SU-8-Based Microchips for Capillary Electrophoresis and Electrospray Ionization Mass Spectrometry

Miniaturization of analytical instrumentation is attracting growing interest in response to the explosive demand for rapid, yet sensitive analytical methods and low-cost, highly automated instruments for pharmaceutical and bioanalyses and environmental monitoring. Microfabrication technology in particular, has enabled fabrication of low-cost microdevices with a high degree of integrated functions, such as sample preparation, chemical reaction, separation, and detection, on a single microchip. These miniaturized total chemical analysis systems (microTAS or lab-on-a-chip) can also be arrayed for parallel analyses in order to accelerate the sample throughput. Other motivations include reduced sample consumption and waste production as well as increased speed of analysis. One of the most promising hyphenated techniques in analytical chemistry is the combination of a microfluidic separation chip and mass spectrometer (MS). In this work, the emerging polymer microfabrication techniques, ultraviolet lithography in particular, were exploited to develop a capillary electrophoresis (CE) separation chip which incorporates a monolithically integrated electrospray ionization (ESI) emitter for efficient coupling with MS. An epoxy photoresist SU-8 was adopted as structural material and characterized with respect to its physicochemical properties relevant to chip-based CE and ESI/MS, namely surface charge, surface interactions, heat transfer, and solvent compatibility. As a result, SU-8 was found to be a favorable material to substitute for the more commonly used glass and silicon in microfluidic applications. In addition, an infrared (IR) thermography was introduced as direct, non-intrusive method to examine the heat transfer and thermal gradients during microchip-CE. The IR data was validated through numerical modeling. The analytical performance of SU-8-based microchips was established for qualitative and quantitative CE-ESI/MS analysis of small drug compounds, peptides, and proteins. The CE separation efficiency was found to be similar to that of commercial glass microchips and conventional CE systems. Typical analysis times were only 30-90 s per sample indicating feasibility for high-throughput analysis. Moreover, a mass detection limit at the low-attomole level, as low as 10E+5 molecules, was achieved utilizing MS detection. The SU-8 microchips developed in this work could also be mass produced at low cost and with nearly identical performance from chip to chip. Until this work, the attempts to combine CE separation with ESI in a chip-based system, amenable to batch fabrication and capable of high, reproducible analytical performance, have not been successful. Thus, the CE-ESI chip developed in this work is a substantial step toward lab-on-a-chip technology.

The effects of environmental factors on biomass and microcystin production by the freshwater cyanobacterial genera Microcystis and Anabaena

Several cyanobacterial genera produce the hepatotoxins, microcystins. Microcystins are produced only in cells that have microcystin synthetase gene (mcy) clusters, which encode enzyme complexes involved in microcystin biosynthesis. Microcystin-producing and nonmicrocystin-producing genotypes of single cyanobacterial genus may occur simultaneously in situ. Previously, the effects of environmental factors on the growth and microcystin production of cyanobacteria have mainly been studied by means of isolated cyanobacteria cultures in the laboratory. Studies in the field have been difficult, owing to the lack of methods to identify and quantify the different genotypes. In this study, genus-specific microcystin synthetase E (mcyE) gene primers were designed and a method to identify and quantify the mcyE copy numbers was developed and used in situ. Microcystis and Anabaena mcyE genes were observed in two Finnish lakes. Microcystis appeared to be the most abundant microcystin producer in Lake Tuusulanjärvi and in one basin of Lake Hiidenvesi. Because the most potent microcystin-producing genus of a lake can be identified, it will be possible in the future to design genus-targeted strategies for lake restoration. Effects of P and N concentrations on the biomass of microcystin-producing and nonmicrocystin-producing Microcystis strains and an Anabaena strain were studied in cultures. P and N concentrations and their combined effect increased cyanobacterial biomass of all Microcystis strains. The biomass of microcystin-producing Microcystis was higher than that of nonmicrocystin-producing strains at high nutrient concentrations. The P concentration increased Anabaena biomass, but the effect of N concentration was statistically insignificant for growth yield, probably due to the ability of the genus to fix molecular N2. P and N concentrations and combined nutrients caused an increase in cellular microcystin concentrations of the Microcystis strain cultivated in chemostat cultures. Cyanobacteria are able to hydrolyse nutrients from organic matter through extracellular enzyme activities. Leucine aminopeptidase (LAP) activity was observed in an axenic N2-fixing Anabaena strain grown in batch cultures. The P concentration caused a statistically significant increase in LAP activity, whereas the effect of N concentration was insignificant. The highest LAP activities were observed in the most eutrophic basins of Lake Hiidenvesi. LAP activity probably originated mostly from attached heterotrophic bacteria and less from cyanobacteria.

