Protecting key pedagogical features in the pivot to online hydrology learning at UWA

The COVID-19 pandemic necessitated a rapid transition to online hydrology instruction at The University of Western Australia (UWA). Key requirements of this transition were to create supportive, inclusive online educational settings, and to maximize student engagement.  Here, we draw on experiences in four hydrology units to illustrate how we used a holistic approach spanning course structure, content delivery, active learning experiences and authentic assessment to protect these key pedagogical features during the transition to online learning.  Learning content that was streamlined, chunked and recorded facilitated effective student-paced learning. Structuring material to support a growth-mindset and providing varied active learning opportunities was also beneficial for establishing a constructive learning culture. Field and laboratory experiences were replaced with digital analogues and “virtual” site visits. While these have limitations for experiential learning, they are also able to span a broader range of conditions than can be physically visited or simulated in the lab. The outcomes in these units as measured by student engagement, enrolment and self-reported satisfaction were positive, with student evaluations remaining similar to those of pre-pandemic levels.  Previous interest in running flipped classrooms and familiarity with technology among instructors and students were helpful in enabling the transition.

The Low-Resolution Structure of Nascent High Density Lipoprotein Reconstituted with DMPC With and Without Cholesterol Reveals A Mechanism for Particle Expansion

High density lipoproteins (HDL) are athero-protective particles under investigation as potential therapeutic agents for cardiovascular disease. We applied small angle neutron scattering (SANS) with contrast variation to obtain the low resolution structure of nascent HDL (nHDL) reconstituted with dimyristoyl phosphatidyl choline (DMPC), apoA1:DMPC (1:80, mol:mol). The overall shape of the entire particle is discoidal, with low resolution architecture of apoA1 visualized as an open, contorted, and slightly out of plane structure with three arms, while the low resolution shape of the lipid phase is an oblate ellipsoid that fits well within the protein shape. Modeling studies incorporating the SANS data indicate that apoA1 within the lipoprotein is folded onto itself, making a hairpin, which was also confirmed independently by both cross-linking mass spectrometry and hydrogen-deuterium exchange mass spectrometry analyses. The open conformation of apoA1 observed coupled with the lipid shape indicate that the lipid is predominantly a bilayer with a small micelle domain between the open apoA1 arms. Collectively, these studies demonstrate that full length apoA1 retains an open architecture that is dictated by its lipid cargo. This configuration may help accommodate potential changing lipid cargo content of the particle by quantized expansion of hairpin structures in apoA

CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing

Results of massive parallel sequencing-by-synthesis vary depending on the sequencing approach. CoolMPS™ is a new sequencing chemistry that incorporates bases by labeled antibodies. To evaluate the performance, we sequenced 240 human non-coding RNA samples (dementia patients and controls) with and without CoolMPS. The Q30 value as indicator of the per base sequencing quality increased from 91.8 to 94%. The higher quality was reached across the whole read length. Likewise, the percentage of reads mapping to the human genome increased from 84.9 to 86.2%. For both technologies, we computed similar distributions between different RNA classes (miRNA, piRNA, tRNA, snoRNA and yRNA) and within the classes. While standard sequencing-by-synthesis allowed to recover more annotated miRNAs, CoolMPS yielded more novel miRNAs. The correlation between the two methods was 0.97. Evaluating the diagnostic performance, we observed lower minimal P-values for CoolMPS (adjusted P-value of 0.0006 versus 0.0004) and larger effect sizes (Cohen's d of 0.878 versus 0.9). Validating 19 miRNAs resulted in a correlation of 0.852 between CoolMPS and reverse transcriptase-quantitative polymerase chain reaction. Comparison to data generated with Illumina technology confirmed a known shift in the overall RNA composition. With CoolMPS we evaluated a novel sequencing-by-synthesis technology showing high performance for the analysis of non-coding RNAs

Assessment of Left Ventricular Geometrical Patterns and Function among Hypertensive Patients at a Tertiary Hospital, Northern Tanzania.

With hypertension, the cardiovascular system changes to adapt to the varying neuro-humoral and hemodynamic changes and this may lead to the development of different left ventricular geometric patterns, each carrying a different risk profile for major adverse cardiovascular events. Using a consecutive sampling technique, a cross-sectional, prospective, hospital based study was done and two hundred and twenty seven (227) hypertensive patients were studied. The distribution of different abnormal LV geometrical patterns was 19.8%, 28.2%, 22% for concentric remodelling, concentric hypertrophy and eccentric hypertrophy respectively. With echocardiographic criteria, the proportion of patients with left ventricular hypertrophy (LVH) was higher when left ventricular mass (LVM) was indexed to height(2.7) than to body surface area (70.0% vs. 52.9%). Duration of hypertension markedly influenced the type of LV geometry with normal LV geometry predominating in early hypertension and abnormal geometrical patterns predominating in late hypertension. The left ventricular fractional shortening decreased with duration of hypertension and was common in patients with eccentric hypertrophy. Age of the patient, systolic blood pressure, duration of hypertension and body mass index were found to be independent predictors left ventricular hypertrophy. About 70% of hypertensive patients had abnormal geometry existing in different patterns. Eccentric hypertrophy had more of clinical and echocardiographic features suggestive of reduced left ventricular systolic function. Hypertensive patients should be recognized as a heterogeneous population and therefore stratifying them into their respective LV geometrical patterns is useful as way of assessing their risk profile as well as instituting appropriate management

