MG4U profile

With the BioMarine Business Convention less than three weeks away, we'll be taking a closer look at the main sponsors and partners.

First up is MG4U...

The EU coordination action Marine Genomics 4 Users (MG4U) responds to several critical bottlenecks. It spreads results from recent and on-going projects in marine genomics and enhances rapid, efficient knowledge transfer to generate interdisciplinary research capacity in Europe. Cutting-edge genomic approaches are now sufficiently mature to advance the knowledge based bio-economy in the marine sector. Marine genomics has enormous potential to improve our lifestyles and prosperity, and to assist with governance and sustainable management of the marine environment.

Today, marine genomics knowledge is a vital part of “blue biotechnology”, and is leading to applications in the management of natural and cultured resources, and preserving marine environments. However, many business leaders and legislators are not yet aware of how marine genomics hold great potential for problem solving and industrial commercial advantage. Valuable knowledge is made accessible and disseminated in user-friendly contexts by Marine Genomics for Users (MG4U). We facilitate knowledge and technology transfer between high-throughput marine genomics, industry and society through dedicated sessions, workshops, face-to-face contacts and access to a knowledge output database.

The EU project Micro B3 on marine microbial Biodiversity, Bioinformatics, and Biotechnology will develop innovative bioinformatic approaches and a legal framework to make large-scale data on marine viral, bacterial, archaeal and protists genomes and metagenomes accessible for marine ecosystems biology and to define new targets for biotechnological applications. Micro B3 will build upon a highly interdisciplinary consortium of 32 academic and industrial partners.

Micro B3 is based on a strong user- and data basis from ongoing European sampling campaigns to long-term ecological research sites. For the first time a strong link between oceanographic and molecular microbial research will be established to integrate global marine data with research on microbial biodiversity and functions. The Micro B3 Information System will provide innovative open source software for data-processing, -integration, -visualisation, and -accessibility. Interoperability will be the key for seamless data transfer of sequence and contextual data to public repositories.

Micro B3 will allow taking full advantage of current sequencing technologies to efficiently exploit large-scale sequence data in an environmental context. Micro B3 will create integrated knowledge to inform marine ecosystems biology and modeling. Moreover, it will facilitate detecting candidate genes to be explored by targeted laboratory experiments for biotechnology and for assigning potential functions to unknown genes. Micro B3 will develop clear IP agreements for the protection and sustainable use of pre-competitive microbial genetic resources and their exploitation in high potential commercial applications.

More information...

Prediction by Tony Haymet

Tony Haymet, Director of Scripps Institution of Oceanography, Vice Chancellor for Marine Sciences-
Co-chair BioMarine since 2008 shares his views on the future of aquaculture.

Sustainable aquaculture is poised to boom in many parts of the globe. In April 2011, I had the opportunity to visit – for the first time – underutilised catfish farms near the Mississippi River. Many exciting futures were discussed, but I found myself wondering how often the ponds would be flooded. As it happened, a month later, the farms were underwater.

As the physicist Niels Bohr wryly pointed out, “prediction is always difficult, especially when it is about the future”. Statistically reliable predictions are required in many regions for aquaculture in order to estimate and amortise risk.

But aquaculture is far from alone. For many commercial activities, in addition to requiring the best science, our community is increasingly asking demanding questions on the prediction of the natural world. What useful chemicals will be discovered from the ocean and ocean mud? Will the steady trend in movement of California precipitation from snow to rain continue, or accelerate? What is the average recurrence time for earthquakes under or near California’s nuclear reactors? Will the sea level continue to rise at its current rate, or faster, or slower? Is methane gas leaking from fracking operations? From a given library of 10,000 marine compounds, how many useful pharmaceuticals may be expected?

Routinely scientists and engineers are criticised for the style of their estimates, relying as we do on “probability distribution functions” rather than “yes or no” responses. My colleagues in climate sciences are often asked to making predictions about future levels of ocean acidity, global temperature, and –yes – river flow. Of course, no one knows, nor can they know precisely. Despite our very advanced understanding of the spectroscopy of trapping heat in the planetary atmosphere, we really don’t know how much CO2 and other greenhouse gases and particulates our communities will emit over the next 50 to 100 years. Although there is no apparent sign of it today, we just might come to our senses and emit less!

Our geophysicists are frequently asked to tell the world when the “big one” will happen. They are correctly hesitant to do so, or even to frame earthquake analysis in terms of prediction. Still their work has been invaluable as a spur to preparedness. One team, for example, has detected a pattern of regularly spaced quakes in the Southern California segment of the San Andreas Fault but has noted that we are currently several decades “overdue” for the next instalment. With some breathtaking science, they attributed the delay to the diminishing weight load of the Salton Sea, an evaporating lake located 130 miles to the east of my office at Scripps Institution of Oceanography, UC San Diego. Now this same team is getting ready to survey the faultlines adjacent to the San Onofre nuclear power plant located in north San Diego County.

