www.ntnu.no/bioteknologi

Annu

al Re

port

2009

Department ofBiotechnology

DEPARTMENT OF BIOTECHNOLOGY, NTNUSem Sælands vei 6/8, 7491 Trondheim, Norway

Phone: +47 73593320 Fax: +47 73591283E-mail: postmottak@biotech.ntnu.no

Head of Department: Kjetil Rasmussen

Vice Head of Department: Professor Kjell M. Vårum

COVER PAGE (Illustration by Edwin Hadley, Univ. of Illinois)

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CONTENTS 1. INTRODUCTION ………………………………………………………………… 4 2. RESEARCH………………………………………………………………………... 5 3. PhD DISSERTATIONS……………………………………………………………. 15 4. PUBLICATIONS…………………………………………………………………... 23 5. EDUCATION………………………………………………………………………. 32 6. ECONOMY………………………………………………………………………… 36 7. LUNCH SEMINARS………………………………………………………………. 37 8. PERSONNEL………………………………………………………………………. 39

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1. INTRODUCTION The Department of Biotechnology has approximately 80 employees. This number has been fairly constant during the last several years. The Department has integrated research activities within the following areas: - Biopolymer chemistry. - Marine biochemistry and bioprospecting. - Molecular genetics, metabolomics and systems biology. - Structural biology and NMR. - Microbial ecology and environmental biotechnology. - Food science. 2009 was a good year for the Department. Most target figures, by which we are commonly judged, increased substantially. From 2007 to 2008 there was a nearly 50% increase in publication points and there was a furter increase by 20% from 2008 to 2009. The Department educated eight PhD and 27 MSc in 2009. It is expected that the number of PhD candidates and the number of MS students will remain high the coming years. The Department is also proud of presenting the target figures related to innovation. Six of NTNUs eight license-agreements came from our department in 2009. It is gratifying that we have experienced that the examination grades of the students have improved and that fewer students fail. We believe that this good trend is, in part, due to increased focus on teaching quality and evaluation of our courses during the last few years. However, we regret that we for economical reason have had to terminate a major laboratory course in biochemistry. On the positive side, we have established a new introductory course in biotechnology which our students have longed for. In addition, we hired senior engineer Martin Gimmestad in August 2009. Gimmestad will both coordinate and take part in teaching our lab courses. Furthermore, in 2010 we will hire a student advisor so that we can offer a better service to all of our students. The Department has been very successful in attracting external funding. For 2009, this funding increased by 49%, exceeding our university budget with 70%. Our research activities are to a large extent based on international and national collaboration, with both large and small projects. During the last year two large projects were initiated. These include the Strategic University Program (SUP) entitled “Development of versatile bacterial expression systems for use in recombinant protein production, metabolic engineering, and systems biology” led by prof. Svein Valla. Prof. Valla is also the project leader of the NTNU-part of the MARZyme project which is a collaboration between research groups at the Umeå University, the University of Tromsø and NTNU. Our project portfolio also

includes many small projects which together give a considerable income, showing that many researchers in our Department are active and successful in grant application. Currently, there is extensive focus on seeking grants from the European Union. In 2009 the EU-project "Promicrobe, Microbes as positive actors for more sustainable aquaculture" was established with prof. Olav Vadstein as NTNUs project leader. The Department has extensive collaboration with SINTEF Materials and Chemistry and SINTEF Fisheries and Aquaculture. Together with the former SINTEF organization, we have continued to develop the mass spectroscopy laboratory for rapid and accurate identification of metabolites (low-molecular-weight cell components) and the high-throughput screening laboratory for automated handling of microorganisms and chemical and enzymatic analyses. These laboratories are of major importance for research projects within systems biology, bioprospecting and several other research projects at our Department. Together with the Department of Chemistry, Department of Biology and SINTEF Materials and Chemistry we are now planning the establishment of an MS-consortium. In August 2009, prof. Arne Strøm retired from his professorship as well as his position as the Head of Department. Engineer Øyvind Johansen retired in October 2009. We are very grateful to them both for many years of positive contributions and great efforts to the wellbeing of the Department. Professor Strøms position has allready been replaced. In Agust 2009 we were happy to welcome prof. Eivind Almås as our new collegue. Professor Almås will work in the field of systems biology. Johansens position will be replaced in 2010. Kjetil Rasmussen Head of Department

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2. RESEARCH Biopolymers and biomaterials – research by NOBIPOL

NOBIPOL (The Norwegian Biopolymer Laboratory) is a multidisciplinary research group within NTNU devoted to the fields of biopolymer engineering and biomaterials, with main focus on the science and technologies of marine polysaccharides, in particular alginates and chitosans. Major collaborating departments at NTNU include the Department of Physics, and the Department of Cancer Research and Molecular Medicine. NOBIPOL also collaborates extensively with SINTEF and industry. Together with the Research Council of Norway NOBIPOL is currently project leader of two KMB projects: Biopolymer Engineering (2007-2012/Partners: SINTEF, FMC NovaMatrix, Ayanda AS, Aqua bio technology ASA, Biotec Pharmacon, and from 01.01.2010 Seagarden A/S) and Microbiocidal coatings (2006-2009/Partner: Tine AS). NOBIPOL is involved in an Ingrated EU project “Bioproduction”, has become partner in a new EU-project entitled “β-cell therapy” and is involved in the “Chicago Diabetes Project”. In addition, NOBIPOL is responsible for or participates in 10-15 externally financed projects. Alginates; new enzymes and sequencing A mutant library of epimerases (>50000) has been created using an error prone PCR approach and effective enzymes are selected using a robotized high throughput screening system. We are now analysing a range of promising candidates in particular some with capacity for generating long G-blocks. The same approach has also given us new alginate degrading enzymes (lyases) with improved specificities.

Together these new enzymes are valuable tools in our new sequencing protocol for alginates. The first sequencing data (block distribution and block length analysis) has been carried out on selected polymers. Based on our patented technology for chemo enzymatic modification of alginates we have produced a range of alginates grafted on the M residues with peptide RGD ligands. The material is currently being tested in various cell models. Cell encapsulation and tissue engineering Activities within tissue engineering have mainly been in connection with the Chicago Project, an international collaboration for a diabetes cure. Human insulin producing pancreatic islets were encapsulated in TAM (Trondheim alginate microcapsule) and cell function evaluated in mice without an immune system. Capsules containing human islets were shown to cure diabetic mice up to the end of the study, 330 days after transplantation. The capsules ability to protect the graft against host destruction was also found to be very promising as encapsulated human islets were protected against the immune system of mice and allowed for the curing of diabetic mice for 100-200 days post transplantation. The cause of failure at a very late stage is the current focus of the research together with baboon studies. Stability of capsules and leakage of capsule products in vitro and in vivo are also being studied. A recently established human full blood assay enables the comparison of different capsules and capsule components in a pre-clinical model of biocompatibility. Capsule properties such as swelling and permeability can be improved by using epimerized alginates. The use of epimerized alginates have allowed a further understanding of the function of alternating sequences in the alginate gel, and functional properties of alginate gels can be tailored. Ongoing studies include cell growth and islet viability in capsules of epimerized alginates. Our research project on immune-protective microcapsule for transplantation of insulin producing cells is ongoing in cooperation with the Chicago Diabetes Project. In addition to ion cross-linked alginate gels, we work on other alginate based materials for tissue engineering including covalently cross-linked alginates, RGD-coupled alginate, alginate/lactose-modified chitosan hydrogels and bio- mineralization of alginate gels.

Academic staff: Christensen, Bjørn E. Professor Skjåk-Bræk, Gudmund Professor Vårum, Kjell Morten Professor Valla, Svein Professor Draget, Kurt Ingar Adjunct professor Smidsrød, Olav Professor emeritus For information regarding staff at other departments, and post docs, Ph.D.-students, please visit our website: http://www.biotech.ntnu.no/nobipol/

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Tissue engineering: Alginate foams Highly purified polysaccharides possess properties making them suitable for preparation of synthetic extra cellular matrices (ECM) relevant for immobilization of cells and tissue regeneration. A new project (Ph.D.-student) focusing on alginate based foams was initiated in 2007 in collaboration with FMC NovaMatrix. Non-viral gene delivery with chitosan New insight into chitosan gene delivery systems have shown that an optimized balance between the stability and the unpacking of the Chitosan-DNA complexes are crucial in order to enhance gene expression levels. Chitosan characterization The relatively high specificity of (concentrated) acid degradation of chitosans has been utilized, where the cleavage rate of a glycosidic linkage following an acetylated unit is about 50 times the cleavage rate following a deacetylated unit. This has been utilized to develop a new method to determine the block length distribution of deacetylated units. The distribution shows that chitosans produced by homogeneous and heterogeneous deacetylation processes show very different block length distribution. Carbonyls in polysaccharides Introduction of small amounts (1-10%) of carbonyls (ketones, aldehydes) in polysaccharides may lead to profound changes in the chemical stability (‘hot spot’ for degradation) and changes in solution properties and interactions with other polymers. A new method based on selective fluorescent or isotope labeling combined with multidetector SEC has been developed in collaboration with Universität für Bodenkultur Wien. We have applied the methods to detect and quantify carbonyls in periodate oxidized alginates, pullulan, dextran as well as Sphagnum pectin. In chitosans, periodate selectively reacts with GlcN residues, leaving GlcNAc intact. Partial oxidation (2-10%) opens the GlcN rings, resulting in a highly flexible joint in an otherwise stiff polymer. Oxidized and unoxidized chitosans, with different FA (content of GlcNAc), were studied by multi detector SEC. We concluded that the intrinsic chain stiffness of chitosans

is only marginally dependent upon FA, but decreases upon oxidation. Interestingly, chitosans are more flexible than mannuronan (homopolymeric alginate), which share the same cellulose-like backbone geometry with chitosans. Oxidized chitosans turn out to have different solubility profiles, and are promising candidates for several biomedical applications such as DNA/siRNA vectors, drug delivery and tissue engineering. Paper ageing In 2007 we started collaboration with SINTEF Energy to study the macromolecular events associated with paper ageing in electrical transformers. The ageing will be monitored at the micro- and nanoscale (SEM, TEM, FT-IR) and at the molecular level (multidetector SEC, microcalorimetry) Marine gelatins Basic research has focused on the improvement of physical properties of marine gelatins by optimizing the extraction conditions. It has been shown that fish gelatin from cold water fish species extracted at room temperature provides gels with higher melting temperatures compared to previous observations (up to 18.5oC). The presence of high molecular weight components is important to achieve such melting temperatures and it has also been found that the presence of low molecular weight molecules perturb and decrease the gelling properties of gelatin. These studies strongly suggest that the standard procedure for the manufacturing of mammalian gelatins is not required nor desired for the production of fish gelatins. The applied research activity has been in cooperation with Ayanda AS, and has focused on issues such as nutraceutical formulations. Several patents regarding a new vehicle for delivery of omega-3 fatty acids to children has been filed during the last five years and by the end of 2009 the manufacturing of this new product was started by Ayanda AS in Båtsfjord, Norway. Alginate oligomers in pharmacy Guluronate oligomers from alginates, manufactured from high-G alginates by hydrolysis and specific extraction procedures, have shown a great potential to modify the mechanical properties of mucin network

To the left: Alginate capsules made from fluorescence labelled Ca-alginate (optical slice of the capsules equator). Photo: Yrr Mørch. To the right: Encapsulated endostatin producing cells (stained with live/dead kit). Photo: Anne Marie Rokstad. Both images are taken with confocal microscopy (CLSM).

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structures. This externally funded research has led to several patents, owned by NTNU's Technology Transfer Office, covering IP both on the treatment of highly viscous mucin secretions as well on drug delivery. Licence agreements have been obtained, and clinical phase 1 has been completed and phase 2 studies on cystic fibrosis symptom relief is planned to commence in 2010. Food coatings and pads The preservative and apparently antimicrobial properties of Sphagnum mosses have been studied with the aim of exploitation in food preservation. A 3 year KMB project involving Tine AS and the Veterinary College (Oslo) was completed in 2009. The project led to a complete revision of the theory for antimicrobial effects. Biologically active β-glucans from Saccharomyces NOBIPOL started a new project as part of a KMB (see above) to investigate macromolecular properties of a commercial preparation of glucans manufactured by Biotec Pharmacon. Several new approaches to study individual macromolecules and their rather peculiar aggregated states have been introduced.

Assosiated with NOBIPOL Researchers: Carlsen, Anne-Ma MSc Ertesvåg, Helga PhD Haug, Ingvild J. PhD Kristiansen, Kåre PhD Mørch, Yrr PhD Strand, Berit L. PhD Strand, Sabina P. PhD Taylor, Cahterine PhD Aachmann, Finn PhD Technical staff: Hansen, Anita I. Strand, Wenche Syversveen, Marit Ulset, Ann-Sissel

Uptake of pDNA-chitosan nanoparticles in HeLa cells. Chitosan was labeled by Alexa 647 (red) and DNA by YOYO-1 (green). Cell nuclei were stained by Hoechst.

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Interactions in planktonic food webs. Copepods and ciliates compete for the same prey, but copepods eat ciliates. (Photos E. Leu, N. Tokle, T. Bardal).

