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SARM1 (sterile alpha and TIR motif containing 1) is responsible for depletion of nicotinamide adenine dinucleotide in its oxidized form (NAD+) during Wallerian degeneration associated with neuropathies. Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors recognize pathogen effector proteins and trigger localized cell death to restrict pathogen infection. Both processes depend on closely related Toll/interleukin-1 receptor (TIR) domains in these proteins, which, as we show, feature self-association-dependent NAD+ cleavage activity associated with cell death signaling. We further show that SARM1 SAM (sterile alpha motif) domains form an octamer essential for axon degeneration that contributes to TIR domain enzymatic activity. The crystal structures of ribose and NADP+ (the oxidized form of nicotinamide adenine dinucleotide phosphate) complexes of SARM1 and plant NLR RUN1 TIR domains, respectively, reveal a conserved substrate binding site. NAD+ cleavage by TIR domains is therefore a conserved feature of animal and plant cell death signaling pathways.

Ancestral sequence reconstruction is a technique which is gaining widespread use in molecular evolution studies and protein engineering. Here we present Graphical Representation of Ancestral Sequence Predictions (GRASP) that can be used to infer and explore ancestral variants of protein families with more than 10,000 members. GRASP uses partial order graphs to represent homology in very large data sets, which are intractable with current inference tools and may, for example, be used to engineer proteins by identifying ancient variants of enzymes. We demonstrate that (1) across three distinct enzyme families, GRASP predicts ancestor sequences, all of which demonstrate enzymatic activity, (2) within-family insertions and deletions can be used as building blocks to support the engineering of biologically active ancestors via a new source of ancestral variation, and (3) generous inclusion of sequence data encompassing great diversity leads to less variance in ancestor sequence.

Additional file 2: Figure S2A. Taxonomic distribution of fungal AAO–PDH. B. Taxonomic distribution of fungal AOx. C. Taxonomic distribution of fungal CDH. D. Taxonomic distribution of fungal GOx-GDH. E. Taxonomic distribution of fungal POx.

Additional file 5: Figure S5. Crystal structure of Komagataella phaffii AOx (5HSA) showing the C-terminal extension (A) and the insertion (B) when compared to AOx-like sequences.

A Thesis Submitted to the Faculty of Graduate Studies and Research In Partial Fulfillment of the Requirements for the Degree of Master of Science in Biology, University of Regina. viii, 86 p. Diurnal aerial insectivores, a guild of birds related by foraging behaviour, are declining rapidly across North America but the reasons for the decline are unknown. One of these guild members, the Common Nighthawk (Chordeiles minor), may have substantial but undocumented populations in Canada’s boreal forest. Any differences between Common Nighthawk population trends in the boreal forest compared to more southern populations may help determine why aerial insectivore populations in general are declining. Wildland fires, common in the boreal forest, transform closed habitat into the open habitat Common Nighthawks prefer. Therefore, I assessed nighthawk abundance in northwestern Ontario in recently burned forest (~5 years since a fire) compared to unburned boreal forest. Based on survey data, Common Nighthawks were significantly more abundant in burned boreal forest than unburned forest, and the probability of detecting birds decreased with distance from a burn. Nighthawks were not more associated with riverine areas than other areas in my study area. I also evaluated forest attributes that may affect local nighthawk abundance. Lesser canopy cover and the number of logs in recently burned forest are likely important factors in habitat use by Common Nighthawks, but these factors are dependent upon the scale used for the evaluation. Common Nighthawks, like other nightjars, often sit on gravel roads at night where they are at risk of being struck by passing traffic, but neither the reasons behind their use of roads nor the frequency of traffic strikes are known. I found no significant vegetation structure variable that predicted nighthawk site use on roads. Further, neither nearby Common Nighthawk abundance nor nearby potential roost availability predicted presence. However, the overall frequency of Common Nighthawks on roads was significantly correlated with lunar phase, which suggests that Common Nighthawks (subfamily Chordeilinae) use roads as a foraging site like other nightjars (subfamily Caprimulginae). The low vehicle-induced mortality I observed likely results from the low traffic rate at my study site, thus the use of gravel roads by Common Nighthawks in the boreal forest, assuming similar levels of traffic, does not appear to be a substantial conservation threat. Student yes