Gonad development in females of fiddler crab Uca rapax (Crustacea, Brachyura, Ocypodidae) using macro and microscopic techniques

The morphology of the ovaries in Uca rapax (Smith, 1870) was described based on macroscopic and microscopic analysis. Females were collected in Itamambuca mangrove, Ubatuba, state of São Paulo, Brazil. In the laboratory, 18 females had their ovaries removed and prepared for histology. Each gonad developmental stage was previously determined based on external and macroscopic morphology and afterwards each stage was microscopically described. The ovaries of U. rapax showed a pronounced macroscopic differentiation in size and coloration with the maturation of the gonad, with six ovarian developmental stages: immature, rudimentary, developing, developed, advanced and spent. During the vitellogenesis, the amount of oocytes in secondary stage increases in the ovary, resulting in a change in coloration of the gonad. Oogonias, primary oocytes, secondary oocytes and follicular cells were histologically described and measured. In female’s ovaries of U. rapax the modifications observed in the oocytes during the process of gonad maturation are similar to descriptions of gonads of other females of brachyuran crustaceans. The similarities are specially found in the morphological changes in the reproductive cells, and also in the presence and arrange of follicle cells during the process of ovary maturation. When external morphological characteristics of the gonads were compared to histological descriptions, it was possible to observe modifications that characterize the process in different developmental stages throughout the ovarian cycle and, consequently, the macroscopic classification of gonad stages agree with the modifications of the reproductive cells.

Preparació de materials híbrids orgànico-inorgànics a partir de sals d'imidazoli

Estudi elaborat a partir d’una estada a l’ Ecole Nationale Supérieure de Chimie de Montpellier, França, durant 2006. S’han sintetitzat materials híbrids orgànico-inorgànics mitjançant el procés sol-gel i altres estratègies sintètiques. En alguns casos, s’ha intentat estructurar aquests materials, ja sigui per autoestructuració o per mitjà de tensioactius. Com a catalitzadors de les reaccions d'hidròlisi i policondensació s’han utilitzat àcids, bases i fluorurs. Els materials obtinguts s’han caracteritzat mitjançant diferents tècniques: BET (Brunauer-Emmett-Teller), TEM (microscopia electrònica de transmissió), SEM (microscòpia electrònica de rastreig), raigs X en pols , IR i RMN (ressonància magnètica nuclear) en estat sòlid. Amb aquests materials es pretén preparar catalitzadors heterogenis de Pd per reaccions d’acoblament creuat, i de Ru per reaccions de metàtesi. També s’han sintetitzat sals d'imidazoli amb cadenes hidrocarbonades llargues amb l'objectiu de preparar gels de sílice amb aquestes molècules atrapades dins la matriu inorgànica. Aquests materials s’utilitzaran com a organocatalitzadors i també es prepararan els corresponents catalitzadors de Pd per reaccions de Heck, Suzuki i Sonogashira. Les sals d’imidazoli s’han utilitzat com a tensioactius en la preparació de gels de sílice estructurats. Aquestes molècules han resultat ser cristalls líquids i s’han caracteritzar mitjançant DSC (differential scanning calorimetry), microscopia òptica i raigs X.

Solid-phase synthesis and NMR studies of modified oligonucleotides forming triplex helix and of oligonucleopeptides mimicking the topoisomerase I-DNA covalent complex

