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: laslora@yahoo.com

Tel/fax:+40 264 425575

Calea Floresti 64

400509, Cluj-Napoca