Biology Seminar Series


Welcome to UTM Biology Seminar Series 2022-2023


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

Where: DV2080 & Live Stream on Zoom (links are posted for each session)


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.

March 31, 2023


Openscapes: Supporting kinder science for future us


At Openscapes, we believe open science can accelerate interoperable, data-driven solutions and increase diversity, equity, inclusion, and belonging in research and beyond. Our main activity is mentoring environmental and Earth science teams in open science, and connecting and elevating them both through tech like R, Python, Quarto, and JupyterHubs and communities including RLadies, Black Women in Ecology Evolution, and Marine Science, Ladies of Landsat, and NASA. We’ll share stories and approaches about supporting open science as a daily practice – better science for future us – and welcome you to join the movement.

Speakers: Dr. Julia Stewart Lowndes, Founder & Co-Director, Openscapes ( )

Julia Stewart Lowndes, PhD is a marine ecologist working at the intersection of actionable environmental science, data science, and open science. Julia’s main focus is mentoring teams to develop technical and leadership mindsets and skills for data-intensive research, grounded in climate solutions, inclusion, and kindness. She founded Openscapes in 2018 as a Mozilla Fellow and Senior Fellow at the National Center for Ecological Analysis and Synthesis (NCEAS), having earned her PhD from Stanford University in 2012 studying drivers and impacts of Humboldt squid in a changing climate.


Ileana Fenwick ( )

NOAA-EPP LMRCSC Undergraduate Graduate

B.S., Marine & Environmental Science

Hampton University

Ileana Fenwick completed an undergraduate degree in Marine and Environmental Science at Hampton University in May 2020. Her past research focused on black sea bass health under Dr. Brad Stevens at the University of Maryland Eastern Shore. After graduating, Ileana continued to do research as an LMRCSC Fellow at Hampton University, investigating oyster reef restoration in the Hampton River.

Ms. Fenwick is pursuing her PhD at UNC Chapel Hill in quantitative fisheries.

2022-2023 Schedule

Jan 13, 2023
Bridget Murphy
Madeleine Oman
 Climate warming delays down regulation of photosynthesis in southern white spruce genotypes compared to northern genotypes
 Modelling the evolution and predictors of mutation rate variation
Dr. Ingo Ensminger
Dr. Rob Ness
Jan 20, 2023
Dr. Anja Groth, University of Copenhagen
 Inheritance of histone modifications/variants across DNA replication and mitosis
CSB Grad Students
Jan 27, 2023
Dr. Lynn Adler, UMass Amherst
 Disease where you dine: The role of floral traits in pollinator-pathogen interactions
Dr. Marc Johnson
Feb 3, 2023
Dr. Douglas Allan, UBC
 Transcriptional regulation of synaptic plasticity in maturing motor neurons by retrograde signals
Dr. Ted Erclik
Feb 10, 2023
Dr. Amy Iler, Northwestern University
 Consequences of environmental variation for plant populations: earlier flowering under climate change and pollinator declines
Dr. Marc Johnson
Feb 17, 2023
Dr. Michelle DiLeo, OMNRF
 The importance of intraspecific variation for ecological prediction
Dr. Helene Wagner
Mar 3, 2023
Dr. Jun Ding, Stanford University
 Cell Type Specific Plasticity in Motor Memory Engrams. 
Dr. Baohua Liu
Mar 10, 2023
Dr. Julia Zeitlinger, Stowers Institute for Medical Research
 Deciphering the cis-regulatory code by interpretable deep learning
Dr. Ho-Sung Rhee
Mar 17, 2023
Dr. Ivana Cvijovic, Stanford University
Dynamics of migration and memory formation in human antibody-mediated immunity
Dr. Alex Nguyen Ba
Mar 24, 2023
Dr. Brady Johnston, University of Western Australia
Blending Proteins: Democratising Access to Beautiful Molecular Landscapes
Mar 31, 2023
Dr. Julia Stewart Lowndes
Ileana Fenwick

Openscapes: Supporting kinder science for future us

Grad Students
Sep 9. 2022
Ahmed Hasan

Dr. Rosemary Martin
How and why does recombination rate vary
Hypoxia sensitivity and patterns of winterkill in larval anisopteran communities in temperate ecosystems
Dr. Rob Ness
Dr. Shannon McCauley
Sep 16, 2022
Dr. Adam Mott
Disease or NAT? RNA control of receptor expression
Dr. Marcus Dillon
Sep 23, 2022

