An object-oriented framework is presented for developing and simulating individual-based models of cell populations. The framework supplies classes to define objects called simulation channels that encapsulate the algorithms that make up a simulation model. These may govern state-updating events at the individual level, perform global state changes, or trigger cell division. Simulation engines control the scheduling and execution of collections of simulation channels, while a simulation manager coordinates the engines according to one of two scheduling protocols. When the ensemble of cells being simulated reaches a specified maximum size, a procedure is introduced whereby random cells are ejected from the simulation and replaced by newborn cells to keep the sample population size constant but representative in composition. The framework permits recording of population snapshot data and/or cell lineage histories. Use of the framework is demonstrated through validation benchmarks and two case studies based on experiments from the literature.

As plastic pollution increases, top marine predators such as marine mammals are becoming increasingly susceptible to plastic particles and their additives. Plastic particles have been found in gastrointestinal tracts and scat of many marine mammals, and quantifying plastic pollution in those that are pelagic can provide insight into plastic pollution in mesopelagic ecosystems that are just beginning to be analyzed. Adapting well-developed laboratory techniques for microplastic (MP) isolation (i.e. density separation and chemical digestion), I isolated MPs from the scat of the deepest diving pinniped, the northern elephant seal (NES), and found that100% of scat samples (n=11) contained high counts of MPs compared to other pinnipeds. Further, as plastic particles move through the digestive tract and potentially translocate into the circulation, body cells may be exposed to these plastic particles. Nanoplastics (NPs;<1μm) have been shown to affect cell viability and redox homeostasis in fish and human cells, while the lipophilic additives bisphenol-a (BPA) and bisphenol-s (BPS) used in plastics production are known endocrine disruptors. However, the effects of plastics (NPs) and plastics additives (BPA and BPS) have not been well-studied in marine mammals. To assess the direct impacts of NPs on marine mammal cells, I exposed fibroblasts isolated from NES skin (n=6 experiments) to polystyrene NPs of two different sizes (0.05μm and 0.5μm) and concentrations (3.64x109 and 3.64x1010 particles/mL) and did not find consistent effects on morphology and viability. Cell viability, which was quantified by an MTT assay, decreased as a result of NP exposure in two experimental replicates, but these results were not reproducible. I found that NPs did not have consistent effects on the morphology or viability of NES fibroblasts, regardless of their size or concentration. Lastly, I examined the effects of plastic additives on the physiology of marine mammal blubber tissue, the primary energy depot and reservoir of lipophilic pollutants. Precision-cut NES blubber slices were exposed to BPA and BPS, alone and in combination with the lipolytic hormone epinephrine, and I assessed their effects on the blubber transcriptome. I found that while BPA and BPS treatments alone did not have a pronounced effect on gene expression, they altered the expression of several genes associated with lipid homeostasis and adipogenesis. These data suggest that NES likely ingest MPs and maybe physiologically affected by exposure to plastic particles and their associated contaminants.

Indiana University-Purdue University Indianapolis (IUPUI) / Articular cartilage is subjected to dynamic mechanical loading during normal daily activities. This complex mechanical loading, including cell deformation and interstitial fluid flow, affects chondrocyte mechano-chemical signaling and subsequent cartilage homeostasis and remodeling. Focal adhesion kinase (FAK) and Src are known to be main mechanotransduction proteins, but little is known about the effect of mechanical loading on FAK and Src under its varying magnitudes and types. In this study, we addressed two questions using C28/I2 chondrocytes subjected to the different types and magnitudes of mechanical loading: Does a magnitude of the mechanical loading affect activities of FAK and Src? Does a type of the mechanical loading also affect their activities? Using fluorescence resonance energy transfer (FRET)-based FAK and Src biosensor in live C28/I2 chondrocytes, we monitored the effects of interstitial fluid flow and combined effects of cell deformation/interstitial fluid flow on FAK and Src activities. The results revealed that both FAK and Src activities in C28/I2 chondrocytes were dependent on the different magnitudes of the applied fluid flow. On the other hand, the type of mechanical loading differently affected FAK and Src activities. Although FAK and Src displayed similar activities in response to interstitial fluid flow only, simultaneous application of cell deformation and interstitial fluid flow induced differential FAK and Src activities possibly due to the additive effects of cell deformation and interstitial fluid flow on Src, but not on FAK. Collectively, the data suggest that the intensities and types of mechanical loading are critical in regulating FAK and Src activities in chondrocytes.

