Department of Biology

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https://hdl.handle.net/10315/6340

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Open Access
A 212-nt long RNA structure in the Tobacco necrosis virus-D RNA genome is resistant to Xrn degradation
(Oxford University Press, 2019) White, K. Andrew; Chaminda, Gunawardene D.; Newburn, Laura R.
Plus-strand RNA viruses can accumulate viral RNA degradation products during infections. Some of these decay intermediates are generated by the cytosolic 5′-to-3′ exoribonuclease Xrn1 (mammals and yeast) or Xrn4 (plants) and are formed when the enzyme stalls on substrate RNAs upon encountering inhibitory RNA structures. Many Xrn-generated RNAs correspond to 3′-terminal segments within the 3′-UTR of viral genomes and perform important functions during infections. Here we have investigated a 3′-terminal small viral RNA (svRNA) generated by Xrn during infections with Tobacco necrosis virus-D (family Tombusviridae). Our results indicate that (i) unlike known stalling RNA structures that are compact and modular, the TNV-D structure encompasses the entire 212 nt of the svRNA and is not functionally transposable, (ii) at least two tertiary interactions within the RNA structure are required for effective Xrn blocking and (iii) most of the svRNA generated in infections is derived from viral polymerase-generated subgenomic mRNA1. In vitro and in vivo analyses allowed for inferences on roles for the svRNA. Our findings provide a new and distinct addition to the growing list of Xrn-resistant viral RNAs and stalling structures found associated with different plant and animal RNA viruses.
Open Access
Actin and myosin inhibitors block elongation of kinetochore fibre stubs in metaphase crane-fly spermatocytes
(Springer Link, 2007-12) Forer, Arthur; Spurck, Tim; Pickett-Heaps, Jeremy
We used an ultraviolet microbeam to cut individual kinetochore spindle fibres in metaphasecrane-fly spermatocytes; then we followed the growth of the “kinetochore stubs”, the remnants of kinetochore fibres that remain attached to kinetochores. Kinetochore stubs elongate with constant velocity by adding tubulin subunits at the kinetochore, and thus elongation is related to flux of tubulin in the kinetochore microtubules. Stub elongation was blocked by cytochalasin D and latrunculin A, actin inhibitors, and by butanedione monoxime, a myosin inhibitor. We conclude that actin and myosin are involved in generating elongation and thus in producing flux of tubulin in kinetochore microtubules. We suggest that actin and myosin act in concert with a spindle matrix to propel kinetochore fibres poleward thereby causing stub elongation and generating anaphasechromosome movement in non-irradiated cells.
Open Access
An adiponectin-S1P axis protects against lipid induced insulin resistance and cardiomyocyte cell death via reduction of oxidative stress
(Biomed Central, 2019-02-21) Botta, Amy; Liu, Ying; Wannaiampikul, Sivaporn; Tungtrongchitr, Rungsunn; Dadson, Keith; Park, Tae-Sik; Sweeney, Gary
Background: Adiponectin exerts several beneficial cardiovascular effects, however their specific molecular mechanisms require additional understanding. This study investigated the mechanisms of adiponectin action in the heart during high fat diet (HFD) feeding or in palmitate (PA) treated H9c2 cardiomyoblasts. Methods: 6-week-old male adiponectin knock out (Ad-KO) mice were fed chow or 60% HFD for 6 weeks then received saline or recombinant adiponectin (3μg/g body weight) for an additional 2 weeks. After acute insulin stimulation (4 U/kg), tissue and serum samples were collected for analysis. H9c2 cardiomyocytes were treated ±0.1 mM PA, the adiponectin receptor agonist AdipoRon, or the antioxidant MnTBAP then assays to analyze reactive oxygen species (ROS) production and cell death were conducted. To specifically determine the mechanistic role of S1P, gain and loss of function studies were conducted with adding S1P to cells or the inhibitors THI and SKI-II, respectively. Results: HFD feeding induced cardiac insulin resistance in