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Researchers in the Faculty of Science are involved in an impressive variety of fields – from astrophysics to zoology, nanotechnology to virtual reality, metabolomics to mathematics and much more!
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Browsing Science by Department "Biological Sciences"
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Item Open Access Alternative splicing of a group II intron in a surface layer protein gene in Clostridium tetani(Oxford Journals, 2013-10) McNeil, Bonnie A; Simon, Dawn M; Zimmerly, StevenGroup II introns are ribozymes and retroelements found in bacteria, and are thought to have been the ancestors of nuclear pre-mRNA introns. Whereas nuclear introns undergo prolific alternative splicing in some species, group II introns are not known to carry out equivalent reactions. Here we report a group II intron in the human pathogen Clostridium tetani, which undergoes four alternative splicing reactions in vivo. Together with unspliced transcript, five mRNAs are produced, each encoding a distinct surface layer protein isoform. Correct fusion of exon reading frames requires a shifted 5' splice site located 8 nt upstream of the canonical boundary motif. The shifted junction is accomplished by an altered IBS1-EBS1 pairing between the intron and 5' exon. Growth of C. tetani under a variety of conditions did not result in large changes in alternative splicing levels, raising the possibility that alternative splicing is constitutive. This work demonstrates a novel type of gene organization and regulation in bacteria, and provides an additional parallel between group II and nuclear pre-mRNA introns.Item Open Access Arabidopsis At5g39790 encodes a chloroplast-localized, carbohydrate-binding, coiled-coil domain-containing putative scaffold protein(BioMed Central, 2008) Lohmeier-Vogel, Elke M.; Kerk, David; Nimick, Mhairi; Wrobel, Susan; Vickerman, Lori; Muench, Douglas G.; Moorhead, Greg B. G.Item Open Access Assembly Pathway of a Bacterial Complex Iron Sulfur Molybdoenzyme(De Gruyter, 2017-08-08) Cherak, Stephana J; Turner, Raymond JProtein folding and assembly into macromolecule complexes within the living cell is a complex process requiring intimate coordination. The biogenesis of complex iron sulphur molybdoenzymes (CISM) requires use of a system specific chaperone – a redox enzyme maturation protein (REMP) – to help mediate final folding and assembly. The CISM Dimethyl sulfoxide (DMSO) reductase is a bacterial anaerobic respiratory oxidoreductase that utilizes DMSO as a final electron acceptor to survive within anoxic conditions. The REMP DmsD strongly interacts with DMSO reductase to facilitate folding, cofactor-insertion, subunit assembly and targeting of the multi-subunit enzyme prior to membrane translocation and final assembly and maturation into a bioenergetic catalytic unit. In this article, we discuss the biogenesis of DMSO reductase as an example of the participant network for bacterial CISM maturation pathways.Item Open Access Behaviors of Western Spruce Budworm Moths (Choristoneura occidentalis) as Defences Against Bat Predation(Springer, 2006-07) Barclay, Robert M. R.; Lloyd, Natasha; Wilson, Joanna M.Item Open Access Bumble Bees of Calgary: A key and illustrated guide for identification of the bumble bee species found in Calgary, Alberta(2023-02-08) Neame, Tobyn; Ritchie, Sarah; Summers, MindiA guide to the natural history, diversity, and identification of Calgary bumble bees.Item Open Access Calgary - A Bee City(2021-12-22) Summers, Mindi; Best, Lincoln; Robinson, Samuel; Seal, Michaela; Purvis, Emily; Vermaak, Sarah; Clarke, Arminty; Gavin, Michael; Miksha, Ron; Eggermont, MarjanVisual summary of Calgary's native bee biodiversity and the 15 native plants found to support the greatest diversity of wild bees.Item Open Access Characterization and functional analysis of seven flagellin genes in Rhizobium leguminosarum bv. viciae. Characterization of R. leguminosarum flagellins(BioMed Central, 2010-08-17) Tambalo, Dinah D.; Bustard, Denise E.; Del Bel, Kate L.; Koval, Susan F.; Khan, Morgan F.; Hynes, MichaelItem Open Access Coleoptera of Alberta: Visual Guide to Common Terrestrial Families (Adults)(University of Calgary, 2022-12-18) Carson, Arminty; Gee, Gabriella; Summers, MindiA visual guide to common Coleoptera families found in Alberta created for undergraduate students and those new to insect identification. Visual images and descriptions are provided for key features and terminology needed to identify common beetles to family. We welcome