Methods and tools for mass spectrometric lipidome analysis

The analysis of lipid compositions from biological samples has become increasingly important. Lipids have a role in cardiovascular disease, metabolic syndrome and diabetes. They also participate in cellular processes such as signalling, inflammatory response, aging and apoptosis. Also, the mechanisms of regulation of cell membrane lipid compositions are poorly understood, partially because a lack of good analytical methods. Mass spectrometry has opened up new possibilities for lipid analysis due to its high resolving power, sensitivity and the possibility to do structural identification by fragment analysis. The introduction of Electrospray ionization (ESI) and the advances in instrumentation revolutionized the analysis of lipid compositions. ESI is a soft ionization method, i.e. it avoids unwanted fragmentation the lipids. Mass spectrometric analysis of lipid compositions is complicated by incomplete separation of the signals, the differences in the instrument response of different lipids and the large amount of data generated by the measurements. These factors necessitate the use of computer software for the analysis of the data. The topic of the thesis is the development of methods for mass spectrometric analysis of lipids. The work includes both computational and experimental aspects of lipid analysis. The first article explores the practical aspects of quantitative mass spectrometric analysis of complex lipid samples and describes how the properties of phospholipids and their concentration affect the response of the mass spectrometer. The second article describes a new algorithm for computing the theoretical mass spectrometric peak distribution, given the elemental isotope composition and the molecular formula of a compound. The third article introduces programs aimed specifically for the analysis of complex lipid samples and discusses different computational methods for separating the overlapping mass spectrometric peaks of closely related lipids. The fourth article applies the methods developed by simultaneously measuring the progress curve of enzymatic hydrolysis for a large number of phospholipids, which are used to determine the substrate specificity of various A-type phospholipases. The data provides evidence that the substrate efflux from bilayer is the key determining factor for the rate of hydrolysis.

Strain-rate sensitivity and microstructural evolution in a Mg-Al-Zn alloy

Strain rate sensitivity measurements are used to identify twinning and changes in deformation mechanisms in a Mg AZ31 alloy over a wide range of temperatures and grain sizes. At low temperatures, there is significant twinning at low strains with strain-rate insensitivity; at large strains, strain rate sensitivity is noted, corresponding to deformation by multiple slip. At high temperatures, there is very little twinning and this leads to a significant strain rate sensitivity from the early stages of deformation. (C) 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Association between molecular variation in the phosphoglucose isomerase (Pgi) locus and migration propensity in the Glanville fritillary butterfly

Habitat fragmentation produces patches of suitable habitat surrounded by unfavourable matrix habitat. A species may persist in such a fragmented landscape in an equilibrium between the extinctions and recolonizations of local populations, thus forming a metapopulation. Migration between local populations is necessary for the long-term persistence of a metapopulation. The Glanville fritillary butterfly (Melitaea cinxia) forms a metapopulation in the Åland islands in Finland. There is migration between the populations, the extent of which is affected by several environmental factors and variation in the phenotype of individual butterflies. Different allelic forms of the glycolytic enzyme phosphoglucose isomerase (Pgi) has been identified as a possible genetic factor influencing flight performance and migration rate in this species. The frequency of a certain Pgi allele, Pgi-f, follows the same pattern in relation to population age and connectivity as migration propensity. Furthermore, variation in flight metabolic performance, which is likely to affect migration propensity, has been linked to genetic variation in Pgi or a closely linked locus. The aim of this study was to investigate the association between Pgi genotype and the migration propensity in the Glanville fritillary both at the individual and population levels using a statistical modelling approach. A mark-release-recapture (MRR) study was conducted in a habitat patch network of M. cinxia in Åland to collect data on the movements of individual butterflies. Larval samples from the study area were also collected for population level examinations. Each butterfly and larva was genotyped at the Pgi locus. The MRR data was parameterised with two mathematical models of migration: the Virtual Migration Model (VM) and the spatially explicit diffusion model. VM model predicted and observed numbers of emigrants from populations with high and low frequencies of Pgi-f were compared. Posterior predictive data sets were simulated based on the parameters of the diffusion model. Lack-of-fit of observed values to the model predicted values of several descriptors of movements were detected, and the effect of Pgi genotype on the deviations was assessed by randomizations including the genotype information. This study revealed a possible difference in the effect of Pgi genotype on migration propensity between the two sexes in the Glanville fritillary. The females with and males without the Pgi-f allele moved more between habitat patches, which is probably related to differences in the function of flight in the two sexes. Females may use their high flight capacity to migrate between habitat patches to find suitable oviposition sites, whereas males may use it to acquire mates by keeping a territory and fighting off other intruding males, possibly causing them to emigrate. The results were consistent across different movement descriptors and at the individual and population levels. The effect of Pgi is likely to be dependent on the structure of the landscape and the prevailing environmental conditions.

