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The concepts of (digital) platform and (digital) infrastructure have been widely used and discussed in recent media research, and in neighbouring fields such as science and technology studies (STS). Yet there is considerable confusion about these concepts and the relations between them. This article seeks to bring these concepts together more coherently by showing how “platformisation” might be understood in terms of its impacts on information infrastructure, including on the principles of openness and generativity underlying early internet architecture, and potential further effects on media and culture deriving from those impacts. To develop this perspective, we draw on research from legal studies which: (a) articulates these principles more fully than in recent media studies and STS; (b) understands infrastructures as resources subject to political contestation; and (c) in the work of Julie Cohen, interprets digital platforms as strategies for disciplining infrastructures. We discuss how such a perspective might complement approaches to digital platforms and infrastructures to be found in political economy of media and internet governance research. We then apply the perspective to a case study: the transition of online music from chaotic experiments with alternative models of distribution in the early century to a thoroughly platformised environment in the 2020s.

The diverse functions of WASP, the deficiency of which causes Wiskott-Aldrich syndrome (WAS), remain poorly defined. We generated three isogenic WAS models using patient induced pluripotent stem cells and genome editing. These models recapitulated WAS phenotypes and revealed that WASP deficiency causes an upregulation of numerous RNA splicing factors and widespread altered splicing. Loss of WASP binding to splicing factor gene promoters frequently leads to aberrant epigenetic activation. WASP interacts with dozens of nuclear speckle constituents and constrains SRSF2 mobility. Using an optogenetic system, we showed that WASP forms phase-separated condensates that encompasses SRSF2, nascent RNA and active Pol II. The role of WASP in gene body condensates is corroborated by ChIPseq and RIPseq. Together our data reveal that WASP is a nexus regulator of RNA splicing that controls the transcription of splicing factors epigenetically and the dynamics of the splicing machinery through liquid-liquid phase separation.

Recent studies using human pluripotent stem cells (hPSCs) have developed protocols to induce kidney-lineage cells and reconstruct kidney organoids. However, the separate generation of metanephric nephron progenitors (NPs), mesonephric NPs, and ureteric bud (UB) cells, which constitute embryonic kidneys, in in vitro differentiation culture systems has not been fully investigated. Here, we create a culture system in which these mesoderm-like cell types and paraxial and lateral plate mesoderm-like cells are separately generated from hPSCs. We recapitulate nephrogenic niches from separately induced metanephric NP-like and UB-like cells, which are subsequently differentiated into glomeruli, renal tubules, and collecting ducts in vitro and further vascularized in vivo. Our selective differentiation protocols should contribute to understanding the mechanisms underlying human kidney development and disease and also supply cell sources for regenerative therapies.

Alzheimer’s Disease (AD) is a complex brain disorder that affects at least one in every ten persons aged 65 and above worldwide. The pathogenesis of this disorder remains elusive. In this work, we utilized a rich set of publicly available gene expression data to elucidate the genes and molecular processes that may underlie its pathogenesis. We developed a new ranking score to prioritize molecular pathways enriched in differentially expressed genes during AD. After applying our new ranking score, GO categories such as cotranslational protein targeting to membrane, SRP-dependent cotranslational protein targeting to membrane, and spliceosomal snRNP assembly were found to be significantly associated with AD. We also confirm the protein-protein interaction between APP, NPAS4 and ARNT2 and explain that this interaction could be implicated in AD. This interaction could serve as a theoretical framework for further analyses into the role of NPAS4 and other immediate-early genes in AD pathogenesis., 2020, Includes bibliography., Degree granted: Thesis (M.S.)--Florida Atlantic University, 2020., Collection: FAU Electronic Theses and Dissertations Collection

Oxidation by reactive oxygen species is the major source of RNA damaging insult in living organisms. Increased RNA oxidation has been strongly implicated in a wide range of human diseases; predominantly neurodegeneration. Oxidized RNA should be removed from the cellular system to prevent their deleterious effect to the cells and organisms. In eukaryotic cells, mitochondria are the major intracellular sources of ROS and may cause greater damage to the mitochondrial RNA. In this study, we first investigated the RNA oxidation, by measuring the level of 8-hydroxy-Guanosine (8-oxo-Guo), inside mitochondria and cytoplasm in cultured human cells. We discovered that the mitochondrial 8-oxo-Guo is higher than its cytoplasmic counterparts under both normal growth and oxidative stress condition. Next, we explored the role of human polynucleotide phosphorylase (hPNPase) in controlling RNA oxidation inside mitochondria and cytoplasm. hPNPase binds to oxidized RNA with higher affinity, reduces the 8-oxo-Guo level in total RNA and protects cells against oxidative stress. In this study, the molecular mechanism of hPNPase in 8-oxo-Guo reduction was investigated. First, the effect of hPNPase activities on the 8-oxo-Guo level in mitochondria and cytoplasm was examined. The knockdown of hPNPase increased both the mitochondrial and cytoplasmic 8-oxo-Guo, whereas overexpression had the opposite effect. Second, our study revealed that hSUV3, an RNA helicase that forms a functional complex with hPNPase in mitochondria, was dispensable in reducing 8-oxo-Guo levels., 2019, Includes bibliography., Degree granted: Dissertation (Ph.D.)--Florida Atlantic University, 2019., Collection: FAU Electronic Theses and Dissertations Collection

