UMB::IKBM::The Protein Engineering and Proteomics Group
Welcome!
The PEP group at UMB (Norwegian University of Life Sciences) is involved in several research projects, which are mainly related to protein science. We belong to the Department of Chemistry, Biotechnology and Food Science.
For dere som helst liker å lese norsk: På våre websider er det flere linker til tekster som er skrevet på norsk, både populærvitenskapelige beskrivelser av det vi driver med og masteroppgaver.
NEWS
30.08.10 The PEP group got a paper accepted for publication in Science!!
01.04.10 - Welcome to Tien-Thanh Nguyen, guest researcher from Austria. During his stay in our group Tien-Thanh is going to develop food grade expression systems.
10.03.10 - Welcome to Lakshmi Prasanna, guest researcher from India. Lakshmi is coming to our lab to clone, express and characterize a thermostable chitinase
01.02.10 - Five new Master student started in the lab. Welcome to Stine, Silje, Rannei, Kristina and Cathrine.
27.01. - Gustav was interviewed on the Norwegian National Radio program Verdt å vite (in Norwegian).
20.01.10 - Svein has published his PhD thesis as a book. Title: Production of Biogas and Bioethanol from Brown Macroalgae. Link to Amazon page
7.9.09 - Welcome to Quang D. Nguyen, guest researcher from Corvinius University, Hungary 1.9.09 - Oskar Bengtsson, with a Ph.D. from Lund University started as a Post-doc on the Biomass2Products project. The project is a joint project with Borregaard.
Celebration!!
UMB::IKBM::The Protein Engineering and Proteomics Group
28.7.09 - Vincent speaks at the Gordon Research Conference on Cellulosomes, Cellulases & Other Carbohydrate Modifying Enzymes. Title of the talk: The roles of processivity and accessory proteins during enzymatic degradation of recalcitrant polysaccharides
11.3.09 - Our close collaborator and dear colleague, Morten Sørlie, turned 40. Pictures 9.3.09 - The PEP group welcomes Berit back from her maternity leave.
25.2.09 - Henrik's paper on processivity in Chitinase A was accepted by JBC. [1]
13.2.09 - The PEP group got several projects on Bioenergy funded. We will work on enzyme technology related to production of both biogass and biotehanol
29.1 - 1.2.09 - The PEP group at the Contact Meeting of the Norwegian Biochemical Society at Røros.
8.1.09 - Birth of Cecilia Lea Karlskås - Congratulations to Ingrid
6.1.09 - Vincent was interviewed by NRK østlandssendingen as part of the 150 years anniversary of the University. Video
10.12.08 - The second PEP bowling competition! Gustav became bowlingchampion of the year! Pictures 18.08.08 - The PEP group welcomes Ingrid Lea as a Ph.D student at the project; "Surface- and secreted proteins in lactobacilli and enterococci and their impact on bacterial adaptation and human health".
29.05.08 - The PEP groups publishes an Opinion paper in Trends in Biotechnology. See Trends in Biotechnology, Vol. 26, Pages 228-235 (May 2008).
29.05.08 - Se på foredraget Vincent holdt 22. mai for lærere i videregående skolen i anledning lansering av boken BIOS Biologi 2.[Biologikurs-Cappelen]
28.02.08 - Lasse Fredriksen and Øyvind Busk teaches High school students DNA profiling techniques commonly used in forensic labs. Ås avisand Østlandets Blad.
18.02.08 - Pictures from the lab
17.02.08 - NBS meeting in Lillehammer 2008, pictures from the event Wintermeeting
12.12.07 - Minister of Agricultur and food Terje Riis Johansen and Minister of Reaserch and Higher Education Tora Aasland visited UMB and the PEP group Thursday 29.11.2007- Pictures more information UMB and Østlandets Blad
16.11.07 - Vincent Eijsink and Svein Horn are developing methods to produce bioethanol from biomass - Østlandets Blad for more information UMB
29.10.07 - The PEP group meets Takeshi Watanabe, one of the founding fathers of chitinase research - Picture
29.10.07 - See the group members at the September 2007 EUCHIS meeting in Antalya - Pictures 22.10.07 - Vincent Eijsink was interviewed about biofuel on NRK2 - En kilde klar og ren
01.09.07 - The PEP group welcomes Lasse Fredriksen as a Ph.D student.
