Mastergrad ved Institutt for biologi ved NTNU. Oversikt over tilbud av masteroppgaver I BIOTEKNOLOGI HØSTEN 2011

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1 Mastergrad ved Institutt for biologi ved NTNU Oversikt over tilbud av masteroppgaver I BIOTEKNOLOGI HØSTEN 2011

2 Kjære student Du som leser dette heftet går antakelig og vurderer om du skal skrive en masteroppgave ved Institutt for biologi. Du klarer kanskje ikke å bestemme deg for hvilket forskningsfelt du skal velge? Mulighetene er mange, og du er sikkert opptatt av å gjøre de riktige valgene. Vi har laget denne oversikten slik at du lettere skal kunne finne fram i det mangfold av forskningsfelt som finnes innen biologi ved NTNU. Du blir kanskje overveldet av mulighetene? La ikke det stoppe deg fra å studere biologi! Du tenker vel på framtidige jobbmuligheter når du skal velge studieretning? Eller, skal du heller velge ut fra egeninteresse? Det er ikke lett å gi gode råd i en slik sak, selv for veiledere som har hatt titalls av masterstudenter. I en periode er det lett å få jobb innen et fagområde, noen år seinere har dette endret seg. Hva som vil skje de neste årene er vanskelig å spå om, og kanskje vet dere det like godt som oss veiledere. Forskningsdelen av en master er krevende, og du skal fordype deg i ett ganske snevert forskningsfelt i flere semestre. Det er derfor ikke tvil om at du vil få best utbytte av en oppgave, og antakelig vil gjøre den beste innsatsen dersom du arbeider med en problemstilling som virkelig opptar deg. Våre råd er derfor at du primært velger en oppgave der du kan arbeide med et området du er interessert i. Mye av arbeidet vil da gå mye lettere! Det blir morsomt, inspirerende og gøy, og ingenting er mer attraktivt i arbeidslivet enn personer som trives og har det morsomt med sitt eget fag. Bruk derfor litt tid på å finne oppgaven din og snakk gjerne med flere veiledere. Oppsøk oss på kontorene, gjerne flere ganger. Har du egne ønsker og ideer, så er det et flott utgangspunkt, og vær ikke redd for å diskutere disse med potensielle veiledere. Studiet er en forberedelse til arbeidslivet, og det vi tror er det viktigste i dette studiet, er at du gjennom å fordype deg i en oppgave, lærer deg forskingsmetoder, kritisk tenking, besluttsomhet og ikke minst kreativitet i forhold til hvordan du skal arbeide praktisk og hvordan du skal uttrykke deg. En ferdig masteroppgave er som et stykke unikt kunstverk: formet og omstrukturert utallige ganger gjennom hardt arbeid og selvkritisk vurdering over lang tid. Alle veilederne som presenterer oppgaver her, vil gjøre sitt beste for at du skal lære mest mulig av faget biologi. Det er derfor vi er her! Lykke til med studiet! Bjørn Munro Jenssen Professor, leder for Institutt for biologi 2

3 Atle Bones Study of molecular defence- and resistance mechanisms against mildew in strawberry (Fragaria x ananassa Duch.) 4 Epigenetic effects of abiotic stress adaption in vegetative off-spring of Fragaria vesca 5 Genomanalyser av kiselalgen Seminavis robusta 6 Genomisk analyse av primærmetabolisme hos kiselalgen Seminavis robusta 7 Jens Rohloff Eco-values as product quality attributes in manufacturing of agricultural food ingredients 8 Berit Johansen A role for inhibition of lipid hormone production in fighting joint inflammation and bone reduction? 9 Martin Kuiper Modelling the links between carbohydrate diet and inflammatory response in humans 10 DNA-based Computing 11 Using text mining tools to extract specific knowledge from PubMed 11 Modelling stress response pathways in Arabidopsis 12 Richard Strimbeck Ecophysiology of dormancy and frost tolerance in boreal and temperate zone conifers 13 Winter light stress and chlorosis in conifer needles 14 Frost tolerance and dehydrins in temperate and boreal fir (edelgran) species 15 Jarle Mork Development and implementation of enzyme and lipososme assays for cryoprotective properties of metabolites and proteins 16 Natural frequency of species hybridization between plaice (Pleuronectes platessa L.) and flounder (Platichtys flesus) in the Trondheimsfjord and adjacent waters. 17 Elin Kjørsvik Mikrostruktur i hvitfisk: Effekt av salting og CAS frysing 18 I tillegg kan følgende oppgaver innen marine sciences være aktuelle: (Ikke beskrevet i dette heftet så ta kontakt ved interesse) Olav Vadstein: Marine microbiology Jana Guenther: Biofouling on aquaculture constructions Øyvind Prestvik: Recirculation Gunvor Øie: First feeding of cod larvae; rotifers and copepods Kjell Inge Reitan: Sustainable aquaculture; using excess nutrients from salmon farming to produce seaweed Trond Størseth: Metagenomics in marine systems Anders Olsen: Marine ecotoxicology Bjørn Henrik Hansen: Marine ecotoxicology Henrik Jensen Kartlegging av gener som påvirker fitness 19 Evolusjon av fuglenes genom 20 Jenny Hagenblad Genetic diversity of Scandinavian hops 21 Chevalier barley one or many varieties? 22 Clonal and seed propagation in ornamental plants 23 Genetic diversity in adaptive genes in barley 24 Gunilla Rosenqvist og/eller Christophe Pelabon Mating behaviour and reproductive success of male guppies from two different breeding regimes in competition.. 25 Evolution in captive populations 26 Evolution of multimodal sexual signaling and animal mating systems in pipefishes 27 Sindre Andre Pedersen Effekter av havforsurnings senarioer og kombinert stress på Raudåte (Calanus finmarchicus) 28 Augustine Arukwe Climate change, emerging pollutants and reproduction dysfunction in fish: Linking quantifiable measures of climate change with pollution and biological consequences (4-5 master thesis) 29 3

