Global Approaches to Elucidate the Function of Post-transcriptional Networks in HIV-1 Infection
Lead Research Organisation:
University of Oxford
Department Name: Biochemistry
Abstract
Human immunodeficiency virus type 1 (HIV-1) is the causative agent of Acquired Immunodeficiency Syndrome (AIDS), which constitutes one of the most important pandemics of our time. From the 60 million people that have been infected with HIV-1, 25 million have dead. Very important advances have been done to better understand HIV-1 infection in the past. However, the technical developments achieved in the last decade open now the possibility of exploring an infected cell in an unprecedented depth.
Once HIV-1 penetrated into the host cell the viral particles disassemble, releasing the genomic RNA that is covered by viral and host proteins. This protein-RNA complex travels towards the nucleus and, during the path, HIV-1 genomic RNA is reverse transcribed into DNA to form the provirus. Once in the nucleus, the provirus is integrated into the cellular chromosome. Synthesis, processing and transport back to the cytoplasm of newly synthesized HIV-1 RNAs are mediated by the host machinery. Importantly, translation of HIV-1 RNAs is exerted by cellular protein synthesis machinery, producing the viral proteins required to generate the viral progeny. Therefore, HIV-1 relies on cellular resources from the entrance in the infected cell to the release of viral progeny. Because HIV-1 strongly relies on host gene expression machinery, scientists envision that inhibition of a cellular function that is required for viral replication and does not compromise cell survival, will represent an alternative strategy to treat HIV-1 infection.
RNA-binding proteins are key "players" of gene expression machinery and this protein class has emerged as crucial regulators of HIV-1 infection. However, to identify novel therapeutic targets, scientists have first to determine the exact repertoire of cellular proteins involved in HIV-1 replication. To date this catalog of host factors is still incomplete in spite of the numerous efforts undertaken to better understand HIV-1-host cell interactions. The methods that I developed during my postdoctoral work offer now the possibility to globally define the scope of host proteins that directly interact with HIV-1 genomic RNA. The repertoire of proteins identified by these methods will be studied in detail in cultured cells and mouse models using different biochemical approaches. Proteins proven by these analyses to play an essential role in HIV-1 replication may represent potential host-based targets to treat the infection. Therefore, this project aims at finding potential therapeutic targets by expanding our knowledge in HIV-1 biology using novel system-wide approaches.
Once HIV-1 penetrated into the host cell the viral particles disassemble, releasing the genomic RNA that is covered by viral and host proteins. This protein-RNA complex travels towards the nucleus and, during the path, HIV-1 genomic RNA is reverse transcribed into DNA to form the provirus. Once in the nucleus, the provirus is integrated into the cellular chromosome. Synthesis, processing and transport back to the cytoplasm of newly synthesized HIV-1 RNAs are mediated by the host machinery. Importantly, translation of HIV-1 RNAs is exerted by cellular protein synthesis machinery, producing the viral proteins required to generate the viral progeny. Therefore, HIV-1 relies on cellular resources from the entrance in the infected cell to the release of viral progeny. Because HIV-1 strongly relies on host gene expression machinery, scientists envision that inhibition of a cellular function that is required for viral replication and does not compromise cell survival, will represent an alternative strategy to treat HIV-1 infection.
RNA-binding proteins are key "players" of gene expression machinery and this protein class has emerged as crucial regulators of HIV-1 infection. However, to identify novel therapeutic targets, scientists have first to determine the exact repertoire of cellular proteins involved in HIV-1 replication. To date this catalog of host factors is still incomplete in spite of the numerous efforts undertaken to better understand HIV-1-host cell interactions. The methods that I developed during my postdoctoral work offer now the possibility to globally define the scope of host proteins that directly interact with HIV-1 genomic RNA. The repertoire of proteins identified by these methods will be studied in detail in cultured cells and mouse models using different biochemical approaches. Proteins proven by these analyses to play an essential role in HIV-1 replication may represent potential host-based targets to treat the infection. Therefore, this project aims at finding potential therapeutic targets by expanding our knowledge in HIV-1 biology using novel system-wide approaches.
Technical Summary
HIV-1 encodes only 15 distinct polypeptides, so it relies heavily on host proteins for replication. After reverse transcription, HIV-1 proviral DNA is integrated into the cellular chromosome. This allows viral RNAs to be synthesized, processed, exported and translated by the host cell machinery. This proposal aims at comprehensively identifying the catalog of host RNA-binding proteins (RBPs) involved in the posttranscriptional regulation of HIV-1 gene expression by applying novel system-wide methodologies built on protocols developed during my postdoctoral work. HIV-1-infected cells will be irradiated with ultraviolet light to crosslink proteins to RNA. HIV-1 RNAs will be isolated through stringent washes using specific locked nucleic acid probes. Co-isolated proteins will be identified by mass spectrometry. I will also analyze the RBPs activated and inactivated by HIV-1 infection using standard "mRNA interactome capture" protocol. Functionally relevant RBPs will be selected by applying sophisticated data analysis and their effects in HIV-1 infection will be evaluated in functional assays. Those RBPs causing strong phenotypes in viral replication will be characterized at the molecular level to understand their role in HIV-1 gene expression. The impact of one selected RBP in systemic HIV-1 infection will be determined using mouse transgenic models. This proposal may reveal the host circuits controlling HIV-1 gene expression, representing an important resource to expand our knowledge in HIV-1 biology.
Planned Impact
HIV-1 is a global health threat that affects millions of people overseas. By the end of 2011, 96,000 people were estimated to be infected with HIV-1 in United Kingdom and almost one million in Western Europe. To design efficient treatments, scientists need first to understand the sophisticated mechanisms developed by HIV-1 to replicate. This proposal aims at providing a comprehensive snapshot of the posttranscriptional regulation of gene expression exerted by this pathogen. Therefore, an improvement of our knowledge in HIV-1 infection may benefit directly and indirectly UK population as well as worldwide patients due to pandemic status of this pathogen. This proposal aims at revisiting HIV-1 infection from a systems biology point of view, making use of the latest high-throughput technologies. Resulting datasets will not be only of interest for scientists, as outlined before, but also for the commercial sector. Conventional antiviral regimens target viral enzymes, blocking viral replication. However, the high rate of errors introduced by the viral retrotranscriptase in each replication round promotes the emergence of drug-resistant variants. For this reason, new generation antiviral drugs target host proteins which are essential for viral replication, but are dispensable for cell survival. This is the case of debio, and inhibitor of the cellular factor cyclophilin A that is essential for hepatitis C virus (HCV) replication. This drug is currently in phase III of clinical trials and has proven to perform excellently when combined with interferons. One of the aims of this proposal is to find host factors playing essential roles in HIV-1 replication that will constitute potential therapeutic targets for HIV-1 treatment. The best candidates for such possibility will be characterized at the molecular level to understand their function in the cellular context. This information will be instrumental to develop strategies to inhibit these proteins. Moreover, the effects of the loss of function of a selected RBP in HIV-1 systemic infection will be explored in a mouse transgenic model. This will instruct about the feasibility and the consequences of using these proteins as targets to block viral replication. Taking together, these data may help to identify host-based therapeutic targets for HIV-1 infection, offering an excellent opportunity to collaborate with pharmaceutical companies in the future. Therefore, the possible outcomes of this project can potentially benefit HIV-1 patients as well as the private sector involved in HIV-1 therapeutic research.
The methods that I will develop for this proposal can serve as a basis for other research projects aiming at studying RBP dynamics in different biological contexts. This may place my future lab as an "epicenter" for collaborative works with other national and international institutions. All these together may contribute to the technological development of UK as well as to the international visibility of the host institution. I also expect that the discoveries made during the accomplishment of this proposal can serve as a starting point for subsequent research projects that may attract funding from international agencies (e.g. ERC).