Dendritic spines are fundamental units of information processing within the nervous system, responsible for independent modulation of synaptic input to neurons. Filopodia, often morphologically indistinguishable from spines, are involved in formation of synapses during neuronal development. Despite the importance of these structures for neuronal function, no detailed study of their presence on motoneurons has yet been made. Here, the presence of spines on hypoglossal motoneurons (HMs) is described at three developmental stages: at P0–2 and P9–11, spines are present at an average density of ~0.1 spines/micron, but at P19 spine density becomes negligible. In P0–2 and P9–11, spines are nonuniformly distributed, occuring in clusters, and at lower density in the most proximal and distal regions to the soma than at intermediate regions. HM spines coincide with a decrease in cell input resistance, which reduces excitability during development. Thus one may speculate that these spines are involved in the formation of new synapses required to maintain adequate excitatory drive. A major difficulty for the study of spines is their small size, which complicates measurement using optical methods. Here, I present a novel method for reconstructing spine morphology using geometric models based on a priori knowledge of spine structure. Tests of the technique using simulated data indicate that it has a resolving capability of up to 40 nm (limited by noise). The technique has been used to measure dendritic spines on HMs, showing that these structures have necks as small as 0.22 micron. For purely passive modulation of synaptic strength, spine necks need to be <~ 0.15 micron. These data suggest that if modulation of synaptic input occurs, biochemical and/or active electrical processes are needed. The methods developed in this Thesis, which have here been applied to HMs, are generally applicable to the study of spine morphology, and its effect on synaptic processing, in all classes of neurons.

During mitosis, adherent animal cells undergo a drastic shape change, from essentially flat to round, in a process known as mitotic cell rounding (MCR). The aim of this thesis was to critically examine the physical and biological basis of MCR. The experimental part of this thesis employed a combined optical microscope-atomic force microscope (AFM) setup in conjunction with flat tipless cantilevers to analyze cell mechanics, shape and volume. To this end, two AFM assays were developed: the constant force assay (CFA), which applies constant force to cells and measures the resultant height, and the constant height assay (CHA), which confines cell height and measures the resultant force. These assays were deployed to analyze the shape and mechanical properties of single cells trans-mitosis. The CFA results showed that cells progressing through mitosis could increase their height against forces as high as 50 nN, and that higher forces can delay mitosis in HeLa cells. The CHA results showed that mitotic cells confined to ~50% of their normal height can generate forces around 50-100 nN without disturbing mitotic progression. Such forces represent intracellular pressures of at least 200 Pascals and cell surface tensions of around 10 nN/µm. Using the CHA to compare mitotic cell rounding with induced cell rounding, it was observed that the intracellular pressure of mitotic cells is at least 3-fold higher than rounded interphase cells. To investigate the molecular basis of the mechanical changes inherent in mitotic cell rounding, inhibitors and toxins were used to pharmacologically dissect the role of candidate cellular processes. These results implicated the actomyosin cortex and osmolyte transporters, the most prominent of which is the Na+/H+ exchanger, in the maintenance of mechanical properties and intracellular hydrostatic pressure. Observations on blebbing cells under the cantilever supported the idea that the actomyosin cortex is required to sustain hydrostatic pressure and direct this pressure into cell shape changes. To gain further insight into the relationship between actomyosin activity and intracellular pressure, dynamic perturbation experiments were conducted. To this end, the CHA was used to evaluate the pressure and volume of mitotic cells before, during and after dynamic perturbations that included tonic shocks, influx of specific inhibitors, and exposure to pore-forming toxins. When osmotic pressure gradients were depleted, pressure and volume decreased. When the actomyosin cytoskeleton was abolished, cell volume increased while rounding pressure decreased. Conversely, stimulation of actomyosin cortex contraction triggered an increase in rounding pressure and a decrease in volume. Taken together, the dynamic perturbation results demonstrated that the actomyosin cortex contracts against an opposing intracellular pressure and that this relationship sets the surface tension, pressure and volume of the cell. The discussion section of this thesis provides a comprehensive overview of the physical basis of MCR by amalgamating the experimental results of this thesis with the literature. Additionally, the biochemal signaling pathways and proteins that drive MCR are collated and discussed. An exhaustive and unprecedented synthesis of the literature on cell rounding (approx. 750 papers as pubmed search hits on “cell rounding”, April 2012) reveals that the spread-to-round transition can be thought of in terms of a surface tension versus adhesion paradigm, and that cell rounding can be physically classified into four main modes, of which one is an MCR-like category characterized by increased actomyosin cortex tension and diminution of focal adhesions. The biochemical pathways and signaling patterns that correspond with these four rounding modes are catalogued and expounded upon in the context of the relevant physiology. This analysis reveals cell rounding as a pertinent topic that can be leveraged to yield insight into core principles of cell biophysics and tissue organization. It furthermore highlights MCR as a model problem to understand the adhesion versus cell surface tension paradigm in cells and its fundamentality to cell shape, mechanics and physiology.

