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Developing new approaches for the single cell manipulations and experimentation

Scientific meeting

Location

Kavli Royal Society Centre, Chicheley Hall, Newport Pagnell, Buckinghamshire, MK16 9JJ

Overview

Satellite meeting organised by Professor Thomas Richards, Dr Ramon Massana and Professor Neil Hall

Monolayer of bacteroidetes cells (false coloured blue) on the surface of the parabasalian protist Barbulonympha. © K Carpenter and P Keeling (University of British Columbia).

Single cell approaches are changing how we study many biological problems. This meeting will bring together biophysicists, molecular biologists and microbial ecologists who are using these technologies to understand the natural world. The aim of this satellite meeting is to report progress, identify areas for synergy and lay down the foundations for further developing this interdisciplinary science.

The schedule of talks and speaker biographies are below. Speaker abstracts will be available closer to the meeting. Recorded audio of the presentations will be available on this page after the meeting has taken place.  

Poster session

There will be a poster session at 16:15 on Wednesday 12 December. If you would like to apply to present a poster please submit your proposed title, abstract (not more than 200 words and in third person), author list, name of the proposed presenter and institution to the Scientific Programmes team with the subject heading "Single cell new approaches: poster abstract" no later than Monday 22 October 2018. Please note that places are limited and posters are selected at the scientific organiser's discretion. Poster abstracts will only be considered if the presenter is registered to attend the meeting.

Attending the event

This is a residential conference, which allows for increased discussion and networking.

  • Free to attend
  • Limited places, advanced registration is essential (request an invitation)
  • Catering and accommodation available to purchase during registration

Enquires: Contact the Scientific Programmes team.

Event organisers

Select an organiser for more information

Schedule of talks

12 December

09:00-12:30

Session 1

5 talks Show detail Hide detail

Chairs

Dr Ramon Massana Institute of Marine Sciences, CSIC, Spain

09:05-09:30 Single cell approaches to study microbe-microbe interactions

Dr Stefan Bertilsson, Uppsala University, Sweden

Abstract

Microbial interactions are central in governing and controlling microbial community composition and function. Yet the bulk approaches normally applied are likely to overlook these interactions that are typically manifested at the microscopic scale. Applying single cell genome sequencing approaches can to begin with help us describe the metabolic capabilities of the largely unculturable natural microbial communities, and with sufficient coverage also identify auxotrophies and metabolic dependencies. Furthermore, when single cell genomics methods are also applied to physically associated cells, we can begin to infer functional interactions from such linkages and combine this information with genome-encoded functional potential. Here Stefan will discuss and present preliminary data highlighting both challenges and opportunities in these and related approaches and provide my personal view on ways to better understand microbe-microbe interactions in the uncultured majority.

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09:45-10:15 Are single-cell approaches useful for evolutionary questions?

Dr Iñaki Ruiz-Trillo, Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Spain

Abstract

Single-cell genomics is a powerful method to get genomic data from uncultured organisms. However, the genome data generated for eukaryotes are usually less than 50% of the genome. The question is then whether this is useful for evolutionary questions. By obtaining single-cell genomic data from three choanoflagellates, Iñaki Ruiz-Trillo investigated whether this methodology can provide valuable data for evolutionary questions. In particular, and given the phylogenetic position of choanoflagellates as the sister-group to animals, the authors analysed the use of these data to address the origin of animals. The potential and the challenges will be discussed.

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10:30-11:00 Coffee

11:00-11:30 Power and challenges of single cell experimentation for the study of the smallest photosynthetic eukaryotes

Dr Gwenaël Piganeau, CNRS, Integrative Biology of Marine Organisms Lab, France

Abstract

Bacterial-sized unicellular eukaryotes of the class Mamiellophyceae are ubiquitous in the marine environment, where they significantly contribute to the primary production. Their ease of manipulation and compact genomes make them ideal models for benchmarking single cell approaches for phytoplanktonic micro-organisms. During this talk, Gwenaël Piganeau will explain how single cell experimentations enable to address two fundamental issues about the mode and tempo of evolution in these microalgae. First, how the set up of mutation accumulation experiment assays in liquid medium allows the segregation of deleterious and slightly deleterious mutations in individual microalgae cells. Whole genome re-sequencing of these lineages in five phytoplanktonic species enabled the estimation of the genome wide spontaneous mutation rate, the ultimate source of genetic diversity in the fate of environmental change. Second, single cell manipulation is required to estimate the phenotypic diversity within isogenic cells. This is particularly important to understand the mechanisms involved in the resistance of microalga to viruses infecting them, and how this impacts the microalga virus ratio, which influences the carbon flux in the sunlit ocean.

