ERA-NET PathoGenoMics
This presentation is the property of its rightful owner.
Sponsored Links
1 / 32

National Contact Point LIFESCIHEALTH Dr. Wilfried Diekmann Königswinterer Str. 522-524, 53227 Bonn PowerPoint PPT Presentation


  • 100 Views
  • Uploaded on
  • Presentation posted in: General

ERA-NET PathoGenoMics Constituent Assembly, October 13-15, 2004 Strategic supporting measures to raise synergies with the European framework programmes and to embedd PathoGenoMics into the European R&D Landscape. National Contact Point LIFESCIHEALTH Dr. Wilfried Diekmann

Download Presentation

National Contact Point LIFESCIHEALTH Dr. Wilfried Diekmann Königswinterer Str. 522-524, 53227 Bonn

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

ERA-NET PathoGenoMics

Constituent Assembly, October 13-15, 2004

Strategic supporting measures

to raise synergies with the European framework programmes and to embedd PathoGenoMics into the European R&D Landscape

National Contact Point LIFESCIHEALTH

Dr. Wilfried Diekmann

Königswinterer Str. 522-524, 53227 Bonn

phone: +49 228 447 698, e-mail: [email protected]

http://www.nks-lebenswissenschaften.de


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

Session overview

W. DiekmannChair &Introduction

Rationale and objectives for strategic support measures

in PathoGenoMics

Current FP6 project portfolio in pathogenomics

Selected FP6 projects of high relevance to PathoGenoMics

M. FroschEUROPATHOGENOMICS

European Virtual Institue for Functional Genomics of Bacterial Pathogens (NoE)

M. VicentemicroMatrix

Workshop on strategies to address antimicrobial resistance through the exploitation of microbial genomics (SSA)

Cooperation with European associations/societies and other stakeholders

E. Ron FEMS

Federation of Microbiological Societies

International perspectives

J. Hacker US Microbe Project

Short statement on current developments


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

Integration

  • Biotechnology Action Plan

FP

National

programmes

project ↔ programme ↔ policy

NoE

ERA-NET

Range

regional/national ↔ transnational ↔ community

Strategic supporting / supervision measures in ERA-NETs Rationale and objectives

“Strategic Supervision“ in an ERA-NET means to support the coherent development of research activities with different range throughout Europe at all relevant levels of integration.

This shall contribute to give a real meaning to the terms “subsidiarity“ and “variable geometry“ for a specific field of research.


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

Strategic supervision in PathoGenoMics, Task 9.4

Objectives and methodology

→ linking with NCP network, industrial associations, scientific societies, …

→ in particular at EU level as FP 6&7, ETIs; but also EUREKA, ESF, …

set-up of powerful communication & multiplication networks for the ERA-NET

continually observe programme design and project portfolios beyond the ERA-NET

raise awareness and embedd the ERA-NET in the European research policy community (in particular beyond the partner countries and in relevant programme-making bodies, as e.g. EAG for FP7 preparation)

supervision of international development

(e.g. INCO target countries, trans-Atlantic cooperation)

→ develop perspectives for financial integration with other programmes

→ show international cooperation perspectives


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

a) Application-orientated genomic approaches

Brain and

diseases of

the nervous

system

Cardiovascular disease,

diabetes

and rare

diseases

Human development

and

the ageing

process

Resis-

tance to antibiotics

and other

drugs

b) Application of knowledge and technologies in the field of genomics and biotechnology for health

TP 1 Life Science, Genomics and Biotechnology for Health

Programme structure and pathogenomics-relevant areas

i) Advanced Genomics and its applications for health

a) Fundamental knowledge & basic tools for functional genomics in all organisms

Comparative genomics

and

population

genetics

Multidisciplinary functional genomics approaches to basic biological processes

Gene

expression

and

proteomics

Bio-informatics

Structural

genomics

Innovative research in post-genomics with

high potential for

application

New preventive and therapeutic tools

(somatic gene and cell

therapies; stem cell and immunotherapies, etc.)

