Browsing by Department "Cell Biology"

As vertebrate embryos grow and develop into adults, their organs must acquire mass and mature tissue architecture to maintain proper homeostasis. While juvenile growth encompasses a significant portion of life, relatively little is known about how individual cells proliferate, with respect to one another, to orchestrate this final maturation. For its simplicity and ease of genetic manipulations, the teleost zebrafish (Danio rerio) was used to understand how the proliferative outputs of individual cells generate an organ from embryogenesis into adulthood.

To define the proliferative outputs of individual cells, a multicolor clonal labeling approach was taken that visualized a large number of cardiomyocyte clones within the zebrafish heart. This Brainbow technique utilizes Cre-loxP mediated recombination to assign cells upwards of ~90 unique genetic tags. These tags are comprised of the differential expression of 3 fluorescent proteins, which combine to give rise to spectrally distinct colors that represent these genetic tags. Tagging of individual cardiomyocytes was induced early in development, when the wall of the cardiac ventricle is a single myocyte thick. Single cell cardiomyocyte clones within this layer expanded laterally in a developmentally plastic manner into patches of variable shapes and sizes as animals grew into juveniles. As maturation continued into adulthood, a new lineage of cortical muscle appeared at the base of the ventricle and enveloped the ventricle in a wave of proliferation that fortified the wall to make it several myocytes thick. This outer cortical layer was formed from a small number (~8) of dominant cortical myocyte clones that originated from trabecular myocytes. These trabecular myocytes were found to gain access to the ventricular surface through rare breaches within the single cell thick ventricular wall, before proliferating over the surface of the ventricle.

These results demonstrated an unappreciated dynamic juvenile remodeling event that generated the adult ventricular wall. During adult zebrafish heart regeneration, the primary source of regenerating cardiomyocytes stems from this outer wall of muscle. Regenerating cardiomyocytes within this outer layer of muscle are specifically marked by the cardiac transcription factor gene gata4, which they continue to express as they proliferate into the wound area.

Using heart regeneration to guide investigation of juvenile cortical layer formation, we found that both processes shared similar molecular and tissue specific responses including expression and requirement of gata4. Additional markers suggested that juvenile hearts were under stress and that this stress could play a role to initiate cortical morphogenesis. Indeed, experimental injury or a physiologic increase in stress to juvenile hearts caused the ectopic appearance of cortical muscle, demonstrating that injury could trigger premature morphogenesis.

These studies detail the cardiomyocyte proliferative events that shape the heart and identify molecular parallels that exist between regeneration and cortical layer formation. They show that adult zebrafish heart regeneration utilizes an injury/stress responsive program that was first used to remodel the heart during juvenile growth.

The tubulin homolog FtsZ provides the cytoskeletal framework for bacterial cell division. FtsZ is an essential protein for bacterial cell division, and is the only protein necessary for Z-ring assembly and constriction force generation in liposomes in vitro. The work presented here utilizes structural and genomic analysis methods to investigate FtsZ function for cell division with three separate questions: (1) What is the function of the C-terminal linker peptide in FtsZ? (2) Are there interacting proteins other than those of the divisome that facilitate FtsZ function? (3) Do lateral contact sites exist between protofilaments in the Z ring, resulting in an organized Z-ring substructure?

The FtsZ protein has an ~50 aa linker between the protofilament-forming globular domain and the C-terminal (Ct) membrane-tethering peptide. This Ct linker is widely divergent across bacterial species, and has been thought to be an intrinsically disordered peptide (IDP). We have made chimeras where we have swapped the Escherichia coli IDP for Ct linkers from other bacteria, and even for an unrelated IDP from human &alpha-adducin. Most of these substitutions allowed for normal cell division, suggesting that sequence of the IDP did not matter -any IDP appears to work (with some exceptions). Length, however, was important: IDPs shorter than 39 or longer than 89 aa's had compromised function. We conclude that the Ct linker of FtsZ functions as a flexible tether between the globular domain of FtsZ in the protofilament, and its attachment to FtsA and ZipA at the membrane. As a worm-like-chain, the Ct linker will function as a stiff entropic spring linking the constricting protofilaments to the membrane.

Previous work from our laboratory found that mutant and foreign FtsZ that do not normally function for cell division can function upon acquisition of a second site suppressor mutation, somewhere in the E. coli genome. We expect that some mutant or foreign FtsZ are partially functional for division in E. coli. As such, these FtsZ require another mutation that further enables their function. These suppressing mutations may reveal proteins interacting with FtsZ and the divisome, that have previously been unknown. In the present study, we have identified, via whole genome re-sequencing, single nucleotide polymorphisms that allow 11 different foreign and mutant FtsZ proteins to function for cell division. While we see a trend toward mutations in genes related to general metabolism functions in the cell, we have also identified mutations in two genes, ispA and nlpI, that may be interacting more directly with the cell division mechanism.

