Fluorescence properties of Baltic Sea phytoplankton

To obtain data on phytoplankton dynamics with improved spatial and temporal resolution, and at reduced cost, traditional phytoplankton monitoring methods have been supplemented with optical approaches. In this thesis, I have explored various fluorescence-based techniques for detection of phytoplankton abundance, taxonomy and physiology in the Baltic Sea. In algal cultures used in this thesis, the availability of nitrogen and light conditions caused changes in pigmentation, and consequently in light absorption and fluorescence properties of cells. In the Baltic Sea, physical environmental factors (e.g. mixing depth, irradiance and temperature) and related seasonal succession in the phytoplankton community explained a large part of the seasonal variability in the magnitude and shape of Chlorophyll a (Chla)-specific absorption. The variability in Chla-specific fluorescence was related to the abundance of cyanobacteria, the size structure of the phytoplankton community, and absorption characteristics of phytoplankton. Cyanobacteria show very low Chla-specific fluorescence. In the presence of eukaryotic species, Chla fluorescence describes poorly cyanobacteria. During cyanobacterial bloom in the Baltic Sea, phycocyanin fluorescence explained large part of the variability in Chla concentrations. Thus, both Chla and phycocyanin fluorescence were required to predict Chla concentration. Phycobilins are major light harvesting pigments for cyanobacteria. In the open Baltic Sea, small picoplanktonic cyanobacteria were the main source of phycoerythrin fluorescence and absorption signal. Large filamentous cyanobacteria, forming harmful blooms, were the main source of the phycocyanin fluorescence signal and typically their biomass and phycocyanin fluorescence were linearly related. Using phycocyanin fluorescence, dynamics of cyanobacterial blooms can be detected at high spatial and seasonal resolution not possible with other methods. Various taxonomic phytoplankton pigment groups can be separated by spectral fluorescence. I compared multivariate calibration methods for the retrieval of phytoplankton biomass in different taxonomic groups. Partial least squares regression method gave the closest predictions for all taxonomic groups, and the accuracy was adequate for phytoplankton bloom detection. Variable fluorescence has been proposed as a tool to study the physiological state of phytoplankton. My results from the Baltic Sea emphasize that variable fluorescence alone cannot be used to detect nutrient limitation of phytoplankton. However, when combined with experiments with active nutrient manipulation, and other nutrient limitation indices, variable fluorescence provided valuable information on the physiological responses of the phytoplankton community. This thesis found a severe limitation of a commercial fast repetition rate fluorometer, which couldn t detect the variable fluorescence of phycoerythrin-lacking cyanobacteria. For these species, the Photosystem II absorption of blue light is very low, and fluorometer excitation light did not saturate Photosystem II during a measurement. This thesis encourages the use of various in vivo fluorescence methods for the detection of bulk phytoplankton biomass, biomass of cyanobacteria, chemotaxonomy of phytoplankton community, and phytoplankton physiology. Fluorescence methods can support traditional phytoplankton monitoring by providing continuous measurements of phytoplankton, and thereby strengthen the understanding of the links between biological, chemical and physical processes in aquatic ecosystems.

Co-Signaling by Neurotrophic Factors and the Extracellular Matrix for Axonal Growth and Neuronal Survival

