BIOPROSP 2009
Radisson SAS Hotel Tromsø, Norway
February 24 – 26, 2009
February 24-25 2009, The Radisson SAS Hotel Conference Centre, Tromsø, Norway
In addition there will be a whole day post conference workshop on new technologies on
February 26 2009 at the Tromsø Science Park (Linken Meeting Centre).
Objectives of the conference:
•
•
•
Confirm BIOPROSPs position as one of the leading international conferences on
marine biotechnology
BIOPROSP will showcase applications and industry utility of discoveries based on
bioprospecting
This year BIOPROSP focus will be on opportunities related to the unique physiology
and metabolism of extremophilic organisms
Target group: Academic and industry researchers, decision makers, regulatory experts,
investors and public facilitators.
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TABLE OF CONTENTS
WELCOME TO BIOPROSP 2009! ......................................................................................................... 3
th
PROGRAM BIOPROSP TUESDAY FEBRUARY 24 ........................................................................... 7
th
PROGRAM BIOPROSP WEDNESDAY FEBRUARY 25 ..................................................................... 8
th
PROGRAM WORKSHOP THURSDAY FEBRUARY 26 ...................................................................... 9
LIST OF SPEAKERS............................................................................................................................ 13
POSTER ABSTRACTS ........................................................................................................................ 41
LIST OF PARTICIPANTS..................................................................................................................... 85
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WELCOME TO BIOPROSP 2009!
This is the 4th International BIOPROSP Conference on Marine Biotechnology, organized by
the research communities in Tromsø and Trondheim. To be held over two days, February
24-25 in the world’s northernmost University City of Tromsø. BIOPROSP 2009 will give
delegates the opportunity to gain a full understanding of the opportunities offered by recent
developments in this interesting field.
The focus if this year’s conference will be extremophiles from beneath the sub Arctic Ocean.
A number of interesting speakers from USA, Russia, Canada, Korea, Germany, England,
Scotland, Sweden and Norway has been invited to bring the delegates up to date with the
latest advances of scientific and commercial aspects in marine bioprospecting. The Minister
of Fisheries and Coastal Affairs will present the Norwegian Government initiative on marine
bioprospecting.
We are pleased to see that it has been good interest in both poster presentations and Post
Conference Workshop. There will be 45 poster presentations, in which 4 of these have been
selected for oral presentation. This year we offer a whole day Post Conference Workshop on
new technologies on February 26 2009, and 80 delegates as registered for this.
We hope that the objectives of BIOPROSP 2009 and your own expectations will be fulfilled,
and we are looking forward to an interesting meeting and an enjoyable stay for all the
participants!
Unn Sørum
Head of the Program Committee
The MABIT program
Tromsø Science Centre, February 11 2009
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BIOPROSP IS SPONSORED BY
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PROGRAMME COMMITTEE
Unn Sørum
Elin Kolsvik
Ole Jørgen Marvik
Klara Stensvåg
Jeanette H. Andersen
Trond Ø. Jørgensen
Svein Valla
Inge W. Nilsen
John-Sigurd Svendsen
Hans-Kristian Kotlar
Sissel Svenning
Grethe Hoel
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PROGRAM BIOPROSP MONDAY FEBRUARY 23th
20:00 . Welcome reception at Polaria, 5 minutes walking distance from the city centre,
offering a maritime and rustic atmosphere. A light meal (tapas) will be served together
with the local beer of Tromsø.
Picture from http://www.polaria.no/
How to get there
– From Radisson SAS Hotel Tromsø to Polaria is a five to ten minute walk.
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PROGRAM BIOPROSP TUESDAY FEBRUARY 24th
From Title
08:00 Registration
09:00 Opening
Welcome on behalf of the program committee
09:15 Welcome to Tromsø
Speaker
Unn Sørum, MABIT, Norway
09:20 Welcome, on behalf of University of Tromsø
Jarle Aarbakke, head of University of Tromsø
09:30 Opening of BIOPROSP: When Little Things Mean a Lot.
The Norwegian Government’s initiative on marine
bioprospecting
MARINE BIOPROSPECTING RESOURCES
09:55 Corals of the Arctic
Helga Pedersen, Minister of Fisheries and
Coastal Affairs, Norway
Chair
Arild Hausberg, mayor of Tromsø
10:15 Extreme in the 4th power!
Lene Buhl-Mortensen, Institute of Marine
Research, Norway
Hans Kristian Kotlar, StatoilHydro, Norway
10:40 Bridging scientific discovery and industry-led innovation
Ole Jørgen Marvik, Innovation Norway
Kjersti Lie
Gabrielsen
University of
Tromsø
11:00 Coffee
Marine genetic resources – the interface between
11:35 international law of the sea and intellectual property
regimes
12:00 MabCent - a Centre for Research-based Innovation of
Arctic marine bioactives and drug discovery
12:20 Marine Extremophiles: Coping and Adaptions to Frozen
and Boiling Life
12:45 The true gold of our planet is not yellow or black, it is vital
Valentina Germani, Law of the Sea, United
Nations, USA
Jeanette H. Andersen, MabCent-CRI,
University of Tromsø, Norway
Geir Gogstad
Rikshospitalet
University
Hospital
John N. Reeve, Ohio State University, USA
Garabed Antranikian, Hamburg University of
Technology, Germany
13:10 Lunch
APPLICATIONS
14:10 Applications of enzymes from the marine cold
environment
14:30 Extremophile enzymes: application and structure
Arne O. Smalås, University of Tromsø,
Norway
Jennifer Littlechild, University of Exeter, UK
14:55 Selected from posters: Exploring natural product
production from symbiotic microorganisms isolated from
corals.
Russell Kerr, University of Prince Edward
Island, Canada
15:05 Selected from posters: Chemical and Physiological traits
of common northern species
15:15 Poster session and coffee
Siv Huseby, MabCent-CRI, University of
Tromsø, Norway
APPLICATIONS
16:15 Antibiotics from the sea
16:35 Ligands of nuclear receptors, novel drug leads to treat
metabolic diseases
17:00 Novel natural products from North-Western Pacific cold
water marine organisms and their bioactivities
17:25 Closing talk day 1: Developing Methods to Discover
Novel Metal Complexes from Marine Invertebrates
17:50 Concluding
20:00 Conference Banquet, SAS Radisson Hotel
John-Sigurd
Svendsen
University of
Tromsø /
Lytix
Biopharma AS
Klara Stensvåg, University of Tromsø, Norway Trond Ø.
Jørgensen
Heonjoong Kang, Seoul National University,
University of
Korea
Tromsø
Valentin Stonik, Russian Academy of Science,
Russia
Marcel Jaspars, University of Aberdeen,
Scotland
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PROGRAM BIOPROSP WEDNESDAY FEBRUARY 25th
From Title
METAGENOMICS / BIOINFORMATICS
08:30 Functional screening of metagenome libraries by the
use of broad-host-range cloning vectors
08:50 Scratching the Surface: Constructing and Screening
Large-insert Soil Metagenomic Libraries
09:15 Predicting genes and protein function in metagenomes:
the large scale challenge
09:40 DNA of the North & South Polar Seas: Metagenomic
screening of high diversity extreme environments
09:55 Coffee
Speaker
Chair
Svein Valla, Norwegian University of Science
and Technology, Norway
Mark Liles, Auburn University, Alabama, USA
Bjarne
Landfald
University of
Tromsø
Peter Meinicke, University of Göttingen,
Germany
Thomas Sicheritz-Ponten, Technical
University of Denmark
TECHNOLOGY / SCALING UP
10:25 Developing and managing a global business based on a Paul Kinnon, ZyGEM Corp. Ltd. USA office
culture collection
10:50 Fragment based drug discovery
Evert Homan, Beactica AB, Sweden
11:15 Large scale purification of biomolecules
Ian Garrard, Brunel University, UK
11:40 Selected from posters: Antimicrobial photodynamic
therapy: Minimization of compound related failure by
optimization of the drug formulation
Hanne Hjorth Tønnesen, University of Oslo,
Norway
11:50 Lunch
APPLICATIONS
12:50 Lactoferrin peptides: From early discovery to the clinical
development
13:15 Functional food and ingredients from the sea
13:40 Discovery of new antibiotics through biosynthetic
engineering and bioprospecting
14:00 Selected from posters: Cultured bacteria and fungi with
bioactivities from the marine sponge Haliclona simulans
14:10 Coffee
APPLICATIONS
14:40 Novel industry based on marine copepods
15:00 Natural products as drugs
15:25 Closing talk: 21st Century Trends in Microbial Ecology &
Biotecnology
15:50 Closing
Ole Jørgen
Marvik
Innovation
Norway
Margit Mahlapuu, PharmaSurgics AB,
Sweden
Fereidoon Shahidi, Memorial University of
Newfoundland, Canada
Sergey B. Zotchev, Biosergen AS/ Norwegian
University of Science and Technology, Norway
Alan Dobsen, University College Cork, Ireland
Inge W. Nilsen
Nofima
Gunnar Rørstad, Calanus AS, Norway
Hans Kr.
Kotlar
Statoilhydro
David Newman, National Cancer Institute,
USA
Eric Mathur, Syntetic Genomics Inc. USA
Trond Ø. Jørgensen, MabCent-CRI,
University of Tromsø, Norway
17.00 Adventures in Tromsø - an optional social program for participants. Separate registration and payment
(Contact [email protected])
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PROGRAM WORKSHOP THURSDAY FEBRUARY 26th
Post Conference Workshop on new technologies at Tromsø Science Park, Linken Meeting
Centre. There will be four different workshops arranged from 08:30 to 15:30. They will be
arranged in parallel sessions.
One or more experts will give a short introduction for selected topics, including
troubleshooting, bottle necks, and challenges with new technology related to the theme. The
delegates are invited to participate with their own problems and/or solutions to the theme for
interactive discussions.
8:30-12-30
WS1: Molecular identification /
Fragment based drug discovery
WS2: Functional and bioinformatic
analyses of metagenome libraries
12:30-13:30 LUNCH
13:30-15:30 WS3: Assay Development Automation WS4: Extraction and purification of
biological material
WS1: Molecular identification / Fragment based drug discovery
Molecular identification (2 hours)
Introduction by Johan K. Svenson, University of Tromsø. Norway, Marcel Jaspars,
University of Aberdeen, Scotland
An accurate structural determination of potentially novel target compounds is imperative to
the bioprospecting scientist. Being able to single out and identify the active compounds is not
only vital for dereplication purposes but also for future developments and patent issues etc. At
this workshop session we will describe some of the recent advancement made in the field of
structural determination of natural product highlighted with relevant examples. The focus of
the session will be on spectroscopic techniques such as NMR and MS. Participants will
actively be able to take part in solving problems and are encouraged to contribute with their
own experiences and potential challenges.
Fragment based drug discovery (2 hours)
Introduction by Evert Homan, Beactica AB, Sweden
Subsets of extremely low-MW (< 250 Da) isolated compounds comprise libraries of 'fragment'
molecules. These are considered as parts of larger molecules, separated parts that each is
capable of interacting with a target of choice. Thus, minor interactions are screened for and
identified, before single fragments are chemically modified / optimized or put together in
seeks of optimized fragment combinations. Alternatively, promising natural fragments are
combined with synthetic fragments in the optimization process.
Beside requirements for highly sensitive screening technologies, working with fragment
libraries represents several challenges in compound identification and in determining
interactions with their respective targets. This workshop session will focus on fragment library
assembly and technology for identification of fragments.
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WS2: Functional and bioinformatic analyses of metagenome libraries
Introduction by Peter Meinicke, University of Göttingen, Germany and Mark Liles, Auburn
University, Alabama, USA
The vast majority of bacteria in nature cannot be efficiently cultivated, and this means that an
enormous potential for gene discovery is lost if one has to rely on cultivation only. One way to
overcome this problem is to construct metagenomic gene libraries which cover all microbial
DNA present in the environment of interest. This DNA can then be expressed and screened
for traits of interest in a conventional host such as Escherichia coli. Alternatively, one may
take advantage of the extremely rapid developments in DNA sequencing technology that
allow direct sequencing of the isolated DNA or the DNA cloned in metagenomic libraries.
Bioinformatics analyses may then be used to search in silico for genes of interest. Both of
these approaches have certain advantages and disadvantages, and in this Workshop these
issues will be discussed, including what can be foreseen to be the long-term trends.
WS3: Assay development automation
Introduction by Phillippe Verwaerde, AlzProtect, France, Ewan S. Grant, Life Science
Automation Europe Beckman Coulter UK Ltd
The early phase of drug discovery involves high-throughput screening and identification of
lead compounds. This phase requires knowledge about assay development as well as
automation and robotics. The workshop should address some of the challenges in this area
and contribute to a better understanding of the requirements for an assay to be well-suited for
automation.
WS4: Extraction and purification of biological material
Introduction by Valentin Stonik, Russian Academy of Science, Russia, Ian Garrard, Brunel
University, UK
In order to extract and purify microbial material like genetic material or low molecular
bioactives, we have to decide what kind of molecules we are looking for at what they are
going to be used for.
If we are going to make a metagenomic library for instance, we have to evaluate certain
issues and evaluate if methods are suitable for use to isolate genetic material that is
representative for the microbial diversity in the sample. The methods might not be rough
enough in order to isolate all of the genetic material available on one hand and on the other
hand gentle enough to preserve long inserts without disruption.
The extraction method of particular small bioactive compounds like secondary metabolites or
peptides from a sample is essential in order to make sure that the sample is representative or
contain all the compounds of interest. This workshop session will focus on the choice of
strategy, methods and scale of techniques.
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Workshop location: LINKEN / Tromsø Science Park
You can order at Taxi at
TROMSØ TAXI (+47) 03011 or DIN TAXI (+47) 02045
BUS 42 stop’s at Sjøgata bus stop, and passes by Tromsø Science Park
(Forskningsparken) You can get of at the bus stop “Gimle” – then you
walk a few minutes back to the Science park. The timetable is also
available at the hotel.
Departure times
from Sjøtata
07.45
07.56
08.15
08.30
08.45
09.00
09.16
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LIST OF SPEAKERS
S1: Arild Hausberg,
Mayor Tromsø municipality
Mr. Hausberg is by education electrical engineer. Before he
became full time politician in 2005 he worked as engineer and
department manager at Troms Kraft, a regional power and
utility company. He has represented the Labour Party
in Tromsø City Council since 1995 and was elected Mayor in
September 2007.
As Mayor Mr. Hausberg puts emphasis on business
development and works to promote Tromsø as a center for
marine based biotechnology.
S2: Jarle Aarbakke,
Rector of the University of Tromsø
Aarbakke has been Professor of Pharmacology and
Clinical Pharmacology at the University of Tromsø since
1982. His main research has been within cancer
pharmacology related to genetic causes of
interindividual differences in drug response.
Aarbakke was elected Rector of the University of
Tromsø in 2002, and was re-elected in 2005 and again
in 2009. Since 2006 he has also chaired the Expert
Committee for the High North - a group appointed by the
Norwegian Ministry of Foreign Affair to give advise on
the development of Norway's High North Policy.
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S3: Helga Pedersen, Minister of Fisheries
and Coastal Affairs
Ms. Helga Pedersen was appointed Minister of Fisheries and
Coastal Affairs on October 17 in 2005. She represents the
Labour Party (Ap).
Education: Intermediate course in History, University of
Tromsø, Foundation course in Russo-Soviet Studies,
University of Bergen, Intermediate course in Russian,
University of Bergen, Baccalaureate after three years of study
at Lycée Alain Chartier (a French Upper Secondary School) in
Bayeux, Normandy, France.
Political experience: From 2007- Deputy Leader of the Labour
Party. Previously, Chairman of the County Council in Finnmark
County, County Council Representative, Finnmark County and
she has been active in the Norwegian Labour Youth League
(AUF), the Norwegian Labour Party’s women’s organisation
and the Labour Party of Tana Municipality.
Picture: Scanpix
Job experience: Head of the Project to Promote Economic and Cultural Development in the
Tanafjord area. Part-time project worker for UNEP/GRID-Arendal. Political advisor to Minister of
Trade and Industry Grete Knudsen. Economic Development and Transport Department in Finnmark
County, tasks associated with restructuring in the interior of Finnmark County
Helga Pedersen, Minister of Fisheries and Coastal Affairs, Norway will open the BIOPROSP
Conference.
BIOPROSP coincides with the Norwegian Government’s initiative on marine bioprospecting, as
embedded in its innovation policy and in the High North strategy
When Little Things Mean a Lot.
The Norwegian Government's initiative on marine bioprospecting
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S4: Lene Buhl-Mortensen,
Institute of Marine Research
Senior scientist
Benthic Habitat and Shellfish Research Group
Institute of Marine Research Bergen, Norway (IMR)
e-mail: [email protected]
Norway
Interests: Benthic habitat and fauna biodiversity,
community structure.
Experience: 25 years experience of marine benthic
fauna studies with particular interest in the relation
between habitat quality and diversity. Author and coauthor of more than 30 papers dealing with topics
ranging from taxonomy and fauna responses to
management. Participation in 6 research cruises as chief
scientist. 2001-2003 visiting scientist on a project on
Coral Ecosystems in Atlantic Canada at Bedford Institute
of Oceanography. Leader of a Norwegian research project investigating the response of benthos to
hypoxia in fjord-basins (2003-2005). Leading the mapping of biodiversity in the MAREANO-program
2006-. From 2007 Program leader of the MAREANO mapping program.
Institute of Marine Research, Bergen, Norway, has the largest group of benthic experts in Norway.
The group is specialised on mapping, monitoring and research on essential and vulnerable habitats
such as deep water corals and sponges. Researchers in the group have experience with providing
advice for coral reef management and mapping.
Corals of the Arctic
The North Atlantic has a rich coral fauna with species having different temperature optima. Most
corals occur in temperatures above zero and many species has their northern limit at the ridges at
the David Strait, Denmark Strait and between Iceland and the Faroe. In Norwegian waters 39 coral
species have been documented (excluding anemones). In comparison > 70 species are known from
the sub arctic zone off Alaska. MAREANO is presently mapping mainly in the sub arctic zone
however, organisms that occur at depth bellow 800 m experience temperatures below zero.
MAREANO has identified 14 coral species, of these four are scleractinians and 10 octocorals. The
reef forming stone-coral Lophelia pertusa do not occur north of the sub-arctic zone. The northern
o
most Lophelia-reef occur just north of Sørøya, at 70 56’N. These refs host a rich fauna of other
corals and sponges. In Norwegian waters the largest coral species are Lophelia, Paragorgia and
o
o
Primnoa. They tolerate temperatures ranging from 3 to 14 C and prefer 5 to 8 C. Corals belonging
to the group Nephtheidae (soft corals) are common and frequently occurring species are Duva
o
florida, Gersemia rubiformis and Drifa glomerata. They tolerate lower temperatures (-1 to 4 C) and
MAREANO have documented them in higher densities below 800 m. This presentation will provide
an overview of coral distribution from earlier registrations and from the MAREANO program (Marine
Area Database for Norwegian Coasts and Sea Areas). For more information about MAREANO see:
www.mareano.no
Coral species from left to right: Duva, Paragorgia (white and red) with orange Primnoa and Lophelia.
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S5: Hans Kristian Kotlar,
StatoilHydro ASA
Senior specialist Biotechnology
StatoilHydro ASA
R&D Centre, Trondheim
[email protected]
Norway
Education: Siv ing .(M. Sc) Technical biochemistry,
The Norwegian Institute of Technology (NTH)
Additional education: Immunology, subject given at the
University of Oslo, Polymer chemistry, subject
given at the University of Oslo. Dr.philos (Ph.D).with
the thesis:" Studies on cell and serum mediated
antitumor activities in early detection of cancer.
Development of the humoral leukocyte adherence
inhibition assay and investigations of its possible use
in cancer diagnosis ".
Experience: Bioengineer at the Vestfold County Hospital, Research scholar at the Norwegian Cancer
Society, Research manager at BIONOR A/S, Section leader, polymer alloys at Statoil, Bamble (later
Borealis), Research adviser in reactive polymer chemistry at Borealis, Research adviser in well
chemistry at Statoil, Research specialist in well chemistry at Statoil, with special emphasize on
laboratory investigations, Petrophysics and Production technology, From 2000 Task
responsible: Applied biotechnology and from 2008, Senior specialist and R&D manager:
Biotechnology Competence.
Main fields of competence: Diagnostic microbiology, immunology, gene technology and early
detection of cancer. Development and production of biotechnological products , Reactive polymer
chemistry, Production technology in E & P. Various areas of well chemistry: Project manager: Scale
and formation damage, Project manager: HPHT scale. Coordination responsible and project
manager: Applied biotechnology in the oil industry, Biotechnology and bioprospecting
Publications/Scientific reports: Within the main fields of competence more than 300 reports/publications/patents/speeches in Norwegian or English. Professional Society of Petroleum Engineers
Memberships, Norwegian Chemical Society
Extreme in the 4th power!
