The methods presented in this study are aimed at the identification of subpopulations (clones) of genetically similar cells within tissue samples through measurement of loci-specific Fluorescence in-situ hybridization (FISH) spot signals for each nucleus and analyzing cell spatial distributions by way of Voronoi tessellation and Delaunay triangulation to robustly define cell neighbourhoods. The motivation for the system is to examine lung cancer patient for subpopulations of Non-Small Cell Lung Cancer (NSCLC) cells with biologically meaningful gene copy-number profiles: patterns of genetic alterations statistically associated with resistance to cis-platinum/vinorelbine doublet chemotherapy treatment. Current technologies for gene-copy number profiling rely on large amount of cellular material, which is not always available and suffers from limited sensitivity to only the most dominant clone in often heterogeneous samples. Thus, through the use of FISH, the detection of gene copy-numbers is possible in unprocessed tissues, allowing identification of specific tumour clones with biologically relevant patterns of genetic aberrations. The tissue-wide characterization of multiplexed loci-specific FISH signals, described herein, is achieved through a fully automated, multicolour fluorescence imaging microscope and object segmentation algorithms to identify cell nuclei and FISH spots within. Related tumour clones are identified through analysis of robustly defined cell neighbourhoods and cell-to-cell connections for regions of cells with homogenous and highly interconnected FISH spot signal characteristics. This study presents experiments which demonstrate the system’s ability to accurately quantify FISH spot signals in various tumour tissues and in up to 5 colours simultaneously or more through multiple rounds of FISH staining. Furthermore, the system’s FISH-based cell classification performance is evaluated at a sensitivity of 84% and specificity 81% and clonal identification algorithm results are determined to be comparable to clone delineation by a human-observer. Additionally, guidelines and procedures to perform anticipated, routine analysis experiments are established.

The thesis is aimed at gaining new knowledge on carrier localization and recombination in InGaN epilayers and structures by using photoluminescence spectroscopy with sub-micrometer spatial resolution. Optical characterization is combined with the structural analysis to provide a deeper insight into peculiarities of InGaN luminescence. Studies of InGaN epitaxial layers showed the relaxed layers to contain nanocolumn-like structures that additionally contribute to inhomogeneous photoluminescence distribution in InGaN layers. The feasibility of suppressing the defect-related emission in InGaN epilayers by laser annealing is demonstrated. The influence of unintentional annealing at elevated temperatures during fabrication of InGaN structures is revealed. A novel interpretation for negative correlation between photoluminescence intensity and band peak wavelength in high-indium-content InGaN multiple quantum wells is suggested. The enhancement of emission efficiency in InGaN quantum wells due to coupling of the optical dipole with localized surface plasmons in silver nanoparticles is investigated and the influence of potential fluctuations on the coupling with localized surface plasmons is revealed. / Disertacija yra skirta krūvininkų lokalizacijos ir rekombinacijos tyrimams InGaN epitaksiniuose sluoksniuose ir dariniuose panaudojant fotoliuminescencinę spektroskopiją su submikrometrine erdvine skyra. Optinius bandinių tyrimus papildo struktūrinė analizė. Darbe parodyta, jog relaksavusiuose InGaN sluoksniuose egzistuoja į nanokolonas panašūs dariniai, kurie papildomai prisideda prie netolygaus fotoliuminescencijos pasiskirstymo InGaN epitaksiniuose sluoksniuose. Pademonstruota galimybė nuslopinti priemaišinės kilmės liuminescenciją InGaN sluoksnyje jį iškaitinus lazerio spinduliuote. Atskleistas netyčinis InGaN darinių aktyviojo sluoksnio iškaitinimas, vykstantis formuojant p tipo sluoksnius, kuris keičia InGaN kvantinių darinių optines sąvybes. Išnagrinėta neigiama koreliacja tarp fotoliuminescencijos intensyvumo ir juostos viršūnės bangos ilgio InGaN kvantiniuose dariniuose ir pasiūlytas naujas šios ypatybės interpretavimo modelis. Lokaliai stebėtas liuminescencijos intensyvumo padidėjimas dėl sąveikos su lokalizuotais paviršiniais plazmonais, indukuotais sidabro nanodalelėse. Parodytas potencialo fliuktuacijų daromas poveikis rezonansinei sąveikai tarp optinių dipolių kvantinėse duobėse ir lokalizuotų paviršinių plazmonų.

