BIO-info (en)

Research – Week 46


QIAGEN Bioinformatics Microbial Genomics hands-on workshop the 7th of Dec. from 9.30 – 16.00.
QIAGEN BIOINFORMATICS HANDS-ON WORKSHOP (7th of Dec from 9.30 to 16.00): From data to discovery with the QIAGEN Microbial Genomics Pro Suite.
The expanding field of metagenomics leaves researchers struggling to convert data generated with a wide range of open source tools into meaningful insights. The Microbial Genomics Pro Suite integrates a comprehensive set of tools for metagenomics into a scalable and user friendly platform.
Metagenomics applications are supported with workflows for the analysis of 16S-, 18S rRNA, or other amplicon data. Further included are workflows for whole metagenome assembly, and the functional analysis of metagenomic data. The recent launch of the CosmosID plugin completes the range of metagenomics applications. The plugin offers best in class taxonomic profiling and pathogen identification and can handle shotgun metagenomics data as input.
To convert microbiome data into biologically meaningful insights, all metagenomics applications are completed with workflows for the statistical analysis of differential abundance in the context of metadata. The user can explore changes in composition or function associated for instance with health or dysbiosis.
A package of workflows for the analysis of outbreaks based on isolate genome data extends the utility of the Microbial Genomics Pro Suite for researchers focusing on epidemiology, food safety and public health.

If you are interested, then join our workshop the 7th of Dec 2016 and learn more about the QIAGEN Microbial Genomics Pro Suite and try it out yourself. You will get a 6 weeks license for you to try out the software with your own data after the workshop

Sign up here

Deadline is 2nd of Dec at 16.00. There is a limit of 20 people for the workshop and registration will be on a first come, first served basis.

Hope to see you there.

Upcoming events – Week 46

Ph.d Trial lecture Alexander Plotkin: “Phylogeny and taxonomy of Polymastiidae (Porifera: Demospongiae)”
Supervisors: Hans Tore Rapp and Endre Willassen.
Evaluating committee: Head of Department Tim J. Littlewood, Department of Life Sciences, Natural History Museum , UK, Associate professor Tomas Cedhagen, Department of Bioscience, Århus University, Denmark, Associate Professor Svein Rune Erga, Department of Biology, University of Bergen
Time and place: Tuesday 22th of November, 12:15 a.m. , Auditoriet Vil Vite, Thormøhlens gt. 51.

Ph.d Trial lecture Oliver Vöcking: “The larval photoreceptors of the mollusk Leptochiton asellus”
Supervisors: Harald Hausen and Jon Vidar Helvik.
Evaluating committee: Professor Dan-Erik Nilsson, Lund Universitet, Sverige, Gruppeleder Juan Ramón Martinez Morales, Pablo de Olavide Universitet, Spania, Førsteamanuensis Ståle Ellingsen. Institutt for biologi, Universitetet i Bergen
Time og place: Monday 28th of November, 10:15 a.m. , Auditoriet Vil Vite, Thormøhlens gt. 51.

Ph.d. Midterm evaluation Oliver Müller: “Microbial communities in arctic environments. The effects of thawing permafrost soils on biogeochemical processes driving the terrestrial and marine carbon cycle development ”
Supervisors: Lise Øvreås, Janet Jansson and Gunnar Bratbak.
Evaluating committee: Førsteamanuensis Anne Bjune(leder), Professor Frede Thingtad, Forsker Sigrunn Eliassen.
Time and place: Friday 25th of November, 14:15 a.m. , Seminarrom K1, Biologen.
All are welcome to the presentations!

New Publications – Week 46

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Brietzke A, Borchel A, Altmann S, Nipkow M, Rebl A, Brunner RM, Goldammer T(2016) Transcriptome sequencing of maraena whitefish (Coregonus maraena). Marine Genomics 29:27-29

Hestetun JT, Pomponi SA, Rapp HT (2016) The cladorhizid fauna (Porifera, Poecilosclerida) of the Caribbean and adjacent waters. Zootaxa 4175

Imsland AK, Reynolds P, Nytrø AV, Eliassen G, Hangstad TA, Jonsdottir ODB, Emaus P-A, , Elvegård TA, Lemmens SCA, Rydland R, Jonassen TM (2016) Effects of lumpfish size on foraging behaviour and co-existence with sea lice infected Atlantic salmon in sea cages. Aquaculture 465:19-27