Report for the scientific sojourn carried out at the Institut de Biologia Molecular de Barcelona of the CSIC –state agency – from april until september 2007. Topoisomerase I is an essential nuclear enzyme that modulates the topological status of DNA, facilitating DNA helix unwinding during replication and transcription. We have prepared the oligonucleotide-peptide conjugate Ac-NLeu-Asn-Tyr(p-3’TTCAGAAGC5’)-LeuC-CONH-(CH2)6-OH as model compound for NMR studies of the Topoisomerase I- DNA complex. Special attention was made on the synthetic aspects for the preparation of this challenging compound especially solid supports and protecting groups. The desired peptide was obtained although we did not achieve the amount of the conjugate needed for NMR studies. Most probably the low yield is due to the intrinsic sensitive to hydrolysis of the phosphate bond between oligonucleotide and tyrosine. We have started the synthesis and the structural characterization of oligonucleotides carrying intercalating compounds. At the present state we have obtained model duplex and quadruplex sequences modified with acridine and NMR studies are underway. In addition to this project we have successfully resolved the structure of a fusion peptide derived from hepatitis C virus envelope synthesized by the group of Dr. Haro and we have synthesized and started the characterization of a modified G-quadruplex.

Drug susceptibility of Brazilian strains of Mycobacterium bovis using traditional and molecular techniques

Transmission of Mycobacterium bovis from cattle to humans has been reported and can cause tuberculosis (Tb) and a problem in certain risk populations. Therefore, knowledge of resistance of M. bovis towards antibiotics used for therapy of human Tb could help avoiding cure delay and treatment cost increase when dealing with drug resistant organisms. We therefore evaluated the susceptibility of M. bovis isolates towards streptomycin, isoniazide, rifampicin, ethambutol, and ethionamide, the first line antibiotics for human Tb. Therefore, 185 clinical samples from cattle with clinical signs of tuberculosis were processed and submitted to culturing and bacterial isolates to identification and drug susceptibility testing using the proportion method. Among 89 mycobacterial strains, 65 were identified as M. bovis and none were resistant to any of the antibiotics used. Confirmation of present results by future studies, enrolling a large number of isolates and designed to properly represent Brazilian regions, may favor the idea of using isoniazide preventive therapy as part of a Tb control strategy in special situations. Also, nucleic acids from bacterial isolates were submitted to rifoligotyping, a recently described reverse hybridization assay for detection of mutations causing resistance towards rifampicin. Concordance between the conventional and the molecular test was 100%, demonstrating the use of such methodology for rapid evaluation of drug susceptibility in M. bovis.

Exploration of alpine orographic precipitation patterns with radar image processing and clustering techniques

A methodology of exploratory data analysis investigating the phenomenon of orographic precipitation enhancement is proposed. The precipitation observations obtained from three Swiss Doppler weather radars are analysed for the major precipitation event of August 2005 in the Alps. Image processing techniques are used to detect significant precipitation cells/pixels from radar images while filtering out spurious effects due to ground clutter. The contribution of topography to precipitation patterns is described by an extensive set of topographical descriptors computed from the digital elevation model at multiple spatial scales. Additionally, the motion vector field is derived from subsequent radar images and integrated into a set of topographic features to highlight the slopes exposed to main flows. Following the exploratory data analysis with a recent algorithm of spectral clustering, it is shown that orographic precipitation cells are generated under specific flow and topographic conditions. Repeatability of precipitation patterns in particular spatial locations is found to be linked to specific local terrain shapes, e.g. at the top of hills and on the upwind side of the mountains. This methodology and our empirical findings for the Alpine region provide a basis for building computational data-driven models of orographic enhancement and triggering of precipitation. Copyright (C) 2011 Royal Meteorological Society .

Evaluation of parasitological and molecular techniques for the diagnosis and assessment of cure of schistosomiasis mansoni in a low transmission area

This study evaluated parasitological and molecular techniques for the diagnosis and assessment of cure of schistosomiasis mansoni. A population-based study was performed in 201 inhabitants from a low transmission locality named Pedra Preta, municipality of Montes Claros, state of Minas Gerais, Brazil. Four stool samples were analysed using two techniques, the Kato-Katz® (KK) technique (18 slides) and the TF-Test®, to establish the infection rate. The positivity rate of 18 KK slides of four stool samples was 28.9% (58/201) and the combined parasitological techniques (KK+TF-Test®) produced a 35.8% positivity rate (72/201). Furthermore, a polymerase chain reaction (PCR)-ELISA assay produced a positivity rate of 23.4% (47/201) using the first sample. All 72 patients with positive parasitological exams were treated with a single dose of Praziquantel® and these patients were followed-up 30, 90 and 180 days after treatment to establish the cure rate. Cure rates obtained by the analysis of 12 KK slides were 100%, 100% and 98.4% at 30, 90 and 180 days after treatment, respectively. PCR-ELISA revealed cure rates of 98.5%, 95.5% and 96.5%, respectively. The diagnostic and assessment of cure for schistosomiasis may require an increased number of KK slides or a test with higher sensitivity, such as PCR-ELISA, in situations of very low parasite load, such as after therapeutic interventions.

