671 research outputs found

    Roadmap of optical communications

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    © 2016 IOP Publishing Ltd. Lightwave communications is a necessity for the information age. Optical links provide enormous bandwidth, and the optical fiber is the only medium that can meet the modern society's needs for transporting massive amounts of data over long distances. Applications range from global high-capacity networks, which constitute the backbone of the internet, to the massively parallel interconnects that provide data connectivity inside datacenters and supercomputers. Optical communications is a diverse and rapidly changing field, where experts in photonics, communications, electronics, and signal processing work side by side to meet the ever-increasing demands for higher capacity, lower cost, and lower energy consumption, while adapting the system design to novel services and technologies. Due to the interdisciplinary nature of this rich research field, Journal of Optics has invited 16 researchers, each a world-leading expert in their respective subfields, to contribute a section to this invited review article, summarizing their views on state-of-the-art and future developments in optical communications

    Single-cell time course analysis of metabolic switching in inducible gene regulatory networks

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    Die Optimierung der Zuckerverwertung ist für Bakterien insbesondere unter variablen Umweltbedingungen essentieller Teil ihrer Überlebensstrategien. Bei zwei konkurrierenden und fluktuierenden Nahrungsangeboten stellt sich die Frage, ob eine homogene oder heterogene Anpassung optimal ist. Um solche Anpassungsmechanismen zu verstehen, wurde metabolisches Schaltverhalten anhand von Genexpression mit Hilfe von Reportergenen sowie zeitaufgelöster Fluoreszenz-Mikroskopie auf Einzelzellebene in Escherichia coli untersucht. Da Genexpression ein inhärent stochastischer Prozess ist, können ausgeprägte Unterschiede zwischen einzelnen Zellen auftreten. Diese Expressionsunterschiede können Teil komplexer Überlebensstrategien sein. In dieser Arbeit wird das Schaltverhalten in Antwort auf eine Nährstoffänderung in direkter bakterieller Umgebung sowie das Umschalten zwischen verschiedenen Verwertungsstrategien als Reaktion auf die Zugabe zweier unterschiedlicher Nährstoffe in verschiedenen Konzentrationen analysiert. Im ersten Teil dieser Arbeit wird das Schaltverhalten im Arabinose-Verwertungssystem untersucht. Hier wurde gezeigt, dass das Abschalten der Genexpression nach Entfernen der induzierend wirkenden Arabinose in allen Zellen innerhalb kurzer Zeit, also homogen abläuft, im Gegensatz zum heterogenen Anschalten. Da die Genexpression in induzierbaren Zuckerverwertungssystemen stark vom Wert der intrazellulären Konzentration des induzierenden Zuckers abhängt, muss zum Abschalten der Genexpression dieser Konzentrationswert unter das zur Induktion nötige Niveau sinken. Ein Absinken der internen Zuckerkonzentration kann entweder über Abbau oder Export des Zuckers geschehen. Innerhalb der hier möglichen Zeitauflösung wurde mit Hilfe einer Mutante, der das Abbauenzymgen araBAD fehlt, keine Abhängigkeit des zeitlichen Abschaltverhaltens von diesem Enzym gefunden. Zusätzlich ist das Abschalten unabhängig von der Expression eines potenziellen Exportproteins des Arabinosesystems. Daher ist möglicherweise ein bisher unbekannter nicht-kanonischer Abbau- oder Exportweg für das schnelle und homogene Abschalten der Genexpression verantwortlich. Der zweite Teil dieser Arbeit beschäftigt sich mit dem Schaltverhalten im Phosphotransferase System, das die Aufnahme zahlreicher Zucker an die Verfügbarkeit von Phosphorgruppen innerhalb der Zelle koppelt. Erstmals wurden quantitative Messungen zum Schaltverhalten des PTS für zwei ausgewählte Zuckerverwertungssysteme, N-acetyl-glucosamine (NAG) und Sorbitol, durchgeführt. Der konkurrierende Prozess um die importlimitierende Ressource Phosphor wurde durch Messung der Genexpression der Systeme sowie durch den konzentrationsabhängigen Einfluss der Zucker auf die Wachstumsrate analysiert. Abhängig von der externen NAG Konzentration zeigten sich zwei Verhaltensweisen: Hohe NAG Konzentrationen führen zu hierarchischem Verwerten der Zucker in Übereinstimmung mit theoretischen Vorhersagen, bei niedrigen Konzentrationen hingegen werden die metabolischen Gene beider Systeme simultan angeschaltet. Mit Hilfe eines mathematischen Modells, das asymmetrische Zuckerqualität sowie variable Kopplung implementiert, kann das gemessene Phasendiagramm der Genexpression reproduziert werden. Daher ist es plausibel, dass die simultane Expression der beiden Systeme unter Bedingungen eines nicht-limitierenden Phosphorflusses von einer Entkopplung der Zuckerverwertungssysteme rührt. Die Tatsache, dass die Zellen für das PTS zwei Schaltverhalten kennen, weist auf eine effiziente Regulation mittels Beschränkung des Phosphorflusses hin und könnte insbesondere bei der Anpassung der metabolischen Überlebensstrategie einer Zelle an vorherrschende Umweltbedingungen ebenso von Nutzen sein wie ein schnelles Abschalten der Genexpression nach Entfernen der externen Arabinose

