Biology Seminar Series

When: Fridays, 12-1pm (unless otherwise indicated)

Where: Zoom

Every Friday during the academic year, the Department of Biology hosts an exciting seminar given by a guest speaker. Topics cover every aspect of biology, from whole organisms to molecular biology. Everyone is welcome to attend.

Full List 2021-2022

October 22, 2021

Dr. Matt Smear, University of Oregon

Neural correlates of time and place in the olfactory bulb of freely-moving mice

Abstract

Odors provide useful navigational and episodic information, but however numerous the odorant receptor genes in an animal’s genome, there is no receptor for time or place. To optimally orient by olfactory information, brains must incorporate odor-driven activity into representations of self-movement and -location. While a feedforward model might predict that such multimodal integration would be implemented in “high-level” areas, recent studies in other sensory modalities demonstrate that motor- and location-related signals are common in primary sensory areas. Motivated by these findings, and given the strong reciprocal connection between olfactory system and hippocampus, we hypothesized that the olfactory bulb might also encode navigational information. To test this hypothesis, we captured the sniffing and movement of mice while recording spiking activity in their olfactory bulb, in the absence of experimenter-applied stimuli or tasks. As previously reported, we found that many units fired preferentially at characteristic times after inhalation. In addition, many units fired preferentially at characteristic sniff frequencies, particularly during free movement, often in correspondence with the rhythmic states of sniffing. In addition to these time-selective signals, we also found that many olfactory bulb neurons are place-selective during free movement. To test whether this position-selective activity carries usable information about the mouse’s location, we decoded position from ensembles of simultaneously recorded units. We could decode the mouse’s position with above-chance accuracy in all sessions. Thus, even during spontaneous behavior and ambient stimuli, information about time and place can be read out from the activity of the olfactory bulb. A mouse needs to know where and when it encountered different smells: olfactory information must be contextualized and incorporated into cognitive maps of environment and self. Our results suggest that this contextualization process begins as soon as olfactory information enters the brain.

Bio

My research focuses on how neural mechanisms coordinate sensing with moving — how do animals sample the environment in order to acquire the information they require to survive? This broad question encompasses a snake flicking its tongue, a primate moving its eyes, or a rodent following its nose. I study the last of these because mice are particularly amenable for studying neural circuits. I am a neuroscientist, born in Saskatchewan, raised in Maryland. I attended Duke and UCSF for school and I did postdocs at Cold Spring Harbor and Janelia Farm. I have been at University of Oregon since 2014.

Host: Dr. Arbora Resulaj

Zoom:  https://utoronto.zoom.us/j/86911860816

October 8, 2021

Dr. Maitreya Dunham - Department of Genome Sciences at University of Washington

Taking yeast experimental evolution out of the lab and into classrooms and breweries. RECORDING

Host: Dr. Alex Nguyen Ba

Abstract:

Microbial experimental evolution has allowed for real time explorations of many important topics in evolution. Now paired with cheap and easy whole genome sequencing, we have been able to explore the genetics of adaptation at a level of molecular detail never before possible. I will talk about two projects where we've been able to apply the approaches and tools we developed to study evolution of yeast cultures in the lab, but now in classroom and industry settings. First, we have simplified our methods to allow high school students to perform experimental evolution as part of a teaching lab, with results contributing to a multi-school research project on how yeast evolve antifungal resistance. Second, we have taken advantage of a natural experiment happening in breweries, where yeast is "repitched" from one fermenter to the next. Using deep sequencing, we found chromosome rearrangements and copy number variants that repeatedly attained high frequency over yeast reuse, even across multiple breweries. We infer that these mutations are beneficial in the brewery environment and affect traits including osmolarity tolerance, flavor, and flocculation. We are hoping to build on these success stories to find new opportunities to study evolution in real time in non-lab environments.

About:

Dr. Maitreya Dunham' research uses high-throughput experimental evolution to understand and exploit evolutionary processes in natural or biotechnological settings. She has set up chemostats to study laboratory and wild microbes in the lab, and exploits next-generation sequencing and advanced bioinformatics pipelines to decipher their genome evolution. She is extremely fun to talk to even for things outside the lab, for example she is involved in multiple breweries around Seattle as she brews her own and grows her own hops. For more information on her research and publications, visit her webpage (https://dunham.gs.washington.edu/home.shtml).

