Correction of the misclassification of species in the Portuguese collection of Cucurbita pepo L. using DNA markers

In this study, the genetic variability among 130 accessions of the Portuguese germplasm collection of Cucurbita pepo L. maintained at the Banco Portugues de Germoplasma Vegetal was assessed using AFLP (amplified fragment length polymorphism) and RAPD (random amplified polymorphic DNA) techniques for the identification of a genetically diverse core group of accessions for field phenotypic analysis. The surprisingly completely different molecular patterns exhibited by multiple accessions was later confirmed in the distribution of the putative C. pepo plants into two clusters drastically separated at a very low level of genetic similarity (DICE coefficient = 0.37). Additional analyses with RAPD and ISSR (inter single sequence repeat) markers and the introduction of standard genotypes of C. maxima L. and C. moschata L. into the analyses allowed the identification of multiple accessions of the last species wrongly included in the C. pepo collection. This study is a good example of the usefulness of DNA markers in the establishment and management of plant germplasm collections.

Contribution to the study of prognostic factors in canine oral squamous cell carcinoma

Tese de Doutoramento em Ciências Veterinárias, na Especialidade de Clínica

Genetic diversity across geographical scales in marine coastal ecosystems: Holothuria arguinensis a model species

Coastal lagoons are considered one of the most productive areas of our planet harboring a large variety of habitats. Their transitional character, between terrestrial and marine environments, creates a very particular ecosystem with important variations of its environmental conditions. The organisms that are able to survive on these ecosystems frequently experience strong selective pressures and constrictions to gene flowwith marine populations, which could contribute to genetic divergence among populations inhabiting coastal lagoon and marine environments. Therefore, the main aims of this study are to asses the genetic diversity and population structure of Holothuria arguinensis across geographical ranges, to test the hypothesis of coastal lagoons as hotspots of genetic diversity in the Ria Formosa lagoon, and to determine the role of exporting standing genetic variation from the lagoon to open sea and their implications to recent geographical expansion events. To reach these objectives, we investigate the genetic structure of H. arguinensis using two mitochondrial DNA markers (COI and 16S) at different spatial scales: i) small, inside Ria Formosa coastal lagoon, South Portugal; 2) large, including most of the geographical distribution of this species (South and Western Portuguese coast and Canary islands); these results will allow us to compare the genetic diversity of lagoonal and marine populations of H. arguinensis. On this framework, its recent geographical expansion events, recorded by Rodrigues (2012) and González-Wangüemert and Borrero-Pérez (2012), will be analyzed considering the potential contribution from lagoonal genetic pool. Non-significant genetic structure and high haplotypic diversity were found inside the Ria Formosa coastal lagoon. Both genes were unable to detect significant genetic differentiation among lagoonal and marine localities, suggesting a high rate of gene flow. The results supported our hypotheses that coastal lagoons are not only acting as hotspots of genetic diversity, but also contributing for the genetic variability of the species, working as a source of new haplotypes and enhancing adaptation to the high variable conditions. Different genetic patterns of colonization were found on H. arguinensis, but they must be studied more deeply.

A possibility for non-invasive diagnosis of superficial scald in 'Rocha' pear based on chlorophyll a fluorescence, colorimetry, and the relation between alpha-farnesene and conjugated trienols