Ad-KO mice, which was reversed following replenishment of normal circulating adiponectin levels. In addition, myocardial total triglyceride was elevated by HFD and lipidomic analysis showed increased levels of ceramides and sphingosine-1 phosphate (S1P), with only the latter being corrected by adiponectin administration. Similarly, treatment of H9C2 cardiomyoblasts with PA led to a significant increase of intracellular S1P but not in conditioned media whereas AdipoRon significantly increased S1P production and secretion from cells. AdipoRon or the antioxidant MnTBAP significantly reduced PA-induced cell death. Gain and loss of function studies suggested S1P secretion and autocrine receptor activation mediated the effect of AdipoRon to attenuate PA-induced ROS production and cell death. Conclusion: Our data establish adiponectin signaling-mediated increase in S1P secretion as a mechanism via which HFD or PA induced cardiomyocyte lipotoxicity, leading to insulin resistance and cell death, is attenuated. Keywords: Adiponectin, Sphingosine-1-phosphate, Ceramide, Cardiomyocyte apoptosis, High fat diet, Palmitate, ROS
Open Access
Anaphase Chromosomes in Crane-Fly Spermatocytes Treated With Taxol (Paclitaxel) Accelerate When Their Kinetochore Microtubules Are Cut: Evidence for Spindle Matrix Involvement With Spindle Forces
(Frontiers, 2018-07-24) Forer, Arthur; Sheykhani, Rozhan; Berns, Michael
Various experiments have indicated that anaphase chromosomes continue to move after their kinetochore microtubules are severed. The chromosomes move poleward at an accelerated rate after the microtubules are cut but they slow down 1–3 min later and move poleward at near the original speed. There are two published interpretations of chromosome movements with severed kinetochore microtubules. One interpretation is that dynein relocates to the severed microtubule ends and propels them poleward by pushing against non kinetochore microtubules. The other interpretation is that components of a putative “spindle matrix” normally push kinetochore microtubules poleward and continue to do so after the microtubules are severed from the pole. In this study we distinguish between these interpretations by treating cells with taxol. Taxol eliminates microtubule dynamics, alters spindle microtubule arrangements, and inhibits dynein motor activity in vivo. If the dynein interpretation is correct, taxol should interfere with chromosome movements after kinetochore microtubules are severed because it alters the arrangements of spindle microtubules and because it blocks dynein activity. If the “spindle matrix” interpretation is correct, on the other hand, taxol should not interfere with the accelerated movements. Our results support the spindle matrix interpretation: anaphase chromosomes in taxol-treated crane-fly spermatocytes accelerated after their kinetochore microtubules were severed.
Open Access
A bee diversity survey in oak savannah habitats in Rondeau Provincial Park, Ontario
(Heritage Resources Centre, University of Waterloo, 2004) Mac, Lily; Bazely, Dawn
A survey of bee diversity was conducted in two oak savannah habitats - Oak Savannah 3 (03) and South Point (SP) - in Rondeau Provincial Park in Southern Ontario, Canada. The bee community composition of 03 and SP were similar in both sites according to a Detrended Correspondence Analysis (DCA) and Sorensen's coefficient of community similarity. However, bees appeared to prefer the SP habitat over 03 as determined by the greater bee species abundance, richness, Shannon diversity, and evenness values found in SP. This is possibly due to the larger habitat area and greater plant species richness and abundance of SP compared to 03. The decline in bee species richness and abundance toward the end of the summer correlated with the decline in plant richness and abundance because bees rely on the nectar and pollen in plants that are flowering as sources of food.
Open Access
Bees collect polyurethane and polyethylene plastics as novel nest materials
(Ecological Society of America, 2013-12-31) MacIvor, Scott; Moore, Andrew E.