Environmental Biotechnology and

Microbial Ecology

Overview Environmental biotechnology is the application of biotechnology for solving environmental problems, both in the environment per se (e.g. bioremediation) or in man made ecosystems (e.g. sewage treatment plants). Environmental biotechnology searchs for technologies that are in accordance with ecological principals, based on a “join them” instead of a “beat them” strategy. Microbial ecology, defined as scientific studies of interactions and basic principles that determine the distribution and abundance of microorganisms, is therefore a basic platform for analyses of problems and for development of technologies. The group is involved in teaching general microbiology, environmental biotechnology and microbial ecology. The research includes studies in both natural and human created ecosystems. The research is coordinated with various groups at NTNU and SINTEF, and involves cooperation both nationally and internationally. A large part of the work is a part of one of NTNU strategic areas – Marine and Maritime research, and is thus coordinated inter departmentally and inter faculty. The main research areas of the group include the following:

Microbial management of marine fish larvae Interactions between fish larvae and bacteria are key factors for development, survival and growth of larvae, and dependent on the bacterial community it may be either detrimental or beneficial. The research within this area includes monitoring of bacterial communities using culture dependent and independent methods, screening for and use of probiotic bacteria (including mechanisms of action), and controlled recolonization of water. Recently we have developed procedures for establishing bacteria free cod larvae as a tool for studying bacteria/larva interaction in gnotobiotic systems. This tool combined with gene expression studies in fish larvae is assumed to boost progress in studies of bacteria/larva interactions, and we are among the first labs in the world to establish bacteria free fish. Recent experiments have revealed that presence of bacteria resulted in a significant up or down regulation of a variety of genes in the host, and the response was dependent on the bacterial species present and whether bacteria were alive or dead. One post doc, one PhD student and several master students have been connected to these activities. Disinfection of ballast water Ballast water from ships is a continuing threat to ecosystem structure and functioning through the introduction of alien species. A new international convention is to be implemented to avoid the problem, but it will require establishments of appropriate disinfection/treatment technologies and strategies. So far focus has been on multi cellular organisms, but our group has focused on inactivation strategies and techniques for bacteria. Our focus has been on limitations of today’s disinfection technology, production of substrate for bacteria due to disinfection, and recolonization of treated water. In laboratory studies we have shown that the disinfection entails an increase in easily degradable organic matter, and thus a substantial increase in bacterial production. One PhD student has been connected to this activity. Biological N removal from process waste water of a CO2 capture plant Combustion of fossil fuels constitutes a major man-made contribution to global warming of our planet due to the greenhouse effect of CO2. Post-combustion capture has been seen as the easiest method to reduce emissions from large point sources such as power plants based on fossil fuels. Such capture may be achieved by absorption with amines. However, a significant operational problem at full scale will be a gradual loss of amines due to irreversible side reactions. Recycled wash and process water must therefore be bled from the system to allow replenishment. This produced waste water may contain large amounts of ammonia as a major degradation product as well as contaminating

Academic staff Professor Kjetill Østgaard Professor Olav Vadstein For information on other participants in the group: www.ntnu.no/bioteknologi/miljobiotek

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levels of the actual amine applied. This is a special waste effluent that should be treated accordingly. Biological N removal is a well established method in wastewater treatment, generally based on a two-step process: The first step denoted nitrification includes lithoautotrophic bacteria that will oxidise ammonium to nitrate. In the second step denoted denitrification, facultative heterotrophops reduce nitrate to nitrogen gas by anaerobic respiration. Long-term model studies have been performed with moving bed biofilm lab reactors, using monoethanol amine (MEA) mixed with ammonia in our wastewater model mix. When interconnected in a post-denitrification configuration, efficient N removal was obtained by adding ethanol as a carbon source for the dentrifying step. When a pre-denitrification configuration with recycling from a second nitrifying reactor was applied, successful N removal was established even with MEA as the only carbon source. Thus, this approach has been shown to be feasible. Other relevant amines are currently being tested. Our research is run in close cooperaton with SINTEF Process Technology as a part of the SOLVit programme involving SINTEF, NTNU, Gasnova and Aker Clean Carbon. Renewable sources for biofuels Raw materials for 2nd or 3rd generation biofuel need to resolve the “food versus fuel” conflict and entail less CO2 emissions during production. Microalgae can be produced with higher yield per area than traditional plants, will not be in conflict with cultivation of food for humans, and in the case of marine microalgae will not be a competitor for fresh-water. We participate in a project “Optimizing Lipid Production by Planktonic Algae” (LIPIDO), initially financed by Nordic Energy Research and continuing with support from the Norwegian Research Council. LIPIDO is coordinated by the Finnish Environment Institute, with collaborating groups in Norway, Germany and Iceland. The goal of the work at NTNU is physiologically oriented and aims to find environmental factor that are critical for the switch between cell division and lipid accumulation. Focus is on growth limiting factors and light regime. We have developed an experimental system for flexible cultivation of microalgae: Algal density is continuously monitored by pigment insensitive optical density measurements and cultivation mode can be varied between batch, fed batch, chemostat and turbidostat. The effect of nutrient stress on lipid content has been studied in the two microalgae Phaeodactylum tricornutum and Isochrysis sp., both under steady state conditions and in detail during 24 hour studies of variations in light and dark periods. One Post. doc. and two master students have been connected to this project.

Ethanol from seaweeds is another form of biofuel, successfully developed in our earlier “Energy from macroalgae” Hydro/NFR project. Current cooperation with Sintef Biotechnology 2009-10 is trying to improve yield of such production by including the alginates of the brown seaweeds in addition to the the previous methods developed for their laminaran and mannitol content. Biogas production may represent an efficient utilization of biodegradable wet organic waste, with an energy potential of about 6 TWh for Norway. Livestock manure constitutes 42% of this. From 2009 on we participate in the NFK financed project “Biogas Trøndelag” on biogas production from cow manure. By utilizing the pilot plant facilities at Bioskiva AS, long-term batch culture development of biogas producing microbial communities are studied in particular at mesophilic conditions. In cooperation with the project partner Sintef Biotechnology, chemical analysis is combined with culture independent microbial methods to monitor the process, in particular how methanogenic Archaea grow and develop over time. Preliminary results are promising. Structure and functioning of natural planktonic ecosystems Natural ecosystems are influenced by a variety of man-made disturbances, including nutrient emissions, pollutants and global warming. Ecosystems have a limited ability to manage such disturbances without loss of ecosystem integrity. Knowledge on this “buffer capacity” of planktonic marine systems is limited, but to provide such information has been a key topic of the group. Lately the focus has been on the primary producers – grazer interactions and with particular emphasize on the impact of omnivory (i.e. one species feeding on several trophic levels, see introductory picture). One PhD-student has been connected to these activities.

Exponentially fed-batch cultures of the diatom Phaeodactylum tricornutum grown under different nutrient conditions: Nitrogen-limitation, full medium and P-limitation. (Photo M Chautón)

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Molecular Biology and Microbiology

Bioprospecting for new antibiotics in the Trondheim fjord Zotchev’s group In this project, we collaborate with SINTEF’s Department of Biotechnology and University of Bergen. We have identified several new biologically active compounds produced by bacteria isolated from upper water layer, sediments, and sponges collected in the Trondheim fjord. Some of the compounds have been purified, their structures determined, and biological properties investigated both in vitro and in vivo. New macrocyclic lactam ML-449 with anti-bacterial and anti-fungal activity produced by Streptomyces bacterium isolated from the Trondheim fjord sediment (Jørgensen et al., 2010, Appl. Envirion. Microbiol. v.76).

We also continue to characterize our bacterial collection through screening, taxonomical analysis, and genetic studies on bacteria from different marine sources (Hakvåg et al., 2009, Mar Drugs v. 7; Jørgensen et al., 2009, Appl. Environ. Microbiol. v. 75; Ian et al., manuscript in preparation). Deciphering antibiotic biosynthesis pathways Access to the genes for antibiotic biosynthesis can provide new possibilities for drug discovery and development. Through changing the biosynthetic genes, it is possible to change the structure of antibiotic molecules, and improve their properties (see www.biosergen.com). We have cloned and analyzed biosynthetic gene clusters for 2 macrolactam and 1 thiopeptide antibiotics from the Trondheim fjord bacteria. Based on the bioinformatic analyses and experimental data, new and unusual biosynthetic pathways have been deduced (Jørgensen et al., 2009, Chem. Biol. v. 16; Engelhardt et al., manuscript in preparation). This information can become useful for design of new drugs. Genome-based bioprospecting We have obtained draft genome sequences of 8 bacterial species isolated from the Trondheim fjord. Genome annotation and gene mining have revealed a large number of undescribed antibiotic biosynthesis gene clusters and unique enzymes with industrial potential. Methods for efficient utilization of these ”genomic treasures” are being currently developed in collaboration with the group of Professor Svein Valla (SUPtek project).

Academic staff David W. Levine Professor Arne Strøm Professor Svein Valla Professor Sergey Zotchev Professor Per Bruheim Associate professor Alexander Dikiy Associate professor Åge Haugen Adjunct professor Jens Nielsen Adjunct professor Trond Ellingsen Adjunct professor

Initiation of the biosynthesis of the macrocyclic lactam BE-14106 (Jørgensen et al., 2009, Chem. Biol. v. 16).

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Alginate Research and Systems Biology Headed by professor Svein Valla and research scientist Helga Ertesvåg Alginate research has been a major topic for a large number of years at our Department, and the molecular biology of synthesis of this industrially important biopolymer has been extensively studied in the bacteria Pseudomonas fluorescens and Azotobacter vinelandii. In 2009 we published the genome sequence of A. vinelandii strain DJ as part of a large consortium collaboration involving several countries. The annotated genome enabled us to mine the genome for alginate-related genes, and the discovery of three new alginate lyases has been published. Alginate lyases have the potential to be used as tools for determining the amount and composition of alginates, and this study was a part of ongoing work aimed at discovering lyases with optimal properties for these purposes.

Another major activity related to the alginate field is Systems Biology, which is an European ERA-Net project coordinated by our group. Partners are from Sweden, Germany, England and locally also SINTEF. In this project large data-sets have been generated in 2009, involving all levels of “omics” analyses, and a computer-based model of carbohydrate metabolism in the organism has been constructed. The model includes all metabolic steps that can be deduced from the genome sequence, including transport processes. The idea is to later use the model to simulate the metabolic network and to help predict how modifications of specified gene activities will influence the synthesis of alginate. We have also screened about 11000 mutants in which genes are randomly inactivated throughout the entire genome. This screening has resulted in the identification of a large number of new and unexpected genes that are required for alginate biosynthesis. Ideally the model described above should be able to explain why these genes are required, and they therefore serve as a test of the validity of the model.

Illustration of the A. vinelandii cell and the key proteins involved in respiratory protection. A number of alginate biosynthetic proteins are produced that direct the formation of an alginate coating around the cell, acting as a physical O2 barrier (black lining). Respiratory proteins including 5 terminal oxidases (dark blue), 4 NADH-ubiquinone oxidoreductases (light blue), 2 ATP synthases (orange), and other proteins involved in respiratory protection (lavender) provide the second line of defense against O2. Proteins sensitive to O2 exposure are outlined in green boxes. (Setubal et al 2009, J. Bacteriol. 191:4534-45)

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Recombinant gene expression and metagenomics Headed by professor Svein Valla This activity concerns the development of recombinant gene expression methods in bacteria. In 2009 we have published four papers in this field, describing the ways to control the gene expression at the levels of transcription and translation. A regulated expression system consists of several elements: a promoter, a regulator of the promoter, a 5' untranslated region, and a gene of interest. We have introduced mutations into these regions (except the gene) in order to study their function in transcriptional and translational processes. These studies resulted in findings that allow us to exert control on expression, i.e. by using the modified element desired expression levels can be obtained. In 2009 we became a partner of a project that aims to identify cellular systems, genes and molecules from marine microorganisms in the Arctic region. This project, MARZymes-Novel enzyme activities from environmental libraries, is a collaboration between the University of Tromsø, Umeå University (Sweden) and NTNU. Our main contribution to this project is to provide bacterial expression platforms that will be used for expressing the genes found in the Arctic region. Yeast – a eukaryote model system to explore DNA damage responses Per Bruheim The yeast Saccharomyces cerevisiae (also known as bakers yeast) is widely used as a eukaryote model organism because of the simple growth requirements, rapid cell division, and ease of genetic manipulation and wealth of experimental tools for genome-wide analysis of biological function, including comprehensive mutant collections that are available for all researchers at reasonable prices. It has been proposed as a suitable tool for identifying human drug targets because > 40% of yeast proteins share some conserved sequence with at least one known or predicted human protein. Furthermore, many pathways are conserved between yeast and human. To form the basis for identification of new genes/ proteins in the DNA damage response of both yeast and mammalian cell an internal research project at NTNU (Department of Biotechnology and Department of Cancer Research and Molecular Medicine) and SINTEF Materials and Chemistry, Department of Biotechnology has been initiated. The project has run for nearly two years with the aims 1. To establish a Yeast System

Biology platform, and 2. To generate results and publications necessary for attracting external funding. It combines basic research in yeast and human cell culture with focus on the important cellular processes to maintain genome integrity. Through this project we expect to identify new proteins and mechanisms important in the DNA damage response. We have used two different experimental approaches: 1. High resolution genome-wide phenotyping using a yeast gene deletion mutant collection with over 5000 mutants and 2. Chemostat cultivations with time series transcriptomics sampling at steady-state conditions. In both approaches, we have used MMS (methyl methanesulphonate, 5-fluorouracil (5FU) and Cisplatin (the two latter are in therapeutic use as anticancer agents) to impose the DNA damage response. The three compounds have different mode of action: MMS is an alkylating agent, 5FU an antimetabolite and nucleoside analog and Cisplatin causes DNA interstrand crosslinks, and will therefore result in different cellular responses. A complete phenotype screen generates over 15 000 growth curves and it is a challenge to efficiently analyze the data to identify mutants with either an increased sensitivity or resistance to the DNA damaging agents. Software for this purpose has been developed, and so far we have identified over 200 mutants with significantly altered phenotype compared to the wild type parental strain. We find that many hits in the phenotype screen and gene expression studies confirm present knowledge. This validates our novel experimental approach. In general, and maybe somewhat unexpectedly, more than 90% of genes that, when deleted, affect DNA damage recovery is not found among the genes that shows changes in expression level upon damage exposure. Thus, neither transcriptional profiling alone nor genomic phenotyping alone, adequately defines the cellular response to DNA damage agents. In conclusion, during this internal project we have established the basis for Yeast Systems biology and a publication based on the most important results is under preparation. Time-series Transcriptome and Metabolome analyses of Yeast Chemostats pulsed with DNA damaging agents.

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Food Science Overview The main research field of the food science group is research on the biochemistry and quality of food raw materials and the changes taking place during processing. Norway is the world’s largest net exporter of seafood. The main focus is research on marine raw materials. In 2009 nine master students graduated (five masters in Technology and four masters in Biotechnology). Two PhD candidates defended their theses. Inger Beate Standal defended her thesis with the title Use of NMR spectroscopy in combination with pattern recognition techniques for elucidation of origin and adulteration of foodstuffs in June 2009. Ida Grong Aursand defended her thesis with the title Low-field NMR and MRI studies of fish muscle in July 2009. Marine by-products Marine by-products are a valuable raw material which can be utilized to produce food ingredients, health food products, pharmaceuticals and cosmetics. Globally more than 91 million tons of fish and shellfish are caught each year. Some of the by-products are utilized today, but huge amounts are wasted. Annual discard from the world fisheries were (FAO) estimated to be approximately 20 million tonnes (25%) per year. Therefore it is a great potential for the fishing industry to utilize more of what is landed. This includes "waste" or by-products or what should really be called rest raw materials. The food science group participates in a Nordic project with the aim to maximize utilization of resources by using fish by-products for value added products where we are looking at production of fish protein hydrolysates. The food science group also participates in a European project together with a Hungarian company where the overall aim of the project is to develop an effective technology for production of high quality fish collagen from by-products from processing of farmed freshwater fish. Superchilling The most important factor for increasing shelf life is the product temperature. Superchilling means storage of food products at 1 to 3 centigrades below their initial freezing point. In practical terms the product is stored at 0˚ to -4˚C. In this way, the ice is magazinated inside the product instead of as external ice, which significantly lowers the demand for extra ice for transport. The purpose of this preservation method is to prolong the shelf life and to improve the biochemical,

microbial and sensorial quality of fresh food. For many food products, superchilling results in better quality compared to conventional chilling. However – there is a need to study the biochemical and physiochemical processes taking place in the food at superchilling temperatures. The Food Science group participates in a large Norwegian project where these aspects are further studied. Calanus The supply of fish oil and fish meal for feed production is expected to be a limiting factor for the fast growing aquaculture industry. Zooplankton, such as Calanus finmarchius, may be an attractive alternative raw material source for production of fish feed. Studies of Calanus have shown large seasonal and geographical variations in lipid content and composition of the lipids. Calanus is subject to rapid degradation after catch, and has active proteolytic and lipolytic enzymes. The proteolytic activity has been characterized with regard to pH and temperature. Low salt products Salting is one of the oldest methods of food preservation. Salting leads to increased shelf life by reducing the water activity. It is also used for taste improvement of food and as a source of mineral ions. However, intake of dietary sodium has been linked to hypertension and consequently increased risk of cardiovascular disease (CVD), greater retention of water in the body and increase thinning of the bones (osteoporosis). Therefore, dietary advice is that the intake of salt should be reduced from 10 g/day to 5 g/day. The main source of salt in the diet is salt from industrially processed food, which accounts for around 80% of our salt intake. The food science group participates in a research project aiming to find more convenient and cost effective methods for reducing levels of salt in food, to identify industrial processes and technological changes needed to ensure acceptable quality and shelf –life of low-salt products. To do this a better understanding of the salting process is needed and one of the aims is to develop a mathematic model to describe salting and technological changes during industrial processes. Ethical slaughtering of white fish The importance of cod aquaculture is increasing and there is therefore a need to find good slaughtering procedures for cod. The slaughtering procedures have to minimize the negative effect on fish welfare and at the same time lead to high quality cod. Slaughtering procedures leading to a minimum of stress can also enable pre-rigor processing of the fish.

