MSc Projects

Every year, several master students join the Institute to develop their master research thesis in one of IGC labs. It is a unique opportunity to get involved and contribute to the research of this international institution, recognized for its research, education and training.

 

 

IGC laboratories welcome students from various universities to develop the Master’s project within the scope of their thesis.

Master students can apply for one of the listed projects. Alternatively, if your interest belongs to another topic, visit our Research Groups and send an application to the Principal Investigator (PI).

 

Eligibility

In order to be eligible to apply, you must be registered with a university on an MSc Degree.

 

To apply

Please contact the chosen project advisor directly through the respective email, with a copy in cc to:  [email protected] and subject title ‘MSc project application’, sending the following documents: 

  • Motivation letter
  • Curriculum vitae

 

Supervisors and projects

List of supervisors and project titles currently accepting students:

Title: Identification of new players in centriole biogenesis

Supervisor: Mónica Bettencourt-Dias and Mariana Lince-Faria

IGC Group: Cell Cycle Regulation Lab

E-mail: [email protected] 

Abstract: Centrioles are subcellular structures essential for the formation of cilia and centrosomes, structures existent in the majority of our cells. Misregulation of the biogenesis of these structures is associated with human disorders such as retinal degeneration, infertility, cystic kidney disease and cancer. The molecular mechanisms regulating centriole biogenesis have only recently started to be unravelled, opening new ways to answer a wide range of questions that have fascinated biologists. A hypothesis-driven siRNA screen previously performed by our lab identified a set of new genes involved in centriole biogenesis. This project aims at the validation of some of the identified candidates. Using different techniques as siRNA mediated gene-knockout in mammalian cells, fluorescence microscopy, Super-resolution microscopy, Expansion microscopy, Western Blot analysis and Drosophila melanogaster genetics, we want to understand the mechanisms of centriole biogenesis regulation as well as its conservation along different species of the eukaryotic kingdom.

Title: Ecology and Evolution in the Gut Microbiome

Supervisors: Isabel Gordo

IGC Group: Evolutionary Biology

E-mail contact: [email protected] 

Abstract: The mammalian gut is home to thousands of species and its diversity is a biomarker of health. In this project we use mice as a model system to understand how dynamic is the gut microbiome and how newly colonisers of the gut evolve. We are interested to discover conditions, such microbe-microbe competition and/or diet supplementation capable of lowering the ability of antibiotic resistant bacteria to persist in the gut. (See Cardoso, Durao, Amicone and Gordo 2020, Nature Ecology & Evolution).

Title: What sets up the asymmetry for early neurogenic divisions in the vertebrate retina?

Supervisor: Caren Norden and Elisa Nerli

IGC Group: Cell Biology of Tissue Morphogenesis

E-mail: [email protected] and [email protected]

Abstract: One fundamental question in developmental biology is how single cells develop into a multicellular organism. Within this process, the generation of cellular diversity is crucial for correct formation and functionality of different organs. The central nervous system is an example in which this diversity is crucial for building neuronal networks and complex functions. To build functional networks, multipotent progenitor cells need to give rise to the correct types of neurons in the proper proportions and with the right timing, while, at the same time, the tissue is still growing. Elucidating these processes requires understanding of how progenitors enter lineage decisions to produce the different neurons at precise timepoints, and how stereotypic these decisions are. To contribute to this question, we focus on the quantitative analysis of a neurogenic lineage in the zebrafish retina, the Ath5 lineage. We use live imaging to perform in vivo lineage tracing of Ath5+ progenitors. Within this lineage, we investigate the outcome of two consecutive cell divisions to understand which fate decisions progenitors make, how plastic or stereotypic they are and what regulates them. Overall, this contributes to understanding how progenitors enter the neurogenic path and form the correct types of neurons at the right time. Two types of projects would be available in this framework to be discussed with potential candidates.

Title: Modifiers of sister chromatid cohesion loss

Supervisor: Raquel Oliveira

IGC Group: Chromosome Dynamics

E-mail: [email protected]

Abstract: Sister chromatid cohesion is essential for faithful mitosis, as premature cohesion loss leads to random chromosome segregation and aneuploidy, resulting in abnormal development. To identify specific conditions capable of restoring defects associated with cohesion loss, we screened for genes whose depletion modulates Drosophila wing development when sister chromatid cohesion is impaired (a first report on the results of this screen can be found here ). This project aims to validate other hits arising from this screen with regard to their ability to modulate defects associated with sister chromatid loss.

Title: Protein complexes by the numbers

Supervisors: Pablo Sartori

IGC Group: Living Physics

E-mail: [email protected]

Abstract: Proteins are the fundamental building blocks of cells. Yet, in order to carry out their function, proteins self assemble into higher order structures referred to as protein complexes. One fundamental difficulty in studying protein complexes is their large diversity. Some complexes, such as microtubules, are polymeric. Others, such as RNA polymerases, grow to well defined size and composition. Some, such as the proteasome, are highly symmetric; whereas others, such as the ribosome, exhibit no symmetries. Similar diversity exists in their kinetics, energetics, composition, etc. In this project we will quantify the above properties of protein complexes by analyzing publicly available databases, curating literature, and doing back of the envelope estimates. Our goal is to come up with a map of the ensemble of protein complexes, and populate it with few representative examples.