Many different research organizations have been searching for the “gold of the ocean” and made important
discoveries of organisms that can produce new compounds as potential new types of antibiotics and anticancer medicine. They have been searching from the high mountain mores to the sediments of the ocean
floor and even in high temperature hydrothermal vents.
In SH we are, however, digging even deeper. Deep down in the oil reservoirs we are finding a whole new
world of microorganisms we know very little of. Deep in the subsurface there are living organisms with
unique properties.
Some day they could be on the pay-list of many different companies. These microorganisms live in the
depth range of 2 – 5 kilometers subsurface or underneath the ocean floor. Another very special feature is
that they are very old. The traditional understanding of the generation of oil reservoirs is through the
sedimentation of river deltas from Cambrian through Jurassic period, i.e. 500 – 200 million years ago,
especially the Jurassic period. During exploration and initial development of a new oil field a lot of cores
and research samples are collected. Furthermore, samples from production wells and sea bed sediments
and seeps, pockmarks have been selectively sampled. All these samples have given a completely new
insight to the abundance and types of organism that can be found. From these types of samples, DNA is
extracted and organisms are identified by traditional molecular genetic approach.
How can this be used?
Finding new oil. Synthesize specific DNA-probes identifying organisms associated with oil
New smart increased oil recovery (IOR) and production methods. Biofuels: Bioconversion of heavy oil.
Bioprospecting - What the nature provides. Outside the oil industry – spin offs
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S6: Ole Jørgen Marvik,
Innovation Norway
Sector Head, Health and Life Sciences
Innovation Norway - London
www.innovationnorway.no/london
5 Regent St., London, SW1Y 4LR, UK
Phone: +44 (0)20 7389 8800
Fax: +44 (0)20 7973 0189
Mobile: +47 911 95 876
[email protected]
Norway
Ole Jørgen Marvik, serves as coordinator for
Innovation Norway’s health and life science sector
programs as well as scientific advisor to their
London office. Ole Jørgen is the founder and former
CEO of Affitech, a drug discovery company based in
Oslo and San Francisco and has been co-founder of
several other biotech start-ups. He has been active
in industry policy through several board positions,
including chairman of the Norwegian Bioindustry
Association and board member of Europabio. Recent projects include involvement in several
emerging Norwegian biomedical clusters and strategy development for national initiatives in areas
such as Norwegian health biobanks and marine bioprospecting. Ole Jørgen has a PhD in
biotechnology from the Univ. of Oslo with 15 years of research experience in molecular and structural
biology. He also holds a master's degree in business management.
Bridging scientific discovery and industry-led innovation
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S7: Valentina Germani,
United Nations
Law of the Sea/Ocean Affairs Officer
United Nations
[email protected]
Italy (nationality); USA (residence)
Ms. Valentina Germani is a Law of the Sea/Ocean Affairs
Officer in the Division for Ocean Affairs and Law of the Sea,
Office of Legal Affairs of the United Nations, where she has
worked for over seven years. Her work at the Division has
focused on sustainable fisheries, marine biological diversity,
and issues relating to the work of the Commission on the
Limits of the Continnetal Shelf. She has acted as Deputy
Secretary for the Review Conference on the UN Fish Stocks
Agreement, the Informal Consultations of States Parties to
the UN Fish Stocks Agreement, the annual consultations for
the negotiation of the United Nations General Assembly resolution on sustainable fisheries, as well as
the Ad Hoc Open-ended Informal Working Group to study issues relating to the conservation and
sustainable use of marine biological diversity beyond areas of national jurisdiction. Before joining the
United Nations in 2001, Ms. Germani worked as a lecturer on the LLM (Master in Law) Programme of
the University of London, where she taught International Law of the Sea and International
Environmental Law at the University College of London and Queen Mary respectively. She graduated
from the London School of Economics in 1999, where she was awarded a Master Degree in Public
International Law. Previously, she obtained a Law Degree from Cardiff Law School.
Marine genetic resources – the interface between international law of the sea and
intellectual property regimes
The presentation will focus on the legal regime under the United Nations Convention on the Law of the Sea
(UNCLOS) applicable to marine genetic resources, both within and beyond the limits of national jurisdiction,
and the implications of the application of relevant intellectual property regimes (both under WTO and WIPO).
In particular, the presentation will outline the various jurisdictional areas established under UNCLOS (internal
waters, territorial sea, exclusive economic zone, continental shelf, etc) and define the rights and duties of
States over marine genetic resources and related activities in those areas. An analysis of the major relevant
aspects of the implementation of intellectual property regimes, in the particular context of such rights and
duties, will then be provided. The presentation will conclude with highlighting issues that may warrant future
consideration by the international community in this area.
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S8: Jeanette H. Andersen,
Marbio, University of Tromsø
Platform leader
Marbio, University of Tromsø
[email protected]
Norway
Jeanette Hammer Andersen (PhD) has
background in the field of antiviral discovery. In the
recent years she has been in charge of
establishing the screening platform, Marbio. Her
work has focused on the development of medium
to high-throughput screening assays within the
fields of antiviral, antibacterial, immunomodulating,
diabetes, antioxidant and anticancer screening.
Marbio is a high-throughput platform for
purification/isolation, screening and identification
of novel bioactivities at the University of Tromsø.
Most of the screening activities are performed in
close collaboration with MabCent-SFI.
MabCent - a Centre for Research-based Innovation of Arctic marine bioactives
and drug discovery
MabCent-SFI is a centre for research based innovation hosted by the University of Tromsø.
Mabcent-SFI focuses on bioactives from Arctic and sub-Arctic organisms searching for
compounds with activities against bacteria, cancer and diabetes as well as compounds with
immunomodulatory and antioxidative effects. Strategies for the extraction, purification, screening
and identification of bioactive compounds will be outlined. The progress and the recent
discoveries from the primary screening will be presented.
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S9: John N. Reeve,
Ohio State University
Professor, Chair of Department
Department of Microbiology
Ohio State University
Columbus, Ohio
[email protected]
Tel:
1-614-292-2301
USA
EDUCATION AND PROFESSIONAL EMPLOYMENT
B.Sc.University of Birmingham, England (1968). Bacteriology.
Ph.D. University of British Columbia, Canada (1971).
Microbiology.
Postdoctoral training:
#1. Univ. of Arizona, Tucson, AZ. 1971-73.
#2. Natl Inst. Med. Res., Mill Hill, England,1973-74.
1974-79. Research Group Director, Max Planck Inst. für Molecular Genetik, W. Berlin, Germany,
1974-79 Associate Professor; 1981-present Professor; 1985- present Dept. Chair; 1999-present Rod
Sharp Endowed Professor, Department of Microbiology, Ohio State University, Columbus, OH, USA
HONORS:
NATO Postdoctoral Fellowship, 1971-1973.
EMBO Postdoctoral Fellowship, 1974.
NIH Research Career Development Award, 1980-85.
Distinguished Research Scholar, Ohio State University, 1989.
Member, Steering Committee, International Society for Extremophiles, 2000-present
International Research Advisor, Priority Program in Genome Function, DFG, Germany, 2000-06
Chair, US DOE Biosciences Council, 2001-06
Fellow, American Academy of Microbiology, 2004
RESEARCH AREAS
Molecular biology, biochemistry and genetics of Extremophiles
Transcription, histones and chromatin in Archaea.
Molecular biology of microbial hydrogen and methane (biogas) production
Marine Extremophiles: Coping and Adaptions to Frozen and Boiling Life
Microorganisms cannot exclude temperature, and the results of investigations of extremophiles that
inhabit and grow in environments at temperatures below 0°C or up to 100°C will be presented.
Microorganisms have been recovered, identified and characterized that were immured in polar or
glacial ice for millennia. The ability of some species to retain metabolic activity within a frozen
environment has been investigated and the results obtained will be discussed. Solar heating of
opaque materials on the surface of ice-fields results in cryoconite hole formation. Every cryoconite
hole constitutes a unique and novel environment, and the isolation of cryconite hole inhabitants will be
described.
Thermococcus kodakaraensis is a hyperthermophilic, anaerobic, heterotrophic Archaeon that was
isolated from a marine, geothermally-heated environment. This hyperthermophile degrades and
ferments several different polysaccharides (e.g. starch, chitin) and peptides. From these abundant
environmental substrates, T. kodakaraensis produces acetate and alanine and generates hydrogen or
hydrogen sulfide, depending on sulfur availability. T. kodakaraensis grows well under laboratory
conditions, optimally at ~85°C, in liquid or on solid media, and we have established genetic
procedures and developed a range of genetic tools for T. kodakaraensis that will be described. With
this genetic technology plus the genome sequence and genome microarrays available, T.
kodakaraensis is now a very practical model system to investigate archaeal gene expression and
regulation, enzyme structure and function, metabolic manipulation and microbial bio-fuel production
under hyperthermophilic conditions. The results of examples of such experiments will be presented.
21
S10: Garabed Antranikian,
Hamburg University of Technology
Head of Institute of Technical Microbiology
Institute of Technical Microbiology, Hamburg
University of Technology, Hamburg,
[email protected]
Tel: +49-(0)40-42878 3117
Germany
Dr. Garabed Antranikian studied Biology as an
undergraduate student at the American University in
Beirut. At the University of Göttingen he completed his
PhD thesis in Microbiology in 1980 in the laboratory of
Professor Gerhard Gottschalk and qualified as a postdoctoral lecturer (Habilitation) in 1988. In 1989 he was
appointed to a professorship in Microbiology at the
Hamburg University of Technology where he has been
the head of the Institute of Technical Microbiology since 1990. From 1993 to 1999 he coordinated the
EU network project Extremophiles. From 2000 to 2003 Prof. Antranikian coordinated the national
network project Biocatalysis and is coordinating the Innovation Center Biokatalyse (ICBio, supported
by DBU) since 2002. He is president of the International Society for Extremophiles, chief editor of the
scientific journal Extremophiles and co-editor of many scientific journals. In 2004 he was awarded the
prize for environment protection by the Federal Environmental Foundation of Germany. Since 2007
he is the coordinator of the “Biocatalysis 2021” Cluster of the Ministry of Education and Research and
he is member of the Academy of Sciences in Hamburg and member of the Union of the German
Academies of Sciences (acatech).
The true gold of our planet is not yellow or black, it is vital
Garabed Antranikian, Institute of Technical Microbiology, Hamburg University of Technology,
Hamburg, Germany
Extremophiles are unique microorganisms that are adapted to survive in ecological niches such as
high or low temperatures, extremes of pH, high salt concentrations and high pressure. The steady
increase in the number of newly isolated extremophilic microorganisms, including Archaea and
Bacteria, and the discovery of their biocatalysts underlines the enormous potential of extremophiles
for application in various fields including energy supply as well as detergent, textile, paper, food,
feed, pharmaceutical and chemical industry (white or industrial biotechnology). Due to the unique
properties of extremozymes, they are expected to play a crucial role in the development of future
biobased industrial processes (biorefinary). A number of heat stable enzymes (hydrolases,
oxidoreductases) with unique properties were identified in extreme thermophilic anaerobic bacteria
and their genes were cloned and expressed in E. coli. The recombinant enzymes are robust towards
temperature and extremes of pH. Their action on the efficient conversion of cellulosic plant material
was investigated after heat and pressure treatment. Further research was performed with other
extremophiles such as the thermoalkaliphilic anaerobic bacterium Anaerobranca gottschalkii (60 °C,
pH 10) and the thermoacidophilic aerobic archaeon Picrophilus torridus (60 °C, pH 0.7). The diversity
of marine microorganisms of samples from the deep sea floor (Mariana Trench), subsea floor, and
terrestrial hot springs was also investigated (collaboration Prof. Horikoshi JAMSTEC). Metagenomic
libraries from these unique habitats were screened for robust enzymes. Using HTS systems a variety
of cold-active and thermoactive enzymes were identified and characterized. Few enzymes show
catalytic activity even below the freezing point of water. These extremozymes are in general superior
to the traditional catalysts, because they provide biocatalysts with unique properties that are active at
extremes of temperature -5 °C and 120 °C, and in the presence of high concentrations of organic
solvents (up to 99 %). By employing modern technologies e.g. directed evolution and synthetic
biology, novel lipases and esterases with altered properties were produced.
22
S11: Arne O. Smalås,
NorStruct, University of Tromsø
Professor
NorStruct, Dept. of chemistry,
Universitetet i Tromsø
[email protected]
Norway
Arne O. Smalås is professor in physical chemistry and
structural biology at the Department of chemistry, University of
Tromsø. He is now the director of the Norwegian Structural
Biology Centre (NorStruct) and the Head of Department of
Chemistry.
NorStruct is a national research and service centre in
structural biology in Norway, providing service and
collaboration in areas like protein production, 3D-structure
investigation and drug discovery and design. In-house projects
at NorStruct cover four main themes; I) Signal transduction – anti cancer drug discovery and design,
II) DNA regulation and modification, III) Host-pathogen interactions, and IV) Extremeophiles and
industrial enzymes
His research interests are within structural biology with X-ray crystallography, molecular modeling and
biophysical methods as main research tools. He is involved in projects connected to cold adaptation
of proteins, industrial applicable enzymes, protein-protein recognition and interactions, and structural
genomics studies on the psychrophilic and fish pathogenic bacterium, V. salmonicida.
Applications of enzymes from the marine cold environments
World-wide, there is an unlimited demand for new efficient products and processes that can lower
energy spending and reduce the production of pollutants and waste, and increase the environmentally
sound production of food and energy. The use of enzymes is rapidly growing in a wide range of
sectors. The current world market (2006) represents a value of 2.8 billion EUROS with an expected
growth of 6.5% the next few years. Europe has been the dominant producer of enzymes and holds
about 70% of the market.
The unique features of cold adapted enzymes have for several decades been exploited in industrial
processes and more recently in various molecular biology applications. However, the potential is
probably much higher, in particular for more specialized applications. In addition to the search for
new enzymes with unique features, we have focused on structure-function relation studies of the cold
active enzymes. A thorough insight into the molecular and structural basis for the unique features will
allow for more sophisticated applications, and further on for redesign to optimize or alter certain
properties by the use of protein engineering.
Comparative studies with enzymes expressed by organisms adapted to higher temperatures have, in
combination with mutational analysis, frequently been used to obtain detailed information about the
structural basis for cold activity. The structure-function relationships are in most cases complex, and
are additionally complicated by the fact that most proteins are in parallel subjected to other adaptive
forces. For extracellular proteins from cold adapted marine organisms for example, the high salt
concentration must be taken into account when deducing the molecular basis for cold activity. Some
features of cold-active enzymes will be exemplified by some of our findings from the last 15 years of
research in this field.
23
S12: Jennifer Littlechild,
University of Exeter
Prof Biological Chemistry
Exeter Biocatalysis Centre,
Henry Wellcome Building for Biocatalysis, School of
Biosciences,
University of Exeter,
EX4 4QD, UK
[email protected]
Professor of Biological Chemistry and Director of the
Exeter Biocatalysis Centre located in the Henry
Wellcome Building for Biocatalysis. The Centre was
opened in November 2003. Prof. Littlechild carried
out her Ph.D. in the Biophysics Laboratory, Kings
College, London University, UK followed by a postdoctoral fellowship at the Biochemistry Department
at Princeton University, USA. In 1975 she became a group leader at the Max-Planck Institute for
Molecular Genetics in Berlin, Germany. In 1980 she returned to the UK to Bristol and in 1991 to
Exeter University. Her current research grants are from UK research councils, BBSRC, EPSRC and
the EU and DTI Technology Transfer Initiative. She is the UK representative for the European Section
on Applied Biocatalysis and was involved in production of the SusChem documentation for White
Biotechnology within the EU Framework 7 programme. Current research studies involve the structural
and mechanistic characterisation of the C-C bond forming enzymes transketolase and aldolase,
vanadium haloperoxidases, Baeyer-Villiger monooxygenases, aminoacylases, novel esterases and
lipases, gamma lactamases, alcohol dehydrogenases, dehalogenases, transaminases and other
enzymes from thermophilic bacteria and archaea. She has published over 110 publications in
refereed high impact journals and presented her research work internationally.
Extremophile enzymes: application and structure
The Exeter Biocatalysis Centre specialises in the isolation and characterisation of novel enzymes
from extremophilic organisms. Many of these enzymes are used in combination with conventional
chemical synthesis for the production of new optically pure drugs of interest to pharmaceutical
companies.
The enzymes have been isolated both by screening for the activity of interest directly from the host
organism or direct amplification using PCR from already sequenced genomes. The enzymes have
been isolated from marine or terrestorial archaea and are cloned and over-expressed in a soluble
form in Escherichia coli.
Thermophilic enzymes are more robust to organic solvents used in the biocatalytic process or in
immobilisation techniques and allow the process to be operated at elevated temperatures where the
substrates are more soluble. Enzymes developed at Exeter that are already used commercially are
the L-aminoacylase from Thermococcus litoralis for the resolution of aminoacids and aminoacid
analogues [1], the gamma lactamase from Sulfolobus solfataricus for the production of optically pure
gamma lactam – the building block for anti-viral carbocyclic nucleotides [2] and alcohol
dehydrogenase from Aeropyrum pernix for the production of optically pure alcohols [3].
Enzymes in development include a transaminase [4] and a dehalogenase [5] from Sulfolobus species.
The transaminase can be used for the asymmetric synthesis of homochiral amines of high
enantioselective purity. The L-2-haloacid dehalogenase has applications both in biocatalysis and in
bioremediation.
The work in the Biocatalysis Centre also involves molecular structure determination of the enzymes to
give an insight into their thermostability, enzymatic mechanistic and substrate specificity.
References
[1] Toogood, H.S., Hollingsworth, E.J., Brown R.C., Taylor I.N., Taylor, S.J.C.,McCague, R.,
Littlechild, J.A. (2002). Extremophiles 6, 111-122.
[2] Toogood,H., Brown, R. Line K., Keene, P. Taylor, S. McCague, Littlechild J. (2004) Tetrahedron
60, 711-716
[3] Guy, J.E., Isupov, M.N. and Littlechild J.A. .(2003) J.Mol.Biol 331, 1041-1051.
[4] Sayer, C. Bommer, M. Ward,J.,Isupov M., Littlechild,J. (2009) J.Mol Biol. in preparation
[5] Rye, C. Isupov, M. Lebedev, A , Littlechild, J. Extremophiles, 2009, 13,179-190.
24
S13: Klara Stensvåg,
University of Tromsø
Professor
Department of Marine Biotechnology, Norwegian
College of Fishery Science, University of Tromsø
[email protected]
Teleph: +47 77 64 45 12
Norway
The University of Tromsø is the northernmost university of
the world. The strategy of the University of Tromsø gives
priority to marine science as one of the research fields
EDUCATION AND PROFESSIONAL EMPLOYMENT
Professor in Marine Biotechnology at the Department of
Marine Biotechnology, Norwegian College of Fishery
Science, University of Tromsø (from 2009).
Associated professor (2003 2008) and researcher (19982003) at UiT. Visiting researcher at Dept. of Biochemistry,
Hollings Marine Laboratory, Medical University of South
Carolina, USA (2006-2007). Dr. Scient University of Tromsø
(1998).
HONORS
Award for commercialisation/research and patenting from the TTO/University of Tromsø (2006)
RESEARCH AREAS
Marine bioprospecting with particularly focus on antibacterial molecules (i.e. peptides) or other natural
active components in marine organisms, to characterise them and to understand their mode of action
and role as host immune factors in the organisms that produce them.
Antibiotics from the sea
Antimicrobial components are widespread and found in all living species studied. The survival of
many marine benthic organisms depends on efficient antimicrobial mechanism to protect themselves
against microbial infections and fouling. These factors may be of protein-like structures coded by
ribosomal genes or organic compounds like secondary metabolites.
Our aim has been to isolate and characterise novel antimicrobial molecules from marine organisms
collected from the Arctic or/and sub-Actic region. Here, we report our recent findings of peptides in
marine crustaceans and echinoderms, and some findings of other compounds from sponges and
tunicates. Using bioassay-guided purification (RP-HPLC) several antimicrobial peptides were isolated
from the blood cells of the small spider crab, Hyas araneus, the king crab, Paralithodes
camtschaticus, and the green sea urchin, Strongylocentrotus droebachiensis. The peptides belong to
different antimicrobial peptide families based on their primary structures and domains. The full gene
sequences obtained indicate that none of the isolated peptides, except for two crustin-like peptides
from H. araneus, show similarity to known antimicrobial peptides. However, they have characteristics
of domains in common with known antimicrobial peptides, like glycine-rich and proline-arginine rich
peptides. One of the peptides seems to contain a modified tyrosine amino acid residue. Mechanisms
of action studies are performed on the peptides to pinpoint their molecular targets in the
microorganisms. Understanding the mechanism of action is vital, both, in terms of basic research, but
also for an eventually later application as clinical tools. Methods are designed to allow a rapid
discrimination between compounds interfering with membrane integrity and compounds interfering
with different stages of bacterial metabolism (DNA replication, transcription, translation). Of the
peptides we have studied so far, we have revealed both membrane lytic peptides and peptides having
intracellular targets. The characterisation of the novel antibacterial molecules, the genes coding for
some of these peptides, and their gene expression will also be presented at the meeting.