    Rendimiento de TCP y Cálculo de Rutas en Redes de Conmutación Óptica de Ráfagas

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    La tecnología de conmutación óptica de ráfagas (Optical Burst Switching, OBS) es una alternativa prometedora para la próxima generación de redes ópticas. Esta tesis estudia el comportamiento de flujos de datos que empleen el protocolo de transporte TCP (Transmission Control Protocol) sobre una red basada en la mencionada tecnología OBS. Así, la tesis estudia el impacto del asentimiento retardado en OBS, propone un modelo teórico que captura el funcionamiento de TCP sobre OBS con múltiples flujos y estudia el efecto de la sincronización de flujos TCP en una red OBS. Además, la tesis propone una técnica de encaminamiento adaptativa y multicamino para OBS, y diseña e implementa un elemento de cálculo de rutas basado en PCE (Path Computation Element) para redes de conmutación de ráfagas OBS con encaminamiento por longitud de onda, conocidas como WR-OBS (Wavelength-Routed OBS).Departamento de Teoría de la Señal y Comunicaciones e Ingeniería Telemátic

    Structural and Functional Characterization of Acetoacetate Decarboxylase-Like Enzymes

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    The acetatoacetate decarboxylase-like superfamily (ADCSF) is a largely unexplored group of enzymes that may be a potential source of new biocatalysts. Bioinformatic analysis has grouped these approximately 2000 enzymes into seven different families based on comparison of predicted active site residues. To date, only the prototypical ADCs (Family I) that catalyze the decarboxylation of acetoacetate have been studied. Analysis of gene context suggests that Family V contains predominantly enzymes predicted to be involved in secondary metabolism. On average, these share about 20% sequence identity to the true ADCs. To learn more about the diversity of chemistries performed by members of Family V, we have been studying two enzymes annotated as acetoacetate decarboxylase in the GenBank database. These are Sbi_00515 from Streptomyces bingchenggensis and Swit_4259 from Sphingomonas wittichii. Steady state analyses of these enzymes demonstrate that both lack decarboxylase activity with any of the substrates tested. This was surprising given that the crystal structures of both enzymes show that their overall folds are almost indistinguishable from that of the prototypical ADCs, though the quaternary structures are different. An important observation from the bioinformatic and crystallographic analyses is that the catalytic lysine and putative acid/base catalyst residues of the true ADCs are retained in both groups of enzymes, but the active site architectures are different. Specifically, two residues shown to be important for the acetoacetate decarboxylase reaction, Arg29 and Glu61 in Clostridium acetobutylicum ADC (CaADC), are not retained in the Family V enzymes. Site-directed mutagenesis, steady state and transient kinetics, and mass spectroscopy data suggest evidence for reversible aldolase-dehydratase and retro-aldolase activities mediated through a Schiff-base mechanism. These are the first Schiff-base-forming aldolases that do not use the TIM barrel fold. Although the physiologically relevant reactions of these Family V enzymes are unknown, these studies illustrate that the ADC fold is a versatile platform that can be adapted to perform different chemistries

    Optoelectronics – Devices and Applications

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    Optoelectronics - Devices and Applications is the second part of an edited anthology on the multifaced areas of optoelectronics by a selected group of authors including promising novices to experts in the field. Photonics and optoelectronics are making an impact multiple times as the semiconductor revolution made on the quality of our life. In telecommunication, entertainment devices, computational techniques, clean energy harvesting, medical instrumentation, materials and device characterization and scores of other areas of R&D the science of optics and electronics get coupled by fine technology advances to make incredibly large strides. The technology of light has advanced to a stage where disciplines sans boundaries are finding it indispensable. New design concepts are fast emerging and being tested and applications developed in an unimaginable pace and speed. The wide spectrum of topics related to optoelectronics and photonics presented here is sure to make this collection of essays extremely useful to students and other stake holders in the field such as researchers and device designers

