BRCA1, a 'complex' protein involved in the maintenance of genomic stability

BRCA1 is a major breast and ovarian cancer susceptibility gene, with mutations in this gene predisposing women to a very high risk of developing breast and ovarian tumours. BRCA1 primarily functions to maintain genomic stability via critical roles in DNA repair, cell cycle checkpoint control, transcriptional regulation, apoptosis and mRNA splicing. As a result, BRCA1 mutations often result in defective DNA repair, genomic instability and sensitivity to DNA damaging agents. BRCA1 carries out these different functions through its ability to interact, and form complexes with, a vast array of proteins involved in multiple cellular processes, all of which are considered to contribute to its function as a tumour suppressor. This review discusses and highlights recent research into the functions of BRCA1-related protein complexes and their roles in maintaining genomic stability and tumour suppression.

Optimisation of singlet oxygen production from photosensitiser-incorporated, medically-relevant hydrogels

Photodynamic therapy and photodynamic antimicrobial chemotherapy are widely used, but despite this, the relationships between fluence, wavelength of irradiation and singlet oxygen (1O2) production are poorly understood. To establish the relationships between these factors in medically-relevant materials, the effect of fluence on 1O2 production from a tetrakis(4-N-methylpyridyl)porphyrin (TMPyP)-incorporated 2-hydroxyethyl methacrylate: methyl methacrylate: methacrylic acid (HEMA:MMA:MAA) copolymer, a total energy of 50.48 J/cm², was applied at varying illumination power, and times. 1O2 production was characterised using anthracene-9,10-dipropionic acid, disodium salt (ADPA) using a recently described method. Using two light sources, a white LED array and a white halogen source, the LED array was found to produce less 1O2 than the halogen source when the same power (over 500-600 nm) and time conditions were applied. Importantly, it showed that the longest wavelength Q band (590 nm) is primarily responsible for 1O2 generation, and that a linear relationship exists between increasing power and time and the production of singlet oxygen.

Optimization of singlet oxygen production from photosensitizer-incorporated, medically relevant hydrogels

Photodynamic therapy and photodynamic antimicrobial chemotherapy are widely used, but despite this, the relationships between fluence, wavelength of irradiation and singlet oxygen ((1) O2 ) production are poorly understood. To establish the relationships between these factors in medically relevant materials, the effect of fluence on (1) O2 production from a tetrakis(4-N-methylpyridyl)porphyrin (TMPyP)-incorporated 2-hydroxyethyl methacrylate: methyl methacrylate: methacrylic acid (HEMA: MMA:MAA) copolymer, a total energy of 50.48 J/cm(2) , was applied at varying illumination power, and times. (1) O2 production was characterized using anthracene-9,10-dipropionic acid, disodium salt (ADPA) using a recently described method. Using two light sources, a white LED array and a white halogen source, the LED array was found to produce less (1) O2 than the halogen source when the same power (over 500 - 600 nm) and time conditions were applied. Importantly, it showed that the longest wavelength Q band (590 nm) is primarily responsible for (1) O2 generation, and that a linear relationship exists between increasing power and time and the production of singlet oxygen. 

YSOVAR: Mid-infrared Variability in the Star-forming Region Lynds 1688

The emission from young stellar objects (YSOs) in the mid-infrared (mid-IR) is dominated by the inner rim of their circumstellar disks. We present IR data from the Young Stellar Object VARiability (YSOVAR) survey of ~800 objects in the direction of the Lynds 1688 (L1688) star-forming region over four visibility windows spanning 1.6 yr using the Spitzer Space Telescope in its warm mission phase. Among all light curves, 57 sources are cluster members identified based on their spectral energy distribution and X-ray emission. Almost all cluster members show significant variability. The amplitude of the variability is larger in more embedded YSOs. Ten out of 57 cluster members have periodic variations in the light curves with periods typically between three and seven days, but even for those sources, significant variability in addition to the periodic signal can be seen. No period is stable over 1.6 yr. Nonperiodic light curves often still show a preferred timescale of variability that is longer for more embedded sources. About half of all sources exhibit redder colors in a fainter state. This is compatible with time-variable absorption toward the YSO. The other half becomes bluer when fainter. These colors can only be explained with significant changes in the structure of the inner disk. No relation between mid-IR variability and stellar effective temperature or X-ray spectrum is found.