Academic staff Turid Rustad Professor Marit Aursand Adjunct professor

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Product quality of farmed cod – effect of handling stress and storage conditions The main objectives are to determine effects of handling stress combined with storage conditions on quality of farmed cod to determine which biochemical changes that are important for the resulting sensory quality. Both proteome analysis, sensory and instrumental quality evaluation will be used identify biochemical markers of handling stress that can be used for prediction of product quality. Refining of marine oil for human consumption Seafood is our main source of healthy lipids. The long-chain omega-3 polyunsaturated fatty acids, EPA and DHA, are known to have a beneficial effect on human health and be a factor in the prevention and treatment of CVD and certain types of cancer and diseases, and in the development and function of the brain. The dominant dietary source of EPA and DHA are oily fish and fish oil supplement. The daily intake of oily fish is currently far below the recommended value, thus it is of interest to produce functional food enriched with omega-3 oils. Natural marine oils with high content of omega-3 intended to be used as a supplement or functional food ingredient has to be processed and refined to obtain safe and neutral blend taste. The food science group participates in a KMB-project “Technology for production of ultra stable marine oils and functional food applications”, where one of the sub-goals is to improve the refining and purification processes of marine oils.

It is of interest to study the different refining steps, with focus on deodorization and molecular distillation, to try to understand how the process affects the quality of the oil. By increasing the knowledge on how the process influences the quality of the oil, one can try to optimize the process so it is more suitable for the refining of marine oils. Lipid and protein oxidation The health beneficial polyunsaturated fatty acids react very easily with oxygen. The oxidation is a highly unwanted reaction because it leads to several problems. Oxidation is the cause of rancid taste in fish and fish products - and oxidation leads to destruction of the healthy fatty acids such as the EPA and the DHA. In addition, it is assumed that some of the oxidation products might be harmful to humans. Lipid oxidation products can react with proteins and lead to changes in protein properties, affecting texture changes in muscle structures, leading to dry and less juicy products. The process of oxidation thus has to be controlled and minimized. To control this we have to understand the oxidation process. Measurement of dissolved oxygen uptake in a special analytical system has shortened the time to measure oxidation rate from days to minutes. The method is well suited to measure the effect of antioxidants, which are compounds that reduces the oxidation rates, and prooxidants, which increase the rate of oxidation. Results show that lipid oxidation is extremely dependent upon temperature. Also a reduction in free iron in processed seafood can reduce the lipid oxidation. This work is done as part of an EU project – Seafoodplus and as part of a Norwegian project.

Measuring texture in Atlantic salmon (Salmo salar).

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3. PhD DISSERTATIONS Ida Grong Aursand, Thesis NTNU, 2009:136 Low-field NMR and MRI studies of fish muscle: Effects of raw material quality and processing. Summary: The present thesis aims at using non-invasive and non-destructive NMR techniques to contribute to a further understanding of fish tissue composition and its characteristics. Moreover, it aims at investigating the water dynamics and the distribution of fat and salt in fish as affected by species, raw material quality and processing from both the chemical and the physical angle at the same time. The applicability of low-field NMR as a tool for the fish processing industry was investigated. The bench top low-field NMR instrument was found suitable for fat and water determination in small Atlantic salmon (Salmo salar) samples, whereas the portable low-field NMR surface scanner (ProFiler) was appropriate for rapid fat determination in minced muscle. Thus, low-field NMR was proven to be good measuring technique, and with the introduction of the NMR surface scanner concept, online quality control may become feasible in the future. Transversal (T2) NMR relaxometry has been demonstrated to contain valuable information about water dynamics in Atlantic salmon and Atlantic cod (Gadus morhua) tissue. The thesis contributes to a further understanding of the relationship between water distribution and microstructure of fish flesh. It has been established that the method is sensitive to fish species, ante-mortem handling, rigor status, freezing/thawing, heating, and brine salting. The tissue T2 relaxation characteristics have been linked to microstructure, salt distribution and salt uptake. It is shown that T2 relaxation components correlate well with water holding capacity during salting. It has been suggested that entrapped and free water, and fat when present, give rise to the main relaxation components in fish muscle tissue. The understanding of the tissue water distribution and dynamics has been improved.

However, the clarification of the relaxation characteristics in fish flesh is still an active area of research. In fatty fish, both fat and water contributes to the T2 NMR relaxation signal. A two dimensional map of the diffusion versus T2 relaxation proved to be a good technique to increase the understanding of water and fat distribution in salmon muscle tissue, by clear separation of the NMR signals from water and fat components into different populations. MR imaging was probed for investigation of fat and salt distribution. 1H MRI was successfully applied to produce separate quantitative water and fat images. Combined 1H and 23Na imaging of brine salted Atlantic salmon revealed that the uptake and distribution of salt in the tissue was highly dependent on the spatial fat distribution. An evident relation was observed between T2 relaxation characteristics of salmon flesh and the sodium distribution in salted fillets. T2 relaxaometry and MR imaging gave further insight into the microstructure and water distribution of fish tissue of different quality and its effect on salt distribution. The combination of these NMR techniques is considered to be a useful tool to increase the understanding of the tissue water distribution and dynamics and for optimization of salting processes. Laila Berg, Thesis NTNU, 2009:46 A mutational analysis of the biotechnologically useful broad-host-range Pm promoter in Escherichia coli. Summary: The Pm promoter originally controls the expression of one of the two operons involved in the catabolism of aromatic hydrocarbons (benzoate derivatives) in the TOL plasmid of Pseudomonas putida. So far, this promoter has been shown to function in at least 16 bacterial species including Escherichia coli. Pm is induced by the binding of

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its positive activator protein, XylS, to two imperfect repeats directly upstream of the promoter −35 element. The XylS protein can only bind to the promoter in a dimeric form which is stabilized by low-cost benzoate effector molecules that enter the cells by passive diffusion. Also, the expression levels from the Pm promoter can easily be controlled by using different alkylbenzoate derivatives and by varying their concentrations. This makes the Pm/xylS promoter system to a useful tool for recombinant gene expression purposes, both at high (recombinant protein production) and low (physiological) levels. The application potential is further broadened by integrating the expression cassette into minimal replicons derived from the broad-host-range plasmid RK2. It is well known that the coding region influences the final protein production level from the promoter system used. One reason for this is believed to be that certain 5′ untranslated transcript region (UTR) and gene coding sequences are unsuited because they form strong secondary structures in the ribosome binding site (RBS) which are unfavorable for efficient translation. Usually, this problem is solved by testing different promoter systems (expression vectors) until (if possible) one is found that gives satisfactory expression levels of the gene of interest. In this thesis the main focus was to gain deeper insights into the role of the DNA region corresponding to the UTR in gene expression by mutational analysis of the UTR DNA sequence. It was decided to use cassette mutagenesis to introduce multiple (in each oligonucleotide) random mutations in the DNA region corresponding to the UTR and the ampicillin resistance gene (bla) as a reporter for the Pm expression levels. Several such complex (large number of mutants) libraries were constructed and later screened. UTR DNA sequences stimulatory to bla gene expression both at the accumulated transcript (up to 7-fold) and protein product (up to 20-fold) levels were isolated. Interestingly, UTR DNA sequences in which the mutations were located more than 7 bps downstream of the transcriptional start site, also displayed a strong stimulatory effect at the accumulated transcript level. In addition, in light of the well known importance of a strong Shine-Dalgarno (SD) sequence and A/U-richness in the UTR to obtain efficient translation, it was surprising that none of the mutations in any of the isolated UTR DNA sequences were located in the SD sequence and about 50 % of them led to the introduction of C’s. Furthermore, these same UTR DNA sequences also displayed a significant stimulatory effect at the accumulated transcript levels (up to 4-fold) of luc

(luciferase from firefly) and celB (phosphoglucomutase from Acetobacter xylinum). However, the stimulatory effect on the protein product formation for these two genes seemed to be strongly dependent on the UTR and gene coding sequence context, because the protein product levels varied between a factor of about 0.6 to 2.1 and 0.7 to 1.5 relative to the wild-type values for luc and celB, respectively. UTR DNA sequences which reduced the bla expression (protein level) to only about 1.5 % of the wild-type value were also identified. Interestingly, this strong down-regulation of the bla gene expression could be obtained even when the SD sequence was kept intact and the mutations were located more than 7 bps downstream of the transcriptional start site. Most of the mutations led to introductions of C or G. These UTR DNA mutations seemed to mainly lower the translational efficiency independent of the coding region, because they also very strongly reduced the protein production from both luc and celB, keeping inducibility intact. These mutants therefore seem to have a general application potential in metabolic engineering studies. Based on the data of the UTR DNA sequences stimulatory to gene expression, it seemed that there apparently is a big potential to increase the gene expression (bla) by mutating the UTR DNA region. There appears however to be a need to adapt the UTR DNA sequence for each specific gene to be expressed, because there seemed to exist a context dependency between the UTR and coding sequences strongly affecting the protein product formation. It was therefore interesting to investigate to what extent the luc and celB gene expression (protein level) could be stimulated by mutating the UTR DNA region. To test this, a synthetic two-cistron operon construct was made to use as a tool for easy identification of Pm UTR DNA sequences leading to improved protein product formation for any gene of interest. The protein production from bla was used as an indicator of the protein formation of the upstream gene, by translational coupling of the bla gene expression to that of the upstream gene. The UTR DNA sequences identified by using the synthetic operon construct led to a significant improvement (up to 1.7-fold) of the protein formation from the already very efficiently expressed celB gene. Also, the UTR DNA sequences adapted to improve the luc gene expression displayed a strong stimulatory effect on the protein production (up to 2.5-fold), but the expression level of this gene was still low. The reason for this is unknown, but most likely is caused by some feature of the luc coding sequence itself. Based on the characterization of the performance of the synthetic operon construct on

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celB and luc expression it appears that the construct is a good tool to achieve improvements of gene expression, although the UTR mutants cannot completely override the limitations imposed by aspects of the gene coding sequences themselves. Interestingly, the UTR DNA sequences isolated by the synthetic operon construct to improve the celB protein formation displayed a strong stimulatory effect on the bla gene expression at both the accumulated transcript (up to 16-fold) and protein product (up to 18-fold) levels. One of these UTR DNA sequences was characterized further, and surprisingly, two independent types of experiments showed that enhanced transcript production was the main cause of the stimulatory effect on transcript accumulation. This is an observation not previously reported in the scientific literature. A 25 bp region in the Pm promoter (including its −10 element) was also randomly mutated by cassette mutagenesis, and the Pm mutants identified in a library based on the best mutant identified in the first round of mutagenesis led to an up to 14-fold stimulatory effect of the bla gene expression. These Pm promoter mutants seemed to lead to a general up-regulation of the gene expression, because they also strongly stimulated the celB and luc gene expression (up to about 10- and 4-fold, respectively). The findings reported in this thesis demonstrate the big potential for increasing gene expression by cassette mutagenesis in promoter control elements even in an already strong promoter like Pm. The identified promoter core mutants seemed to stimulate expression of any gene, presumably by generating more transcripts. The stimulatory effect displayed by the isolated UTR DNA sequences, on the other hand, appeared to be more dependent of the context between the UTR and coding sequences. The probably scientifically most interesting new finding was that the UTR may play a critical role in the transcription process. The mechanism behind this is currently not known, but based on the literature there are direct contacts between the RNA polymerase (RNAP) and UTR DNA sequence both during the formation of the open transcription initiation RNAP complex and during RNAP promoter escape. In addition, the UTR sequence itself might directly influence the clearing of the RNA exit channel during the promoter escape. Based on the phenotypes displayed by the mutant UTR DNA sequences reported here, high level gene expression seems to require a compromise in the UTR DNA sequence between transcriptional and translational stimulation, in addition to its assumed significance for mRNA turnover rates.

Sigrid Hakvåg, Thesis NTNU, 2009:168 Antibiotic-producing bacteria from the surface microlayer in the Trondheim fjord, Norway. Summary: The marine environment has so far been poorly utilized in the search for (producers of) novel antimicrobial compounds. Marine bioprospecting might therefore be a promising field of research for the pharmaceutical industry as an alternative to terrestrial sources and synthetic production of pharmaceuticals. In this project, over 4000 cultivable isolates have been isolated from different locations in the Trondheim fjord and along the coast of Trøndelag, Norway. Over 1000 of these bacteria were isolated from the sea surface microlayer, whereas the rest originated from sediment samples. The diversity of the isolates from the sea surface microlayer have been investigated by studying cultivable bacteria from two sampling locations as ‘model-samples’. Whole-cell based antimicrobial assays revealed surprisingly high numbers of isolates displaying antagonistic activity among the assayed streptomycetes. 16S rDNA analyses indicated that several isolates seemed to be closely related, and studies on the PKS type I genes present in these samples revealed that recent horizontal gene transfer might have taken place. The results indicate that de-replication of isolates cannot be performed based on 16S rDNA sequences alone, and the identification of unique KS-sequences in some of these isolates further supports this statement. Two streptomycete isolates from the sea surface microlayer displayed activity against a vancomycin-resistant Enterococcus sp. Analysis of the bacterial extracts indicated that this might be due to the production of a novel antibacterial compound. Plasmids play an important role in the horizontal gene transfer among bacterial species. The genes involved in the biosynthesis of the antifungal polyene macrolide candicidin were found to be present on a linear plasmid in one on the isolated strains. Production of candicidin was found to be widely distributed among Streptomyces bacteria isolated from the Trondheim fjord, and it is thought that the plasmid might be involved in spreading the gene cluster in the marine environment. A Gram-negative strain in the isolate collection showing antibacterial activity was show to be a new strain of the genus Collimonas. The Collimonas CT (Coast of