Disertacija yra skirta krūvininkų lokalizacijos ir rekombinacijos tyrimams InGaN epitaksiniuose sluoksniuose ir dariniuose panaudojant fotoliuminescencinę spektroskopiją su submikrometrine erdvine skyra. Optinius bandinių tyrimus papildo struktūrinė analizė. Darbe parodyta, jog relaksavusiuose InGaN sluoksniuose egzistuoja į nanokolonas panašūs dariniai, kurie papildomai prisideda prie netolygaus fotoliuminescencijos pasiskirstymo InGaN epitaksiniuose sluoksniuose. Pademonstruota galimybė nuslopinti priemaišinės kilmės liuminescenciją InGaN sluoksnyje jį iškaitinus lazerio spinduliuote. Atskleistas netyčinis InGaN darinių aktyviojo sluoksnio iškaitinimas, vykstantis formuojant p tipo sluoksnius, kuris keičia InGaN kvantinių darinių optines sąvybes. Išnagrinėta neigiama koreliacja tarp fotoliuminescencijos intensyvumo ir juostos viršūnės bangos ilgio InGaN kvantiniuose dariniuose ir pasiūlytas naujas šios ypatybės interpretavimo modelis. Lokaliai stebėtas liuminescencijos intensyvumo padidėjimas dėl sąveikos su lokalizuotais paviršiniais plazmonais, indukuotais sidabro nanodalelėse. Parodytas potencialo fliuktuacijų daromas poveikis rezonansinei sąveikai tarp optinių dipolių kvantinėse duobėse ir lokalizuotų paviršinių plazmonų. / The thesis is aimed at gaining new knowledge on carrier localization and recombination in InGaN epilayers and structures by using photoluminescence spectroscopy with sub-micrometer spatial resolution. Optical characterization is combined with the structural analysis to provide a deeper insight into peculiarities of InGaN luminescence. Studies of InGaN epitaxial layers showed the relaxed layers to contain nanocolumn-like structures that additionally contribute to inhomogeneous photoluminescence distribution in InGaN layers. The feasibility of suppressing the defect-related emission in InGaN epilayers by laser annealing is demonstrated. The influence of unintentional annealing at elevated temperatures during fabrication of InGaN structures is revealed. A novel interpretation for negative correlation between photoluminescence intensity and band peak wavelength in high-indium-content InGaN multiple quantum wells is suggested. The enhancement of emission efficiency in InGaN quantum wells due to coupling of the optical dipole with localized surface plasmons in silver nanoparticles is investigated and the influence of potential fluctuations on the coupling with localized surface plasmons is revealed.

Wheat bulb fly (WBF) (Delia coarctata, Fallén, Diptera: Anthomyiidae) is a pest of commercial importance in cereal crops. Control is dependent on organophosphates some of which are restricted in the UK, while current oviposition monitoring techniques are labour intensive and subjective. Eggs are not laid in association with a host-plant, therefore, prompt location of a suitable host is critical to the survival of the newly hatched larvae. Wheat bulb fly larvae have been shown to exhibit a positive chemotactic response to wheat and other host-plant seedlings and their root exudates. The objective of this study was to improve the control and population monitoring methodology associated with WBF, by investigating the ecology and specifically the chemical ecology of the WBF. Bioassays were used to investigate the behavioural response of WBF to known chemical constituents of host-plant exudates. Four secondary metabolites were found to be attractive while CO2 was found to alter the behaviour of larvae. Wheat bulb fly oviposition was assessed in field situations to describe egg laying spatially and through time. Geostatistical and ecological techniques were used to observe the spatial dependence and dispersion of oviposition and construct contour maps or scale-sized dot graphs of oviposition density. The traditional single line transect sampling pattern was compared against a more intensive sampling regime. Oviposition monitoring was conducted over a three year period to ascertain the time of peak egg density of this fly. A molecular based diagnostic test to assess WBF egg populations for damage forecasting was developed. A real time polymerase chain reaction (PCR) protocol was produced to estimate field populations of WBF eggs through the quantification of eggs from field samples. In addition endpoint PCR was used to identify the presence or absence of eggs from samples. This study gives the potential to advance current control methodology by providing the basis for the development of a lure and kill or confusion/disruption strategy, while offering a more accurate sampling system and a molecular diagnostic test, for improvement of the management of WBF.

No description available.

