Alan Perelson’s 70th Birthday Conference: Viral Dynamics: Past, Present and Future

Sankalp and I have just returned from a weekend trip to Santa Fe for the Viral Dynamics conference in honour of Alan Perelson’s 70th birthday.

The conference itself was very high quality – excellent talks throughout from some extremely eminent people in virus research. I particularly appreciated David Ho’s opening talk and Alan Perelson’s closing keynote; David’s talk on HIV dynamics reminding me just how good Alan and Avidan Neumann’s modelling contribution was: it wasn’t about developing big complex models, or doing very fancy mathematics; it was about doing the right simple model to make the most use of the data. Alan’s talk focussed on his earlier work in theoretical immunology – very many interesting examples showing how much you can learn by thinking in mathematical/computational ways.

The best part of the conference was meeting up with people – whether old friends from the short time I spent in LANL (Alan, Jack) and my PhD days (Ruy, Sebastian) – or brilliant people I hadn’t met before with whom I had some very stimulating conversations.

What was also evident was the warmth felt by so many people towards Alan. I only spent 3 months in the lab in 1994 – in between my degree and PhD – and went back for another month in the summer of 1995 – and yet when Ruy Ribeiro sent the invitation I immediately felt that this was a meeting I couldn’t miss. Many people there had collaborated with Alan for many years. And while Alan’s contribution to science is enormous, the plaque that the organizers made for him was for friendship, collaboration and mentorship, with a network graph of his collaborative research outputs. In this, Alan is a positive example for us all.

We went with a poster:


which was Sankalp’s first conference poster presentation! I thought that this would be a good opportunity for him; although Sankalp’s model is about bacteriophage in the context of AMR, while the conference focussed on human disease viruses, the conference attendees mainly worked in mathematical models of virus dynamics. This meant that Sankalp was among people who understood what he was doing and why he was doing it, speaking the same language. Sankalp was busy – he had people speaking with him for the full 2 hours of the poster session – and we received many interesting ideas and suggestions from these conversations.

Nearly new publication: Metal Resistance and Its Association With Antibiotic Resistance. Advances in Microbial Physiology

Last month the review that Sankalp and I contributed to was published on line by Advances in Microbial Physiology. This review was led by Jon Hobman, with considerable writing by Chandan Pal. It is a real honour to have co-authored with the amazing Joakim Larsson. My own contribution was small: Sankalp contributed some review material on modelling, and I got stuck in with Joakim and Jon in the editing phase to ensure we had a coherent story. Overall, this is a very nice and timely review, and we have had a lot of interest in it already. Citation and abstract:

Pal C, Asiani K, Arya S, Rensing C, Stekel DJ, Larsson DGJ and Hobman JL 2017. Metal Resistance and Its Association With Antibiotic Resistance. Advances in Microbial Physiology. DOI:


Antibiotic resistance is recognised as a major global threat to public health by the World Health Organization. Currently, several hundred thousand deaths yearly can be attributed to infections with antibiotic-resistant bacteria. The major driver for the development of antibiotic resistance is considered to be the use, misuse and overuse of antibiotics in humans and animals. Nonantibiotic compounds, such as antibacterial biocides and metals, may also contribute to the promotion of antibiotic resistance through co-selection. This may occur when resistance genes to both antibiotics and metals/biocides are co-located together in the same cell (co-resistance), or a single resistance mechanism (e.g. an efflux pump) confers resistance to both antibiotics and biocides/metals (cross-resistance), leading to co-selection of bacterial strains, or mobile genetic elements that they carry. Here, we review antimicrobial metal resistance in the context of the antibiotic resistance problem, discuss co-selection, and highlight critical knowledge gaps in our understanding.

On AMR Panel with Lord Jim O’Neill at University of Nottingham Chancellor’s Lecture

Last night I had the enormous privilege of being on a panel following Lord Jim O’Neill’s lecture on AMR as part of the University of Nottingham’s Chancellor’s Lecture series.


It was a real coup for the university to have Jim O’Neill speak. It was a great event – well attended by alumni and many other’s. The lecture was brilliant: O’Neill is a very engaging speaker and spoke with confidence and passion on the findings of his report. He mainly focussed on the ten point plan:



It was especially interesting seeing AMR from the perspective of an economist: not just in quantifying the problem in monetary terms (his argument that $40B spend will save $100T costs is compelling) but also how he breaks down the solutions into ‘supply’ and ‘demand’ side solutions and especially his emphasis on the importance of reducing demand for antibiotics through 6 of his points. (I’m not sure where our emphasis on waste management fits into that – but that is another matter – and actually having an economist (Steve Ramsden) on our project also helps framing it).

