A new self-assessment teaching assistant survey for growth and development

During their time as Teaching Assistants (TAs), graduate students develop a variety of skills, knowledge, and attitudes, based on teaching and related facilitation experiences. As TAs move on to future opportunities, their prior experiences form a foundation upon which additional teaching experience builds. Presently, there are few tools to gauge pedagogical growth during graduate student involvement as TAs in a specific post-secondary course, or as a consequence of their participation in a specialized TA training or teaching program.  We created a model for TA development in SCIE 113 (First-year Seminar in Science) at the University of British Columbia. Based on this model, we designed a new survey for TAs to self-assess skills, knowledge and attitudes that they bring with them from prior experience, and those that they develop or further during their time as a TA in SCIE113. We administered the survey to 18 current and past SCIE 113 TAs as of December 2015, representing the complete population of TAs. The results showed that SCIE 113 TAs with similar levels of experience shared similar skills, knowledge, and attitudes as assessed by this survey. Those TAs with the most experience had greater abilities in roles previously identified as unique to the course. Others working with graduate students can use or adapt the survey questions to investigate and stimulate the growth of TAs in their course or program

Critical analysis of figures is as helpful as reading the whole paper: The data-centric ‘Figure Facts’ activity leads students to practice graph interpretation and helps them understand research papers better

Learning to interpret scholarly literature is critical training for evidence-based decision makers, including scientists. In a second-year organismal biology class, we compared the efficacy of two different activities, a ‘Summary Activity’ and ‘Figure Facts’, in directing students to practice graph interpretation and in promoting their comprehension of selected research papers. For the Summary Activity, students briefly summarized a research paper, presumably reading as they normally would. In contrast, the data-centric Figure Facts activity prompted students to interpret the article’s figures and link methods to results, and was previously shown to improve students’ data interpretation ability in an advanced neurobiology course (Round and Campbell 2013). In this study, after each activity, students self-reported reading behaviours via surveys and answered multiple choice questions measuring their understanding of the articles. Significantly more students engaged in figure interpretation when completing Figure Facts. Students also spent more time on the Results section and less time on the Abstract when doing Figure Facts compared to the Summary Activity. On multiple choice questions, students who prepared with Figure Facts outperformed peers who did summaries. Most students reported highly desirable learning gains from Figure Facts. However, when choosing to complete either activity, most students chose whichever they tried first. We conclude that a simple data-centred reading tool can compel students to practice data interpretation and enhance their grasp of scientific literature. Round, J. E., & Campbell, A. M. (2013). Figure Facts: encouraging undergraduates to take a data-centered approach to reading primary literature. CBE—Life Sciences Education, 12(1), 39-46

How the Fungi got into shape : cellular organization and morphogenetic gene evolution in phylum Chytridiomycota reveals mechanisms underlying the evolution of fungal body diversity

With their threadlike hyphal cells, fungi can invade the surface of a cheese, secreting digestive enzymes and soaking up the spoils. Although most fungi feed with hyphae, phylum Chytridiomycota produces various alternative cell shapes. Here I address three hypotheses regarding the evolution of cell shape. Firstly, Fungi inherited core genes for cellular morphogenesis from their most recent common ancestor and diversification of these genes through evolutionary time potentially contributed to morphological novelty. My phylogenomic surveys revealed duplications in seven families of actin-binding proteins predating the radiation of fungal phyla. Synthesizing previous studies of the function, localization and evolutionary history of septin, myosin, and actin-binding proteins in yeasts and hyphal fungi enabled me to further hypothesize their roles during development in Chytridiomycota. Since Chytridiomycota diverged from moulds and mushrooms, each group evolved unique mechanisms for constructing different cell shapes using a shared ancestral molecular toolkit. Hyphal growth and septation require actin. My second hypothesis was that actin, a major cytoskeletal component, is also involved in morphogenesis in Chytridiomycota. Using fluorescence microscopy, I documented rhodamine phalloidin-stained actin cables, patches, sheets and perinuclear shells through development in Chytriomyces hyalinus. I disrupted the actin cytoskeleton with the chemical inhibitor latrunculin B. Observing actin patches concentrated at rhizoid tips and at cytoplasmic cleavage planes, and finding that actin integrity was essential for rhizoid proliferation in C. hyalinus both support a conserved role for actin in polarized growth and cytokinesis. Thirdly, I hypothesized that sustained tip growth and nuclear migration underlie the convergent evolution of hyphae and hypha-like growth forms. Chytriomyces hyalinus shows determinate growth that ceases once a zoosporangium matures. Phylogenies indicate that filamentous species in Chytridiomycota with indeterminate growth arose independently from ancestors with a determinate growth mode. I determined that actin organization and nuclear migration patterns in each species differed from one another and from hyphae, most likely as a result of their independent origins. In combination, phylogenetic analyses, molecular genetics, and microscopy are tearing away the curtains of time that mask the ever-changing molecular machinery that gave rise to an astounding diversity of form and function in modern fungi.Science, Faculty ofBotany, Department ofGraduat