Temperatura e luz na germinação do endemismo algarvio Tuberaria major

Dissertação mest., Gestão Sustentável de Espaços Rurais, Universidade do Algarve, 2009

Object segregation and local gist vision using low-level geometry

Multi-scale representations of lines, edges and keypoints on the basis of simple, complex and end-stopped cells can be used for object categorisation and recognition (Rodrigues and du Buf, 2009 BioSystems 95 206-226). These representations are complemented by saliency maps of colour, texture, disparity and motion information, which also serve to model extremely fast gist vision in parallel with object segregation. We present a low-level geometry model based on a single type of self-adjusting grouping cell, with a circular array of dendrites connected to edge cells located at several angles.

WTS-1-TvD

Brown sample with two mains domains. The general clast shape ranges from sub-angular to sub-rounded. The first one is light brown with closely clustered clasts ranging from small to large. Lineations are common amongst the smaller clasts. Grain crushing is commonly seen with larger clasts. The other domain is a darker brown with better dispersed clasts ranging from small to medium. Lineations are common in this domain.

Développement du cartilage articulaire équin du fœtus à l’adulte : imagerie par résonance magnétique et microscopie en lumière polarisée

La structure du cartilage articulaire adulte est caractérisée par la présence de couches créées par l’orientation des fibres de collagène (Benninghoff, 1925). Avant de présenter la structure adulte classique en arcades “de Benninghoff”, le cartilage subit une série de changements au cours de sa maturation (Julkunen et al., 2010; Lecocq et al., 2008). Toutefois, un faible nombre d’études s’est intéressé à la structure du collagène du cartilage articulaire in utero. Notre objectif était d’étudier la maturation de la surface articulaire de l’épiphyse fémorale distale chez le cheval, en employant à la fois l’imagerie par résonance magnétique (IRM) et la microscopie en lumière polarisée après coloration au rouge picrosirius, au niveau de sites utilisés dans les études de réparation tissulaire et de sites prédisposés à l’ostéochondrose (OC). Le but était de décrire le développement normal du réseau de collagène et la relation entre les images IRM et la structure histologique. Des sections provenant de cinq sites de l’épiphyse fémorale distale de 14 fœtus et 10 poulains et adultes ont été colorées au rouge picrosirius, après que le grasset ait été imagé par IRM, dans l’optique de visualiser l’agencement des fibres de collagène de type II. Les deux modalités utilisées, IRM et microscopie en lumière polarisée, ont démontré la mise en place progressive d’une structure en couches du réseau de collagène, avant la naissance et la mise en charge de l’articulation.

Etude spectroscopique d’un plasma micro-onde à la pression atmosphérique et son application à la synthèse de nanostructures

