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Journeys in Science and Enterprise

eSCAMPS

Hughes Hall, Cambridge. 20th September 2024.

About

eSCAMPS is a one-day conference that explores the success stories of leading scientists and students. By combining keynote speakers, panel-led discussions, and speed-dating sessions, we hope to inspire your 'Journey in Science and Enterprise.' 

Keynote Speakers

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Sharon Peacock is Master Elect of Churchill College and a member of Council of the University of Cambridge. She is Professor of Microbiology and Public Health at the University of Cambridge, and Non-Executive Director on the Board of Cambridge University Hospitals NHS Foundation Trust.

 

Sharon has built her scientific expertise around pathogen genomics, antimicrobial resistance, and several tropical diseases. She was the founding Director of the COVID-19 Genomics UK Consortium (COG-UK), formed in April 2020 to provide SARS-CoV-2 genomes towards the UK pandemic response.

 

Prior to this, she dedicated more than a decade to the translation of pathogen sequencing into clinical and public health microbiology, as well as using sequencing to examine the transmission of antibiotic-resistant bacteria between humans, livestock, and the environment.

 

She is a Fellow of the Academy of Medical Sciences, Fellow of the American Academy of Microbiology, an elected Member of the European Molecular Biology Organization (EMBO), and an Honorary Fellow of the Royal College of Physicians (London).

 

Sharon was awarded the Unilever Colworth Prize in 2018 and the Marjory Stephenson Prize in 2023 for outstanding contributions to the discipline of microbiology. Sharon was awarded a CBE for services to Medical Microbiology in 2015, and in 2021 received the Medical Research Council Millennium Medal.

Sharon Peacock

Master Elect of Churchill College, Cambridge

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Jason Mellad

Jason is a scientist and entrepreneur dedicated to transforming innovative technologies into improved patient outcomes.
 

As the CEO and co-founder of Start Codon, an accelerator based in Cambridge, UK, he focuses on identifying groundbreaking healthcare founders and innovations globally.

 

He provides seed funding and utilizes the outstanding resources of the Cambridge cluster to mitigate risks and propel the success of their start-ups.

CEO and Founder of Start Codon 

Highlights

01.

Student presentations

Quotient Therapeutics have kindly donated £200 to be awarded to the person judged best presenter on the day. Details on submissions will be released shortly.

02.

Panels and speed dating 

Discuss driving change, having an impact, and forging your own career with leaders in science education, policy, public engagement, public health, academia, and industry. 

03.

Science Improv Session

Our friends from the Cambridge University Science Improv Society will be leading this session. Don't miss out on our stand-up comedy show!

04.

Networking and Happy Hour at The Lab

Cambridge Gravity has generously agreed to host our Happy Hour. Mix and mingle with conference attendees; who knows, your next company or job might start there!

Panelists

Panel 1 - Innovation and Entrepreneurship

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Elena Arciero is statistical genetics and target assessment lead at Quotient Therapeutics.

Jon Teague

Jon Teague is a bioinformatician and Director of COSMIC, with a keen interest in making data publicly available for both industry and academic use.

Hemalvi-Patani

Hemalvi Patani is a Senior Scientist at Quotient Therapeutics

Panel 2 - Pathways in Science

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Sharon Peacock is Master Elect of Churchill College and a Professor of Microbiology and Public Health at the University of Cambridge.

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Alex Cagan is an assistant professor at the University of Cambridge, where he investigates investigates evolutionary processes in somatic tissue. In addition to his research, he works as a scientific illustrator.

GunesTaylor

Güneş Taylor is a postdoctoral research scientist at The Francis Crick Institute with a strong passion for scientific communication.

Treasa-Creavin

Treasa Creavin leads the digital learning programme at Wellcome Connecting Science where she has gained extensive experience in the field of scientific communication and education.

