Overview

Stefano Pagliara studied Physics at the University of Salento (Italy) where he also obtained a PhD in Nanoscience applying physical and engineering tools to biological problems such as biomineralization. Stefano then moved to the the Cavendish Laboratory, University of Cambridge, where he carried out post-dotoral research on membrane transport. In 2013 Stefano obtained a Leverlhulme Early Career Fellowship to carry out research on antibiotic accumulation in individual bacteria. In 2014 he moved to the University of Exeter where he is now a Senior Lecturer leading a group based in the Living Systems Institute and working on phenotypic heterogeneity. 

Single-cell biology

We have recently begun to understand that there are important differences between cells which have the same genetic make-up. Therefore, we need to study the behaviour of thousands individual cells within a population, this requiring the development of single-cell technologies including novel microfluidic and imaging tools. Our research group uses these tools to understanding how individual cells within a population specialise to perform specific functions with an emphasis on their capabilities to exchange molecules with their environment and with other cells. Our aims are:

1. To determine the environmental factors and the molecular mechanisms underlying heterogeneity in molecular uptake in unicellular organisms such as bacteria, fungi and mammalian cells.

2. To elucidate the mechanisms underlying survival to antimicrobials of subsets within clonal microbial populations.

3. To understand the dynamics of inter-species interactions at the scale of the individual cell, particularly between the host and its pathogen as well as between symbionts.

4. To investigate how ageing shapes the composition of clonal microbial populations.

Qualifications

Master in Physics, University of Salento, Lecce, Italy (2006)

PhD in Nanoscience, University of Salento, Lecce, Italy (2010)

Career

Sep 2010 - Sep 2013 Postdoctoral research associate, Cavendish Laboratory, University of Cambridge

Oct 2013 - Sept 2014 Leverhulme Early Career Fellow, Cavendish Laboratory, University of Cambridge

Sep 2014 - Oct 2014  Non-stipendiary Fellowship, Clare Hall, University of Cambridge

Oct 2014 - Sep 2016 Leverhulme Early Career Fellow, Biosciences, University of Exeter

Oct 2016 - Sept 2017 Lecturer, Biosciences, University of Exeter

Oct 2017 - July 2022  Senior Lecturer, Living Systems Institute, University of Exeter

Aug 2022 - Date         Associate Professor, Living Systems Institute, University of Exeter

Links

• Pagliara group website

Research group links

• Microbial Evolutionary Ecology

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Research

Research interests

1. Membrane transport

Molecular exchange across cellular membranes is at the basis of life and has been investigated via ensemble measurements. Our research sheds new light on the heterogeneity of molecular uptake within populations of bacteria with the same genetic makeup which is paramount for improving drug therapy and the yield of food production.

2. Host-pathogen interactions

Individual cells interact with their neighbours in a variety of different ways both beneficial and detrimental for the wellbeing. Our research focuses on the study of the relationship between bacteria and their bacteriophage which is relevant for next generation phage therapy as well as the interaction between microalgae and bacteria and viruses associated to their surface which is crucial for achieving a better understanding and a tighter control of algal blooms.

3. Drug efficacy

Antibiotics play a fundamental role in modern medicine, but drug-resistant pathogens now exist for all known antibiotics. In combination with a major void in antibiotic discovery, this has led to predictions that bacterial infections will cause 10 million premature deaths annually by 2050. Our research tackle this crucial societal issue by quantifying both the uptake of existing and novel drugs in individual bacterial pathogen as well as the efficacy of such drugs in completely clearing out a bacterial infection.

4. Ageing

Ageing is the decline in reproductive success and survival with advancing age and has been well documented across a diverse range of multicellular organisms  where it is thought to arise from the progressive accumulation of defects. Our research investigates the mechanisms underlying the natural course of ageing in unicellular organisms, such as bacteria, in the absence of external stressors.

