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The goal of this Creative Project was to write a model text on the principles and practices of specifications writing for landscape architecture students.The goals of the text were to provide: 1) an overview of the principles and practices of specifications writing as advocated by the Construction Specifications Institute; 2) examples of contract documents used by the landscape architect; and 3) a source of reference information specifically for landscape architects.The text consists of nine chapters. Each chapter begins with a set of goals, followed by the text content, and ends with a set of review questions. The text contains figures and appendices which provide examples and sources of information useful to specifications writers. / Department of Landscape Architecture

“The scientist, by the very nature of his commitment, creates more and more questions, never fewer. Indeed the measure of our intellectual maturity, one philosopher suggests, is our capacity to feel less and less satisfied with our answers to better problems.” ~G.W. Allport, Becoming, 1955 It will be interesting to look back at this thesis in a few decades and reflect on how the questions and interpretation of data in the field of developmental biology have changed. Indeed, a biologist currently in their twilight years might reflect on their youth, before the discovery of hereditary material, and compare that bookend with the range of genome sequences and related knowledge currently available. How long will it take before this thesis reads like a debate about whether the male or female contributed the ‘homunculus,’ a miniature preformed human to the embryo that grows into an adult? In this thesis I asked three related questions: whether the role of Oct4 during embryogenesis provides insight into its contribution to pluripotency; how surfaceome changes contribute to functional maturation of neural stem cells and to what extent the murine genome is imprinted. Our data indicate that Oct4 is required for posterior expansion. We propose that the function of the protein is conserved, but that its expression has been coopted to yield different cell types based on its combination with different factors. We show that fundamental aspects of cell biology are altered during the maturation from pluripotent populations to neural stem cells, and identify mediators of proliferation, survival and adhesion that distinguish neural stem cell regulation from their precursors. Finally, we validated discovery of a dozen novel imprinted transcripts using a genomic approach. These discoveries will contribute to a holistic view of the causes and consequences of imprinting, but do not support a paradigm shift in the scale and consequences of imprinting.

“The scientist, by the very nature of his commitment, creates more and more questions, never fewer. Indeed the measure of our intellectual maturity, one philosopher suggests, is our capacity to feel less and less satisfied with our answers to better problems.” ~G.W. Allport, Becoming, 1955 It will be interesting to look back at this thesis in a few decades and reflect on how the questions and interpretation of data in the field of developmental biology have changed. Indeed, a biologist currently in their twilight years might reflect on their youth, before the discovery of hereditary material, and compare that bookend with the range of genome sequences and related knowledge currently available. How long will it take before this thesis reads like a debate about whether the male or female contributed the ‘homunculus,’ a miniature preformed human to the embryo that grows into an adult? In this thesis I asked three related questions: whether the role of Oct4 during embryogenesis provides insight into its contribution to pluripotency; how surfaceome changes contribute to functional maturation of neural stem cells and to what extent the murine genome is imprinted. Our data indicate that Oct4 is required for posterior expansion. We propose that the function of the protein is conserved, but that its expression has been coopted to yield different cell types based on its combination with different factors. We show that fundamental aspects of cell biology are altered during the maturation from pluripotent populations to neural stem cells, and identify mediators of proliferation, survival and adhesion that distinguish neural stem cell regulation from their precursors. Finally, we validated discovery of a dozen novel imprinted transcripts using a genomic approach. These discoveries will contribute to a holistic view of the causes and consequences of imprinting, but do not support a paradigm shift in the scale and consequences of imprinting.

In order to remain competitive, modem systems developers are increasingly under pressure to produce software solutions to complex problems faster and cheaper, whilst at the same time maintaining a high level of quality in the delivered product. One of the key quality measures is the delivery of a system that meets the customer's requirements. Failure to meet the customer's requirements may engender significant re-design, which in turn will cost money, delay product introduction and may seriously damage the developer's credibility. For these reasons, the problem of developing a precise and unambiguous statement of requirements for a proposed system is perhaps one of the most challenging problems within software engineering today. Formal, model-based specification languages such as the Z notation have been widely adopted within the context of requirements engineering, to provide a vehicle for the development of precise and unambiguous specifications. However, the mathematical foundation upon which these notations are based often makes them unapproachable and difficult to assimilate by a non-specialist reader. The problem then faced is that if the customer cannot understand the semantics of the specification, how can the customer agree that the specification is indeed a true reflection of the requirements for the desired system? Several researchers have proposed that rapid prototyping and animation of specifications can be used to increase the customer's understanding of the formal specification. This is achieved by executing specification components on candidate data and observing that the behaviour is as expected. However this requires that the original formal specification be reliably transformed into a representation capable of being executed within a computer system. To achieve this aim requires the support of computer-based tools able to assist the requirements engineer in capturing, manipulating and transforming the formal specification in an efficient and consistent manner. This thesis describes the research and development of the TranZit tool, which is a Z notation editor, checker and transformation system. TranZit supports the efficient capture and maintenance of Z notation specifications using the Windows Graphical User Interface, supported by a suite of powerful language-driven features. In addition TranZit contains a highly integrated and optimised syntax and type checker, combining traditional compiler design techniques with innovative use of object-oriented data structures and methods, to assist the requirements engineer in ensuring the internal consistency of the captured specification. Most importantly, TranZit contains a novel transformation engine, which is capable of transforming a captured Z specification into an executable representation based on extensions to LISP, suitable for direct execution in an animation environment. This process is supported by an eclectic strategy combining automated transformation with user assistance, to overcome many of the well-documented problems associated with transforming non-executable clauses in formal specifications.

