Early Stage Researchers in HONOURs

 

+ESR1: Cormac Kinsella, Academic Medical Center of the University of Amsterdam (AMC)

       Cormac KinsellaDuring my BSc in Zoology (Cardiff University) I became interested in parasite and pathogen biology while working on helminth ectoparasites of fish. This directed the focus of my MSc research, carried out during the Erasmus Mundus Master Programme in Evolutionary Biology (MEME). First at LMU Munich, I delved into aspects of cell signalling in Trypanosoma brucei, the causative agent of sleeping sickness. Next at Harvard University I utilised deep sequencing for both genomic surveillance of Jamestown Canyon Virus, a neuroinvasive Orthobunyavirus, and viral discovery. At Uppsala University I worked with 10X Genomics linked-read sequencing data to better understand the evolution of an unusual ‘parasitic’ chromosome system present in some avian species.

My doctoral project will focus on viral pathogen discovery, primarily utilising the VIDISCA method developed by Dr. Lia van der Hoek at  the AMC. Despite the availability of accurate diagnostic tests for many viruses, a significant proportion of suspected viral  disease cases in humans cannot be assigned to a known pathogen, and remain undiagnosed. Undiscovered viruses are suspected to be responsible for part of this disease burden, necessitating targeted discovery approaches. I will identify viruses in available biobanks at the AMC, simultaneously studying the whole virome of patients and controls to identify patterns that underlie health. In a separate line of investigation, I will utilise molecular biology methods to capture and identify insect-vectored pathogens of relevance to human and animal health directly from homogenised insect samples.

+ESR2: Ceren Simsek, Katholieke Universiteit Leuven (KU Leuven)

       ceren simsekI have studied molecular biology and genetics in Bilkent University, Turkey. During my master’s I have joined AgroParisTech and had a chance to work as an intern at Collège de France and INRA. During my last internship, I have participated in the analysis of genetic control of chicken gut microbiota using bioinformatics tools. The diverse world of gut microbiota intrigued me and I decided to continue my graduate studies in this field.For my doctoral project, the main goal is to study the longitudinal dynamics of the microbial gut community during the 1st year of life in infants. To study the virus component (virome) in the gut we will use the NetoVir protocol, which was developed by the host laboratory. The initial steps of this protocol are sample homogenization, physical removal of cells and cellular debris using filtration and centrifugation, followed by nuclease treatment. Then the viral nucleic acids will be extracted, cDNA library will be prepared by random amplification, and Illumina NGS will be used to deep sequence these viromes. The sequences will be assembled, annotated and analyzed further using in-house developed pipelines as well as tools developed for ocean viromics, allowing the identification of highly divergent phages. Furthermore, we will also investigate the bacterial dynamics using 16S analyzes, as well as shotgun bacterial metagenomics on a subset of samples to infer relationships between bacteria and bacteriophages. The aforementioned analyses will allow us to study in great detail the influence of diet, medication, vaccination and diseases on the infant gut microbiota development.

+ESR3: Pauline Dianne Santos, Friedrich-Loeffler-Institut (FLI)

       Pauline Santos.jpegI studied Biology (BSc) and Microbiology (MSc) at the Institute of Biology, University of the Philippines Diliman (UPD). My master’s thesis focused on the optimization of protocols for Salmonella subtyping using PCR-based techniques and their application on isolates collected from retail meat. While pursuing my postgraduate degree, I also worked as research associate at the Natural Science Research Institute-UPD where I handled two research topics. The first project focused on molecular-based screening of Salmonella and its subtypes in food and animal samples, and protocol development for faster detection of Salmonella in meat. As part of my thesis and project, I took part on a 10-month internship program hosted by United Nations University-Gwangju Institute of Science and Technology in Republic of Korea in 2014, where I optimized the protocol for PCR-based Salmonella O-serogrouping assay. As my side project, I contributed on the determination of efficiency of DNA extraction and qPCR methodologies for the enumeration of E. coli collected in environmental samples.

