Recruiting for 26 PhD Vacancies - Application closed!
For the project 'Preparing for vector-borne virus outbreaks in a changing world: a One Health Approach' we are currently recruiting for 26 PhD positions.
On this page you can read all about the PhD vacancies per pillar. Go to the Application form below to apply for any of the 26 PhD vacancies.
Regarding the process and timing:
- deadline for applications: 31 October 2019
- in November we will start the selection procedure
- the selected candidates are supposed to start early 2020 (January/February), as the duration of the project is limited
Please keep in mind that you can apply for a maximum of three vacancies. Per position you need to upload a specific cover letter and a CV.
If you have any questions, please call +31 (0)10 – 704 36 65 or send an email to nwa.onehealth@erasmusmc.nl.
Vacancies Pillar A: Ecosystem mapping
Project description
The PhD will sample and monitor mosquito densities in potential hotspot zones identified through a recently completed ZonMw project (Eco-alert). The mosquito sampling scheme will be closely linked in space and time to other sampling schemes to allow cross-species analyses. Mosquito diversity and abundance will be compared with data collected through environmental surveillance, where diversity and abundance of mosquitos is assessed through next-generation-sequencing (NGS) of environmental water samples. This set-up is also used through living lab experiments to test impact of different types of environmental pollution in collaboration in Pillar B (Leiden University). In parallel, a mosquito identification citizen science project will be done by the general public and by high-school students, and mosquito burdens will be assessed through the “Muggenradar”.
Hosting institute: Wageningen University, Entomology group
Primary supervisor: dr. Sander Koenraadt (WUR)
Co-supervisor: prof. dr. Frederique Bartumeus (CSIC, Barcelona), dr. Maarten Schrama (LU)
Promotor: prof. M. Dicke
Collaborators: prof. dr. Frederique Bartumeus, dr. Maarten Schrama, dr. Fred de Boer, dr. Bas Oude Munnink (ErasmusMC), dr. Eefje Schrauwen
Specific requirements for the projects
We invite PhD candidates with an MSc degree in Ecology/Biology, experience with molecular techniques (PCR, NGS etc.) and statistical modelling. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
The PhD will increase and optimize current arbovirus surveillance in wild birds as set up under the Eco-alert pilot, and develop systematic sampling of target birds in areas designated as hotspots (Esser et al. 2019), and of animal species proposed by Pandit et al., 2018, such as rodents and bats. Sampling of wild birds in other European countries will be set up to study the international spread and evolution of arboviruses that are of relevance for the Netherlands. For USUV and possible other viruses the PhD will study the pathogenicity and epidemiology in vector and host species using surveillance results of live and dead amplifying and dead-end hosts, pathology results of dead birds, ring-recapture studies and longitudinal studies of certain animal populations. Spatial-temporal differences to virus exposure will be analysed in relation to other environmental conditions.
Hosting institute: ErasmusMC
Primary Supervisor: dr. Reina Sikkema (Erasmus MC)
Co-supervisors: dr. Judith van de Brand, dr. Henk van der Jeugd (NIOO)
Promotor: prof. dr. Marion Koopmans (Erasmus MC)
Collaborators (secondments): dr. Judith van de Brand (UU), dr. Fred de Boer, dr. Kevin Matson (WUR Resource Ecology Group), nVWA
Specific Requirements for the projects
We invite PhD candidates with a background in general ecology, disease ecology, ornithology, and / or veterinary medicine. Experience with the design of epidemiological studies, and expertise in study protocols involving live animals is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
The PhD will analyse the impact of emerging arboviruses on the population dynamics of wild birds using surveillance data, data on temporal trends and distribution of key hosts, ring-recapture studies and population modelling using the USUV – mosquito - blackbird system as a model. The potential influence of local and regional spread of viruses through local bird movements and migration will be analysed in relation to the variation in local conditions, and species community composition. The interplay between virus and host evolution will be studied through intensive, longitudinal studies of selected populations of blackbirds and possibly other host species. Movement patterns of USUV-infected blackbirds will be studied using tracking devices.