24.08.07 - Both Lasse Fredriksen and Øyvind Busk successfully defended their master thesis this week.
Congratulations!
12.08.07 - Research pages updated.
03.07.07 - Fra tre til tank via sopp - Vincent i forskning.no.
13.06.07 - Anita Sveen successfully defended her Master thesis. Congratulations!
16.04.07 - The group welcomes Bjørge Westereng to work as a post-doc on the ADDBAR project.
UMB::IKBM::The Protein Engineering and Proteomics Group
10.04.07 - Torkild Andersen og Ida Evenrød ønskes velkommen som nye masterstudenter i PEP-gruppa.
UMB::IKBM::The Protein Engineering and Proteomics Group
News
30.08.10 The PEP group got a paper accepted for publication in Science!!
01.04.10 Welcome to Tien-Thanh Nguyen, guest researcher from Austria. Tien-Thanh is going to develop food grade expression system during his stay in our group.
10.03.10 Welcome to Lakshmi Prasanna, guest researcher from India. Lakshmi is coming to our lab to clone, express and characterize a thermostable chitinase
20.01.10 Svein has published his PhD thesis as a book. Title: Production of Biogas and Bioethanol from Brown Macroalgae. Can be bought at Amazon.com
7.9.09 - Welcome to Quang D. Nguyen, guest researcher from Corvinius University, Hungary
1.9.09 Oskar Bengtsson started in the group. He works as a Postdoc on the Biomass2Products project in close collaboration with Borregaard. Oscar has a Ph.D. from Lund University,
28.7.09 - Vincent speaks at the Gordon Research Conference on Cellulosomes, Cellulases & Other Carbohydrate Modifying Enzymes. Title of the talk: The roles of processivity and accessory proteins during enzymatic degradation of recalcitrant polysaccharides
11.3.09 - Our close collaborator and dear colleague, Morten Sørlie, turned 40. Pictures.
9.3.09 - The PEP group welcomes Berit back from her maternity leave.
25.2.09 - Henrik's paper on processivity in Chitinase A was accepted by JBC. [1]
13.2.09 - The PEP group got several projects on Bioenergy funded. We will work on enzyme technology related to production of both biogass and biotehanol
29.1 - 1.2.09 - The PEP group at the Contact Meeting of the Norwegian Biochemical Society at Røros.
Celebration!!
UMB::IKBM::The Protein Engineering and Proteomics Group
8.1.09 - Birth of Cecilia Lea Karlskås - Congratulations to Ingrid
6.1.09 - Vincent was interviewed by NRK østlandssendingen as part of the 150 years anniversary of the University. Video
10.12.08 - The second PEP bowling competition! Gustav became bowlingchampion of the year! Pictures 18.08.08 - The PEP group welcomes Ingrid Lea as a Ph.D student at the project; "Surface- and secreted proteins in lactobacilli and enterococci and their impact on bacterial adaptation and human health".
29.05.08 - The PEP groups publishes an Opinion paper in Trends in Biotechnology. See Trends in Biotechnology, Vol. 26, Pages 228-235 (May 2008).
29.05.08 - Se på foredraget Vincent holdt 22. mai for lærere i videregående skolen i anledning lansering av boken BIOS Biologi 2.[Biologikurs-Cappelen]
28.02.08 - Lasse Fredriksen and Øyvind Busk teaches High school students DNA profiling techniques commonly used in forensic labs Ås avis and Østlandets Blad.
18.02.08 - Pictures from the lab
17.02.08 - NBS meeting in Lillehammer 2008, pictures from the event Wintermeeting
12.12.07 - Minister of Agricultur and food Terje Riis Johansen and Minister of Reaserch and Higher Education Tora Aasland visited UMB and the PEP group Thursday 29.11.2007- Pictures more information UMB and Østlandets Blad
16.11.07 - Vincent Eijsink and Svein Horn are developing methods to produce bioethanol from biomass - Østlandets Blad for more information UMB
29.10.07 - The PEP group meets Takeshi Watanabe, one of the founding fathers of chitinase research - Picture
29.10.07 - See the group members at the September 2007 EUCHIS meeting in Antalya - Pictures
22.10.07 - Vincent Eijsink was interviewed about biofuel on NRK2 - En kilde klar og ren
01.09.07 - The PEP group welcomes Lasse Fredriksen as a Ph.D student.
