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Distortion Invariant Feature Extraction with Echo State Networks
No full textIn complex pattern recognition tasks data usually exhibits many local distortions which significantly disturb the recognition process. A method for extracting temporal features from a signal that are invariant to these distortions is presented in this report. The idea is to use Echo State Network to generate a rich high-dimensional representation of data. Temporal features are then extracted by finding projections of the high-dimensional representation that are minimally influenced by the selected distortions while still carrying most of the information about the underlying signal required for the performed task. The algorithm performance is analyzed on synthetic signals as well as on high-dimensional handwriting data for shift and scale distortions. It is shown that the algorithm is capable to extract a low dimensional feature set from a reservoir which is invariant to the selected distortions and relevant to the performed task
Use of protein engineering to study DNA recognition by the E.coli DNA methyltransferase (EcoDam)
No full textDNA methylation carried out by DNA methyltransferases (MTases) is widespread in prokaryotes and eukaryotes. In this study, we have changed the target specificity of EcoDam from GATC to GATT by directed evolution, combining different random mutagenesis methods with restriction protection at GATT sites for selection and screening. The new methyltransferases are fully functional in vivo and in vitro. The EcoDam and T4Dam DNA-(adenine N6)-methyltransferases both methylate the adenine residue in GATC sites. They are highly related in amino acid sequence and structure but deviate in their contact to the first base pair of the target sequence. We have transplanted the T4Dam DNA recognition module into EcoDam and show that the EcoDam K9A/Y138R double mutant is highly active and specific. The evolutionary intermediates of this transition were studied as well: the EcoDam K9A variant showed low activity and loss of recognition of the first base pair, whereas; the EcoDam Y138R variant is fully active and specific. This result indicates that there exists a smooth evolutionary pathway changing the EcoDam DNA recognition mode to the T4Dam mode without loss of activity. Finally, in an attempt to enhance the preference of the L122A EcoDam for hemimethylated DNA to generate an artificial epigenetic system that can propagate patterns of GATC site methylation potentially useful for gene regulation, the L122, P134 and V133 residues were replaced with other amino acids using site directed mutagenesis. Our results showed that, in addition to L122A, the L122A/V133L EcoDam variant was able to sense the methylation status of the GATC target recognition site and methylated only hemimethylated DNA
Efficient multichannel image partitioning : theory and application
No full textSegmentation is an important tool in image processing. The principal goal of the segmentation process is to separate the structures of interest from the background and from each other. The focus of the current work is to explore and develop a range of efficient segmentation approaches for multichannel image data. As main examples of application, we use synthetic color images as well as medical and biomedical image data. In our studies the objective is to divide the entire image into subregions. Such a procedure is often called partitioning. We start from a generalization of grayscale segmentation techniques to multichannel data by converting it to a scalar field. We propose a procedure that converts color to scalar data while preserving as many salient features as possible which is important for segmentation purposes. We apply standard segmentation techniques to the converted data and discuss the advantages and limitations of such conversion. Apart from that, we propose an approach that allows for the direct segmentation and surface extraction mechanisms for color data. Our approach consists of several automated steps and an intuitive mechanism for user-guided feature selection. Often operating only in the feature space is not fully adequate, and algorithms which operate both in feature and object space are preferable. We analyze several global multichannel image partitioning approaches using minimum description length. We develop a novel extension of the approach to multichannel image partitioning. In certain highly specialized segmentation tasks, prior knowledge, e. g., feature and shape characteristics, about the areas to be extracted might be useful. For such problems a relatively simple partitioning can be used in combination with several post-processing steps. We apply such approach for evaluation of certain cell types. We discuss the results and limitations of the individual processing steps as well as of the overall automatic quantification approach
Hybrid organic-inorganic polyoxotungstates functionalized by diorganotin and -antimony linkers
No full textThe present work summarizes our research done in the field of Polyoxotungstates functionalized by organotin and –antimony linkers.
After an introduction on iso- and heteropolyoxometalates (generally referred as Polyoxometalates, or POMs) and some of their most important applications a discussion is devoted to the analytical techniques used in the characterization of Polyoxometalates. The next chapters are dedicated to the chemistry of mono- and diorganotin functionalized iso- and heteropolytungstates, starting with a more specific introduction on the subject, followed by five chapters in which the new synthesized compounds are treated in detail, starting from their synthetic procedure and characterization in the solid state and in solution (where applies), and ending with a discussion of their structural features and conclusion remarks. The chapters are organized in terms of the dimensionality of the novel materials synthesized, i.e. 3-, 2-, 1-dimensional and discrete molecular assemblies.
Following the same organization as that used for the chapters devoted to organotin functionalized iso- and heteropolyoxometalates; the next one deals with organoantimony functionalized POMs; including a discussion on the first polyoxotungstate polyanion functionalized with three monophenylantimony groups in a sandwich type structure.
