Cumulative Effects of Coastal Watershed Land Use on Chironomidae (Insecta: Diptera) Communities of Neotropical Estuaries in Costa Rica

University of Minnesota Ph.D. dissertation. July 2017. Major: Entomology. Advisor: Leonard Ferrington, Jr.. 1 computer file (PDF); xiii, 158 pages.Chironomidae assemblages are likely to provide a useful measure of biotic integrity in Neotropical estuaries of Costa Rica, which lack an intensive estuarine bioassessment tool to support environmental monitoring. However, little is known about chironomid communities in these estuaries and the cumulative effects of watershed land use on chironomid communities have not been studied. The purpose of this dissertation was to (1) quantify land cover change of six watersheds on the Caribbean coast of Costa Rica between 2001 and 2014, (2) describe all steps of the Chironomidae surface-floating pupal exuviae method in detail, including sample collection, laboratory processing, slide mounting, and genus identification, (3) investigate Chironomidae species diversity of nine estuaries across a land use gradient on the Caribbean coast of Costa Rica, (4) compare the relative effectiveness of five different DNA extraction protocols and direct PCR in isolation of DNA from chironomid pupal exuviae, and (5) assess the efficiency of using standard DNA barcoding for species identification of chironomid pupal exuviae. I found that watershed-scale land use analyses showed agricultural expansion and deforestation in watersheds on the northeastern coast and secondary forest regrowth on the southeastern coast of Costa Rica. I identified 228 morphospecies and 70 genera from 17,071 Chironomidae surface-floating pupal exuviae collected from nine Neotropical estuaries and that a Chironomidae Index of Biotic Integrity successfully discriminated estuaries with differing degrees of stress across a land use gradient. I extracted genomic DNA from 61.2% of 570 sampled pupal exuviae. The NucleoSpin® Tissue XS Kit, DNeasy® Blood and Tissue kit, and QuickExtract™ DNA Extraction Solution provided the best results in isolating DNA from single pupal exuviae. A total of 36.3% of 190 sampled pupal exuviae resulted in high-quality sequences for Costa Rica, but none matched known species. This knowledge is important if these aquatic communities are to be used more effectively in future biological monitoring, conservation, and integrated water resource management of Neotropical estuaries

Teacher-Initiated Discourse Moves in Reformed Undergraduate STEM Learning Environments

Faculty advisor: Abdi WarfaThis research was supported by the Undergraduate Research Opportunities Program (UROP)

DNA barcoding for species identification of insect skins: A test on Chironomidae (Diptera) pupal exuviae

Chironomidae (Diptera) pupal exuviae samples are commonly used for biological monitoring of aquatic habitats. DNA barcoding has proved useful for species identification of chironomid life stages containing cellular tissue, but the barcoding success of chironomid pupal exuviae is unknown. We assessed whether standard DNA barcoding could be efficiently used for species identification of chironomid pupal exuviae when compared with morphological techniques and if there were differences in performance between temperate and tropical ecosystems, subfamilies, and tribes. PCR, sequence, and identification success differed significantly between geographic regions and taxonomic groups. For Norway, 27 out of 190 (14.2%) of pupal exuviae resulted in high-quality chironomid sequences that match species. For Costa Rica, 69 out of 190 (36.3%) Costa Rican pupal exuviae resulted in high-quality sequences, but none matched known species. Standard DNA barcoding of chironomid pupal exuviae had limited success in species identification of unknown specimens due to contaminations and lack of matching references in available barcode libraries, especially from Costa Rica. Therefore, we recommend future biodiversity studies that focus their efforts on understudied regions, to simultaneously use morphological and molecular identification techniques to identify all life stages of chironomids and populate the barcode reference library with identified sequences

Data from: Trace DNA from insect skins: a comparison of five extraction protocols and direct PCR on chironomid pupal exuviae

