Fundamental knowledge and basic tools for functional genomics in ...

clatteringlippsBiotechnology

Dec 5, 2012 (4 years and 6 months ago)

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La génomique

dans l’
E
space
E
uropéen de la
R
echerche



Le 6ème programme cadre


Le contexte politique





FOOD QUALITY AND SAFETY
Coherent
development
(€50M)
Strengthening the foundations
of the ERA
(€320M)
Coordination
of research
activities
(€270M)
Structuring the ERA
(€2.605M)
Research &
innovation
(€290M)
Human
resources &
mobility
(€1.580M)
Research
infrastructures
(€655M)
Science and
society
(€80M)
Priority Thematic Areas
(€11.285M)
Life sciences,
genomics
&
biotech. for health
(€2.255M)
Information society
technologies
(€3.625M)
Nanotechn
and
nanosciences
(€1.300M)
Aeronautics and space
(€1.075M)
Food quality and safety
(€685M)
Sustainable
devel
, global change
and ecosystems
(€2.120M)
Citizens & governance in the
knowledge society
(€225M)
Activities covering a wider field of research
(€2.06M)
Supporting policies and anticipating
scientific needs
(€555M)
Specific SME activities
(€430M)
Specific international cooperation
(€315M)
Non
-
nuclear JRC activities
(€760M)
Focusing and Integrating European Research
(€13.345M)
Sixth Framework
Programme
2002
-
2006
(Global budget European Community 16.270 M €)
FP5/QoL : mio


2.2

FP6/TP1+TP5 : mio


3.0

1800 Projects

~ 400 TI

~ 200 NI

80%

20%

LESS with MORE : less projects, higher focussing
but more organisation implied

5th Framework
Programme

(1998
-

2002)


The 6th Framework
Programme

(2002
-

2006)


Quality of Life programme

Thematic Priority 1 or 5

Public

dialogue

Innovation

and

technology

transfer

initiatives

“wet”

science

Bioethics

Research

Socio
-
economic

research









Ethics

Public

dialogue

Innovation

and

competitiveness

“wet” science

Academia
-


Industry
-

Engineering

Regulation

and governance

Fragmentation


Life Sciences, Genomics and Biotechnology for Health (FP6)

Life Sciences, Genomics &

biotechnology for health



Advanced Genomics and its applications for health (1100 M

)




Fundamental knowledge and basic tools for functional genomics


in all organisms


(Structural genomics; proteomics; comparative genomics; bioinformatics;


Multidisciplinary genomics approaches to basic biological processes)




Application of knowledge and technologies in the field of


genomics and biotechnology for health


(Technology platforms; support to start
-
up companies)


Combating major diseases (1155 M

)




Application
-
oriented approach to medical genomics knowledge


(Cardiovascular disease, diabetes and rare diseases ; resistance to


antibiotics ; Studying the brain and combating diseases of the nervous


system ; Studying human development and the ageing process)






Broader biomedical approach


(cancer, poverty
-
related infectious diseases)

Fundamental knowledge and basic tools
for functional genomics in all organisms


Structural genomics

LSH
-
2003
-
1.1.2
-
1: Comparative structural biology of viral
replication


IP.

The focus should be on developing new
approaches, tools and technologies for collecting comprehensive
structural information on the replicative machinery of RNA
viruses to facilitate the identification of potential new drug targets.


LSH
-
2003
-
1.1.2
-
2: Structure determination of large protein
complexes


IP
.
The focus should be on the high throughput
isolation of cellular protein complexes under physiological
conditions and their structural analysis.