The last chapter deals with two structures without organometallic moieties attached to the POM framework, which nevertheless presents very interesting structural attributes. Finally, the appendix includes already published as well as submitted and accepted material in specialized journals based on the work from this manuscript
Improved methodology for the preparation of chiral amines
No full textThe importance of α-chiral amines as building blocks in pharmaceutical drugs, natural products, fine chemicals and agrochemicals have encouraged scientists to develop different methodologies for their preparation. Their main goal was to develop a step wise efficient and low waste production methodology which utilizes inexpensive starting material for the synthesis of α-chiral amines in high yields and enantioselectivity. Different methodologies have been developed aiming to meet these criteria. These strategies are discussed and their importance and limitations are critically analyzed.
Reductive amination is a powerful methodology for the synthesis of chiral amines in high yields and enantioselectivity. It is a two step strategy beginning from the prochiral carbonyl compound to the primary chiral amine. The historical development and the latest milestones in this field are discussed in chapter three. Different drugs and natural products which are prepared utilizing reductive amination as a key step in their synthesis are summarized in chapter four.
Reductive amination utilizing chiral auxiliary/Lewis acid/ heterogeneous catalyst/ molecular hydrogen has been investigated in our group over the last five years. This combination allowed the preparation of alkyl-alkyl’ α-chiral amines in mediocre to good yields and enantioselectivities. This group of amines is known historically to be difficult synthetic task. We developed a new asymmetric reductive amination procedure using Yb(OAc)3 (50-110 mol %) that allows increased diastereoselectivity (6-15% units) for alkyl-alkyl’ α-chiral amines that previously only provided mediocre to good diastereoselectivity. Different Lewis acids were tested under different reaction conditions of temperature, pressure and solvents and the results of these experiments are discussed in chapter five.
The use of catalytic Lewis acids in reductive amination has never been reported in literatures. We demonstrated the beneficial use of 10-15 mol % of Yb(OAc)3 or Ce(OAc)3 or Y(OAc)3 in suppressing alcohol formation and promoting reductive amination in good yield but without enhanced stereoselectivity. Despite the fact that the use of Brønsted acids in reductive amination is well established no literature reports are available. We have performed and extensive study on the use of commercially available Brønsted and mineral acids in reductive amination. The scope of the reaction and the substrate categories are summarized in chapter six.
A mechanism for the reaction has been proposed and the basic mechanistic experiments have been performed. An in situ cis- to trans-ketimine isomerization mechanism, promoted by Yb(OAc)3, has been proposed to account for the observed increase in diastereoselectivity. The experiments and the proposed mechanism are summarized in chapter seven
Exploring the influence of biological variability on pattern formation in Dictyostelium discoideum
No full textThis thesis explores the systematic influence of biological variability on self-organized pattern formation of the slime mold Dictyostelium discoideum (Dd). Potential applications beyond Dd are to all systems that follow some form of excitable dynamics and, consequently, organize their collective behavior in terms of target waves and spiral waves. Computational studies of several mathematical models for Dd signaling have been performed and analyzed regarding the processes of target and spiral wave generation as well as the statistical allocation of these waves relative to the position of specific fractions of cells that guide the respective processes of self-organization. By considering a large number of numerical simulations, the total space of asymptotic patterns that is supported by a specific arrangement of cell properties can be identified. These analyses were performed using a suite of custom software, based on the established phase singularity technique for the identification of spiral waves and on a novel noise-resistant 3D fitting algorithm for the identification of target waves developed in this thesis
Weak binding of antibiotics in bacterial porins : measurement and biological relevance
No full textThe outer membrane of Gram--negative bacteria, acting as a selectively permeable barrier, is a major factor in broad--spectrum antibiotic resistance. This selective permeability may be investigated extit[in vitro], by focussing on the individual constituents of the outer membrane. It has been shown that a weak affinity of hydrophilic antimicrobials to the interior of general diffusion porins in the bacterial wall enhances their translocation through the pore, resulting in greater accumulation of the antibiotic in the bacterium. In this work, a method is developed to ascertain with molecular detail the membrane translocation route of antibiotics, using a combination of high--resolution conductance measurements on a single porin in an artificial bilayer, fluorescence resonance energy transfer measurements and molecular dynamics simulations. A porin--based route of entry is shown for moxifloxacin, and a pathway through the lipid for nalidixic acid (a hydrophilic and hydrophobic quinolone). The translocation kinetics and affinity of other quinolone antibiotics have been measured by pore conductance fluctuations. An understanding of the detailed molecular interactions between the antibiotic and its entry channel may be used to develop new antibiotics with improved uptake kinetics. To facilitate future measurements a novel microfluidics--based planar lipid bilayer measurement system has been developed capable of high--resolution, low noise recordings and double sided perfusion. The system has the potential to screen a large number of specific outer membrane channels against a library of antibiotics