Dr. Santiago Herrera
Lehigh University
Advancing eDNA as a Tool for Exploration in Deepwater Environments
Dr. Cassidy D'Aloia
Sep 30, 2022
Dr. Ninon Meyer, University of Newcastle
Wildlife connectivity : teaming up with local people to enhance conservation
Dr. Helene Wagner
Oct 7, 2022
Dr. Josef Nissimov, University of Waterloo
Algal viruses: friends or foes?
Dr. Steven Short
Oct 21, 2022
Dr. Dmitry Rinberg,
NYU Grossman School of Medicine
Cracking the Olfactory Coding using Behavior
Dr. Arbora Resulaj
Oct 28, 2022
Dr. Francois Robert,
The Roles of FACT during Transcription Elongation
Dr. Ho-Sung Rhee
Nov 4, 2022
Dr. Megan Bontrager, U of T
Local adaptation at range edges and under anomalous climates
Dr. Peter Kotanen
Nov 11, 2022
Dr. Uwe Rascher, Julich Research Center
Understanding the diurnal and seasonal dynamics of photosynthesis – from the molecular regulation of photosynthetic light conversion to the global carbon fluxes
Dr. Ingo Ensminger
Nov 18, 2022
Dr. Tziana Gelmi Candusso, U of T
The spatial ecology of urban mammals in Toronto
Dr. Christoph Richter
Nov 25, 2022
Dr. Fiona Hunter,
Brock University
How do co-circulating viruses interact within mosquitoes? 
Dr. Rosalind Murray
Dec 2, 2022
Dr. Shaun Killen, University of Glasgow
Fuel and friends: Links between metabolism and social behaviours in fish
EEB Grad Students
Dec 9, 2022
Dongyan Tan, Stony Brook University
Histone variants, the diverse building-block of chromatin in transcriptional regulation. Virtual
Dr. Mark Currie


Milena Russo Design

Blending Proteins: Democratising Access to Beautiful Molecular Landscapes


Crucial to the field of structural biology is clear and compelling visualisations. While this has mostly been the realm of dedicated scientific software, graphical fidelity is not usually the focus, which makes communication with those who aren’t experts in the field difficult. While dedicated 3D modelling and animation programs exist, they are unable to work with the data formats that are used in various structural biology pipelines.

 I will be presenting my journey through molecular visualisation, starting out using PyMol and ChimeraX to do run-of-the-mill crystallography, and how this lead to pursuing 3D modelling and animation inside of Blender. This resulted in the creation of my own bespoke plugin for the software, which enables the import of structural biology data formats such a .pdb files, electron microscopy densities and molecular dynamics simulations. Loading this data natively inside of Blender allows the user to harness the full power of an industry-leading 3D animation program to create compelling visualisations of molecular data. These visualisations enable clearer communication with non-experts, and create compelling images and movies to explain complicated concepts to others in the field.

Dynamics of migration and memory formation in human antibody-mediated immunity

Antibodies are crucial in defending against pathogens, but unlike most proteins, they aren't genetically encoded at birth. Instead, they arise in a stochastic evolutionary process in specialized immune cells called B cells. Studying this process is essential for understanding how antibody-mediated immunity develops, is maintained, and evolves throughout life. Recent advances in sequencing technologies allow us to study this at scale by sequencing the genes that encode antibodies. Although most samples used for studying B cell repertoires are collected from peripheral blood, B cells migrate between lymphatic tissues as they proliferate and differentiate. Thus, it is not clear whether the population of circulating B cells in the peripheral blood is representative of the B cell system as a whole. This gap is particularly important because it is known that the majority of circulating antibody proteins come from cells that reside in the bone marrow, and it is unclear how these cells are related to those residing in other lymphatic organs. Our study addresses this gap by examining human antibody cells from various lymphatic tissues in the same individual. Our findings reveal extensive exchange between these tissues, but also significant differences among B cells residing in different locations. These insights help us better understand the process by which B cells commit to long-term memory and the statistics governing this active process. Specifically, our results shed light on the tempo and pace at which B cells make decisions about committing to long-term memory.

Dr. Cvijovic uses a combination of theory and next-generation genomics tools to study stochastic processes such as evolution. She is an expert in analyzing genomics data from natural evolution, and these days she is at the front in computational immunology by leading a B-cell/T-cell consortium. As a theorist going into wet-lab experiments, she has some of the craziest science stories I've ever heard and she is one of the most fun person to talk to outside the lab.

