Genome-wide transcriptional responses to shade: Linking shade avoidance and auxin

Plants have the ability to use the composition of incident light as a cue to adapt development and growth to their environment. Arabidopsis thaliana as well as many crops are best adapted to sunny habitats. When subjected to shade, these plants exhibit a variety of physiological responses collectively called shade avoidance syndrome (SAS). It includes increased growth of hypocotyl and petioles, decreased growth rate of cotyledons and reduced branching and crop yield. These responses are mainly mediated by phytochrome photoreceptors, which exist either in an active, far-red light (FR) absorbing or an inactive, red light (R) absorbing isoform. In direct sunlight, the R to FR light (R/FR) ratio is high and converts the phytochromes into their physiologically active state. The phytochromes interact with downstream transcription factors such as PHYTOCHROME INTERACTING FACTOR (PIF), which are subsequently degraded. Light filtered through a canopy is strongly depleted in R, which result in a low R/FR ratio and renders the phytochromes inactive. Protein levels of downstream transcription factors are stabilized, which initiates the expression of shade-induced genes such as HFR1, PIL1 or ATHB-2. In my thesis, I investigated transcriptional responses mediated by the SAS in whole Arabidopsis seedlings. Using microarray and chromatin immunoprecipitation data, we identified genome-wide PIF4 and PIF5 dependent shade regulated gene as well as putative direct target genes of PIF5. This revealed evidence for a direct regulatory link between phytochrome signaling and the growth promoting phytohormone auxin (IAA) at the level of biosynthesis, transport and signaling. Subsequently, it was shown, that free-IAA levels are upregulated in response to shade. It is assumed that shade-induced auxin production takes predominantly place in cotyledons of seedlings. This implies, that IAA is subsequently transported basipetally to the hypocotyl and enhances elongation growth. The importance of auxin transport for growth responses has been established by chemical and genetic approaches. To gain a better understanding of spatio-temporal transcriptional regulation of shade-induce auxin, I generated in a second project, an organ specific high throughput data focusing on cotyledon and hypocotyl of young Arabidopsis seedlings. Interestingly, both organs show an opposite growth regulation by shade. I first investigated the spatio-transcriptional regulation of auxin re- sponsive gene, in order to determine how broad gene expression pattern can be explained by the hypothesized movement of auxin from cotyledons to hypocotyls in shade. The analysis suggests, that several genes are indeed regulated according to our prediction and others are regulated in a more complex manner. In addition, analysis of gene families of auxin biosynthetic and transport components, lead to the identification of essential family members for shade-induced growth re- sponses, which were subsequently experimentally confirmed. Finally, the analysis of expression pattern identified several candidate genes, which possibly explain aspects of the opposite growth response of the different organs.

Keraamisten laattojen luokittelu väripiirteiden avulla

Vaikka keraamisten laattojen valmistusprosessi onkin täysin automatisoitu, viimeinen vaihe eli laaduntarkistus ja luokittelu tehdään yleensä ihmisvoimin. Automaattinen laaduntarkastus laattojen valmistuksessa voidaan perustella taloudellisuus- ja turvallisuusnäkökohtien avulla. Tämän työn tarkoituksena on kuvata tutkimusprojektia keraamisten laattojen luokittelusta erilaisten väripiirteiden avulla. Oleellisena osana tutkittiin RGB- ja spektrikuvien välistä eroa. Työn teoreettinen osuus käy läpi aiemmin aiheesta tehdyn tutkimuksen sekä antaa taustatietoa konenäöstä, hahmontunnistuksesta, luokittelijoista sekä väriteoriasta. Käytännön osan aineistona oli 25 keraamista laattaa, jotka olivat viidestä eri luokasta. Luokittelussa käytettiin apuna k:n lähimmän naapurin (k-NN) luokittelijaa sekä itseorganisoituvaa karttaa (SOM). Saatuja tuloksia verrattiin myös ihmisten tekemään luokitteluun. Neuraalilaskenta huomattiin tärkeäksi työkaluksi spektrianalyysissä. SOM:n ja spektraalisten piirteiden avulla saadut tulokset olivat lupaavia ja ainoastaan kromatisoidut RGB-piirteet olivat luokittelussa parempia kuin nämä.

Evidence for daily and weekly rhythmicity but not lunar or seasonal rhythmicity of physical activity in a large cohort of individuals from five different countries.

