Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Abstract Background From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas.

Embryonic development and larval stages of Steindachneridion parahybae (Siluriformes: Pimelodidae): implications for the conservation and rearing of this endangered Neotropical species

Steindachneridion parahybae is a freshwater catfish endemic to the Paraíba do Sul River and is classified as an endangered Neotropical species. An increasing number of conservation biologists are incorporating morphological and physiological research data to help conservation managers in rescue these endangered species. This study investigated the embryonic and larval development of S. parahybae in captivity, with emphasis in major events during the ontogeny of S. parahybae. Broodstocks were artificially induced to reproduce, and the extrusion occurred 200-255 degree-hours after hormonal induction at 24°C. Larval ontogeny was evaluated every 10 minutes under microscopic/stereomicroscopic using fresh eggs samples. The main embryogenic development stages were identified: zygote, cleavage, including the morula, blastula, gastrula phase, organogenesis, and hatching. The extruded oocytes showed an average diameter of 1.10 ± 0.10 mm, and after fertilization and hydration of eggs, the average diameter of eggs increased to about 1.90 ± 0.60 mm, characterized by a large perivitelline space that persisted up to embryo development, the double chorion, and the poles (animal and vegetative). Cell division started about 2 minutes after fertilization (AF), resulting in 2, 4, 8 (4 x 2 arrangement of cells), 16 (4 x 4), 32 (4 x 8) and 64 (2 x 4 x 8) cells. Furthermore, the blastula and gastrula stages followed after these cells divisions. The closed blastopore occurred at 11 h 20 min AF; following the development, the organogenetic stages were identified and subdivided respectively in: early segmentation phase and late segmentation phase. In the early segmentation phase, there was the establishment of the embryonic axis, and it was possible to distinguish between the cephalic and caudal regions; somites, and the optic vesicles developed about 20 h AF. Total hatching occurred at 54 h AF, and the larvae average length was 4.30 ± 0.70 mm. Gradual yolk sac reduction was observed during the first two days of larval development. The first feeding occurred at the end of the second day. During the larval phase, cannibalism, heterogeneous larval growth and photophobia were also observed. This information will be important in improving the artificial reproduction protocols of S. parahybae in controlled breeding programs.

What Happened to Participation? Urban Development and Authoritarian Upgrading in Cairo's Informal Neighbourhoods

Participation appeared in development discourses for the first time in the 1970s, as a generic call for the involvement of the poor in development initiatives. Over the last three decades, the initial perspectives on participation intended as a project method for poverty reduction have evolved into a coherent and articulated theoretical elaboration, in which participation figures among the paraphernalia of good governance promotion: participation has acquired the status of “new orthodoxy”. Nevertheless, the experience of the implementation of participatory approaches in development projects seemed to be in the majority of cases rather disappointing, since the transformative potential of ‘participation in development’ depends on a series of factors in which every project can actually differ from others: the ultimate aim of the approach promoted, its forms and contents and, last but not least, the socio-political context in which the participatory initiative is embedded. In Egypt, the signature of a project agreement between the Arab Republic of Egypt and the Federal Republic of Germany, in 1998, inaugurated a Participatory Urban Management Programme (PUMP) to be implemented in Greater Cairo by the German Technical Cooperation (Deutsche Gesellschaft für Technische Zusammenarbeit, GTZ) and the Ministry of Planning (now Ministry of Local Development) and the Governorates of Giza and Cairo as the main counterparts. Now, ten years after the beginning of the PUMP/PDP and close to its end (December 2010), it is possible to draw some conclusions about the scope, the significance and the effects of the participatory approach adopted by GTZ and appropriated by the Egyptian counterparts in dealing with the issue of informal areas and, more generally, of urban development. Our analysis follows three sets of questions: the first set regards the way ‘participation’ has been interpreted and concretised by PUMP and PDP. The second is about the emancipating potential of the ‘participatory approach’ and its ability to ‘empower’ the ‘marginalised’. The third focuses on one hand on the efficacy of GTZ strategy to lead to an improvement of the delivery service in informal areas (especially in terms of planning and policies), and on the other hand on the potential of GTZ development intervention to trigger an incremental process of ‘democratisation’ from below.