Title: Ironing out the details of myeloid ferritin in the control of organismal homeostasis

Supervisors: Miguel Soares and Rui Martins

IGC Group: Inflammation

E-mail: [email protected]

Abstract: Myeloid cells, such as monocyte/macrophages play a central role in the maintenance of organismal homeostasis, beyond their well-described innate immune functions. This is illustrated for example in the context of iron metabolism, where tissue-resident macrophages recycle up to 95% of the iron required to sustain erythropoiesis. The iron is acquired and extracted from the prosthetic heme groups of hemoglobin through erythrophagocytosis of senescent red blood cells (RBC) by tissue-resident macrophages in the spleen and liver. Iron is than exported from macrophages via ferroportin or stored inside ferritin, a multimeric protein composed of 24 heavy/heart chain (FtH) and light/liver chain (FtL) subunits. Expression of FtH plays a non-redundant physiologic role during embryonic development, and as such its constitutive deletion is embryonically lethal. Our group recently revealed that conditional deletion of FtH in adult mice using a tamoxifen-inducible R26CreERT2FtHlox/lox (FtH∆/∆) mouse model, leads to a fast loss of body weight andtemperature with concomitant disruption of energy homeostasis, mitochondrial function, and organ dysfunction ultimately leading to death. Recently, we found that the lethality of FtH∆/∆mice is rescued upon bone marrow transplant of cells expressing normal levels of FtH, which is sufficient to maintain body weight and temperature, and fully support organismal homeostasis. Furthermore, this rescue effect is dependent on the expression of FtH by myeloid cells (e.g. macrophages), as the transplant of bone marrow cells lacking expression of FtH in either LysM or Cx3CR1 lineages is not able to rescue the mice from tamoxifen-induced FtH deletion and subsequent loss of organismal homeostasis and death. This surprising observation indicates that FtH expression by cells of myeloid lineage is sufficient to maintain organismal homeostasis in mice following inducible FtH deletion. Our work is now focused on understanding the cellular and molecular basis of how myeloid- expressed ferritin is able to sustain energy and organismal homeostasis. For this project, we willreconstitute FtH∆/∆ mice by transplanting bone marrow cells from reporter mice where LysM+cells are tagged with a fluorescent protein (dTomato). This will allow us to initially characterize the FtH-expressing cell population responsible for the rescue effect using multi-color flow cytometry followed by single-cell sorting and RNAseq analysis of sorted dTomato+ cells to understand the transcriptional programs underlying the rescue effect upon tamoxifen-induced FtH deletion.

Title: Haematopoiesis in Drosophila: mechanistic control of haemocyte proportions during larval development

Supervisor: Élio Sucena

IGC Group: Evolution and Development

E-mail: [email protected]

Title: Chasing the genetic bases of resistance and tolerance in Drosophila melanogaster

Supervisor: Élio Sucena

IGC Group: Evolution and Development

E-mail: [email protected]

Title: Optimization of Sample Processing for Electron Microscopy

Supervisor: Erin Tranfield

IGC Group: Electron Microscopy Facility E-mail contact: [email protected]

Abstract: Sample processing for Electron Microscopy is a technique that is surrounded by habit and old standard conventions. There are a lot of reports in the literature of different protocols, but it is hard to know which protocol is the best for a given sample when there have never been side by side comparisons of conditions. The purpose of this Masters project will be to compare different methods of sample preservation on the same sample(s) and to evaluate the effectiveness, and overall quality of ultrastructural preservation. There are many different conditions that can be tested and many different models that can be used so the specifics of this project will be discussed between the PI and the student to see what is most interesting for the student. This project would be excellent for a chemistry student interested in learning more about biology or a biology student interested in learning more about the chemistry behind sample preservation and fixation.

Title: Comparative demography of endangered species using genomic data

Supervisors: Lounès Chikhi, Olivier Mazet and Beatriz Mourato

IGC group: Population and Conservation Genetics (Collaboration with “Institut de Mathématiques de Toulouse”, Toulouse, France)

E-mail contact: [email protected] ([email protected], [email protected])

Abstract: Genomic data have become increasingly available for many taxa including endangered species. In addition, the computational methods used to reconstruct the recent evolutionary history of species from genomic data have become increasingly sophisticated. However, despite the increasing amount of data, most studies focus on one species making it difficult to determine whether the history reconstructed informs us only on that particular species or provides a general information on past changes in habitat or on the influence of human populations on endangered species. Comparative studies are crucially needed but difficult to carry out. In our group we are studying how models of population structure influence the inference of the demographic history of species. In this project the student will analyse in close collaboration with the supervisors the properties of genomic data from species living in the same habitats. We will compare the results of computer simulations and real data from endangered species from the same or neighbouring regions for which genomic data are available. We are thus looking for a candidate who would like to explore with us the properties of past changes in connectivity on genomic data from co-distributed endangered species. The candidate will perform coalescent simulations under varying scenarios (using scripts that have been already developed in the team, she/he will also be able to develop her/his own depending on her/his interests). Simulations will be compared to real data sets from endangered species. More specific details of the project will be discussed with the candidates, as this is an ongoing project.