Hosting institute: NIOO
Primary supervisor: dr. Henk van der Jeugd (NIOO)
Co-supervisor: prof. dr. Marion Koopmans (Erasmus MC), dr. Fred de Boer (WUR)
Promotor: dr. Fred de Boer (WUR), co-promotor dr. Henk van der Jeugd (NIOO)
Collaborators (secondments): Erasmus MC, UU, RIVM, dr. Kevin Matson (WUR)
Specific Requirements for the projects
We invite PhD candidates with a background in population dynamics and modelling. Experience with capturing, handling, and sampling of birds, capture-recapture modelling or animal tracking are considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
The PhD will combine data on bird host densities and movements from Sovon, Vogeltrekstation, Eurobirdportal, and Trektellen to monitor avian host occurrence in time and space on near real-time basis for a set of suitable host/risk species by constructing a Live-Atlas model that predicts spatial patterns of occurrence and relative densities. The Sovon-DWHC dead bird and mammal surveillance will be developed further, to automatically detect unusual patterns of mortality at an early stage. Monitoring of rodent, bat and mammalian hosts, will be developed together with the Mammal Society, building on existing initiatives for a priority list of mammalian hosts, and will be integrated with the sampling scheme of these species. In collaboration with PhD 3, short and long-distance dispersal of several potential host species will be quantified using tracking devices and ringing data, in relation to differences in local densities and ecological and physiological factors.
Hosting institute: NIOO
Primary supervisor: dr. Henk van der Jeugd (NIOO)
Co-supervisor: dr. Kevin Matson (WUR), prof. dr. Ruud Foppen
Promotor: prof. dr. Ruud Foppen, co-promotor dr. Henk van der Jeugd, dr. Kevin Matson (WUR)
Collaborators (secondments): Erasmus MC, WUR environmental sciences, WUR Bioveterinary Research, WUR Quantitative Veterinary Epidemiology, UU, Deltares, LU, Sovon
Specific Requirements for the projects
We invite PhD candidates with a background in computational ecology,
experience with geostatistical modelling, handling of large databases and a good working knowledge of R is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
The PhD will model arbovirus introduction and amplification risk based on in depth knowledge on microclimate, habitat suitability and migratory routes of vectors and hosts, and effects of change scenario’s on all of these. Building from previous work in Ecoalert, and the data gathered in PhD projects 1 to 4, and in collaboration with Pillar B, the PhD will develop dynamic risk maps that can be used to visualize (changing) risks in real time.
Hosting institute: WUR Resource Ecology Group
Primary supervisors: dr. Fred de Boer (WUR)
Co-supervisor: dr. Kevin Matson (WUR)
Collaborators (secondments): Erasmus MC, WUR environmental sciences, WUR Quantitative Veterinary Epidemiology, UU, Deltares, LU
Specific Requirements for the projects
We invite PhD candidates with a background in epidemiology or ecology. Experience with modelling, GIS and/or remote sensing is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
eHealth modules combined with self-sampling by (returning) travellers will be used to assess importation risk. This will be done by building on already available apps used to target travellers, that will be extended for targeted and prospective syndromic surveillance of travelers to detect imported infections. Impact of arbovirus infection may differ depending on the history of earlier exposures, as antibodies to flaviviruses cross react and may interact with incoming viruses leading to changes in the infection pathway. The relevance of this background will be studied in collaboration with PhD project 20 (system serology). Given the expansion of arboviral disease in Europe, studies will include travelers to non-tropical destinations. This includes regions in The Netherlands in case of a threat of arbovirus emergence. A preparedness protocol will be developed to allow targeted studies in case of suspected arbovirus circulation in The Netherlands and eHealth approaches and self-sampling will be targeted to this group of travellers.
