Stretching single DNA-molecules with temperature-stabilized optical tweezers

This thesis consists of two parts; in the first part we performed a single-molecule force extension measurement with 10kb long DNA-molecules from phage-λ to validate the calibration and single-molecule capability of our optical tweezers instrument. Fitting the worm-like chain interpolation formula to the data revealed that ca. 71% of the DNA tethers featured a contour length within ±15% of the expected value (3.38 µm). Only 25% of the found DNA had a persistence length between 30 and 60 nm. The correct value should be within 40 to 60 nm. In the second part we designed and built a precise temperature controller to remove thermal fluctuations that cause drifting of the optical trap. The controller uses feed-forward and PID (proportional-integral-derivative) feedback to achieve 1.58 mK precision and 0.3 K absolute accuracy. During a 5 min test run it reduced drifting of the trap from 1.4 nm/min in open-loop to 0.6 nm/min in closed-loop.

Molecular Tuning of Rhodopsins for High Visual Sensitivity in Different Light Environments : Variation in Absorbance Spectrum and Opsin Sequence within and between Species

Visual pigments of different animal species must have evolved at some stage to match the prevailing light environments, since all visual functions depend on their ability to absorb available photons and transduce the event into a reliable neural signal. There is a large literature on correlation between the light environment and spectral sensitivity between different fish species. However, little work has been done on evolutionary adaptation between separated populations within species. More generally, little is known about the rate of evolutionary adaptation to changing spectral environments. The objective of this thesis is to illuminate the constraints under which the evolutionary tuning of visual pigments works as evident in: scope, tempo, available molecular routes, and signal/noise trade-offs. Aquatic environments offer Nature s own laboratories for research on visual pigment properties, as naturally occurring light environments offer an enormous range of variation in both spectral composition and intensity. The present thesis focuses on the visual pigments that serve dim-light vision in two groups of model species, teleost fishes and mysid crustaceans. The geographical emphasis is in the brackish Baltic Sea area with its well-known postglacial isolation history and its aquatic fauna of both marine and fresh-water origin. The absorbance spectrum of the (single) dim-light visual pigment were recorded by microspectrophotometry (MSP) in single rods of 26 fish species and single rhabdoms of 8 opossum shrimp populations of the genus Mysis inhabiting marine, brackish or freshwater environments. Additionally, spectral sensitivity was determined from six Mysis populations by electroretinogram (ERG) recording. The rod opsin gene was sequenced in individuals of four allopatric populations of the sand goby (Pomatoschistus minutus). Rod opsins of two other goby species were investigated as outgroups for comparison. Rod absorbance spectra of the Baltic subspecies or populations of the primarily marine species herring (Clupea harengus membras), sand goby (P. minutus), and flounder (Platichthys flesus) were long-wavelength-shifted compared to their marine populations. The spectral shifts are consistent with adaptation for improved quantum catch (QC) as well as improved signal-to-noise ratio (SNR) of vision in the Baltic light environment. Since the chromophore of the pigment was pure A1 in all cases, this has apparently been achieved by evolutionary tuning of the opsin visual pigment. By contrast, no opsin-based differences were evident between lake and sea populations of species of fresh-water origin, which can tune their pigment by varying chromophore ratios. A more detailed analysis of differences in absorbance spectra and opsin sequence between and within populations was conducted using the sand goby as model species. Four allopatric populations from the Baltic Sea (B), Swedish west coast (S), English Channel (E), and Adriatic Sea (A) were examined. Rod absorbance spectra, characterized by the wavelength of maximum absorbance (λmax), differed between populations and correlated with differences in the spectral light transmission of the respective water bodies. The greatest λmax shift as well as the greatest opsin sequence difference was between the Baltic and the Adriatic populations. The significant within-population variation of the Baltic λmax values (506-511 nm) was analyzed on the level of individuals and was shown to correlate well with opsin sequence substitutions. The sequences of individuals with λmax at shorter wavelengths were identical to that of the Swedish population, whereas those with λmax at longer wavelengths additionally had substitution F261F/Y in the sixth transmembrane helix of the protein. This substitution (Y261) was also present in the Baltic common gobies and is known to redshift spectra. The tuning mechanism of the long-wavelength type Baltic sand gobies is assumed to be the co-expression of F261 and Y261 in all rods to produce ≈ 5 nm redshift. The polymorphism of the Baltic sand goby population possibly indicates ambiguous selection pressures in the Baltic Sea. The visual pigments of all lake populations of the opossum shrimp (Mysis relicta) were red-shifted by 25 nm compared with all Baltic Sea populations. This is calculated to confer a significant advantage in both QC and SNR in many humus-rich lakes with reddish water. Since only A2 chromophore was present, the differences obviously reflect evolutionary tuning of the visual protein, the opsin. The changes have occurred within the ca. 9000 years that the lakes have been isolated from the Sea after the most recent glaciation. At present, it seems that the mechanism explaining the spectral differences between lake and sea populations is not an amino acid substitution at any other conventional tuning site, but the mechanism is yet to be found.