Neurotrophic factors (NTFs) and the extracellular matrix (ECM) are important regulators of axonal growth and neuronal survival in mammalian nervous system. Understanding of the mechanisms of this regulation is crucial for the development of posttraumatic therapies and drug intervention in the injured nervous system. NTFs act as soluble, target-derived extracellular regulatory molecules for a wide range of physiological functions including axonal guidance and the regulation of programmed cell death in the nervous system. The ECM determines cell adhesion and regulates multiple physiological functions via short range cell-matrix interactions. The present work focuses on the mechanisms of the action of NTFs and the ECM on axonal growth and survival of cultured sensory neurons from dorsal root ganglia (DRG). We first examined signaling mechanisms of the action of the glial cell line-derived neurotrophic factor (GDNF) family ligands (GFLs) on axonal growth. GDNF, neurturin (NRTN) and artemin (ART) but not persephin (PSPN) promoted axonal initiation in cultured DRG neurons from young adult mice. This effect required Src family kinase (SFK) activity. In neurons from GFRalpha2-deficient mice, NRTN did not significantly promote axonal initiation. GDNF and NRTN induced extensive lamellipodia formation on neuronal somata and growth cones. This study suggested that GDNF, NRTN and ARTN may serve as stimulators of nerve regeneration under posttraumatic conditions. Consequently we studied the convergence of signaling pathways induced by NTFs and the ECM molecule laminin in the intracellular signaling network that regulates axonal growth. We demonstrated that co-stimulation of DRG neurons with NTFs (GDNF, NRTN or nerve growth factor (NGF)) and laminin leads to axonal growth that requires activation of SFKs. A different, SFK-independent signaling pathway evoked axonal growth on laminin in the absence of the NTFs. In contrast, axonal branching was regulated by SFKs both in the presence and in the absence of NGF. We proposed and experimentally verified a Boolean model of the signaling network triggered by NTFs and laminin. Our results put forward an approach for predictable, Boolean logics-driven pharmacological manipulation of a complex signaling network. Finally we found that N-syndecan, the receptor for the ECM component HB-GAM was required for the survival of neonatal sensory neurons in vitro. We demonstrated massive cell death of cultured DRG neurons from mice deficient in the N-syndecan gene as compared to wild type controls. Importantly, this cell death could not be prevented by NGF the neurotrophin which activates multiple anti-apoptotic cascades in DRG neurons. The survival deficit was observed during first postnatal week. By contrast, DRG neurons from young adult N-syndecan knock-out mice exhibited normal survival. This study identifies a completely new syndecan-dependent type of signaling that regulates cell death in neurons.

Direct somatic embroygenesis from immature embryos of rosewood (Dalbergia latifolia Roxb.)

Direct regeneration of somatic embryos was obtained from immature zygotic embryos of Dalbergia latifolia. Immature embryos dissected from green pods 90 d after flowering gave the highest frequency of somatic embryo formation. Preculture on high 2,4-D medium for 4 weeks induced direct somatic embryogenesis, which was expressed during the second culture phase in the presence of low 2,4-D along with a high sucrose concentration. Embryos were separated and transferred to the maturation medium containing MS + 0.5-1.0 mg/L BAP, where embryos developed into plantlets. Somatic embryos failed to convert into complete plants without BAP treatment. This method of direct regeneration of somatic embryos without a callus phase has direct application for genetic manipulation studies.

High vacuum tribology of polycrystalline diamond coatings

Polycrystalline diamond coatings have been grown on unpolished side of Si(100) wafers by hot filament chemical vapour deposition process. The morphology of the grown coatings has been varied from cauliflower morphology to faceted morphology by manipulation of the growth temperature from 700 degrees C to 900 degrees C and methane gas concentration from 3% to 1.5%. It is found that the coefficient of friction of the coatings under high vacuum of 133.32 x 10(-7) Pa (10(-7) torr) with nanocrystalline grains can be manipulated to 0.35 to enhance tribological behaviour of bare Si substrates.

Inside out: Why do so many great buildings have drab interiors?

An extravaganza of shapes now forms our city skylines. CAD and BIM with their inbuilt links to manufacturing and construction processes has made possible this kind of effusive architectural expression, at least externally. Building developers clearly understand the enormous marketing potential for impact expression. The skilled manipulation of 3D CAD software enables architects to achieve usable gross floor space within an enticingly sinuous, but build-able, envelope. This critical factor is resulting in a fundamental change to the appearance of our cities. It has become plausible, at least, to design and build complex and non-repetitive buildings without incurring prohibitive additional labor costs.However The ground level lobby spaces often do manage to retain some of the external. However, the interior working spaces, particularly in commercial office buildings tend to loose this grand gesture. However - the internal activity - the very reason for the existence of the building – often takes place in monotonous spaces that seem driven predominately by the need to accommodate workstation furniture and functions in dire need of reconsideration.

Novel fluorescence detection technique for non-contact temperature sensing in microchip PCR

DNA amplification using Polymerase Chain Reaction (PCR) in a small volume is used in Lab-on-a-chip systems involving DNA manipulation. For few microliters of volume of liquid, it becomes difficult to measure and monitor the thermal profile accurately and reproducibly, which is an essential requirement for successful amplification. Conventional temperature sensors are either not biocompatible or too large and hence positioned away from the liquid leading to calibration errors. In this work we present a fluorescence based detection technique that is completely biocompatible and measures directly the liquid temperature. PCR is demonstrated in a 3 ILL silicon-glass microfabricated device using non-contact induction heating whose temperature is controlled using fluorescence feedback from SYBR green I dye molecules intercalated within sensor DNA. The performance is compared with temperature feedback using a thermocouple sensor. Melting curve followed by gel electrophoresis is used to confirm product specificity after the PCR cycles. (c) 2007 Elsevier B.V. All rights reserved.