These researchers have done much to characterise the next quake we can expect from this region – temporally and spatially – and have succeeded in managing expectations of their predictive prowess. At least I hope so. Who can forget that Italian scientists were charged with manslaughter in 2011 for (in my own words) not successfully predicting a quake that killed 308 people in 2009. Who knows if this sort of reaction will reach California when the next catastrophic quake hits?

Quite properly, scientists and engineers respond with “if … then” scenarios, along the lines of “if we emit this many gigatons of CO2-equivalent, and this level of black carbon soot, we can expect this range of warming”. It is remarkable how often scientists and engineers are criticised harshly for responding responsibly using the “if …then” format. And yet I confidently predict that this state of things will not change soon.

Institutions such as my own will have to gear up to handle more frequent requests for larger-scale predictions. I believe that we are up to the task of helping society manage its future, but we all have a role in keeping expectations reasonable.

Read more about Tony Haymet here.

Martin Beaulieu

Martin Beaulieu co-owner and Director of Operations at innoVactiv. Rimouski, Canada 

He is also the acting Chair for the Accord Marine Sciences and Technologies Cluster. He holds a master's degree in protein chemistry and a Ph.D. in physical chemistry of polymers (Laval University).

Prior to joining innoVactiv’s team he held a research position at the Nestlé Research Center (Lausanne, Switzerland) where he was coordinating the research for Coffee Mate and Tea Time products.

Since 2004, he has been Associate Professor in the Department of Food Science and Nutrition at Laval University. Dr. Beaulieu is also a scientific advisor for various Canadian research organizations. He has conducted research visits to the Departments of Food Science of the University of Guelph (Canada) and University of Georgia in Athens (USA).

His research interests focus on the structure / function relationship of compounds from natural extracts for application in the fields of food, nutrition and cosmetics. To date, seven patents and more than sixty scientific communications are originating from the research he contributed to.

Interview: Meredith Lloyd Evans and Johanna Wesnigk, MG4U

Interview For Pierre Erwes, Biomarine 2012, Think Tank

Q1: PE to both of you: In a few words could you tell us who you are?

Johanna: I am a project manager for European research projects focussing on marine environmental, genomic and biotechnological issues. My background is in bioremediation and marine microbiology.

Meredith: I run a biosciences innovation consultancy that specialises in challenging new areas, of which blue biotech and industrial biotech are two. My background is in the pharmaceutical industry, veterinary medicine, IP management and general technology consultancy.

Q2: PE to Johanna.  For our audience could you explain the scope of marine genomics in our biomarine industry?

With Marine Genomics we can mine data, not resources. This is important, as strong points for using marine resources are the high bio- and chemical diversity in the sea, many bio-active substances are in use in the fight for survival. However, it is hard to get sufficient quantities of the resources, it’s expensive to extract them, and the harvest  of commercially useful amounts is neither sustainable nor guaranteed over time.

Marine genomics can help us with the following issues:

1. Better understanding of marine ecosystems, enhanced through in-depth knowledge of the molecular repertoire of marine organisms.
2. Insights into the large number of genes with unknown functions and possibilities to use this potential for us.
3. Utilisation of novel variations of known enzymes with improved characteristics (cold- heat-pressure stability, inert to saline environment, e.g. in the EU-funded Mamba project).
4. Determining optimum expression conditions (examples could be nitrogen limitation or light stimulation) to avoid costly high-throughput screening.

Marine environmental genomic information thus can also enable better cultivation of interesting microorganisms to learn more about their exotic enzymes which then could be heterologously expressed in the known microbial workhorses, or if we are ambitious and patient enough, in new model marine microorganisms.

Q3: PE to Meredith: BioBridge is a relay between research and industry. How do you see marine genomics applied research in major developments of tomorrow’s biomarine industry?

Johanna has highlighted the main attractions; the key is to marry together some interesting industrial needs with the possibilities we have. Needs we know about include new enzymes for green applications – biocatalysis, avoidance of petroleum-dependency, reduced energy and carbon use; new therapeutic agents for difficult diseases (not just cancers); and robust and novel materials, some of which may even be capable of taking their place in nanotechnology and new data-processing methods, as well as for industrial and medical uses. Exploring Blue Biotech also gives scope for innovation in the important support areas of laboratory-based analytical technologies, micro-engineering and microfluidics, extreme-environment engineering and new bioprocess systems.

In all of these, marine genomics plays a role – in identifying the targets, in collaborating with modern genetic engineering and synthetic biology, in ensuring that engineering innovation is appropriate, in addition to stimulating the search to pin down what previously unknown genes may actually do.

