Signal transduction-related responses to phytohormones and environmental challenges in sugarcane

Abstract Background Sugarcane is an increasingly economically and environmentally important C4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. Sugarcane originated from crosses of Saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. Environmental stresses limit enormously sugarcane productivity worldwide. To investigate transcriptome changes in response to environmental inputs that alter yield we used cDNA microarrays to profile expression of 1,545 genes in plants submitted to drought, phosphate starvation, herbivory and N2-fixing endophytic bacteria. We also investigated the response to phytohormones (abscisic acid and methyl jasmonate). The arrayed elements correspond mostly to genes involved in signal transduction, hormone biosynthesis, transcription factors, novel genes and genes corresponding to unknown proteins. Results Adopting an outliers searching method 179 genes with strikingly different expression levels were identified as differentially expressed in at least one of the treatments analysed. Self Organizing Maps were used to cluster the expression profiles of 695 genes that showed a highly correlated expression pattern among replicates. The expression data for 22 genes was evaluated for 36 experimental data points by quantitative RT-PCR indicating a validation rate of 80.5% using three biological experimental replicates. The SUCAST Database was created that provides public access to the data described in this work, linked to tissue expression profiling and the SUCAST gene category and sequence analysis. The SUCAST database also includes a categorization of the sugarcane kinome based on a phylogenetic grouping that included 182 undefined kinases. Conclusion An extensive study on the sugarcane transcriptome was performed. Sugarcane genes responsive to phytohormones and to challenges sugarcane commonly deals with in the field were identified. Additionally, the protein kinases were annotated based on a phylogenetic approach. The experimental design and statistical analysis applied proved robust to unravel genes associated with a diverse array of conditions attributing novel functions to previously unknown or undefined genes. The data consolidated in the SUCAST database resource can guide further studies and be useful for the development of improved sugarcane varieties.

Order induced charge carrier mobility enhancement in columnar liquid crystal diodes

Discotic molecules comprising a rigid aromatic core and flexible side chains have been promisingly applied in OLEDs as self-organizing organic semiconductors. Due to their potentially high charge carrier mobility along the columns, device performance can be readily improved by proper alignment of columns throughout the bulk. In the present work, the charge mobility was increased by 5 orders of magnitude due to homeotropic columnar ordering induced by the boundary interfaces during thermal annealing in the mesophase. State-of-the-art diodes were fabricated using spin-coated films whose homeotropic alignment with formation of hexagonal germs was observed by polarizing optical microscopy. The photophysical properties showed drastic changes at the mesophase-isotropic transition, which is supported by the gain of order observed by X-ray diffraction. The electrical properties were investigated by modeling the current−voltage characteristics by a space-charge-limited current transport with a field dependent mobility.

Análisis del uso de las redes neuronales artificiales en el diseño de filtros antispam : una propuesta basada en arquitecturas neuronales no supervisadas

[ES]El spam, o correo no deseado enviado masivamente, es una amenaza que afecta al correo electrónico y otros medios de comunicación telemática. Su alto volumen de circulación genera pérdidas temporales y económicas considerables. Se presenta una solución a este problema: un sistema inteligente híbrido de filtrado antispam, basado en redes neuronales artificiales (RNA) no supervisadas. Consta de una etapa de preprocesado y de otra de procesado, basadas en distintos modelos de computación: programada (con 2 fases: manual y computacional) y neuronal (mediante mapas autoorganizados de Kohonen, SOM), respectivamente. Este sistema ha sido optimizado usando, como cuerpo de datos, ham de “Enron Email” y spam de dos fuentes diferentes. Se analiza la calidad y el rendimiento del mismo mediante diferentes métricas.

La piattaforma BTSSOC-Cellulat per la simulazione di sistemi biochimici

Il lavoro svolto in questa tesi verte sullo sviluppo e l'integrazione del modello teorico conosciuto come Biochemical Tuple Spaces for Self-Organizing Coordination, in breve BTSSOC, in una piattaforma completa, chiamata BTSSOC-Cellulat, per la simulazione di sistemi biochimici, sviluppata utilizzando i linguaggi Java, Prolog, TuCSoN e ReSpecT.