X-ray and neutron scattering studies on some nanoscale structures in molecular biology

Scattering of X-rays and neutrons has been applied to the study of nanostructures with interesting biological functions. The systems studied were the protein calmodulin and its complexes, bacterial virus bacteriophage phi6, and the photosynthetic antenna complex from green sulfur bacteria, chlorosome. Information gathered using various structure determination methods has been combined to the low resolution information obtained from solution scattering. Conformational changes in calmodulin-ligand complex were studied by combining the directional information obtained from residual dipole couplings in nuclear magnetic resonance to the size information obtained from small-angle X-ray scattering from solution. The locations of non-structural protein components in a model of bacteriophage phi6, based mainly on electron microscopy, were determined by neutron scattering, deuterium labeling and contrast variation. New data are presented on the structure of the photosynthetic antenna complex of green sulfur bacteria and filamentous anoxygenic phototrophs, also known as the chlorosome. The X-ray scattering and electron cryomicroscopy results from this system are interpreted in the context of a new structural model detailed in the third paper of this dissertation. The model is found to be consistent with the results obtained from various chlorosome containing bacteria. The effect of carotenoid synthesis on the chlorosome structure and self-assembly are studied by carotenoid extraction, biosynthesis inhibition and genetic manipulation of the enzymes involved in carotenoid biosynthesis. Carotenoid composition and content are found to have a marked effect on the structural parameters and morphology of chlorosomes.

Information Technology in Construction – Domain Definition and Research Issues

This article discusses the scope of research on the application of information technology in construction (ITC). A model of the information and material activities which together constitute the construction process is presented, using the IDEF0 activity modelling methodology. Information technology is defined to include all kinds of technology used for the storage, transfer and manipulation of information, thus also including devices such as copying machines, faxes and mobile phones. Using the model the domain of ITC research is defined as the use of information technology to facilitate and re-engineer the information process component of construction. Developments during the last decades in IT use in construction is discussed against a background of a simplified model of generic information processing tasks. The scope of ITC is compared with the scopes of research in related areas such as design methodology, construction management and facilities management. Health care is proposed as an interesting alternative (to the often used car manufacturing industry), as an IT application domain to compare with. Some of the key areas of ITC research in recent years; expert systems, company IT strategies, and product modelling are shortly discussed. The article finishes with a short discussion of the problems of applying standard scientific methodology in ITC research, in particular in product model research.

Detecting Earnings Management Using Neural Networks

Detecting Earnings Management Using Neural Networks. Trying to balance between relevant and reliable accounting data, generally accepted accounting principles (GAAP) allow, to some extent, the company management to use their judgment and to make subjective assessments when preparing financial statements. The opportunistic use of the discretion in financial reporting is called earnings management. There have been a considerable number of suggestions of methods for detecting accrual based earnings management. A majority of these methods are based on linear regression. The problem with using linear regression is that a linear relationship between the dependent variable and the independent variables must be assumed. However, previous research has shown that the relationship between accruals and some of the explanatory variables, such as company performance, is non-linear. An alternative to linear regression, which can handle non-linear relationships, is neural networks. The type of neural network used in this study is the feed-forward back-propagation neural network. Three neural network-based models are compared with four commonly used linear regression-based earnings management detection models. All seven models are based on the earnings management detection model presented by Jones (1991). The performance of the models is assessed in three steps. First, a random data set of companies is used. Second, the discretionary accruals from the random data set are ranked according to six different variables. The discretionary accruals in the highest and lowest quartiles for these six variables are then compared. Third, a data set containing simulated earnings management is used. Both expense and revenue manipulation ranging between -5% and 5% of lagged total assets is simulated. Furthermore, two neural network-based models and two linear regression-based models are used with a data set containing financial statement data from 110 failed companies. Overall, the results show that the linear regression-based models, except for the model using a piecewise linear approach, produce biased estimates of discretionary accruals. The neural network-based model with the original Jones model variables and the neural network-based model augmented with ROA as an independent variable, however, perform well in all three steps. Especially in the second step, where the highest and lowest quartiles of ranked discretionary accruals are examined, the neural network-based model augmented with ROA as an independent variable outperforms the other models.