This dissertation addresses the ultimate strength analysis of nonlinear beam-columns under axial compression, the sensitivity of the ultimate strength, structural optimization and reliability analysis using ultimate strength analysis, and Reliability-Based Design Optimization (RBDO) of the nonlinear beam-columns. The ultimate strength analysis is based on nonlinear beam theory with material and geometric nonlinearities. Nonlinear constitutive law is developed for elastic-perfectly-plastic beam cross-section consisting of base plate and T-bar stiffener. The analysis method is validated using commercial nonlinear finite element analysis. A new direct solving method is developed, which combines the original governing equations with their derivatives with respect to deformation matric and solves for the ultimate strength directly. Structural optimization and reliability analysis use a gradient-based algorithm and need accurate sensitivities of the ultimate strength to design variables. Semi-analytic sensitivity of the ultimate strength is calculated from a linear set of analytical sensitivity equations which use the Jacobian matrix of the direct solving method. The derivatives of the structural residual equations in the sensitivity equation set are calculated using complex step method. The semi-analytic sensitivity is more robust and efficient as compared to finite difference sensitivity. The design variables are the cross-sectional geometric parameters. Random variables include material properties, geometric parameters, initial deflection and nondeterministic load. Failure probabilities calculated by ultimate strength reliability analysis are validated by Monte Carlo Simulation. Double-loop RBDO minimizes structural weight with reliability index constraint. The sensitivity of reliability index with respect to design variables is calculated from the gradient of limit state function at the solution of reliability analysis. By using the ultimate strength direct solving me

Summary: Oxidative stress (OS) is strongly implicated in age-related neurodegeneration and other diseases. Under OS, the production of excessive oxidants leads to increased damages to cellular components. Recently, RNA has been discovered as a major target of oxidative damage, including the creation of abasic sites. In this work, we developed a method for quantifying abasic RNA in cell. Using this method, we have examined the potential role of the RNA-processing cellular foci, stress granule (SG) and processing bodies (PB) in eliminating abasic RNA in situ. We demonstrated that RNA is a major target of oxidative damage, constituting the majority of OS-induced abasic nucleic acids in HeLa cell. Importantly, the level of abasic RNA is strongly correlated with SG abundance. Furthermore, inhibition of SG/PB formation causes accumulation of abasic RNA, suggesting that SG/PB participates in removing oxidized RNA and protects cells under OS, which offers novel targets for therapeutic intervention in age-related diseases., 2016, Includes bibliography., Degree granted: Thesis (M.S.)--Florida Atlantic University, 2016., Collection: FAU Electronic Theses and Dissertations Collection

A novel approach is proposed to unwrap the phase maps of two fringe patterns in fringe pattern projection-based profilometry. In contrast to existing techniques, where spatial frequencies (i.e., the number of fringes on a pattern) of the two fringe patterns must be integers and coprime, the proposed method is applicable for any two fringe patterns with different fringe wavelengths (i.e., the number of pixels in a fringe) and thus provides more flexibility in the use of fringe patterns. Moreover, compared to the existing techniques, the proposed method is simpler in its implementation and has better antierror capability. Theoretical analysis and experiment results are presented to confirm the effectiveness of the proposed method.

High penetration of variable generation such as wind power increases the demands on frequency control. The same applies to island operation and in particular if this involves variable generation, which is planned at the Danish island Bornholm. While it is obvious that the frequency control need to be considered, the disturbances caused to this control by the hourly dispatch of generation has received less attention and is the focus of this paper. Based on years of recorded PMU data, statistics of frequency events and analysis of frequency quality are made to demonstrate the relation between the frequency deviations and hourly scheduled generation. A simple model is given to reproduce these deterministic frequency variations. Simulations indicate that smaller system size as is typical for island operation does not necessarily increase these frequency variations provided load, generation, load response characteristic and system inertia are reduced with the same factor as compared to the large system.