Hosting institute: LUMC
Primary supervisor, promotor: prof. dr. Leo Visser (LUMC)
Co-supervisor: prof. dr. Marion Koopmans (Erasmus MC)
Collaborators (secondments): prof. dr. Eric van Gorp (Travel clinic ErasmusHaven), prof. dr. Frederique Bartumeus (CSIC Barcelona), prof. dr. Zaaijer (Sanquin), dr. Patricia Bruijning (Julius Centre and RIVM)
Specific Requirements for the projects
We invite PhD candidates with a background in medicine, public health, and / or epidemiology. Experience with population studies is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
In the citizen science project high school students are involved to collect data of birds and of mosquito populations (abundance, biting rates, nuisance) to investigate bird mortality and mosquito behaviour and prevalences in the Netherlands. This project will combine traditional methods (bird/mosquito surveys), molecular approaches to mosquito sampling (environmental DNA) and virtual interfaces (smartphones applications) to collect citizen science data. It will also explore how these data types can be used to model risk of arbovirus emergence.
Hosting institute: Erasmus MC
Primary supervisor, promotor: prof. dr. Frederique Bartumeus (CSIC Barcelona), prof. dr. Eric van Gorp (Erasmus MC)
Co-supervisor: dr. Sander Koenraadt (WUR), dr. Henk van der Jeugd (NIOO)
Collaborators (secondments): dr. Sander Koenraadt (WUR), prof. dr. Marion Koopmans (Erasmus MC)
Specific Requirements for the projects
We invite PhD candidates with a background and/or interest in infectious diseases, public education and communication, citizen science, youth, data analysis and the skills to work in an international multidisciplinary team and the flexibility to travel. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
Arboviruses may impact livestock as well as humans, but livestock may also serve as sentinels for human health risks. Therefore, a truly integrated early warning system would combine data collected from different reservoirs, and be adaptable in response to potential alerts. The PhD will develop a national mapping study of baseline seroprevalence to the priority viruses studied, using a systematic sample of the main livestock species, as input for the model development (Pillar B). Where possible, these will be derived from ongoing national surveillance programs for other diseases, that are monitored as part of statutory surveillance, and include risk targeted-sampling based on data on animal movements in Europe. In addition, in liaison with the PhDs focussing on human infections, a protocol will be developed to allow sampling in response to an alert, either by targeting live-stock or by use of sentinel animals. Analytical methods will be harmonized across species, including humans.
Hosting institute: Wageningen Bioveterinary Research
Primary supervisor/ promotor: prof. dr. Wim van der Poel (Wageningen Bioveterinary Research)
Co Supervisor: dr. Fred de Boer (WUR), prof. dr. Marion Koopmans (Erasmus MC)
Promotor: prof. dr. Wim van der Poel (Wageningen Bioveterinary Research)
Collaborators (secondments): WUR, Erasmus MC
Specific Requirements for the projects
We invite PhD candidates with a background in veterinary medicine, epidemiology, biology. Experience with epidemiological studies including basic laboratory analyses is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Vacancies Pillar B: Forecasting and early detection
Project description
Emergence of mosquito-borne diseases critically depends on the presence, abundance, and interplay between hosts, vectors, and pathogens. The spatial and temporal scales at which these interactions take place make it particularly challenging to predict and prepare for outbreaks. In this project, the candidate will use the several data streams collected in Pillar A to reconstruct zoonotic outbreaks, characterize the main drivers of emergence and spread, and determine the risk and spatial extent of outbreaks under current and future scenarios.
Hosting institute: Wageningen University, Quantitative veterinary epidemiology
Primary supervisor: dr. Quirine ten Bosch (WUR)
Promotor: prof. dr. Mart de Jong (WUR)
Collaborators (secondments): prof. dr. Marten Scheffer (WUR), prof. dr. Hans Heesterbeek (Utrecht University), dr. Eline Boelee (Deltares), dr. Maarten Schrama (LU), prof. dr. Marion Koopmans (Erasmus MC)
Specific Requirements for the projects
We invite PhD candidates with a background in epidemiology, ecology, applied mathematics, mathematical biology, or related fields. Experience with mathematical and statistical modelling, programming (R, python, C++, or similar), and Geographic Information Systems is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
The dynamics of a given vector species, the animal species it needs for reproduction and survival, a potential pathogen it transmits, and the host species of this pathogen are influenced by the ecosystem context in which they all live. The ecosystem context has a defining influence on the capability of a (group of) host species to maintain a pathogen or to act as a reservoir of infection for humans. If we are to quantify emergence capabilities for VBD then understanding the influence of the ecosystem context and interactions is important. A recently developed modelling approach that fully merges ecological and epidemiological dynamics will be extended to study vector-borne pathogens. First, we focus on invasion/emergence (of vector and/or pathogen) using R0, characterizing maintenance communities and reservoirs for human infection, relative contributions of species (groups) to R0, and explore the way in which scenarios of change in the ecosystem impact these. In a second part, we introduce a method to differentiate between minor and major outbreaks. We will explore the use of concepts like reactivity in the context of vector-borne pathogens to quantify the vulnerability of an ecosystem to the successful emergence of key vector species and of the pathogens they can transmit.