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Trøndelag) produces the blue pigmented compound violacein, and genome scanning identified genes for biosynthesis of this compound, as well as several other gene clusters for the production of secondary metabolites of potential industrial interest. Hanne Jørgensen, Thesis NTNU, 2009:86 Analysis of genes for the biosynthesis of polyene macroclyclic compounds in streptomycetes isolated from the Trondheimsfjord Summary: The isolation of microbial producers of bioactive natural products from environmental samples has historically been a great success and laid the foundation for the modern medical science we enjoy the fruits of today. To sustain and further improve the treatment of diseases, we rely upon the continued discovery and development of new bioactive compounds. The work presented in this thesis describes the screening of more than 4000 actinomycete isolates recovered from sediment and neuston layer samples collected in the Trondheimsfjord. The objective was to discover producers of new compounds with antifungal or cytotoxic activity. The primary screening approach based on assays with Candida strains uncovered a large number of isolates producing bioactive compounds; however, spectroscopic analyses of extracts from these isolates revealed that a high percentage of the isolates were potentially producing the same compound. LC-MS-TOF analysis of the extracts identified the compound in question as the polyene macrolide candicidin. A genetic analysis of eight isolates showed that they all contained the candicidin biosynthetic gene cluster and that the cluster was present on a large plasmid in one of the isolates. The plasmid’s ability for transfer to other Streptomyces strains was investigated, but interspecific transfer could not be detected. A “cured” strain unable to produce candicidin was obtained by incubation of the plasmid-containing isolate at a high temperature and reintroduction of the plasmid restored the candicidin production, thus indicating that the plasmid is transmissible by conjugation. It is possible that the plasmid may have been responsible for the dissemination of the

candicidin biosynthetic gene cluster among actinomycetes in sediments and neuston layer of the Trondheimsfjord, although the results from this study were not conclusive. Candidates selected based on the primary screening against Candida strains were further evaluated in assays with different cancer cell lines. A compound displaying good cytotoxic activity was identified as the previously described macrolactam antibiotic BE-14106 by LC-MS-TOF analysis and NMR spectroscopy. A genomic library was III IV constructed for the BE-14106 producer and screened with a molecular probe targeting polyketide synthase genes. The biosynthetic gene cluster was successfully identified and sequenced and the biosynthetic pathway leading to production of BE-14106 was elucidated. The proposal for the biosynthetic pathway is supported by results from gene inactivation experiments, enzyme assays with heterologously expressed proteins and feeding studies with isotope labeled components. A second macrolactam, ML-449, was identified in the primary screening against the Candida strains. LC-MS-TOF analysis indicated structural resemblance to BE-14106. The complete structure of ML-449 was obtained by NMR spectroscopy, showing that BE-14106 and ML-449 only differ in the length of the acyl side chain. The ML-449 biosynthetic gene cluster was subsequently cloned, sequenced and compared to the BE-14106 biosynthetic gene cluster. The two clusters were found to be remarkably similar, differing only in the genes encoding the polyketide synthases synthesizing the acyl side chain. Phylogenetic analyses pointed to common ancestry for the two clusters as well as an evolutionary relationship with other macrolactam biosynthetic gene clusters. Krista Michelle Kaster, Thesis NTNU, 2009:41 Analysis and applications of microoganisms from a chalk oil reservoir in the North Sea. Summary: Ekofisk a chalk oil reservoir in the Norwegian sector of the North Sea was found to harbour an active and diverse microbial community. Microbial

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actives may be deleterious in nature as in reservoir souring or maybe advantageous as in microbial enhanced oil recovery. The aim of this study was to characterise the microbial communities in the Ekofisk oil reservoir and to gain insight into the microbial mechanisms important for the a) control of reservoir souring, and b) which can be utilized in enhanced oil recovery. Produced water samples from the Ekofisk oil reservoir were analysed using both culture-dependent and -independent techniques. The Ekofisk microbial community was found to be dominated by thermophilic microorganisms many of which were capable of either sulphidogenic or methanogenic physiologies. They were similar to organisms that have been previously identified from oil reservoir fluids. The dominant organisms identified directly from the produced water samples had sequences similar to members of the genera Thermotoga, Caminicella, Thermoanaerobacter, Archaeoglobus, Thermococcus, and Methano-bulbus. Enrichment cultures obtained from the produced water samples were dominated by sheathed rods. Sequence analyses of the cultures indicated predominance of the genera Petrotoga, Arcobacter, Archaeoglobus and Thermococcus. Reservoir souring caused by sulphide production due the activity of sulphate reducing prokaryotes (SRP) may be reduced by the injection of nitrate or nitrite. Nitrate or nitrite mitigates sulphide production either by the stimulation of nitrate reducing bacteria (NRB) through nitrate addition or via metabolic inhibition of the reduction of sulphite to sulphide by nitrite. Here we found that nitrate addition was ineffective at controlling souring whereas nitrite proved very effective at inhibiting sulphate reduction even at very low concentrations (0.25 mM - 1 mM) in both batch culture and bioreactor studies. To investigate microbial utilization in MEOR two fermentative enrichment cultures from the Ekofisk and Draugen oil reservoirs were used in a series of models experiments. In the course of this study we were able to determine that L- fructose, D-galacturonic acid, turnose, pyruvic acid and pyruvic acid methyl ester were the substrates preferred by the Ekofisk ferementative enrichment culture. We were also able to determine that the microbial cells themselves in Draugen fermentative enrichment cultures were able to cause emulsion. In addition, oil reservoir enrichment cultures caused wettability changes. As shown in two experiments; 1) by a change of height of the oil-water meniscus in a capillary tube mode, and 2) by the change of contact angle due to biofilm growth on polycarbonate coupons. In the latter experiment the contact angle changed from 154° on the control to

0° due to the growth of a biofilm on the coupon. This change in wettability may lead to enhanced oil recovery. This study found that nitrite was an effective method of controlling oil reservoir souring. In addition this study revealed that the biofilm may play an important role in reservoir souring as evidenced by the change in wettability. Therefore by gaining a better understanding of oil reservoir microbial community we will be better able to control both their deleterious and positive effects. Kåre Andre Kristiansen, Thesis NTNU, 2009:49 Specific interactions of chitosans with lysozyme and wheat germ agglutinin (WGA). Summary: Polysaccharides are important biopolymer materials, which have vital functions in almost all living systems. They serve as energy storage, play active parts in cell signalling processes and/or offer mechanical structure to cell walls. Today, we also rely on polysaccharides in many commercial products, often to give them a specific texture. A carbonyl group or more precisely an aldehyde (predominantly), is present in all polysaccharides masked as a hemiacetal at its reducing end. In some cases additional carbonyls may also be introduced. Such carbonyls (aldehydes or ketones) can be formed naturally by oxidation in the presence of oxygen and light, or be introduced as a result of chemical processing deliberately or un-deliberately. The chemical stability and structural properties are affected by the introduction of carbonyl groups. Several methods exist for their detection, but the majority of these have a low detection limit and/or provide only a measure of the average carbonyl content. Because of this, these methods offer limited information for polydisperse polysaccharide samples containing small amounts of carbonyl functionalities. This thesis deals with the detection of carbonyl group profiles within polysaccharides, and the use of periodate oxidation to introduce carbonyl groups into different alginate materials, resulting in altered chemical and physical properties.

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In the first part of the study, the carbonyl structure and content in the pectic polysaccharide sphagnan was re-investigated. Previous literature describes the presence of a novel monosaccharide named 5-keto-D-mannuronic acid (5-KMA) in sphagnan, and points it out as the main reason for the preservation of organic material in peat bogs. Through the work of this thesis and other recent publications it is shown that the carbonyl content in sphagnan is a tenfold lower than previously published, and that 5-KMA do not exist in sphagnan. The latter was demonstrated by reacting sphagnan with different amino compounds. A flaw in the original colorimetric assay for detecting 5-KMA was also revealed. The tanning ability of sphagnan was tested, but it was found that it did not meet the demands to be classified as a true ‘tanning agent’. Although the carbonyl content was found to be lower than first anticipated, it was higher than in other polysaccharides, possessing only the reducing end carbonyl group. During this work it became clear that a better general method for carbonyl profile detection in polysaccharides dissolved in water was needed. Such a method was therefore developed. The method involves labelling of the polysaccharide with either tritium or fluorescent labels. The labelling technique should be chosen depending on the structure of the polysaccharide. After labelling, the polysaccharide is analysed by size exclusion chromatography (SEC) with multiangular laser light scattering (MALLS) coupled with tritium or fluorescence detection. The chain stiffness and extensions of various in vitro epimerized alginates, and periodate oxidized alginates, were studied using SEC-MALLS with on-line viscosity detection. The chain conformation and extensions were evaluated using the exponent in the Mark-Houwink-Sakurada (MHS) relationship and the persistence length (q) from Bohdanecký analysis. The study revealed no significant difference in chain stiffness and extension between alginates with varying content of mannuronic acid (M) and guluronic acid (G), while alginates subjected to partial periodate oxidation and reduction showed a pronounced difference. For instance, a reduction of 35% in the MHS exponent (a) was observed between an unoxidized and a 44 mol% oxidized sample. In the last part of the study, periodate oxidized and borohydride reduced mannuronan were studied by NMR and the main peaks in the spectrum assigned. Later, oxidized/reduced mannuronan was used as a substrate for the C-5 epimerases AlgE4 or AlgE6. The fraction of G-residues (FG) decreased as the fraction of oxidized residues (P0) increased. The main reason for this was that the stretches of M-residues, which the enzyme could attach, were shortened. Finally, mannuronan was oxidized/

reduced (P0 = 0.02-0.08) before or after epimerization and studied by NMR, SEC-MALLS with on-line viscometry and small-strain oscillatory measurements. The results from the latter method showed that the dynamic storage modulus (G’) decreased rapidly as P0 increased. By comparing the oxidized/reduced alginates with alginate from Laminaria hyperborea (leaf and stipe) and Durvillea antarctica with similar molecular weight (MW) and average G-block length (NG>1), it was concluded that the decrease in G’ was mainly due to an increased flexibility of the polymer and not simply a reduction in MW and NG>1. Rahmi Lale, Thesis NTNU, 2009:266 The xylS/Pm expression cassette: New functional insights and application potentials. Summary: Positively regulated expression systems are widely used to control gene expression for applied and basic studies in bacteria (Paper I). XylS/Pm, originating from the Pseudomonas putida TOL plasmid is an example of such a system which had previously been coupled with the minimal replicons of the plasmid RK2 to create broad-host-range expression vectors (Blatny et al. 1997a). These systems have been used as versatile expression tools which cover a wide range of properties and applications, and the wild type XylS/Pm system was proven to be useful for production of recombinant proteins in Escherichia coli at industrial levels (Sletta et al. 2004; 2007). RK2 replicons are functional in at least 58 Gram-negative (Toukdarian, 2004; Trond Erik Vee Aune, personal communication) and in at least one Gram-positive bacterium, Clavibacter xyli (Thomas & Helinski 1989). Both the replicon and the xylS/Pm expression cassette contribute to the broad-host-range properties of this system (Winther-Larsen et al. 2000b; Fu et al. 2008). Important characteristics of these vectors include adjustable copy number (between 4 and 100 per chromosome), several different and inexpensive benzoic acid derivatives such as m-toluic acid can be used as inducers. They act in a dose-dependent manner apparently not requiring an active uptake system (Lambert & Stratford 1999), further simplifying the use of the system across species barriers.

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One of the aims of the work reported in this thesis was to further improve the expression levels from XylS/Pm and to gain new insights about the underlying mechanisms involved in determination of the levels of expression. For these studies E. coli was used as the main model system. The 5’-UTR region was the first DNA regulatory element to be studied. Large mutant libraries covering this region were created (using doped synthetic oligonucleotide mixtures) and screened with respect to expression levels, using bla (encoding β-lactamase) as reporter gene. This screening system has the important advantage that it allows very strong selection for enhanced expression levels by simply plating cells from the library on agar media supplied with a gradient of increasing levels of ampicillin (Winther-Larsen et al. 2000a). As an outcome of this work mutations in the 5’-UTR were found to represent an efficient tool for enhancing gene expression (up to over 20-fold compared to the wild type). Interestingly, some of the mutations were found to act by stimulating transcription, whereas the 5’-UTR has previously been considered to be mainly involved in control of mRNA stability and translation. Further inspection on the variant 5’-UTR sequences revealed that certain nucleotides were repeatedly substituted, such as the A to C transversion at position +10 (11 out of 14) relative to the transcriptional start site (Paper II). To investigate further the contribution of each base position, this region was also studied for identifying low-level expression variants. Mutant libraries covering the 5’-UTR were constructed with the same set-ups as described above but were, this time, screened to identify low-level expression variants. Sequencing of candidates revealed that they were not exhibiting any obvious positional hot-spots, but variants could be identifed which displayed a strongly reduced background expression in the absence of the inducer. Interestingly, these variants had not lost their inducibility properties, although the maximum level of induction was reduced relative to the wild type. Such variants will have a potential use in studies such as metabolic engineering and expression of toxic genes (Paper III). In a collaborative project the variant 5’-UTR sequences are currently being analysed by bionformatic tools, and the preliminary results indicate that generating in silico 5’-UTR sequences with predicted and desired properties may become possible (Skancke, unpublished). In parallel to the work on the 5’-UTR, other conceptually similar activities have resulted in identification of many up-regulated variants of the Pm promoter and the positive regulator XylS sequences. Similar to the 5’-UTR studies it was found that the expression from Pm can be strongly stimulated by introducing mutations in the promoter

region (Bakke et al. 2009) or in the XylS regulator coding sequence (Aune et al. 2009). Interestingly, when several variants from each element (XylS, Pm and 5’-UTR) were combined in a single construct, much stronger stimulation (both at the transcriptional and translational levels) was observed than that of the each variant element separately (Paper IV). An important conclusion from the work presented in this thesis is, therefore, that expression levels can be improved by mutating the regulatory elements, even in a case where the wild type version of the cassette can express proteins at industrial levels. These findings are likely to be relevant also for other well established expression cassettes. Inger Beate Standal, Thesis NTNU, 2009:114 Use of NMR spectroscopy in combination with pattern recognition techniques for elucidation of origin and adulteration of foodstuffs. Summary:

Consumers and food authorities are, to an increasing extent, concerned about factors such as the origin of food, how it is produced, and if it is healthy and safe. There are methods for general quality control to map the safety and nutritional value; however there is a need for suitable analytical methods to verify information such as the production method (wild/farmed), geographical origin, species, and process history of foods.

This thesis evaluates the applicability of using nuclear magnetic resonance (NMR) spectroscopy combined with pattern recognition techniques for authentication of foodstuffs. Fish and marine oils were chosen as materials. 13C NMR was applied to authenticate marine oils and muscle lipids of both fatty and lean fish, according to production method (wild/farmed), geographical origin, species, and process history. 1H NMR was applied on low molecular weight compounds extracted from cod muscle to authenticate fish according to species and processing conditions.

13C NMR combined with pattern recognition techniques enabled the differentiation of marine oils according to wild/farmed and geographical origin

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of the raw material. It is suggested that this was mainly due to the different diets of the fish from which the oil was produced. It was also possible to authenticate marine oils according to species, and to say something about the level of mixtures detectable. The sn-2 position specificity of fatty acids in triacylglycerols was shown to be an important characteristic to separate oils of different species. Esterified fish oil (concentrates) could easily be differentiated from natural fish oil by their 13C NMR profile.