Peritoneal dialysis and neurological outcome in infants and small children

Although improved outcomes for children on peritoneal dialysis (PD) have been seen in recent years, the youngest patients continue to demonstrate inferior growth, more frequent infections, more neurological sequelae, and higher mortality compared to older children. Also, maintain-ing normal intravascular volume status, especially in anuric patients, has proven difficult. This study was designed to treat and monitor these youngest PD patients, which are relatively many due to the high prevalence of congenital nephrotic syndrome of the Finnish type (CNF, NPHS1) in Finland, with a strict protocol, to evaluate the results and to improve metabolic balance, growth, and development. A retrospective analysis of 23 children under two years of age at onset of PD, treated between 1995 and 2000, was performed to obtain a control population for our prospective PD study. Respectively, 21 patients less than two years of age at the beginning of PD were enrolled in prospective studies between 2001 and 2005. Medication for uremia and nutrition were care-fully adjusted during PD. Laboratory parameters and intravascular volume status were regu-larly analyzed. Growth was analyzed and compared with midparental height. In a prospective neurological study, the risk factors for development and the neurological development was determined. Brain images were surveyed. Hearing was tested. In a retrospective neurological study, the data of six NPHS1 patients with a congruent neurological syndrome was analyzed. All these patients had a serious dyskinetic cerebral palsy-like syndrome with muscular dysto-nia and athetosis (MDA). They also had a hearing defect. Metabolic control was mainly good in both PD patient groups. Hospitalization time shortened clearly. The peritonitis rate diminished. Hypertension was a common problem. Left ventricular hypertrophy decreased during the prospective study period. None of the patients in either PD group had pulmonary edema or dialysis-related seizures. Growth was good and catch-up growth was documented in most patients in both patient groups during PD. Mortality was low (5% in prospective and 9% in retrospective PD patients). In the prospective PD patient group 11 patients (52%) had some risk factor for their neuro-development originating from the predialysis period. The neurological problems, detected be-fore PD, did not worsen during PD and none of the patients developed new neurological com-plications during PD. Brain infarcts were detected in four (19%) and other ischemic lesions in three patients (14%). At the end of this study, 29% of the prospectively followed patients had a major impairment of their neurodevelopment and 43% only minor impairment. In the NPHS1+MDA patients, no clear explanation for the neurological syndrome was found. The brain MRI showed increased signal intensity in the globus pallidus area. Kernic-terus was contemplated to be causative in the hypoproteinemic newborns but it could not be proven. Mortality was as high as 67%. Our results for young PD patients were promising. Metabolic control was acceptable and growth was good. However, the children were significantly smaller when compared to their midparental height. Although many patients were found to have neurological impairment at the end of our follow-up period, PD was a safe treatment whereby the neurodevelopment did not worsen during PD.

Criticality of the exponential rate of decay for the largest nearest-neighbor link in random geometric graphs

Let n points be placed independently in d-dimensional space according to the density f(x) = A(d)e(-lambda parallel to x parallel to alpha), lambda, alpha > 0, x is an element of R-d, d >= 2. Let d(n) be the longest edge length of the nearest-neighbor graph on these points. We show that (lambda(-1) log n)(1-1/alpha) d(n) - b(n) converges weakly to the Gumbel distribution, where b(n) similar to ((d - 1)/lambda alpha) log log n. We also prove the following strong law for the normalized nearest-neighbor distance (d) over tilde (n) = (lambda(-1) log n)(1-1/alpha) d(n)/log log n: (d - 1)/alpha lambda <= lim inf(n ->infinity) (d) over tilde (n) <= lim sup(n ->infinity) (d) over tilde (n) <= d/alpha lambda almost surely. Thus, the exponential rate of decay alpha = 1 is critical, in the sense that, for alpha > 1, d(n) -> 0, whereas, for alpha <= 1, d(n) -> infinity almost surely as n -> infinity.

