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Successful mammalian development to term requires that embryonic and extra-embryonic tissues communicate and grow in coordination, to form the body. After implanting into the uterus, the mouse embryo is comprised of three cell lineages: first, the embryonic epiblast (EPI) that forms the embryo proper, second, the extra-embryonic ectoderm (ExE) which contributes to the foetal portion of the placenta, and third, the visceral endoderm (VE) that contributes to the yolk sac. These three tissues form a characteristic ‘egg-cylinder’ structure, which allows signals to be exchanged between them and sets the stage for body axis establishment and subsequent tissue patterning. The mechanisms underlying this process are difficult to study in vivo because a different genetically manipulated mouse line must be generated to investigate each factor involved. This difficulty has prompted efforts to model mammalian embryogenesis in vitro, using cell lines, which are more amenable to genetic manipulation. The pluripotent state of the EPI can be captured in vitro as mammalian embryonic stem cells (ESCs). Although mouse ESCs have been shown to contribute to all adult tissues in chimeric embryos, they cannot undertake embryogenesis when allowed to differentiate in culture. Previous studies have shown that ESCs formed into three-dimensional (3D) aggregates, called embryoid bodies, can become patterned and express genes associated with early tissue differentiation. However, embryoid bodies cannot recapitulate embryonic architecture and therefore may not accurately reflect what happens in the embryo. In this study, a new technique was developed to model early mouse development which is more faithful to the embryo. ESCs were co-cultured with stem cells derived from the ExE, termed trophoblast stem cells (TSCs), embedded within extracellular matrix (ECM). These culture conditions lead to the self-assembly of embryo-like structures with similar architecture to the mouse egg cylinder. They were comprised of an embryonic compartment derived from ESCs abutting an extra-embryonic compartment derived from TSCs, and hence were named ‘ETS-embryos’. These structures developed a continuous cavity at their centre, which formed via a similar sequence of events to those that lead to pro-amniotic cavity formation in the mouse embryo, and required active Nodal/Activin signalling. After cavitation, ‘ETS-embryos’ developed regionalised mesodermal tissue and primordial germ cell-like cells originating at the boundary between embryonic and extra-embryonic compartments. Inhibitor studies revealed that this occurred in response to endogenous Wnt and BMP signalling, pathways which also govern these tissue specification events in the early mouse embryo. To demonstrate that ‘ETS-embryos’ were comparable to mouse embryos at the global transcriptional level, RNA-sequencing was then performed on different tissue regions of ‘ETS-embryos’ and the resulting transcriptomes were compared to datasets from mouse embryos. These data showed that ‘ETS-embryos’ were highly similar to mouse embryos at post-implantation stages in their overall gene expression patterns. Taken together, these results indicate that ‘ETS-embryos’ are an accurate in vitro model of mammalian embryogenesis, which can be used to complement studies undertaken in vivo to investigate early development.

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Recent breakthroughs in microscopy techniques and fluorescence probes enable the recording of mouse embryogenesis at the cellular level for days, easily generating terabyte-level 3D time-lapse data. Since millions of cells are involved, this information-rich data brings a natural demand for an automated tool for its comprehensive analysis. This tool should automatically (1) detect and segment cells at each time point and (2) track cell migration across time. Most existing cell tracking methods cannot scale to the data with such large size and high complexity. For those purposely designed for embryo data analysis, the accuracy is heavily sacrificed. Here, we present a new computational framework for the mouse embryo data analysis with high accuracy and efficiency. Our framework detects and segments cells with a fully probability-principled method, which not only has high statistical power but also helps determine the desired cell territories and increase the segmentation accuracy. With the cells detected at each time point, our framework reconstructs cell traces with a new minimum-cost circulation-based paradigm, CINDA (CIrculation Network-based DataAssociation). Compared with the widely used minimum-cost flow-based methods, CINDA guarantees the global optimal solution with the best-of-known theoretical worst-case complexity and hundreds to thousands of times practical efficiency improvement. Since the information extracted from a single time point is limited, our framework iteratively refines cell detection and segmentation results based on the cell traces which contain more information from other time points. Results show that this dramatically improves the accuracy of cell detection, segmentation, and tracking. To make our work easy to use, we designed a standalone software, MIVAQ (Microscopic Image Visualization, Annotation, and Quantification), with our framework as the backbone and a user-friendly interface. With MIVAQ, users can easily analyze their data and visually check the results. / Doctor of Philosophy / Mouse embryogenesis studies mouse embryos from fertilization to tissue and organ formation. The current microscope and fluorescent labeling technique enable the recording of the whole mouse embryo for a long time with high resolution. The generated data can be terabyte-level and contains more than one million cells. This information-rich data brings a natural demand for an automated tool for its comprehensive analysis. This tool should automatically (1) detect and segment cells at each time point to get the information of cell morphology and (2) track cell migration across time. However, the development of analytical tools lags far behind the capability of data generation. Existing tools either cannot scale to the data with such large size and high complexity or sacrifice accuracy heavily for efficiency. In this dissertation, we present a new computational framework for the mouse embryo data analysis with high accuracy and efficiency. To make our framework easy to use, we also designed a standalone software, MIVAQ, with a user-friendly interface. With MIVAQ, users can easily analyze their data and visually check the results.