This study aimed to identify physiological markers in superficially scalded 'Rocha' pear (Pyrus communis L 'Rocha') that would relate to chlorophyll a fluorescence (CF), allowing a non-invasive diagnosis of the disorder. Conditions chosen before shelf life provided two fruit groups with different developing patterns and severity of superficial scald: T fruit fully developed the disorder in storage, while C fruit developed it progressively throughout shelf life. Principal component analysis (PCA) of all the measured variables, and simple linear correlations among several major parameters and scald index (SI)/shelf life showed that scald and ripening/aging were concurring processes, and that it was not possible to isolate a particular variable that could deliver a direct non-invasive diagnosis of the disorder. For both fruit groups the SI resulted from the balance between the reducing power (OD200) and the content of conjugated trienols (CTos) and alpha-farnesene (alpha-Farn) in the fruit peel. At OD200 > 150 there was a linear relationship between CTos and OD200, suggesting that the level of antioxidants was self-adjusted in order to compensate the CTos level. However, at OD200 < 150 this relationship disappeared. A consistent linear relationship between dos and alpha-Farn existed throughout shelf life in both fruit groups, contrarily to the early storage stage, when those compounds do not relate linearly. The CF variables F-0, F-v/F-m, and the colorimetric variables, L* and h degrees were used in multi-linear regressions with other physiological variables. The regressions were made on one of the fruit groups and validated through the other. Reliable regressions to alpha-Farn and CTos were obtained (R approximate to 0.6; rmsec approximate to rmsep). Our results suggest that a model based on CF and colorimetric parameters could be used to diagnose non-invasively both the contents and the relationship between alpha-Farn and CTos and hence the stage of scald development. (C) 2011 Elsevier By. All rights reserved.

Correction of the misclassification of species in the Portuguese collection of Cucurbita pepo L. using DNA markers

In this study, the genetic variability among 130 accessions of the Portuguese germplasm collection of Cucurbita pepo L. maintained at the Banco Portugues de Germoplasma Vegetal was assessed using AFLP (amplified fragment length polymorphism) and RAPD (random amplified polymorphic DNA) techniques for the identification of a genetically diverse core group of accessions for field phenotypic analysis. The surprisingly completely different molecular patterns exhibited by multiple accessions was later confirmed in the distribution of the putative C. pepo plants into two clusters drastically separated at a very low level of genetic similarity (DICE coefficient = 0.37). Additional analyses with RAPD and ISSR (inter single sequence repeat) markers and the introduction of standard genotypes of C. maxima L. and C. moschata L. into the analyses allowed the identification of multiple accessions of the last species wrongly included in the C. pepo collection. This study is a good example of the usefulness of DNA markers in the establishment and management of plant germplasm collections.

Flow around a hemisphere-cylinder at high angle of attack and low Reynolds number. Part I: Experimental and numerical investigation

Three-dimensional Direct Numerical Simulations combined with Particle Image Velocimetry experiments have been performed on a hemisphere-cylinder at Reynolds number 1000 and angle of attack 20◦. At these flow conditions, a pair of vortices, so-called “horn” vortices, are found to be associated with flow separation. In order to understand the highly complex phenomena associated with this fully threedimensional massively separated flow, different structural analysis techniques have been employed: Proper Orthogonal and Dynamic Mode Decompositions, POD and DMD, respectively, as well as criticalpoint theory. A single dominant frequency associated with the von Karman vortex shedding has been identified in both the experimental and the numerical results. POD and DMD modes associated with this frequency were recovered in the analysis. Flow separation was also found to be intrinsically linked to the observed modes. On the other hand, critical-point theory has been applied in order to highlight possible links of the topology patterns over the surface of the body with the computed modes. Critical points and separation lines on the body surface show in detail the presence of different flow patterns in the base flow: a three-dimensional separation bubble and two pairs of unsteady vortices systems, the horn vortices, mentioned before, and the so-called “leeward” vortices. The horn vortices emerge perpendicularly from the body surface at the separation region. On the other hand, the leeward vortices are originated downstream of the separation bubble, as a result of the boundary layer separation. The frequencies associated with these vortical structures have been quantified.

Tuberculosis in alpacas (Lama pacos) caused by Mycobacterium bovis

We report three cases of tuberculosis in alpacas from Spain caused by Mycobacterium bovis. The animals revealed two different lesional patterns. Mycobacterial culture and PCR assay yielded positive results for M. bovis. Molecular typing of the isolates identified spoligotype SB0295 and identical variable-number tandem repeat (VNTR) allele sizes.

