Hybrid model for vascular tree structures

This paper proposes a new representation scheme of the cerebral blood vessels. This model provides information on the semantics of the vascular structure: the topological relationships between vessels and the labeling of vascular accidents such as aneurysms and stenoses. In addition, the model keeps information of the inner surface geometry as well as of the vascular map volume properties, i.e. the tissue density, the blood flow velocity and the vessel wall elasticity. The model can be constructed automatically in a pre-process from a set of segmented MRA images. Its memory requirements are optimized on the basis of the sparseness of the vascular structure. It allows fast queries and efficient traversals and navigations. The visualizations of the vessel surface can be performed at different levels of detail. The direct rendering of the volume is fast because the model provides a natural way to skip over empty data. The paper analyzes the memory requirements of the model along with the costs of the most important operations on it.Postprint (published version

Molecular factors involved in the formation of secondary vascular tissues and lignification in higher plants

The formation of secondary vascular tissues involves complex processes and many steps, a number of which have been examined in detail in this study. A novel CuZn-SOD, with a high pI and thus denoted hipI-SOD, was identified and characterized in Pinus sylvestris. Results from immunolocalisation analyses indicated that it is localised in lignified structures, suggesting that SOD might participate in the formation of secondary cell walls and lignification. To further investigate its role in these processes, a Zinnia mesophyll cell system was set up. This enabled us to follow the differentiation from mesophyll cell to tracheary element. Various inhibitors against SOD and H2O2-production were applied. The results suggested that HipI-SOD might have a novel and important function in secondary cell wall formation and lignification processes. The expression pattern and localization of the protein during formation of tracheary elements support this assumption. The other part of this study involved analysis of transcription factors and their regulation, especially in secondary vascular tissues. The genes encoding three MYB-transcription factors and one novel Zinc-finger transcription factor were found in an EST-library from the cambial region of hybrid aspen (Populus tremula L. x tremuloides Michx.). The genes were cloned and characterized and their regulation by hormones, sucrose and gravity was investigated. The genes were found to be under hormone and sucrose control, and their expression altered during tension wood formation. Transgenic plants were constructed, carrying one of two antisense constructs of MYB-genes, PttMYB46 or PttMYB76, which were strongly expressed in lignified tissues. Analysis of plants with either of these constructs displayed a complex phenotype, including reduced growth, increased concentration of some phenolic acids and changes in lignin composition. Some of the phenotypic traits were indicative of strong investment in defensive characters

A Framework for Directional and Higher-Order Reconstruction in Photoacoustic Tomography

Photoacoustic tomography is a hybrid imaging technique that combines high optical tissue contrast with high ultrasound resolution. Direct reconstruction methods such as filtered backprojection, time reversal and least squares suffer from curved line artefacts and blurring, especially in case of limited angles or strong noise. In recent years, there has been great interest in regularised iterative methods. These methods employ prior knowledge on the image to provide higher quality reconstructions. However, easy comparisons between regularisers and their properties are limited, since many tomography implementations heavily rely on the specific regulariser chosen. To overcome this bottleneck, we present a modular reconstruction framework for photoacoustic tomography. It enables easy comparisons between regularisers with different properties, e.g. nonlinear, higher-order or directional. We solve the underlying minimisation problem with an efficient first-order primal-dual algorithm. Convergence rates are optimised by choosing an operator dependent preconditioning strategy. Our reconstruction methods are tested on challenging 2D synthetic and experimental data sets. They outperform direct reconstruction approaches for strong noise levels and limited angle measurements, offering immediate benefits in terms of acquisition time and quality. This work provides a basic platform for the investigation of future advanced regularisation methods in photoacoustic tomography.Comment: submitted to "Physics in Medicine and Biology". Changes from v1 to v2: regularisation with directional wavelet has been added; new experimental tests have been include

