Biological Sciences

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    A genome resource for 192 Verticillium dahliae isolates infecting potatoes across Canada
    (ACS Publications, 2023) Arseneault, Tanya; Lafond-Lapalme, Joël; Gonzalez, Chary Esteban Quinche; Jordan, Katerina S.; Yevtushenko, Dmytro P.; Barrett, Ryan; Van der Heyden, Hervé; Chen, Dahu; Tenuta, Mario; Mimee, Benjamin
    Verticillium dahliae is an important soilborne pathogen causing Verticillium wilt. It is also the primary causal agent of potato early dying, a disease complex involving the root-lesion nematode. Here, we report the whole-genome sequencing of 192 isolates of V. dahliae originating from the major potato production areas across Canada. Our results yielded a resource of 277,010 genetic variations that will be useful for genetic analyses and revealed the presence of two major lineages, both present in all provinces but exhibiting differences in regional prevalence.
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    A new record of Stylophorum diphyllum (Michx.) Nutt. in Canada: a case study of the value and limitations of building species distribution models for very rare plants
    (BioOne, 2019) McCune, Jenny L.
    Stylophorum diphyllum (Michx.) Nutt. is an endangered plant of rich floodplain forests in southern Ontario, Canada. Prior to 2015 there were only four known populations in Ontario. I built a species distribution model (SDM) based on the known occurrences, and tested it by surveying 156 forest sites that varied in their predicted suitability. An indicator species analysis showed that sites predicted to be suitable had significantly higher frequency and abundance of common species usually associated with S. diphyllum, demonstrating the ability of the SDM to pinpoint similar habitat, although none of these sites contained S. diphyllum. The most important predictors used by the SDM to determine habitat suitability were growing season precipitation, surficial geology, and soil texture. I discovered a new population of S. diphyllum more than 50 km north of the known populations, at one of the sites not predicted to be suitable. This demonstrates a clear example of SDM overfitting, which may occur when models are built based on few, spatially limited occurrence records. Nonetheless, the key environmental predictors remained the same in an updated SDM including the new record. Stylophorum diphyllum provides a case study of both the value and the limitations of using SDMs to predict suitable habitat for very rare and geographically restricted plants, and the need for more rare plant surveys even in human-dominated landscapes.
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    A survey of Helicotylenchus, Paratylenchus, Pratylenchus, and Tylenchorhynchus nematodes in potato fields in Alberta, 2018 and 2019
    (Taylor & Francis, 2021) Robertson, C. J.; Yevtushenko, Dmytro P.; Snowdon, E.; Harding, M. W.
    The prevalence of Helicotylenchus, Paratylenchus, Pratylenchus and Tylenchorhynchus genera of nematodes is not well understood across the prairie provinces of Canada. These nematodes can cause economic damage by feeding on the host crop directly or serve as vectors of plant diseases. While conducting a larger project, nematode populations were quantified in the soil of three commercial potato fields planted with cultivar ‘Russet Burbank’; one in 2018 and two in 2019. The nematodes were extracted from soil samples, identified morphologically, and then quantified as numbers per kg of fresh soil. All four genera were detected in all fields, but the population sizes varied between fields and across time within fields.
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    Agrobacterium-mediated stable genetic transformation of Populus angustifolia and Populus balsamifera
    (Frontiers Media, 2016) Maheshwari, Priti; Kovalchuk, Igor
    The present study demonstrates Agrobacterium tumefaciens-mediated stable genetic transformation of two species of poplar – Populus angustifolia and Populus balsamifera. The binary vector pCAMBIA-Npro-long-Luc containing the luciferase reporter gene was used to transform stem internode and axillary bud explants. Putative transformants were regenerated on selection-free medium using our previously established in vitro regeneration method. Explant type, genotype, effect of pre-culture, Agrobacterium concentration, a time period of infection and varying periods of co-culture with bacteria were tested for the transformation frequency. The highest frequency of transformation was obtained with stem internode explants pre-cultured for 2 days, infected with Agrobacterium culture at the concentration of OD600 D 0.5 for 10 min and co-cultivated with Agrobacterium for 48 h. Out of the two genotypes tested, P. balsamifera exhibited a higher transformation rate in comparison to P. angustifolia. The primary transformants that exhibited luciferase activity in a bioluminescence assay under the CCD camera when subjected to polymerase chain reaction and Southern blot analysis revealed a stable single-copy integration of luc in their genomes. The reported protocol is highly reproducible and can be applied to other species of poplar; it will also be useful for future genetic engineering of one of the most important families of woody plants for sustainable development.