Routti H, Lille-Langøy R, Berg MK, Fink T, Harju M, Kristiansen K, Rostkowski P, Rusten M, Sylte I, Øygarden L, Goksøyr A (2016) Environmental Chemicals Modulate Polar Bear (Ursus maritimus) Peroxisome Proliferator-Activated Receptor Gamma (PPARG) and Adipogenesis in Vitro. Environmental Science & Technology 50:10708-10720

Van Ekert E,Chauvigne F, Finn RN, Mathew LG, Hull JJ, Cerda J, Fabrick JA (2016) Molecular and functional characterization of Bemisia tabaci aquaporins reveals the water channel diversity of hemipteran insects. Insect Biochemistry and Molecular Biology 77:39-51


Hamre K, Sissener NH, Lock E-J, Olsvik PA, Espe M, Torstensen BE, Silva J, Johansen J, Waagbø R, Hemre G-I.(2016) Antioxidant nutrition in Atlantic salmon(Salmo salar) parr and post-smolt,fed diets with high inclusion of plantingredients and graded levels ofmicronutrients and selected amino acids.
PeerJ 4:e2688




Upcoming events – Week 44

Master exam- Ida Vee:  Towards improved management of deep-sea sponge grounds in Norwegian waters

Ida Vee will on Friday 4th of November give the final presentation of her master thesis in Biology – marine biology

Supervisors: Hans Tore Rapp, Joana Xavier.  External examiner:  Jussi Evertsen, Frøya videregående skole. Internal examiner:  Bjørn Arild Hatteland

Time and location: Friday 4th of November at 10:15, Lille auditorium, HIB

All are welcome to the presentation


Ph.d. Trial lecture Jon Thomassen Hestetun:  ” Evolutionary and ecological adaptations to life in the deep-sea”.

Evaluating committee:  Associate Professor Ida Helene Steen, Forsker Anne Helene Solberg Tandberg,  Postdoc Joana R Xavier

Time and place: Wednesday 9th of November at 10:15.  Seminar room K3, Blokk B, Biologen

All are welcome to the presentation


Ph.d. Trial lecture Oliver Vocking:  “Circadian rhythms and evolution”.

Evaluating committee: Researcher Elsa Denker, Associate Professor Odd Andre Karlsen, Associate Professor Ståle Ellingsen

Time and place: Friday 11th of November Group room 209N1, 2. etasje, datablokken, HIB

All are welcome to the presentation


Have we forgotten the biology in all the technology?

Debate on Wednesday, November 2nd, (19:30-21:30) in Boksalongen in Østre Skostredet.

Read more on Facebook.


Fish swimming course – Summer 2017

Read more here: Fish swimming AD 2017.

Using Insects for Feed Purposes

NICE seminar Bergen

New publications – Week 44

Eggestol HO, Wegeland HI, Ronneseth A, Tollefsen KE, Haugland GT (2016) Distribution of the potential DC-markers DEC205, Langerin, DC-LAMP and DC-SIGN within tissues of Atlantic salmon (Salmo salar L.) and their response upon challenge with microbes. European Journal of Immunology 46: 943-944

Harvey AC, Juleff G, Carvalho GR, Taylor MI, Solberg MF, Creer S, Dyrhovden L, Matre IH, Glover KA (2016a) Does density influence relative growth performance of farm, wild and F-1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions? Royal Society Open Science 3

Harvey AC, Solberg MF, Glover KA, Taylor MI, Creer S, Carvalho GR (2016b) Plasticity in response to feed availability: Does feeding regime influence the relative growth performance of domesticated, wild and hybrid Atlantic salmon Salmo salar parr? Journal of Fish Biology 89: 1754-1768

Jansson E, Taggart JB, Wehner S, Dahle G, Quintela M, Mortensen S, Kvamme BO, Glover KA (2016) Development of SNP and microsatellite markers for goldsinny wrasse (Ctenolabrus rupestris) from ddRAD sequencing data. Conservation Genetics Resources 8: 201-206 10.1007/s12686-016-0532-0

Rojas-Garcia CR, Applebaum SL, Morais S, Ronnestad I (2016) Trans-intestinal absorption rates differ between free amino acids during larval development in Atlantic herring (Clupea harengus). Aquaculture 464: 222-228

Skarpaas O, Meineri E, Bargmann T, Potsch C, Topper J, Vandvik V (2016) Biomass partitioning in grassland plants along independent gradients in temperature and precipitation. Perspectives in Plant Ecology Evolution and Systematics 19: 1-11