25
S14: Heonjoong Kang,
Seoul National University
Heonjoong Kang
Director
Center for Marine Natural Products and Drug
Discovery (CMDD), Seoul National University
[email protected]
Korea
1989-1994 Ph.D. University of California, San Diego,
SIO, Marine Natural Products Chemistry (Professor
William Fenical)
1994-1998 Postdoctoral Training, Salk Institute,
Biomedicine (Professor Ronald M. Evans)
1998-present Associate Professor , IPGE and SEES,
Seoul National University
2004- present Director, CMDD, Seoul National University
The Center for Marine Natural Products and Drug Discovery (CMDD), the only marine drug discovery
program in Korea, is a research center established in October 2004. The program will run for ten
years with a budget exceeding 70 million US dollars. The main focus of CMDD is to develop drugs
based on marine natural products to treat metabolic diseases, immune diseases and infectious
diseases. To achieve such goal we adopt various disciplines that include marine natural products
chemistry, synthetic chemistry, molecular modeling and combinatorial chemistry, molecular biology,
endocrinology, immunology, microbiology, toxicology, pharmacology, molecular medicine and clinical
biology. We utilize various platforms such as target-based high throughput screening, lead
optimization with molecular modeling and combinatorial chemistry, total synthesis, in vivo evaluation
with animal disease models, pharmacokinetics and clinical biology, which will give totally innovated
drugs that were never encountered in terrestrial systems.
Ligands of nuclear receptors, novel drug leads to treat metabolic diseases
The nuclear receptors are ligand-activated transcription factors which regulate many aspects of
metabolism, development and inflammation. The receptors thus become promising drug targets for
treatment of metabolic syndrome. Among them, the oxycholesterol receptors LXRs up-regulate genes
for bile acid biosynthesis, while the bile acid receptor FXR counteracts the process. LXR also
regulates fatty acid biosynthesis in liver. In addition, FXR is involved in obstructive cholestasis and
inflammatory bowel diseases. Recently in collaboration with Professor Evans we identified that
targeted activation of the peroxisome proliferator-activated receptor PPARδ in mice selectively
activates genes of glucose catabolism, fatty acid oxidation, energy uncoupling and signaling
pathways in anti-inflammatory process. These findings suggest that PPARδ serves as a widespread
regulator of glucose- and fat-burning and a key transcriptional factor regulating inflammation.
A combination of natural product isolation, chemical modification and automated bioassays led to
identification of various natural products as agonists and antagonists for nuclear receptors. The
compounds had been modified based on molecular modeling studies to give potent ligands, for
example, for PPARδ with EC50 value as low as sub-nanomolar. The ligands also had good selectivity
toward PPARδ over the other subtypes, PPARα and PPARγ. Treatment of mice with the newly
developed ligands showed that the treated mice gained much less body weight than controls. As
expected, the treated mice showed reduced adiposity and improved glucose tolerance. The
compounds also attenuated lesion progression in a hypercholesterolemic mouse model. These
results clearly demonstrate ligands of nuclear receptors as drug leads to treat metabolic diseases
such as obesity, diabetes, hypercholesterolemia, atherosclerosis and etc.
26
S15: Valentin Stonik,
Russian Academy of Sciences
Director, Head of laboratory, Professor
Pacific Institute of Bioorganic Chemistry, Far-Eastern
Branch of the Russian Academy of Sciences;
tel: +7-4232-311430;
fax: +7-4232-314050;
mob: 8-4232-722987
[email protected], [email protected]
RUSSIA
V.A.Stonik: Chemists; b. Dec.4,1942; D.Sc. (1988),
M.M. Shemyakin Prize (1995); Corresponding
Member of the Russian Academy Sciences (RAS)
(1997); Full Member of RAS (2003); Head of the
Laboratory of Marine Natural Products Chemistry
(1977), Director of the Pacific Institute of Bioorganic
Chemistry (PIBOC), Far-Eastern Branch of RAS (2002). Field: natural products chemistry and chemistry
of physiologically active compounds (secondary metabolites). Author and co-authors of more than 260
publications in Russian and international journals; 3 monographs; 16 patents. Member of the Editorial
Boards: Natural Product Communications, the Russian Journal of Bioorganic Chemistry, etc.
PIBOC is founded in 1964, has staff of 320 pers. including 147 scientists (100 PhD., 25 DSc., 2
Corresponding Members, 2 Full Members of RAS). There are three leading Russian scientific
schools. Main scientific trends: bioorganic chemistry, biochemistry, organic chemistry, molecular
biology and immunology, marine microbiology, biotechnology, taxonomy of higher plants. Facilities:
laboratory building, vivarium, marine experimental station, experimental plant, research vessel
“Akademik Oparin”. General equipment: GLC and HPLC chromatographs; NMR “Bruker” 300, 500
and 700 MHz; MALDI, EI and ES mass-spectrometers; “Farmascan” tomograph, etc.
Novel natural products from North-Western Pacific cold water marine organisms and
their bioactivities
V.A. Stonik, D.L. Aminin, S.A. Avilov, V.I. Kalinin, A.A. Kicha, N.V. Ivanchina, E.V. Levina
Pacific Institute of Bioorganic Chemistry, 690022, Vladivostok, prospect 100-letya Vladivostoka, 159
North-Western Pacific cold water organisms, including both marine macro- and microorganisms have
been studying systematically at the Pacific Institute of Bioorganic Chemistry of the Russian Academy
of Sciences during the last thirty years. These organisms (marine invertebrates, bacteria, and fungi)
were collected in the Sea of Okhotsk during mainly marine expeditions aboard the research vessel
“Akademik Oparin”. Some biological materials were also founded in the North part of the Atlantic
Ocean (Maine, USA). Recently, we have isolated six new triterpene glycosides from the sea
cucumber Cucumaria okhotensis, five new natural products of the same series from the North Atlantic
C. frondosa, about thirty new polar steroids from different starfish species, one unusual ubiquinone
derivative 3-demethylubiquinone Q2 from the ascidian Aplydium glabrum, etc. Structures of all the
metabolites isolated were established using 2D NMR experiments, different variants of mass
spectrometry, and chemical transformations.
Some triterpene glycosides from sea cucumbers were shown to possess a potent immunostimulatory
effect. The molecular mechanisms of action were studied using proteomics and transcriptomics
methods. Polar steroids from starfish demonstrate interesting neurotrophic properties and stimulate
differentiation and development of neurons. 3-Demethylubiquinone Q2 inhibits the EGF-induced
+
malignant JB6 P Cl 41 cell transformation and the growth of the solid Ehrlich sarcoma tumor in mice.
This compound induces apoptosis of different human tumor cells, has potential for development of
new antitumor agents in cancer prophylactics and treatment.
27
S16: Marcel Jaspars,
University of Aberdeen
Professor of Organic Chemistry
Marine Biodiscovery Centre
University of Aberdeen
[email protected]
Scotland, UK
Prof Marcel Jaspars is professor of organic chemistry
at the University of Aberdeen. Research in the Jaspars
group focuses on the functions and applications of
natural products, particularly those from marine
organisms. The goal of the work is to determine the
biological role of selected natural products as well as
using others as pharmaceuticals, tools for biomedical
research, fluorosensors and catalysts.
Prof Jaspars was educated at Cambridge, where he enjoyed being supervised by Dudley Williams
and obtained his PhD from Trinity College Dublin, Eire under the supervision of Tony Davis on
organosilicon chemistry. A postdoc in Texas was swiftly followed by a longer postdoctoral stint in
California with Phil Crews working on marine natural products. During this period he co-authored a
textbook entitled 'Organic Structure Analysis'. Marcel Jaspars joined the faculty at Aberdeen in 1995
and was promoted to full professor in 2003. He was awarded the 2003 Matt Suffness award by the
American Society of Pharmacognosy and has recently received a Research Development Fellowship
from the UK’s Biotechnology and Biological Sciences Research Council on “Biosynthesis and
Exploitation of Marine-Derived Post-Translationally Modified Ribosomal Peptides”. Marcel is Chair of
the editorial board of the Royal Society of Chemistry journal “Natural Product Reports”, is a visiting
Professor at MabCent at the University of Tromsø, and acts as science manager for marine and
aquatic biotechnology for the Bioscience for Business Knowledge Transfer Network. Marcel also
consults for a number of UK marine biotechnology companies.
Developing Methods to Discover Novel Metal Complexes from Marine Invertebrates
The marine ecosystem presents an extremely broad spectrum of dissolved metal ions but contains
very low levels of physiologically important ones except sodium and potassium. For this reason it is
believed that marine organisms have developed unique capabilities for the acquisition, sequestration
and utilisation of these important trace metal ions. It is speculated that for marine invertebrates these
processes may involve secondary metabolites, many of which have structural features such as polar
functional groups in chelate-like arrangements and sometimes macrocyclic cavities which suggest
potential metal chelating properties. Amongst the marine invertebrates ascidians (seasquirts) are
generally known to hyperaccumulate metals from the surrounding seawater, with high concentrations
of V, Ti, Cr, Mn, Fe, Co, Cu, Zn, Rb, Zr, Nb, Mo, Cs, Ta and Sn having been found. There has been
much speculation regarding the organic complexation of these metals in the ascidians, but little
research has been conducted in this area. Ascidians are therefore an important source in the search
for metal complexing compounds from marine sources.
We have been developing methodology to allow parallel on-line element specific and molecular
specific detection. This is achieved by coupling the outflow of an LC system to an inductively coupled
plasma mass spectrometer (ICP-MS) and an electrospray mass spectrometer (ES-MS) in parallel.
Using this approach we were able to identify an intact metal-ligand complex present in a crude
organism extract. This is the first time that an intact metal-ligand complex has been recovered from
an ascidian extract, which has significant implications for the elucidation of the ecological function of
these ligands and the metal accumulation abilities of these organisms. Potential uses of these
complexes are as selective complexation agents for diseases of metal homeostasis, as biomedical
research tools, and as many carry fluorophores, as fluorescent metal chemosensors.
28
S17: Svein Valla,
Norwegian University of Science and
Technology
Professor
Department of Biotechnology, Norwegian University
of Science and Technology
[email protected]
Norway
Position: Professor in Molecular Genetics
Research: Molecular genetics of prokaryotes. Broad
experience in the use of modern gene technology in
numerous bacterial species. Main research activities now
running: a. Alginate biosynthesis and genetics in
Pseudomonas fluorescens and Azotobacter vinelandii. b.
Basic and applied studies of recombinant gene expression
in E. coli and other bacteria. c. Cloning and expression of
DNA from bacteria in marine environments
(bioprospecting).
Membership in academic and professional bodies: Editor in Microbial Biotechnology. Invited
member of The Royal Norwegian Society of Sciences and Letters and The American Society for
Biochemistry and Molecular Biology. National delegate for European Federation of Biotechnology.
Reviewer for many scientific journals.
Selected recent papers:
Rozeboom, H., Bjerkan, T.M., Kalk, K.H., Ertesvåg, E., Holtan, S., Aachmann, F., Valla, S., and
Dijkstra, B.W. 2008. Structural and mutational characterization of the catalytic A-module of the
mannuronan C-5-epimerase AlgE4 from Azotobacter vinelandii. J. Biol. Chem. 283: 23819-23828.
Berg, L., Lale, R., Bakke, I., and Valla, S. 2008. The expression of recombinant genes in Escherichia
coli can be strongly stimulated at the transcript production level by mutating the DNA-region
corresponding to the 5′-untranslated part of mRNA. Microb. Biotechnol. In press
Functional screening of metagenome libraries by the use of broad-host-range cloning
vectors
The majority of microorganisms present in natural environments cannot be readily cultivated, but their
DNA can be cloned in standard laboratory hosts such as Escherichia coli. This approach also has its
limitations in that the heterologous DNA is not necessarily expressed in the new host, the inserts may
become too small to cover all the genes needed to represent an entire pathway of interest, the library
of clones may not be of sufficient size to ensure that all genes of interest are represented, and
screening methods may limit what can be detected. To identify functions of interest one may
sequence the DNA from the environment and use bioinformatics tools to analyse the resulting
sequence data. This method, which is becoming more and more relevant due to technological
progress, also has its limitations. However it can be supplemented by functional screening, which in
principle makes the researcher independent of the problem of being able to predict function
bioinformatically. We have recently shown that it is possible to extend the applicability of the current
tools for functional screening by converting well established plasmid vectors limited to replication in E.
coli, into broad-host-range vectors that can be transferred to numerous gram-negative species.
Furthermore, the vectors could hold and stably maintain very large inserts (up to 200 kb) in a tested
alternative host, Pseudomonas fluorescens. This means that if environmental DNA is cloned in the
new vectors the corresponding gene functions may be screened in a variety of bacterial species.
Since it is well known that far from all genes are expressed in E. coli, this opens up the possibility of
detecting many more new functions by functional screening. Libraries constructed in E. coli can be
efficiently transferred to new hosts by conjugation, and this may for example allow for screening in
cold-water adapted hosts, such that the activities of proteins functional only at low temperatures can
be detected.
29
S18: Mark Liles,
Auburn University
Assistant Professor
Auburn University
[email protected]
USA
1991 Received B.S. in Biology at Tulane University,
New Orleans, LA
1991-1992 Employed as a research technician at a
research institute in New Orleans, LA
1992-1998 Graduate Fellow at Northwestern University,
Chicago, IL
1998 Received Ph.D. in Microbiology
1998-2005 Postdoctoral Fellow in Bacteriology at
University of Wisconsin, Madison, WI -postdoctoral
mentors Dr. Jo Handelsman and Dr. Robert Goodman
2005- Assistant Professor, Department of Biological
Sciences, Auburn University, AL
Research in the Liles laboratory focuses on the use of microbial community genomics to describe
lateral gene transfer of antibiotic resistance and for the discovery of natural products from diverse
microbial species. Research efforts employ molecular microbiology, bioinformatics, and biochemical
methodologies. Currently the Liles laboratory has 17 members, including 1 technician, 9 graduate
students, and 6 undergraduate students.
Auburn University is the land grant university for the State of Alabama, USA. The Department of
Biological Sciences has 36 tenure-track faculty representing diverse biological disciplines and
currently training 133 graduate students
Scratching the Surface:
Constructing and Screening Large-insert Soil Metagenomic Libraries
There are both opportunities and challenges in exploiting the diversity of microbial natural products
using a community genomic approach. By directly isolating and cloning genes isolated from
environmental samples it is possible to overcome the bias of cultivation in sampling the biosynthetic
potential of diverse microorganisms. Yet other biases remain that can impair efforts to discover
natural products produced heterologously from recombinant clones in a community genomic
(“metagenomic”) library. Improvements have been made in the isolation, purification, and cloning of
high molecular weight (HMW) metagenomic DNA from soil microorganisms that have resulted in
qualitatively improved metagenomic libraries. Specifically, the use of a formamide denaturation step to
purify HMW DNA has significantly improved cloning efficiency, especially for environmental samples
that were previously recalcitrant to cloning due to co-purification of inhibitory compounds. Both BAC
and fosmid libraries have been generated from soil microbial communities. These metagenomic
libraries have been screened by a variety of methodologies, including functional and sequence-based
screens. A collection of Type I polyketide synthase (PKS)-containing clones has been isolated via
hybridization of library clone DNAs to a degenerate probe, with most of these PKSs showing
divergence from previously described PKSs. Antibiotic- producing and antibiotic-resistant clones have
been identified via functional screens, using a panel of bacterial tester strains and clinically relevant
antibiotics, respectively. Many of these clones do not show significant homology to sequences within
the GenBank database and may be expressing novel mechanisms of antibiotic synthesis/resistance.
Expression of metagenomic clones in heterologous hosts, whether for antibiotic biosynthesis or other
functions, will benefit from the use of heterologous hosts besides E. coli. A novel Gram-negative
shuttle BAC vector has been constructed that permits transfer and expression of metagenomic
libraries in a broader spectrum of prokaryotic hosts. Current metagenomic technology will benefit from
a next generation of shuttle vectors, high-throughput screening platforms, innovative bioassays, and
increased sequencing throughput.
30
S19: Peter Meinicke,
University of Göttingen
Senior research fellow
Bioinformatics Department,
Institute of Microbiology and Genetics,
University of Göttingen
[email protected]
Germany
Dr. Peter Meinicke received his doctoral
degree in informatics from the University of
Bielefeld in Germany where he developed
new machine learning techniques. As a postdoctoral
researcher, he worked in the field of neurolinguistics
where he developed methods for the analysis of EEG
time series. In 2003, he turned to Computational
Biology at the Bioinformatics Department of the
Biological Faculty in Göttingen as a senior researcher
and group leader. There, he pursues the design and
application of machine learning methods for the
analysis of diverse biological data from highthroughput measurements in metabolomics, transcriptomics, proteomics and (meta)genomics. In
addition, he gives several lectures about machine learning and data mining in computational biology.
The University of Göttingen is an old and traditional institution founded in 1737, with about 20000
students today. The Bioinformatics Department is only six years old, but already has a strong
reputation in software development for sequence alignment and all kinds of gene prediction.
Predicting genes and protein function in metagenomes: the large scale challenge
Metagenomics is a central approach for the analysis of microbial communities, that is based on DNA
sequences from environmental samples. The identification of protein coding genes on these sequence
fragments provides a basis for functional profiling of habitats and for the discovery of new biomolecules
and new metabolic pathways. The restricted length of sequencing reads, often not exceeding a few
hundred base pairs, requires specialized methods for the prediction of genes and protein function in
metagenomes. Progress in sequencing technologies implicates a rapidly increasing quantity of
metagenomic data, but only few methods are available which can cope with the limited length and the vast
amount of DNA. Therefore, fast and reliable methods are urgently needed to encounter the emerging
sequence avalanche in metagenomics.
31
S20: Thomas Sicheritz-Ponten,
Technical University of Denmark
Center for Biological Sequence Analysis
DTU Systems Biology
Department of Systems Biology
Technical University of Denmark
Denmark
Dr. Thomas Sicheritz-Ponten PhD, is associate
professor with a background in Bioinformatics and
Molecular Evolution from Uppsala University,
Sweden and heads the Metagenomics group at
CBS. His primary interests are in microbial
genome analysis, metagenomics, microbiomics
and the detection and study of lateral gene
transfers. A major part of his research is
metatranscriptomics of the human microbiome corelating changes in the human microbiome with changes in human health ,where he is currently
coodrinating DTU's involvement in the EU project Metagenomics of the human intestinal tract
(MetaHIT).
TSP has been a scientific member of the Danish expedition GalatheaIII, collecting microbial DNA
from deep sea for the metagenomic project "DNA of the polar seas". He has been developing
new methods for the analysis of genomic and metagenomic data and he also has a strong research
track record in machine learning methods and large scale data analysis. Some examples are
NetPhosK, a neural network based phoshorylation predictor and SPyPhy - automatic, large-scale
reconstructions of phylogenetic relationships of complete genomes.
DNA of the North & South Polar Seas: Metagenomic screening of high diversity
extreme environments
Metagenomics provides us with a mechanism for analysing previously unknown organisms that are
not easily cultured in a laboratory and enables us to take a closer look at their natural environment. At
the Center for Biological Sequence Analysis at the Technical University of Denmark, we are involved
in both metagenomic data collection and tool development. During the project "DNA of the Polar
Seas", on board of the Danish Galathea3 expedition, we collected bacterial DNA from several
thousand meters depth around the South Pole and Greenland. Here our reasearch is focusing on
three of the challenges metagenomics brings us: a) Who is in there? b) What are they doing? and c)
How are they doing it? For a) Who is in there - we are developing tools for predicting taxonomy and
comparing bacterial diversity between north and south polar seas as well as deep vs surface marine
environments. b) What are they doing - Combining the results from massively parallel sequencing
techniques with high-density mRNA micro array profiling tools enables us to identify differences in
genes and pathways expression between different aquatic environments and finally, c) How are they
doing it - to facilitate metagenomic mining of enzymes adapted to cold and/or high pressure
environments we are currently developing an enzyme discovery and comparison pipeline.
32
S21: Paul Kinnon,
ZyGEM Corp. Ltd
President and Chief Executive Officer
ZyGEM Corp. Ltd. USA office
www.ZyGEM.com
Tel: +1 858 720 8333
Fax: +1 858 720 8339
[email protected]
USA
Paul Kinnon was appointed President and CEO in October
2007. A life science industry veteran, he brings ZyGEM
more than 18 years of management experience in
developing and marketing innovative products and
solutions to diverse customers. Paul joined ZyGEM from
Invitrogen Corp., where he held the positions of Vice
President of Global Strategic Alliances and Vice President
and General Manager of the Applied Markets Business
Unit. Previously, he was Vice President of Sales and
Marketing at Guava Technologies and Vice President of Sales at Cellomics. Earlier in his career, he
held marketing and management positions at leading companies including Porvair, Caliper, Whatman
and Thermo Instrumentation. Paul was awarded a Bachelor of Applied Chemistry from Coventry
University in the UK and a Diploma of Marketing from Chartered Institute Of Marketing He is a
member of the Chartered Institute Marketing and Association of Strategic Alliance Professionals
(ASAP). Paul is based at ZyGEM’s U.S. headquarters near San Diego, California."
