Mining microarray datasets in nutrition: expression of the GPR120 (n-3 fatty acid receptor/sensor) gene is down-regulated in human adipocytes by macrophage secretions

Microarray datasets are a rich source of information in nutritional investigation. Targeted mining of microarray data following initial, non-biased bioinformatic analysis can provide key insight into specific genes and metabolic processes of interest. Microarrays from human adipocytes were examined to explore the effects of macrophage secretions on the expression of the G-protein-coupled receptor (GPR) genes that encode fatty acid receptors/sensors. Exposure of the adipocytes to macrophage-conditioned medium for 4 or 24 h had no effect on GPR40 and GPR43 expression, but there was a marked stimulation of GPR84 expression (receptor for medium-chain fatty acids), the mRNA level increasing 13·5-fold at 24 h relative to unconditioned medium. Importantly,expression of GPR120, which encodes an n-3 PUFA receptor/sensor, was strongly inhibited by the conditioned medium (15-fold decrease in mRNA at 24h). Macrophage secretions have major effects on the expression of fatty acid receptor/sensor genes in human adipocytes, which may lead to an augmentation of the inflammatory response in adipose tissue in obesity

Embracing innovation in microbiology education: Integrating online interactive simulation and F-2-F practical inquiry when teaching MADLI-TOF

Diagnostic laboratories routinely use Matrix-Assisted Laser Desorption/Ionisation-Time Of Flight (MALDI-TOF) to identify bacteria present in patient samples (Patel, 2013). MALDI-TOF quickly and accurately identifies organisms, yet, it is uncommon for undergraduate students to use this equipment; being limited to theoretical application only. To address this, we combined F-2-F laboratory classes with a MALDI-TOF simulation to teach students how to process clinical samples from start to finish. On completing the F-2-F and online simulation, students should understand the microbiological steps required to process diverse clinical samples; understand which follow-up tests will confirm the identity of the organism; understand how to prepare a sample for MALDI-TOF; and correctly analyse and interpret MALDI-TOF data. Third-year Infectious diseases students (n=37, mean age 22.2±4.9, mean GPA 5.46±0.84) at the University of South Australia participated in this study. In weeks 1 to 6 of semester, students learnt how to process clinical samples in a microbiology laboratory. In the mid-semester break, students used the simulation to process a patient sample (e.g. blood, sputum, or CSF). Students had to choose the correct culture medium, incubation conditions and interpret Gram stain results. Once isolated, single colonies were picked, processed and analysed using MALDI-TOF. The output was used to confirm the identity of the bacterial species. Written and video instructions were provided to teach students on use of the simulation. The MALDI-TOF data generated were interpreted while referring to laboratory data. On completion, students submitted a written laboratory report for assessment. Student feedback was obtained through a 5-point Likert-style questionnaire. Thematic analysis was performed on the free text written feedback. Students “agreed” that the simulation reinforced the logic required to analyse a patient sample (taught in the F-2-F sessions). They “agreed” that using the simulation in conjunction with F-2-F practicals was beneficial to their learning and that the simulation enhanced their ability to combine laboratory data (e.g. biochemical testing) with MALDI-TOF data. Prior to the simulation student understanding of MALDI-TOF was 2.6±0.54 (out of 5), increasing significantly to 3.1±0.55 after completing the simulation (Students t test; p < 0.0004). The mean score for the written report was 16.2±3.1 SD (max of 20), with only 2 students failing to achieve a minimum passing score. The combination of F-2-F laboratory and online MALDI-TOF effectively integrated all steps required to identify bacterial species in a clinical sample. While some aspects of navigating the simulation were identified as challenging for students, there were noted improvements in student understanding. We will continue to improve the flow of the simulation as well as the representation of culture plates for the different bacterial species. REFERENCE Patel R. (2013). Matrix-assisted laser desorption ionization-time of flight mass spectrometry in clinical microbiology. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America, 57(4), 564–572. https://doi.org/10.1093/cid/cit24

From virtual to practical: Integrating an online simulation and face-to-face learning to enable hemocytometer proficiency

