Structure, Dynamics, and Regulation of Collective Cell Migration

Collective migration is the process by which cells organize individual motions to productively migrate as a group and plays a fundamental role in organism development, tissue regeneration, and cancer invasion. In development, coordinated migration facilitates the formation of complex organ structures and is required for proper dissemination of neural crest cells throughout an organism. After injury, this process allows breaches in epithelial layers to be repaired while maintaining tissue integrity, and in cancer, collective behavior enhances invasion of tumor cells into the surrounding tissue. Chapter 1 provides an introduction for the role of collective migration across an organism’s lifespan, the mechanisms used by cells to generate motile force, and the emergence of collective behavior. Chapter 2 dissects the intertwined roles of three fundamental parameters often altered in collective migration processes: cell density, cell adhesion, and cell-cell contractility through the Rho-ROCK-Myosin II signaling axis. Through quantitative analysis of large-scale time-lapse imaging and mathematical modeling, I identify force-sensitive contractility and cell packing as mediators of two distinct classes of collective migration. From these results, I formulate a phase-diagram of collective cell migration and test predictions in an in-vivo epithelium using genetic manipulations to drive collective motion between predicted migratory phases. In Chapter 3, the effect of phenotypic heterogeneity on the organization of cells is examined, providing insight into the effects of early cancer progression on epithelial dynamics. I find that mutant cells within an otherwise wild-type tissue impact organization through local and field-effects, disrupting normal dynamics and leading to cell-type segregation. Chapter 4 provides a theoretical framework for quantitatively understanding and predicting the dynamics of protein interactions underlying biological processes including collective migration. Traditional chemical kinetics approaches break down in situations where components are slow diffusing or in countable numbers, requiring the formulation of new models that take into account this level of complexity. Here I develop an event-driven algorithm that bridges well-mixed and unmixed systems and use it to predict the effect of apparent changes in enzymatic efficiency due to alterations in mobility that may be caused by protein complex formation. Overall the work in this dissertation advances our understanding of the structure and dynamics of collective migration and the parameters governing this process by combining quantitative statistical analysis, mathematical modeling, and in-vivo live imaging

Light-sheet microscopy: a tutorial

This paper is intended to give a comprehensive review of light-sheet (LS) microscopy from an optics perspective. As such, emphasis is placed on the advantages that LS microscope configurations present, given the degree of freedom gained by uncoupling the excitation and detection arms. The new imaging properties are first highlighted in terms of optical parameters and how these have enabled several biomedical applications. Then, the basics are presented for understanding how a LS microscope works. This is followed by a presentation of a tutorial for LS microscope designs, each working at different resolutions and for different applications. Then, based on a numerical Fourier analysis and given the multiple possibilities for generating the LS in the microscope (using Gaussian, Bessel, and Airy beams in the linear and nonlinear regimes), a systematic comparison of their optical performance is presented. Finally, based on advances in optics and photonics, the novel optical implementations possible in a LS microscope are highlighted.Peer ReviewedPostprint (published version

SWD\u27s in Higher Education

My research paper consists of researching the experiences of students with disabilities in higher education as well as the history of disabilities acts, what has changed for SWD\u27s in higher education and how we can make more accommodations for higher education. Furthermore, I will be discussing the stigma behind disability as well as include research about accommodation strategies and how accommodations have improved in recent years. The research paper will also entail how online learning during the COVID pandemic has affected students with disabilities in higher education and how inequity as well as the lack of face to face interaction has hindered students with disabilities during the pandemic. This would also explain the difference university/college size has on the individual. I decided to also include my story as a student with a hidden disability. My educational story would entail the extra hard work and resilience I had to display only went to showcase that most student\u27s with disabilities, hidden or not, have to work two to three times as hard as the typical student. My abstract conveys how SWD\u27s pursuing higher education should and would benefit from accommodations.Finally, my research is to apply how we must prioritize SWD\u27s needs, find new ways to innovate our college curriculum, and provide the necessary counseling for those students as they are considered high risk of dropping out. This research paper is also to demonstrate how with the right guidance and installment of transformative leadership for all educators helping their students in need

