Bruk av genteknologi og lyskvalitet for å kontrollere strekningsvekst hos julestjerne (Euphorbia pulcherrima Willd ex Klotzsch)

Poinsettia (Euphorbia pulcherrima Willd ex Klotzsch) is a non-food and non-feed, vegetatively propagated ornamental plant which is among the economically most important ornamentals worldwide. Desirable plant height is one of the most important traits in such species. To obtain compact plants, growers are regularly using chemical growth retardants such as CCC (chlormequat chloride) or alar/daminozide (dimethylaminosuccinamic acid), which inhibit the gibberellin (GA) biosynthesis, resulting in compact plants. However, growth retardants have negative impacts on the environment and human health among others by potentially being carcinogenic. Thus, it is highly desirable to further restrict their use. This PhD project has explored the use of a plant genetic engineering approach and regulation of light quality by using light emitting diodes (LEDs) to control shoot elongation in poinsettia. The SHORT INTERNODES gene from Arabidopsis thaliana (AtSHI) was introduced into poinsettia by the use of an Agrobacterium-based transformation system (paper I). Light quality effects on plant morphology was investigated in greenhouse compartments and growth chambers by comparing use of traditional high pressure sodium (HPS) lamps as supplementary light with a combination of 80% red (R) and 20% blue (B) light from light emitting diodes (LED) (paper II). Also, the effect a 30 min end-of-day (EOD) treatment provided by R LED light was investigated in both light regimes (Paper II). To investigate the effect of manipulation of the phytochrome system on hormone physiology, and since the knowledge on hormone physiology in poinsettia was limited, the effects of EOD-R and EOD-FR on hormone levels were compared (paper III). Three independent transgenic lines (TL1, TL2, TL3) harbouring AtSHI were identified by PCR, and stable integration was confirmed by Southern blot analysis (paper I). When grown under short (SD; 10 h) or long day (LD; 16 h) conditions all three transgenic lines showed reduced shoot elongation compared to untransformed wild type (WT) control plants. TL1 showed the shortest stems and internodes under SD with 52% and 49% reduction, respectively, compared to the WT. This correlated with the highest AtSHI expression, and a trend of 31% lower levels of indole-3 acetic acid (IAA) in TL1 compared to the WT. All three cultivars tested (‘Christmas Spirit’, ‘Christmas Eve’ and ‘Advent Red’) showed reduced plant height (20-34%) under 20% B and 80% R provided by LED light compared to the traditionally used HPS lamps (5% B) (paper II). The phytochrome photostationary state (PPS) under the LED and HPS was very similar, indicating that B light receptors such as cryptochromes are important to control stem elongation of poinsettia. Furthermore, in ‘Advent Red’ exposure to EOD-R resulted in reduced stem extension by 13% when HPS was used as supplementary light (paper II). By contrast, under the B-R supplementary LED light, EOD-R did not reduce shoot elongation, suggesting that the light-receptor dependent inhibition of shoot elongation had already been saturated due to the high content of B and R. In the other cultivar tested, ‘Christmas Eve’, no effect of the EOD-R-treatment was observed under any of the two light regimes. This might be due to differences in phytochrome light receptors or their action. Lower plants under EOD-R compared to EOD-FR correlated with lower levels of IAA, gibberellin (GA) and abscisic acid (21%, 28% and 19%, respectively) in shoot tips (paper III). The GA analyses revealed that the 13-hydroxylation pathway of GA biosynthesis is probably dominating over the non-13-hydroxylation pathway. In conclusion, these results demonstrates the potential for using genetic engineering and exploiting light quality responses in order to reduce the use of plant growth retardants in greenhouse production of poinsettia. However, the difference in response to EOD-R in the tested cultivars emphasizes the importance of investigating light quality responses in different