4 Atle Bones Jens Rohloff, Jahn Davik Study of molecular defence- and resistance mechanisms against mildew in strawberry (Fragaria x ananassa Duch.) * The demand for strawberries is increasing due to the fruits flavour and health-beneficial phytochemicals * Mildew infection occurs on leaves, but additional infection of berries leads to severe yield loss * MLO genes (mildew resistant locus o) are activated in F. x ananassa upon pathogen attack Studies in other crop species have been shown that induced resistance against pathogens, including barley, tomato and potato, might be obtained. The hypothesis is that the pathogen needs a specific plant protein produced by MLO genes in order to infestate the organism. If the proteins are not produced in their correct form, or not produced at all, the plant might become resistant. MLO genes have also been shown to be active in the plant model Arabidopsis (AtMLO2, AtMLO6, AtMLO12) with high homology to strawberry. Goals and approaches in Fragaria * Characterization of MLO-genes and related defence transcripts by qrt-pcr * Study of direct and systemic defenced responses through application of metabolite profiling 4

5 Atle Bones Jens Rohloff, Jahn Davik Epigenetic effects of abiotic stress adaption in vegetative offspring of Fragaria vesca * Plants must respond and adapt to abiotic stresses to survive in various environmental conditions, e.g. low temperatures * Genome-wide analyses have revealed networks controling transcription, protein modification, and metabolism * Epigenetic regulation via changes in nucleosome distribution, histone modification, and DNA methylation plays a key role in abiotic stress gene networks The woodland strawberry (Fragaria vesca) has been introduced as a new model plant for the Rosaceae familily, and its draft genome has recently been published. The project will be integrated as part of on-going project activities for the development of freezing tolerant strawberry varieties (Graminor AS, Bioforsk, HIH, IUPUI/IN and NTNU), were genomic, proteomic, and metabolomic approaches are applied. The question, in which way epigenetic regulation impacts on plant adaption toward abiotic stress, will be adressed in this master project. Single and combined effects of (a) abiotic stress (cold), and (b) artificial triggers (methyl jasmonate) will be studied against control groups. Experiments are intended to run over multiple generations in order to deduce generation-togeneration effects. Plant samples will primarily be subjected to metabolite profiling to trace changes in metabolic phenotypes, but other molecular methods are likely to be applied, too. 5

6 Atle Bones Tore Brembu, Per Winge Genomanalyser av kiselalgen Seminavis robusta Kiselalger er encellete fotosyntetiske organismer som finnes både i fersk- og saltvann. De regnes for å være den viktigste gruppen av eukaryotiske planteplankton, og står for rundt 40 % av primærproduksjonen i havet. Kiselalger er også en svært artsrik gruppe, med opptil arter. Til nå har genomet til to kiselalger blitt kartlagt. Vi er i ferd med å sekvensere genomet til en tredje art, Seminavis robusta; selve sekvenseringen antas å være fullført våren Foreløpige analyser tyder på at S. robusta-genomet inneholder minst dobbelt så mange gener som de to kartlagte kiselalgene. En hovedoppgave blir derfor å identifisere genmodeller, dvs. finne start og stoppkodon til gener samt exon/intron overganger. Et av programmene vi vil benytte her er FGENESH++ fra Softberry.com, hvor vi vil benytte kjente genmodeller fra andre diatomer som guide. I tillegg vil vi sette opp en genomviewer (GBrowse) hvor en kan analysere og annotere genene (gi navn og beskrive de ulike genene). Vi planlegger også i løpet av året å lage en microarray chip for Seminavis robusta som vil bli brukt til å analysere gen transkripsjon under ulike eksperimentelle betingelser. En del av Master oppgaven kan derfor også påregnes brukt ved analyser av disse datasettene. Vi ser derfor etter en Master student som er interessert i generell bioinformatikk og som har kjennskap til databaser og kan litt programmering. Det er også en fordel at man har kjennskap til Linux/Unix operativsystemer da det meste av software er skrevet for disse systemene. Beregningsbasert biologi 6

7 Atle Bones Tore Brembu, Per Winge Genomisk analyse av primærmetabolisme hos kiselalgen Seminavis robusta Kiselalger er encellete fotosyntetiske organismer som finnes både i fersk- og saltvann. De regnes for å være den viktigste gruppen av eukaryotiske planteplankton, og står for rundt 40 % av primærproduksjonen i havet. Kiselalger er også en svært artsrik gruppe, med opptil arter. Til nå har genomet til to kiselalger blitt kartlagt. Vi er i ferd med å sekvensere genomet til en tredje art, Seminavis robusta; selve sekvenseringen antas å være fullført i.l.a. våren Foreløpige analyser tyder på at S. robusta-genomet inneholder minst dobbelt så mange gener som de to kartlagte kiselalgene. Oppgaven går ut på å karakterisere de metabolske sporene som er involvert i primærmetabolisme hos S. robusta. Ved hjelp av databasesøk (BLAST) og enzymdatabaser (KEGG) vil gener som koder for enzymer involvert i disse prosessene bli identifisert. Analysen vil inkludere studier av genfamiliene for de ulike enzymene med tanke på for eksempel ulik substratspesifisitet. Evolusjonære analyser vil bli gjort for å studere opprinnelse og slektskap til ulike gener og metabolske spor. Disse studiene kan suppleres med en praktisk del om ønskelig. Beregningsbasert biologi 7