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    Altered radiation responses of breast cancer cells resistant to hormonal therapy
    (Impact Journals, 2015) Luzhna, Lidiya; Lykkesfeldt, Anne E.; Kovalchuk, Olga
    Endocrine therapy agents (the selective estrogen receptor (ER) modulators such as tamoxifen or the selective ER down-regulators such as ICI 182,780) are key treatment regimens for hormone receptor-positive breast cancers. While these drugs are very effective in controlling ER-positive breast cancer, many tumors that initially respond well to treatment often acquire drug resistance, which is a major clinical problem. In clinical practice, hormonal therapy agents are commonly used in combination or sequence with radiation therapy. Tamoxifen treatment and radiotherapy improve both local tumor control and patient survival. However, tamoxifen treatment may render cancer cells less responsive to radiation therapy. Only a handful of data exist on the effects of radiation on cells resistant to hormonal therapy agents. These scarce data show that cells that were resistant to tamoxifen were also resistant to radiation. Yet, the existence and mechanisms of cross-resistance to endocrine therapy and radiation therapy need to be established. Here, we for the first time examined and compared radiation responses of MCF-7 breast adenocarcinoma cells (MCF-7/S0.5) and two antiestrogen resistant cell lines derived from MCF-7/S0.5: the tamoxifen resistant MCF-7/TAMR-1 and ICI 182,780 resistant MCF-7/182R-6 cell lines. Specifically, we analyzed the radiation-induced changes in the expression of genes involved in DNA damage, apoptosis, and cell cycle regulation. We found that the tamoxifen-resistant cell line in contrast to the parental and ICI 182,780-resistant cell lines displayed a significantly less radiationinduced decrease in the expression of genes involved in DNA repair. Furthermore, we show that MCF-7/TAMR-1 and MCF-7/182R-6 cells were less susceptible to radiation-induced apoptosis as compared to the parental line. These data indicate that tamoxifen-resistant breast cancer cells have a reduced sensitivity to radiation treatment. The current study may therefore serve as a roadmap to the future analysis of the mechanisms of cross-resistance between hormonal therapy and radiation.
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    Ancestral exposure to stress epigenetically programs preterm birth risk and adverse maternal and newborn outcomes
    (BioMed Central, 2014) Yao, Youli; Robinson, Alexandra M.; Zucchi, Fabiola C. R.; Robbins, Jerrah C.; Babenko, Olena M.; Kovalchuk, Olga; Kovalchuk, Igor; Olson, David M.; Metz, Gerlinde A. S.