L’objectif de ce mémoire de maîtrise est de caractériser la distribution axiale des plasmas tubulaires à la pression atmosphérique créés et entretenus par une onde électromagnétique de surface ainsi que d’explorer le potentiel de ces sources pour la synthèse de matériaux et de nanomatériaux. Un précédent travail de thèse, qui avait pour objectif de déterminer les mécanismes à l’origine de la contraction radiale du plasma créé dans des gaz rares, a mis en lumière un phénomène jusque-là inconnu dans les plasmas d’onde de surface (POS). En effet, la distribution axiale varie différemment selon la puissance incidente ce qui constitue une différence majeure par rapport aux plasmas à pression réduite. Dans ce contexte, nous avons réalisé une étude paramétrique des POS à la pression atmosphérique dans l’Ar. À partir de nos mesures de densité électronique, de température d’excitation et de densité d’atomes d’Ar dans un niveau métastable (Ar 3P2), résolues axialement, nous avons conclu que le comportement axial de l’intensité lumineuse avec la puissance n’est pas lié à un changement de la cinétique de la décharge (qui est dépendante de la température des électrons et de la densité d’atomes d’Ar métastables), mais plutôt à une distribution anormale de dissipation de puissance dans le plasma (reliée à la densité d’électrons). Plus précisément, nos résultats suggèrent que ce dépôt anormal de puissance provient d’une réflexion de l’onde dans le fort gradient de densité de charges en fin de colonne, un effet plus marqué pour de faibles longueurs de colonnes à plasma. Ensuite, nous avons effectué une étude spectroscopique du plasma en présence de précurseurs organiques, en particulier le HMDSO pour la synthèse de matériaux organosiliciés et l’IPT pour la synthèse de matériaux organotitaniques. Les POS à la PA sont caractérisés par des densités de charges très élevées (>10^13 cm^-3), permettant ainsi d’atteindre des degrés de dissociation des précurseurs nettement plus élevés que ceux d'autres plasmas froids à la pression atmosphérique comme les décharges à barrière diélectrique. Dans de tels cas, les matériaux synthétisés prennent la forme de nanopoudres organiques de taille inférieure à 100 nm. En présence de faibles quantités d’oxygène dans le plasma, nous obtenons plutôt des nanopoudres à base d’oxyde de silicium (HMDSO) ou à base de titanate de silicium (IPT), avec très peu de carbone.

Growth of metal and semiconductor nanostructures for nonlinear optical applications

Nonlinear optics has been a rapidly growing field in recent decades since the invention of lasers. The systematic progress in the laser technology increases our efficiency in the generation and control of coherent optical radiations. Nonlinear optics is based on the study ofeffects and phenomena related to the interaction of intense coherent light radiation with matter. Compared to other light sources laser radiation can provide high directionality, high monochromaticiry, high brightness and high photon degeneracy. At such a very intense incident beam, the matter responds in a nonlinear manner to the incident radiation fields, which endows the media :1 characteristic to change the refractive index or absorption coe fflcient of the media or the wavelength, or the frequency of the incident electromagnetic waves. This thesis encompasses the fabrication of nonlinear optical devices based on semiconductor and metal nanostructures. The presented work focus on the experimental and theoretical discussions on nonlinear optical effects especially nonlinear absorption and refraction exhibitted by metal and semiconductor nanostructures

“Spatial and Temporal Variation of Phytoplankton Community and Their Growth Limiting Factors in Cochin Backwater”

The influence of salinity on phytoplankton varies widely, because different species have different salinity preferences. Like marine and aquatic species, many phytoplankton species exhibit tolerance to certain salinity, beyond which, it can inhibit their growth. Light is the most important factor that influences phytoplankton growth. In aquatic environments (lakes, sea or estuary) the light incident on the surface is rapidly reduced exponentially with depth (Krik, 1994). In estuaries, the major factor influencing the light availability is the suspended particulate matter, which attenuates and scatters the light. The light changes with time of the day and the season, affecting the amount of light penetrating the water column. Similarly, biological factor like copepod grazing is a major factor influencing the standing crop of phytoplankton. The copepod can actively graze up to 75% of the phytoplankton biomass in a tropical estuary (Tan et. al., 2004). It is in the context that the present study investigates the salinity, light (physical factors) and copepod grazing (biological factor) phytoplankton as the factors controlling phytoplankton growth and distribution

Hyperspectral field measurements to determine dry matter yield and nutritive value of legume-grass swards