BACKGROUND Accurately identifying and counting cells using a hemocytometer are essential skills for cell biology students (Delgado et al., 2021). Learning to use a hemocytometer can be challenging for students, while confirming that the correct technique has been used is challenging for the educator. Students must correctly identify different cell types, disregard cellular debris, and distinguish between viable vs dead cells. These challenges make it difficult for students to attain proficiency in this vital skill. AIMS On completing the online exercise, students should understand how a hemocytometer can quantify cells; how to count different cell populations correctly; evaluate, analyse and interpret experimental data; understand how variations in samples can affect the quality of the cell count; and identify errors in the counting process. DESCRIPTION OF INTERVENTION First-year Laboratory Medicine students at the University of South Australia (UniSA) were first taught the principles of a hemocytometer, how it works, how cells are counted, and how cell density and viability are calculated. Students then used an online virtual hemocytometer to count two samples containing enriched lymphocytes and neutrophils. All samples had red blood cell and platelet contamination. Detailed instructions on how to use the virtual hemocytometer, count viable and trypan blue dead cells, and undertake cell density and viability calculations were also included. Student feedback was obtained through a 5-point Likert questionnaire with free text responses. DESIGN AND METHODS As part of the online training report, students calculated the cell count, density, and viability for two samples counted using the virtual hemocytometer. Students then completed a 5-point Likert-style questionnaire with free text responses to assess student understanding, benefits to their learning when faced with a F-2-F laboratory setting and perception of strengths/weaknesses of the teaching approach. Likert data were converted to a numeric scale, averaged across all responses, and compared using a Student t-test where possible. Written responses were assessed through a thematic analysis. RESULTS In most cases, cell density and viability data calculated using the online hemocytometer closely matched the expected computer-generated results. The online simulation faithfully replicated issues typically seen when using a real hemocytometer. This included contaminating cells, cell clumps, and cells falling across two adjacent grids. Students strongly indicated that the virtual hemocytometer training would aid their use of a hemocytometer in an F-2-F setting. Students responded as “strongly enjoying” the approach, finding it engaging and able to replicate a real-world experience. Student confidence increased significantly after using the simulation in all aspects, especially in calculating cell density and viability, two common areas of mistakes. CONCLUSIONS An online hemocytometer faithfully taught all aspects of hemocytometer use. Students were better able to count cells correctly and perform all required calculations. Moving forward, this approach will continue to be used, but we will improve the graphical representation of the individual cell types. REFERENCES Delgado, T., Bhark, SJ., & Donahue, J. (2021). Pandemic Teaching: Creating and teaching cell biology labs online during COVID‐19. BAMBED, 49(1), 32-37

Injury-Dependent and Disability-Specific Lumbar Spinal Gene Regulation following Sciatic Nerve Injury in the Rat

Allodynia, hyperalgesia and spontaneous pain are cardinal sensory signs of neuropathic pain. Clinically, many neuropathic pain patients experience affective-motivational state changes, including reduced familial and social interactions, decreased motivation, anhedonia and depression which are severely debilitating. In earlier studies we have shown that sciatic nerve chronic constriction injury (CCI) disrupts social interactions, sleep-wake-cycle and endocrine function in one third of rats, a subgroup reliably identified six days after injury. CCI consistently produces allodynia and hyperalgesia, the intensity of which was unrelated either to the altered social interactions, sleep-wake-cycle or endocrine changes. This decoupling of the sensory consequences of nerve injury from the affective-motivational changes is reported in both animal experiments and human clinical data. The sensory changes triggered by CCI are mediated primarily by functional changes in the lumbar dorsal horn, however, whether lumbar spinal changes may drive different affective-motivational states has never been considered. In these studies, we used microarrays to identify the unique transcriptomes of rats with altered social behaviours following sciatic CCI to determine whether specific patterns of lumbar spinal adaptations characterised this subgroup. Rats underwent CCI and on the basis of reductions in dominance behaviour in resident-intruder social interactions were categorised as having Pain & Disability, Pain & Transient Disability or Pain alone.We examined the lumbar spinal transcriptomes two and six days after CCI. Fifty-four ‘disability-specific’ genes were identified. Sixty-five percent were unique to Pain & Disability rats, two-thirds of which were associated with neurotransmission, inflammation and/or cellular stress. In contrast, 40% of genes differentially regulated in rats without disabilities were involved with more general homeostatic processes (cellular structure, transcription or translation). We suggest that these patterns of gene expression lead to either the expression of disability, or to resilience and recovery, by modifying local spinal circuitry at the origin of ascending supraspinal pathways