Optimizing countershading camouflage

Countershading, the widespread tendency of animals to be darker on the side that receives strongest illumination, has classically been explained as an adaptation for camouflage: obliterating cues to 3D shape and enhancing background matching. However, there have only been two quantitative tests of whether the patterns observed in different species match the optimal shading to obliterate 3D cues, and no tests of whether optimal countershading actually improves concealment or survival. We use a mathematical model of the light field to predict the optimal countershading for concealment that is specific to the light environment and then test this prediction with correspondingly patterned model “caterpillars” exposed to avian predation in the field. We show that the optimal countershading is strongly illumination-dependent. A relatively sharp transition in surface patterning from dark to light is only optimal under direct solar illumination; if there is diffuse illumination from cloudy skies or shade, the pattern provides no advantage over homogeneous background-matching coloration. Conversely, a smoother gradation between dark and light is optimal under cloudy skies or shade. The demonstration of these illumination-dependent effects of different countershading patterns on predation risk strongly supports the comparative evidence showing that the type of countershading varies with light environment.

Numerical simulations of significant orographic precipitation in Madeira island

High-resolution simulations of high precipitation events with the MESO-NHmodel are presented, and also used to verify that increasing horizontal resolution in zones of complex orography, such as in Madeira island, improve the simulation of the spatial distribution and total precipitation. The simulations succeeded in reproducing the general structure of the cloudy systems over the ocean in the four periods considered of significant accumulated precipitation. The accumulated precipitation over theMadeirawas better represented with the 0.5 km horizontal resolution and occurred under four distinct synoptic situations. Different spatial patterns of the rainfall distribution over the Madeira have been identified

Analytics and Methods for Logistic System Design and Operations Management

Analytics is the technology working with the manipulation of data to produce information able to change the world we live every day. Analytics have been largely used within the last decade to cluster people’s behaviour to predict their preferences of items to buy, music to listen, movies to watch and even electoral preference. The most advanced companies succeded in controlling people’s behaviour using analytics. Despite the evidence of the super-power of analytics, they are rarely applied to the big data collected within supply chain systems (i.e. distribution network, storage systems and production plants). This PhD thesis explores the fourth research paradigm (i.e. the generation of knowledge from data) applied to supply chain system design and operations management. An ontology defining the entities and the metrics of supply chain systems is used to design data structures for data collection in supply chain systems. The consistency of this data is provided by mathematical demonstrations inspired by the factory physics theory. The availability, quantity and quality of the data within these data structures define different decision patterns. Ten decision patterns are identified, and validated on-field, to address ten different class of design and control problems in the field of supply chain systems research.

The ontogeny of bipedalism: insights from the study of talar growth

The development of bipedal locomotion was gradual during evolution, and with the increase in discoveries of fossils and, in particular, in discoveries of pedal bones, the attention to this problematic has grown in the last decades. Moreover, the discoveries of juveniles fossil foot bones has led the attention to the evolution and the development of bipedal locomotion. The study of the development of human gait in children may help in shedding light to the development of human locomotion. The human talus plays a pivotal role, linking the leg to the foot and receiving and distributing the weight, while permitting a wide range of foot movements. It is also present at birth, and this makes a perfect bone to study to disentangle how the bone structure acts to cope with the changes in locomotion and body weight. Here, I analyze the external and internal morphology of the human talus from the perinatal period to adolescence, to investigate how the different phases of the acquisition of bipedal gait affect talar morphology, and how the bone copes with the weight gain during growth. Results show that the talar internal and external morphologies change in line with the different activities and loading of the foot. Initially, at around birth, the talus has a very globular and immature external shape, with a very dense trabecular architecture, composed of thin, numerous, and densely packed trabeculae, with a rather isotropic structure. External and internal morphologies change in relation to the different loading patterns which follow during growth, showing a more specialized structure, both in the external and internal morphology, linked to the maturation of bipedal locomotion, until the adult-like pattern is reached, during adolescence.