Hosting institute: Utrecht University; Faculty of Veterinary
Primary supervisor/ Promotor: prof. dr. Hans Heesterbeek (UU)
Co-supervisor: dr. Quirine ten Bosch (WUR)
Collaborators (secondments): dr. Fred de Boer (WUR ), prof. dr. Marten Scheffer (WUR), prof. dr. Mart de Jong (WUR), dr. Eline Boelee (Deltares), dr. Maarten Schrama (LU), prof. dr. Marion Koopmans (Erasmus MC), prof. dr. Mick Roberts (Massey University, Auckland)
Specific Requirements for the projects
We invite PhD candidates with a strong background in theoretical ecology, theoretical/mathematical biology, mathematics. Experience with mathematical modelling is essential; experience with ecosystem modelling and ecosystem dynamics, is considered an advantage We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
Complex systems that approach a critical point have been shown to display generic dynamical symptoms such as critical slowing down. In this project we will explore how those fundamental principles may apply to the dynamics of vector-borne disease outbreaks. Most work will be based on analyses of models developed in cooperation with the projects described for positions 10 and 11, but we will also explore ways of scanning data obtained from various sources including social media data and google search behavior.
Hosting institute: Wageningen University, Environmental Sciences
Primary supervisor: dr. Ingrid van de Leemput (WUR), dr. Quirine ten Bosch (WUR)
Promotor: prof. dr. Marten Scheffer (WUR)
Collaborators (secondments): prof. dr. Mart de Jong (WUR), prof. dr. Hans Heesterbeek (Utrecht University), dr. Eline Boelee (Deltares), dr. Maarten Schrama (LU), prof. dr. Marion Koopmans (Erasmus MC)
Specific Requirements for the projects
We invite PhD candidates with a strong background in theoretical ecology, theoretical/mathematical biology or applied mathematics. Experience with mathematical modelling is essential; experience with analysing complex data sets or computer programming is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
Spatially explicit predictions will be generated for ranges and combinations of stressors under each of the four scenarios, predicting mosquito abundance, exposure and transmission risk and, eventually, tipping points (together with projects 10, 11). These predictions will be based on own data collection of current mosquito abundance (in collaboration with project 1), land use cover and changes therein (collaboration with Deltares) and experiments on key mosquito species (project 15).
Hosting Institute: Leiden University
Primary supervisor: dr. Maarten Schrama (LU)
Promotor: prof. dr. Peter van Bodegom
Collaborators (secondments): dr. Ingrid vd Leemput (WUR Environmental sciences), dr. Quirine ten Bosch (WUR quantitative veterinary epidemiology), dr. Gertjan Geerling (Deltares), dr. Barry Rockx (Erasmus MC), prof. dr. Hans Heesterbeek (UU)
Specific Requirements for the projects
We invite PhD candidates with a background/interest in disease ecology, infectious diseases, vector biology, spatially explicit modeling. Eeperience in data analysis skills or environmental sciences are an advantage. We expect prospective PhD candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
Vector competence is the ability of a mosquito to transmit a specific virus, a trait that is influenced by both biotic, abiotic, and genetic factors. In this project, vector competence of native and invasive mosquito species, Culex pipiens and Aedes albopictus, will be assessed. The effect of different climatic and environmental factors on transmission potential for priority arboviruses will be studied in a comparative manner. Specifically, different temperatures that reflect typical Dutch climatic conditions, as well as projected conditions including unusually warm summers, and increased nighttime temperatures will be studied.
