http://repub.eur.nl/res/aut/3465/ List of Publications en http://repub.eur.nl/static-eur/img/logo.png http://repub.eur.nl http://repub.eur.nl/res/pub/39447/ 2013-03-21T00:00:00Z Major shifts in the availability of palatable plant resources are of key relevance to the ecology of leaf-cutting ants in human-modified landscapes. However, our knowledge is still limited regarding the ability of these ants to adjust their foraging strategy to dynamic environments. Here, we examine a set of forest stand attributes acting as modulating forces for the spatiotemporal architecture of foraging trail networks developed by Atta cephalotes L. (Hymenoptera: Formicidae: Attini). During a 12-month period, we mapped the foraging systems of 12 colonies located in Atlantic forest patches with differing size, regeneration age, and abundance of pioneer plants, and examined the variation in five trail system attributes (number of trails, branching points, leaf sources, linear foraging distance, and trail complexity) in response to these patch-related variables. Both the month-to-month differences (depicted in annual trail maps) and the steadily accumulating number of trails, trail-branching points, leaf sources, and linear foraging distance illustrated the dynamic nature of spatial foraging and trail complexity. Most measures of trail architecture correlated positively with the number of pioneer trees across the secondary forest patches, but no effects from patch age and size were observed (except for number of leaf sources). Trail system complexity (measured as fractal dimension; Df index) varied from 1.114 to 1.277 along the 12 months through which ant foraging was monitored, with a marginal trend to increase with the abundance of pioneer stems. Our results suggest that some leaf-cutting ant species are able to generate highly flexible trail networks (via fine-tuned adjustment of foraging patterns), allowing them to profit from the continuous emergence/recruitment of palatable resources. http://repub.eur.nl/res/pub/35010/ 2012-01-10T00:00:00Z Regulatory DNA elements such as enhancers, silencers and insulators are embedded in metazoan genomes, and they control gene expression during development. Although they fulfil different roles, they share specific properties. Herein we discuss some examples and a parsimonious model for their function is proposed. All are transcription units that tether their target promoters close to, or distant from, transcriptional hot spots (or 'factories'). http://repub.eur.nl/res/pub/34627/ 2011-08-02T00:00:00Z The project Services@MediGRID consortium established a tool set of grid-based biomedical services since 2008. The services are related to genetic analysis, genome data visualization, and pharmacokinetic modeling. Furthermore, business concepts for these services have been examined which are supported by an accounting and billing service. While the tools cover a whole service chain for biomedicine, the business concepts are rather heterogeneous. However, the overall addressed target market areas show promising potential. In addition, a structured coaching process reduces friction in the technology transfer from grid computing to biomedicine. This should be considered for similar future endeavors. http://repub.eur.nl/res/pub/23944/ 2010-11-16T00:00:00Z For the present efforts in dynamic IT outsourcing environments like Grid or Cloud computing security and trust are ongoing issues. SLAs are a proved remedy to build up trust in outsourcing relations. Therefore, it is necessary to determine whether SLAs can improve trust from the perspective of the outsourcing customer by integration of security measures. The conducted survey indicates that customers see SLAs as an approach to increase their level of trust in IT outsourcing partners. In addition, security measures in SLAs are of high relevance to support trust but not yet integrated appropriately. However, SLAs are very important for the technology transfer of eScience projects in Grid computing. Again, Grid based outsourcing of biomedical IT services requires security measures in SLAs. Thus, the technology transfer process of dynamic IT outsourcing infrastructures requires adequate SLAs in order to be successful. http://repub.eur.nl/res/pub/23946/ 2010-11-15T00:00:00Z The amount of information is growing exponentially with ever-new technologies emerging and is believed to be always at the limit. In contrast, huge resources are obviously available, which are underused in the IT sector, similar as e.g. in the renewable energy sector. This is especially for grid with its fast turnover rates very astonishing considering the barriers for further development put forward by the inability to satisfy the need for such resources. The phenomenon is a typical example of the Inverse Tragedy of the Commons, i.e. resources are underexploited in contrast to the unsustainable and destructing overexploitation in the Classic Tragedy of the Commons. An analysis of IT and the grid sector which attempts to share resources for better usage efficiency, reveals two challenges, which lead to the heart of the paradox: i) From a macro perspective all grid infrastructures involve not only mere technical solutions but also dominantly all of the autopoietic social sub-systems ranging from religion to policy. ii) On the micro level the individual players and their psychology and risk behaviour are of major importance for acting within the macro autopoietic framework. Consequently, the challenges of grid implementation are similar to those of other pressing global issues as e.g. climate protection. This is well described by extending the Human Ecology triangle