Effect of Strain Rate on Evolution of the Deformation Microstructure and Texture in Polycrystalline Copper and Nickel

The evolution of crystallographic texture in polycrystalline copper and nickel has been studied. The deformation texture evolution in these two materials over seven orders of magnitude of strain rate from 3 x 10(-4) to similar to 2.0 x 10(+3) s(-1) show little dependence on the stacking fault energy (SFE) and the amount of deformation. Higher strain rate deformation in nickel leads to weakerh < 101 > texture because of extensive microband formation and grain fragmentation. This behavior, in turn, causes less plastic spin and hence retards texture evolution. Copper maintains the stable end < 101 > component over large strain rates (from 3 x 10(-4) to 10(+2) s(-1)) because of its higher strain-hardening rate that resists formation of deformation heterogeneities. At higher strain rates of the order of 2 x 10(+3) s(-1), the adiabatic temperature rise assists in continuous dynamic recrystallization that leads to an increase in the volume fraction of the < 101 > component. Thus, strain-hardening behavior plays a significant role in the texture evolution of face-centered cubic materials. In addition, factors governing the onset of restoration mechanisms like purity and melting point govern texture evolution at high strain rates. SFE may play a secondary role by governing the propensity of cross slip that in turn helps in the activation of restoration processes.

High-Temperature (1023 K to 1273 K 750 degrees C to 1000 degrees C]) Plastic Deformation Behavior of B-Modified Ti-6Al-4V Alloys: Temperature and Strain Rate Effects

A minor addition of B to the Ti-6Al-4V alloy, by similar to 0.1 wt pct, reduces its as-cast prior beta grain size by an order of magnitude, whereas higher B content leads to the presence of in situ formed TiB needles in significant amounts. An experimental investigation into the role played by these microstructural modifications on the high-temperature deformation behavior of Ti-6Al-4V-xB alloys, with x varying between 0 wt pct and 0.55 wt pct, was conducted. Uniaxial compression tests were performed in the temperature range of 1023 K to 1273 K (750 degrees C to 1000 degrees C) and in the strain rate range of 10(-3) to 10(+1) s(-1). True stress-true strain responses of all alloys exhibit flow softening at lower strain rates and oscillations at higher strain rates. The flow softening is aided by the occurrence of dynamic recrystallization through lath globularization in high temperature (1173 K to 1273 K 900 degrees C to 1000 degrees C]) and a lower strain rate (10(-2) to 10(-3) s(-1)) regime. The grain size refinement with the B addition to Ti64, despite being marked, had no significant effect on this. Oscillations in the flow curve at a higher strain rate (10(0) to 10(+1) s(-1)), however, are associated with microstructural instabilities such as bending of laths, breaking of lath boundaries, generation of cavities, and breakage of TiB needles. The presence of TiB needles affected the instability regime. Microstructural evidence suggests that the matrix cavitation is aided by the easy fracture of TiB needles.

Correlations between frequency of infra-red active vibrational modes and copper-oxygen distance in copper oxides. Application to superconductors

The infra-red spectra of a large number of ternary Cu(II) oxides with at least a quasi square-planar coordination of oxygen around the copper ions have been studied. The frequency of the bands with the highest frequency,v max, is found to correlate extremely well with the shortest Cu–O distance.v max increases at an impressive rate of sim20 cm–1 per 0.01 Å when the Cu–O distance becomes less than 1.97 Å, which is the Cu2+–O2– distance in square-planar CuO4 complexes as obtained from empirical ionic radii considerations. The marked sensitivity may be used as a ldquotitrationrdquo procedure not only to assign bands but also to obtain diagnostic information about local coordination in compounds derived, for example, from the YBa2Cu3O7–d structure such as LaCaBaCu3O7–d . The only example where this correlation fails is in the two-layer non-superconducting oxides derived from La2(Ca, Sr)Cu2O6. The significance of this result is discussed. The marked dependence of frequency on the bond-distance is qualitatively examined in terms of an increased electron-phonon coupling to account for the observed tendency of the superconducting transition temperature to go through a maximum as the average basal plane Cu–O distance is decreased.