The second project ignited my passion for virus research. I was involved on the production of recombinant hemagglutinin (H3) that potentially induce protection against broad range of Influenza A strains. To pursue my interest on virus research, I participated on 2017 Summer Internship Program hosted by Taiwan International Graduate Program at the Institute of Molecular Biology, Academia Sinica. My project focused on structural and functional analyses of Vaccinia H3 envelope protein.

My doctoral project will focus on further optimization of methodologies for direct analysis of nucleic acids using multiplex RT-qPCR, pan viral microarray, and next generation sequencing. I will apply these techniques on archived samples and samples from suspected current outbreaks that are available at the Friedrich-Loeffler-Institute. In addition, the identified virus will undergo thorough characterization.

+ESR4: Ignacio Postigo Hidalgo, Charité - Universitätsmedizin Berlin

       Ignacio Postigo.jpeg

During my Biology Bachelor´s degree studies at the Universidad de Salamanca (Spain) I developed a multidisciplinary interest for science that motivated me to study different biological fields such as animal reproduction or cellular and molecular biology, but also technical areas like programming. At the end of my undergraduate studies, I spent six months in Dresden (Germany), first as an Erasmus student, and later on working as a research assistant in proteomics for 9 additional months.

It was not until I started my Masters studies in Biology at Uppsala University (Sweden) that I directed the focus of my interest to infectious diseases and public health. As part of my masters studies, I had the opportunity to participate in the Pan American Health Organization (PAHO) intern program, in Washington DC (US). There, I provided support to their activities regarding the integrated epidemiological surveillance of arboviral diseases, contributed to an ongoing  dengue virus genotyping project and helped with the development of their mosquito epidemiological surveillance system. After the completion of the internship I got hired for the rest of the year as an international consultant to keep working on my duties at PAHO. At the same time, I worked on my Masters Thesis on the molecular epidemiology of dengue in Central America. 

My PhD project at the Charité Universitätsmedizin, Berlin will focus on the detection and quantification of novel viruses, together with the development of serologic tools and enrichment techniques for diagnostics through next-generation sequencing. In addition, the evolutionary history of the novel viruses will be investigated through phylogenetic inference methods.

 

+ESR5

+ESR6: Lisa Falk, Academic Medical Center of the University of Amsterdam (AMC)

       Lisa Falk

I studied Biomedical Science and Biochemistry with main focus on molecular and cellular biology of infectious diseases at the Ernst-Moritz-Arndt University Greifswald, Germany. During my Master thesis I investigated human primary macrophages to establish a model for immune evasion strategies of the CA-MRSA strain USA300. In the course of my doctorate, I aim to continue research on host-pathogen interactions with primary cell culture models that demonstrate high morphological and physiological similarity to the in vivo host tissue environment.

With regard to respiratory infections, the human airway epithelium (HAE) serves as an initial entry point and primary target tissue for respiratory pathogens. In vitro models of primary HAE cells were shown to be highly permissive to infection with various human respiratory viruses, including influenza A virus, human bocavirus and respiratory syncytial virus. In my PhD project, I will inoculate HAE cultures with clinical respiratory sample isolates derived from the GRACE cohort. Upon successful infection and replication, virus isolates will be investigated by VIDISCA-NGS, followed by analysis of the viral mRNA. By application of single-cell RNA sequencing of infected cells, I want to determine cell tropism, identify the cellular receptor engaged for viral entry, characterize replication strategies, and study the pathogenesis of previously un-culturable or unknown respiratory viruses to identify potential targets for anti-viral strategies.

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+ESR8: Kinga Böszörményi, Biomedical Primate Research Centre (BPRC)

       KingaI graduated in 2015 as a biologist with specialization for molecular-, immune- and microbiology at the Eötvös Lornánd University, Faculty of Science in Budapest, Hungary. As an undergraduate student, I worked in the Molecular and Comparative Virology group at the Institute for Veterinary Medical Research, Hungarian Academy of Sciences. For my Master thesis, I was screening exotic mammal samples for novel adenoviruses. During that time, I determined the complete genome sequence of a novel exotic adenovirus, the polar bear adenovirus, by primer walking method. After receiving my degree, I started working in this laboratory as a junior scientist for 2 years.