The expiration day effect of indexoptions and index futures on the underlying shares

This paper studies the effect of the expiration day of index options and futures on the trading volume, variance and price of the underlying shares. The data consists of all trades for the underlying shares in the FOX-index for expiration days during the period October 1995 to the mid of yer 1999. The main results seem to support the findings of Kan 2001, i.e. no manipulation on a larger scale. However, some indication of manipulation could be found if certain characteristics are favorable. These characteristics include: a) a large quantity of outstanding futures or at/in the money options contracts, b) there exists shares with high index weight but fairly low trading volume. Lastly, there is some indication that manipulation might be more popular towards the end of the examined time period.

Time Scale Separated Nonlinear Partial Integrated Guidance and Control of Interceptors in the Terminal Phase

The paper proposes a time scale separated partial integrated guidance and control of an interceptor for engaging high speed targets in the terminal phase. In this two loop design, the outer loop is an optimal control formulation based on nonlinear model predictive spread control philosophies. It gives the commanded pitch and yaw rates whereas necessary roll-rate command is generated from a roll-stabilization loop. The inner loop tracks the outer loop commands using the dynamicinversion philosophy. However, unlike conventional designs, in both the loops the Six degree of freedom (Six-DOF) interceptor model is used directly. This intelligent manipulation preserves the inherent time scale separation property between the translational and rotational dynamics, and hence overcomes the deficiency of current IGC designs, while preserving its benefits. Six-DOF simulation studies have been carried out accounting for three dimensional engagement geometry. Different comparison studies were also conducted to measure the performance of the algorithm.

Environmental and climatic dependences of stable isotope ratios in tree rings on different temporal scales

This work examines stable isotope ratios of carbon, oxygen and hydrogen in annual growth rings of trees. Isotopic composition in wood cellulose is used as a tool to study past climate. The method benefits from the accurate and precise dating provided by dendrochronology. In this study the origin, nature and the strength of climatic correlations are studied on different temporal scales and at different sites in Finland. The origin of carbon isotopic signal is in photosynthetic fractionation. The basic physical and chemical fractionations involved are reasonably well understood. This was confirmed by measuring instantaneous photosynthetic discrimination on Scots pine (Pinus sylvestris L.). The internal conductance of CO2 was recognized to have a significant impact on the observed fractionation, and further investigations are suggested to quantify its role in controlling the isotopic signal of photosynthates. Isotopic composition of the produced biomass can potentially be affected by variety of external factors that induce physiological changes in trees. Response of carbon isotopic signal in tree ring cellulose to changes in resource availability was assessed in a manipulation experiment. It showed that the signal was relatively stable despite of changes in water and nitrogen availability to the tree. Palaeoclimatic reconstructions are typically based on functions describing empirical relationship between isotopic and climatic parameters. These empirical relationships may change depending on the site conditions, species and timeframe studied. Annual variation in Scots pine tree ring carbon and oxygen isotopic composition was studied in northern and in central eastern Finland and annual variation in tree ring latewood carbon, oxygen and hydrogen isotopic ratio in Oak (Quercus robur L.) was studied in southern Finland. In all of the studied sites at least one of the studied isotope ratios was shown to record climate strongly enough to be used in climatic reconstructions. Using the observed relationships, four-century-long climate reconstructions from living Scots pine were created for northern and central eastern Finland. Also temporal stability of the relationships between three proxy indicators, tree ring growth and carbon and oxygen isotopic composition was studied during the four-hundred-year period. Isotope ratios measured from tree rings in Finland were shown to be sensitive indicators of climate. Increasing understanding of environmental controls and physiological mechanisms affecting tree ring isotopic composition will make possible more accurate interpretation of isotope data. This study also demonstrated that by measuring multiple isotopes and physical proxies from the same tree rings, additional information on tree physiology can be obtained. Thus isotopic ratios measured from tree ring cellulose provide means to improve the reliability of climate reconstructions.