24.08.07 - Both Lasse Fredriksen and Øyvind Busk successfully defended their master thesis this week.
Congratulations!
UMB::IKBM::The Protein Engineering and Proteomics Group
12.08.07 - Research pages updated.
03.07.07 - Fra tre til tank via sopp - Vincent i forskning.no.
13.06.07 - Anita Sveen successfully defended her Master thesis. Congratulations!
16.04.07 - The group welcomes Bjørge Westereng to work as a post-doc on the ADDBAR project.
10.04.07 - Torkild Andersen og Ida Evenrød ønskes velkommen som nye masterstudenter i PEP-gruppa.
05.03.07 - The group welcomes Zhanliang Liu to work as a post-doc on deacetylases.
15.02.07 - Britt Dahl og Helle Akselsen ønskes velkommen som nye masterstudenter i PEP-gruppa.
02.01.07 - Berit Bjugan Aam har begynt i gruppen som forsker per 1. januar.
23.11.06 - PEP-gruppa publiserer i PNAS om kitinnedbryting og bioetanol.
20.11.06 - Updated: Upcoming conferences of interest to PEP members.
31.10.06 - IKBM har undertegnet kontrakt med ENEnergy Ltd. om Bioethanol. Les mer.
16.10.06 - A paper titled "Costs and Benefits of Processivity in Enzymatic Degradation of Recalcitrant Polysaccharides", authored by Svein Jarle Horn and other group members, gets accepted to PNAS!
Update: Pictures from the celebration.
02.10.06 - The PEP group welcomes Henrik Zakariassen as a Ph.D student.
09.09.06 - EUCHIS 06 - Gustav Vaaje-Kolstad wins the Braconnot price!
09.09.06 - EUCHIS 06 - See the PEP group in action in sunny Montpellier.
31.08.06 - The PEP group welcomes the visiting Diploma student Elisabeth Halbmayr!
18.08.06 - Jarl Andreas Anmarkrud successfully defended his Master thesis. Congratulations!
19.06.06 - The PEP group welcomes Liv Anette Bøhle as a Ph.D. student to work with proteomics on Enterococci.
23.03.06 - A Wiki has been set up for our members. Please contribute with your best recipes, tips and protocols.
UMB::IKBM::The Protein Engineering and Proteomics Group
10.12.05 - Vincent and Lars Axelsson (Matforsk) have a "News and views" article in December issue of Nature Biotechnology (pdf).
28.11.05 - Gustav and Vincent are in the news (in Norwegian) with CBP21.
24.11.05 - The CBP21 links the PEP group to the Biomotive network (in Norwegian).
21.11.05 - The PEP group gets its very own domain pep.umb.no!
04.11.05 - The PEP group celebrates professor Eijsinks 100th peer reviewed article!
01.09.05 - New master projects are now available!
01.08.05 - Gustav Vaaje-Kolstad gets receives the honour of "article of the week" for his latest article describing the function of chitin binding protein CPB21 in Journal of Biological Chemistry. Se more here.
03.05.05 - Minor overhaul of the site to make updates and corrections.
01.05.05 - Crystals of Chitinase G from Streptomyces coelicolor have just been produced, and work has commenced to solve the structure.
29.04.05 - Ph.D.-dissertation of Gustav Vaaje-Kolstad. Follow this link.
28.04.05 - Master student Ellinor Heggset and Ph.D student Ingunn Alne Hoell have succeeded in refolding a chitinase from pine tree (with 16 cysteins!!) from inclusion bodies. This must be said to be a big
breakthrough - as protein production is a vitally important (and limiting) element in proteomics. The work was done in collaboration with Skogforsk.
18.04.05 - The group is now involved in a new EU project that deals with making useful compounds from brewers spent grain (in other words, waste products). Follow this link to the project homepage.
18.04.05 - New master projects are now available!
News archive
UMB::IKBM::The Protein Engineering and Proteomics Group
The PEP group focuses on proteins and enzymes in a variety of contexts. Our projects range from fundamental structure-function studies on the folding, stability and functionality of individual proteins to applied studies in enzyme technology. In addition we have a protein- and proteomics-oriented research activity in the field of lactic acid bacteria. The best way to get a complete overview over our activities in the past years is to take a look at our list of publications.