The packaging and product supply chain is currently undergoing a digital transformation that changes the way organizations manage data. Cloud-based software is an emerging technological innovation entirely focused on harnessing the power of packaging/product specifications to create efficiencies. These applications coordinate the data that millions of SKUs worldwide are generating into a harmonized system that will not only organize the SKUs but also create valuable information that will allow stakeholders to make decisions based upon data-driven insights. Specifications are the DNA-level information of packaging and products. Items such as the bill of materials, technical drawings, and inventory are stored together to create a traceable trail of information for stakeholders along the supply chain to refer to in the face of recalls, sustainability reports, and root cause analysis of procurement delays. Organizations have gone from storing this data on paper to creating a digital trail with manual processes and legacy systems on the computer. However, these systems cannot contend with the sheer amount of data companies now possess, wasting time and money trying to organize it all. In addition, packaging and product specification data lacks a common language that creates consistency and reduces errors; tracing an item to its source is a laborious endeavor; and resource investment is trying to solve the problem with existing manual processes and legacy systems when funding should go towards an innovative, cloud-based solution. Such a system would be able to process data and create a standardized template for specifications. This organization would allow for fast querying and advanced analytics that turn into visualizations that illustrate the insights. This framework would create a single point of truth for specifications that would enhance how companies along the supply chain collaborate and share information and streamline packaging and product creation workflow. Software solutions for specification data management exist in varying levels of involvement and installation that allow stakeholders to find a model that fits their needs in an ever-changing supply chain management landscape.

Muscle satellite cells are a distinct population of myogenic progenitors that mediate the postnatal growth and regeneration of skeletal muscle. To gain insight into the genetic regulation of satellite cell function during muscle regeneration, genes expressed specifically in these cells were identified by representational difference analysis of cDNAs. Notably, the paired-box transcription factor Pax7 was isolated as a gene specifically expressed in quiescent and activated satellite cells. Cell culture and histological analysis of PaxZ-deficient muscle revealed a complete absence of satellite cells. This result demonstrates a requirement for Pax7 upstream of MyoD and Myf5 in the specification of muscle satellite cells. Consistent with their lack of satellite cells, adult PaxT mice displayed an aggravated muscle wasting phenotype characterized by spinal kyphosis and reduced muscle mass. Acute muscle damage led to extensive calcification and deposition of adipose and fibrotic tissues with the appearance of rare regenerated myofibers. Importantly, analysis of Pax7 muscle suspensions indicated that myogenic cells expressing Pax3 and MyoD were responsible for this low level of regeneration. To characterize the role of adult stem cells in skeletal muscle, we investigated the myogenic potential of muscle-derived CD45+:Sca1+ cells in vivo during regeneration and in vitro using coculture assays. CD45+ and Sca1+ cells isolated from uninjured muscle were uniformly non-myogenic. Strikingly, 7-10% of CD45+:Sca1+ cells purified from regenerating muscle activated the myogenic program by a Pax7-dependent mechanism in response to activation of the Wnt signaling pathway. Furthermore, expression of Pax7 was sufficient to induce myogenic commitment in CD45f+Scal cells from uninjured muscle. This result demonstrates that non-satellite cell derived myogenic progenitors possess a physiological role in muscle regeneration and tissue homeostasis. Taken together, this work establishes a requirement for Pax7 in the specification of muscle satellite cells and for the myogenic recruitment of adult stem cells populations during tissue repair. Importantly, these studies also suggest that targeted therapies to activate Wnt signaling and Pax7 expression in adult stem cells will be effective for promoting muscle regeneration in patients with degenerative neuromuscular diseases or muscular dystrophies. / Thesis / Doctor of Philosophy (PhD)

No description available.