to a rectangle: invironment-individual-society-environment. By applying this extension of this classical field of interdisciplinary basic and applied research to the grid sector, i.e. by further extension to an e-Human Grid Ecology rational, the Grid Inverse Tragedy of the Commons can be understood and approached regarding the internalization challenge into e-Society and e-Life, from which then guidelines for the day-to-day management can be derived. This is of general importance for many complex fields and thus with similar paradoxes and challenges. http://repub.eur.nl/res/pub/23949/ 2010-07-16T00:00:00Z Bringing new users into grids is a top priority for all grid initiatives and one of the most challenging tasks. Especially in life sciences it is essential to have a certain amount of users to establish a critical mass for a sustainable grid and give feedback back to the technological middleware layer. Based on the presumable lack of grid IT knowledge it is notably more arduous to satisfy user demands although here the requirements are especially demanding. Therefore, the development of an information- and learning platform could support the efforts of grid experts to guide new users. By providing a platform about grid technology and their feasibilities for users of the community of biomedicine potential, users could be supported using the high potential of their discipline. http://repub.eur.nl/res/pub/23956/ 2010-07-16T00:00:00Z The genome architecture in cell nuclei plays an important role in modern microscopy for the monitoring of medical diagnosis and therapy since changes of function and dynamics of genes are interlinked with changing geometrical parameters. The planning of corresponding diagnostic experiments and their imaging is a complex and often interactive IT intensive challenge and thus makes high-performance grids a necessity. To detect genetic changes we recently developed a new form of fluorescence in situ hybridization (FISH) - COMBinatorial Oligonucleotide FISH (COMBO-FISH) - which labels small nucleotide sequences clustering at a desired genomic location. To achieve a unique hybridization spot other side clusters have to be excluded. Therefore, we have designed an interactive pipeline using the grid-based GLOBE 3D Genome Viewer and Platform to design and display different labelling variants of candidate probe sets. Thus, we have created a grid-based virtual "paper" tool for easy interactive calculation, analysis, management, and representation for COMBO-FISH probe design with many an advantage: Since all the calculations and analysis run in a grid, one can instantly and with great visual ease locate duplications of gene subsequences to guide the elimination of side clustering sequences during the probe design process, as well as get at least an impression of the 3D architectural embedding of the respective chromosome region, which is of major importance to estimate the hybridization probe dynamics. Beyond, even several people at different locations could work on the same process in a team wise manner. Consequently, we present how a complex interactive process can profit from grid infrastructure technology using our unique GLOBE 3D Genome Platform gateway towards a real interactive curative diagnosis planning and therapy monitoring. http://repub.eur.nl/res/pub/23960/ 2010-07-16T00:00:00Z Especially in the life-science and the health-care sectors the huge IT requirements are imminent due to the large and complex systems to be analysed and simulated. Grid infrastructures play here a rapidly increasing role for research, diagnostics, and treatment, since they provide the necessary large-scale resources efficiently. Whereas grids were first used for huge number crunching of trivially parallelizable problems, increasingly parallel high-performance computing is required. Here, we show for the prime example of molecular dynamic simulations how the presence of large grid clusters including very fast network interconnects within grid infrastructures allows now parallel high-performance grid computing efficiently and thus combines the benefits of dedicated super-computing centres and grid infrastructures. The demands for this service class are the highest since the user group has very heterogeneous requirements: i) two to many thousands of CPUs, ii) different memory architectures, iii) huge storage capabilities, and iv) fast communication via network interconnects, are all needed in different combinations and must be considered in a highly dedicated manner to reach highest performance efficiency. Beyond, advanced and dedicated i) interaction with users, ii) the management of jobs, iii) accounting, and iv) billing, not only combines classic with parallel high-performance grid usage, but more importantly is also able to increase the efficiency of IT resource providers. Consequently, the mere "yes-we- can" becomes a huge opportunity like e.g. the life-science and health-care sectors as well as grid infrastructures by reaching higher level of resource efficiency. http://repub.eur.nl/res/pub/23951/ 2010-01-01T00:00:00Z Germ line gene transposition technology has been used to generate "libraries" of flies and worms carrying genomewide mutations. Phenotypic screening and DNA sequencing of such libraries provide functional information resulting from insertional events in target genes. There is also a great need to have a fast and efficient way to generate mouse mutants in vivo to model developmental defects and human diseases. Here we describe an optimized mammalian germ line transposition system active during early mouse spermatogenesis using the Minos transposon. Transposon-positive