8 Jens Rohloff Tor-Henning Iversen Eco-values as product quality attributes in manufacturing of agricultural food ingredients * Worldwide, a growing demand for green, healthy and ethically produced, i.e. eco-branded food products is evident * Development of eco-branded food needs to be monitored in the entire value chain ("fra jord til bord") * Production of new and healthier agricultural food ingredients is imperative to replace non eco-friendly elements Focus on locally produced food ingredients with low carbon foot-print is one major focus of the master project, which will be integrated as part of a 4-years NFR-project between NHH Business School in Bergen and NTNU. Due to on-going agreements between funding industry partners, and the project group, the content of biologically and food-related issues is not yet defined. However, essential key topics, which have been predefined as Case Studies, might be adressed as part of the master project, and include: I Substitution of palm oil with e.g. rapeseed oil, study of locally produced oil quality and test products II Local cultivation of fruits and berries, mapping of health-beneficial chemical parameters in raw materials and value-added products 8

9 Navn på biveiledere etc. Kort arbeidstit tel Kort beskrivelse av oppgaven (opptil 60 ord) Grundig beskrivelse (opptil 300 ord) Prof. Berit Johansen Astrid J. Feuerherm, Randi M. Sommerfelt, Thuy Nguyen, Mari Sæther A role for inhibition of lipid hormone production in fighting joint inflammation and bone reduction? Prostanoids are important signalling molecules involved in a wide range of inflammatory diseases. A better understanding of the signalling pathways leading to prostanoid production may contribute to the development of new generation pharmaceutics to combat disease. The master thesis will aim to reveal some of the signalling events in a rheumatoid joint. The involvement of eicosanoids in inflammation is well known, as reducing the activity of enzymes responsible for their synthesis efficiently reduces the symptoms of inflammation: heat, redness, oedema, pain and loss of function. In general, eicosanoids have pleiotropic effects and may contribute in regulating various cellular processes: growth, proliferation, apoptosis, migration, inflammation, pain, tissue homeostasis. A resulting cellular behaviour during various environmental conditions will perhaps be determined by the ratio of the various eicosanoids present. The maintenance of adequate bone mass is dependent upon the controlled and timely removal of old, damaged bone. This complex process is performed by the highly specialized, multinucleated osteoclast. Over the past 15 years, a detailed picture has emerged describing the origins, differentiation pathways and activation stages that contribute to normal osteoclast function. These findings include the identification of the RANK- RANKL-OPG system as a primary mediator of osteoclastogenesis, the characterization of ion transport and cellular attachment mechanisms and the recognition that matrix-degrading enzymes are essential components of resorptive activity. Another example of joint inflammation is engagement of Toll-like receptors 2 or 4 (TLR2/4), which is reported to mediate bone loss. Though inflammatory bone loss in experimental diseases models can be produced by engagement of TLR4, it is uncertain which mechanisms are included, like if and which matrix-degrading enzymes and regulators are engaged. In a cellular model for rheumatoid arthritis we have observed that SW982 synoviocytes respond by secreting PGE2 in response to cytokines like IL-1 and TNF. Thus, TNF-stimulation reduces the expression of the bone protector OPG mrna, suggesting a role for PLA2 and COX enzymes and their metabolites in bone maintenance. Possible master theses: 1) OPG/DKK1/RANKL Elisa on TNF induced SW982 cells, an osteoclast disease modell. Identification of a novel therapeutic target. 2) Characterisation of TLR2/4-induced responses, and possible involvement of cpla2 in an opsteoclast cell model 3) Development of an Immunhistochemic detection method of cpla2 group IVa and its phosphorylated form by confocal laser microscopy. 9

10 Navn på hovedveileder: Navn på biveiledere etc. Kort arbeidstittel på oppgaven (Opptil 20 ord) oppgaven (opptil 60 ord) Grundig beskrivelse (opptil 300 ord) Lenke 1 Lenke 2 Martin Kuiper Berit Johansen Modelling the links between carbohydrate diet and inflammatory response in humans The student will model the response cascade that link carbohydrate-rich diets to known inflammatory processes. Information will come from public datasources, and a comprehensive model will be generated in the network editing program CellDesigner. Different submodules will be defined, corresponding to different steps in the signalling cascade, and model checking will be done with functional genomics datasets including microarray data. We hypothesise that a carbohydrate-rich diet may cause a major deregulation of hormonal balance, causing both acute and chronic systemic inflammatory reactions mediated by white blood cells; we have preliminary evidence that this is caused by a carbohydrate-rich diet. This project is part of an integrated multidisciplinary systems biology approach to identify the hormones, genes and pathways specifically responding to a dietary carbohydrate reduction. We will use existing small regulatory networks for macrophages, monocytes and dendritic cells that we will extend with public and project data to model onset of inflammatory cascades. We will exploit existing biomodels including those of various kinases (ERK/MAPK, insulin receptor, growth hormone), lipid kinases (ex. PI3K/AKT), JAK/STAT, WNT/B-catenin, transcription factors (NFkB, CREB, SREBP-1c, PPARa and more) pathways. The modeling will be performed with CellDesigner, a pathway editing software developed for biologists. The project has the following phases: -Getting familiar with CellDesigner and the various databases that contain plant stress response information. -Convert appropriate insulin-signaling and inflammatory response information into CellDesigner models -Identify specific modules in these networks related to signaling cascade step, select a module and extensively test it for descriptive and simulation results -Further enhance a module by analysing available literature with the help of text mining tools (ihop, LitInspector) -Further enhance a module by analysing available functional genomics data, based on analysis of descriptive and simulation properties, in the framework of current experiments ongoing in the labs of Kuiper and Johansen. Systems Biology 10