Literaturnaja skazka A.M. Remizova (1900-1920-e gody)

Literary tale of A.M. Remizov (1900’s – 1920’s) The thesis is devoted to a detailed historical-literary description of a tale as a genre tradition in the creative work of Alexei Mikhailovich Remizov (1877-1957), one of the major Russian prose writers of the 20’s century. This very approach allows to specify the place and functional meaning of this genre in literary practice of the writer and to appeal to one of the key problems of the 20-21 century literature history – a specific of modernistic literature composition principle and a role of montage techniques in its formation. Remizov was working on tales during his whole life, though the most productive years of folklore studies fell to 1900’s – 1910’s. During this period he intensively studied folklore materials, narrated several hundreds of folk tales and in 1900’s – 1920’s published eight tale collections which played a significant role in the formation of stylistic and compositional principles of his prose of the 1910’s – 1920’s, especially montage techniques, which in its turn influenced the development of the narrative forms in the Russian post-revolutionary literature. At the same time a tale has specified not only poetics but also problematics of Remizov’s creative work, as when choosing folklore sources the writer always alluded to modern themes and relevant intellectual trends. The current research work, based on various archive materials and a wide spectrum of modern historical-literary data, complies four chapters with a consistent description of creation history, publication and critics’ reviews of Remizov’s tale collections and single tales contributing to his creative evolution characteristic. Furthermore, the work refers to composition and subject of the particular collections. On the whole it enables to follow up genre dynamics. The first chapter of the work is devoted to Posolon’ (Sunwise), the earliest tale collection of Remizov. The main feature of the collection is that its composition is oriented on the agrarian calendar and the subject – on the system of mythological views reflected in the Russian folklore. This very collection to a large extent corresponds to the writer’s views on the myth represented in Pis’mo v redaktsiyu (Letter to the Editor). The history of this manifesto appearing is analyzed in the second chapter. The incident which caused its forthcoming contributed to ‘legitimization’ of Remizov’s narrations as a relevant genre of modern literature and to upgrading the writer in professional hierarchy. The third chapter analyzes Remizov’s collections of 1900’s – early 1920’s, a result of Remizov’s scrupulous work with a specific tale material. He is acting here as a tale repertory researcher and in some cases as a collector as well. The means of such collections’ topical organization is not the myth but the hero of the tale. According to this principle single pieces are grouped into cycles, which then form complicated montage constructs. Texts themselves can be viewed as a sort of hyper-quotations, as they in fact entirely coincide with their original sources. Besides, collections usually have their own ideal patterns. In the fourth chapter a connection of Remizov’s creative work with folk fun culture and a tradition of the folklore noel story is being demonstrated on Zavetnyie skazy (Secret Tales) material. A consistent collections’ history creation analysis convinces us that the tale was a sort of laboratory in which main writer’s prose methods were being worked out.