A denotational semantics for the generalized ER model and a simple ER algebra

The recent spurt of research activities in Entity-Relationship Approach to databases calls for a close scrutiny of the semantics of the underlying Entity-Relationship models, data manipulation languages, data definition languages, etc. For reasons well known, it is very desirable and sometimes imperative to give formal description of the semantics. In this paper, we consider a specific ER model, the generalized Entity-Relationship model (without attributes on relationships) and give denotational semantics for the model as well as a simple ER algebra based on the model. Our formalism is based on the Vienna Development Method—the meta language (VDM). We also discuss the salient features of the given semantics in detail and suggest directions for further work.

Optical trapping and transportation of carbon nanotubes made easy by decorating with palladium

Individual carbon nanotubes being substantially smaller than the wavelength of light, are not much responsive to optical manipulation. Here we demonstrate how decorating single-walled carbon nanotubes with palladium particles makes optical trapping and manipulation easier. Palladium decorated nanotubes (Pd/SWNTs) have higher effective dielectric constant and are trapped at much lower laser power level with greater ease. In addition, we report the transportation of Pd/SWNTs using an asymmetric line trap. Using this method carbon nanotubes can be transported in any desired direction with high transportation speed. (c) 2006 Optical Society of America.

Irradiation effects in graphene and related materials

Nanomaterials with a hexagonally ordered atomic structure, e.g., graphene, carbon and boron nitride nanotubes, and white graphene (a monolayer of hexagonal boron nitride) possess many impressive properties. For example, the mechanical stiffness and strength of these materials are unprecedented. Also, the extraordinary electronic properties of graphene and carbon nanotubes suggest that these materials may serve as building blocks of next generation electronics. However, the properties of pristine materials are not always what is needed in applications, but careful manipulation of their atomic structure, e.g., via particle irradiation can be used to tailor the properties. On the other hand, inadvertently introduced defects can deteriorate the useful properties of these materials in radiation hostile environments, such as outer space. In this thesis, defect production via energetic particle bombardment in the aforementioned materials is investigated. The effects of ion irradiation on multi-walled carbon and boron nitride nanotubes are studied experimentally by first conducting controlled irradiation treatments of the samples using an ion accelerator and subsequently characterizing the induced changes by transmission electron microscopy and Raman spectroscopy. The usefulness of the characterization methods is critically evaluated and a damage grading scale is proposed, based on transmission electron microscopy images. Theoretical predictions are made on defect production in graphene and white graphene under particle bombardment. A stochastic model based on first-principles molecular dynamics simulations is used together with electron irradiation experiments for understanding the formation of peculiar triangular defect structures in white graphene. An extensive set of classical molecular dynamics simulations is conducted, in order to study defect production under ion irradiation in graphene and white graphene. In the experimental studies the response of carbon and boron nitride multi-walled nanotubes to irradiation with a wide range of ion types, energies and fluences is explored. The stabilities of these structures under ion irradiation are investigated, as well as the issue of how the mechanism of energy transfer affects the irradiation-induced damage. An irradiation fluence of 5.5x10^15 ions/cm^2 with 40 keV Ar+ ions is established to be sufficient to amorphize a multi-walled nanotube. In the case of 350 keV He+ ion irradiation, where most of the energy transfer happens through inelastic collisions between the ion and the target electrons, an irradiation fluence of 1.4x10^17 ions/cm^2 heavily damages carbon nanotubes, whereas a larger irradiation fluence of 1.2x10^18 ions/cm^2 leaves a boron nitride nanotube in much better condition, indicating that carbon nanotubes might be more susceptible to damage via electronic excitations than their boron nitride counterparts. An elevated temperature was discovered to considerably reduce the accumulated damage created by energetic ions in both carbon and boron nitride nanotubes, attributed to enhanced defect mobility and efficient recombination at high temperatures. Additionally, cobalt nanorods encapsulated inside multi-walled carbon nanotubes were observed to transform into spherical nanoparticles after ion irradiation at an elevated temperature, which can be explained by the inverse Ostwald ripening effect. The simulation studies on ion irradiation of the hexagonal monolayers yielded quantitative estimates on types and abundances of defects produced within a large range of irradiation parameters. He, Ne, Ar, Kr, Xe, and Ga ions were considered in the simulations with kinetic energies ranging from 35 eV to 10 MeV, and the role of the angle of incidence of the ions was studied in detail. A stochastic model was developed for utilizing the large amount of data produced by the molecular dynamics simulations. It was discovered that a high degree of selectivity over the types and abundances of defects can be achieved by carefully selecting the irradiation parameters, which can be of great use when precise pattering of graphene or white graphene using focused ion beams is planned.