Little is known about the behavior of juvenile brown trout (Salmo trutta) during winter in boreal streams. Harsh winter conditions presumably affect overwinter survival negatively in small streams, where ice may have a large effect on survival of young salmonids. The aim of this study was to examine the effect of over-head ice cover on the spatial positioning of small brown trout in a boreal stream. I hypothesized that during the day brown trout will use the middle of the stream to a greater extent in the presence of over-head ice cover than in its absence. In the absence of ice cover, trout were predicted to hold station near the shore. At night, I hypothesized that there will be little effect of ice cover on the spatial positioning of the trout, with trout expected to occupy the entire stream width. Analysis of the results for the entire study period revealed a strong positive correlation between the tendency to be positioned towards the middle of the stream during daytime and the presence of ice cover. An analysis based on the period when water temperature was around 0o C (< 0,3o C) showed that trout used the entire width of the stream in the presence of surface ice but were restricted to the margins in the absence of ice. My hypothesis regarding the spatial distribution of trout at night was not supported by the data, as there was no difference in their spatial distribution during the day and at night. / Det råder stor okunskap om hur vinterförhållanden påverkar överlevnaden av juvenila öringar (Salmo trutta) i boreala områden. Isformationer och dess bildningsprocesser kan ha avgörande effekt på mortaliteten hos unga öringar som övervintrar i mindre vattendrag. Denna studie handlar om istäckets påverkan på öringens positionering längs vattendragets bredd. Hypoteserna är 1) att närvaron av istäcket ger öringen större möjlighet att kunna utnyttja mer metaboliskt gynnsamma ståndplatser i vattendraget än utan is och 2) att istäcket har effekt på daglig respektive nattlig positionering ifrån strandkanten. Resultaten i studien visar ett starkt positivt förhållande mellan ökad andel istäckningsgrad och positionering längre ut från strandkanten mot mitten av vattendraget. Vidare visar mina resultat, som baseras på perioden när vattentemperaturen var runt 0o C (< 0,3o C), att öringen använde sig av hela vattendragets bredd i närvaro av istäcke, men var nära strandkanten vid frånvaro av istäcket. Min hypotes angående öringens rumsliga fördelning under natten stöds inte av resultatet, då det inte fanns någon skillnad i deras rumsliga fördelning under dagen respektive på natten.

The methods presented in this study are aimed at the identification of subpopulations (clones) of genetically similar cells within tissue samples through measurement of loci-specific Fluorescence in-situ hybridization (FISH) spot signals for each nucleus and analyzing cell spatial distributions by way of Voronoi tessellation and Delaunay triangulation to robustly define cell neighbourhoods. The motivation for the system is to examine lung cancer patient for subpopulations of Non-Small Cell Lung Cancer (NSCLC) cells with biologically meaningful gene copy-number profiles: patterns of genetic alterations statistically associated with resistance to cis-platinum/vinorelbine doublet chemotherapy treatment. Current technologies for gene-copy number profiling rely on large amount of cellular material, which is not always available and suffers from limited sensitivity to only the most dominant clone in often heterogeneous samples. Thus, through the use of FISH, the detection of gene copy-numbers is possible in unprocessed tissues, allowing identification of specific tumour clones with biologically relevant patterns of genetic aberrations. The tissue-wide characterization of multiplexed loci-specific FISH signals, described herein, is achieved through a fully automated, multicolour fluorescence imaging microscope and object segmentation algorithms to identify cell nuclei and FISH spots within. Related tumour clones are identified through analysis of robustly defined cell neighbourhoods and cell-to-cell connections for regions of cells with homogenous and highly interconnected FISH spot signal characteristics. This study presents experiments which demonstrate the system’s ability to accurately quantify FISH spot signals in various tumour tissues and in up to 5 colours simultaneously or more through multiple rounds of FISH staining. Furthermore, the system’s FISH-based cell classification performance is evaluated at a sensitivity of 84% and specificity 81% and clonal identification algorithm results are determined to be comparable to clone delineation by a human-observer. Additionally, guidelines and procedures to perform anticipated, routine analysis experiments are established.

Diss. (sammanfattning). Umeå : Sveriges lantbruksuniv., 2003. / Härtill 4 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2004. / Härtill 4 uppsatser.

Diss. (sammanfattning) Umeå : Sveriges lantbruksuniv., 2003. / Härtill 5 uppsatser.