Department of Biological Sciences

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https://hdl.handle.net/20.500.14078/6

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Nature kids: out and about
(2024) Haines, Jessica A.
How well do you know Alberta’s waterfowl? Test your identification skills on a few of our species by matching the photos with the descriptions of these wonderful waterfowl below.
Impacts of garlic mustard (Alliaria petiolata, Brassicaceae) invasion on oribatid mites in urban forest soils vary with the size of the invaded patch
(2024) Flaherty, Leah; Hills, Melissa; Giacobbo, Victoria; Kuczmarski, Paige; Momborquette, Morgan; Lumley, Lisa
Investment in non-native species management should be informed by knowledge of impact, including on native biodiversity and ecosystem function. Oribatid soil mites may be useful to evaluate the impacts of plant invasions since they are bioindicators of disturbance and soil ecosystem health. Still, more research is needed to characterize their responses to plant invasion, especially at the species level. Our objective was to determine the effect of invasion of urban forest understories by an allelopathic weed (garlic mustard, Alliaria petiolata (Brassicaceae)) on belowground oribatid mite species and communities. At two sites in central Alberta (Canada), over two years, we examined adult oribatid (≥ 300 µm) community assemblages, species richness, evenness, diversity, and abundance in plots invaded with garlic mustard and uninvaded plots with native vegetation. Environmental covariates known to be associated with soil invertebrate communities were also evaluated. Results suggest that the spatial extent of the garlic mustard invasion (patch area) mediates its impact on oribatid mite communities. However, there were no community-level impacts when considering invasion as binary (garlic mustard vs. native vegetation). Garlic mustard patch area influenced oribatid community composition and was positively related to species richness and several abundance metrics. The oribatid species we observed benefiting from garlic mustard invasion have been previously associated with disturbed soils. The mechanisms driving these patterns need more research, but we hypothesize they may relate to patch-specific resident times. Site was also a dominant factor influencing oribatid mite communities, and impacts of year, litter depth, and canopy cover were also detected at the species and/or community level. These findings contribute to our understanding of the impact of an invasive weed on bioindicating soil mite communities and species and highlight the importance of considering invasion context, including spatial extent when evaluating the impacts of invasive species on belowground invertebrate communities.
Microsporidia in fish
(2014) Kent, Michael L.; Shaw, Ross W.; Sanders, Justin L.; Weiss, Louis M.; Becnel, James J.
The importance of microsporidia in captive fishes continues to increase with the continued dramatic increase in finfish aquaculture. Most microsporidia of fish are transmitted without intermediate hosts, and hence, cultured fish are particularly susceptible to microsporidian infections due to high stocking densities, compared to their wild counterparts. There are several examples of microsporidia causing disease in cultured food fishes. Early investigations of fish microsporidia included some observations of host response. Several drugs have been used to treat microsporidian infections in fish, mostly on an experimental basis. Most reports of successful treatments were with fumagillin. This drug is an antimicrobial agent developed for treating Nosema apis infections in honeybees and is the most widely used drug used for treating microsporidiosis in fishes.
Galapagos giant tortoise trafficking case demonstrates the utility and applications of long-term comprehensive genetic monitoring
(2023) Quinzin, Maud C.; Bishop, Anusha P.; Miller, Joshua M.; Poulakakis, Nikos; Tapia, W.; Torres-Rojo, F.; Sevilla, C.; Caccone, Adalgisa
Illegal Wildlife Trade (IWT) is a cause for global concern as pressure stemming from IWT threatens wild species and can even lead to extinction. Galapagos giant tortoises (Chelonoidis sp.) are a group of threatened species protected under CITES, which forbids their import–export for international trade; however, IWT of this group persists. In this study, we describe the use of two extensive genetic repositories of mitochondrial and nuclear microsatellite markers for Galapagos giant tortoises to identify an unsuspected source of trafficked juvenile tortoises. Our genetic analyses, together with morphological and captive-born registry data, provide evidence that the smuggled juveniles were from two breeding centers dedicated toward conservation located on the Galapagos islands of San Cristobal and Isabela. This is the first documentation of smuggled tortoises being taken from breeding centers rather than the wild. The findings from our genetic analysis provided key evidence that enabled legal investigation. This case demonstrates the importance of the comprehensive genetic characterization of Galapagos giant tortoises and the suitability of standard genetic markers for identifying the species and islands of origin of trafficked animals. We also discuss the efficacy, adequacy, and reach of existing measures against IWT. Overall, this case illustrates an important application of long-term and comprehensive genetic repositories of endangered species and the crucial role of collaborations among academic laboratories maintaining those repositories, local practitioners responsible for species protection, and the bodies that implement and enforce antitrafficking regulations.