Hosting institute: WUR-entomology
Primary supervisor: dr. Sander Koenraadt (WUR)
Co-supervisors: dr. Gorben Pijlman (WUR), prof. dr. Ronald van Rij (Radboudumc), dr. Barry Rockx (Erasmus MC)
Collaborators (secondments): dr. Maarten Schrama (LU), prof. dr. Marion Koopmans (Erasmus MC)
Specific Requirements for the projects
We invite PhD candidates with a background in Molecular Life Sciences, Biomedical Sciences or a related study and a strong background in molecular cell biology. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
Mosquitoes lack the adaptive immune responses of vertebrates, yet they possess a sophisticated and complex immune response to pathogen infections. This immune response is a critical determinant for pathogen transmission (vector competence). In this project, we will study the immune response of native and invasive mosquitoes (Culex pipiens and Aedes albopictus) to arbovirus infection, and how these responses affect pathogen transmission. Transcriptomic and functional studies in adult mosquitoes will be performed to define the activation of innate immune pathways and small RNA-based immunity. In addition, we will analyze how different temperatures, climatic conditions and stressors after vector immunity.
Hosting institute: RadboudUMC
Primary supervisor: prof. dr. Ronald van Rij (RadboudUMC)
Collaborators (secondments): dr. Gorben Pijlman (WUR), dr. Sander Koenraadt (WUR), LU, Erasmus MC
Specific Requirements for the projects
We invite PhD candidates with an MSc degree in Molecular Life Sciences, Biomedical Sciences or a related study and a strong background in molecular cell biology. Experience with next generation-sequencing and the analyses of large sequence datasets is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
To quantify the effect of (ranges of) stressors on parameters that are directly related to disease risk (larval mortality rate, larval development rate, rate of adult emergence), this project will use a range of different experiment designs (full-factorial microcosms, mesocosms) to expose the main vector of WNV and USUV, Culex pipiens as well as potential other disease vectors to ranges and combinations of selected stressors. Moreover, this project will evaluate the outcome of these small experiments in large scale field setting using an eDNA approach.
Hosting institute: Leiden University
Primary supervisor: dr. Maarten Schrama (LU)
Co Supervisor: dr. Eline Boelee (Deltares)
Promotor: prof. dr. Peter van Bodegom (LU)
Collaborators (secondments): dr. Eline Boelee (Deltares), dr. Gertjan Geerling (Radboud University), dr. Barry Rockx ( Erasmus MC), WUR virology
Specific Requirements for the projects
We invite PhD candidates with a background in ecology or population biology. Experience with eDNA, experimental ecology, and entomology are considered advantages. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes to be willing to do secondments in one of the partner institutes.
Vacancies Pillar C: Impact and severity assessment
Project description
Reservoir competence (presence of susceptible vertebrate hosts) is a key variable for the emergence of vector borne diseases. We will perform in vitro and in vivo studies to determine the susceptibility of a range of indigenous vertebrate species, in the Netherlands, (informed by wildlife surveillance studies), to infection with priority VBD (such as USUV and WNV) and evaluate the pathogenesis and their role in the transmission cycle. We will map relevant host/virus interactions using innovative tissue micro-arrays, precision-cut organ slices, primary cell cultures and relevant experimental animal studies in order to identify the breadth of potential reservoir species in the Netherlands. These data will be important for guiding surveillance and modelling (project 2), and to prepare for the need of rapid assessments in case of new introductions of vector born diseases (project 21).
Hosting institute: Utrecht University
Primary supervisor: dr. Judith van den Brand (Utrecht University)
Co-supervisor: dr. Barry Rockx (Erasmus MC)
Promotor: prof. dr. Andrea Gröne (Utrecht University)
Collaborators: Erasmus MC, prof. dr. Jeroen Kortekaas (WUR bioveterinary research), WUR resource ecology
Specific Requirements for the projects
We invite PhD candidates with a background in (veterinary) medical science. Experience with experimental animals, (histo)pathology, or virology is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
The risk for sustained transmission of vector-borne diseases requires sufficient levels of the virus in saliva of a competent vector as well as in the blood of a susceptible host. It is known that the presence of mosquito saliva can enhance arbovirus infection and viremia but it remains unknown whether the saliva of different mosquito species vary in their ability to do so. Moreover, it is unknown whether this ability to enhance infection is similar for different viruses and different vertebrate hosts.