progeny carry on average more than 2 new transpositions, and 45 to 100% of the progeny carry an insertion in a gene. The optimized Minos-based system was tested in a small rapid dominant functional screen to identify mutated genes likely to cause measurable cardiovascular "disease" phenotypes in progeny/embryos. Importantly this system allows rapid screening for modifier genes. Copyright http://repub.eur.nl/res/pub/17552/ 2009-08-13T00:00:00Z The current fast growth of genome-wide association studies (GWAS) combined with now common computationally expensive imputation requires the online access of large user groups to high-performance computing resources capable of analyzing rapidly and efficiently millions of genetic markers for ten thousands of individuals. Here, we present a web-based interface—called GRIMP—to run publicly available genetic software for extremely large GWAS on scalable super-computing grid infrastructures. This is of major importance for the enlargement of GWAS with the availability of whole-genome sequence data from the 1000 Genomes Project and for future whole-population efforts. http://repub.eur.nl/res/pub/17884/ 2009-06-17T00:00:00Z The sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. Long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 9 106 to 3.0 9 107 bp from Archaea, Bacteria, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens. The local correlation coefficients show a species-specific multi-scaling behaviour: close to random correlations on the scale of a few base pairs, a first maximum from 40 to 3,400 bp (for Arabidopsis thaliana and Drosophila melanogaster divided in two submaxima), and often a region of one or more second maxima from 105 to 3 9 105 bp. Within this multi-scaling behaviour, an additional fine-structure is present and attributable to codon usage in all except the human sequences, where it is related to nucleosomal binding. Computer-generated random sequences assuming a block organization of genomes, the codon usage, and nucleosomal binding explain these results. Mutation by sequence reshuffling destroyed all correlations. Thus, the stability of correlations seems to be evolutionarily tightly controlled and connected to the spatial genome organization, especially on large scales. In summary, genomes show a complex sequential organization related closely to their three-dimensional organization. http://repub.eur.nl/res/pub/17555/ 2009-06-01T00:00:00Z Genomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the general sequential, three-dimensional and regulatory organization. Here, we present the GLOBE 3D Genome Platform a completely novel grid based virtual “paper” tool and in fact the first system-biological genome browser integrating the holistic complexity of genomes in a single easy comprehensible platform: Based on a detailed study of biophysical and IT requirements, every architectural level from sequence to morphology of one or several genomes can be approached in a real and in a symbolic representation simultaneously and navigated by continuous scale-free zooming within a unique three-dimensional OpenGL and grid driven environment. In principle an unlimited number of multi-dimensional data sets can be visualized, customized in terms of arrangement, shape, colour, and texture etc. as well as accessed and annotated individually or in groups using internal or external data bases/facilities. Any information can be searched and correlated by importing or calculating simple relations in real-time using grid resources. A general correlation and application platform for more complex correlative analysis and a front-end for system-biological simulations both using again the huge capabilities of grid infrastructures is currently under development. Hence, the GLOBE 3D Genome Platform is an example of a grid based approach towards a virtual desktop for genomic work combining the three fundamental distributed resources: i) visual data representation, ii) data access and management, and iii) data analysis and creation. Thus, the GLOBE 3D Genome Platform is the novel system-biology oriented information system urgently needed to access, present, annotate, and to simulate the holistic genome complexity in a unique gateway towards a real understanding, educative presentation and curative manipulation planning of this tremendous evolutionary information grail – genomes. http://repub.eur.nl/res/pub/17559/ 2009-06-01T00:00:00Z Advanced visualization technologies are gaining major importance to allow presentation and manipulation of high dimensional data. Since new health technologies are constantly increasing in complexity, adequate information processing is required for diagnostics and treatment. Therefore, the German DGrid initiative started to build visualization centers in 2008, which have recently been embedded into the existing compute and storage infrastructure. This paper describes an analysis of this infrastructure and the interplay with life science applications for 3D and 4D visualization and manipulation. Furthermore, the performance and business aspects regarding accounting, pricing and billing are investigated. The results show the viability and the opportunities for further optimization of this novel service approach and the possibilities for a sustainable business scenario. http://repub.eur.nl/res/pub/17563/ 2009-06-01T00:00:00Z With ever-new technologies emerging also the amount of information to be stored and processed is growing exponentially and is believed to be always at the limit. In contrast, however, huge resources are available in the IT sector alike e.g. the renewable energy sector, which are