Structure and dynamics of supramolecular assemblies studied by advanced solid-state NMR spectroscopy

Ziel der vorliegenden Arbeit ist die Aufklärung von Struktur und Dynamik komplexer supramolekularer Systeme mittels Festkörper NMR Spektroskopie. Die Untersuchung von pi-pi Wechselwirkungen, welche einen entscheidenden Einfluss auf die strukturellen und dynamischen Eigenschaften supra- molekularer Systeme haben, hilft dabei, die Selbst- organisationsprozesse dieser komplexen Materialien besser zu verstehen. Mit dipolaren 1H-1H and 1H-13C Wiedereinkopplungs NMR Methoden unter schnellem MAS können sowohl 1H chemische Verschiebungen als auch dipolare 1H-1H und 1H-13C Kopplungen untersucht werden, ohne dass eine Isotopenmarkierung erforderlich ist. So erhält man detaillierte Informationen über die Struktur und die Beweglichkeit einzelner Molekül- segmente. In Verbindung mit sogenannten nucleus independent chemical shift (NICS) maps (berechnet mit ab-initio Methoden) lassen sich Abstände von Protonen relativ zu pi-Elektronensystemen bestimmen und so Strukturvorschläge ableiten. Mit Hilfe von homo- und heteronuklearen dipolaren Rotationsseitenbandenmustern könnenaußerdem Ordnungs- parameter für verschiedene Molekülsegmente bestimmt werden. Die auf diese Weise gewonnenen Informationen über die strukturellen und dynamischen Eigenschaften supramolekularer Systeme tragen dazu bei, strukturbestimmende Molekül- einheiten und Hauptordnungsphänomene zu identifizieren sowie lokale Wechselwirkungen zu quantifizieren, um so den Vorgang der Selbstorganisation besser zu verstehen.

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

Liquid crystalline elastomers as stimuli-responsive microactuators

Liquid crystalline elastomers (LCEs) are known to perform a reversible change of shape upon the phase transition from the semi-ordered liquid crystalline state to the chaotic isotropic state. This unique behavior of these “artificial muscles” arises from the self-organizing properties of liquid crystals (mesogens) in combination with the entropy-elasticity of the slightly crosslinked elastomer network. In this work, micrometer-sized LCE actuators are fabricated in a microfluidic setup. The microtubular shear flow provides for a uniform orientation of the mesogens during the crosslinking, a perquisite for obtaining actuating LCE samples. The scope of this work was to design different actuator geometries and to broaden the applicability of the microfluidic device for different types of liquid crystalline mesogens, ranging from side-chain to main-chain systems, as well as monomer and polymer precursors. For example, the thiol-ene “click” mechanism was used for the polymerization and crosslinking of main-chain LCE actuators. The main focus was, however, placed on acrylate monomers and polymers with LC side chains. A LC polymer precursor, comprising mesogenic and crosslinkable side-chains was synthesized. Used in combination with an LC monomer, the polymeric crosslinker promoted a stable LC phase, which allowed the mixture to be isothermally handled in the microfluidic reactor. If processed without the additional LC components, the polymer precursor yielded actuating fibers. A suitable co-flowing continuous phase facilitates the formation of a liquid jet and lowers the tendency for drop formation. By modification of the microfluidic device, it was further possible to prepare core-shell particles, comprised of an LCE shell and filled with an isotropic liquid. In analogy to the heart, a hollow muscle, the elastomer shell expels the inner liquid core upon its contraction. The feasibility of the core-shell particles as micropumps was demonstrated. In general, the synthesized LCE microactuators may be utilized as active components in micromechanical and lab-on-chip systems.

Untersuchung der Auswirkungen verschiedener Variationsbereiche des differenziellen Lernens und Lehrens im weiten Sinn auf ausgewählte technische Grundfertigkeiten im Hallenhockey

Die Frage wie großmotorische Bewegungen gelernt werden beschäftigt nicht nur Sportler, Trainer und Sportlehrer sondern auch Ärzte und Physiotherapeuten. Die sportwissenschaftlichen Teildisziplinen Bewegungs- und Trainingswissenschaft versuchen diese Frage sowohl im Sinne der Grundlagenforschung (Wie funktioniert Bewegungslernen?) als auch hinsichtlich der praktischen Konsequenzen (Wie lehrt man Bewegungen?) zu beantworten. Innerhalb dieser Themenfelder existieren Modelle, die Bewegungslernen als gezielte und extern unterstützte Ausbildung zentralnervöser Bewegungsprogramme verstehen und solche, die Lernen als Selbstorganisationsprozess interpretieren. Letzteren ist das Differenzielle Lernen und Lehren (Schöllhorn, 1999) zuzuordnen, das die Notwendigkeit betont, Bewegungen durch die Steigerung der Variationen während der Aneignungsphase zu lernen und zu lehren. Durch eine Vielzahl an Variationen, so die Modellannahme, findet der Lernende ohne externe Vorgaben selbstorganisiert ein individuelles situatives Optimum. Die vorliegende Arbeit untersucht, welchen Einfluss Variationen verschiedener Art und Größe auf die Lern- und Aneignungsleistung großmotorischer Bewegungen haben und in wie fern personenübergreifende Optima existieren. In zwei Experimenten wird der Einfluss von räumlichen (Bewegungsausführung, Bewegungsergebnis) und zeitlichen Variationen (zeitliche Verteilung der Trainingsreize) auf die Aneignungs- und Lernleistung großmotorischer sportlicher Bewegungen am Beispiel zweier technischer Grundfertigkeiten des Hallenhockeys untersucht. Die Ergebnisse der Experimente stützen die bisherige Befundlage zum Differenziellen Lernen und Lehren, wonach eine Zunahme an Variation in der Aneignungsphase zu größeren Aneignungs- und Lernleistungen führt. Zusätzlich wird die Annahme bestätigt, dass ein Zusammenhang von Variationsbereich und Lernrate in Form eines Optimaltrends vorliegt. Neu sind die Hinweise auf die Dynamik von motorischen Lernprozessen (Experiment 1). Hier scheinen individuelle Faktoren (z. B. die Lernbiografie) als auch die Phase im Lernprozess (Aneignung, Lernen) Einfluss zu haben auf den Umfang und die Struktur eines für die optimale Adaptation notwendigen Variationsbereichs. Darüber hinaus weisen die Befunde auf verschiedene Aneignungs- und Lerneffekte aufgrund alleiniger Variation der zeitlichen Verteilung bei ansonsten gleichen Trainingsreizen hin (Experiment 2). Für zukünftige Forschungsarbeiten zum Erlernen großmotorischer Bewegungen und für die sportliche Praxis dürfte es daher erkenntnisreich sein, die Historie der intrinsischen Dynamik der lernenden Systeme stärker zu berücksichtigen. Neben Fragestellungen für die Grundlagenforschung zum (Bewegungs-)Lernen ließen sich hieraus unmittelbar praxisrelevante Erkenntnisse darüber ableiten, wie Bewegungslernprozesse mittels verschiedener Variationsbereiche strukturiert und gesteuert werden könnten.

