Cilia are polarized extensions of the cells microtubule-based cytoskeleton dedicated to sensory, signaling and motility-related functions. In mammals, there are two main types of cilia, immotile and motile, where motile cilia generate/modulate fluid flow at the embryonic node, in respiratory airways, cerebral ventricles and the oviduct in addition to sperm propulsion via the flagellum. Defects in cilia motility cause a rare genetic disorder called Primary Ciliary Dyskinesia (PCD). In this thesis, I present functional and molecular characterisation of two PCD causing genes HEATR2 and ZMYND10. Core cilia genes are transcriptionally activated by members of the winged-helix transcription factors of the RFX family. The forkhead transcription factor FOXJ1, additionally activates motility genes such as the ones encoding components of axonemal dynein motors which transfer the chemical energy released from ATP hydrolysis to kinetic motion necessary for ciliary motility. I present data in this thesis which show that Heatr2 and Zmynd10 are both targets of the RFX3-FOXJ1 transcriptional module which co-operatively switches on genes required to make motile cilia Mutations in both HEATR2 and ZMYND10 cause the same subtype of PCD (loss of inner and outer arm dyneins in cilia). I characterise a human PCD causing mutation in HEATR2 in this thesis. Additionally, using genetic null mouse models generated using the CRISPR technology, I describe the phenotypic effects of complete loss of Zmynd10 in mice. Zmynd10 mutant mice display characteristic PCD-like features. Adding to my functional studies, I present proteomic data to propose mechanisms by which HEATR2 and ZMYND10 proteins control cilia motility. Mass spectrometry and protein interaction studies support distinct roles for HEATR2 and ZMYND10 in intracellular transport and pre-assembly of axonemal dynein motors. The multisystem approaches described in this thesis to characterise the roles of HEATR2 and ZMYND10 highlight the molecular complexity underlying the assembly and delivery of axonemal dyneins to motile cilia and provide novel functional and molecular insights into the pathophysiology of PCD.

Ciliopathies are a group of heterogeneous diseases associated with ciliary dysfunction. Diseases in this group display considerable phenotypic variation within individual diseases as well as overlapping phenotypes among clinically distinct diseases. In particular, mutations in CEP290 cause phenotypically diverse ciliopathies ranging from isolated retinal degeneration, nephronophthisis (NPHP), and Bardet-Biedl Syndrome (BBS) to the neonatal lethal Meckel-Gruber syndrome (MKS). However, the underlying mechanisms of the variable expressivity in ciliopathies are not well understood. This thesis focuses on evaluating the molecular and biological processes behind the retinal degeneration and obesity observed in cilia disorders with respect to CEP290 and other ciliopathy genes using the zebrafish and mouse model systems. CEP290 is the most frequently mutated gene underlying the non-syndromic blinding disorder, Leber's congenital amaurosis (LCA). We first aimed to characterize the function of various CEP290 domains and to characterize a zebrafish model aimed at progressing towards future therapy for patients with CEP290 LCA. To this end, an antisense oligonucleotide [Morpholino(MO)] was used for gene knockdown. We showed that cep290 MO-injected embryos have reduced Kupffer's vesicle size and delays in melanosome transport, two phenotypes that are observed upon knockdown of BBS genes in zebrafish. More importantly, the embryos had a statistically significant reduction in visual function, and this vision impairment caused by the disruption of cep290 can be rescued by expressing only the N-terminal region of the human CEP290 protein. These data indicate a specific region of the CEP290 protein, which is necessary for visual function. We examined the contribution of BBS genes to the clinical variability of CEP290-associated ciliopathies. We demonstrated that the BBSome binds to the N-terminal region of CEP290 and co-localizes with CEP290 to the centriolar satellite in ciliated cells and to the connecting cilium of photoreceptor cells. We further showed that the BBSome is required for proper localization of CEP290 in these structures. Genetic interactions were tested using Cep290rd16, a Cep290 hypomorphic allele with an in-frame deletion of 299 residues, and Bbs4 null mutant mouse lines. Additional loss of Bbs4 alleles in Cep290rd/rd mutants results in increased body weight and accelerated photoreceptor degeneration compared to mice without Bbs4 mutations. Furthermore, double heterozygous mice (Cep290+/rd16; Bbs4+/-) have increased body weight compared to single heterozygous animals. Our data indicated that genetic interactions between the BBSome components and CEP290 underlie the variable expression and overlapping phenotypes of ciliopathies caused by CEP290 mutations. Finally, this work was extended to other cilia disorders through the characterization of genetic interactions between CEP290 and other ciliopathy genes. We found that different NPHP and MKS proteins interact with CEP290 via its different regions, suggesting the central role of CEP290 in CEP290 biological/cellular functions. To characterize the functional interaction between these proteins, we used in vitro systems to double knockdown CEP290 with other NPHP and MKS genes and showed that depletion of a certain combination set of these proteins disrupted the localization of proteins into the cilia. The data indicated that the phenotypic variability of human ciliopathies is associated with different degree of compromise of cilia function.