Parameters Affecting the Extraction of Polycyclic Aromatic Hydrocarbons with Pressurised Hot Water

Pressurised hot water extraction (PHWE) exploits the unique temperature-dependent solvent properties of water minimising the use of harmful organic solvents. Water is environmentally friendly, cheap and easily available extraction medium. The effects of temperature, pressure and extraction time in PHWE have often been studied, but here the emphasis was on other parameters important for the extraction, most notably the dimensions of the extraction vessel and the stability and solubility of the analytes to be extracted. Non-linear data analysis and self-organising maps were employed in the data analysis to obtain correlations between the parameters studied, recoveries and relative errors. First, pressurised hot water extraction (PHWE) was combined on-line with liquid chromatography-gas chromatography (LC-GC), and the system was applied to the extraction and analysis of polycyclic aromatic hydrocarbons (PAHs) in sediment. The method is of superior sensitivity compared with the traditional methods, and only a small 10 mg sample was required for analysis. The commercial extraction vessels were replaced by laboratory-made stainless steel vessels because of some problems that arose. The performance of the laboratory-made vessels was comparable to that of the commercial ones. In an investigation of the effect of thermal desorption in PHWE, it was found that at lower temperatures (200ºC and 250ºC) the effect of thermal desorption is smaller than the effect of the solvating property of hot water. At 300ºC, however, thermal desorption is the main mechanism. The effect of the geometry of the extraction vessel on recoveries was studied with five specially constructed extraction vessels. In addition to the extraction vessel geometry, the sediment packing style and the direction of water flow through the vessel were investigated. The geometry of the vessel was found to have only minor effect on the recoveries, and the same was true of the sediment packing style and the direction of water flow through the vessel. These are good results because these parameters do not have to be carefully optimised before the start of extractions. Liquid-liquid extraction (LLE) and solid-phase extraction (SPE) were compared as trapping techniques for PHWE. LLE was more robust than SPE and it provided better recoveries and repeatabilities than did SPE. Problems related to blocking of the Tenax trap and unrepeatable trapping of the analytes were encountered in SPE. Thus, although LLE is more labour intensive, it can be recommended over SPE. The stabilities of the PAHs in aqueous solutions were measured using a batch-type reaction vessel. Degradation was observed at 300ºC even with the shortest heating time. Ketones and quinones and other oxidation products were observed. Although the conditions of the stability studies differed considerably from the extraction conditions in PHWE, the results indicate that the risk of analyte degradation must be taken into account in PHWE. The aqueous solubilities of acenaphthene, anthracene and pyrene were measured, first below and then above the melting point of the analytes. Measurements below the melting point were made to check that the equipment was working, and the results were compared with those obtained earlier. Good agreement was found between the measured and literature values. A new saturation cell was constructed for the solubility measurements above the melting point of the analytes because the flow-through saturation cell could not be used above the melting point. An exponential relationship was found between the solubilities measured for pyrene and anthracene and temperature.

Computational Methods for Locating and Analyzing Conserved Gene Regulatory DNA Elements

This thesis presents methods for locating and analyzing cis-regulatory DNA elements involved with the regulation of gene expression in multicellular organisms. The regulation of gene expression is carried out by the combined effort of several transcription factor proteins collectively binding the DNA on the cis-regulatory elements. Only sparse knowledge of the 'genetic code' of these elements exists today. An automatic tool for discovery of putative cis-regulatory elements could help their experimental analysis, which would result in a more detailed view of the cis-regulatory element structure and function. We have developed a computational model for the evolutionary conservation of cis-regulatory elements. The elements are modeled as evolutionarily conserved clusters of sequence-specific transcription factor binding sites. We give an efficient dynamic programming algorithm that locates the putative cis-regulatory elements and scores them according to the conservation model. A notable proportion of the high-scoring DNA sequences show transcriptional enhancer activity in transgenic mouse embryos. The conservation model includes four parameters whose optimal values are estimated with simulated annealing. With good parameter values the model discriminates well between the DNA sequences with evolutionarily conserved cis-regulatory elements and the DNA sequences that have evolved neutrally. In further inquiry, the set of highest scoring putative cis-regulatory elements were found to be sensitive to small variations in the parameter values. The statistical significance of the putative cis-regulatory elements is estimated with the Two Component Extreme Value Distribution. The p-values grade the conservation of the cis-regulatory elements above the neutral expectation. The parameter values for the distribution are estimated by simulating the neutral DNA evolution. The conservation of the transcription factor binding sites can be used in the upstream analysis of regulatory interactions. This approach may provide mechanistic insight to the transcription level data from, e.g., microarray experiments. Here we give a method to predict shared transcriptional regulators for a set of co-expressed genes. The EEL (Enhancer Element Locator) software implements the method for locating putative cis-regulatory elements. The software facilitates both interactive use and distributed batch processing. We have used it to analyze the non-coding regions around all human genes with respect to the orthologous regions in various other species including mouse. The data from these genome-wide analyzes is stored in a relational database which is used in the publicly available web services for upstream analysis and visualization of the putative cis-regulatory elements in the human genome.