Multiple choice questions to combat plagiarism and encourage conceptual learning

Academic dishonesty (i.e., plagiarism or cheating in plain English) discredits and compromises the validity of University qualifications. All the effort an academic puts into the construction, administration and delivery of their courses is undermined if students are cheating. There are a number of studies describing methods for detecting plagiarism in written assignments. For example, there is software which can detect high levels of similarity between students’ work (Moeck 2002; Hamilton 2003), and there has been a special interest in identifying Internet-related cheating (Young 2001), commercial ghost-writing (Hammer 1976) and in alerting academics to other forms of electronically based plagiarism (McMurtry 2001; Heberling 2002). At first glance, these issues seem less relevant to our large Biochemistry and Molecular Biology classes (which have enrolments of between 200-700 students) because our assessment is based on laboratory work (including individualised practical skills tests) and end-of-semester examinations. However, not only is it clear that a great deal of cheating can occur in the examination room (especially when large numbers of multiple choice questions are employed), our experiences have also made us realise that the detection of cheating causes tremendous stress of itself. Thus the central theme of this paper is that it is a waste of time to employ sophisticated plagiarism detection solutions for in-semester written work if those assignments contribute relatively little to the final mark (as would be the case if the bulk of the final assessment is an easily corrupted multiple choice examination). Additionally, we believe that it is better to make multiple choice examinations that cannot be plagiarised than to burden oneself with the problem of dealing with suspected plagiarism. To this end we have developed examination solutions that prevent cheating and which, as a by-product, allows for flexibility in question design that facilitates the grading of individual options within multiple choice questions

A Review of the History, Advocacy and Efficacy of Data Management Plans

Data management plans (DMPs) have increasingly been encouraged as a key component of institutional and funding body policy. Although DMPs necessarily place administrative burden on researchers, proponents claim that DMPs have myriad benefits, including enhanced research data quality, increased rates of data sharing, and institutional planning and compliance benefits. In this article, we explore the international history of DMPs and describe institutional and funding body DMP policy. We find that economic and societal benefits from presumed increased rates of data sharing was the original driver of mandating DMPs by funding bodies. Today, 86% of UK Research Councils and 63% of US funding bodies require submission of a DMP with funding applications. Given that no major Australian funding bodies require DMP submission, it is of note that 37% of Australian universities have taken the initiative to internally mandate DMPs. Institutions both within Australia and internationally frequently promote the professional benefits of DMP use, and endorse DMPs as ‘best practice’. We analyse one such typical DMP implementation at a major Australian institution, finding that DMPs have low levels of apparent translational value. Indeed, an extensive literature review suggests there is very limited published systematic evidence that DMP use has any tangible benefit for researchers, institutions or funding bodies. We are therefore led to question why DMPs have become the go-to tool for research data professionals and advocates of good data practice. By delineating multiple use-cases and highlighting the need for DMPs to be fit for intended purpose, we question the view that a good DMP is necessarily that which encompasses the entire data lifecycle of a project. Finally, we summarise recent developments in the DMP landscape, and note a positive shift towards evidence-based research management through more researcher-centric, educative, and integrated DMP services

Using ASELL as a framework for driving change

A 2009 Australian Council of Deans of Science report (Rice, Thomas and O'Toole, 2009) identified the quality of undergraduate laboratory curricula as an important issue in tertiary science education. Evaluation of undergraduate labs traditionally relies on anecdotal evidence about what works and why; changes are often ad-hoc. We need an appropriate evidence-based methodology to clearly articulate the goals and aims of the teaching labs, and evaluate the curricula against these. Fortunately, such a methodology exists: the ASELL framework (ASELL, 2012) employs research-led surveys and workshops to identify pedagogical and logistical issues with science laboratory experiments, and an iterative process for improvement. Building on past experience with this framework, we are using the ASELL tools to examine laboratory experiments in the Schools of Physics and Molecular Bioscience at the University of Sydney to gain feedback about the level, relevance, degree of challenge, experimental techniques and class logistics. We will identify several experiments at the first year (physics) and second year (biochemistry) level to focus on, and implement changes based on the ASELL analysis — and so armed, to influence colleagues to spread the framework across the Faculty. J.W. Rice, S.M. Thomas, P. O'Toole, Tertiary Science Education in the 21st Century, Australian Learning & Teaching Council, 2009. ASELL, Advancing Science by Enhancing Learning in the Laborotory (2012), http://www.asell.or

