CTP promotes efficient ParB-dependent DNA condensation by facilitating one-dimensional diffusion from parS

Faithful segregation of bacterial chromosomes relies on the ParABS partitioning system and the SMC complex. In this work, we used single-molecule techniques to investigate the role of cytidine triphosphate (CTP) binding and hydrolysis in the critical interaction between centromere-like parS DNA sequences and the ParB CTPase. Using a combined optical tweezers confocal microscope, we observe the specific interaction of ParB with parS directly. Binding around parS is enhanced by the presence of CTP or the non-hydrolysable analogue CTPγS. However, ParB proteins are also detected at a lower density in distal non-specific DNA. This requires the presence of a parS loading site and is prevented by protein roadblocks, consistent with one-dimensional diffusion by a sliding clamp. ParB diffusion on non-specific DNA is corroborated by direct visualization and quantification of movement of individual quantum dot labelled ParB. Magnetic tweezers experiments show that the spreading activity, which has an absolute requirement for CTP binding but not hydrolysis, results in the condensation of parS-containing DNA molecules at low nanomolar protein concentrations

Fundamental studies in geodynamics

Research in fundamental studies in geodynamics continued in a number of fields including seismic observations and analysis, synthesis of geochemical data, theoretical investigation of geoid anomalies, extensive numerical experiments in a number of geodynamical contexts, and a new field seismic volcanology. Summaries of work in progress or completed during this report period are given. Abstracts of publications submitted from work in progress during this report period are attached as an appendix

A functional model of similarity

In the first chapters, the prevalent conception of the nature of similarity is shown to be too narrow, and the argument is developed that models of similarity must encompass both analytic and synthetic components. Some general problems of measurement and the testing of psychological models are also discussed.A review of the philosophical treatment of the concept of similarity is made in order to understand the origins of the models found in the present psychological literature. These are then analysed in terms of their implicit object representations and cognitive processes. The distinction between the'class inclusion' and 'distance relation' models of similarity is shown tobe qualitative in nature, and to correspond to the analytic-synthetic distinction in terms of cognitive process.A functional model of the psychological processes and object representations involved in similarity judgements is then proposed. The fundamental idea involved in this model is that the global properties of referents are synthetically evaluated in terms of their contextual relations, whilst an analytic 'pattern matching' of local properties is made. Various theoretical aspects of the model are examined experimentally, and its general applicability is indicated in a series of applied studies.The scope of the argument is finally broadened to encompass a development of Torgerson's (196.5) conception of the nature of the dimensions resulting from MDS analysis. Dimensions may be considered as 'virtual' artifacts of the experimental task and the individual's conception of it. This possibility allows the methodology to escape the dominating influence of its psychophysical tradition, and become a conceptually deeper tool for cognitive psychology

Magnetic and Mechanical Properties of Ultrasoft Magnetorheological Elastomers

Magnetorheological elastomers (MREs), composite materials consisting of magnetic particles embedded in a non-magnetic elastomeric matrix, can reversibly modulate their mechanical and magnetic properties through tuning the applied magnetic field H. Recently, ultrasoft MREs have received tremendous attention due to their great potential in biomedical applications. However, the effects of the polymer stiffness and magnetic particle concentration on the magnetic and mechanical properties of ultrasoft MREs still need to be better understood. In this dissertation, the author presents a comprehensive investigation of the magnetic and mechanical properties of ultrasoft MREs as well as their biomedical applications. The effect of polymer stiffness on magnetization reversal of MREs has been investigated using a combination of magnetometry measurements and computational modeling. The magnetic hysteresis loops of the softer MREs exhibit a characteristic pinched loop shape with almost zero remanence and loop widening at intermediate fields that monotonically decreases with increasing polymer stiffness. A two-dipole model that incorporates magneto-mechanical coupling not only confirms that micron-scale particle motion along the applied magnetic field direction plays a defining role in the magnetic hysteresis but also reproduces the observed loop shapes and widening trends for MREs with varying polymer stiffnesses. Measurements of the moduli and surface roughness of ultrasoft MREs at various H’s reveal a sensitive dependence on the magnetic particle concentration and H. As increases from 0 to 23%, ultrasoft MREs at =95.5 kA/m (1200 Oe) show an increase of ≈41×,11×,and 11× in their shear storage, Young’s modulus, and surface roughness, respectively. The moduli and surface roughness can be fit to quadratic functions of and H. The presented magnetic and mechanical properties of ultrasoft MREs provides the framework for applying the MREs as dynamic platforms in biomedical engineering. Ultrasoft MREs have been applied to investigate the response of cells to 2D and 3D dynamic mechanical stimuli. Furthermore, the field-dependent particle motion observed in ultrasoft MREs has inspired an application for creating 3D heterogeneous cellular gradients. This work was performed under the guidance of the author’s thesis advisor, Professor Xuemei Cheng