Developing and managing a global business based on a culture collection
The presentation will cover the following topics:
ZyGEM’s history and the challenges of building a business based on a culture collection
The importance of developing the right strategy along with the associated risks and pitfalls link to a
culture collection and technology company
An outline of the ZyGEM culture collection and its potential applications
33
S22: Evert J. Homan,
Beactica AB
Senior Research Scientist,
Computational Chemistry & Informatics
Beactica AB,
Box 567, Uppsala
[email protected]
Sweden
Beactica is a specialist drug discovery company,
utilising its proprietary methodologies to evaluate the
biophysical interaction of molecules in order to
generate novel therapeutics. The company
specializes in fragment-based drug discovery by
employing a surface plasmon resonance (SPR)
technology platform. SPR-based fragment screening
allows for rapid identification of efficient starting
points for lead generation. In-depth SPR analyses
provide unique protein-ligand interaction data that
can be used to quickly optimize leads and prioritize drug candidates. Dr Evert Homan is responsible
for Beactica’s SPR-integrated computational chemistry and informatics infrastructure. More than ten
years of industrial experience from Pharmacopeia, Pharmacia, Biovitrum and Beactica have given
him broad knowledge of the preclinical drug discovery process, with particular focus on computational
medicinal chemistry. Dr Homan holds a masters degree in pharmacy and a Ph.D. in medicinal
chemistry from the University of Groningen, the Netherlands.
Fragment based drug discovery
Although the impact of fragment-based drug discovery (FBDD) on delivering new clinical
medicines has yet to be proven, this recently introduced approach has the potential to reduce
attrition and shorten lead times in drug discovery pipelines. As opposed to the high-throughputdriven technologies introduced in the mid-90’s, such as high-throughput screening and
combinatorial chemistry, FBDD allows for the identification of highly efficient starting points that are
amenable to iterative synthetic optimization. Importantly, these fragments lack the pharmacokinetic
flaws usually encountered in hits obtained from conventional screening approaches. Furthermore,
screening of less complex substances allows for a more extensive exploration of the accessible
chemical space, and hence increases the chances of finding hits. This presentation will introduce
common aspects and commonly employed techniques in the field of FBDD, and discuss
(dis)advantages in comparison with other approaches. In addition, some of the special features of
surface plasmon resonance-based FBDD, as employed by Beactica, will be highlighted with
examples.
34
S23: Ian Garrard,
Brunel University
Manager of Advanced Bioprocessing Centre
Brunel Institute for Bioengineering, Brunel
University, London, UK
[email protected]
UK
Dr Ian Garrard is Manager of the Advanced Bioprocessing
Centre (ABC) at Brunel University, London, UK. This is a
£1.5 million laboratory facility dedicated to research into
liquid-liquid technology. Dr Garrard joined Brunel University
from an industrial background, having spent more than 15
years working for the natural products research company
Xenova and the pharmaceutical giant, Pfizer and was
experienced in the purification of biomolecules and natural products. Having encountered the
technique of countercurrent chromatography in industry, seen its potential and identified the reasons
why industry is slow to adopt it, Dr Garrard moved to Brunel University to research the scale up of the
technology. Current research projects include: the large scale purification of monoclonal antibodies,
the continuous extraction of a crude natural products mixture, and the use of the instrument as a
combined bioreactor/separator.
Large Scale Purification of Biomolecules
Ian Garrard, Derek Fisher and Ian A Sutherland
Brunel Institute for Bioengineering, Brunel University, West London, UB8 3PH, UK
There are a number of distinct advantages to having a liquid stationary phase for large scale
purifications including: a very high sample loading, the ability to inject crude particulates, 100%
recovery of all components, no drifting of peak retention times, easy recycling of the solvent used, and
no expensive columns to replace [1, 2].
Variously known as dynamic extraction, centrifugal partition chromatography or counter current
chromatography according to the instrument used, all these techniques use two immiscible liquids as
the mobile and the stationary phase of a separation. Each of these techniques will be briefly
described, with recent advances in both machine design and understanding detailed. With modern
instruments, the separations are provided in minutes, the injection loadings are in the grams to
hundreds-of-grams scale, the equipment is robust, and the scale-up from analytical to pilot level has
been shown to be quick and easy [3, 4].
A number of case studies will be presented including.
1. The use of aqueous two phase systems for protein extraction and purification.
2. The direct scaling of a natural product purification from milligram to kilogram quantities.
3. The latest research on the purification of biological particles such as plasmids or viruses.
4. The continuous extraction of a complex mixture by true countercurrent flow of both liquid
phases.
[1]
[2]
[3]
[4]
Garrard IJ, Fisher D, Sutherland IA. Dynamic extraction: a high speed, high capacity purification process that is rapidly
scaleable. LC/GC North America, vol.26, No.5, pp.2-7, May 2008.
Garrard IJ, Janaway L, Fisher D. Minimising Solvent Usage in High Speed, High Loading and High Resolution Isocratic
Dynamic Extraction. Journal of Liquid Chromatography & Related Technologies, 30, 151-163, 2007.
Wood P, Ignatova S, Janaway L, Keay D, Hawes D, Garrard IJ, Sutherland IA. Counter-Current Chromatography
Separation Scaled up from an Analytical Column to a Production Column. Journal of Chromatography A, 1151, 25-30,
2007.
Sutherland IA, Fisher D. Dynamic extraction technology. Innovations in Pharmaceutical Technology, October, 68-71,
(2004).
35
S24: Margit Mahlapuu,
PharmaSurgics AB
Position: CSO
PharmaSurgics AB
[email protected]
Sweden
PharmaSurgics AB is a biotech company founded in
2005. The company originates from collaboration
between Sahlgrenska Academy and Chalmers
University of Technology and is located in close
proximity to Sahlgrenska University Hospital, in
Biotech Center in Gothenburg, Sweden. Currently,
PharmaSurgics employs 8 FTEs complemented with
several expert consultants in key areas.
PharmaSurgics develops and commercialises a
novel treatment for the prevention of harmful
scarring (adhesions) after surgery. The company’s
core technology constitutes a patented family of
peptide compounds with highly beneficial antiinflammatory and anti-microbial effects, which
promote the healing process. The multifunctional
properties of the compounds offer the potential for multiple commercialisation projects to be
conducted in parallel.
Margit Mahlapuu joined PharmaSurgics in 2007 as a CSO. M. Mahlapuu holds a PhD in Molecular
biology from Göteborg University and has previously worked at AstraZeneca, Arexis AB and Biovitrum
AB.
Lactoferrin peptides: From early discovery to the clinical development
Pharmasurgics main project focuses on development of novel treatments for prevention of internal
post-surgical scar formation - adhesions. Adhesions are a significant source of post-surgical
complications for millions of patients, a world-wide dilemma for surgeons and a major burden on the
healthcare systems. Existing therapies, based on medical device products, which physically
separate the tissue surfaces, have failed to show efficacy and have been associated with severe
adverse effects and/or complicated application procedure.
Pharmasurgics’ core technology constitutes patented pharmaceutical compounds with highly
beneficial anti-inflammatory and anti-microbial effects that promote the healing process and prevent
adhesion formation. PharmaSurgics’ peptides are integrated into a lubricating vehicle covering tissue
surfaces exposed to the risk of developing post-surgical adhesions. The combined effect of a
physical barrier and a pharmacologically active compound directly affecting the mechanism behind
adhesion formation is unique and provides a base for more comprehensive treatment of postsurgical complications.
The presentation summons our experience in the development of the PharmaSurgics’ focus project
from the early discovery into the first clinical phases.
36
S25: Fereidoon Shahidi,
Memorial University of Newfoundland
University Research Professor
Memorial University of Newfoundland, Biochemistry
Department
St. John’s, NL A1B 3X9
[email protected], [email protected]
Canada
Brief Biodata of Professor Fereidoon Shahidi
Fereidoon Shahidi, Ph.D., FACS, FAOCS, FCIC, FCIFST,
FIAFoST, FIFT, FRSC is a university research professor, the
highest academic level, in the Department of Biochemistry at
Memorial University of Newfoundland (MUN). He also is crossappointed to the Department of Biology, Ocean Sciences Centre,
and the aquaculture program at MUN. Dr. Shahidi is the author
of over 600 research papers and book chapters, has also
authored or edited over 50 books, and has given over 400
presentations at scientific conferences. Dr. Shahidi’s current
research interests include different areas of nutraceuticals and
functional foods as well as marine foods and natural antioxidants.
Dr. Shahidi serves as the editor-in-chief of the Journal of Food Lipids and Journal of Functional Foods, an editor
of Food Chemistry as well as an editorial board member of the Journal of Food Science, Journal of Agricultural
and Food Chemistry, Nutraceuticals and Food; and the International Journal of Food Properties and serves on
the editorial advisory board of Inform. He has received numerous awards, including the He was the 1996 William
J. Eva Award from the Canadian Institute of Food Science and Technology in recognition of his outstanding
contributions to food science in Canada through research and service. He also received the 1998 Earl P. McFee
Award from the Atlantic Fisheries Technological Society, the 2002 ADM Award from the American Oil Chemists’
Society, the 2005 Stephen Chang Award from the Institute of Food Technologists. In 2006, Dr. Shahidi was
inducted the Fellow of the International Academy of Food Science and Technology and was a most highly cited
th
st
(7 ) and a most published (1 ) individual in the area of food, nutrition and agricultural science for 1996-2006 as
th
listed by ISI; this standing has now been revised to the 4 . Dr. Shahidi was the 2007 recipient of the
Advancement of Agricultural and Food Chemistry Award from the Agricultural and Food Chemistry Division of the
American Chemical Society (ACS) and its 2008 Distinguished Service Award. He has served as executive
member of several societies and their divisions and an organizer of many conferences and symposia. Dr.
Shahidi served as a member of the Expert Advisory Panel of Health Canada on Standards of Evidence for Health
Claims for Foods, the Standards Council of Canada on Fats and Oils, the Advisory Group of Agriculture and AgriFood Canada on Plant Products, and the Nutraceutical Network of Canada. He also served as a member of the
Washington-based Council of Agricultural Science and Technology on Nutraceuticals. Dr. Shahidi is currently
serving as a member of the Expert Advisory Committee of the Natural Health Products Directorate of Health
Canada. Dr. Shahidi is a founder of the International Society for Nutraceuticals and Functional Foods (ISNFF)
which is a not-for-profit organization <isnff.org>.
Functional Food and Ingredients from the Sea
Marine functional food and ingredients from the aquatic environment appear to constitute an ever increasing
sector of the functional foods and nutraceutical industries in Canada and around the world. This is created,
in part, by more interest in foods containing omega-3 fattty acids and their extracted omega-3 oils. The oils
so obtained are used as dietary supplements and in preparation of fortified foods and beverages. The
benefits of omega-3 oils are due to their lowering of serum triacylglycerol and amiliorating the incidences of
arrhythmias. Ohter benefits of omega-3 fatty acids are related to their potential positive effects in type 2
diabetes, inflammmatory diseases, including mental depressions and other related disorders. Obviously,
these oils need to be stabilized so that flavour characteristuic of the products are not compromised.
Meanwhile, glucosamine and its precursors, chitosan and chitin, are also of interest for preceived beneficial
effects on joint health. In addition to these, biopeptides produced upon hydrolysis of marine products are
considered important in health promotion and disease risk eduction by varied mechanisms, including ACEinhibitory effects. Finally, the use of algal products / seaweeds and seaweed derived products is of much
interest to the health food and nutraceutical industries. The presentation will provide a cursory account of
marine bioactives in the context of bioresources from the aquatic environment. Processing by-products from
the seafod industies play an important role in the development of healthful products.
37
S26: Sergey B. Zotchev,
Biosergen AS/ NTNU
Chief Scientific Officer/Professor
Biosergen AS/ The Norwegian University of Science
and Technology (NTNU)
[email protected]
Norway
Sergey Zotchev's major field of expertise is
molecular genetics of actinomycete bacteria, with
focus on genetics and biochemistry of antibiotic
biosynthesis. He defended his PhD thesis at the
Research Institute for Genetics and Selection of
Industrial Microorganisms (Moscow, Russia) in
1991. After several years of postdoctoral studies in
Germany (University of Osnabrueck), USA
(University of Wisconsin-Madison), and Sweden
(Karolinska Institute), he has joined NTNU in 1996
as a Research Fellow. In 2001, Sergey took up an appointment as an Associate Professor at the
Department of Biotechnology, and established his own research group. Later, his research interests
have expanded to bioprospecting, with main focus on discovery of new and rare actinobacteria in
marine environment capable of producing antimicrobial and antitumor compounds.
Sergey Zotchev is currently a Professor at the Department of Biotechnology, NTNU, and a Chief
Scientific Officer at the biotech start-up company Biosergen AS. The latter company has been
established based on the results obtained at NTNU and SINTEF on biosynthetic engineering of the
antifungal antibiotic nystatin analogues. Sergey’s vision for the future is to create a robust pipeline for
drug development based on the integration of bioprospecting, biosynthetic engineering, and
bio/chemoinformatics.
Discovery of new antibiotics through biosynthetic engineering and bioprospecting
There exists an unmet medical need for efficient and safe antimicrobial and anticancer agents.
Actinomycete bacteria have long since been known as producers of diverse biologically active
compounds, many of which are being currently used as antibiotics and anticancer drugs. One of the
approaches towards development of new drug candidates is represented by a relatively new field of
bacterial biosynthetic engineering. The latter requires full understanding of genetics and
biochemistry of the compound’s biosynthesis, and the ability to manipulate the biosynthetic genes
with predictable outcome for compound’s structure. This approach will be illustrated by the
successful development of new antifungal antibiotics at Biosergen AS. The company, together with
NTNU and SINTEF, has managed to drastically improve the pharmacological properties of nystatin
through manipulation of genes for its biosynthesis.
Yet another promising way to new drugs lies through bioprospecting focused on bacterial secondary
metabolites, which will be illustrated by the latest developments in the bioprospecting project at
NTNU and SINTEF. Major challenge of this approach is very frequent re-discovery of already known
compounds, which can be circumvented by focusing on unique environmental niches and rare
bacterial species. At NTNU and SINTEF we have developed techniques for efficient isolation and
characterization of actinomycete bacteria from marine sediments, sponges and sea surface
microlayer. Novel compounds shown to be active against multi-resistant bacterial and fungal
species, and several cancer cell lines have been identified. This work is being paralleled by the
search for biosynthetic genes for these new compounds, which may open possibility for their
improvement through biosynthetic engineering.
38
S27: Gunnar Rørstad,
Calanus AS
Managing Director & Co-Founder
Calanus AS
[email protected]
Norway
Calanus AS (www.calanus.no) is a private company
founded with a vision to develop novel biomarine industry
based on ecologically sustainable harvesting of the
zooplankton Calanus finmarchicus, the largest harvestable
biomass in the North Atlantic ocean.
Gunnar Rørstad has broad experience from the
biotechnology industry, including tenure as CEO of Biotec
Pharmacon ASA (1994-2006), a Norwegian public
biopharmaceutical company which he also co-founded.
Novel industry based on marine copepods
Calanus finmarchicus is the major zooplankton species in the North Atlantic food-web, and it has a
biochemical composition which makes it very attractive as a raw material for ingredients and bioactive
products for diverse applications.
Calanus AS has in collaboration with industrial and academic partners invented technology for
sustainable harvesting of Calanus finmarchicus, and is developing processing methods and products
on basis of this exiting new raw material for the biomarine industry.
The Company’s products in development include protein hydrolysates and powders with attractive
tastes and nutrient profiles, and a dietary oil composition rich in stearidonic acid, other long-chain n-3
fatty acids, and astaxanthin.
Calanus AS has, moreover, identified a truly novel and unique pharmaceutical product candidate for a
major disease indication, which the Company intends to bring forward through preclinical and early
clinical development.
39
S28: David Newman,
National Cancer Institute
Chief, Natural Products Branch
National Cancer Institute
[email protected]
USA
Born in the UK, trained originally as an analytical
chemist, moved to synthetic organic chemistry and then
received a DPhil in microbial chemistry in 1968 from
Sussex. Moved to USA in ’68 as a post-doc, worked as
a biological chemist (mainly antibiotics and marine
natural products) in industry from 1970 to 1991, then
joined the Natural Products Branch (NPB), NCI in 1991
and was appointed Chief in 2006.
The NCI is the largest Institute in the National Institutes of Health (a US gov’t institution) and NPB is
part of the Developmental Therapeutics Program whose sole task is to find new treatments for
cancer. NPB is responsible for obtaining natural products from microbe, marine and plant sources
that are then used as sources of leads for novel agents.
Natural Products as Drugs:
Will discuss a little history of the topic and then move into the marine/microbial arena demonstrating
with current compounds, how the interplay of marine invertebrates and microbes is leading to novel
chemistries that have potential not only in cancer but in antiinfectives and pain management.
40
S29: Erik Mathur, Synthetic Genomics,
Inc.
Eric J. Mathur
Vice President, Genomic Research
Synthetic Genomics, Inc.
[email protected]
USA
Synthetic Genomics, Inc., a privately held company
founded in 2005, is dedicated to developing and
commercializing genomic-driven solutions to address
global energy and environmental challenges. The scientific
strength at Synthetic Genomics lies in the decades of
pioneering scientific research by J. Craig Venter, Ph.D.
and Nobel Laureate Hamilton O. Smith, M.D. The
company's scientific team includes leading researchers with expertise in areas such as metabolic
engineering, microbiology, biochemistry, bioinformatics, plant genomics, climate change and energy
policies. In addition to the in-house research at Synthetic Genomics, the company is also funding
synthetic genomic research at the J. Craig Venter Institute, a not-for-profit research organization with
more than 400 staff and scientists dedicated to the advancement of the science of genomics,
understanding its implications for society, and communicating those results to the scientific
community, the public and policymakers.
21st Century Trends in Microbial Ecology & Biotechnology
Eric J. Mathur; Synthetic Genomics, Inc. La Jolla, CA
It is only recently that scientists have begun to realize the important role marine microorganisms play
in shaping our biosphere. Microbes have been shown to impact many biogeochemical processes
including carbon sequestration, anaerobic oxidation of methane, nutrient cycling and even can affect
ocean productivity resulting from global dust storms. The biotechnology revolution has led to the
development of a new suite of sophisticated cellular and molecular tools including modern
phylogenetic techniques, novel microbial cultivation methods, high throughput & single cell genomics,
functional genomics and more recently, metagenomic sequencing technologies. Microbial
biotechnology has made a tremendous impact on the quality of modern life resulting in cures for
disease, improvements in health, nutritional advances, unravelling new sources of alternative energy
and progressing toward solutions for food security, pollution control and bioremediation of toxic waste
sites. In addition to facilitating the development of innovative and efficient industrial processes, these
advances have provided molecular ecologists with the necessary tools to enable a better
understanding of the roles microorganisms play in affecting the structure and function of ecosystems
and ultimately how they help drive global geochemical processes.
41
POSTER ABSTRACTS
Poster 1
The Aquapharm Marine Microbial Collection: Culturing Commercial
Possibilities
Authors:
Kimberley McKendrick, Liming Yan, Claire Treasurer, Anish Senan and Andrew Mearns Spragg.
Address:
Aquapharm Biodiscovery, European Centre for Marine Biotechnology, Dunstaffnage, Scotland, United
Kingdom PA37 1QA
Abstract:
Aquapharm is a leading marine biotechnology company pioneering the discovery, isolation and
subsequent development of novel bio-chemicals isolated from the under-explored biological diversity
of marine microbes. Its core competence is the ability to find and develop products derived from its
growing and proprietary library of marine micro-organisms using “SeaRch™”, a novel screening
technology. SeaRch™ is providing the Company with a large diversity of new chemical compounds,
an excellent “hit-rate” of new anti-infectives and further high value products useful in other commercial
sectors. Aquapharm’s central asset is its unique and growing collection of over 7000 isolates of
marine microorganisms collected from a wide range of habitats. The business seeks to exploit the
abundance of diverse and novel chemistry contained within this proprietary library to serve as an
invaluable resource for its commercial activities.
42
Poster 2
Bioprospecting services: from nature to biotechnological
development
Authors Diaz-Cidoncha Garcia Alberto, CPD Ciencia Services supporting science research
Institution address C / Sangenjo , 34.
28034 Madrid , Spain.
Tel: +34913781432
Fax: +34917390931
Email: [email protected]
Web page: www.cpdciencia.com
Summary of presentation
Project Azores deep sampling 2007-2010
During 2008 CPD Ciencia was Bioprospecting marine and terrestrial samples at the Azores Island, in
collaboration with the University of Azores Department of Oceanography and fisheries (DOP).
