry.

This thesis presents the research and development of sustainable design guidelines for the furniture and wood products industry, suitable for sustainably enhancing design, manufacturing and associated activities. This sustainable guideline is based on secondary research conducted on subject areas such as ‘eco’ design, ‘green’ branding and ‘green’ consumerism, as well as an examination of existing certifications and sustainable tools techniques and methodologies, national and international drivers for sustainable development and an overview of sustainability in the Irish furniture manufacturing context. The guideline was further developed through primary research. This consisted of a focus group attended by leading Irish designers, manufacturers and academics in the area of furniture and wood products. This group explored the question of ‘green branding’ saturation in the market and the viability of investing in sustainability just yet. Participants stated that they felt the market for ‘green’ products is evolving very slowly and that there is no metric or legal framework present to audit whether or not companies are producing products that really embody sustainability. All the participants believed that developing and introducing a new certification process to incorporate a sustainable design process was a viable and necessary solution to protecting Irish furniture and wood manufacturers going forward. For the purposes of the case study, the author investigated a ‘sustainable’ design process for Team woodcraft, Ltd., through the design and development of a ‘sustainable’ children’s furniture range. The case study followed a typical design and development process; detailing customer design specifications, concept development and refinement and cumulating in final prototype, as well as associated engineering drawings. Based on this primary and secondary research, seven fundamental core principles for this sustainable guideline have been identified by the author. The author then used these core principles to expand into guidelines for the basis of proposed new Irish sustainable design guidelines for the furniture and wood products industry, the concept of which the author has named ‘Green Dot’. The author suggests that the ‘Green Dot’ brand or logo could be used to market an umbrella network of Irish furniture designers and manufactures who implement the recommended sustainable techniques.

Experimental design for acquiring relevant data to address the issue of comparing consecutively manufactured tools and firearms

The comparison of consecutively manufactured tools and firearms has provided much, but not all, of the basis for the profession of firearm and toolmark examination. The authors accept the fundamental soundness of this approach but appeal to the experimental community to close two minor gaps in the experimental procedure. We suggest that "blinding" and attention to appropriateness of other experimental conditions that would consolidate the foundations of our profession. We do not suggest that previous work is unsound.

Design and analysis of ChIP-Seq experiments for nuclear factor I DNA-binding proteins

SUMMARY : Eukaryotic DNA interacts with the nuclear proteins using non-covalent ionic interactions. Proteins can recognize specific nucleotide sequences based on the sterical interactions with the DNA and these specific protein-DNA interactions are the basis for many nuclear processes, e.g. gene transcription, chromosomal replication, and recombination. New technology termed ChIP-Seq has been recently developed for the analysis of protein-DNA interactions on a whole genome scale and it is based on immunoprecipitation of chromatin and high-throughput DNA sequencing procedure. ChIP-Seq is a novel technique with a great potential to replace older techniques for mapping of protein-DNA interactions. In this thesis, we bring some new insights into the ChIP-Seq data analysis. First, we point out to some common and so far unknown artifacts of the method. Sequence tag distribution in the genome does not follow uniform distribution and we have found extreme hot-spots of tag accumulation over specific loci in the human and mouse genomes. These artifactual sequence tags accumulations will create false peaks in every ChIP-Seq dataset and we propose different filtering methods to reduce the number of false positives. Next, we propose random sampling as a powerful analytical tool in the ChIP-Seq data analysis that could be used to infer biological knowledge from the massive ChIP-Seq datasets. We created unbiased random sampling algorithm and we used this methodology to reveal some of the important biological properties of Nuclear Factor I DNA binding proteins. Finally, by analyzing the ChIP-Seq data in detail, we revealed that Nuclear Factor I transcription factors mainly act as activators of transcription, and that they are associated with specific chromatin modifications that are markers of open chromatin. We speculate that NFI factors only interact with the DNA wrapped around the nucleosome. We also found multiple loci that indicate possible chromatin barrier activity of NFI proteins, which could suggest the use of NFI binding sequences as chromatin insulators in biotechnology applications. RESUME : L'ADN des eucaryotes interagit avec les protéines nucléaires par des interactions noncovalentes ioniques. Les protéines peuvent reconnaître les séquences nucléotidiques spécifiques basées sur l'interaction stérique avec l'ADN, et des interactions spécifiques contrôlent de nombreux processus nucléaire, p.ex. transcription du gène, la réplication chromosomique, et la recombinaison. Une nouvelle technologie appelée ChIP-Seq a été récemment développée pour l'analyse des interactions protéine-ADN à l'échelle du génome entier et cette approche est basée sur l'immuno-précipitation de la chromatine et sur la procédure de séquençage de l'ADN à haut débit. La nouvelle approche ChIP-Seq a donc un fort potentiel pour remplacer les anciennes techniques de cartographie des interactions protéine-ADN. Dans cette thèse, nous apportons de nouvelles perspectives dans l'analyse des données ChIP-Seq. Tout d'abord, nous avons identifié des artefacts très communs associés à cette méthode qui étaient jusqu'à présent insoupçonnés. La distribution des séquences dans le génome ne suit pas une distribution uniforme et nous avons constaté des positions extrêmes d'accumulation de séquence à des régions spécifiques, des génomes humains et de la souris. Ces accumulations des séquences artéfactuelles créera de faux pics dans toutes les données ChIP-Seq, et nous proposons différentes méthodes de filtrage pour réduire le nombre de faux positifs. Ensuite, nous proposons un nouvel échantillonnage aléatoire comme un outil puissant d'analyse des données ChIP-Seq, ce qui pourraient augmenter l'acquisition de connaissances biologiques à partir des données ChIP-Seq. Nous avons créé un algorithme d'échantillonnage aléatoire et nous avons utilisé cette méthode pour révéler certaines des propriétés biologiques importantes de protéines liant à l'ADN nommés Facteur Nucléaire I (NFI). Enfin, en analysant en détail les données de ChIP-Seq pour la famille de facteurs de transcription nommés Facteur Nucléaire I, nous avons révélé que ces protéines agissent principalement comme des activateurs de transcription, et qu'elles sont associées à des modifications de la chromatine spécifiques qui sont des marqueurs de la chromatine ouverte. Nous pensons que lés facteurs NFI interagir uniquement avec l'ADN enroulé autour du nucléosome. Nous avons également constaté plusieurs régions génomiques qui indiquent une éventuelle activité de barrière chromatinienne des protéines NFI, ce qui pourrait suggérer l'utilisation de séquences de liaison NFI comme séquences isolatrices dans des applications de la biotechnologie.