11 Hovedveileder: Martin Kuiper Pauline Haddow DNA-based Computing We will extend on published results on hybridisation based computing, using array-based ligation and PCR to detect or amplify specific DNA sequences that represent the match between DNA array patterns and a substrate that represents a question. This is a new area at NTNU, and the project will be designed and executed together with the Department of Informatics / IDI. Biotechnology / Information Technology / Synthetic Biology Martin Kuiper Heri Ramampiaro - IDI Using text mining tools to extract specific knowledge from PubMed Today s high throughput experiments yield enormous amounts of data, and analysis of these data may provide large numbers of hypotheses. It is impossible to verify all these individual hypotheses, so we are developing an approach to integrate a wide diversity of information to see if this additional knowledge will help to highlight and prioritise particular hypotheses for experimental investigation. A tremendous amount of knowledge is hidden in the scientific literature, and the challenge is to find and extract such knowledge through automated means. Several text mining tools exist, a selection of these will be tried to optimise the detection of information about pairs of specific genes or gene products: the relationship between a transcription factor and a target gene regulated and expressed through that transcription factor. The results of this automated text mining will be entered into a database and used to asses high throughput hypotheses. Biotechnology / Integrative Biology / Information Technology 11

12 Navn på hovedveileder: Navn på biveiledere etc. Kort arbeidstittel på oppgaven (Opptil 20 ord) oppgaven (opptil 60 ord) Grundig beskrivelse (opptil 300 ord) Lenke 1 Lenke 2 Martin Kuiper Atle Bones Modelling stress response pathways in Arabidopsis Plants have an elaborate system to deal with environmental stresses. In this project a comprehensive model of the Arabidopsis stress response pathways will be produced from public datasources, in the network editing program CellDesigner. Different modules will be defined in this network, covering various abiotic and biotic stresses. The response of the different pathways will be tested with microarray datasets. Plants have to cope with a large variety of environmental stresses like drought, heat, cold, or fungal and insect attacks, just to name a few. In agriculture, these stresses can cause great losses in production of food and feed, and plant stress response is the subject of many studies. Much of the information from these efforts is available in public literature, or in databases. The challenge is to assemble much of these data in pathway models that can help to understand the dynamics of stress responses. Models lie at the foundation of systems biology, and in this project we will build response models that can be tested against public and laboratory data to check the model s descriptive accuracy. Models will be built in CellDesigner, a software program specifically developed for biologists to build network models and analyse them by overlaying for instance microarray data, or use them for computer simulations. The project will have the following phases: -Getting familiar with CellDesigner and the various databases that contain plant stress response information. -Convert appropriate stress response information into CellDesigner models -Identify specific modules in these networks related to stress type, select a module and extensively test it for descriptive and simulation results -Further enhance a module by analysing available literature with the help of text mining tools (ihop, LitInspector) -Further enhance a module by analysing available functional genomics data, based on analysis of descriptive and simulation properties, in the framework of current experiments ongoing in the labs of Kuiper and Bones. Systems Biology 12

13 Navn på hovedveileder: Navn på biveiledere etc. Kort arbeidstittel på oppgaven (Opptil 20 ord) oppgaven (opptil 60 ord) Grundig beskrivelse (opptil 300 ord) Førsteamanuensis Richard Strimbeck Ecophysiology of dormancy and frost tolerance in boreal and temperate zone conifers Over the course of a winter, monitor frost tolerance and determine chilling requirements and temperature sums for dehardening and bud break in Norway spruce, Scots pine, or other conifer species. As part of our ongoing research on the winter ecophsyiology of conifers, we need baseline data on seasonal changes in frost tolerance and dormancy in several pine, spruce, and fir species. The development of dormancy and frost tolerance in needles of conifers from temperate and boreal regions is fine-tuned to local light and temperature environments to ensure that they can survive light and low-temperature stress and minimize respiratory losses during the dormant season. Dormancy and frost acclimation is triggered by short days and reinforced by low temperature. Trees and shrubs generally have chilling and temperature sum requirements for loss of dormancy, but these are not known for many species. Bud forcing and deacclimation experiments can provide important information about these responses. The results are relevant to understanding and predicting the effects of climate change on the phenology of dormancy and growth. Lenke

14 Navn på hovedveileder: Navn på biveiledere etc. Kort arbeidstittel på oppgaven (Opptil 20 ord) oppgaven (opptil 60 ord) Grundig beskrivelse (opptil 300 ord) Førsteamanuensis Richard Strimbeck Winter light stress and chlorosis in conifer needles Monitor the development of winter chlorosis and conduct experiments to develop a more complete picture of the ecophysiology of winter light stress in Norway spruce and Scots pine. In winter, the needles of evergreen conifers are exposed to a combination of low temperature and bright light that sometimes results in severe chlorosis or yellowing. Although various aspects of this phenomenon have been studied, a combination of field study and lab experiments should yield a more complete picture of the separate and interacting effects of temperature and light and some of the physiological processes resulting in chlorosis. The project would include field monitoring of trees in high and low stress locations, and lab experiments involving exposure to low temperature and light. Applicable methods include image analysis to quantify the color change, chlorophyll fluorescence, measurement of pigment concentrations via HPLC, and Western blotting of photosynthetic proteins. Field work will include sample collection and field measurements during winter in Estandstadmarka or Bymarka, so good ski skills will also be useful! Lenke