Leveraging genomic load estimates to optimize captive breeding programmes
(2024) Jensen, Evelyn L.; Gray, Rachel; Miller, Joshua M.
Rapid biodiversity loss threatens many species with extinction. Captive populations of species of conservation concern (such as those housed in zoos and dedicated breeding centres) act as an insurance should wild populations go extinct or need supplemental individuals to boost populations. Limited resources mean that captive populations are almost always small and started from few founding individuals. As a result, captive populations require careful management to minimize negative genetic impacts, with decisions about which individuals to breed together often guided by the principle of minimizing relatedness. Typically this strategy aims to retain 90% of genetic diversity over 200 years (Soulé et al., Zoo Biology, 1986, 5, 101), but it has a weakness in that it does not directly manage for genetic load. In this issue of MolecularEcology Resources, Speak et al. (Molecular Ecology Resources, 2024, e13967) present a novel proof-of-concept study for taking this next step and incorporating estimates of individual genetic load into the planning of captive breeding, using an approach that is likely to be widely applicable to many captive populations.
Generation of pancreatic ductal organoids and whole-mount immunostaining of intact organoids
(2018) Rezanejad, Habib; Hollister Lock, Jennifer; Sullivan, Brooke A.; Bonner-Weir, Susan
Traditionally, studies of cells and tissues have been performed on isolated primary cells or immortalized cell lines by culturing them in 2D culture dishes or flasks. However, a caveat regarding 2D culture is that the cells poorly recapitulate their in vivo counterparts, mainly due to a lack of 3D cell-cell and cell–extracellular matrix interactions. In recent years, the development of in vitro organoids as 3D culture has gained substantial attention as a model to study different tissues. In adults, pancreatic ductal cells are considered as a source of stem or progenitor cells, so developing new methods to study ductal cells would be useful. Here, we provide a protocol to isolate mouse pancreatic ductal cells and a cost-effective protocol to generate 3D organoid structures from such ductal cells. Additionally, we have devised a protocol for immunostaining of intact whole organoids without sectioning.
Pancreatic ductal cell heterogeneity: insights into the potential for β-cell regeneration in diabetes
(2025) Britt, Madelaine; Abdilmasih, Nicholas; Rezanejad, Habib
Diabetes mellitus is a significant and fast-growing health problem worldwide. Cost, donor shortages, and immune rejection limit current treatment strategies. While considerable progress has been made in creating β-cells in vitro with remarkable morphological and functional resemblance to those in primary pancreatic islets, exploring alternative sources for β-cell replacement is crucial. With adult pancreatic stem cells still not conclusively identified, researchers focus their attention on heterogeneity within pancreatic ductal epithelial cells, exploring these cells as a potential source of progenitor cells for pancreatic regeneration and β-cell formation. Recent studies using techniques such as fluorescence-activated cell sorting, immunostaining and single cell RNA-sequencing have identified ductal cell heterogeneity with several subpopulations of ductal cells with progenitor-like properties and their capacity for differentiation into insulin producing cells. Here, we have reviewed the most recent studies on pancreatic ductal cell subpopulations that offer insights into potential stem-cell populations to form β-cells in diabetes treatment.