commercially grown cultivars.Julestjerne (poinsettia; Euphorbia pulcherrima Willd ex Klotzsch), som verken benyttes til fôr eller mat og formeres vegetativt, er blant de økonomisk viktigste potteplantekulturer i verden. Kontroll av plantehøyden er av avgjørende betydning i slike arter. For å oppnå kompakte planter benyttes regelmessig behandling med kjemiske veksthemmere som CCC (chlormequat chloride) eller alar/daminozide (dimethylaminosuccinamic acid). Disse hemmer gibberellin- (GA) biosyntesen. Kjemiske veksthemmere har imidlertid negative effekter på miljøet og human helse, blant annet ved å være potensielt kreftframkallende. Det er derfor sterkt ønskelig å begrense bruken av disse ytterlige. Dette PhD-arbeidet har undersøkt muligheten for å benytte genteknologi og manipulering av lyskvalitet ved hjelp av lys-dioder (LED; fra engelsk «light emitting diodes») til å kontrollere strekningsveksten hos julestjerne. «SHORT INTERNODES»-genet fra vårskrinneblom (Arabidopsis thaliana) (AtSHI) ble satt inn i julestjerne ved hjelp av Agrobacterium-basert genteknologi (artikkel 1). Effekter av lyskvalitet på plantemorfologi ble undersøkt i veksthus og vekstkammere ved å sammenligne bruk av tradisjonelle høytrykksnatriumlamper (HPS; fra engelsk «high pressure sodium») som tilleggslys med bruk av LED-lys som ga en kombinasjon av 80% rødt (R) og 20% blått (B) lys (artikkel II). I tillegg ble effekten av en 30 minutters behandling med R LED-lys på slutten av dagen (EOD; fra engelsk «end of day») studert (artikkel II). For å undersøke effekten av manipulering av fytokromsystemet på hormonfysiologien, og siden kunnskapen om hormonfysiologien i julestjerne var begrenset, ble effektene av 30 minutter med EOD-R og EOD-mørkerødt (MR) på plantenes hormoninnhold sammenlignet (artikkel III). Tre uavhengige transgene linjer (T1, T2, T3) med innsatt AtSHI ble identifisert ved hjelp av PCR og stabil integrering bekreftet ved hjelp av southern blot-analyse (artikkel I). Ved dyrking under kort (KD; 10 timer) og lang dag (16 timer) viste alle tre linjer redusert strekningsvekst sammenlignet med ikke-tranformerte villtype-kontrollplanter. TL1 hadde de korteste stenglene og internodiene under KD med henholdsvis 52 % og 49 % reduksjon sammenlignet med villtypen. Dette korrelerte med det høyeste AtSHI-uttrykket og en tendens til lavere (31 %) nivåer av indol-3-eddiksyre (IAA) i TL1 sammenlignet med villtypen. Alle de tre testede julestjernesortene (‘Christmas Spirit’, ‘Christmas Eve’ og ‘Advent Red’) viste redusert plantehøyde (20-34 %) under 20 % B and 80 % R fra LED, sammenlignet med de tradisjonelt brukte HPS lampene (5 % B) (artikkel II). Fytokromstatus var svært lik under LED og HPS og dette tyder på at B-lysreseptorer som kryptokromer er viktige i å kontrollere strekningsveksten i julestjerne. I ‘Advent Red’ førte EOD-R til 13 % reduksjon i stengelstrekningen når HPS ble brukt som tilleggslys i veksthuset, sammenlignet med bruk av kun HPS uten EOD-R (artikkel II). I motsetning til dette, ble strekningsveksten ikke redusert av EOD-R-eksponering under B-R-LED-lysbehandlingen. Dette kan tyde på at lysavhengig hemming av stengelstrekning i dette tilfellet allerede var mettet på grunn av det høye nivået av B og R-lys. I den andre testede julestjernesorten, ‘Christmas Eve’, ble det ikke observert noen effekt av EOD-R under noen av de to lysregimene. Forskjellen mellom sortene kan muligens skyldes forskjeller i fytokrom-lysreseptorer eller deres virking. Lavere planter under EOD-R sammenlignet ned EOD-MR korrelerte med lavere nivåer av IAA, GA og abscisinsyre (henholdsvis 21 %, 28 % og 19 %) i skuddspissene (artikkel III). Analysene viste at 13-hydroksylerte gibberelliner forekom i større mengder enn ikke-13-hydroksylerte. De oppnådde resultatene viser potensial for å benytte genmodifisering og utnytte responser på lyskvalitet for å redusere bruk av kjemiske veksthemmere i veksthusdyrking av julestjerne. Forskjellene i respons på EOD-R i ulike julestjernesorter understreker imidlertid betydningen av å undersøke lyskvalitetsresponser i forskjellige kommersielt dyrkede sorter.Joint Proof-of-Concept Fun

