An extensive English language bibliography on graph theory and its applications, supplement 1

Graph theory and its applications - bibliography, supplement

Proceedings of the 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization

International audienceThe Cologne-Twente Workshop (CTW) on Graphs and Combinatorial Optimization started off as a series of workshops organized bi-annually by either Köln University or Twente University. As its importance grew over time, it re-centered its geographical focus by including northern Italy (CTW04 in Menaggio, on the lake Como and CTW08 in Gargnano, on the Garda lake). This year, CTW (in its eighth edition) will be staged in France for the first time: more precisely in the heart of Paris, at the Conservatoire National d’Arts et Métiers (CNAM), between 2nd and 4th June 2009, by a mixed organizing committee with members from LIX, Ecole Polytechnique and CEDRIC, CNAM

Digital Single-Cell Analysis of Plant Organ Development Using 3DCellAtlas

Diverse molecular networks underlying plant growth and development are rapidly being uncovered. Integrating these data into the spatial and temporal context of dynamic organ growth remains a technical challenge. We developed 3DCellAtlas, an integrative computational pipeline that semiautomatically identifies cell types and quantifies both 3D cellular anisotropy and reporter abundance at single-cell resolution across whole plant organs. Cell identification is no less than 97.8% accurate and does not require transgenic lineage markers or reference atlases. Cell positions within organs are defined using an internal indexing system generating cellular level organ atlases where data from multiple samples can be integrated. Using this approach, we quantified the organ-wide cell-type-specific 3D cellular anisotropy driving Arabidopsis thaliana hypocotyl elongation. The impact ethylene has on hypocotyl 3D cell anisotropy identified the preferential growth of endodermis in response to this hormone. The spatiotemporal dynamics of the endogenous DELLA protein RGA, expansin gene EXPA3, and cell expansion was quantified within distinct cell types of Arabidopsis roots. A significant regulatory relationship between RGA, EXPA3, and growth was present in the epidermis and endodermis. The use of single-cell analyses of plant development enables the dynamics of diverse regulatory networks to be integrated with 3D organ growth

Combinatorial Optimization

This report summarizes the meeting on Combinatorial Optimization where new and promising developments in the field were discussed. Th

The Potts model and the independence polynomial:Uniqueness of the Gibbs measure and distributions of complex zeros

Part 1 of this dissertation studies the antiferromagnetic Potts model, which originates in statistical physics. In particular the transition from multiple Gibbs measures to a unique Gibbs measure for the antiferromagnetic Potts model on the infinite regular tree is studied. This is called a uniqueness phase transition. A folklore conjecture about the parameter at which the uniqueness phase transition occurs is partly confirmed. The proof uses a geometric condition, which comes from analysing an associated dynamical system.Part 2 of this dissertation concerns zeros of the independence polynomial. The independence polynomial originates in statistical physics as the partition function of the hard-core model. The location of the complex zeros of the independence polynomial is related to phase transitions in terms of the analycity of the free energy and plays an important role in the design of efficient algorithms to approximately compute evaluations of the independence polynomial. Chapter 5 directly relates the location of the complex zeros of the independence polynomial to computational hardness of approximating evaluations of the independence polynomial. This is done by moreover relating the set of zeros of the independence polynomial to chaotic behaviour of a naturally associated family of rational functions; the occupation ratios. Chapter 6 studies boundedness of zeros of the independence polynomial of tori for sequences of tori converging to the integer lattice. It is shown that zeros are bounded for sequences of balanced tori, but unbounded for sequences of highly unbalanced tori

Bacterial Mechanosensitive Channel of Large Conductance (MscL) in Mammalian Cells for Novel Mechanobiology Applications

Mechanobiology, a relatively young field that centers on how external physical forces on cells or tissues and their intrinsic mechanical properties can influence physiology and disease, has become a pillar in cell biology. Indeed, cells experience a myriad of external, mechanical stimuli such as shear stress, stretch, substrate and matrix rigidity, surface topography, compression, and inter-cellular junction forces. Mechanosensors on the cell surface interfacing with the external environment (e.g., receptors, mechanosensitive ion channels, focal adhesions) and within the cell (e.g. the cytoskeleton) can sense, transmit, and amplify these inputs. This results in a cascade of intracellular biochemical signaling that leads to altered gene expression, protein expression, and finally, altered cell behavior and function. This process is known as mechanotransduction. Mechanotransduction at the cellular-scale has perceptible, large-scale implications such as proper organism development, our ability to sense sound and touch, function and homeostasis of organ systems, and disease progression. Previous work in mechanobiology has focused on investigating or capitalizing on native, endogenous mechanotransduction. This dissertation work proposes a relatively unexplored frontier in mechanobiology: exogenous mechanotransduction, by demonstrating a novel approach towards achieving signal transduction and mechanically driven behavior in cells through the introduction of exogenous mechanosensory components. Here we demonstrate how the functional expression of the E. coli membrane tension gated mechanosensitive channel of large conductance (MscL) in mammalian cells endows the cells with new mechano-sensing capabilities such as the activation of MscL in the plasma membrane through membrane tension resulting from (1) osmotic down-shock and (2) new interactions with native mechano-sensory components, as well as altered cell function such as (3) impairment of cell migration in metastasis in vivo and narrow, 3D confinement in vitro. The first major contribution in this thesis was to show that MscL can be expressed in mammalian cells, localize to cellular membranes, and responds to membrane tension via osmotic down-shock. The second contribution was demonstrating that the activation of the bacterial MS channel expressed in mammalian cells can be mediated through localized membrane stress that is dependent on the native actin-cytoskeleton. This was done by using acoustic tweezing cytometry (ATC) where acoustic excitation of microbubbles targeted to surface integrin receptors generated localized forces that robustly gated MscL. Impermeable, fluorescent dye uptake was used to report MscL activation; also showing that activated MscL can deliver large molecules into the cell. Lastly, we investigated the effect of MscL mechanotransduction on the cell function of migration in cancer metastasis and then more specifically, 3D-confinements. Our findings in our in vivo mouse model showed that there was a marked reduction in metastasis to the lung for MscL expressing cancer cells compared to controls. In vitro migration experiments using a biomimetic microfluidic device revealed that MscL activation due to 3D-confined migration could be responsible for the observed reduction in metastasis. We found that ~46% of MscL-expressing cancer cells that entered extremely narrow confinements of 30 µm2 cross-section had activated MscL and only 11% of these cells were able to fully enter the channel and migrate. Implications of this thesis are that MscL: (1) can be used as a molecular delivery tool for live-cells via mechanical stimulus; (2) can provide insight into the metastatic cascade and mechanobiology focused therapies; and (3) in mammalian cells can serve to study existing mechanotransduction or potentially engineer new mechanical properties and signaling in cells.PHDMechanical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/144021/1/heureaux_1.pd