Dendritic spines are fundamental units of information processing within the nervous system, responsible for independent modulation of synaptic input to neurons. Filopodia, often morphologically indistinguishable from spines, are involved in formation of synapses during neuronal development. Despite the importance of these structures for neuronal function, no detailed study of their presence on motoneurons has yet been made. Here, the presence of spines on hypoglossal motoneurons (HMs) is described at three developmental stages: at P0–2 and P9–11, spines are present at an average density of ~0.1 spines/micron, but at P19 spine density becomes negligible. In P0–2 and P9–11, spines are nonuniformly distributed, occuring in clusters, and at lower density in the most proximal and distal regions to the soma than at intermediate regions. HM spines coincide with a decrease in cell input resistance, which reduces excitability during development. Thus one may speculate that these spines are involved in the formation of new synapses required to maintain adequate excitatory drive. A major difficulty for the study of spines is their small size, which complicates measurement using optical methods. Here, I present a novel method for reconstructing spine morphology using geometric models based on a priori knowledge of spine structure. Tests of the technique using simulated data indicate that it has a resolving capability of up to 40 nm (limited by noise). The technique has been used to measure dendritic spines on HMs, showing that these structures have necks as small as 0.22 micron. For purely passive modulation of synaptic strength, spine necks need to be <~ 0.15 micron. These data suggest that if modulation of synaptic input occurs, biochemical and/or active electrical processes are needed. The methods developed in this Thesis, which have here been applied to HMs, are generally applicable to the study of spine morphology, and its effect on synaptic processing, in all classes of neurons.

Dendritic spines are fundamental units of information processing within the nervous system, responsible for independent modulation of synaptic input to neurons. Filopodia, often morphologically indistinguishable from spines, are involved in formation of synapses during neuronal development. Despite the importance of these structures for neuronal function, no detailed study of their presence on motoneurons has yet been made. Here, the presence of spines on hypoglossal motoneurons (HMs) is described at three developmental stages: at P0–2 and P9–11, spines are present at an average density of ~0.1 spines/micron, but at P19 spine density becomes negligible. In P0–2 and P9–11, spines are nonuniformly distributed, occuring in clusters, and at lower density in the most proximal and distal regions to the soma than at intermediate regions. HM spines coincide with a decrease in cell input resistance, which reduces excitability during development. Thus one may speculate that these spines are involved in the formation of new synapses required to maintain adequate excitatory drive. A major difficulty for the study of spines is their small size, which complicates measurement using optical methods. Here, I present a novel method for reconstructing spine morphology using geometric models based on a priori knowledge of spine structure. Tests of the technique using simulated data indicate that it has a resolving capability of up to 40 nm (limited by noise). The technique has been used to measure dendritic spines on HMs, showing that these structures have necks as small as 0.22 micron. For purely passive modulation of synaptic strength, spine necks need to be <~ 0.15 micron. These data suggest that if modulation of synaptic input occurs, biochemical and/or active electrical processes are needed. The methods developed in this Thesis, which have here been applied to HMs, are generally applicable to the study of spine morphology, and its effect on synaptic processing, in all classes of neurons.

Dendritic spines are fundamental units of information processing within the nervous system, responsible for independent modulation of synaptic input to neurons. Filopodia, often morphologically indistinguishable from spines, are involved in formation of synapses during neuronal development. Despite the importance of these structures for neuronal function, no detailed study of their presence on motoneurons has yet been made. Here, the presence of spines on hypoglossal motoneurons (HMs) is described at three developmental stages: at P0–2 and P9–11, spines are present at an average density of ~0.1 spines/micron, but at P19 spine density becomes negligible. In P0–2 and P9–11, spines are nonuniformly distributed, occuring in clusters, and at lower density in the most proximal and distal regions to the soma than at intermediate regions. HM spines coincide with a decrease in cell input resistance, which reduces excitability during development. Thus one may speculate that these spines are involved in the formation of new synapses required to maintain adequate excitatory drive. A major difficulty for the study of spines is their small size, which complicates measurement using optical methods. Here, I present a novel method for reconstructing spine morphology using geometric models based on a priori knowledge of spine structure. Tests of the technique using simulated data indicate that it has a resolving capability of up to 40 nm (limited by noise). The technique has been used to measure dendritic spines on HMs, showing that these structures have necks as small as 0.22 micron. For purely passive modulation of synaptic strength, spine necks need to be <~ 0.15 micron. These data suggest that if modulation of synaptic input occurs, biochemical and/or active electrical processes are needed. The methods developed in this Thesis, which have here been applied to HMs, are generally applicable to the study of spine morphology, and its effect on synaptic processing, in all classes of neurons.