    Abstract Background: Chronic stress is considered to be one of many causes of human preterm birth (PTB), but no direct evidence has yet been provided. Here we show in rats that stress across generations has downstream effects on endocrine, metabolic and behavioural manifestations of PTB possibly via microRNA (miRNA) regulation. Methods: Pregnant dams of the parental generation were exposed to stress from gestational days 12 to 18. Their pregnant daughters (F1) and grand-daughters (F2) either were stressed or remained as non-stressed controls. Gestational length, maternal gestational weight gain, blood glucose and plasma corticosterone levels, litter size and offspring weight gain from postnatal days 1 to 30 were recorded in each generation, including F3. Maternal behaviours were analysed for the first hour after completed parturition, and offspring sensorimotor development was recorded on postnatal day (P) 7. F0 through F2 maternal brain frontal cortex, uterus and placenta miRNA and gene expression patterns were used to identify stress-induced epigenetic regulatory pathways of maternal behaviour and pregnancy maintenance. Results: Progressively up to the F2 generation, stress gradually reduced gestational length, maternal weight gain and behavioural activity, and increased blood glucose levels. Reduced offspring growth and delayed behavioural development in the stress cohort was recognizable as early as P7, with the greatest effect in the F3 offspring of transgenerationally stressed mothers. Furthermore, stress altered miRNA expression patterns in the brain and uterus of F2 mothers, including the miR-200 family, which regulates pathways related to brain plasticity and parturition, respectively. Main miR-200 family target genes in the uterus, Stat5b, Zeb1 and Zeb2, were downregulated by multigenerational stress in the F1 generation. Zeb2 was also reduced in the stressed F2 generation, suggesting a causal mechanism for disturbed pregnancy maintenance. Additionally, stress increased placental miR-181a, a marker of human PTB. Conclusions: The findings indicate that a family history of stress may program central and peripheral pathways regulating gestational length and maternal and newborn health outcomes in the maternal lineage. This new paradigm may model the origin of many human PTB causes.
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    An anomalous northern saw-whet owl (Aegolius acadicus) egg
    (Ottawa Field-Naturalists' Club, 2012) Burg, Theresa M.; Lauff, Randolph F.
    An anomalously large and coloured egg was found within a clutch of the Northern Saw-whet Owl (Aegolius acadicus) in Nova Scotia; all other eggs of the clutch were within the normal size and colour range for the species. Analysis of three mitochondrial genes suggests all eggs in the clutch were laid by Northern Saw-whet Owl(s) with similar genetic make-up. This is the first report of an anomalous egg from this species, and a rare example of added pigment.
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    Are we accurately estimating the potential role of pollution in the decline of species at risk in Canada?
    (Canadian Science Publishing, 2019) McCune, Jenny L.; Colla, Sheila R.; Coristine, Laura E.; Davy, Christina M.; Flockhart, D. T. Tyler; Schuster, Richard; Orihel, Diane M.
    Pollution is a pervasive, albeit often invisible, threat to biodiversity in Canada. Currently, the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) relies on expert opinion to assess the scope (i.e., the proportion of a species’ population that may be affected) of pollution to species at risk. Here, we describe a spatially explicit, quantitative method for assessing the scope of pollution as a threat to species at risk in Canada. Using this method, we quantified the geographic co-occurrence of 488 terrestrial and freshwater species and pollution sources and determined that, on average, 57% of the mapped occurrences of each species at risk co-occurred with at least one pollution source. Furthermore, we found a weak correlation between the scope of the threat of pollution as assessed by COSEWIC expert panels and the geographic overlap of species occurrences and pollution sources that we determined with our quantitative method. Experts frequently identified scope of pollution as absent or negligible even for species with extensive co-occurrence with pollution sources, especially vascular plants. Clearly, a quantitative approach is needed to make accurate estimates of the scope of pollution as a threat to species at risk in Canada.
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    Assessing public comitment to endangered species protection: a Canadian case study
    (Canadian Science Publishing, 2017) McCune, Jenny L.; Carlsson, Anja M.; Colla, Sheila; Davy, Christina; Favaro, Brett; Ford, Adam T.; Fraser, Kevin C.; Martins, Eduardo G.
    Preventing the extinction of species will require limiting human activities in key areas, but it is unclear to what extent the public is committed to these limits and the associated costs. We commissioned an online survey of 1000 Canadians and asked them if it is important to prevent the extinction of wild species in Canada. We used specific scenarios illustrating the need for limits to personal activities, private property rights, and industrial development to further test their support. The respondents were strongly committed to species conservation in principle (89% agree), including the need to limit industrial development (80% agree). There was less support for limiting private property rights (63% agree), and more uncertainty when scenarios suggested potential loss of property rights and industry-based jobs. This highlights the high level of public concern regarding the economic impacts of preventing extinctions, and the need for more programs to encourage voluntary stewardship of endangered species on private land. Opinion polls that measure public support for conservation without acknowledging the concessions required may result in overly optimistic estimates of the level of support. Most Canadians in our sample supported endangered species conservation even when the necessity of limiting human activities was explicitly stated.
