Leading Researchers: Priscilla Akyaw and Élio Sucena, Evolution & Development laboratory, IGC
Website

External collaboration
David Duneau, Institute of Evolutionary Biology at Edinburgh University.
Country: Scotland
Duration: 1 to 2 months

Abstract:
Host resistance to pathogens and disease tolerance of established infections are known major components of immunity. In insects, both resistance and disease tolerance contribute significantly to host survival upon oral infection, ultimately ensuring the return to physiological homeostasis. Studies into understanding host response to infection have given comparatively little attention to disease tolerance and have targeted the mechanisms of resistance, i.e. active pathogen elimination, both in vertebrate and invertebrate organisms, especially in Drosophila melanogaster. Indeed, disease tolerance mechanisms, which pertain to the host´s ability to withstand and/or repair damage inflicted either directly by the invading pathogen (virulence or pathogen-associated injury) or indirectly by the host’s own immune effectors during the process of resistance (immunopathology), are poorly understood. Also, little attention has been given to the larval stages in which exposure to pathogens is likely to be more severe, as most studies focus on the adult stage and its response to both systemic and oral infections. However, we have recently developed protocols to characterize separately the disease tolerance components of the immune response in D. melanogaster adults after infection with a range of bacterial pathogens differing in their virulence via either route of infection. Here, we propose to explore the uncharted territory of larval responses by testing these protocols in larvae to determine the relative contribution of each of these immune components in the death of orally infected individuals and potentially compare it the one obtained in adults. We propose to also test the range of responses deployed using a wide range of bacteria differing in their type and virulence. Finally, we wish to test the behaviour of larvae under each of these conditions and the role of choice/avoidance as to ascertain the contribution of such pre-emptive component in the overall biological response repertoire of Drosophila larvae facing bacterial pathogenic agents.

Brief description of the research approach
This Project will be developed using the model organism Drosophila melanogaster. One specific tool, unique to this system, that will constitute the basis of our experimental approach is the DGRP (Drosophila Genetic reference Panel). This is a set of around 200 lines in which every individual is genetically identical (isogenic) and for which each line has its full genome sequenced. Each trait considered in this project, from survival and reproduction to behaviour, will be studied using the DGRP infected with different pathogens. This comprehensive phenotypic description will allow developing a Genome-Wide Association Study (GWAS) that will provide candidate genes that may be tested and validated functionally.

Lay summary/ Impact of the study:
The way we respond to attacks from pathogens is multi-layered. Our bodies, as those of most multicellular organisms, can trigger counter-attacks that we generically call immunity. However, this response, this immunity, can be seen as including other types and levels of response. For example, upstream of the body response we typically consider, one can identify behavioural traits, which can simply be avoidance of the pathogen source by, for example, limiting contact with infected individuals. Another layer, that acts in parallel with the classical attack of the invading pathogen we call “resistance”, involves the ability to cope with that unwanted presence and its nefarious effects on health. Our body´s capacity to tolerate the pathogen-induced damage and repair it, called generically “disease tolerance”, is as important as the mentioned resistance mechanisms that contain pathogen numbers. Many such mechanisms are share between humans and other animals, including the model insect Drosophila melanogaster. For this reason, we propose to use this system and its vast array or tools to contribute to the identification of the genetic bases of such mechanisms. We will explore this approach under a number of different conditions including host life-stage and pathogen type/virulence as to gather the most comprehensive description of these phenomena and their mechanistic bases. This knowledge will inform, as in many other cases in the past, on the types of mechanisms at play in human immune response and provide new clues towards development of novel therapeutics.