Identification of the Best Practices for Design, Construction, and Repair of Bridge Approches, 2005

Bridge approach settlement and the formation of the bump is a common problem in Iowa that draws upon considerable resources for maintenance and creates a negative perception in the minds of transportation users. This research study was undertaken to investigate bridge approach problems and develop new concepts for design, construction, and maintenance that will reduce this costly problem. As a result of the research described in this report, the following changes are suggested for implementation on a pilot test basis: • Use porous backfill behind the abutment and/or geocomposite drainage systems to improve drainage capacity and reduce erosion around the abutment. • On a pilot basis, connect the approach slab to the bridge abutment. Change the expansion joint at the bridge to a construction joint of 2 inch. Use a more effective joint sealing system at the CF joint. Change the abutment wall rebar from #5 to #7 for non-integral abutments. • For bridges with soft foundation or embankment soils, implement practices of better compaction, preloading, ground improvement, soil removal and replacement, or soil reinforcement that reduce time-dependent post construction settlements.

Identification of the Best Practices for Design, Construction, and Repair of Bridge Approaches, January 2005

Bridge approach settlement and the formation of the bump is a common problem in Iowa that draws upon considerable resources for maintenance and creates a negative perception in the minds of transportation users. This research study was undertaken to investigate bridge approach problems and develop new concepts for design, construction, and maintenance that will reduce this costly problem. As a result of the research described in this report, the following changes are suggested for implementation on a pilot test basis: • Use porous backfill behind the abutment and/or geocomposite drainage systems to improve drainage capacity and reduce erosion around the abutment. • On a pilot basis, connect the approach slab to the bridge abutment. Change the expansion joint at the bridge to a construction joint of 2 inch. Use a more effective joint sealing system at the CF joint. Change the abutment wall rebar from #5 to #7 for non-integral abutments. • For bridges with soft foundation or embankment soils, implement practices of better compaction, preloading, ground improvement, soil removal and replacement, or soil reinforcement that reduce time-dependent post construction settlements.

iLOGP: A Simple, Robust, and Efficient Description of n-Octanol/Water Partition Coefficient for Drug Design Using the GB/SA Approach.

The n-octanol/water partition coefficient (log Po/w) is a key physicochemical parameter for drug discovery, design, and development. Here, we present a physics-based approach that shows a strong linear correlation between the computed solvation free energy in implicit solvents and the experimental log Po/w on a cleansed data set of more than 17,500 molecules. After internal validation by five-fold cross-validation and data randomization, the predictive power of the most interesting multiple linear model, based on two GB/SA parameters solely, was tested on two different external sets of molecules. On the Martel druglike test set, the predictive power of the best model (N = 706, r = 0.64, MAE = 1.18, and RMSE = 1.40) is similar to six well-established empirical methods. On the 17-drug test set, our model outperformed all compared empirical methodologies (N = 17, r = 0.94, MAE = 0.38, and RMSE = 0.52). The physical basis of our original GB/SA approach together with its predictive capacity, computational efficiency (1 to 2 s per molecule), and tridimensional molecular graphics capability lay the foundations for a promising predictor, the implicit log P method (iLOGP), to complement the portfolio of drug design tools developed and provided by the SIB Swiss Institute of Bioinformatics.