Student Speakers

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Leonie Lorenz

EMBL-EBI

The human pathogen Streptococcus pneumoniae is a major cause of diseases, including pneumonia and meningitis. The introduction of multi-valent vaccines against S. pneumoniae successfully reduced the burden of disease and the prevalence of targeted strains. However, S. pneumoniae strains not included in the vaccine have benefitted from the vaccine introduction as over time they replace the targeted strains. To prevent the rise of pathogenic strains, it is crucial to understand which of the untargeted S. pneumoniae strains will dominate the replacement. This strain replacement can be modelled through negative frequency-dependent selection (NFDS) on the genome content. NFDS is a type of balancing selection for which the benefit of a given trait negatively correlates with the prevalence of that trait within a population. By extending a previously published model, we developed a faster and more flexible mathematical model that describes the post-vaccine dynamics of S. pneumoniae populations. Here we show that our model reliably identifies the S. pneumoniae strains which increase in prevalence and that it is applicable across different populations and vaccines. We demonstrate that the model with NFDS is significantly better than null models without NFDS. Our model is faster and easier to reuse than previous implementations, and the use of modern bioinformatic tools facilitates the application and reuse in other datasets and species. The model output can be used to predict burden of disease, advise policy decisions, and inform future vaccine design.
Mechanistic modelling of Streptococcus pneumoniae population dynamics after vaccine introduction
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Stephanie McGimpsey

Wellcome Sanger Institute

The English Channel is a small body of ocean wedged between the UK and France that is has kilometres of beach resort towns. Both countries have polices that allow for the release of untreated sewage into water ways that contribute the English Channel. It is also a busy shipping channel with potential for spread of bacteria via ballast water and contamination from jettisoned ship waste. So with all this potential human contamination does this affect the microbial diversity of the English Channel and is the water safe to swim in? I filtered sea water over a five month period encompassing the warmest to the coolest sea temperatures to produce pure cultures for short read sequencing. These genomes were then assembles, QC'd and had their taxonomy classified using GTDB. The species present were then used to create a phylogenetic tree based on bacterial core genes. The abundance of each species was plotted over the five month sampling period to identify trends. The species present were then compared with the Tara Oceans project to identify any species that were unexpected. I found multiple opportunistic pathogens that traditionally inhabit the ocean as well as a few puzzling species. The abundance of species varied over the 5 month period with Bacillus and Vibrio genera contributing to the largest number of genomes sequenced. So is the water safe to swim in? You'll have to come to the talk to find out.
Should you swim in the English Channel?
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Lucia Ramirez Navarro

Wellcome Sanger Institute

Crohn’s disease (CD), is an immune-mediated condition and a subtype of inflammatory bowel disease (IBD), characterised by chronic inflammation and damage in the gastrointestinal tract. The causes of CD are poorly understood, but it is hypothesised to be driven by a dysregulated immune response against commensal gut bacteria in genetically susceptible individuals. To understand the immune-mediated mechanisms underlying CD, we investigated immune cells from both the gut and bloodstream, focusing on how their transcriptional profile changes as they migrate to inflamed tissues. We generated a single-cell atlas of paired ileal and circulating immune cells from 125 patients, analysing over half a million cells. Our study identified unique and shared immune cell states, including tissue-specific subsets of Gamma Delta T cells and Tregs. Heritability enrichment analysis showed that T cell-specific programs are enriched in disease risk loci, emphasizing the role of the microenvironment in understanding the genetic component of IBD. Additionally, leveraging clinical data from our cohort, we identified many genes with significant tissue-specific correlations with disease severity or medication status. Notably, many effects were observed exclusively in ileal Gamma Delta T cells, suggesting that the biology of IBD progression or severity is more accurately captured at the primary disease site. In summary, our study provides a comprehensive characterization of tissue-specific and systemic transcriptional states within the immune system of CD patients. Our findings suggest that examining both local and circulating immune cells offers better insights into how the immune system contributes to the disease process in different contexts.
A multi-tissue perspective of the immune system's dysregulation in Crohn’s disease
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Tung Nguyen

University of Cambridge

Viral load, measured by diagnostic RT-qPCR cycle-threshold (Ct) values, is crucial in pandemics like COVID-19 for assessing the patient severity and stage of SARS-CoV-2 infection. Obtained from clinical nasopharyngeal swabs, it also helps minimize spurious mutational artifacts due to insufficient starting genomic material. Despite extensive sequencing efforts using tiled amplicon-based library preparation, many SARS-CoV-2 genomes lack metadata or clinical quantitative assays to ascertain viral load. We propose a novel method that uses raw sequencing metrics, particularly coverage unevenness, to train a simple and fast random forest regressor for predicting Ct values from raw amplicon-based sequences. Analyzing nearly 20,000 samples from a hospital in Houston, Texas, half of which lack Ct values, our model achieved an adjusted R² of 85% for linear prediction across the Ct spectrum and demonstrated generalizability across different library preparation methods. We applied the model to logistic regressions on higher “infectious” viral loads (Ct
coverCt: uneven sequencing coverage predicts viral loads and is correlated with the COVID-19 clinical condition.
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Mujar Minette Shalo

