Pattern Formation and Organization of Epithelial Tissues

Developmental biology is a study of how elaborate patterns, shapes, and functions emerge as an organism grows and develops its body plan. From the physics point of view this is very much a self-organization process. The genetic blueprint contained in the DNA does not explicitly encode shapes and patterns an animal ought to make as it develops from an embryo. Instead, the DNA encodes various proteins which, among other roles, specify how different cells function and interact with each other. Epithelial tissues, from which many organs are sculpted, serve as experimentally- and analytically-tractable systems to study patterning mechanisms in animal development. Despite extensive studies in the past decade, the mechanisms that shape epithelial tissues into functioning organs remain incompletely understood. This thesis summarizes various studies we have done on epithelial organization and patterning, both in abstract theory and in close contact with experiments. A novel mechanism to establish cellular left-right asymmetry based on planar polarity instabilities is discussed. Tissue chirality is often assumed to originate from handedness of biological molecules. Here we propose an alternative where it results from spontaneous symmetry breaking of planar polarity mechanisms. We show that planar cell polarity (PCP), a class of well-studied mechanisms that allows epithelia to spontaneously break rotational symmetry, is also generically capable of spontaneously breaking reflection symmetry. Our results provide a clear interpretation of many mutant phenotypes, especially those that result in incomplete inversion. To bridge theory and experiments, we develop quantitative methods to analyze fluorescence microscopy images. Included in this thesis are algorithms to selectively project intensities from a surface in z-stack images, analysis of cells forming short chain fragments, analysis of thick fluorescent bands using steerable ridge detector, and analysis of cell recoil in laser ablation experiments. These techniques, though developed in the context of zebrafish retina mosaic, are general and can be adapted to other systems. Finally we explore correlated noise in morphogenesis of fly pupa notum. Here we report unexpected correlation of noise in cell movements between left and right halves of developing notum, suggesting that feedback or other mechanisms might be present to counteract stochastic noise and maintain left-right symmetry.PHDPhysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/138800/1/hjeremy_1.pd

Anisotropic Müller glial scaffolding supports a multiplex lattice mosaic of photoreceptors in zebrafish retina

Abstract Background The multiplex, lattice mosaic of cone photoreceptors in the adult fish retina is a compelling example of a highly ordered epithelial cell pattern, with single cell width rows and columns of cones and precisely defined neighbor relationships among different cone types. Cellular mechanisms patterning this multiplex mosaic are not understood. Physical models can provide new insights into fundamental mechanisms of biological patterning. In earlier work, we developed a mathematical model of photoreceptor cell packing in the zebrafish retina, which predicted that anisotropic mechanical tension in the retinal epithelium orients planar polarized adhesive interfaces to align the columns as cone photoreceptors are generated at the retinal margin during post-embryonic growth. Methods With cell-specific fluorescent reporters and in vivo imaging of the growing retinal margin in transparent juvenile zebrafish we provide the first view of how cell packing, spatial arrangement, and cell identity are coordinated to build the lattice mosaic. With targeted laser ablation we probed the tissue mechanics of the retinal epithelium. Results Within the lattice mosaic, planar polarized Crumbs adhesion proteins pack cones into a single cell width column; between columns, N-cadherin-mediated adherens junctions stabilize Müller glial apical processes. The concentration of activated pMyosin II at these punctate adherens junctions suggests that these glial bands are under tension, forming a physical barrier between cone columns and contributing to mechanical stress anisotropies in the epithelial sheet. Unexpectedly, we discovered that the appearance of such parallel bands of Müller glial apical processes precedes the packing of cones into single cell width columns, hinting at a possible role for glia in the initial organization of the lattice mosaic. Targeted laser ablation of Müller glia directly demonstrates that these glial processes support anisotropic mechanical tension in the planar dimension of the retinal epithelium. Conclusions These findings uncovered a novel structural feature of Müller glia associated with alignment of photoreceptors into a lattice mosaic in the zebrafish retina. This is the first demonstration, to our knowledge, of planar, anisotropic mechanical forces mediated by glial cells.https://deepblue.lib.umich.edu/bitstream/2027.42/139592/1/13064_2017_Article_96.pd

Equal Graph Partitioning on Estimated Infection Network as an Effective Epidemic Mitigation Measure

Controlling severe outbreaks remains the most important problem in infectious disease area. With time, this problem will only become more severe as population density in urban centers grows. Social interactions play a very important role in determining how infectious diseases spread, and organization of people along social lines gives rise to non-spatial networks in which the infections spread. Infection networks are different for diseases with different transmission modes, but are likely to be identical or highly similar for diseases that spread the same way. Hence, infection networks estimated from common infections can be useful to contain epidemics of a more severe disease with the same transmission mode. Here we present a proof-of-concept study demonstrating the effectiveness of epidemic mitigation based on such estimated infection networks. We first generate artificial social networks of different sizes and average degrees, but with roughly the same clustering characteristic. We then start SIR epidemics on these networks, censor the simulated incidences, and use them to reconstruct the infection network. We then efficiently fragment the estimated network by removing the smallest number of nodes identified by a graph partitioning algorithm. Finally, we demonstrate the effectiveness of this targeted strategy, by comparing it against traditional untargeted strategies, in slowing down and reducing the size of advancing epidemics