Effect of favorable pressure gradient on transitional spot formation rate

The calculation of the transitional boundary layer requires estimates of the extent of the transition zone, which in turn depends on the rate at which turbulent spots are formed. This rate has been found to scale with local boundary layer thickness and viscosity, and the resulting nondimensional group (called crumble) is a function of the pressure gradient, among other parameters. Available experimental data are analyzed to show that the crumble increases slowly with increasing favorable pressure gradients, being about four times as large as in constant-pressure flow when the Thwaites pressure gradient parameter at the effective origin of the resulting turbulent boundary layer is 0.1 and when transition is driven by free-stream turbulence.

Measurement of the corrosion rate of aluminium in sodium hydroxide using holographic interferometry

The application of holographic interferometry to the measurement of the corrosion rate of aluminium in sodium hydroxide is investigated. Details of the fabrication of the corrosion cell and the experimental procedure are given. Thickness loss of aluminium was found for different dissolution times and compared with the conventional weight-loss method using a microbalance.

Production process of Scots pine.

The accompanying collective research report is the result of the research project in 1986­90 between The Finnish Academy and the former Soviet Academy of Sciences. The project was organized around common field work in Finland and in the former Soviet Union and theoretical analyses of tree growth determining processes. Based on theoretical analyses, dynamic stand growth models were made and their parameters were determined utilizing the field results. Annual cycle affects the tree growth. Our theoretical approach was based on adaptation to local climate conditions from Lapland to South Russia. The initiation of growth was described as a simple low and high temperature accumulation driven model. Linking the theoretical model with long term temperature data allowed us to analyze what type of temperature response produced favorable outcome in different climates. Initiation of growth consumes the carbohydrate reserves in plants. We measured the dynamics of insoluble and soluble sugars in the very northern and Karelian conditions. Clear cyclical pattern was observed but the differences between locations were surprisingly small. Analysis of field measurements of CO2 exchange showed that irradiance is the dominating factor causing variation in photosynthetic rate in natural conditions during summer. The effect of other factors is so small that they can be omitted without any considerable loss of accuracy. A special experiment carried out in Hyytiälä showed that the needle living space, defined as the ratio between the shoot cylindric volume and needle surface area, correlates with the shoot photosynthesis. The penetration of irradiance into Scots pine canopy is a complicated phenomenon because of the movement of the sun on the sky and the complicated structure of branches and needles. A moderately simple but balanced forest radiation regime submodel was constructed. It consists of the tree crown and forest structure, the gap probability calculation and the consideration of spatial and temporal variation of radiation inside the forest. The common field excursions in different geographical regions resulted in a lot of experimental data of regularities of woody structures. The water transport seems to be a good common factor to analyse these properties of tree structure. There are evident regressions between cross-sectional areas measured at different locations along the water pathway from fine roots to needles. The observed regressions have clear geographical trends. For example, the same cross-sectional area can support three times higher needle mass in South Russia than in Lapland. Geographical trends can also be seen in shoot and needle structure. Analysis of data published by several Russian authors show, that one ton of needles transpire 42 ton of water a year. This annual amount of transpiration seems to be independent of geographical location, year and site conditions. The produced theoretical and experimental material is utilised in the development of stand growth model that describes the growth and development of Scots pine stands in Finland and the former Soviet Union. The core of the model is carbon and nutrient balances. This means that carbon obtained in photosynthesis is consumed for growth and maintenance and nutrients are taken according to the metabolic needs. The annual photosynthetic production by trees in the stand is determined as a function of irradiance and shading during the active period. The utilisation of the annual photosynthetic production to the growth of different components of trees is based on structural regularities. Since the fundamental metabolic processes are the same in all locations the same growth model structure can be applied in the large range of Scots pine. The annual photosynthetic production and structural regularities determining the allocation of resources have geographical features. The common field measurements enable the application of the model to the analysis of growth and development of stands growing on the five locations of experiments. The model enables the analysis of geographical differences in the growth of Scots pine. For example, the annual photosynthetic production of a 100-year-old stand at Voronez is 3.5 times higher than in Lapland. The share consumed to needle growth (30 %) and to growth of branches (5 %) seems to be the same in all locations. In contrast, the share of fine roots is decreasing when moving from north to south. It is 20 % in Lapland, 15 % in Hyytiälä Central Finland and Kentjärvi Karelia and 15 % in Voronez South Russia. The stem masses (115­113 ton/ha) are rather similar in Hyytiälä, Kentjärvi and Voronez, but rather low (50 ton/ha) in Lapland. In Voronez the height of the trees reach 29 m being in Hyytiälä and Kentjärvi 22 m and in Lapland only 14 m. The present approach enables utilization of structural and functional knowledge, gained in places of intensive research, in the analysis of growth and development of any stand. This opens new possibilities for growth research and also for applications in forestry practice.

