Showing papers by "Tallinn University of Technology published in 2007"

Mouse and rat BDNF gene structure and expression revisited

Abstract: Brain-derived neurotrophic factor (BDNF) has important functions in the development of the nervous system and in brain plasticity-related processes such as memory, learning, and drug addiction. Despite the fact that the function and regulation of rodent BDNF gene expression have received close attention during the last decade, knowledge of the structural organization of mouse and rat BDNF gene has remained incomplete. We have identified and characterized several mouse and rat BDNF transcripts containing novel 5′ untranslated exons and introduced a new numbering system for mouse and rat BDNF exons. According to our results both mouse and rat BDNF gene consist of eight 5′ untranslated exons and one protein coding 3′ exon. Transcription of the gene results in BDNF transcripts containing one of the eight 5′ exons spliced to the protein coding exon and in a transcript containing only 5′ extended protein coding exon. We also report the distinct tissue-specific expression profiles of each of the mouse and rat 5′ exon-specific transcripts in different brain regions and nonneural tissues. In addition, we show that kainic acid-induced seizures that lead to changes in cellular Ca2+ levels as well as inhibition of DNA methylation and histone deacetylation contribute to the differential regulation of the expression of BDNF transcripts. Finally, we confirm that mouse and rat BDNF gene loci do not encode antisense mRNA transcripts, suggesting that mechanisms of regulation for rodent and human BDNF genes differ substantially. © 2006 Wiley-Liss, Inc.

Novel neurotrophic factor CDNF protects and rescues midbrain dopamine neurons in vivo

Abstract: In Parkinson's disease, brain dopamine neurons degenerate most prominently in the substantia nigra. Neurotrophic factors promote survival, differentiation and maintenance of neurons in developing and adult vertebrate nervous system. The most potent neurotrophic factor for dopamine neurons described so far is the glial-cell-line-derived neurotrophic factor (GDNF). Here we have identified a conserved dopamine neurotrophic factor (CDNF) as a trophic factor for dopamine neurons. CDNF, together with its previously described vertebrate and invertebrate homologue the mesencephalic-astrocyte-derived neurotrophic factor, is a secreted protein with eight conserved cysteine residues, predicting a unique protein fold and defining a new, evolutionarily conserved protein family. CDNF (Armetl1) is expressed in several tissues of mouse and human, including the mouse embryonic and postnatal brain. In vivo, CDNF prevented the 6-hydroxydopamine (6-OHDA)-induced degeneration of dopaminergic neurons in a rat experimental model of Parkinson's disease. A single injection of CDNF before 6-OHDA delivery into the striatum significantly reduced amphetamine-induced ipsilateral turning behaviour and almost completely rescued dopaminergic tyrosine-hydroxylase-positive cells in the substantia nigra. When administered four weeks after 6-OHDA, intrastriatal injection of CDNF was able to restore the dopaminergic function and prevent the degeneration of dopaminergic neurons in substantia nigra. Thus, CDNF was at least as efficient as GDNF in both experimental settings. Our results suggest that CDNF might be beneficial for the treatment of Parkinson's disease.

LRRTM1 on chromosome 2p12 is a maternally suppressed gene that is associated paternally with handedness and schizophrenia

Abstract: Left–right asymmetrical brain function underlies much of human cognition, behavior and emotion. Abnormalities of cerebral asymmetry are associated with schizophrenia and other neuropsychiatric disorders. The molecular, developmental and evolutionary origins of human brain asymmetry are unknown. We found significant association of a haplotype upstream of the gene LRRTM1 (Leucine-rich repeat transmembrane neuronal 1) with a quantitative measure of human handedness in a set of dyslexic siblings, when the haplotype was inherited paternally (P = 0.00002). While we were unable to find this effect in an epidemiological set of twin-based sibships, we did find that the same haplotype is overtransmitted paternally to individuals with schizophrenia/schizoaffective disorder in a study of 1002 affected families (P = 0.0014). We then found direct confirmatory evidence that LRRTM1 is an imprinted gene in humans that shows a variable pattern of maternal downregulation. We also showed that LRRTM1 is expressed during the development of specific forebrain structures, and thus could influence neuronal differentiation and connectivity. This is the first potential genetic influence on human handedness to be identified, and the first putative genetic effect on variability in human brain asymmetry. LRRTM1 is a candidate gene for involvement in several common neurodevelopmental disorders, and may have played a role in human cognitive and behavioral evolution. Molecular Psychiatry (2007) 12, 1129–1139; doi:10.1038/sj.mp.4002053; published online 31 July 2007