Transcriptome and proteome analysis of xylose-metabolising Saccharomyces cerevisiae

Increasing concern about global climate warming has accelerated research into renewable energy sources that could replace fossil petroleum-based fuels and materials. Bioethanol production from cellulosic biomass by fermentation with baker s yeast Saccharomyces cerevisiae is one of the most studied areas in this field. The focus has been on metabolic engineering of S. cerevisiae for utilisation of the pentose sugars, in particular D-xylose that is abundant in the hemicellulose fraction of biomass. Introduction of a heterologous xylose-utilisation pathway into S. cerevisiae enables xylose fermentation, but ethanol yield and productivity do not reach the theoretical level. In the present study, transcription, proteome and metabolic flux analyses of recombinant xylose-utilising S. cerevisiae expressing the genes encoding xylose reductase (XR) and xylitol dehydrogenase (XDH) from Pichia stipitis and the endogenous xylulokinase were carried out to characterise the global cellular responses to metabolism of xylose. The aim of these studies was to find novel ways to engineer cells for improved xylose fermentation. The analyses were carried out from cells grown on xylose and glucose both in batch and chemostat cultures. A particularly interesting observation was that several proteins had post-translationally modified forms with different abundance in cells grown on xylose and glucose. Hexokinase 2, glucokinase and both enolase isoenzymes 1 and 2 were phosphorylated differently on the two different carbon sources studied. This suggests that phosphorylation of glycolytic enzymes may be a yet poorly understood means to modulate their activity or function. The results also showed that metabolism of xylose affected the gene expression and abundance of proteins in pathways leading to acetyl-CoA synthesis and altered the metabolic fluxes in these pathways. Additionally, the analyses showed increased expression and abundance of several other genes and proteins involved in cellular redox reactions (e.g. aldo-ketoreductase Gcy1p and 6-phosphogluconate dehydrogenase) in cells grown on xylose. Metabolic flux analysis indicated increased NADPH-generating flux through the oxidative part of the pentose phosphate pathway in cells grown on xylose. The most importantly, results indicated that xylose was not able to repress to the same extent as glucose the genes of the tricarboxylic acid and glyoxylate cycles, gluconeogenesis and some other genes involved in the metabolism of respiratory carbon sources. This suggests that xylose is not recognised as a fully fermentative carbon source by the recombinant S. cerevisiae that may be one of the major reasons for the suboptimal fermentation of xylose. The regulatory network for carbon source recognition and catabolite repression is complex and its functions are only partly known. Consequently, multiple genetic modifications and also random approaches would probably be required if these pathways were to be modified for further improvement of xylose fermentation by recombinant S. cerevisiae strains.

Modelling boreal forest CO2 exchange and seasonality

Man-induced climate change has raised the need to predict the future climate and its feedback to vegetation. These are studied with global climate models; to ensure the reliability of these predictions, it is important to have a biosphere description that is based upon the latest scientific knowledge. This work concentrates on the modelling of the CO2 exchange of the boreal coniferous forest, studying also the factors controlling its growing season and how these can be used in modelling. In addition, the modelling of CO2 gas exchange at several scales was studied. A canopy-level CO2 gas exchange model was developed based on the biochemical photosynthesis model. This model was first parameterized using CO2 exchange data obtained by eddy covariance (EC) measurements from a Scots pine forest at Sodankylä. The results were compared with a semi-empirical model that was also parameterized using EC measurements. Both of the models gave satisfactory results. The biochemical canopy-level model was further parameterized at three other coniferous forest sites located in Finland and Sweden. At all the sites, the two most important biochemical model parameters showed seasonal behaviour, i.e., their temperature responses changed according to the season. Modelling results were improved when these changeover dates were related to temperature indices. During summer-time the values of the biochemical model parameters were similar at all the four sites. Different control factors for CO2 gas exchange were studied at the four coniferous forests, including how well these factors can be used to predict the initiation and cessation of the CO2 uptake. Temperature indices, atmospheric CO2 concentration, surface albedo and chlorophyll fluorescence (CF) were all found to be useful and have predictive power. In addition, a detailed simulation study of leaf stomata in order to separate physical and biochemical processes was performed. The simulation study brought to light the relative contribution and importance of the physical transport processes. The results of this work can be used in improving CO2 gas exchange models in boreal coniferous forests. The meteorological and biological variables that represent the seasonal cycle were studied, and a method for incorporating this cycle into a biochemical canopy-level model was introduced.

