Seminar Series in Quantitative Biology and Ecology

Information

The seminar series in Quantitative Biology and Ecology is part of the Serrapilheira/ICTP-SAIFR TRAINING PROGRAM IN QUANTITATIVE BIOLOGY AND ECOLOGY. This Program trains young Brazilian and other Latin American scientists for world-class research on biology and ecology using the quantitative methods of mathematics, physics, and computer science. It strategically makes use of the country’s well-established excellence in mathematics and physics to tap into Brazil’s tremendous potential in life sciences.

The invited speakers of the Seminar Series cover different topics in Ecology and Biology, also showing the different theoretical and quantitative approaches they use in their research. The seminar series will happen regularly every Wednesday until the end of November. On special occasions, we might have seminars on other weekdays.

As part of our Training Program to prepare better scientists, we also organize Talks on transversal themes in Science (such as Women in Science, Mental Health in Science, Scientific Communication, among others). The Talks on transversal themes in Science will happen regularly every Monday until the end of November.

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Previous Seminars

Quantifying and integrating molecules for a more precise medicine (click to watch)
Speaker: Helder Nakaya – Albert Einstein Instituto Israelita de Ensino e Pesquisa
Date: July 28, 2022 14:30
Abstract: Diseases are mostly a consequence of an abnormality in multiple genes. Network Medicine investigates how genes interact to each other in complex intracellular and intercellular networks. The talk will show the recent advances on this emerging field of research and its impact on precision medicine and drug repositioning in Chikungunya, Zika, Malaria and Yellow Fever.

Theory, Models and Methods in Macroecology (click to watch)
Speaker: José Alexandre Felizola Diniz Filho – Universidade Federal de Goiás
Date: August 4, 2022 14:30
Abstract: Macroecology, as a relatively new field in Ecology, holds distinct methodological characteristics that lead to profound philosophical changes in the nature of evidence to support and build theories and models. One reason for this is the impracticability of controlled or manipulative experimental studies at broad spatial and temporal scales, as well as historical contingencies and the complexity of ecological dynamics at these scales. We follow here a model-based reasoning for building scientific theories and show in particular how computer simulation models, applied to different case studies in diversity gradients, can be successfully used in macroecology as mediating theory and data.

Assessing risks to biodiversity from climate change using macroecological and macroevolutionary models
Speaker: Andreas L. S. Meyer – University of Cape Town
Date: August 11, 2022 14:30
Abstract: Climate change is already causing local biodiversity losses, affecting ecosystems, and disrupting the life-supporting services they provide to people. However, our ability to forecast biodiversity responses and identify species most at risk from climate change remains insufficient. Here, I will explore how macroecological and macroevolutionary models can help us predict ecological and evolutionary responses of biodiversity to climate change. I will also show how simple, intuitive models can provide unprecedented information to assess risks and improve conservation prioritization and decision-making processes.

Unveiling complexity in ecology and evolution (click to watch)
Speaker: Flávia Maria Darcie Marquitti – Universidade Estadual de Campinas / ICTP-SAIFR
Date: August 18, 2022 14:30
Abstract: Mathematical and computational models are powerful tools to investigate patterns and delve into the processes behind them, making sense of the complexity of natural systems, from individuals to communities. In this talk, I will present the two main lines that guide my research: interaction networks and evolutionary models. In the first part, I will discuss how interactions across different levels of organization are shaped in nature and discuss the theoretical processes that may have resulted in observed interaction patterns. In the second part, I will address how genetic structure is important for the evolution of strategies and how the evolutionary process leaves signals in phylogenetic trees.

Tipping points and resilience: the case of the Amazonian ecosystems (click to watch)
Speaker: Marina Hirota – Universidade Federal de Santa Catarina
Date: August 25, 2022 14:30
Abstract: Not available.

Population genomics in space and time: insights from ancient DNA (click to watch)
Speaker: Prof Fernando Racimo – University of Copenhagen
Date: September 14, 2022 11:30
Abstract: The sequencing of ancient genomes has provided an unprecedented opportunity to study human evolutionary history over thousands of years, in different regions of the world. Here, I will describe several methods developed in our group to relate genomic data to informative parameters about population expansions, movement and adaptation, while explicitly accounting for both spatial and temporal dimensions. These include a new way to model the spread of ancestry in ancient genomes across a landscape, along with a new simulation framework for easily generating spatial simulations of arbitrary complexity. We have recently applied some of these methods to a new dataset including thousands of ancient human genomes and used them to infer major population movements over the past 13 millennia of Eurasian history.