In general terms, the group work is currently working on the following topics:
Structure-function studies of enzymes that act on chitin and related polymers The applied goal of this work is to convert chitin and related polymers to bioactive oligosaccharides. In this project we collaborate very closely with Dr. Morten Sørlie and his co-workers at our institute and with the Norwegian Biopolymer Laboratory in Trondheim (NOBIPOL). Most of our protein engineering and directed evolution work, a key competence area for the group, is done in connection to the chitin work.
Enzymatic degradation and valorization of biomass
Recently, we have been particularly interested in the conversion of lignocellulosic biomass used for the production of second generation biethanol. This is a relatively new activity that has been boosted by two major breakthrough findings in our reserach on chitin, as well as by great political interest. Our work on biomass conversion includes some bioprospecting, i.e. finding new enzymatic tools in nature.
Lactic acid bacteria (LAB)
We have been working for many years in this field, partly in collaboration with professors Ingolf Nes and Leiv Sigve Håvarstein at our institute and with Dr. Lars Axelsson at Matforsk. Together these research groups have reached the final of Norwegian
competition for Centres of Excellence (og which Norway has only about 20 in total) two consecutive times (2002 & 2006). In the PEP group, we have been working with
bacteriocins and gene expression. Current work is focussed on the following two topics:
(1) exploitation of lactic acid bacteria, in particular lactobacilli, as (in situ) cell factories for medicinal proteins such as cancer vaccines, and (2) use of functional genomics, in particlar (surface) proteomics, to study how LAB interact with and respond to human cells.
CBP21
wheat straw
Overexpression of PepN in Lactobacillus
UMB::IKBM::The Protein Engineering and Proteomics Group
Group Members
Vincent Eijsink Group leader Office: 3B.41
Originally from Arnhem, Netherlands Phone: +47 6496 5892
Email: vincent.eijsink[AT]umb.no Ellen Hasle Kokkim
Senior Engineer
Lab 3B.14 Office 3.B.35
Originally from Sarpsborg, Norway Phone: +47 6496 5875
Email: ellen.hasle.kokkim[AT]umb.no Morten Skaugen
Senior Engineer
Lab 1B.08 Office 1.B.44
Originally from Arendal, Norway Phone:
Email: morten.skaugen[AT]umb.no Svein J. Horn
M.S., Ph.D.; Norwegian university of Science and technology, Trondheim, Norway Post doc
Office 3.B.43
Originally from Brønnøysund, Norway Phone: +47 6496 5907
Email: sveiho[AT]umb.no Geir Mathiesen
M.S., Ph.D.; Norwegian university of Life Sciences, Ås, Norway Post doc
Office 3.B.40
Originally from Furnes, Ringsaker, Norway Phone: +47 6496 5899
Email: geir.mathiesen[AT]umb.no
UMB::IKBM::The Protein Engineering and Proteomics Group
Gustav Vaaje-Kolstad
M.S., Ph.D.; Norwegian university of Life Sciences, Ås, Norway Post doc
Office 3.B.39
Originally from Lampeland, Norway Phone: +47 6496 5905
Email: gustko[AT]umb.no Janneke Treimo
M.S., Ph.D.; Norwegian university of Life Sciences, Ås, Norway Post doc
Office
Originally from Fredrikstad, Norway Phone:
Email: janneke.treimo[AT]umb.no Berit Bjugan Aam
Siv.ing.: University of Tromsø
Dr. Scient: University of Oslo/Norwegian Defence Research Establishment Post doc
Office 3.A.42
Originally from Trondheim/Klæbu, Norway Phone: +47 9186 6719
Email: berit.aam[AT]umb.no Bjorge Westereng
M.Sc:Norwegian university of Life Sciences, Ås,
Norway PhD: University of Oslo,School of
pharmacy Post doc
Office 3.B.42
Originally from Ås, Norway Phone:+ 47 6496 5909
Email: bjorge.westereng[AT]umb.no Zhanliang Liu