In this project, we will determine the efficiency by which the virus can infect a susceptible host via different routes and what factors (mosquito bite, virome, microbiome) will affect this. To this end, we will use in vitro models of key target organ systems in transmission of arboviruses including, skin, and the circulatory system as well as relevant in vivo transmission models, and infect them with biologically relevant doses of arboviruses in the presence or absence of different co-infections, the presence or absence of saliva extracted from different resident and invasive mosquito species and/or from the same mosquito species impacted by different anthropogenic stressors. We will study the potential effects of each of these variables on the outcome of infection and specifically on viremia as a measure of transmission risk in collaboration with projects 16, 18 and 19.
Hosting institute: Erasmus MC
Primary supervisor: dr. Barry Rockx (Erasmus MC)
Co-supervisor: dr. Martijn van Hemert
Promotor: prof. dr. Marion Koopmans (Erasmus MC)
Collaborators: dr. Maarten Schrama (LU), dr. Judith van de Brand (UU), dr. Sander Koenraad (WUR) entomology, dr. Gorben Pijlman (WUR), prof. dr. Ronald van Rij (RaboudUMC)
Specific Requirements for the projects
We invite PhD candidates with a background in virology or a related field of study. Experience with Biosafety level 3, experimental animal studies or mosquitoes, is considered a strong advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in at least one of the partner institutes.
Project description
This PhD student will develop in vitro and in vivo models to study interactions of arboviruses with the central nervous system (CNS). The student will assess the ability of arboviruses to gain access to the CNS (neuro-invasiveness), infect cells of the CNS (neurotropism), and their ability to cause neurological disease (neurovirulence) in humans and animals. The susceptibility of neurons differentiated from induced pluripotent stem cells (iPSCs) as well as glial cells, such as astrocytes, will be evaluated. To study the arboviruses in more complex systems, experiments with organoids and formalin-fixed paraffin-embedded CNS tissues, collected from natural target species, will be performed. The experiments will focus on virulence factors and innate- and epigenetic host responses in collaboration with projects 16, 17 and 19. The ultimate objective is to prioritize neuropathogenic arboviruses for countermeasure development.
Hosting institute: WUR
Primary supervisor: prof. dr. Jeroen Kortekaas (WUR)
Co-supervisor: dr. Barry Rockx (Erasmus MC)
Promotor: prof. dr. Jeroen Kortekaas (WUR), prof. dr. Marion Koopmans (Erasmus MC)
Collaborators: dr. Judith vd Brand (UU), dr. Marjolein Kikkert (LUMC)
Specific Requirements for the projects
We invite PhD candidates with a background in virology or cell biology. Experience with BSL3, experimental animals, or primary cell culture is considered and advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
This PhD student will develop reverse genetics systems for a collection of arbovirus strains that will be made available to other partners within the consortium to allow for standardization. These viruses will be characterised in vitro, in cell culture models and - in collaboration with other partners - also in mosquitoes and animal models. Innate immune responses in primary target organ systems will be characterized using cell culture-based and ex vivo models (e.g. skin explants) of human, reservoir and other hosts. In this manner, we aim to identify key innate immunity pathways and their effects on local virus replication, cellular immune responses and tissue damage (connect to projects 6/8, 18 and 19a). Subsequently, viral innate immune evasion mechanisms will be identified and dissected at a molecular level (changes in these mechanisms in response to various host and environmental factors will be identified in other projects). Using reverse genetics, the relative contribution of various evasion mechanisms will be assessed. Based on this knowledge, the PhD student will engineer virus mutants that are affected in their innate immune evasion capabilities. The attenuation of these viruses and the (enhanced) innate immune responses they should elicit will be assessed in cell culture-based and small-animal models (collaboration with Erasmus MC, project 18).