Position and Feed-Rate Control for Contouring Numerical-Control Systems

Numerical control (NC) for contouring operations requires precise control of position and feed rate for approximating the contour by linear moves of the cutter. A control scheme, for generating linear moves with desired slopes for the cutter, is described. This scheme provides for nine successive linear moves, and may be either expanded or implemented in succession, for approximating a contour.

HDL subspecies : association with low HDL-C, obesity, and metabolic syndrome

AIMS An independent, powerful coronary heart disease (CHD) predictor is a low level of high-density lipoprotein cholesterol (HDL-C). Discoidal preβ-HDL particles and large HDL2 particles are the primary cholesterol acceptors in reverse cholesterol transport, a key anti-atherogenic HDL mechanism. The quality of HDL subspecies may provide better markers of HDL functionality than does HDL-C alone. We aimed I) to study whether alterations in the HDL subspecies profile exist in low-HDL-C subjects II) to explore the relationship of any changes in HDL subspecies profile in relation to atherosclerosis and metabolic syndrome; III) to elucidate the impact of genetics and acquired obesity on HDL subspecies distribution. SUBJECTS The study consisted of 3 cohorts: A) Finnish families with low HDL-C and premature CHD (Study I: 67 subjects with familial low HDL-C and 64 controls; Study II: 83 subjects with familial low HDL-C, 65 family members with normal HDL-C, and 133 controls); B) a cohort of 113 low- and 133 high-HDL-C subjects from the Health 2000 Health Examination Survey carried out in Finland (Study III); and C) a Finnish cohort of healthy young adult twins (52 monozygotic and 89 dizygotic pairs) (Study IV). RESULTS AND CONCLUSIONS The subjects with familial low HDL-C had a lower preβ-HDL concentration than did controls, and the low-HDL-C subjects displayed a dramatic reduction (50-70%) in the proportion of large HDL2b particles. The subjects with familial low HDL-C had increased carotid atherosclerosis measured as intima-media-thickness (IMT), and HDL2b particles correlated negatively with IMT. The reduction in both key cholesterol acceptors, preβ-HDL and HDL2 particles, supports the concept of impaired reverse cholesterol transport contributing to the higher CHD risk in low-HDL-C subjects. The family members with normal HDL-C and the young adult twins with acquired obesity showed a reduction in large HDL2 particles and an increase in small HDL3 particles, which may be the first changes leading to the lowering of HDL-C. The low-HDL-C subjects had a higher serum apolipoprotein E (apoE) concentration, which correlated positively with the metabolic syndrome components (waist circumference, TG, and glucose), highlighting the need for a better understanding of apoE metabolism in human atherosclerosis. In the twin study, the increase in small HDL3b particles was associated with obesity independent of genetic effects. The heritability estimate, of 73% for HDL-C and 46 to 63% for HDL subspecies, however, demonstrated a strong genetic influence. These results suggest that the relationship between obesity and lipoproteins depends on different elements in each subject. Finally, instead of merely elevating HDL-C, large HDL2 particles and discoidal preβ-HDL particles may provide beneficial targets for HDL-targeted therapy.