For 2009-2010 this project is considering the use of an autonomous submarine to have access to the
biodiversity of sea bottoms up to 500 m.
Project sampling European Union outermost regions from 2004
Bioprospecting for the collection of biological samples for research and industrial using in different
ecosystems from all European Union outermost regions : Canary Island since 2004 , Azores 20072010, Reunion 2009, Netherland Antilles 2008 - 2010, Madeira 2010 French Guyana 2010 Martinique
and Guadaloupe 2011.
Project European countries
Sampling in special ecosystem from European Union countries
Crete (Greece) 2007, Sweden 2007- 2008, Formentera (Spain) 2008, Sicily (Italy) 2008, Scotland
(U.K) 2009, Bulgaria 2009, Pantelleria (Italy) 2009.
Project For the Ministry of Science and Technology of Mozambique. Design and implementation
of the National Center of Marine biotechnology in Mozambique.
Increase the basic resources for the developing of marine Biotechnology in Mozambique:
1. - Creation of a Marine Biotechnology unit, including equipment and “training”.
2. - Creation of a marine organisms bank from Mozambique’s organisms, for taxonomy and
Biotechnology purpose, including sediments, marine invertebrates, marine vertebrates and seaweed,
to achieve basic development of science and possible commercial use and Biotechnological benefits.
3. - Identification and creation of “Protected Areas” for the conservation of the marine Biodiversity,
biotechnological use and the environmental protection.
4. - Study and advising, for carrying out a law project for the protection, access and benefit sharing to
the Mozambique’s marine genetic resources.
43
Poster 3
Barents BioCentre
Erling Sandsdalen, Norut
Barents BioCentre (BBC) is a new biotech centre to be established in a new building in Tromsø
Science Park. BBC will be a centre housing activities from the university of Tromsø, several biotech
companies and Northern Research Institute’s new biotech department. The centre offers modern
laboratories with advanced equipment meant to cover the growing biotech industry needs both for
R&D services and modern laboratories. The main goal for BBC is to contribute to industrial growth.
BBC is established as a result of a common initiative between several biotech companies, the
University of Tromsø and Northern Research Institute.
44
Poster 4
Marbank – a repository for marine organisms
Authors
Marbank (Kjersti Lie Gabrielsen, Robert Johansen, Sten-Richard Birkely)
Institution /address
Marbank, University of Tromsø, N-9037 Tromsø, Norway
Abstract
As a result of Norway’s increased focus and research effort on marine bioprospecting a marine
repository, Marbank, is established in Tromsø, Norway. Marbank has a national responsibility for
collecting, preserving and cataloguing marine organisms from Norwegian waters (and especially from
Arctic areas) for research, commercial and exploitation purposes. The mission of Marbank is to
provide an accessible repository of frozen marine biological samples for R&D institutions and industry
that search for novel compounds in marine organisms.
In general, a high diversity in marine organisms increases the possibility to discover new, unique
molecules by bioprospecting and hence Marbank aims for a widest possible assortment of samples.
The material archived and stored in the repository includes taxonomy samples, genetic and biological
material from marine microorganisms, plankton, algae, invertebrates and vertebrates. The vast
majority of organisms are rather rare and small making the sampling for a certain amount of biomass
rather demanding. So far Marbank has samples from approximately 500 organisms in the collection.
Marbank is funded by the Norwegian Ministry of fisheries and coastal affairs and the University of
Tromsø.
45
Poster 5
MARINE BIOTECNOLOGY
MARINE BIOTECHNOLOGY
Bachelor- and master degree programmes at the Norwegian College of Fishery Science,
University of Tromsø
Marine Biotechnology is considered as technology that uses marine microorganisms, plant- and
animal cells, or parts of these for useful purposes in a controlled fashion to produce and alter products
that is important for us. That can i.e. be products with a healthy effect, drugs to cure cancer,
compounds for industrial application, etc.
The discipline marine biotechnology is changing very fast, and highly competent candidates are
demanded. The prospect of work is divers and varying from locally, nationally and internationally.
Both research and commercialisation is future challenges within this field of research.
The Norwegian College of Fishery Science is offering bachelor- and master programmes in Marine
Biotechnology. The master study is new and is offered for the first time in autumn 2009.
Parts of the teaching at the bachelor level in Marine Biotechnology will take place on the Universities
research vessels, in modern laboratories and in collaboration with the life science industry.
The master degree study is applying specialization within chemicals of aliments and industrial
biotechnology, but also courses within entrepreneurship and commercialisation.
Additional information about the study will be presented at the meeting.
Contact person Professor Klara Stensvåg +47 77 64 45 12
More about the study
http://uit.no/studieprogram/2008/host/b-marinbio
46
Poster 6
Screening for compounds from Arctic and sub-Arctic marine
invertebrates with anti-cancer activities
Trine Stiberg, Maria Perander, Jeanette Hammer Andersen, Trond Jørgensen. MabCent-SFI, Tromsø
Science Park, University of Tromsø, 9037 Tromsø
The objective of the anti-cancer screening project at MabCent-SFI is to identify compounds from
marine invertebrates, bacteria and algae that kill cancer cells or inhibit the progression of cancer. Two
strategies to identify drugs with potential anticancer activities are used. The first is a classical
approach where marine extracts are screened for cytotoxic or cytostatic activities towards a panel of
cancer cell lines. The second strategy is to target signaling pathways or proteins with important
functions in cancer initiation and progression. Biochemical and cell-based assays are currently being
employed or developed to identify inhibitors of cancer cell growth, the NF-κB signaling pathway, and
members of the protein kinase superfamily.
47
Poster 7
Screening for Compounds with Antioxidant Activities from Arctic
and sub-Arctic Marine Organisms
1
1
2
2
Tim Hofer , Tonje Engevik Eriksen , Ida-Johanne Jensen , Edel Oddny Elvevoll , Jeanette Hammer3
2
Andersen , Ragnar Ludvig Olsen
1
2
3
MabCent-SFI , Norwegian Fishery College and Marbio , University of Tromsø, N-9037 Tromsø,
Norway
MabCent-SFI is a centre for research based innovation hosted by the University of Tromsø, Norway,
that focuses on the identification of bioactive compounds from Arctic and sub-Arctic marine
organisms. MabCent-SFI covers the pipeline from sampling to bioassay screening and research with
the identification of drug leads with potential commercial interests as the main objective.
The antioxidant screening program at MabCent-SFI includes:
i)
identification of compounds with activities in cell based assays such as the CAA (cellular
antioxidant activity) assay
ii)
antioxidant activities in ‘wet chemistry’ assays including FRAP (ferric reducing antioxidant
power) and ORAC (oxygen radical absorbance capacity)
iii)
antioxidant protection from H2O2-induced cellular oxidative DNA damage using the Comet
assay, which can also be used to test cytotoxic effects to the genome
Novel compounds are compared to known antioxidants including flavonoids, tocopherols and
carotenoids.
48
Poster 8
Discovery of anti-diabetic agents from marine invertebrates
Steinar Paulsen, Marte Albrigtsen, Jeanette Hammer Andersen, Trond Jørgensen
MabCent-SFI, Tromsø Science Park, University of Tromsø, NO-9037 Tromso, Norway
Eating is essential to life, and its episodic nature requires physiological adaptations to avoid excess or
insufficiency in circulating fuels, especially glucose and lipids. Our modern lifestyle with an increasing
imbalance between energy intake and energy expenditure, often resulting in obesity, is a challenge to
this fine tuned energy adaptation. Chronic disruption of the energy balance causes plasma glucose
imbalance, hypertrophy and hyperplasia of adipocytes causing metabolic disorders such as type 2
diabetes (T2D). A number of potential drug targets have been identified and investigated with respect
to treatment of metabolic syndromes and T2D. Developed and released drugs have revealed
moderate efficiency and many have shown low specificity with adverse effects. The drug screening
campaign at MabCent is focused on two targets: The enzyme PTB-1B involved in the insulin
signalling cascade, and nuclear receptors regulating the expression of genes involved in the control of
lipid metabolism, glucose homeostasis and inflammatory processes. Our HTS campaign rely on both
isolated target and cell based assays. Screening strategy and preliminary results will be presented.
49
Poster 9
Shilajit: A Himalayan Natural Resource for the Prevention of
Diabetes
1,3
2
1
Purusotam Banset , Akihito Takano , Katsuko Komatsu
1
Institute of Natural Medicine, University of Toyama, Sugitani, Toyama, JAPAN
2
Showa Pharmaceutical University, Medicinal Plant Garden, Machida -Tokyo, JAPAN
3
The National Research Center in Complimentary and Alternative Medicine (NAFKAM),
University of Tromsø, Tromsø, Norway
The old report of WHO shows that the population of diabetics was 60 millions in 1980, 118 millions in
1995 and there will be 220 millions in 2010. Currently, it has been estimated that there are already
246 millions population are diabetics. Therefore, it is very important to focus on the research to find
the cure to such disease, which is not only killing the lives of one person per second the lives and
deteriorating the health but also, a huge social and economical burden to the nations. One of the
major causes of the diabetes is the gradual destruction of insulin producing β−cells in the pancreas.
On this regard, the role of GAD-65, IRS, Th1 and Th2 cells activities, and reactive oxygen spices
(ROS) including SOD-activity has been studied. Vitamin C, vitamin E, nicotinamide, lipoic acid, Nacetyl-L-cysteine are some of the examples showing the preventive action on diabetes. However,
there is no systematic study on the role of natural medicines and their actions in preventing diabetes.
Shilajit is one of the crucial elements in several formulations including those of Rasayana, a therapy in
Ayurveda (a traditional medicine practiced in South Asia). It has been used in the prevention of aging
and mental disorder. Although, Shilajit is widely used for the treatment of diabetes, no satisfactory
scientific reports are available up to now. The crude Shilajit in the market is a dark brown or black
rock-like substance with a strong smell of cow’s stale urine, however, its quality remains to be
determined.
In our studies, Shilajit (collected in the central Himalayan region) prevented the diabetes in female
nonobese diabetic (NOD) mice model. Shilajit also prevented the diabetes in the rats against the
action of multiple low-dose (10 mg/kg, i.v., 5 times) of streptozotocin. On the other hand, Shilajit did
not show antioxidative activity. The preventive action of Shilajit on diabetes is mainly focused on the
Th1 and Th2 cell activities, since Th2 cells activity was found to be significantly upregulated. Shilajit,
however, showed a mild action in controlling the blood sugar level in young, old, and mild diabetic
rats, but not in the severe diabetic rats. It also stimulated the nitric oxide production in macrophages.
Based on these evidences, the antidiabetic activities of Shilajit appear to be immunomodulative by
protecting insulin producing β-cells in the pancreas. Further systematic research on constituents of
Shilajit and its quality evaluation is necessary to enable the use of Shilajit in the prevention and/or
treatment of diabetes.
50
Poster 10
Screening for immunomodulating compounds in Arctic marine
organisms
1
2
3
3
2
Karianne F. Lind , Kirsti Helland , Bjarne Østerud , Karl-Erik Eilertsen , Jeanette H. Andersen and
1
Trond Ø. Jørgensen
1
2
3
MabCent-SFI, University of Tromsø, Norway. Marbio, University of Tromsø, Norway. Institute of
Medical Biology, Medical Faculty, University of Tromsø, Norway.
Marine extracts are analysed in vitro for both anti-inflammatory and immunostimulatory activity using
the monocyte/macrophage cell-line THP-1 and studying the secretion of TNFα. In addition, an IL-1β
ELISA will be implemented in the primary screening to supplement the TNFα assay.
Different
signalling pathways involved in inflammation will thus be targeted in the screening. Fractions that
show activity in the primary assays are further tested in a whole blood model for their ability to
modulate the expression of tissue factor (TF) in mononuclear cells and inflammatory cytokines in
plasma.
To be able to screen a high number of marine extracts it is necessary to automate the ELISA assays.
Adaptation of an ELISA assay to high-throughput (HTS) format is not always straightforward due to
the fact that some reagents in the ELISA kits are light and/or temperature sensitive. An in-house
ELISA for the IL-1β with light-stable reagents was therefore developed and adapted to a HTS format.
Data from the assay development will be presented.
51
Poster 11
Dunaliella salina CNM-AV-02 – source of biologic active
compounds.
Iulia Iatco, Ludmila Rudi, Cepoi Liliana, Rudic Valeriu
Organisation: Institute of Microbiology and Biotechnology
Moldova Academy of Sciences
Laboratory Phycobiotechnology
Dunaliella salina is a green unicellular halophill microalgae. It can be a model for haloadoptation
studies, not only for algae, but for high plants too. Dunaliella produces a high amount of valuable
biologic active compounds, as ß – carotene, polyunsaturated fatty acids (essential for animals and
people), and lipids. Salt stress increases the basic physiologic functions in alga – photosynthesis and
photorespiration, and changes in lipids composition.
It grows on high salt concentrations, due this it is very rare contaminated with other cultures. And in
countries with warm climate Dunaliella is grown in open ponds.
We propose the technologies of fatty acids direct synthesis in Dunaliella salina, and their prospective
using in different industries – for bio fuel production, in pharmacy, zootechny, medicine est.
As methods for lipids quantity increasing are proposed some metals coordinating compounds,
temperature and irradiation regulating.
52
Poster 12
Exploring natural product production from symbiotic
microorganisms isolated from corals.
Bradley Haltli, Fabrice Berrué and Russell Kerr
Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada
While marine invertebrates are well known as a prolific source of bioactive natural products with
varied applications in human health a critical concern that often arises is the question of a sustainable
supply. In part due to such reasons, many research groups have examined marine bacteria from
sediment as a source of novel natural products. The microbial communities of marine invertebrates
are not well characterized with the exception of the sponges. Over the past few years, we have
examined the bacterial communities in selected gorgonian corals using both culture-independent and
culture-dependent techniques and such studies have indicated substantial diversity. We have been
investigating approaches to screen a variety of conditions to produce natural products via the culture
of bacteria derived from corals and recent progress will be discussed.
Selected for oral presentation
53
Poster 13
Characterization of Streptomyces spp. isolated from the sea
surface microlayer in the Trondheim fjord, Norway
1
1
2
1
Sigrid Hakvåg , Espen Fjærvik , Kjell D. Josefsen , Elena Ian ,
2
Trond E. Ellingsen and Sergey B. Zotchev
1
1
Department of Biotechnology, Norwegian University of Science and Technology,
N-7491 Trondheim, Norway
E-mail: [email protected]
2
Department of Biotechnology, SINTEF Materials and Chemistry, N-7034 Trondheim, Norway
Summary: The water surface microlayer is still poorly explored, although it has been shown to
contain a high density of metabolically active bacteria, often called bacterioneuston. Actinomycetes
from the surface microlayer in the Trondheim fjord, Norway, have been isolated and characterized. A
total of 217 isolates from two separate samples morphologically resembling the genus Streptomyces
have been further investigated in this study. Antimicrobial assays showed that about 80% of the
isolates exhibited antagonistic activity against non-filamentous fungus, Gram-negative, and Grampositive bacteria. Based on the macroscopic analyses and inhibition patterns from the antimicrobial
assays, the sub-grouping of isolates was performed. Partial 16S rDNAs from the candidates from
each subgroup were sequenced and phylogenetic analysis performed. 7 isolates with identical 16S
rDNA sequences were further studied for the presence of PKS type I genes. Sequencing and
phylogenetic analysis of the PKS gene fragments revealed that horizontal gene transfer between
closely related species might have taken place. Identification of unique PKS genes in these isolates
implies that de-replication can not be performed based solely on the 16S rDNA sequences. The
results obtained in this study suggest that streptomycetes from the neuston population may be an
interesting source for discovery of new antimicrobial agents.
Keywords: Sea surface microlayer, streptomycetes, antimicrobial activity, phylogenetic analysis
Acknowledgements
This project is financed by the Research Council of Norway.
54
Poster 14
The cysteine-rich antimicrobial peptides from the sea urchin
Chun Li, Tor Haug, Olaf B. Styrvold, Trond Ø. Jørgensen and Klara Stensvåg
Department of Marine Biotechnology, The Norwegian College of Fishery Science, University of
Tromsø, Breivika, N-9037 Tromsø, Norway
Abstract
Here we report the purification and characterization of two cysteine-rich antibacterial peptides (5.6
and 5.8 kDa) from coelomocyte extracts of the green sea urchin, Strongylocentrotus droebachiensis.
The peptides display potent activities against Gram-negative and Gram-positive bacteria. They also
show the low hemolytic activity. The cDNA encoding the peptides and genomic sequences were
isolated and sequenced. The two peptides (named strongylocin 1 and 2) have putative isoforms (1b
and 2b), similar to two putative proteins from the purple sea urchin S. purpuratus. Strongylocin 1
consists of 83 amino acids that include a preprosequence of 35 amino acids, whereas strongylocin 2a
and 2b are composed of 89 and 90 amino acids, respectively, where 38 amino acids represent a
preprosequence. The genes of putative strongylocins from S. purpuratus were constructed into
PET30-EK/LIC vector and were expressed in E. coli (C43-BL21). The recombinant products show
antibacterial activity against both Gram-negative and Gram-positive bacteria. Therefore, strongylocins
are suggested to play an important role in sea urchins innate immunity.
55
Poster 15
Characterization of crustins from the hemocytes of the spider crab,
Hyas araneus, and the red king crab, Paralithodes camtschaticus
1
Sigmund V. Sperstad , Tor Haug, Victoria Paulsen, Tone Mari Rode , Guro Strandskog, Stein Tore
Solem, Olaf B. Styrvold, Klara Stensvåg
Department of Marine Biotechnology, The Norwegian College of Fishery Science, University of
Tromsø, N-9037 Tromsø, Norway
1
Present address: Matforsk AS, Nofima Food, Osloveien 1, N-1430 Ås.
Abstract
Crustins are distributed across the decapods and are believed to play a significant part in the humoral
defence system of their host. In this study, two crustin isoforms from Hyas araneus hemocytes were
purified and tested for antimicrobial activity against selected microorganisms. They show both
antibacterial and antifungal activity, with highest activity against the Gram-positive bacteria
Corynebacterium glutamicum. Sequencing of the transcripts showed them to have a mature peptide
of 90 amino acids and differing in three positions in the mature peptide. They were named CruHa1
and CruHa2. Real-time RT-PCR revealed that they mainly are expressed in hemocytes. Screening a
cDNA library detected a crustin sequence in P. camtschaticus hemocytes, coding for a mature
peptide of 98 amino acids. It was named CruPc. Based on phylogenetic inference and primary
structure, CruHa1 and CruHa2 were placed within the Type I group of crustins, while CruPc belongs
to the Type II
56
Poster 16
Mechanisms of action of the antimicrobial peptide, arasin 1, from
Hyas araneus.
Authors:
Victoria Paulsen, Hans-Matti Blenche, Tor Haug, Olaf Styrvold, Klara Stensvåg
The increasing resistance of bacteria to conventional antibiotics has stimulated the isolation and
characterization of antimicrobial peptides (AMPs) for potential use as new target antibiotics. AMPs are
important components of the innate immune system of both vertebrate and invertebrate animals.
Arasin 1, isolated form haemocytes of the spider crab (Hyas araneus) belongs to the proline-rich
family of antibacterial peptides. The peptide is 37 amino acids long, and it is composed of two
domains, a proline/arginine-rich N-terminal domain and a C-terminal domain containing two disulphide
linkages. In this study the antimicrobial activity and mechanism of action of arasin 1 was examined
using transmission electron microscopy (TEM), and different antimicrobial assays.
57
Poster 17
Extreme possibilities in extreme environments – a large reservoir
of biological diversity waiting to be discovered
Hans Tore Rapp, Christoffer Schander, Lise Øvreås, Ida Helene Steen, Vigdis Lid Torsvik, Harald
Furnes, Ingunn Hindenes Thorseth, Rolf-Birger Pedersen
Centre for Geobiology, Universitetet i Bergen, Postboks 7803, 5020 Bergen, Norway
The newly discovered deep sea hydrothermal vents on the Mohn and Knipovich ridges north of Jan
Mayen holds a unique biodiversity. Biodiversity of our planet is not only wonderful and beautiful for the
human eye, but also holds and invaluable source of genetic material and ecosystem services that we
and future generations need for a sustainable future on this planet. Two new and exiting venting
areas have been identified in Norwegian oceans; one shallow at 550-700 meters, and a deeper, more
northerly one at 2400 meters. The shallow field consists of areas with low temperature seepage and,
white smokers and brine seepage, while the deeper field consists of a large area with high
temperature black smokers.
In both areas dense fields of microbial mats are found, which are currently being
characterized. Several new and little studied microbes have been identified, both within Bacteria and
Archaea. Many of these seem to be well adapted to these extreme environments, and their potential
as sources for bioactive compounds can not be overestimated.
The fauna surrounding the shallow vent region seems mostly to be closely related to the
fauna of the deep sea, even if some potentially endemic species and some anomalies have been
noted. The deep vents hold a more specialized and more typical vent fauna, with high densities of
vent endemic molluscs, crustaceans, cnidarians and annelids.