A different shade of hypha : cytological and molecular phylogenetic evidence for the independent rise of the hyphal habit in the class Monoblepharidomycetes (Chytridiomycota)

Once the ancestors of fungi stopped moving and instead started reaching out with hyphae, their filamentous growth made possible new variety in form and habitat. Hyphae mediated substrate colonization, absorptive nutrition, mating and reproduction. Although shared across most familiar terrestrial fungal lineages, little was known about where hyphae evolved in early fungi. In chapter one, I review the phylogenetic origins of hyphae and current understanding of the cytology of hyphal tips. Better understanding of fungal phylogeny and hyphal growth near the base of the fungal tree was needed. In Chapter 2, I investigated the phylogeny and cytology in the Class Monoblepharidomycetes (Chytridiomycota), a group of deeply diverging, zoosporic fungi, encompassing a range of body types. Species can be either crescent or rod-shaped unicells or sprawling hyphal growths. I inferred a phylogeny of the fungi based on 28S ribosomal DNA sequence data using maximum likelihood (ML) and Bayesian inference methods. I recovered the monophyly of modern fungal phyla and the topology was comparable to the most taxonomically diverse and gene–rich phylogeny of the fungi to date. I used likelihood methods to trace the origins of hyphae on my likelihood tree, concluding that hyphae arose independently in the Monoblepharidomycetes and at least three other times in the fungi. Next, I searched for evidence of convergent evolution in the cellular organization of hyphal Monoblepharidomycetes using fluorescence and transmission electron microscopy. I showed that the hyphae of Monoblepharidomycetes have a novel form with an unusual microtubule cytoskeleton and without a typical fungal Spitzenkörper. This constitutes the first report on the cytology of hyphae from the Chytridiomycota. In Chapter 3, I discuss the significance of my research and possible future directions including cytological experiments on the Monoblepharidomycetes cytoskeleton.Science, Faculty ofBotany, Department ofGraduat

Diverse organizations of actin and nuclei underpin the evolution of indeterminate growth in Chytridiomycota and Dikarya

Indeterminate growth, as in the hyphae of the “Humongous Fungus” of Michigan requires sustained nuclear migration and cell wall remodeling. We compare actin organization and patterns of nuclear positioning among four distantly related, indeterminate species of phylum Chytridiomycota: Cladochytrium replicatum, Physocladia obscura, Nowakowskiella sp., and Polychytrium aggregatum. We combined light microscopy, nuclear staining with DAPI, and actin staining with rhodamine phalloidin to analyze actin distribution and nuclear migration during somatic growth in the four Chytridiomycota species. Actin formed plaques, filaments, cables and perinuclear shells in patterns that varied across the four species. All four species initiated indeterminate growth by extending branching, anucleate rhizomycelium,The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs