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    The Biology and Management of Southern Alberta's Cottonwoods
    (Lethbridge, AB : University of Lethbridge, 1991, 1991-02) Rood, Stewart B.; Mahoney, John M.
    Proceedings of the University of Lethbridge conference, May 4 to 6, 1990.
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    Caloric restriction extends lifespan in a clonal plant
    (Wiley, 2024) Chmilar, Suzanne L.; Luzardo, Amanda C.; Dutt, Priyanka; Pawluck, Abbe; Thwaites, Victoria C.; Laird, Robert
    When subjected to dietary caloric restriction (CR), individual animals often outlive well-fed conspecifics. Here, we address whether CR also extends lifespan in plants. Whereas caloric intake in animals comes from ingestion, in plants it derives from photosynthesis. Thus, factors that reduce photosynthesis, such as reduced light intensity, can induce CR. In two lab experiments investigating the aquatic macrophyte Lemna minor, we tracked hundreds of individuals longitudinally, with light intensity—and hence, CR—manipulated using neutral-density filters. In both experiments, CR dramatically increased lifespan through a process of temporal scaling. Moreover, the magnitude of lifespan extension accorded with the assumptions that (a) light intensity positively relates to photosynthesis following Michaelis–Menten kinetics, and (b) photosynthesis negatively relates to lifespan via a power law. Our results emphasize that CR-mediated lifespan extension applies to autotrophs as well as heterotrophs, and suggest that variation in light intensity has quantitatively predictable effects on plant aging trajectories.
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    Campylobacter jejuni colonization is associated with a dysbiosis in the cecal microbiota of mice in the absence of prominent inflammation
    (Public Library of Science, 2013) Lone, Abdul G.; Selinger, L. Brent; Uwiera, Richard R. E.; Xu, Yong; Inglis, G. Douglas
    Background: Campylobacter jejuni causes enterocolitis in humans, but does not incite disease in asymptomatic carrier animals. To survive in the intestine, C. jejuni must successfully compete with the microbiota and overcome the host immune defense. Campylobacter jejuni colonization success varies considerably amongst individual mice, and we examined the degree to which the intestinal microbiota was affected in mice (i.e. a model carrier animal) colonized by C. jejuni at high relative to low densities. Methods: Mice were inoculated with C. jejuni or buffer, and pathogen shedding and intestinal colonization were measured. Histopathologic scoring and quantification of mRNA expression for α-defensins, toll-like receptors, and cytokine genes were conducted. Mucosa-associated bacterial communities were characterized by two approaches: multiplexed barcoded pyrosequencing and terminal restriction fragment length polymorphism analysis. Results: Two C. jejuni treatments were established based on the degree of cecal and colonic colonization; C. jejuni Group A animals were colonized at high cell densities, and C. jejuni Group B animals were colonized at lower cell densities. Histological examination of cecal and colonic tissues indicated that C. jejuni did not incite visible pathologic changes. Although there was no significant difference among treatments in expression of mRNA for α-defensins, tolllike receptors, or cytokine genes, a trend for increased expression of toll-like receptors and cytokine genes was observed for C. jejuni Group A. The results of the two methods to characterize bacterial communities indicated that the composition of the cecal microbiota of C. jejuni Group A mice differed significantly from C. jejuni Group B and Control mice. This difference was due to a reduction in load, diversity and richness of bacteria associated with the cecal mucosa of C. jejuni Group A mice. Conclusions: High density colonization by C. jejuni is associated with a dysbiosis in the cecal microbiota independent of prominent inflammation.
