Dynamic spot analysis in the 2D electrophoresis gels images

Práce shrnuje faktory a parametry, které ovlivňují výsledky 2D elektroforézy, se zaměřením na zpracování obrazu jako jeden ze způsobů snížení nesprávné interpretace jejích výstupů. Proces zpracování obrazu využívá jako zdroj dat především obrazů z opakovaných provedení téhož pokusu, neboli víceplik. Pomocí analýzy obrazů víceplik je možno pozorovat nebo korigovat změny jednoho pokusu a také porovnávat je s výstupy jiných pokusů. Cílem práce je poskytnout podporu specialistovi, který má na starosti popsat vlastnosti struktur nacházejících se v elektroforetických obrazech.The text briefly describes factors and parameters which influence the results of 2D electrophoresis focusing on image processing as one manner to reduce incorrect interpretation of its outputs. As dataset, image processing performance uses images from repeated execution of one experiment also known as multiplicates. Using multiplicates analysis it is possible to observe or lower the changes of one experiment and to compare them with outputs of other experiments. The aim of this work is to provide support for specialist who takes care about describing the character patterns located in electrophoretic images.

Implications of hybridisation and cytotypic differentiation in speciation assessed by AFLP and plastid haplotypes : a case study of Potentilla alpicola La Soie

Background: Hybridisation is presumed to be an important mechanism in plant speciation and a creative evolutionary force often accompanied by polyploidisation and in some cases by apomixis. The Potentilla collina group constitutes a particularly suitable model system to study these phenomena as it is morphologically extensively variable, exclusively polyploid and expresses apomixis. In the present study, the alpine taxon Potentilla alpicola has been chosen in order to study its presumed hybrid origin, identify underlying evolutionary processes and infer the discreteness or taxonomic value of hybrid forms. Results: Combined analysis of AFLP, cpDNA sequences and ploidy level variation revealed a hybrid origin of the P. alpicola populations from South Tyrol (Italy) resulting from crosses between P. pusilla and two cytotypes of P. argentea. Hybrids were locally sympatric with at least one of the parental forms. Three lineages of different evolutionary origin comprising two ploidy levels were identified within P. alpicola. The lineages differed in parentage and the complexity of the evolutionary process. A geographically wide-spread lineage thus contrasted with locally distributed lineages of different origins. Populations of P. collina studied in addition, have been regarded rather as recent derivatives of the hexaploid P. argentea. The observation of clones within both P. alpicola and P. collina suggested a possible apomictic mode of reproduction. Conclusions: Different hybridisation scenarios taking place on geographically small scales resulted in viable progeny presumably stabilised by apomixis. The case study of P. alpicola supports that these processes played a significant role in the creation of polymorphism in the genus Potentilla. However, multiple origin of hybrids and backcrossing are considered to produce a variety of evolutionary spontaneous forms existing aside of reproductively stabilised, established lineages

Research reports: 1991 NASA/ASEE Summer Faculty Fellowship Program

The basic objectives of the programs, which are in the 28th year of operation nationally, are: (1) to further the professional knowledge of qualified engineering and science faculty members; (2) to stimulate an exchange of ideas between participants and NASA; (3) to enrich and refresh the research and teaching activities of the participants' institutions; and (4) to contribute to the research objectives of the NASA Centers. The faculty fellows spent 10 weeks at MSFC engaged in a research project compatible with their interests and background and worked in collaboration with a NASA/MSFC colleague. This is a compilation of their research reports for summer 1991

Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

Solutions to decision-making problems in management engineering using molecular computational algorithms and experimentations

制度:新 ; 報告番号:甲3368号 ; 学位の種類:博士(工学) ; 授与年月日:2011/5/23 ; 早大学位記番号:新568

<i>Plasmodium </i>Condensin Core Subunits SMC2/SMC4 Mediate Atypical Mitosis and Are Essential for Parasite Proliferation and Transmission

Condensin is a multi-subunit protein complex regulating chromosome condensation and segregation during cell division. In Plasmodium spp., the causative agent of malaria, cell division is atypical and the role of condensin is unclear. Here we examine the role of SMC2 and SMC4, the core subunits of condensin, during endomitosis in schizogony and endoreduplication in male gametogenesis. During early schizogony, SMC2/SMC4 localize to a distinct focus, identified as the centromeres by NDC80 fluorescence and chromatin immunoprecipitation sequencing (ChIP-seq) analyses, but do not form condensin I or II complexes. In mature schizonts and during male gametogenesis, there is a diffuse SMC2/SMC4 distribution on chromosomes and in the nucleus, and both condensin I and condensin II complexes form at these stages. Knockdown of smc2 and smc4 gene expression reveals essential roles in parasite proliferation and transmission. The condensin core subunits (SMC2/SMC4) form different complexes and may have distinct functions at various stages of the parasite life cycle