13C NMR on muscle lipids, combined with pattern recognition techniques enabled the classification of wild and farmed salmon. The classification according to geographical origin was somewhat more complicated. A combination of analytical methods may be the best approach to obtain reliable results on geographical origin of fish. The analysis of lean fish showed that it was possible to classify lean gadoids according to species, and two stocks of Atlantic cod could be differentiated. There were also minor differences in the sn-2 position specificity of 22:6n-3 in phosphatidylcholine (PC) and phosphatidylethanolamine (PE) among the species investigated.

1H NMR on water soluble extracts of fish muscle provided information about a wide range of compounds, and the two species investigated (cod and haddock) displayed different 1HNMR profiles. Dimethylamine (DMA) was used as a marker for frozen, non processed fish. When applying the 1H NMR data in pattern recognition techniques, frozen fish could be differentiated from non-frozen fish, and in the classification of the cod of the different processing methods 80% of the samples were correctly classified.

Common for the methods presented in this thesis, NMR spectroscopy combined with pattern recognition for authentication of traceability data on foodstuffs, is the need for databases with analytical data on reference samples, covering the natural variation among the samples to be classified. Databases for marine oils need not be as extensive as for fish, since marine oils are generally produced from fish batches. Oils can also be analyzed directly without extensive sample preparation, and the greatest potential for official application may lie in the analysis of oils.

Studying the effect of handling on the quality of cod.

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4. PUBLICATIONS Publications in refereed journals 1. Aachmann, Finn Lillelund; Aune, Trond Erik Vee. Use of cyclodextrin and its derivatives for increased transformation efficiency of competent bacterial cells. Applied Microbiology and Biotechnology 2009 ;Volum 83.(3) s. 589-596

2. Aakvik, Trine; Degnes, Kristin F.; Dahlsrud, Rannveig; Schmidt, Frank; Dam, Ragnar; Yu, Lihua; Völker, Uwe; Ellingsen, Trond Erling; Valla, Svein. A plasmid RK2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species. FEMS Microbiology Letters 2009 ;Volum 296.(2) s. 149-158

3. Aune, Trond Erik Vee; Aachmann, Finn Lillelund. Methodologies to increase the transformation efficiencies and the range of bacteria that can be transformed. Applied Microbiology and Biotechnology 2009, 13s.

4. Aursand, Ida Grong; Veliyulin, Emil; Böcker, Ulrike; Ofstad, Ragni; Rustad, Turid; Erikson, Ulf. Water and salt distribution in Atlantic Salmon (Salmo salar) studied by low-field 1H NMR, 1H and 23Na MRI and light microscopy: Effects of raw material quality and brine salting. Journal of Agricultural and Food Chemistry 2009 ;Volum 57.(1) s. 46-54

5. Aursand, Marit; Standal, Inger Beate; Prael, A; McEvoy, L; Irvine, Joe; Axelson, David E. 13C NMR Pattern Recognition Techniques for the Classification of Atlantic Salmon (Salmo salar L.) According to Their Wild, Farmed, and Geographical Origin. Journal of Agricultural and Food Chemistry 2009 ;Volum 57.(9) s. 3444-3451

6. Axelson, DE; Standal, Inger Beate; Martinez, I; Aursand, Marit. Classification of Wild and Farmed Salmon Using Bayesian Belief Networks and Gas Chromatography-Derived Fatty Acid Distributions. Journal of Agricultural and Food Chemistry 2009 ;Volum 57.(17) s. 7634-7639

7. Bakke, Ingrid; Berg, Laila; Aune, Trond Erik Vee; Brautaset, Trygve; Sletta, Håvard; Tøndervik, Anne; Valla, Svein. Random mutagenesis of the Pm promoter as a powerful strategy for improvement of recombinant-gene expression. Applied and Environmental Microbiology 2009 ;Volum 75.(7) s. 2002-2011

8. Ballance, Simon; Aarstad, Olav Andreas; Aachmann, Finn Lillelund; Skjåk-Bræk, Gudmund; Christensen, BE. Preparation of high purity monodisperse oligosaccharides derived from mannuronan by size-exclusion chromatography followed by semi-preparative high-performance anion-exchange chromatography with pulsed amperometric detection. Carbohydrate Research 2009 ;Volum 344. s. 255-259

9. Berg, Laila; Lale, Rahmi; Bakke, Ingrid; Burroughs, Nigel; Valla, Svein. 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. Microbial Biotechnology 2009 ;Volum 2.(3) s. 379-389

10. Brautaset, Trygve; Lale, Rahmi; Valla, Svein. Minireview - Positively regulated bacterial expression systems. Microbial Biotechnology 2009 ;Volum 2.(1) s. 15-30

11. Carvajal, Ana Karina; Rustad, Turid; Mozuraityte, Revilija; Storrø, Ivar. Kinetic Studies of Lipid Oxidation Induced by Hemoglobin Measured by Consumption of Dissolved Oxygen in a Liposome Model System. Journal of Agricultural and Food Chemistry 2009 ;Volum 57.(17) s. 7826-7833

12. De Vos, Paul; Bucko, Marek; Gemeiner, Peter; Navrátil, Marián; Svitel, Juraj; Faas, Marijke; Strand, Berit Løkensgard; Skjåk-Bræk, Gudmund; Mørch, Yrr Asbjørg; et.al. Multiscale requirements for bioencapsulation in medicine and biotechnology. Biomaterials 2009 ;Volum 30.(13) s. 2559-2570

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13. Donati, Ivan; Mørch, Yrr Asbjørg; Strand, Berit Løkensgard; Skjåk-Bræk, Gudmund; Paoletti, Sergio. Effect of Elongation of Alternating Sequences on Swelling Behavior and Large Deformation Properties of Natural Alginate Gels. Journal of Physical Chemistry B 2009 ;Volum 113.(39) s. 12916-12922

14. Eysturskard, Jonhard; Haug, Ingvild; Elharfaoui, Nadia; Djabourov, Madeleine; Draget, Kurt Ingar. Structural and mechanical properties of fish gelatin as a function of extraction conditions. Food Hydrocolloids 2009 ;Volum 23.(7) s. 1702-1711

15. Eysturskard, Jonhard; Haug, Ingvild; Ulset, Ann-Sissel Teialeret; Draget, Kurt Ingar. Mechanical properties of mammalian and fish gelatins based on their weight average molecular weight and molecular weight distribution. Food Hydrocolloids 2009 ;Volum 23.(8) s. 2315-2321

16. Funami, Takahiro; Fang, Yapeng; Noda, Sakie; Ishihara, Sayaka; Nakauma, Makoto; Draget, Kurt Ingar; Nishinari, Katsuyoshi; Phillips, Glyn O.. Rheological properties of sodium alginate in an aqueous system during gelation in relation to supermolecular structures and Ca2+ binding. Food Hydrocolloids 2009 ;Volum 23.(7) s. 1746-1755

17. Ghim, CM; Almaas, Eivind. Two-Component Genetic Switch as a Synthetic Module with Tunable Stability. Physical Review Letters 2009 ;Volum 103.(2), 4 s.

18. Gimmestad, Martin; Ertesvåg, Helga; Heggeset, Tonje Marita; Aarstad, Olav Andreas; Svanem, Britt Iren Glærum; Valla, Svein. Characterization of Three New Azotobacter vinelandii Alginate Lyases, One of Which Is Involved in Cyst Germination. Journal of Bacteriology 2009 ;Volum 191.(15) s. 4845-4853

19. Hakvåg, Sigrid; Fjærvik, Espen; Klinkenberg, Geir; Borgos, Sven Even F.; Josefsen, Kjell D.; Ellingsen, Trond Erling; Zotchev, Sergey. Violacein-producing Collimonas sp. from the sea surface microlayer of costal waters in Trøndelag, Norway. Marine Drugs 2009 ;Volum 7. s. 576-588

20. Haug, Ingvild; Vegarud, G.E.; Langsrud, T.; Draget, Kurt Ingar; Skar, Hilde Margareta. Electrostatic effects on β-lactoglobulin transitions during heat denaturation as studied by differential scanning calorimetry. Food Hydrocolloids 2009 ;Volum 23.(8) s. 2287-2293

21. Heggset, Ellinor Bævre; Hoell, Ingunn A.; Kristoffersen, Marius; Eijsink, Vincent G.H.; Vårum, Kjell Morten. Degradation of chitosans with chitinase G from Streptomyces coelicolor A3(2): Production of chito-oligosaccharides and insight into subsite specificities. Biomacromolecules 2009 ;Volum 10. s. 892-899

22. Jakobsen, Øyvind Mejdell; Brautaset, Trygve; Degnes, Kristin F.; Heggeset, Tonje M.B.; Balzer, Simone; Flickinger, Michael C.; Valla, Svein; Ellingsen, Trond Erling. Overexpression of wild-type aspartokinase increases L-lysine production in the thermotolerant methylotrophic bacterium Bacillus methanolicus. Applied and Environmental Microbiology 2009 ;Volum 75.(3) s. 652-661

23. Jørgensen, Hanne; Degnes, Kristin F.; Sletta, Håvard; Fjærvik, Espen; Dikiy, Alexander; Herfindal, Lars; Bruheim, Per; Klinkenberg, Geir; Bredholt, Harald; Nygård, Gyrid; Døskeland, Stein O.; Ellingsen, Trond E.; Zotchev, Sergey. Biosynthesis of macrolactam BE-14106 involves two distinct PKS systems and amino acid processing enzymes for generation of the aminoacyl starter unit. Chemistry and Biology 2009 ;Volum 16. s. 1109-1121

24. Jørgensen, Hanne; Fjærvik, Espen; Hakvåg, Sigrid; Bruheim, Per; Bredholt, Harald; Klinkenberg, Geir; Ellingsen, Trond Erling; Zotchev, Sergey. Candicidin Biosynthesis Gene Cluster Is Widely Distributed among Streptomyces spp. Isolated from the Sediments and the Neuston Layer of the Trondheim Fjord, Norway. Applied and Environmental Microbiology 2009 ;Volum 75.(10) s. 3296-3303

25. Kaster, Krista Michelle; Bonaunet, K; Berland, H; Kjeilen-Eilertsen, G; Brakstad, OG. Characterisation of culture-independent and -dependent microbial communities in a high-temperature offshore chalk petroleum reservoir. Antonie van Leeuwenhoek 2009 ;Volum 96.(4) s. 423-439

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26. Kortner, Trond Moxness; Overrein, Ingrid; Øie, Gunvor; Kjørsvik, Elin; Arukwe, Augustine. Modulation of hormonal regulation and digestive capasity in Atlantic cod larvae (Gadus morhua) as influenced by prey. Special Publications (European Aquaculture Society) 2009 (38) s. 205-206

27. Kristiansen, Kåre Andre; Ballance, Simon; Potthast, A; Christensen, Bjørn Erik. An evaluation of tritium and fluorescence labelling combined with multi-detector SEC for the detection of carbonyl groups in polysaccharides. Carbohydrate Polymers 2009 ;Volum 76.(2) s. 196-205

28. Kristiansen, Kåre Andre; Schirmer, Bjørn Christian; Aachmann, Finn Lillelund; Skjåk-Bræk, Gudmund; Draget, Kurt Ingar; Christensen, Bjørn Erik. Novel alginates prepared by independent control of chain stiffness and distribution of G-residues: Structure and gelling properties. Carbohydrate Polymers 2009 ;Volum 77.(4) s. 725-735

29. Kristinova, Vera; Mozuraityte, Revilija; Storrø, Ivar; Rustad, Turid. Antioxidant activity of phenolic acids in lipid oxidation catalyzed by different prooxidants. Journal of Agricultural and Food Chemistry 2009 ;Volum 57. s. 10377-10385

30. Lee, Byung Cheon; Dikiy, Alexander; Kim, Hwa-Young; Gladyshev, Vadim N.. Functions and evolution of selenoprotein methionine sulfoxide reductases. Biochimica et Biophysica Acta - General Subjects 2009 ;Volum 1790. s. 1471-1477

31. Lelu, Sylvie; Davies, Catharina de Lange; Reitan, Nina Kristine; Strand, Sabina P. Gene delivery with chitosan: influence of chain length on intracellular trafficking and dissociation. European Biophysics Journal 2009 ;Volum 38. Suppl. 1 s. S89

32. Mørkved, Eva Henmo; Andreassen, Trygve; Bruheim, Per. Zinc azaphthalocyanines with pyridin-3-yloxy peripheral substituents. Polyhedron 2009 ;Volum 28.(13) s. 2635-2640

33. Nowicka, Katja; Gernata, Tim; Almaas, Eivind; Stubbs, Lisa. Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proceedings of the

National Academy of Science of the United States of America 2009 ;Volum 106.(52) s. 22358-22363

34. Olderøy, Magnus Østgård; Xie, Minli; Strand, Berit Løkensgard; Flaten, Ellen Marie; Sikorski, Pawel; Andreassen, Jens-Petter. Growth and nucleation of calcium carbonate vaterite crystals in presence of alginate. Crystal Growth & Design 2009 ;Volum 9.(12) s. 5176-5183

35. Preobrazhenskaya, Maria N.; Olsufyeva, Evgenia N.; Solovieva, Svetlana E.; Tevyashova, Anna N.; Reznikova, Marina I.; Luzikov, Yuryi N.; Terekhova, Larisa P.; Trenin, Aleksei S.; Galatenko, Olga A.; Treshalin, Ivan D.; Mirchink, Elena P.; Bukhman, Vladimir M.; Sletta, Håvard; Zotchev, Sergey. Chemical modification and biological evaluation of new semisynthetic derivatives of 28,29-didehydronystatin A1 (S44HP), a genetically engineered antifungal polyene macrolide antibiotic. Journal of Medicinal Chemistry 2009 ;Volum 52. s. 189-196

36. Preobrazhenskaya, Maria N.; Olsufyeva, Evgenia N.; Tevyashova, Anna N.; Printsevskaya, Svetlana S.; Solovieva, Svetlana E.; Reznikova, Marina I.; Trenin, Aleksey S.; Galatenko, Olga A.; Treshalin, Ivan D.; Pereverzeva, Eleonora R.; Mirchink, Elena P.; Zotchev, Sergey. Synthesis and study of the antifungal activity of new mono- and disubstituted derivatives of a genetically engineered polyene antibiotic 28,29-didehydronystatin A1 (S44HP). Journal of antibiotics (Tokyo. 1968) 2009 s. 1-10

37. Reitan, Nina Kristine; Maurstad, Gjertrud; Davies, Catharina de Lange; Strand, Sabina P.. Characterizing DNA condensation by structurally different chitosans of variable gene transfer efficacy. Biomacromolecules 2009 ;Volum 10.(6) s. 1508-1515

38. Riebroy, Siriporn; Benjakul, Soottawat; Visessanguan, Wonnop; Erikson, Ulf; Rustad, Turid. Acid-induced gelation of natural actomyosin from Atlantic cod (Gadus morhua) and burbot (Lota lota). Food Hydrocolloids 2009 ;Volum 23. s.26-39

39. Saage, Aandrea; Vadstein, Olav; Sommer, Ulrich. Feeding behaviour of adult Centropages hamatus (Copepoda, Calanoida): Functional response and selective feeding experiments. Journal of Sea Research 2009 ;Volum 62.(1) s. 16-21