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    Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine
    (Public Library of Science, 2017) Zaheer, Rahat; Bony-Dugat, Eric; Holman, Devon; Cousteix, Elodie; Xu, Yong; Munns, Krysty D.; Selinger, Lorna J.; Barbieri, Rutn; Alexander, Trevor W.; McAllister, Tim A.; Selinger, L. Brent
    Escherichia coli O157:H7 is a foodborne pathogen that colonizes ruminants. Cattle are considered the primary reservoir of E. coli O157:H7 with super-shedders, defined as individuals excreting>104 E. coli O157:H7 CFU g-1 feces. The mechanisms leading to the super-shedding condition are largely unknown. Here, we used 16S rRNA gene pyrosequencing to examine the composition of the fecal bacterial community in order to investigate changes in the bacterial microbiota at several locations along the digestive tract (from the duodenum to the rectal-anal junction) in 5 steers previously identified as super-shedders and 5 non-shedders. The overall bacterial community structure did not differ by E. coli O157:H7 shedding status; but several differences in the relative abundance of taxa and OTUs were noted between the two groups. The genus Prevotella was most enriched in the non-shedders while the genus Ruminococcus and the Bacteroidetes phylum were notably enriched in the super-shedders. There was greater bacterial diversity and richness in samples collected from the lower- as compared to the upper gastrointestinal tract (GI). The spiral colon was the only GI location that differed in terms of bacterial diversity between super-shedders and non-shedders. These findings reinforced linkages between E. coli O157:H7 colonization in cattle and the nature of the microbial community inhabiting the digestive tract of supershedders.
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    Characterizing the performance of ecosystem models across time scales: a spectral analysis of the North American Carbon Program site-level synthesis
    (American Geophysical Union, 2011) Dietze, Michael C.; Vargas, Rodrigo; Richardson, Andrew D.; Stoy, Paul C.; Barr, Alan G.; Anderson, Ryan S.; Arain, M. Altaf; Baker, Ian T.; Black, T. Andrew; Chen, Jing M.; Philippe, Ciais; Flanagan, Larry B.; Gough, Christopher M.; Grant, Robert F.; Hollinger, David Y.; Izaurralde, R. Cesar; Kucharik, Christopher J.; Lafleur, Peter M.; Liu, Shugang; Lokupitiya, Erandathie; Luo, Yiqi; Munger, J. William; Peng, Changhui; Poulter, Benjamin; Price, David T.; Ricciuto, Daniel M.; Riley, William J.; Sahoo, Alok Kumar; Schaefer, Kevin; Suyker, Andrew E.; Tian, Hanqin; Tonitto, Christina; Verbeeck, Hans; Verma, Shashi B.; Wang, Weifeng; Weng, Ensheng
    Ecosystem models are important tools for diagnosing the carbon cycle and projecting its behavior across space and time. Despite the fact that ecosystems respond to drivers at multiple time scales, most assessments of model performance do not discriminate different time scales. Spectral methods, such as wavelet analyses, present an alternative approach that enables the identification of the dominant time scales contributing to model performance in the frequency domain. In this study we used wavelet analyses to synthesize the performance of 21 ecosystem models at 9 eddy covariance towers as part of the North American Carbon Program’s site-level intercomparison. This study expands upon previous single-site and single-model analyses to determine what patterns of model error are consistent across a diverse range of models and sites. To assess the significance of model error at different time scales, a novel Monte Carlo approach was developed to incorporate flux observation error. Failing to account for observation error leads to a misidentification of the time scales that dominate model error. These analyses show that model error (1) is largest at the annual and 20–120 day scales, (2) has a clear peak at the diurnal scale, and (3) shows large variability among models in the 2–20 day scales. Errors at the annual scale were consistent across time, diurnal errors were predominantly during the growing season, and intermediate-scale errors were largely event driven. Breaking spectra into discrete temporal bands revealed a significant model-by-band effect but also a non significant model-by-site effect, which together suggest that individual models show consistency in their error patterns. Differences among models were related to model time step, soil hydrology, and the representation of photosynthesis and phenology but not the soil carbon or nitrogen cycles. These factors had the greatest impact on diurnal errors, were less important at annual scales, and had the least impact at intermediate time scales.
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    Circadian disruption and breast cancer: an epigenetic link?