Deciphering the cis-regulatory code by interpretable deep learning

The cis-regulatory code that instructs gene regulation, also known as the genome’s second code, is a fundamentally unresolved problem. It is estimated that >80% of disease-causing mutations in the human genome are found in cis-regulatory regions, but since we cannot read the code, we cannot predict which genetic variants disrupt gene regulation. Recent progress in using neural networks for learning DNA sequence has however provided proof-of-principle that this complex cis-regulatory code can be learned. This new approach is fundamentally different from traditional methods in that it is an inverted learning paradigm. Traditionally, cis-regulatory sequence rules are hypothesized manually and tested by statistical overrepresentation, but applying the learned rules results in poor performance when applied to specific genomic regions. In the inverted learning paradigm, the sequence rules are learned inside a black box directly from genomic sequences through their ability to better predict a specific genomics data set. Only upon achieving high accuracy, are the rules extracted from the model using interpretation tools. This dramatically improves the predictive performance, but requires rigorous approaches for extracting, understanding and validating the learned sequence rules to make sure that they represent biology. I will describe how we use this approach to understand specific processes underlying gene regulation using mouse cell types or Drosophila embryos as model systems. In all cases, we uncover unexpected sequence rules that we can validate with experiments. These results illustrates a path forward towards understanding the rules and molecular mechanisms underlying the cis-regulatory code.

The importance of intraspecific variation for ecological prediction

Different individuals of the same species are diverse in their traits and interactions with the environment. Yet ecological models typically ignore this variation by assuming average responses across individuals and populations. This has prompted calls for ecologists to build more reality into models of connectivity, invasions, range dynamics, and responses to climate change. However, the level of detail needed for accurate predictions remains an open question. In this talk I will present our recent work characterizing the variation and potential drivers of individual dispersal in the Glanville fritillary butterfly across a metapopulation in the Åland Islands, Finland. I will show that the factors that maintain dispersal variation are complex, but that there are clear consequences when we ignore it in models of gene flow, colonization, and extinction risk. I will finish by discussing my group’s ongoing work using whole-genome sequencing and common garden experiments to characterize spatial variation in plastic and locally adapted responses to climate across the butterfly’s European range.

Consequences of environmental variation for plant populations: earlier flowering under climate change and pollinator declines

Earlier flowering is one of the most widespread biological responses to climate change, and these shifts in the timing of flowering are especially pronounced at high elevations and high latitudes, places were climate change is occurring rapidly. This talk will therefore begin by examining what is driving these changes in flowering dates, using subalpine plants in the Colorado Rocky Mountains as a case study. After thinking about drivers of earlier flowering, we will consider population-level consequences of earlier flowering. Another type of environmental variation that my group thinks about a lot is fluctuations in pollinator services, and this talk will conclude by examining the effects of altered pollination for plant population dynamics, something we know surprisingly little about.  

In Person POSTER

Algal viruses: friends or foes?

Marine viruses are now viewed as major drivers of biogeochemical cycles and as crucial components that shape microbial food webs. Our main understanding of these viruses stems predominantly from their study in marine habitats, where viruses are entangled in complicated but detrimental co-evolutionary arms race with their algal host. To that end, it is widely accepted that marine viruses can control the abundance of dominant microalgal communities, decide the faith of blooms, and affect the diversity of microorganisms in coastal and oceanic environments. Nevertheless, despite the ecological and societal importance of freshwater environments, our understanding of the role of viruses in freshwater habitats is at its infancy. In this talk I will first present an overview of some of the positive effects that virus infection of cosmopolitan marine microalga such as Emiliania huxleyi have. I will then ask the questions of whether virus infection in freshwater environments is as important as in marine systems, whether virus infection of toxic algae is contributing to the control of harmful algal blooms (HABs), or whether freshwater viruses actually contribute to worsening the effects of HABs.   