SECOND CALL TOPICS

Fundamental knowledge and basic tools
for functional genomics in all organisms

Multidisciplinary functional genomics
approaches to basic biological processes

MITOCHECK (IP)

Regulation of mitosis by phosphorylation

FUNGENES (IP)

Functional genomics in engineered mouse ES cells

No project selected


LYMPH/ANGIOGENOMICS (IP)

Genome wide discovery and functional analysis of
novel genes in lymph/angiogenesis

FIRST CALL TOPICS


PROJECTS FUNDED

The cell cycle


Non
-
human embryonic
stem cells

Erythroid development
and disorders

Lymph/angiogenesis

Epigenetics


Chronic inflammation


Ubiquitin
-
proteasome
pathway


Fundamental knowledge and basic tools
for functional genomics in all organisms

Multidisciplinary functional genomics
approaches to basic biological processes

FIRST CALL TOPICS


PROJECTS FUNDED

THE EPIGENOME (NoE)

Epigenetic plasticity of the genome +

The European epigenetics network

MAIN (NoE)

Targeting cell migration in chronic
inflammation

No project selected

Fundamental knowledge and basic tools
for functional genomics in all organisms

Multidisciplinary functional genomics
approaches to basic biological processes

SECOND CALL TOPICS

LSH
-
2003
-
1.1.5
-
1: Functional genomics approaches in animal models to study
human kidney disease


IP/NOE
.

The focus should be on integrating different
expertise, animal models and functional genomics platforms to discover the genetic
mechanisms that underlie kidney development and cause kidney disease.


LSH
-
2003
-
1.1.5
-
2: Functional genomics approaches to the study of peroxisomes
in health and disease


IP/NOE.

The focus should be on using functional genomics
approaches and cell and animal models to decipher the entire spectrum of biological
functions performed by peroxisomes and to evaluate their roles in disease.



LSH
-
2003
-
1.1.5
-
5: DNA damage and repair mechanisms in health and
disease


IP.

The focus

should be on using multidisciplinary functional genomics
approaches to decipher the core molecular mechanisms of DNA damage and
repair.



LSH
-
2003
-
1.1.5
-
6: Functional genomics approaches in animal models to
study human immunological disease


IP/NOE.

The focus should be on
bringing together different expertise from academic and industrial (including
SMEs) laboratories to generate a joint programme of activities that combines
research on model organisms and functional genomics to investigate the immune
system for elucidating the genetic basis of immunological disease, thereby
facilitating the development of new diagnostics and therapeutic tools.


Fundamental knowledge and basic tools
for functional genomics in all organisms

Multidisciplinary functional genomics
approaches to basic biological processes

SECOND CALL TOPICS


Fundamental knowledge and basic
tools


for functional genomics in all
organisms


Multidisciplinary functional
genomics for basic mechanisms
of:

Transcription activation, signal
transduction, intracellular
communication, non coding
genomic information, integration
of genes, in silico predicion and
simulation of regulatory
networks

STREPs and CAs

16 STREPs funded

Low abundance mRNAs and
proteins, role of small RNAs,
nanomachines, apoptosis,
comparative genomics in
protozoa, standardisation, in silico
modelling of macromolecules.

CA:

Structuring mouse genomics
and other models, systems
biology, model organisms
resources, biobanks

FIRST CALL TOPICS


SECOND CALL TOPICS

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


Rational

and

accelerated

development

of

new,

safer

and

more

effective

drugs

including

pharmacogenomics

approaches



Development

of

new

diagnostics



Development

of

new

in
-
vitro

tests

to

replace

animal

experimentation


Development

and

testing

of

new

preventive

and

therapeutic

tools
,


such

as

somatic

gene

and

cell

therapies

(in

particular

stem

cell

therapies,

for

example

those

on

neurological

and

neuromuscular

disorders)

and

immunotherapies


Innovative

research

in

post
-
genomics
,

which

has

high

potential

for

application






New

drugs

(
6
)


Protein
-
kinases

-

novel

drug

targets

(IP)


Drugs

for

depression

(IP)

Replication

&

integration

of

HIV

(IP)

Individualised

medicines

(missing)

Blood

substitutes

G
-
protein

coupled

receptors

European

Labcourse
:

gene

vectors

(SSA)

Application of knowledge and technologies in

the field of genomics and biotechnology for health




Diagnostics

(
2
)


