Project acronym VERCORS
Project Verification of Concurrent Data Structures
Researcher (PI) Marieke Huisman
Host Institution (HI) UNIVERSITEIT TWENTE
Call Details Starting Grant (StG), PE6, ERC-2010-StG_20091028
Summary Increasing performance demands, application complexity and explicit multi-core parallelism makes concurrency omnipresent in software applications. However, due to the complex interferences between threads in an application, concurrent software is also notoriously hard to get correct. Instead of spending large amounts of money to fix incorrect software, formal techniques are needed to reason about the behaviour of concurrent programs.
In earlier work, we developed a variant of permission-based separation logic that is particularly suited to reason about multithreaded Java programs with dynamic thread creation and termination, and reentrant locks. The VerCors project will extend expressiveness of the logic, to specify and verify concurrent data structures. The verification logic will be parameterised over the locking policy, so that a high-level specification of the behaviour of a data structure can be reused for different implementations. Thus the implementation of a concurrent data structure can be changed, without affecting correctness of the applications using it.
The logic will also be parameterised with concurrency and synchronisation primitives, so that a logic for a different programming language can be defined as an instance of the general logic. It will also be adapted to reason about programs with benign data races, i.e., data races where the same value is written simultaneously by different threads. Also techniques to generate part of the specifications automatically will be developed. Finally, the logic will be adapted to a distributed setting, where data consistency between the different sites has to be maintained.
All results will be integrated in a tool set that generates and proves proof obligations automatically. It will be validated on realistic case studies.
Summary
Increasing performance demands, application complexity and explicit multi-core parallelism makes concurrency omnipresent in software applications. However, due to the complex interferences between threads in an application, concurrent software is also notoriously hard to get correct. Instead of spending large amounts of money to fix incorrect software, formal techniques are needed to reason about the behaviour of concurrent programs.
In earlier work, we developed a variant of permission-based separation logic that is particularly suited to reason about multithreaded Java programs with dynamic thread creation and termination, and reentrant locks. The VerCors project will extend expressiveness of the logic, to specify and verify concurrent data structures. The verification logic will be parameterised over the locking policy, so that a high-level specification of the behaviour of a data structure can be reused for different implementations. Thus the implementation of a concurrent data structure can be changed, without affecting correctness of the applications using it.
The logic will also be parameterised with concurrency and synchronisation primitives, so that a logic for a different programming language can be defined as an instance of the general logic. It will also be adapted to reason about programs with benign data races, i.e., data races where the same value is written simultaneously by different threads. Also techniques to generate part of the specifications automatically will be developed. Finally, the logic will be adapted to a distributed setting, where data consistency between the different sites has to be maintained.
All results will be integrated in a tool set that generates and proves proof obligations automatically. It will be validated on realistic case studies.
Max ERC Funding
1 306 500 €
Duration
Start date: 2011-02-01, End date: 2016-01-31
Project acronym Viral Host Factors
Project Identification of Host Determinants for Virus
Entry using a Haploid Genetic Approach
Researcher (PI) Thijn Reinout Brummelkamp
Host Institution (HI) STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS
Call Details Starting Grant (StG), LS6, ERC-2012-StG_20111109
Summary The most powerful and direct way to get insight into complex biological systems is to remove individual components and observe the consequences. Cultured human cells are widely used to model and study aspects of human disease. Although human cells can be analyzed and manipulated in numerous ways, their genome has remained refractory to efficient mutagenesis-based analysis.
We have developed an insertional mutagenesis-based approach in haploid and near-haploid human cells. We have shown that this approach enables the generation of null alleles for most human genes and can be used to pinpoint genes that are involved in phenotypes of interest. We have made use of parallel sequencing approaches to generate high-density genetic overviews of genes that are required for phenotypic cell states. In a variety of genetic screens we have identified host factors required for infection of cells by influenza virus, the first entry receptor for a Clostridium Difficile toxin and a set of host factors that play a role in the entry of Ebola virus. Importantly, we can carry out and analyze a genetic screen in a period of weeks in a cost-effective manner.
This application outlines experiments aimed at identification and detailed characterization of host factors that play a role in Filovirus infection. Moreover, we propose a number of experiments to gain mechanistic insight in the role of the Niemann-Pick C1 cholesterol transporter in entry, tropism and the fusion process of Ebola virus. Furthermore we propose to develop refinements in our screening approach. Finally, we will apply our haploid screening platform to generate a “Host Factors Atlas’ for 50 diverse viruses that infect the human population. We foresee that the outlined experiments will provide an detailed and accurate overview of the unusual entry-route used by Filoviridae, will make our screening platform more powerful and will generate a much-needed overview of host factors used by a compendium of viruses.
Summary
The most powerful and direct way to get insight into complex biological systems is to remove individual components and observe the consequences. Cultured human cells are widely used to model and study aspects of human disease. Although human cells can be analyzed and manipulated in numerous ways, their genome has remained refractory to efficient mutagenesis-based analysis.