Q4: PE to Meredith. Most of the projects in marine genomics are conducted by innovative SMEs, unfortunately after a few years they tend to disappear. What is the blocking factor to their development and what are the winning strategies for SMEs in Europe versus North America.

The blocking factor in Europe is usually insufficient funding for the pre-profit trajectory of a company. Those that focus on using marine genomics as a service or contract research tool may indeed survive because of this, since they can achieve cash-flow if they are effective as deliverers of what industry wants. I generally take it as a ‘rule of thumb’ that the US has at least 10 times as much money available for investment in start-ups and is several times more willing to invest in innovation than is the case in Europe. Also, there is a strong support in USA for government-funded SME links with innovative research, to embed new science in companies. National and EU funding in blue biotech has been poorly correlated and aligned in the past; SMEs often found it hard to be involved in and benefit from EU consortia, for example. This is hopefully changing.

Q5: PE to Johanna. MG4U is a European program dedicated to marine genomics. Could you tell us what are the main points of interests and what is at stake?

MG4U is “Marine Genomics for Users” in full. Our remit is to spread knowledge on the manifold outcomes of national and international research projects on marine -omics, from the FP6 Network of Excellence MGE to new large projects like the French Oceanomics and the European Micro B3. We are addressing marine researchers, policy makers and especially industry, potentially interested in the many innovative developments for diverse sectors. Tools within MG4U are a knowledge database, workshops and training courses, dedicated MG sessions at conferences and establishing/furthering one-to-one contacts between academia and industries.

Q6: PE to Johanna: when it comes to the necessary tools used in marine genomics Bioinformatics is always top of the list. Could you explain the concept?

In -omics you have to deal with increasingly large amounts of sequence data, esp. since the high-throughput and next-generation sequencing technologies have taken over and data are “exploding”. Thus novel bioinformatics techniques and infrastructures are urgently needed to turn data into sensible information and into knowledge. This ranges from data- and quality management (cleaning), aligning, annotating the raw data; to data-mining, text-mining, data integration, statistics and modelling tasks. To make ultimate sense and predict, e. g. novel functions of genes, genomic data need to be merged with environmental, biological and biochemical knowledge. This has led to a new discipline called environmental bioinformatics, which will be addressed in the Micro B3 project. Starting out as a set of techniques bioinformatics has become a technology and a new research discipline. Also companies are emerging to provide bioinformatics services.

Q7: PE to Meredith & Johanna: In October in London both of you will be involved in one of the Biomarine Think-tanks on marine biotechnology. What do you expect from such a brainstorming?

We are working together to encourage industry to propose strategic needs where a better understanding of genes and their functions is going to make a difference. One outcome should be enhanced understanding between industry and academia of marine-genomic based processes of interest leading to industrial bio-products. Also, part of the function of a think-tank like this is to create new contacts and networks, with a view for future activities. So, questions to answer are
            what are topics/areas/ approaches for industry-academia cooperation for marine biotechnology, and
            how can typical problems i.e. those between industry and researchers or those facing        industry in establishing new developments be solved or avoided?

We also see that big industry understands and uses genomics in many ways already, so we want to investigate not only
            what the overall research needs of industry are but also
            how SMEs can be enabled to use the marine bioresources potential, and
            what kind of research collaboration they are open for, and what they would pay for?

We need to define the exact area in this value chain, where academia can hand over research results to industry. At the moment it seems too often that industry wants things ‘on a plate’ - which is far too far along the chain, and too expensive, for most research innovators to achieve, even with government funding support for collaborations.

Finally, we will use the think-tank to set some of the agenda items and identify some of the contributors for the BioMarine 2013 conference.

Q8: PE to Johanna: You are familiar with European project funding processes. Do you know if marine genomics is still a priority for the European Commission? Could you elaborate?

In the final stages of FP7 marine biotechnology and environmental genomics can be found as part of many medium and large projects, in the Ocean of Tomorrow calls, as well as in dedicated KBBE and a few environmental calls. In basic research funding the ERC (European Research Council) grants often include -omics elements as they are an integral part of many marine, environmental and life sciences research questions.

As to the future within Horizon 2020, not too much detail has been put down yet. The ERC grants will continue, with the new team “Synergy” grants potentially enabling even larger ‑omics projects to be tackled. Marine and maritime research will be a part of the KBBE societal challenge sub-programme, thus applied projects will become stronger. Finally biotechnology is named as one of the Key Enabling Technologies, with marine input as a potentially very innovative element in technology development, as we tackle very diverse taxa from which are emerging new model species and novel knowledge, e.g. on evolution for certain biotech applications.

So there are three major opportunities for marine -omics to be funded, from creating new knowledge, to addressing societal challenges, all the way to biotech demonstration plan(t)s.