Applying Equity Literacy’s Four Abilities to Middle Schools for the Benefit of Students Experiencing Homelessness

In this essay, I use the McKinney-Vento Homeless Education Assistance Improvements Act of 2001 to define homelessness and describe its prevalence in United States public schools. I present readers with statistics about student homelessness and situate Gorski’s equity literacy within the progressive, equity-oriented foundations of the middle school movement and as a means by which stakeholders could begin to address homelessness in their contexts. After presenting the four abilities of equity literate educators, I apply the abilities to the nuances of student homelessness in the middle grades

Doctor of Philosophy

dissertationIt is surprising that there are only about 80 described congenital diseases that result from mutations in any of the 1% of genes in the human genome (~200-250 genes) dedicated to protein glycosylation. It is these glycosylation events that provide tremendous protein diversity and contribute to proper protein folding, function, and subcellular localization. Thus, the rarity with which human congenital disorders of glycosylation (CDGs) are observed despite the myriad of genes involved in this process and the apparent critical role for proper protein form and function suggests that glycosylation is critical for proper development. However, the role of glycans in development has been largely understudied and there are only a few genetic models of human CDGs in existence. Glycosylation occurs by the enzymatic addition of sugar-derived molecules and is estimated to provide 10-104 times more diversity than the unmodified proteome alone. Glycans are present on the surface of nearly every cell within multicellular organisms and are capable of facilitating communication with the cell and its environment and with other cells and also have structural roles as critical components of extracellular matrix. However, the complexity of glycan formation makes it difficult to understand the diverse and pleiotropic roles glycans play in cellular biology. The utility of Drosophila to elucidate the role of glycans in development as well as disease has only been appreciated recently. Herein, I further demonstrate the utility of Drosophila to understand the roles of both N- and O-glycans in development and cell signaling. Furthermore, I utilize the fly to understand the biology of glycans in a human disorder of congenital disease, Peters Plus Syndrome. I demonstrate that the previously reported Dpp signal antagonism achieved by the sugar derivative UDP-N-Acetyglucosamine (GlcNAc) is carried out by the synthesis of a chondroitin-sulfate sink produced in the embryonic cardiac mesoderm and by the addition of GlcNAc to the type I receptor Saxophone to limit Dpp signal through Tkv exclusively. Furthermore, loss of the Drosophila ortholog of the human B3GLCT gene, sugarcoated, demonstrates a critical role for O-linked mucins in cell hypertrophic growth during larval development and oogenesis and demonstrates a potential role for human mucins in chondrocyte hypertrophy-an event required for the majority of human bone growth-and a potential mechanistic reason for growth defects observed in Peters Plus Syndrome patients

Learning Through Crisis and Paradox in Justice-Oriented Teacher Education

In this article we explore some of the challenges, constraints, and what we refer to as glimmers of revelation that occurred during an experiential, community-based teacher education course that we designed and co-taught in spring 2015. Trying to take seriously Kumashiro’s (2009) notions that justice oriented teacher education happens “only when we ourselves are still struggling with questions about the ‘what else,’ ‘how else,’ and ‘where else’ that are involved” in this kind of teaching [emphasis added] (p. xxv), we explore moments where we grappled with the paradox, partiality, uncertainty, and discomfort (Kumashiro, 2009) that often accompany our commitments as middle grades teacher educators attempting to enact anti-oppressive teaching practices

Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench

Recently, high-throughput sequencing (HTS) has revealed compelling details about the small RNA (sRNA) population in eukaryotes. These 20 to 25 nt noncoding RNAs can influence gene expression by acting as guides for the sequence-specific regulatory mechanism known as RNA silencing. The increase in sequencing depth and number of samples per project enables a better understanding of the role sRNAs play by facilitating the study of expression patterns. However, the intricacy of the biological hypotheses coupled with a lack of appropriate tools often leads to inadequate mining of the available data and thus, an incomplete description of the biological mechanisms involved. To enable a comprehensive study of differential expression in sRNA data sets, we present a new interactive pipeline that guides researchers through the various stages of data preprocessing and analysis. This includes various tools, some of which we specifically developed for sRNA analysis, for quality checking and normalization of sRNA samples as well as tools for the detection of differentially expressed sRNAs and identification of the resulting expression patterns. The pipeline is available within the UEA sRNA Workbench, a user-friendly software package for the processing of sRNA data sets. We demonstrate the use of the pipeline on a H. sapiens data set; additional examples on a B. terrestris data set and on an A. thaliana data set are described in the Supplemental Information. A comparison with existing approaches is also included, which exemplifies some of the issues that need to be addressed for sRNA analysis and how the new pipeline may be used to do this

Global discovery and characterization of small non-coding RNAs in marine microalgae

Background Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi. Results Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions. Conclusions This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and maybe used for acclimation to environmental conditions

The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs

Motivation: RNA interference, a highly conserved regulatory mechanism, is mediated via small RNAs (sRNA). Recent technical advances enabled the analysis of larger, complex datasets and the investigation of microRNAs and the less known small interfering RNAs. However, the size and intricacy of current data requires a comprehensive set of tools, able to discriminate the patterns from the low-level, noise-like, variation; numerous and varied suggestions from the community represent an invaluable source of ideas for future tools, the ability of the community to contribute to this software is essential. Results: We present a new version of the UEA sRNA Workbench, reconfigured to allow an easy insertion of new tools/workflows. In its released form, it comprises of a suite of tools in a user-friendly environment, with enhanced capabilities for a comprehensive processing of sRNA-seq data e.g. tools for an accurate prediction of sRNA loci (CoLIde) and miRNA loci (miRCat2), as well as workflows to guide the users through common steps such as quality checking of the input data, normalization of abundances or detection of differential expression represent the first step in sRNA-seq analyses