Plastic waste pervades the global landscape. Although adverse impacts on both species and ecosystems have been documented, there are few observations of behavioral flexibility and adaptation in species, especially insects, to increasingly plastic-rich environments. Here, two species of megachilid bee are described independently using different types of polyurethane and polyethylene plastics in place of natural materials to construct and close brood cells in nests containing successfully emerging brood. The plastics collected by each bee species resembled the natural materials usually sought; Megachile rotundata, which uses cut plant leaves, was found constructing brood cells out of cut pieces of polyethylene-based plastic bags, and Megachile campanulae, which uses plant and tree resins, had brood cells constructed out of a polyurethane-based exterior building sealant. Although perhaps incidentally collected, the novel use of plastics in the nests of bees could reflect ecologically adaptive traits necessary for survival in an increasingly human-dominated environment.
Open Access
Borrowing from Peter to pay Paul: managing threatened predators of endangered and declining prey species
(2019-10-15) Dupuis-Desormeaux, Marc; Davidson, Zeke; Dheer, Arjun; Pratt, Laura; Preston, Elizabeth; Gilicho, Saibala; Mwololo, Mary; Chege, Geoffrey; MacDonald, Suzanne E.; Doncaster, C Patrick
Conservation policy and practice can sometimes run counter to their mutual aims of ensuring species survival. In Kenya, where threatened predators such as lion deplete endangered prey such as Grevy’s zebra, conservation practitioners seek to ensure species success through exclusive strategies of protection, population increase and preservation. We found strong selection for the endangered Grevy’s zebra by both lion and hyena on two small fenced conservancies in Kenya. Despite abundant diversity of available prey, Grevy’s zebra were selected disproportionately more than their availability, while other highly available species such as buffalo were avoided. Lions were therefore not alone in presenting a credible threat to Grevy’s zebra survival. Conservation practitioners must consider interlinked characteristics of prey selection, resource availability and quality, the interplay between carnivore guild members and landscape scale population trends performance in wildlife management decisions.
Open Access
CAPA neuropeptides and their receptor form an anti-diuretic hormone signalling system in the human disease vector, Aedes aegypti
(Nature, 2020) Sajadi, Farwa; Uyuklu, Ali; Paputsis, Christine; Lajevardi, Aryan; Wahedi, Azizia; Ber, Lindsay Taylor; Matei, Andreea; Paluzzi, Jean-Paul
Insect CAPA neuropeptides are homologs of mammalian neuromedin U and are known to influence ion and water balance by regulating the activity of the Malpighian ‘renal’ tubules (MTs). Several diuretic hormones are known to increase primary fluid and ion secretion by insect MTs and, in adult female mosquitoes, a calcitonin-related peptide (DH31) called mosquito natriuretic peptide, increases sodium secretion to compensate for the excess salt load acquired during blood-feeding. An endogenous mosquito anti-diuretic hormone was recently described, having potent inhibitory activity against select diuretic hormones, including DH31. Herein, we functionally deorphanized, both in vitro and in vivo, a mosquito anti-diuretic hormone receptor (AedaeADHr) with expression analysis indicating highest enrichment in the MTs where it is localized within principal cells. Characterization using a heterologous in vitro system demonstrated the receptor was highly sensitive to mosquito CAPA neuropeptides while in vivo, AedaeADHr knockdown abolished CAPA-induced anti-diuretic control of DH31-stimulated MTs. CAPA neuropeptides are produced within a pair of neurosecretory cells in each of the abdominal ganglia, whose axonal projections innervate the abdominal neurohaemal organs, where these neurohormones are released into circulation. Lastly, pharmacological inhibition of nitric oxide synthase (NOS) and protein kinase G (PKG) signaling eliminated anti-diuretic activity of CAPA, highlighting the role of the second messenger cGMP and NOS/PKG in this anti-diuretic signaling pathway.