Development and performance assessment of a Plasma Focus electron beam generator for Intra-Operative Radiation Therapy

The Plasma Focus is a device designed to generate a plasma sheet between two coaxial electrodes by means of a high voltage difference. The plasma is then driven to collapse into a “pinch”, where thermonuclear conditions prevail. During the “pinch phase” charged particles are emitted, with two main components: an ion beam peaked forward and an electron beam directed backward. The electron beam emitted backward by Plasma Focus devices is being investigated as a radiation source for medical applications, using it to produce x-rays by interaction with appropriate targets (through bremsstrahlung and characteristic emission). A dedicated Plasma Focus device, named PFMA-3 (Plasma Focus for Medical Applications number 3), has been designed, put in operation and tested by the research groups of the Universities of Bologna and Ferrara. The very high dose rate (several gray per discharge, in less than 1 µs) is a peculiarity of this device that has to be investigated, as it might modify the relative biological effectiveness (RBE). Aim of this Ph.D. project was to investigate the main physical properties of the low-energy x-ray beams produced by a Plasma Focus device and their potential medical applications to IORT treatments. It was necessary to develop the optimal geometrical configuration; to evaluate the x-rays produced and their dose deposited; to estimate the energy electron spectrum produced in the “pinch phase”; to study an optimal target for the conversion of the x-rays; to conduct simulations to study the physics involved; and in order to evaluate the radio-biological features of the beam, cell holders had to be developed for both irradiations and cell growth conditions.

Development and application of a GC system for NMHC analyses of air samples from the CARIBIC aircraft project

The subject of this thesis is the development of a Gaschromatography (GC) system for non-methane hydrocarbons (NMHCs) and measurement of samples within the project CARIBIC (Civil Aircraft for the Regular Investigation of the atmosphere Based on an Instrument Container, www.caribic-atmospheric.com). Air samples collected at cruising altitude from the upper troposphere and lowermost stratosphere contain hydrocarbons at low levels (ppt range), which imposes substantial demands on detection limits. Full automation enabled to maintain constant conditions during the sample processing and analyses. Additionally, automation allows overnight operation thus saving time. A gas chromatography using flame ionization detection (FID) together with the dual column approach enables simultaneous detection with almost equal carbon atom response for all hydrocarbons except for ethyne. The first part of this thesis presents the technical descriptions of individual parts of the analytical system. Apart from the sample treatment and calibration procedures, the sample collector is described. The second part deals with analytical performance of the GC system by discussing tests that had been made. Finally, results for measurement flight are assessed in terms of quality of the data and two flights are discussed in detail. Analytical performance is characterized using detection limits for each compound, using uncertainties for each compound, using tests of calibration mixture conditioning and carbon dioxide trap to find out their influence on analyses, and finally by comparing the responses of calibrated substances during period when analyses of the flights were made. Comparison of both systems shows good agreement. However, because of insufficient capacity of the CO2 trap the signal of one column was suppressed due to breakthroughed carbon dioxide so much that its results appeared to be unreliable. Plausibility tests for the internal consistency of the given data sets are based on common patterns exhibited by tropospheric NMHCs. All tests show that samples from the first flights do not comply with the expected pattern. Additionally, detected alkene artefacts suggest potential problems with storing or contamination within all measurement flights. Two last flights # 130-133 and # 166-169 comply with the tests therefore their detailed analysis is made. Samples were analyzed in terms of their origin (troposphere vs. stratosphere, backward trajectories), their aging (NMHCs ratios) and detected plumes were compared to chemical signatures of Asian outflows. In the last chapter a future development of the presented system with focus on separation is drawn. An extensive appendix documents all important aspects of the dissertation from theoretical introduction through illustration of sample treatment to overview diagrams for the measured flights.