Mutations in BBS6 cause two clinically distinct syndromes, Bardet-Biedl syndrome (BBS), a syndrome caused by defects in cilia transport and function, as well as McKusick-Kaufman syndrome, a genetic disorder characterized by congenital heart defects. Congenital heart defects are rare in BBS, and McKusick-Kaufman syndrome patients do not develop retinitis pigmentosa. Therefore, the McKusick-Kaufman syndrome allele may highlight cellular functions of BBS6 distinct from the presently understood functions in the cilia. In support, we find that the McKusick-Kaufman syndrome disease-associated allele, BBS6H84Y; A242S, maintains cilia function. We demonstrate that BBS6 is actively transported between the cytoplasm and nucleus, and that BBS6H84Y; A242S, is defective in this transport. We developed a transgenic zebrafish with inducible bbs6 to identify novel binding partners of BBS6, and we find interaction with the SWI/SNF chromatin remodeling protein Smarcc1a (SMARCC1 in humans). We demonstrate that through this interaction, BBS6 modulates the sub-cellular localization of SMARCC1 and find, by transcriptional profiling, similar transcriptional changes following smarcc1a and bbs6 manipulation. Our work identifies a new function for BBS6 in nuclear-cytoplasmic transport, and provides insight into the disease mechanism underlying the congenital heart defects in McKusick-Kaufman syndrome patients.

A leading cause of male infertility is genetic variation in genes required for sperm formation and/or function. There is evidence to suggest PACRG is involved in mammalian spermatogenesis. Specifically, the loss of Pacrg function causes a spermatogenic defect and male infertility in mice. To investigate if PACRG plays a similar role in human spermatogenesis, the localisation of PACRG was determined in human testis. Using an immunohistochemical approach, this study demonstrated that PACRG is localised to the human sperm flagella. To investigate a potential role for PACRG in human male infertility, sequence analysis and an association study were performed. Sequence analysis did not identify any pathological alterations. However, 1 of 3 variants identified (rs9347683) was shown to be significantly associated with male infertility by association analysis (p=0.009, Odds Ratio=1.6, n=766). / A high degree of structural and functional conservation exists between different types of motile cilia/flagella. Evidence from studies in C.reinhardtii and T.brucei indicate Pacrg is necessary for axoneme formation and microtubule stability. To test the role of the mammalian homologue, this study characterised the Pacrg knockout mouse, quakingviable (qkv) and generated Pacrg transgenic qkv mice (qkv-Tg). Using immunohistochemistry and immunoelectron microscopy this study demonstrated that Pacrg was localised to the axonemal microtubule doublets of sperm and ependymal cilia. The absence of Pacrg was associated with compromised sperm flagella formation and male infertility. In addition, histological and MRI analysis of qkv mutant mice revealed hydrocephalus. Specifically, qkv mutant mice showed a ~2.5 fold expansion of the lateral ventricle area compared to wildtype mice. The hydrocephalus phenotype was associated with a reduction in ependymal cilial beat frequency (CBF). Transgenic expression of Pacrg was sufficient to rescue the hydrocephalus and infertility phenotypes. In conclusion, this study has demonstrated that Pacrg is a novel axonemal protein in a subset of motile cilia and loss of Pacrg function results in spermiogenic defects and hydrocephalus in mice. Further, this study has shown that variations in the human PACRG promoter are a risk factor in human male infertility. Collectively these data provide evidence for a conserved role of PACRG in the cilial axoneme. This suggests the protein may be a candidate for a variety of human diseases characterised by cilial dysfunction.

How tissues and organs develop into their final shape during embryogenesis is a fascinating and long-standing question in developmental biology. Tissue morphogenesis is driven by a variety of events at the cellular level and individual cell shape change is one of the central morphogenetic engines. Thus, it is crucial to understand what signals specify the correct cell behavior in specific groups of cells during development. For my doctoral studies, I have focused on two cell shape change events, apical constriction and cilia assembly. First, we present data demonstrating that Shroom3 is essential for cell shape changes and morphogenesis in the developing vertebrate gut, where Shroom3 transcription requires the Pitx1 transcription factor. We identified a Pitx-responsive regulatory element in the genomic DNA upstream of Shroom3, and showed that Pitx proteins directly activated Shroom3 transcription in Xenopus. Moreover, we showed that ectopic expression of Pitx proteins was sufficient to induce Shroom3-dependent cytoskeletal reorganization and epithelial cell shape change. These data demonstrated new breadth to the requirements for Shroom3 in morphogenesis, and also provided a cell-biological mechanism for Pitx transcription factors action during morphogenesis. Next, we focused on understanding the transcriptional regulation of ciliogenesis. We first showed that Rfx2 transcription factor broadly controlled ciliogenesis, and by RNA- and ChIP-sequencing, we showed that Rfx2 directly regulated a wide range of genes encoding diverse ciliogenic machinery. Finally, in addition to ciliogenesis regulation, a large number of non-ciliary genes in our Rfx2 dataset led us to identify a novel role of Rfx2 in controlling insertion of multi-ciliated cells into the overlying mucociliary epithelium. Moreover, we showed here that Slit2, a target of Rfx2, was involved in multi-ciliated cell movements, possibly through mediating cortical E-cadherin level. This work allowed us to begin building a genetic network controlling multi-ciliated cells in mucociliary epithelium. Together, we showed a transcriptional regulation of apical constriction driving gut morphogenesis and a comprehensive transcriptional network that governs multi-ciliated cell development. / text