Finally, we have devised a screen to identify mutations in FtsZ that may be involved in lateral bonding between protofilaments. There are presently two proposed models of FtsZ substructure: the scattered or the ribbon model. A major difference between these models is that the scattered model proposed no interaction between adjacent protofilaments in the Z ring, while the ribbon model suggests that adjacent protofilaments are bonded laterally to create an organized substructure of aligned protofilaments. Our screen was designed to identify complementary surface-exposed residues that may be involved in lateral bonding. We initially identified two lateral contact candidate residues: R174, and E250 and mutated them to abrogate FtsZ function. We also mutated L272, which is known to make contacts across the protofilament interface, to look for compensating mutations in these contact residues. Using the screen, we identified a number of secondary mutations in FtsZ that can complement these initial loss-of-function mutations. While this screen has not yielded strong candidates for lateral bonding partners, it has emerged as a high-throughput method for screening large libraries of mutant FtsZ proteins in order to identify compensating mutation pairs.

Sex determination is a critical biological process for all sexually reproducing animals. Despite its significance, evolution has provided a vast array of mechanisms by which sexual phenotype is determined and elaborated even within amniote vertebrates. The most prevalent systems of sex determination in this clade are genetic and temperature dependent sex determination. These two systems are sometimes consistent within large groups of species, such as the mammals who nearly ubiquitously utilize XY genetic sex determination, or they can be much more mixed as in reptiles that use genetic or temperature dependent systems and even both simultaneously. The turtles are a particularly diverse group in the way they determine sex with multiple different genetic and temperature based systems having been described. We investigated the nature of the temperature based sex determination system in Trachemys scripta elegans to ascertain whether it behaved as a purely temperature based system or if some other global source of sex determining information might be apparent within thermal regions insufficient to fully induce male or female development. These experiments found that sex determination in this species is much more complex and early acting than previously thought and that each gonad within an individual has the same sexual fate established enough that it can persist even without further communication between. We established a best practice for the assembly and annotation of de novo whole transcriptomes from T. scripta RNA-seq and utilized the technique to quantify the gene regulatory events that occur across the thermal sensitive period.

Evidence is entirely lacking on the resolution of TSD when eggs are incubated at the pivitol temperature in which equal numbers or males and females are produces. We have produced a timecourse data set that allowed for the elucidation of the gene expression events that occur at both the MPT and FPT over the course of the thermal sensitive period. Our data suggests that early establishment of a male or female fate is possible when temperature is sufficiently strong enough as at MPT and FPT. We see a strong pattern of mutually antagonistic gene expression patterns emerging early and expanding over time through the end of the period of gonad plasticity. In addition, we have identified a strong pattern of differential expression in the early embryo at stages prior to the formation of the gonad. Even without the known systemic signaling attributed to sex hormones emanating from the gonad, the early embryo has a clear male and female gene expression pattern. We discuss how this early potential masculinization or feminization of the embryo may indicate that the influence of temperature may extend beyond the determination of gonadal sex or even metabolic adjustments and how this challenges the well-defined paradigm in which gonadal sex determines peripheral sexual characteristics.