In my PhD project, I will work on the characterization of the pathogenic potential of novel emerging flaviviruses, with focus on the description of early pathological events following Usutu and Zika virus infection. I will infect primary cells and cell cultures derived from nonhuman primates as model systems for human flavivirus infection. Viral stocks will be prepared on mosquito or nonhuman primate cells. In the project, I will also apply immunohistological straining, molecular biology, and cell culture methods to investigate viral replication, pathogenesis and tissue tropism.

 

+ESR9: Alba Folgueiras González, MSD Animal Health (MSD-AH)

       Alba Folgueiras GonzálezI have studied a BSc in Biotechnology at Universidad de Oviedo (Asturias, Spain) with a year abroad at Swansea University (Wales, UK), touching on a broad range of areas from immunology and physiology to physics and chemical engineering. During my fourth year, I wrote my dissertation about the glucose transporters regulation by antitumoral natural compounds. However, after graduating, amazed by the opportunities that synthetic biology could bring to different fields of science, I decided to pursue an MSc in Synthetic Biology and Biotechnology at The University of Edinburgh. I spent my four last months there conducting “blue-skies” research in biocompatible chemistry at Wallace Lab in order to develop catalytically active exopolysaccharide slimes by using engineered bacteria, synthetic sugars and “click-chemistry” reactions.

Synthetic biology could also be a great tool to control infectious diseases, discover new viruses and develop novel vaccines and in-vitro culture systems with the help of new technologies such as CRISPR-Cas editing system or Next Generation Sequencing, among others. In the course of my PhD, held at MSD Animal Health in Boxmeer, and with close collaboration with the AMC in Amsterdam, I will work in the identification and characterization of novel viruses in veterinary patient samples, which includes the fulfillment of Koch’s postulates. At the same time, I will be involved in the development of novel culture systems for proof of concept studies and also to increase the viral titers of already known viruses with the final aim of improving the vaccine development process

+ESR10: Alexis Hoste, INGENASA

       Alexis HosteI studied Biological Engineering at the University of Technology of Compiègne in France with a focus on the Design and Innovation of Bio-Products. For my Master’s degree I completed two six months internships in pharmaceuticals companies. The first internship was in Ceva Santé Animale, an animal health company in the United States of America. During this stay I worked on the development of a new line of swine vaccine against the Porcine Circo Virus II, by purification of a recombinant swine cytokine expressed in the E. coli system. My second internship took place in Sanofi Pasteur, in France, where I developed new fermentation processes for the expression of a recombinant protein included in a human vaccine using the E. coli system.

My PhD project will take place in an animal health biotech company (INGENASA) based in Madrid, Spain and in collaboration with the University of Leeds, UK. This project will focus on the detection of zoonotic viruses of the Order Bunyaviridae, such as the Crimean-Congo hemorrhagic fever virus (CCHFV) and the Rift Valley fever virus (RVFV). CCHFV is the causative agent of Crimean-Congo hemorrhagic fever, which is the most widespread tick-borne viral infection of humans and has a fatality rate up to 40%. RVFV primarily affects animals but can also infect humans with some mild to severe symptoms that can cause death. These two viruses will be the main target for the development of new diagnostic tests, as there are still some gaps in the diagnosis and surveillance of these viruses in animals. After producing the target immunogenic proteins, specific monoclonal antibodies will be obtained and used for the development of different immunoassays such as ELISAs and lateral flow assays. Besides, multiplex serology tests will be developed for the differential diagnosis between CCHFV, RVFV and other related pathogens.

+ESR11: Tim Passchier, University of Leeds

       Tim PasschierAfter obtaining a BSc in Biomedical Sciences from Utrecht University, in the Netherlands, I decided to pursue a Master’s in Molecular and Cellular Life Sciences, also at Utrecht University. I directed my Master’s programme towards Virology and conducted two research projects. The major project centred on the molecular and functional characterisation of a coronavirus accessory protein, in particular its role in integrated stress response antagonism. My minor project, on placement at the University of Oxford, focussed on the influence of the secondary and higher-order structure of viral RNA on persistence in its natural hosts. Finally, I wrote my Master’s thesis on the role of ISG15 in the intra- and extracellular, innate and adaptive immune responses, the structural similarities and differences between it and diubiquitins, and the specificity determinants of viral deubiquitinases/deISGylases.