We have developed an insertional mutagenesis-based approach in haploid and near-haploid human cells. We have shown that this approach enables the generation of null alleles for most human genes and can be used to pinpoint genes that are involved in phenotypes of interest. We have made use of parallel sequencing approaches to generate high-density genetic overviews of genes that are required for phenotypic cell states. In a variety of genetic screens we have identified host factors required for infection of cells by influenza virus, the first entry receptor for a Clostridium Difficile toxin and a set of host factors that play a role in the entry of Ebola virus. Importantly, we can carry out and analyze a genetic screen in a period of weeks in a cost-effective manner.
This application outlines experiments aimed at identification and detailed characterization of host factors that play a role in Filovirus infection. Moreover, we propose a number of experiments to gain mechanistic insight in the role of the Niemann-Pick C1 cholesterol transporter in entry, tropism and the fusion process of Ebola virus. Furthermore we propose to develop refinements in our screening approach. Finally, we will apply our haploid screening platform to generate a “Host Factors Atlas’ for 50 diverse viruses that infect the human population. We foresee that the outlined experiments will provide an detailed and accurate overview of the unusual entry-route used by Filoviridae, will make our screening platform more powerful and will generate a much-needed overview of host factors used by a compendium of viruses.
Max ERC Funding
1 495 200 €
Duration
Start date: 2013-01-01, End date: 2017-12-31
Project acronym VIVARNASILENCING
Project Antiviral Defense in the Vector Mosquito Aedes aegypti: induction and suppression of RNA silencing pathways
Researcher (PI) Ronald Van Rij
Host Institution (HI) STICHTING KATHOLIEKE UNIVERSITEIT
Call Details Consolidator Grant (CoG), LS6, ERC-2013-CoG
Summary BACKGROUND: Mosquitoes and other blood-feeding arthropods transmit important human and animal viruses (arthropod-borne viruses, arboviruses). With the increasing global threat of arboviruses, it is essential to understand the virus-vector interactions that determine virus transmission. The mosquito antiviral immune response is a key determinant of virus replication and transmission. We recently showed that arboviruses are targeted by a poorly-understood RNA silencing pathway in the major vector mosquito Aedes aegypti: the Piwi-interacting RNA (piRNA) pathway. Our (published and unpublished) observations imply that the piRNA pathway contributes to antiviral defense against different classes of viruses in somatic tissues of mosquitoes. Moreover, we identified a novel class of endogenous gene-derived piRNAs in mosquitoes that may form a new paradigm for piRNA-based regulation of cellular gene expression.
AIM: This proposal has a three-fold aim: i) to delineate the biogenesis and function of the novel classes of virus- and gene-derived piRNAs, ii) to characterize mechanisms by which (arbo)viruses suppress or evade antiviral RNA silencing pathways, and by doing so, iii) to establish mosquitoes as an experimental model to characterize the complex piRNA machinery.
APPROACH: We will use Aedes cell lines that recapitulate all aspects of piRNA biogenesis. This allows us to use a unique, powerful approach of genomic, cell biological, biochemical, and proteomic methodologies to study piRNA biogenesis and function.
IMPORTANCE AND INNOVATION: This is the first study to comprehensively characterize viral and cellular piRNA biogenesis and function in mosquitoes. This proposal provides novel insights into the antiviral response in mosquitoes and may uncover novel regulatory functions of endogenous piRNAs. Moreover, it establishes a platform for functional and biochemical dissection of the complex biogenesis of piRNAs - the most enigmatic class of small silencing RNAs.
Summary
BACKGROUND: Mosquitoes and other blood-feeding arthropods transmit important human and animal viruses (arthropod-borne viruses, arboviruses). With the increasing global threat of arboviruses, it is essential to understand the virus-vector interactions that determine virus transmission. The mosquito antiviral immune response is a key determinant of virus replication and transmission. We recently showed that arboviruses are targeted by a poorly-understood RNA silencing pathway in the major vector mosquito Aedes aegypti: the Piwi-interacting RNA (piRNA) pathway. Our (published and unpublished) observations imply that the piRNA pathway contributes to antiviral defense against different classes of viruses in somatic tissues of mosquitoes. Moreover, we identified a novel class of endogenous gene-derived piRNAs in mosquitoes that may form a new paradigm for piRNA-based regulation of cellular gene expression.
AIM: This proposal has a three-fold aim: i) to delineate the biogenesis and function of the novel classes of virus- and gene-derived piRNAs, ii) to characterize mechanisms by which (arbo)viruses suppress or evade antiviral RNA silencing pathways, and by doing so, iii) to establish mosquitoes as an experimental model to characterize the complex piRNA machinery.
APPROACH: We will use Aedes cell lines that recapitulate all aspects of piRNA biogenesis. This allows us to use a unique, powerful approach of genomic, cell biological, biochemical, and proteomic methodologies to study piRNA biogenesis and function.
IMPORTANCE AND INNOVATION: This is the first study to comprehensively characterize viral and cellular piRNA biogenesis and function in mosquitoes. This proposal provides novel insights into the antiviral response in mosquitoes and may uncover novel regulatory functions of endogenous piRNAs. Moreover, it establishes a platform for functional and biochemical dissection of the complex biogenesis of piRNAs - the most enigmatic class of small silencing RNAs.
Max ERC Funding
2 000 000 €
Duration
Start date: 2014-08-01, End date: 2019-07-31