Research projects

Research themes

• Understanding the role of membrane transport in pharmacotherapy
• Novel polypeptide therapeutics for gram-negative infections
• A biophysical approach to identify genes underlying antibiotic tolerance
• Developing microfluidic platforms to fight bio-threats
• Transporters in uncultivated marine microbes
• Host immunosuppression by anti-CRISPR phages

Prospective Interdisciplinary PhD Projects

Tackling antibiotic resistance by measuring and modelling the uptake of viruses and antibiotics in single cell (co-supervised with Prof Krasimira Tsaneva-Atanasova)

This interdisciplinary project will provide novel understanding on the biological mechanisms underlying antibiotic and phage uptake in gram-negative bacteria which is paramount for our battle against infectious diseases. In this project we aim to quantitate the accumulation of antibiotics and bacteriophage in gram negative species such as Escherichia coli and Pseudomonas aeruginosa, combining fluorescent drug derivatives, stained phage and single-bacterium imaging. These data will be rationalised by using a mathematical model that describes the temporal changes in antibiotic or phage concentration in single bacteria and will inform how phenotypic heterogeneity, in both the bacterial and phage populations, impacts on population and evolutionary dynamics. Taken together the information unlocked using this novel combination of experiment, modelling and statistical inference will be essential for the rational design of the next generation of therapeutics against infections caused by gram-negative pathogens.

Bioengineering lineage segregation from human naïve stem cells to recapitulate early human development (co-supervised with Prof Austin Smith)

This project is a fusion of stem cell biology with bioengineering and physics of living systems. The aim is to engineer formation of a blastocyst, the paramount structure in development of the early mammalian embryo. To achieve this we will use human naïve stem cells, which have the capacity to produce all types of cell. In order to regulate and organise differentiation precisely in four dimensions, a combination of chemical and mechanical cues will be applied to defined numbers of stem cells confined within microfluidic chambers. Morphological, cellular and molecular criteria will be applied to evaluate blastocyst structures generated from naïve stem cell building blocks. Finally, the effects of specific genetic and environmental perturbations will be interrogated by real-time imaging and single cell ‘omics.

Modelling the mechanisms that allow bacteria to change shape in response to the environment (co-supervised with Dr David Richards)

This project will use a combination of mathematical modelling and wet-lab experiments to investigate the shape of cells. In particular, you will determine how bacteria change their shape in response to different environments. This will involve (i) writing simple mathematical models of cell shape, (ii) computationally simulating these models, (iii) obtaining real time-lapse microscopy images of how bacteria respond to a variety of environments, and (iv) designing image analysis software to automatically extract the cell shape from these images. This is an excellent opportunity to learn both the experimental and modelling sides of modern research, ideal for a future career in academia or elsewhere. You are not expected to already know both mathematical modelling and wet-lab techniques; full training will be provided in both areas during the PhD.

Funding

• BBSRC Responsive Mode Award - Anti-CRISPR phage therapy
• BBSRC TDRF - Phytofluidics
• Gordon Betty Moore Foundation Project Grant - Membrane trasnport in the sea
• MRC Proximity to Discovery Award - Novel peptides to overcome antibiotic tolerance  
• Leverhulme Trust Early Career Fellowship - Single-cell membrane transport

Links

• Exeter antimicrobial resistance website
• SINGEK Marie Curie Network
• INNOGLY Cost Action
• Pagliara group website

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Publications

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Teaching

This course is part of the Bio3073 module Specialist Topics in Chemical Sciences. The course focuses on molecular exchange across cellular membranes which is one of the most fundamental phenomena in biology. Life relies on the delicate balance between influx and efflux processes: cells survive if they are able to keep the intracellular level of accumulated poisonous molecules below a toxic threshold while obtaining a quantity of nutrients sufficient for subsistence. This course reviews the structure and composition of the lipid bilayer as well as the repertoire of membrane proteins that function as molecule transporters in prokaryotic and eukaryotic cells. The course will cover the main mechanisms underlying molecular transport across biological membranes including passive diffusion, channel-facilitated diffusion, primary and secondary active transport. The course concludes with a theoretical workshop on the state-of-the-art technologies for studying membrane transport and a practical workshop on investigating membrane transport by using the microfluidics and microscopy facilities available at Exeter.

Microfluidics and Lab-on-a-Chip Technologies

This course is part of the NSCM006 Module Further Advanced Topics in Chemistry. The course introduces cutting-edge technologies intersecting chemistry, physics and biotechnology that have become pivotal to molecular biology, DNA analysis and point-of-care diagnosis of diseases. The course covers the theoretical and experimental basis of microfluidics including the physical laws governing the movement of fluids at the micro- and nano-scale and some of the most relevant applications of lab-on-a-chip technologies. The course concludes with a theoretical workshop on the state-of-the-art of microfluidics and a practical workshop hands-on the fabrication and handling of microfluidic devices in the lab where students get to make their first microfluidic chips.

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Supervision / Group

Postdoctoral researchers

Postgraduate researchers

Alumni

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