B.Sc: Hebei University, China
M.Sc, PhD: Agricultural University of Hebei, China Researcher
Office 3A.40
Originally from Baoding, China Phone: +47 6496 5899
Email: zhanl[AT]umb.no Sigrid Gåseidnes
M.Sc, PhD: Norwegian university of Life Sciences, Ås, Norway Post doc
Office 3.B.39
UMB::IKBM::The Protein Engineering and Proteomics Group
Originally from Trondheim Phone: +47 6496 5890
Email: sigrid.gaseidnes[AT]umb.no Liv Anette Bøhle
M.S.; Norwegian university of Life Sciences, Ås, Norway PhD student
Office 3.B.38
Originally from Spydeberg, Norway Phone:
Email: liv.bohle[AT]umb.no Henrik Zakariassen
M.S.; Norwegian university of Life Sciences, Ås, Norway PhD student
Office 3.B.38
Originally from Tønsberg, Norway Phone: +47 6496 6249
Email: henrik.zakariassen[AT]umb.no Lasse Fredriksen
PhD student Office 3.B.45
Originally from Råde, Norway Phone:
Email: lasse.fredriksen[AT]gmail.com Anne Cathrine Bunæs
M.S.; Norwegian university of Life Sciences, Ås, Norway Lab Engineer
Lab 3.B.06 Office 3.B.35
Originally from Setskog, Norway Phone: +47 6496 6158
Email: anne.bunes[AT]umb.no Ingrid Lea Karlskås
Master of Technology (Siv.ing), Molecular Biotechnology, University of Tromsø PhD Student
Office 3.B.45
Originally from Bodø, Norway Phone: +47 6496 6251 Email: ingrid.lea[AT]umb.no Oskar Bengtsson
M.S.; Lund University, Lund, Sweden
UMB::IKBM::The Protein Engineering and Proteomics Group
Post Doc Office 3.B.44
Originally from Knislinge, Sweden Phone: +47 6496 5911
Email: oskar.bengtsson[AT]umb.no Hong Zhai
B.Sc: Hebei University, China M.Sc: Åbo Akademi University, Finland PhD student
Office 3.B.44
Originally from Baoding, China Phone: +47 6496 5911
Email: hong.zhai[AT]umb.no Zarah Forsberg
M.Sc: Swedish University of Agricultural Sciences, Uppsala, Sweden PhD student
Originally from Uppsala, Sweden Phone: +47 6496 5862
Email: zarah.forsberg[AT]umb.no Phil Pope
PhD: Griffith University Post doc
Office 3.A.38
Originally from NSW (Australia) Email: phillip.b.pope[AT]gmail.com Alasdair Mackenzie
PhD: Swedish University of Agricultural Sciences, Uppsala, Sweden Post doc
Office 3.A.41
Originally from Tasmania (Australia) Email:alasdair.mackenzie[AT]umb.no Vivekanand
PhD: Indian Institute of Technology (IIT) Roorkee, Roorkee, India Post doc
Office 3.A.41
Originally from Gorakhpur, India Email: vivekanand[AT]umb.no Jane Agger
PhD:
Lab Engineer Office 3.B.42 Originally from
UMB::IKBM::The Protein Engineering and Proteomics Group
Email: jane.agger[AT]umb.no
Sophanit Mengesha Master student Lab 3.B.06
Originally from Addis Ababa, Ethiopia
Email: sophanit.mengesha[AT]student.umb.no
Trine Isaksen Master student Lab 3.B.06
Originally from Oslo, Norway
Email: trine.isaksen1[AT]student.umb.no Graduated students and former members here.
UMB::IKBM::The Protein Engineering and Proteomics Group
Publications in international journals
2010
Profiling brewers’ spent grain for composition and microbial ecology at the site of production; JA Robertson, K Ianson, JR Treimo, CB Faulds, T Brocklehurst, VGH Eijsink, KW Waldron. LWT - Food Science and Technology, 43 (2010) 890-896.
Signatures of activation parameters reveal substrate-dependent rate determining steps in
polysaccharide turnover by a family 18 chitinase; H Zakariassen, VGH Eijsink, M Sørlie. Carbohydrate Polymers, 81 (2010) 14-20.
Comparison of allosamidin binding to the three chitinases of Serratia marcescens; differences in the thermodynamic signatures; J Baban, S Sakuda, VGH Eijsink, M Sørlie. J. Phys. Chem. B, 114 (2010) 6144-6149.
Enzymatic hydrolysis of steam exploded hardwood using short processing times; SJ Horn, VGH Eijsink. Biosci. Biotechnol. Biochem., 74 (2010) 1157-1163.