In vitro differentiation of adipose-tissue-derived mesenchymal stem cells into neural retinal cells through expression of human PAX6 (5a) gene
(2014) Rezanejad, Habib; Soheili, Zahra-soheila; Haddad, Farhang; Matin, Maryam M.; Samiei, Shahram; Manafi, Ali; Ahmadieh, Hamid
The neural retina is subjected to various degenerative conditions. Regenerative stem-cell-based therapy holds great promise for treating severe retinal degeneration diseases, although many drawbacks remain to be overcome. One important problem is to gain authentically differentiated cells for replacement. Paired box 6 protein (5a) (PAX6 (5a)) is a highly conserved master control gene that has an essential role in the development of the vertebrate visual system. Human adipose-tissue-derived stem cell (hADSC) isolation was performed by using fat tissues and was confirmed by the differentiation potential of the cells into adipocytes and osteocytes and by their surface marker profile. The coding region of the human PAX6 (5a) gene isoform was cloned and lentiviral particles were propagated in HEK293T. The differentiation of hADSCs into retinal cells was characterized by morphological characteristics, quantitative real-time reverse transcription plus the polymerase chain reaction (qPCR) and immunocytochemistry (ICC) for some retinal cell-specific and retinal pigmented epithelial (RPE) cell-specific markers. hADSCs were successfully isolated. Flow cytometric analysis of surface markers indicated the high purity (97 %) of isolated hADSCs. After 30 h of post-transduction, cells gradually showed the characteristic morphology of neuronal cells and small axon-like processes emerged. qPCR and ICC confirmed the differentiation of some neural retinal cells and RPE cells. Thus, PAX6 (5a) transcription factor expression, together with medium supplemented with fibronectin, is able to induce the differentiation of hADSCs into retinal progenitors, RPE cells and photoreceptors.
Heterogeneity of SOX9 and HNF1β in pancreatic ducts is dynamic
(2018) Rezanejad, Habib; Ouziel-Yahalom, Limor; Keyzer, Charlotte A.; Sullivan, Brooke A.; Hollister-Lock, Jennifer; Li, Wan-Chun; Guo, Lili; Deng, Shaopeng; Lei, Ji; Markmann, James; Bonner-Weir, Susan
Pancreatic duct epithelial cells have been suggested as a source of progenitors for pancreatic growth and regeneration. However, genetic lineage-tracing experiments with pancreatic duct-specific Cre expression have given conflicting results. Using immunofluorescence and flow cytometry, we show heterogeneous expression of both HNF1β and SOX9 in adult human and murine ductal epithelium. Their expression was dynamic and diminished significantly after induced replication. Purified pancreatic duct cells formed organoid structures in 3D culture, and heterogeneity of expression of Hnf1β and Sox9 was maintained even after passaging. Using antibodies against a second cell surface molecule CD51 (human) or CD24 (mouse), we could isolate living subpopulations of duct cells enriched for high or low expression of HNF1β and SOX9. Only the CD24high (Hnfβ high/Sox9 high) subpopulation was able to form organoids.
Reinforcing one-carbon metabolism via folic acid/Folr1 promotes β-cell differentiation
(2021) Karampelias, Christos; Rezanejad, Habib; Rosko, Mandy; Duan, Likun; Lu, Jing; Pazzagli, Laura; Bertolino, Philippe; Cesta, Carolyn E.; Liu, Xiaojing; Korbutt, Gregory S.; Andersson, Olov
Diabetes can be caused by an insufficiency in β-cell mass. Here, we performed a genetic screen in a zebrafish model of β-cell loss to identify pathways promoting β-cell regeneration. We found that both folate receptor 1 (folr1) overexpression and treatment with folinic acid, stimulated β-cell differentiation in zebrafish. Treatment with folinic acid also stimulated β-cell differentiation in cultures of neonatal pig islets, showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets, the increased β-cell differentiation originated from ductal cells. Mechanistically, comparative metabolomic analysis of zebrafish with/without β-cell ablation and with/without folinic acid treatment indicated β-cell regeneration could be attributed to changes in the pyrimidine, carnitine, and serine pathways. Overall, our results suggest evolutionarily conserved and previously unknown roles for folic acid and one-carbon metabolism in the generation of β-cells.