Reverse Engineering tools: development and experimentation of innovative methods for physical and geometrical data integration and post-processing

In recent years, the use of Reverse Engineering systems has got a considerable interest for a wide number of applications. Therefore, many research activities are focused on accuracy and precision of the acquired data and post processing phase improvements. In this context, this PhD Thesis deals with the definition of two novel methods for data post processing and data fusion between physical and geometrical information. In particular a technique has been defined for error definition in 3D points’ coordinates acquired by an optical triangulation laser scanner, with the aim to identify adequate correction arrays to apply under different acquisition parameters and operative conditions. Systematic error in data acquired is thus compensated, in order to increase accuracy value. Moreover, the definition of a 3D thermogram is examined. Object geometrical information and its thermal properties, coming from a thermographic inspection, are combined in order to have a temperature value for each recognizable point. Data acquired by an optical triangulation laser scanner are also used to normalize temperature values and make thermal data independent from thermal-camera point of view.

The development and deployment of FOTOS: a fast observation of trace organics system

Flüchtige organische Bestandteile (engl.: VOC) sind in der Atmosphäre in Spuren vorhanden, spielen aber trotzdem eine wichtige Rolle in der Luftchemie: sie beeinflussen das Ozon der Troposphäre, städtischen Smog, Oxidationskapazität und haben direkte und indirekte Auswirkungen auf die globale Klimaveränderung. Eine wichtige Klasse der VOC sind die Nicht-Methan-Kohlenwasserstoffe (engl.: NMHC), die überwiegend von anthropogenen Quellen kommen. Aus diesem Grund ist für Luftchemiker ein Messinstrument nötig, das die VOC, die NMHC eingeschlossen, mit einer höheren Zeitauflösung misst, besonders für Echtzeitmessungen an Bord eines Forschungsflugzeuges. Dafür wurde das System zur schnellen Beobachtung von organischen Spuren (engl.: FOTOS) entworfen, gebaut für den Einsatz in einem neuen Wissenschaftlichen Flugzeug, das in großen Höhen und über weite Strecken fliegt, genannt HALO. In der Folge wurde FOTOS in zwei Messkampagnen am Boden getestet. FOTOS wurde entworfen und gebaut mit einem speziell angefertigten, automatisierten, kryogenen Probensystem mit drei Fallen und einem angepassten, erworbenen schnellen GC-MS. Ziel dieses Aufbaus war es, die Vielseitigkeit zu vergrößern und das Störungspotential zu verringern, deshalb wurden keine chemischen Trocknungsmittel oder adsorbierenden Stoffe verwendet. FOTOS erreichte eine Probenfrequenz von 5.5 Minuten, während es mindestens 13 verschiedene C2- bis C5-NMHC maß. Die Drei-Sigma-Detektionsgrenze für n- und iso-Pentan wurde als 2.6 und 2.0 pptv ermittelt, in dieser Reihenfolge. Labortests bestätigten, dass FOTOS ein vielseitiges, robustes, hochautomatisiertes, präzises, genaues, empfindliches Instrument ist, geeignet für Echtzeitmessungen von VOC in Probenfrequenzen, die angemessen sind für ein Forschungsflugzeug wie HALO. Um die Leistung von FOTOS zu bestätigen, wurde vom 26. Januar bis 4. Februar 2010 ein Zwischenvergleich gemacht mit dem GC-FID-System am Meteorologischen Observatorium Hohenpeißenberg, einer WMO-GAW-globalen Station. Dreizehn verschiedene NMHC wurden innerhalb des Rahmens der GWA Data Quality Objectives (DQO) analysiert und verglichen. Mehr als 80% der Messungen von sechs C3- bis C5-NMHC erfüllten diese DQO. Diese erste Messkampagne im Feld hob die Robustheit und Messgenauigkeit von FOTOS hervor, zusätzlich zu dem Vorteil der höheren Probenfrequenz, sogar in einer Messung am Boden. Um die Möglichkeiten dieses Instrumentes im Feld zu zeigen, maß FOTOS ausgewählte leichte NMHC während einer Messkampagne im Borealen Waldgebiet, HUMPPA-COPEC 2010. Vom 12. Juli bis zum 12. August 2010 beteiligte sich eine internationale Gruppe von Instituten und Instrumenten an Messungen physikalischer und chemischer Größen der Gas- und Partikelphasen der Luft über dem Borealen Wald an der SMEAR II-Station nahe Hyyttiälä, Finnland. Es wurden mehrere Hauptpunkte von Interesse im Mischungsverhältnis der Alkane und im Isomerenverhätnis von Pentan identifiziert, insbesondere sehr unterschiedliche Perioden niedriger und hoher Variabilität, drei Rauchschwaden von Biomassen-Verbrennung von russischen Waldbränden und zwei Tage mit extrem sauberer Luft aus der Polarregion. Vergleiche der NMHC mit anderen anthropogenen Indikatoren zeigten mehrere Quellen anthropogener Einflüsse am Ort auf und erlaubten eine Unterscheidung zwischen lokalen und weiter entfernten Quellen. Auf einen minimalen natürlichen Beitrag zum 24h-Kreislauf von NOx wurde geschlussfolgert aus der Korrelation von NOx mit Alkanen. Altersschätzungen der Luftmassen durch das Isomerenverhältnis von Pentan wurden erschwert durch sich verändernde Verhältnisse der Quellen und durch Besonderheiten der Photochemie während des Sommers im hohen Norden. Diese Messungen zeigten den Wert des Messens leichter NMHC, selbst in abgelegenen Regionen, als einen zusätzlichen spezifischen Marker von anthropogenem Einfluss.