15 Navn på hovedveileder: Navn på biveiledere etc. Kort arbeidstittel på oppgaven (Opptil 20 ord) oppgaven (opptil 60 ord) Førsteamanuensis Richard Strimbeck Frost tolerance and dehydrins in temperate and boreal fir (edelgran) species Monitor frost tolerance and relative dehydrin levels in several fir species Grundig beskrivelse (opptil 300 ord) Lenke 1 The arboretum at the Ringve Botanical Garden includes thirteen species of fir (Abies spp.), with seven of the same and two more species available for study in the Lippes arboretum in Bymarka. These collections offer an opportunity for comparative study of frost tolerance in a broad range of temperate and boreal species within the genus. We have already been successful in using this approach to characterize differences in frost tolerance and acclimation patterns in several conifer species. The project will involve seasonal monitoring of frost tolerance by controlled freezing and electrolyte leakage, and extraction and detection of dehydrins, key proteins involved in stress tolerance, via Western blotting. There is also the possibility of doing some 2D gel electrophoresis to identify other proteins involved in frost tolerance. Data analysis involves advanced non-linear curve fitting using statistical software. The results should contribute toward an understanding of the biochemistry and biophysical mechanisms of extreme frost tolerance, and will complement the results of a master s project on spruce (Picea spp.) that is currently underway. Lenke 2 15

16 Navn på hovedveileder: Navn på biveiledere etc. Kort arbeidstittel på oppgaven (Opptil 20 ord) oppgaven (opptil 60 ord) Grundig beskrivelse (opptil 300 ord) Førsteamanuensis Richard Strimbeck Development and implementation of enzyme and lipososme assays for cryoprotective properties of metabolites and proteins 1. Measure enzyme activity after freezing 2. Measure leakage from fluorescein dye filled liposomes after freezing; over a range of temperatures to develop freezing response curves, with and without cryoprotective substances. Numerous substances, including sucrose and other sugars, some specialized proteins, and some low molecular weight metabolites, are known or purported to protect proteins, cells, or tissues from the destructive effects of freezing. While there are some existing assays for these effects, they are problematic because they involve enzymes that are not notably freeze-labile and have not to date been applied across a full range of freezing treatments to full characterize they nature of the response. I need to find one or more enzymes that respond to freezing and improve on an existing liposome assay so that I can use these assays to characterize the cryoprotective properties of proteins extracted from super frost tolerant Siberian spruce and other species. The student will also gain experience in data analysis using non-linear curve fitting. The work might also extend to using Modulated differential scanning calorimetry (MDSC) to quantify glass transitions in sugar-protein mixtures. The results of this work may ultimately lead to improvements in techniques for frozen and dried preservation of biological materials. Lenke 1 Lenke 2 16

17 Navn på hovedveileder: Navn på biveiledere etc. Kort arbeidstittel på oppgaven (Opptil 20 ord) oppgaven Jarle Mork, IBI, NTNU Henk van der Veer, Niox, Nederland Natural frequency of species hybridization between plaice (Pleuronectes platessa L.) and flounder (Platichtys flesus) in the Trondheimsfjord and adjacent waters. Plaice and flounder are genetically close species, and are easily hybridized by artificial fertilization. Hybridization is known to occur in nature, but to an unknown and maybe different degree in different areas. Speies hybrids are easily identified by isozyme-based techniques in the laboratory. The project will collect flatfishes (all sizes) for freezer stoarage and later species/hybrid identification by electrophoresis and histochemical staining of enzymes in tissue samples. The results will be analyzed relative to biogical and microgeographic factors. Cooperation will be established with the internationally wellreputated flatfish expert Henk van dr Veer at NIOX, Texel, The Netherlands. Field work will involve ~ 3 months collection of flatfishes from different locations in thetrøndelag region vinter/spring/summer in one year. The lab work will take place in the genetics lab at Trondhjem Biological Station in Bynesveien. Lenke 1 Lenke

18 Elin Kjørsvik Ulf Erikson Mikrostruktur i hvitfisk: Effekt av salting og CAS frysing Konsistens/teksturegenskapene til både fersk og prosessert fisk er viktige for produktets kvalitet. Ulike analysemetoder benyttes for å måle ulike parametre som karakteriserer et produkts konsistens. Dette kan f.eks. være mekanisk sammenpressing, bestemmelse av vanninnhold, vannbindingsevne, fordeling av fritt og bundet vann, og proteinenes løselighetsegenskaper. Dersom en i tillegg kan bestemme produktets mikrostruktur, vil en kunne få en bedre forståelse av hvordan prosesseringen påvirker et fiskeprodukts funksjonelle egenskaper. Oppgaven vil gå ut på å studere mikrostruktur i fersk, frosset/tint, og saltet hvitfisk. Resultatene skal korreleres opp mot resultatene fra de andre målemetodene nevnt ovenfor. Oppgaven er knyttet opp mot to prosjekter ved SINTEF Fiskeri og havbruk: (1) KMB DANTEQ tar sikte på å fremskaffe ny kompetanse og utvikle metoder for å optimalisere håndtering av fisk ombord på fiskefartøy. I en av arbeidspakkene, Refrigeration technology and fish quality, skal en blant annet studere en nye frysemetode, Cells Alive System (CAS). Oppgaven vil her knyttes til CAS frysing av fersk fisk. (2) I prosjektet KMB Low salt products er målet å redusere saltinnholdet i fiskeprodukter (farse). I oppgaven vil en her se på hvordan ferskt vs frosset/tint råstoff, og ulike saltkonsentrasjoner, påvirker sluttproduktets (farse) egenskaper. Marine Coastal Development 18