The ERK-MAPK pathway is a dynamic signaling module, conserved across Eukarya, and capable of processing a myriad of environmental and cellular signals. It has been implicated in controlling important cell fate decisions in many cell types and species. In mES cells, growth factor activation of the ERK-MAPK pathway is involved in the earliest stages of lineage segregation, however very little is currently known about the mechanism by which this is accomplished. Taking a loss-of-function gene targeting approach I have reexamined the relative contribution of ERK2 activity to FGF-ERK signaling. Although ERK2 depletion results in an attenuation of the combined ERK1/2 activity, this is compensated for by the hyperactivation of the remaining ERK1 isozyme. Normal ERK1/2 function can be restored to ERK2 deficient cells by transgenic expression of either ERK1 or ERK2, indicating a degree of functional redundancy between both isoforms. When subjected to the appropriate cues, lineage commitment proceeded normally in ERK2 deficient cells, however increased self-renewal was observed under standard culture conditions. Several attempts were made to further probe ERK1/2 function by siRNA depletion, and dominant negative inhibition of ERK1 in Erk2 knockout cells, however both approaches failed to provide further insight. Furthermore, taking a candidate approach, the role of Srf, a canonical target of ERK1/2 signaling, was examined. Initial experiments indicated a role for SRK in neural differentiation, however due to issues of culture adaptation and instability in several cell lines it was not possible to conclude this line of research within the time frame of this thesis. IP-MS/MS analysis identified several proteins known to interact with ERK2 and indicated an involvement in nuclear pore function through TPR as well as transcriptional and translational regulation through RSK proteins. Moreover, this study identified DUSP6 and DUSP9 as the primary induced dual specificity phosphatases that regulate ERK2 activity in mES cells. To further probe the functional significance of the ERK:p90RSK interaction I examined a mES cell line genetically depleted for PDK1, a crucial regulator of p90RSK function. This cell line exhibits no detectable p90RSK activity, however in contrast to studies in other cell lines, p90RSK activity is dispensable for mitogen-induced cFos expression in mES cells. Subsequent experiments demonstrated a requirement for PDK1 activity in either the specification or maintenance of mES cell derived neurons. Further analysis indicated that p90RSK may be involved in a negative feedback loop regulating ERK1/2 activity, and if so may represent a point whereby ERK1/2 activity can be manipulated. To examine this I determined the effect pharmacological inhibition of p90RSK has on ERK1/2 activity and self-renewal using a novel p90Rsk inhibitor, BI-D1870. Although treatment with BI-D1870 correlated with enhanced ERK1/2 phosphorylation, the offtarget effects this molecule exhibits made it impossible to draw any firm conclusions from these experiments. Overall this study has demonstrated a degree of redundancy between ERK1/2 isozymes in mES cells. It has highlighted the complex nature of ERK1/2 regulation as well as the robustness of this pathway to perturbations in ERK dose. Furthermore, it has underscored some of the common pitfalls encountered when studying differentiation phenotypes in mES cells. Although this study failed to highlight anything more than a coincidental relationship between ERK1/2 activity and self-renewal capacity of mES cells, it has helped to highlight some important behavioral characteristics of the FGF-MAPK pathway in mES cells and provide a platform for further study.

During embryonic development, multipotent cardiovascular progenitor cells (MCPs) are specified from early mesoderm. Although the core cardiac transcriptional machinery acting during cardiac cell differentiation is relatively well known, the molecular mechanism acting upstream of these cardiac transcriptional factors, and promoting cardiac progenitor specification from early mesoderm remains poorly understood. We used embryonic stem cell (ESC) differentiation as a model to dissect the molecular mechanisms implicated in cardiovascular progenitor specification. Using ESCs, in which gene expression can be temporally regulated, we showed that transient expression of Mesp1 dramatically accelerates and enhances multipotent cardiovascular progenitor specification through an intrinsic and cellular autonomous mechanism. Using genome wide transcriptional analysis, we found that Mesp1 rapidly activates and represses a discrete set of genes. Using chromatin immunoprecipitation, we showed that Mesp1 directly binds to regulatory DNA sequences located in the promoter of many key genes belonging to the core cardiac transcriptional machinery, resulting in their rapid upregulation. Mesp1 also directly and strongly represses the expression of key genes regulating other early mesoderm and endoderm cell fates. Using engineered ESC expressing the green fluorescent protein under the control of the Mesp1 promoter, we isolated Mesp1 expressing cells in differentiating ESCs allowing characterization of the cellular and molecular mechanisms underlying cardiovascular specification. Our results demonstrate that Mesp1 acts as a key regulatory switch during cardiovascular specification, residing at the top of the hierarchy of the gene network responsible for cardiovascular cell fate determination. Moreover our results place Mesp1 upstream of the specification of both first and second heart fields and provide novel and important insights into the molecular mechanisms underlying the earliest step of cardiovascular specification. We identified cell surface markers expressed allowing the isolation of early cardiovascular progenitors and provide potentially novel methods for dramatically increasing the number of cardiovascular cells for cellular therapy in humans.