Molecular Biodiversity Laboratory

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Molecular Biodiversity Laboratory

• Leveraging Molecular Biodiversity to build novel
  bioinformatic systems, both applied to human
  health in order to monitor safety and
• risks - and to agro-industrial, to trace products
  along food production and supply chains

Luigi Di Pace - IBM MBLab Director email
luigi_dipace_at_it.ibm.com
09/07/2009
Title slide
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Biology has become an Information Science
Thanks to new disciplines such as genomic,
proteomic, meta-genomics, metabolonics, etc. we
take smart decisions in a much more broader space
in a number of domains. Biodiversity and Genetic
Information are becoming a new information source
for Smart Decisions
One of the main engine of the biology is
Information. This is stored and coded and
transmitted in several ways The main information
repository is our DNA, this database is
replicated in each cell of our body, and any cell
of living organisms has a DNA. DNA includes the
genes which are the information needed to govern
structural and functional activities in our
bodies. Every living species has specific
molecular diversity that include all
information derived from genetic that distinguish
a living species form another. Molecular
biodiversity is one of the most powerful tools
used by bioinformatics to build IT applications
able to analysis and interpreted such diversity
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Research-driven activities
IBM Research Labs
Research Disciplines
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IBM Research Bioinformatics Life Sciences
researches

• General areas of interest in Life Sciences
  research
• developing analytics in the absence of knowledge
  of the nature of the data. These algorithms are
  generic in their nature and consequently
  applicable to a very large number of the problems
  one encounters in the field of Life Sciences.
• developing methodologies that are of relevance to
  molecular dynamics and using simulations to study
  and understand important biological systems
• driving the definition of standards for
  information interchange relevant in Life Sciences
  (e.g. HL7, etc.)
• generating practical solutions that are based on
  developed algorithms, in order to showcase the
  great value that these methods hold for solving
  many problems from the Life Sciences, including
  ones of critical importance.

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Project/Topic driven activities
Leveraging IBM unique abilities in IBM Research
and other organizations that can be applied to
the molecular biodiversity topic, to develop
real-world business applications
Computational Biology Center (R. Ajay )
Yorktown
External Partners
Ontologies (B. Schloos)
Almaden
Analytics (J. Kreulen)
IBM Italy GBS Innovation Center
Search (S. Vaithyanathan)
IBM Research
Molecular Biodiversity Center
Haifa
Healthcare (P. Vortman)
IBM Global Business Services
Zurich
Molecular Dynamics (A. Curioni)
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Molecular Biodiversty Laboratory
MBLab is a private-public research initiative,
involved in the study and the use of Molecular
Biodiversity. It aims to build novel
bioinformatic systems, both applied to human
health in order to monitor safety and risks -
and to agro-industrial, to trace products along
food production and supply chains
Project co-funded by Italian Minister of Research
(MIUR) and it is a 7M investment Fondo FAR -
Legge 297/1999 Art. 12/lab Project Grant DM19410
www.mblabproject.it
Institutional partners

• Organization
• Lab Director is Luigi Di Pace (IBM)
• Scientific Board
• Prof. Annamaria Colao (University Federico II
  of Napoli)
• Prof. Floriana Esposito (University of Bari)
• Dott. Pietro Leo (IBM)
• Prof. Graziano Pesole (University of Bari)
• Prof. Cecilia Saccone (CNR-ITB University of
  Bari)
• Dott. Angelo Visconti (CNR-ISPA)

IBM GBS Innovation Center Italy (Project
Coordinator)
Università degli Studi di Bari Facoltà di Scienze
Biotecnologiche Labo-Biotech
C.N.R. - Istituto di Scienze delle Produzioni
Università degli Studi di Napoli Federico
II Dipartimento di Endocrinologia ed Oncologia
Molecolare e Clinica
C.N.R. - Istituto di Tecnologie Biomediche -
Sezione di Bari
ITB
Univeresità Telematica G. Marconi
Università degli Studi di Bari Dipartimento di
Informatica
Ministero dellistruzione delluniversità e della
ricerca
Provincia autonoma di Trento
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Molecular Biodiversity Lab partnership and
StrategyMixing and balancing public and private
resources, in an Open Research Collaboration
style, to build an operative research network to
provide high-value services and products based on
molecular biodiversity
Project co-funded by Italian Minister of Research
(MIUR) - Fondo FAR - Legge 297/1999 Art. 12/lab
Project Grant DM19410
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What is Molecular Biodiversity and why the study
of it is relevant from an industrial perspective?
Wine Deep Tracing
Example 1 Wine Deep Tracing By using a
biomolecular signature from grapevine and
microbioma biodiversity