Astrocytes, the perisynaptic glial cells of the brain, display a complex morphology that is strongly linked to their functions at the synapse. Primary processes radiating from the astrocyte cell soma branch out to secondary and tertiary processes, which further ramify into tiny perisynaptic astrocyte processes, giving a mature astrocyte its characteristic arborized structure. Astrocyte processes dynamically ensheath the pre- and post-synapse to provide instructive cues for synapse formation, maturation, and function. Perturbations in astrocyte-synapse interactions result in synaptic deficits, leading to excitation/inhibition imbalance and aberrant neural circuitry. However, the mechanisms linking astrocyte morphology and function to neuronal contact and synaptic adhesion are poorly understood. In a candidate-based reverse genetic screen utilizing rodent cortical neurons and astrocytes, I identified two genes, HepaCAM and CTNND2, as regulators of astrocyte morphogenesis in response to neuronal adhesion.HepaCAM is an astrocyte-enriched cell adhesion molecule that participates in cell-cell and cell-ECM interactions to regulate cell migration and proliferation. shRNA-mediated silencing of hepaCAM expression in astrocytes resulted in decreased astrocyte complexity in vitro and in vivo. HepaCAM stabilizes the gap junction protein connexin 43 (Cx43) at cell-cell junctions. We used stimulated emission depletion (STED) microscopy to show that hepaCAM and Cx43 colocalize at astrocyte processes in the mouse cortex and performed native affinity purifications followed by liquid chromatography-coupled high-resolution mass spectrometry (AP-MS) to demonstrate that Cx43 binds to hepaCAM. Finally, utilizing the same shRNA silencing approach, we found that hepaCAM and Cx43 were epistatic to each other in the regulation of astrocyte morphogenesis. Through mosaic analysis with double markers (MADM), we found that hepaCAM knockout astrocytes lost their ability to tile and had mislocalized Cx43. Consequently, gap junction coupling is impaired in astrocytes without hepaCAM. Additionally, we found decreased colocalization of hepaCAM puncta with synapses, a marked decrease in inhibitory synapses density, and a significant decrease in amplitude of miniature inhibitory postsynaptic currents, suggesting that loss of astrocytc hepaCAM disrupts the balance between synaptic excitation and inhibition. During development, astrocytes need to form non-overlapping territories within which they dynamically ensheathe synapses within discrete regions of neuropil. Taken together, our findings suggest that hepaCAM and Cx43 are critical proteins at the intersection of these two processes to ensure the proper molecular regulation of astrocyte self-organization and territory formation for normal circuit formation and function. Next, we identified Ctnnd2 (protein: δ-catenin) as another key regulator of astrocyte morphological complexity. δ-catenin was previously thought to be a neuron-specific protein that regulates dendrite morphology. Utilizing RNA fluorescence in situ hybridization (RNA-FISH) and immunohistochemistry, we found Ctnnd2 mRNA and δ-catenin is also highly expressed by astrocytes during the critical period of astrocyte morphological maturation and synapse formation during cortical development. shRNA-mediated silencing of Ctnnd2 expression in astrocytes resulted in decreased astrocyte complexity in vitro and in vivo. δ-catenin is hypothesized to mediate transcellular interactions through the cadherin family of cell adhesion proteins. We used structural modeling and surface biotinylation assays in both HEK293T and purified astrocyte cultures to reveal that δ-catenin interacts with N-cadherin juxtamembrane domain to promote N-cadherin surface expression. An autism-linked δ-catenin point mutation impaired N-cadherin cell surface expression and reduced astrocyte complexity. In the developing mouse cortex, only lower-layer cortical neurons express N-cadherin. Remarkably, when we silenced astrocytic N-cadherin throughout the cortex, only lower-layer astrocyte morphology was disrupted. These findings show that δ-catenin controls astrocyte-neuron cadherin interactions that regulate layer-specific astrocyte morphogenesis.

Bone development and homeostasis are governed by a number of developmental signals, transcription factors and cellular metabolism. This process is also dependent on the orchestration of multiple cell types including osteoblasts, chondrocytes, skeletal stem cells and osteoclasts. Osteoblasts are the principal bone forming cells responsible for producing and secreting the type I collagen rich extracellular bone matrix. Protein synthesis is an energetically and biosynthetically demanding process. This requires copious amounts of ATP and amino acids amongst other metabolites. However, the precise mechanisms and systems that osteoblasts utilize to meet these synthetic demands are poorly understood. Previous studies have shown amino acid consumption is increased in osteoblasts during differentiation. This process is regulated by transcription factors ATF4 and FOXO. Additionally, osteogenic signals like WNT and PTH can stimulate amino acid uptake. For example, WNT signaling can rapidly stimulate glutamine uptake and metabolism required for osteoblast differentiation. Unfortunately, transporters mediating glutamine uptake in osteoblasts are unknown. Moreover, the mechanism by which WNT stimulates increased glutamine consumption is also unknown. We identified two amino acid transporters, Slc7a7 and Slc1a5, as the primary glutamine transporters in response to WNT. Slc7a7 is responsible for the rapid WNT-induced glutamine uptake via the -catenin dependent pathway. Conversely, Slc1a5 sustains basal glutamine uptake, which is regulated by ATF4 downstream of the mTORC1 pathway. In summary, these data demonstrate the biphasic role of WNT signaling in regulating glutamine consumption, by two amino acid transporters Slc7a7 and Slc1a5, during osteoblast differentiation. While we have shown the importance of glutamine in bone cells, the role of other amino acids is not clear. Proline has long been considered as a critical amino acid due to its enrichment in collagens. Furthermore, PTH stimulates proline consumption in osteoblasts. The transport of proline is characterized by its dependency on sodium and sensitivity to MEAIB. However, the precise transport system responsible for proline import is not known. Here we identified the amino acid transporter Slc38a2, which encodes SNAT2, as the primary proline transporter in osteoblasts. Deletion of Slc38a2 results in defects in both intramembranous and endochondral ossifications. The phenotype is associated with defective osteoblast differentiation highlighted by reduction of proline enriched proteins (e.g. RUNX2, OSX and COL1A1). Slc38a2 provides proline to support osteoblast differentiation through two mechanisms. First, majority of proline is directly incorporated into proteins and does not contribute to amino acid biosynthesis. Second, proline oxidation regulates bioenergetics required for osteoblast differentiation. These findings highlight the multifaceted functions of proline, which is provided by Slc38a2, in osteoblast differentiation and bone formation. Collectively, my work demonstrates the critical role of amino acid transporters in osteoblast differentiation and provides novel insights in their potential applications in treatments of bone diseases like osteoporosis and bone fracture.

