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    The auxiliary replicons of Butyrivibrio proteoclasticus : a thesis presented in fulfilment of the Doctorate of Philosophy degree at Massey University, Palmerston North, New Zealand
    (Massey University, 2009) Yeoman, Carl
    Butyrivibrio proteoclasticus B316T is the most recently described species of the Butyrivibrio / Pseudobutyrivibrio assemblage and now the first to have its genome sequenced. The genome of this organism was found to be spread across four replicons: a 3.5 Mb major chromosome and three additional large replicons: 186, 302 and 361 Kb in size. This thesis describes the sequencing, analysis, annotation and initial characterisation of all three B. proteoclasticus auxiliary replicons. Most significantly, these analyses revealed that the 302-Kb replicon is a second chromosome. This small chromosome, named BPc2, encodes essential systems for the uptake and/or biosynthesis of biotin and nicotinamide adenine mononucleotide, as well as the enzymes required for utilisation of fumarate as the terminal electron acceptor during anaerobic respiration, none of which are found on the main chromosome. In addition, BPc2 contains two complete rRNA operons, a large number of enzymes involved in the metabolism of carbohydrates, nitrogen and fatty acids. In contrast to BPc2, both megaplasmids appear largely cryptic, collectively encoding 421 genes not previously described in public databases. Nevertheless, only the 186-Kb, but not 361-Kb megaplasmid, could be cured from Butyrivibrio proteoclasticus B316T. The largest megaplasmid has a copy number of 5, while all other replicons are present at a copy number of 1. %GC content and codon usage analyses strongly suggests that all three auxiliary replicons have co-resided with the major chromosome for a significant evolutionary period. Moreover, the replication machineries of these three replicons are conserved. Interestingly, a survey of a number of Butyrivibrio / Pseudobutyrivibrio species revealed that the megaplasmids are widespread in this assemblage, however these other large plasmids do not show concordance with their 16S rRNA phylogeny and appear distinct to those of B. proteoclasticus B316T. A microarray analysis of gene expression in a co-culture experiment between B. proteoclasticus and the important ruminal methanogen, Methanobrevibacter ruminantium M1, revealed a potentially mutualistic interspecies interaction. In this relationship M. ruminantium appears to provide B. proteoclasticus with glutamate, essential to the final step of NAD+ biosynthesis, while B. proteoclasticus appears to provide M. ruminantium with formate, hydrogen and carbon dioxide, each important substrate for methanogenesis.
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    Conceptual replication of Seo (2008), “Self-efficacy as a mediator in the relationship between self-oriented perfectionism and academic procrastination”
    (12/12/2021) Williams M; Edwards SR
    Introduction Self-oriented perfectionism is the tendency to set high standards for oneself and evaluate one’s behaviour accordingly. Based on a study of 692 students in Korea, Seo (2008) reported finding a negative relationship between self-oriented perfectionism and academic procrastination – i.e., the tendency to procrastinate on academic tasks. Furthermore, Seo reported that this relationship was completely mediated by self-efficacy. Seo’s study has been influential in the literature but to our knowledge has not yet been independently replicated. In this study we report a preregistered conceptual replication testing five hypotheses based on Seo’s key findings. Material and methods A detailed preregistration (including data processing and analysis syntax) was lodged in advance of data collection at https://osf.io/xfvd8. Participants were 575 students recruited from OECD countries using prolific.co. Academic procrastination was measured via an adapted version of the Procrastination Assessment Scale – Students, while self-oriented perfectionism was measured via the 5-item self-oriented perfectionism subscale of the Big Three Perfectionism Scale. Self-efficacy was measured via the New General Self-Efficacy Scale. Both ordinary least squares regression and structural equation modelling were used to test hypotheses. Results We found no evidence of a bivariate relationship between self-oriented perfectionism and academic procrastination in either set of analyses. However, we did find evidence of a small and negative indirect effect of self-oriented perfectionism on academic procrastination via self-efficacy. Conclusions We were only able to partially replicate Seo’s key findings, having found no evidence of a negative relationship between self-oriented perfectionism and academic procrastination.
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    What do incoming university students believe about open science practices in psychology?
    (SAGE Publications, 11/07/2022) Beaudry JL; Williams M; Philipp MC; Kothe EJ
    Background: Understanding students’ naive conceptions about the norms that guide scientific best practice is important so that teachers can adapt to students’ existing understandings. Objective: We examined what incoming undergraduate students of psychology believe about reproducibility and open science practices. Method: We conducted an online survey with participants who were about to start their first course in psychology at a university (N = 239). Results: When asked to indicate how a researcher should conduct her study, most students endorsed several open science practices. When asked to estimate the proportion of published psychological studies that follow various open science practices, participants’ estimates averaged near 50%. Only 18% of participants reported that they had heard the term “replication crisis.” Conclusion: Despite media attention about the replication crisis, few incoming psychology students in our sample were familiar with the term. The students were nevertheless in favour of most open science practices, although they overestimated the prevalence of some of these practices in psychology. Teaching Implications: Teachers of incoming psychology students should not assume pre-existing knowledge about open science or replicability.