This thesis focuses on the design, fabrication and characterization of polymeric smart structures that are able to alter their geometry and thus their properties upon the application of external stimuli in a reversible and controllable manner. Two different responsive structures are studied that both contain poly dimethyl-siloxane (PDMS) and differ in the design, geometry, and actuation mechanism. The first structure is a surface decorated by a square array of posts (cilia) made of PDMS reinforced with magnetic particles and is actuated magnetically. The structures are meant to mimic cilia, a hair-like structure found in nature. The physical parameters necessary for the magnetic response of the cilia including physical dimensions and filler concentration are investigated. In addition, the elastic modulus of the composites is measured and the microstructure is examined in order to determine the dispersion and homogeneity of the composites. The second structure is a planar hetero-structure consisting of a PDMS substrate and a nanoporous (NP) metal foam film which is actuated thermally or chemically by tuning the generation and release of residual stresses at the NP metal foam/PDMS interface. The effect of strain, applied to the PDMS substrate prior to the deposition of the NP metal foam and the effect of the PDMS and NP metal foam thicknesses on the shape/size of the planer hetero-structure after the actuation is investigated.

Thesis (Ph.D.)-- University of Adelaide, Dept. of Physics, 1956. / Typewritten copy. Includes bibliographical references (leaves 141-144).

Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.

Human congenital heart disease (CHD) is the most common cause of non-infectious neonatal death affecting 1-2% of live births (Hoffman and Kaplan, 2002). Treatment of CHD requires major surgery and quality of life is often significantly reduced despite treatment. With the discovery of single gene mutations that cause CHD in model animals (Lyons et al., 1995), the role of genetics in CHD has become appreciated. The genetic basis of CHD is poorly understood, with different members of the same family presenting with different types of CHD (Schott et al., 1998), suggesting the causes of CHD are multifactorial. Cardiogenesis is intimately associated with the establishment of the left-right (L-R) body axis, with the two processes sharing several important transcription factors. Heart looping, in which the heart turns dextrally, is the earliest physical manifestation of L-R asymmetry. L-R patterning disorders are associated with an increased risk of CHD; heterotaxy (in which L-R asymmetry is neither normal nor mirror image) accounts for about 3% of all CHD (Zhu et al., 2006).Investigating cardiogenesis and the causes of CHD necessitates the use of animal models, typically mice, chicks, zebrafish and Xenopus. Recently a strain of mouse with a mutation in a gene essential for cardiac development was isolated from an ENU mutagenesis screen (Kile et al., 2003) using mice carrying a balancer chromosome. It has been subsequently found that the most likely candidate gene codes for the protein Prpf8, an integral component of the spliceosome. The mutation is homozygous lethal, with homozygous mice having a grossly deformed heart, developmental delay and a high incidence of heart looping reversal, indicative of a L-R patterning disorder. In depth characterisation of homozygous mutant embryos revealed defects in the morphology of the embryonic node, nodal cilia and the expression pattern of L-R axis genes. We also investigated the expression of Prpf8 during embryogenesis, and the effect that the point mutation we found in our homozygous embryos has on splicing kinetics.

After more than a century, there are no analytical solutions for the Navier-Stokes equations to describe complex fluid behavior, and we often resort to different computational methods to find solutions under specific conditions. In particular, to address many biological questions, we need to use techniques which are accurate at the mesoscale regime and computationally efficient, since atomistic simulations are still incredibly computationally costly, and continuum methods based on Navier-Stokes present challenges with complicated moving boundaries, in the presence of fluctuations. Here, we use a novel particle-based coarse-grained method, known as MPCD, to study ciliated swimmers. Using experimentally measured beating patterns, we show how we recapitulate the emergence of metachronal waves (MCW) on planar surfaces, and present new results on curved surfaces. To quantitatively study these waves, we also analyzed their effect on beating intervals, energy fluctuations, and fluid motion. We then extended our model to realistic cellular geometries, using experimentally obtained Basal Bodies locations.\par In the second part of our study, we focused on the intracellular fluid motion, neglecting hydrodynamic interactions. We developed the Digital Confocal Microscopy Suite (DCMS) that can run on multiple platforms using GPUs and can input realistic cell shapes and optical properties of the confocal microscope. It has this ability to simulate both (Fluorescence Recovery After Photobleaching) FRAP and Fluorescence Correlation Spectroscopy (FCS) experiments, as well as the capability to model photo-switching of fluorophores, acquisition photo-bleaching, and reaction-diffusion systems. With this platform, in collaboration with the Vidali Lab, we were able to elucidate the role of boundaries in interpreting FRAP experiments in \textit{moss} and estimate the binding rates of myosin XI.