Basement membranes (BMs) are conserved, cell-associated, sheet-like networks of extracellular matrices that provide structural support to tissues. BMs also function as a signaling scaffold, directing cellular processes including self-renewal, adhesion, and proliferation. However, the role of BMs in mediating interactions between tissues is an active area of inquiry. Using C. elegans, which are highly amenable to genetic and visual manipulation, I investigated the role of BMs in mediating inter-tissue interactions within the reproductive system: in tissue separation (gonad and body wall muscle), in tissue linkage (uterine utse and epidermal seam), and in stem cell-niche interactions (germ stem cells and niche). To probe BM function, I used live-cell imaging of endogenous localization of BM components, conditional knockdown, RNAi screening, and genetic mutant alleles. In Chapter 1, I discuss what is known about BMs in the separation and linkages of reproductive tissues, BM function in the germ stem cell niche, and introduce the advantages of using C. elegans as a model. In Chapter 2, I explore the role of BMs in mediating niche enwrapment. In Chapter 3, I show that failed BM separation between the gonad and body wall muscle leaks germ cells into the body cavity to become enwrapped by abnormally protrusive muscle cells. In Chapter 4, I find that discoidin domain receptor-2 directs adhesion of uterine utse BM and epidermal seam BM to connect reproductive tissues. In Chapter 5, I discuss the impact of these findings.

Osteoarthritis (OA) is one of the leading causes of disability in the United States, afflicting over 27 million Americans and imposing an economic burden of more than $128 billion each year (1, 2). OA is characterized by progressive degeneration of articular cartilage together with sub-chondral bone remodeling and synovial joint inflammation. Currently, OA treatments are limited, and inadequate to restore the joint to its full functionality.

Over the years, progresses have been made to create biologic cartilage substitutes. However, the repair of degenerated cartilage remains challenging due to its complex architecture and limited capability to integrate with surrounding tissues. Hence, there exists a need to create not only functional chondral constructs, but functional osteochondral constructs, which could potentially enhance affixing properties of cartilage implants utilizing the underlying bone. Furthermore, the molecular mechanisms driving chondrogenesis are still not fully understood. Therefore, detailed transcriptomic profiling would bring forth the progression of not only genes, but gene entities and networks that orchestrate this process.

Bone-marrow derived mesenchymal stem cells (MSCs) are routinely utilized to create cartilage constructs in vitro for the study of chondrogenesis. In this work, we set out to examine the underlying mechanisms of these cells, as well as the intricate gene correlation networks over the time course of lineage development. We first asked the question of how transforming growth factors are determining MSC differentiation, and subsequently utilized genetic engineering to manipulate this pathway to create an osteochondral construct. Next, we performed high-throughput next-generation sequencing to profile the dynamics of MSC transcriptomes over the time course of chondrogenesis. Bioinformatics analyses of these big data have yielded a multitude of information: the chondrogenic functional module, the associated gene ontologies, and finally the elucidation of GRASLND and its crucial function in chondrogenesis. We extended our results with a detailed molecular characterization of GRASLND and its underlying mechanisms. We showed that GRASLND could enhance chondrogenesis, and thus proposed its therapeutic use in cartilage tissue engineering as well as in the treatment of OA.

Abstract

Adult zebrafish demonstrate a remarkable capacity to regenerate heart tissue following injury, and thus have served as a valuable model for developing our understanding of cardiac repair and regeneration. Recent work has identified and characterized multiple cardiac mitogens all of which can drive cardiomyocyte (CM) division in the absence of injury. Despite these impressive responses, little is known regarding the shared specific molecular mechanisms of CM proliferation that lie downstream of these unique ligand-receptor interactions. Here, we found that the tumor suppressor p53 was significantly suppressed during regeneration which correlated with increases in the transcription of p53’s primary negative regulator Mdm2. Using established and newly generated transgenic lines we demonstrated that experimentally altering cellular p53 levels affects CM proliferation. Inducible overexpression of the cardiac mitogens Nrg1 and Vegfaa demonstrated similar findings with increased mdm2 transcription and p53 suppression during regeneration along with augmented CM proliferation with loss of p53. Furthermore, we observed significant overlap between gata4 and mdm2 gene expression domains during development, following heart injury, and with mitogen stimulation suggesting potential interactions between these two genes.  Our findings indicate a novel injury and mitogen-induced function of Mdm2 to repress p53 during zebrafish heart regeneration. Here we also investigated the presence of additional cardiac mitogens, specifically HB-EGF, an ErbB ligand. We found that both HB-EGF paralogs are both present in the zebrafish heart and are both transcriptionally upregulated near the site of injury. A newly generated set of novel HB-EGF transgenic reporters, knock-outs, and overexpression lines will further investigate the importance of these early findings and HB-EGF signaling which will add to our understanding of heart regeneration.