Variation i kvinnors namnfraser i officiella dokument i Helsingfors 1780-1930 : Socioonomastiska synvinklar på makt och identitet

This dissertation is an onomastic study of variation in women s name phrases in official documents in Finland during the period 1780−1930. The aim is to discuss from a socio-onomastic perspective both the changeover from patronymics to inherited family names and the use of surnames after marriage (i.e. whether women adopted their husbands family names or retained their maiden names), before new laws in this area entered into force in Finland in the early 20th century. In 1920, a law on family names that required fixed names put an end to the use of the patronymic as a person s only surname. After 1929, it was no longer possible for a married woman to retain her maiden name. Methodologically, to explain this development from a socio-onomastic perspective, I have based my study on a syntactic-semantic analysis of the actual name phrases. To be able to demonstrate the extensive material, I have elaborated a scheme to divide the 115 different types of name phrases into 13 main categories. The analysis of the material for Helsinki is based on frequency calculations of the different types of name phrases every thirtieth year, as well as on describing variation in the structure and semantic content of the name phrases, e.g. social variation in the use of titles and epithets. In addition to this, by applying a biographic-genealogical method, I have conducted two case studies of the usage of women s name phrases in the two chosen families. The study is based on parish registers from the period 1780−1929, estate inventory documents from the period 1780−1928, registration forms for liberty of trade from the period 1880−1908, family announcements on newspapers from the period 1829−1888, gravestones from the period 1796−1929 and diaries from the periods 1799−1801 and 1818−1820 providing a corpus of 5 950 name phrases. The syntactic-semantic analysis has revealed the overall picture of various ways of denoting women in official documents. In Helsinki, towards the end of the 19th century, the use of inherited family names seems to be almost fully developed in official contexts. At the late 19th century, a patronymic still appears as the only surname of some working-class women whereas in the early 20th century patronymics were only entered in the parish register as a kind of middle name. In the beginning of the 19th century, most married women were still registered under their maiden names, with a few exceptions among the bourgeoisie and upper class. The comparative analysis of name phrases in diaries, however, indicates that the use of the husband s family name by married women was a much earlier phenomenon in private contexts than in official documents. Keywords: socio-onomastics, syntactic-semantic analysis, name phrase, patronymic, maiden name, husband s family name

Characterization and evaluation of melibiose as novel excipient in tablet compaction

Lactose is probably the most used tablet excipient in the field of pharmacy. Although lactose is thoroughly characterized and available in many different forms there is a need to find a replacer for lactose as a filler/binder in tablet formulations because it has some downsides. Melibiose is a relatively unknown disaccharide that has not been thoroughly characterized and not previously used as an excipient in tablets. Structurally melibiose is close to lactose as it is also formed from the same two monosaccharides, glucose and galactose. Aim of this research is to characterize and to study physicochemical properties of melibiose. Also the potential of melibiose to be used as pharmaceutical tablet excipient, even as a substitute for lactose is evaluated. Current knowledge about fundamentals of tableting and methods for determinating of deformation behavior and tabletability are reviewed. In this research Raman spectroscopy, X-ray powder diffraction (XRPD), near-infrared spectroscopy (NIR) and Fourier-transform infrared spectroscopy (FT-IR) were used to study differences between two melibiose batches purchased from two suppliers. In NIR and FT-IR measurements no difference between materials could be observed. XPRD and Raman however found differences between the two melibiose batches. Also the effects of moisture content and heating to material properties were studied and moisture content of materials seems to cause some differences. Thermal analytical methods, differential scanning calorimetry (DSC) and thermogravimetry (TG) were used to study thermal behaviour of melibiose and difference between materials was found. Other melibiose batch contains residual water which evaporates at higher temperatures causing the differences in thermal behaviour. Scanning electron microscopy images were used to evaluate particle size, particle shape and morphology. Bulk, tapped and true densities and flow properties of melibiose was measured. Particle size of the melibiose batches are quite different resulting causing differences in the flowability. Instrumented tableting machine and compression simulator were used to evaluate tableting properties of melbiose compared to α-lactose monohydrate. Heckel analysis and strain-rate sensitivity index were used to determine deformation mechanism of melibiose monohydrate in relation to α–lactose monohydrate during compaction. Melibiose seems to have similar deformation behaviour than α-lactose monohydrate. Melibiose is most likely fragmenting material. Melibiose has better compactibility than α – lactose monohydrate as it produces tablets with higher tensile strength with similar compression pressures. More compression studies are however needed to confirm these results because limitations of this study.