Open Access
Characteristics of expanding and stable populations of garlic mustard in Carolinian parks
(Heritage Resources Centre, University of Waterloo, 2002) Firanski, J. Carrie; Falkenberg, Nancy; Koh, Saewan; Bazely, Dawn
Garlic Mustard (Alliaria petiolata) is a short-lived monocarpic perennial introduced to North America in 1868 which reached Canada in 1879. It was first introduced to Point Pelee National Park in 1969 and Rondeau Provincial Park in the 1980s. Both parks have long histories of human-induced disturbance, with most recently high deer grazing pressure. We show that garlic mustard has become (Point Pelee NP) and is becoming (Rondeau PP) a predominant understorey herb from 1994 to the present, and that the two parks are in different phases of colonization. Our research suggests that the garlic mustard population at Point Pelee has stabilized while the Rondeau population is continuing to expand. We found a significant negative relationship between species diveristy and garlic mustard density for both of the parks. However, it is unknown whether garlic mustard is supressing native herbaceous species diversity, or whether low diversity is an outcome of the intense long-term grazing pressure exerted by deer on the native species. Interestingly, the garlic mustard populations at both parks have alternate years of high and low flowering densities, driven by intraspecific density effects. This may expalin the lack of negative association in garlic mustard density and native diversity in some years. Further research will include experiments with native species transplants into garlic mustard dominated sites to determine competitive interactions, and analysis of changes in distribution throughout the transects to determine rate of spread of expanding garlic mustard populations at Rondeau.
Open Access
A checklist for choosing between R packages in ecology and evolution
(Wiley, 2020) Lortie, Christopher; Braun, Jenna; Filazzola, Alessandro; Miguel, Maria Florencia
The open source and free programming language R is a phenomenal mechanism to address a multiplicity of challenges in ecology and evolution. It is also a complex ecosystem because of the diversity of solutions available to the analyst. Packages for R enhance and specialize the capacity to explore both niche data/experiments and more common needs. However, the paradox of choice or how we select between many seemingly similar options can be overwhelming and lead to different potential outcomes. There is extensive choice in ecology and evolution between packages for both fundamental statistics and for more specialized domain‐level analyses. Here, we provide a checklist to inform these decisions based on the principles of resilience, need, and integration with scientific workflows for evidence. It is important to explore choices in any analytical coding environment—not just R—for solutions to challenges in ecology and evolution, and document this process because it advances reproducible science, promotes a deeper understand of the scientific evidence, and ensures that the outcomes are correct, representative, and robust.
Open Access
Chromosomes selectively detach at one pole and quickly move towards the opposite pole when kinetochore microtubules are depolymerized in Mesostoma ehrenbergii spermatocytes.
(Springer Link, 2018-02) Forer, Arthur; Fegaras, Eleni
In a typical cell division chromosomes align at the metaphase plate before anaphase commences. This is not the case in Mesostoma spermatocytes. Throughout prometaphase the three bivalents persistently oscillate towards and away from either pole, at average speeds of 5-6 μm/min., without ever aligning at a metaphase plate. In our experiments nocodazole (NOC) was added to prometaphase spermatocytes to depolymerize the microtubules. Traditional theories state that microtubules are the producers of force in the spindle, either by tubulin depolymerizing at the kinetochore (PacMan) or at the pole (Flux). Accordingly, if microtubules are quickly depolymerized, the chromosomes should arrest at the metaphase plate and not move. However, in 57/59 cells at least one chromosome moved to a pole after NOC treatment, and in 52 of these cells all three bivalents moved to the same pole. Thus the movements are not random to one pole or other. After treatment with NOC chromosome movement followed a consistent pattern. Bivalents stretched out towards both poles, paused, detached at one pole, and then the detached kinetochores quickly moved towards the other pole, reaching initial speeds up to more than 200 μm/min., much greater than anything previously recorded in this cell. As the NOC concentration increased the average speeds increased and the microtubules disappeared faster. As the kinetochores approached the pole they slowed down and eventually stopped. Similar results were obtained with colcemid treatment. Confocal immunofluorescence microscopy confirms that microtubules are not associated with moving chromosomes. Thus these rapid chromosome movements may be due to non-microtubule spindle components such as actin-myosin or the spindle matrix.