recommendations for additions and updates from the entomological community.Item Open Access A collaboration in creating digital natural history collections: A case study of Alberta native bees(2021-10-16) Alexander, Rob; Ruddock, Kathryn; Summers, MindiAt the University of Calgary, a collaboration among staff and students in the Department of Biological Sciences, Department of Mechanical Engineering, and Libraries and Cultural Resources, sought to explore how we could make our Biological Sciences natural history collections (invertebrate, vertebrate, and herbarium) accessible to a range of diverse stakeholders interested in biodiversity conservation. Using native bees as a case study, we digitized over 230 species of bee, producing 368 public records that includes three photographs of each bee specimen: lateral, anterior, and dorsal, along with associated metadata. This work involved the launch of a biodiversity website and digital collections where these photographs and student-created natural history illustrations are now available as open educational resources. Our digitization work is continuing for bees as well as other insect groups, and we are currently expanding our digitization capabilities to create 3D models. These 3D models will be annotated for students in biology and engineering courses, and used to train both students and citizen scientists in insect identification. Our collaboration has generated campus-wide interest in bees, with recent collaborations with the Office of Sustainability leading to the University of Calgary becoming a BeeUniversity and the start of the Calgary pollinator Count citizen-science initiative.Item Open Access Comparative proteomic analysis of proliferating and functionally differentiated mammary epithelial cells(American Society for Biochemistry and Molecular Biology Inc., 2003) Desrivieres, S.; Prinz, T.; Palomino-Laria, N. C.; Meyer, M.; Boehm, G.; Schafer, J.; Neumann, T.; Groner, B.; Shemanko, Carrie S.Item Open Access Concurrent profiling of indole-3-acetic acid, abscisic acid, and cytokinins and structurally related purines by high-performance-liquidchromatography tandem electrospray mass spectrometry(BioMed Central, 2012-10-12) Farrow, Scott C; Emery, RJ NeilItem Open Access Considering multiple anthropogenic threats in the context of natural variability: Ecological processes in a regulated riverine ecosystem(Wiley, 2020-06-09) Sinnatamby, R. Niloshini; Mayer, Bernhard; Kruk, Mary K.; Rood, Stewart B.; Farineau, Anne; Post, John R.Rivers are among the most altered environments globally, but identifying which threats are responsible for observed biotic and abiotic changes is complicated by natural drivers of variation. The Bow River, Canada provides an ideal model to resolve these influences and explore spatial relationships. It originates from pristine Rocky Mountain headwaters and is subsequently impacted by typical human alterations: damming, municipal channelization and effluent release, and agricultural impacts (nutrient enrichment and water withdrawal for irrigation). By coordinating studies of the Bow River's biota, we demonstrate how threat–driver interactions depend on season and the abiotic factor and biotic community or species of interest. We conclude that impact severity and riverine recovery depend on the threat magnitude, its longitudinal position and proximity to other threats and natural drivers. We found that river regulation, water extraction and bank armouring interact to limit geomorphic processes resulting in depleted riparian woodlands and numbers of fish species, though a large, undammed tributary nearby allows quick recovery downstream. We highlight the implications of the longitudinal position of the threats because cold-water fish species are disproportionately impacted through the area where the human impacts on the Bow River overlap. We illustrate how the interactions between flow, nutrients and temperature lead to macrophyte- or algae-dominated communities and associated shifts in fish composition and biomass. Finally, we applied our increased understanding of ecological riverine processes to conclude that management techniques such as flushing flows or functional environmental flows are likely to have only minimal or conditional success in the Bow River.Item Open Access Creating digital collections of biological specimens: Lessons for teaching and learning(2021-08-11) Ruddock, Kathryn; Summers, Mindi; Vamosi, JanaUniversity of Calgary Libraries has partnered with faculty in Biological Sciences since 2016 to digitize, describe and share herbarium and invertebrate specimens