Production of chitooligosaccharides and their potential applications in medicine; BB Aam, EB Heggset, AL Norberg, M Sørlie, KM Vårum, VGH Eijsink. Marine Drugs, 8 (2010) 1482-1517.
Structure and Function of Enzymes Acting on Chitin and Chitosan; I.A. Hoell, G. Vaaje-Kolstad, VGH Eijsink. Biotechnology and Genetic Engineering Reviews, in press.
Effect of enzyme processivity on the efficacy of a competitive chitinase inhibitor; H Zakariassen, L Klemetsen, S Sakuda, G Vaaje-Kolstad, KM Vårum, M Sørlie, VGH Eijsink. Carbohydrate Polymers, 82 (2010) 779–785.
Identification of proteins related to the stress response in Enterococcus faecalis V583 caused by bovine bile; LA Bøhle, EM Færgestad, E Veiseth-Kent, H Steinmoen, IF Nes, VGH Eijsink, G Mathiesen. Proteome Science, 8 (2010) 37.
Degradation of Chitosans with a novel family 46 Chitosanase from Streptomyces coelicolor A3(2); E Heggset, A Dybvik, IA Hoell, AL Norberg, M Sørlie, VGH Eijsink, KM Varum. Biomacromolecules, 11 (2010) 2487–2497.
Dissecting Factors that Contribute to Ligand-Binding Energetics for Family 18 Chitinases; AL Norberg, VGH Eijsink, M Sørlie. Thermochimica Acta, 511 (2010) 189-193.
An oxidative enzyme boosting the enzymatic conversion of recalcitrant polysaccharides. G Vaaje- Kolstad, B Westereng, SJ Horn, Z Liu, H Zhai, M Sørlie, VGH Eijsink. Science, 330 (2010) 219-222.
Abstract Fulltext
Cell wall anchoring of the 37 kDa oncofetal antigen by Lactobacillus plantarum for mucosal cancer vaccine delivery; L Fredriksen, G Mathiesen, M Sioud, VGH Eijsink. Appl. Environm. Microbiol., 76 (2010) 7359-7362.
Determination of substrate binding energies to individual subsites of a family 18 chitinase . AL Norberg, V Karlsen, IA Hoell, I Bakke, VGH Eijsink, M Sørlie. FEBS Letters, 584 (2010) 4581-4585.
Dissecting concurrent enzyme reactions and binding events for chitinases interacting with chitosan
UMB::IKBM::The Protein Engineering and Proteomics Group
oligosaccharides by high resolution mass spectrometry; FH Cederkvist, M Mormann, M Froesch, VGH Eijsink, M Sørlie, J Peter-Katalinić. Intern. J. Mass Spectrom., in press.
1H, 13C, 15N resonance assignment of the non-catalytic Chitin-binding Protein CBP21 from Serratia marcescens; G Vaaje-Kolstad, VGH Eijsink, FL Aachmann. Biomolecular NMR Assignments, in press.
2009
Improving catalytic properties of chitinase by directed evolution. C. Songsiriritthigul, P. Pesatcha, V.G.H. Eijsink, M. Yamabhai. Biotechnology Journal, 4 (2009) 501-509.
Use of Lactobacilli and their pheromone-based regulatory mechanism in gene expression and drug delivery. D.B. Diep, G. Mathiesen, V.G.H. Eijsink, I.F. Nes. Curr. Pharmac. Biotechnol., 10 (2009) 62-73.
Release of non-cellulosic glucose and arabinoxylan from brewers’ spent grain by microbial proteases;
C.B. Faulds, S. Collins, J.A. Robertson, J. Treimo, V.G.H. Eijsink, S. Hinz, H.A. Scholsc, J. Buchertd, K.W. Waldron. J. Cereal Science, 50 (2009) 332-336.
Degradation of chitosans with chitinase G from Streptomyces coelicolor A3(2) - Production of chito- oligosaccharides and insight into subsite specificities; E.B. Heggset, I.A. Hoell, M. Kristoffersen, V.G.H.
Eijsink, K.M. Vårum. Biomacromolecules, 10 (2009) 892-899.
Enzymatic solubilization of brewer`s spent grain by combined action of carbohydrases and peptidases;
J. Treimo, B. Westereng, S.J. Horn, P. Forssell, J. Robertson, C. Faulds, K.W. Waldron, J. Buchert, V.G.H. Eijsink. J. Agric. Food Chem., 57 (2009) 3316-3324.