Leading Researcher: Lounes Chikhi
Website

External collaboration
Institut de Mathématiques de Toulouse, Institut National des Sciences Appliquées de Toulouse, UNiov. Toulouse, France (collab. Prof. Olivier Mazet) – Département de Biologie Animale, Université de Mahajanga, Madagascar (collab. Prof. Solofonirina RASOLOHARIJAONA)
Country: France or Madagascar
Duration external collaboration: 3-4 months

Abstract:
The Population and Conservation Genetics (PCG) group at the IGC is interested in using genomic data to understand the recent evolutionary history of species. More specifically, we wish to identify environmental changes that have influenced and may still influence the genomic diversity of species across their distribution. These environmental changes may be ancient or recent, and they can result from human activities or natural cycles, including climate change. The project advertised here focuses on the impact of population structure, connectivity and habitat loss and fragmentation on the genomic diversity of various vertebrate species. In the last 17 years we have been particularly interested in endangered species of Madagascar but we have also been working on the evolutionary history of humans. The PCG group has been using several angles: (i) field work, (ii) genetic and genomic analyses, and (iii) computer simulations and statistical modelling. In a few words, we can use samples obtained in Madagascar to study the genomic diversity of several vertebrates (lemurs or rodents, mainly), or we can obtain published genomic data from species of interest (humans, Neanderthals, lemurs, etc.). We then use simulations and statistical inference to compare evolutionary models of ancient and changing population connectivity. Specifically, we aim at identifying periods during which habitats or populations were disconnected and periods of high connectivity. We are also interested in understanding what is happening in the field, in Madagascar to help protect populations of endangered species. The project is therefore open to students from any field of natural sciences, including biology, ecology, geography, physics, computer science or mathematics, among others. The selected student will work on one or several aspects of the projects currently developed between Madagascar, Toulouse and Oeiras. If a computationally-oriented student is selected s/he will mostly work at the IGC and with colleagues from the Institut de Mathématiques de Toulouse and INSA, Toulouse. If a student with an interest in lab work is selected s/he s/he will spend more time in the lab at the IGC and will then have the possibility to do field work in Madagascar (if the covid situation allows, and the project requires it) or with colleagues from the Evolution & Diversité Biologique, lab in Toulouse.

Brief description of the experimental approach

The scientific methods/approaches used during the project will depend on the background and interest of the student (laboratory genetic analysis, data analysis, simulations and statistical modelling). Biology students should not be worried by the statistical and theoreticals aspects whereas physicists and mathematicians should not fear the lab and biological or field work aspects. Students should focus on the parts that attract them. The project is flexible.

Below are thus briefly described the different types of tasks. The final candidate is expected to perform one or two of them (for instance field work + data analyses, or field work + modelling, or field work + lab work + modelling, etc.):

1.  Field work: The field work is carried out in the north and northwest of Madagascar in collaboration with Prof Solofonirina RASOLOHARIJAONA from Mahajanga University, and Emmanuel Rasolondraiube who manages the field work teams)
2. Lab work: once the samples are obtained, they are sent to the IGC where DNA is extracted. Genomic analyses are mostly but not only outsourced. PCR is mainly used to amplify DNA for mitochondrial for species identification and to study genetic diversity across the species range. Genetic analyses are also carried out from either faecal samples (with specifically designed technique).
3. Data analysis: Genetic and genomic data are routinely analysed using classical population genetics software to quantify diversity within forest fragments and differentiation between them. Geographical Information System (GIS) modelling is also used to map diversity and distribution together with forest types and other geographical features (roads, rivers, villages, etc.). Genomic data are also used to infer important aspects of the species demographic history (bottlenecks, expansions, etc.).
4. Modelling: we collaborate with O: Mazet from Istitut de Mathématiques de Toulouse to develop methods and software to analyze genetic and genomic data. We use modelling approaches to infer parameters of the demographic history of populations. For instance, we aim at determining whether the patterns of genetic diversity found in endangered species are influenced by recent anthropogenic changes (deforestation) or by ancient changes such as climatic changes that have taken place in the Indian Ocean in the last 10 000 to 100,000 years. We also ask how different models of human evolution, including Neanderthal admixture, can explain genomic diversity.

The candidate is expected to be strong in (or strongly motivated by) at least one of these aspects of the work. Candidates will be offered the possibility to learn about the others, if they wish to.

