12:30-1:30 pm - Feb., 7,2018, Using Next Generation Molecular Fungicides to Protect Canada's Crops1/29/2019
 Dr. Mark Belmont, University of Manitoba
This seminar will provide insights into the utility of next generation, RNAi-based molecular fungicides and their applicability to control crop pathogens. Sclerotina sclerotiorum, the causal agent of white mold, infects over 450 species of plants worldwide. This fungal phytopathogen has become a major threat to crops including canola which contributes $27 billion to the Canadian economy. Sclerotinia is a persistent problem for canola growers that has traditionally been managed using broad-spectrum fungicides. However, current fungicide strategies have proven to be ineffective. Thus, there is an immediate need to manage Sclerotinia using novel species-specific control methods. Our strategy exploits the inherent cellular defense process known as RNA interference (RNAi). Upon encountering a double stranded RNA (dsRNA) molecule, the cell processes the dsRNA specifically targeting transcripts with sequence homology. Sclerotinia-specific target genes were identified using bioinformatics. RNAi knockdown was confirmed using qRT-PCR on RNA isolated from fungal cultures. Transgenic plants over-expressing the dsRNA showed a profound and prolonged tolerance to Sclerotinia.  Dr. Adam Mott, Dept Biology, Univ Toronto, Scarborough Campus
To thrive, plants must be able to quickly recognize and respond to changing environmental conditions and pathogen attack. The perception of many signals is accomplished through the collective action of members of the leucine-rich repeat receptor kinase (LRR-RK) family, of which there are 225 in Arabidopsis. Upon detection of an extracellular signal, these receptors physically interact to form signaling-competent structures able to integrate complex signals to guide plant defence and growth. Using a high-throughput interaction screen we determined the physical interactions between 200 of the LRR-RLKs from Arabidopsis. Using network analysis and community detection we have detected distinct, but interconnected, subnetworks that show evidence of specialized biological activity and demonstrated novel function for several previous unstudied receptors. In addition, we show that the overall network structure is critical for proper signaling responses, and disruptions can have unexpected consequences at a distance.  Dr. Jacqueline Bede, Dept Plant Science, McGill University
Plant responses to biotic and abiotic stresses require prioritizing different pathways to appropriate regulate metabolic flux. Some caterpillar species have honed into this “cross-talk” and evolved strategies to manipulate plant signaling pathways to minimize induced plant responses. Bede’s lab studies this close, complex interaction from both the plant and insect perspective. Research in her laboratory also investigates how these plant-insect interactions may be influenced by future climatic conditions, in particular elevated atmospheric carbon dioxide.  Dr. George diCenzo, Dept of Biology, University of Florence, Italy
Approximately 10% of bacterial species contain a genome divided between two or more large (> 300 kb) DNA replicons. One such organism is Sinorhizobium meliloti, a soil-dwelling a-proteobacterium that can enter into N2-fixing endosymbiotic interactions with leguminous plants. A synthetic genome reduction approach was used to construct a S. meliloti derivative lacking both of its secondary replicons, which together encode 2900 genes. High-throughput growth assays and soil mesocosm experiments demonstrated that the secondary replicons likely have small contributions to growth in bulk soil despite encoding a broad range of metabolic capabilities. Instead, in silico modelling of S. meliloti metabolism suggested that the metabolic properties of the secondary replicons are associated with specific environments, such as the rhizosphere. Consistent with this being a generalizable property, comparative genomics of ~300 strains from the family Burkholderiaceae suggested that their secondary replicons are enriched in environmental adaptation genes. Nevertheless, massively-parallel transposon-sequencing uncovered extensive genetic interactions between the S. meliloti replicons. Similarly, transcriptomics (RNA-seq) and non-targeted metabolomics illustrated that the more conserved secondary replicon of S. meliloti has become integrated into the general metabolic and transcriptomic networks of the cell. This integration is due, at least in part, to the transfer of core genes from the chromosome to the secondary replicon. Overall, these systems-level data support a model in which large secondary replicon(s) provide increased genome flexibility, facilitating more rapid adaptation to novel environments. These results can have implications in elucidating the genomics of host-adaptation, which is applicable to the many human pathogens and plant symbionts that harbour divided genomes. Tues, Nov 27, 10:30am, Rm 1103// Animal Genomes, Large and Small (EEB talk of interest to MCIB)11/14/2018
 Dr. T. Ryan Gregory, Dept. Integrative Biology, Univ of Guelph
The extraordinary diversity in genome sizes (haploid nuclear DNA contents, or “C-values”) among eukaryote species has remained a major puzzle in genetics for over 60 years. The size of a genome size bears no relationship to the number of coding genes it contains or to the complexity of the organism in which it is found, a finding so surprising to early researchers that it became known as the “C-value paradox”. While the discovery of non-coding DNA has solved this paradox, it has raised a series of new questions regarding the origins, mechanisms of spread and loss, phenotypic consequences, and reasons for differential abundance of non-coding DNA in different species. This seminar explores these questions, with a particular emphasis on the connection between genome size and such important phenotypic characteristics as cell size, body size, metabolism, and development in animals. Nov 13, 2018 // Uncovering mechanisms that regulate age-related decline and reproductive senescence11/7/2018
 Dr. Nicole Templeman, Lewis-Sigler Institute for Integrative Genomics & Dept. of Molecular Biology, Princeton University.
