An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance

BACKGROUND: Motif finding algorithms have developed in their ability to use computationally efficient methods to detect patterns in biological sequences. However the posterior classification of the output still suffers from some limitations, which makes it difficult to assess the biological significance of the motifs found. Previous work has highlighted the existence of positional bias of motifs in the DNA sequences, which might indicate not only that the pattern is important, but also provide hints of the positions where these patterns occur preferentially.RESULTS: We propose to integrate position uniformity tests and over-representation tests to improve the accuracy of the classification of motifs. Using artificial data, we have compared three different statistical tests (Chi-Square, Kolmogorov-Smirnov and a Chi-Square bootstrap) to assess whether a given motif occurs uniformly in the promoter region of a gene. Using the test that performed better in this dataset, we proceeded to study the positional distribution of several well known cis-regulatory elements, in the promoter sequences of different organisms (S. cerevisiae, H. sapiens, D. melanogaster, E. coli and several Dicotyledons plants). The results show that position conservation is relevant for the transcriptional machinery.CONCLUSION: We conclude that many biologically relevant motifs appear heterogeneously distributed in the promoter region of genes, and therefore, that non-uniformity is a good indicator of biological relevance and can be used to complement over-representation tests commonly used. In this article we present the results obtained for the S. cerevisiae data sets.publishersversionpublishe

Modulating intermolecular interactions and rheological properties in silk fibroin using ultrasound frequencies

info:eu-repo/semantics/draf

Rice quality profiling to classify germplasm in breeding programs

The objective of this work was to define a quality space for assessing rice varieties. Eleven long grain varieties, seven commercial and four new advanced lines were assessed to obtain complete quality profile considering appearance, physicochemical parameters, water absorption behaviour, pasting profile and textural attributes. Commercial varieties were chosen to provide the widest variation in properties, applying the variability analysis concepts of the Taguchi method, including Japonicas, Indicas, hybrids and aromatics. Quality parameters were measured in five different dimensions of quality space (totalling 50). Variable reduction techniques were applied to chose 3 parameters in each dimension (totalling 15 quality indicators) that would describe the whole space with greatest orthogonality, accuracy and yet explaining a significant proportion of the whole variance of data. The analysis of the quality space thus defined and similarities between varieties is illustrated with the conclusion of how the 4 new advanced lines perform in terms of quality behaviour, where it is concluded that one of them is very promising as an improvement over European (Indica) towards the behaviour of a pure Guyana (Indica), whereas 3 others have significant shortcomings in various aspects of the quality space compared to all others, albeit their greater closeness to Japonicas

Salmonella spp. in pet reptiles in Portugal : prevalence and chlorhexidine gluconate antimicrobial efficacy

Research Areas: Infectious Diseases ; Pharmacology & PharmacyABSTRACT - A fraction of human Salmonella infections is associated with direct contact with reptiles, yet the number of reptile-associated Salmonellosis cases are believed to be underestimated. Existing data on Salmonella spp. transmission by reptiles in Portugal is extremely scarce. The aim of the present work was to evaluate the prevalence of Salmonella spp. in pet reptiles (snakes, turtles, and lizards), as well as evaluate the isolates’ antimicrobial resistance and virulence profiles, including their ability to form biofilm in the air-liquid interface. Additionally, the antimicrobial effect of chlorhexidine gluconate on the isolates was tested. Salmonella was isolated in 41% of the animals sampled and isolates revealed low levels of antimicrobial resistance. Hemolytic and lypolytic phenotypes were detected in all isolates. The majority (90.63%) of the Salmonella isolates were positive for the formation of pellicle in the air-liquid interface. Results indicate chlorhexidine gluconate is an effective antimicrobial agent, against the isolates in both their planktonic and biofilm forms, demonstrating a bactericidal effect in 84.37% of the Salmonella isolates. This study highlights the possible role of pet reptiles in the transmission of non-typhoidal Salmonella to humans, a serious and increasingly relevant route of exposure in the Salmonella public health framework.info:eu-repo/semantics/publishedVersio

Locomotion gait optimization for a quadruped robot

This article describes the development of a gait optimization system that allows a fast but stable robot quadruped crawl gait. We focus in the development of a quadruped robot walking gait locomotion that combine bio-inspired Central Patterns Generators (CPGs) and Genetic Algorithms (GA). The CPGs are modelled as autonomous differential equations, that generate the necessary limb movement to perform the walking gait, and the Genetic Algorithm perform the search of the CPGs parameters. This approach allows to explicitly specify parameters such as amplitude, offset and frequency of movement and to smoothly modulate the generated trajectories according to changes in these parameters. It is therefore easy to combine the CPG with an optimization method. A genetic algorithm determines the best set of parameters that generates the limbs movements. We intend to obtain a walking gait locomotion that minimizes the vibration and maximizes the wide stability margin and the forward velocity. The experimental results, performed on a simulated Aibo robot, demonstrated that our approach allows low vibration with a high velocity and wide stability margin for a quadruped walking gait locomotion

Head motion stabilization during quadruped robot locomotion: combining CPGs and stochastic optimization methods