The methods that I will develop for this proposal can serve as a basis for other research projects aiming at studying RBP dynamics in different biological contexts. This may place my future lab as an "epicenter" for collaborative works with other national and international institutions. All these together may contribute to the technological development of UK as well as to the international visibility of the host institution. I also expect that the discoveries made during the accomplishment of this proposal can serve as a starting point for subsequent research projects that may attract funding from international agencies (e.g. ERC).
Organisations
- University of Oxford (Lead Research Organisation)
- UNIVERSITY OF OXFORD (Collaboration)
- Duke University (Collaboration)
- École normale supérieure de Lyon (ENS Lyon) (Collaboration)
- Karolinska Institute (Collaboration)
- German Cancer Research Center (Collaboration)
- European Molecular Biology Laboratory (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- DIAMOND LIGHT SOURCE (Collaboration)
- University of Vienna (Collaboration)
- University of Tartu (Collaboration)
- University of Glasgow (Fellow)
People |
ORCID iD |
| Alfredo Castello Palomares (Principal Investigator / Fellow) |
Publications
Avolio R
(2018)
Protein Syndesmos is a novel RNA-binding protein that regulates primary cilia formation.
in Nucleic acids research
Bach-Pages M
(2017)
Plant RNA Interactome Capture: Revealing the Plant RBPome.
in Trends in plant science
Bach-Pages M
(2020)
Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method.
in Biomolecules
Beckmann BM
(2016)
The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions.
in Pflugers Archiv : European journal of physiology
Castello A
(2015)
Metabolic Enzymes Enjoying New Partnerships as RNA-Binding Proteins.
in Trends in endocrinology and metabolism: TEM
Castello A
(2017)
Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap.
in Nature protocols
Castello A
(2016)
Comprehensive Identification of RNA-Binding Domains in Human Cells.
in Molecular cell
Castello A
(2015)
The emerging universe of RNA binding proteins
in The Biochemest
Castello A
(2016)
Comprehensive Identification of RNA-Binding Proteins by RNA Interactome Capture.
in Methods in molecular biology (Clifton, N.J.)
| Description | Development of CLIP-seq and iCLIP for plants |
| Amount | £90,716 (GBP) |
| Funding ID | 0007038 |
| Organisation | University of Oxford |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 11/2019 |
| End | 10/2020 |
| Description | John Fell Fund |
| Amount | £57,651 (GBP) |
| Funding ID | 0006735 |
| Organisation | University of Oxford |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 11/2019 |
| End | 10/2020 |
| Description | John Fell Funds |
| Amount | £50,367 (GBP) |
| Funding ID | 151/055 |
| Organisation | University of Oxford |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 05/2016 |
| End | 04/2017 |
| Description | Marie-Sklodowska-Curie awarded to Manuel-Garcia Moreno |
| Amount | € 195,454 (EUR) |
| Funding ID | 700184 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 05/2017 |
| End | 05/2019 |
| Description | PROTEOME-WIDE IDENTIFICATION OF RNA-BINDING PROTEINS PLAYING CRITICAL ROLES IN VIRUS INFECTION |
| Amount | £439,272 (GBP) |
| Funding ID | MR/R021562/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2018 |
| End | 11/2021 |
| Description | RNA ReguNet - a Marie Sklowdowska Curie PhD Programme - https://cordis.europa.eu/project/id/101073094 |
| Amount | € 2,915,150 (EUR) |
| Funding ID | 101073094 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 04/2023 |
| End | 03/2026 |
| Description | Towards the discovery of cellular RNA-binding proteins with master regulatory roles in virus infection |
| Amount | € 2,000,000 (EUR) |
| Funding ID | 101001634 vRNP-capture |
| Organisation | European Research Council (ERC) |
| Sector | Public |
| Country | Belgium |
| Start | 12/2021 |
| End | 11/2026 |
| Title | Comparative RNA interactome capture |
| Description | RNA interactome capture has been broadly used to identify RNA binding proteins in cultured cells (Castello et al., Cell 2012). However, it was not adapted to compare the RNA-bound proteome of cells under different physiological states. For this, we combined SILAC (stable isotope labeling by amino acids in cell culture) with the RNA interactome workflow. This fusion now allows accurate estimation of the amount of protein interacting with RNA in two or more experimental conditions. As a proof of principle, we challenged cells with sindbis virus and found that more than two hundred RNA-binding proteins (RBPs) respond to the infection either increasing or decreasing their association with RNA. Further functional characterisation demonstrated that responsive RBPs play important roles in infection. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | We showed that RNA-binding protein dynamics is an excellent method to identify proteins that are functionally required by viruses. The proof of principle work was published in Molecular Cell and the method has now been applied to other viruses such as influenza A virus and human immunodeficiency virus, revealing host factors with master regulatory roles in infection. These works will be published between 2019 and 2020. Moreover, this research built the foundations of an MRC grant recently awarded to us and allowed us to establish many international collaborations. We plan to write a manuscript on the method to make it fully available to the community in a protocol format. |
| URL | https://www.sciencedirect.com/science/article/pii/S1097276519300371#gs4 |
| Title | Fluorescence-activated cell sorting of cells under different stages of HIV infection |
| Description | We have developed a fully infective HIV variant expressing mCherry (a red fluorescent protein) fused to an accessory protein. This virus has been proven very useful to monitor HIV infection in real time using both microscopy and a CO2-controlled plate reader. Basically, cells become red when they express the viral protein fused to mCherry. Taking advantage of this virus as well as an effective antibody recognising a viral (late) structural protein, we can sort with high purity cells under different stages of infection using Fluorescence-activated cell sorting (FACS). This technical advance will allow us to study the host cell-virus interactions occurring at different stages of infection. This method will have a big impact in bulk and single cell analyses and will be of broad interest in the field. |
| Type Of Material | Technology assay or reagent |
| Provided To Others? | No |
| Impact | We noticed that HIV infected cells are highly heterogeneous. This is in part because HIV infection is asynchronic, exhibiting enormous cell-to-cell variations. Asynchronous infection is associated to i) the high variability of the pre-integration step that can take from 4 to 12h, ii) the non-parallel transcriptional activation of the provirus after integration and iii) the short nature of the early phase (2-4 h). Moreover, we and others noticed that an important proportion of cells do not show traces of HIV even when infected with excess of virus. This suggests that these cells are either more refractory to infection or that the provirus has entered into a dormant state (latency). The handful on transcriptomic and proteomic studies available to date disregarded these facts and has used "time post infection" to separate HIV infection stages. Having a reliable and easy-to-apply method to separate cells under different stages of infection, we will be able to perform transcriptomic and proteomic analyses in homogeneous population of cells, which will increase the signal of the assay over the experimental noise and intra-sample variations. Global analyses of primary cells have remained a challenge so far due to the low penetrance of HIV infection in these cultures (~10%). Our approach can separate the infected cells from the uninfected ones, being compatible with primary cultures. This will open the possibility to study inter-individual variations of HIV infection. Moreover, our approach can be applied to single cell studies to identify inter-cellular variations of HIV infection and cellular responses. |
| Title | In-virion RNA interactome capture |
| Description | We adapted RNA interactome capture to purified viral particles (HIV and Sindbis virus) to detect protein-RNA interactions taking place inside capsids. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | Recent evidence suggests that viruses incorporate cellular proteins into the capsid core that can interact with the viral RNA genome and have important roles in the early phase of new infections. A system-wide method to detect such interactions and their biological relevance was missing. This technique allowed the identification of dozens of RNA-binding proteins important for HIV and Sindbis virus infection. Many of these proteins have never been linked to virus infection before and are thus novel targets to inhibit viral replication. We expect two research articles (one based on HIV and another based on Sindbis virus) at the beginning of next year revealing the virion-incorporated RNA-binding proteome that will be of interest for virologists and immunologists. |
| Title | Integrase-Scarlet tagged HIV |
| Description | We generated a fully infective HIV virus encoding Integrase tagged with the red fluorescent protein Scarlet. In addition, we also generated a single-round replication virus tagged in the same way. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Infection of human cells with this virus results in the release of new viral particles fluorescently labelled. They are very useful to track the fate of HIV capsids in a newly infected cell by fluorescent microscopy, including live cell imaging. This allows the study of RNA-binding (and other) proteins in the early phase of HIV infection. We expect a research publication in the current year or beginning of next revealing the role of RNA-binding proteins in early HIV infection. |
| Title | Jurkat FlpIn TRex cells |
| Description | Jurkat CD4+ cells containing FRT sites for stable integration of genes of interest. In addition, cells contain a tetracycline repressor and thus expression is inducible by doxycycline addition. |