Saami reindeer pastoralism under climate change: Applying a generalized framework for vulnerability studies to a sub-arctic social–ecological system

Abstract: A generalized vulnerability framework was used to structure an interdisciplinary and intercultural examination of factors that influence the ways in which reindeer pastoralism in Finnmark (northern Norway) may be affected by climate change. Regional and local (downscaled) climate projections included scenarios that can potentially influence foraging conditions for reindeer. None of the projections were without precedent; several climate change events in Finnmark during the last 100 years were at least as great as those projected in the next 20–30 years. Herders’ traditional responses to changes in both the natural and the socio-economic environments have depended on a flexibility in herding practice that is currently being eroded by several non-climate factors. The reduced of freedom of action resulting from loss of habitat, predation and aspects of governance (especially economic and legal constraints) potentially dwarves the putative effects of projected climate change on reindeer pastoralism. It may, however, also lead to situations in which new climatic conditions threaten the system in unprecedented ways. Developing appropriate methodologies for assessing the adaptive capacity, the vulnerability and the resilience of social–ecological systems to global changes remains a challenge. Recognition of the knowledge systems of Arctic cultures and the full engagement of local people throughout the process are key elements of the solution.

Arabidopsis thaliana myosin XIK is involved in root hair as well as trichome morphogenesis on stems and leaves

Abstract: Myosins form a large superfamily of molecular motors that move along actin filaments. The functions of myosins in plant cells are thought to be related to various processes: cell division, movement of mitochondria and chloroplasts, cytoplasmic streaming, rearrangement of transvacuolar strands, and statolith positioning. Class VIII and XI myosins are represented in the Arabidopsis thaliana genome by 4 and 13 potential genes, respectively. The roles of individual class XI myosins and their cellular targets in A. thaliana are still unclear. In this work we implemented a reverse genetic approach to analyse the loss-of-function mutants of XIK, a representative of class XI myosins in A. thaliana. Three different T-DNA insertion mutants in the myosin XIK gene showed similar phenotypes: impaired growth of root hair cells, twisted shape of stem trichomes, and irregular size, branch positioning, and branch expansion of leaf trichomes. Morphometric analysis of mutant seedlings showed that the average length of root hairs was reduced up to 50% in comparison with wild-type root hairs, suggesting an involvement of the class XI myosin XIK in tip growth. On leaves, the proportion of trichomes with short branches was doubleed in mutant plants, and the mutant trichomes possessed a mildly twisted shape. Therefore, we concluded that myosin XIK is involved also in the elongation of stalks and branches of trichomes.

Fiscal Policies and Business Cycles in an Enlarged Euro Area

Abstract: This paper compares the cyclical properties of fiscal policies across the 12 original eurozone countries and the future members from Central and Eastern Europe. For the sample period 1995-2005, the fiscal balance exhibits less inertia and is more counter-cyclical in Central and Eastern European countries than in members of the eurozone. The main differences arise from the revenue side. Differences in the formation of fiscal policy between current and future eurozone countries decrease over time. Autonomous fiscal policy has little or no effect on cyclical variability in either of the two groups of countries. Counter-cyclical fiscal policy appears to be effective in Central and Eastern European countries, but largely ineffective in eurozone countries.