Identification and quantification techniques in mass spectrometry-based proteomics

Résumé La protéomique basée sur la spectrométrie de masse est l'étude du proteome l'ensemble des protéines exprimées au sein d'une cellule, d'un tissu ou d'un organisme - par cette technique. Les protéines sont coupées à l'aide d'enzymes en plus petits morceaux -les peptides -, et, séparées par différentes techniques. Les différentes fractions contenant quelques centaines de peptides sont ensuite analysées dans un spectromètre de masse. La masse des peptides est enregistrée et chaque peptide est séquentiellement fragmenté pour en obtenir sa séquence. L'information de masse et séquence est ensuite comparée à une base de données de protéines afin d'identifier la protéine d'origine. Dans une première partie, la thèse décrit le développement de méthodes d'identification. Elle montre l'importance de l'enrichissement de protéines comme moyen d'accès à des protéines de moyenne à faible abondance dans le lait humain. Elle utilise des injections répétées pour augmenter la couverture en protéines et la confiance dans l'identification. L'impacte de nouvelle version de base de données sur la liste des protéines identifiées est aussi démontré. De plus, elle utilise avec succès la spectrométrie de masse comme alternative aux anticorps, pour valider la présence de 34 constructions de protéines pathogéniques du staphylocoque doré exprimées dans une souche de lactocoque. Dans une deuxième partie, la thèse décrit le développement de méthodes de quantification. Elle expose de nouvelles approches de marquage des terminus des protéines aux isotopes stables et décrit la première méthode de marquage des groupements carboxyliques au niveau protéine à l'aide de réactifs composé de carbone 13. De plus, une nouvelle méthode, appelée ANIBAL, marquant tous les groupements amines et carboxyliques au niveau de la protéine, est exposée. Summary Mass spectrometry-based proteomics is the study of the proteome -the set of all expressed proteins in a cell, tissue or organism -using mass spectrometry. Proteins are cut into smaller pieces - peptides - using proteolytic enzymes and separated using different separation techniques. The different fractions containing several hundreds of peptides are than analyzed by mass spectrometry. The mass of the peptides entering the instrument are recorded and each peptide is sequentially fragmented to obtain its amino acid sequence. Each peptide sequence with its corresponding mass is then searched against a protein database to identify the protein to which it belongs. This thesis presents new method developments in this field. In a first part, the thesis describes development of identification methods. It shows the importance of protein enrichment methods to gain access to medium-to-low abundant proteins in a human milk sample. It uses repeated injection to increase protein coverage and confidence in identification and demonstrates the impact of new database releases on protein identification lists. In addition, it successfully uses mass spectrometry as an alternative to antibody-based assays to validate the presence of 34 different recombinant constructs of Staphylococcus aureus pathogenic proteins expressed in a Lactococcus lactis strain. In a second part, development of quantification methods is described. It shows new stable isotope labeling approaches based on N- and C-terminus labeling of proteins and describes the first method of labeling of carboxylic groups at the protein level using 13C stable isotopes. In addition, a new quantitative approach called ANIBAL is explained that labels all amino and carboxylic groups at the protein level.