Emergence of new types of Theileria orientalis in Australian cattle and possible cause of theileriosis outbreaks

Theileria parasites cause a benign infection of cattle in parts of Australia where they are endemic, but have, in recent years, been suspected of being responsible for a number of outbreaks of disease in cattle near the coast of New South Wales. The objective of this study was to identify and characterize the species of Theileria in cattle on six farms in New South Wales where disease outbreaks have occurred, and compare with Theileria from three disease-free farms in Queensland that is endemic for Theileria. Special reference was made to sub-typing of T. orientalis by type-specific PCR and sequencing of the small subunit (SSU) rRNA gene, and sequence analysis of the gene encoding a polymorphic merozoite/piroplasm surface protein (MPSP) that may be under immune selection. Nucleotide sequencing of SSU rRNA and MPSP genes revealed the presence of four Theileria genotypes: T. orientalis (buffeli), T. orientalis (ikeda), T. orientalis (chitose) and T. orientalis type 4 (MPSP) or type C (SSU rRNA). The majority of animals showed mixed infections while a few showed single infection. When MPSP nucleotide sequences were translated into amino acids, base transition did not change amino acid composition of the protein product, suggesting possible silent polymorphism. The occurrence of ikeda and type 4 (type C) previously not reported to occur and silent mutation is thought to have enhanced parasite evasion of the host immune response causing the outbreak

Bicycle Diversion Evaluation Project

The primary purpose of the Bicycle Diversion Evaluation Project (“The BDE Project”) is to determine whether or not wayfinding signage specifically targeted at cyclists, is effective at changing the behaviour of cyclists by encouraging cyclists to use designated bicycle routes. The goal of the wayfinding signs is to encourage cyclists to use routes that are less busy in order to reduce the number of pedestrian-cyclist conflicts on the UBC Vancouver campus. The BDE Project fills a gap in the literature as it is unique. The case studies that were examined in the literature review broadly suggests that signage is effective in changing the behaviour of pedestrians, cyclists or drivers. Despite not clearly being able to identify that bike wayfinding can alter the route choice behaviour of cyclists, the case studies suggest that wayfinding signs will be successful in altering cyclist route choice behaviour. As there is no case study that directly answers the research question being posed in the BDE Project, the BDE Project is an important study that fills a gap in the academic literature on the effectiveness of bike wayfinding signage at changing the behaviour of cyclists. Results from the BDE Project show that the percent change in cyclists choosing to travel away from the Pedestrian Priority Zone in the before-implementation and after-implementation counting period is not significantly different. As a result, the BDE Project cannot confidently conclude that the specific bike wayfinding signs that have been implemented on the UBC Vancouver campus have an effect at altering the route choice behaviour of cyclists. Despite this finding, it is important to understand that there are a number of limitations that likely contributed to this result. One major limitation is the lack of time between the implementation of the wayfinding signs and the beginning of the post-implementation counting. Another limitation of the wayfinding signs is that they are not placed at consistent locations in intersections and have small font size making them hard to read. Further studies looking at the design of bike wayfinding signs are recommended and need to be done before it can be concluded that all bike wayfinding signs are ineffective at altering the route choice behaviour of cyclists. Disclaimer: “UBC SEEDS provides students with the opportunity to share the findings of their studies, as well as their opinions, conclusions and recommendations with the UBC community. The reader should bear in mind that this is a student project/report and is not an official document of UBC. Furthermore readers should bear in mind that these reports may not reflect the current status of activities at UBC. We urge you to contact the research persons mentioned in a report or the SEEDS Coordinator about the current status of the subject matter of a project/report.”Applied Science, Faculty ofCommunity and Regional Planning (SCARP), School ofUnreviewedGraduat

Expression profiling and comparative sequence derived insights into lipid metabolism

Expression profiling and genomic DNA sequence comparisons are increasingly being applied to the identification and analysis of the genes involved in lipid metabolism. Not only has genome-wide expression profiling aided in the identification of novel genes involved in important processes in lipid metabolism such as sterol efflux, but the utilization of information from these studies has added to our understanding of the regulation of pathways participating in the process. Coupled with these gene expression studies, cross species comparison, searching for sequences conserved through evolution, has proven to be a powerful tool to identify important non-coding regulatory sequences as well as the discovery of novel genes relevant to lipid biology. An example of the value of this approach was the recent chance discovery of a new apolipoprotein gene (apo AV) that has dramatic effects upon triglyceride metabolism in mice and humans

Selective DNA amplification from complex genomes using universal double-sided adapters

There is a rapidly developing need for new technologies to amplify millions of different targets from genomic DNA for high throughput genotyping and population gene-sequencing from diverse species. Here we describe a novel approach for the specific selection and amplification of genomic DNA fragments of interest that eliminates the need for costly and time consuming synthesis and testing of potentially millions of amplicon-specific primers. This technique relies upon Type IIs restriction enzyme digestion of genomic DNA and ligation of the fragments to double-sided adapters to form closed-circular DNA molecules. The novel use of double-sided adapters, assembled through the combinatorial use of two small universal sets of oligonucleotide building blocks, provides greater selection capacity by utilizing both sides of the adapter in a sequence-specific ligation event. As demonstrated, formation of circular structures results in protection of the desired molecules from nuclease treatment and enables a level of selectivity high enough to isolate single, or multiple, pre-defined fragments from the human genome when digested at over five million sites. Priming sites incorporated into the adapter allows the utilization of a common pair of primers for the amplification of any adapter-captured DNA fragment of interest