Host: Dr. Steven Short

Advancing eDNA as a Tool for Exploration in Deepwater Environments
Environmental DNA (eDNA) sequencing and quantification complement established tools to assess the biodiversity of vulnerable benthic ecosystems. Offshore, marine eDNA may be transported long distances by complex ocean currents until it dilutes or degrades and is no longer detectable using PCR-based methods. A comprehensive understanding of the impact of marine physicochemical conditions on eDNA persistence has not been established. This gap in knowledge obscures the source location of eDNA from benthic ecosystems. In the mesophotic and deep ocean, below 30 meters depth, temperature, pH and dissolved oxygen concentration vary with depth and location. We conducted eDNA persistence experiments using eDNA derived from a deep-sea coral to determine the degradation rate among the natural combinations of temperature, pH and dissolved oxygen concentration that occur commonly in the deep ocean. The eDNA degradation process was best explained by a model with two phases with different decay rate constants. During the initial phase, eDNA degraded rapidly, and the rate was independent of physicochemical factors. During the second phase, eDNA degraded slowly, and the rate was strongly controlled by temperature and weakly controlled by pH. We did not find evidence that dissolved oxygen concentration from 0.1 mg/L to fully saturated conditions influenced eDNA degradation rate. Based on our results and publications using similar methods, we estimate that marine eDNA can persist at quantifiable concentrations for over 2 weeks at low temperatures (≤ 10 °C) but for a week or less at ≥ 20 °C. We propose a general temperature-dependent model to predict the maximum persistence time of eDNA detectable through single-species eDNA quantification methods. The relationship between temperature and eDNA persistence appears to be independent of the source taxa, however further experiments with other marine invertebrates are necessary. Community-wide sequencing data from eDNA samples at an offshore, mesophotic reef will test predictions regarding the transport extent of eDNA from benthic organisms and the application of eDNA analyses in these habitats. This research is supported by NOAA OER award NA18OAR0110289.

Host: Dr. Cassidy D'Aloia

In Person POSTER
Wildlife connectivity : teaming up with local people to enhance conservation
Maintaining connectivity among remaining habitat fragments is key to conserve biodiversity in a rapidly changing world. Effective landscape connectivity requires both a strong scientific basis to identify areas of conservation concern, and socio-political considerations to successfully protect these priority areas. I will present case studies from Panama, Australia, and Europe where efforts to maintain/restore connectivity for terrestrial mammals are currently being undertaken. After estimating functional connectivity for a suite of species using a combination of approaches (i.e., movement, occurrence, genetics), and identifying areas that would best facilitate species movement, I outline the different strategies that are being implemented together with local initiatives and Indigenous people to enhance the conservation of wildlife and their habitat

Host: Prof. Helene Wagner

Disease or NAT? RNA control of receptor expression
The LRR-RLK family of cell surface receptors is the largest group of receptor-like kinases in plants. They regulate plant growth, development, and stress responses including immune activation. To optimize these processes and overall plant fitness, their expression and activation are tightly controlled. As a result, many LRR-RLKs show tissue-specific, developmentally regulated, or stress-induced expression patterns. What remains unclear is how the plant achieves this level of expression specificity and inducibility to a wide-range of signals. Our work shows that the LRR-RLKs are significantly associated with regulatory non-coding RNA molecules. The expression of these regulatory RNAs is often tissue-specific and/or stress-induced, suggesting that their activity could explain the regulation of LRR-RLK expression in response to diverse cues. Using several examples, we demonstrate a variety of regulatory effects and mechanisms by which these RNAs control LRR-RLK expression in a tissue-dependent manner. This work provides a novel mechanism for regulation of a variety of plant growth and immune responses mediated by LRR-RLKs. 

Host: Dr. Marcus Dillon

Ahmed Hasan – In Person
Ph.D. Candidate, Dept. of Cell and Systems Biology
Ness Lab,
How and why does recombination rate vary?
Recombination rate varies at multiple scales across nature; between species, individuals, and across genomes. Here, I present some work on inferring variation in recombination rate and investigating its causes and consequences across the genome, as well as ongoing work to develop software for fast and efficient detection of recombination in bulk sequencing reads.
Dr. Rosemary Martin - Zoom
McCauley Lab
Hypoxia sensitivity and patterns of winterkill in larval anisopteran communities in temperate ecosystems
The depletion of dissolved oxygen in lakes and ponds as a result of extended ice coverage can lead to large die-offs of fish, a phenomenon known as winterkill. Hypoxic winter conditions act as an environmental filter and can shape fish communities in mid and high latitude ecosystems by selecting against hypoxia sensitive species. Most aquatic invertebrates remain active under ice, but it is generally unknown how periods of winter hypoxia affect activity levels and survival for many taxa. We surveyed larval dragonfly communities in 18 lakes in Michigan and Ontario for a total of 6 years of pre and post winter samples and identified dragonflies Anax junius and Leucorrhinia intacta as winterkill candidates. We experimentally tested relative sensitivity to low oxygen conditions in odonate species. Mortality of A. junius in hypoxic treatments was significantly higher compared with oxic treatments, but not for other dragonflies. Hypoxic conditions may contribute to patterns of overwinter declines in A. junius, a large bodied voracious top predator. Because of A. junius’s apparently higher sensitivity to hypoxia, habitats that become hypoxic in winter could be seasonal refuges from predation for aquatic organisms that are able to tolerate hypoxic conditions. Climate change is decreasing ice coverage duration which could decrease occurrences of hypoxia under ice. Reduced hypoxia could lead to greater numbers of A. junius present in spring communities and consequently increase predation pressure on aquatic invertebrates and other prey species.

