Mapping intra- and inter-annual dynamics in wetlands with multispectral, thermal and SAR time series

Kartierung der intra- und interannuellen Dynamik von Feuchtgebieten mit multispektralen, thermischen und SAR-Zeitreihen Die Analyse der aktuellen räumlichen Verbreitung und der zeitlichen Entwicklung von Feuchtgebieten stellt eine äußerst komplexe Aufgabe dar, welche durch die Saisonalität, die schwierige Zugänglichkeit und die besonderen Eigenschaften als Ökoton bedingt ist. Erdbeobachtungssysteme sind somit das am besten geeignete Werkzeug, um zeitliche und räumliche Muster von Feuchtgebieten auf globaler Ebene zu beobachten (saisonale Veränderungen und Langzeit-Trends) und um den Einfluss der menschlichen Aktivitäten auf ihre physischen und biologischen Eigenschaften zu untersuchen. Zur Kartierung von raum-zeitlichen Mustern wurden Zeitreihen von Radar- (Sentinel-1), Multispektral- (Sentinel-2) und Thermal-Satellitendaten (MODIS) in fünf Untersuchungsgebieten, mit für Feuchtgebiete unterschiedlichen typischen Charakteristika, untersucht. In Kapitel 1 werden die Problematik in Bezug auf die Definition von Feuchtgebieten erläutert und allgemeine Degradations-Trends beschrieben. Die Kapitel 2 und 3 behandeln einen Algorithmus, der Veränderungen mithilfe von SAR-Zeitreihen feststellt, sowie die Vorteile des Cloud-Computings für das operationelle Monitoring saisonaler Muster und die Erkennung kurzfristig auftretender Veränderungen. In den Kapiteln 4 und 5 werden die zwei Hauptursachen für den Verlust von Feuchtgebieten betrachtet: der Staudammbau und die Ausdehnung landwirtschaftlicher Flächen. In Kapitel 4 werden dichte Zeitreihen multispektraler (Sentinel-2) und SAR-Daten (Sentinel-1) verwendet, um die Feuchtgebiete Albaniens – eines Landes in dem konträre Pläne zum Ausbau seines Wasserkraftpotentials und dem Schutz intakter Flussökosysteme zu Spannungen führen – landesweit zu kartieren. Die synergetischen Vorteile, die sich durch die Fusionierung von multispektralen und SAR-Daten für die Klassifikation ergeben, werden dabei herausgestellt. Kapitel 5 veranschaulicht, dass die Kilombero-Überschwemmungsebene in Tansania ein großes und bedeutendes Feuchtgebiet ist, das in den vergangenen Jahren infolge der weitgehend unkontrollierten Ausbreitung landwirtschaftlicher Flächen in seiner Ausdehnung und seiner Ökologie stark beeinträchtigt wurde. Um die Auswirkungen der Landnutzungsänderungen des Feuchtgebietes während der vergangenen 18 Jahre zu analysieren, wurden eine Zeitreihe (2000 bis 2017) thermaler Daten (MODIS) analysiert. Die drei für die Zeitreihenanalyse angewandten Modelle zeigen, wie landwirtschaftliche Praktiken die Landoberflächentemperatur in den landwirtschaftlich genutzten Gebieten sowie in den angrenzenden natürlichen Feuchtgebieten erhöht haben.Due to wetlands’ seasonality, their difficult access and ecotone character, determining their actual extension and trends over time is a complex task. Earth Observation systems are the most appropriate tool to monitor their spatio-temporal patterns (seasonal changes and long term trends) at global scales, and to study the effects that human activities have in their physical and biological properties. In this work I use time series of radar (Sentinel-1), multispectral (Sentinel-2) and thermal (MODIS) imagery to map the spatio-temporal patterns in 5 wetlands of different characteristics. First, I introduce in chapter 1 the problematic of wetlands’ definitions and their degradation trends. I continue with a brief introduction on remote sensing, time series analysis, and their applications on wetlands’ research and management. In chapters 2 and 3 I implement an algorithm for change detection of time series of Sentinel-1 images and demonstrate the