The mouse embryonic gonad provides an outstanding model to study the complex mechanisms involved in cell fate specification and maintenance. At the bipotential stage, both XX and XY gonads are capable of becoming testes or ovaries upon specific molecular cues. The specification of the supporting cell lineage (as either Sertoli cells in the male or granulosa cells in the female) initiates the testis or ovary program, leading to male or female fate. However, there are significant gaps in our understanding of how the somatic cells in the gonad arise, are competent to differentiate, and determine and maintain their fates. In this dissertation, we addressed these questions.

We found that NUMB (an antagonist of Notch signaling) serves as competence factor for somatic cell differentiation during early gonadogenesis. The asymmetric allocation of NUMB to the basolateral domain of actively dividing coelomic epithelial (CE) cells is indispensable to (1) maintain the totipotent stem cell-like reservoir at the CE domain, and (2) give rise to progenitor cells that can further differentiate into supporting and interstitial cell lineages. Deletion of Numb; Numbl resulted in disruption of cell polarity in the CE domain as well as a reduction of multiple differentiated cell lineages within XX and XY gonads, including supporting cells and male steroidogenic cells, which were most severely affected. We detected elevated Notch downstream signaling in the Numb; Numbl mutant gonads. Moreover, treatment of DAPT (which blocks Notch signaling) rescued the Numb; Numbl mutant phenotypes, strongly suggesting that upregulation of Notch is responsible.

Previous experiments indicate that when supporting cells commit to the male (Sertoli) fate, they must repress the alternative female (granulosa) cell fate. In another line of experiments, we investigated the hypothesis that the Polycomb repressive complex (PRC1) plays a critical role in repressing the female pathway during male gonad patterning. We found that loss of Ring1B (a component of PRC1) led to the disruption of XY gonad development specific to the posterior region of male gonads. Sry, the upstream driver of the male pathway, was not appropriately expressed in the posterior domain, which contained cells expressing female markers and, in some cases, small aggregates of undifferentiated cells. Using ChIP-Seq, we identified potential targets of PRC during male gonad development. Moreover, a key gene in the male pathway, SOX9, interacts with Ring1B, based on immunoprecipitation results, leading to the hypothesis that it may be involved in the recruitment of PRC to its target sites to execute the repression of female genes in male gonads.

Our findings provide insight into how somatic cell fate is determined and maintained during mammalian sex determination. Our results may be valuable for patients with disorders of sexual development with unidentified genetic contributions.

The formation of the heart is a critical part of development that, if defective, can lead to congenital malformations incompatible with life. An improved understanding of the cellular and molecular processes that build the heart is essential to elucidate the causes of congenital defects and to design appropriate therapies. Relatively little is known about how the cardiac chambers adopt distinct forms to follow their specialized functions. Here, I have used a multicolor genetic labeling system to trace the progeny of zebrafish atrial cardiomyocytes as they expand to form the mature atrial myocardium. By comparing the observed cellular dynamics to those previously mapped in the ventricle, I identified characteristics of chamber development, including wall thickening, wall composition, and internal muscle formation, that contribute to the structural divergence of the chambers. As coronary vessel formation is one such chamber-specific morphogenetic process, I then explored the effect of a chamber-specific growth factor on cardiac development and homeostasis. Using a transgenic reporter and an inducible overexpression tools, I found ectopic expression of this growth factor stimulates cardiomyocyte proliferation. However, overexpression also blocks regeneration, possibly due to the abolition of an endogenous gradient localized to the site of injury. These findings not only provide new details for how the cardiac chambers form, but also demonstrate how understanding developmental phenomena can provide insights into important concepts of regenerative medicine.