Spatial structure of the 8200 cal yr BP event in northern Europe

Abstract: . A synthesis of well-dated high-resolution pollen records suggests a spatial structure in the 8200 cal yr BP event in northern Europe. The temperate, thermophilous tree taxa, especially Corylus, Ulmus, and Alnus, decline abruptly between 8300 and 8000 cal yr BP at most sites located south of 61° N, whereas there is no clear change in pollen values at the sites located in the North-European tree-line region. Pollen-based quantitative temperature reconstructions and several other, independent palaeoclimate proxies, such as lacustrine oxygen-isotope records, reflect the same pattern, with no detectable cooling in the sub-arctic region. The observed patterns challenges the general view of the wide-spread occurrence of the 8200 cal yr BP event in the North Atlantic region. An alternative explanation is that the cooling during the 8200 cal yr BP event took place mostly during the winter and spring, and the ecosystems in the south responded sensitively to the cooling during the onset of the growing season. In contrast, in the sub-arctic area, where the vegetation was still dormant and lakes ice-covered, the cold event is not reflected in pollen-based or lake-sediment-based records.

QSPR modeling of flash points: An update

Abstract: Quantitative structure–property relationship (QSPR) models for the flash points of 758 organic compounds are developed using geometrical, topological, quantum mechanical and electronic descriptors calculated by CODESSA PRO software. Multilinear regression models link the structures to their reported flash point values. We also report a nonlinear model based on an artificial neural network. The results are discussed in the light of the main factors that influence the property under investigation and its modeling.

Nonlinear Components of Ship Wake Waves

Abstract: Nonlinear components of wakes from large high-speed ships at times carry a substantial part of the wake energy and behave completely differently compared to the classical Kelvin wave system. This overview makes an attempt to summarize the descriptions of nonlinear parts of a ship’s wake. For completeness, also the basic properties of the Kelvin wake are sketched. The central topic is the generation of solitons by ship motion both in channels and in unbounded sea areas. The discussion is mostly limited to disturbances on the surface of nonstratified water. The optional nonlinear components of the ship wake such as the very narrow V-like wake components, packets of monochromatic waves, ship-generated depression areas, and supercritical bores are also discussed. Specific features of solitonic ship waves and their interactions have numerous applications in naval and coastal engineering, and in adjacent areas of applied mechanics. An overview of the practical use of certain properties of phase shifts, and particularly high wave humps occurring during Mach reflection and nonlinear interaction of solitons in decreasing the wave resistance at supercritical speeds and in the freak wave theory, is also presented. The final part of the paper describes the results of studies of far-field properties of nonlinear wakes and possible consequences of the increase of local hydrodynamic activity. There are 263 references cited in this review article.

Improvement of Lock-in Electrical Bio-Impedance Analyzer for Implantable Medical Devices

Abstract: A novel solution for improving lock-in electrical bio-impedance (EBI) analyzers by suppressing errors caused by higher odd harmonics of rectangular wave pulses is proposed. The solution is based on a newly developed method of shortening the rectangular full duty cycle pulses, which are commonly used in correlation-type lock-in EBI measurements. Comparison of the proposed method to a common method of regular rectangular waveforms is given. The results show that the measurement errors of the three-element EBI equivalent become several tens of times smaller when shortening the excitation and reference signals separately by different values, for example, by 30 deg and 18deg. Shortening of only a single signal (either excitation or reference) can also give significant progress. Improved accuracy of the EBI phasor measurement makes the proposed method reliable for most clinical applications. Due to its simplicity, the method is appropriate for on-chip realization in implantable devices

Random Forest for Gene Expression Based Cancer Classification: Overlooked Issues

Abstract: Random forest is a collection (ensemble) of decision trees. It is a popular ensemble technique in pattern recognition. In this article, we apply random forest for cancer classification based on gene expression and address two issues that have been so far overlooked in other works. First, we demonstrate on two different real-world datasets that the performance of random forest is strongly influenced by dataset complexity. When estimated before running random forest, this complexity can serve as a useful performance indicator and it can explain a difference in performance on different datasets. Second, we show that one should rely with caution on feature importance used to rank genes: two forests, generated with the different number of features per node split, may have very similar classification errors on the same dataset, but the respective lists of genes ranked according to feature importance can be weakly correlated.