How do co-circulating viruses interact within mosquitoes? 

West Nile virus is a flavivirus that is amplified in a "bird-Culex mosquito-bird" transmission cycle until it "spills over" into the mammalian population, generally late in the season. A model to predict when human cases of West Nile virus - based on 21 years of mosquito surveillance and viral testing data - will be presented. With global climate change, and the introduction of new mosquito vectors and new viruses, the possibility of more than one virus circulating in the environment increases. Information will be presented on what happens in cell culture and in live mosquitoes when more than one virus is present. The role of superinfection exclusion - when a non-pathogenic insect specific virus is present alongside a medically important virus such as West Nile virus, Zika virus or Mayaro virus - will be presented. 


Host: Dr. Rosalind Murray

Fuel and friends: Links between metabolism and social behaviours in fish

Individuals within species show tremendous variation in physiological and behavioural traits. Over the last decade there has been a surge of interest in the ecological and evolutionary importance of this diversity, but the vast majority of this work has been performed on isolated animals. In reality, however, most animals - from insects to mammals - do not live in a vacuum, but instead live within complex social structures. Social influences may override links between traits that exist in solitary animals. Conversely, an individual's standing within a group may be an important factor generating intraspecific variation. In this talk I will review some of our recent work examining the interplay between social behaviours and metabolic traits within various fish species and how such links may be modulated by environmental factors, and relevance for issues associated with fishing-induced selection.

We stream live here:

Speaker: Dr. Dongyan Tan, Department of Pharmacological Sciences, Stony Brook University

Zoom link:

Host: Dr. Mark Currie

Title: Histone variants, the diverse building-block of chromatin in transcriptional regulation


Histone variants are nonallelic isoforms of canonical histones that confer unique properties on chromatin. In recent years, there has been a renaissance of interest in understanding how histone variants shape the chromatin landscape in cells during multicellular organism and disease development. We use cryo-EM and complimentary biochemistry to elucidate the mechanism-of-actions of two H2A family variants, H2A.Z and macroH2A. Variant H2A.Z, an essential protein for aminal survival, has well-established functions in transcription. Our study in H2A.Z provides the structural basis for the dual-function of H2A.Z in transcriptional control. In the meantime, we undertake the effort to understand how unique properties of variant H2A.Z promote its associations with chromatin regulators such as heterochromatin protein 1 (HP1). Variant macroH2A, on the other hand, is primarily known for its role in X-chromosome inactivation in female mammals. Our latest results indicate that a conserved sequence in the linker region of macroH2A is responsible for its unusual ability to stabilize linker DNA on nucleosomes and for its function in transcription repression.

The spatial ecology of urban mammals in Toronto

Wildlife is a key part of the urban ecosystem, and while considered pests by many inhabitants, mesopredator mammals play an invaluable role in maintaining a healthy ecological dynamic. The effect of their presence can cascade across multiple trophic levels, as they control small mammal populations and disperse seeds. To better conserve them while managing the negative implications of their presence, we aim to understand how mammals navigate the city and how urban life may affect their species' interactions. In this seminar, we will illustrate how we have been studying urban wildlife in Toronto using both tracking data and camera traps. We will discuss our results on habitat selection, landscape connectivity, and net displacement of urban coyotes, the use of machine learning to accelerate camera trap data identification, and briefly describe the projects that have arisen from our camera trap data, which aim at better understanding mammal ecology in cities. 

We will live stream here:

Title: Cracking the Olfactory Coding using Behavior


Two of the most fundamental questions of sensory neuroscience are: 1) how is stimulus information represented by neuronal activity? and 2) what features of this activity are read out to guide behavior? The first question has been the subject of a large body of work across different sensory modalities. The second question remains a significant challenge, since one needs to establish a causal link between neuronal activity and behavior.

