Lab presentation2011


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Lab presentation2011

  1. 1. Genomics – Proteomics Core Facility PROTEOcore
  2. 2. ORGANISATION – PROTEOcoreMicroarray System Cell culturelaboratory biology Transgenic animal model Proteomics DNA Sequencing Laboratory Post-genomic Bioinformatics & Histology, cytology, Biostatistics morphology Imaging High throughput Glassware & Lab maintenance analytical chemistryTranslational research
  3. 3. Research & Co-operation– Alliance of local members of the cluster by competition and supply relationships or common interests– examples at ILS:
  4. 4. Research Topics
  5. 5. Technology Transfer Management Biomedical Informatics Joint technology platforms Genomics / proteomics Molecular farming Agro-biotechnology Moleculebank Microbial genomics / proteomics / transcriptomics omics High throughput screening Fermentation/Bioprotect Transcriptomics DNS → animal breeding Metabolomics Safety pharmacology Safety pharmacology Microarray platformmeasurement Oral antidiabetics Biomedical Proteomic platform Sclerosis Multiplex, POCD, Alzheimer Nanotechnology Chemiotherapy Enriched egg
  6. 6. Proteomics – Genomics Even more different… Gene/ RNA Protein dynamic dynamicHandle Stable molecules Fragile molecules Handling cheap/ easy Handling dependent Minimal modification Labile modification Works in isolation Protein-interaction Localization dependentTech Sequencing (established) MS related (not yet) DNA array / genotyping/ Protein Chip (not yet)HTP expression / CGH/ Antibodies array (not yet)
  7. 7. PROTEOcore – Research & Co-operation– 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
  8. 8. J Assouline, Genome-wide measurement of gene expression
  9. 9. MIAME - cADN• Sample QC microarray• Sample MIAMEtreatment• Metadata Hybridization protocol• mARNs QCExtraction protocolQC Sample Hybridization Array• Targetpreparation • Array design QC(labeling) - QC • Image acquisition and quantification • Database building QC • Statistical analysis • Filtering • Data mining • Normalization 6 STEPS of a Microarray Experiment (S. Sansone)
  10. 10. 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
  11. 11. Proteomics
  12. 12. • 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
  13. 13. 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
  14. 14. USAMV Rector supports • 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 ofAgricultural 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 tobiotechnology is a lost opportunity for students and for the nation." 17
  15. 15. • For more information on future partnerships, contact Dr. Ramona SUHAROSCHI Email: Helping Hands for Addressing Tel/fax:+40 264 425575Excellence in Research, Education and Training Needs for Biotechnology Calea Floresti 64 400509, Cluj-Napoca 18