During mitosis, adherent animal cells undergo a drastic shape change, from essentially flat to round, in a process known as mitotic cell rounding (MCR). The aim of this thesis was to critically examine the physical and biological basis of MCR. The experimental part of this thesis employed a combined optical microscope-atomic force microscope (AFM) setup in conjunction with flat tipless cantilevers to analyze cell mechanics, shape and volume. To this end, two AFM assays were developed: the constant force assay (CFA), which applies constant force to cells and measures the resultant height, and the constant height assay (CHA), which confines cell height and measures the resultant force. These assays were deployed to analyze the shape and mechanical properties of single cells trans-mitosis. The CFA results showed that cells progressing through mitosis could increase their height against forces as high as 50 nN, and that higher forces can delay mitosis in HeLa cells. The CHA results showed that mitotic cells confined to ~50% of their normal height can generate forces around 50-100 nN without disturbing mitotic progression. Such forces represent intracellular pressures of at least 200 Pascals and cell surface tensions of around 10 nN/µm. Using the CHA to compare mitotic cell rounding with induced cell rounding, it was observed that the intracellular pressure of mitotic cells is at least 3-fold higher than rounded interphase cells. To investigate the molecular basis of the mechanical changes inherent in mitotic cell rounding, inhibitors and toxins were used to pharmacologically dissect the role of candidate cellular processes. These results implicated the actomyosin cortex and osmolyte transporters, the most prominent of which is the Na+/H+ exchanger, in the maintenance of mechanical properties and intracellular hydrostatic pressure. Observations on blebbing cells under the cantilever supported the idea that the actomyosin cortex is required to sustain hydrostatic pressure and direct this pressure into cell shape changes. To gain further insight into the relationship between actomyosin activity and intracellular pressure, dynamic perturbation experiments were conducted. To this end, the CHA was used to evaluate the pressure and volume of mitotic cells before, during and after dynamic perturbations that included tonic shocks, influx of specific inhibitors, and exposure to pore-forming toxins. When osmotic pressure gradients were depleted, pressure and volume decreased. When the actomyosin cytoskeleton was abolished, cell volume increased while rounding pressure decreased. Conversely, stimulation of actomyosin cortex contraction triggered an increase in rounding pressure and a decrease in volume. Taken together, the dynamic perturbation results demonstrated that the actomyosin cortex contracts against an opposing intracellular pressure and that this relationship sets the surface tension, pressure and volume of the cell. The discussion section of this thesis provides a comprehensive overview of the physical basis of MCR by amalgamating the experimental results of this thesis with the literature. Additionally, the biochemal signaling pathways and proteins that drive MCR are collated and discussed. An exhaustive and unprecedented synthesis of the literature on cell rounding (approx. 750 papers as pubmed search hits on “cell rounding”, April 2012) reveals that the spread-to-round transition can be thought of in terms of a surface tension versus adhesion paradigm, and that cell rounding can be physically classified into four main modes, of which one is an MCR-like category characterized by increased actomyosin cortex tension and diminution of focal adhesions. The biochemical pathways and signaling patterns that correspond with these four rounding modes are catalogued and expounded upon in the context of the relevant physiology. This analysis reveals cell rounding as a pertinent topic that can be leveraged to yield insight into core principles of cell biophysics and tissue organization. It furthermore highlights MCR as a model problem to understand the adhesion versus cell surface tension paradigm in cells and its fundamentality to cell shape, mechanics and physiology.

Indiana University-Purdue University Indianapolis (IUPUI) / Endothelial Colony Forming Cells (ECFCs) are highly proliferative endothelial progenitor cells with clonal proliferative potential and in vivo vessel forming ability. While endothelial cells have been derived from human induced pluripotent stem cells (hiPS) or human embryonic stem cells (hES), they are not highly proliferative and require ectopic expression of a TGFβ inhibitor to restrict plasticity. Neuropilin-1 (NRP-1) has been reported to identify the emergence of endothelial precursor cells from human and mouse ES cells undergoing endothelial differentiation. However, the protocol used in that study was not well defined, used uncharacterized neuronal induction reagents in the culture medium, and failed to fully characterize the endothelial cells derived. We hypothesize that NRP-1 expression is critical for the emergence of stable endothelial cells with ECFC properties from hES cells. We developed a novel serum and feeder free defined endothelial differentiation protocol to induce stable endothelial cells possessing cells with cord blood ECFC-like properties from hES cells. We have shown that Day 12 hES cell-derived endothelial cells express the endothelial markers CD31+ NRP-1+, exhibit high proliferative potential at a single cell level, and display robust in vivo vessel forming ability similar to that of cord blood-derived ECFCs. The efficient production of the ECFCs from hES cells is 6 logs higher with this protocol than any previously published method. These results demonstrate progress towards differentiating ECFC from hES and may provide patients with stable autologous cells capable of repairing injured, dysfunctional, or senescent vasculature if these findings can be repeated with hiPS.