In olfaction, it has been proposed that information about odors is encoded in spatial distribution of receptor activation and the next level mitral/tufted cells, as well as in their relative timing and synchrony. However, the role of different features of neural activity in guiding behavior remains unknown. Using mouse olfaction as a model system, we developed both technological and conceptual approaches to study sensory coding by perturbing neural activity at different levels of information processing during sensory driven behavioral tasks. We performed quantitative behavioral experiments to measure psychophysical limits of the readability of different features of the neural code, and quantify their behavioral relevance. Based on these results, we built a detailed mathematical model of the behavioral relevance of the different features of spatiotemporal neural activity. Our approach can be potentially generalized to other sensory systems.

Host: Dr. Arbora Resulaj

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The roles of FACT during transcription elongation


In living cells, transcription occurs in the context of chromatin. During transcription elongation, RNA polymerase II therefore must negotiate with a series of nucleosomes that need to be disassembled in order for the polymerase to access the DNA template strand. Because nucleosomes are the hosts of epigenetic information (either as histone post-translational modifications or by the presence of histone variants), however, cells have evolved mechanisms to ensure their proper reassembly in the wake of transcription. Transcription is therefore coupled to a delicate balance of nucleosome disassembly and reassembly, a process that involves several chromatin regulators including histone chaperones FACT and Spt6. In this presentation, I will review our work on the role of FACT in preserving nucleosomes and their modifications, and propose a detailed mechanism for FACT recruitment to genes. I will also present data assessing the role of the high mobility group protein Nhp6 in FACT’s function.

Host: Dr. Ho-Sung Rhee

We stream live here:

Local adaptation at range edges and under anomalous climates

Species’ geographic ranges are limited on the landscape. A major focus of work in the Bontrager lab is identifying which evolutionary and ecological forces interact to shape species’ geographic distributions and limit adaptation. In addition, populations are frequently adapted to their local environments, and my lab works to identify which components of the environment are the most important factors driving local adaptation. To test the effects of gene flow at range edges, we deployed a large common garden experiment at the northern range edge of the wildflower Clarkia pulchella. Our results indicate that gene flow has generally positive effects at this edge and that these effects can be attributed to both heterosis and the movement of alleles from warm climates. We then conducted a quantitative synthesis of transplant experiments to 1) examine how climate change is altering patterns of local adaptation, 2) evaluate the relative importance of temperature and precipitation to local adaptation and 3) examine how the magnitude of local adaptation changes from range centres to range edges. We found that temperature adaptation is a major component of local adaptation, and that as little as two degrees of warming is adequate to disrupt patterns of local adaptation. This work confirms temperature as a critical driver of plant population performance and characterizes general patterns of adaptation across species' ranges. 

Host: Dr. Peter Kotanen

In Person
We live stream:

Understanding the diurnal and seasonal dynamics of photosynthesis – from the molecular regulation of photosynthetic light conversion to the global carbon fluxes
Institute of Bio- and Geosciences, IBG-2: Plant Science, Forschungszentrum Jülich, Leo-Brandt-Str, 52425 Jülich, Germany
Plant photosynthesis is maybe one of the best understood biophysical and biochemical biological pathway, which combines photosynthetic light absorption, the usage of the energy in light reactions and the biochemical fixation of atmospheric CO2. Decades of basic and applied research have produced a good mechanistic understanding of the underlying mechanisms and their regulatory properties as well as a large amount of methods to non-invasively quantify the dynamics of photosynthesis. Fluorescence techniques are a widely used approach to directly quantify charge separation at photosystem II and to quantify the efficiency of photosynthetic light reactions non-invasively. Because of the rapid development of optical sensors and cameras, also fluorescence techniques have been greatly refined in the past years and nowadays fluorescence sensors can capture the fluorescence signal from larger distances enabling fluorescence measurements even from aircraft and satellite sensors.
In this seminar I will re-visit our current scientific understanding of the mechanistic link between the fluorescence signal and the functional properties of photosynthetic light reactions. I will give an update on the rapid development of new fluorescence measurement concepts, which include laser-induced fluorescence transients and the retrieval of solar-induced fluorescence from airborne and satellite plattforms. These novel data, which for the first allow to see and monitor the large scale dynamics of photosynthetic efficiency are exemplified with selected case studies, where we combined genetically modified plants with large scale, ecosystem modelling. Finally, I will briefly introduce the FLEX satellite mission concept (FLEX, FLuoresence EXplorer), which is currently implemented by the European Space Agency as Earth Explorer 8 and which will be launched in 2025. FLEX will have a spatial resolution of 300 meters and will provide global maps of solar-induced fluorescence and actual photosynthetic rates, which will allow for the first time to study the spatio-temporal dynamics of vegetation fluorescence and actual photosynthesis.
Selected recent publications
Mohammed G.H., Colombo R, Middleton E.M., Rascher U., van der Tol C., Nedbal L., Goulas Y., Pérez-Priego O., Damm A., Meroni M., Joiner J., Cogliati S., Verhoef W., Malenovský Z., Gastellu-Etchegorry J.-P., Miller J.R., Guanter L., Moreno J., Moya I., Berry J.A., Frankenberg C. & Zarco-Tejada P.J. (2019) Remote sensing of solar-induced chlorophyll fluorescence (SIF) in vegetation: 50 years of progress. Remote Sensing of Environment, 231, article no. 111177, doi: 10.1016/j.rse.2019.04.030.
Acebron K., Matsubara S., Jedmowski C., Emin D., Muller O. & Rascher U. (2021) Diurnal dynamics of non-photochemical quenching in Arabidopsis npq mutants assessed by solar-induced fluorescence and reflectance measurements in the field. New Phytologist, 229, 2104-2119, doi: 10.1111/nph.16984.
Porcar-Castell A., Malenovský Z., Magney T., Van Wittenberghe S., Fernández-Marín B., Maignan F., Zhang Y., Maseyk K., Atherton J., Albert L.P., Robson T.M., Zhao F., Garcia-Plazaola J.-I., Ensminger I., Rajewicz P.A., Grebe S., Tikkanen M., Kellner J.R., Ihalainen J.A., Rascher U. & Logan B. (2021) Chlorophyll a fluorescence illuminates a path connecting plant molecular biology to Earth-system science. Nature Plants, 7, 998-1009, doi: 10.1038/s41477-021-00980-4.