Evaluation of First-Order Actuator Dynamics and Linear Controller for a Bio-Inspired Rotating Empennage Fighter Aircraft

This paper considers the problem of stabilizing a bio-inspired fighter aircraft variant at its Air Combat Maneuver Condition. The aircraft equations of motion are linearized, and an infinite-horizon linear quadratic regulator design is conducted for this aircraft. Included in the dynamics are first-order actuator models, which have the effect of slowing actuator responses. This is particularly important for the bio-inspired variant because it requires rotation of the empennage, which has relatively large inertia. The bio-inspired variant open-loop system is unstable in the short period and Dutch roll modes, which is mitigated in the closed-loop system. Monte Carlo simulation responses to initial condition dispersions, aerodynamic model errors, and atmospheric turbulence are presented for the controlled aircraft system. These simulations demonstrate the robust properties of the presented control design. Discussion is dedicated to control designs neglecting input from throttle and the rotating tail, and corresponding successes. Whereas the bio-inspired variant aircraft can be successfully controlled without rotating tail input, effects from neglecting throttle input show throttle should be included, but perhaps in an alternate loop such as a speed controller

Self-assembly of Fmoc-tetrapeptides based on the RGDS cell adhesion motif

Self-assembly in aqueous solution has been investigated for two Fmoc [Fmoc ¼ N-(fluorenyl)-9-methoxycarbonyl] tetrapeptides comprising the RGDS cell adhesion motif from fibronectin or the scrambled sequence GRDS. The hydrophobic Fmoc unit confers amphiphilicity on the molecules, and introduces aromatic stacking interactions. Circular dichroism and FTIR spectroscopy show that the self-assembly of both peptides at low concentration is dominated by interactions among Fmoc units, although Fmoc-GRDS shows b-sheet features, at lower concentration than Fmoc-RGDS. Fibre X-ray diffraction indicates b-sheet formation by both peptides at sufficiently high concentration. Strong alignment effects are revealed by linear dichroism experiments for Fmoc-GRDS. Cryo-TEM and smallangle X-ray scattering (SAXS) reveal that both samples form fibrils with a diameter of approximately 10 nm. Both Fmoc-tetrapeptides form self-supporting hydrogels at sufficiently high concentration. Dynamic shear rheometry enabled measurements of the moduli for the Fmoc-GRDS hydrogel, however syneresis was observed for the Fmoc-RGDS hydrogel which was significantly less stable to shear. Molecular dynamics computer simulations were carried out considering parallel and antiparallel b-sheet configurations of systems containing 7 and 21 molecules of Fmoc-RGDS or Fmoc-GRDS, the results being analyzed in terms of both intermolecular structural parameters and energy contributions

MicroRNAs Associated with Caste Determination and Differentiation in a Primitively Eusocial Insect

In eusocial Hymenoptera (ants, bees and wasps), queen and worker adult castes typically arise via environmental influences. A fundamental challenge is to understand how a single genome can thereby produce alternative phenotypes. A powerful approach is to compare the molecular basis of caste determination and differentiation along the evolutionary trajectory between primitively and advanced eusocial species, which have, respectively, relatively undifferentiated and strongly differentiated adult castes. In the advanced eusocial honeybee, Apis mellifera, studies suggest that microRNAs (miRNAs) play an important role in the molecular basis of caste determination and differentiation. To investigate how miRNAs affect caste in eusocial evolution, we used deep sequencing and Northern blots to isolate caste-associated miRNAs in the primitively eusocial bumblebee Bombus terrestris. We found that the miRNAs Bte-miR-6001-5p and -3p are more highly expressed in queen- than in worker-destined late-instar larvae. These are the first caste-associated miRNAs from outside advanced eusocial Hymenoptera, so providing evidence for caste-associated miRNAs occurring relatively early in eusocial evolution. Moreover, we found little evidence that miRNAs previously shown to be associated with caste in A. mellifera were differentially expressed across caste pathways in B. terrestris, suggesting that, in eusocial evolution, the caste-associated role of individual miRNAs is not conserved

miRCat2: Accurate prediction of plant and animal microRNAs from next-generation sequencing datasets

Motivation: MicroRNAs are a class of ∼21-22 nucleotide small RNAs which are excised from a stable hairpin-like secondary structure. They have important gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in eukaryotes. There are several computational tools for miRNA detection from next-generation sequencing (NGS) datasets. However, many of these tools suffer from high false positive and false negative rates. Here we present a novel miRNA prediction algorithm, miRCat2. miRCat2 incorporates a new entropy-based approach to detect miRNA loci, which is designed to cope with the high sequencing depth of current NGS datasets. It has a user-friendly interface and produces graphical representations of the hairpin structure and plots depicting the alignment of sequences on the secondary structure. Results: We tested miRCat2 on a number of animal and plant datasets and present a comparative analysis with miRCat, miRDeep2, miRPlant and miReap. We also use mutants in the miRNA biogenesis pathway to evaluate the predictions of these tools. Results indicate that miRCat2 has an improved accuracy compared with other methods tested. Moreover, miRCat2 predicts several new miRNAs that are differentially expressed in wildtype versus mutants in the miRNA biogenesis pathway. Availability: miRCat2 is part of the UEA small RNA Workbench and is freely available from http://srnaworkbench.cmp.uea.ac.uk