often even not at all used. This underusage bares any rational especially in the IT sector where e.g. virtualisation and grid approaches could be fast implemented due to the great technical and fast turnover opportunities. Here, we describe this obvious paradox for the first time as the Inverse Tragedy of the Commons, in contrast to the Classical Tragedy of the Commons where resources are overexploited. From this perspective the grid IT sector attempting to share resources for better efficiency, reveals two challenges leading to the heart of the paradox: i) From a macro perspective all grid infrastructures involve not only mere technical solutions but also dominantly all of the autopoietic social sub-systems ranging from religion to policy. ii) On the micro level the individual players and their psychology and risk behaviour are of major importance for acting within the macro autopoietic framework. Thus, the challenges of grid implementation are similar to those of e.g. climate protection. This is well described by the classic Human Ecology triangle and our extension to a rectangle: invironment-individual-society-environment. Extension of this classical interdisciplinary field of basic and applied research to an e-Human Grid Ecology rational, allows the Inverse Tragedy of the Commons of the grid sector to be understood and approached better and implies obvious guidelines in the day-today management for grid and other (networked) resources, which is of importance for many fields with similar paradoxes as in (e-)society. http://repub.eur.nl/res/pub/17564/ 2009-06-01T00:00:00Z Sustainability is a top priority for nearly all grid communities. The German grid communities in the area of life sciences are continuing their dissemination efforts in order to bring the grid to scientists. With cloud computing another concept for distributed IT infrastructures is on the rise. In this regard the grid has a different focus and matches better with life science compute power demands. A comparison of both grid and cloud in addition to the background and present status of the German life science grid give a contemporary impression of the future perspectives of MediGRID. http://repub.eur.nl/res/pub/17890/ 2008-05-18T00:00:00Z Many scenarios in medical research are predestined for grid computing. Large amounts of data in complex medical image, biosignal and genome processing demand large computing power and data storage. Integration of distributed, heterogeneous data, e.g. correlation between phenotype and genotype data are playing an essential part in life sciences. Sharing of specialized software, data and processing results for collaborative work are further tasks which would strongly benefit from the use of grid infrastructures. However, two major barriers are identified in existing grid environments that prevent extensive use within the life sciences community: Extended security requirements and appropriate usability. To meet these requirements, the MediGRID project is enhancing the basic D-Grid infrastructure along with the implementation of prototype applications from different fields of biomedical research. In this paper, we focus on the developments for ease-of-use under consideration of different aspects of security. They encompass not only security within the grid infrastructure, but also the boundary conditions of network security on the site of the research institutions. For medical grids, we propose a strictly webportal- based access to grid resources for end-users, with user-guiding, application specific, graphical interfaces. Different levels of authorization are implemented, from fully authorized users to guests without certificate authentication in order to allow hands-on experience for potential grid users. http://repub.eur.nl/res/pub/17899/ 2008-04-18T00:00:00Z The immunoglobulin heavy-chain (Igh) locus is organized into distinct regions that contain multiple variable (V(H)), diversity (D(H)), joining (J(H)) and constant (C(H)) coding elements. How the Igh locus is structured in 3D space is unknown. To probe the topography of the Igh locus, spatial distance distributions were determined between 12 genomic markers that span the entire Igh locus. Comparison of the distance distributions to computer simulations of alternative chromatin arrangements predicted that the Igh locus is organized into compartments containing clusters of loops separated by linkers. Trilateration and triple-point angle measurements indicated the mean relative 3D positions of the V(H), D(H), J(H), and C(H) elements, showed compartmentalization and striking conformational changes involving V(H) and D(H)-J(H) elements during early B cell development. In pro-B cells, the entire repertoire of V(H) regions (2 Mbp) appeared to have merged and juxtaposed to the D(H) elements, mechanistically permitting long-range genomic interactions to occur with relatively high frequency. http://repub.eur.nl/res/pub/17901/ 2008-02-18T00:00:00Z Microtubule (MT) plus end – tracking proteins (+TIPs) specifi cally recognize the ends of growing MTs. +TIPs are involved in diverse cellular processes such as cell division, cell migration, and cell polarity. Although +TIP tracking is important for these processes, the mechanisms underlying plus end specifi city of mammalian +TIPs are not completely understood. Cytoplasmic linker protein 170 (CLIP-170), the prototype +TIP, was proposed to bind to MT ends with high affi nity, possibly by copolymerization with tubulin, and to dissociate seconds later. However, using fl uorescence-based approaches, we show that two +TIPs, CLIP-170 and endbinding protein 3 (EB3), turn over rapidly on MT ends. Diffusion