LeishGEM.org

About LeishGEM

LeishGEM (the Leishmania genetic modification project) will use high throughput genetic tools to understand how Leishmania parasites are such successful pathogens.

This collaborative project will have two genome-wide reverse genetics screens as a foundation, followed up with cutting edge molecular biology, cell biology and data science.

LeishGEM will determine which proteins are needed for Leishmania parasites to progress through their life cycle and survive in their hosts, which stages they're important for and where they are found in the cell.

This approach will not just find important proteins, it will find the most important proteins. We can then start assembling this knowledge to find the most important pathways for pathogenicity.

The two genome-wide screens which are the LeishGEM foundations will also be community resources: Deletion bar-seq and Leishtag. These will transform our understanding Leishmania molecular cell biology. 

Deletion bar-seq

This sub-project will will generate deletion mutants for every Leishmania protein-coding gene, with each mutant carrying a unique genetic barcode. We will put pools of these mutants through series of assays in host organisms, host cells or in vitro imitations of host environments, then sequence the barcodes in the population (bar-seq) to determine which genes are required under each condition. It builds on the success of our previous, smaller, bar-seq experiments to understand Leishmania molecular cell biology (Beneke et al. 2019, Baker et al. 2021).

The deletion bar-seq fitness data will be made available as it is generated. This will become a genome-wide database of quantitative parasite fitness defects across multiple in vitro and in vivo conditions caused by deletion of a gene. The approximately 170 pooled populations of 48 barcoded deletion mutants, together covering the entire genome, will be cryopreserved as a resource for the future.

LeishTag

LeishTag will determine the subcellular localisation of Leishmania proteins, prioritising proteins which appear to be recent evolutionary adaptations in Leishmania or identified as important for pathogenicity by deletion bar-seq. This will be supplemented with LOPIT-DC evidence. It builds on to the success of TrypTag, carried out in the related parasite Trypanosoma brucei and prioritises genes not conserved in T. brucei.

The LeishTag data will be made available as it is generated on LeishTag.org. This will be a database of microscope images of the promastigote and amastigote life cycle stages and annotations of the protein subcellular localisation.

Jobs

We are currently hiring for 5 posts. Informal enquiries welcome.

Location

LeishGEM is a collaborative project being carried out primarily in the UK. There are three key sites.

Glasgow

Gluenz lab (Wellcome Centre for Integrative Parasitology, University of Glasgow)

Eva Gluenz's group will have a main focus on the cell biology of Leishmania mutants in vitro. Bar-seq deletion mutant generation and in vitro phenotyping will be carried out here.

York

Mottram lab (in the York Biomedical Research Institute, University of York)

Work in Jeremy Mottram's group will focus on understanding the interaction of the Leishmania parasite with its host. Bar-seq deletion in vitro and in vivo phenotyping will be carried out here, as will the LOPIT-DC contribution to LeishTag.

Oxford

Sunter lab (Department of Biological and Medical Sciences, Oxford Brookes University)
Wheeler lab (Peter Medawar Building for Pathogen Resarch, University of Oxford)

The Oxford-based research groups will focus on subcellular protein localisation. Jack Sunter's group will focus on microscopy of Leishmania and will host the LeishTag sub-project. Richard Wheeler's group will focus on computational analysis and integration of the different data types from the different LeishGEM sites.

Other collaborators

Collaborators will include Petr Volf (Charles University, Prague) for work in the sandfly vector and Samuel Dean (University of Warwick) for his expertise from TrypTag.

Open positions

Post-doc (University of Glasgow)

This researcher will take a leading role in the generation of barcoded deletion mutants and in designing and carrying out in vitro phenotyping assays to determine the fitness of mutants, together with the research assistant. This role will involve collaboration on phenotyping data analysis with other partners in the project and it will provide opportunities to develop and pursue individual projects that address specific biological questions linked to the wider research interests of the lab.

Apply here (closed 22 April 2021)

Please send enquiries to: eva.gluenz@glasgow.ac.uk

Research assistant (University of Glasgow)

This research assistant will be responsible, together with the post-doc, for the high-throughput generation of barcoded deletion mutants, involving molecular biology and parasite cell culture.

Apply here (closed 22 April 2021)

Please send enquiries to: eva.gluenz@glasgow.ac.uk

Post-doc (University of York)

This researcher will carry out in vitro and in vivo phenotyping assays for the bar-seq library to determine the fitness of mutants. He/she will also develop LOPIT-DC proteomics of Leishmania infected macrophages to contribute to LeishTag validation. This role will involve collaboration on phenotyping data analysis with other partners in the project and it will provide opportunities to develop and pursue individual projects that address specific biological questions linked to the wider research interests of the lab.

Apply here (closed 2 May 2021)

Please send enquiries to: jeremy.mottram@york.ac.uk

Research assistant (Oxford Brookes University)

The primary role of this research assistant will be the high-throughput generation of the protein subcellular localisation data, involving molecular biology, parasite cell culture and microscopy. In addition, there will be opportunity for phenotype analysis with other partners towards the end of the project.

Apply here (closed 23 May 2021)

Please send enquiries to: jsunter@brookes.ac.uk

Post-doc (University of Oxford)

The primary role for this post-doc position will be analysis, visualisation and enabling access to the genome-wide data from LeishGEM (deletion bar-seq, LeishTag). Wider roles include incorporating other data (bioinformatic predictions, phylogenetic analysis and existing protein localisation databases) to add value to LeishGEM datasets and build evidence for important functional cohorts of proteins for pathogenicity which can then be experimentally tested. This is a primarily computational role.

Apply here (closed 4th June 2021)

Please send enquiries to: richard.wheeler@ndm.ox.ac.uk

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LeishGEM is funded by a Wellcome Trust Collaborative Award.