Since most biological processes require nutrients, signaling networks that respond to nutrient levels play important roles in regulating many functions, including growth, reproduction, and tissue maintenance with age. In organisms ranging from invertebrates to mammals, genetic loss-of-function of signaling components in nutrient-sensing pathways—such as the insulin/insulin-like growth factor-1 signaling (IIS) pathway—can thereby slow the physiological deterioration that characterizes aging, and extend lifespan. In Caenorhabditis elegans, loss-of-function of the daf-2 IIS receptor also significantly delays the age-related decline in reproductive capacity, one of the earliest hallmarks of aging. To identify mechanisms that directly control aging of the reproductive system, we compared the transcriptomes of aged daf-2(-) and wild-type oocytes. Remarkably, inhibiting one group of oocyte-specific IIS transcriptional targets, cathepsin B cysteine proteases, can improve oocyte quality in aging C. elegans, even when inhibition takes place partway through the reproductive period. This suggests that it is possible to slow age‑related reproductive decline with mid‑life interventions. In addition to evaluating molecular changes downstream of key nutrient-sensing signaling networks like the IIS pathway, I am interested in determining whether we can uncover new mechanisms of age-related decline by looking at other major regulators of growth, energy balance, and metabolism. The cAMP response element-binding protein (CREB) is a highly conserved transcription factor that regulates numerous processes, including growth and nutrient storage. I found that in C. elegans, CREB also regulates oocyte quality and reproductive capacity with age, which is a previously unknown function of CREB signaling. Interestingly, this targeted effect on reproductive aging is due to CREB’s activity in the C. elegans hypodermis, an epithelial tissue transcriptionally similar to mammalian liver and adipose tissue. Collectively, these projects have revealed some of the intricacies by which tissue-specific signaling events exert nuanced effects on complex systemic functions, and uncovered new mechanistic regulators of age-related decline.  Dr. Matthew Pamenter, Dept. Biology, University of Ottawa
I am interested in the physiological and related molecular mechanisms that underlie natural metabolic adaptations to low oxygen stress and enable central nervous system function and viability in hypoxia and ischemia. Specifically, I use hypoxia-tolerant comparative model organisms (African mole rats, western painted turtles, goldfish) and oxygen-sensitive mammalian cells and tissues (mouse, human) to investigate cellular and systemic mechanisms involved in hypoxia-tolerance and neuroprotection. The long-term aim of my research is to discover cellular pathways and molecular candidates that enable endogenous systemic tolerance to low oxygen stress in hypoxia-adapted species, and to translate these mechanisms to hypoxia-intolerant mammals in order to reduce or reverse brain cell injury caused by pathological conditions that compromise oxygen supply to the tissue (e.g. stroke, heart attack, COPD, etc).  Dr. Adam Bewick, Department of Genetics, University of Georgia
Heritable, genetic changes that contribute to phenotypic differences are the foundations of the Modern Synthesis. However, epigenetics, the molecular mechanism of heritable gene expression changes that cannot be attributed to changes in DNA sequence, potentially offers an alternative path for evolution. Despite what we know about the association of epigenomic variation to phenotypic variation, we lack a framework for understanding epigenetics in the context of the Modern Synthesis. An ongoing question is can epigenetics have a role in adaptive evolution through natural selection? If so, then do we see evidence of potentially adaptive epigenomic variation between and within species? Through phylogenetic comparative methods and functional genetics in plants, I have found substantial epigenomic variation between species. Contributors to epigenome divergence between plant species include lineage-specific genetic innovations that establish and maintain the epigenome. This variation is echoed at the population level, is heritable, and contributes to phenotypic differences among individuals, possibly meeting the requirements of natural selection. Thus, future work aims to identify adaptive epigenomic variation and its phenotypic consequences in plant populations by applying established population genetic theory to an epigenetic context. Extensions of this work include applied epigenetics for agricultural improvement. Ultimately, describing the role of epigenetics in evolution will require placing our knowledge in the context of the Modern Synthesis.  Boris Mayer, PhD Candidate, Dept. Plant Science, McGill University
With the onset of climate change, it has become increasingly relevant to understand how plants respond to changing environmental conditions. Yet, temperate plants regularly face seasonal change and, to persist in these conditions, have adapted by adjusting their stress tolerance, phenology and development. Understanding how temperate plants follow seasonal cues during their development can help elucidate adaptation in plants. Cold acclimation (CA) and vernalization (VRN) are processes that ensure persistence in temperate climates by regulating freezing tolerance and flowering time respectively. However, how these two processes are integrated into a coordinated developmental response remains poorly understood. The model grass Brachypodium distachyon has emerged as a model to study CA and VRN in temperate cereals. By identifying key seasonal cues that occur within the native range of the species, we designed a diurnal freezing treatment (DF) that combines prevailing summer-to-winter transition signals. Under DF, B. distachyon accessions of different climatic origins manifest coordinated and novel cold acclimation and vernalization responses. Altogether, our results demonstrate a direct link between CA and VRN, and that typically used constant-temperature cold treatments induce an “over-vernalized” molecular state at the expense of freezing tolerance. This work also stresses the importance of reproducing natural signals in laboratory conditions. Dr. Rajendhran Rajakumar, Department of Genetics, Harvard Medical School  |