19 Navn på hovedveileder: Navn på biveiledere etc. Kort arbeidstittel på oppgaven (Opptil 20 ord) oppgaven (opptil 60 ord) Grundig beskrivelse (opptil 300 ord) Henrik Jensen Bernt-Erik Sæther og Ingelin Steinsland (Institutt for matematiske fag) Kartlegging av gener som påvirker fitness Disse to oppgavene vil gi deg en unik mulighet for å lære stateof-the-art genomiske teknikker, og å bruke disse til å besvare spørsmål knytta til økologi og evolusjon i naturlige bestander. Fitness er en kombinasjon av overlevelse og reproduksjon, og måles ofte som bidraget til framtidige generasjoner. Målet med denne oppgava er å bruke data fra et langtidsstudie på gråspurv i tre naturlige populasjoner på Helgelandskysten for å: a) finne ut hvor på kromosomene gener som påvirker fitness ligger, og b) undersøke om noen av disse genene ligger på kjønnskromosomene. Dataene som vil bli brukt er genetisk informasjon på ca SNPs fra ca gråspurv med kjent slektskapsforhold. Denne informasjonen vil kombinieres med fenotypiske data på fitnessrelaterte trekk i QTL-analyser for å finne ut hvor i genomet slike gener befinner seg. Hovedsakelig vil det inngå analyser av store mengder genetiske data og statistisk modellering, men litt feltarbeid kan også være aktuelt. Lenke 1 Lenke Bioteknologi, Evolusjonsbiologi og systematikk/taksonomi, Økologi 19

20 Navn på hovedveileder: Navn på biveiledere etc. Kort arbeidstittel på oppgaven (Opptil 20 ord) oppgaven (opptil 60 ord) Grundig beskrivelse (opptil 300 ord) Henrik Jensen Bernt-Erik Sæther og Ingelin Steinsland (Institutt for matematiske fag) Evolusjon av fuglenes genom Disse to oppgavene vil gi deg en god mulighet for å lære hvordan en kan bruke de enorme mengdene genetisk informasjon som finnes i for eksempel GenBank til å besvare viktige evolusjonære spørsmål. Oppbygning av genomet og hvordan dette endrer seg over tid er viktige spørsmål i evolusjonsbiologien. To viktige spørsmål i denne sammenhengen er for det første hvor raskt (mellom arter) rekkefølge av gener på kromosomene endrer seg, og for det andre hva slags faktorer som påvirker hvor ofte nye allelkombinasjoner testes ut ved rekombinasjon. Målet med denne oppgava er å bruke genetiske data fra naturlige gråspurvbestander, og sammenligne dette med genetisk informasjon fra andre fuglearter lagra i for eksempel GeneBank for å undersøke: a) Om kromosomene har samme oppbygning hos ulike fuglearter, og b) Om rekombinasjonsrater varierer mellom ulike fuglearter, eller mellom kjønnene. Lenke 1 Lenke 2 Dataene som vil bli brukt er genetisk informasjon på ca SNPs fra ca gråspurv med kjent slektskapsforhold. Denne informasjonen vil sammenlignes med genetiske data fra de samme genene hos andre fuglearter som for eksempel høne og sebrafink. Hovedsakelig vil det inngå komparative analyser av store mengder genetiske data og statistisk modellering, men litt feltarbeid kan også være aktuelt hvis du ønsker det. Bioteknologi, Evolusjonsbiologi og systematikk/taksonomi, Økologi 20

21 Jenny Hagenblad Else-Marie Karlsson Strese Genetisk diversitet i Skandinavisk humle Genetic diversity of Scandinavian hops Hops has long been valued as an important ingredient in beer production and it has been cultivated in Scandinavia since the 10th century. It is a bisexual plant, but in cultivation it is clonally reproduced as it is only the female plants that are of interest to hops growers and beer makers. Historic cultivation of hops is fairly well described in old litterature, but not well understood from a genetic perspective. Previous studies have been unable to shed light on the cultivation history of hops. Where were hops introduced from or was native hops used? How clonal are hops plants? Are the hops plants that can be found today at old mansions the remnants of old hops gardens? In this project you will visit old mansions, primarily in Sweden, that are shown on historical maps to have cultivated hops. There you will collect hops plants that may be descendants of hops cultivated in 17th century hops gardens. You will then work in the lab and genotype these using microsatellite markers to learn both about the cultivation history of hops and its propagation biology. You will learn lab techniques such as DNA extraction, PCR and microsatellites analysis and some standard genetic analysis methods. You will also learn about the history of hops cultivation. Ecology, evolution, molecular biology. 21

22 Jenny Hagenblad Chevalier-bygg en eller flera sorter? Chevalier barley one or many varieties? Plant breeding efforts and improvement of barley begun during the late 19th and early 20th century. One of the early varieties developed was the hugely popular Chevalier variety, that was cultivated over large areas. However, it was not always that names was used strictly for a genetically distinguished variety, but sometimes it was used to describe a range of varieties of similar morphological type. Chevalier barley has been preserved in genebanks, but it is also available from a large number of locations, preserved in historical seed collections. In this project you will work in the lab and genotype Chevalier barley from many different sources, both live and 100-year-old seeds, using microsatellite loci. You will determine both the within-population genetic diversity and see if and how much Chevalier barley samples differ from each other. Is what is called Chevalier barley in the genebank the same as what was cultivated as Chevalier barley 100 years ago? You will learn lab techniques such as DNA extraction, PCR and microsatellites analysis and some standard genetic analysis methods. Evolution, molecular biology. 22