advantages of cloud computation for operational monitoring. In chapters 4 and 5 I address two of the main causes of wetland degradation: dam building and agricultural expansion. In chapter 4 I use dense time series of Sentinel-1 and Sentinel-2 images map all the wetlands of Albania; a country struggling between developing its large hydropower potential or preserving its intact and valuable river ecosystems. I evaluate the synergic advantages of fusing multispectral and radar imagery in combination with knowledge-based rules to produce classification of higher thematic and spatial resolutions. In chapter 5 I present how the Kilombero Floodplain, in Tanzania, has been degraded during the last years due to uncontrolled farmland expansion. I use a time series of thermal imagery (MODIS) from 2000 until 2017 to analyze the effect of land use changes on the wetland. I compare three models for time series analysis and reveal how farming practices have increased the surface temperature of the farmed area, as well as in adjacent natural wetlands.Mapeo de las dinámicas inter- e intra-anuales en humedales con series temporales de imágenes multiespectrales, termales y de radar Debido a la estacionalidad de los humedales, su difícil acceso y sus características de ecotono, determinar su actual extensión y sus tendencias a lo largo del tiempo es una tarea compleja. Los sistemas de observación terrestres son la herramienta más apropiada para monitorear sus patrones espacio-temporales (estacionalidad y tendencias a largo plazo) a escalas globales, y para estudiar los efectos que las actividades humanas causan en sus propiedades físicas y biológicas. En esta tesis uso series temporales de imágenes radar (Sentinel-1), multiespectrales (Sentinel-2) y termales (MODIS) para mapear los patrones espacio-temporales de 5 humedales de diferentes características. En el capítulo 1 describo los retos que derivan de las diferentes definiciones que existen de los humedales. También presento las tendencias globales de degradación que la mayoría de los humedales continúan experimentando en los últimos años. Continúo con una breve introducción de los sistemas de teledetección remota, análisis de series temporales, y sus aplicaciones a la investigación y gestión de los humedales. En los capítulos 2 y 3 implemento un algoritmo de detección de cambios para series temporales de imágenes radar, y muestro las ventajas de usar sistemas de computación en la nube para monitorear cambios en la cobertura del suelo a corto plazo. En los capítulos 4 y 5 trato con dos de las causas más comunes de degradación de humedales: la construcción de presas y la expansión de la agricultura. En el capítulo 4 uso series temporales de imágenes multiespectrales (Sentinel-2) y radar (Sentinel-1) para mapear todos los humedales Albania; un país que se debate entre desarrollar su potencial hidroenergético o preservar sus valiosos e intactos ecosistemas de rivera. Mediante la fusión de imágenes radar y multiespectrales y el uso de reglas de decisión genero un mapa de suficiente resolución espacial y temática para que pueda ser usado por sectores interesados y gestores. En el capítulo 5 presento como las llanuras inundables de Kilombero, en Tanzania, han sido degradadas durante los últimos años debido a la expansión incontrolada de la agricultura. Usando series temporales de imágenes termales (MODIS) desde 2000 hasta 2017 y mapas de cambios de usos del suelo, determino los efectos que estos cambios han tenido en el humedal. Comparo 3 modelos diferentes de análisis de series temporales y muestro cómo la expansión de la agricultura ha incrementado la temperatura superficial terrestre, no solo de la zona cultivada, sino también de zonas adyacentes aún naturales