Smage SB, Frisch K, Brevik OJ, Watanabe K, Nylund A (2016) First isolation, identification and characterisation of Tenacibaculum maritimumin Norway, isolated fromdiseased farmed sea lice cleaner fish Cyclopterus lumpus L. Aquaculture 464: 178-184

Steinum TM, Karatas S, Martinussen NT, Meirelles PM, Thompson FL, Colquhoun DJ (2016) Multilocus Sequence Analysis of Close Relatives Vibrio anguillarum and Vibrio ordalii. Applied and Environmental Microbiology 82: 5496-5504


Professor T. Frede Thingstad, Institute of Biology, University of Bergen turns 70 on December 21st, 2016 and will soon retire. On that occasion, the research environment in Bergen will honor Frede for his pioneering research by arranging an open scientific seminar on December 2nd from 10:00-15:00 at VilVite.

Frede is one of the world’s leading researchers in marine microbial ecology, and his work on the design of conceptual and mathematical models of the microbial food webhas had great impact on the research field. In 1983, he was central in shaping the concept “The Microbial Loop” which led to a paradigm shift in the field, and in 1997 he launched “Killing- the-Winner” as a key concept for analyzing the relationship between processes and participants in the marine microbial food chain .

To honor Frede, we have invited four internationally renowned scientists and challenged them to elucidate Frede’s work from different perspectives. These researchers are:

  • Farooq Azam (Scripps Institution of Oceanography): Marine microbiology
  • Forest Rohwer (San Diego State University): Molecular ecology and “omics”
  • Christiane Lancelot (Université Libre de Bruxelles): Ecosystem models and theory
  • Dag O Hessen (University of Oslo): General biology and evolution

Frede Thingstad

Welfare, HR and HSE – Week 44

New employees

Siri Vatsø Haugum

Siri Vatsø Haugum: hired 12th of September 2016 as a PhD candidate in plant community ecology.

Karina Dale

Karina Dale: hired 17th of October 2016 as a PhD candidate in environmental toxicology.

Lindsey Moore Camilla Osberg

Lindsey Moore and Camilla Osberg were hired in permanent positions from 1st of October 2016 as senior engineers connected to the research groups in fish health and the teaching of fish health students.


Renate Hvidsten Skoge: hired 16th of August 2016 as a researcher in reverse genetics.


New assembly point in case of fire

The assembly point is next to the Propella between Data-block and VilVite sentre.


New doctorate

Perpetra Akite was awarded her doctorate under a cotutelle agreement between UiB and the University of Makerere, Uganda. She was a PhD student on the Matrix project and her thesis was on the spatial and matrix influences on the biogeography of insect taxa in forest fragments in central Uganda, supervised by Richard Telford (EECRG) and Anne Akol and Hugh Rowell (Makerere University). Her defence presentation on the 20 October 2016 was rated as excellent.

Congratulations to Dr Perpetra Akite.


Here is a photo of her at her defence, demonstrating using a sling! Photo by Amy Eycott.

Upcoming events – Week 42


bioCEED seminar series

Making (use of) videos in Teaching and Learning, read more here!
Time and place: 26 Oct, 14:15-15:00, Biologen, Seminar room K1.

Everyone welcome!

Master exam- Andreas Gilje Sjøberg: Physiological characterization of a novel strain within Rhodobacteracea, isolated from a biolfilm sample on a barite chimney at the Loki’s Castle Vent Field
Andreas Gilje Sjøberg hold Thursday 27th October the final presentation of his master thesis in Biology – Microbiology  (Biogeology)
Supervisors: Ida H. Steen, Håkon Dahle
External examiner: Mette Svenning, UiT
Internal sensor: Gunnar Bratbak
Time and place: 27th October, 13:00 på Senter for geobiologi, lunchrommet

Master exam- Roar Leksen: Traceable lice strain of Lepeophtheirus salmonis (Krøyer 1837) as a tool for studying lice dispersion.
Roar Leksen hold Friday 28th of October the final presentation of his master thesis in Aquaculture Biology.
Supervisor: Frank Nilsen.
Internal examiner: Kristin Hamre.
Sensor: Ørjan Karlsen, HI
Time and place: Friday 28th of October, 10:15, Seminarrom K3, Biologen.

Everyone welcome!