Nuorisokodista maailmalle : Kokemuksia nuorisokodissa elämisestä ja aikuisiässä selviytymisestä

This thesis studies the experiences of women who have lived in a youth home as girls. There are two main themes: 1) experiences of living in a youth home, and 2) experiences of coping as an adult. Data on the first theme is purely subjective; it derives from personal, recalled experiences. Data on the second theme is partly based on experiences and partly on facts about the current life situation of the research participants. A third theme of the thesis is concerned with the question of how the research participants’ placement in a youth home influenced their later life. The thesis contributes valuable knowledge concerning the experiences of young people who have been raised in substitute care, a topic that is rare in the literature. The empirical data of the study consists of responses to an initial inquiry and subsequent interviews. The inquiry was sent to 116 former inhabitants of a youth home. 62 altogether returned the inquiry, and 34 participated in the interview. The purpose of the inquiry was to produce an overview of the life situations of the research participants and to invite them to participate in the interview. In addition, the inquiry sought to produce an overview of how the participants enjoyed living in a youth home and how they saw its significance in terms of their later lives. The interviews concentrated on the research participants’ experiences concerning the processes of getting into a youth home, living there, and coping independently in life afterwards. The most central result relating to the first main theme was that the experiences were both shared and non-shared. Living in a youth home was characterized by six general sentiments: “wonderful, real home”, “new world!”, “safe haven”, “place to live”, “penal institution”, and “nightmare”. These sentiments seemed to be related first and foremost to whether one’s own, individual needs and expectations had been met in the youth home. The strongest and most common needs, as experienced, were the needs for safety, belongingness and respect. On the basis of the experiences, meeting these needs can be considered as the most important task of a youth home. The results relating to the second main theme of the study were examined in two different ways. Comparisons with the general female population (education, situation in working life and financial circumstances) showed that research participants had coped less well. Differences were also found to exist in family structures: nuclear families and single mother families were more unusual among research participants, and stepfamilies more common, than in the general population. More of the participants’ children than of the general population’s lived with somebody other than their parent. However, the experience of coping well was common among research participants, although the beginning of independent living had been generally experienced as difficult: feelings of loneliness, insecurity and restlessness were dominant. Later, a sense of life control developed and strengthened through joining with others (family, work, friends), through accepting one’s own life history and through creating one’s own model of living. As the most significant explanation of their coping, the research participants identified their own (innate) strength and will to cope. The majority of the research participants felt that the youth home had a positive influence on their later lives. Positive influences can be grouped in three “levels”: I) getting out of the home, II) having good experiences and learning useful things, and III) the essential effect on one’s own way of thinking and living. The second level’s influence includes strengthened self-esteem, increased social understanding and new knowledge and skills. Some research participants did not think the youth home had any significance in terms of their later lives, and some thought it had negative significance.

Molecular Genetics of Lactase Deficiencies

Congenital lactase deficiency (CLD) (MIM 223000) is a rare autosomal recessive gastrointestinal disorder characterized by watery diarrhea in infants fed with breast milk or other lactose-containing formulas. The CLD locus was previously assigned by linkage and linkage disequilibrium analyses on 2q21 in 19 Finnish families. In this study, the molecular background of this disorder is reported. The CLD locus was refined in 32 CLD patients in 24 families by using microsatellite and single nucleotide polymorphism (SNP) haplotypes. Mutation analyses were performed by direct sequencing. We identified 5 distinct mutations in the lactase (LCT) gene, encoding the enzyme that hydrolyzes lactose in the intestinal lumen. These findings facilitate genetic testing of CLD in clinical practice and enable genetic counseling. The present data also provide the basis for detailed characterization of the molecular pathogenesis of this disorder. Adult-type hypolactasia (MIM 223100) (lactase non-persistence, lactose intolerance) is an autosomal recessive gastrointestinal condition that is a result of a decline in the activity of lactase in the intestinal lumen after weaning. Adult-type hypolactasia is considered to be a normal phenomenon among mammals and symptoms are remarkably milder than experienced in CLD. Recently, a variant C/T-13910 was shown to associate with the adult-type hypolactasia trait, locating 13.9 kb upstream of the LCT gene. In this study, the functional significance of the C/T-13910 variant was determined by studying the LCT mRNA levels in intestinal biopsy samples in children and adults with different genotypes. RT-PCR followed by solid-phase minisequencing was applied to determine the relative expression levels of the LCT alleles using an informative SNP located in exon 1. In children, the C-13910 allele was observed to be downregulated after five years of age in parallel with lactase enzyme activity. The expression of the LCT mRNA in the intestinal mucosa in individuals with the T-13910 A-22018 alleles was 11.5 times higher than that found in individuals with the C-13910, G-22018 alleles. These findings suggest that the C/T-13910 associated with adult-type hypolactasia is associated with the transcriptional regulation of the LCT gene. The presence of the T-13910 A-22018 allele also showed significant elevation lactase activity. Galactose, the hydrolysing product of the milk sugar lactose, has been hypothesized to be poisonous to ovarian epithelial cells. Hence, consumption of dairy products and lactase persistence has been proposed to be a risk factor for ovarian carcinoma. To investigate whether lactase persistence is related to the risk of ovarian carcinoma the C/T-13910 genotype was determined in a cohort of 782 women with ovarian carcinoma 1331 individuals serving as controls. Lactase persistence did not associate significantly with the risk for ovarian carcinoma in the Finnish, in the Polish or in the Swedish populations. The findings do not support the hypothesis that lactase persistence increases the risk for ovarian carcinoma.