October 1, 2021

Dr. Cassidy D'Aloia, University of New Brunswick

Genetic approaches to uncovering marine connectivity RECORDING

Host: Dr. Bailey McMeans

Abstract:

Over 70% of marine species disperse as tiny larvae that develop in ocean currents. Determining where those larvae go—and how they get there—has been a major challenge in marine ecology. Genetic relatedness analyses that identify first-order kin, such as parents and their offspring or full siblings, have become a popular tool for documenting marine larval dispersal events. But these analyses come with their own drawbacks. Mainly, these studies are spatially and temporally constrained due to their sampling intensity, rendering them ill-suited for detecting long-distance dispersal and/or temporal fluctuations in connectivity patterns. In this talk, I’ll present recent work that integrates multiple genetic approaches to detecting larval dispersal across spatial and temporal scales. We assess the benefits and shortcomings of our own genetic relatedness studies. Collectively, we find evidence of consistently limited dispersal in a coral reef fish, despite the fact that individuals develop and feed offshore in pelagic waters for nearly a month. These results pave the way for new integrative lines of research that explore the behavioral and oceanographic mechanisms driving these dispersal patterns.

Bio:

I am a molecular ecologist and marine field biologist who grew up in landlocked upstate NY. My interest in EEB and marine science was first sparked while studying as an undergraduate at Middlebury College and the Universidad Austral de Chile. After that, I spent five years (often underwater!) studying coral reef fishes in Belize during my PhD. I completed postdocs at Woods Hole Oceanographic Institution and the University of Toronto before moving to the University of New Brunswick as an Assistant Professor. In January 2022 I am joining the UTM Department of Biology.

Website: https://www.cassidydaloia.com/

September 24, 2021

Dr. Susan Gasser, Director of ISREC - Swiss Institute for Experimental Cancer Research

How heterochromatin preserves genome stability and tissue identity in worms. Recording

Abstract: 

Development of an organism is governed by a carefully orchestrated program of gene regulation, controlled on the level of both chromatin and DNA sequence. Histone modifications are the primary drivers of chromatin structure, which shape the epigenetic information of any cell. Methylation of lysine 9 of histone H3 (H3K9me) characterizes the transcriptionally silent heterochromatin in organisms from yeast to man. It ensures genome stability by silencing repeats (1)  and it silences some genes as cells differentiate (2). In multicellular animals the aberrant gain or loss of heterochromatin and its segregation at the nuclear envelope has been correlated with a loss of tissue integrity, aging and cancer (e.g., 2,3,4).  Nonetheless, how H3K9me restricts expression remains unknown. Here we show in C. elegans that loss of H3K9me results in the limited depression of genes which in some tissues and/or embryos carry H3K9 methylation. We find that the pattern of gene derepression by loss of H3K9me is distinct in embryos and in terminally differentiated cells (5). During organismal development, we find that H3K9me is lost from genes that must be expressed, and is gained on genes that were expressed in prior developmental stages. Active H3K9me maintenance by MET-2/SETDB1 is necessary to ensure silencing, even in post mitotic cells. Despite the fact that H3K9me generally restricts chromatin accessibility at promoters and enhancers, as measured by ATAC-seq, we find that changes in accessibility do not necessarily correlate with gene derepression. Rather, the binding of a specific subset of TFs is controlled in differentiated tissues by H3K9me.  This substantiates the long-standing hypothesis that heterochromatin controls gene expression. Although derepression can be independent of stable chromatin opening, expression reflects the ability of TFs to access gene promoters (5).

1. Zeller, P. et al. Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability. Nat Genet 48, 1385-1395, doi:10.1038/ng.3672 (2016).

2. Nicetto, D. et al. H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification. Science 363, 294-297, doi:10.1126/science.aau0583 (2019).

3. Chen, M. W. et al. H3K9 histone methyltransferase G9a promotes lung cancer invasion and metastasis by silencing the cell adhesion molecule Ep-CAM. Cancer Res 70, 7830-7840, doi:10.1158/0008-5472.CAN-10-0833 (2010).

4. Harr, J.C., et al. Loss of an H3K9me-anchor rescues laminopathy-linked changes in nuclear organization and muscle function in an EDMD model. Genes & Dev. 34, 560 - 579. doi: 10.1101/gad.332213.119. (2020).