Professor Liz Sockett kindly asked me to serve on the panel (along side Dr Mat Diggle from EmPath) – this was a new experience for me – I was a little nervous – but the questions were good and interesting. The first couple of questions were more clinically focussed and answered by Liz and Mat. A question came up about how we prevent rapid spread of resistance to any new antibiotics we might discover. Mat gave a good answer from a clinical perspective, and I was able to add that there would need to be very wise use (if at all) of any new clinically important antibiotics in veterinary use. (To be fair, that point is  made in the O’Neill report anyway!) And then got a question direct to me about agricultural waste  management practises in developing countries. This was a nice one – as I have recently visited China and then had visitors from South Africa. So I was able to speak about the challenges of AMR from pig farming in China – the Chinese government are very committed to environmental research and China has a very well-funded research programme; South Africa is also very interesting because there is a mix of modern farming where the challenge of reducing antibiotic use is similar to in the UK, and then traditional subsistence farming, where nutrition is the biggest challenge, and the antibiotic challenge is more about access to antibiotics rather than use reduction.

After the talk, many interesting people came to speak with me, which was really nice, while Professor Christine Dodd looked after our stand and she also received many questions.

Official photographs will follow. The photograph at the top is thanks to Adam Roberts (from his twitter feed).





Research Associate/Fellow in Science and Technology Studies (STS)

We are now advertising the next postdoctoral job for the EVAL-FARMS project. This is a part time role (3 days/week) for three years.

Research Associate/Fellow in Science and Technology Studies (STS)

Sociology & Social Policy

Location:  Sutton Bonington
Salary:  £26,052 to £38,183 per annum, pro rata depending on skills and experience (minimum £29301 with relevant PhD). Salary progression beyond this scale is subject to performance
Closing Date:  Friday 02 December 2016
Reference:  SOC323516

We are seeking an excellent researcher in Science and Technology Studies.

The post-holder will conduct qualitative ethnographic work and interviews on social and cultural aspects of knowledge on antimicrobial resistance in laboratory and farm settings, with the University of Nottingham, UK as the main focus.

Applicants must have a PhD (or be near to completion)  in science and technology studies (STS), human geography or related field, including postgraduate training in social science research methods, or have equivalent relevant knowledge, skills and experience. You must be able to engage with a wide range of stakeholders, including scientists and farmers, as you would be part of a highly multidisciplinary team. Excellent oral and written English language skills are essential. Applicants must be highly motivated, ambitious and have a proven track record of timely research publications (from PhD or beyond).

The post is funded by the NERC EVAL-FARMS project (Evaluating the Threat of Antimicrobial Resistance in Agricultural Manures and Slurries), and will be jointly supervised by the School of Sociology and Social Policy (Institute for Science and Society/ISS) and the School of Geography.

The Associate/Fellow will be primarily located in the School of Biosciences and expect to be physically present on the Sutton Bonington campus, where the scientific work in EVAL-FARMS will be carried out. The fellow will spend roughly a third of their time on University Park where the Schools of Sociology and Social Policy, and of Geography are located.


Informal enquiries may be addressed to Sujatha Raman tel: 0115 846 7039 or email Please note that applications sent directly to this email address will not be accepted.

Research Technician (2 Posts – 1 Full-time & 1 Part-time)

We are now recruiting for two technician positions for the EVAL-FARMS project.

Closing Date
Friday, 28th October 2016
Job Type
Technical Services
School of Biosciences – Technical Services
£22249 to £26537 per annum (pro rata if applicable), depending on skills and experience. Salary progression beyond this scale is subject to performance

Applications are invited for the above full-time and part-time posts which are based within the School of Biosciences at the Sutton Bonington Campus.

The post is to provide technical support on a NERC funded research project “Evaluating the Threat of Antimicrobial Resistance in Agricultural Manures and Slurries”.

The role holder will assist with the collection of soil & slurry samples & processing the samples for microbiological, genomic, wet chemistry & water quality indicators and will require working off-site.

Duties will include:

  • Processing samples for further analysis by LC-MS, ICP/AAS, PCR and microbiological analysis and culture,general microbiological analysis & culture at ACDP 2,assessing water quality indicators using UV vis spectrophotometer
  • Ensuring stocks & equipment in own areas of responsibility are maintained & available for use.
  • Maintaining a safe working environment in accordance with statutory & University Health & Safety procedures.

Full details can be found in the job description.

