lab presentation2011
TRANSCRIPT
Genomics – Proteomics Core
Facility
PROTEOcore
ORGANISATION –
PROTEOcore
Cell culture
Transgenic animal
model
DNA Sequencing
Post-genomic
Histology, cytology,
morphology
Imaging
Glassware & Lab
maintenance
Microarray
laboratory
Proteomics
Laboratory
Bioinformatics &
Biostatistics
High throughput
analytical chemistry
Translational
research
System
biology
– Alliance of local members of the cluster by
competition and supply relationships or
common interests
– examples at ILS:
Research & Co-operation
Research Topics
om
ics
Transcriptomics
High throughput screening
Moleculebank
Genomics / proteomics
Sclerosis Multiplex, POCD,
Alzheimer
Oral antidiabetics
Sa
fety
ph
arm
aco
logy
Chemiotherapy Nanotechnology
Proteomic platform
Microbial genomics /
proteomics / transcriptomics
Fermentation/Bioprotect
DNS → animal breeding
Molecular farming
Safety pharmacology
Microarray platform
Bio
me
dic
al
me
asu
rem
ent
Agro
-bio
tech
nolo
gy
Metabolomics
Enriched egg
Technology Transfer Management
Biomedical Informatics
Joint technology platforms
Proteomics – GenomicsEven more different…
Gene/ RNA
dynamic
Protein
dynamic
Stable molecules
Handling cheap/ easy
Minimal modification
Works in isolation
Fragile molecules
Handling dependent
Labile modification
Protein-interaction
Localization dependent
Handle
Tech
HTP
Sequencing (established) MS related (not yet)
DNA array / genotyping/ expression / CGH/
Protein Chip (not yet)
Antibodies array (not yet)
– Indication areas at ILS
• Diseases of the Central Nervous System;
• Inflammatory Diseases; Food Allergens
• Cancer; Biomarkers (proteins, peptides)
• Proteomics (food proteins and bioactive peptides)
• Probiotics, Functional Food.
– Indication areas are based on:
• Regional resources, know how and research co-
operations within the local institutes and companies
• Global market expectations
– Focus increases the efficiency of Innovation
PROTEOcore – Research &
Co-operation
J Assouline, Genome-wide measurement of gene expression
MIAME - cADN
microarray
6 STEPS of a Microarray Experiment
Array
• Array design
Hybridization protocol
• Statistical analysis
• Data mining
• Image acquisition and
quantification
• Database building
• Filtering
• Normalization
HybridizationSample
(S. Sansone)
MIAME • Sample QC
• Sample
treatment
• Metadata
• mARNs
Extraction protocol
QC
• Target
preparation
(labeling) - QC
QC
QC
QC
PROTEOMICS
• Sample preparation
• 1st dimension (1D)
– Gel-based
– Gel free
• 2nd dimension (2D)
• Detection of protein spots
• Imaging analysis & 2D gel databases
• Spot handling: excision, in gel digestion
Proteomics
• Need of standards in Proteomics
• HUPO-PSI
– Organization
– Standard data formats
– MIAPEs
• PEFF: A Common Sequence Database Format in Proteomics
• PRIDE
• Standard data format converters
Future vision
• Continue work on important data analysis problems in
bioinformatics and language technology
– Applications, including fielded and commercialized ones
– Theory and method development
– Collaboration across units, disciplines, industry
• Future emphasis on
– Mining rich public biological databases
• Discovery of patterns in complex irregular structures,
discovery of similarities and analogies
– Methods for semantic analysis of large text collections
• language and domain-independence, efficiency
USAMV Rector supports
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• Doru PAMFIL, PhD — an accomplished professor of genetics, he has expertise in the management of many national and international projects and veteran of large, public research institutions.
– Throughout his career he has focused on expanding undergraduate research opportunities and improving the education and professional experience of graduate students, with a focus on underrepresented groups.
– Pamfil’s academic work focuses on Biotechnology (marker assisted selection, detection of GMOs, genetic transformation, micropropagation, microbiology). The GMOs Laboratory – CERTOMG - was included in EUROPEAN NETWORK OF GMO LABORATORIES (ENGL) in 2009
"The problem solving, systems thinking, and teamwork aspects of biotechnology can benefit all students,
whether or not they ever pursue an scientific career," said Doru PAMFIL, Rector of the University of
Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, head of INSTITUTE OF LIFE SCIENCES
(LIS).
"An biotechnology education and science curricula that does not include at least some exposure to
biotechnology is a lost opportunity for students and for the nation."
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Helping Hands for Addressing
Excellence in Research, Education
and Training Needs for
Biotechnology
• For more information on future partnerships, contact Dr. Ramona SUHAROSCHI
Email: [email protected]
Tel/fax:+40 264 425575
Calea Floresti 64
400509, Cluj-Napoca