Virus and satellite in ecological coexistence (click to watch)
Speaker:Adriana L Sanz Garcia – Georgia Institute of Technology
Date: September 21, 2022 14:30
Abstract: Cooperation is a main driver of biological complexity at all levels. In the viral world, gene sharing among viral genomes, complementation between genomes or interactions within quasispecies are frequently observed. In this contribution, we explore the effects of flexible associations between fully fledged viruses and subviral entities, such as virus satellites, in viral dynamics and, in particular, in stable viral coexistence. We devise a mathematical model to compare different situations of competition between two viruses and to quantify how the association with a satellite qualitatively modifies dynamical equilibria. The relevant parameter is the invasion fitness of each virus or of the virus-satellite tandem, which in the model depends on the transmission rate of viruses and on their effect on host survival. In a virus-virus competition, one of the viruses becomes eventually extinct, recasting the competitive exclusion law of ecology. However, an association with a satellite might change the outcome of the competition in two ways, either to favor the less competitive virus (regardless of whether it is the helper virus or not) or to allow for the stable coexistence of the two viruses and the satellite. The virus-satellite association differs from other mechanisms proposed in ecology to date to enhance species coexistence. We hypothesize that such an association constitutes a parsimonious evolutionary pathway towards more stable cooperative associations, such as bipartite viral forms, a collaborative association unique to viruses.

Upcoming Seminars

Unraveling the complexity of the plasma membrane from studies of symmetric and asymmetric model membranes

Thais A. Enoki

Cornell University

September 27, 2022 14:30

Cell membranes play important roles in cell function. The plasma membrane (PM) has the fundamental structure of a lipid bilayer, and has thousands lipid species that evolved to have physico-chemical properties that promote, for instance, a non-random lateral organization. This physical barrier protects the cell, and is composed of two leaflets of different lipid composition, thus is termed “asymmetric”. These PM leaflets have very different phase behavior. The exoplasmic leaflet, which faces the extracellular environment, is well studied using symmetric bilayers. The coexistence of liquid phases, named liquid disordered (Ld) and liquid ordered (Lo), is related to cell biology concepts of membrane rafts in the cell PM and is important to understand protein sorting and trafficking, membrane signal transduction, and viral assembly. We report a domain size transition tuned by the lipid composition, which can be explained by competing interactions between the line tension and dipole-dipole repulsion. In this transition, phase domain size abruptly changes without changes in the phase properties. Moreover, we observe notable patterns of modulated phases as the domain line tension decreases along the domain size transition. We also found a simple and accessible method to measure domain sizes below optical resolution (~200 nm). In contrast, the cytoplasmic leaflet lacks the high melting lipids, which with cholesterol could form the Lo phase. Thus, we need to consider a more complex model of the plasma membrane, which includes leaflets of distinct lipid composition. We first describe a new method to prepare asymmetric vesicles. Here, we use the hemifusion of giant unilamellar vesicles (GUVs) and a supported lipid bilayer (SLB) to engineer asymmetric GUVs, (aGUVs). We use different fluorescent dyes to monitor the inner and the outer leaflets of these unsupported aGUVs, and confirm that all newly exchanged lipids in the aGUVs are found in their outer leaflets. To model the plasma membrane, we prepare aGUVs that have one leaflet that phase separates into Ld+Lo phases, whereas the apposed leaflet forms a single fluid phase in an ordinary symmetric vesicle. For asymmetric vesicles, dye partition reveals induced ordered domains. We observed different cases where an ordered domain can induce order in the apposed leaflet. In addition, our results suggest that the induced ordered domains of the PM model are enriched in cholesterol. Therefore, the cytoplasmic leaflet may have “raft-like” domains induced by the exoplasmic leaflet.

 

Informal Meetings

During the period of September 12 – December 2, 2022, 28 distinguished international researchers in the fields of biology and ecology will be participating in the advanced module of the Serrapilheira/ICTP-SAIFR Training Program in Quantitative Biology and Ecology. In order to discuss common research interests which may lead to future collaborations, ICTP-SAIFR is organizing weekly informal meetings of Brazilian PhD students, postdocs and professors with these distinguished researchers.

The informal meetings will occur for a few hours in the late afternoon of one day during the visit of the researcher. The precise dates will be decided later, and if you would like to participate in one or more of these informal meetings, please fill out the application form at least one month before the visit of the researcher. You can request to participate in up to 10 informal meetings, and you will be asked to order in priority from 1 to 10 the researchers whom you would like to meet.

The application form and the list of names and dates of the visiting researchers are at https://www.ictp-saifr.org/informalqbio/

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