Numerical Chromosome Variation and Mitotic Segregation Defects in Cells Generated in the Adult Brain of Teleost Fish
No full textIn contrast to most other vertebrates, teleost fish exhibit an unparalleled capacity to generate new cells in both the intact and the injured adult brain. This dissertation is focused on the occurrence, the extent and the fate of aneuploid cells (genome-modified individual cells characterized by the loss or gain of whole chromosomes) generated in the teleostean brain. Aneuploidy is observed in 80% of the newly-generated cells of the adult brain, but occurs at a very low rate in liver tissue, as shown by metaphase chromosome spreads and flow-cytometric DNA content analysis. To further analyze this phenomenon, the mitotic machinery of adult brain cells was examined for chromosome segregation defects which showed lagging chromosomes at metaphase and anaphase, as well as micronuclei and anaphase bridges, in the intact adult brain. To identify the fate of aneuploid cells in the adult brain, the Sphase cell cycle marker 5-bromo-2-deoxyuridine (BrdU) was injected into the fish, which were kept for various postadministration survival times. In the 100- and 860-day BrdU survival periods, the rate of mitotic segregation defects was significantly reduced, compared to the 2h and the 30-day survival times. These findings suggest that a good portion of the cells with mitotic defects were eliminated, possibly by apoptotic cell death. The analysis of post BrdU administration survival times in Apteronotus leptorhynchus up to 860 days, and up to 203 days in Danio rerio, revealed that a significant proportion of cells which exhibit nuclear abnormalities after mitosis survived for the rest of the life of the fish. In conclusion, this thesis demonstrates the evidence of the generation and maintenance of aneuploid cells in the adult fish brain that arise through chromosome missegregation which is a widespread phenomenon in the teleostean central nervous system
Chances and barriers for the prolongation of working life : interaction between state and company policies in Poland and Western Germany
No full textThis study examines the institutional and organisational determinants of the early exit trend in Germany and Poland and future prospects thereof. It adopts a diachronic time frame (from the 1970s till present) and analyses legislative changes in the field of pension and labour market policy (macro level), changes of individual retirement preferences (micro level) and changes of firm policies with regard to older workers (micro level). The applied methods are qualitative case studies in 31 German and Polish establishments, analysis of policy documents and scholarly literature and secondary analysis of official statistical data. The results confirm theories which combine rational choice and institutional approaches, as proposed by Mayntz/Scharpf (1995) or Windhoff-Héritier (1991). In particular, firms (and individual workers) slowly adapt to opportunities and restrictions, as well as to normative expectations, set by institutions (e.g. the raised retirement age). However, structural determinants like the situation on the sales and labour market, rationalisation processes and ownership transformations clearly influence when and which adaptation patterns will be adopted. The cross-national comparison has revealed that differences between Polish and German firms with regard to the effect their personnel policy has on the integration, resp. externalisation of older workers exceed branch similarities across both countries. That can be explained with the country-specific national and sectoral institutions which create restrictions and opportunities for firm behaviour, and with socio-economic constraints. With regard to institutional determinants of early exit, Germany is better positioned than Poland and is more likely to further raise the employment rate of older workers
Ecological aspects of the marine planctomycete Rhodopirellula baltica SH1T : a whole genome array approach
No full textSince the first microbial genome has been finished in the year 1995 more than 800 sequenced microorganisms are publicly available and many more are on their way. Bioinformatic analysis of the sequence information is required to process this huge amount of data and to generate sound hypotheses in terms of physiology and ecology of an organism as well as to efficiently screen for candidate genes for biotechnological relevant enzymes.However, high-throughput lab-methods are more than ever required for the subsequent verification of initial bioinformatic findings and hypotheses. Post-genomic approaches like DNA microarrays have revolutionised molecular biology by enabling a new dimension of parallelism in expression profiling. Eight years ago, the Max Planck Institute for Marine Microbiology has initiated a genomics project for the complete genome sequencing and analysis of environmental relevant marine bacteria. Rhodopirellula baltica was selected as a marine representative of the globally distributed and environmentally important bacterial phylum Planctomycetales. It is a model organism for aerobic carbohydrate degradation in marine systems, where polysaccharides represent the dominant components of biomass. The complete genome sequence of R. baltica has been determined and functional annotation was performed. However, pure in silico predictions left about 55% of the genes without functional assignment. The availability of the whole genome sequence has already stimulated a set of follow-up studies ranging from proteomics to protein crystallization as well as biotechnological applications. This work presents the establishment of, and the results gained with, the first whole genome microarray for a Planctomycete. It shows that massive expression profiling under defined environmental conditions can take the challenge to bridge the gap between classical studies on the cell biology and physiology of Planctomycetes and their active genetic repertoire