    (Impact Journals, 2015) Kochan, David Z.; Kovalchuk, Olga
    Breast cancer is already the most common malignancy affecting women worldwide, and evidence is mounting that breast cancer induced by circadian disruption (CD) is a warranted concern. Numerous studies have investigated various aspects of the circadian clock in relation to breast cancer, and evidence from these studies indicates that melatonin and the core clock genes can play a crucial role in breast cancer development. Even though epigenetics has been increasingly recognized as a key player in the etiology of breast cancer and linked to circadian rhythms, and there is evidence of overlap between epigenetic deregulation and breast cancer induced by circadian disruption, only a handful of studies have directly investigated the role of epigenetics in CD-induced breast cancer. This review explores the circadian clock and breast cancer, and the growing role of epigenetics in breast cancer development and circadian rhythms. We also summarize the current knowledge and next steps for the investigation of the epigenetic link in CD-induced breast cancer.
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    Collateral benefits: river flow normalization for endangered fish enabled riparian rejuvenation
    (Wiley, 2024) Rood, Stewart B.; Hoffman, Gregory C.; Merz, Norm; Anders, Paul; Benjankar, Rohan; Burke, Michael; Egger, Gregory; Polzin, Mary Louise; Soults, Scott
    Like most rivers worldwide, the transboundary North American Kootenay/i River has experienced multiple impacts including watershed developments, river channelization, and floodplain clearing, draining, and diking. Construction of Libby Dam was authorized by the 1964 Columbia River Treaty (CRT) between the United States and Canada, and in 1975 began regulating downstream flows for flood risk management and hydropower generation. Following cumulative impacts, the endemic Kootenai River White Sturgeon population collapsed and was designated as endangered in 1994 (U.S. Endangered Species Act). Subsequent Biological Opinions from the U.S. Fish and Wildlife Service prescribed Libby Dam operations to provide springtime flow pulses for sturgeon spawning. These provided the unanticipated benefit of substantial seedling recruitment of native and introduced riparian cottonwoods and willows. The regulated flow regime was further adaptively managed to provide a more normative (natural) regime, to balance ecological functions with flood risk management and hydropower generation. The broadened ecological considerations would be consistent with the proposed priorities for the modernization of the international CRT. The observed responses revealed that (1) diverse aquatic and riparian organisms are dependent on common river flow characteristics; (2) a normalized flow regime provided substantial ecological benefits; and (3) due to multiple influences, hybrid ecosystems develop along regulated rivers, with a blending of natural and altered processes and communities. For other regulated rivers, we recommend that (1) high springtime flows be allowed, as feasible; (2) followed by the gradual post-peak recession; and (3) the maintenance of sufficient flows through the warm and dry interval of mid to late summer.
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    Combining air sampling and DNA metabarcoding to monitor plant pathogens
    (APS Publications, 2023) Reich, Jonathan; Chen, Wen; Radford, Devon; Turkington, Kelly; Yevtushenko, Dmytro P.; Hamelin, Richard; Chatterton, Syama
    Monitoring the air for airborne plant pathogens is an increasingly common method for the management of economically important plant diseases. In Alberta, Canada, several commodity clusters, including dry bean, canola, potato, and wheat, currently support air monitoring research programs for airborne pathogens of interest. In this study, we assessed the feasibility of monitoring for these, and more, plant fungal pathogens simultaneously using two different sampler types (cyclone versus rotation impaction) and by metabarcoding the ITS1 region using the Illumina sequencing platform. We collected air samples from four geographically distant sites across Alberta and monitored four crop types in southern Alberta. Overall, we found weak, but statistically significant, effects of geographic location and crop type on the aeromycobiota community composition. A few common taxa, such as Ramularia, Alternaria, and Epicoccum, constituted the vast majority of reads across all samples. Nevertheless, in each sample, we identified many plant pathogens of interest and organisms that previous research has found antagonistic to those pathogens, highlighting the utility of these approaches in understanding the pathobiome. In assessing the real-world implications of read counts, we discovered that they were only weakly correlated with spore counts quantified by qPCR. The two types of samplers collected different community profiles, reinforcing the importance of carefully considering which sampler type to use in monitoring programs. Taken together, our results show promise for the future of monitoring the air pathobiome, although much more work is required to understand the relationship of airborne communities to their in-field impact on disease development.