Chemical aging of m-xylene secondary organic aerosol: laboratory chamber study

Secondary organic aerosol (SOA) can reside in the atmosphere for a week or more. While its initial formation from the gas-phase oxidation of volatile organic compounds tends to take place in the first few hours after emission, SOA can continue to evolve chemically over its atmospheric lifetime. Simulating this chemical aging over an extended time in the laboratory has proven to be challenging. We present here a procedure for studying SOA aging in laboratory chambers that is applied to achieve 36 h of oxidation. The formation and evolution of SOA from the photooxidation of m-xylene under low-NO_x conditions and in the presence of either neutral or acidic seed particles is studied. In SOA aging, increasing molecular functionalization leads to less volatile products and an increase in SOA mass, whereas gas- or particle-phase fragmentation chemistry results in more volatile products and a loss of SOA. The challenge is to discern from measured chamber variables the extent to which these processes are important for a given SOA system. In the experiments conducted, m-xylene SOA mass, calculated under the assumption of size-invariant particle composition, increased over the initial 12–13 h of photooxidation and decreased beyond that time, suggesting the existence of fragmentation chemistry. The oxidation of the SOA, as manifested in the O:C elemental ratio and fraction of organic ion detected at m/z 44 measured by the Aerodyne aerosol mass spectrometer, increased continuously starting after 5 h of irradiation until the 36 h termination. This behavior is consistent with an initial period in which, as the mass of SOA increases, products of higher volatility partition to the aerosol phase, followed by an aging period in which gas- and particle-phase reaction products become increasingly more oxidized. When irradiation is stopped 12.4 h into one experiment, and OH generation ceases, minimal loss of SOA is observed, indicating that the loss of SOA is either light- or OH-induced. Chemical ionization mass spectrometry measurements of low-volatility m-xylene oxidation products exhibit behavior indicative of continuous photooxidation chemistry. A condensed chemical mechanism of m-xylene oxidation under low-NO_x conditions is capable of reproducing the general behavior of gas-phase evolution observed here. Moreover, order of magnitude analysis of the mechanism suggests that gas-phase OH reaction of low volatility SOA precursors is the dominant pathway of aging in the m-xylene system although OH reaction with particle surfaces cannot be ruled out. Finally, the effect of size-dependent particle composition and size-dependent particle wall loss rates on different particle wall loss correction methods is discussed

Yields of oxidized volatile organic compounds during the OH radical initiated oxidation of isoprene, methyl vinyl ketone, and methacrolein under high-NO_x conditions

We present first-generation and total production yields of glyoxal, methylglyoxal, glycolaldehyde, and hydroxyacetone from the oxidation of isoprene, methyl vinyl ketone (MVK), and methacrolein (MACR) with OH under high NO_x conditions. Several of these first-generation yields are not included in commonly used chemical mechanisms, such as the Leeds Master Chemical Mechanism (MCM) v. 3.2. The first-generation yield of glyoxal from isoprene was determined to be 2.1 (±0.6)%. Inclusion of first-generation production of glyoxal, glycolaldehyde and hydroxyacetone from isoprene greatly improves performance of an MCM based model during the initial part of the experiments. In order to further improve performance of the MCM based model, higher generation glyoxal production was reduced by lowering the first-generation yield of glyoxal from C5 hydroxycarbonyls. The results suggest that glyoxal production from reaction of OH with isoprene under high NO_x conditions can be approximated by inclusion of a first-generation production term together with secondary production only via glycolaldehyde. Analogously, methylglyoxal production can be approximated by a first-generation production term from isoprene, and secondary production via MVK, MACR and hydroxyacetone. The first-generation yields reported here correspond to less than 5% of the total oxidized yield from isoprene and thus only have a small effect on the fate of isoprene. However, due to the abundance of isoprene, the combination of first-generation yields and reduced higher generation production of glyoxal from C5 hydroxycarbonyls is important for models that include the production of the small organic molecules from isoprene

Analysis of photochemical and dark glyoxal uptake: Implications for SOA formation

The dependence of glyoxal uptake onto deliquesced ammonium sulfate seed aerosol was studied under photochemical (light + hydroxyl radical (OH)) and dark conditions. In this study, the chemical composition of aerosol formed from glyoxal is identical in the presence or absence of OH. In addition, there was no observed OH dependence on either glyoxal uptake or glyoxal-driven aerosol growth for this study. These findings demonstrate that, for the system used here, glyoxal uptake is not affected by the presence of OH. In combination with previous studies, this shows that the exact nature of the type of seed aerosol, in particular the presence of a coating, has a large influence on fast photochemical uptake of glyoxal. Due to the challenge of relating this seed aerosol dependence to ambient conditions, this work highlights the resulting difficulty in quantitatively including SOA formation from glyoxal in models

α-pinene photooxidation under controlled chemical conditions – Part 2: SOA yield and composition in low- and high-NO_x environments

The gas-phase oxidation of α-pinene produces a large amount of secondary organic aerosol (SOA) in the atmosphere. A number of carboxylic acids, organosulfates and nitrooxy organosulfates associated with α-pinene have been found in field samples and some are used as tracers of α-pinene oxidation. α-pinene reacts readily with OH and O_3 in the atmosphere followed by reactions with both HO_2 and NO. Due to the large number of potential reaction pathways, it can be difficult to determine what conditions lead to SOA. To better understand the SOA yield and chemical composition from low- and high-NO_x OH oxidation of α-pinene, studies were conducted in the Caltech atmospheric chamber under controlled chemical conditions. Experiments used low O_3 concentrations to ensure that OH was the main oxidant and low α-pinene concentrations such that the peroxy radical (RO_2) reacted primarily with either HO_2 under low-NO_x conditions or NO under high-NO_x conditions. SOA yield was suppressed under conditions of high-NO_x. SOA yield under high-NO_x conditions was greater when ammonium sulfate/sulfuric acid seed particles (highly acidic) were present prior to the onset of growth than when ammonium sulfate seed particles (mildly acidic) were present; this dependence was not observed under low-NO_x conditions. When aerosol seed particles were introduced after OH oxidation, allowing for later generation species to be exposed to fresh inorganic seed particles, a number of low-NO_x products partitioned to the highly acidic aerosol. This indicates that the effect of seed acidity and SOA yield might be under-estimated in traditional experiments where aerosol seed particles are introduced prior to oxidation. We also identify the presence of a number of carboxylic acids that are used as tracer compounds of α-pinene oxidation in the field as well as the formation of organosulfates and nitrooxy organosulfates. A number of the carboxylic acids were observed under all conditions, however, pinic and pinonic acid were only observed under low-NO_x conditions. Evidence is provided for particle-phase sulfate esterification of multi-functional alcohols