MODELLING THE INFLUENCE OF NUCLEUS ELASTICITY ON CELL INVASION IN FIBER NETWORKS AND MICROCHANNELS

Cell migration in highly constrained extracellular matrices is exploited in scaffold-based tissue engineering and is fundamental in a wide variety of physiological and pathological phenomena, among others in cancer invasion and development. Research into the critical processes involved in cell migration has mainly focused on cell adhesion and proteolytic degradation of the external environment. However, rising evidence has recently shown that a number of cell-derived biophysical and mechanical parameters, among others nucleus stiffness and cell deformability, plays a major role in cell motility, especially in the ameboid-like migration mode in 3D confined tissue structures. We here present an extended cellular Potts model (CPM) first used to simulate a micro-fabricated migration chip, which tests the active invasive behavior of cancer cells into narrow channels. As distinct features of our approach, cells are modeled as compartmentalized discrete objects, differentiated in the nucleus and in the cytosolic region, while the migration chamber is composed of channels of different widths. We find that cell motile phenotype and velocity in open spaces (i.e., 2D flat surfaces or large channels) are not significantly influenced by cell elastic properties. On the contrary, the migratory behavior of cells within subcellular and subnuclear structures strongly relies on the deformability of the cytosol and of the nuclear cluster, respectively. Further, we characterize two migration dynamics: a stepwise way, characterized by fluctuations in cell length, within channels smaller than nucleus dimensions and a smooth sliding (i.e., maintaining constant cell length) behavior within channels larger than the nuclear cluster. These resulting observations are then extended looking at cell migration in an artificial fiber network, which mimics cell invasion in a 3D extracellular matrix. In particular, in this case, we analyze the effect of variations in elasticity of the nucleus on cell movement. In order to summarize, with our simulated migration assays, we demonstrate that the dimensionality of the environment strongly affects the migration phenotype and we suggest that the cytoskeletal and nuclear elastic characteristics correlate with the tumor cell's invasive potentia

Patterning nanocrystals using DNA

One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made.[1] Here, we have sought to assemble larger and more complex nanostructures. Gold-DNA conjugates with 50 to 100 bases self-assembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure [2][3] that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA ''trimer.'' This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices to a length greater than 20 {micro}m, and collecting atomic force microscopy (AFM) images up to 30 {micro}m. We found the lattices' requirement of divalent magnesium cations to stabilize Holliday junctions to be incompatible with the stability of charge-stabilized gold nanoparticles used for the experiments here, and gold particles added indiscriminately to the lattice surface through non-specific binding. Redesigning the lattices to avoid magnesium may improve results

Field-control, phase-transitions, and life's emergence

Instances of critical-like characteristics in living systems at each organizational level as well as the spontaneous emergence of computation (Langton), indicate the relevance of self-organized criticality (SOC). But extrapolating complex bio-systems to life's origins, brings up a paradox: how could simple organics--lacking the 'soft matter' response properties of today's bio-molecules--have dissipated energy from primordial reactions in a controlled manner for their 'ordering'? Nevertheless, a causal link of life's macroscopic irreversible dynamics to the microscopic reversible laws of statistical mechanics is indicated via the 'functional-takeover' of a soft magnetic scaffold by organics (c.f. Cairns-Smith's 'crystal-scaffold'). A field-controlled structure offers a mechanism for bootstrapping--bottom-up assembly with top-down control: its super-paramagnetic components obey reversible dynamics, but its dissipation of H-field energy for aggregation breaks time-reversal symmetry. The responsive adjustments of the controlled (host) mineral system to environmental changes would bring about mutual coupling between random organic sets supported by it; here the generation of long-range correlations within organic (guest) networks could include SOC-like mechanisms. And, such cooperative adjustments enable the selection of the functional configuration by altering the inorganic network's capacity to assist a spontaneous process. A non-equilibrium dynamics could now drive the kinetically-oriented system towards a series of phase-transitions with appropriate organic replacements 'taking-over' its functions.Comment: 54 pages, pdf fil

Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP.

Important insights into nuclear function would arise if gene loci physically interacting with particular subnuclear domains could be readily identified. Immunofluorescence microscopy combined with fluorescence in situ hybridization (immuno-FISH), the method that would typically be used in such a study, is limited by spatial resolution and requires prior assumptions for selecting genes to probe. Our new technique, immuno-TRAP, overcomes these limitations. Using promyelocytic leukemia nuclear bodies (PML NBs) as a model, we used immuno-TRAP to determine if specific genes localize within molecular dimensions with these bodies. Although we confirmed a TP53 gene-PML NB association, immuno-TRAP allowed us to uncover novel locus-PML NB associations, including the ABCA7 and TFF1 loci and, most surprisingly, the PML locus itself. These associations were cell type specific and reflected the cell's physiological state. Combined with microarrays or deep sequencing, immuno-TRAP provides powerful opportunities for identifying gene locus associations with potentially any nuclear subcompartment