of CLIP-170 and EB3 appears to be rate limiting for their binding to MT plus ends. We also report that the ends of growing MTs contain a surplus of sites to which CLIP-170 binds with relatively low affi nity. We propose that the observed loss of fl uorescent +TIPs at plus ends does not refl ect the behavior of single molecules but is a result of overall structural changes of the MT end. http://repub.eur.nl/res/pub/17895/ 2008-01-01T00:00:00Z The immunoglobulin heavy-chain (Igh) locus is organized into distinct regions that contain multiple variable (VH), diversity (DH), joining (JH) and constant (CH) coding elements. How the Igh locus is structured in 3D space is unknown. To probe the topography of the Igh locus, spatial distance distributions were determined between 12 genomic markers that span the entire Igh locus. Comparison of the distance distributions to computer simulations of alternative chromatin arrangements predicted that the Igh locus is organized into compartments containing clusters of loops separated by linkers. Trilateration and triplepoint angle measurements indicated the mean relative 3D positions of the VH, DH, JH, and CH elements, showed compartmentalization and striking conformational changes involving VH and DH-JH elements during early B cell development. In pro-B cells, the entire repertoire of VH regions (2 Mbp) appeared to have merged and juxtaposed to the DH elements, mechanistically permitting long-range genomic interactions to occur with relatively high frequency. http://repub.eur.nl/res/pub/17567/ 2007-11-01T00:00:00Z Die elektronische Patientenakte gilt als Schlüsselapplikation der Gesundheitstelematik. Um sie optimal nutzen zu können, sind verteilte Anwendungen nötig. Die Grid-Technik liefert dafür erste Konzepte. Für einen Vortrag zum Thema erhielt der Autor den Telemed-Preis. http://repub.eur.nl/res/pub/17902/ 2007-09-01T00:00:00Z Het Erasmus Medisch Centrum en de Hogeschool Rotterdam zijn in 2005 een samenwerking begonnen teneinde de ongeveer 95% onbenutte rekencapaciteit van hun computers beschikbaar te maken voor onderzoek en onderwijs. Deze samenwerking heeft geleid tot het Erasmus Computing GRID (ECG), een virtuele supercomputer met na voltooiing een rekencapaciteit van 20 Teraflops. Dit artikel schetst enige achtergronden van grid computing, beschrijft een aantal toepassingen die mogelijk zijn met een grid infrastructuur en geeft de wijze weer waarop het ECG wordt vormgegeven. In het verlengde hiervan bevat het een pleidooi om grid computing binnen het onderwijs een betere basis te geven om op die manier vanuit het onderwijs een substantiële bijdrage te leveren aan het versterken van (rekenintensief) onderzoek. http://repub.eur.nl/res/pub/17566/ 2007-08-22T00:00:00Z Despite the major advancements during the last decade with respect to both knowledge of higher order chromatin organization in the cell nucleus and the elucidation of epigenetic mechanisms of gene control, the true three-dimensional (3D) chromatin structure of endogenous active and inactive gene loci is not known. The present study was initiated as an attempt to close this gap. As a model case, we compared the chromatin architecture between the genetically active and inactive domains of the imprinted Prader–Willi syndrome (PWS) locus in human fibroblast and lymphoblastoid cell nuclei by 3D fluorescence in situ hybridization and quantitative confocal laser scanning microscopy. The volumes and 3D compactions of identified maternal and paternal PWS domains were determined in stacks of light optical serial sections using a novel threshold-independent approach. Our failure to detect volume and compaction differences indicates that possible differences are below the limits of light optical resolution. To overcome this limitation, spectral precision distance microscopy, a method of localization microscopy at the nanometer scale, was used to measure 3D distances between differentially labeled probes located both within the PWS region and in its neighborhood. This approach allows the detection of intranuclear differences between 3D distances down to about 70–90 nm, but again did not reveal clearly detectable differences between active and inactive PWS domains. Despite this failure, a comparison of the experimental 3D distance measurements with computer simulations of chromatin folding strongly supports a non-random higher order chromatin configuration of the PWS locus and argues against 3D configurations based on giant chromatin loops. Our results indicate that the search for differences between endogenous active and inactive PWS domains must be continued at still smaller scales than hitherto possible with conventional light microscopic procedures. The possibilities to achieve this goal are discussed. http://repub.eur.nl/res/pub/17904/ 2007-04-02T00:00:00Z Personalized Medicine is of paramount interest for many areas in Medical Informatics. Therefore genotype data as well a phenotype data about patients have to be available. This data will be stored in Electronic Health Records or – patient controlled - in Personal Health Records. As the amount of (raw) data is rising continuously, methods for a secure data administration have to be found. Grid Services offer data storage, can support data retrieval and the presentation of the data. The basic security services could be provided by the German health professional infrastructure, but there are many security challenges to be faced. http://repub.eur.nl/res/pub/10809/ 2006-08-01T00:00:00Z The human small glutamine-rich TPR-containing protein (hSGT) is essential for cell division since RNA-interference-mediated strong reduction of hSGT protein