| Type Of Material | Cell line |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | The FlpIn TRex system is widely used by the scientific community in overexpression studies or in experiments requiring tagged proteins with different purposes (for example, fluorescent microscopy, co-immunoprecipitation and protein-protein interactions, co-immunoprecipitation and RNA-protein interactions). However, a FlpIn TRex T-cell line susceptible for HIV infection (CD4+) was missing until now. We are using such cells in our lab to study the function of specific RNA-binding proteins in an HIV-infection context. We expect to include these results in coming research publications. |
| Title | Plate reader assay to monitor life virus replication |
| Description | A protocol was established to enable cultivation of tissue culture sample in a temperature and CO2 controlled plate reader while simultaneously measuring viral replication. The viral replication is assessed using a fluorescence tag inserted into the virus which will be a surrogate measure for viral replication. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Currently used methods to determine virus replication are end point based assays, often needing cellular lysis to asses the amount of virus e.g. via luciferase assays. The new method allows continuous measurement over multiple days, allowing to detect changes in viral replication kinetic with an accuracy which have not been possible before. In addition, this method is easily scalable, allowing medium throughput screens for factors impacting on viral replication e.g. in 96 well plates. This protocol was used in a recent Molecular cell publication doi: 10.1016/j.molcel.2019.01.017 and we plan to write a manuscript on the method to make it fully available to the community in a protocol format. |
| URL | https://www.cell.com/molecular-cell/fulltext/S1097-2765(19)30037-1 |
| Title | RBDmap, a novel method for system-wide profiling of RNA-binding domains |
| Description | This method employs UV crosslinking, oligo(dT) capture of poly(A) RNA, controlled proteolysis and mass spectometry to determine the protein regions engaged in RNA-binding in living cells in a system-wide scale. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | 1. Publication in Mol Cell with the biological data. 2. Full protocol published in Nature Protocols. |
| URL | https://www.nature.com/articles/nprot.2017.106 |
| Title | RNA interactome capture in suspension cells |
| Description | RNA interactome capture has so far only been produced in adherent cells. However in order to investigate how HIV-1 infection is reshaping the RBPome, we needed to optimise and adopt the method for CD4+ lymphocytes which are suspension cells. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | The RNA interactome capture in non-adherent cells allows the investigation of RBPome changes in any type of suspension cells including lymphocytes and macrophages, the target cells for HIV-1. However, this can also be applied to study other infections of the blood. In addition, this opens the way to investigate the RBPome any haemapoetic cell type, including those with heritable diseases or cancer. The method was shared in 2015 in collaboration with Ervin Fodor. |
| Title | SP3, a highly sensitive proteomics method |
| Description | The quality of proteomic analysis depends largely on the sample preparation method. To facilitate our work with very limited and precious samples (HIV-1 infected cells), we needed to implement and further develop a novel sample preparation method called SP3, which is more sensitive than conventional ones. It uses HILIC style binding to bind proteins to carboxylate-coated beads. After washing, proteins are eluted by tryptic digestion. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | This method allowed us to identify which cellular RNA-binding proteins play key roles in HIV-1 infection. This will be published in detail and is now available for other groups in the Advanced Proteomics Facility of the Department of Biochemistry, University of Oxford. |
| URL | https://www.cell.com/molecular-cell/fulltext/S1097-2765(19)30037-1 |
| Title | mCherry tagged HIV |
| Description | HIV-1 clones were generated harbouring mCherry. Different clones were generated, producing HIV-1 which expresses this fluorescent protein either early or late in it's replication cycle. The cloning was performed both in wild type HIV-1 (strain NL4.3) as well as a single round replicon. The fluorescent tagging allows monitoring of viral spread and viral replication in the different stages of gene expression and can be assessed either on a population level e.g. fluorescence measurement or on a cell by cell level via flow cytometry. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Such tagged viruses allow an easy way to measure not only infection rate, but also enable us to measure speed of viral replication under different conditions. The proof of principle work was published in Molecular Cell, where the method has also applied to other viruses such as SINV, revealing host factors with master regulatory roles in infection. Further viruses including Vaccinia are currently getting tagged and further work utilizing the HIV tagged constructs will be published between 2019 and 2020. Moreover, this research built the foundations of an MRC grant recently awarded to us and allowed us to establish many international collaborations. We plan to write a manuscript on the method to make it fully available to the community in a protocol format. |
| URL | https://www.cell.com/molecular-cell/fulltext/S1097-2765(19)30037-1 |
| Title | mCherry tagged SINV |
| Description | Sindbis virus (SINV) clones were generated harbouring mCherry at a second subgenomic locus. The fluorescent tagging allows monitoring of viral spread and viral replication in the different stages of gene expression and can be assessed either on a population level e.g. fluorescence measurement or on a cell by cell level via flow cytometry. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Such tagged viruses allow an easy way to measure not only infection rate, but also enable us to measure speed of viral replication under different conditions. The proof of principle work was published in Molecular Cell, where the method has also applied to HIV replicons, revealing host factors with master regulatory roles in infection. Further viruses are currently getting tagged. Moreover, this research built the foundations of an MRC grant recently awarded to us and allowed us to establish many international collaborations. We plan to write a manuscript on the use of the resource to make it fully available to the community in a protocol format. |
| URL | https://www.cell.com/molecular-cell/fulltext/S1097-2765(19)30037-1 |
| Title | Proteomic data describing the remodeling of the cellular proteome and RBPome upon viral infection |
| Description | Whole cell proteomic and RBPome data generated for a recent publication (DOI: 10.1016/j.molcel.2019.01.017) describing how virus infection remodels the cell on these global scales were made available as raw and processed proteomic data. They have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009789. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | This data has been used as the basis for a recent publication (DOI: 10.1016/j.molcel.2019.01.017) |
| URL | http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009789 |
| Title | RBDmap - A comprehensive collection of RNA-binding domains |
| Description | We have recently published a method called RBDmap; which can determine the RNA-binding site of RNA-binding proteins in living cells. This method combines UV crossliking on living cells to covalently link nucleotides and amino acids placed at zero distances. After lysis, protein-RNA complexes are isolated under denaturing conditions and eluates are treated with a protease that cleaves every 17 amino acids in average. The RNA with the protein portion still crosslinked to it are purified with oligo (dT). After tryptic digestion, peptides are identified by mass spectrometry. This has been recently published in Molecular Cell (Castello et al., Mol Cell, 2016). Following this protocol, we can identify the sites of contact between proteins and RNA. In particular, we identified more than 1,100 RNA binding sites mapped to 529 human proteins. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | This is the first in vivo established repertoire of RNA-binding domains. This dataset is of high interest for RNA-biologists working with proteins displaying and uncanonical mode of RNA binding. This is also very useful for people interested in iCLIP and similar methods to study protein-RNA interactions. The paper describing this method has been published in a high impact journal, Molecular Cell and it has been already cited 14 times in half a year since its publication. I have been invited to a number of seminars and conferences to present this work. |
| URL | http://www-huber.embl.de/users/befische/RBDmap/ |
| Title | RNA sequencing data describing the remodeling of the cellular transcriptome upon viral infection |
| Description | RNAsequencing data for the recent publication (DOI: 10.1016/j.molcel.2019.01.017) as raw and processed data are available at GEO: GSE125182. Similarily the iCLIP-seq data is available under the same GEO. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The data has been used for a recent publication DOI: 10.1016/j.molcel.2019.01.017 |
| URL | http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE125182 |
| Title | The core viral RNA interactome |
| Description | This is a compendium of the cellular RNA-binding proteins that interact with the RNAs of alphavirus, coronavirus and flavivirus. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | This dataset has established the foundations of future research. The identification of cellular factors that engage with the RNAs of viruses from different families may lead to the identification of antivirals with broad-range therapeutic activity. |
| URL | https://doi.org/10.1016/j.tibs.2021.08.002 |
| Title | Virus-linked RNA interactome |
| Description | Collection of RNA-binding proteins linked to virus infection of immunity. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | This database has been published in WIREs RNA journal as a review article (doi: 10.1002/wrna.1498) and is useful for the scientific community in the fields of virology, immunology and RNA. |