Non
-
invasive advances in prenatal
diagnosis (NoE)


Molecular diagnostics of kidney disease

Diagnostic for prion diseases (missing)




In

Vitro

alternatives

(
3
)


Hazard

and

risk

assessment

of

reproductive

toxicity

(IP)

In

vitro

assays

for

long

term

toxicity

Alternative

methods

(SSA)





New

Therapies

(
9
)


European

consortium

for

stem

cell

research

(IP)

Allogeneic

stem

cell

transplantation

(IP)

Mesenchymal

stem

cells

for

connective

tissue

disorders

(IP)

Genome

&

protein

information

for

immune

recognition

Stem

cells

for

myocardial

repair

Dendritic

-

cells

/

-

Vaccines

/

-

Cancer

European Labcourse: therapy (SSA)





Post

Genomics

(
6
)


New

approaches

for

autoimmune

diseases

(IP)

Pharmaceuticals

from

plants

(IP)

Antibiotic

resistance

-

Gyrase

inhibitors

/

-

Glycopeptides

Genomics
-

Biocatalysis

Post
-
genomics

drug

discovery



Post Genomics

Exploitation of fungal genomics and
filamentous fungal biotechnology for
human health
CA

RNA as a human

therapeutic tool
IP

Post
-
genomics approach to the study

of human pathogens
NoE

Induction of transplant

tolerance
IP

Novel biosafe propagation

deficient virus vectors

aimed at prevention and treatment

of infectious diseases
STREP

New bioassays and biosensors


for detection of harmful microbes
STREP


FIRST CALL:





New approaches for autoimmune diseases (IP)

Pharmaceuticals from plants (IP)

Antibiotic resistance
-

Gyrase inhibitors /
-

Glycopeptides

Genomics
-

Biocatalysis

Post
-
genomics drug discovery

SECOND CALL

Fungall cell
-
wall as a target

of antifungal therapies
STREP

Use of RNAi as tool of post
-
genomic
analysis
SSA

Application of knowledge and

technologies in the field of genomics and
biotechnology for health

Priority 5

Food Quality and Safety




Epidemiology of food related diseases and allergies



Impact of food on health



Traceability processes



Methods of analysis/detection and control of chemical


contaminants and pathogenic microorganisms



Safer production methods and healthier foodstuffs



Impact of Animal feed on Human Health



Environmental health risks



strategic objectives


-

nutrition science benefiting from new genomic
technologies


-

virtual centre of excellence


-

transferring acquired knowledge to stakeholders’ groups





process of activities











Joint
Research
Integration
Spreading
of
excellence
Joint
Research
Integration
Spreading
of
excellence
Figure 1. The three concentric activities of NuGO

integrating activities











Integrating
Activites
Technology
integration
Methods
& Models
Information
systems
Bioinformatics
Integrating
Activites
Technology
integration
Methods
& Models
Information
systems
Bioinformatics
Integrating
Activites
Technology
integration
Methods
& Models
Information
systems
Bioinformatics
joint research activities











Joint Research
Gut
functions
Metabolic
health
Risk
Benefit
Evaluation
Life
stage
nutrition
Joint Research
Gut
functions
Metabolic
health
Risk
Benefit
Evaluation
Life
stage
nutrition
Joint Research
Gut
functions
Metabolic
health
Risk
Benefit
Evaluation
Life
stage
nutrition
activities to spread excellence











Spreading of excellence

Activities

Training

Commercialisation

Dissemination

Nutrigenomics and society

The main NuGO Activities to Spread Excellence


Grain Legumes Integrated Project

Grain legumes studied
:

pea, bean, faba bean, chickpea, lentil and lupin (the legume
Medicago
truncatula

is used as a model system)

Proposed budget:

Total Costs:


28.153.743

Requested EC Contribution


16.961.701

(50% budget requested by 10 partners)