levels causes mitotic arrest (M. Winnefeld, J. Rommelaere, and C. Cziepluch, The human small glutamine-rich TPR-containing protein is required for progress through cell division, Exp. Cell Res. 293 (2004), 43–57). Analysis of HeLa cells expressing a histone 2A-YFP fusion protein revealed the continuous presence of few mislocalized chromosomes close to the spindle poles as possible cause for hSGT depletion-dependent prometaphase arrest. Cells unable to rescue these mislocalized chromosomes into the metaphase plate died at this stage through apoptosis. In order to address hSGT function at the molecular level, mass spectrometry analysis of proteins which co-immunoprecipitated with Flag-tagged hSGT was performed. Thereby, Hsp70 and Bag-6/Bat-3/Scythe were identified as novel hSGT interaction partners while interaction with Hsc70 was confirmed. Results obtained with truncated versions of the hSGT protein revealed that Bag-6/Bat-3/Scythe and Hsp70 or Hsc70 were independently able to form complexes with hSGT. Interaction of hSGT with Hsc70, Hsp70 or Bag-6/Bat-3/Scythe was demonstrated in prometaphase, thereby suggesting a possible role for complexes containing hSGT and distinct (co)-chaperones during mitosis. Finally, cells from populations with reduced levels of Bag-6/Bat-3/Scythe also displayed persistence of mislocalized chromosomes and mitotic arrest, which strongly indicated that hSGT-Bag-6/Bat-3/Scythe complexes could be directly or indirectly required for complete chromosome congression. http://repub.eur.nl/res/pub/10808/ 2005-11-01T00:00:00Z The distribution and formation of foraging trails have largely been neglected as factors explaining harvesting patterns of leaf-cutting ants.We applied fractal analysis, circular, and conventional statistics to published and newly recorded trailmaps of seven Atta colonies focusing on three aspects: permanence, spatio-temporal plasticity and colony life stage. In the long term, trail patterns of young and mature Atta colonies revealed that foraging activities were focused on distinct, static sectors that made up only parts of their potentially available foraging range. Within these foraging sectors, trails were typically ephemeral and highly variable in space and time. These ephemeral trails were concentrated around permanent trunk trails in mature and around nest entrances in young colonies. Besides these similarities, the comparison of trail systems between the two life stages indicated that young colonies exploited fewer leaf sources, used smaller and less-complex systems of foraging trails, preferred different life forms as host plants, and switched hosts more often compared with mature colonies. Based on these analyses, we propose a general hypothesis which describes the foraging pattern in Atta as a result of initial foraging experiences, spatio-temporal distribution of suitable host plants, energetic constraints, and other factors such as seasonality and interspecific predation http://repub.eur.nl/res/pub/10806/ 2004-04-26T00:00:00Z The effect of trichostatin A (TSA)-induced histone acetylation on the interphase chromatin structure was visualized in vivo with a HeLa cell line stably expressing histone H2A, which was fused to enhanced yellow fluorescent protein. The globally increased histone acetylation caused a reversible decondensation of dense chromatin regions and led to a more homogeneous distribution. These structural changes were quantified by image correlation spectroscopy and by spatially resolved scaling analysis. The image analysis revealed that a chromatin reorganization on a length scale from 200 nm to >1 mm was induced consistent with the opening of condensed chromatin domains containing several Mb of DNA. The observed conformation changes could be assigned to the folding of chromatin during G1 phase by characterizing the effect of TSA on cell cycle progression and developing a protocol that allowed the identification of G1 phase cells on microscope coverslips. An analysis by flow cytometry showed that the addition of TSA led to a significant arrest of cells in S phase and induced apoptosis. The concentration dependence of both processes was studied. http://repub.eur.nl/res/pub/10807/ 2004-01-01T00:00:00Z Telomeres are specialized structures at the ends of the chromosomes that, with the help of proteins ± such as the telomere repeat-binding factor TRF2 ±, form protective caps which are essential for chromosomal integrity. Investigating the structure and three-dimensional (3D) distribution of the telomeres and TRF2 in the nucleus, we now show that the telomeres of the immortal HaCaT keratinocytes are distributed in distinct non-overlapping territories within the inner third of the nuclear space in interphase cells, while they extend more widely during mitosis. TRF2 is present at the telomeres at all cell cycle phases. During mitosis additional TRF2 protein concentrates all around the chromosomes. This change in staining pattern correlates with a significant increase in TRF2 protein at the S/G2 transition as seen in Western blots of synchronized cells and is paralleled by a cell cycle-dependent regulation of TRF2 mRNA, arguing for a specific role of TRF2 during mitosis. The distinct territorial localization of telomeres is abrogated in aHaCaT variant that constitutively expresses c- Myc ± a protein known to contribute to genomic instability. These cells are characterized by overlapping telomere territories, telomeric aggregates (TAs), that are accompanied by an overall irregular telomere distribution and a reduced level in TRF2 protein. These TAs which are readily detectable in interphase nuclei, are similarly present in