MNK2 deficiency potentiates β-cell regeneration via translational regulation
(2022) Karampelias, Christos; Watt, Kathleen; Mattsson, Charlotte L.; Ruiz, Angel Fernández; Rezanejad, Habib; Mi, Jiarui; Liu, Xiaojing; Chu, Lianhe; Locasale, Jason W.; Korbutt, Gregory S.; Rovira, Meritxell; Larsson, Ola; Andersson, Olov
Regenerating pancreatic β-cells is a potential curative approach for diabetes. We previously identified the small molecule CID661578 as a potent inducer of β-cell regeneration, but its target and mechanism of action have remained unknown. We now screened 257 million yeast clones and determined that CID661578 targets MAP kinase-interacting serine/threonine kinase 2 (MNK2), an interaction we genetically validated in vivo. CID661578 increased β-cell neogenesis from ductal cells in zebrafish, neonatal pig islet aggregates and human pancreatic ductal organoids. Mechanistically, we found that CID661578 boosts protein synthesis and regeneration by blocking MNK2 from binding eIF4G in the translation initiation complex at the mRNA cap. Unexpectedly, this blocking activity augmented eIF4E phosphorylation depending on MNK1 and bolstered the interaction between eIF4E and eIF4G, which is necessary for both hypertranslation and β-cell regeneration. Taken together, our findings demonstrate a targetable role of MNK2-controlled translation in β-cell regeneration, a role that warrants further investigation in diabetes.
Multi-spatial and temporal assessments of impacts and recovery of epibenthic species and habitats under mussel farms in the Marlborough Sounds, New Zealand
(2024) Davidson, Robert J.; Scrimgeour, Garry J.; Richards, Laura A.; Locky, David
Benthic habitat and macrobenthos recovery were measured over an 11-y period beginning in January 2002 following the closure of a green-lipped mussel farm in the Marlborough Sounds, New Zealand. Habitats and abundance of eight invertebrate species were compared under two types of farming structures (production backbones and warps) used to grow mussels and secure the farm to the seabed, adjacent areas unaffected by farming served as the control reference. The mean percent of the seabed covered by mussel shells under backbones declined from 38% to 0% after 11 y whereas deposition of shells beneath warps was low (<4%) and resembled that at reference sites after only 3 y. One month following farm closure, mean species densities beneath warps, where the upper confidence limit of mean percent shell cover was 7%, did not differ from reference sites. By contrast, the mean densities of two macrobenthic species beneath backbones exceeded that at reference sites whereas the densities of three species were less than that at reference sites. The mean densities of the remaining three species did not differ (P > 0.05) between backbones, warps, and reference sites. The mean abundance of invertebrates was significantly and positively (three species) or negatively (three species) related to the percent shell cover on the seabed. Recovery of four epibenthic species was rapid with mean densities beneath backbones similar to reference sites after 1- to 2-y following farm closure. Densities of the fifth species resembled that at reference sites after 10 y whereas the remaining three species did not differ from controls. Multivariate analyses showed that epibenthic invertebrate communities beneath warps were similar to reference sites throughout the entire 11-y study period. Communities beneath the two backbones differed initially from reference sites but were similar to reference sites 6- and 8-y postfarm closure. After establishing the importance of percent shell cover as an indicator of effects on epibenthic species, data from multiple mussel farms in the Marlborough Sounds were analyzed. These analyses showed that the mean percent of mussel shells beneath backbones (x̄ = 29.5%, range = 0%–100%), exceeded that beneath warps (x̄ = 2.3%), and at reference sites (x̄ = 0.08%). Analyses also showed that the mean maximum distance of mussel shell deposition was 13.5 m distance (range = 1.5–26.5 m) away from farms and was positively (P < 0.01) related to the depth of water where farms were located. Based on multiple mussel farms, mean mussel shell cover declined to below a possible impact threshold of 7% by 7.5 m distance for farms in <12 m depth and 18.5 m distance for farms located in deeper water (>20 m depth). Taken together, the effects of mussel farm on epibenthic species abundance as well as overall community structure showed relatively localized impacts, that recovery occurred within 1–10 y following farm removal and that percent shell cover appears to be a useful indicator of effects of mussel farming on the epibenthos.