Summary: tmRNA is a small stable RNA present in Eubacteria. Through a mechanism called trans-translation, tmRNA mediates ribosome rescue and quality control of proteins and mRNA. In this study, the Escherichia coli (E. coli) mutant lacking tmRNA was demonstrated hypersensitive to oxidative stress. The role of tmRNA-mediated surveillance mechanism in protecting E. coli cell under oxidative stress condition was examined. The tmRNA-mediated tagged protein levels were elevated in cells under oxidative stress condition, demonstrating the enhanced need for tmRNA under such condition. Our results suggest that mRNA damage by oxidative stress may cause reduced cell viability, and that tmRNA is required to rescue cells under such condition. Furthermore, our observations showed that tmRNA is required for the optimal growth of E. coli under normal aeration but not under anaerobic condition, suggesting that oxidation ofmRNA is the major reason for requirement oftmRNA during normal aeration., 2007, Includes bibliography., Degree granted: Thesis (M.S.)--Florida Atlantic University, 2007., Charles E. Schmidt College of Science, Collection: FAU Electronic Theses and Dissertations Collection

Summary: Three important exoribonucleases degrading RNAs in sequence-independent manner, RNase II, RNase Rand polynucleotide phosphorylase (PNPase), were shown to protect cells against oxidative stress. This is presumably due to the function of the exoribonucleases in the removal of oxidized RNA in cells. MutT pyrophosphohydrolase .was previously reported to scavenge oxidized nucleotides 8-oxoGTP and 8-oxoGDP, prevent their incorporation into RNA. Deficiency of MutT may lead to an increase in the level of 8-oxoG in RNA, which may enhance the requirement of the RNA surveillance function of the exoribonucleases. This study focuses on the roles of the RNA-degradation exoribonucleases in the removal of oxidatively-damaged RNA in the mutT background. This work shows that mutT mutation enhances the sensitivity of the RNase mutants to hydrogen peroxide. Growth defect of the pnp mutT mutant was detected even under normal aeration, but was rescued to the level of pnp mutant under anaerobic conditions. The pnp mutT mutant shows high mutator activity observed from LacZ reporter system and high level of 8-oxoG in RNA, strongly suggest that PNPase is responsible for removing 8-oxoG containing RNAs elevated in mutT background. Additionally, genetic instability observed from the mutant lacking RNase II and MutT supports the idea that RNase II may adopt a distinct pathway to reduce deleterious effect from oxidation challenge., 2007, Degree granted: Thesis (M.S.)--Florida Atlantic University, 2007.

Summary: Exoribonucleases degrade RNA and are important in RNA metabolism and gene expression. Mycoplasma genitalium, a bacterium with the smallest genome known, has only one identified exoribonuclease, RNase R (MgR). In this work RNA degradation properties of purified MgR were examined. As observed in Escherichia coli RNase R (EcR) studies, MgR degrades poly(A), rRNA, and oligoribonucleotides in 3'--->5' direction, though its substrate specificity and optimal activity requirements vary. Interestingly, MgR is sensitive to 2-O-methylation stopping downstream of such modifications in native rRNA and synthetic oligoribonucleotides. MgR removes the 3' trailer sequence from a tRNA precursor of M. genitalium and generates products equal to the mature tRNA, demonstrating a role of MgR in tRNA maturation. The 3' terminal CCA sequence and the acceptor stem of tRNA play a role in determining the formation of such products by MgR. These results suggest multiple functions of RNase R in RNA metabolism in Mycoplasma., Charles E. Schmidt College of Science, Degree granted: Thesis (M.S.)--Florida Atlantic University, 2006., Collection: FAU Electronic Theses and Dissertations Collection

Summary: In this work, we report that the only exoribonuclease in M. genitalium, RNase R, is able to generate mature 3'-ends. The aminoacyl-acceptor stem, CCA terminus and discriminator residue plays an important role in stopping RNase R digestion at the mature 3'-end. Disruption of the stem causes partial or complete degradation of the pre-tRNA, whereas extension of the stem results in the formation of a mature 3’-end. CC residues in CCA terminus and A or G residues at discriminator position are the most preferred residues for precise stopping of RNase R at mature 3’ end. The significance of this works shows that M. genitalium RNase R generates mature tRNA in a single step by recognizing features in the terminal domains of tRNA, a process requiring multiple RNases in most bacteria., 2013, Includes bibliography., Dissertation (Ph.D.)--Florida Atlantic University, 2013.