Elongation of the vertebrate rostrocaudal axis depends on localised populations of axial progenitors. Previous work has demonstrated the presence of Neuromesodermal (NM) progenitors that behave as multipotent stem cells, which contribute to the neurectoderm and mesoderm throughout axis elongation. They have been localised to the Node-­‐Streak Border (NSB) in the primitive streak region, and the Chordoneural Hinge (CNH) in its descendant, the tail bud. At primitive streak stages, the Caudal Lateral Ectoderm (CLE) on either side of the primitive streak itself is also fated for neurectoderm and mesoderm. However, fate mapping studies in mouse and chick have suggested that these progenitors are more transitory than those in the NSB and CNH, leading to the idea that two different types of progenitor cell exist in the primitive streak region; long-­‐term (stem cell-­‐like) and transient progenitors. In this thesis, I have examined the potency of the CLE cells by heterotopically grafting them into the NSB. Anterior CLE cells are exquisitely sensitive to their position and differentiate predominantly as neurectoderm, mesoderm, or both, depending on their exact location in the NSB. Most significantly, their descendants are retained in the CNH, indicating that CLE cells show equal potential to NSB progenitors on transplantation to the border environment. The relationship between fate and potency within the streak stage embryo suggest a mechanism by which stem cells are maintained not only by their intrinsic stem cell program, but are also influenced by their location. Furthermore, I have investigated the expression of candidate markers of NM-­‐progenitors, and have found that the combined expression of Sox2 and T genes in the progenitor area coincides with observed NM-­‐potency, and could serve as a marker for this stem cell population. Over time, axial elongation comes to a halt and NM-­‐progenitors are thereafter not longer active. It is still unclear how exactly this process occurs and specifically whether axial elongation ceases because NM progenitors are eliminated. I have investigated the events occurring immediately before the end of axial elongation. Morphological and gene expression analysis shows that apoptosis reaches a peak only after the complete axis has been laid down, and is not dramatically elevated in the progenitors themselves before that. In order to test signalling pathways that lead to progenitor maintenance, I have developed an in vitro tail growth assay that recapitulates in vivo development, as measured by several morphometric criteria. I show that, even though FGF signalling is critical for most cells in the tail bud including NM-­‐progenitors, it is not sufficient for NM-­‐ progenitor maintenance. In contrast, exposing tail buds to elevated Wnt/β-­‐catenin signalling does prolong the lifetime of NM-­‐progenitors in the ageing tail bud, as judged by the presence of Sox2-­‐T double-­‐positive cells. In this regard we have found that the time of cessation coincides with the disappearance of Sox2-­‐T double-­‐positive cells, the disappearance of Wnt3a and concomitant neuralisation of the progenitor region. This data suggest an important governing role for Wnt signalling in both maintenance and fate decision of NM progenitors. Thus the disappearance of Wnt signalling in the tail bud over time could well be the main reason for triggering the halt of caudal elongation.

The morphogenetic events that give rise to the early post-implantation mouse embryo (egg cylinder) have not been thoroughly studied and our knowledge is restricted to "snap-shot" descriptions of embryos recovered at different stages of implantation from the mother. A central feature of the egg cylinder is the pro-amniotic cavity, which spans the embryo and participates in formation of the extraembryonic membranes. The major aims of my PhD studies have been to reveal how this cavity is formed (Aim 1) and then how the egg cylinder grows (Aim 2). In order to address how the pro-amniotic cavity forms (Aim 1), I first characterised in detail development of the architecture of the extra-embryonic ectoderm (ExE), which has to be remodelled to permit cavity formation. My findings indicate that the ExE comprises cells in direct contact with a basement membrane and cells that lie deeper in the tissue. The ExE originates in the polar trophectoderm, a monolayer covering the epiblast of the blastocyst, which expands and undergoes invagination to form a slit-like cavity. By carrying out analyses of fixed specimens and live imaging of cultured embryos, I have found that the epiblast and ExE cavity extend towards each other through the formation and resolution of multiple rosette structures. This leads to the fusion of the ExE and epiblast cavities to form the unified pro-amniotic cavity. I show that this process is dependent on signalling cues stemming from the underlying basement membrane that activate the b1-integrin signalling pathway to regulate cell polarity, ExE tissue architecture and rosette formation. In addition to the basement membrane's role in b1-integrin signalling, it also has physical functions that I characterise in the second part of my study (Aim 2). High resolution imaging revealed that the basement membrane underlying the epiblast is highly perforated during the implantation stages. These perforations are initially evenly distributed and then accumulate asymmetrically at the future posterior part of the embryo, just prior to gastrulation. Finally, I demonstrate that remodelling of the basement membrane requires the expression of matrix metalloproteinases (MMPs) in the epiblast under the control of Nodal. The anterior visceral endoderm inhibits Nodal signalling and hence MMP inhibition in the anterior. I demonstrate that activity of the MMPs and perforations in the basement membrane are essential for embryo growth. The domain of posterior basement membrane perforations persists beyond gastrulation suggesting a potential role for these perforations in primitive streak formation and extension. Together, my studies bring new important insights into the understanding of early mouse embryo morphogenesis.