Open Access
The Churchill Community of Knowledge: An Open Access Digital Archive
(Poster presented at the 7th International Biocuration Conference 6-9 April 2014, Toronto, Canada, 2014-04-06) Untershats, Netta; Kosavic, Andrea; Cooke, Fred; Jefferies, Susan; Sivakumaran, Jeevika; Bekit, Natan; Bazely, Dawn
This poster was presented at the 7th International Biocuration Conference (ISB2014), University of Toronto, Toronto, Canada, April 6-9, 2014. The Churchill Community of Knowledge Digital Archive is a YorkSpace Institutional Repository research project led by IRIS (Institute for Research & Innovation in Sustainability) and York University Libraries. Its overall goal is to document, coalesce and mobilize long-term ecological research from Wapusk National Park and, more broadly, Churchill, Manitoba. To date, the project has engaged 10 undergraduate & graduate Biology students in developing metadata for copyrightâ€‘cleared digital media & uploading items. Diverse communities, including the public, can access the Open Access archive via Google searches
Open Access
Coaching for life -- my life
(Association of Universities and Colleges of Canada, 2005-11) Bazely, Dawn
Juggling a demanding academic career with family responsibilities â€“ sound familiar? I nearly called it quits. Instead, I called a coach
Open Access
Colonization and usage of an artificial urban wetland complex by freshwater turtles
(2018-08-08) Dupuis-Desormeaux, Marc; Davy, Christina; Lathrop, Amy; Followes, Emma; Ramesbottom, Andrew; Chreston, Andrea; MacDonald, Suzanne E.
Conservation authorities invest heavily in the restoration and/or creation of wetlands to counteract the destruction of habitat caused by urbanization. Monitoring the colonization of these new wetlands is critical to an adaptive management process. We conducted a turtle mark-recapture survey in a 250 ha artificially created wetland complex in a large North American city (Toronto, Ontario). We found that two of Ontario’s eight native turtle species (Snapping turtle (SN), Chelydra serpentina, and Midland Painted (MP) turtle, Chrysemys picta marginata) were abundant and both were confirmed nesting. The Blanding’s turtle (Emydoidea blandingii) was present but not well established. Species richness and turtle density were not equally distributed throughout the wetland complex. We noted SN almost exclusively populated one water body, while other areas of the wetland had a varying representation of both species. The sex ratios of both SN and MP turtles were 1:1. We tracked the movement of Snapping and Blanding’s turtles and found that most turtles explored at least two water bodies in the park, that females explored more water bodies than males, and that 95% of turtles showed fidelity to individual overwintering wetlands. We performed DNA analysis of two Blanding’s turtles found in the created wetlands and could not assign these turtles to any known profiled populations. The genetic data suggest that the turtles probably belong to a remnant local population. We discuss the implications of our results for connectivity of artificial wetlands and the importance of the whole wetland complex to this turtle assemblage.
Open Access
Comparing motion capture cameras versus human observer monitoring of mammal movement through fence gaps: a case study from Kenya
(2016) Dupuis-Desormeaux, Marc; Davidson, Zeke; Mwololo, Mary; Kisio, Edwin; MacDonald, Suzanne E.
Monitoring the movement and distribution of wildlife is a critical tool of an adaptive management framework for wildlife conservation. We installed motion‐triggered cameras to capture the movement of mammals through two purpose‐built migration gaps in an otherwise fenced conservancy in northern Kenya. We compared the results to data gathered over the same time period (1 Jan 2011–31 Dec 2012) by the human observers monitoring mammal tracks left at the same fence gaps in a sandy loam detection strip. The camera traps detected more crossing events, more species and more individuals of each species per crossing event than did the human track observers. We tested for volume detection differences between methods for the five most common species crossing each gap and found that all detection rates were heavily weighted towards the camera‐trap method. We review some of the discrepancies between the methods and conclude that although the camera traps record more data, the management of that data can be time‐consuming and ill‐suited to some time‐sensitive decision‐making. We also discuss the importance of daily track monitoring for adaptive management conservation and community security.