Hosting institute: LUMC
Primary supervisors: dr. Marjolein Kikkert, dr. Martijn van Hemert
Promotor: prof. dr. Eric Snijder
Collaborators (secondments): dr. Barry Rockx (Erasmus MC), prof dr. Jeroen Kortekaas (WUR BVR), dr. Ronald van Rij (Radboud UMC), dr. Judith van den Brand (UU)
Specific Requirements for the projects
We invite PhD candidates with a background in (Innate) Immunology, Virology and/or Molecular Biology. Experience with ex vivo skin cultures, or innate immune response analyses is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one or more of the partner institutes.
Project description
Arbovirus-specific antibodies from previous exposures may prevent or enhance subsequent infections. In this PhD track, we will determine the antibody repertoire to differentiate between related arbovirus exposures using B-cell profiling. To determine how previous exposures impact subsequent infections, we will define the molecular determinants of human protective and enhancing antibodies using B-cell immortalization combined with recombinant antibody technology and functional in vitro assays. This work will be performed in close collaboration with PhD project 6, 17, 22 and 26.
Hosting institute: Erasmus MC
Primary supervisor: dr. Gijs van Nierop (Erasmus MC)
Co-supervisor: prof. dr. Leo Visser
Promotor: prof. dr. Marion Koopmans (Erasmus MC)
Co-supervisor: prof. dr. Leo Visser
Collaborators (secondments): prof. dr. Zaaijer (Sanquin), prof. dr. Duits (blood bank of Curaçao)
Specific Requirements for the projects
We invite PhD candidates with a background in infections and immunity and experience in primary lymphocyte culture and molecular biology to apply for this project. Experience with multiplex serological assays and flow cytometry is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Vacancies Pillar D: Interventions
Project description
This PhD will focus on bridging from (basic) research to understanding what outcomes would be actionable during outbreaks or for preparedness planning. Results from the different PhD projects will be used to design intervention strategies aimed at altering human behavior (involving citizens and influencing traveler behavior), manipulating the environment (water infrastructure and management, emission reduction, vegetation management) to reduce mosquito density, and preventing novel introductions of autochthonous vector and virus species to prevent reaching tipping points.
Hosting institute: Erasmus MC
Primary supervisor (promoters): prof. dr. Marion Koopmans (Erasmus MC), prof. dr. Aura Timen (RIVM, VU)
Collaborators (secondments): dr. Maarten Schrama (LU), dr. Eline Boelee (Deltares), prof. dr. Heiman Wertheim (RadboudUMC), WP leaders
Specific Requirements for the projects
We invite PhD candidates with a background in life sciences (medicine, veterinary medicine, biology) with a demonstrable interest in public health and proven experience with qualitative and quantitative research methods. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
This work focusses on development of innovative serological tools. The work will involve using aptamers and monoclonal antibodies to identify antigens that can be used in a multiplex test to detect antibodies in multiple species and allow serological differentiation between antigenically related arboviruses, to be employed in Pillar A studies. Fieldable versions of optimal assays will be developed using lateral-flow or spot-based tests, involving participants in citizen science studies to assess user-friendliness
Hosting institute: Utrecht University
Primary supervisor: dr. Helene Verheije (Utrecht University)
Co-supervisor: dr. Reina Sikkema (Erasmus MC), Aart van Amerongen (WUR)
Promotor: prof. dr. Andrea Gröne (Utrecht University)
Collaborators (secondments): prof. dr. Marion Koopmans (Erasmus MC), WUR-BVR, WUR-Food & Biobased
Specific Requirements for the projects
We invite PhD candidates with a background in molecular biology. Experience with protein/antigen expression, cell culture, or Elisa is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
The fast development of sequencing platforms has opened up unique opportunities for pathogen detection, tracking, and characterisation. In addition, fast and fieldable metagenomic sequencing allows for unprecedented deep and unbiased analysis of all genetic material in a sample, which can be exploited for pathogen discovery, systems profiling and tracking of gene flows. This project will focus on the development and use of existing and novel approaches like sequencing methods and bioinformatic workflows including phylogenetic analyses to study the ecology and epidemiology of known and new arboviruses at the human-animal interface in near to real-time settings.
