Kein Folientitel - ERA-NET PathoGenoMics

noisymaniacalΒιοτεχνολογία

20 Φεβ 2013 (πριν από 4 χρόνια και 5 μήνες)

145 εμφανίσεις

Nationale


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1


National Contact Point LIFESCIHEALTH


Dr. Wilfried Diekmann


Königswinterer Str. 522
-
524, 53227 Bonn

phone: +49 228 447 698, e
-
mail: wilfried.diekmann@dlr.de

http://www.nks
-
lebenswissenschaften.de

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

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Session overview

W. Diekmann

Chair &

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. Frosch

EUROPATHOGENOMICS


European Virtual Institue for Functional Genomics of Bacterial

Pathogens (NoE)


M. Vicente

microMatrix


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



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

ERA
-
NET

NoE

FP

Biotechnology Action Plan

National

programmes


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.

regional/national ↔ transnational ↔ community

Range


project ↔ programme ↔ policy

Integration

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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)







Strategic supervision in PathoGenoMics, Task 9.4

Objectives and methodology

→ develop perspectives for financial integration with other programmes


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

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

→ show international cooperation perspectives

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

Gene

expression

and

proteomics

Structural

genomics

Comparative
genomics

and

population

genetics

Bio
-
informatics

Multidisciplinary
functional genomics
approaches to basic
biological processes

i) Advanced Genomics and its applications for health

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

New,

safer,more
effective drugs

(incl. pharmaco
-
genomics)

New

diagnostics

New
in vitro

tests to

replace animal

experimentation

New preventive and
therapeutic tools

(somatic gene and cell

therapies; stem cell and
immunotherapies, etc.)

Innovative
research in post
-
genomics with

high potential for

application

ii) Combating major diseases

b) Cancer

c) Poverty
-

related diseases




HIV / AIDS



Malaria



Tuberculosis


Cardiovascular
disease,

diabetes

and rare

diseases

Resis
-

tance to
antibiotics

and other

drugs

Brain and

diseases of

the nervous

system

Human
development

and

the ageing

process

a) Application
-
orientated genomic approaches

TP 1 Life Science, Genomics and Biotechnology for Health

Programme structure and pathogenomics
-
relevant areas

Nationale


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6

Activity Code

Areas addressed

Instr.

LIFESCIHEALTH
-
1.1

Fundamental genomics

LSH
-
2002
-
1.1.0
-
1/2

Topics for STREP/CA/SSA across the Fundamental genomics area in all organisms

SSA, CA, STREP

LIFESCIHEALTH
-
1.2

Applied genomics

LIFESCIHEALTH
-
1.2.5

Innovative research in post
-
genomics

LSH
-
2002
-
1.2.5
-
3

Combinatorial biosynthesis as a tool for generating new drug candidates

STREP

LIFESCIHEALTH
-
2

Combating major diseases


LIFESCIHEALTH
-
2.1.2

Combating resistance to antibiotics and other drugs


LSH
-
2002
-
2.1.2
-
1

Management of respiratory tract infections

NoE

LSH
-
2002
-
2.1.2
-
3

Broadening the knowledge base on the molecular mechanisms behind resistance

STREP
,
CA

LSH
-
2002
-
2.1.2
-
4

Workshop on the structuring of European research activities to more effectively
combat drug resistant hospital infections

SSA

LSH
-
2002
-
2.1.2
-
5

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

SSA

LIFESCIHEALTH
-
2.3

Confronting the major communicable diseases linked to poverty


LSH
-
2002
-
2.3.0
-
4

Tuberculosis vaccine development

IP, NoE

LSH
-
2002
-
2.3.0
-
5

Development of mucosal vaccines for poverty
-
related diseases

IP
,
NoE

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

Selected pathogenomics
-
relevant areas

Nationale


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7


























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

Nationale


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8


























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


Nationale


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9


























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

Nationale


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10


























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

Nationale


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11


























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

Nationale


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12


























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

Nationale


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13

Activity Code

Areas addressed

Instr.

LIFESCIHEALTH
-
1.1

Fundamental genomics

LIFESCIHEALTH
-
1.1.3

Comparative genomics and population genetics

LSH
-
2003
-
1.1.3
-
2

Standardisation and integration of genomic and phenotypic information to characterise
bacterial diversity with relevance to human health

NoE

LSH
-
2003
-
1.1.0
-
1/2/3

Topics for STREP/CA/SSA across the Fundamental genomics area in all organisms

SSA, CA, STREP

LIFESCIHEALTH
-
1.2

Applied genomics

LIFESCIHEALTH
-
1.2.5

Innovative research in post
-
genomics

LSH
-
2003
-

1.2.5
-
2

Post
-
genomic approaches to the study of human pathogens

NoE

LSH
-
2003
-

1.2.5
-
4

New bioassays & biosensors using post
-
genomic approaches to detect harmful microbes

STREP

LSH
-
2003
-

1.2.5
-
5

The fungal cell
-
wall as a target of antifungal therapies

STREP

LSH
-
2003
-

1.2.5
-
6

Biotechnological & post
-
genomic approaches for the development of novel biosafe
propagation deficient virus vectors aimed at prevention & treatment of infectious diseases
(e.g. enteric, respiratory)

STREP

LSH
-
2003
-

1.2.5
-
7

Exploitation of fungal genomics and filamentous fungal biotechnology for human health

CA

LIFESCIHEALTH
-
2

Combating major diseases

LIFESCIHEALTH
-
2.1.2

Combating resistance to antibiotics and other drugs

LSH
-
2003
-
2.1.2
-
1

Functional genomics of antibiotics
-
producing organisms

IP

LSH
-
2003
-
2.1.2
-
2

New molecular targets to develop drugs against pathogens causing severe resistance
problems

IP

LSH
-
2003
-
2.1.2
-
3

Novel approaches to address antimicrobial resistance through non
-
antimicrobial based
therapies

STREP,
CA

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

Selected pathogenomics
-
relevant areas

Nationale


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14

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

Selected pathogenomics
-
relevant areas

Activity Code

Areas addressed

Instr.