Genetic and morphological variation and differentiation of Raja clavata populations in the European seas: marker development and preliminary data

In this study the population structure and connectivity of the Mediterranean and Atlantic Raja clavata (L., 1758) were investigated by analyzing the genetic variation of six population samples (N = 144) at seven nuclear microsatellite loci. The genetic dataset was generated by selecting population samples available in the tissue databases of the GenoDREAM laboratory (University of Bologna) and of the Department of Life Sciences and Environment (University of Cagliari), all collected during past scientific surveys (MEDITS, GRUND) from different geographical locations in the Mediterranean basin and North-east Atlantic sea, as North Sea, Sardinian coasts, Tuscany coasts and Cyprus Island. This thesis deals with to estimate the genetic diversity and differentiation among 6 geographical samples, in particular, to assess the presence of any barrier (geographic, hydrogeological or biological) to gene flow evaluating both the genetic diversity (nucleotide diversity, observed and expected heterozygosity, Hardy- Weinberg equilibrium analysis) and population differentiation (Fst estimates, population structure analysis). In addition to molecular analysis, quantitative representation and statistical analysis of morphological individuals shape are performed using geometric morphometrics methods and statistical tests. Geometric coordinates call landmarks are fixed in 158 individuals belonging to two population samples of Raja clavata and in population samples of closely related species, Raja straeleni (cryptic sibling) and Raja asterias, to assess significant morphological differences at multiple taxonomic levels. The results obtained from the analysis of the microsatellite dataset suggested a geographic and genetic separation between populations from Central-Western and Eastern Mediterranean basins. Furthermore, the analysis also showed that there was no separation between geographic samples from North Atlantic Ocean and central-Western Mediterranean, grouping them to a panmictic population. The Landmark-based geometric morphometry method results showed significant differences of body shape able to discriminate taxa at tested levels (from species to populations).