Candidates must have a HNC in a relevant subject or equivalent qualifications plus considerable relevant technical/scientific experience OR substantial work experience in a relevant technical or scientific role.

Candidates should have experience of working with ACDP 2 pathogens and proven technical and/or experimental expertise in techniques for water quality analysis including filtration, COD analysis, molecular biology & PCR technologies.

These posts are available as soon as possible on a fixed-term contract for a period of 15 months.

Informal enquiries may be addressed to: Dov Stekel tel: 0115 9516294 Or email Please note that applications sent directly to this email address will not be accepted.

The University of Nottingham is an equal opportunities employer and welcomes applications from all sections of the community.

PhD Opportunity: Geospatial modelling the spread of antimicrobial resistance in the environment

We are looking for an excellent candidate for a PhD in Geospatial modelling the spread of antimicrobial resistance in the environment, funded by the NERC Envision doctoral training programme, supervised jointly by myself, Stuart Marsh (Nottingham Geospatial Institute), Malcolm Bennett (School of Veterinary Medicine and Science) and Andrew Singer (Centre for Ecology and Hydrology). Details of the project are below. Please apply by 6th January on

Project Description

Antimicrobial resistance (AMR) is a major global challenge. It is estimated that globally 700,000 human deaths per year are due to AMR, predicted to rise to 10 million by 2050. While much research is in medical/agricultural contexts, the spread of AMR in the environment is often neglected. Antimicrobials and antimicrobial resistant genes (ARGs) and organisms have sources in agriculture and wastewater treatment plants (WWTP), which are spread on land through slurry, manures or sewage sludge, or released directly into rivers. Soil and water polluted by antimicrobials and resistant bacteria can impact crops, animals and humans. Thus, AMR presents both an environmental and human health hazard.

Our vision is to develop mathematical models that can predict AMR spread in the environment. Such modelling will require numerous factors, including: prevalence of ARGs and the relative role of different AMR sources, pathways, drivers and receptors. These models would be used to inform policy on the priorities for controlling AMR in agriculture and the wider natural environment and on the most appropriate specific actions following an outbreak of an AMR pathogen. They will also help prioritise AMR surveillance. Most mathematical modelling for the environmental spread of AMR operates locally, e.g. in a slurry tank, field soil or a WWTP, or a smaller still, e.g. a biofilm. A challenge is to develop predictive models at much larger environmental scales.

This PhD project will begin to address this challenge, by following four novel modelling approaches: incorporation of the heterogeneity of AMR agents; using a combination of deterministic and stochastic models to account for both microscopic and population level scales; up-scaling the current approaches to an environmental scale by using methods developed for geospatial modelling of pollutants; and calibrating the models with geospatially explicit environmental AMR surveillance data from our projects and those of our collaborators.

Funding Notes

Applicants should hold a minimum of a UK Honours Degree at 2:1 level or equivalent in any relevant scientific discipline with considerable quantitative component (mathematics, physics, computer science, engineering). They must be able to evidence excellent mathematical and computer programming skills, a willingness to work across multi-disciplinary boundaries, including physical geography and microbiology.

Full studentships are available to UK/EU candidates who’ve been ordinarily resident in the UK throughout the 3-year period immediately preceding the date of an award. EU candidates who’ve not been resident in the UK for the last 3-years are eligible for “tuition fees-only” awards (no maintenance grant).

Welcome to Laurence Shaw

We are delighted to have Lauence Shaw in our laboratory as a postdoctoral researcher from the end of August until the end of December. Laurence will be working on an EPSRC ODA project analyzing AMR data in collaboration with Yongguan Zhu at the Institute of Urban Environment, Chinese Academy of Sciences, Xiamen. Laurence writes:

I am a statistician and my role here is to perform a statistical analysis on soil data from China with the aim of understanding the development of Anti-Microbial Resistance.  As an undergraduate I studied mathematics at Homerton College, Cambridge before coming to the University of Nottingham to undertake a masters in statistics. This led to a PhD in the School of Mathematical Sciences In Nottingham in which I used probability theory to model the spread of epidemics.

During my PhD I got involved in teaching statistics, both to mathematics undergraduates and to PhD students outside of mathematics who had data but did not necessarily know what to do with it. This sparked an interest in using my statistical background to collaborate with other departments and I have undertaken small data analysis projects with Crop Sciences (where I first worked with Dov), Medicine & Health and Engineering at Nottingham. This had brought me to my current position in Biosciences.

In my spare time I run a local pool team, and am one of a group of quizmasters who set the Monday pub quiz at the Malt Cross in Nottingham.