LIFESCIHEALTH
-
2.3

Confronting the major communicable diseases linked to poverty

LSH
-
2003
-
2.3.0
-
1

Highly innovative approaches for the development of new interventions for HIV,
malaria and tuberculosis

STREP

LSH
-
2003
-
2.3.0
-
2

Coordination of European research on HIV, malaria and tuberculosis at the global level

SSA

LSH
-
2003
-
2.3.0
-
3

Networking of European SMEs active in the area of poverty related diseases

SSA

Nationale


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15


























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


Nationale


Kontaktstelle

Lebenswissenschaften

16


























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

Nationale


Kontaktstelle

Lebenswissenschaften

17


























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“


Nationale


Kontaktstelle

Lebenswissenschaften

18


























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


Nationale


Kontaktstelle

Lebenswissenschaften

19


























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


Nationale


Kontaktstelle

Lebenswissenschaften

20


























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


Nationale


Kontaktstelle

Lebenswissenschaften

21


























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

Nationale


Kontaktstelle

Lebenswissenschaften

22


























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

Nationale


Kontaktstelle

Lebenswissenschaften

23


























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

Nationale


Kontaktstelle

Lebenswissenschaften

24


























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

Nationale


Kontaktstelle

Lebenswissenschaften

25


























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

3
D

structures





structural

&

molecular

biology

protocol

for

examining

promising

drug
-

protein

fit

pairs





Coordination
:

Eotvos

Lorand

Tudomanyegyetem,

HU

Nationale


Kontaktstelle

Lebenswissenschaften

26


























FP6 project portfolio in pathogenomics

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

Genome
-

and

HLA
-

wide

scanning

and

validation

of

cytotoxic

CD
8

T

cell

responses

against

Mycobacterium

tuberculosis

(VACCINES
4
TB)



STREP,

retained

for

funding


Genomics/proteomics

based

platform

for

antigen
-

and

epitope
-
discovery

with

relevance

to

human

immune

CD
8

cytotoxic

T

cells

responses

against

M
.

tuberculosis





Methodology
:


high
-
throughput

methods

from

immunology

and

bioinformatics





Coordination
:

Technical

University

of

Denmark
,

DK

Nationale


Kontaktstelle

Lebenswissenschaften

27


























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

Nationale


Kontaktstelle

Lebenswissenschaften

28


























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

Nationale


Kontaktstelle

Lebenswissenschaften

29


























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

Nationale


Kontaktstelle

Lebenswissenschaften

30


























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

Nationale


Kontaktstelle

Lebenswissenschaften

31


























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

Nationale


Kontaktstelle

Lebenswissenschaften

32

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

Selected pathogenomics
-
relevant areas

Activity Code

Areas addressed

Instr.

LIFESCIHEALTH
-
1.1

Fundamental genomics

LSH
-
2004
-
1.1.0
-
1/2/3

Topics for STREP/CA/SSA across the Fundamental genomics area in all organisms

SSA, CA, STREP

LIFESCIHEALTH
-
1.2

Applied genomics



LIFESCIHEALTH
-
1.2.5

Innovative research in post
-
genomics


LSH
-
2004
-
1.2.5
-
4

Post genomic approaches for tackling complex multifactorial diseases (except Cancer)

STREP

LIFESCIHEALTH
-
2

Combating major diseases

LIFESCIHEALTH
-
2.1.2

Combating resistance to antibiotics and other drugs

LSH
-
2004
-
2.1.2
-
1

Management of lower respiratory tract infections

NoE

LSH
-
2004
-
2.1.2
-
2

The role of mobile genetic elements in the generation of antimicrobial resistance

STREP

LSH
-
2004
-
2.1.2
-
3

Improved understanding of ecological factors with impact on the genetic and molecular
determinants of fitness and virulence of resistant bacterial pathogens

STREP

LSH
-
2004
-
2.1.2
-
4

Control of anti
-
fungal drug resistance (especially orientated towards SMEs)

STREP

LSH
-
2004
-
2.1.2
-
5

Workshop on translation of research results on antimicrobial resistance into clinical practice

SSA

LSH
-
2004
-
2.1.2
-
6

Workshop for set up of a centrally supported system for annotation of microbial genomics

SSA

LIFESCIHEALTH
-
2.2

Combating cancer

LSH
-
2004
-
2.2.0
-
3

Research on tumours associated with infectious agents

IP

LIFESCIHEALTH
-
2.3

Confronting the major communicable diseases linked to poverty

LSH
-
2004
-
2.3.0
-
4

Development of new drugs for the treatment of tuberculosis

IP

LSH
-
2004
-
2.3.0
-
7

Research in poverty
-
related diseases (PRD) by SMEs

STREP

LSH
-
2004
-
2.3.0
-
9

Coordination of PRD activities between biotech industry, bioincubators & biotech investors

CA