Insect skins (exuviae) are of extracellular origin and shed during moulting. The skins do not contain cells or DNA themselves, but epithelial cells and other cell-based structures might accidentally attach as they are shed. This source of trace DNA can be sufficient for PCR amplification and sequencing of target genes and aid in species identification through DNA barcoding or association of unknown life stages. Species identification is essential for biomonitoring programs, as species vary in sensitivities to environmental factors. However, it requires a DNA isolation protocol that optimizes the output of target DNA. Here, we compare the relative effectiveness of five different DNA extraction protocols and direct PCR in isolation of DNA from chironomid pupal exuviae. Chironomidae (Diptera) is a species-rich group of aquatic macroinvertebrates widely distributed in freshwater environments and considered a valuable bioindicator of water quality. Genomic DNA was extracted from 61.2% of 570 sampled pupal exuviae. There were significant differences in the methods with regard to cost, handling time, DNA quantity, PCR success, sequence success and the ability to sequence target taxa. The NucleoSpin® Tissue XS Kit, DNeasy® Blood and Tissue kit, and QuickExtract™ DNA Extraction Solution provided the best results in isolating DNA from single pupal exuviae. Direct PCR and DTAB/CTAB methods gave poor results. While the observed differences in DNA isolation methods on trace DNA will be relevant to research that focuses on aquatic macroinvertebrate ecology, taxonomy and systematics, they should also be of interest for studies using environmental barcoding and metabarcoding of aquatic environments

Increasing Student Engagement through Course Attributes, Community, and Classroom Technology: Lessons from the Pandemic.

While many STEM (science, technology, engineering, and mathematics) instructors returned to in-person instruction in fall 2021, others found themselves continuing to teach via online, hybrid, or hybrid flexible (i.e., hyflex) formats. Regardless of one's instructional modality, the findings from our own and other studies provided insight into effective strategies for increasing student engagement and decreasing cognitive overload. As part of this perspective, we included data from undergraduate students, many of whom are first generation and low income and from marginalized backgrounds, to identify instructional practices that helped them thrive and succeed during the recent COVID-19 pandemic. More specifically, we explored the various pedagogies and technologies utilized during emergency remote teaching to identify best practices as we considered the future of teaching. In sharing best practices at our institution, we aimed to provide a framework for deep reflection among the readers and the identification of practices to start, stop, and/or continue at their own institutions

Norway Chironomidae Pupal Exuviae Specimen Data

Specimen data for Chironomidae pupal exuviae voucher specimens submitted to the NTNU University Museum

DNA quantity data

DNA quantity data organized by DNA extraction method associated with individual chironomid pupal exuviae DNA extract samples

Handling time, PCR success, Sequence success, and Target sequence success data

Handling time, PCR success, sequence success, and target sequence success for chironomid pupal exuviae samples

If you are learner‐centered and you know it, raise your hand: Perspectives on and implementation of pedagogical changes by science instructors during the COVID‐19 pandemic

Students at Minority-Serving Institutions (MSIs) faced significant hardships while trying to learn through emergency remote teaching (ERT) during the COVID-19 pandemic. Our research aims to investigate if science, technology, engineering, and mathematics (STEM) instructors thought about and enacted more learner-centered teaching practices to alleviate some of this stress encountered by their students. Using semi-structured interviews and classroom observations, we utilized inductive and deductive qualitative research methods to examine two questions: (1) To what extent were STEM instructor's perceived pedagogical changes learner-centered during ERT?; and (2) To what extent were STEM instructor's teaching behaviors and discourse practices learner-centered during ERT? Our findings revealed that during ERT, STEM instructors described using a variety of pedagogical changes that we identified as learner-centered under the Weimer framework, including ideas such as enacting flexible late policies and increased usage of formative assessment. Interestingly, we found that many of these learned-centered changes were happening outside of the classroom. Classroom observations assessing instructor behaviors and discourse demonstrated that STEM instructors enacted practices that aligned with Weimer's five constructs of learner-centered teaching. Our research highlights implications of learner-centered teaching practices for STEM instructors as well as researchers