Characterisation of the Lactococcus lactis sp. lactis chitinase and chitin binding protein; G. Vaaje- Kolstad, A.C. Bunæs, G. Mathiesen V.G.H. Eijsink. FEBS J., 276 (2009) 2402-2415
Aromatic Residues in the Catalytic Center of Chitinase A From Serratia marcescens Affect
Processivity, Enzyme Activity and Biomass-converting Efficiency. H. Zakariassen, B.B. Aam, S.J. Horn, K.M. Vårum, M. Sørlie, V.G.H. Eijsink. J. Biol. Chem., 284 (2009) 10610-10617.
Structural and functional characterization of a putative polysaccharide deacetylase of the human parasite Encephalitozoon cuniculi. J.E. Urch, R. Hurtado-Guerrero, D. Brosson, C. Texier, Z. Liu, V.G.H. Eijsink, D.M.F. van Aalten. Protein Science, 18 (2009) 1197-1209.
Genome-wide analysis of signal peptide functionality in Lactobacillus plantarum WCFS1. G Mathiesen, A Sveen, MB Brurberg, L Fredriksen, L Axelsson, VGH Eijsink. BMC Genomics, 10 (2009) 425.
2008
Towards new enzymes for biofuels: lessons from chitinase research. V.G.H. Eijsink, G. Vaaje-Kolstad, K.M. Vårum,S.J. Horn. Trends in Biotechnology, Vol. 26, Pages 228-235 (May 2008)
Bacteriocins from plant pathogenic bacteria. I. Holtsmark, V.G.H. Eijsink, M.B. Brurberg, FEMS Microbiol. Lett. 280 (2008) 1-7.
Heterologous protein secretion by Lactobacillus plantarum using homologous signal peptides. G.
Mathiesen, A. Sveen, J.C. Piard, L. Axelsson, V.G.H Eijsink, J. Appl. Microbiol. 105 (2008) 215-226.
Expression and characterization of endochitinase C from Serratia marcescens and its purification by a one-step “general” chitinase purification method; B. Synstad, G. Vaaje-Kolstad, F.H. Cederkvist, S.F.
Saua, S.J. Horn, V.G.H. Eijsink, M. Sørlie; Biosci. Biotechnol. Biochem. 72 (2008) 715-723.
Inhibition of a Glycoside Hydrolase Family 18 by Chitooligosaccharides; F.H. Cederkvist, M. Parmer, K.M. Vårum, V.G.H. Eijsink, M. Sørlie, Carbohyd. Polym. 74 (2008) 41-49.
Towards new enzymes for biofuels: lessons from chitinase research; V.G.H. Eijsink, G. Vaaje-Kolstad, K.M. Vårum, S.J. Horn; Trends Biotechnol. 26 (2008) 228-235.
UMB::IKBM::The Protein Engineering and Proteomics Group
High-level expression of recombinant beta-galactosidases in Lactobacillus plantarum and
Lactobacillus sakei using a sakacin P-based expression system; E. Halbmayr, G. Mathiesen, T.H.
Nguyen, C. Peterbauer, V.G.H. Eijsink and D. Haltrich; J. Agric. Food Chem. 56 (2008) 4710-4719.
Enzymatic solubilisation of proteins in Brewer’s Spent Grain; J. Treimo, S.I. Aspmo, V.G.H. Eijsink, S.J. Horn; J. Agric. Food Chem. 56 (2008) 5359-5365.
Hydrolysis of brewer’s spent grain by carbohydrate degrading enzymes; P. Forssell, H. Kontkanen1, H.A. Schols, S. Hinz, V.G.H. Eijsink, J. Treimo, J,A. Robertson, K.W. Waldron, C.B. Faulds, J.
Buchert. J. Inst. Brewing, in press
2007
The tomato pathogen Clavibacter michiganensis subsp. michiganensis: producer of a broad spectre of antimicrobial substances; I. Holtsmark, D. Mantzilas, V.G.H. Eijsink, M.B. Brurberg; J. Appl. Microbiol.
102 (2007) 416-423.
Evaluation of seasonal variation in cod viscera hydrolysates used in a growth medium for lactic acid bacteria. S.J. Horn, S.I. Aspmo, V.G.H. Eijsink. Enzyme Micr. Technol. 40 (2007) 1328-1334.