Embryonic cells of many species polarise and the cell polarity is often important for the normal developmental progression. In the mouse embryo, the prototype of epithelial cell polarity, namely apico-basal polarisation, become established at the 2.5 days' post-fertilisation, when the embryos are at the 8-cell stage. The formation of apical domain is necessary and sufficient for the first segregation of extra-embryonic and embryonic cell lineages, as well as the following up morphogenetic transitions, such as the blastocyst formation. This study aims to explore the molecular pathways triggering the first cell polarity establishment in the mouse embryo, and to reveal the mechanism that programmes the timing of this event in the mouse embryo. The results showed that cell polarity establishment during the 8-cell stage development can be divided into two major phases: in the first phase actomyosin complex became polarised to the cell-contact free surface; and in the second phase apical proteins recruited to the actomyosin enriched cell-contact free cortex, they further became centralised in the cell-contact free surface, excluding the local actomyosin meshwork, resulting in the formation of actomyosin ring. The activation and assembly of actomyosin meshwork during the first phase, but not its contractility, was essential for apical protein recruitment. Factors responsible for actin cytoskeleton reorganisation included Phospholipase C (PLC) - Protein Kinase C (PKC) pathway components, they directly activated actomyosin in the first phase through the Rho proteins such as RhoA. Further results showed that the apical protein centralisation step required a proximate transcriptional input that was induced by two transcription factors, Tfap2c and Tead4. RNAi and Genetic depletion of these two factors prevented apical protein centralisation and the final apical domain assembly. The protein expression profile indicated that Tfap2c and Tead4 expression, and therefore their activity, were induced by zygotic genome activation. Significantly, overexpression of Tfap2c, Tead4, together with constitutively activated Rho proteins were sufficient to advance the timing of apical domain formation, indicating that the timer of cell polarity establishment at the 8-cell stage is set by the Rho proteins activation, and the zygotic transcriptional accumulation of Tfap2c and Tead4. Together, these results characterised the molecular events during the cell polarity establishment at the 8-cell stage mouse embryo, and identified the timing regulation of this event.

Assisted reproductive technology (ART) has been rapidly expanding since the birth of Louise Brown, the first test tube baby, in 1978. Although an increasingly complex array of laboratory skills and procedures have been developed for infertility treatments, the success rate of ART remains low. In an attempt to make ART safer and more efficient, international medical practice is trending towards single embryo transfers and the use of innovative, sophisticated technologies to identify promising gametes and embryos with the highest potential to generate a pregnancy. Laser technology is increasingly being used to accomplish these aims. The application of lasers for ART has been successfully employed in clinical practice for some time now and is continually the subject of investigative research in order to generate new methods to improve operations. Moreover, lasers serve as a powerful tool at the forefront of investigative research in the reproductive sciences, assisting in broadening our understanding of reproductive and developmental biology. Nevertheless, there is a paucity of literature pertaining to the safe standardisation of such laser procedures with evidence at the molecular level. The primary aim of this thesis was to optimise applications of laser technology for clinical ART and research applications in the reproductive sciences. This thesis utilised the mouse embryo model to investigate potential deleterious effects of different laser treatment applications, both by the operator and hardware manufacturer. Safe and unsafe laser operator parameters were elucidated by assessing deleterious effects to the plasma membrane integrity, blastocyst survival rate, DNA fragmentation levels, and changes in gene expression of key developmental genes. The effect of altering the laser hardware to lower the power output was evaluated and it was determined that if a lower power laser is used to deliver a set amount of energy over a longer period of time, a smaller amount of damage is incurred. Work in this thesis also established a new method in which laser technology can be used as a research tool for the reproductive sciences, by creating a novel stimuli-responsive laser-activated nanoparticle delivery system with spatial control and increased efficiency in a mammalian cell model. The field of reproductive science continues to benefit greatly from laser application clinically to improve infertility treatments, and in research, to elucidate mechanisms underlying infertility, with a hope of increasing our understanding and eventually developing new treatment options.