Multiwavelength studies of regolith effects in planetary remote sensing

A large proportion of our knowledge about the surfaces of atmosphereless solar-system bodies is obtained through remote-sensing measurements. The measurements can be carried out either as ground-based telescopic observations or space-based observations from orbiting spacecraft. In both cases, the measurement geometry normally varies during the observations due to the orbital motion of the target body, the spacecraft, etc.. As a result, the data are acquired over a variety of viewing and illumination angles. Surfaces of planetary bodies are usually covered with a layer of loose, broken-up rock material called the regolith whose physical properties affect the directional dependence of remote-sensed measurements. It is of utmost importance for correct interpretation of the remote-sensed data to understand the processes behind this alteration. In the thesis, the multi-angular effects that the physical properties of the regolith have on remote-sensing measurements are studied in two regimes of electromagnetic radiation, visible to near infrared and soft X-rays. These effects are here termed generally the regolith effects in remote sensing. Although the physical mechanisms that are important in these regions are largely different, notable similarities arise in the methodology that is used in the study of the regolith effects, including the characterization of the regolith both in experimental studies and in numerical simulations. Several novel experimental setups have been constructed for the thesis. Alongside the experimental work, theoretical modelling has been carried out, and results from both approaches are presented. Modelling of the directional behaviour of light scattered from a regolith is utilized to obtain shape and spin-state information of several asteroids from telescopic observations and to assess the surface roughness and single-scattering properties of lunar maria from spacecraft observations. One of the main conclusions is that the azimuthal direction is an important factor in detailed studies of planetary surfaces. In addition, even a single parameter, such as porosity, can alter the light scattering properties of a regolith significantly. Surface roughness of the regolith is found to alter the elemental fluorescence line ratios of a surface obtained through planetary soft X-ray spectrometry. The results presented in the thesis are among the first to report this phenomenon. Regolith effects need to be taken into account in the analysis of remote-sensed data, providing opportunities for retrieving physical parameters of the surface through inverse methods.

Polymeereillä stabiloitu amorfinen formulaatio

Nowadays growing number of new active pharmaceutical ingredients (API) have large molecular weight and are hydrophobic. The energy of their crystal lattice is bigger and polarity has decreased. This leads to weakened solubility and dissolution rate of the drug. These properties can be enhanced for example by amorphization. Amorphous form has the best dissolution rate in the solid state. In the amorphous form drug molecules are randomly arranged, so the energy required to dissolve molecules is lower compared to the crystalline counterpart. The disadvantage of amorphous form is that it is unstable. Amorphous form tends to crystallize. Stability of amorphous form can be enhanced by adding an adjuvant to drug product. Adjuvant is usually a polymer. Polymers prevent crystallization both by forming bonds with API molecules and by steric hindrance. The key thing in stabilizing amorphous form is good miscibility between API and polymer. They have to be mixed in a molecular level so that the polymer is able to prevent crystallization. The aim of this work was to study miscibility of drug and polymer and stability of their dispersion with different analytical methods. Amorphous dispersions were made by rotary evaporator and freeze dryer. Amorphicity was confirmed with X-ray powder diffraction (XRPD) right after preparation. Itraconazole and theophylline were the chosen molecules to be stabilized. Itraconazole was expected to be easier and theophylline more difficult to stabilize. Itraconazole was stabilized with HPMC and theophylline was stabilized with PVP. Miscibility was studied with XRPD and differential scanning calorimetry (DSC). In addition it was studied with polarized light microscope if miscibility was possible to see visually. Dispersions were kept in stressed conditions and the crystallization was analyzed with XRPD. Stability was also examined with isothermal microcalorimetry (IMC). The dispersion of itraconazole and theophylline 40/60 (w/w) was completely miscible. It was proved by linear combination of XRPD results and single glass transition temperature in DSC. Homogenic well mixed film was observed with light microscope. Phase separation was observed with other compositions. Dispersions of theophylline and PVP mixed only partly. Stability of itraconazole dispersions were better than theophylline dispersions which were mixed poorer. So miscibility was important thing considering stability. The results from isothermal microcalorimetry were similar to results from conventional stability studies. Complementary analytical methods should be used when studying miscibility so that the results are more reliable. Light microscope is one method in addition to mostly used XRPD and DSC. Analyzing light microscope photos is quite subjective but it gives an idea of miscibility. Isothermal microcalorimetry can be one option for conventional stability studies. If right conditions can be made where the crystallization is not too fast, it may be possible to predict stability with isothermal microcalorimetry.