Technology Development and Consumer Acceptance of Innovation in Fruit Production

Precision Agriculture (PA) and the more specific branch of Precision Horticulture are two very promising sectors. They focus on the use of technologies in agriculture to optimize the use of inputs, so to reach a better efficiency, and minimize waste of resources. This important objective motivated many researchers and companies to search new technology solutions. Sometimes the effort proved to be a good seed, but sometimes an unfeasible idea. So that PA, from its birth more or less 25 years ago, is still a “new” management, interesting for the future, but an actual low adoption rate is still reported by experts and researchers. This work aims to give a contribution in finding the causes of this low adoption rate and proposing a methodological solution to this problem. The first step was to examine prior research about Precision Agriculture adoption, by ex ante and ex post approach. It was supposed as important to find connections between these two phases of a purchase experience. In fact, the ex ante studies dealt with potential consumer’s perceptions before a usage experience occurred, therefore before purchasing a technology, while the ex post studies described the drivers which made a farmer become an end-user of PA technology. Then, an example of consumer research is presented. This was an ex ante research focused on pre-prototype technology for fruit production. This kind of research could give precious information about consumer acceptance before reaching an advanced development phase of the technology, and so to have the possibility to change something with the least financial impact. The final step was to develop the pre-prototype technology that was the subject of the consumer acceptance research and test its technical characteristics.

Building Peace and/or Gender Equality. Changing Attitudes around Peace, Development and Security in International Cooperation in Rwanda.

The times following international or civil conflicts but also violent revolutions often come with unequal share of the peace dividend for men and women. Delusions for women who gained freedom of movement and of roles during conflict but had to step back during reconstruction and peace have been recorded in all regions of the world. The emergence of peacebuilding as a modality for the international community to ensure peace and security has slowly incorporated gender sensitivity at the level of legal and policy instruments. Focusing on Rwanda, a country that has obtained significant gender advancement in the years after the genocide while also obtaining to not relapse into conflict, this research explores to what extent the international community has contributed to this transformation. From a review of evaluations, findings are that many of the interventions did not purse gender equality, and overall the majority understood gender and designed actions is a quite superficial way which would hardly account for the significative advancement in combating gender discrimination that the Government, for its inner political will, is conducting. Then, after a critique from a feminist standpoint to the concept of human security, departing from the assumption (sustained by the Governemnt of Rwanda as well) that domestic violence is a variable influencing level of security relevant at the national level, a review of available secondary data on GBV is conducted an trends over the years analysed. The emerging trends signal a steep increase in prevalence of GBV and in domestic violence in particular. Although no conclusive interpretation can be formulated on these data, there are elements suggesting the increase might be due to augmented reporting. The research concludes outlining possible further research pathways to better understand the link in Rwanda between the changing gender norms and the GBV.

Aerobic biodegradation of chlorinated solvents and plastics in batch and continuous-flow bioreactors: process development, and identification of suitable chemical pre-Treatments

The purpose of the first part of the research activity was to develop an aerobic cometabolic process in packed bed reactors (PBR) to treat real groundwater contaminated by trichloroethylene (TCE) and 1,1,2,2-tetrachloroethane (TeCA). In an initial screening conducted in batch bioreactors, different groundwater samples from 5 wells of the contaminated site were fed with 5 growth substrates. The work led to the selection of butane as the best growth substrate, and to the development and characterization from the site’s indigenous biomass of a suspended-cell consortium capable to degrade TCE with a 90 % mineralization of the organic chlorine. A kinetic study conducted in batch and continuous flow PBRs and led to the identification of the best carrier. A kinetic study of butane and TCE biodegradation indicated that the attached-cell consortium is characterized by a lower TCE specific degredation rates and by a lower level of mutual butane-TCE inhibition. A 31 L bioreactor was designed and set up for upscaling the experiment. The second part of the research focused on the biodegradation of 4 polymers, with and with-out chemical pre-treatments: linear low density polyethylene (LLDPE), polyethylene (PP), polystyrene (PS) and polyvinyl chloride (PVC). Initially, the 4 polymers were subjected to different chemical pre-treatments: ozonation and UV/ozonation, in gaseous and aqueous phase. It was found that, for LLDPE and PP, the coupling UV and ozone in gas phase is the most effective way to oxidize the polymers and to generate carbonyl groups on the polymer surface. In further tests, the effect of chemical pretreatment on polyner biodegrability was studied. Gas-phase ozonated and virgin polymers were incubated aerobically with: (a) a pure strain, (b) a mixed culture of bacteria; and (c) a fungal culture, together with saccharose as a co-substrate.