| URL | https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fwrna.1498&file=wrna1498-sup-... |
| Description | Data analysis |
| Organisation | German Cancer Research Center |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | We have performed the experiments and generated the data. 1. We have implemented RNA interactome capture (Castello et al., Cell, 2012; Nat Protocols, 2013) to: > Suspension cells: the CD4+ lymphocytic cell line SubT1. > Adherent cells (Hek293) infected or not with sindbis virus. > Adherent cells (Hek293T) infected or not with vaccinia virus. > Adherent cells (A549) infected or not with influenza virus. > Suspension cells (SupT1) infected or not with human immunodeficiency virus. 2. We have also generated proteome and transcriptome samples from infected and mock cells. 3. We have performed all the follow up experiments. |
| Collaborator Contribution | 1. The Ficher lab has analysed has generated an analytical pipeline to compare RNA interactomes (repertoire of RNA-binding proteins) generated under different physiological conditions (infected and not infected). The analytical pipelines are "ready to apply" to any similar dataset generated with RNA interactome capture. This has already been used to analyse the following RNA interactomes: > Suspension cells: the CD4+ lymphocytic cell line SubT1. > Adherent cells (Hek293) infected or not with sindbis virus. > Adherent cells (Hek293T) infected or not with vaccinia virus. > Adherent cells (A549) infected or not with influenza virus. > Suspension cells (SupT1) infected or not with human immunodeficiency virus. 2. They have generated an analytic pipeline to analyse whole cell proteomes under differential conditions using the state-of-the-art statistical methods. This has been already applied to: > Adherent cells (Hek293) infected or not with sindbis virus. 3. They have generated an analytical pipeline to analyse transcriptomic data from multiple angles. In particular, the pipeline focus on identifying steps in RNA metabolism affected by viruses (or any other cellular perturbation). This pipeline has been applied to: > Adherent cells (Hek293) infected or not with sindbis virus. 4. They have worked a way to make the data available in an intuitive, "easy-to-use" website (e.g. http://www-huber.embl.de/users/befische/RBDmap/). These sites will be released upon publication and will be open access. |
| Impact | Our collaborator Bernd Fischer sadly passed away in 2017. 2 publications in Molecular Cell and 1 publication in Nature Protocols. |
| Start Year | 2014 |
| Description | Emiliano Ricci - Gene editing using next generation CRISPR/cas9 systems |
| Organisation | École normale supérieure de Lyon (ENS Lyon) |
| Country | France |
| Sector | Academic/University |
| PI Contribution | We are supporting them with mass spectrometry analyses. |
| Collaborator Contribution | Emiliano has helped us to generate in a systematic manner, knock-out (KO) and knock-in lines using the latest CRISPR/cas9 technology. He has generated a new CRISPR/cas9 system, called nanoblades, in which protein and guide RNA are self-packaged into virus like particles (VLPs). By incubating cells refractory to conventional transfection such as T lymphocytes we obtain 50-70% of editing events making the generation of multiple KO lines in these challenging systems feasible. |
| Impact | Our collaboration led to a peer-reviewed publication in Molecular Cell (https://www.sciencedirect.com/science/article/pii/S1097276519300371#gs4) and will generate three more publications by the end of 2019 and beginning of 2020. |
| Start Year | 2017 |
| Description | Establishment of multi-virus screening assay |
| Organisation | University of Tartu |
| Country | Estonia |
| Sector | Academic/University |
| PI Contribution | 1- We have replaced fluorescence tags in some of the virus constructs (we received from our collaborator), so all the viruses are mCherry tagged. 2- We have implemented these additional viruses in our multi-virus screening assay(described in the method section) |
| Collaborator Contribution | They provided fluorescence -tagged viruses covering two different virus families: Alphaviruses (Sindbis, Semiliki, Ross river and O'nyong'nyong) and Flaviviruses ( ZIKA, Yellow-fever and Dengue2) |
| Impact | Establishment of multi-virus screening assay |
| Start Year | 2019 |
| Description | Global analysis of influenza virus interactions with the host RNA biology machinary |
| Organisation | University of Oxford |
| Department | Sir William Dunn School of Pathology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I am co-supervising a PhD student from Ervin Fodor lab in the Dunn School of Pathology to investigate the interactions of Influenza virus and the host RNA machinery. For this work, the Fodor lab applied RNA interactome capture to cells infected with Influenza, method that we have already established for HIV and other viruses. This collaboration is in an early stage, but our preliminary results are very encouraging. |
| Collaborator Contribution | Benjamin Nilsson (PhD in the Fodor lab) have adapted our RNA interactome protocol to A549 lung epithelial cells. After the successful determination of the RNA-bound proteome of A549 cells, Benjamin applied this method to A549 infected with Influenza virus and out preliminary results are very promising, suggesting broad alterations of the RNA-bound proteome triggered after infection. |
| Impact | 1. We have generated the first RNA inteactome of a lung epithelial cell line, A549 2. We identified dozens of novel lung epithelial-specific RNA-binding proteins. 3. We have optimised the protocol to monitor RNA binding globally in A549 cells infected with Influenza virus. 4. We have determined the RBPome of influenza virus-infected cells. 5. We have analysed whole proteome and transcriptome of influenza virus-infected cells. A manuscript will be submitted for publication in Summer 2019. |
| Start Year | 2015 |
| Description | Gracjan Michlewski - Role of TRIM25 RNA-binding activity on virus infection |
| Organisation | University of Edinburgh |
| Department | Division of Pathway Medicine |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The aim of this project is to understand the role of the RNA-binding activity of the antiviral protein TRIM25 in Sindbis virus infection. We have studied the effect of deletion or overexpression of different domains of TRIM25, tracking in real-time the replication of Sindbis virus labelled with mCherry in a fluorescence plate reader. In addition, we have obtained cell lysates from different KO cell lines infected with Sindbis virus to be analysed by CLIP-seq in order to detect RNA-binding sites of TRIM25. |
| Collaborator Contribution | Gracjan Michlewski lab has provided knock-out and knock-in TRIM25 cells and has perfomed CLIP-seq experiment and analysis with the lysates produced by our lab. |
| Impact | Gracjan Michleswki and other member of his lab are co-authors of our research article (doi: 10.1016/j.molcel.2019.01.017). We have obtained exciting results that are expected to be published in the next year. |
| Start Year | 2018 |
| Description | Ilan Davis |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Our Proteomic work has provided insight into which proteins are involved in shaping the RNA interactome upon viral infection. In order to understand the implications on this data further we now generated transcriptome analysis in infected and uninfected states using RNA sequencing approaches. Furthermore, we generated a variety of genetically modified cell lines to investigate the changes observed during infection on a molecular level. |
| Collaborator Contribution | Ilan Davis provided help and expertise in super-resolution microscopy to further our understanding of candidate proteins. Furthermore his group is providing expertise in data-analysis. In particular bioinformatic expertise to process transcriptome data - in particular RNA sequencing and iCLIP - via a dedicated postdoc Aino Jarvelin. |
| Impact | So far this collaboration has led to contribution to multiple figures in a recent publication in Molecular Cell. |
| Start Year | 2016 |
| Description | Jane McKeating - Effect of hypoxia invirus infection |
| Organisation | University of Oxford |
| Department | Nuffield Department of Medicine |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This collaborative project aims at understanding the effect of oxygen tension on HIV infection using transcriptomics and quantitative proteomics. Our research team contributes to this project by perfoming HIV work in a Category 3 containment laboratory, generating and processing samples for RNA sequencing and mass spectrometry. |
| Collaborator Contribution | Jane McKeating lab contributes to the project by providing cell lines and hypoxia chambers to perform experiments under different O2 conditions. Shabaz Mohammed lab provides mass spectrometry reagents, equipment and data analysis. |
| Impact | The lab was awarded a John Fell Fund from University of Oxford to support this project for 1 year (covering postdoc salary plus research costs). The collaboration is multi-disciplinary involving virology and hypoxia fields plus transcriptomics and quantitative proteomics. |
| Start Year | 2019 |
| Description | Javier Martinez - tRNA splicing ligase complex in HIV-1 infection |
| Organisation | University of Vienna |
| Department | Max F. Perutz Laboratories (MFPL) |
| Country | Austria |
| Sector | Academic/University |
| PI Contribution | We have performed the experiments and generated the data for the functional analysis of the human tRNA splicing ligase in HIV-1 infection. In particular, we have tested HIV-1 fitness assays on cells lacking components of the tRNA ligase complex. We have also performed protein-protein interaction analyses of subunits of the tRNA splicing ligase complex in HIV-1 infection context, and we have analysed the data. |
| Collaborator Contribution | The Martinez lab have provided their expertise in the molecular biology of the human tRNA splicing ligase complex to instruct our experiments. They have also performed in vitro analysis of the tRNA ligase activity. They have also provided key reagents and protocols. |
| Impact | Impact of the tRNA splicing ligase in HIV-1 infection. |
| Start Year | 2015 |
| Description | Maria Harkiolaki, Ilan Davis and Ian Dobbie - Correlative microscopy in virus-infected cells |