Towards Understanding Powder Behavior Via Simulation

The aim of this study was to investigate powder and tablet behavior at the level of mechanical interactions between single particles. Various aspects of powder packing, mixing, compression, and bond formation were examined with the aid of computer simulations. The packing and mixing simulations were based on spring forces interacting between particles. Packing and breakage simulations included systems in which permanent bonds were formed and broken between particles, based on their interaction strengths. During the process, a new simulation environment based on Newtonian mechanics and elementary interactions between the particles was created, and a new method for evaluating mixing was developed. Powder behavior is a complicated process, and many of its aspects are still unclear. Powders as a whole exhibit some aspects of solids and others of liquids. Therefore, their physics is far from clear. However, using relatively simple models based on particle-particle interaction, many powder properties could be replicated during this work. Simulated packing densities were similar to values reported in the literature. The method developed for describing powder mixing correlated well with previous methods. The new method can be applied to determine mixing in completely homogeneous materials, without dividing them into different components. As such, it can describe the efficiency of the mixing method, regardless of the powder's initial setup. The mixing efficiency at different vibrations was examined, and we found that certain combinations of amplitude, direction, and frequencies resulted in better mixing while using less energy. Simulations using exponential force potentials between particles were able to explain the elementary compression behavior of tablets, and create force distributions that were similar to the pressure distributions reported in the literature. Tablet-breaking simulations resulted in breaking strengths that were similar to measured tablet breaking strengths. In general, many aspects of powder behavior can be explained with mechanical interactions at the particle level, and single particle properties can be reliably linked to powder behavior with accurate simulations.

Opettajien roolit alakoulun samanaikaisopetuksessa

Teachers work is changing from independent work towards a collegial cooperation, and one form of cooperation can be co-teaching. Co-teaching is also discussed in the three level model of supporting in Special education strategy (Ministry of Education 2007). Efforts have been made to increase co-teaching in Helsinki with the help of a merit pay system. The purpose of this study is to describe teachers' roles in planning, implementing and evaluating co-teaching and to resolve how teachers have ended up with these roles, what advantages and disadvantages there are in different roles and what kind of roles are experienced meaningful. This study is made from a class teacher or a special class teacher point of view. The research material was collected using a qualitative web-inquiry in Autumn 2010. The questionnaire was answered by 35 teachers. The material was studied using content analysis methods. Three different co-teaching roles were formed on the basis of the research material. These roles differ in the way of dividing responsibility of planning and implementing co-teaching. Responsibility Sharers divided the responsibility evenly, Primary Responsible had one teacher with main responsibility and Single Responsible had only one teacher having all the responsibility of planning and teaching. The more responsibility the class teacher had, the more the special education teacher was limited to answer for students with special needs. Distribution of work with Responsibility Sharers was mostly based on good cooperation, while Primary Responsible and Single Responsible had work distribution mostly affected by absence of common planning time. The most satisfied with their co-teaching roles were the Responsibility Sharers, while the Single Responsible were the most unhappy group. However, it seems that individuals' persona affects to what kind of co-teaching was experienced meaningful.