New in vitro

tests to

replace animal

experimentation

New,

safer,more effective drugs

(incl. pharmaco-genomics)

New

diagnostics

ii) Combating major diseases

c) Poverty-

related diseases

b) Cancer

  • HIV / AIDS

  • Malaria

  • Tuberculosis


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

1st Call (FP-2002-LIFESCIHEALTH, deadline: 25.03.2003)

Selected pathogenomics-relevant areas


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Fundamental Genomics, Outcome 1st Call

Bacterial stress management relevant to infectious diseases and biopharma-ceuticals (BACELL HEALTH) –STREP, retained for funding

Integrated study of the response of Gram-positive bacteria to stresses encountered by pathogens during infection and by industrial strains during industrial bioprocesses:

understand and model regulatory networks/processes that comprise cell stress management systems

identify key targets for novel anti-infectives and improving industrial bioprocesses

Species:Bacillus subtilis, B. anthracis, B. cereus; Listeria monocytogenes, Staphylococcus aureus, Streptococcus pneumoniae

Coordination: University Newcastle, UK


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Applied Genomics, Outcome 1st Call

Development of New Gyrase Inhibitors by combinatorial biosynthesis (COMBIGYRASE) –STREP, retained for funding

Generation of novel inhibitors of gyrase and topoisomerase IV, in particular of the aminocoumarin and cyclothialidine type

engineering complete biosynthetic pathways of natural inhibitors

cloning and sequencing of complete gene clusters

Species:Streptomyces spec.

Methodology: Biophysics, X-ray crystallography, enzyme and antibacterial assays, animal experimentation

Coordination: University Tübingen, DE


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Major Diseases, Outcome 1st Call

Combating resistance to antibiotics by broadening the knowledge on molecular mechanisms behind resistance to inhibitors of cell wall synthesis (COBRA)

–STREP, retained for funding

Elucidation of molecular mechanisms of resistance to inhibitors of cell wall synthesis in bacteria responsible for severe nosocomial and community-aquired infections:

indepth understanding of resistance mechanisms based on ß-lactamases, penicillin-binding proteins, t-RNAdependent ligases, and other principles

assess the modification of structure, function, dynamics of relevant pathways

develop novel diagnostic and therapeutic tools

Species:Pseudomonas, Acinobacter, S. pneumoniae, S. aureus, Enterococcus

Methodology:structural genomics, crystallography, biochemistry,

clinical microbiology, genetics

Coordination: INSERM, FR


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Major Diseases, Outcome 1st Call

Molecular mechanisms of resistance, virulence and epidemicity in Streptococcus pneumoniae (PREVIS) –STREP, retained for funding

Identification of bacterial genetic determinants and host factors associated with invasise disease, drug resistant pneumococcal clones and spread of epidemic S. pneumoniae clones

frequency and clonal types of drug resistant and drug susceptible pneumococci

old age homes and AIDS hospice as ecological reservoirs of resistant strains

transcriptional profiling involving DNA microarrays

sequencing of S. mitis, a frequent source of gene fragments resulting in resistance

threshhold levels of antibiotic consumption in the community

Species:Streptococcus pneumoniae

Methodology:genomics, transcriptomics, clinical microbiology

Coordination: Swedish Institute for Infectious Disease Control, SE


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Major Diseases, Outcome 1st Call

Workshop on strategies to address antimicrobial resistance through the exploitation of microbial genomics (micro MATRIX) –SSA, retained for funding

Workshop to organise the European expertise needed to further apply functional genomics for fighting antimicrobial resistance:

reveal novel anti-microbial targets

discover new antibiotics

understand the controls required to avoid the emergence of resistances

discover regulatory notes and structural elements essential for resistance

form a framework of leading experts and a concerted approach for further research

Methodology: gene expression, physiology, stress response, adhesion,

pathogenesis, and resistance mechanisms,

Coordination: Consejo Superior de Investigaciones Científicas (CSIC), ES


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Poverty-related diseases, Outcome 1st Call