Background Biological rhythmicity has been extensively studied in animals for many decades. Although temporal patterns of physical activity have been identified in humans, no large-scale, multi-national study has been published, and no comparison has been attempted of the ubiquity of activity rhythms at different time scales (such as daily, weekly, monthly, and annual). Methods Using individually worn actigraphy devices, physical activity of 2,328 individuals from five different countries (adults of African descent from Ghana, South Africa, Jamaica, Seychelles, and the United States) was measured for seven consecutive days at different times of the year. Results Analysis for rhythmic patterns identified daily rhythmicity of physical activity in all five of the represented nationalities. Weekly rhythmicity was found in some, but not all, of the nationalities. No significant evidence of lunar rhythmicity or seasonal rhythmicity was found in any of the groups. Conclusions These findings extend previous small-scale observations of daily rhythmicity to a large cohort of individuals from around the world. The findings also confirm the existence of modest weekly rhythmicity but not lunar or seasonal rhythmicity in human activity. These differences in rhythm strength have implications for the management of health hazards of rhythm misalignment. Key Messages Analysis of the pattern of physical activity of 2,328 individuals from five countries revealed strong daily rhythmicity in all five countries, moderate weekly rhythmicity in some countries, and no lunar rhythmicity or seasonal rhythmicity in any of the countries.

Correcció postural esportiva utilitzant un sensor Kinect

Aquest projecte s’emmarca dins de l’àmbit de la visió per computador, concretament en la utilització de dades de profunditat obtingudes a través d’un emissor i sensor de llum infraroja.El propòsit principal d’aquest projecte és mostrar com adaptar aquestes tecnologies, a l’abast de qualsevol particular, de forma que un usuari durant la pràctica d’una activitat esportiva concreta, rebi informació visual continua dels moviments i gestos incorrectes que està realitzant, en base a uns paràmetres prèviament establerts.L’objectiu d’aquest projecte consisteix en fer una lectura constant en temps real d’una persona practicant una selecció de diverses activitats esportives estàtiques utilitzant un sensor Kinect. A través de les dades obtingudes pel sensor Kinect i utilitzant les llibreries de “skeleton traking” proporcionades per Microsoft s’haurà d’interpretar les dades posturals obtingudes per cada tipus d’esport i indicar visualment i d’una manera intuïtiva els errors que està cometent en temps real, de manera que es vegi clarament a quina part del seu cos realitza un moviment incorrecte per tal de poder corregir-lo ràpidament. El entorn de desenvolupament que s’utilitza per desenvolupar aquesta aplicació es Microsoft Viusal Studio 2010.El llenguatge amb el qual es treballarà sobre Microsoft Visual Studio 2010 és C#

Diffantom: Whole-Brain Diffusion MRI Phantoms Derived from Real Datasets of the Human Connectome Project.

Food allergies are believed to be on the rise and currently management relies on the avoidance of the food. Hen's egg allergy is after cow's milk allergy the most common food allergy; eggs are used in many food products and thus difficult to avoid. A technological process using a combination of enzymatic hydrolysis and heat treatment was designed to produce modified hen's egg with reduced allergenic potential. Biochemical (SDS-PAGE, Size exclusion chromatography and LC-MS/MS) and immunological (ELISA, immunoblot, RBL-assays, animal model) analysis showed a clear decrease in intact proteins as well as a strong decrease of allergenicity. In a clinical study, 22 of the 24 patients with a confirmed egg allergy who underwent a double blind food challenge with the hydrolysed egg remained completely free of symptoms. Hydrolysed egg products may be beneficial as low allergenic foods for egg allergic patients to extent their diet. This article is protected by copyright. All rights reserved.

Laboratory automation in clinical bacteriology: what system to choose?

Automation was introduced many years ago in several diagnostic disciplines such as chemistry, haematology and molecular biology. The first laboratory automation system for clinical bacteriology was released in 2006, and it rapidly proved its value by increasing productivity, allowing a continuous increase in sample volumes despite limited budgets and personnel shortages. Today, two major manufacturers, BD Kiestra and Copan, are commercializing partial or complete laboratory automation systems for bacteriology. The laboratory automation systems are rapidly evolving to provide improved hardware and software solutions to optimize laboratory efficiency. However, the complex parameters of the laboratory and automation systems must be considered to determine the best system for each given laboratory. We address several topics on laboratory automation that may help clinical bacteriologists to understand the particularities and operative modalities of the different systems. We present (a) a comparison of the engineering and technical features of the various elements composing the two different automated systems currently available, (b) the system workflows of partial and complete laboratory automation, which define the basis for laboratory reorganization required to optimize system efficiency, (c) the concept of digital imaging and telebacteriology, (d) the connectivity of laboratory automation to the laboratory information system, (e) the general advantages and disadvantages as well as the expected impacts provided by laboratory automation and (f) the laboratory data required to conduct a workflow assessment to determine the best configuration of an automated system for the laboratory activities and specificities.

Security Authentication using Phase-Encoded Nanoparticle Structures and Polarized Light

Phase encoded nano structures such as Quick Response (QR) codes made of metallic nanoparticles are suggested to be used in security and authentication applications. We present a polarimetric optical method able to authenticate random phase encoded QR codes. The system is illuminated using polarized light and the QR code is encoded using a phase-only random mask. Using classification algorithms it is possible to validate the QR code from the examination of the polarimetric signature of the speckle pattern. We used Kolmogorov-Smirnov statistical test and Support Vector Machine algorithms to authenticate the phase encoded QR codes using polarimetric signatures.