Lung epithelium, the lining that covers the inner surface of the respiratory tract, is directly exposed to the environment and thus susceptible to airborne toxins, irritants, and pathogen-induced damages. In adult mammalian lungs, epithelial cells are generally quiescent but can respond rapidly to repair damaged tissues. Evidence from experimental injury models in rodents and human clinical samples has led to the identification of these regenerative cells, as well as pathological metaplastic states specifically associated with different forms of damages. The primary alveolar stem cell, alveolar type-2 cells (AT2s) are sparsely distributed and make up only 5% of the surface area. Despite this organization, AT2s are still able to maintain tissue homeostasis and achieve efficient repair after injury. However, the underlying mechanisms of stem cell activation, injury response, and subsequent cell-cell communication signals mediating resolution of injury and restoration of alveolar homeostasis remain elusive. Additionally, modulation of these regenerative cells for therapeutic potential has not been well established, primarily due to a lack of viable gene editing tools and vehicles for gene delivery to the alveolar stem cells, and neighboring niche. First, to better target the lung alveolus, we screened and identified cell-type specific adeno-associated virus (AAV) serotypes, enabling efficient targeting and gene expression of exogenous genes in alveolar stem cells as well neighboring mesenchyme. These tools were also capable for both in vitro and in vivo gene editing, forgoing the need for development of complex genetic mouse models as well as enabling diverse, viral-based screens. Second, using 3-dimensional, thick tissue imaging we reveal that a single AT2 cell can enface multiple alveolar compartments by virtue of a unique, multi-apical domain architecture. Lineage tracing and live imaging coupled with genetic and AAV-mediated selective ablation of AT2s was used to show robust recovery of AT2 numbers and distribution via clonal proliferation and migration, even after three successive rounds of ablation. Clonal tracing revealed that a single AT2 can differentiate to cover multiple alveolar cups. During injury repair, AT2s dynamically reorganize their apical domains to facilitate either migration or differentiation. Single- cell transcriptome profiling, genetic and pharmacologic disruption of actin dynamics, and evaluation of multiple physiologically relevant disease states identified the roles of actin cytoskeleton, cell migration, and multi-apical domains in AT2 recovery and regenerative potency. Lastly, using cell-type specific ablation of alveolar type 1 cells (AT1s), we identified novel mechanisms of epithelium-mediated signaling to mesenchymal fibroblasts, thereby uncovering novel mechanisms of fibrosis initiation and progression. Modulation of AT1 ablation dynamics preferentially drives fibrosis or, in contrast, emphysema, both at histological and physiological levels, as assessed by whole body plethysmography. Single-cell sequencing identified the epithelial and mesenchymal cell identities involved in regenerative processes, as well as identification of a PDGFA signaling axis between AT1s and resident alveolar fibroblasts necessary for fibroblast maintenance. We demonstrate that modulation of these signaling pathways during lung regeneration could enhance fibrosis or convert fibrosis to emphysema. In sum, the work presented herein both develops functional tools for perturbation of alveolar stem cells, as well as an improved understanding of alveolar architecture, stem cell dynamics during injury repair, homeostatic intercellular signaling, and mechanisms of disease progression.

The formation of a single lumen during tubulogenesis is crucial for the development and function of many organs. Although 3D cell culture models have identified molecular mechanisms controlling lumen formation in vitro, their function during vertebrate organogenesis is poorly understood. In this work we used the zebrafish gut as a model to investigate single lumen formation during tubulogenesis. Previous work has shown that multiple small lumens enlarge through fluid accumulation and coalesce into a single lumen. However, since lumen formation occurs in the absence of apoptosis, other cellular processes are necessary to facilitate single lumen formation.

Using light sheet microscopy and genetic approaches we identified a distinct intermediate stage in lumen formation, characterized by two adjacent un-fused lumens. These lumens are separated by cell contacts that contain basolateral adhesion proteins. We observed that lumens arise independently from each other along the length of the gut and do not share a continuous apical surface. Resolution of this intermediate phenotype into a single, continuous lumen requires the remodeling of basolateral contacts between adjacent lumens and subsequent lumen fusion.

Furthermore, we provide insight into the genetic mechanisms regulating lumen formation through the analysis of the Hedgehog pathway. We show that lumen resolution, but not lumen opening, is impaired in smoothened (smo) mutants, indicating that fluid-driven lumen enlargement and resolution are two distinct processes. We also show that smo mutants exhibit perturbations in the Rab11 trafficking pathway, which led us to demonstrate that Rab11-mediated recycling, but not degradation, is necessary for single lumen formation. Taken together, this work demonstrates that lumen resolution is a distinct genetically-controlled process, requiring cellular rearrangement and lumen fusion events, to create a single, continuous lumen in the zebrafish gut.

The means by which cells, tissues, and organisms undergo morphogenesis are variable and highly regulated, and the mechanisms that govern cellular changes in response to signaling cues are poorly understood. This study seeks to address the role of a newly characterized protein in zebrafish in translating signaling cues into physical changes within a cell.

The Cordon–bleu (Cobl) gene is widely conserved in vertebrates, with developmentally regulated axial and epithelial expression in mouse and chick embryos. In vitro, Cobl can bind monomeric actin and nucleate formation of unbranched actin filaments, while in cultured cells it can modulate the actin cytoskeleton. However, an essential role for Cobl in vivo has yet to be determined. We have identified the zebrafish cobl ortholog and have used zebrafish as a model to assess the requirements for Cobl in embryogenesis. We find that cobl shows enriched expression in ciliated epithelial tissues during zebrafish organogenesis. The utilization of antibodies developed against Cobl shows that the protein is concentrated along the apical domain of ciliated cells, in close proximity to the apical actin cap.