Host: Dr. Ingo Ensminger

Madeleine Oman

PhD Student, Ness Lab

Modelling the evolution and predictors of mutation rate variation

Mutation introduces the genetic variation that facilitates adaptive evolution, but those mutations can also give rise to diseases such as cancer and age-related illnesses. Although mutation is random, the relative rate of mutation at each position, or mutability, is not uniform across the genome. Variation in mutability has been demonstrated at multiple scales and the rate at which mutations occur can vary from site to site across the genome more than 100-fold. Thus, individual sites and regions across the genome have the potential to participate in evolution and genetic pathologies at varying rates. 
Investigating how molecular processes and genomic properties predict mutation is an active area of study, and many factors have merged as strong predators of mutation. These factors include molecular processes (e.g. DNA repair), protein associations (e.g. nucleosome occupancy) and genetic sequence (e.g. the CpG effect), with sequence context emerging as one of the strongest predictors. 
Here I use models to understand how mutation rate variation evolved and what mechanisms best predict it. Analysing the drivers and patterns of mutability variation can help us understand the mutagenic mechanisms of human disease and the forces that generate the variation available to evolution.


Bridget Murphy

PhD Student, Ensminger Lab

Climate warming delays downregulation of photosynthesis in southern white spruce genotypes compared to northern genotypes

Temperature and photoperiod are critical environmental cues for the seasonal regulation of carbon uptake in boreal conifers. During autumn, the downregulation of photosynthesis is triggered by decreasing temperatures and shortening photoperiods. While photoperiod will be unaffected by climate change, it is unclear how future warming and reduced water availability will impact the regulation of autumn cold acclimation. Genetic variation may also affect the timing of cold acclimation due to local adaptions to environment and photoperiod. The goal of our project is to understand the impacts of warming and reduced precipitation on the timing of cold acclimation in two latitudinally distinct white spruce (Picea glauca) genotypes. The experimental design consisted of four treatments in replicate field plots: (1) control, (2) reduced precipitation, (3) warming and (4) warming combined with reduced precipitation. Warming was achieved through a temperature free-air enhancement experimental set up and precipitation was reduced by ~50% using rainout structures. Warming impacted photosynthetic activity and the development of low temperature protection of the chloroplast in late autumn time points. Additionally, compared to the northern genotype, the southern genotype had higher photosynthetic activity and reduced low temperature protection. This allowed carbon uptake longer into autumn. Our findings indicate that warming delays the downregulation of photosynthesis and the upregulation of low temperature protective mechanisms, with a greater delay in a slow-growing southern genotype compared to a fast-growing northern genotype.