| Organisation | Diamond Light Source |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | The Castello and Davis lab have obtained and processed samples for correlative microscopy using a new platform for imaging cells in 3D, under cryogenic conditions. We used Hela cells expressing MOV10-YFP (marker of P-bodies) and labelled with fluorescent organelle-specific dyes, infected with Sindbis mCherry virus. |
| Collaborator Contribution | Our partners built the microscopes (cryo-structured illumination fluorescence microscope and soft X-ray tomography), acquired and analysed the images. |
| Impact | This collaboration led to a manuscript that is under preparation and will be submitted in March 2020. This is a multi-disciplinary collaboration that involves virology and molecular biology (Castello and Davis lab) and super-resolution fluorescent and X-ray microscopy (including physicists and engineers in Micron Oxford and Diamond Light Source). |
| Start Year | 2018 |
| Description | Maria Harkiolaki, Ilan Davis and Ian Dobbie - Correlative microscopy in virus-infected cells |
| Organisation | University of Oxford |
| Department | Micron Oxford Advanced Bioimaging Unit |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Castello and Davis lab have obtained and processed samples for correlative microscopy using a new platform for imaging cells in 3D, under cryogenic conditions. We used Hela cells expressing MOV10-YFP (marker of P-bodies) and labelled with fluorescent organelle-specific dyes, infected with Sindbis mCherry virus. |
| Collaborator Contribution | Our partners built the microscopes (cryo-structured illumination fluorescence microscope and soft X-ray tomography), acquired and analysed the images. |
| Impact | This collaboration led to a manuscript that is under preparation and will be submitted in March 2020. This is a multi-disciplinary collaboration that involves virology and molecular biology (Castello and Davis lab) and super-resolution fluorescent and X-ray microscopy (including physicists and engineers in Micron Oxford and Diamond Light Source). |
| Start Year | 2018 |
| Description | Quantitative Proteomics |
| Organisation | University of Oxford |
| Department | Department of Chemistry |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have performed the experiments and generated the data. 1. We have implemented RNA interactome capture (Castello et al., Cell, 2012; Nat Protocols, 2013) to: > Suspension cells: the CD4+ lymphocytic cell line SubT1. > Adherent cells (Hek293) infected or not with sindbis virus. > Adherent cells (Hek293T) infected or not with vaccinia virus. > Adherent cells (A549) infected or not with influenza virus. > Suspension cells (SupT1) infected or not with human immunodeficiency virus. 2. We have also generated proteome and transcriptome samples from infected and mock cells. 3. We have performed protein-protein interaction analysis in sindbis virus infected cells of three of the candidates identified from the above studies. 4. We are performing all the follow up data analysis. |
| Collaborator Contribution | 1. The Mohammed lab has helped us to combine the RNA interactome capture protocol (Castello et al., Nature Prot, 2013) with SILAC labelling for quantitative proteomics. This has been already applied to: > Suspension cells: the CD4+ lymphocytic cell line SubT1. > Adherent cells (Hek293) infected or not with sindbis virus. > Adherent cells (Hek293T) infected or not with vaccinia virus. > Adherent cells (A549) infected or not with influenza virus. > Suspension cells (SupT1) infected or not with human immunodeficiency virus. 2. They have combined SILAC and fractionation to study in high depth the proteome of infected cells. 3. They have implemented a new method for mass spectrometry sample preparation called SP3. This method allow us to reduce the scale of the experiments. 4. They have processed immunoprecipitations from 3 candidate proteins derived from the studies above to study their protein-protein interaction partners in infected cells. |
| Impact | 1. Determination of the RBPome (repertoire of RNA-binding proteins) of SupT1 cells 2. Determination of the alterations in the RBPome induced by sindbis virus infection. 3. Determination of the alterations in the RBPome induced by human immunodeficiency virus infection - In progress. 4. Determination of the alterations in the RBPome iinduced by to vaccinia virus infection. 5. Determination of the alterations in the RBPome induced by influenza virus infection. 6. Impact of the alterations of the RBPome in response to sindbis virus infection on the cellular and viral proteome. Our collaboration led to a peer-reviewed publication in Molecular Cell (https://www.sciencedirect.com/science/article/pii/S1097276519300371#gs4) and will generate three more publications by the end of 2019 and beginning of 2020. |
| Start Year | 2015 |
| Description | Reader of RNA modifications in HIV-1 infection |
| Organisation | Duke University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We are performing the mass spectrometry based RNA interactome capture in wt and KO lines for enzymes which modify RNA with the aim to identify the RNA binding proteins which are affected by a given RNA modification. This will potentially highlight readers and affectors of RNA modifications, in particular two which have importance on HIV-1 replication. |
| Collaborator Contribution | The laboratory of Professor Bryan Cullen identified several RNA modifying enzymes which have an effect on HIV-1 replication. Although the enzymes show a phenotype, the underlying molecular mechanisms is still not fully understood. |
| Impact | Collaboration still in progress. No formal outcome yet. In order to further understand the results of RNA modifications of HIV-1, as identified by the Cullen lab, we are now using our expertise on RNA biology to identify the underlying molecular mechanism, in particular how these modifications are translated by the cell. |
| Start Year | 2019 |
| Description | Vicent Pelechano - RNA sequencing analysis in virus-infected cells |
| Organisation | Karolinska Institute |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | We are generating RNA preparations from virus infected cells |
| Collaborator Contribution | Vicent Pelechano's team is processing or cDNA libraries using cutting edge technologies to improve our understanding on the architecture of the transcriptome of virus infected cells. |
| Impact | Our collaboration led to a peer-reviewed publication in Molecular Cell (https://www.sciencedirect.com/science/article/pii/S1097276519300371#gs4) and will submit one additional manuscript by the end of 2019 and beginning of 2020. |
| Start Year | 2016 |
| Description | Visualisation of SARS-CoV-2 RNA - smFISH |
| Organisation | University of Oxford |
| Department | Department of Biochemistry |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | With our expertise to work in CL3 conditions, we establishing the methodology/procedures and provided sample of Calu-3 cells infected with SARS-CoV-2 under CL3 conditions for use in smFISH. |
| Collaborator Contribution | Ilan Davis is an expert in RNA biology with a strong expertise in super resolution microscopy. He has a setup to visualise single molecule RNA in cells (single molecule fluorescence in situ hybridisation - smFISH) and adapted his protocols for us to visualise SARS-CoV-2 RNA in individual infected cells. Jane McKeating is an expert virologist with a strong collaborative network, which recently started studying SARS-CoV-2 infection under hypoxia. Our smFISH setup helped her to address aspects of SARS-CoV-2 RNA replication for her work. We continue this collaboration to address the early stages of RNA replication in individual cells and their effect on bystander cells on an single molecule level, allowing us to follow even very early stages of viral RNA replication in detail. |
| Impact | Publication under review in "Cell reports": "Hypoxic and Pharmacological Activation of HIF Inhibits SARS-CoV-2 Infection of Lung Epithelial Cells" https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3720002 Further publication in preparation. |
| Start Year | 2020 |
| Description | Visualisation of SARS-CoV-2 RNA - smFISH |
| Organisation | University of Oxford |
| Department | Nuffield Department of Medicine |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | With our expertise to work in CL3 conditions, we establishing the methodology/procedures and provided sample of Calu-3 cells infected with SARS-CoV-2 under CL3 conditions for use in smFISH. |
| Collaborator Contribution | Ilan Davis is an expert in RNA biology with a strong expertise in super resolution microscopy. He has a setup to visualise single molecule RNA in cells (single molecule fluorescence in situ hybridisation - smFISH) and adapted his protocols for us to visualise SARS-CoV-2 RNA in individual infected cells. Jane McKeating is an expert virologist with a strong collaborative network, which recently started studying SARS-CoV-2 infection under hypoxia. Our smFISH setup helped her to address aspects of SARS-CoV-2 RNA replication for her work. We continue this collaboration to address the early stages of RNA replication in individual cells and their effect on bystander cells on an single molecule level, allowing us to follow even very early stages of viral RNA replication in detail. |
| Impact | Publication under review in "Cell reports": "Hypoxic and Pharmacological Activation of HIF Inhibits SARS-CoV-2 Infection of Lung Epithelial Cells" https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3720002 Further publication in preparation. |
| Start Year | 2020 |
| Description | enhanced and comparative RNA interactome capture |
| Organisation | European Molecular Biology Laboratory |
| Department | European Molecular Biology Laboratory Heidelberg |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | This collaboration is combining our comparative RNA interactome capture approach, including the bioinformatic processing with the eRIC approach from our collaboration partners to provide a unified state-of-the-art protocol for the community to follow |
| Collaborator Contribution | Our partners developed and LNA based RNA interactome capture called eRIC approach, which we combine with our cRIC to provide a unified state-of-the-art protocol for the community to follow. |