through digital collections as a resource for students. These collections are used by students and are created in partnership with students as part of course assignments. COVID-19 and online instruction made the collection and training resources even more valuable to our learners than we originally envisioned. Join us to learn how we created these collections, uses for the digital objects in teaching and learning, and limitations of the digital collection when the physical specimen is not accessible.Item Open Access Diet reconstructions for end-Pleistocene Mammut americanum and Mammuthus based on comparative analysis of mesowear, microwear, and dental calculus in modern Loxodonta africana(Elsevier, 2020-01) Cammidge, Tasha S.; Kooyman, Brian; Theodor, Jessica M.We analyse mesowear, microwear, and dental calculus for end-Pleistocene Mammut and Mammuthus from North America, and modern Loxodonta africana to reconstruct diet. These three methods allow both short- and long-term diets to be distinguished. As microwear analysis shows a negative correlation between the numbers of pits and scratches counted, the proportions of pits/(pits + scratches) were used for analyses rather than gross counts. The three types of analyses confirm that modern Loxodonta africana are grazers or mixed-feeders. Microwear analysis demonstrates that end-Pleistocene Mammut were primarily browsers but may have changed their diets opportunistically or seasonally to graze. Mesowear analysis of end-Pleistocene Mammuthus indicates a grazing diet, but microwear analysis indicates a mixed-feeding diet. Dental calculus analysis demonstrates that all three species were mixed-feeding to varying degrees. Results show that extinct proboscidean diet was more complex than previously thought, and may contradict previous work suggesting that Mammut were browsers and Mammuthus were grazers. Using mesowear and microwear, we found no significant differences in pre- and post-glacial diet for fossil proboscideans. However, using dental calculus, we found that for pre-glacial specimens there was a larger proportion of tiny (i.e. less than 8 μm wide) grass starch granules, whereas for post-glacial specimens there is a larger proportion of large (i.e. greater than 20 μm wide) grass starch granules with lamellae, suggesting with a shift in Mammut and Mammuthus diet during the end-Pleistocene. Specimens commonly had different dietary signals depending on the method utilized, suggesting that a multi-faceted approach is required to fully elucidate proboscidean diet.Item Open Access Displacement affinity chromatography of protein phosphatase one (PP1) complexes(2008-11-10) Moorhead, Greg B. G.; Trinkle-Mulcahy, Laura; Nimick, Mhairi; De Wever, Veerle; Campbell, David G.; Gourlay, Robert; Lam, Yun Wah; Lamond, Angus I.Item Open Access DNA based prenatal testing for the skin blistering disorder epidermolysis bullosa simplex(John Wiley & Sons, 2000) Rugg, E. L.; Baty, D.; Shemanko, Carrie S.; Magee, G.; Polak, S.; Bergman, R.; Kadar, T.; Boxer, M.; Falik-Zaccai, T.; Borochowitz, Z.; Lane, E. B.Item Open Access Effects of body size on investment in individual broods by male pine engravers (Coleoptera: Scolytidae)(National Research Council Press, 1995) Reid, Mary L.; Roitberg, Bernard D.Item Open Access Effects of intrinsic and extrinsic factors on ruminating, grazing, and bedding time in bighorn sheep (Ovis canadensis)(Public Library of Science, 2018-10-29) Wang, Muyang; Alves, Joana; Tucker, Meghan; Yang, Weikang; Ruckstuhl, Kathreen ERumination is the repeated process of regurgitation of a food bolus, followed by chewing, swallowing, and regurgitation, which enhance nutrient assimilation. Time spent in lateral recumbency (i.e., bedded, lying) has often been used as a proxy for time spent ruminating due to difficulties of observing detailed rumination behavior in the field. The actual proportion of time spent ruminating, or other activities, will in turn be affected by the age and sex of an individual but also with changes in food quality. We studied the effects of intrinsic and extrinsic factors on time spent ruminating, bedding, proportion of bedding time spent ruminating, and grazing of individually marked bighorn sheep (Ovis canadensis). Our results show that bighorn sheep spent more time ruminating and less time grazing in summer and autumn. Overall, females spent less time ruminating, and more time grazing than males. Bighorn sheep decreased their time spent ruminating with increasing acid detergent fiber (ADF) content in the forage. Age influenced the time spent grazing, bedded and proportion of bedded time spent ruminating. Older sheep not only increased their bedding time but also their time spent bedded without ruminating compared to younger individuals. The proportion of time spent grazing was also affected by age, with a decrease in the proportion of time spent grazing with increasing age. Our results suggest that these four behaviors are plastic and variable. We thus conclude that bedding time does not reflect time spent ruminating but that the latter is affected by both intrinsic and extrinsic factors.Item Open Access The efficacy of different antimicrobial metals at preventing the formation of, and eradicating bacterial biofilms of pathogenic indicator strains.