Advances in genetics and fluorescent protein chemistry have enabled us to fuse fluorescent probes directly to biomolecules in stably growing organisms; making it easier to image the precise position and movement of cells in three dimensions. Fluorescent stains and dyes can be employed in a similar fashion to visualize nano-scale fluctuations in active cellular structures without fixation. While informative and exciting on a qualitatively level, microscopy truly becomes powerful when we can extract meaningful quantitative information. To accomplish this, custom MATLAB (Mathworks, Natick, MA) image analysis algorithms were developed to specifically measure the biophysical parameters related to pathogenesis and function in microbes and mammalian cells. These parameters can then be exploited in the development of biophysical models to validate current measurements, and make critical predictions about the system's behavior, often addressing quantities inaccessible by experimental methods. The following research chapters of this dissertation thoroughly describe how these techniques were developed and applied to study the biophysical mechanisms of bacterial and cellular invasion.

This work revealed what is at the core of a particular group of prospective teachers that underlie their commitment to teach in under-resourced schools and districts. Prospective teachers committed to teaching in under-resourced schools have qualities or attributes of recognition and respect for students and families who come from low-income and culturally different backgrounds and experiences. These prospective teachers were able to recognize complex interactions that students and their families face at the individual, social and institutional level. They also sought ways to address their students' learning needs by drawing from students' experiences to make meaningful connections between home and school. To identify students' and families' lived experiences, cultural practices, and language as resources to draw from, are acts of recognition and respect towards students and their families who are, for many prospective teachers, different from themselves. Recognition and respect for difference are essential attributes that underlie a socially just and humanistic pedagogy which can positively impact the learning outcomes for students who are historically poorly served by our public schools. This work highlights a different view that prospective teachers from majority White European backgrounds have about social others. It also provides a new framework using social otherness as a lens to reveal prospective teachers' understandings and knowledge about students and families from low-income backgrounds.

Traditional undergraduate biology courses are content intensive, requiring students to understand and remember large amounts of information in short periods of time. Yet most students maintain little of the material encountered during their education. Poor knowledge retention is a main cause of academic failure and high undergraduate attrition rates. Characterizing strategies that support robust learning is critical for ensuring student success. One such strategy is testing effect, the observation that repeated testing can improve the fidelity and durability of retained knowledge more than an equal quantity of restudy. Numerous investigations have described the nature and boundaries of testing effect. Very few, however, have characterized its efficacy in actual classroom practice. The current study investigated whether repeated testing or repeated study affected student retention and understanding of complex biological concepts. The study was conducted in a large (~320 students) introductory biology class. All study conditions and assessments were required components of the course. Student retention of two fundamental molecular biology "big ideas" was targeted; (1) the relationship between genotype and phenotype, and (2) the relationship between gene expression and cell function. Students were randomly assigned to one of three repeated quiz or study conditions. For four weeks, students encountered various combinations of multiple-choice (MC) questions and review material related to big ideas 1&2 and/or unrelated lecture topics. Five weeks after the last quiz, all students completed identical MC final exam questions related to both big ideas. To determine the quality of "understanding" assessed by the MC questions, a subset of students also completed a short answer (SA) test prior to the final exam. Both question formats assessed the same knowledge (2 big ideas) at the same level (comprehension and application). Final exam performance supported the finding that repeated retrieval improves long-term retention of knowledge relative to repeated study. Novel to other previous work conducted at the undergraduate level, the current findings suggest that repeated testing affects student retention and understanding of sophisticated concepts. Careful design and analysis of parallel multiple-choice and short answer questions demonstrated that each can target and elicit similar qualities and types of knowledge.

This study investigated whether participation in the Partnership for Research and Education in Plants (PREP), a long-term authentic plant research project, in conjunction with explicit verses implicit instruction can change high school students' conceptions of the nature of science (NOS). The participants included a total of 134 students comprised of three groups from 10 total classes over the course of two academic years. Participants in four classes (two each year) participated in PREP and received explicit instruction on NOS. Participants in four other classes (two each year) participated in PREP and received implicit only instruction on NOS. Additionally, two classes (one each year) of high-achieving freshmen participated in PREP and received explicit instruction on NOS. This third group was used as a comparative group to the other two groups, due to their high achievement in middle school math and science. The treatment for all three groups spanned 8 weeks and included participation in an authentic plant research project. An open-ended questionnaire (modified Views of Nature of Science - VNOS), in conjunction with semi-structured interviews, was used to assess students' conceptions before and after the intervention. Results showed that all three groups improved their conceptions of NOS equally. The high-achieving group began with significantly higher-scoring views prior to the completion of the intervention, and improved to the same degree as the other two groups. A comparison of the explicit group to the implicit only group showed that there was no significant difference in their improvement, as both groups improved equally. Implications for the teaching and learning of NOS are discussed.