New strategies to improve grain legumes for food and feed

:



to increase competitiveness of grain legumes in Europe



to improve Europe’s self
-
sufficiency in plant proteins

66 partners from 19 countries

(~80 labs; 9 SMEs):

UK
; BE; BG; CH; CZ; DE; DK; ES; FR; HU; IL; IT; NL; NO; PL; PT; SE; AU;
US

Grain Legumes Integrated Project

Genetic &


genomic tools

food, feed

& health

Economic &

environmental

impact

Seed composition

& quality

Crop functioning

& seed quality

Bioinformatics

Coordination

& training

Dissemination

& transfer

TTP


~10 SMEs

Cooperation and coordination of national
or regional research and innovation
activities (i.e. programmes)


ERA
-
NET”



Participants
: ERA
-
PG builds on national research programmes in plant
genomics (
NL
, AT, BE, DK, FI FR, DE, IT, NO, SP, UK). Other states may join
(BG, EE, GR, HU, IE, PO, PT, RO, SW)


Objectives
:


Improved co
-
ordination

of national plant genomics research programmes



Optimising investments

for plant genomics research and supporting policies



Creating long term perspectives

and improved validation of RTD strategies



Means
: information exchange, web portal, short
-
term exchange of pgm
managers, benchmarking, joint database of experts, position papers

ERA
-
NET co
-
ordination action in
plant genomics (ERA
-
PG)

A European Strategy for Life Sciences and
Biotechnology: The Action Plan
-

COM (2002) 27

1. Harvesting the Potential



The resource Base


investing in people


generating and exploiting knowledge


intellectual property protection


capital base


Networking Europe’s
Biotechnology Communities


A pro
-
active role for public
authorities


3. Responding to global
challenge


A European agenda for
international collaboration


Europe’s responsibilities
towards the developing world



2. Governing Life Sciences
and Biotechnology



Societal scrutiny and dialogue


Developing Life Sciences and
Biotechnology in harmony
with ethical values and social
goals


Demand
-
driven applications
through informed choice


Confidence in science
-
based
regulatory oversight


4. Implementation and
coherence across policies,
sectors and actors

TECHNOLOGY PLATFORMS


European Council in March 2003

“ ...European Research and Innovation Area to be
strengthened to the benefit of all in the enlarged EU by
creating
European technology platforms bringing together
technological know
-
how, industry, regulators and financial
institutions

to develop a strategic agenda for leading
technologies, in areas such as plant genomics …”



Technology Platforms have been identified as important
elements for increasing competitiveness in the
Communication “Industrial policy in an enlarged Europe”
(Dec. 2002) and

the “3% action plan” (April 2003)

3% Action Plan:


better use of public financing to increase leverage effect on
private investment;


R&D in corporate strategies and management.


Progress jointly (open process of co
-
ordination;
European
technology platforms
)


Improve public support to research and innovation (human
resources; academia
-
industry links; mix of public financing
instruments; ..);


Redirect public spending towards research and innovation
(refocus public spending; state aid rules; public procurement; ...)

Plant Genomics

SHARED PLATFORM

EPSO

Industry

Farmers cooperatives

Biotech
entrepreneurs

Consumer groups

Environmental NGO

Policy
-
makers

Policy DGs

Improving the
diagnostic and
therapeutic arsenal
for health care

LIFE SCIENCES, GENOMICS AND

BIOTECHNOLOGY FOR HEALTH

TOWARDS JOINT INDUSTRIAL PROJECTS


Treaty on the European Union




Article 171

The Community may set up
joint undertakings

or any other
structure necessary for the efficient execution of Community
research, technological development and demonstration programmes

E.g. GALILEO Joint Undertaking

Members are
EC
,
ESA
,
EIB
,
private enterprises
. A tendering
process is foreseen. Encompasses R&D, validation of
developments, demonstration, coordination with national
activities. Mio


5.0 to be subscribed by entrerprises, down to


250 000 for SMEs

European
Research Council

Joint Industrial
Projects