(Nature, 2017-02-15) Gugala, Natalie; Lemire, Joe A.; Turner, Raymond J.The emergence of multidrug resistant pathogens and the prevalence of biofilm-related infections have generated a demand for alternative antimicrobial therapies. Metals have not been explored in adequate detail for their capacity to combat infectious disease. Metal compounds can now be found in textiles, medical devices, and disinfectants – yet, we know little about their efficacy against specific pathogens. To help fill this knowledge gap, we report on the antimicrobial and antibiofilm activity of seven metals; silver, copper, titanium, gallium, nickel, aluminum and zinc against three bacterial strains, Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli. In order to evaluate the capacity of metal ions to prevent the growth of, and eradicate biofilms and planktonic cells, bacterial cultures were inoculated in the Calgary Biofilm Device (MBEC™) in the presence the metal salts. Copper, gallium, and titanium were capable of preventing planktonic and biofilm growth, and eradicating established biofilms of all tested strains. Further, we observed that the efficacies of the other tested metal salts displayed variable efficacy against the tested strains. Further, contrary to the enhanced resistance anticipated from bacterial biofilms, particular metal salts were observed to be more effective against biofilm communities versus planktonic cells. In this study, we have demonstrated that the identity of the bacterial strain must be considered prior to treatment with a particular metal ion. Consequently, as the use of metal ions as antimicrobial agents to fight multidrug resistant and biofilm related infections increases, we must aim for more selective deployment in a given infectious setting.Item Open Access Enamel hypoplasia and dental wear of North American late Pleistocene horses and bison: An assessment of nutritionally based extinction models(Cambridge, 2019-06-03) Jass, Christopher I.; Austen, Jennifer; Theodor, Jessica M.; Barrón-Ortiz, Christina I.; Barrón-Corvera, RaúlApproximately 50,000–11,000 years ago many species around the world became extinct or were extirpated at a continental scale. The causes of the late Pleistocene extinctions have been extensively debated and continue to be poorly understood. Several extinction models have been proposed, including two nutritionally based extinction models: the coevolutionary disequilibrium and mosaic-nutrient models. These models draw upon the individualistic response of plant species to climate change to present a plausible scenario in which nutritional stress is considered one of the primary causes for the late Pleistocene extinctions. In this study, we tested predictions of the coevolutionary disequilibrium and mosaic- nutrient extinction models through the study of dental wear and enamel hypoplasia of Equus and Bison from various North American localities. The analysis of the dental wear (microwear and mesowear) of the samples yielded results that are consistent with predictions established for the coevolutionary disequilibrium model, but not for the mosaic-nutrient model. These ungulate species show statistically different dental wear patterns (suggesting dietary resource partitioning) during preglacial and full-glacial time intervals, but not during the postglacial in accordance with predictions of the coevolutionary disequilibrium model. In addition to changes in diet, these ungulates, specifically the equid species, show increased levels of enamel hypoplasia during the postglacial, indicating higher levels of systemic stress, a result that is consistent with the models tested and with other climate-based extinction models. The extent to which the increase in systemic stress was detrimental to equid populations remains to be further investigated, but suggests that environmental changes during the late Pleistocene significantly impacted North American equids.