Practical security analysis of e-voting systems

Abstract: We adapt game theoretic methods for studying the security of two evoting systems: the Estonian E-Voting System (EstEVS) and Secure Electronic Registration and Voting Experiment (SERVE) performed in the United States of America. While these two systems are quite similar from technical side, security experts have made totally different decisions about their security--EstEVS was indeed used in practical elections while SERVE was decided to be insecure. The aim of this work is to clarify if the minor technical differences between these two systems were indeed a sufficient reason to distinguish between their security. Our analysis is oriented to practical security against large-scale attacks. We define a model for the real-life environment in which voting takes place and analyze the behavior of adversaries. We show that in our model EstEVS is secure and SERVE is not. The reliability of the results is still questionable because of our limited knowledge about many of the parameters. It turns out though that our main results are quite robust with respect to the choice of parameters.

Synchronous Sampling and Demodulation in an Instrument for Multifrequency Bioimpedance Measurement

Abstract: Direct sampling of known carriers is the preferred digital method for measuring biomodulation of tissue impedance. Due to limited resolution and conversion rate of analog-to-digital converters and limited processing power of available digital processors and/or lack of energy resources, conventional discrete-Fourier-transform-based algorithms are not efficient in small medical devices. Knowing exactly the frequencies of carriers (and excitations), an energy-saving fast signal processing method can be developed and implemented. When sampling synchronously with a carrier, it is possible to minimize the complexity of calculations and to introduce a digital-to-analog feedback for enhancement of resolution by digitizing only the small variations between adjacent samples. The proposed system is qualified on proprietary hardware.

Encapsulation of β-carotene from sea buckthorn (Hippophaë rhamnoides L.) juice in furcellaran beads

Abstract: The objective of this study was to prepare and evaluate furcellaran beads as an encapsulation material for β-carotene from sea buckthorn ( Hippophae rhamnoides L.) juice. Beads were prepared by ionotropic gelation. The influence of bead formulation factors on the particle size and firmness was investigated and the encapsulation efficiency of β-carotene in beads was studied. The nature of the cation, the polymer and cation concentration, and the proportion of volumes of the outer to the inner phase influenced the size and firmness of furcellaran beads. With increasing proportion of sea buckthorn juice in the formulae, firmness of furcellaran beads decreased. The encapsulation efficiency of β-carotene from sea buckthorn juice in furcellaran capsules was 97%. It suggested that furcellaran beads may be applied for β-carotene encapsulation. Industrial relevance Encapsulation is a rapidly emerging area with multitude of applications in biotechnology, one of them being the controlled release of active biomolecules. The sensitivity to the environmental factors makes furcellaran a promising material for the controlled release of pharmaceuticals, (pro)biotica, and bioactive materials. Entrapment of these materials into the furcellaran beads by protecting them against degradation processes could solve the problem to incorporate health promoting ingredients into food without reducing their bioavailability or functionality. The change of pH in the digestive system could cause degradation of the beads followed by release of bioactive materials in the organism. It does create a basis for new product development in food industry. However, more work regarding to the improvements of bead stability and the release of entrapped materials are required.

Myosin inhibitors block accumulation movement of chloroplasts in Arabidopsis thaliana leaf cells

Abstract: Chloroplasts alter their distribution within plant cells depending on the external light conditions. Myosin inhibitors 2,3-butanedione monoxime (BDM), N-ethylmaleimide (NEM), and 1-(5-iodonaphthalene-1-sulfonyl)-1H-hexahydro-1,4-diazepine hydrochloride (ML-7) were used to study the possible role of myosins in chloroplast photorelocation in Arabidopsis thaliana mesophyll cells. None of these agents had an effect on the chloroplast high-fluence-rate avoidance movement but all of the three myosin inhibitors blocked the accumulation movement of chloroplasts after a high-fluence-rate irradiation of the leaves. The results suggest that myosins have a role in A. thaliana chloroplast photorelocation.