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11:45-12:15 Dissecting trophic interactions among microbes in the ocean

Dr Susanne Wilken, University of Amsterdam, The Netherlands

Abstract

Predatory protists have long been recognised for their role in aquatic food webs, often exerting control on microbial abundance and community structure. Nevertheless, little is known about the relative importance and activity of different predatory groups, let alone the specific predator-prey interactions that drive population dynamics of individual taxa in the ocean. Resolving such interactions is complicated by the extreme diversity of the predators involved, both in terms of their distant evolutionary histories spanning the eukaryotic tree of life, as well as their functional diversity that includes the combination of photosynthetic with predatory nutrition in a mixotrophic lifestyle. Here, single-cell and population level cell sorting based on the presence of acidic food vacuoles were used to identify actively feeding microbes in the NE Pacific Ocean. Prey assimilation by predators feeding on the most abundant photosynthetic microbe Prochlorococcus was further verified by RNA-stable isotope probing. Both of these approaches suggested the quantitative importance of choanoflagellates as microbial predators in both productive coastal and nutrient-poor oceanic waters. Finally, the suitability of transcriptional patterns to indicate a predatory, phagotrophic nutrition will be discussed. Collectively, these approaches help to dissect the diverse trophic roles of microbial eukaryotes that shape the marine carbon cycle.

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12:30-13:30

Lunch

13:30-18:00

Session 2

5 talks Show detail Hide detail

Chairs

Professor Karin Rengefors, Lund University, Sweden

13:30-14:00

Dr Colomban de Vargas, Station Biologique de Roscoff, France

Show speakers

14:15-14:45

15:00-15:30 Tea

15:30-16:00 Understanding microbial interactions with eukaryotes at a single cell level

Dr Alistair Darby, University of Liverpool, UK

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16:15-18:00 Poster session

13 December

09:00-12:30

Session 3

5 talks Show detail Hide detail

Chairs

Professor Neil Hall, Earlham Institute, UK

09:00-09:30 Shaping the environment for single microorganisms

Dr Vicente Fernandez, ETH Zürich, Switzerland

Abstract

Variability between individual microorganisms is driven by both internal factors, such as phenotypic heterogeneity, and external factors, through spatially and temporally stochastic interactions with the environment. As new methods are developed to measure the responses of single cells, it is of equal importance to have flexible and accurate approaches to experimentally manipulate the environment at the single-cell level, in order to mimic or isolate components of their natural habitat. This involves challenges in controlling the chemical composition, temporal dynamics, and spatial distributions at the scale of individual cells. Vicente Fernandez will present new approaches combining microfluidics and image analysis for recreating interactions between bacteria and phytoplankton from aquatic environments, and for further simplifying these interactions to study the behavioural and growth responses of hundreds to thousands of single cells in parallel. These approaches unlock the possibility of understanding and quantifying fundamental marine processes from the perspective of the individual microorganisms that drive them.

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09:45-10:15 Exploring deep opisthokont evolution through single-cell approaches

Dr Purificacion Lopez-Garcia, CNRS - Université Paris-Sud, France

Abstract

Opisthokonts were early recognised as one of the major eukaryotic super-groups based on molecular phylogenetic analyses. They cluster in two major lineages, the Holomycota and the Holozoa, which encompass well known multicellular organisms, respectively Fungi and Metazoa, together with a cohort of unicellular relatives. Phylogenetic and functional analyses have shown that many genes typically involved in metazoan multicellularity were already present in the unicellular relatives of animals. On the holomycotan branch, the situation is complex because the boundaries defining Fungi are fuzzy and, at the same time, environmental 18S rRNA metabarcoding combined with more classical taxonomic studies have revealed a wide diversity of previously unrecognized lineages branching deeply within classical Fungi (osmotrophic lineages, including chytrids) and prior to their divergence (eg, aphelids, rozellids or cryptomycotes, microsporidians, nucleariids). Many of these lineages encompass uncultured species for which gaining information is challenging. Single-cell genomic and transcriptomic approaches offer a suitable solution to fill gaps on our knowledge about early-branching holomycotan lineages. Purificacion Lopez-Garcia will present ongoing studies of her lab to obtain phylogenomic and gene content data with the aim of unraveling hallmark evolutionary processes leading to the evolution of fungi.