| Impact | Protocol written and submitted to Nature Protocols. Currently under review. |
| Start Year | 2019 |
| Description | 12th Blizard Institute HIV Symposium - Oral presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation of the work to an HIV expert audience to engage experts in the field. Multiple people asked questions about the work following the talk and engaged me on the topic afterwards, indicating that the topic is of great interest to the expert audience. |
| Year(s) Of Engagement Activity | 2019 |
| Description | 4 lectures in virology |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | I introduced the basics on virology and the outcomes of this fellowship to students in the 3th and 4th year of Biochemistry (University of Oxford). |
| Year(s) Of Engagement Activity | 2018 |
| Description | 8th Symposium on Structural Proteomics |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | I was invited to give a talk in this conference that brings together some of the most prestigious experts in proteomics. My talk was very well received and helped to establish new collaborations. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.ssp2018.de/ |
| Description | Alfredo Castello - Midlands RNA saloon - Online talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited to give an online talk in the Midlands RNA saloon. Several hundreds people attended and there was a nice discussion afterwards. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.midrna.co.uk/ |
| Description | Alfredo Castello - Online Conference - PMF proteomic meeting - Keynote speaker |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited to give the keynote lecture at the online PMF proteomics meeting. Several hundreds of people attended and there was a nice discussion afterwards. I established a collaboration with Kathryn Lilley (Cambridge). |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.proteomicsmethodsforum.org.uk/conferences/2020-cambridge/ |
| Description | British Society for Proteome Research conference - Invited talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at the British Society for Proteomic Research. Great discussions |
| Year(s) Of Engagement Activity | 2022 |
| Description | Career Development talk for the Biochemistry postdoctoral association - Transition to a PI position |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | I explained my experience at applying to career development fellowships and provide my advises on how to build a strong research group. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Castello, Davis, Fulga & Raff Labs retreat 2015 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was giving a presentation regarding the research undertaken in front of 3 different research groups. These groups are local to the area and we are interested in fostering links regarding potential collaborations with these groups. This already resulted in us gaining help using microscopy equipment. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Chairman and Talk in the conference: EMBO Protein Synthesis and Translational Control |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I acted as chairman of the 'RNP complexes' session of this prestigious conference. I introduced to all the speakers and gave a 30 min talk on the project. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.embl.de/training/events/2019/TRC19-01/ |
| Description | Chromosomal and RNA biology group presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation in a departmental talk series. Presentation was well received with several group leaders commenting positively on the presentation. Valuable feedback gained. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Communication of our work in the Spanish National Radio (RNE) |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | My role was to write the script for the locutor. He spoke about our work on OAS1 and SARS-CoV-2 published in Science |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.rtve.es/play/audios/el-laboratorio-de-jal/laboratorio-jal-defensas-innatas-heroicas-cont... |
| Description | Department of Biochemistry - University of Cambridge |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited speaker for an online seminar |
| Year(s) Of Engagement Activity | 2021 |
| Description | Departmental talk 2015 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Departmental talk series to gain feedback on the project and presentation skills. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Departmental talk 2016 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Departmental talk series to gain feedback on the project and presentation skills. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Departmental talk 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Departmental talk series to gain feedback on the project and presentation skills. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Departmental talk 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of the work to members of the Department in a Seminar series. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Development of the Castellolab website in blog format |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I generated and updated regularly our lab website. It is designed in a blog format that we use to post interesting research news, our scientific achievements, job opportunities, etc. |
| Year(s) Of Engagement Activity | 2015,2016,2017,2018,2019,2020 |
| URL | http://castellolab.com/ |
| Description | ECMC Scientific Advisory Board, Department of Oncology, Oxford |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | I advise oncologists using drugs against RNA-binding proteins on how to understand/investigate the effects of these drugs in cancer cells. |
| Year(s) Of Engagement Activity | 2017,2018 |
| URL | http://www.ecmcnetwork.org.uk/oxford |
| Description | ECMC Scientific Advisory Board, Department of Oncology, Oxford |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | I advise oncologists using drugs against RNA-binding proteins on how to understand/investigate the effects of these drugs in cancer cells. |
| Year(s) Of Engagement Activity | 2018 |
| Description | EMBO Workshop Pathogen Immunity and Signalling 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation on HIV-interactome capture, to present the work to an expert audience and gain feedback. Talked with several group leaders about the work and they showed great interest. Discussed possible follow up strategies. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Functional Genomics Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presented at the workshop to foster collaboration within the Oxford high throughput functional genomics community. There was great interest in the poster throughout the two days of the conference. |
| Year(s) Of Engagement Activity | 2016 |
| Description | GRC Physical Virology - Invited Speaker |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at a large GRC conference in virology. A lot of interactions and new connections were made. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Interview in Spanish national radio - RNE |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Interview in the Spanish National Radio to speak about our work in SARS-CoV-2, which was published in Mol Cell. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.rtve.es/play/audios/marca-espana/marca-espana-nuevas-estrategias-terapeuticas-contra-inf... |
| Description | Invited Talk in the EMBO RNA: structure meets function conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was a large conference with hundreds of attendants |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://meetings.embo.org/event/18-rna |
| Description | Invited speaker - Conference - Molecular life of stem cells - Ljubljana (Slovenia) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented my research in global analysis of protein-RNA interactions in infected cells |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.fkkt.uni-lj.si/fileadmin/datoteke/Obvestila/Utrip/brochure_MLSC_.pdf |
| Description | Keynote speaker of the RNA club University of Leeds, York and Sheffield. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited as keynote speaker for the RNA club organised between the University of Leeds, York and Sheffield |
| Year(s) Of Engagement Activity | 2019 |
| Description | Lecture in a Master programme - G3: Frontiers in RNA Biology HS16 (#13186-01) - FMI, Basel (Switzerland) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Lecture on viruses; gene organisation and host-virus interactions |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.fmi.ch/Training/Teaching/courseDetails.html?course=127 |
| Description | MRC Centre for Reproductive Health - University of Edinburgh |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited speaker in an institutional seminar |
| Year(s) Of Engagement Activity | 2022 |
| Description | Member of the Committee of experts in AREF Research Development Fellowships |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I participate in the panel that awards the AREF fellowships to African postdoctoral fellows interested in improving their skills |
| Year(s) Of Engagement Activity | 2016,2017 |
| URL | https://www.africaresearchexcellencefund.org.uk/2017/04/04/aref-research-development-fellowships-201... |
| Description | Open the Castello lab Twitter |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We open our twitter account to communicate with other researchers and with the wider public. We post and explain our work and help to expand and share the work of others. @Castello_lab |
| Year(s) Of Engagement Activity | 2019,2020 |
| URL | https://twitter.com/castello_lab |
| Description | Oral presentation in Chromosome&RNA Biology Group meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation in Chromosome&RNA Biology Group meeting in the Department of Biochemistry (University of Oxford). |
| Year(s) Of Engagement Activity | 2018 |
