Transposable elements and genome size dynamics in Gossypium

Although eukaryotic organisms display a wide range in genome size, from as little as 9 Megabases (Mb) in some fungi to over 690,000 Mb in the diatom Navicula pelliculosa, there is only an approximate 20-fold variation in the number of protein coding genes. Additionally, this variation in genome size is not directly correlated with organismal or morphological/physiological complexity. This striking contradiction has historically been termed the C-value paradox . Research conducted over the past half century has revealed that most genome size variation in plants can be ascribed to the repetitive fraction of the genome, particularly LTR-retrotransposons. Furthermore, recent studies in maize and rice have revealed the tremendously dynamic nature of LTR-retrotransposons, where transposition has occurred recently and rapidly, resulting in a highly dynamic genome. To date, most studies of genome size evolution and transposable element dynamics has been conducted in the grasses, or among a few distantly related model dicots. In the work presented here, the cotton genus, Gossypium, was used to study genome size evolution and transposable element dynamics among closely related, long-lived species, whose members diverged within the last 5-7 million years. Provided is a description of the various types of repetitive sequences present and their relative contributions to overall extant genome size among three Gossypium species and a phylogenetic outgroup, Gossypioides kirkii.Results indicate that one type of gypsy-like LTR-retrotransposon, Gorge3, is responsible for much of the genome size variation in the genus. However, different transposable elements behave differently in different genomes, and estimated copy numbers are not always correlated with genome size. Further detailed analysis of the evolutionary history of Gorge3 suggests that this LTR-retrotransposon underwent lineage-specific proliferation in each clade, and that these proliferation events occurred in an episodic manner at different time points in each of the genomes investigated. Using a novel modeling approach, it is shown that although lineage-specific transposition of Gorge3 has occurred in the taxa having small genomes, the magnitude of DNA removal outweighs DNA gain through transposition, ultimately leading to genome downsizing. Investigation of the transpositional nature and timing of two other relatively abundant repetitive sequences, copia-like LTR-retrotransposons and non-LTR LINEs, indicates that lineage-specific amplification has occurred for each sequence type in each lineage. Copia-like LTR-retrotransposons, similar to that found for Gorge3, undergo episodic proliferation at different time points in each genome. In contrast, non-LTR LINEs appear to accumulate in a more stochastically regular manner, and phylogenetic analysis suggests that the majority of the Gossypium LINE population is dominated by ancient sequences that predate divergence events within the genus. The cumulative results of this dissertation work indicate that transposable element proliferation has occurred recently and rapidly in all genomes investigated and their differential accumulation or retention contributes significantly to variation in genome size in Gossypium

Cooking up concept maps

Concept maps allow students to visually work through an idea for potentially useful search terms. A common roadblock students experience in the research process is identifying central concepts in their research questions and devising useful ways to reframe search terms. Concept mapping is one instructional strategy that can be used to help students better identify the central concepts in their research questions and expand on other ways these concepts are articulated in the literature

Whipping up the “Why Paper”: Inquiry into diverse perspectives

Students are introduced to various databases that provide access to alternative perspectives and to an advanced organizer designed to foster critical evaluation of sources. In a Valuing Cultural Diversity course, required for all undergraduate education majors, students are asked to write a Why paper to investigate and understand alternative perspectives, looking particularly at the perspectives of a cultural group different from their own

New avenues for integrating information literacy into the curriculum

A generally understood mission of library instruction programs is to promote information literacy (IL) and critical thinking across the curriculum. The majority of programmatic IL collaborations with higher education core curricula are found in introductory composition or communication courses. Other more unconventional avenues offer potentially more effective ways to teach students the basic IL concepts and skills. At the University of Nevada, Las Vegas (UNLV), conversations with College of Education faculty helped librarians identify a strategic and unique point of entry for IL instruction. Using the ADDIE model as a conceptual framework, librarians and an instructional designer met with the course coordinators for the Valuing Cultural Diversity course to collaboratively develop tools and assignments that deconstruct and scaffold the research process for students. The systematic approach for identifying this course, developing the partnership, creating the assessment tools, and refining instruction and assignments based on our findings will be discussed

Planar and spherical stick indices of knots

The stick index of a knot is the least number of line segments required to build the knot in space. We define two analogous 2-dimensional invariants, the planar stick index, which is the least number of line segments in the plane to build a projection, and the spherical stick index, which is the least number of great circle arcs to build a projection on the sphere. We find bounds on these quantities in terms of other knot invariants, and give planar stick and spherical stick constructions for torus knots and for compositions of trefoils. In particular, unlike most knot invariants,we show that the spherical stick index distinguishes between the granny and square knots, and that composing a nontrivial knot with a second nontrivial knot need not increase its spherical stick index

Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy

Chimeric antigen receptor (CAR) T-cell therapy has produced remarkable anti-tumor responses in patients with B-cell malignancies. However, clonal kinetics and transcriptional programs that regulate the fate of CAR-T cells after infusion remain poorly understood. Here we perform TCRB sequencing, integration site analysis, and single-cell RNA sequencing (scRNA-seq) to profile CD8+ CAR-T cells from infusion products (IPs) and blood of patients undergoing CD19 CAR-T immunotherapy. TCRB sequencing shows that clonal diversity of CAR-T cells is highest in the IPs and declines following infusion. We observe clones that display distinct patterns of clonal kinetics, making variable contributions to the CAR-T cell pool after infusion. Although integration site does not appear to be a key driver of clonal kinetics, scRNA-seq demonstrates that clones that expand after infusion mainly originate from infused clusters with higher expression of cytotoxicity and proliferation genes. Thus, we uncover transcriptional programs associated with CAR-T cell behavior after infusion.Published versio

Can programme theory be used as a 'translational tool’ to optimise health service delivery in a national early years’ initiative in Scotland: a case study

Background Theory-based evaluation (TBE) approaches are heralded as supporting formative evaluation by facilitating increased use of evaluative findings to guide programme improvement. It is essential that learning from programme implementation is better used to improve delivery and to inform other initiatives, if interventions are to be as effective as they have the potential to be. Nonetheless, few studies describe formative feedback methods, or report direct instrumental use of findings resulting from TBE. This paper uses the case of Scotland’s, National Health Service, early years’, oral health improvement initiative (Childsmile) to describe the use of TBE as a framework for providing feedback on delivery to programme staff and to assess its impact on programmatic action.<p></p> Methods In-depth, semi-structured interviews and focus groups with key stakeholders explored perceived deviations between the Childsmile programme 'as delivered’ and its Programme Theory (PT). The data was thematically analysed using constant comparative methods. Findings were shared with key programme stakeholders and discussions around likely impact and necessary actions were facilitated by the authors. Documentary review and ongoing observations of programme meetings were undertaken to assess the extent to which learning was acted upon.<p></p> Results On the whole, the activities documented in Childsmile’s PT were implemented as intended. This paper purposefully focuses on those activities where variation in delivery was evident. Differences resulted from the stage of roll-out reached and the flexibility given to individual NHS boards to tailor local implementation. Some adaptations were thought to have diverged from the central features of Childsmile’s PT, to the extent that there was a risk to achieving outcomes. The methods employed prompted national service improvement action, and proposals for local action by individual NHS boards to address this.<p></p> Conclusions The TBE approach provided a platform, to direct attention to areas of risk within a national health initiative, and to agree which intervention components were 'core’ to its hypothesised success. The study demonstrates that PT can be used as a 'translational tool’ to facilitate instrumental use of evaluative findings to optimise implementation within a complex health improvement programme.<p></p&gt