23 Jenny Hagenblad Klonal förökning och fröförökning hos prydnadsväxter Clonal and seed propagation in ornamental plants Many ornamental plants are propagated clonally but taking cuttings or shoots from the mother plant. This means that the daughter plant will be genetically identical to the mother plant which is advantageous for the gardener as it ensures that fragrance, leaf shape and flower appearance continues to have the desirable appearance. Genetic analysis of clonally propagated ornamental plants, however, sometimes gives a conflicting message as different members of the same clone have distinct genetic profiles. There are several possible explanations for this. There can be mutations in the genetic markers, markers can be erronously genotyped or maybe the clone is not a clone but the result of seed propagation. In this project you will sample individuals of a clonally reproduced ornamental or other cultivated plant (e.g. peony, rose, tulip, hops, rhubarb or onion) that you chose. You will then genotype the individuals with one of several marker types of your choice and examine to what extent seed propagation is present, to what extent different markers mutate and how reliable different markers are for genotyping. You will learn lab techniques such as DNA extraction, PCR and analysis of microsatellites and other markers as well as some standard genetic analysis methods. Evolution, ecology, molecular biology. 23

24 Jenny Hagenblad Genetisk diversitet i adaptiva gener i bygg Genetic diversity in adaptive genes in barley Unimproved landraces are believed to be genetically more variable than modern varieties and analysis of neutral genetic markers such as microsatellites shows this to be true. However, landraces are also expected to be adapted to the climate and growth conditions of their geographic origin and genes involved in this should be less variable than neutral markers. This has, however, never been investigated and in genetic studies of cultivated plant single individuals are usually investigated and assumed to be representative for the whole variety. In this project you will use 100-year-old seeds of barley from Scandinavia and Europe. You will genotype these for flowering time genes that should have been important for adaptation to growth at different lattitudes. By sequencing these for multiple individuals from the same landrace population you will gain an understanding of the within and between population diversity at adaptive genes. You will also be able to analyse your data for signals of selection and show if the genes have indeed been involved in adaptation. You will learn lab techniques such as DNA extraction, PCR and sequencing as well as some standard genetic analysis methods. Evolution, ecology, molecular biology. 24

25 Gunilla Rosenqvist, Christophe Pelabon Tonje Aronsen Mating behaviour and reproductive success of male guppies from two different breeding regimes in competition. This project aims at testing whether the absence of sexual selection in captive populations may affect the competitive ability of males to sire offspring In a project started in 1998 small populations of guppy (Poecilia reticulata) have been bred in captivity for 12 generations, under two different breeding regimes. In the first type of breeding regime, the 10 males and 10 females comprised in the population at each generation were allowed to interact freely thereby experiencing sexual selection via mate choice and intra sexual competition. In the second breeding regime, breeding pairs with one male and one female, chosen to be the most distant genetically were placed together, therefore preventing any sexual selection. This experimental designed produced a set up of 10 polygamous vs. 9 monogamous lines of guppies maintained under different breeding regimes during 12 generations. We expect that during these 12 generation differences occurred in the selection pressures with respect to sexually selected traits favoured by male-male competition. in the two breeding regimes, and that males from the two breeding regimes may have evolved differently and that males from the polygamous populations may perform better than males from the monogamous populations in pre- and postmating competition. In this experiment, males from the two breeding regimes will be placed in a real competition situation over a female. Courtship behaviour and mating activity will be recorded. After the trial the female will be isolated in a tank to give birth. Microsatelite markers will be used to resolve paternity. This should therefore tell us whether behavioural observations of mating preference are in agreement with paternity data. Etologi, ekologi, molekulär 25

26 Gunilla Rosenqvist, Christophe Pelabon Geir Bolstad Evolution in captive populations Study of evolution in captive populations is important both for our understanding of evolution, and for conservation. With this project we want to understand if female choice can explain evolved morphological differences in captive populations. Morphological, behavioral and genetic divergence of isolated populations is the basis of speciation and therefore the biodiversity we observe today. It has been often suggested that sexual selection and particularly mate preference can strongly affect the frequency and the speed of this process, because divergence in mating preference can affect directly the reproductive isolation. This project will test whether divergence in female preference can happen after only few generations of isolation. We have ten populations of guppies, originating from a common population, that have been in the lab since 1998 (11 generations). These populations have evolved morphological differences in sexually selected traits. We now want to know if female preference for the sexually selected traits in males have also diverged among populations, and if the differences in female choice can explain the morphological differences observed in males. The female preference for the sexually selected traits will be obtained by mate choice experiments, where female guppies inspect several different male guppies visually, and we record how the female behave. The data obtained from this experiment will be very interesting since we both have population differences, and diverging selection pressures that leads to population differentiation. This has very rarely been obtained before. Key words: Behavioral ecology; Conservation biology; Quantitative genetics; Guppy; Lab. Økologi, Etologi, Evolusjonsbiologi, Molekylærbiologi 26

27 Gunilla Rosenqvist, Anders Berglund, Josefin Sundin (Uppsala Universitet) Evolution of multimodal sexual signaling and animal mating systems in pipefishes Investigate the evolution of signaling under various environmental regimes, and how signaling constraints may affect sexual selection and mating systems. The study organisms are the deep-snouted pipefish Syngnathus typhle, the straight-nose pipefish Nerophis ophidion. These two marine species are sex-role reversed, i.e. in mating; males are the limiting resource which females compete for. Females likely rely on multiple cues to communicate with males and to compete with other females in order to increase their mating success. The eutrophication in our waters leads to an explosive growth of filamentous algae; this will increase water turbidity and reduce visibility. Consequently, sexual selection on visual signals may be impaired, and females may be forced to use other signals. Here we will investigate if environmental perturbation has any effect on sensory modalities, such as visual, olfactory and auditory cues. Predictions about population density, biodiversity changes and the intensity of sexual selection to assess unexpected consequences from climate change will be tested. The study will be conducted on Gotland. Økologi, Etologi, Evolusjonsbiologi, Molekylærbiologi 27