Background: Septins are cytoskeletal proteins important in cell division and in establishing and maintaining cell polarity. Although septins are found in various eukaryotes, septin genes had the richest history of duplication and diversification in the animals, fungi and protists that comprise opisthokonts. Opisthokont septin paralogs encode modular proteins that assemble into heteropolymeric higher order structures. The heteropolymers can create physical barriers to diffusion or serve as scaffolds organizing other morphogenetic proteins. How the paralogous septin modules interact to form heteropolymers is still unclear. Through comparative analyses, we hoped to clarify the evolutionary origin of septin diversity and to suggest which amino acid residues were responsible for subunit binding specificity. Results: Here we take advantage of newly sequenced genomes to reconcile septin gene trees with a species phylogeny from 22 animals, fungi and protists. Our phylogenetic analysis divided 120 septins representing the 22 taxa into seven clades (Groups) of paralogs. Suggesting that septin genes duplicated early in opisthokont evolution, animal and fungal lineages share septin Groups 1A, 4 and possibly also 1B and 2. Group 5 septins were present in fungi but not in animals and whether they were present in the opisthokont ancestor was unclear. Protein homology folding showed that previously identified conserved septin motifs were all located near interface regions between the adjacent septin monomers. We found specific interface residues associated with each septin Group that are candidates for providing subunit binding specificity. Conclusions: This work reveals that duplication of septin genes began in an ancestral opisthokont more than a billion years ago and continued through the diversification of animals and fungi. Evidence for evolutionary conservation of ~ 49 interface residues will inform mutagenesis experiments and lead to improved understanding of the rules guiding septin heteropolymer formation and from there, to improved understanding of development of form in animals and fungi.Science, Faculty ofNon UBCBotany, Department ofReviewedFacult

A multigene phylogeny of Olpidium and its implications for early fungal evolution

Background: From a common ancestor with animals, the earliest fungi inherited flagellated zoospores for dispersal in water. Terrestrial fungi lost all flagellated stages and reproduce instead with nonmotile spores. Olpidium virulentus (= Olpidium brassicae), a unicellular fungus parasitizing vascular plant root cells, seemed anomalous. Although Olpidium produces zoospores, in previous phylogenetic studies it appeared nested among the terrestrial fungi. Its position was based mainly on ribosomal gene sequences and was not strongly supported. Our goal in this study was to use amino acid sequences from four genes to reconstruct the branching order of the early-diverging fungi with particular emphasis on the position of Olpidium. Results: We concatenated sequences from the Ef-2, RPB1, RPB2 and actin loci for maximum likelihood and Bayesian analyses. In the resulting trees, Olpidium virulentus, O. bornovanus and non-flagellated terrestrial fungi formed a strongly supported clade. Topology tests rejected monophyly of the Olpidium species with any other clades of flagellated fungi. Placing Olpidium at the base of terrestrial fungi was also rejected. Within the terrestrial fungi, Olpidium formed a monophyletic group with the taxa traditionally classified in the phylum Zygomycota. Within Zygomycota, Mucoromycotina was robustly monophyletic. Although without bootstrap support, Monoblepharidomycetes, a small class of zoosporic fungi, diverged from the basal node in Fungi. The zoosporic phylum Blastocladiomycota appeared as the sister group to the terrestrial fungi plus Olpidium. Conclusions: This study provides strong support for Olpidium as the closest living flagellated relative of the terrestrial fungi. Appearing nested among hyphal fungi, Olpidium's unicellular thallus may have been derived from ancestral hyphae. Early in their evolution, terrestrial hyphal fungi may have reproduced with zoospores.Botany, Department ofScience, Faculty ofNon UBCReviewedFacult

New insights into the evolutionary history of Fungi from a 407 Ma Blastocladiomycota fossil showing a complex hyphal thallus

Zoosporic fungi are key saprotrophs and parasites of plants, animals and other fungi, playing important roles in ecosystems. They comprise at least three phyla, of which two, Chytridiomycota and Blastocladiomycota, developed a range of thallus morphologies including branching hyphae. Here we describe Retesporangicus lyonii gen. et sp. nov., an exceptionally well preserved fossil, which is the earliest known to produce multiple sporangia on an expanded hyphal network. To better characterize the fungus we develop a new method to render surfaces from image stacks generated by confocal laser scanning microscopy. Here, the method helps to reveal thallus structure. Comparisons with cultures of living species and character state reconstructions analysed against recent molecular phylogenies of 24 modern zoosporic fungi indicate an affinity with Blastocladiomycota. We argue that in zoosporic fungi, kinds of filaments such as hyphae, rhizoids and rhizomycelium are developmentally similar structures adapted for varied functions including nutrient absorption and anchorage. The fossil is the earliest known type to develop hyphae which likely served as a saprotrophic adaptation to patchy resource availability. Evidence from the Rhynie chert provides our earliest insights into the biology of fungi and their roles in the environment. It demonstrates that zoosporic fungi were already diverse in 407 million-year-old terrestrial ecosystems. This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’

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