Inheritance of histone modifications/variants across DNA replication and mitosis

In dividing cells, faithful replication of the genome must be accompanied by reproduction of the chromatin landscape on newly synthesized DNA. Research in the Groth lab aims to elucidate how chromatin organization is propagated across cell division to maintain genome stability and function. A key goal is to identify mechanisms that underpin epigenetic cell memory and understand their roles in cell fate decision during development and in disease. We have developed a panel of tailored technologies to address chromatin replication and epigenetic cell memory (NCC proteomics, ChOR-seq, SCAR-seq, RepliATAC-seq, iDEMS). Combining these technologies with structure-function studies of histone chaperones, we have made advances in understanding inheritance of histone-based information, restoration of chromatin organization in the wake of replication and how chromatin replication integrates with DNA repair. I will present our latest results on how histones are handled at the replication fork and the role of histone recycling in maintaining cell identity and cell fate.

Disease where you dine: The role of floral traits in pollinator-pathogen interactions

Food resources can alter host-pathogen dynamics not only via nutrition, but in some cases via chemical or mechanical traits that reduce infection. Many pollinator species are declining due to a range of factors including parasites and pathogens, but the potential for specific plant species to structure pollinator-pathogen interactions is largely unrecognized. Our previous work discovered that consuming sunflower pollen (Helianthus annuus) dramatically and consistently reduced infection by the gut pathogen Crithidia bombi in the common eastern bumble bee, Bombus impatiens. We have since expanded this work to consider (a) the breadth of this effect, in terms of both the extent of plant species whose pollen reduces Crithidia and the range of bee castes and species that are responsive, (b) the mechanism underlying this effect and (c) the field consequences of sunflower pollen for pollinator health. Our work demonstrates the role that a single key floral resource could play in pollinator-pathogen dynamics. Our current future research goals are to link our understanding of this system across scales from molecular to landscape.

Transcriptional regulation of synaptic plasticity in maturing motor neurons by retrograde signals


Retrograde signaling from synapses is a poorly understood yet critical contributor to transcriptional changes in neuron’s required for presynaptic maturation. Retrograde BMP signaling in Drosophila motor neurons has long served as a paradigm to study how retrograde signals control synaptic function, where it is required for neuromuscular junction (NMJ) growth, maturation and competence to express synaptic homeostasis and plasticity. 

I will describe our work defining the target genes of retrograde BMP signaling and the underlying gene regulatory mechanisms. I will also discuss recent studies revealing novel roles for a family of BMP-induced genes with emerging critical roles in synaptic function from flies to vertebrates. 



Cell Type Specific Plasticity in Motor Memory Engrams.


Learning and consolidation of new motor skills require plasticity in the motor cortex and striatum, two key motor regions of the brain. Yet, how neurons undergo synaptic changes and become recruited during motor learning to form a memory engram remains unknown. Here, we train mice on a motor learning task and use a genetic approach to identify and manipulate behavior-relevant neurons selectively in the primary motor cortex (M1). We find that the degree of M1 engram neuron reactivation correlates with motor performance. We further demonstrate that learning-induced dendritic spine reorganization specifically occurs in these M1 engram neurons. Additionally, we find that motor learning leads to an increase in the strength of M1 engram neuron outputs onto striatal spiny projection neurons (SPNs) and that these synapses form clusters along SPN dendrites. These results identify a highly specific synaptic plasticity during the formation of long-lasting motor memory traces in the corticostriatal circuit. 

May 5, 2023 Dr. Stephan Pless

Mar 10, 2023 Dr. Julia Zeitlinger

Mar 3, 2023, Dr. Jun Ding

Feb 17, 2023 Dr. Michelle DiLeo

Feb 10, 2023 Dr. Amy Iler

Feb 3, 2023 Dr. Douglas Allan

Jan 27, 2023 Dr. Lynn Adler

Dec 9, 2022 Dr. Dongyan Tan

Dec 2, 2022 Dr. Shaun Killen

Nov 25, 2022  Dr. Fiona Hunter

Nov 18, 2022 Dr. Tiziana Gelmi Candusso

Nov 11, 2022 Dr. Uwe Racher

Nov 4, 2022 Dr. Megan Bontrager

Oct 28, 2022 Dr. Robert Francois

Oct 21, 2022 Dr. Dmitri Rinberg

Oct 7, 2022 Dr. Josef Nissimov

Sep 30, 2022 Dr. Santiago Herrera

Sep 23, 2022 Dr. Ninon Meyer

Sep 16, 2022 Dr. Adam Mott