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40. Setubal, Joao C.; dos Santos, Patricia; Goldman, Barry S.; Ertesvåg, Helga; Espín, Guadalupe; Rubio, Luis M.; Valla, Svein; Almeida, Nalvo F.; Balasubramanian, Divya; Cromes, Lindsey; Curatti, Leonardo; Du, Zijin; Godsy, Eric; Goodner, Brad; Hellner-Burris, Kaitlyn; Hernandez, José A.; Houmiel, Katherine; Imperial, Juan; Kennedy, Christina; Larson, Timothy J.; Latreille, Phil; Ligon, Lauren S.; Lu, Jing; Mærk, Mali; Miller, Nancy M.; Norton, Stacie; O’Carroll, Ina P.; Paulsen, Ina; Raulfs, Estella C.; Roemer, Rebecca; Rosser, James; Segura, Daniel; Slater, Steve; Stricklin, Shawn L.; Studholme, David J.; Sun, Jian; Viana, Carlos J.; Wallin, Erik; Wang, Baomin; Wheeler, Cathy; Zhu, Huijun; Dean, Dennis R.; Dixon, Ray; Wood, Derek. Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. Journal of Bacteriology 2009 ;Volum 191.(14) s. 4534-4545

41. Slizyte, Rasa; Mozuraityte, Revilija; Martinez-Alvarez, Oscar; Falch, Eva; Fouchereau-Peron, Martine; Rustad, Turid. Functional, bioactive and antioxidative properties of hydrolysates obtained from cod (Gadus morhua) backbones. Process Biochemistry 2009 ;Volum 4.(6) s. 668-677 42. Solgaard, Geir; Thorsen, Kaspar Høye; Draget, Kurt Ingar. Encapsulation of a proteolytically active novel bioproduct; controlling the release of proteinous components. Food and Bioproducts Processing 2009 ;Volum 87.(C1) s. 40-45

43. Stalheim, Torunn; Ballance, Simon; Christensen, Bjørn Erik; Granum, P.E. Sphagnan – a pectin-like polymer isolated from Sphagnum moss can inhibit the growth of some typical food spoilage and food poisoning bacteria by lowering the pH. Journal of Applied Microbiology 2009 ;Volum 106.(3) s. 967-976

44. Standal, Inger Beate; Axelson, David E.; Aursand, Marit. Differentiation of Fish Oils According to Species by 13C-NMR Regiospecific Analyses of Triacyglycerols. Journal of the American Oil Chemists Society 2009 ;Volum 86.(5) s. 401-407

45. Stockmann, Vegar; Bakke, Jan Magnus; Bruheim, Per; Fiksdahl, Anne. Formation of new 4-isocyanobut-2-enenitriles by thermal ring cleavage of 3-pyridyl azides. Tetrahedron 2009 ;Volum 65.(18) s. 3668-3672

46. Valla, Svein. The future is artificial. Microbial Biotechnology 2009 ;Volum 2.(2) s. 152-153

47. Zakariassen, H; Aam, BB; Horn, SJ; Vårum, Kjell Morten; Sorlie, M; Eijsink, VGH. Aromatic Residues in the Catalytic Center of Chitinase A from Serratia marcescens Affect Processivity, Enzyme Activity, and Biomass Converting Efficiency. Journal of Biological Chemistry 2009 ;Volum 284.(16) s. 10610-10617

48. Zotchev, Sergey; Caffrey, Patrick. Genetic analysis of nystatin and amphotericin biosynthesis. Methods in Enzymology 2009 ;Volum 459. s. 243-258

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Conference contributions 1. Aachmann, Finn Lillelund. NMR. Nettverkssamling for realfag; 2009-10-29 - 2009-10-29

2. Aachmann, Finn Lillelund; Larsen, Kim L.; Wimmer, Reinhard. Investigations of Cyclodextrin-Aromatic Amino Acid Interactions -Basis for Interactions with Proteins. First European Cyclodextrin Conference; 2009-10-11 - 2009-10-13

3. Aachmann, Finn Lillelund; Sal, Lena Solli; Dikiy, Alexander. Structural Characterization of Mammalian Methionine Sulfoxide Reductase B1 and its Functional Peculiarities. 30th Danish NMR Meeting; 2009-01-26 - 2009-01-27

4. Aachmann, Finn Lillelund; Sal, Lena Solli; Hwa-Young, Kim; Gladyshev, Vadim N.; Dikiy, Alexander. Functional insights into the catalytic mechanism of methionine sulfoxide reductase B1 through its structural analysis. Euromar 2009; 2009-07-05 - 2009-07-09

5. Bantle, Michael; Bergvik, Maria; Rustad, Turid. Freezing time and its influence on enzymatic activities and lipid composition in Calanus finmarchicus. 3rd Joint Trans-Atlantic Fisheries Technology Conference; 2009-09-15 - 2009-09-28

6. Bossier, P.; Dierckens, K.; Van Delsen, B.; Defoirdt, T.; De Schryver, P.; Vadstein, Olav; Aasen, Inga-Marie; Gatesoupe, F.J.; Verreth, J.; Smidt, H.; Skjermo, Jorunn; Verdegem, M.J.C.; Boon, N.; Olsen, Yngvar; Van Breusegem, F.; Sorgeloos, P.. The role of microbiota in aquaculture target organisms and their environment. Aquaculture Europe 2009; 2009-08-14 - 2009-08-17

7. Bruheim, Per; Sletta, Håvard; Klinkenberg, Geir; Ellingsen, Trond Erling; Krokan, Hans Einar; Otterlei, Marit. Systems biology and high resolution genome-wide phenotyping of yeast used for identification of cellular and molecular effects of DNA damaging agents. 3rd US-EU Workshop "Systems level understanding of DNA damage responses"; 2009-03-30 - 2009-04-01

8. Buchinger, Edith; Aachmann, Finn Lillelund; Iwai, Hideo; Skjåk-Bræk, Gudmund; Valla, Svein; Wimmer, Reinhard. Segmental labelled AlgE4- an alginate epimerase. Euromar 2009; 2009-07-05 - 2009-07-09

9. Buchinger, Edith; Aachmann, Finn Lillelund; Iwai, Hideo; Valla, Svein; Skjåk-Bræk, Gudmund; Wimmer, Reinhard. Segmental labelled AlgE4- an alginate epimerase. The VIII European Symposium of the; 2009-06-14 - 2009-06-18

10. Carvajal, Ana Karina; Rustad, Turid; Mozuraityte, Revilija; Storrø, Ivar. Kinetic studies of lipid oxidation in marine lipids induced by hemoglobin. 25th LipidForum Symposium; 2009-06-15 - 2009-06-17

11. Crescente, Christian Miguel; Afrapoli, Mehdi Shabani; Jonstad, T.; Rasmussen, Kjetil; Torsæter, Ole; Hultmann, Lisbeth; Strøm, Arne Reidar; Kowalewski, Espen. Effects of wettability and salinity on microbial enhanced oil recovery with Rhodococcus sp.094.. International Symposium of the Society of Core Analysts; 2009-09-27 - 2009-09-30

12. Davies, Catharina De Lange; Berg, Lars S; Reitan, Nina Kristine; Lelu, Sylvie; Maurstad, Gjertrud; Olderøy, Magnus Østgård; Strand, Sabina P.. DNA-chitosan nanoparticles in gene delivery: Chitosan structure and physiological barriers for efficient delivery. 100th Annual Meting 2009; 2009-04-18 - 2009-04-22

13. Davies, Catharina De Lange; Reitan, Nina Kristine; Maurstad, Gjertrud; Olderøy, Magnus Østgård; Berg, Lars S; Strand, Sabina P.. Barriers for delivery of pDNA-chitosan vectors. The Norwegian Biochemical Society 45th Contact Meeting; 2009-01-29 - 2009-02-01

14. Draget, Kurt Ingar. Chemical and Physical Properties and some Bioactive and Biomedical Considerations. 3rd International Hydrocolloids Forum: Hydrocolloids as Dietary Fibre: Characterisation and Functionality; 2009-06-29 - 2009-06-30

28

15. Draget, Kurt Ingar. The impact of the chemical and physical properties of alginates on biofunctionality. The 15th Gums and Stabilisers for the Food Industry; 2009-06-22 - 2009-06-25

16. Dragset, Marte Singsås; Steigedal, Magnus; Flo, Trude Helen; Valla, Svein. Searching future therapies for tuberculosis: Identification of genes involved in /Mycobacterium avium/ intracellular survival in macrophages. NBS kontaktmøte; 2009-01-29 - 2009-02-01

17. Engelhardt, Kerstin; Sletta, Håvard; Degnes, Kristin F.; Klinkenberg, Geir; Kemmler, M.; Bredholt, Harald; Ian, Elena; Fjærvik, Espen; Ellingsen, Trond Erling; Zotchev, Sergey. Isolation of the biosynthetic gene cluster for TP1161, a novel thiazolyl peptide from a marine-derived Nocardiopsis sp.. Symposium on the Biology of Streptomyces; 2009-10-07 - 2009-10-11

18. Forberg, Torunn; Vadstein, Olav; Arukwe, Augustine. HOST RESPONSES TO BACTERIA IN GNOTOBIOTIC ATLANTIC COD (GADUS MORHUA) LARVAE. Aquaculture Europe 2009; 2009-08-14 - 2009-08-17

19. Forberg, Torunn; Vadstein, Olav; Arukwe, Augustine. Strategies to unravel gene expression responses of host-microbe interactions in cod (Gadus morhua) larvae. LARVI’09 – 5th Fish & shellfish symposium; 2009-09-07 - 2009-09-10

20. Haug, Ingvild. Fra forskning til skjønnhet?. Tronett-møte, Teknas kvinnenettverk; 2009-01-13 - 2009-01-13

21. Heggset, Ellinor Bævre; Dybvik, Anette Israelsen; Hoell, Ingunn A.; Eijsink, Vincent G.H.; Sørlie, M.; Vårum, Kjell Morten. Chitosan Degradation with Chitosanase Q9RJ88 from /Streptomyces coelicolor/ A3(2). 9th Internation Conference of the European Chitin Society, Euchis 2009; 2009-05-23 - 2009-05-26

22. Heggset, Ellinor Bævre; Hoell, Ingunn A.; Kristoffersen, Marius; Eijsink, Vincent G.H.; Vårum, Kjell Morten. Degradation of chitosans with chitinase G from /Streptomyces coelicolor A3(2)/. 9th Internation Conference of the European Chitin Society, Euchis 2009; 2009-05-23 - 2009-05-26

23. Ian, Elena; Fjærvik, Espen; Bredholt, Harald; Zotchev, Sergey. Analysis of cultivable actinobacteria isolated from two marine sponges collected in the Trondheim fjord, Norway.. Symposium on the Biology of Streptomyces; 2009-10-07 - 2009-10-11

24. Jørgensen, Hanne; Degnes, Kristin F.; Sletta, Håvard; Fjærvik, Espen; Dikiy, Alexander; Herfindal, Lars; Bruheim, Per; Klinkenberg, Geir; Bredholt, Harald; Nygård, Gyrid; Døskeland, Stein O.; Ellingsen, Trond Erling; Zotchev, Sergey. The biosynthesis of macrolactam BE-14106: a new way of generating an aminoacyl starter unit. The Fifteenth International Symposium on the Biology of Actinomycetes 2009 (ISBA15); 2009-08-20 - 2009-08-25

25. Jørgensen, Hanne; Engelhardt, Kerstin; Sletta, Håvard; Fjærvik, Espen; Klinkenberg, Geir; Degnes, Kristin F.; Ian, Elena; Bredholt, Harald; Kemmler, M.; Terekhova, Larissa P.; Galatenko, Olga A.; Dikiy, Alexander; Bruheim, Per; Ellingsen, Trond Erling; Zotchev, Sergey. Streptomycetes and other actinobacteria from the Trondheim fjord (Norway): diversity, secondary metabolites, and genes for their biosynthesis. Symposium on the Biology of Streptomyces; 2009-10-07 - 2009-10-11

26. Kortner, Trond Moxness; Overrein, Ingrid; Øie, Gunvor; Kjørsvik, Elin; Arukwe, Augustine. Modulation of hormonal regulation and digestive capasity in Atlantic cod larvae (Gadus morhua) as influenced by prey. Larvi 2009 - 5th fish & shellfish larviculture symposium; 2009-09-07 - 2009-09-10

27. Mærk, Mali. Genteknologi. Byen, bygdene og kunnskapen; 2009-03-25 - 2009-03-25

28. Mærk, Mali; Ellingsen, Trond E.; Ertesvåg, Helga; Jakobsen, Øyvind M.; Klinkenberg, Geir; Sletta, Håvard; Tøndervik, Anne; Valla, Svein. Bacterial alginate biosynthesis: New genes identified by high-throughput screening. 10th International Conference on Systems Biology; 2009-08-30 - 2009-09-04

29

29. Mærk, Mali; Lien, Stina Katrine; Ertesvåg, Helga; Bruheim, Per; Valla, Svein. An Entner-Doudoroff pathway mutation in Pseudomonas fluorescens causes cell death during alginate production. The Norwegian Biochemical Society 45th Contact Meeting; 2009-01-29 - 2009-02-01

30. Olderøy, Magnus Østgård; Xie, Minli; Østnæs, Simen; Andreassen, Jens-Petter; Strand, Berit Løkensgard; Sikorski, Pawel. Alginate/CaCO3 Biomaterials. Bone-Tec 2009; 2009-10-08 - 2009-10-11

31. Olsen, Yngvar; Larssen, Harald; Overrein, Ingrid; Evjemo, Jan Ove; Rainuzzo, Jose R.. Fatty acid composition of phospholipids in prey organisms and their incorporation efficiency in cod larvae during early first feeding. World Aquaculture 2009; 2009-09-25 - 2009-09-29

32. Skjåk-Bræk, Gudmund. Alginate microcapsules for cell transplantation. Can they be improved?. Beta Cell Therapy lectures; 2009-10-20 - 2009-10-20

33. Skjåk-Bræk, Gudmund. Characterization of alginates relevant to their use as immobilisation matrix for living cells. Int Workshop on Bioencapsulation; 2009-04-24 - 2009-04-25

34. Skjåk-Bræk, Gudmund. Spanskesyken, hva var det, og hva kan vi lære av den?. Tekns - teknisk-naturvitenskapelig forening; 2009-08-20 - 2009-08-20

35. Stafsnes, Marit Hallvardsdotter. Microbial production of carotenoids. Høstmøtet i NBS Trøndelag; 2009-10-05 - 2009-10-06

36. Strand, Berit Løkensgard. Finnes det en kur for diabetes?. Gløshaugen akademiske klubb; 2009-11-19 - 2009-11-19

37. Strand, Berit Løkensgard; Skjåk-Bræk, Gudmund. Encapsulation with alginates. Particles 2009 - Micro and Nano Encapsulation; 2009-07-11 - 2009-07-14

38. Strand, Sabina P. Chitosans for gene and siRNA delivery. 9th International Conference of the European Chitin Society; 2009-05-23 - 2009-05-26

39. Strand, Sabina P.; Issa, M.; Malmo, Jostein; Artursson, P.; Vårum, Kjell Morten. Tailoring of chitosans for siRNA delivery. Congress of European Society of Gene and Cell Therapy; 2009-11-20 - 2009-11-25