Receptor-like kinases (RLKs) make up one of the largest gene families in Arabidopsis thaliana. These genes are required for various biological processes, including response to biotic stress, cell elongation, cell proliferation, and cell fate patterning. An emerging theme in Arabidopsis and other plants is that networks of RLKs are required to regulate a specific process throughout development involving spatial and temporal regulation of transcription factors. However, there are still many RLKs (>50%) with no known function.Several RLKs regulate epidermal development by contributing to early embryonic epidermal maintenance or to epidermal differentiation. In my first analysis, I characterize the role of two related RLKs GASSHO1 (GSO1) and GSO2 in epidermal differentiation. gso1 gso2 double mutants initially form an epidermis during embryogenesis, but analysis of post-embryonic root development indicates the mis-expression of epidermal-specific genes. Three previously characterized RLKs that are involved in epidermal development are also involved in meristem maintenance. In order to decipher the RLK gene networks controlling epidermal development and meristem maintenance, it is necessary to identify additional RLKs involved in both of these processes. I further identified roles for GSO1 and GSO2 in maintaining root growth and root apical meristem (RAM) activity. A future goal will be to elucidate the networks of RLKs, including GSO1 and GSO2 in regulating epidermal and RAM development.The development of the vasculature in plants is controlled by a vascular meristem, the procambium. Oriented cell divisions from the procambium produce phloem, to the periphery, and xylem, to the center of the plant. In a reverse genetic screen to determine to roles of the remaining RLKs with unknown function, we identified the RLK XYLEM INTERMIXED WITH PHLOEM1 (XIP1) that is required for vascular development. We show XIP1 is required for regulating the differentiation of the phloem and for the organization of xylem vessel elements. Our analysis indicates that XIP1 is part of a vascular meristem network, further emphasizing the importance of social networks of RLKs regulating a specific process in development.

The phylo-geography and population genetics of three Crotalus species in Southern Arizona (C. atrox, C. cerastes, and C. scutulatus) were examined using mitochondrial DNA genes and nuclear microsatellite DNA markers. My focus was twofold: (1) the phylo-geography and population structure in Southern Arizona and (2) possible genetic signatures of population fragmentation by linear barriers on rattlesnakes populations at Picacho Peak. My results show genetic signatures of geneflow restrictions in one species (C. atrox) which coincide with Interstate 10. I did not observe similar genetic effects in C. cerastes or scutulatus, possibly caused by smaller sample sizes and marker numbers. I found limited phylo-geographic and population genetic structure for all three species in Southern Arizona indicating large interconnected populations. This study provides wildlife management with a powerful genetic toolset and provides important baseline data for future assessment and monitoring efforts of important predators and their populations in the Sonoran desert habitat.

An early event in animal development is the formation of the three primary germ layers that define the body plan. During gastrulation, cells migrate through the primitive streak of the embryo and undergo changes in morphology and gene expression, thus creating the mesodermal and endodermal cell layers. Gastrulation requires expression of Fibroblast Growth Factor (FGF), Wnt, and Platelet-Derived Growth Factor (PDGF). Embryos treated with FGF inhibitors fail to gastrulate, as cell migration is completely halted. During gastrulation, 44 microRNAs are expressed in the primitive streak of G. gallus embryos, and six (microRNAs -let7b, -9, -19b, -107, -130b, and -218) are strongly upregulated when FGF signaling is blocked. The abundance of these six FGF-regulated microRNAs is controlled at various stages of processing: most are regulated transcriptionally, and three of them (let7b, 9, and 130b) are blocked by the presence of Lin28B, an RNA-binding protein upregulated by FGF signaling. These microRNAs target various serine/threonine and tyrosine kinase receptors. We propose a novel pathway by which FGF signaling downregulates several key microRNAs (partially through Lin28B), upregulating gene targets such as PDGFRA, which permits and directs cell migration during gastrulation. These findings add new layers of complexity to the role that FGF signaling plays during embryogenesis. FGF signaling is also required for the formation of the heartfields, and has an overlapping pattern of expression with BMP (Bone Morphogenetic Protein). A microarray experiment using inhibitors of FGF and BMP found that thousands of genes in pre-cardiac mesoderm are affected by FGF signaling, BMP signaling, or a cooperative effect of the two. The promoter regions of similarly regulated genes were queried for over-represented transcription factor binding sites or novel DNA motifs. Cluster analysis of over-represented sites determined candidate transcriptional modules that were tested in primary cardiac myocyte and fibroblast cultures. About 75% of predicted modules in FGF-upregulated genes proved to be functional enhancers or repressors. Functional enhancers among FGF-upregulated genes contained clusters of CdxA and NFY sites, and increased transcription in the presence of a constitutively active FGF receptor.