    Towards light based dynamic control of synthetic biological systems

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    For the field of synthetic biology, the adaptation of principles, from the well established traditional engineering disciplines, like mechanical and electrical engineering, in order to realise complex synthetic biological circuits, is an intriguing prospect. These principles can enable a forward engineering, rational design and implementation approach, where a system's properties can be predicted or designed in silico followed by the manufacturing of the in vivo system, that can be tested, used or redesigned in the most efficient possible way. Achieving control over these circuits, is one of the important topics of the field, for these applications to become robust and render useful functions applicable to energy, medicine, pharmaceuticals and agriculture industries. In this work, I attempt to explore light, as a promising control 'dial' for synthetic circuitry. Light is fast, economic compared to chemicals, it can be interfaced with electronics, it is reversible in its effect and can be applied at a fine spatio-temporal resolution. These characteristics, are absent from the classically used chemical inducers, meaning that light, can open new possibilities for the user to control synthetic systems, or even facilitate the cell to cell communication, within population based networks. This work, is a contribution towards harnessing the advantages of light, for achieving control over synthetic circuits. More specifically, I start with the detailed theoretical and experimental study of the Cph8 two component system, a synthetic chimeric receptor which is responsive to red light. This is done, in order to develop a sufficient theoretical understanding of it, through detailed mechanistic modelling, in order to connect the specific system with the toggle switch and the dual feedback oscillator, in an optimal way and achieve control of these devices through light. The developed model, was able to highlight the main aspects and mechanisms inherent to its structure, describe most of the observations from the experimental system, to also make quantitative predictions. The second part of this work, was the development of novel promoters, that can be regulated by a commonly used transcription factor, such as LacI, but also, light responsive regulators like OmpR and CcaR. This yielded a direct way to integrate light and chemical inputs, into a single output, while the dual regulation, allowed to connect and modulate the toggle switch without the need of additional transcription factors. The latter, a light tuneable toggle switch, showed indications that it can function as a memory controller that can be reset by light. Finally, I show the design and modelling of a light tuneable dual feedback oscillator, where light of one wavelength can be used to tune the amplitude, while another wavelength can tune the period. The developed models and synthetic circuits are expected to contribute towards implementing finely tuned and controlled synthetic circuits through light.Open Acces

    Single-molecule spectroscopy: investigations of protein folding to multi-laboratory consistencies on proteins

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    The investigation of complex biological processes has been challenging and require a variety of sophisticated tools to interpret the underlying processes. The study of the folding process in proteins is one of the focuses of this thesis work. To this end, both spontaneous and chaperone- assisted folding mechanisms were investigated. Single-molecule fluorescence spectroscopy has been extensively applied to the study of biomolecular bindings, conformational changes, and their dynamics due to its high sensitivity, time resolution, and its ability to differentiate between homogenous and heterogenous populations. Specifically, single-molecule Förster Resonance Energy Transfer (smFRET) studies on protein folding have elucidated the basic mechanisms of spontaneous protein folding, and properties of the chaperone-substrate interactions. The possibility to measure at low concentrations making it possible to avoid the aggregation, which is difficult to avoid in ensemble experiments. To investigate the spontaneous folding mechanisms in large multi-domain proteins, two-color smFRET studies were carried out on a slowly folding version of the two-domain Maltose- binding protein (MBP). Three-color smFRET, an extension of typical two-color smFRET to three-colors, was applied on specifically labeled MBP to visualize the co-ordination between the domains as they fold. Chaperone-substrate interactions are crucial to process the substrates and thus enable them to carry out their physiological function. Cavity confinement effect of GroEL/ES, a bacterial Hsp60 on MBP folding landscape was demonstrated. Another substrate protein, p53-DNA-binding domain was probed concerning the combined action of Hsp70 and Hsp90 chaperone on its folding. To conclude the thesis work, a smFRET comparison study on proteins involving 16 laboratories was undertaken to assess the accuracy and precision of smFRET measurements as well as to determine a detection limit for dynamic motions in proteins
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