The Distinctive Regulation of Cyanobacterial Glutamine Synthetase

Glutamine synthetase (GS) features prominently in bacterial nitrogen assimilation as it catalyzes the entry of bioavailable nitrogen in form of ammonium into cellular metabolism. The classic example, the comprehensively characterized GS of enterobacteria, is subject to exquisite regulation at multiple levels, among them gene expression regulation to control GS abundance, as well as feedback inhibition and covalent modifications to control enzyme activity. Intriguingly, the GS of the ecologically important clade of cyanobacteria features fundamentally different regulatory systems to those of most prokaryotes. These include the interaction with small proteins, the so-called inactivating factors (IFs) that inhibit GS linearly with their abundance. In addition to this protein interaction-based regulation of GS activity, cyanobacteria use alternative elements to control the synthesis of GS and IFs at the transcriptional level. Moreover, cyanobacteria evolved unique RNA-based regulatory mechanisms such as glutamine riboswitches to tightly tune IF abundance. In this review, we aim to outline the current knowledge on the distinctive features of the cyanobacterial GS encompassing the overall control of its activity, sensing the nitrogen status, transcriptional and post-transcriptional regulation, as well as strain-specific differences.Deutsche Forschungsgemeinschaft KL 3114/2-1Ministerio de Economía y Competitividad BIO2016-75634-PFEDER BIO2016-75634-

Predicting Species and Structural Diversity of Temperate Forests with Satellite Remote Sensing and Deep Learning

Anthropogenically-driven climate change, land-use changes, and related biodiversity losses are threatening the capability of forests to provide a variety of valuable ecosystem services. The magnitude and diversity of these services are governed by tree species richness and structural complexity as essential regulators of forest biodiversity. Sound conservation and sustainable management strategies rely on information from biodiversity indicators that is conventionally derived by field-based, periodical inventory campaigns. However, these data are usually site-specific and not spatially explicit, hampering their use for large-scale monitoring applications. Therefore, the main objective of our study was to build a robust method for spatially explicit modeling of biodiversity variables across temperate forest types using open-access satellite data and deep learning models. Field data were obtained from the Biodiversity Exploratories, a research infrastructure platform that supports ecological research in Germany. A total of 150 forest plots were sampled between 2014 and 2018, covering a broad range of environmental and forest management gradients across Germany. From field data, we derived key indicators of tree species diversity (Shannon Wiener Index) and structural heterogeneity (standard deviation of tree diameter) as proxies of forest biodiversity. Deep neural networks were used to predict the selected biodiversity variables based on Sentinel-1 and Sentinel-2 images from 2017. Predictions of tree diameter variation achieved good accuracy (r2 = 0.51) using Sentinel-1 winter-based backscatter data. The best models of species diversity used a set of Sentinel-1 and Sentinel-2 features but achieved lower accuracies (r2 = 0.25). Our results demonstrate the potential of deep learning and satellite remote sensing to predict forest parameters across a broad range of environmental and management gradients at the landscape scale, in contrast to most studies that focus on very homogeneous settings. These highly generalizable and spatially continuous models can be used for monitoring ecosystem status and functions, contributing to sustainable management practices, and answering complex ecological questions.publishedVersio

Intrinsically disordered inhibitor of glutamine synthetase is a functional protein with random-coil-like pKa values

The sequential action of glutamine synthetase (GS) and glutamate synthase (GOGAT) in cyanobacteria allows the incorporation of ammonium into carbon skeletons. In the cyanobacterium Synechocystis sp. PCC 6803, the activity of GS is modulated by the interaction with proteins, which include a 65-residue-long intrinsically disordered protein (IDP), the inactivating factor IF7. This interaction is regulated by the presence of charged residues in both IF7 and GS. To understand how charged amino acids can affect the binding of an IDP with its target and to provide clues on electrostatic interactions in disordered states of proteins, we measured the pKa values of all IF7 acidic groups (Glu32, Glu36, Glu38, Asp40, Asp58, and Ser65, the backbone C-terminus) at 100 mM NaCl concentration, by using NMR spectroscopy. We also obtained solution structures of IF7 through molecular dynamics simulation, validated them on the basis of previous experiments, and used them to obtain theoretical estimates of the pKa values. Titration values for the two Asp and three Glu residues of IF7 were similar to those reported for random-coil models, suggesting the lack of electrostatic interactions around these residues. Furthermore, our results suggest the presence of helical structure at the N-terminus of the protein and of conformational changes at acidic pH values. The overall experimental and in silico findings suggest that local interactions and conformational equilibria do not play a role in determining the electrostatic features of the acidic residues of IF7.Ministerio de Economía y Competitividad CTQ 2015-64445-R, BFU2013- 41712-P, BIO2016-75634PJunta de Andalucía BIO-284Generalitat Valenciana Prometeo 018/201