| Description | Oral presentation in Chromosome&RNA Biology Group meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk in Department Of Biochemistry (University of Oxford) in the Chromosome&RNA Biology Group seminar series. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation in Department of Biochemistry Annual Recess |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation in the Department of Biochemistry Annual Recess addressed to all researchers in our department. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Oral presentation in UK RNA Meeting 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation in UK RNA meeting involving researchers in the field of RNA biology based on UK. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Outreach in local school |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Representation as a STEM parent ambassador at a local school (St. Gregory the Great) as part of their summer party. The aim was to engage not only children but also motivate parents to participate in STEM related activities together with their children to increase the impact from a "one-off" activity to a more sustainable engagement in science. More than 100 pupils attended the party with about 5 science activities at our stall being highly popular. Further information material suggesting further STEM activities at home was handed out in addition to direct engagement on the day. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Oxford Science Fair |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Volunteer at a stall at the Oxford Science Fair representing the Department of Biochemistry. A lot of interest on the stall. I personally engaged particularly with school aged children. However, got the comment from accompanying parents that they now understand this as well. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Postdoc poster session in the Department |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation within the department with the aim to foster contacts and collaboration with not directly related research groups. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster at the RNA society meeting 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a poster with details of the impact of HIV infection on RNA binding protein activity. The poster sparked questions and discussion with multiple PIs as well as postdocs. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.rnasociety.org/conferences/rna-2017/ |
| Description | Poster presentation in EMBO Pathogen immunity and signalling |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation in international meeting in Oxford, involving researchers in the field of immunity. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation in Positive-Strand RNA virus Symposia |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation in international meeting in Killarney (Ireland), involving researchers in the field of positive-strand RNA viruses. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation in RNA Society Meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation in RNA meeting Prague 2017, involving researchers in the field of RNA biology from all around the world. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Presentation to Departmental Support Staff |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Supporters |
| Results and Impact | A presentation in lay terms of the research the group is undertaking to non academic support staff at the department. The intention was to inform staff not involved in research about the research happening in the department and foster an understanding about the worth and contribution of their work in supporting medical research at the department. The presentation was designed to engage the audience to ask questions at any stage which got a great response followed by a informal coffee with further discussion. Multiple staff member reported a changed appreciation of the impact the research and their contribution is having. People commenting even weeks later on the exciting research we are undertaking. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Press release in Advanced Science News |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press released explaining our review article (doi: 10.1002/wrna.1498) to a broad audience. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.advancedsciencenews.com/unconventional-rna-binding-proteins-step-into-the-virus-host-bat... |
| Description | Press release in Medical Sciences Division Oxford Website |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Press release in the Medical Sciences Division and Department of Biochemistry News section, addressed to the University of Oxford Scientific Community, explaining in lay language our research article (doi: 10.1016/j.molcel.2019.01.017). |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.medsci.ox.ac.uk/news/discovering-the-cellular-rna-binding-proteins-controlling-virus-inf... |
| Description | Press release in UAM Gazette |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Press release in outreach website from the Autonomous University of Madrid to explain our research article (doi: 10.1016/j.molcel.2019.01.017) to a broad audience (mainly undergraduate students but also researchers in different disciplines). |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.uam.es/ss/Satellite?c=UAM_NotCientific_FA&cid=1446777217997&language=es&pagename=Universi... |
| Description | Press release in our work on the composition of SARS-CoV-2 ribonucleoproteins |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press release in our work in SARS-CoV-2 for the Department of Biochemistry, University of Oxford. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.bioch.ox.ac.uk/article/new-therapeutic-possibilities-at-the-heart-of-sars-cov-2-life-cyc... |
| Description | Press release in our work on the composition of SARS-CoV-2 ribonucleoproteins |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | A press release in our work in SARS-CoV-2. This was press release was echoed by many newspapers, magazines and news agencies some examples below: https://www.heraldscotland.com/news/19326873.coronavirus-glasgow-university-study-paves-way-treatments/ https://news.stv.tv/scotland/covid-19-study-could-lead-to-treatments-for-future-viruses?top |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.gla.ac.uk/news/archiveofnews/2021/may/headline_791504_en.html |
| Description | Press release in our work on the composition of SARS-CoV-2 ribonucleoproteins - University of Oxford |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press release of our work in SARS-CoV-2 at the University of Oxford website. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.ox.ac.uk/news/2021-05-27-sars-cov-2-rna-discovery-unlocks-new-potential-treatments |
| Description | Press release in our work on the composition of SARS-CoV-2 variants |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press release for our work on single molecule analysis of SARS-CoV-2 replication and its implications for new variants. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.gla.ac.uk/researchinstitutes/iii/newsevents/headline_836247_en.html |
| Description | Project website (hRBP-virion) |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Website to explain a research project and the outcome in lay language for researchers in other fields and a broad audience. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://hrbpvirion.wordpress.com/ |
| Description | RNA & Transcription meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Interdepartmental talk series. The focus was on presenting the labs research scope and spark collaborations. |
| Year(s) Of Engagement Activity | 2016 |
| Description | RNA UK conference (Windermere, UK) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Selected talk at a national conference for scientists working on RNA biology in the UK. Several scientist including group leaders remarked on the interest the talk had to them. I also got told by two group leaders that they will get in contact with Alfredo regarding potential collaborations. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://rnauk2016.wordpress.com/ |
| Description | RNA localisation FOR2333 - Invited speaker |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | It was the German RNA meeting. I met several scientists and started collaborations. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://for2333.de/index.php?browse=356248&newsid=325700 |
| Description | Randall Seminar at the King College |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar about our investigations in virus-host interactions. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.kcl.ac.uk/lsm/newsevents/eventrecords/2016/apr/Randall-Seminar-Dr-Castello.aspx |
| Description | Results in brief (hRBP-virion) |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press release explaining the outcome of a research project to a broad audience. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://cordis.europa.eu/article/id/413352-tracing-the-early-steps-of-hiv-infection-via-protein-sign... |
| Description | Seminar at the Centro Nacional de Biotecnologia (CNB), Spain |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited to present my work in a formal seminar at the Centro Nacional de Biotecnologia (Madrid, Spain). Following up discussing led to potential collaborations with groups there. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Seminar at the DKFZ, Heidelberg, Germany |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | I was invited to give a talk in the DKFZ in Heidelberg, Germany. Some of the most recognised virologists in Europe attended and they liked very much my talk. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Seminar at the Department of Biochemistry, ETH, Zurich |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | I was invited to present the scientific outcomes of this fellowship to experts in RNA biology |
| Year(s) Of Engagement Activity | 2018 |
| Description | Seminar at the Department of Pathology, Cambridge |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | I was invited to present the scientific outcomes of this fellowship to virologists and pathologists from the University of Cambridge |
| Year(s) Of Engagement Activity | 2019 |
| Description | Seminar at the Dunn School of Pathology - University of Oxford - Invited by the postdoc association |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | A talk invited by the postdoc association with focus on Research and Career Development Discussions. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Seminar at the LMCB, London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | I was invited to present the scientific outcomes of this fellowship to experts in RNA biology |