The vent fields are currently being intensely studied by researchers from the Centre of
Geobiology at the University of Bergen in collaboration with national and international collaborators.
Although bioprospecting so far has not been a main goal for the research at the centre, a regular
sampling scheme at the institute allows for further exploration and collaboration also in this area.
58
Poster 18
Norwegian sponges, corals and ascidians: Rich sources of
bioactive natural products
1,2
3
Hans Tore Rapp , Friederike Hoffmann , Sven Possner, Karsten Fehler, Christoffer Schander
1
1,2
Centre for Geobiology, University of Bergen, PO Box 7803, 5020 Bergen, Norway.
[email protected]
2
University of Bergen, Department of Biology, Bergen High-Technology Center, 5020 Bergen,
Norway.
3
Sars Centre for Marine Molecular Biology. Sars International Centre For Marine Molecular Biology,
Thormøhlensgate 55, 5008 Bergen, Norway
The diversity of secondary metabolism of sponges, corals and ascidians is the reason that many
natural products with interest to human society have been discovered in these groups of animals.
Several species of these groups commonly found along the Norwegian coast contain new and
unusual compounds with a commercial potential. e.g. the sponges Phakellia ventilabrum,
Hymedesmia paupertas and Geodia barretti, and the corals Antothela grandiflora, Primnoa
resedaeformis and Paragorgia arborea and ascidians of the genus Ascidia.
In these organisms the secondary metabolites act like a chemical defense, and they possess
antimicrobial, antiviral, antifungal and cytotoxic properties. As an example the main component in the
sponge G. barretti, the indole alkaloid Barettin, shows strong antifouling activity. The compounds are
either produced by the organism itself, by associated bacteria, or through a interplay between these.
Development of a new drug or product must always include a plan to supply enough of the compound
for the preclinical and clinical tests. Some species have elsewhere been collected on a large scale to
enable further development of their bioproducts, but due to their slow growth and low recovery rates
in natural systems it is obvious that harvesting from natural resources is not an option for durable
large-scale production. Culture systems are therefore recommended, and to solve the supply problem
we have developed cultivation techniques for several species of boreal sponges.
59
Poster 19
Antimicrobial compounds from marine sponges and tunicates
a
b
b
c
a
Margey Tadesse , Veronika Tørfoss , Morten B. Strøm , Espen Hansen , Klara Stensvåg and Tor
a
Haug
a
Department of Marine Biotechnology and Centre for Research-based Innovation on Marine
Bioactivities and Drug Discovery (MabCent), The Norwegian College of Fishery Science, University of
Tromsø, Breivika, N-9037 Tromsø, Norway
b
Department of Pharmacy and MabCent, Faculty of Medicine, University of Tromsø, Breivika, N-9037
Tromsø, Norway
c
MabCent, University of Tromsø, Breivika, N-9037 Tromsø, Norway
Abstract
Benthic marine invertebrates collected from sub-Arctic regions of northern Norway, were found to be
a promising source of novel bioactive compounds against human and fish pathogenic bacteria and
fungi. Lyophilized material from seven species of ascidians, six sponges and one soft alcyonid coral
were extracted with 60% acidified acetonitrile (ACN). After separation into an ACN-rich phase (ACN
extract) and an aqueous phase, and subsequent solid phase extraction of the aqueous phase,
fractions differing in polarity were obtained and screened for antibacterial and antifungal activities,
along with the more lipophilic ACN-extracts. Antimicrobial activity was determined against two Gramnegative, two Gram-positive bacteria, and two strains of fungi. Notably, all the invertebrate species in
the study showed activity against all four strains of bacteria and the two strains of fungi. In general,
the aqueous fractions displayed highest antimicrobial activity. An antibacterial compound was further
isolated from the ascidian Dendrodoa aggregata. The full structure of the compound was determined
by NMR and mass spectrometry.
60
Poster 20
Bioactive metabolites in marine sponges
1, 3
Ingrid Varmedal
2
3
1
, Espen Hansen , Ragnar L. Olsen , Trond Jørgensen , Jeanette Hammer
2
Andersen
1
2
MabCent, University of Tromsø, N-9037 Tromsø, Norway and Marbio, University of Tromsø, N3
9037 Tromsø, Norway and Norwegian College of Fishery Science, University of Tromsø, N-9037,
Norway
Marine sponges have in the past proven to be a rich source of bioactive metabolites. The goal of this
project was to identify and isolate bioactive components from Arctic sponges.
Semi-purified fractions from organic and aqueous extracts were tested for anticancer, antibacterial
and antioxidative activities. Several bioactive fractions were found in the primary screening and these
fractions were further purified and retested for biological activity. The purified fractions with biological
activity were analyzed by LC-MS in order to identify the active components. The approach and results
will be presented in detail in the poster.
[email protected]
61
Poster 21
Cultured bacteria and fungi with bioactivities from the marine
sponge Haliclona simulans.
Jonathan Kennedy, Paul W. Baker and Alan D.W. Dobson
Environmental Research Institute and Microbiology Department, University College Cork, Lee Road ,
Cork, Ireland.
Samples of the marine sponge Haliclona simulans were collected from Irish coastal waters and both
bacteria and fungi were cultured from these samples. Phylogenetic analyses of the cultured isolates
showed that 4 different bacterial phyla were represented; Bacteriodetes, Actinobacteria,
Proteobacteria and Firmicutes. Over 80 fungi were isolated from 19 different genotypes. These were
classified within Agaricomycotina, Mucrromycotina, Saccharomycotina and Pezizomycotin; with the
majority of the isolates associated with the latter class. Some of the fungal isolates showed
antimicrobial inhibition of Escherichia coli, Bacillus sp., Staphylococcus aureus and Candida glabrata
(1).
The sponge bacterial isolates were assayed for the production of antimicrobial substances and
biological activities against Gram-positive and Gram-negative bacteria and fungi were demonstrated.
Further testing using clinical indicator strains showed that the antimicrobial activities extended to the
important
pathogens
Pseudomonas
aeruginosa,
Clostridium
difficile,
multi-drug
resistant
Staphylococcus aureus and pathogenic yeast strains (2). The presence of potential antibiotic
encoding polyketide synthase and nonribosomal peptide synthase genes revealed that these
secondary metabolites were present in most of the bacterial phyla, and were particularly prevalent
among the Actinobacteria and Proteobacteria.
This study demonstrates that the culturable fraction of microbes, including fungi; from the sponge H.
simulans is quite diverse and appears to posses much potential as a source for the discovery of new
medically relevant biological active agents.
1. Baker, P.W., Kennedy, J., Dobson, A.D.W. and Marchesi, J.R. (2008). Phylogenetic diversity
and antimicrobial activities of fungi associated with Haliclona simulans isolated from Irish
coastal waters. Marine Biotechnology. (in press).
2. Kennedy et al., (2008) Isolation and analysis of bacteria with antimicrobial activities from the
marine sponge Haliclona simulans isolated from Irish waters. Marine Biotechnology. (in
press) PMID: 18953608
Selected for oral presentation
62
Poster 22
Isolation of antimicrobial molecules from the marine sponge
Haliclona sp.2
Lena C. Vaagsfjord, Tor Haug, Terje Vasskog, Klara Stensvåg
Department of Marine Biotechnology, The Norwegian College of Fishery Science, University of
Tromsø, Breivika, N-9037 Tromsø, Norway
Porifera has by far become the leading source of natural bioactive products when comparing the
number of compounds isolated. The pharmacological potential of sessile invertebrates in general and
sponges in particular is enormous because of the way they feed and the environment they live in.
Sponges also have a wide diversity of symbionts that secrete metabolites making the diversity of
natural products isolated even higher.
The aim of this study (masters thesis) is to isolate and characterise antimicrobial molecules from the
marine sponge Haliclona sp.2. Freeze dried tissue was extracted with acetonitrile (ACN 60%) and a
solid phase extraction was performed on the aqueous phase. Antibacterial screening was conducted
and the most active extract (40% SPE) was subjected to RP-HPLC. Continual testing and isolation of
the compounds from fractions where the activity was located was conducted. Active fractions were
further analysed using mass spectrometry MS and LC-MS to revile information about molecular
structure. Up till now several antibacterial compounds with different polarity have been found and the
preliminary results will be presented at the meeting.
63
Poster 23
The DIABOL project – Mining for genes, proteins, metabolites,
nanoscale structures and molecular machinery of marine algae.
Atle M. Bones, Marianne Nymark, Kristin C. Valle, Kjersti Andresen, Mari-Ann Østensen, Kasper
Hancke, Geir Johnsen and Tore Brembu
Cell and Molecular Biology Section and Marine Biology Section, Department of Biology, Norwegian
University of Science and Technology, NTNU, N-7491 Trondheim, Norway
Diatoms are unicellular photosynthetic eukaryotes found in all aquatic and moist environments. They
are responsible for ~25% of global CO2 fixation. Diatoms have come to the age of genomics, and
sequencing projects will add new genome information within the next years. The genomes of the
diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum have been sequenced. Molecular
biology and genomics techniques have been established for both species; together with the
sequenced genomes, these tools/techniques make these diatoms attractive for molecular analyses.
The DIABOL project was initiated in 2007, and aims to combine knowledge on marine algae and
competence on molecular biology, functional genomics and molecular imaging in order to mine for
compounds and functions in algae. We will search for genes, proteins and metabolites and study
basic processes such as morphogenesis, cell division, light perception and acclimatization to
changing conditions. Here we will present and discuss the genomics of light acclimatization in
Phaeodactulum tricornutum.
64
Poster 24
Broad-host-range cloning/expression vectors
Rahmi Lale and Svein Valla
Department of Biotechnology, Norwegian University of Science and Technology (NTNU),
N-7491 Trondheim, Norway. [email protected]
Current efforts in metagenomics generate vast amounts of sequence information. Once these
data sets are processed it results in large number of putative genes. At this stage expression
tools become indispensable as their use is necessary in production of enzymes, bioactive
molecules, drugs or any gene product that has either academic or commercial interest.
In recent years we have developed two new systems based on the broad-host-range plasmid
RK2 in which (i) the XylS/Pm 1, and (ii) the ChnR/Pb 2 positive regulator/promoter system has
been integrated. The XylS/Pm system has many very attractive properties, among them are high
induced expression levels in many hosts, possibilities for fine-tuning of the expression levels due
to graded response to inducer concentrations, and the fact that the inducers (benzoic acid and
derivatives thereof) are cheap, do not require a host up-take system, and are not metabolised by
most bacteria. In this system there are several DNA control elements that we have been our
interest over the years: Pm (promoter), xylS (gene encoding positive regulator of Pm, acts in the
presence of inducer), 5'-UTR (5' untranslated region at the mRNA level), trfA (gene encoding
plasmid replication initiation protein). Throughout the years by mutagenesis studies we have
identified variants of these regulatory sequences that lead to changed expression levels (both
increased and decreased compared to wild-type forms) by using Escherichia coli as host
organism. Currently we have, for example, achieved over a hundred-fold stimulation of
expression from the XylS/Pm system, by combining variant forms of the Pm, xylS and 5'-UTR in
E. coli. And in addition by the use of 5'-UTR variants we have also brought the basal level
expression to negligible levels without compromising the inducibility, which is an important
characteristic in tightly controlled expression. With these modifications we have been able to
show that this system can be used to control expression over a continuous five-log factor range.
These achievements, for us, are important as the XylS/Pm system has already been shown to be
useful both for industrial level recombinant protein production and for metabolic engineering
purposes across species barriers in its wild-type form1,3. The second ChnR/Pb system has similar
abilities such that inducer (cyclohexanone) displays concentration-dependent response and does
not need any particular transport system, and both systems function well in different gramnegative
species.
E. coli is the most widely used vehicle both for cloning and protein production. Despite its wide
use it is known that it may not be suitable for all types of applications4. Therefore having a
system that can operate in different bacterial species can create flexibility in testing different
hosts, depending on the protein to be produced. As the systems that are presented above are
known to function in numerous bacterial hosts they represent features that are suitable for
expression of target genes that are identified in metagenomic DNA preparations.
1 Blatny, J. et al., Appl. Env. Microbiol. 63: 370-379 (1997).
2 Steigedal, M, Valla, S. Met. Eng. (2008). doi:10.1016/j.ymben.2007.08.002
3 Sletta, H. et al., Appl. Env. Microbiol. (2004). doi: 10.1128/AEM.70.12.7033-7039.2004
4 Structural Genomics Consortium, et al., Nature Methods (2008). doi:10.1038/NMETH.F.202
65
Poster 25
Broad-host-range plasmid vector for metagenome construction
b
a
a
b
b
Kristin Fløgstad Degnes , Rannveig Skrede , Trine Aakvik , Lihua Yu , Trond Erling Ellingsen and
a,
Svein Valla *.
a
Department of Biotechnology, Norwegian University of Science and Technology, 7491 Trondheim,
Norway.
b
SINTEF Materials and Chemistry, Department of Biotechnology, SINTEF, Trondheim, 7465
Trondheim, Norway.
Abstract
The majority of microorganisms in natural environments are difficult to cultivate, and their genes
are therefore commonly studied via metagenome libraries. To enhance the chances that such cloned
genes become expressed we here report the construction of a broad-host-range plasmid vector
(pRS44) for fosmid and BAC cloning. pRS44 can be conjugatively transferred to and maintained in
almost any Gram-negative bacterium due to the presence of the origins of transfer and replication,
oriT and oriV, from the broad-host-range plasmid RK2. This means that metagenomic libraries
constructed in this vector can be transferred to many different hosts at high efficiencies, making it
possible to perform various screens in hosts with different expression capabilities. This feature will
increase the chances for novel compounds to be found. The vector replicates in Eschericha coli via
the plasmid F origin and was found to be remarkably stable (also with insert) in this host due to the
presence of two independent stabilization systems. A metagenomic fosmid library (20 000 clones) has
been constructed in pRS44, and 16S rRNA analysis of the cloned DNA confirms that the library
represents many different genotypes. BAC clones with insert sizes up to around 200 kb have also
been generated, confirming the capability of the vector to hold large inserts. Both the entire fosmid
library and selected fosmid- and BAC clones have successfully been transferred by mobilized
conjugation to two other tested species, Pseudomonas fluorescens and Xanthomonas campestris.
66
Poster 26
Phylogenetic analysis of a metagenomic library from a high-arctic
environment
Matthias Zielke, SFI MabCent, University of Tromsø, Norway
Hans-Matti Blencke, Norwegian College of Fishery Science, University of Tromsø, Norway
Bjarne Landfald, Norwegian College of Fishery Science, University of Tromsø, Norway
Environmental microorganisms are fundamental to ecosystem function as drivers in processes such
as primary production, global biogeochemical cycling and bioremediation of pollution. The very long
evolutionary history of microorganisms has generated a plethora of physiologies and molecular
adaptations - some of which may be valuable tools for biochemical and technical processes. Due to
the fact that the vast majority of microorganisms are not culturable even by today´s state-of-the-art
techniques, cultivation-independent approaches have to be used to uncover potentially valuable
compounds. One such approach, metagenomics, involves direct isolation of environmental DNA
followed by cloning into a cultured host organism. Depending on the aim of the following studies,
either sequence-driven or function-driven analysis can be conducted.
We are under way with a phylogentic screening of a metagenomic library obtained from a
high-arctic intertidal zone environment. The library, which is based on fosmid vectors with 35 kbp
average insert size, contains about 30.000 clones. The objective of the project is to pick out the
expected 1-2 percent of fosmid clones which carry the 16S rRNA gene, in order to establish which
bacterial phylotypes are present in this highly challenging environment. Preliminary results indicate a
diverse pool of bacteria, including representatives of elusive groups such as Planctomycetales and
Verrucomicrobiales, which have not been encountered in strain collections from the same location.
Inserts of fosmids that can be assigned to uncommon or sparsely described groups will be sequenced
in their entirety to screen for genes coding for enzymes of biotechnological interest. A PCR based
16S rDNA screening and sequencing approach for fosmid pools has been developed. However, there
are several practical challenges to be overcome before the entire metagenome library has been
screened and a complete picture of the bacterial diversity is established.
67
Poster 27
Identification of cold-adapted lipolytic enzymes from an Arctic
intertidal zone metagenome
Juan Fu*, Hans Matti Blencke, Bjarne Landfald
(Norwegian College of Fishery Science, University of Tromsø, NO-9037 Tromsø, Norway)
Lipolytic enzymes include esterases and lipases which catalyze the hydrolysis and synthesis of
short-chain (≤C10) and long-chain (≥C10) acylglycerols, respectively. Lipolytic enzymes are highly
versatile and widely used in the food, detergent, pharmaceutical, leather, textile, cosmetics, and paper
industries. Most of the lipolytic enzymes used in industry are microbial. Bacterial lipolytic enzymes
have been classified into 8 families according to their conserved sequence motifs and biological
properties. To search for new cold-adapted lipolytic enzymes, a metagenomic library was constructed
by using environmental DNA from a Svalbard intertidal zone sediment. About 60,000 fosmid clones
were screened on tributyrin plates at 12°C and 139 positive clones were obtained. Two of them also
showed lipase activity on triolein plates. The average insert size of the fosmids is about 35kb. The
complete sequences of 17 positive fosmids were determined by shotgun sequencing and putative
lipolytic enzyme genes were identified. Eighty-two additional fosmids were fragmented and
subcloned. Subclones showing lipolytic enzyme activity have been sequenced. Until now, putative
lipolytic enzyme genes have been identified from 42 positive subclones. The metagenomic lipolytic
enzyme genes show large diversity and about 10 genuinely novel genes have been identified.
Selected genes will be subjected to expression cloning and more detailed biochemical and structural
analyses of the recombinant products.
*Corresponding author.
Email address: [email protected]
68
Poster 28
Evo Array; a novel tool for high throughput bioprospecting and
sequence mining
BO Karlsen (1,2) , T Furmanek (3) , M Andreassen (1) , Å Emblem (1) , TE Jørgensen (2) ,
P Kettunen (3) , K Luukko (3) , J Nordeide (2) , DH Coucheron (1) , T Moum (2) ,
SD Johansen (1,2)
1 Department of Molecular Biotechnology, IMB, University of Tromsø, Norway; 2 Faculty of
Biosciences and Aquaculture, Bodø University College, Norway; 3 Division of Anatomy and Cell
Biology, Department of Biomedicine, University of Bergen, Norway
Key words: Large scale sequencing, bioprospecting, Evo Array, Atlantic cod development, cyclins,
miRNA.
Background: The 454 pyrosequencing technology and other next generation sequencing
technologies require new software and hardware solutions capable of handling the large output of
sequences that are being produced. In the need for global sequence mining, clustering and
integration of databases that are relevant to such projects we developed a novel bioinformatic tool
called Evo Array (Evolutionary image Array). The Evo Array tool should benefit the bioprospecting
community in implementation of large scale approaches to gene mining of organisms and tissues of
interests.
Results: As a proof of principle, we used 200 000 reads of developmentally expressed genes from
Atlantic cod (Gadus morhua) that were fed into the program for analysis and comparison against 20
000 human reference genes. In an in silico subtraction approach, against the 180 000 cod EST
downloaded from NCBI, we find approximately 500 core genes, potentially important for
understanding the developmental processes in Gadus morhua. As the key regulators of cell cycle
progression and hence early development, we selected the cyclins for further analysis. The cononical
A, B, D and E type cyclins were identified. Also all the cyclin CDK (cyclin dependent kinases) partners
were found in this screen. Combining the 454 data and NCBI EST reads from cod, we assembled a
1586 bp read from 34 contigs, representing cyclin B1. We aligned it to the zebrafish cyclin B1 full
length cDNA 1446 bp cds, with a 3’ UTR of 204 bp and estimated the cod 3’ UTR to be 281 bp
without the poly(A) signal.
By analysing the cod cyclin B1 3’ UTR, 5’ UTR and ORF, by 10 000 reads of developmentally
expressed miRNA, and also the adult stage specific miRNA (10 000 reads), we find a more complex
pattern of miRNA expressed that target the B1 cyclin gene in the early cell cycles. How cyclin B1 is
regulated in these early cell cycles is of major interest, especially in the pre-fertilized oocytes, and in
the formation and development of the vertebrate tissues.
Reference: Biotechnology Annual Review, 2009, Vol 15, in press Large-scale sequence
analyses of Atlantic cod
Steinar D. Johansen*,1,2, Dag H. Coucheron 1,3, Morten Andreassen 1
, Bård Ove Karlsen 1,2, Tomasz Furmanek 4, Tor Erik Jørgensen 2, Åse Emblem 1
, Ragna Breines 1, Jarle T. Nordeide 2
, Truls Moum 2 , Alexander J. Nederbragt 5, Nils C. Stenseth 5 and Kjetill S. Jakobsen 5
69
Poster 29
Metagenomic approaches to access and exploit the metabolic
diversity of the sponge microbial consortia.
Jonathan Kennedy, David Lejon and Alan D.W. Dobson.
Environmental Research Institute and Microbiology Department, University College Cork, Lee Road,
Cork, Ireland.