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10:30-11:00 Coffee

11:00-11:30

Dr Adam Monier, Living Systems Institute, University of Exeter, UK

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11:45-12:15 Single-cell approaches for investigating planktonic archaea

Dr Alyson Santoro, University of California, Santa Barbara, USA

Abstract

Though archaea have been known in the marine water column for nearly 30 years, many questions remain about their ecology, physiology, and interactions with other members of the microbial community. In particular, the interactions between archaea and eukaryotic plankton are poorly understood. Indeed, aside from the well-known relationship between methanogenic archaea and their ciliate hosts in anaerobic environments, no archaeal symbionts of eukaryotes have been identified. To investigate this, over 400 individual protist cells were isolated using fluorescence-activated cell sorting, genome amplified, and screened for the presence of associated archaea. Despite the identification of multiple protist-bacteria associations, no archaeal-eukaryote relationships were identified. Single-cell amplified genomes (SAGs) of archaeal cells, however, have revealed interesting biogeographic differences in different oceanic regions. Further discussed is the growing availability of metagenome-assembled genomes (MAGs) for planktonic archaea and the relative utility of MAGs versus SAGs for understanding archaeal biogeography and physiology.

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12:30-13:30

Lunch

13:30-17:00

Session 4

5 talks Show detail Hide detail

Chairs

Professor Tom Richards, University of Exeter, UK

13:30-14:00 Improving the read accuracy of Oxford Nanopore Technology sequencers to enable the high-throughput analysis of isoform-level single cell transcriptomes

Dr Christopher Vollmers, University of California Santa Cruz, USA

Abstract

Christopher Vollmers has previously shown that Oxford Nanopore Technology (ONT) cDNA sequencing can uncover transcript isoform diversity in single cells in unprecedented detail. Now, his group has developed a new method to increase the accuracy of cDNA reads generated by the ONT MinION. These more accurate reads can be used to demultiplex high-throughput single cell cDNA libraries and identify base-accurate full-length transcript isoforms. Further, his group has benchmarked this new method by analysing a cDNA pool of 96 B cells and found isoform diversity with potential implications for cancer treatment.

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14:15-14:45 Early metazoan cell type diversity and regulation by single-cell RNA-seq analysis

Dr Arnau Sebé-Pedrós, Weizmann Institute of Science, Israel

Abstract

A fundamental characteristic of animals is their ability to form large cell populations that are capable of cooperating through interaction between different archetypical functional programs, which are sometimes called cell types. The deployment and maintenance of these cell type-specific transcriptional programs is coordinated by transcription factor regulatory networks. However, the phylogenetic relationships and evolutionary dynamics underlying cell type hierarchies and their regulation are poorly understood. To gain insights into this question Arnau’s group profiled thousands of single-cell transcriptomes in the cnidarian Nematostella vectensis and other early-branching animals. The resulting whole-organism cell type classification atlases reveal an unanticipated high diversity of cell types in some of these species, particularly neuronal types. Moreover, the group identifies the gene modules specific to these cell behaviours, as well as the master transcription factors regulating them at different levels of the cell type hierarchy. These results provide the first glimpses to early-multicellular cell type complexity and the regulatory principles that orchestrate it.

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15:00-15:30 Tea

15:30-16:00 Single cell multi-omics: multiple measurements from single cells

Dr Iain Macaulay, Earlham Institute, UK

Abstract

The ability to analyse the genomes, epigenomes and transcriptomes of individual cells has offered a new way in which to explore cellular heterogeneity in a diverse array of living systems. The Macaulay group has focussed on the development of technologies that enable us to explore, in parallel, multiple omic parameters of single cells – enabling combined gene expression and genome sequencing from the same cell. Another major focus of the group's work in this area is the understanding of alternative splicing in individual cells using long-read sequencing. In this talk Iain Macaulay will give an overview of the group’s approaches, how they aim to apply them in a wide array of applications across mammalian, plant and microbial biology.

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16:15-17:00 Panel discussion/overview

Related events

Developing new approaches for the single cell manipulations and experimentation

Satellite meeting organised by Professor Thomas Richards, Dr Ramon Massana and Professor Neil Hall

Kavli Royal Society Centre, Chicheley Hall Newport Pagnell Buckinghamshire MK16 9JJ
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