AtomLbs: An Atom Based Convolutional Neural Network for Druggable Ligand Binding Site Prediction

Despite advances in drug research and development, there are few and ineffective treatments for a variety of diseases. Virtual screening can drastically reduce costs and accelerate the drug discovery process. Binding site identification is one of the initial and most important steps in structure-based virtual screening. Identifying and defining protein cavities that are likely to bind to a small compound is the objective of this task. In this research, we propose four different convolutional neural networks for predicting ligand-binding sites in proteins. A parallel optimized data pipeline is created to enable faster training of these neural network models on minimal hardware. The effectiveness of each method is assessed on well-established ligand binding site datasets. It is then compared with the state-of-the-art and widely used methods for ligand binding site identification. The result shows that our methods outperform most of the other methods and are comparable to the state-of-the-art methods

Advanced microwave embedded sensors for infrastructure health monitoring

Microwave sensor systems have been widely investigated for many applications due to their ability to provide non-destructive, noncontact, one-sided and wireless testing. Among these applications infrastructure health monitoring of bridges, building, and dams using microwave sensors, which are mounted on or embedded in composite structures of infrastructure has been attracting an increasing interest. One of the current needs of infrastructure health monitoring includes the detection and monitoring of disbonding and gaps in concrete-based structures, which are also required for simultaneous characterization of concrete. A recently proposed microwave sensor technique exploiting a relatively simple waveguide sensor embedded in a concrete-metal structure such as a concrete-filled steel tube exhibited great potential. However, it suffers from a few drawbacks that need to be solved. This thesis aims to develop and investigate advanced microwave embedded sensors to solve main problems in the current microwave sensory technique including characterization of concrete in concrete-based structures at different stage of its life, size of the interface under inspection, detection and monitoring of a small gap between concrete and dielectric material surfaces and sensitivity to gaps. To achieve this aim the following five research contributions have been made: The first contribution is the methodology for the determination of the complex dielectric permittivity of concrete using both measurement data and simulation results at different stages (fresh, early-aged and dry) of its life. Firstly, it is developed and tested for a single flanged open-ended waveguide sensor with a hardened concrete specimen, and then the methodology is modified for the developed sensors embedded in concrete-based composite structures with fresh, early-age and dry concrete. Modern computational tool CST Microwave Studio and a performance network analyser are used for simulation and measurement, respectively, throughout this research work. The second contribution is a dual waveguide sensor, which is proposed, designed and applied for the detection and monitoring of a small gap in concrete-metal composite structures. It consists of two waveguide sections and a metal plate and uses the transmission of electromagnetic waves along gap when it occurs between the metal plate and concrete surfaces. It provides more measurement data than the single waveguide sensor for characterising concrete-metal structures such as transmission properties of guided waves along the gap and reflection properties of the metal–concrete interface at two different places at the same stage of concrete. As a result, the proposed sensor increases the size of the interface under inspection and sensitivity to the gap using the magnitude of reflection coefficient and magnitude of transmission coefficient together and/or independently. The third contribution is the design and application of a dual waveguide sensor with rectangular dielectric insertions that is proposed and tested for the characterisation of concrete–metal structures at different stages of the concrete life including its fresh stage. The dielectric insertions are designed and implanted in the waveguide sections in such a way that they create the resonant response of the sensor and prevent water and concrete entering the sections. The resonant properties of the sensor allow long-term monitoring of the concrete hydration, including the detection of the transition from fresh to hardened concrete on its first day. The proposed sensor along with the modified algorithm provides the determination of the complex dielectric permittivity of fresh concrete. The fourth contribution is a dual waveguide sensor with tapered dielectric insertions. Each tapered dielectric insertion is designed with a tapered part and rectangular part to reduce wave reflection from the insertions over an entire frequency band. The proposed sensor has improved performance at the resonant responses of a quarter-wavelength resonator formed by an open end at the tapered part and shorted end at the rectangular part of each insertion. The last contribution is the development of dual waveguide sensors with attached dielectric layer and their application for the detection and monitoring of gap between dielectric materials and concrete in metal-dielectric layer-concrete composites as well as the determination of complex dielectric permittivity of concrete at different stages of its life. One of the most attractive designs is the sensor with empty waveguide sections due to its simplicity and robustness, and capability of the layer for preventing penetration of the obstacles and water, and for optimization of the sensor. On the other hand, the sensors with dielectric insertions and the layer demonstrate a significantly higher magnitude of transmission coefficient. The proposed DWSs can be applied to characterise fresh concrete in a dielectric mould or on-line, and to investigate the shrinkage of different categories of concrete