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    Common coulee plants of Southern Alberta
    ([Lethbridge, Alta : University of Lethbridge] ; Lethbridge, Alta. : distributed by University of Lethbridge Digital Herbarium, 2014, 2014) Bain, John; Flanagan, June; Kuijt, Job
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    Comparative genomic analysis of Escherichia coli 0157:H7 isolated from super-shedder and low-shedder cattle
    (Public Library of Science, 2016) Munns, Krysty D.; Zaheer, Rahat; Xu, Yong; Stanford, Kim; Laing, Chad R.; Gannon, Victor P. J.; Selinger, L. Brent; McAllister, Tim A.
    Cattle are the primary reservoir of the foodborne pathogen Escherichia coli O157:H7, with the concentration and frequency of E. coli O157:H7 shedding varying substantially among individual hosts. The term ‘‘super-shedder” has been applied to cattle that shed 104 cfu E. coli O157:H7/g of feces. Super-shedders have been reported to be responsible for the majority of E. coli O157:H7 shed into the environment. The objective of this study was to determine if there are phenotypic and/or genotypic differences between E. coli O157:H7 isolates obtained from super-shedder compared to low-shedder cattle. From a total of 784 isolates, four were selected from low-shedder steers and six isolates from super-shedder steers (4.01–8.45 log cfu/g feces) for whole genome sequencing. Isolates were phage and clade typed, screened for substrate utilization, pH sensitivity, virulence gene profiles and Stx bacteriophage insertion (SBI) sites. A range of 89–2473 total single nucleotide polymorphisms (SNPs) were identified when sequenced strains were compared to E. coli O157:H7 strain Sakai. More non-synonymous SNP mutations were observed in low-shedder isolates. Pan-genomic and SNPs comparisons did not identify genetic segregation between supershedder or low-shedder isolates. All super-shedder isolates and 3 of 4 of low-shedder isolates were typed as phage type 14a, SBI cluster 3 and SNP clade 2. Super-shedder isolates displayed increased utilization of galactitol, thymidine and 3-O-β-D-galactopyranosyl-Darabinose when compared to low-shedder isolates, but no differences in SNPs were observed in genes encoding for proteins involved in the metabolism of these substrates. While genetic traits specific to super-shedder isolates were not identified in this study, differences in the level of gene expression or genes of unknown function may still contribute to some strains of E. coli 0157:H7 reaching high densities within bovine feces.
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    Comparative phylogeographic analysis suggests a shared history among eastern North American boreal forest birds
    (Oxford Academic, 2021) Ralston, Joel; FitzGerald, Alyssa M.; Burg, Theresa M.; Starkloff, Naima C.; Warkentin, Ian G.; Kirchman, Jeremy J.
    Phylogeographic structure within high-latitude North American birds is likely shaped by a history of isolation in refugia during Pleistocene glaciations. Previous studies of individual species have come to diverse conclusions regarding the number and location of likely refugia, but no studies have explicitly tested for biogeographic concordance in a comparative phylogeographic framework. Here we use a hierarchical approximate Bayesian computation analysis of mitochondrial DNA sequences from 653 individuals of 6 bird species that are currently co-distributed in the boreal forest of North America to test for biogeographic congruence. We find support for congruent phylogeographic patterns across species, with shallow divergence dating to the Holocene within each species. Combining genetic results with paleodistribution modeling, we propose that these species shared a single Pleistocene refugium south of the ice sheets in eastern North America. Additionally, we assess modern geographic genetic structure within species, focusing on Newfoundland and disjunct high-elevation populations at the southern periphery of ranges. We find evidence for a “periphery effect” in some species with significant genetic structure among peripheral populations and between peripheral and central populations. Our results suggest that reduced gene flow among peripheral populations, rather than discordant biogeographic histories, can explain the small differences in genetic structure and levels of genetic diversity among co-distributed boreal forest birds