Summary: Productivity, botanical composition and forage quality of legume-grass swards are important factors for successful arable farming in both organic and conventional farming systems. As these attributes can vary considerably within a field, a non-destructive method of detection while doing other tasks would facilitate a more targeted management of crops, forage and nutrients in the soil-plant-animal system. This study was undertaken to explore the potential of field spectral measurements for a non destructive prediction of dry matter (DM) yield, legume proportion in the sward, metabolizable energy (ME), ash content, crude protein (CP) and acid detergent fiber (ADF) of legume-grass mixtures. Two experiments were conducted in a greenhouse under controlled conditions which allowed collecting spectral measurements which were free from interferences such as wind, passing clouds and changing angles of solar irradiation. In a second step this initial investigation was evaluated in the field by a two year experiment with the same legume-grass swards. Several techniques for analysis of the hyperspectral data set were examined in this study: four vegetation indices (VIs): simple ratio (SR), normalized difference vegetation index (NDVI), enhanced vegetation index (EVI) and red edge position (REP), two-waveband reflectance ratios, modified partial least squares (MPLS) regression and stepwise multiple linear regression (SMLR). The results showed the potential of field spectroscopy and proved its usefulness for the prediction of DM yield, ash content and CP across a wide range of legume proportion and growth stage. In all investigations prediction accuracy of DM yield, ash content and CP could be improved by legume-specific calibrations which included mixtures and pure swards of perennial ryegrass and of the respective legume species. The comparison between the greenhouse and the field experiments showed that the interaction between spectral reflectance and weather conditions as well as incidence angle of light interfered with an accurate determination of DM yield. Further research is hence needed to improve the validity of spectral measurements in the field. Furthermore, the developed models should be tested on varying sites and vegetation periods to enhance the robustness and portability of the models to other environmental conditions.

Exploratory and dust-bathing behaviour in laying hens kept in commercial aviaries and furnished cages

The aim of the present thesis was to identify management factors that affect the extent of exploratory behaviour (ground pecking, scratching) as well as quantitative and qualitative as-pects of dust-bathing behaviour in laying hens kept in commercial furnished cages (‘small group housing’) and aviaries. Based on the results, it should be considered which management measures can be recommended for farmers to enhance hen welfare. The feasibility of direct observations of dust-bathing behaviour as well as video observations of exploratory and dust-bathing behaviour was tested in two aviaries. The direct observations were judged to be unfeasible under the conditions encountered. For the analysis of the video recordings, different sampling intervals for instantaneous scan sampling, different extents of observation time, and intra- and inter-observer reliabilities were compared and the most ap-propriate observation scheme selected. Applying the selected scheme (observing the first 16 minutes of every hour distributed over two consecutive light days with a sample interval of two minutes), within the range of environmental conditions found in 22 aviaries, pecking, scratching and dust-bathing behaviour was performed on average 25, 2 and 7 % of the obser-vation time. Hen numbers in the litter were positively associated with stocking density and group size. More scratching was performed with increasing litter height as well as in humid litter. If no litter had been provided, thus substrate consisted of dust and faeces, a reduced proportion of dust-bathing was found. The same method was then used in 16 furnished cage systems. On average 12 % of the total hen number were found on the scratching mats. The hens spent 8 % of the observed time pecking at the mat, 4 % dust-bathing and 0.4 % scratch-ing. Higher proportions were found on the mats and more dust-bathing behaviour occurred, if substrate was provided. Also with increasing light intensity and stocking density more hens were observed on the mats. More pecking and scratching occurred in conditions of higher stocking density, probably due to social facilitation, and of increased mat area per hen. With increasing mat numbers per cage less pecking was observed. Wider mats led to increased dust-bathing behaviour. Finally, 129 dust-baths recorded in 17 aviaries were analysed in detail. On average they lasted 17 minutes, with the tossing phase taking 69 % of this time, including on average 2 vertical wing shakes and 3 scratches with one leg per minute tossing phase. Dust-bath duration de-creased with increasing litter height. Litter type influenced all recorded parameters: dust-bath duration was highest on straw and lowest on fine material and fine material mixed with straw, where on both also the proportion of the tossing phase was lowest. The number of vertical wing shakes during the dust-bath was highest on straw and lowest on fine material mixed with straw as against the frequency of vertical wing shaking that was lowest on straw and highest on fine material. If dust-bathing hens were disturbed twice or more, dust-bathing duration decreased. With increasing light intensity a decreased proportion of the tossing phase as well as a reduced number of vertical wing shakes were recorded. Possibly the light stimulated the hens to dust-bath more often with less tossing behaviour per performance. The observed variation of the dust-bathing parameters could reflect successful adaptation or frustration of the hens. The litter and light conditions on the investigated farms were predominantly restrictive in terms of stimulation of exploration and dust-bathing behaviour. Thus, it was only possible to analyse possible associations between these factors and exploration and dust-bathing behav-iour within the range found. Based on the results the following management recommendations can be given: To allow hens in furnished cages more normal activity, substrate availability should be improved and mat space and light intensity increased. With regard to aviaries as well litter availability should be improved. Litter height should not be too low. Disturbances during dust-bathing should be prevented, but no influencing factors could be identified.