My PhD project at the University of Leeds focuses on the expression and structural elucidation of nucleoproteins and nucleocapsid complexes of various emerging zoonotic viruses, using protein crystallography and cryo-electron microscopy. Of primary interest are members of the Bunyaviridae and Paramyxoviridae families. Once resolved, the molecular structures of these proteins may improve our mechanistic understanding of the viral life cycle and aid in the design of novel therapeutics, directly targeting these proteins or the interactions with their binding partners.

+ESR12: Kevin Szillat, Friedrich-Loeffler-Institut (FLI)

       ESR12_SzillatOriginally from Germany, I studied Biology and Molecular Health Sciences at the Swiss Federal Institute of Technology in Zurich (ETH). While my Bachelor studies gave me a broad overview of natural sciences, I focused more on health-related research during my Master program, working on thyroid dysfunctions, cancer and wound healing. In the meantime, my part time job at a vaccine developing company gave me a first impression of industrial research.

During the course of my doctoral project, I will focus on the in vitro and in vivo characterization of viral pathogens (under different biosafety levels, BSL2 to BSL3+). Potentially suitable cell cultures will be selected from the collection of cell lines at the FLI, accommodating more than 1250 different cell lines, ranging from farm animals to fishes, reptiles and insects. Cell culture systems for newly identified viruses might not be available immediately, therefore, in vivo inoculation is a necessary step in order to promote virus replication and obtain reference material for further diagnostic and phylogenetic evaluation. In vivo characterization also aims to determine the disease course and pathologic association with the infection and could also enable adaptation of the virus in order to facilitate its subsequent cell culture isolation.

+ESR13: Joyce Odeke Akello, University of Bern (UB)

       Joyce_Odeke_AkelloI completed my BSc in Biomedical Science at the University of Greenwich (2013), then I obtained my MSc in Molecular Biology of Infectious Diseases in 2015 from the London School of Hygiene and Tropical Medicine. As part of my MSc, I undertook a 3-month lab-based research project entitled “Molecular epidemiology of norovirus genotypes associated with community cases of infectious intestinal disease in the UK”, within the Enteric Virus Unit at Public Health England (PHE) under the supervision of Dr. David James Allen. Following my graduation, I Joined PHE as a Project Scientist to work on a Food Standards Agency-funded research project entitled “Assessing the contribution made by the food chain to the burden of UK-acquired Norovirus infection”. At the end of this grant-funded position, I maintained a research position at PHE, implementing molecular methodologies to capture, concentrate, and detect enteric viruses from environmental samples.

My PhD project will involve methodological development and application of molecular biology assays to identify and characterise new and emerging viruses in environmental and clinical samples. The clinical research and development project will take place at the institute for Infectious Diseases (IFIK, University of Bern, Switzerland), with a specific focus on the detection and whole-genome characterisation of adenoviruses in clinical samples as a model for establishing protocols and assays for host-switching pathogens. The aim of this PhD project will be to evaluate and optimise sample preparation and sequencing protocols for clinical samples and to further contribute to the development of bioinformatics and phylogenetic pipelines to characterise genomic structure and features, and phylogeny of adenoviruses in clinical samples. I will undertake the environmental research and development project at the Spiez Laboratory, Switzerland, working on characterising PCR-positive samples for vector-borne diseases including TBEV in ticks, USUV in mosquito, and PUUV in rodents by two independent approaches. The first approach, which represents the main focus of the PhD project, aims at developing a vector specific sample preparation protocol suitable for robust metagenomics analysis. Furthermore, I will compare and evaluate three NGS approaches and several bioinformatics tools to optimize the phylogenetic classification of the candidate viruses involved in vector-borne diseases. The second approach aims at establishing methods for the in-vitro characterisation of potential viral candidates by optimising cell culture and organotypic culture protocols for each virus type. Organotypic brain slice cultures will be applied to investigate cellular and molecular processes of infection.