40. Strand, Sabina P.; Berg, Lars S; Lelu, Sylvie; Davies, Catharina De Lange; Artursson, Per; Vårum, Kjell Morten. Molecular design of chitosan gene delivery systems with an optimized balance between polyplex stability and unpacking. Congress of European Society of Gene and Cell Therapy; 2009-11-20 - 2009-11-25 Molecular design of chitosan gene delivery systems with an optimized balance between polyplex stability and polyplex unpacking. Congress of European Society of Gene and Cell Therapy; 2009-11-20 - 2009-11-25

41. Tøndervik, Anne; Aarstad, Olav Andreas; Sletta, Håvard; Skjåk-Bræk, Gudmund. Use of high throughput screening technology for development of alginate-modifying enzymes with novel properties. Polysaccharides as a source for advanced materials EPNOE 2009; 2009-09-21 - 2009-09-24

42. Vadstein, Olav. Resirkulering i akvakultur: Mer enn avfallshåndtering. Akvakultur - muligheter og trusler i vann; 2009-05-13 - 2009-05-13

43. Valla, Svein. Bioteknologiens utvikling – en fare for samfunnet? Foredrag ved Gløshaugen Akademiske Klubb; 2009-02-05 - 2009-02-05

44. Valla, Svein. Pm/xylS coupled to broad-host-range RK2 replicons: an advanced system for accurate control of gene expression at a wide range of levels in bacteria. Norsk Biokjemisk Selskaps kontaktmøte Røros; 2009-01-29 - 2009-02-01

45. Vestrum, Ragnhild Inderberg; Forberg, Torunn; Vadstein, Olav. Impact of live versus dead bacteria on survival, growth, and gene expression in Atlantic cod (Gadus morhua) larvae. LARVI’09 – 5th Fish & shellfish symposium; 2009-09-07 - 2009-09-10

30

46. Wentzel, Alexander. The metabolic switch in streptomyces coelicolor studied by high time-resolution ‘omics analysis of closely-monitored submerged batch cultivations. 15th Int. Symposium on the Biology of Actinomycetes; 2009-08-20 - 2009-08-25

47. Wentzel, Alexander; Jakobsen, Øyvind M.; Øverby, Anders; Hoel, Sunniva; Bruheim, Per; Sletta, Håvard; Strøm, Arne Reidar; Ellingsen, Trond Erling. A systems biology approach towards understanding metabolic switching from primary to secondary metabolism in Streptomyces coelicolor. NBS Vintermøte; 2009-01-29 - 2009-02-01

48. Xie, Minli; Olderøy, Magnus Østgård; Strand, Berit Løkensgard; Andreassen, Jens-Petter; Sikorski, Pawel. Alginate/CaCO3 Composite Biomaterials. NTNU Nanolab Usermeet. 2009; 2009-05-12 - 2009-05-14

49. Xie, Minli; Olderøy, Magnus Østgård; Strand, Berit Løkensgard; Andreassen, Jens-Petter; Sikorski, Pawel. Alginate/CaCO3 Composite Biomaterials. NANOMAT conference 2009; 2009-06-16 - 2009-06-17

50. Zotchev, Sergey. Discovery of new antibiotics through biosynthetic engineering and bioprospecting. BIOPROSP 2009; 2009-02-24 - 2009-02-24

51. Zotchev, Sergey. Evolution of secondary metabolite biosynthesis in actinobacteria: insights from genetics and biochemistry. Symposium on Miscobial Genome Dynamics and Evolution; 2009-05-07 - 2009-05-08

52. Zotchev, Sergey. New and Improved Antifungal Polyene Macrolides through Biosynthetic and Chemical Engineering. Zing Natural Products Conference; 2009-03-01 - 2009-03-04

53. Zotchev, Sergey; Jørgensen, Hanne; Degnes, Kristin F.; Sletta, Håvard; Fjærvik, Espen; Dikiy, Alexander; Herfindal, L.; Bruheim, Per; Klinkenberg, Geir; Bredholt, Harald; Nygård, G.; Døskeland, Stein O.; Ellingsen, Trond Erling. Small-ring macrolactams with acyl side chain: new insights into the biosynthesis and its evolution. 15th International Symposium on the Biology of Actinomycetes; 2009-08-20 - 2009-08-25

Chapters in books

1. Bantle, Michael; Eikevik, Trygve Magne; Rustad, Turid. Atmospheric freez-drying of calanus finmarchicus and its effects on proteolytic and lipolytic activities. I: Atmospheric freez-drying of calanus finmarchicus and its effects on proteolytic and lipolytic activities : June 17th to 19th 2009, Reykjavik, IcelandProceedings of the 4th Nordic Drying Conference NDC2009 : June 17th to 19th 2009, Reykjavik, Iceland. Høgskolen i Oslo 2009 ISBN 978-82-594-3406-7.

2. Ertesvåg, Helga; Valla, Svein; Skjåk-Bræk, Gudmund. Enzymatic Alginate Modification. I: Alginates: Biology and Applications. Springer 2009 ISBN 978-3-540-92678-8. s. 95-115

3. Espevik, Terje; Rokstad, Anne Mari; Kulseng, Bård Eirik; Strand, Berit Løkensgard; Skjåk-Bræk, Gudmund. Mechanisms of the host immune response to alginate microcapsules. I: The Bioartificial

Pancreas and Other Biohybrid Therapies. Kerala, India: Transworld Research Network 2009 ISBN 978-81-7895-415-8. s. 279-290

4. Falch, Eva; Overrein, Ingrid; Solberg, Christel; Slizyte, Rasa. Composition and calories. I: Handbook of Seafood and Seafood Products Analysis. CRC Press 2009 ISBN 978-1-4200-4633-5. s. 257-285

5. Forberg, Torunn; Vadstein, Olav; Arukwe, Augustine. Strategies to unravel gene expression responses of host-microbe interactions in cod (Gadus morhua) larvae. I: Larvi 2009 -European Aquaculture Society Special Publication No 38. Oostende, Belgia: European Aquaculture Society 2009 ISBN 9789090245638. s. 116-118

6. Haug, Ingvild; Draget, Kurt Ingar. Gelatin. I: Handbook of Hydrocolloids, 2nd Ed. Woodhead Publishing Limited 2009 ISBN 978-1-84569-414-2. s. 142-162

31

7. Jacobsen, Charlotte; Rustad, Turid; Nielsen, Nina Skall; Falch, Eva; Jansson, Stig; Storrø, Ivar. Processing of marine lipids and factors affecting their quality when used for functional foods. I: Marine functional food. Wageningen Academic Publishers 2009 ISBN 978-90-8686-078-4. s. 89-114

8. Myklestad, Sverre M.; Granum, Espen. Biology of (1,3)- β -glucans and related glucans in protozoans and chromistans. I: Chemistry, Biochemistry and Biology of (1,3)-Beta Glucans and Related Polysaccharides. Academic Press 2009 ISBN 978-0-12-373971-1. s. 353-385

9. Myklestad, Sverre M.; Smidsrød, Olav; Indergaard, Mentz Petter. Nils Andreas Sørensen og tang- og tare instituttet. I: "Proffen" Nils Andreas Sørensen. En minnebok. Trondheim: Fakultet for naturvitenskap og teknologi 2009 ISBN 978-82-998249-0-3. s. 133-190

10. Mørch, Yrr Asbjørg; Strand, Berit Løkensgard; Skjåk-Bræk, Gudmund. Alginate structure function relationships relevant to their use for cell encapsulation. I: The Bioartificial Pancreas and Other Biohybrid Therapies. Kerala, India: Transworld Research Network 2009 ISBN 978-81-7895-415-8. s. 51-66

11. Rustad, Turid. Lipid oxidation. I: Handbook of Seafood and eafood Products Analysis. CRC Press 2009 ISBN 978-1-4200-4633-5. s. 87-95

12. Rustad, Turid. Peptides and proteins. I: Handbook of Seafood and Seafood Products Analysis. CRC Press 2009 ISBN 978-1-4200-4633-5. s. 11-19 13. Vadstein, Olav. Interactions in the planktonic food web. I: Ecosystem Barents Sea. Tapir Akademisk Forlag 2009 ISBN 978-82-519-2461-0. s. 251-266 14. Valla, Svein; Ertesvåg, Helga; Tonouchi, Naoto; Fjærvik, Espen. Bacterial cellulose production: Biosynthesis and applications. I: Microbial production of biopolymers and polymer precursors. : Caister academic press 2009 ISBN 978-1-904455-36-3. s. 43-77 15. Vestrum, Ragnhild Inderberg; Forberg, Torunn; Vadstein, Olav. Impact of live versus dead bacteria on survival, growth, and gene expression in Atlantic cod (Gadus morhua) larvae. I: Larvi 2009 -European Aquaculture Society Special Publication No 38. Oostende, Belgia: European Aquaculture Society 2009 ISBN 9789090245638. s. 478-481 16. Zotchev, Sergey. Antibiotics: Biosynthesis. I: Wiley Encyclopedia of Chemical Biology. John Wiley & Sons, Inc. 2009 ISBN 978-0471-75477-0. s. 89-98

Reports Mærk, Mali. Rapport fra kurs i systembiologi. : Norsk Biokjemisk Selskap 2009 2 s. NBS-nytt (4/2009)

Rygh Refseth, Ingun; Johansen, Berit; Arbo, Ingerid Brænne; Rustad, Turid. Multiplex analyse av biomarkører relatert til kosthold i humant plasma og serum. Trondheim: NTNU, Institutt for bioteknologi 2009 192 s.

32

5. EDUCATION Department of Biotechnology

The Department of Biotechnology is involved in two different studies in Biotechnology. Both are 5 year programs leading either to Master of Technology in biotechnology (Sivilingeniørstudiet) or a Master of Science in biotechnology. The two programs have common basic courses in biochemistry, microbiology and molecular genetics. The major difference is the focus on chemistry and chemical engineering the first two years of study of the Master of Technology/ Sivilingeniørstudiet in biotechnology as compared to natural science and cell biology in the Master of Science in biotechnology. Students with relevant bachelor degrees from other universities, technical institutes or colleges are offered a 2 year Master program in biotechnology.

Courses Master courses

Course no. Credits Title Lectures Started/

Passed TBT 4102 7.5 Biochemistry, Basic course S. Zotchev / K. Vårum 145 / 130 TBT 4107 7.5 Biochemistry, Advanced course G. Skjåk-Bræk 71 / 59 TBT 4110 7.5 Microbiology O.Vadstein / P. Bruheim 80 / 63 TBT 4125 7.5 Food Chemistry T. Rustad 33 / 33 TBT 4130 7.5 Environmental Biotechnology K. Østgaard 12 / 11 TBT 4135 7.5 Biopolymers B.E. Christensen 42 / 38 TBT 4140 7.5 Biochemical Engineering P. Bruheim 27 / 27 TBT 4145 7.5 Molecular Genetics S. Valla 64 / 50 TBT 4150 7.5 Biochemical Engineering, plant design T. Ellingsen 5 / 5 TBT 4155 7.5 Increased Value of Marine Biological Resources K. I. Draget 3 / 3 TBT 4160 7.5 Organic Chemistry and Biochemistry B. E. Christensen 34 / 31 TBT 4500 15 Biotechnology, Specialization project P. Bruheim 15 / 15 TBT 4505 7.5 Biotechnology, Specialization course P. Bruheim 42 / 42 TBT 4850 7.5 Experts in Team, Interdisciplinary project O. Vadstein 22 / 22 PhD courses

Course no. Credits Title Lectures Started/ Passed

BT 8101* 9.0 Microbial Ecology O. Vadstein / K. Østgaard BT 8102 7.5 Molecular and Cellular Bioinformatics S. Valla 3 / 3 BT 8103 7.5 Molecular Mechanisms of Toxicology Aa. Haugen 17 / 16 BT 8104* 9.0 NMR Biomolecular Spectroscopy O. Dikiy BT 8105 7.5 Prokaryote Molecular Biology A.R. Strøm 10 / 10 BT 8106* 7.5 Glycobiology–Complex Carbohydrates,

Structure and Biological Function G. Skjåk-Bræk

BT 8114 7.5 Marine Biochemistry K.M. Vårum 8 / 8 BT 8115 7.5 Protein Structures O. Dikiy 13 / 13 BT 8110 9.0 Food Science, Advanced T. Rustad 5 / 5 BT 8112 5.0 Fish Salting T. Rustad 5 / 5 BT 8113* 7.5 Biomaterials K.I. Draget BT 8116* 7.5 Exp. methods in biopol./glycobiology B.E. Christensen

BT 8117 7.5 Marine lipids M. Aursand 7 / 7

*Course is given next time in 2010

33

Master students

Master of Science

Student Title Advisor

Ateba, Madeleine S. Assomo Effect of storage and processing of crab as raw material for emulsion based products (in Norwegian)

Turid Rustad

Brunsvik, Anders MS2 and MS3 mass spectral libraries and confirming analysis on LC/MS Iontrap (in Norwegian)

Per Bruheim

Buarø, Marita Lipids and selected enzymatic activities in Atlantic salmon(Salmo salar). (in Norwegian)

Turid Rustad

Finnstun, Elin Investigation of the functionality of the Pm//XylS cassette in Bacillus subtilis (in Norwegian)

Svein Valla

Gabrielsen, Christina Investigating use of the XylS/Pm expression system for production of recombinant proteins in Streptomyces spp.

Svein Valla

Haverstad, Ane Sunniva Characterization of transposon mutants in Azotobacter vinelandii (in Norwegian)

Svein Valla

Kim, Chung-Eun Determination of protein and lipid oxidation by near-infrared spectroscopy

Turid Rustad

Konradsen, Therese Aursand Characterization of genes that influences the biosynthesis of alginate in Pseudomonas fluorescens

Svein Valla

Kristoffersen, Venke Some properties of chemo- and enzymatically modified alginates Gudmund Skjåk-Bræk

Lieungh, Ida Is Lipocalin 2 involved in protection against bacterial urinary tract infections?

Svein Valla

Madsen, Birgitte Bargård Automated extraction of marine lipids (in Norwegian) Marit Aursand Vestrum, Ragnhild Inderberg Functionality of bacteria/cod larvae interactions (in Norwegian) Olav Vadstein

Lise Mari Klepp Andersen working hard in the lab. Photo: Cecilie Skagfjord.