University of Cambridge

Enteric fever is a common cause of morbidity and mortality in underdeveloped countries, where it is endemic. Clinical management and control of the disease rely on prompt diagnosis and effective treatment. Nevertheless, current diagnostic methods are not sufficiently specific and sensitive while antimicrobial resistance is becoming widespread, limiting treatment efficacy. Significant delays to treatment are currently caused because widely-used blood culture diagnostics take several days to return a result and have limited sensitivity of only 40–60% (Parry et al., 2011). CRISPR AMR Dx seeks to engineer an affordable, sensitive multiplex Cas12a-based biosensor for the diagnosis of enteric fever caused by typhoidal Salmonella and identify related antibiotic resistant genes. A fusion domain (villin head piece) was added to the N-terminal of enASCas12a to improve stability, solubility, and affinity to the target DNA, thus improving the processivity of the enzyme. Preamplification methods SSB-Helicase Assisted Rapid PCR (SHARP) and Loop Mediated Isothermal Amplification (LAMP) are being optimized to increase the diagnostic sensitivity. With the help of a collaborator, the improved assay will be integrated into a multichannel microfluidic device. This will enhance specificity and sensitivity while reducing complexity and the need for instrumentation, in line with the REASSURED criteria for point-of-care diagnostics (Land et al., 2019).
CRISPR AMR DX: An Optimised CRISPR/CAS12A Based Multiplex Biosensor For Rapid Diagnosis Of Enteric Fever And Antimicrobial Resistance
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Vote for best speaker here!

Symposium Agenda

Session 1

8:00 - 8:35

H Room (Next to Pavilion Room)

Registration & Breakfast

8:45 - 9:00

Pavilion Room

Introduction

9:00 - 10:00

Pavilion Room

Keynote Lecture 1

Dr. Jason Mellad, CEO and Founder of Start Codon

10:00 - 10:15

Pavilion Room & Antechamber

Tea and Coffee

10:15 - 10:45

Pavilion Room

Selected Oral Presentations - Session 1

Leonie Lorenz, European Bioinformatics Institute (EMBL-EBI)

​Lucia Ramirez Navarro, Wellcome Sanger Institute

Mujar Minette Shalo, University of Cambridge

10:45 - 11:00

Pavilion Room & Antechamber

Tea and Coffee

11:00 - 11:45

Pavilion Room

Selected Oral Presentations - Session 2

Stephanie McGimpsey, Wellcome Sanger Institute

Tung Nguyen, National Institute of Allergy and Infectious Diseases (NIAID, NIH)

Lunch & Poster Session

11:45 - 12:00

Pavilion Room & Antechamber

Word from our sponsors

12:00 - 13:00

Pavilion Room & Antechamber

Lunch

including Poster exhibition & Sponsor showcase from 12.15

Session 2

13:00 - 13:30

Peter Richards Room

Cambridge Improv Science Society

13:30 - 14:30

Peter Richards Room

Panel 1:

Pathways in Science

Prof. Sharon Peacock, Master-elect of Churchill College

Dr. Gunes Taylor, Postdoctoral Fellow, Francis Crick Institute

Dr. Treasa Creavin, Wellcome Connecting Science

Dr. Alex Cagan, Assistant Professor, University of Cambridge & Scientific Illustrator

14:30 - 14:40

Peter Richards Room

Break

14:40 - 15:30

Peter Richards Room

Panel 2: Innovation and Entrepreneurship

Dr. Elena Arciero, Quotient Therapeutics

Dr. Jon Teague, Director of COSMIC

Dr Hemalvi Patani, Senior Scientist, Quotient Therapeutics

15:30 - 16:30

Peter Richards Room

Speed-dating

Join our keynote speakers, panellists, and sponsors for open conversations about pathways in science!

16:45 - 17:45

Peter Richards Room

Keynote Lecture 2

Prof Sharon Peacock, Master-elect of Churchill College, Professor of Microbiology and Public Health

17:45 - 18:00

Peter Richards Room

Closing remarks

18:00 - 18:30

Walk to The Lab

18:30

Award Ceremony & Happy Hour @ The Lab

Quotient therapeutics logo
COSMIC logo
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EMBL-EBI logo
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Cambridge Gravity logo
Hughes Hall College logo

In support of accessibility

Sharon Peacock

Organising Committee

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