Less Traditional – More Conceptual: Enhancing Student Learning in First-Year Biology

Over the last two decades, a number of influential reports have called for fundamental changes to undergraduate science education. Most importantly, these reports advocate a shift from traditional lecture-based teaching formats to ones that use student-focused pedagogies to encourage deep student learning about key conceptual ideas in science. Based on these reports, and the underlying research, the University of Calgary completed an extensive redesign of its first-year biology courses in 2011, resulting in two courses: Energy Flow in Biological Systems and DNA, Inheritance and Evolution. These courses focus student learning on two foundational concepts and use student-centered pedagogies to encourage the development of critical-thinking and problem-solving skills. Pre/post data collected from one year of the previous introductory courses and two years of the redesigned courses were used to determine the impact of the transition to a conceptual-based curriculum and the incorporation of active learning strategies including clickers and in-class group assignments on student learning gains measured via normalized change using questions from Biological Concept Inventory, Respiration and Photosynthesis Diagnostic Question Clusters and the Conceptual Inventory of Natural Selection. Student motivations and approaches for learning (e.g. deep versus surface approaches) using the published Approaches and Study Skills Inventory for Students (ASSIST) survey and the Experiences of Teaching and Learning Questionnaire (ETLQ). Data show significantly higher learning gains during the two consecutive years of implementation of the redesigned courses than those achieved in the previous format. Additionally, students reported that lecture activities allowed them being more engaged with course content. We are currently analyzing student written responses, which will provide further insight into the impact of course redesign on content knowledge and critical reasoning skills on student success

Evaluating student learning in large introductory biology courses: predictors of student success and lessons for course redesign

In 2009, the University of Calgary began an extensive redesign of its first-year biology courses based on survey feedback from both students and faculty, as well as the extensive literature showing the effectiveness of student-centered pedagogies in enhancing student learning, engagement and retention in large classes. The two newly designed courses, Energy Flow in Biological Systems and DNA, Inheritance and Evolution are concept-based courses that emphasize the integration of key concepts from biomolecules to the biosphere within a student-centered learning environment; these courses begin in Fall 2011. In order to understand the factors influencing student success in first-year biology, we have initiated a three-year mixed-methods investigation of students’ a priori knowledge, motivations, and approaches to learning. In our current first-year courses, we collected data related to changes in both student motivation and learning over the entire first year for 750 students. The strongest predictors of student success, based on grades earned in the lecture component of the course, were multiple-choice pre-test scores (

Applied Meteorology Unit (AMU) Quarterly Report Second Quarter FY-14

This report summarizes the Applied Meteorology Unit (AMU) activities for the second quarter of Fiscal Year 2014 January - March 2014)

Applied Meteorology Unit (AMU) Quarterly Report First Quarter FY-14

NASA's LSP and other programs at Vandenberg Air Force Base (VAFB) use wind forecasts issued by the 30th Operational Support Squadron (30 OSS) to determine if they need to limit activities or protect property such as a launch vehicle due to the occurrence of warning level winds at VAFB in California. The 30 OSS tasked the AMU to provide a wind forecasting capability to improve wind warning forecasts and enhance the safety of their customers' operations. This would allow 30 OSS forecasters to evaluate pressure gradient thresholds between pairs of regional observing stations to help determine the onset and duration of warning category winds. Development of such a tool will require that solid relationships exist between wind speed and the pressure gradient of one or more station pairs. As part of this task, the AMU will also create a statistical climatology of meteorological observations from the VAFB wind towers

Homoplastic microinversions and the avian tree of life

Background: Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasyfree evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution. Results: We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots. Conclusions: Microinversions can provide valuable phylogenetic information, although power analysis indicate

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology

Characteristics of Adults in the Hepatitis B Research Network in North America Reflect Their Country of Origin and Hepatitis B Virus Genotype

Chronic hepatitis B virus (HBV) infection is an important cause of cirrhosis and hepatocellular carcinoma worldwide; populations that migrate to the US and Canada might be disproportionately affected. The Hepatitis B Research Network (HBRN) is a cooperative network of investigators from the United States and Canada, created to facilitate clinical, therapeutic, and translational research in adults and children with hepatitis B. We describe the structure of the network and baseline characteristics of adults with hepatitis B enrolled in the network

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century