Reduction of cobl by antisense morpholinos reveals an essential role in embryonic morphogenesis and organ development. A requirement for Cobl was shown for the proper function of various and ciliated epithelial organs. Cobl appears to direct the elongation of motile cilia in organs such as Kupffer’s vesicle and the pronephros. In Kupffer’s vesicle, the reduction in Cobl coincides with a reduction in the amount of apical F-actin. Additionally, Cobl may play a role during gastrulation cell movements and convergence and extension morphogenesis during early embryonic development. Thus, Cobl may represent a molecular activity that couples developmental patterning signals with local intracellular cytoskeletal dynamics to support elongation of motile cilia and tissue morphogenesis.

Regeneration is a remarkable feat of developmental regrowth and patterning. The blastema is a mass of progenitor cells that enables complete regeneration of amputated salamander limbs or fish fins. Despite years of study, methodologies to identify and track blastemal cell progenies have been deficient, restricting our understanding of appendage regeneration at a cellular and molecular level. To bridge this knowledge gap, gene expression analysis, the generation of transgenic and mutant zebrafish, qualitative and quantitative analyses, morphological measurements, and chemical treatments were used to assess molecular and cellular processes involved in fin regeneration. Two main findings arose from these methods. The first provides evidence that connective tissue progenitors are rapidly organized into a scalable blueprint of lost structures, and that amputation stimulates resident cells to reset proximodistal positional information. The second identifies a fibroblast subpopulation near uninjured fin joints that contributes to the blastemal progenitor population. These findings reveal insights on cellular and molecular mechanisms of appendage regeneration and provide a basis for work exploring how cells in an adult vertebrate bone appendage coordinately rebuild a new structure.

Codon usage bias is a fundamental aspect of the genetic code. For many years synonymous mutations to a coding sequence were considered to be functionally “silent.” We now appreciate that is not the case and that synonymous codon choice can have drastic implications for gene expression and protein production. A major debate in the field remains whether codon usage bias is evolutionarily selected for to drive efficient translation in a tissue-specific manner. Here we perform an organism wide screen in Drosophila using codon modified reporters to reveal tissue-specific responses to codon usage bias. We uncover a strict limit on rare codon usage for protein expression, and this limit coincides with the rareness limit of endogenous genes in Drosophila. We find that rare codon usage near the edge of this limit is sufficient to impart tissue-specific gene expression, notably in the testis and brain. We define a new codon usage metric, the tissue-apparent Codon Adaptation Index (taCAI) to reveal a conserved enrichment in rare codons in endogenous testis genes of both flies and humans. We further demonstrate that rare codons in the evolutionarily young gene, RpL10Aa, are required for female fertility.

Concurrent with the global escalation of the AIDS pandemic, cryptococcal infections are increasing and are of significant medical importance. Although improvements in antifungal therapy have advanced the treatment of cryptococcosis, the mortality rate is approximately 12% in medically advanced countries, and approaches 50% in less developed regions. Additionally, C. neoformans can cause infection in seemingly healthy individuals, elevating its status as a primary human pathogen. Although numerous studies have examined virulence properties, less is understood regarding host immune factors in the lungs during early stages of fungal infection. In the present thesis studies, I examined the roles played by pulmonary surfactant proteins in response to C. neoformans in vitro and in vivo. We demonstrate that SP-D, but not SP-A, binds to the yeast and increases phagocytosis of poorly encapsulated yeast cells by macrophages, yet concomitantly protects the pathogenic microbes from macrophage-mediated defense mechanisms. Furthermore, we show that SP-D functions as risk factor in vivo by protecting the yeast cells against oxidant species and thus facilitating disease progression. The results of these studies provide a new paradigm on the role played by surfactant protein D during host responses to C. neoformans and, consequently, impart insight into potential future treatment strategies for cryptococcosis.

The cells of the budding yeast Saccharomyces cerevisiae undergo a robust morphological cycle, involving reorganization of the actin cytoskeleton, septin ring formation, and polarized growth. These events are crucial to the formation of a fully-equipped and properly-shaped bud, which gives rise to the daughter cell. The budding yeast, as a well-established genetic model system, has attracted numerous investigations aimed at uncovering the underlying principles of morphogenesis.

Despite the important roles of the septin ring and collar in morphogenesis and cytokinesis, little is known about how they are assembled. We found that septins are recruited to the ring and collar following a tri-linear assembly/disassembly scheme.

Polarization of actin cables enable directed secretion and growth. The formin Bni1p, an actin nucleator, is thought to polarize actin cables in response to the direct regulation by the master polarity regulator, Cdc42p. However, we found that all the known Bni1p-regulatory pathways are dispensable, including the direct regulation by Cdc42p, and we uncovered a novel pathway linking Bni1p to Cdc42p via the Cdc42p effector, Gic2p.

Yeast morphogenesis is tightly coupled with the cell cycle. Contrary to the prevailing model, we found that G1-CDK activity, albeit required for bud emergence, is not needed to trigger polarization. This finding suggests that cells are in a default polarized state, which is negatively regulated by the G2-CDK.