Cell polarity is an important regulator of cellular processes and is vital in helping to prevent metaplasia and tumorigenesis. There are three many polarity complexes that regulate and maintain epithelial cellular polarity. The Par and Crumbs complexes locate to the apical membrane of the cell, while the Scribble complex is located basolaterally. Of the Scribble complex components, the polarity protein Hugl1, also known as Mgl1 in mice, is especially important in helping to maintain apical basolateral and planar polarity, and is lost in multiple types of cancer. When Hugl1 expression is lost in epithelial cells, it results in a mesenchymal phenotype. We now show that the loss of Hugl1 fundamentally shifts the cellular phenotype and specifically alters EGFR trafficking and signaling. Loss of Hugl1 results in the nuclear translocation of Taz and Slug, increased migration, and the mislocalization of EGFR (Epidermal Growth Factor Receptor), driving cellular growth. Hugl1 regulates the expression of multiple cell identity markers and its loss results in stem cell characteristics, including the increased expression of CD44, and a decrease of CD49f and CD24 expression. The loss of Hugl1 also results in increased growth in soft-agar and prolonged survival when transplanted into NOD-SCID mice; its loss also results in EGF-dependent migration which aids in increasing mammosphere survival. Furthermore, isolated EGFR mislocalization via a point mutation (P667A) also drives these same phenotypes, including activation of Akt and Taz nuclear translocation, indicating the importance of Hugl1 in the regulation of EGFR localization and its signaling. In mice, the loss of total Mgl1 is lethal within days of birth due to hydrocephaly and results in the formation of rosette like structures in the brain that are reminiscent of neuroectodermal tumors. We designed a targeted Mgl1 knockout in the mammary epithelial cells using the Cre/Lox system to evaluate the effects of Mgl1 loss in murine mammary gland development and tumorigenesis. The loss of Mgl1 expression in mice inhibits ductal outgrowth, increases side branching and epithelial layers, and results in the mislocalization of EGFR. While overt mammary tumors did not develop, some individuals did develop hyperplastic nodules that could progress into cancer. The knockdown of Hugl1 in vitro and Mgl1 in vivo reveal how the loss of polarity and presence of Hugl1 results in cancer stem cell characteristics, increased migration, and abnormal signaling due to the mislocalization of EGFR. While these changes result in metaplasia and a potential pre-cancerous state, the loss of Hugl1 alone is not enough to drive the cancer progression, indicating that other mutations or factors are necessary for the development of breast cancer. Because of the key role polarity plays in the prevention of breast cancer development we investigated if the addition of Hugl1 back into breast cancer cells could revert the cancerous cells to a normal epithelial phenotype. Most of the breast cancer cells transfected with Hugl1 expression did not survive, indicating that the re-expression of polarity regulators forces cancer cells to die. The small percentage of cells that did survive re-expression of Hugl1 had retarded growth in soft agar and a decrease in EGFR expression. Together, these data indicate that Hugl1 expression and EGFR activity are closely related and that Hugl1 is required for the proper localization and signaling of EGFR. When Hugl1 is lost, EGFR is mislocalized and fails to be degraded properly, promoting pre-neoplastic changes.

Recent research effort (measured in number of publications) on genes is biased towards genes that have been studied heavily in the past. Some factors for why this occurs is that many of these historically studied genes are important for survival or there are more tools available that make genetic studies of them much more accessible. Studies of research effort on \textit{Saccharomyces cerevisiae} genes characterized with genetic or protein interactions found that there is an aversion to studying lesser-known genes in networks. As well, in a study of three human protein families, many of the genes that have recently been discovered to have association with complex disease, through methods such as genome wide association studies (GWAS), are understudied in the present compared to the small number of historically heavily studied genes. In this study we explore possible causes of and diversion from this preferential bias with gene conservation and human genes being disease-associated. We find there is some evidence of conservation driving biases in research effort for essential genes in \textit{Saccharomyces cerevisiae}, but inconclusive evidence in other organisms. We look for effects of disease association through Mendelian and complex diseases in a historical, pre-GWAS, and contemporary, post-GWAS, context. Within both contexts we find that Mendelian disease genes may drive preferential study bias. For contemporary research effort we utilize a model of publication rates and find that there are individual GWAS genes that tend to be investigated more than predicted compared to non-GWAS genes. It appears that the proportion of GWAS genes that had highly unexpected increases in publication rate compared to model predictions rose fairly quickly but has been declining. Our analysis suggests that GWAS has had a small impact on what genes some scientists study despite preferential study biases. However GWAS gene-disease association's impact on research effort appears to be declining, possibly due to scientists not being as interested in GWAS results as time goes on.

A recurring theme in biology is the aggregation of mRNA-protein complexes (mRNPs) into higher order assemblies. Often these complexes play important roles in the regulation of gene expression, but the function of the conserved cytoplasmic mRNP assemblies - P bodies and stress granules, is not known. It is believed that the misregulation of granule assembly is related to disorders like Amyotrophic Lateral Sclerosis and Frontotemporal Lobe Degeneration. Determining the complete composition of these granules may hold the key to understanding the function and mechanism of assembly of these granules. This work describes multiple approaches taken to identify new protein and mRNA components of P bodies and stress granules. New members of the P body and stress granule proteome reveal a role for these granules in diverse cellular processes including signal transduction, transcription and metabolism. Additionally, a new stress granule resident complex - the CCT complex, was also identified as a novel regulator of granule disassembly. This work also describes the first purification scheme for stress granules and presents a new system for in vitro study of stress granules. Together, the findings shed new light on the composition, function, structure and regulation of P bodies and stress granules in yeast.