Lay summary/ Impact of the study:
Madagascar is famous worldwide for its unique biodiversity and for the negative impact that humans have had on its environments. Even though humans arrived on the island less than 3000 to 10,000 years ago it is believed that they drove to extinction many species that were endemic to Madagascar including such species as the elephant-bird, pygmy hippopotamus, and giant lemurs. The impact of humans on Madagascar probably increased around 1000 years ago, and later when the French colonized the island causing major changes in agricultural practices. This continued in the 20^th century due to the demographic increase from less than 3 million people in 1900 to 27 million today. The exploitation of natural resources by foreign companies and local populations has led to an increased deforestation of the island and many forest-dwelling species are now threatened. Lemurs are forest-dwelling primates and are thus particularly affected by forest degradation. They are unique to Madagascar and include some of the most threatened primate species in the world. It is estimated that more than 94% of the lemur species are endangered. Twenty years ago, it was believed that there were only 34 lemur species whereas now ~110 species are recognized. This means that for most of these new lemur species even the most basic data on their ecology, distribution and population sizes are to a large extent absent. The consequence is that to improve their conservation status (critically endangered, threatened, vulnerable, etc.) it is necessary to collect new information. We have also no data on the genetic diversity of most lemur species and on how this diversity has been shaped by past and on-going environmental changes events. In parallel to the work carried out in the field in Madagascar, we have been increasingly interested in determining whether genomic diversity can be interpreted in a framework involving populations that have seen their connectivity vary through time. Our work suggests that some features of genomic diversity found today in many endangered species are better explained by models of population structure rather than models involving population size changes. We work in collaboration with mathematicians from Toulouse, and study the properties of genomic data under complex demographic models. Altogether we want to build a general framework that will help researchers better understand genomic data from populations of many species. We will obtain new data on several species of lemurs and small vertebrates that live in the north and northwest of Madagascar. The new data will be very important to update their conservation status, which defines how they can be protected. Finally, in a period global change, our work will provide important insights into the long-term genomic effects of ancient climatic changes.

Leading Researcher: Luís Teixeira and Lounès Chikhi, Instituto Gulbenkian de Ciência
Website

External Collaboration:
Julien Cote, Universite Toulouse 3 Paul Sabatier/ Station d’Ecologie Théorique et Expérimentale (SETE) UMR CNRS-UT3 5321
Country: France
Duration: 2x 2months

Abstract:
Drosophila melanogaster development and physiology is dependent on its interaction with microorganisms, including yeasts and bacteria. We have isolated and identified hundreds of bacterial strains of the Acetobacter genus associated with the gut microbiota of wild flies. These isolates show variation in their impact on the host development and in their capacity to colonize the gut of the fly. Some are very efficient in this colonization and in their capacity to promote the development and fertility of D. melanogaster. This led us to propose that D. melanogaster farms beneficial bacteria by carrying a stable gut colonizing bacteria population in them and spreading them as it lays eggs, thus promoting the development of the next generation. Therefore, it would be advantageous to carry gut colonizing bacteria in an ecological scenario where D. melanogaster explores its environment. In this project we will test this hypothesis by comparing the fitness of fly populations with and without gut colonizing bacteria in field conditions.

Brief description of the research approach

In this project we will test in lab conditions, at IGC, the capacity of different Acetobacter isolates to colonize the gut, and impact the physiology of D. melanogaster in terms of development time and fertility. Simultaneously we will sequence the genomes of these isolates to determine their phylogenetic relation and identify genetics differences determining different phenotypes. The main objective is to identify closely related bacteria with a) similar impact on the fly fitness in lab conditions but different capacity of gut colonization, b) similar capacity of gut colonization but differences in the impact of fly development. We will analyse how the different Acetobacter isolates, identified and characterized in the lab, impact D. melanogaster fitness in field conditions. We will perform this at the Metatron, at SETE, a simulator of ecosystems dedicated to the study of ecological processes inside semi-controlled environments. We will release populations of flies, carrying different bacteria isolates, in 100m² outside population cages. Fitness will be assessed by measuring time of development and fertility of these flies, and population growth. We will measure the benefit of these bacteria to flies under dispersal conditions, by manipulating the connection between cages with corridors. Therefore, we will use these semi-field conditions to test if carrying beneficial, gut-colonizing bacteria represents a fitness advantage to D. melanogaster in ecological conditions that include migration. 