Organelle transport in eukaryotic cells is regulated by a precisely coordinated activity of phosphoinositide lipids, small GTPases, and molecular motors. Despite the extensive study of functional activities of individual regulators, how these activities promote precise deliveries of particular membrane proteins to specific cellular locations remained unclear. Ankyrin-B, which is previously well recognized as a plasma membrane adaptor that assembles diverse specialized plasma membrane domains, exhibited an unexpected role in intracellular transport. This thesis establishes ankyrin-B as a master integrator of the polarized long range organelle transport via direct interactions with Rab GTPase Activating Protein 1 Like (RabGAP1L), phosphatidylinositol 3-phosphate (PI3P) and dynactin 4. In Chapter 2, I identified an ankyrin-B death domain binding partner, RabGAP1L, that specifically interacts with ankyrin-B on intracellular organelles and requires ankyrin-B for its proper localization. In Chapter 3, I demonstrated that ankyrin-B is a PI3P-effector in mouse embryonic fibroblasts (MEFs) and promotes the polarized transport of associated organelles in migrating cells in a RabGAP1L-dependent manner. I continued to investigate what membranes/membrane-associated proteins utilize the ankyrin-B/RabGAP1L pathway in Chapter 4 and identified α5β1-integrin as a cargo whose polarized transport and recycling are ankyrin-B-dependent. I further presented that ankyrin-B, through recruiting RabGAP1L to PI3P-positive/Rab22A-associated endosomes containing α5β1-integrin, promotes polarized recycling of α5β1-integrin in migrating mouse embryonic fibroblasts. In collaboration with James Bear (UNC Chapel Hill), we further demonstrated that this ankyrin-B/RabGAP1L-mediated pathway is required for haptotaxis along fibronectin gradients. In Chapter 5, I elucidated the in vivo interaction between ankyrin-B and RabGAP1L. I demonstrated that ankyrin-B specifically interacts with RabGAP1L at long axon tracts in the brain and at costameres in the skeletal muscle. I also show the phenotypic analysis of ankyrin-B floxDD mice as an initial attempt to determine the physiological function of the ankyrin-B death domain in vivo. Together, this thesis dissects an ankyrin-B-mediated molecular mechanism for polarized endosomal trafficking and α5β1-integrin recycling during directional cell migration, and provides new insights into how phosphoinositide lipids, Rab GTPases, and molecular motor activities are coordinated to control the directional transport of specialized membrane cargos.

The differentiation of human induced pluripotent stem cells (hiPSCs) to prescribed cell fates enables the engineering of patient-specific tissue types, such as hyaline cartilage, for applications in regenerative medicine, disease modeling, and drug screening. In many cases, however, these differentiation approaches are poorly controlled and generate heterogeneous cell populations. In this dissertation, we demonstrate robust cartilaginous matrix production in multiple hiPSC lines using a robust and reproducible differentiation protocol. To purify chondroprogenitors produced by this protocol, we engineered a COL2A1-GFP knock-in reporter hiPSC line by CRISPR-Cas9 genome editing. Purified chondroprogenitors demonstrated an improved chondrogenic capacity compared to unselected populations, improved matrix homogeneity, and reduced variability between tissues. We next demonstrated the ability of the system to serve as a high-throughput system for arthritis disease modeling using cytokine stimuli. Finally, we used this platform to screen for transcription factors whose activation might be involved in chondrogenic lineage specification of hiPSCs. Taken together, these studies describe the generation of a high-throughput system for chondrogenesis and its application for screens and arthritis disease modeling. Future applications of this platform may be useful for identifying pathways regulating cartilage regeneration and novel therapeutics for arthritis.

As development progresses, many tissues lose their ability to regenerate via cellular proliferation. In some tissues, including the human heart and kidneys, injury activates a non-proliferative cellular response known as hypertrophy- an increase in cell size to restore lost organ mass. Although the connection between development and injury response is often observed, little is known about the developmental signals that terminate and switch injury responses. Moreover, the role of non-proliferative injury responses in restoring function to recovering tissues remains unexplored.

In this dissertation, I identify the Drosophila hindgut pylorus, an intestinal valve, as a new model to study the developmental regulation of injury responses. By using Drosophila genetics and developing a new method for site-specific genetic ablation, I discovered that the Drosophila pylorus switches its injury responses during tissue development. Injury to the larval pylorus results in accelerated mitotic cycles while injury to the adult pylorus leads to endocycles (DNA replication without division) and hypertrophy. My work identifies developmental hormones and transcription factors that act to regulate the injury response switch through control of fizzy-related, an evolutionary-conserved mitotic inhibitor. Last, I found that under chronic growth conditions, endocycles and hypertrophy protect the pyloric epithelial barrier function. Together my work explores both regulation and function of a developmental injury response switch.