Molecular diagnostic: from research to application

Transcription

1 FEM2 Ambiente S.r.l. spin-off dell' UNIVERSITA' DEGLI STUDI DI MILANO-BICOCCA Molecular diagnostic: from research to application Emanuele Ferri & Andrea Galimberti Le biotecnologie nel mondo della criminologia Seconda Edizione ( )

2 Summary Part I Who we are and what we do Part II DNA barcoding as an instrument to identify living beings Part III DNA barcoding applications Part IV Pyrosequencing Part V Pyrosequencing applications

3 Summary Part I Who we are and what we do Part II DNA barcoding as an instrument to identify living beings Part III DNA barcoding applications Part IV Pyrosequencing Part V Pyrosequencing applications

4 FEM2 Ambiente S.r.l. ZooPlantLab Massimo Labra Assistant professor at UNIMIB Maurizio Casiraghi Assistant professor at UNIMIB Fabizio De Mattia President FEM2-Ambiente Emanuele Ferri CEO FEM2-Ambiente

5 FEM2 Ambiente S.r.l. ZooPlantLab Andrea Galimberti Emanuele Panunzi Michela Barbuto Silvia Sironi

6 DNA barcoding Services Animal organisms identification Vegetal organisms identification Identification of fungi, bacteria, complexes matrices Pathogens screening Characterization of microbial communities By Sanger sequencing of libraries By multiplexing pyrosequencing Molecular sexing and avian pathologies Amphibian pathologies

7 Products

8 Summary Part I Who we are and what we do Part II DNA barcoding as an instrument to identify living beings Part III DNA barcoding applications Part IV Pyrosequencing Part V Pyrosequencing applications

9 Laboratory DNA barcoding

10 Summary Part I Who we are and what we do Part II DNA barcoding as an instrument to identify living beings Part III DNA barcoding applications Part IV Pyrosequencing Part V Pyrosequencing applications

11 DNA barcoding: our cases Food traceability - identification of market fish: Diffusion of processed rather than whole fish; Discrimination systems are welcomed; Our work is in collaboration with the Milan Fish Market, the distribution industries, the Italian food control agency (N.A.S. Carabinieri)

12 DNA barcoding: our cases Commercial cases (1): Common smooth-hound (Mustelus mustelus and Mustelus asterias)

13 DNA barcoding: our cases Commercial cases (1): Triakidae Palombo (Mustelus mustelus and Mustelus asterias) 29 % 71 % Squalidae Carcarinidae Lamnidae

14 DNA barcoding: our cases Commercial cases (2): flatfish Pleuronectes platessa Solea solea 80 % Platichthys flesus

15 DNA barcoding: our cases Commercial cases (3): Perca fluviatilis Italian rice Risotto with European perch ( risotto con pesce persico )

16 DNA mini-barcoding in progress Examination of baby food composed of flounder coxi of Sus scrofa domesticus

17 DNA barcoding: our cases Identification of commercial plant species Economically relevant topic; In some cases lack of high level of quality control; Plants used in alternative medicine, dietary supplements, nutraceutics, cosmetics, food (spices)

18 DNA barcoding: our cases Italian bats project identification of Italian bats: Bats are an intriguing and unknown topic; High level of molecular diversity is found in this group of mammals; Our work is in collaboration with the Italian Bat Association ( Italian bats represent 33 species out of 39 european species

19 DNA barcoding: our cases Identification of commercial and invasive exotic species Economically relevant topic: 3B /year; Trade of endangered species; Works on a single feather; Molecular sex determination as an additive output: service activated

20 DNA barcoding: other cases

21 DNA barcoding: our cases Identification of plant species from pollen Bees are used as pollen collectors; Identification of plants from pollen

22 Summary Part I Who we are and what we do Part II DNA barcoding as an instrument to identify living beings Part III DNA barcoding applications Part IV Pyrosequencing Part V Pyrosequencing applications

23 Metagenomic: our cases Pyrosequencing on: Soils (characterization of soil s meiofauna ) Pollens (as an alternative to classic melissopalinologic analysis) Water (characterization of water meiobenthos ) Bacteria (microbic characterization of complexes matrices)

24 Microbic characterization

25 Microbic characterization How to keep the analysis effective, but reduce the costs?

26 Microbic characterization Biochimical multiplexing FEM2 Ambiente has a library made up by 20 chimeric primer. Combining 10 chimeric primer For with 10 chimeric primer Rev allow the characterization of up to 100 different samples. With 1/8 454 plate is possible to obtain sequences/samples of 100 samples at cost of IVA.

27 Microbic characterization Not standard data management (Ribosomal Database Project) FEM2 Ambiente we are developing an identification pipeline based on NCBI BLAST: PYROBLAST-MULTICLASSIFIER

28 Microbic characterization