Open Access
Conservation Genomics of the Declining North American Bumblebee Bombus terricola Reveals Inbreeding and Selection on Immune Genes
(Frontiers Media, 2018-08-10) Kent, Clement; Dey, Alivia; Patel, Harshilkumar; Tsvetkov, Nadejda; Tiwari, Tanushree; MacPhail, Victoria J.; Gobeil, Yann; Harpur, Brock; Gurtowski, James; Schatz, Michael; Colla, Sheila R.; Zayed, Amro
The yellow-banded bumblebee Bombus terricola was common in North America but has recently declined and is now on the IUCN Red List of threatened species. The causes of B. terricola’s decline are not well understood. Our objectives were to create a partial genome and then use this to estimate population data of conservation interest, and to determine whether genes showing signs of recent selection suggest a specific cause of decline. First, we generated a draft partial genome (contig set) for B. terricola, sequenced using Pacific Biosciences RS II at an average depth of 35×. Second, we sequenced the individual genomes of 22 bumblebee gynes from Ontario and Quebec using Illumina HiSeq 2500, each at an average depth of 20×, which were used to improve the PacBio genome calls and for population genetic analyses. The latter revealed that several samples had long runs of homozygosity, and individuals had high inbreeding coefficient F, consistent with low effective population size. Our data suggest that B. terricola’s effective population size has decreased orders of magnitude from pre-Holocene levels. We carried out tests of selection to identify genes that may have played a role in ameliorating environmental stressors underlying B. terricola’s decline. Several immune-related genes have signatures of recent positive selection, which is consistent with the pathogen-spillover hypothesis for B. terricola’s decline. The new B. terricola contig set can help solve the mystery of bumblebee decline by enabling functional genomics research to directly assess the health of pollinators and identify the stressors causing declines.
Open Access
The dark side of facilitation: native shrubs facilitate exotic annuals more strongly than native annuals in net abundance
(Pensoft, 2019-04) Lucero, Jacob; Noble, Taylor; Haas, Stephanie; Westphal, Michael; Butterfield, H. Scott; Lortie, Christopher
Open Access
Data files for "Molecular Modeling the Proteins from the exo-xis Region of Lambda and Shigatoxigenic Bacteriophages"
(MDPI, 2021-10-20) Donaldson, Logan
Open Access
Determining an appropriate fire frequency for restoration and maintenance of oak savannas in Pinery Provincial Park.
(Society for Ecological Restoration, 2004-08) Etwell, Tracey; Bazely, Dawn
Oak Savanna habitat is globally rare. Prescribed burning is currently a widely-adopted management approach for restoring and maintaining these communities. We examined patterns of habitat recovery in the largest existing remnant in Southern Ontario, Pinery Provincial Park, while setting up a long-term monitoring program aimed at evaluating the success of the long-term prescribed burn plan. Initial results suggest that there is a three year burn lag during which cover of typical oak savanna species increases over this time period following burning. Future studies will determine where the peak of maximum diversity of oak savanna species occurs with respect to time- since- burning.
Open Access
Determining appropriate fire frequencies for oak savannas in two Ontario Provincial Parks
(Heritage Resources Centre, University of Waterloo, 2004) Etwell, Tracey; Bazely, Dawn
Prescribed burning is a popular management tool in many prairie and savanna restorations. In Ontario's globally rare oak savanna plant communities it is viewed as a means of restoring historic disturbance regimes essential for the maintenance of native species. Prescribed burn plans have been implemented at two Carolinian provincial parks, Rondeau and Pinery. Our goals are to establish a framework for the restoration of oak savanna communities that is based on the principles of restoration ecology and adaptive management. Since burning has both short and long-term effects, effective monitoring of plant community responses is essential. A key to success will be ensuring that protocols for measuring long-term plant community responses to burning, that are designed to be carried out by researchers with varying levels of field expertise yield sound data.