Trade-offs constrain adaptive pathways to type VI secretion system survival
(2023) MacGillivray, Kathryn A.; Ng, Siu Lung; Wiesenfeld, Sophia; Guest, Randi L.; Jubery, Tahrima; Silhavy, Thomas J.; Ratcliff, William C.; Hammer, Brian K.
The Type VI Secretion System (T6SS) is a nano-harpoon used by many bacteria to inject toxins into neighboring cells. While much is understood about mechanisms of T6SS-mediated toxicity, less is known about the ways that competitors can defend themselves against this attack, especially in the absence of their own T6SS. Here we subjected eight replicate populations of Escherichia coli to T6SS attack by Vibrio cholerae. Over ∼500 generations of competition, isolates of the E. coli populations evolved to survive T6SS attack an average of 27-fold better, through two convergently evolved pathways: apaH was mutated in six of the eight replicate populations, while the other two populations each had mutations in both yejM and yjeP. However, the mutations we identified are pleiotropic, reducing cellular growth rates, and increasing susceptibility to antibiotics and elevated pH. These trade-offs help us understand how the T6SS shapes the evolution of bacterial interactions.
Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation
(2024) Gupta, Meera; Johnson, Alex N. T.; Cruz, Edward R.; Costa, Eli J.; Guest, Randi L.; Li, Sophia Hsin-Jung; Hart, Elizabeth M.; Nguyen, Thao; Stadlmeier, Michael; Bratton, Benjamin P.; Silhavy, Thomas J.; Wingreen, Ned S.; Gitai, Zemer; Wühr, Martin
Protein turnover is critical for proteostasis, but turnover quantification is challenging, and even in well-studied E. coli, proteome-wide measurements remain scarce. Here, we quantify the turnover rates of ~3200 E. coli proteins under 13 conditions by combining heavy isotope labeling with complement reporter ion quantification and find that cytoplasmic proteins are recycled when nitrogen is limited. We use knockout experiments to assign substrates to the known cytoplasmic ATP-dependent proteases. Surprisingly, none of these proteases are responsible for the observed cytoplasmic protein degradation in nitrogen limitation, suggesting that a major proteolysis pathway in E. coli remains to be discovered. Lastly, we show that protein degradation rates are generally independent of cell division rates. Thus, we present broadly applicable technology for protein turnover measurements and provide a rich resource for protein half-lives and protease substrates in E. coli, complementary to genomics data, that will allow researchers to study the control of proteostasis.
A periplasmic phospholipase that maintains outer membrane lipid asymmetry in Pseudomonas aeruginos
(2023) Guest, Randi L.; Lee Michael J.; Wang, Wei; Silhavy, Thomas J.
The outer membrane of Gram-negative bacteria is unique in both structure and function. The surface-exposed outer leaflet is composed of lipopolysaccharide, while the inner leaflet is composed of glycerophospholipids. This lipid asymmetry creates mechanical strength, lowers membrane permeability, and is necessary for virulence in many pathogens. Glycerophospholipids that mislocalize to the outer leaflet are removed by the Mla pathway, which consists of the outer membrane channel MlaA, the periplasmic lipid carrier MlaC, and the inner membrane transporter MlaBDEF. The opportunistic pathogen Pseudomonas aeruginosa has two proteins of the MlaA family: PA2800 and PA3239. Here, we show that PA2800 is part of a canonical Mla pathway, while PA3239 functions with the putative lipase PA3238. While loss of either pathway individually has little to no effect on outer membrane integrity, loss of both pathways weakens the outer membrane permeability barrier and increases production of the secondary metabolite pyocyanin. We propose that mislocalized glycerophospholipids are removed from the outer leaflet by PA3239 (renamed MlaZ), transferred to PA3238 (renamed MlaY), and degraded. This pathway streamlines recycling of glycerophospholipid degradation products by removing glycerophospholipids from the outer leaflet prior to degradation.