5. Methot, S.P., Padeken, J., et al., H3K9me selectively blocks transcription factor activity to ensure differentiated tissue integrity.  In final revision, Nat Cell Biol. (2021).

September 17, 2021

Dr. Santiago Claramunt, Associate Curator of Birds, Department of Natural History, Royal Ontario Museum & Assistant Professor, Department of Ecology and Evolutionary Biology, University of Toronto

“Integrative approaches to the study of bird diversification” RECORDING

Phylogenetic approaches are revolutionizing the study of macroevolution but inferences about diversification require accurate time-scaled phylogenies and attention to the fundamental causal processes. Here I show how we can make progress in both fronts using bids as an example. I show new approaches for the calibration of molecular clocks and how new avian time-trees reveal a striking correlation between global temperatures and diversification rates. Then, I show how dispersal ability can be estimated from wing shape and explore the relationship between dispersal ability and diversification rates. These new approaches have great potential for further our understanding of the process of diversification.

Bio:

I was born and raised in Uruguay, where I became interested in science and nature, and obtained a BSc in Biology. I moved to the USA for doctoral studies at Louisiana State University, followed by a postdoctoral position at the American Museum of Natural History in New York. After teaching biogeography and evolutionary biology for two years in Peru, I moved to Toronto where I am Associate Curator of Birds at the Royal Ontario Museum and Assistant Professor—Status Only—at the Department of Ecology and Evolutionary Biology of the University of Toronto.

September 10, 2021

James Santangelo, PhD Student (Robert Ness & Marc Johnson Supervisors)

Parallel adaptation to the world’s urban jungles

Abstract:

Urbanization dramatically transforms environments in ways that alter the evolution of life. We examined whether global urbanization drives convergent environmental change and parallel evolution by sampling 110,019 white clover plants from 6,169 populations in 160 cities spanning diverse climates. Plants were assayed for hydrogen cyanide—a Mendelian antiherbivore defence that also affects tolerance to abiotic stressors. Urban environments were consistently hotter, less vegetated, and had more impervious surfaces than nonurban areas, which were associated with the evolution of phenotypic clines in 47% of cities throughout the world. Sequencing 520 genomes from 26 cities revealed that parallel clines were best explained by adaptive evolution, and environmental analyses showed that variation in HCN clines was explained by multiple interacting environmental factors. Our results demonstrate that ongoing urban environmental change is leading to parallel evolution globally.

Dr. Jimena Leyria, PostDoctoral Fellow (Angela Lange Supervisor)

A bite, a blood cocktail, and successful reproduction: control of egg-laying in a major vector of Chagas Disease

Abstract:

In the blood-sucking Rhodnius prolixus, a vector of Chagas disease, the nutrients incorporated by a blood meal have a high epidemiological impact since in adult mated females, each meal results in a bout of egg laying, and thereby the production of hundreds of offspring. In insects, insulin-like peptide (ILP) signalling along with the target of rapamycin (ToR) are involved in detecting and interpreting nutrient levels. By means of RNA-Sequencing we have examined how a blood meal influences mRNA expression of the ILP/ToR signalling pathway in key tissues involved in reproduction (fat body and ovaries). Although there is an up-regulation of the genes involved in ILP/ToR signalling in unfed insects, western blot analysis reveals that this signalling is only activated after a blood meal, i.e. phosphorylation of proteins. Immunofluorescence and RNA interference (RNAi) studies suggest that during the unfed condition, FoxO signalling may be responsible for the up-regulation of transcripts involved in the ILP/ToR signalling cascade. Moreover, exogenous insulin stimulates protein phosphorylation in the fat body and ovaries from unfed insects, suggesting that those females are in a sensitized state and respond to food by rapidly activating ILP signalling. Also, by RNAi and ex vivo assays we show that ILP/ToR pathway is involved in juvenile hormone (JH) synthesis and release, a hormone that coordinates the synthesis of yolk protein precursors by the fat body, which in turn influences the numbers of eggs laid per female. Our study reveals a network of regulatory pathways implicated in reproductive performance. These analyses serve as a starting point for new investigations that increase the chances of developing novel strategies for vector population control by translational research, with less impact on the environment and more specificity for a particular organism.

2021-2022 Schedule

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