A compositional neural architecture for language

Hierarchical structure and compositionality imbue human language with unparalleled expressive power and set it apart from other perception–action systems. However, neither formal nor neurobiological models account for how these defining computational properties might arise in a physiological system. I attempt to reconcile hierarchy and compositionality with principles from cell assembly computation in neuroscience; the result is an emerging theory of how the brain could convert distributed perceptual representations into hierarchical structures across multiple timescales while representing interpretable incremental stages of (de) compositional meaning. The model's architecture—a multidimensional coordinate system based on neurophysiological models of sensory processing—proposes that a manifold of neural trajectories encodes sensory, motor, and abstract linguistic states. Gain modulation, including inhibition, tunes the path in the manifold in accordance with behavior and is how latent structure is inferred. As a consequence, predictive information about upcoming sensory input during production and comprehension is available without a separate operation. The proposed processing mechanism is synthesized from current models of neural entrainment to speech, concepts from systems neuroscience and category theory, and a symbolic-connectionist computational model that uses time and rhythm to structure information. I build on evidence from cognitive neuroscience and computational modeling that suggests a formal and mechanistic alignment between structure building and neural oscillations and moves toward unifying basic insights from linguistics and psycholinguistics with the currency of neural computation

Coassembled nanostructured bioscaffold reduces the expression of proinflammatory cytokines to induce apoptosis in epithelial cancer cells

The local inflammatory environment of the cell promotes the growth of epithelial cancers. Therefore, controlling inflammation locally using a material in a sustained, non-steroidal fashion can effectively kill malignant cells without significant damage to surrounding healthy cells. A promising class of materials for such applications is the nanostructured scaffolds formed by epitope presenting minimalist self-assembled peptides; these are bioactive on a cellular length scale, while presenting as an easily handled hydrogel. Here, we show that the assembly process can distribute an anti-inflammatory polysaccharide, fucoidan, localized to the nanofibers within the scaffold to create a biomaterial for cancer therapy. We show that it supports healthy cells, while inducing apoptosis in cancerous epithelial cells, as demonstrated by the significant down-regulation of gene and protein expression pathways associated with epithelial cancer progression. Our findings highlight an innovative material approach with potential applications in local epithelial cancer immunotherapy and drug delivery

Extracellular Matrix Remodeling and the Control of Branching Morphogenetic Programs.

Epithelial cells and endothelial cells initiate distinct branching morphogenetic programs during their coordinated invasion and proliferation into the interstitial compartment, a tissue comprised of mesenchymal stromal cells and extracellular matrix (ECM). While mammary gland development occurs in a specialized stromal environment dominated by adipocytes and fibroblasts, endothelial cell branching proceeds throughout all tissues in the absence of a specific stromal cell population. Nevertheless, both epithelial cells and endothelial cells engaged in morphogenetic responses have been posited to mobilize proteolytic enzymes to penetrate ECM barriers. However, transgenic mouse models have failed to identify required proteolytic effectors or uncover the mechanisms whereby proteolytic changes in tissue microenvironments regulate cell behavior. Herein, we characterize functional roles performed by the two dominant transmembrane proteinases expressed during epithelial and endothelial cell branching processes, the membrane-anchored matrix metalloproteinases, MT1-MMP and MT2-MMP. Using a series of transgenic mouse models, we identify new and unanticipated roles for MT1-MMP and MT2-MMP in mammary gland morphogenesis as well as angiogenesis. Tissue-specific targeting of MT1-MMP and MT2-MMP demonstrate that early mammary gland branching, which takes place within an immature ECM, proceeds independently of either proteinase. Instead, both proteinases play important, but diametrically opposed, roles in mammary gland adipocytes, where MT1-MMP stimulates adipogenesis and lipid metabolism, while MT2-MMP represses the development of thermogenic beige/brown adipocytes. In marked contrast, during the major phases of postnatal mammary gland development where a mature ECM is actively deposited, branching requires stromal cell-, rather than epithelial cell-, derived MT1-MMP, where the proteinase regulates branching by remodeling a periductal network of ECM macromolecules dominated by type I collagen. Endothelial cells also rely on MT1-MMP to direct branching, but unexpectedly, the proteinase also controls proliferative responses via a novel regulatory axis wherein pericellular proteolysis of the ECM governs the cytoskeletal-nuclear membrane interactions responsible for regulating transcriptional activity. Together, these data create new paradigms relevant to morphogenesis and tissue remodeling, as well as identify novel roles for membrane-anchored metalloproteinases in governing ECM proteolysis and associated transcriptional programs.PHDCellular and Molecular BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/120758/1/tyfei_1.pd

Tailoring Cellular Function: The Contribution of the Nucleus in Mechanotransduction

Cells sense a variety of different mechanochemical stimuli and promptly react to such signals by reshaping their morphology and adapting their structural organization and tensional state. Cell reactions to mechanical stimuli arising from the local microenvironment, mechanotransduction, play a crucial role in many cellular functions in both physiological and pathological conditions. To decipher this complex process, several studies have been undertaken to develop engineered materials and devices as tools to properly control cell mechanical state and evaluate cellular responses. Recent reports highlight how the nucleus serves as an important mechanosensor organelle and governs cell mechanoresponse. In this review, we will introduce the basic mechanisms linking cytoskeleton organization to the nucleus and how this reacts to mechanical properties of the cell microenvironment. We will also discuss how perturbations of nucleus-cytoskeleton connections, affecting mechanotransduction, influence health and disease. Moreover, we will present some of the main technological tools used to characterize and perturb the nuclear mechanical state