An Integrated project for the design and testing of vaccine candidates against tuberculosis: Identification, development and clinical studies (TB-VAC)

–IP, retained for funding

Development of improved TB vaccines, particularly for the young adult population:

identify and develop novel vaccines or antigen components

optimize the delivery and composition of candidate vaccines

evaluate candidate vaccines in animal models as well as in Phase I clinical trials

GMP production of vaccine candidates

Coordination: Institut Pasteur, FR


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

2nd Call (FP-2003-LIFESCIHEALTH-I, deadline: 13.11.2003)

Selected pathogenomics-relevant areas


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

2nd Call (FP-2003-LIFESCIHEALTH-3, deadline 24.03.2004)

Selected pathogenomics-relevant areas


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Fundamental Genomics, Outcome 2nd Call

Genetics of Sepsis in Europe (GenOSept) - STREP, retained for funding

Multidisciplinary fundamental genomics approach to examine genetic predisposition to sepsis (life threatening infection)

identify candidate genes including those controlling programmed cell death

epidemiology studies of genetic disposition to sepsis-related mortality and

morbidity in European intensive care units

gender-related aspects of sepsis patients

target risk subpopulations

Methodology:gene expression, structural genomics, population genetics,

genetic epidemiology, biometrics, high-throughput genotyping

Coordination: European Society of Intensive Care Medicine (ESICM), BE


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Functional Genomics, Outcome 2nd Call

Functional genomic characterization of the bacterial Tat complex as a nanomachine for biopharmaceutical production and a target for novel anti-infectives (Tat machine) –STREP, retained for funding

Multidisciplinary functional genomic characterization of the Twin-arginine translocation (Tat) machinery, which is a widely conserved system for bacterial protein secretion:

improve and use the Tat nanomachine for biopharmaceutical production

use the Tat nanomachine of major Gram-positive and -negative pathogens as potential target for novel anti-infectives

Species:Bacillus, E. coli, Streptomyces, E. coli O 157,

Pseudomonas aeruginosa

Methodology : bioinformatics, comparative and structural geniomics, proteomics

Coordination: University of Groningen, NL


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Applied Genomics, Outcome 2nd Call

European Virtual Institute for Functional Genomics of Bacterial Pathogens – (EUROPATHOGENOMICS/EPG) - NoE, retained for funding

Network to form a durable alliance of the best pathogenomics research capacities

bring together relevant epidemiological, basic and applied research

stimulate collaborative, multidisciplinary research activities

foster biotechnological applications and technology transfer (in terms of innovative diagnostic tools, anti-infectious agents, antigens and/or host defence mechanisms)

Methodology : molecular biology, immunology, cell biology, structural biology

Coordination: University of Würzburg, DE

Nationales Kompetenzzentrum

“Genomanalyse pathogener Mikroorganismen“


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Applied Genomics, Outcome 2nd Call

Electrical bio sensor arrays for analyses of harmful microorganisms and microbial toxins (eBIOSENSE) - STREP, retained for funding

Advanced technology platform for analysis of food and water born harmful microorganisms and /or their toxins (e.g. mycotoxins):

electric biochip arrays enabling the parallel and simultaneous identification of nucleic acids, microbial proteins and toxins (based on nm-sized interdigital gold electrodes)

design of portable instruments furnished with disposable chips

Species:Escherichia coli (STEG, ETEC, EHEC), Salmonella enteridis,

Bacillus cereus, Staphylococci, Legionella

Methodology : genomics, proteomics,bioinformatics, advanced silicon and

microsystem technologies

Coordination: Kungliga Tekniska Högskolan, SE


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Applied Genomics, Outcome 2nd Call

SLIC-Biosensors in Molecular Diagnostics: Nanotechnology for the analysis of species-specific microbial transcripts (SLIC) - STREP, retained for funding