Assessment of Weathering Steel Bridge Performance in Iowa and Development of Inspection and Maintenance Techniques, RB17-012, 2013

Weathering steel is commonly used as a cost-effective alternative for bridge superstructures, as the costs and environmental impacts associated with the maintenance/replacement of paint coatings are theoretically eliminated. The performance of weathering steel depends on the proper formation of a surface patina, which consists of a dense layer of corrosion product used to protect the steel from further atmospheric corrosion. The development of the weathering steel patina may be hindered by environmental factors such as humid environments, wetting/drying cycles, sheltering, exposure to de-icing chlorides, and design details that permit water to pond on steel surfaces. Weathering steel bridges constructed over or adjacent to other roadways could be subjected to sufficient salt spray that would impede the development of an adequate patina. Addressing areas of corrosion on a weathering steel bridge superstructure where a protective patina has not formed is often costly and negates the anticipated cost savings for this type of steel superstructure. Early detection of weathering steel corrosion is important to extending the service life of the bridge structure; however, written inspection procedures are not available for inspectors to evaluate the performance or quality of the patina. This project focused on the evaluation of weathering steel bridge structures, including possible methods to assess the quality of the weathering steel patina and to properly maintain the quality of the patina. The objectives of this project are summarized as follows:  Identify weathering steel bridge structures that would be most vulnerable to chloride contamination, based on location, exposure, environment, and other factors.  Identify locations on an individual weathering steel bridge structure that would be most susceptible to chloride contamination, such as below joints, splash/spray zones, and areas of ponding water or debris.  Identify possible testing methods and/or inspection techniques for inspectors to evaluate the quality of the weathering steel patina at locations discussed above.  Identify possible methods to measure and evaluate the level of chloride contamination at the locations discussed above.  Evaluate the effectiveness of water washing on removing chlorides from the weathering steel patina.  Develop a general prioritization for the washing of bridge structures based on the structure’s location, environment, inspection observations, patina evaluation findings, and chloride test results.

Validation of tissue modelization and classification techniques in T1-weighted MR brain images

We propose a deep study on tissue modelization andclassification Techniques on T1-weighted MR images. Threeapproaches have been taken into account to perform thisvalidation study. Two of them are based on FiniteGaussian Mixture (FGM) model. The first one consists onlyin pure gaussian distributions (FGM-EM). The second oneuses a different model for partial volume (PV) (FGM-GA).The third one is based on a Hidden Markov Random Field(HMRF) model. All methods have been tested on a DigitalBrain Phantom image considered as the ground truth. Noiseand intensity non-uniformities have been added tosimulate real image conditions. Also the effect of ananisotropic filter is considered. Results demonstratethat methods relying in both intensity and spatialinformation are in general more robust to noise andinhomogeneities. However, in some cases there is nosignificant differences between all presented methods.

Studies on the characterization of dental whitening process by using both hyperspectral imaging and colorimeter techniques

A beautiful smile is directly related with white teeth. Nowadays oral care has increased and developed processes for beautiful smiles. Dental bleaching is frequently used in odontology, not just for health care also for aesthetic treatment. With the possibility of teeth bleaching, now the importance is in, how white the tooth is? Because color is relate to an individual perception. In order to assets teeth correct color identification has been developed many color guides, models, spaces and analytical methods. Spite all of these useful tools the color interpretation depends on environmental factors, position of the sample in the data acquisition and most importantly the instrument sensitivity. The commons methods have proved to be useful. They are easy to handle, some are portable but they do not have a high sensitivity. The present work is based on the integration of a new analytical technique for color acquisition. High spectral Image (HSI) is able to performed image analysis with high quality and efficiency. HSI is used in many fields and we used it for color image analysis within the bleaching process. The main comparison was done with the HSI and the colorimeter through the processes of two different bleaching protocols. The results showed that HSI has higher sensitivity than the colorimeter. During the analysis the dental surface with the HSI we were able to notice surface changes. These changes were analyzed by roughness studies.

Selenium content of Finnish oats in 1997-1999 : effect of cultivars and cultivation techniques

Selostus: Suomalaisen kauran seleenipitoisuus vuosina 1997-1999