Integration von Heizern in thermotrope flüssigkristalline Elastomer-Aktoren und deren Anwendung beim technischen Nachbau eines menschlichen Auges

Flüssigkristalline Elastomere (LCE) zeigen eine reversible Kontraktion und werden in der Literatur auch als „künstliche Muskeln“ bezeichnet. In dieser Arbeit werden sie mit einem integrierten Heizer versehen, um eine schnelle und präzise Ansteuerung zu ermöglichen. Anschließend werden diese als Aktoren zur Realisierung eines technischen Nachbaus des menschlichen Auges verwendet. rnDas einzigartige Verhalten der flüssigkristallinen Elastomere beruht auf der Kombination der Entropie Elastizität des Elastomers mit der Selbstorganisation der flüssigkristallinen Einheiten (Mesogene). Diese beiden Eigenschaften ermöglichen eine reversible, makroskopische Verformung beim Phasenübergang des Flüssigkristalls in die isotrope Phase. Hierbei ist es wichtig eine homogene Orientierung der Mesogene zu erzeugen, was in dieser Arbeit durch ein Magnetfeld erreicht wird. Da es sich um ein thermotropes flüssigkristallines Elastomer handelt, werden in dieser Arbeit zwei Ansätze vorgestellt, um den LCE intern zu heizen. Zum einen werden Kohlenstoffnanoröhren integriert, um diese über Strahlung oder Strom zu heizen und zum anderen wird ein flexibler Heizdraht integriert, welcher ebenfalls über Strom geheizt wird. rnUm den technischen Nachbau des menschlichen Auges zu realisieren, ist die Herstellung einer flüssigkristallinen Iris gezeigt. Hierzu wird ein radiales Magnetfeld aufgebaut, welches eine radiale Orientierung des Mesogene ermöglicht, wodurch wiederum eine radiale Kontraktion ermöglicht wird. Außerdem sind zwei Konzepte vorgestellt, um eine Elastomer Linse zu verformen. Zum einen wird diese mit einem ringförmigen LCE auseinandergezogen und somit abgeflacht. Zum anderen sind acht Aktoren über Anker an einer Linse angebracht, welche ebenfalls eine Vergrößerung der Linse bewirken. In beiden Fällen werden LCE mit dem zuvor präsentierten integrierten Heizdraht verwendet. Abschließend ist das Zusammensetzen des technische Nachbaus des menschlichen Auges dargestellt, sowie Aufnahmen, welche mit diesem erzeugt wurden.

Radiation metabolomics. 1. Identification of minimally invasive urine biomarkers for gamma-radiation exposure in mice

Gamma-radiation exposure has both short- and long-term adverse health effects. The threat of modern terrorism places human populations at risk for radiological exposures, yet current medical countermeasures to radiation exposure are limited. Here we describe metabolomics for gamma-radiation biodosimetry in a mouse model. Mice were gamma-irradiated at doses of 0, 3 and 8 Gy (2.57 Gy/min), and urine samples collected over the first 24 h after exposure were analyzed by ultra-performance liquid chromatography-time-of-flight mass spectrometry (UPLC-TOFMS). Multivariate data were analyzed by orthogonal partial least squares (OPLS). Both 3- and 8-Gy exposures yielded distinct urine metabolomic phenotypes. The top 22 ions for 3 and 8 Gy were analyzed further, including tandem mass spectrometric comparison with authentic standards, revealing that N-hexanoylglycine and beta-thymidine are urinary biomarkers of exposure to 3 and 8 Gy, 3-hydroxy-2-methylbenzoic acid 3-O-sulfate is elevated in urine of mice exposed to 3 but not 8 Gy, and taurine is elevated after 8 but not 3 Gy. Gene Expression Dynamics Inspector (GEDI) self-organizing maps showed clear dose-response relationships for subsets of the urine metabolome. This approach is useful for identifying mice exposed to gamma radiation and for developing metabolomic strategies for noninvasive radiation biodosimetry in humans.