Brand formative design - development and assessment of product design from a future, brand and consumer perspective

With this dissertation research we investigate intersections between design and marketing and in this respect, which factors do contribute that a product design becomes brand formative. We have developed a Brand Formative Design (BFD) framework, which investigates individual design features in a holistic, comparable, brand relevant, and consumer specific context. We discuss what kinds of characteristics contribute to BFD but also illuminate how they should be applied and examine: rnA holistic framework leading to Brand Formative Design. Identification and assessment of BFD Drivers. The dissection of products into three Distinctive Design Levels. The detection of surprising design preferences. The appropriate degree of scheme deviation with evolutionary design. Simulated BFD development processes with three different products and the integration of consumers. Future oriented objectification, comparability and assessment of design. Recommendations for the management of design in a brand specific context. Design is a product feature, which contributes significantly to the success of products. However, the development of new design contains challenges. Design can hardly be objectified; many people have an opinion concerning the attractiveness of new products but cannot formulate their future preferences. Product design is widely developed based on intuition, which can be difficult for the management of design. Here the concept of Brand Formative Design can provide a framework which contributes to structure, objectify, develop and assess new evolutionary design in brand and future relevant contexts, but also integrates consumers and their preferences without restricting creativity too much.

Development and application of mass-spectrometric methods for the quantification and characterization of organic compounds in ice cores

Eisbohrkerne stellen wertvolle Klimaarchive dar, da sie atmosphärisches Aerosol konservieren. Die Analyse chemischer Verbindungen als Bestandteil atmosphärischer Aerosole in Eisbohrkernen liefert wichtige Informationen über Umweltbedingungen und Klima der Vergangenheit. Zur Untersuchung der α-Dicarbonyle Glyoxal und Methylglyoxal in Eis- und Schneeproben wurde eine neue, sensitive Methode entwickelt, die die Stir Bar Sorptive Extraction (SBSE) mit der Hochleistungsflüssigchromatographie-Massenspektrometrie (HPLC-MS) kombiniert. Zur Analyse von Dicarbonsäuren in Eisbohrkernen wurde eine weitere Methode entwickelt, bei der die Festphasenextraktion mit starkem Anionenaustauscher zum Einsatz kommt. Die Methode erlaubt die Quantifizierung aliphatischer Dicarbonsäuren (≥ C6), einschließlich Pinsäure, sowie aromatischer Carbonsäuren (wie Phthalsäure und Vanillinsäure), wodurch die Bestimmung wichtiger Markerverbindungen für biogene und anthropogene Quellen ermöglicht wurde. Mit Hilfe der entwickelten Methoden wurde ein Eisbohrkern aus den Schweizer Alpen analysiert. Die ermittelten Konzentrationsverläufe der Analyten umfassen die Zeitspanne von 1942 bis 1993. Mittels einer Korrelations- und Hauptkomponentenanalyse konnte gezeigt werden, dass die organischen Verbindungen im Eis hauptsächlich durch Waldbrände und durch vom Menschen verursachte Schadstoffemissionen beeinflusst werden. Im Gegensatz dazu sind die Konzentrationsverläufe einiger Analyten auf den Mineralstaubtransport auf den Gletscher zurückzuführen. Zusätzlich wurde ein Screening der Eisbohrkernproben mittels ultrahochauflösender Massenspektrometrie durchgeführt. Zum ersten Mal wurden in diesem Rahmen auch Organosulfate und Nitrooxyorganosulfate in einem Eisbohrkern identifiziert.

Desarrollo y Perspectivas de los Sistemas de Andenerías en los Andes Centrales del Perú (Development and Perspectives of Irrigated Terrace Systems in the Peruvian Central Andes) [Rezension]

Book review of: Kendall, Ann Rodríguez, Abelardo. Desarrollo y Perspectivas de los Sistemas de Andenerías en los Andes Centrales del Perú (Development and Perspectives of Irrigated Terrace Systems in the Peruvian Central Andes). Cuzco, Peru. ISBN: 978-9972-691-93-5.