A concurrent region growing algorithm guided by circumscribed contours

Image segmentation of natural scenes constitutes a major problem in machine vision. This paper presents a new proposal for the image segmentation problem which has been based on the integration of edge and region information. This approach begins by detecting the main contours of the scene which are later used to guide a concurrent set of growing processes. A previous analysis of the seed pixels permits adjustment of the homogeneity criterion to the region's characteristics during the growing process. Since the high variability of regions representing outdoor scenes makes the classical homogeneity criteria useless, a new homogeneity criterion based on clustering analysis and convex hull construction is proposed. Experimental results have proven the reliability of the proposed approach

Avaliação quimiométrica da distribuição de metais pesados em composto de lixo urbano domiciliar

The main obstacle to the use of compost from urban waste in agriculture is the presence of heavy metals. Once in the soil, their effect is accumulative and they may contaminate crops and water. The present study reports the evaluation of the chemical distributions of Cu, Pb, Mn and Zn in three different sized fractions (unsieved, < 1,18mm and > 1,18mm) of compost, by means of a sequencial extraction procedure and a chemometric analysis of the total content of all metals in each fraction. The pattern recognition methods showed significant differences in total heavy metal contents for the different fractions. The finest one was the most contaminated. Meanwhile, this fraction presented lower amounts of metals in avaliable forms. This behavior can be attributed to the presence of metal particles in their elemental states in this fraction.

Classificação de água de coco processada e natural por meio de HCA, PCA e teores de íons metálicos determinados por ICP OES

Inductively Coupled Plasma Optical Emission Spectrometry was used to determine Ca, Mg, Mn, Fe, Zn and Cu in samples of processed and natural coconut water. The sample preparation consisted in a filtration step followed by a dilution. The analysis was made employing optimized instrumental parameters and the results were evaluated using methods of Pattern Recognition. The data showed common concentration values for the analytes present in processed and natural samples. Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) indicated that the samples of different kinds were statistically different when the concentrations of all the analytes were considered simultaneously.

Espectroscopia de impedância eletroquímica aplicada ao estudo das reações heterogêneas em ânodos dimensionalmente estáveis

This paper discusses different aspects related to the application of electrochemical impedance spectroscopy (EIS) in the study of heterogeneous electrochemical reactions occurring on Dimensionally Stable anodes (DSA®). The most relevant aspects of the semiconductor/electrolyte interface, the application of the EIS classical equivalent circuit approach and the ac porous model in DSA are presented. The paper shows that DSA type electrodes can be consistently investigated by using the ac porous model and an analysis is presented showing the advantage of applying this kind of approach to study heterogeneous reactions on DSA electrodes. Furthermore, some preliminary results on Ti/Ru0,3Ti(0,7-x)Sn x O2 based electrodes are presented to exemplify the use of the ac porous model analysis.

25 anos de quimiometria no Brasil

Chemometric activities in Brazil are described according to three phases: before the existence of microcomputers in the 1970s, through the initial stages of microcomputer use in the 1980s and during the years of extensive microcomputer applications of the ´90s and into this century. Pioneering activities in both the university and industry are emphasized. Active research areas in chemometrics are cited including experimental design, pattern recognition and classification, curve resolution for complex systems and multivariate calibration. New trends in chemometrics, especially higher order methods for treating data, are emphasized.

Reconhecimento de padrões por métodos não supervisionados: explorando procedimentos quimiométricos para tratamento de dados analíticos

An activity for introducing hierarchical cluster analysis (HCA) and principal component analysis (PCA) during the Instrumental Analytical Chemistry course is presented. The posed problem involves the discrimination of mineral water samples according to their geographical origin. Thirty-seven samples of 9 different brands were considered and the results from the determination of Na, K, Mg, Ca, Sr and Ba were taken into account. Non-supervised methods for pattern recognition were explored to construct a dendrogram, score and loading plots. The devised activity can be adopted for introducing Chemometrics devoted to data handling, stressing its importance in the context of modern Analytical Chemistry.

Classificação de biodiesel na região do visível

Classification of biodiesel by oilseed type using pattern recognition techniques is described. The spectra of the samples were performed in the Visible region, requiring noise removal by use of a first derivative by the Savitzky-Golay method, employing a second-order polynomial and a window of 21 points. The characterization of biodiesel was performed using HCA, PCA and SIMCA. For HCA and PCA methods, one can observe the separation of each group of biodiesel in a spectral region of 405-500 nm. SIMCA model was used in a test group composed of 28 spectral measurements and no errors are obtained.