Development of alternative technologies for direct genotyping and/or screening of the transcriptome for multiparametric testing systems usable in clinical diagnostics:

use of tmRNA transcripts of the bacterial ssrA gene

based on a self-assembled lipid bilayer membrane that integrates a synthetic ligand-gated ion-channel (so-called SLIC-Nanobiosystem)

monitoring via electrical impedance sopectroscopy

ultra-sensitive qunatification and identification of bacterial species in a single homogenous assay format

prototypes of miniaturized/compact and cost-effective instruments

Methodology: transcriptomics, genomics, electronics

Coordination: Ayanda Biosystems, CH


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Applied Genomics, Outcome 2nd Call

The fungal cell wall as a target for antifungal therapies (FUNGWALL)

- STREP, retained for funding

Research programme on core cell wall complexes which are common to all pathogenic fungi:

characterise the enzymes and reactions associated with chitin synthesis,

glucan branching and cross-linking of chitin and 1-3 glucan

signalling mechanisms allowing fungi to adapt to/survive cell wall damages

define novel antifungal targets and compounds effecting cell wall integrity

Species: Candida albicans, Aspergillus fumigatus

Coordination: Institut Pasteur, FR


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Major Diseases, Outcome 2nd Call

Integrating genomics-based applications to exploit Actinomyces as a resource for new antibiotics (ActinoGEN) - IP, retained for funding

Genomics-based approach to exploit hitherto overlooked genetic resources for new antibiotics:

assess new biosynthetic pathways from diverse species

activate cryptic pathways from well-characterised species

engineer novel hybrid antibiotics by combinatorial biosynthesis

Methodology:multidiscipliar post-genomics, biochemistry, physiology, chemistry

Species: Actinomycetes,

in particular Streptomyces coelicolor (genome completely sequenced)

Coordination: University of Wales Swansea, UK


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Major Diseases, Outcome 2nd Call

Inhibition of new targets for fighting antibiotic resistance (EUR-INTAFAR)

- IP, retained for funding

Coherent set of converging approaches to study and design novel targets (i.e. enzyme inhibitors and/or agents perturbing protein-protein interactions) interfering with bacterial peptidoglycan biosynthesis and cell morphogenesis:

inhibitors for penicillin-resistant transpeptidases

inhibitors of the glycosyltransferase domain of class A penicillin-binding proteins

inhibiting synthesis and transport of cell wall subunits at the plasma membrane

interfering cell morphogenesis and its regulation

Methodology:biotechnology, bacterial physiology, cell biology

Species: streptocooci, staphylococci, enterococci, chlamydiae

Coordination: Université de Liège, BE


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Major Diseases, Outcome 2nd Call

New methods of treatment of antibiotic-resistant pneumococcal disease (PNEUMOPEP) - STREP, retained for funding

New targets/lead compounds as well as adjunctive therapy and drug delivery approaches against pneumonia and meningitis (including the related acute toxaemia caused by pro-inflammatory pneumococcal toxins as e.g. pneumolysin):

targets: pneumolysin; cell surface proteinases involved in adhesion and invasion

treatment approach based on binding peptides and small molecules isolated from large phage display libraries

drug formulation in chitosan for nasal delivery

pharmacological testsin animal models of pneumonia, bacteraemia and meningitis,

Species: multiresistant strains of Streptococcus pneumoniae

Coordination: University of Leicester, UK


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Major Diseases, Outcome 2nd Call

Antimicrobials by Immune Stimulation (AMIS) - STREP, retained for funding

Innovative approach to use the strength of the human immune system to design new antimicrobial drugs and/or to broaden the approaches in therapeutic intervention:

Target: antimicrobial proteins that trigger inflammatory signals

(i.e. in one single molecule)

Screen and modify novel “dual mode of action effector molecules”

as potential drug candidates

Species: various extra- and intracellular bacteria

Coordination: University Medical Centre Utrecht, NL


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Poverty-related diseases, Outcome 2nd Call

Finding promising drug candidates against tuberculosis with multidisciplinary protocol based non-conventional search (scrIN-SILICO)

