Nov 22, 2018 // Divide and conquer: the contribution of the divided bacterial genome in conquering multiple niches
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.
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.
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.
Nov., 8, 2018// Digging up the evolutionary origins of hypoxia-tolerance: physiological and biochemical adaptations to acute hypoxia in African mole rats
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.
Nov 1, 2018 // Developing under a changing environment: cold acclimation and vernalization in Brachypodium distachyon
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.
Oct., 18th, 2018/ From Gene Networks to Social Networks: Integrating Development, Ecology, and Evolution.
Dr. Alex Koo, Department of Philosophy, University of Toronto
Scientific realism is the view that our current scientific theories are approximately true. While certainly appealing, scientific anti-realists argue that believing in the approximate truth of our theories is naïve when placed in the context of the history of science. The primary event to be accounted for is the transition from Newtonian physics to the current quantum model. A problem with this approach is that while philosophy of science has contributed significantly to the understanding of fundamental physics, it does not seem to apply to other scientific theories. I will present the standard debate between realism and anti-realism, and will attempt to frame the discussion under the context of the shift from classical to molecular genetics. I suggest that this shift represents an acute problem for a realist interpretation of genetics. This problem can be solved, but it requires a dramatic reconception of the gene. Whether or not this is tolerable to practicing geneticists is up to you.
OCT 4th, 2018 // Application of Plant Phenotyping Techniques for Trait Discovery towards Crop Improvement and Food Security
Dr. Stephen Hunt. President and CEO, Qubit Systems Inc. Adjunct Professor, Dept. Biological Sciences, Queen’s University.
Feeding the world is a challenging business, especially in the face of climate change, drought, saline soils, soil nutrient depletion, fungal infections, insect herbivory – this list goes on. Researchers are scrambling to develop new plant varieties that can maintain high yields under conditions that limit the productivity of current crops. However, identification of the few individual plants with beneficial phenotypic traits requires that thousands of plants are screened, preferably at the same stage of development and at the same time following imposition of stress. This seminar will describe high throughput plant phenotyping platforms designed to meet these challenges in the greenhouse, growth room and field. Imaging technologies for RGB and morphometric analysis, thermal analysis, hyperspectral analysis and, critically, analysis of chlorophyll fluorescence kinetics will be discussed. The latter technique, as a tool for rapid monitoring of photosynthetic processes, is extremely useful in identifying the early onset of numerous stresses, as well as recovery from such stresses after amelioration. The presentation will also review techniques for root phenotyping, and will consider issues concerning the plasticity of the plant phenotype as a product of genotype-environment interaction.