+ESR14: Beatriz Álvarez Rodríguez, University of Leeds

       Beatriz AlvarezDuring my Biochemistry studies at the Universidad Autónoma de Madrid (UAM) I had the opportunity to work at the Centro de Biología Molecular Severo Ochoa in Madrid, where I studied the translational control of viruses supervised by Dr. Iván Ventoso. Keeping on with the research on infectious diseases, I took part in a project based on the in vitro activities of the agent Bedaquiline in non-tuberculous mycobacteria within the Erasmus+ programme, supervised by Prof. Peter Van Damme and Dr. Anandi Martin at the LM-UGent (Belgium). Subsequently, I decided to start a MSc in Molecular Nanoscience and Nanotechnology coordinated by the Universitat de València in 2016. During this period, I did my master thesis at IMDEA-nanoscience institute under the supervision of Dr. Álvaro Somoza with a grant funded by the UAM. My work there was focused on the development of gold-based nanostructures for uveal melanoma treatment.

My PhD project combines these two areas of research: infectious diseases and nanotechnology. My research is going to be focused on the study of viral proteins to further develop nanosensors to detect them in biological samples. We will concentrate our work on the nucleocapsid protein of negative single stranded RNA zoonotic viruses. After protein synthesis and purification, we aim to do structural analysis using electron microscopy and crystallographic techniques. Additionally, we will raise antibodies and Affimers targeted to these proteins to use them as the detecting components of our nanosensor systems. These studies will help to a better understanding of the biology of zoonotic viruses and will lead to a rapid detection system of emerging viruses, which is a critical component of disease surveillance and management.

+ESR15: Joan Martí i Carreras, Katholieke Universiteit Leuven (KU Leuven)

       Joan Marti I CarrerasI studied my bachelor in Genetics by the Autonomous University of Barcelona (Barcelona, Spain) where I conducted basic research in the evolution of piwi-interacting-RNA genes. Later, I obtained my masters in Bioinformatics by the Pompeu Fabra University (Barcelona, Spain), reconstructing metagenomic and metatranscriptomic data from marine samples for studying global patterns of mercury-degradating genes. In the course of my doctorate, we aim to study the single-host and population variability of the human cytomegalovirus genome, as well its expression dynamics by optimizing ultra-long read sequencing platform from Oxford Nanopore Technologies ™.

Human cytomegalovirus (HCMV), the prototype member of the herpesvirus subfamily Betaherpesvirinae, is a ubiquitous virus with seroprevalences ranging from 45 to 100% in adults. Primary infections of healthy children and adults are usually asymptomatic but the virus establishes a lifelong persistence as a latent infection, from which it can reactivate to spread infectious progeny. HCMV can cause serious sequelae during infection of immunocompromised individuals and foetuses. Worldwide, HCMV is the most common congenital infection, with an overall birth prevalence of 0.64%, causing sensorineural hearing loss and neurodevelopmental delays in new-borns. HCMV encodes a double-stranded DNA (dsDNA) genome of 235 kbp, one of the largest genomes of all human viruses. Sequence analyses of viral genes encoding glycoproteins and immune-modulating factors have established the existence of separate clusters of polymorphisms or genotypes and attracted interest into the genetic variability and its potential implications for viral pathogenicity. Until recently, only a hundred of complete genome sequences had been characterised from clinical isolates, both because of the size of the genome and the relatively low viral loads in clinical isolates; albeit, those genomes were assembling short reads, oversimplifying the strain classification and diversity of the samples. In my PhD, additional sequences from clinical isolates will be obtain from different countries, within and without EU, and we will optimise the ultra-long read sequencing platform from Oxford Nanopore Technologies ™, in order to better apprehend the intra-host and inter-host genetic diversity and the coding capacity of wild-type HCMV strains.

HONOURs

Host switching pathogens, infectious outbreaks and zoonosis; a Marie Sklodowska-Curie Innovative Training Network.

This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 721367.