A review of the history, advocacy and efficacy of data management plans

Data management plans (DMPs) have increasingly been encouraged as a key component of institutional and funding body policy. Although DMPs necessarily place administrative burden on researchers, proponents claim that DMPs have myriad benefits, including enhanced research data quality, increased rates of data sharing, and institutional planning and compliance benefits. In this manuscript, we explore the international history of DMPs and describe institutional and funding body DMP policy. We found that economic and societal benefits from presumed increased rates of data sharing was the original driver of mandating DMPs by funding bodies. Today, 86% of UK Research Councils and 63% of US funding bodies require submission of a DMP with funding applications. Given that no major Australian funding bodies require DMP submission, it is of note that 37% of Australian universities have taken the initiative to internally mandate DMPs. Institutions both within Australia and internationally frequently promote the professional benefits of DMP use, and endorse DMPs as ‘best practice’. We analyse one such typical DMP implementation at a major Australian institution, finding that DMPs have low levels of apparent translational value. Indeed, an extensive literature review suggests there is very limited published systematic evidence that DMP use has any tangible benefit for researchers, institutions or funding bodies. We are therefore led to question why DMPs have become the go-to tool for research data professionals and advocates of good data practice. By delineating multiple use-cases and highlighting the need for DMPs to be ft for intended purpose, we question the view that a good DMP is necessarily that which encompasses the entire data lifecycle of a project. Finally, we summarise recent developments in the DMP landscape, and note a positive shift towards evidence-based research management through more researcher-centric, educative, and integrated DMP services

Why do Students Still Bother to Come to Lectures When Everything is Online?

With the recent emergence of an extensive range of online resources: everything from electronic lecture notes, slides, mp3 podcasts to the fully-downloadable recorded lecture with coordinated audio and visual images, the obvious question is: “Why do students still bother to come to lectures?” To explore this question, a preliminary survey was carried out within junior, intermediate and senior courses taught by School of Molecular Bioscience, The University of Sydney during second semester, 2009. This simple voluntary survey, which was mounted on WebCT, had two simple questions, each of which allowed both constrained and open responses. Do you attend lectures? How would you feel if there were no face-to-face lectures and lectures were only available online? Of those students who responded to the survey, the overwhelming majority, surprisingly, attended most lectures. For a voluntary on-line survey which was only accessible over a two-week period, the response rate was very encouraging. Most respondents also submitted abundant, enthusiastic free-form comments. The students were keen to give their opinion; many of the comments contained more than one reason for their attendance pattern. Because of this, the results (both numerical data and comments) provide a rich resource of student opinion for analysis. This conference provides the ideal opportunity to reflect on our data with assistance from a wider audience

Why do Students Still Bother Coming to Lectures, When Everything is Available Online?

Web-based lecture technologies (WBLTs), which deliver recorded lectures and notes online, are increasingly common. However, there is concern that they may reduce lecture attendance. Since we did not observe a significant drop in attendance following the introduction of WBLTs in the School of Molecular Bioscience at the University of Sydney, we surveyed 563 students to discover why they attended lectures despite the availability of copious online materials. 82 % of responding students reported they always or mostly attend lectures and 74% expressed a negative emotion when asked how they would feel if lectures were abolished. Free-form comments indicated that students attend lectures for reasons either positive about lectures or negative about WBLTs. Students feel that lectures provide a disciplined learning environment where they can concentrate in a scholarly community. Lectures intrinsically contribute to the ‘university experience’ and the social aspect is also important. Some students are motivated to attend through habit, guilt or by financial concerns. Negative comments highlighted perceptions that WBLTs do not fully capture lecture content, can be inefficient and unreliable, and predispose students to procrastination. The majority of students use WBLTs in addition to attending lectures and perceive distinct roles for each mode. Most students who did not attend lectures claimed they were unable to for logistical reasons, although some cited inconvenience, overcrowding or peer-distraction. Students also make strategic decisions to prioritise competing commitments. Only a minority of students prefer WBLTs to attendance. These students prefer the ability to work at a time, place and pace of their choosing. This study supports the contention that WBLTs alone do not reduce lecture attendance, and highlights features of lectures which can be improved to increase attendance and student engagement