Enteroinvasive Escherichia coli vs. Shigella flexneri : how different patterns of gene expression affect virulence

Important features of the enteroinvasive Escherichia coli (EIEC) phenotype and gene expression likely to confer EIEC with a lower ability to cause disease than Shigella flexneri were described here for the first time. To confirm the lower pathogenicity of EIEC, we have analyzed the keratoconjunctivitis developed in guinea-pigs with EIEC or S. flexneri. Shigella flexneri induced a more pronounced proinflammatory response, whereas EIEC induced a mild form of the disease. EIEC showed a significantly less efficient cell-to-cell Caco-2 dissemination when compared with S. flexneri. Plaques formed by EIEC during intercellular spreading were four times smaller than those formed by S. flexneri. At the molecular level, the lower expression of virulence genes by EIEC during infection of Caco-2 cells highlighted the importance of effective gene transcription for bacterial pathogenicity.

Ventilation Patterns Influence Airway Secretion Movement

BACKGROUND: Retention of airway secretions is a common and serious problem in ventilated patients. Treating or avoiding secretion retention with mucus thinning, patient-positioning, airway suctioning, or chest or airway vibration or percussion may provide short-term benefit. METHODS: In a series of laboratory experiments with a test-lung system we examined the role of ventilator settings and lung-impedance on secretion retention and expulsion. Known quantities of a synthetic dye-stained mucus simulant with clinically relevant properties were injected into a transparent tube the diameter of an adult trachea and exposed to various mechanical-ventilation conditions. Mucus-simulant movement was measured with a photodensitometric technique and examined with image-analysis software. We tested 2 mucus-simulant viscosities and various peak flows, inspiratory/ expiratory flow ratios, intrinsic positive end-expiratory pressures, ventilation waveforms, and impedance values. RESULTS: Ventilator settings that produced flow bias had a major effect on mucus movement. Expiratory How bias associated with intrinsic positive end-expiratory pressure generated by elevated minute ventilation moved mucus toward the airway opening, whereas intrinsic positive end-expiratory pressure generated by increased airway resistance moved the mucus toward the lungs. Inter-lung transfer of mucus simulant occurred rapidly across the ""carinal divider"" between interconnected test lungs set to radically different compliances; the mucus moved out of the low-compliance lung and into the high-compliance lung. CONCLUSIONS: The movement of mucus simulant was influenced by the ventilation pattern and lung impedance. Flow bias obtained with ventilator settings may clear or embed mucus during mechanical ventilation.

Macromolecular array patterns of silk gland secretion in social Hymenoptera larvae

The cocoon, produced by most holometabolous insects, is built with silk that is usually produced by the larval salivary gland. Although this silk has been widely studied in the Lepidoptera, its composition and macromolecular arrangement remains unknown in the Hymenoptera. The macromolecular array patterns of the silk in the larval salivary gland of some meliponids, wasps, and ants were analyzed with polarized-light microscopy, and they were compared with those of Bombyx mori (Lepidoptera). There is a birefringent secretion in the glandular lumen of all larvae, due to filamentous structural proteins that display anisotropy. The silk in the distal, middle and proximal regions of the secretory portion of Formicidae and Vespidae glands presented a lattice optical pattern. We found a different pattern in the middle secretory portion of the Meliponini, with a zigzag rather than a lattice pattern. This indicates that the biopolymer fibers begin their macromolecular reorganization at this glandular region, different from the Formicidae and the Vespidae, in which the zigzag optical pattern was only found at the lateral duct. Probably, the mechanism of silk production in the Hymenoptera is a characteristic inherited from a common ancestor of Vespoidea and Sphecoidea; the alterations in the pattern observed in the Meliponini could be a derived characteristic in the Hymenoptera. We found no similarity in the macromolecular reorganization patterns of the silk between the Hymenoptera species and the silkworm.

Neutrophil extracellular traps identification in tegumentary lesions of patients with paracoccidioidomycosis and different patterns of NETs generation in vitro

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)