Natural products isolated from sponges are an important source of new biologically active compounds
(1). However, the development of these compounds into drugs is often restricted by the difficulties in
achieving a sustainable supply of these complex molecules for pre-clinical and clinical development.
Increasing evidence implicates
microbial symbionts as a likely source of many of these biologically active compounds. However, the
vast majority of the sponge microbial community remains uncultured and the biochemical diversity of
the sponge microbial consortia is therefore largely inaccessible using traditional microbiological
methods. A metagenomic approach offers a biotechnological solution to this problem (2).
The metagenome of the sponge Haliclona simulans has been shown to contain diverse
microorganisms and genes and gene clusters typical for the biosynthesis of biologically active natural
products (3).
A functional metagenomic approach is currently being employed to access the
metabolic diversity of this sponge, utilising several expression hosts to maximise expression and
subsequent detection of activities which are likely to have remained largely inaccessible by employing
other methods. Data will be presented on metagenomic library construction and on various screening
protocols that are currently being employed.
1. Newman, D.J. (2008). Natural products as leads to potential drugs: an old process or the
new hope for drug discovery? J. Med. Chem. 51 (9) : 2589-2599.
2. Kennedy, J., Marchesi, J.R. and Dobson, A.D.W. (2007). Metagenomic approaches to exploit
the biotechnological potential of the microbial consortia of marine sponges. Appl. Microbiol.
Biotechnol. 75, 11-20.
3. Kennedy, J., Codling, C.E, Jones, B., Dobson, A.D.W. and Marchesi, J.R. (2008). Diversity
of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish
waters and identification of polyketide synthase genes from the sponge metagenome.
Environ. Microbiol. 10 (7): 1888-1902.
70
Poster 30
Some statistical methods in comparative genomics of
environmental adaptation.
Steinar Thorvaldsen1, Tor Flå1 and Nils P. Willassen2
1Dept of Mathematics and Statistics, Faculty of Science, 2The Norwegian Structural Biology Centre,
University of Tromsø, 9037 Tromsø - Norway. [email protected]
In the toolbox DeltaProt we present statistical methods and trend-tests that are useful when the
protein sequences in alignments can be divided into two or more groups based on known phenotypic
traits such as preference of temperature, pH, salt concentration or pressure. The approach has been
successfully applied in the research on extremophile organisms. We also provide procedures to plot
the output from these tests for visualisations. DeltaProt is a Matlab companion Toolbox that can be
used freely for academic, non-profit purposes. Available from http://www.math.uit.no/bi/deltaprot/
We particularly work on identifying proteome-wide, and protein-specific, characteristics of cold
adaptation (psycrophily). This is done by using comparative genomics on cold-adapted organisms,
and similar genes from organisms with normal growth temperatures (mesophiles). In particular we
have studied gamma-Proteobacteria from the order Vibrionales, where many genomes with different
optimum growth temperature (Topt) are already completed.
Statistical methods
The toolbox consists of a set of statistical routines with a variety of modelling functions. We consider
both the amino acid sequence compositions, and the substitution patterns, to determine whether there
are underlying trends that explain the observed variation between the phenotypic groups to be
analysed. More than 80 different physicochemical properties of the amino acid may also be applied in
order to reduce the sequence alphabet to measurements. Each situation is analysed by appropriate
statistical methods:
•
Composition: Linear regression
•
Substitutions: Fisher’s exact test, Chi-square tests, Mantel-Haenszel test
•
Properties: Wilcoxon paired test, Non-parametric regression based on Mann-Kendall
statistics
Fig. The ranked distribution of slope coefficients for change of hydrophobicity at the surface of 65 membrane proteins as
estimated from a linear regression model.
71
Poster 31
DNA of the North & South Polar Seas: Metagenomic screening of
high diversity extreme environments
Thomas Sicheritz-Ponten*, Marcelo Bertalan*, Rasmus Blom* and Nikolaj Blom**
*Center for Biological Sequence Analysis (CBS) Technical University of Denmark **current address:
Novozymes A/S, Denmark
We present a metagenomic analysis of microbial communities at some of the coldest (-1,5 C) and
deepest (4000m) parts of the polar seas. As part of the Danish marine expedition Galathea 3 in 20062007, we collected water samples in the arctic oceans around Greenland and Antarctica. The
microbial fraction was collected by filtration and total genomic DNA was sequenced using Sanger and
454 technology. 16S rRNA analysis is used to illustrate the high diversity and the distribution of
bacterial and archaeal species and compare across various depths and geographic locations. One
observation is that conservation is greater between samples at similar depths (horizontally, but far
apart ca.2000km) than between samples at the same location, but at various depths (vertically,
4000m).
In addition, preliminary results from 454 metagenomic sequencing of selected Antarctic deep and cold
stations show a high quantity and diversity of homologues to known enzymes, enzyme-like
sequences and completely unknown ORFs with potentially industrially relevant functions.
To facilitate metagenomic mining of enzymes adapted to cold and/or high pressure environments we
are currently developing an enzyme comparison pipeline. This pipeline performs comparative analysis
of protein sequences derived from different microbial environments from one or more organisms. The
analysis is automated: the input proteins are first processed by a number of analysis and prediction
methods, the results are then remapped onto a multiple alignment and compared. All the differences
found between the homologues are then projected and visualized on a 3D protein structure.
72
Poster 32
Immobilisation and Use of Thermophilic Biocatalysts in
Miniaturised Flow Reactors
a
b
b
b
b
Anne Marie Hickey , Bongkot Ngamsom , Leanne Marle , Gillian M Greenway , Paul Watts , Tom
b
a
McCreedy and Jennifer A Littlechild
a
Henry Wellcome Building for Biocatalysis, School of Biosciences, University of Exeter, Stocker Road,
Exeter, EX4 4QD, UK.
b
Department of Chemistry, Cottingham Road, University of Hull, Hull, HU6 7RX, UK.
The exploitation of enzymes for biocatalysis and biotransformation and their potential application in
new drug discovery have been the focus of much academic research. While a number of enzymes
are commercially available, their use in an industrial setting is often limited to functions that have been
proven to be cost-effective and they are rarely investigated further. However, the development of
miniaturised flow reactor technology has meant that the cost of such research, once considered costand time-inefficient, would be much less prohibitive. The use of miniaturised flow reactors for enzyme
screening offers a number of advantages over batch enzyme assay systems. Since the assay is
performed on a miniaturised scale, enzyme, substrate and co-factor quantities required are
significantly reduced, thus reducing the cost in the case of expensive substrates and co-factors for
laboratory-scale investigations.
Since they use microfluidic systems, where the substrate and
products flow out of the system, the problems of negative feedback encountered upon build-up of
products by certain enzymes are avoided.
Quite often enzymes fulfil a single use function in
biotransformation, however, enzyme immobilisation allows enzyme re-use and, in some cases, helps
to increase enzyme stability. Two enzymes with potential for biotransformation reactions have been
successfully immobilised in miniaturised flow reactors. Both are from thermophilic archaea, an Laminoacylase from Thermococcus litoralis and an amidase from Sulfolobus solfataricus.
Two
approaches to enzyme immobilisation were examined, both involving enzyme cross-linking. The first
reactor type used monoliths, to which the enzymes were attached, the second contained previously
cross-linked enzymes trapped using frits, in the microfluidic channels. Two different microreactor
designs were used in the investigation, microreactor chips for the monoliths and capillary tubes for the
cross-linked enzymes. These systems allowed passage of the substrate(s) and product(s) through
the system while retaining the enzyme performing the catalytic conversion.
73
Poster 33
Design of enzymes for natural product screening
Richard A. Engh (1), Ulli Rothweiler (1,2), Alexander Pflug (1,3), Taiana Oliveira (1), Tad Holak (2),
Dirk Bossemeyer (3)
(1) Institutt for Kjemi og NORSTRUCT, Universitetet i Tromsø, Norway
(2) Max Planck Institute für Biochemie, Martinsried, Germany
(3) German Cancer Research Center, Heidelberg, Germany
The most prominent motivation for modern bioprospecting efforts is the discovery of new drugs.
Indeed, natural substances have historically been their richest source. However, modern chemistry
and structure based research methods enable the targeted creation of chemical diversity, minimizing
some of the technical difficulties associated with natural products, in particular chemical synthesis.
The two approaches become synergistic when natural biodiversity, with its evolutionary selection of
specifically bioactive substances, can be combined with modern structure based drug discovery
methods.
As the major drug targets for cancer (and other diseases), protein kinases provide many examples of
natural products as starting points for drug development. Because initial hits will typically undergo a
series of modifications before final compounds are selected, the priority for bioprospecting screening
lies in the identification of new classes of bioactive compounds, and not in the discovery of "market
ready"
substances. As a consequence, in vitro screens that identify even weakly binding substances to a
broad class of targets, especially the protein kinases, should be designed to maximize technical
efficiency and relevant hit rates. We illustrate these principles with examples taken from current
protein kinase inhibitor research.
74
Poster 34
Antimicrobial photodynamic therapy: Minimization of compoundrelated failure by optimization of the drug formulation
Hanne Hjorth Tønnesen, Anne Bee Hegge, Tone Haukvik and Solveig Kristensen
School of Pharmacy, University of Oslo
Department of Pharmaceutics,
P.O.Box 1068 Blindern,
0316 Oslo,
Norway
Many substances that show biological effect during a screening program are discarded early in the
process due to lack of a proper formulation. For a drug candidate to be developed the compound
must dissolve in body fluids, be absorbed through a membrane and generate an adequate drug
concentration at the pharmacologically relevant site so that the desired action is obtained in a
reproducible manner. Further, the substance must possess sufficient stability to allow for production,
e.g. isolation, purification and sterilization. Most of the compounds that reach to the market have high
membrane permeability. One of the major reasons for clinical failure of a new drug substance is
therefore poor bioavailability due to low solubility, dissolution rate or high logP (octanol/water
distribution coefficient). It is postulated that >90% of new molecular entities under development have
a solubility problem. The present work focuses on the formulation of natural photosensitizers to be
used in antimicrobial photodynamic therapy (aPDT). The main advantages of aPDT are high target
specificity, few undesired side effects and almost no development of resistance mechanisms in known
pathogens. The reason for the latter is the generalized action of the light-activated drug on vital cell
structures once the drug has accumulated inside the target cell. Most photosensitizers do however;
possess poor drugability (i.e. unfavorable solubility, logP and stability). The aim of the present work is
to overcome some of these problems by developing formulations based on bioadhesive nanocarriers
like alginate based devices combined with cyclodextrins or micelles. Preliminary studies show
promising results on both gram positive and gram negative bacteria. The work emphasizes the
importance of drug formulation as part of the development process and the anticipated advantage of
developing drugs with novel mechanisms in the battle against bacterial resistance.
Selected for oral presentation
75
Poster 35
An oxidized tryptophan facilitates copper-binding in
Methylococcus capsulatus secreted protein MopE
1
2
2
2
2
Ronny Helland , Anne Fjellbirkeland , Odd Andre Karlsen , Thomas Ve , Johan R. Lillehaug , Harald
2
B. Jensen .
1
Norwegian Structural Biology Centre , Faculty of Science, University of Tromso, N-9073 Tromso,
2
Norway and the Department of Molecular Biology , University of Bergen, N-5020 Bergen, Norway.
Address correspondence to: Professor Harald B. Jensen, Department of Molecular Biology, HIB,
University of Bergen, Thormøhlensgate 55, N-5020 Bergen, Norway, Phone: +47 55 58 64 22, Fax:
+47 55 58 96 83, E-mail: [email protected]
Methylococcus capsulatus (Bath) is a gram-negative bacterium which is able to use methane as a
sole carbon and energy source. The oxidation of methane to methanol is catalyzed by methane
monooxygenase, an enzyme which is produced in two forms (sMMO and pMMO) depending on the
copper-to-biomass ratio in the growth medium. Other morphological and physiological changes in M.
capsulatus are also regulated by the copper-to-biomass ratio.
MopE ( Methylococcus outer membrane protein E) is a protein secreted into the growth medium in
large amounts when the bacterium is grown under copper-limited conditions. The crystal structure of
M. capsulatus MopE has been solved to 1.35Å and revealed a copper-binding site with a geometry
not described before, including an oxidized tryptophan and two histidines. The oxidation of the
tryptophan is essential for copper binding since MopE recombinantly produced in E. coli does not
carry the modification (demonstrated by the crystal structure), nor does it bind copper; copper is not
seen in the crystal structure, nor is it detected in ICP analysis.
The identification of the kynurenine reported here is an important observation of a structural difference
between a wild-type protein and its heterologously expressed counterpart. It thus provides a warning
example that a heterologously expressed protein does not always exert the same properties as that
from the wild-type organism. In the case of MopE, the modification takes place only when
endogenously expressed in M. capsulatus, and thus appears to be linked to its biological function. In
this case, the general use of recombinant proteins for structure studies may have made the detection
of the kynurenine elusive.
76
Poster 36
The 1.4 Å crystal structure of the large and cold-active Vibrio sp.
alkaline phosphatase
1
1
2
Ronny Helland , Renate Lie Larsen and Bjarni Ásgeirsson
1
The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037
Tromsø, Norway
2
Science Institute, Department of Biochemistry, University of Iceland, Dunhaga 3, IS-107 Reykjavik,
Iceland
The removal or transfer of phosphoryl groups is an important function in cellular metabolism and
regulation. Alkaline phosphatases (APs) are enzymes involved in removing phosphate groups from
proteins and DNA.
The AP from the cold-adapted Vibrio strain G15-21 is among the variants with the highest known kcat
value, and it is one of the largest APs identified to date. The structure of the enzyme at 1.4 Å
resolution reveals that the Vibrio AP has four large inserts compared to APs from E. coli, human
placenta, shrimp and the Antarctic bacterium strain TAB5. The Vibrio AP forms a dimeric structure,
although its monomers are without the long N-terminal helix that embraces the other subunit in many
other APs. Instead, one of the long insertion loops, previously noted as a special feature of the Vibrio
AP, serves a similar function. The "crown" domain is the largest observed in known APs, and parts of
it slopes over the catalytic site suggesting that the substrates may be small molecules.
77
Poster 37
Salmon goose-type lysozyme (SalG): kinetics, thermodynamics and
structure.
1, 2
2
2
1
2
Peter Kyomuhendo , Bjørn O. Brandsdal , Ronny Helland , Bjørnar Myrnes , Arne O. Smalås ,
1
and Inge W. Nilsen .
1
2
Nofima Marin, Tromsø, Norway, and NorStruct, Dep. of Chemistry, University of Tromsø, Norway
Animal lysozymes belong to one of three subtypes of an enzyme class that specifically hydrolyses
peptidoglycans protecting bacterial cells. Recently, vertebrates have been shown to contain two of
these lysozymes; the chicken (c-) and the goose (g-) type. We have cloned and expressed SalG, a gtype lysozyme from Atlantic salmon. Like other fish g-type lysozymes the SalG protein lacks cysteins
and hence structure-stabilizing disulphide bridges found in other vertebrates as well as in
invertebrates. We here report the following findings:
1. alternative splicing produces a protein with / without a signal peptide for secretion
2. the enzyme is cold-active as well as “thermo-tolerant” (= reversible heat inactivation)
3. differential scanning calorimetry demonstrated i) a TM consistent with kinetic results,
and ii) spontaneous refolding of SalG protein consistent with the “thermo-tolerance”
4. correct refolding and enzyme reactivation after heating is concentration-dependent
5. explanation for why goose lysozyme and not SalG is a target for the bacterial inhibitor Ivy
6. 3D crystal structure features
78
Poster 38
Flexibility studies of cold adapted uracil-DNA glycosylase from
Atlantic cod
1
2
1
2
Laila Niiranen , Netsanet Assefa Gisaw , Arne O. Smalås , Nils Peder Willassen and Elin Moe
1
1
2
The Norwegian Structural Biology Center (NorStruct), Institute of Chemistry, and Department of
Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, Norway
Abstract
Cold adapted enzymes are characterized by high catalytic efficiency, low temperature optimum for
activity and low temperature stability when compared to their mesophilic homologues. The catalytic
domain of Uracil-DNA N-glycosylase (UNG) from Atlantic cod is cold adapted and displays the
features described above compared to UNG from humans. The crystal structures of the enzymes are
very similar and consist of a classic single domain
α/β-fold with a central four stranded parallel and
twisted β--sheet surrounded by eleven α-helices.
Biochemical and structural analysis of mutants suggests that the cold adapted features of cod UNG
(cUNG) are caused by more flexible loops and a more optimized electrostatic potential around the
active site of the enzyme. The main hypothesis about the improved features of the cold adapted
enzymes is that they are more flexible compared to their mesophilic homologues, and here we
describe experiments that have been performed in order to study the flexibility of cUNG compared to
hUNG. We have performed Small Angle X-ray scattering (SAXS) experiments on both enzymes, and
analyzed their stability using Differential Scanning Calorimetry (DSC) and Isothermal Titration
Calorimetry (ITC). We have also constructed, characterized and crystallized mutants that based on
Molecular Dynamics (MD) simulation experiments were proposed to be more unstable than the native
proteins. So far, the structure of one hUNG mutant has been determined. Results from these
experiments will be reported.
79
Poster 39
Sialic acid synthesis in Aliivibrio salmonicida
1
1
2
1
Bjørn Altermark , Inger Lin U. Ræder , Martina Hadrovic , Ingar Leiros and Arne O. Smalås
1
1
NorStruct, Dep. of Chemistry, University of Tromsø, Norway
Dep. of Molecular Biology, University of Zagreb, Croatia
2
Summary:
Sialic acids are nine carbon sugars found associated with both bacterial and eukaryal cells. They are
vastly important for cell-cell communication, pathogen interaction and immune recognition. Sugar
modifying enzymes can be utilized in many different areas in molecular biology and medicine. The
combination of chemical- and enzymatic synthesis will bring forward new saccharides which can have
useful properties. The genome of the psychrophilic and fish pathogenic bacterium Aliivibrio
salmonicida LFI1238 reveals that it possesses the ability to synthesize the two sialic acids Neuraminic
Acid and Legionaminic acid. We have recombinantly expressed several of the proteins belonging to
the pathways leading to these sugars. Our aim is to understand more about the roles the sialic acids
play in the bacterium, and to characterize the enzymes which synthesize them
The sugar molecules can be modified by a whole range of enzymes that can acetylate, methylate,
phosphorylate etc. which will change the bacterium’s antigenic properties. Furthermore, knock out of
genes from these two pathways might give answers about their functions and possible roles in
virulence. Since A.salmonicida is a psychrophile, it might produce cold adapted versions of the sialic
acid synthesizing enzymes. Cold adapted enzymes are often known to be more efficient compared to
mesophilic counterparts, which renders them highly interesting as targets for commercial exploitation.
The commercial potential will be further investigated through the characterization of the enzymes.
Assays and methods for purifying and analyzing the products of the enzymatic reactions are being
developed. Other enzymes associated with the two pathways are also targeted for further studies.
The presence of a capsule, other glycosylated surface proteins and/or N-acetylneuraminic acid in A.
salmonicida will be tested. Tools like electron microscopy, NMR and mass spectrometry will be used
for these purposes. X-ray crystallography are also being used to solve the three dimensional structure
of the enzymes.
80
Poster 40
Hunting for enzymes in the cold North
1
2
1
2
3
Atle N. Larsen , Laila Niiranen , Kirsti M. Johannessen , Solrun Finstad and Nils Peder Willassen
1
MabCent-SFI and Department of Molecular Biotechnology, Institute of Medical Biology, University of
Tromsø, Norway
2
NorStruct and Department of Chemistry, Faculty of Science, University of Tromsø, Norway
3
NorStruct and Department of Molecular Biotechnology, Institute of Medical Biology, University of
Tromsø, Norway
Abstract
By far the largest proportion of the Earth’s biosphere is comprised of organisms that thrive in cold
environments and are referred to as psychrophiles or cold-adapted organisms. In order to survive and
proliferate in the harsh cold environment, marine organisms must possess a capacity to synthesize
cold-adapted enzymes. Cold-adapted enzymes have evolved a range of structural features that are
necessary to perform their action at low temperatures and are in general more catalytically efficient
and possess usually a lower thermal stability compared to enzymes from organisms adapted to
warmer
climate.
These
characteristics
make
cold-adapted
enzymes
very
interesting
for
biotechnological and industrial purposes.
Microorganisms represent an enormous reservoir of biodiversity, but only about 1 % is readily
cultivable. Using metagenomics as a tool one can in principle access 100 % of the genetic resources
of an environment. The MabCent enzyme group searches for cold-adapted enzymes by taking
advantage of a metagenomic library created from a Svalbard intertidal zone sample as well as the
fully sequenced and annotated genome of the psychrophilic fish pathogen Vibrio salmonicida. In order
to achieve a detailed picture of each target’s biotechnological and/or industrial potential, interesting
enzyme targets are submitted to a state of the art protein production pipeline including recombinant
protein expression, purification, biochemical/biophysical characterization and 3D-structure
determination.