Hosting institute: Erasmus MC
Primary supervisor: dr. Richard Molenkamp, dr. Bas Oude Munnink (Erasmus MC)
Co-supervisor: dr. Maarten Schrama (LU)
Promotor: prof. dr. Marion Koopmans (Erasmus MC)
Collaborators (secondments): prof. dr. Ronald van Rij (RadboudUMC), Eefje Schrauwen
Specific Requirements for the projects
We invite PhD candidates with a background in life sciences, preferably with specialisation in genomic epidemiology, including experience in bio-informatics and NGS techniques. Candidates need to have experience and interest in wet lab in addition to the data analysis. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
Like all multicellular organisms, mosquitoes have a resident microbiome and virome that may affect their immune system and therefore their ability to transmit viruses. This PhD project will identify resident insect viruses and bacteria in Dutch mosquitoes and analyze how these affect vector competence (the ability of a mosquito to transmit specific arboviruses). For vector competence-modifying bacterial or viral species, their distribution and stability in the Dutch ecosystem we will be analyzed. Moreover, newly identified insect-specific viruses will be used to modulate mosquito immunity using as a putative approach to inhibit arbovirus transmission.
Hosting institute: RadboudUMC
Primary supervisor: prof. dr. Ronald van Rij (RadboudUMC)
Co-supervisor: dr. Gorben Pijlman (WUR)
Collaborators (secondments): WUR-Virology, LU, Erasmus MC
Specific Requirements for the projects
We invite PhD candidates with an MSc degree in Molecular Life Sciences, Biomedical Sciences or a related study and a strong background in molecular cell biology. Experience with next generation-sequencing and the analyses of large sequence datasets is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.
Project description
Results from the different projects will inform us on worrisome arbovirus variants with (potentially) changed transmission or pathogenicity features. In collaboration with colleagues from LUMC (project 6 and 19) and Erasmus MC (projects 17 and 18), the PhD student will apply reverse genetics techniques to recreate such variants and characterize their properties in cell culture, ex-vivo and small-animal models (with EMC) to assess the contribution of specific mutations to pathogenesis, (innate) immune evasion, and immune responses. For example, the role of NS1 (e.g. glycosylation variants) in the replication of USUV and disease outcome will be studied in comparison with WNV (and other flaviviruses). To increase our preparedness for emerging arboviruses, innovative approaches for the development of live attenuated vaccines will be explored, using platforms already available at LUMC and using engineered virus mutants with diminished immune evasion capabilities. In collaboration with projects 18, 19 and 26, the efficacy of these vaccine candidates will be studied in the mosquito-mouse infection model.
Hosting institute: LUMC
Primary supervisors: dr. Martijn van Hemert, dr. Marjolein Kikkert
Co-supervisor: dr. Barry Rockx (Erasmus MC)
Promotor: prof. dr. Eric Snijder
Collaborators (secondments): dr. Richard Molekamp (Erasmus MC), prof. dr. Leo Visser (LUMC), dr. Judith van den Brand (UU), dr. Gorben Pijlman (WUR)
Specific Requirements for the projects
We invite PhD candidates with a background in Immunology and/or Virology. Experience with Animal Model Studies or Vector Biology is considered an advantage. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one or more of the partner institutes.
Project description
We aim to specifically activate vertebrate antiviral responses modifying their dinucleotide composition to attenuate vector-borne viruses and develop this into universal approach to generate safe and effective live-attenuated vaccines. We will investigate the immunogenicity, pathogenicity and safety of recoded candidate vaccines using in vitro and in vivo infection models developed in WP6.
Hosting institute: WUR
Primary supervisor: dr. Jelke Fros (WUR)
Promotor: prof. dr. Jeroen Kortekaas (WUR)
Co-supervisor: dr. Gorben Pijlman (WUR)
Collaborators (secondments): LUMC, dr. Barry Rockx (Erasmus MC) (in vivo studies)
Specific Requirements for the projects
We invite PhD candidates with an MSc degree in Molecular Life Sciences, Biomedical Sciences or a related study and a strong background in molecular cell biology. We expect candidates to be interested in working in a multidisciplinary team, as part of this joint program. Candidates need to be willing to do secondments in one of the partner institutes.