34

Master of Technology

Eide, Kjersti Meldahl Alginate capsules for cell therapy - Effect of viscosity on capsule properties

Gudmund Skjåk-Bræk

Gustavesen, Bård Karsten Analylsis of gene expression data and genome-wide phenotype screen of Saccharomyces cerevisiae treated with DNA damaging cytostatica

Per Bruheim

Holm, Øyvind Underdal Characterization of mutants in the sucrose porins ScrY1 and ScrY2 from Azotobacter vinelandii (in Norwegian)

Helga Ertesvåg

Johansen, Arne Magne Properties of fish protein hydrolysates: Comparison of commercial and laboratory made hydrolysates

Turid Rustad

Klementsaune, Liv Kvistad Gene Therapy: Chitosan based nanoparticles for siRNA in human cells

Kjell Morten Vårum

Kvammen, Marita Helen Microbial shelf life of low-salt products. Effect of salt (NaCl) reduction in shrimps in brine

Marit Aursand

Lundesgaard, Therese Depolymerization mechanisms and degradation of Sodium Hyaluronat (in Norwegian)

B.E. Christensen

Malmo, Jostein Gene Therapy: Chitosan-based nanoparticles for siRNA delivery in human cells (in Norwegian)

Kjell M. Vårum

Moholdt, Øystein Distribution of water in fresh and frozen codmuscle studied by NMR (in Norwegian)

Marit Aursand

Ntaganda, Denis Alginate sequencing - Determination of absolute block length in native and epimerised alginates

Gudmund Skjåk-Bræk

Pedersen, Christin Thrane Examination of AVPR1A and KANK1 as autism susceptibility genes

Svein Valla

Poon, Cheau Ling Studies of lipid oxidation in salmon by near infrared spectroscopy

Turid Rustad

Refseth, Ingun Rygh Multiplexanalysis of biomarkes in human plasma and serum related to diet (in Norwegian)

Turid Rustad

Tomren, Henrik Berg Tissue engineering: Degradable alginate (in Norwegian) Bjørn E. Christensen

Wennberg, Aina Charlotte PCR-detection of Vibrio cholerae in ballast water Sergey Zotchev

Anne-Ma H. Carlsen and Magnus Hattrem happily posing for the photographer Cecilie Skagfjord.

35

Student exchange To Department of Biotechnology 2009

Name Institution Borges Colaço, Ana Instituto Superior Técnico Portugal Buchinger, Edith Aalborg University Denmark Halavaara, Monika Tampere University of Technology Finland Han, SangHee Dongguk University Rep. of Korea /

South-Korea Janze, Ann-Kathrin Lise Meitner Schule, Berlin Germany Krause, Benjamin University of Freiburg, Germany Germany Kristinova, Vera Brno University of Technology Czech Republic Lee, Hyejeong Dongguk Univeristy Rep. of Korea / Sør-

Korea Mainusch, Yvonne University Bonn (Rheinische-Friedrich-

Wilhelms-Universität) Germany

Mertens, Alan RWTH Aachen Germany Ovissipour, Mahmoudreza Tarbiat Modares University Iran Röderstein, Eva-Maria Lise-Meitner-Schule, Berlin Germany Shmidt, Alexander St Petersburg State Polytechnic

University Russian Federation

From Department of Biotechnology 2009 Name Master-

program Institution Egeland, Live MSc University of California, San Diego USA Evensen, Ida Maria MSc University of Glasgow Scotland Heien, Hilde Rau MSc University of Glasgow Scotland Røyrvik, Brita MSc University of California, San Diego USA Daviknes, Ingrid Marie Eriksen MT National University of Singapore Singapore Gytri, Stine Angeltveit MT Danmarks Tekniske Universitet Denmark Steine, Jan MT Newcastle University UK Hektoen, Helga Helseth MT University of California, Santa Barbara USA Møller, Elen Kristine MT University of California, Santa Barbara USA Sundrønning, Silje Beate MT University of California, Santa Barbara USA Sætrang, Henriette Elisabeth Myhr MT University of California, Santa Barbara USA Østnæs, Simen Johnsen MT University of California, Santa Barbara USA

36

6. ECONOMY The department income consists of university funding and overhead from external projects. In 2009 the income was 20.607.000, of which 75% was used to pay salaries to the permanent staff. In addition, the department has a high externally funded activity. In 2009 the total external income was 35.156.000,-. The number of external projects was approximately 60, and most of these were funded by the Norwegian Research Council. The expenses for external projects are mainly wages and overhead to the faculty. 55 technicians, PhD-students, post docs and researchers were externally funded in 2009. Accounts 2006 2007 2008 2009Income Public funding 15 886 000 16 535 000 19 481 464 20 607 144Overhead external projects 766 580 972 100 0* 0*Sum income 16 652 580 17 507 100 19 481 464 20 607 144Expenses Wages 13 724 606 14 060 711 14 209 033 15 390 305Operating expenses 3 950 796 3 270 038 4 604 835 5 317 094Sum expenses 17 675 402 17 330 749 18 813 868 20 707 399 Result -1 022 822 176 351 667 596 -100 255

*All overhead income is transferred to the faculty.

37

7. LUNCH SEMINARS Tid: Hver onsdag 12.15-13.00. Sted: Lunsjrom/bibliotek 039.

Programutkast (revidert 14.05) våren 2009:

Dato Uke Serie* Navn og tittel: 7/1 2 Pro Helga Ertesvåg: Pseudomonas aeruginosa biofilm development - - Bacterial multicellular behaviour to defeat our defences 14/1 3 Pro Geir Martin Haarberg, Inst. for materialtek.: Electrolysis for sustainable development – - New technologies for molten salts and for restoration of Lake Biwa 21/1 5 Asp Turid Rustad: Om melk og ost 28/1 4 Pro Olav Vadstein: Microbes as negative and positive actors in marine fish fry

production: - An ecological perspective 4/2 6 Pro Johan Pettersen, MISA as: Case biogas – perspectives & environmental systems

performance 11/2 7 Pro Trond Erik Vee Aune, Vectron Biosolutions AS: Synthetic biology 18/2 8 Avlyst grunnet allmøte med dekan 25/2 9 PhD Kari Johanne Kihle Attramadal: Recirculation as a microbial control strategy in

Marine fry production 4/3 10 Pro Bjørn Henrik Hansen, SINTEF Marin miljøtek.: Raudåte (Calanus finmarchicus) – - en ny og relevant testorganisme for vurdering av effekter av forurensning 11/3 11 Pro Oleksandr Dykyy: Structural BioNMR research at the NT Faculty NMR Center 18/3 12 Pro Finn Aachmann: Functional insights into the catalytic mechanism of methionine sulfoxide reductase B1 through structural analysis 25/3 13 Pro Yi-Qian Sun: Systems biology of a genetically engineered Pseudomonas fluorescens with inducible exo-polysaccharide production – Identification of transposon insertion mutants with altered alginate production 1/4 14 Pro Kurt I. Draget: Alginate oligomers in biomedicine 15 PÅSKE 15/4 16 Asp Sylvi Gaut, NGU: Hyttebrønner – om grunnvann og mikrober 22/4 17 PhD Hanne Jørgensen: Analysis of genes for the biosynthesis of polyene macrocyclic compounds in streptomycetes isolated from the Trondheim fjord 29/4 18 Asp Mentz Indergaard, NTNU Infoavd.: Illustrert institutthistorie 6/5 19 Asp Vibeke Videm, Inst. for laboratoriemedisin: Sant og usant om ernæring 13/5 20 Pro Øystein Grimstad, Hudavdelingen, St.Olavs Hospital: Atopic dermatitis and the skin barrier 20/5 21 Pro Martina Klučáková & Miloslav Pekař, Faculty of Chemistry, Brno University of Technology: Biocolloid research at FCH BUT 27/5 22 Asp Arne Strøm & Svein Valla: Crystal ball 2009 3/6 23 Asp Håvar Fuglem, Politiets sikkerhetstjeneste PST: Bioterror? Forebyggende virksomhet mot spredning av masseødeleggelsesvåpen 10/6 24 Asp Gudmund Skjåk-Bræk: Spanskesyken, hva var det, og hva kan vi lære av den når vi

nå står overfor en ny pandemi? 17/6 25 PhD Rahmi Lale: Improved features of the XylS/Pm expression system Sommeravslutning med kake. *Kode Fast under-tittel / kommentar:

Pro ”Hva gjør vi? Hva har vi lyst til å gjøre?”* * Vi i betydn. kongelig entall eller ”gruppa”. Lyst til i betydn. kommende 3-årsperiode. / Bidrag fra proffer, proffe forskere / post doc. og vitensk. ansatte.

PhD ”Graden min, den blir så fin!” / Bidrag fra PhD-studenter i alle faser av studiet. MoU ”Jeg forteller gjerne - om min diplom med * !” / Bidrag fra Masters of the Univers(ity); nyansatte og hovedfags-

studenter. Asp = Annet spennende!* * I betydn. med snev av fag, kultur, eller begge deler. / Bidrag fra gjester og andre. Hvem som

vil, egentlig.

38

Program (14/12) for høsten 2009:

Dato Uke Serie* Navn og tittel: 19/8 34 PhD Sigrid Hakvåg: Antibiotic-producing bacteria from the sea surface microlayer in the Trondheim fjord 26/8 35 Pro Shiho Suzuki: Film properties of enzymatically synsthesized amylose 2/9 36 PhD Murside Kes: Degradation of polysaccharides and paper studied by microcalorimetry 9/9 37 Pro Indra de Soysa, Dep. of Sociology and Political Science: Does globalization generate conflict or peace? 16/9 38 Asp Bjørg Ulsaker: Årets soppkurs 23/9 39 Pro Mette Langaas, Anvendt klinisk forskning DMF: Biostatistics - crossdisciplinary research and an example from analysing qPCR data 30/9 40 Pro Olav Vadstein: Mitt favoritt-økosystem 7/10 41 PhD Marie Hjelmseth Aune, Inst. kreftforskning: Evasion of immune response – Toll-like receptors and the Black Death 14/10 42 Pro Eivind Almaas: Network biology: From pretty pictures to deep insights 21/10 43 Pro Trond Erik Vee Aune, Vectron Biosolutions AS: Going commercial – the Vectron experience 28/10 44 Pro Aslak Einbu, Sintef Prosessteknologi: Post-combustion CO2 capture by amine absorption 4/11 45 Pro Alexander Wentzel: A systems biology approach to study the metabolic switch in Streptomyces coelicolor 11/11 46 PhD Marit Stafsnes: Microbial production of carotenoids 18/11 47 Asp Gunn Midtøy, Kjeldsberg kaffebrenneri: Fra bønne til kopp 25/11 48 Pro Marit Otterlei, Inst. for kreftforskning og molekylærbiologi DMF: Identification of a novel and widespread PCNA interacting motif with potential use in chemotherapy 2/12 49 PhD Fen Qin: Macromolecular properties of bioactive beta glucans from Saccharomyces

cerevisae 9/12 50 AsP Kjetill Østgaard: In Borderland 1: Norway East of Istanbul 16/12 51 Asp Olena Dobrovolska, Olga Sekurova and Irina V. Vodyanova: Waiting for Ded Moroz –how to celebrate X-mas Russian style *Kode Fast under-tittel / kommentar:

Pro ”Hva gjør vi? Hva har vi lyst til å gjøre?”* * Vi i betydn. kongelig entall eller ”gruppa”. Lyst til i betydn. kommende 3-årsperiode. / Bidrag fra proffer, proffe forskere / post doc. og vitensk. ansatte.

PhD ”Graden min, den blir så fin!” / Bidrag fra PhD-studenter i alle faser av studiet. MoU ”Jeg forteller gjerne - om min diplom med * !” / Bidrag fra Masters of the Univers(ity); nyansatte og hovedfags-

studenter. Asp = Annet spennende!* * I betydn. med snev av fag, kultur, eller begge deler. / Bidrag fra gjester og andre. Hvem som

vil, egentlig.

39

8. PERSONNEL

Kjetil Rasmussen

Eivind Almaas,

Professor Per Bruheim,

Assoc. Professor Bjørn E. Christensen,

Professor Olexandr Dikiy, Assoc. Professor

David Levine,

Professor Turid Rustad,

Professor Gudmund Skjåk-Bræk, Professor

Olav Vadstein, Professor

Svein Valla,

Professor Kjell M. Vårum,

Professor (Vice head)Sergey Zotchev,

Professor Kjetill Østgaard,

Professor

Head of department

Scientific staff

40

Unni Bragstad,

Secretary Wenche Lindseth,

Higher Executive Officer Cecilie Skagfjord, Executive Officer

Marit Aursand Kurt Ingar Draget Trond E Ellingsen Åge Haugen

Jens Nielsen

Hans Grasdalen Sverre M. Myklestad Olav Smidsrød Arne Strøm

Administrative staff

Adjunct professors

Professor emeritus

41

Trygve Andreassen,

Staff Engineer Kristin Antonsen,

Staff Engineer Anne Bremnes,

Engineer Merethe Christensen,

Staff Engineer

Åse Marie Fjelldal,

Engineer Martin Gimmestad

Senior Engineer Anita Hansen, Staff Engineer

Øyvind Johansen, Engineer

Marika H. Krogstad

Trainee Kjersti Ljones,

Engineer Tonje Stavne Staff Engineer

Siri Stavrum, Engineer

Anita Storsve,

Engineer Wenche Strand, Staff Engineer

Marit Syversveen, Staff Engineer

Gerd Inger Sætrom, Staff Engineer

Ann-Sissel Ulset, Staff Engineer

Randi Utgård, Staff Engineer

Technical staff

42

Ingrid Bakke Laila Berg Sven Even Borgos Anne-Ma H. Carlsen

Matilde S. Chauton Anne Sissel Duun Helga Ertesvåg Elin Finnstun

Espen Fjærvik Ingvild Haug Lisbeth Hultmann Elena Ian

Hanne Jørgensen Trygve D. Kjellsen Kåre A. Kristiansen Anna Lewin

Yrr Mørch

Aina Nedal

Catherine T.

Nordgård

Olga Sekurova

Researchers, Post docs.

43

Hege Sletvold Berit Strand Sabina Strand Yi-Qian Sun

Shiho Suzuki Alexander Wentzel Finn Aachmann

Researchers, Post docs.

44

Therese Andersen Simone Balzer Edith Buchinger Ana Karina Carvajal

Hanne Digre Elena Dobrovolskaya Marte S. Dragset Anette I. Dybvik

Kerstin Engelhardt Jonhard Eysturskard Torunn Forberg Kirsti Greiff

Ida Grong Aursand

Sigrid Hakvåg

Ellinor B. Heggset

Ole-Kristian Hess-

Erga

Murside Kes Thang Trung Khong Anne Krog Veronika Kucharova

Ph.D. students

45

Rahmi Lale Stina Katrine Lien Jostein Malmo Mali Mærk

Ingrid Overrein Fen Qin Marit Stafsnes Inger Beate Standal

Frederike Stüttgen Irina V. Vodyanova Zahra Zavareh Trine Aakvik

Olav Aarstad

Ph.D. students

DEPARTMENT OF BIOTECHNOLOGY, NTNUSem Sælands vei 6/8, 7491 Trondheim, Norway

Phone: +47 73593320 Fax: +47 73591283E-mail: postmottak@biotech.ntnu.no

Head of Department: Kjetil Rasmussen

Vice Head of Department: Professor Kjell M. Vårum

NTNUThe Norwegian University of Science and Technology (NTNU) in Trondheim represents academic eminence in technology and the natural sciences as well as in other academic disciplines ranging from the social sciences, the arts, medicine, teacher education, architecture to fi ne art. Cross-disciplinary cooperation results in innovative breakthroughs and creative solutions with far-reaching social and economic impact.

Address, contact informationDepartment of Biotechnology, NTNUN-7491 Trondheim NORWAY

E-mail: postmottak@biotech.ntnu.no Phone: (+47) 73593320

www.ntnu.no/bioteknologi

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