In this work, the authors propose a combined approach based on a controller architecture that is able to generate locomotion for a quadruped robot and a global optimization algorithm to generate head movement stabilization. The movement controllers are biologically inspired in the concept of Central Pattern Generators (CPGs) that are modelled based on nonlinear dynamical systems, coupled Hopf oscillators. This approach allows for explicitly specified parameters such as amplitude, offset and frequency of movement and to smoothly modulate the generated oscillations according to changes in these parameters. The overall idea is to generate head movement opposed to the one induced by locomotion, such that the head remains stabilized. Thus, in order to achieve this desired head movement, it is necessary to appropriately tune the CPG parameters. Three different global optimization algorithms search for this best set of parameters. In order to evaluate the resulting head movement, a fitness function based on the Euclidean norm is investigated. Moreover, a constraint-handling technique based on tournament selection was implemented

Hydro-sedimentary processes in a beach-headland system

Understanding hydro-sedimentary processes in space-limited environments as embayed beaches is a key question to reconstruct preterit and predict future coastal evolution forced by the mean sea level rise. Moreover, such knowledge is a fundamental management tool in areas where coastal erosion is currently a worrying fact. This work aims thus to assess the sedimentary contribute, provided by the alongshore transport, to feed embayed beaches. At the southernmost rocky coast of Portugal (Algarve), beaches occurring at the cliffs’ foot are separated by headlands connected to shore platforms forming littoral cells as a consequence of the extremely karstified carbonate landscape. The survival of those beaches depends almost exclusively on the alongshore drift.info:eu-repo/semantics/publishedVersio

Bacteriocin production of the probiotic Lactobacillus acidophilus KS400

In the last years, the use of probiotics, including Lactobacillus species, has received much attention to prevent and treat vaginal disorders. These species have been described as having the ability to colonize the epithelial surface and produce antimicrobial metabolites that are able to control the remaining vaginal microflora. This study aimed to identify and characterize, for the first time, a bacteriocin natively produced by Lactobacillus acidophilus KS400 (probiotic strain from Gynoflor®-Medinova AG, Switzerland) and its antimicrobial activity against relevant urogenital pathogens. After organic acids and hydrogen peroxide neutralization in the fermented Lactobacillus acidophilus KS400 culture medium, bacteriocin activity was tested against the indicator microorganism Lactobacillus delbrueckii ATCC9649. The fermentation of Lactobacillus acidophilus KS400 for bacteriocin production was carried out in batch mode, and its antimicrobial activity, optical density and pH were monitored. After production and extraction, the bacteriocin molecular weight was estimated by electrophoresis and tested against vaginal pathogenic microorganisms. As described for other bacteriocins, batch fermentation profiles indicated that bacteriocin production occurs during the exponential growth phase of the lactobacilli, and declines during their stationary growth phase. The molecular weight of the bacteriocin is approximately 7.5 kDa. The bacteriocin containing protein extract was shown to inhibit the growth of Gardnerella vaginalis, Streptococcus agalactiae, Pseudomonas aeruginosa and the indicator strain Lactobacillus delbrueckii ATCC9649. We conclude that L. acidophilus KS400 produces bacteriocin with antimicrobial activity against relevant urogenital pathogens.Project POCI-01-0145-FEDER-007491; Medinovainfo:eu-repo/semantics/publishedVersio

Development of dioctadecyldimethylammonium bromide/monoolein liposomes for gene delivery

The artificial introduction of nucleic acids (NA) into mammalian cells (transfection) has become, in recent years, a well-established procedure in basic and applied research, which allowed the study of gene function and regulation. The advances in this area have made possible the use of these methods for gene-based medicines, which constitute alternative therapeutic approaches. One of the most prominent methods is lipofection that uses cationic liposome/NA complexes (a.k.a. lipoplexes) for the complexation, transport and release of therapeutic sequences into target cells. Although yielding lower transfection efficiencies compared with viral gene delivery, lipofection vectors are much safer for medical applications because no significant mutational or toxicological risk exist. Dioctadecyldimethylammonium Bromide (DODAB)/Monoolein (MO) liposomes have recently been described as a new promising alternative to common transfection reagents, due to the pioneering application of MO as helper lipid in lipoplex formulations. In this chapter, we will review the effect of MO on the physicochemical properties of DODAB/MO liposomes and pDNA/DODAB/MO lipoplexes. How lipoplex properties may affect the interaction with different extracellular components and their cell uptake and trafficking will be discussed. The importance of lipoplex biocompatibility towards efficient gene therapy will also be approached presenting pDNA/DODAB/MO system as a lipoplex model, supporting the use of MO as new helper lipid in lipofection.FCTCOMPETEThis work was supported by FCT research project PTDC/QUI/69795/2006, which is cofunded by the program COMPETE from QREN with co-participation from the European Community fund FEDER; CFUM [PEst-C/FIS/UI0607/2011]; CBMA [Pest C/BIA/UI4050/2011]; J.P.N. Silva holds a PhD Grant (SFRH/BD/46968/2008); A. C.N. Oliveira holds a PhD grant (SFRH/BD/68588/2010)