mitotic cells, including cells in telophase. Thus, we propose that TAs, which subsequently also cluster their respective chromosomes, contribute to genomic instability by forcing an abnormal chromosome segregation during mitosis. http://repub.eur.nl/res/pub/10805/ 2003-08-19T00:00:00Z Although methods for light microscopy of chromatin are well established, there are no quantitative data for nucleosome concentrations in vivo. To establish such a method we used a HeLa clone expressing the core histone H2B fused to the enhanced yellow fluorescent protein (H2B-EYFP). Quantitative gel electrophoresis and fluorescence correlation spectroscopy (FCS) of isolated oligonucleosomes show that 5% of the total H2Bs carry the fluorescent tag and an increased nucleosome repeat length of 204 bp for the fluorescent cells. In vivo, the mobility and distribution of H2BEYFP were studied with a combination of FCS and confocal imaging. With FCS, concentration and brightness of nascent molecules were measured in the cytoplasm, while in the nucleoplasm a background of mobile fluorescent histones was determined by continuous photobleaching. Combining these results allows converting confocal fluorescence images of nuclei into calibrated nucleosome density maps. Absolute nucleosome concentrations in interphase amount up to 250 mM locally, with mean values of 140(^28) mM, suggesting that a condensationcontrolled regulation of site accessibility takes place at length scales well below 200 nm. http://repub.eur.nl/res/pub/10803/ 2003-05-01T00:00:00Z Transport and binding of molecules to specific sites are necessary for the assembly and function of ordered supramolecular structures in cells. For analyzing these processes in vivo, we have developed a confocal fluorescence fluctuation microscope that allows both imaging of the spatial distribution of fluorescent molecules with confocal laser scanning microscopy and probing their mobility at specific positions in the cell with fluorescence correlation spectroscopy and continuous fluorescence photobleaching (CP). Because fluorescence correlation spectroscopy is restricted to rapidly diffusing particles and CP to slower processes, these two methods complement each other. For the analysis of binding-related contributions to mobility we have derived analytical expressions for the temporal behavior of CP curves from which the bound fraction and/or the dissociation rate or residence time at binding sites, respectively, can be obtained. In experiments, we investigated HeLa cells expressing different fluorescent proteins: Although enhanced green fluorescent protein (EGFP) shows high mobility, fusions of histone H2B with the yellow fluorescent protein are incorporated into chromatin, and these nuclei exhibit the presence of a stably bound and a freely diffusing species. Nonpermanent binding was found for mTTF-I, a transcription termination factor for RNA polymerase I, fused with EGFP. The cells show fluorescent nucleoli, and binding is transient. CP yields residence times for mTTF-I-EGFP of ;13 s. http://repub.eur.nl/res/pub/10802/ 2003-02-18T00:00:00Z http://repub.eur.nl/res/pub/9413/ 2003-01-01T00:00:00Z Genomes are one of the major foundations of life due to their role in information storage, process regulation and evolution. However, the sequential and three-dimensional structure of the human genome in the cell nucleus as well as its interplay with and embedding into the cell and organism only arise scarcely from the unknown, despite recent successes e. g. in the linear sequencing efforts and growing evidence for seven genomic organization levels. To achieve a deeper understanding of the human genome the structural, scaling and dynamic properties in the simulation of interphase chromosomes and cell nuclei are determined and combined with the analysis of long-range orrelations in completely sequenced genomes as well as the analysis of the chromatin distribution in vivo: This integrative approach reveals that the chromatin fiber is most likely folded according to the Multi-Loop-Subcompartment (MLS) model in which the chromatin fiber bents into 63–126 kbp big loops aggregated to rosettes connected by again 63–126 kbp linkers. The MLS model exhibits fine-structured multi-scaling and predicts correctly the transport of molecules by moderately obstructed/anomalous diffusion. On the basic sequence level, genomes show fine-structured positive long-range correlations, allowing classification and tree construction. This, DNA fragment distributions after carbon ion irradiation and on the highest structural level, the nuclear morphology visualized by histone autofluorescent protein fusions in vivo, agrees again best with the MLS model. Thus, the local, global and dynamic characteristics of cell nuclei are not only tightly inter-connected, but also are integrated holisticly to fulfill the overall function of the genome. http://repub.eur.nl/res/pub/10800/ 2002-05-08T00:00:00Z http://repub.eur.nl/res/pub/10799/ 2002-04-01T00:00:00Z Several GFP variants have been developed for multicolor labeling in vivo. Here we report that simultaneous co-transfection of fluorescent protein chimeras can give falsepositive results caused by the conversion of spectral properties. Under standard transfection conditions, approximately 8% of cells produce false-positive results, but, depending on the conditions, up to 26% of the cells permanently express altered fusion proteins. This compromises the interpretation of the results. The conversion is independent of transfection methods or cell types. Our results show that the effect is based on homologous recombination/repair/replication process events that