Hardware implementation of daubechies wavelet transforms using folded AIQ mapping

The Discrete Wavelet Transform (DWT) is a popular tool in the field of image and video compression applications. Because of its multi-resolution representation capability, the DWT has been used effectively in applications such as transient signal analysis, computer vision, texture analysis, cell detection, and image compression. Daubechies wavelets are one of the popular transforms in the wavelet family. Daubechies filters provide excellent spatial and spectral locality-properties which make them useful in image compression. In this thesis, we present an efficient implementation of a shared hardware core to compute two 8-point Daubechies wavelet transforms. The architecture is based on a new two-level folded mapping technique, an improved version of the Algebraic Integer Quantization (AIQ). The scheme is developed on the factorization and decomposition of the transform coefficients that exploits the symmetrical and wrapping structure of the matrices. The proposed architecture is parallel, pipelined, and multiplexed. Compared to existing designs, the proposed scheme reduces significantly the hardware cost, critical path delay and power consumption with a higher throughput rate. Later, we have briefly presented a new mapping scheme to error-freely compute the Daubechies-8 tap wavelet transform, which is the next transform of Daubechies-6 in the Daubechies wavelet series. The multidimensional technique maps the irrational transformation basis coefficients with integers and results in considerable reduction in hardware and power consumption, and significant improvement in image reconstruction quality

pH Development Analysis of Alkaline and Low Salinity Water Flooding in sandstone cores

Master's thesis in Petroleum EngineeringLow salinity (LS) water flooding has been in the center of interest for conventional oil recovery in sandstone reservoir for more than two decades because of its low cost and potential for increased oil recovery. Though hundreds of researches have been done on LS EOR method, the mechanism behind the oil recovery is still debatable. Recently, Smart Water group of University of Stavanger has proposed a new chemical wettability alteration mechanism where protons (H+) from LS water replaces metal ions such as Ca2+, Na+ from the clay surface and made the surface more water wet by releasing polar organic oil components due to a pH increase. As a result, more oil is displaced towards production well and increases oil recovery. As the proton (H+) is adsorbed, pH of the produced water is increased and using this theory, Aksulu et. al. (2012) established a pH screening test as an experimental tool to check the LS potential for sandstone. pH of the system can also be increased by injecting alkaline water of high pH instead of creating in situ pH increase by LS water flooding. In this thesis, the transportability of alkalinity and development of pH was investigated for LS and alkaline water flooding. Three outcrop sandstone cores of different mineralogy were used for 12 pH screening tests at different temperatures. In addition with the pH screening test, pressure changes, density changes and ion chromatography tests were done during the flooding to observed the changes of produced water. pH-screening tests with alkaline water injection showed low potential for extra alkalinity compared with LS water injection. Almost two pH unit of injected high alkaline water is reduced by the minerals and formation water. On the other hand, the results of the pH-screening tests for LS water injection showed a potential for increasing the effluent LS water pH up to two units in comparison to its initial pH-value. Both the LS and alkaline water showed same trend of pH buildup though they had a big difference in bulk pH (almost 5 pH unit). Transportation of alkalinity through a mineral system with large surface area seemed to be challenging due to pH buffering from brine/mineral interactions as well as from chemical interactions involving inorganic cations from the formation water. It can be concluded after the thesis that an in-situ generation of alkaline conditions in the reservoir by injecting LS water seemed to have a larger potential for EOR purposes than transporting alkalinity by injecting high pH alkaline water through the reservoir