Contact details of presenting author:
Family name: Larsen
Telephone: +47 77644478
First name: Atle Noralf
Fax: +47 77645350
Title: Dr.
E-mail: [email protected]
Organisation: MabCent-SFI and Department of Molecular Biotechnology,
Institute of Medical Biology, University of Tromsø, Norway
Address: Breivika, 9037 Tromsø, Norway
81
Poster 41
High-resolution mass spectrometry – a valuable tool for
dereplicating marine natural products
Marianne Hjerpset, Espen Hansen, Jeanette H. Andersen
Marbio and MabCent, University of Tromsø, N-9037 Tromsø, Norway
Marbio is a high-throughput platform at the University of Tromsø, Norway, for purification, isolation,
screening and identification of novel bioactive compounds from marine organisms. In order to focus
the available resources on the most promising lead candidates, a rapid and reliable identification of
known compounds is essential. This process is known as dereplication. In Marbio we use highresolution mass spectrometry to assign the accurate mass and isotope distribution of active
compounds from the screening. The elemental composition is calculated and used to search
databases in order to eliminate known bioactive compounds from further investigations.
82
Poster 42
Chemical vs. Physiological traits of common northern spring
bloom diatoms
Hansen, E.; Degerlund, M; Huseby, S; Ingebrigtsen, R.; Eriksen, G.K.; Eilertsen, H.C.
MabCent, Norwegian College of Fishery Science, University of Tromsø,
N-9037 NORWAY
Abstract
The taxonomical groups marine algae and animals contain a bevildering variability with respect to
morphology, chemistry and physiology, and some guiding principles hypothesizing “where to find
what” would be of great significance in bioprospecting as well as in ecological work. The underlying
intention legetimating all taxonomical evaluations is to be able to categorize organisms also with
respect to physiological and chemical traits. Natural variations in these traits makes it understandable
why diversity is maintained by mechanisms where organisms “outgrow” each in that they have
adapted different strategies. Examples of such traits are e.g. high growth rates at low temperatures
and production of allelochemicals. Here we compare the taxonomical status of some common
northern diatoms with their physiological ablities and chemical status, this with the intention to test the
hypothesis “Can the species concept (classical morphological or more ecologically defined) be used
to predict the chemical composition as well as physiological capabilities of organisms or groups of
organisms?”.
Selected for oral presentation
83
Poster 43
Use of an adapted Chemical Diversity Index (CDI) to evaluate
biochemical composition vs. morphological taxonomy of common
northern diatoms.
Huseby, S; Hansen, E.; Degerlund, M; Eriksen, G.K.; Ingebrigtsen, R.; Eilertsen, H.C.
MabCent, Norwegian College of Fishery Science, University of Tromsø,
N-9037 NORWAY
Abstract
Databases where organisms (species – groups) are sorted hierarchically according to “probability to
detect certain compounds” may prove a valuable tool in future bioprospecting as well as in ecological
contexts. Practicing chemical taxonomy first and foremost presupposes a reliable and up to date
“classical” taxonomical description (species – genus) as well as comprehensive chemical profiling of
the organisms in question. The challenge that arises subsequent to the laboratory analyses is: What
criteria to use to group the chemical data? Here we test out an adapted biological Similarity/Diversity
index as a tool to categorize and compare the chemical profiles of some common northern diatoms.
84
Poster 44
Mechanistic EnLightenment – Mode of Action studies on
Antimicrobial Substances with Marine Origin
1
1
2
1
1
1
Hans-Matti Blencke , Victoria Paulsen , Matti Karp , Chun-Li , Tor Haug , Sigmund Sperstad , Klara
Stensvåg
1
Understanding the mechanism of action of novel antimicrobial agents as e.g. antimicrobial peptides
(AMP) is vital, both, in terms of basic research, and for a later application as clinical tools. This is also
true for effective antimicrobial substances with unwanted side effects. This is because each new
antimicrobial substance might point to a hitherto unknown bacterial Achilles heel. This in turn can be
used to design drugs with the same target and therefore the same antimicrobial activity without having
the side effects of the originally discovered substance – the so called drug lead compound. Because
of the large variety of antimicrobial action and the large amount of hits in a HTS environment it is often
necessary to concentrate on the most interesting candidates for further characterization. Therefore
HTS methods for a quick characterization of basic modes of action together with a chemical
characterization would allow a more rational selection of new interesting hits and indicate the direction
of follow up studies.
Together with our collaborators we have been establishing a battery of methods which will allow us
to evaluate the modes of action of new AMPs. The first set of methods is designed for high throughput
screening and will allow a rapid discrimination between compounds interfering with membrane
integrity and compounds interfering with different stages of bacterial metabolism. In a later stage a
second set of methods is going to be applied to pinpoint the interaction partners of the AMPs on a
molecular level.
1 University of Tromsø, Norwegian College of Fishery Science, Institute for marine biotechnology,
Norway
2 Tampere University of Technology, Environmental Engineering and Biotechnology, Finland
85
LIST OF PARTICIPANTS
Name
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Abildgaard Christina
Abolhassani Abbas
Abrahamsen Hogne
Albrigtsen Marte
Aldridge Susan
Altermark Bjørn
Amlie Kari Elisabeth
Andersen Jeanette
Antranikian Garabed
Arnesen Jan Arne
Arntzen Dagfinn
Aune Line Kristin
Aune Trond Erik
Basnet Purusotam
Bayer Annette
16
17
18
19
Benjaminsen Arne
Berge Gunnar
Bergseth Steinar
Bertalan Marcelo
Bjørsvik Magnus
Støback
Blencke Hans-Matti
Blom Nikolaj
Blom Rasmus
Organization
Research Council of Norway/ Ministry
of Fisheries and Coastal Affairs
Azad University
NFH, University of Tromsø
MabCent-SFI, University of Tromsø
Aldridge Associates Ltd
University of Tromsø
Sigma-Aldrich Norway AS
Marbio, University of Tromsø
Hamburg University of Technology
Nofima Marin
Nerliens Meszansky AS
Ministry of Foreign Affairs
Vectron Biosolutions AS
NAFKAM / University of Tromsø
University of Tromsø
Ministry of Fisheries and Coastal
Affairs
Pronova Biopharma AS
The Research Council of Norway
Danish Technical University
NFH, University of Tromsø
NFH, University of Tromsø
Novozymes A/S
Zitogene
IRIS-International Research Institute of
24 Boccadoro Kate
Stavanger
25 Bohne Victoria
Nofima Ingredients
Norwegian University of Science and
26 Bones Atle M.
Technology
27 Buhl-Mortensen Lene Institute of Marine Research
28 Christopeit Tony
Uppsala University
29 Coucheron Dag H.
University of Tromsø
30 Danielson Helena
Uppsala University
31 Degerlund Maria
NFH, University of Tromsø
Diaz-Cidoncha
CPD Ciencia - Services Supporting
32 Garcia Alberto
Science Research
33 Dobson Alan
University College Cork
34 Eilertsen Hans Chr.
NFH, University of Tromsø
35 Eilertsen Karl-Erik
MabCent-SFI, University of Tromsø
36 Einarsson Hjörleifur
University of Akureyri
37 Elde Morten
Biotec Pharmacon
38 Ellingsen Trond
SINTEF Materials and chemistry
39 Engh Richard
University of Tromsø
40 Engqvist Magnus
Lytix Biopharma AS
Eriksen Gunilla
41 Kristina
University of Tromsø
Eriksen Tonje
MabCent-SFI, University of Tromsø
42 Engevik
43 Eriksson Jonas
Lytix Biopharma AS
44 Fegatella Fitri
Charoen Pokphand Indonesia
45 Fernandes Jorge
Bodø University College
20
21
22
23
Country
E-mail address
Category
Norway
Iran
Norway
Norway
UK
Norway
Norway
Norway
Germany
Norway
Norway
Norway
Norway
Norway
Norway
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Norway
Norway
Norway
Denmark
[email protected]
[email protected]
[email protected]
[email protected]
Norway
Norway
Denmark
Denmark
[email protected]
[email protected]
[email protected]
[email protected]
Norway
Norway
[email protected]
[email protected]
Norway
Norway
Sweden
Norway
Sweden
Norway
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
P23
S4
Spain
Ireland
Norway
Norway
Iceland
Norway
Norway
Norway
Norway
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
P2
P21, oral
Norway
[email protected]
Norway
Norway
Indonesia
Norway
[email protected]
[email protected]
[email protected]
[email protected]
P39
Exhibition
S8, Com
S10
Exhibition
P9
P31
P44
P33
86
46
47
48
49
50
51
52
53
54
55
56
57
Finstad Solrun
Fu Juan
Føre Thomas K.
Gabrielsen Kjersti Lie
Garrard Ian
Germani Valentina
Gjellesvik Dag Rune
Gloppen Hans Inge
Gogstad Geir
Gotaas Geir
Grant Ewan
Gudimova Elena
NorStruct
NFH, University of Tromsø
Norinnova AS
Marbank
Brunel University
United Nations
Biotec Pharmacon ASA
Finnmark County
Rikshospitalet University Hospital
University of Tromsø
Beckman Coulter Europe
PINRO
Norwegian University of Science and
Technology
Norinnova AS
University of Prince Edward Island
Marbio, University of Tromsø
University of Tromsø
NFH, University of Tromsø
University of Tromsø
Tromsø municipality
Marbio, University of Tromsø
University of Tromso
Troms county
University of Bergen
University of Tromsø
MabCent-SFI, University of Tromsø
Norway
Norway
Norway
Norway
UK
USA
Norway
Norway
Norway
Norway
England
Russia
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
58
59
60
61
62
63
64
65
66
67
68
69
70
71
Hakvåg Sigrid
Hall Bård
Haltli Bradley
Hansen Espen
Hansen Ida Kristine
Haug Tor
Haugen Peik
Hausberg Arild
Helland Kirsti
Helland Ronny
Helstad Kjetil
Herfindal Lars
Hjerde Erik
Hjerpset Marianne
Hjorth Tønnesen
Hanne
Hoel Grethe
Hofer Tim
Homan Evert
Hovland Ragnar
Norway
Norway
Canada
Norway
Norway
Norway
Norway
Norway
Norway
Norway
Norway
Norway
Norway
Norway
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
P13
University of Oslo
TTO Nord AS
MabCent-SFI, University of Tromsø
Beactica AB
Pronova BioPharma
Norway
Norway
Norway
Sweden
Norway
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
P34, oral
Com
P7
S22, WS1
77 Huseby Siv
78 Hustad Ulf
MabCent-SFI, University of Tromsø
SIVA
[email protected]
[email protected]
79 Iatco Iulia
Ingebrigtsen Richard
80 Andre
81 Ingebrigtsen Truls
82 Jakobsen Anne-Gry
83 Jarlbæk Henrik
84 Jaspars Marcel
85 Jensen Ida-Johanne
86 Jessen Emil B.
Johannessen Kirsti
87 Merete
Moldova Academy of Sciences
Norway
Norway
Rep.
Moldova
University of Tromsø
University of Tromsø
VWR International
Danish Technical University
Aberdeen University
NFH, University of Tromsø
Innovation Norway
Norway
Norway
Norway
Danmark
Scotland
Norway
Norway
MabCent-SFI, University of Tromsø
Norway
Tromsø municipality
University of Tromsø
Norwegian University of Science and
Technology
VWR International AS
MabCent-SFI, University of Tromsø
Troms Kråkebolle AS
Seoul National University
Northern Biolabs
Norway
Norway
[email protected]
[email protected]
[email protected]
Exhibition
[email protected]
[email protected]
S16; WS 1
[email protected]
[email protected]
[email protected]
t.no
[email protected]
o
[email protected]
Norway
Norway
Norway
Norway
Korea
Norway
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
72
73
74
75
76
88 Johansen Jan Eirik
89 Johansen Steinar
90
91
92
93
94
95
Johnsen Geir
Johnsen Åshild
Jørgensen Trond Ø.
Jørgensen Øyvind
Kang Heonjoong
Karlsen Bård Ove
[email protected]
P27
P4
S23, WS4
S7
WS3
S1
P35, P36
P41
P42, P43,
oral
P11
Exhibition
Com
S14
P28
87
96 Kennedy Jonathan
97
98
99
100
101
102
103
104
105
Kerr Russell
Kinnon Paul
Kjellsen Trine
Klinkenberg Geir
Kollboth Kjersti
Kolsvik Elin
Kotlar Hans Kristian
Kristoffersen Jan
Kyomuhendo Peter
106
107
108
109
110
111
112
113
Lale Rahmi
Lall Santosh
Landfald Bjarne
Lanes Olav
Larsen Atle Noralf
Leeson Frederick
Li Chun
Liles Mark
Lind Karianne
Fredenfeldt
Lind Rikke
Lindeman Ole
Andreas
Littlechild Jennifer
Lorentzen Marit Sjo
Lundberg Urban
Mahlapuu Margit
Malla Nabin
Marvik Ole Jørgen
Mathur Eric
McKendrick
Kimberley
McMichael Jonny
Meinicke Peter
Mykletun Jostein
Myrnes Bjørnar
Nematzadehsaeidkh
anloo Meysam
Newman David
Nicolaisen Alexander
Niiranen Laila
Nilsen Gerd
Nilsen Inge Waller
Nordal Harald
Nour Reza
Olsen Ragnar L.
Olsen Rolf Erik
Olsson Gunn Berit
Paulander Wilhelm
Paulin Lars
Paulsen Steinar
Paulsen Victoria
Pedersen Hege
Lynum
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145 Pedersen Helga
University College Cork
Atlantic Veterinary College, University
of Prince Edward Island
ZyGEM Corp Ltd
OneMed AS
SINTEF Materials and Chemistry
RDA2-Tromsø
Innovation Norway
StatoilHydro ASA
Norinnova Forvaltning AS
Nofima Marin
Norwegian University of Science and
Technology
National Research Council
NFH, University of Tromsø
Biotec Pharmacon
MabCent-SFI, University of Tromsø
Lytix Biopharma A/S
NFH, University of Tromsø
Auburn University
Ireland
[email protected]
P29
Canada
USA
Norway
Norway
Norway
Norway
Norway
Norway
Norway
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
P12, oral
S21
Exhibition
Norway
Canada
Norway
Norway
Norway
Norway
Norway
USA
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
P24
MabCent-SFI, University of Tromsø
Ministry of Trade and Industry
Norway
Norway
[email protected]
[email protected]
Ministry of Trade and Industry
University of Exeter
University of Tromsø
Orthogenics AS
PharmaSurgics AB
University of Tromsø
Innovation Norway
Synthetic Genomics, Inc.
Norway
UK
Norway
Norway
Sverige
Norway
Norway
USA
Aquapharm Biodiscovery
Charles River
University of Göttingen
Ministry of Foreign Affairs
Nofima Marin
Scotland
UK
Germany
Norway
Norway
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected].
uk
[email protected]
[email protected]
[email protected]
[email protected]
Azad University
National Cancer Institute
Sigma-Aldrich Norway AS
University of Tromsø
Biotec Pharmacon
Nofima Marin
Hyperthermics Holding as
Medinor AS
NFH, University of Tromsø
Institute of Marine Research
Nofima Marin
Orthogenics
University of Helsinki
MabCent-SFI, University of Tromsø
NFH, University of Tromsø
Iran
USA
Norway
Norway
Norway
Norway
Norway
Norway
Norway
Norway
Norway
Norway
Finland
Norway
Norway
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
University of Tromsø
Ministry of Fisheries and Coastal
Affairs
Norway
[email protected]
Norway
[email protected]
Com
S5, Com
P40
P14
S18, WS2
P10
S12, P32
S24
S6, Com
S29
P1
S19, WS2
S28
Exhibition
P38
Com, P37
Exhibition
P8
P16
S3
88
146 Perander Maria
MabCent-SFI, University of Tromsø
Norwegian University of Science and
Technology
Norway
[email protected]
Norway
[email protected]
Troms Kråkebolle AS
Norway
[email protected]
NFH, University of Tromsø
International Research Institute of
Stavanger-IRIS
University of Bergen
Marealis AS
Ohio State University
Ministry of Fisheries and Coastal
Affairs
Norwegian Ministry of Trade and
Industry
University of Tromso
Norwegian University of Science and
Technology
Tromsø
[email protected]
Norway
Norway
Norway
USA
[email protected]
[email protected]
[email protected]
[email protected]
Norway
[email protected]
Norway
Norway
[email protected]
[email protected]
Norway
[email protected]
University of Tromsø
Nerliens Meszansky AS
Bioparken AS
Calanus AS
Azad University
Azad University
University Hospital of North Norway
Norut
University of Tromsø
TTO Nord AS
University of Tromsø
Memorial University of Newfoundland
Norway
Norway
Norway
Norway
Iran
Iran
Norway
Norway
Norway
Norway
Norway
Canada
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Technical University of Denmark
SINTEF Materials and Chemistry
NorStruct, University of Tromsø
Denmark
Norway
Norway
[email protected]
[email protected]
[email protected]
University of Tromsø
University of Tromsø
NFH, University of Tromsø
Norinnova AS
Norway
Norway
Norway
Norway
[email protected]
[email protected]
[email protected]
[email protected]
Norway
[email protected]
178 Steinsli Jartrud
179 Stenberg Even
Innovation Norway
Ministry of Fisheries and Coastal
Affairs
Nofima
Norway
Norway
[email protected]
[email protected]
180
181
182
183
184
University of Tromsø
Marbio, University of Tromsø
Russian Academy of Sciences
University of Tromsø
NFH, University of Tromsø
Norway
Norway
Russia
Norway
Norway
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
S15, WS4
University of Tromsø
Norinnova AS
University of Tromsø
Medinor AS
Norwegian University of Science and
Technology
MABIT, Norinnova AS
NFH, University of Tromsø
Norway
Norway
Norway
Norway
[email protected]
[email protected]
[email protected]
[email protected]
Com
Com
WS1
Exhibition
Norway
Norway
Norway
[email protected]
[email protected]
[email protected]
Com
P19
147 Pettersen Ragnhild
Ponnerassery
148 Sudeesh
Prebensen Nina
149 Katrine
150
151
152
153
Provan Fiona
Rapp Hans Tore
Rauø Jaran
Reeve John N.
154 Riise Tore
155 Rossum Kari
156 Rothweiler Ulli
157 Rye Morten
Ræder Inger Lin
158 Uttakleiv
159 Rødsten Lise
160 Rønning Ketil
161 Rørstad Gunnar
162 Sadeghi Edris
163 Sadeghi Milad
164 Samuelsen Ørjan
165 Sandsdalen Erling
166 Savinova Tatiana
167 Seppola Magnus
168 Seternes Ole Morten
169 Shahidi Fereidoon
Sicheritz-Ponten
170 Thomas
171 Sletta Håvard
172 Smalås Arne O.
Sollid Johanna
173 Ericson
174 Solstad Runar Gjerp
175 Sperstad Sigmund
176 Steffensen Rudi
Steien Svein
177 Hallbjørn
185
186
187
188
Stensvåg Klara
Stiberg Trine
Stonik Valentin
Strøm Morten B.
Styrvold Olaf B.
Svendsen John S.
Mjøen
Svenning Sissel
Svenson Johan
Sæterøy Trude
189 Søreide Fredrik
190 Sørum Unn
191 Tadesse Margey
P6
P17, P18
S9
Exhibition
S27
P3
S25
S20
S11
P15
S13, Com,
P5
89
192
193
194
195
Tande Kurt
Thorvaldsen Steinar
Tore Normann
Tveter Ida
196 Valla Svein
Valseth Marit
197 Sommerfelt
198 Vang Birthe
199 Varmedal Ingrid
200 Vasskog Terje
201 Verwaerde Philippe
Vaagsfjord Lena
202 Christine
203 Wahl Trond
204 Wedø Charlotte
205 Wilandt Artur
206 Willassen Nils Peder
207 Zielke Matthias
208 Zotchev Sergey
209 Østerud Bjarne
210 Øverbø Kersti
211 Aakvik Trine
212 Aarbakke Jarle
Bodø University College
University of Tromsø
Norinnova AS
NFH, University of Tromsø
Norwegian University of Science and
Technology
Norway
Norway
Norway
Norway
[email protected]
[email protected]
[email protected]
[email protected]
Norway
[email protected]
S17, Com
Innovation Norway
NFH, University of Tromsø
MabCent-SFI, University of Tromsø
MabCent-SFI, University of Tromsø
AlzProtect
Norway
Norway
Norway
Norway
France
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
P20
NFH, University of Tromsø
OneMed AS
University of Tromsø
BioVico
University of Tromsø
MabCent-SFI, University of Tromsø
Norwegian University of Science and
Technology / Biosergen AS
University of Tromsø
Nofima Marin
Norwegian University of Science and
Technology
University of Tromsø
Norway
Norway
Norway
Poland
Norway
Norway
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Norway
Norway
Norway
[email protected]
[email protected]
[email protected]
S26
Norway
Norway
[email protected]
[email protected]
P25
S2
P30
WS3
P22
Exhibition
P26