How does a protein fold? A time series segmentation study

In this work, we perform time series segmentation on average velocity time series of penta-alanine protein simulated in water. We then cluster the segments according to their fluctuation characteristics and discover periods of weak overall fluctuations surrounded by well-aligned segment boundaries. We speculate that these quiet periods may correspond to the folded state of the protein and that the well-aligned segment boundaries surrounding them may indicate the folding and unfolding processes. We then proceed to systematically identify such global transitions, measure the lifetimes of the quiet periods and the folding/unfolding events, and identify plausible precursor segments leading the transitions. We then check our findings of possible folding events against traditional methods of comparing molecular structures and measuring the radius of gyration. Finally, we extended the work by including atomic cross correlation analysis on various quiet periods and transitions to identify possible hydrogen bond formation and to better understand the folding dynamics of the protein.Bachelor of Science in Physic

Additional file 11: Figure S6. of Anisotropic Müller glial scaffolding supports a multiplex lattice mosaic of photoreceptors in zebrafish retina

Expression of cdh2 transcripts in differentiating photoreceptors (A-A”’) In situ hybridization for cdh2 transcripts (A, white or A”, A”’, magenta) in a retinal cross-section from the Müller glial reporter line, Tg(gfap:EGFP) (A’-A”’, green). (PDF 2467 kb

Additional file 5: Figure S2. of Anisotropic MĂźller glial scaffolding supports a multiplex lattice mosaic of photoreceptors in zebrafish retina

Immature UV cones have rounded apical profiles in the pre-column area. (PDF 939 kb

Additional file 10: Movie S4. of Anisotropic Müller glial scaffolding supports a multiplex lattice mosaic of photoreceptors in zebrafish retina

Red cones in the pre-column zone (magenta dots) and in the mature mosaic (white dots) are surrounded by Müller glial scaffolding. Higher magnification of a portion of the field shown in Fig. 4A–D and Additional file 9: Movie S3: Müller glia (green) and Red cones (red). Weak GFP signals of immature Müller glia first appear in the proliferative zone (toward the right). The intensity of the GFP signal increases in differentiating Müller glia and their processes surround photoreceptors, including differentiating Red cones (magenta dots) at the level of the OLM. Emergence of the hexagonal distribution of Red cones (white dots) is accompanied by morphological maturation of Müller glia. (AVI 4600 kb

Additional file 8: Figure S5 of Anisotropic MĂźller glial scaffolding supports a multiplex lattice mosaic of photoreceptors in zebrafish retina

MĂźller glial apical processes are preferentially distributed into parallel, inter-column bands. (PDF 1085 kb

Additional file 4: Movie S2. of Anisotropic Müller glial scaffolding supports a multiplex lattice mosaic of photoreceptors in zebrafish retina

Live imaging of the photoreceptor mosaic emerging at the retinal margin in rapidly growing juvenile zebrafish. Confocal z-stack series of live multiphoton confocal imaging at the dorsal retinal margin in a double transgenic ruby zebrafish; Tg(trß2:tdTomato) in red and Tg(crx:mCFP) in cyan. The crx promoter is expressed in all cone and rod photoreceptors; the mCFP reporter localizes to the plasma membrane. The tdTomato+ proliferative retinal progenitors are randomly distributed in the most peripheral region of the germinal zone (asterisks). The first cone column (arrow and inset) is composed of tdTomato+ Red cones alternately separated by mCFP-labeled profiles of one or three immature cones (white dots), as predicted by the organization of cone types in a column in the mature mosaic. Mature cones develop long apical projections, including conical-shaped outer segments that are strongly labeled by the crx:mCFP reporter. (See also Fig. 2D.) (AVI 1851 kb

Additional file 9: Movie S3. of Anisotropic Müller glial scaffolding supports a multiplex lattice mosaic of photoreceptors in zebrafish retina

Müller glial apical processes provide scaffolding for differentiating photoreceptor cells. 3D–reconstruction (maximum intensity z-projection) of live multiphoton confocal imaging from a double transgenic ruby zebrafish, with reporters for Müller glia (gfap:EGFP in green) and Red cones (trß2:tdTomato in red). Müller glial processes extend laterally at the level of OLM to surround profiles of individual Red cones and other photoreceptors. (See also Fig. 4A–D.) (AVI 4930 kb