NADP(+)-isocitrate dehydrogenase from the cyanobacterium Anabaena sp. strain PCC 7120: purification and characterization of the enzyme and cloning, sequencing, and disruption of the icd gene

NADP(+)-isocitrate dehydrogenase (NADP(+)-IDH) from the dinitrogen-fixing filamentous cyanobacterium Anabaena sp. strain PCC 7120 was purified to homogeneity. The native enzyme is composed of two identical subunits (M(r), 57,000) and cross-reacts with antibodies obtained against the previously purified NADP(+)-IDH from the unicellular cyanobacterium Synechocystis sp. strain PCC 6803. Anabaena NADP(+)-IDH resembles in its physicochemical and kinetic parameters the typical dimeric IDHs from prokaryotes. The gene encoding Anabaena NADP(+)-IDH was cloned by complementation of an Escherichia coli icd mutant with an Anabaena genomic library. The complementing DNA was located on a 6-kb fragment. It encodes an NADP(+)-IDH that has the same mobility as that of Anabaena NADP(+)-IDH on nondenaturing polyacrylamide gels. The icd gene was subcloned and sequenced. Translation of the nucleotide sequence gave a polypeptide of 473 amino acids that showed high sequence similarity to the E. coli enzyme (59% identity) and with IDH1 and IDH2, the two subunits of the heteromultimeric NAD(+)-IDH from Saccharomyces cerevisiae (30 to 35% identity); however, a low level of similarity to NADP(+)-IDHs of eukaryotic origin was found (23% identity). Furthermore, Anabaena NADP(+)-IDH contains a 44-residue amino acid sequence in its central region that is absent in the other IDHs so far sequenced. Attempts to generate icd mutants by insertional mutagenesis were unsuccessful, suggesting an essential role of IDH in Anabaena sp. strain PCC 7120.España, Dirección General de Investigación Científica y Técnica (grant PB91-0127

Implantación de la metodología Seis Sigma en varias plantas en un mismo grupo industrial

El objetivo principal del este proyecto fin de carrera es el de generar en primer lugar documentación de apoyo acerca de la metodología 6-sigma, a un nivel intermedio entre lo que es el nivel “Green-belt” y el nivel “Black-belt” tal y como los entienden las empresas multinacionales como General Electric, que abogan por éste tipo de metodología, para luego y a modo de aplicación, seguir ésta metodología siguiendo sus distintos pasos para el estudio de las características críticas de una pieza eólica, en concreto la torre de un aerogenerador. Se trata de un P.F.C. que nos orientará acerca de las distintas herramientas de calidad y de las herramientas estadísticas más apropiadas (disponibles en el programa Minitab) a emplear a lo largo de las 5 etapas de las que consta un proyecto 6-sigma.Ingeniería IndustrialIndustria Ingeniaritz