Lay summary/ Impact of the study:
Animals live with populations of microbes within their guts, the gut microbiota, that can strongly impact their health. We use the fruit fly to understand basic principles of how the microbiota and animals interact. The fruit fly has a simpler microbiota composition than humans, and has been traditionally used for its powerful genetics. We have been studying in the lab how bacteria can grow in the gut of fruit flies and how it can be beneficial for flies. In this project we want to move from understanding these interactions in controlled lab conditions to studying them in large populations of flies in natural conditions. This is important because it will tell us the real impact of having stable associations with gut bacteria for wild animals. Also, it will help us to establish principles on how to translate lab results to real life conditions.

Bibliography
Pais, I. S., Valente, R. S., Sporniak, M., Teixeira, L. 2018. Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria. PLoS Biol. 16, e2005710

Leading Researcher: Pablo Sartori
Website

External collaboration
Technical University Dresden
Country: Germany
Duration: 1 to 2 months

Abstract:
From chemical pollution to temperature changes, humans are altering the conditions of water around the globe. As consequence, the rich diversity of microbial species that swim in these waters is changing their behaviour. To predict the response of such behavioural shift to environmental changes we need to quantitatively measure microbial swimming behavior in controlled settings at a large and affordable scale. This project aims at developing a low-cost and high-throughput imaging platform capable of imaging in parallel dozens of swimming single-cell organisms in a controlled environment. The platform will be endowed with a software package that computationally processes the data and thus quantifies how environmental changes, e.g. changes in temperature, shape behavioral response. As a test case, we will use this platform to quantify the behavioral space of the phototactic algae Chlamydomonas to changes in light and temperature.

Brief description of the research approach
We will use a low-magnification low-cost objective coupled to a Raspberry Pi camera in a 3D printed mechanical stage to image swimming microbes. Due to the low cost (ca 100EUR) we will parallelize imaging, creating a compact array of dozens of such microscopes automated via microcontrollers.

Lay summary/ Impact of the study:
Human induced environmental changes are affecting the aquatic microbial biosphere. Our platform will allow to obtain large amounts of data of microbial swimming in response to such changes at a low cost. The latter will make our platform available for a wide range of users.

Leading Researcher: Marco Fumasoni, Genome Maintenance and Evolution lab, Instituto Gulbenkian de Ciencia
Website

External collaboration
Andrea Giometto Lab, Cornell University, USA
Duration: 2 months

Abstract:
Advances in comparative genomics are demonstrating remarkable biodiversity in how different organisms perform important cellular functions. Sometimes genes that were considered essential for viability are found missing in newly sequenced organisms, shaking our understanding of essential cellular processes. For instance, proteins required to begin chromosomal DNA replication, and previously considered universal, have been recently found lacking in a group of protists called Carpediemona. How these organisms lost these proteins while keep replicating their DNA remains mysterious. This project aims to experimentally investigate the evolutionary transitions which allow DNA replication mutants to resume cell division and viability.

Brief description of the research approach
Mutants of the gene CDC6, missing in Carpediemona will be generated by genetically manipulating the budding yeast S. cerevisiae. Additional UV mutagenesis will be employed to generate viable suppressors, which will be then experimentally evolved in the lab. The final population of cells, capable of efficiently replicating their genomes in the absence of CDC6, will be sequenced. We will then analyze their genomes to identify adaptive mutations and unveil their mode of chromosomal DNA replication.

Lay summary/ Impact of the study:
This study will reveal alternative strategies that cells can use to initiate chromosomal DNA replication. This will be important to interpret the biodiversity of genome maintenance present in nature, and how it can be evolutionarily achieved. Importantly, inhibitors of DNA replication are vastly used in medical treatments for pathogen infections and in cancer treatment. Understanding how cells resume cell division when the beginning of their DNA replication is impaired will inform about the emergence of resistance to these inhibitors and thus be clinically relevant.