• Biodiversity refers to the variety of the living
  forms existing on Earth and the ecosystems they
  participate in. The biodiversity we observe today
  is the result of a million-years evolution it
  can be considered at molecular, species and
  ecosystem biodiversity levels.
• Molecular Biodiversity is the research focus area
  of MBLab and, under our vision and perspective,
  it aims to generate new insights, at the
  molecular level, trying to combine data coming
  from multiple Information biodiversity axes.
• MBLab aims to design and build bioinformatic
  molecular biodiversity applications applied to
  various ecosystems, both natural, a specific
  geographic area, a living organism, as well as
  man-made, an agro-food supply chain, a wine
  fermentation silos, etc.

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What is Molecular Biodiversity and why the study
of it is relevant from an industrial perspective?
Wine Deep Tracing
Example 1 Wine Deep Tracing By using a
biomolecular signature from grapevine and
microbioma biodiversity

• Biodiversity refers to the variety of the living
  forms existing on Earth and the ecosystems they
  participate in. The biodiversity we observe today
  is the result of a million-years evolution it
  can be considered at molecular, species and
  ecosystem biodiversity levels.
• Molecular Biodiversity is the research focus area
  of MBLab and, under our vision and perspective,
  it aims to generate new insights, at the
  molecular level, trying to combine data coming
  from multiple Information biodiversity axes.
• MBLab aims to design and build bioinformatic
  molecular biodiversity applications applied to
  various ecosystems, both natural, a specific
  geographic area, a living organism, as well as
  man-made, an agro-food supply chain, a wine
  fermentation silos, etc.

Wine
Biodiversity
(0-10 total species)
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What is Molecular Biodiversity and why the study
of it is relevant from an industrial perspective?
Wine Deep Safety
Example 2 Wine Deep Safety By studing molecular
ecosystem biodiversity and conditions of
grapevine and microbioma to avoid the negative
effects of dangerous species

• Biodiversity refers to the variety of the living
  forms existing on Earth and the ecosystems they
  participate in. The biodiversity we observe today
  is the result of a million-years evolution it
  can be considered at molecular, species and
  ecosystem biodiversity levels.
• Molecular Biodiversity is the research focus area
  of MBLab and, under our vision and perspective,
  it aims to generate new insights, at the
  molecular level, trying to combine data coming
  from multiple Information biodiversity axes.
• MBLab aims to design and build bioinformatic
  molecular biodiversity applications applied to
  various ecosystems, both natural, a specific
  geographic area, a living organism, as well as
  man-made, an agro-food supply chain, a wine
  fermentation silos, etc.

Ochratoxin A (OTA) is a mycotoxin of considerable
concern for human health and is said to have
carcinogenic, nephrotoxic and genotoxic
properties OTA is a naturally produced by a
number of Fungi (mold) species at particular
biological and environmental conditions
Facts
FAO estimates that the 25 of Food in the world
is contained by mycotoxins Just few fungi
species are responsible for producing OTA in food
and feed. In the wine the major responsible is
just one species Aspergillus Carbonarius
Can we know molecular ecosystem conditions that
lead fungi produce the OTA mycotoxyn?
Challenges
Can we inhibit OTA mycotoxyn production? Can we
have simple and fast molecular tools to verify if
fungi into a crop or a food silos belong to a
dangerous species?
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Biodiversity Axes Traditional Approach
Life Taxonomy
Bi-dimentional investigation area
Organisms
Intra-species studies
Iter-species studies
A Food Production Chain
A controlled production Enviromentt
A wine fermentation Silos
A Blood Sample
A living Organisms
A production field
Geographic Area
Planet
A Ship
Ecosystems
Large size
The traditional Biodiversity investigation area
Generate insights from a combined observation of
taxonomy (organisms) and data about ecosystems in
which organisms live.
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Biodiversity Axes in the post-genomic era
Life Taxonomy
Bi-dimentional investigation area
Organisms
Intra-species studies
Iter-species studies
A Food Production Chain
A controlled production Enviromentt
A wine fermentation Silos
A Blood Sample
A living Organisms
A production field
Geographic Area
Planet
A Ship
Ecosystems
Large size
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The Molecular Biodiversity Lab aims to develop a
number of molecular diagnostic tools and
bioinformatic resources targeting both human
safety and agricultural applications, by
exploiting a number of molecular biodiversity,
including DNA Barcoding, techniques and know-how
Molecular Biodiversity
Molecular diagnostic tools and resources