Dynamics of biofilm re-growth in drinking water distributions systems

The majority of biomass within water distribution systems is in the form of attached biofilm. This is known to be central to drinking water quality degradation following treatment yet little understanding of the dynamics of these highly heterogeneous communities exists. This paper presents original information on such dynamics with findings demonstrating patterns of material accumulation, seasonality and influential factors. Rigorous flushing operations repeated over a one-year period on an operational, chlorinated system in the UK are presented. Intensive monitoring and sampling were undertaken including time series turbidity and detailed microbial analysis using 16S rRNA Illumina MiSeq sequencing. Results show bacterial dynamics were influenced by differences in the supplied water and by the material remaining attached to the pipe wall following flushing. Turbidity, metals and phosphate were the main factors correlated with the distribution of bacteria in the samples. Coupled with the lack of inhibition of biofilm development due to chlorine residual, this suggests that limiting inorganic nutrients, other than organic carbon, might be a viable component in treatment strategies to manage biofilms. The research also showed that repeat flushing exerted beneficial selective pressure, thus also a viable advantageous biofilm management option. This work advances our understanding of microbiological processes in drinking water distribution systems and helps inform strategies to optimise asset performance. IMPORTANCE: This research provides with novel information regarding dynamics of biofilm formation in real drinking water distribution systems made of different materials. This new knowledge on microbiological process in water supply systems can be used to optimise the performance of the distribution network and to guarantee safe and good quality drinking water to consumers

Role of aldehyde chemistry and NO_x concentrations in secondary organic aerosol formation

Aldehydes are an important class of products from atmospheric oxidation of hydrocarbons. Isoprene (2-methyl-1,3-butadiene), the most abundantly emitted atmospheric non-methane hydrocarbon, produces a significant amount of secondary organic aerosol (SOA) via methacrolein (a C_4-unsaturated aldehyde) under urban high-NO_x conditions. Previously, we have identified peroxy methacryloyl nitrate (MPAN) as the important intermediate to isoprene and methacrolein SOA in this NO_x regime. Here we show that as a result of this chemistry, NO_2 enhances SOA formation from methacrolein and two other α, β-unsaturated aldehydes, specifically acrolein and crotonaldehyde, a NO_x effect on SOA formation previously unrecognized. Oligoesters of dihydroxycarboxylic acids and hydroxynitrooxycarboxylic acids are observed to increase with increasing NO_2/NO ratio, and previous characterizations are confirmed by both online and offline high-resolution mass spectrometry techniques. Molecular structure also determines the amount of SOA formation, as the SOA mass yields are the highest for aldehydes that are α, β-unsaturated and contain an additional methyl group on the α-carbon. Aerosol formation from 2-methyl-3-buten-2-ol (MBO232) is insignificant, even under high-NO_2 conditions, as PAN (peroxy acyl nitrate, RC(O)OONO_2) formation is structurally unfavorable. At atmospherically relevant NO_2/NO ratios (3–8), the SOA yields from isoprene high-NO_x photooxidation are 3 times greater than previously measured at lower NO_2/NO ratios. At sufficiently high NO_2 concentrations, in systems of α, β-unsaturated aldehydes, SOA formation from subsequent oxidation of products from acyl peroxyl radicals+NO_2 can exceed that from RO_2+HO_2 reactions under the same inorganic seed conditions, making RO_2+NO_2 an important channel for SOA formation

Rho1 regulates adherens junction remodeling by promoting recycling endosome formation through activation of myosin II

Once adherens junctions (AJs) are formed between polarized epithelial cells they must be maintained because AJs are constantly remodeled in dynamic epithelia. AJ maintenance involves endocytosis and subsequent recycling of E-cadherin to a precise location along the basolateral membrane. In the Drosophila pupal eye epithelium, Rho1 GTPase regulates AJ remodeling through Drosophila E-cadherin (DE-cadherin) endocytosis by limiting Cdc42/Par6/aPKC complex activity. We demonstrate that Rho1 also influences AJ remodeling by regulating the formation of DE-cadherin–containing, Rab11-positive recycling endosomes in Drosophila postmitotic pupal eye epithelia. This effect of Rho1 is mediated through Rok-dependent, but not MLCK-dependent, stimulation of myosin II activity yet independent of its effects upon actin remodeling. Both Rho1 and pMLC localize on endosomal vesicles, suggesting that Rho1 might regulate the formation of recycling endosomes through localized myosin II activation. This work identifies spatially distinct functions for Rho1 in the regulation of DE-cadherin–containing vesicular trafficking during AJ remodeling in live epithelia