Adaptive Materialbereitstellung in flexiblen Produktionssystemen auf Grundlage einer agentenbasierten Transportsteuerung

Zur Sicherstellung einer schnellen und flexiblen Anpassung an sich ändernde Anforderungen sind innerbetriebliche Materialbereitstellungskonzepte in immer stärkerem Maße zu flexibilisieren. Hierdurch kann die Erreichung logistischer Ziele in einem dynamischen Produktionsumfeld gesteigert werden. Der Beitrag stellt ein Konzept für eine adaptive Materialbereitstellung in flexiblen Produktionssystemen auf Grundlage einer agentenbasierten Transportplanung und -steuerung vor. Der Fokus liegt hierbei auf der Planung und Steuerung der auf Basis von Materialbedarfsmeldungen ausgelösten innerbetrieblichen Transporte. Neben Pendeltouren zur Versorgung des Produktionssystems findet auch das dynamische Pickup-and-Delivery-Problem Berücksichtigung. Das vorgestellte Konzept ist an den Anforderungen selbstorganisierender Produktionsprozesse ausgerichtet.

Towards an Emergent Semantic Web

In his in uential article about the evolution of the Web, Berners-Lee [1] envisions a Semantic Web in which humans and computers alike are capable of understanding and processing information. This vision is yet to materialize. The main obstacle for the Semantic Web vision is that in today's Web meaning is rooted most often not in formal semantics, but in natural language and, in the sense of semiology, emerges not before interpretation and processing. Yet, an automated form of interpretation and processing can be tackled by precisiating raw natural language. To do that, Web agents extract fuzzy grassroots ontologies through induction from existing Web content. Inductive fuzzy grassroots ontologies thus constitute organically evolved knowledge bases that resemble automated gradual thesauri, which allow precisiating natural language [2]. The Web agents' underlying dynamic, self-organizing, and best-effort induction, enable a sub-syntactical bottom up learning of semiotic associations. Thus, knowledge is induced from the users' natural use of language in mutual Web interactions, and stored in a gradual, thesauri-like lexical-world knowledge database as a top-level ontology, eventually allowing a form of computing with words [3]. Since when computing with words the objects of computation are words, phrases and propositions drawn from natural languages, it proves to be a practical notion to yield emergent semantics for the Semantic Web. In the end, an improved understanding by computers on the one hand should upgrade human- computer interaction on the Web, and, on the other hand allow an initial version of human- intelligence amplification through the Web.

Software Development in the Cloud: Exploring the Affordances of Platform-as-a-Service

Software development teams increasingly adopt platform-as-a-service (PaaS), i.e., cloud services that make software development infrastructure available over the internet. Yet, empirical evidence of whether and how software development work changes with the use of PaaS is difficult to find. We performed a grounded-theory study to explore the affordances of PaaS for software development teams. We find that PaaS enables software development teams to enforce uniformity, to exploit knowledge embedded in technology, to enhance agility, and to enrich jobs. These affordances do not arise in a vacuum. Their emergence is closely interwoven with changes in methodologies, roles, and norms that give rise to self-organizing, loosely coupled teams. Our study provides rich descriptions of PaaS-based software development and an emerging theory of affordances of PaaS for software development teams.

Timed mind maps using MINDMANAGER & MS-PROJECT for educational innovation

The adaptation to the European Higher Education Area (EHEA) is becoming a great challenge for the University Community, especially for its teaching and research staff, which is involved actively in the teaching-learning process. It is also inducing a paradigm change for lecturers and students. Among the methodologies used for processes of teaching innovation, system thinking plays an important role when working mainly with mind maps, and is focused to highlighting the essence of the knowledge, allowing its visual representation. In this paper, a method for using these mind maps for organizing a particular subject is explained. This organization is completed with the definition of duration, precedence relationships and resources for each of these activities, as well as with their corresponding monitoring. Mind maps are generated by means of the MINDMANAGER package whilst Ms-PROJECT is used for establishing tasks relationships, durations, resources, and monitoring. Summarizing, a procedure and the necessary set of applications for self organizing and managing (timed) scheduled teaching tasks has been described in this paper.