Planificación y optimización de redes ópticas en el Internet del futuro

[SPA] Las estrictas exigencias requeridas por la futura red 5G, junto a las elevadas previsiones de crecimiento de tráfico IP, principalmente cimentadas en la proliferación de numerosos servicios basados en la nube, crean un panorama futuro lleno de incógnitas desde la perspectiva de las grandes redes ópticas de telecomunicaciones. Las tareas de planificación y optimización serán esenciales para asegurar que los requisitos pueden cumplirse de una manera económicamente viable. Esta tesis trata de analizar, en primer lugar, la validez de las predicciones de crecimiento tráfico, a la luz de las actuales aplicaciones y en un escenario donde los requisitos de latencia implican la evolución de los CDNs con el despliegue de micro-datacenters. Se analizará en particular el efecto de esta evolución en el tráfico soportado por las redes ópticas troncales. Segundo, la tesis estudia opciones que permitan abordar los requisitos esperados de la red, desde tres enfoques: a) optimización en el diseño y gestión de CDNs, b) control programable de la red basado, en redes definidas por software (SDN) y con virtualización en las funciones de red (NFV) y por último, c) posible introducción de tecnología SDM (Space Division Multiplexing) para expandir la capacidad de las redes de transporte como soporte efectivo del incremento de tráfico IP. Los resultados de este trabajo concluyen, en primera instancia, que la evolución del tráfico troncal en el Internet del futuro dependerá de la naturaleza de los servicios que las aplicaciones ofrezca, siendo el balance entre el tráfico de usuario y de sincronización especialmente determinante. Por otro lado, los resultados sugieren que un acercamiento del contenido a los usuarios puede tener el efecto neto de disminuir la cantidad de tráfico soportada por las redes core, en relación con las previsiones actuales. Los casos de uso analizados en el entorno SDN-NFV determinan la necesidad de optimización para proporcionar flexibilidad y programabilidad en la migración hacia sistemas virtualizados en las redes, siendo este conjunto de funcionalidades esenciales para satisfacer los requerimientos de los futuros servicios en el paradigma 5G. Además, las pruebas de concepto presentadas avalan la optimización conjunta de recursos de red e IT para la asistencia de service chains en redes basadas en SDN-NFV. Finalmente, para las redes ópticas basadas en SDM, la propuesta presentada de restricción de canal espacial (SCC) emerge como una opción válida a implementar en ROADMs para contextos flex-grid. La validez de tal propuesta reside en la reducción de coste de implementación dada por su menor complejidad y mayor disponibilidad de equipamiento, a costa de mínimas pérdidas en rendimiento, respecto de opciones totalmente permisivas.[ENG] The strict requirements required for the future 5G network, jointly with the high growth forecasts of IP traffic, mainly based on the proliferation of cloud services, create a future panorama full of uncertainties from the perspective of large optical telecommunications networks. Planning and optimization tasks are essential to ensure that the requirements are satisfied in an economically viable manner. This thesis tries to analyze, in the first place, the validity of traffic growth predictions, in the light of current applications in a scenario where the latency requirements imply the evolution of CDNs with the deployment of micro-datacenters. In particular, the effect of this traffic evolution, supported by the optical backbone networks, will be analyzed. Second, the thesis studies some options that allow addressing the expected requirements of the network, from the perspective of three major approaches: a) optimization in the design and management of CDNs, b) programmable control of the network based on software-defined networking and with virtualization in network functions and finally, c) possible introduction of the Space Division Multiplexing (SDM) technology to expand the capacity of transport networks as effective support for the increase of IP traffic. The outcomes of this work conclude, in the first instance, that the evolution of the backbone traffic in the future Internet will depend on the nature of the services that the applications offer, being the balance between user traffic and synchronization one especially determining. On the other hand, the results suggest that place the content close to the users can have direct effect of decreasing the amount of traffic supported by the core networks, in relation to the current forecasts. The use cases analyzed in the SDN-NFV environment determine the need for optimization providing flexibility and programmability in the migration to virtualized systems in the networks. This set of functionalities are essential to satisfy the requirements of the future services in the 5G paradigm. In addition, the proof of concept presented in this thesis supports the joint optimization of network and IT resources for the assistance of service chains in networks based on SDN-NFV. Finally, for SDM-based optical networks, the proposal presented for space channel restriction (SCC) emerges as a valid option to be implemented in ROADMs for flex-grid environments. The validity of this proposal lies in the significant reduction in terms of implementation cost due to its lower complexity and the current availability of the equipment, at the expense of minimal performance degradations, compared to totally permissive options.Escuela Internacional de Doctorado de la Universidad Politécnica de CartagenaUniversidad Politécnica de CartagenaPrograma de Doctorado en Tecnologías de la Información y las Comunicaciones por la Universidad Politécnica de Cartagen