Research recast(ed): S3E19 - The distinguished world of musical insects
(2024) Leschyshyn, Brooklyn; Smadis, Natalie; Judge, Kevin
On today's episode, Dr. Kevin Judge is back on the podcast! Dr. Kevin Judge, an expert in the field of crickets, discusses his research on how the European species Roesel’s Katydid showed up in North America. He shares how his fascination with singing insects led him to study their behaviors, including mating displays and competitive interactions. Dr. Judge's work not only sheds light on the ecological implications of species dispersal but also highlights the importance of paying attention to the often-overlooked world of insects. He reflects on the honor of receiving the Distinguished Research Award and offers advice to students and listeners to persevere in pursuing their dreams.
Research recast(ed): S2E13 - Mating, romance, and cannibalism in the insect world with Dr. Kevin Judge
(2023) Miskiman, Megan; Schabert, Reinette; Judge, Kevin
In today’s episode, associate professor of the Biology Department here at MacEwan, Dr. Kevin Judge, discusses his research on the sexual selection and mating system of insects part of the genus, Cyphoderris.
Research recast(ed): S3E2 - Microplastics, fish bellies, and the wonderful world of biology with Dr. David Locky
(2023) Leschyshyn, Brooklyn; Smadis, Natalie; Locky, David
In today’s episode, Dr. David Locky tells us about his work in wetland ecology and land use impact. Diving underwater, we learn about microplastics in freshwater and organisms. Dr. David Locky is passionate about his research and is excited about the impact his students will make.
Large‐scale bioacoustic monitoring to elucidate the distribution of a non‐native katydid
(2023) Caouette, Alexandre P.; Bayne, Erin M.; Judge, Kevin
1. For animals that produce species-specific audible sounds, environmental recordings combined with automated acoustic monitoring software (passive acoustic monitoring [PAM]) may be an effective monitoring tool because it allows audio data from many, widely distributed autonomous recording units (ARUs) to be processed in a relatively short period of time. Males of many insect species produce loud, species-specific mating songs, yet acoustic insects have received less attention from PAM relative to vertebrates. 2. We evaluated the use of PAM to monitor, Roeseliana roeselii (Orthoptera, Tettigoniidae), an acoustic insect that has expanded its range to Alberta, Canada, far outside its naturalized North American range. We analysed environmental recordings from ARUs: (1) at two control sites known to be occupied by R. roeselii and (2) across Alberta established by the Alberta Biodiversity Monitoring Institute (ABMI) to search for new populations. 3. PAM successfully detected R. roeselii at the two control sites, but not at any of the 73 ABMI sites that we analysed. Despite the failure to detect new locations of R. roeselii, our analysis of ABMI environmental recordings detected several other species of acoustic insects, including Orchelimum gladiator, Gryllus sp. and Allonemobius spp. 4. Our results add to the growing body of work showing the feasibility of using PAM for acoustic insects. We make suggestions for how to maximize the effectiveness of this monitoring tool for the conservation and management of singing insects in North America.
Research recast(ed): S2E2 - The Aquatic Biosphere project, with Dr. Ross Shaw
(2022) Ekelund, Brittany; Cave, Dylan; Shaw, Ross W.
Today we sat down with Dr. Ross Shaw to get a sneak peek into a very exciting new project being pitched, which would bring a wet and wild wonderland to our prairie city. It’s the Aquatic Biosphere project! Looking at the life cycle of water in Alberta and combining education and conservation. We also speak to Ross about his part in the creation of Life on The Edge, a new biology-based video game designed to be fun. You can download Life on the Edge on Steam for free.

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