–STREP, retained for funding

Development of a protocol capable of identifying novel drug binding sites and novel

drug-protein complexes of Mycobacterium tuberculosis proteins consisting of:

a method to identify surface indentation patterns in protein 3D structures

structural & molecular biology protocol for examining promising drug-protein fit pairs

Coordination: Eotvos Lorand Tudomanyegyetem, HU


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Poverty-related diseases, Outcome 2nd Call

Genome- and HLA- wide scanning and validation of cytotoxic CD8 T cell

responses against Mycobacterium tuberculosis(VACCINES4TB)

–STREP, retained for funding

Genomics/proteomics based platform for antigen- and epitope-discovery with

relevance to human immune CD8 cytotoxic T cells responses against M. tuberculosis

Methodology: high-throughput methods from immunology and bioinformatics

Coordination: Technical University of Denmark, DK


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Poverty-related diseases, Outcome 2nd Call

Molecular markers of M. tuberculosis early interactions with host phagocytes (MM-TB) –STREP, retained for funding

Comparative genomics approach to develop new markers of protection and to identify novel molecular patterns, both in the microbe and in the host cells, being associated with early interactions between M. tuberculosis and phagocytic cells

microarrays to simultaneously study the entire expressed genomes of both the mammalian host (macrophages, dendritic cells) and the microbial parasite during their interaction

reveal patterns of the induced gene expression

novel targets for vaccine design

molecular markers and pathways associated with protection

Methodology: transcriptional profiling approaches

Coordination: Technical University of Denmark, DK


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Poverty-related diseases, Outcome 2nd Call

Development of a molecular platform for the simultaneous detection

of Mycobacterium tuberculosis resistance to rifampicin and fluoroquinolones

(TB-DRUG OLIGOCOLOR) –STREP, retained for funding

Molecular platform for the identification of Mycobacterium tuberculosis in clinical specimens and simultaneous detection of resistance to rifampicin & fluoroquinolones:

Methodology: microplates, enzymatic chromogen detection systems

Coordination: Institute of Tropical Medicine, BE


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Poverty-related diseases, Outcome 2nd Call

Strategy for characterisation of the worldwide population structure of Mycobacterium tuberculosis in relation to the efficacy of new tuberculosis vaccines (TB World Collection) –SSA, retained for funding

Preparing a strategy for collecting isolates in a non-biased way in order to characterise the worldwide population structure of M. tuberculosis:

meeting of relevant specialists and contacts from developing countries

develop a strategy for determining the evolutionary divergence worldwide

standard set of most significant strains regarding the current TB epidemic

Coordination: National Institute of Public Health and the Environment, NL


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Poverty-related diseases, Outcome 2nd Call

The diversity of Mycobacterium tuberculosis strains in China: tracing the origins of the worldwide dispersion of the multidrug-resistant Beijing genotype

(TB China) –SSA, retained for funding

Organization of the analysis of a large collection of strains (3000) from the 31 Provinces of China:

genotyping and multidrug-resistance (MDR) assessment

clinical information as e.g. BCG status, age and gender of the patients

technical knowledge exchange to Chinese laboratories

Coordination: University of Paris, FR


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

FP6 project portfolio in pathogenomics

TP LSH, Poverty-related diseases, Outcome 2nd Call

Establishing a TB Treatment Efficacy Marker (TB Treatment Marker)

–SSA, retained for funding

Strategy development for monitoring TB progression and the efficacy of TB treatment as well as for guiding clinical decision-making in TB management

blood plasma protein suPAR level as a potential useful marker

pilot study in Guinea-Bissau (one of the highest TB incidences in the world !)

Coordination: ViroGates ApS, FR


National contact point lifescihealth dr wilfried diekmann k nigswinterer str 522 524 53227 bonn

3rd Call (FP-2004-LIFESCIHEALTH-5, deadline: 16.11.2004)

Selected pathogenomics-relevant areas


  • Login