Revisiting core traffic growth in the presence of expanding CDNs

Traffic growth forecasts announce a dramatic future for core networks, struggling to keep the pace of traffic augmentation. Internet traffic growth primarily stems from the proliferation of cloud services and the massive amounts of data distributed by the content delivery networks (CDNs) hosting these services. In this paper, we investigate the evolution of core traffic in the presence of growing CDNs. Expanding the capacities of existing data centers (DCs) directly translates the forecasted compound-annual-growth-rate (CAGR) of user traffic to the CAGR of carried core link traffic. On the other hand, expanding CDNs by building new geographically dispersed DCs can significantly reduce the predicted core traffic growth rates by placing content closer to the users. However, reducing DC-to-user traffic by building new DCs comes at a trade-off with increasing inter-DC content synchronization traffic. Thus, the resulting overall core traffic growth will depend on the types of services supported and their associated synchronization requirements. In this paper, we present a long-term evolution study to assess the implications of different CDN expansion strategies on core network traffic growth considering a mix of services in proportions and growth rates corresponding to well-known traffic forecasts. Our simulations indicate that CDNs may have significant incentive to build more DCs, depending on the service types they offer, and that current alarming traffic predictions may be somewhat overestimated in core networks in the presence of expanding CDNs. (C) 2019 The Authors. Published by Elsevier B.V.The research leading to these results has received funding from the European Commission for the H2020-ICT-2016-2 METRO-HAUL project (G.A. 761727) and it has been partially funded by the Spanish national project ONOFRE-2(TEC2017-84423-C3-1-P, MINECO/AEI/FEDER, UE)

Transcription of glutamine synthetase genes (glnA and glnN) from the cyanobacterium Synechocystis sp. strain PCC 6803 is differently regulated in response to nitrogen availability

In the cyanobacterium Synechocystis sp. strain PCC 6803 we have previously reported the presence of two different proteins with glutamine synthetase activity: GSI, encoded by the glnA gene, and GSIII, encoded by the glnN gene. In this work we show that expression of both the glnA and glnN genes is subjected to transcriptional regulation in response to changes in nitrogen availability. Northern blot experiments and transcriptional fusions demonstrated that the glnA gene is highly transcribed in nitrate- or ammonium-grown cells and exhibits two- to fourfold-higher expression in nitrogen-starved cells. In contrast, the glnN gene is highly expressed only under nitrogen deficiency. Half-lives of both mRNAs, calculated after addition of rifampin or ammonium to nitrogen-starved cells, were not significantly different (2.5 or 3.4 min, respectively, for glnA mRNA; 1.9 or 1.4 min, respectively, for glnN mRNA), suggesting that changes in transcript stability are not involved in the regulation of the expression of both genes. Deletions of the glnA and glnN upstream regions were used to delimit the promoter and the regulatory sequences of both genes. Primer extension analysis showed that structure of the glnA gene promoter resembles those of the NtcA-regulated promoters. In addition, mobility shift assays demonstrated that purified, Escherichia coli-expressed Synechocystis NtcA protein binds to the promoter of the glnA gene. Primer extension also revealed the existence of a sequence related to the NtcA binding site upstream from the glnN promoter. However, E. coli-expressed NtcA failed to bind to this site. These findings suggest that an additional modification of NtcA or an additional factor is required for the regulation of glnN gene expression.Dirección General de Investigación Científica y Técnica PB91-0127 PB94-144