Diffusion of the synthetic pyrethroid permethrin into bed-sediments

Bed-sediments are a sink for many micro-organic contaminants in aquatic environments. The impact of toxic contaminants on benthic fauna often depends on their spatial distribution, and the fate of the parent compounds and their metabolites. The distribution of a synthetic pyrethroid, permethrin, a compound known to be toxic to aquatic invertebrates, was studied using river bed-sediments in lotic flume channels. trans/cis-Permethrin diagnostic ratios were used to quantify the photoisomerization of the trans isomer in water. Rates were affected by the presence of sediment particles and colloids when compared to distilled water alone. Two experiments in dark/light conditions with replicate channels were undertaken using natural sediment, previously contaminated with permethrin, to examine the effect of the growth of an algal biofilm at the sediment-water interface on diffusive fluxes of permethrin into the sediment. After 42 days, the bulk water was removed, allowing a fine sectioning of the sediment bed (i.e., every mm down to 5 mm and then 5-10 mm, then every 10 mm down to 50 mm). Permethrin was detected in all cases down to a depth of 5-10 mm, in agreement with estimates by the Millington and Quirk model, and measurements of concentrations in pore water produced a distribution coefficient (K-d) for each section, High K-d's were observed for the top layers, mainly as a result of high organic matter and specific surface area. Concentrations in the algal biofilm measured at the end of the experiment under light conditions, and increases in concentration in the top 1 mm of the sediment, demonstrated that algal/bacterial biofilm material was responsible for high K-d's at the sediment surface, and for the retardation of permethrin diffusion. This specific partition of permethrin to fine sediment particles and algae may enhance its threat to benthic invertebrates. In addition,the analysis of trans/cis-permethrin isomer ratios in sediment showed greater losses of trans-permethrin in the experiment under light conditions, which may have also resulted from enhanced biological activity at the sediment surface.

Monitoring and modelling the three-dimensional flow of water under drip irrigation

The interpretation of soil water dynamics under drip irrigation systems is relevant for crop production as well as on water use and management. In this study a three-dimensional representation of the flow of water under drip irrigation is presented. The work includes analysis of the water balance at point scale as well as area-average, exploring uncertainties in water balance estimations depending on the number of locations sampled. The water flow was monitored by detailed profile water content measurements before irrigation, after irrigation and 24 h later with a dense array of soil moisture access tubes radially distributed around selected drippers. The objective was to develop a methodology that could be used on selected occasions to obtain 'snap shots' of the detailed three-dimensional patterns of soil moisture. Such patterns are likely to be very complex, as spatial variability will be induced for a number of reasons, such as strong horizontal gradients in soil moisture, variations between individual sources in the amount of water applied and spatial variability is soil hydraulic properties. Results are compared with a widely used numerical model, Hydrus-2D. The observed dynamic of the water content distribution is in good agreement with model simulations, although some discrepancies concerning the horizontal distribution of the irrigation bulb are noted due to soil heterogeneity. (c) 2006 Elsevier B.V. All rights reserved.