occur between the nucleotide sequences of the fluorescent proteins. Consecutive transfection or low sequence similarities avoided recombination. The appearance of conversion facilitates exchanges of spectral properties in fusion proteins, the creation of libraries, or the assembly of DNA fusion constructs in vivo. The detailed quantification of the conversion rate allows the investigation of recombination/repair/replication processes in general. http://repub.eur.nl/res/pub/10801/ 2002-02-21T00:00:00Z http://repub.eur.nl/res/pub/17892/ 2002-01-01T00:00:00Z To approach the still largely unknown sequential and three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated on the 30 nm chromatin fiber level with Monte Carlo, Brownian Dynamics and parallel computing methods. Differences between used models explain various experimental conditions, favouring a Multi-Loop-Subcompartment model with 63-126 kbp loops aggregated to possibly rosettes connected by 63-126 kbp linkers, and predict correctly the transport of molecules by moderately obstructed diffusion excluding the Inter-Chromosomal Domain hypothesis. Correlation analyses of completely sequenced Archaea, Bacteria and Eukarya chromosomes revealed fine-structured positive long-range correlations due to codon, nucleosomal or block organization of the genomes, allowing classification and tree construction. By construction and expression of fusionproteins from the histones H1, H2A, H2B, H3, H4 and mH2A1.2 with the autofluorescent proteins CFP, GFP, YFP, DsRed-1 and DsRed-2, the chromatin morphology could be investigated in vivo during interphase, mitosis or apoptosis and revealed different interphase morphologies for cell lines, quantifiable by scaling analyses. Finally, construct conversions in simultaneous co-transfections due to recombination/repair/replication were discovered in ≤25 % of cells and led to a variety of new applications. http://repub.eur.nl/res/pub/9414/ 2001-04-20T00:00:00Z Recombinant human erythropoietin (Epo)and granu l o cy t e - c o l o ny - s t i mulating factor (G-CSF) are used to stimulate hematopoiesis in patients with malignant dise a s e s . These cytokines transduce their biological signal via the Epo receptor (EpoR) and G-CSF receptor (G-CSF-R) into the cell. We therefore investigated in human tumor cell lines the expression of these receptors in tumor cells as well as their response to Epo and G-CSF. Methods and study design: The expression of EpoR and G-CSF-R mRNA was analy zed with rev e rse transcription-poly m e r a s e chain reaction (RT-PCR). EpoR protein expression was further monitored with Western blot and immunocytochemistry analys i s . The cellular response to various concentrations of Epo was evaluated using 3[H]-thymidine uptake, Northern blot of cfos expression and tyrosine kinase activity assay. The proliferation after G-CSF incubation was analyzed with the MTS assay. Results: In this study EpoR mRNA and protein were detected in various human tumor cell lines. Treatment with Epo did not influence the pro l i feration rate of examined EpoR-positive tumor cell lines.Epo did not stimulate the tyrosine kinase activity nor did it affect the c-fos mRNA in these cell lines.G-CSF-R mRNA was only detected in two myeloid cell lines. Treatment with G-CSF did not increase the proliferation of these cells. C o n c l u s i o n s : These results demonstrate that Epo and G-CSF did not modulate the growth rate of examined receptor-positive tumor cell lines; the presence of the Epo receptor seems not essential for cell growth of these tumor cells in cell culture. http://repub.eur.nl/res/pub/9360/ 2000-01-01T00:00:00Z http://repub.eur.nl/res/pub/9416/ 1999-01-01T00:00:00Z http://repub.eur.nl/res/pub/9415/ 1998-09-01T00:00:00Z http://repub.eur.nl/res/pub/32173/ 1998-02-04T00:00:00Z Dreidimensionale Organisation von Chromosomen Domänen in Simulation und Experiment Um Aussagen über die dreidimensionale Organisation von Chromosomen in der Interphase zu machen, wurden Monte-Carlo und Brownsche-Dynamik Simulationen von Chromosomenterritorien mit Hilfe eines Polymeransatzes durchgeführt. Daraus wurden Observable (verschiedene Abstandsverteilungen zwischen genomischen Markern, Aufenthaltswahrscheinlichkeit und Dichte) berechnet, die für die Vorhersage und Interpretation von Experimenten dienen. Damit können Modelle der chromosomalen Organisation, insbesondere das Random-Walk/Giant-Loop- (MLS) und das Multi-Loop-Subcompartment Modell, unterschieden werden. Für die Bestimmung von Abstandsverteilungen zwischen genomischen Markern der Prader-Labhart-Willi/Angelmann (PLW/A) Region wurden Experimente mit einem konfokalen Laser-Scanning-Mikroskop (CLSM) durchgeführt. Zellkerne von Fibroblasten wurden mit schonender Fluoreszenz in situ Hybridisierung (FISH) präpariert. Über die Signal-Brightness, das Signalvolumen, die Intergrierte Fluoreszenz Intensität (IFI) und den Abstand homologer Chromosomen wurden ebenfalls Aussagen gemacht. Vergleiche zwischen Simulation und Experiment ergaben starke Hinweise für das MLS Modell, sowie eine unterschiedliche Organisation zwischen mütterlichem und väterlichem Chromosom 15. Im Hinblick auf zukünftige komplexere Fragestellungen der Gesamtorganisation des Zellkerns stellte sich die Theorie der Fraktale für neue Analysemethoden als geeignet heraus. Die Ergebnisse der Simulationen zeigten dabei multifraktales Verhalten. Erstmals könnte damit die Fraktalität und Multifraktalität einer zellulären Organisationsstruktur gezeigt worden sein. Damit besteht nun die Möglichkeit aus der fraktalen Struktur Aussagen über Diffusionseigenschaften und andere Organisationsmerkmale im Zellkern zu treffen.