Title: Testing the confounding impact of sampling schemes and spatial structure on signals of population size change and admixture

Supervisors: Lounès Chikhi and Rémi Tournebize

IGC group: Population and Conservation Genetics

E-mail contact: [email protected] ([email protected])

Abstract: A major interest in population genetics is to reconstruct the demographic history of species using genetic data. Yet, although species evolve in space and time, a large amount of research largely oversees the importance of space. Consequently, several methods used to reconstruct that history assume that population structure, including spatial structure, can be neglected. In other words individuals are analysed as if they were sampled from large populations (often representing continents) wherein individuals reproduce freely without considering spatial distances. By ignoring spatial structure (i.e. the heterogeneous geographic distribution of allele frequencies across a species distribution), these methods can produce results that are interpreted in terms of population size change, admixture or selection when spatial structure might be a contributing factor. Our team is interested in the use of alternative models of species demography that integrate population structure. Previous research suggests that spatial structure can generate signatures that are interpreted as admixture by several commonly used tests or statistics such as the ABBA-BABA test. Still several studies have identified admixture events in lemurs or humans on the basis of this test. In this project the student will carry out spatial simulations in close collaboration with the two supervisors to study the properties of this and other statistics in models with and without admixture. We are thus looking for a candidate who would like to explore with us the properties of spatial processes with applications in endangered species or in the human species. The candidate will perform coalescent simulations under varying scenarios (using scripts that have been already developed in the team, she/he will also be able to develop her/his own depending on her/his interests). Simulations will be compared to real data sets from endangered species or from humans. More specific details of the project will be discussed with the candidates, as this is an ongoing project.

Title: Regulation of stem cell centrosomes during ageing

Supervisors: Pilar Okenve-Ramos / Mónica Bettencourt-Dias 

IGC group: Cell Cycle Regulation, Insitituto Gulbenkian de Ciência, Oeiras

E-mail contact: [email protected]

Abstract: With an increasing older population, age is the main risk factor for multiple debilitating and deadly diseases, such as dementias or cancer. Each tissue and cell type can react differently to the same insults to maintain homeostasis. For instance, certain adult tissues have active stem cells which ensure, by asymmetrically dividing, both self-renewal and the production of new young differentiated cells, regulating the homeostasis of the tissue. But with age also stem cells get affected, with Intestinal Stem Cells for instance, over-proliferating and leading to dysplasia, inflammation or commensal dysbiosis. An essential organelle, which regulate the asymmetric division and impacts on stem cell proliferation or quiescence state, are centrosomes. We propose to study the effects of ageing and one of its main primary hallmarks (autophagy dysfunction) in centrosomes in two active stem cell types in the adult fly (Drosophila). The project will involve fly genetics, cell biology and microscopy, including live imaging and super-resolution. With this project we will further our understanding on centrosome maintenance and their dysfunction, and their contribution to ageing.

Title: Role of DNA repair mechanisms in budding yeast karyotype evolution

Supervisors: Marco Fumasoni

IGC group: Genome Maintenance and Evolution

E-mail contact: [email protected]

Abstract: Karyotype, the physical organization of the genetic material into chromosomes, is a characteristic property of a species.  Changes in karyotype can play an important role in the evolution of eukaryotic organisms as they can constitute a barrier to sexual reproduction. Which forces drive karyotype evolution and which mechanisms dictate the optimal number of chromosomes for a given species remain unanswered questions, especially because of the shortage of experimental approaches available. Recently, CRISPR technology has been used to engineer budding yeast cells carrying the 12Mb genome, usually organized in 16 chromosomes, in progressively fewer number of larger chromosomes. Strains having a single chromosome have been shown to have cellular fitness and transcription profiles remarkably similar to wild type cells carrying 16 chromosomes. This suggests how, under optimal laboratory conditions, largely different karyotypes are equally sustainable in buddying yeast. We propose that despite these similarities, different karyotypes will severely impact cell’s ability to repair DNA lesions and we hypothesize that strains with different number of chromosomes will behave substantially different under genotoxic conditions. To investigate this hypothesis, we will take advantage of the recently generated panel of S.cerevisiae strains carrying different karyotypes and use a combination of genetics, cell biology and experimental evolution approaches. The results obtained from this project will help to elucidate the forces determining the optimal number of chromosomes in yeast and increase our understanding of karyotype evolution.

 

Please check our website for research interests and recent work from the various groups.

 

MSc Project Committee: 
Ricardo Henriques
Vera Martins
Elias Barriga
Maria João Amorim (consultant)
Gabriel Martins (consultant)

 

More information:
[email protected]
Tel: +351 214 464 549