| Year(s) Of Engagement Activity | 2018 |
| Description | Seminar at the London RNA club |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited speaker in the London RNA club, which includes very prestigious RNA biologists in the UK (e.g. Prof. Jernej Ule, UCL). The talk was very appreciated by the audience and helped to forge new collaborations. I was then included as member of the London RNA club. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://londonrnaclub.uk/ |
| Description | Seminar at the Ludwig Institute, Oxford |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited to give a talk in the Ludwig Institute for Cancer Research. The audience was very interested in applying my methods to a cancer-related project and indeed I establish a collaboration with Dr. Gareth Bond. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Seminar at the RNA Club Munich |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited speaker in the RNA Club in Munich. This club is form by internationally recognised laboratories in the RNA field (E.g. Prof. Elena Conti, MPI), based in Munich. The talk was very well perceived and it was a very interesting follow up discussion. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Seminar at the Universidad Federico II di Napoli |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar about our research in host-virus interactions - Excellent feedback. A collaboration was forged with Franca Esposito's lab and one PhD student in her lab (Rosario Avolio) has worked in my lab as academic visitor for five months in a common project. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Seminar at the bugg session of the Dunn School of Pathogly, University of Oxford |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | The aim of this talk was to show to other labs interested in host-pathogen interactions in Oxford, the work that we are currently doing in our laboratory. This talk have helped to foster a potential collaboration with Prof. Acuto (Dunn School of Pathology). |
| Year(s) Of Engagement Activity | 2016 |
| Description | Seminar for the University of Indiana |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Online seminar - Invited speaker |
| Year(s) Of Engagement Activity | 2021 |
| Description | Talk about the use of Mass spectrometry to PhD students |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Presentation about in which way mass spectrometry can be used to answer biological questions in research projects. One of the PhD student has since contacted us regards doing a rotation project with us and is considering a research project with us for her PhD. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Talk at FMI, Basel (Switzerland) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk about our research in global protein-RNA interactions analyses in infected cells |
| Year(s) Of Engagement Activity | 2016 |
| Description | Talk at Frankfurt RNA meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | We presented the scientific outcomes of this fellowship in a meeting organised by the RNA community in Germany - I was invited speaker. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Talk at at the MRC-University of Glasgow Centre for Virus Research |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | I presented the outcomes of this fellowship to experts in virology |
| Year(s) Of Engagement Activity | 2017 |
| Description | Talk at the EMBO conference: Eukaryotic RNA turnover |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I presented the scientific outcomes of this fellowship to experts in RNA biology. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://meetings.embo.org/event/17-rna-turnover |
| Description | Talk at the LMB, Cambridge (UK) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk about our research in global protein-RNA interactions in infected cells |
| Year(s) Of Engagement Activity | 2016 |
| Description | Talk at the London RNA club |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Presented our work on the changes in RNA binding protein activity upon virus infection to a non virology audience. ~40 researchers from a variety of fields in RNA biology were present. The talk sparked questions and discussion afterwards with multiple people contacting me regarding an interest in collaboration. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Talk at the MRC Centre for Virus Research, University of Glasgow |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited to give a seminar for one of the best institutions in virology in the UK |
| Year(s) Of Engagement Activity | 2020 |
| Description | Talk at the RNA UK meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I gave a talk in the RNA UK meeting, which brings together all the RNA biology groups in the UK. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.rnauk2020.org/ |
| Description | Talk at the RNA society meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | My abstract was selected for talk at the RNA society 2019, Krakow. 11th-16th Jun 2019. I spoke in front of a very large audience of international researchers. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www2.rnasociety.org/conferences/rna-2019/ |
| Description | Talk at the RNA society meeting 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | We presented the scientific outcomes of this fellowship in the most prestigious conference in RNA biology. Only few abstracts were selected out of more than 300 applications. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.rnasociety.org/conferences/rna-2017/ |
| Description | Talk at the Roslin Institute - University Edinburgh |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | I presented the scientific outcomes of this fellowships to an audience of experts in virology |
| Year(s) Of Engagement Activity | 2018 |
| Description | Talk at the SciLifeLab, Karolinska Institutet, Solna, Sweden |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | I presented the scientific outcomes of this fellowship |
| Year(s) Of Engagement Activity | 2017 |
| Description | Talk at the University of Salamanca (Spain) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk about our studies in global protein-RNA interaction analyses in infected cells |
| Year(s) Of Engagement Activity | 2016 |
| Description | Talk at the ViroOx meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | This is an initiative to bring the diverse group of groups working on viruses in Oxford together to foster collaboration. The presentation got high interest, with over lots of questions. Different people requested samples and plasmids, were interested in getting access to the preprint of the paper presented. Furthermore, I discussion ensued about applying for additional funding as a collaboration project to apply our technology in a wider context. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Talk at the WT Center for Cell Biology - University of Edinburgh (UK) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | A talk about our studies in global protein-RNA interactions in infected cells |
| Year(s) Of Engagement Activity | 2016 |
| Description | Talk in the functional genomics workshop in Oxford |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | The aim of this event was to bring together different laboratories in the Oxford campus interested in functional genomics. We were invited as experts in RNA biology and high-throughput methods. It was a great initiative and there are multiple collaborations arising from it. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Talk in the symposium in memoriam Bernd Fischer |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | We presented the work we have done in collaboration with Bernd Fischer in the symposium in his memory. Unfortunately our collaborator passed away in Feb 2017 |
| Year(s) Of Engagement Activity | 2017 |
| Description | Two poster presentations in Postdoc Poster Sessions |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Two poster presentations in yearly Postdoc Poster Session organized by the Postdoc Associations in the Deparment of Biochemistry, Department of Physiology, Anatomy& Genetics, and the Dunn School of Pathology (University of Oxford). |
| Year(s) Of Engagement Activity | 2018,2019 |
| Description | Video explaining our research in SARS-CoV-2 variants |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | The CVR recorded a video of me explaining our research in SARS-CoV-2 variants. The video was released in all the institutional social media. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://twitter.com/i/status/1493193315692335108 |
| Description | Wellcome Chromosome Biology Programme - Proteomics course |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Talk to PhD students in their first year to demonstrate the scope of questions which can be addressed by mass spectrometry. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Workshop: Introduction to RNA biology and epigenetics in stem cells - Ljubljana (Slovenia) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | In this workshop I explained the latest technologies in RNA biology to graduate and master students at the University of Ljubljana (Slovenia) |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.fkkt.uni-lj.si/fileadmin/datoteke/Obvestila/Utrip/brochure_MLSC_.pdf |
| Description | XXXVIII Reunión Anual Sociedad de Bioquímica y Biología Molecular de Chile |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited speaker in a symposium about RNA biology that included very prestigious international speakers working in this field such as Prof. Melissa Moore (University of Massachusetts Medical School). The auditorium was full for this symposium and there was a very vibrant discussion after my talk. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www.sbbmch.cl/?page_id=429 |
| Description | https://theknowshowpodcast.podbean.com/e/understanding-the-role-of-rna-binding-proteins-in-virus-infection-dr-alfredo-castello/ |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Interview in the Know Show, a podcast with international impact and a broad audience |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://theknowshowpodcast.podbean.com/e/understanding-the-role-of-rna-binding-proteins-in-virus-inf... |