Developmental biology of wood formation

The wood-forming vascular cambium is responsible for the production of a large part of the biomass on this planet. Yet, there is only limited knowledge on how cell proliferation and differentiation in the cambial meristem are regulated. In this thesis the wood-forming tissues of aspen were used as a model system to identify and characterize molecular factors related to cambial meristem activity. An important regulator of cambial meristem activity is the plant hormone auxin. As polar transport is crucial for the delivery of auxin to the cambial zone, we identified homologues of known regulators of polar auxin transport and described their regulation by environmental and developmental factors. Translating changes in auxin concentration into changes in gene expression involves members of the Aux/IAA gene family. Aspen homologues of Aux/IAA genes were cloned and found to be expressed in a highly tissue-specific fashion, which is further influenced by developmental events and changes in the environment. A major response of trees to environmental changes is the suspension of meristematic growth during winter dormancy. A comparison of gene expression in active and dormant cambia revealed dramatic changes in the transcriptome including the expression of many cold and stress related genes during winter. During the process of wood formation, cells originating in the vascular cambium go through an elaborate process of cell division, cell expansion, secondary wall formation and programmed cell death. Large-scale analysis of gene expression was used to create transcriptional maps of the differentiation process. This extensive dataset allowed us to confirm the proposed functions of various genes involved in wood formation, assign other known genes to specific stages along the developmental gradient and identify a large number of novel potential regulators of wood formation. The data further suggest that the cambial meristem shares regulatory mechanisms with other meristems in addition to its own, specific factors

Diversification and expression of the PIN, AUX/LAX, and ABCB families of putative auxin transporters in \u3cem\u3ePopulus\u3c/em\u3e

Intercellular transport of the plant hormone auxin is mediated by three families of membrane-bound protein carriers, with the PIN and ABCB families coding primarily for efflux proteins and the AUX/LAX family coding for influx proteins. In the last decade our understanding of gene and protein function for these transporters in Arabidopsis has expanded rapidly but very little is known about their role in woody plant development. Here we present a comprehensive account of all three families in the model woody species Populus, including chromosome distribution, protein structure, quantitative gene expression, and evolutionary relationships. The PIN and AUX/LAX gene families in Populus comprise 16 and 8 members respectively and show evidence for the retention of paralogs following a relatively recent whole genome duplication. There is also differential expression across tissues within many gene pairs. The ABCB family is previously undescribed in Populus and includes 20 members, showing a much deeper evolutionary history, including both tandem and whole genome duplication as well as probable gene loss. A striking number of these transporters are expressed in developing Populus stems and we suggest that evolutionary and structural relationships with known auxin transporters in Arabidopsis can point toward candidate genes for further study in Populus. This is especially important for the ABCBs, which is a large family and includes members in Arabidopsis that are able to transport other substrates in addition to auxin. Protein modeling, sequence alignment and expression data all point to ABCB1.1 as a likely auxin transport protein in Populus. Given that basipetal auxin flow through the cambial zone shapes the development of woody stems, it is important that we identify the full complement of genes involved in this process. This work should lay the foundation for studies targeting specific proteins for functional characterization and in situ localization

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees.

BackgroundOne of the great advantages of next generation sequencing is the ability to generate large genomic datasets for virtually all species, including non-model organisms. It should be possible, in turn, to apply advanced computational approaches to these datasets to develop models of biological processes. In a practical sense, working with non-model organisms presents unique challenges. In this paper we discuss some of these challenges for ChIP-seq and RNA-seq experiments using the undomesticated tree species of the genus Populus.ResultsWe describe specific challenges associated with experimental design in Populus, including selection of optimal genotypes for different technical approaches and development of antibodies against Populus transcription factors. Execution of the experimental design included the generation and analysis of Chromatin immunoprecipitation-sequencing (ChIP-seq) data for RNA polymerase II and transcription factors involved in wood formation. We discuss criteria for analyzing the resulting datasets, determination of appropriate control sequencing libraries, evaluation of sequencing coverage needs, and optimization of parameters. We also describe the evaluation of ChIP-seq data from Populus, and discuss the comparison between ChIP-seq and RNA-seq data and biological interpretations of these comparisons.ConclusionsThese and other "lessons learned" highlight the challenges but also the potential insights to be gained from extending next generation sequencing-supported network analyses to undomesticated non-model species

Mathematical modelling of angiogenesis and vascular adaptation

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A Review of Mathematical Models for the Formation of\ud Vascular Networks

Mainly two mechanisms are involved in the formation of blood vasculature: vasculogenesis and angiogenesis. The former consists of the formation of a capillary-like network from either a dispersed or a monolayered population of endothelial cells, reproducible also in vitro by specific experimental assays. The latter consists of the sprouting of new vessels from an existing capillary or post-capillary venule. Similar phenomena are also involved in the formation of the lymphatic system through a process generally called lymphangiogenesis.\ud \ud A number of mathematical approaches have analysed these phenomena. This paper reviews the different modelling procedures, with a special emphasis on their ability to reproduce the biological system and to predict measured quantities which describe the overall processes. A comparison between the different methods is also made, highlighting their specific features