28 Sindre Andre Pedersen Bjørn Munro Jenssen ++ Effekter av havforsurnings senarioer og kombinert stress på Raudåte (Calanus finmarchicus) Masterstudenten(e) vil utføre eksperimentelle studier for å avdekke mulige negative konsekvenser av nært forestående havforsurnings senarioer på nøkkelarten Raudåte. Siden Raudåte har en nøkkelrolle i det pelagiske næringsnettet i Nordsjøen og Barentshavet kan negative effekter få alvorlige konsekvenser på økosystemnivå. Det er derfor behov for data på langtidseffekter av realistiske senarioer for havforsurning. Det er også viktig å undersøke effekten av forhøyet CO 2 konsentrasjon opp mot andre viktige miljøfaktorer som temperatur (global oppvarming), mattilgang og miljøforurensning (f.eks olje) siden økt CO 2 konsentrasjon kan forsterke effekten av disse stressfaktorene. Masterstudenten(e) vil bli integrert i et nytt forskningsprosjekt som er et samarbeid mellom NTNU, SINTEF og Biotrix. Prosjektet er finansiert an Norges Forskningsråd og vil pågå over fire år. Forsøkene vil bli utført ved NTNUs nye fasiliteter ved SeaLab. I tillegg til fitness relaterte parametere som overlevelse og reproduktiv suksess vil det også bli fokusert på bruk av molekylærbiologiske hjelpemidler (Realtime-PCR, Microarray, Proteomics) for å avdekke virkningsmekanismer og potensielle biomarkører. De verdifulle resultatene som genereres av de eksperimentelle studiene vil bli integrert i datasimulerings verktøy som utvikles ved SINTEF for å kunne predikere effekter av forhøyet CO 2 på naturlig populasjoner i Norskehavet samt Barentshavet og derved sikre en fornuftig forvalting av både Raudåte og fiskeslagene som er avhengige av denne arten. For nærmere informasjon kontakt Sindre A. Pedersen (kontor: EU2-167; Sindre.Pedersen@bio.ntnu.no) eller Bjørn Munro Jenssen (kontor: EU2-173; bjorn.munro.jenssen@bio.ntnu.no). Lenke 1: Lenke 2: Lenke 3: home/people/ Fysiologi, Celle og molekylærbiologi, Marinbiologi 28

29 Arbeidstittel på oppgaven (max 20 ord): oppgaven (max 300 ord): Augustine Arukwe Marianne olufsen Climate change, emerging pollutants and reproduction dysfunction in fish: Linking quantifiable measures of climate change with pollution and biological consequences Emerging pollutants such as perfluorinated organic compounds (PFCs) are notorious environmental contaminants and have been detected globally in wildlife and humans. Particularly, PFCs have received a lot of societal attention because of their unique chemistry (as both water and oil repellent and reduction of surface tension), persistence, bioaccumulation and toxic effects. Because of this unique chemistry, PFCs represent a group of emerging compounds with not well-understood toxicological properties. The limited database indicates a need for further studies and most importantly integrating the climate change phenomenon. The increase in the average temperature on the Earth's near-surface air and oceans since the mid-twentieth century and it s projected continuation is generally termed Global warming. Current models predict a global warming of about C between 1990 and These predictions are based on a wide range of assumption about the main forces driving future emissions that include population growth and technological advances. Increasing global temperature will cause sea levels to rise, and is expected to increase the intensity of extreme weather events and to change the amount and pattern of precipitation. Other effects of global warming include changes in agricultural yields, trade routes, glacier retreat, species extinctions and increases in the ranges of disease vectors and susceptibility of organisms to environmental contaminants. Increases in temperature and carbon dioxide (CO2) are the two most discussed and quantifiable measures of climate change. Increased CO2 concentrations produces lower ph and with overt physiological effects to aquatic animals. Oxygen depletion (or hypoxia) is a phenomenon that occurs in aquatic environments because the concentration of dissolved oxygen (DO; molecular oxygen dissolved in the water) is so low that it becomes detrimental to aquatic organisms, including reductions in biosynthetic processes. The depletion of O2 may result from a number of natural factors, but it is most often seen as a consequence of pollution and eutrophication in which plant nutrients enter a river, lake, or ocean, and phytoplankton blooms are encouraged. Thus, hypoxia is defined as a shortage of oxygen (O2) to <2 ml/l or <2.8 mg/l and is known to be a pressing global problem and a significant portion of world freshwater and marine ecosystem is already affected by hypoxia, including areas in central Norway and the Baltic sea. Furthermore, changes in temperature and hypoxic stress have been shown to affect contaminants distribution in the environment and in organisms through partitioning in different environmental matrixes. Until recently, comprehensive studies aimed at understanding the combined effects of climate change and contaminants on biological processes are lacking and their implications with regard to associations can only be understood through integrated, empirical and systematic research approaches. This project is a research council financed project that will use Atlantic cod in both in vitro and in vivo exprements. 4 master students are needed to focus on respective issues in this project related to lipid homeostasis, biotransformation, oxidative stress and endocrine disruption using biochemical, cellular and molecular methods. Oppgaven passer for (angi Environmental Toxicology, Cell and Molecular Biology, Biotechnology 29