Natural Substrate Assay for Chitinases Using High Performance Liquid Chromatography: A
Comparison with Existing Assays; I.M. Krokeide, B. Synstad, S. Gåseidnes, S. J. Horn, V.G.H. Eijsink, M. Sørlie. Anal. Biochem.363 (2007) 128-134.
Precise and Continuous Enzyme Assay for Chitinase Catalyzed Hydrolysis of Tetra-N-
acetylchitotetraose Using Isothermal Titration Calorimetry. I.-M. Krokeide, V.G.H. Eijsink, M. Sørlie.
Thermochimica Acta 454 (2007) 144-146.
Mucolytic activity of bacterial and human chitinases. N. N. Sanders, V.G.H. Eijsink, P.S. van den Pangaart, R.J. van Neerven, P.J. Simons, S.C. De Smedt, J. Demeester, Biochim. Biophys. Acta 1770 (2007) 839-846.
A thermodynamic analysis of allosamidin binding to a family 18 chitinase. F.H. Cederkvist, S.F. Saua, V. Karlsen, S. Sakuda, V.G.H. Eijsink, M. Sørlie; Biochemistry 47 (2007) 12347-12354.
2006
Comparative studies of chitinases A, B, and C from Serratia marcescens. S.J. Horn, M. Sørlie, A.L.
Norberg, B. Synstad, G. Vaaje-Kolstad, K.M. Vårum, V.G.H. Eijsink; Biocatalysis and Biotransformation, 24 (2006) 39-53.
In vitro evolution of a subfamily 10 histidine protein kinase (SppK) from Lactobacillus. G. Mathiesen, G.W. Axelssen, L. Axelsson, V.G.H. Eijsink; Arch. Microbiol. 184 (2006) 327-334.
Endo/exo mechanism and processivity of family 18 chitinases produced by Serratia marcescens. S.J.
Horn, A. Sørbotten, B. Synstad, P. Sikorski, M. Sørlie, K.M. Vårum, V.G.H. Eijsink; FEBS J. 273 (2006) 491-503.
Identification of non-covalent glycosidase chitooligosaccharide complexes by (+) nanoelectrospray quadrupole time-of-flight mass spectrometry. F.C. Cederkvist, A. Zamfir, V.G.H. Eijsink, M. Sørlie, J.
Peter-Katalinic, M.G. Peter; Ang Chemie Int Ed. 45(2006) 2429-2434
Molecular cloning, characterization, and real-time expression studies of a novel endochitinase gene (ech30) from the mycoparasite Trichoderma atroviride strain P1. S.S. Klemsdal, J.L. Clarke, I.A. Hoell, V.G.H. Eijsink, M.B. Brurberg; FEMS Microbiol. Lett. 256(2006) 282-289.
Synthesis and evaluation of a 99mTc-HYNIC-labeled chitin-binding protein as potential specific radioligand for the in vivo detection of fungal infections in mice. R. Siaens, V.G.H. Eijsink, G. Vaaje- Kolstad, K. Vandenbulcke, B. Cornelissen, R. Dierckx, G. Slegers, Quart. J. Nucl. Medic. Mol.
UMB::IKBM::The Protein Engineering and Proteomics Group
Imaging 50 (2006)155-166.
Serratia marcescens chitinases with “tunnel-shaped” substrate-binding grooves show endo-activity and different degrees of processivity during enzymatic hydrolysis of chitosan; P. Sikorski, A. Sørbotten, S. J. Horn, V. G. H. Eijsink, K. M. Vårum; Biochemistry, 45(2006) 9566-9574.
Purification, characterization and gene sequence of michiganin type B lantibiotic produced by the tomato pathogen Clavibacter michiganensis subsp. michiganensis; I. Holtsmark, D. Mantzilas, V.G.H.
Eijsink, M.B. Brurberg; Appl. Environm. Microbiol. 72(2006) 5814-5821.
Crystal structure and enzymatic properties of a bacterial family 19 chitinase reveal differences with plant enzymes; I.A. Hoell, B. Dalhus, E.B. Heggset, S.I. Aspmo, V.G.H. Eijsink; FEBS J. 273 (2006) 4889-4900.
Enzymatic degradation of recalcitrant polysaccharides: costs and benefits of processivity S.J. Horn, P.
Sikorski, J.B. Cederkvist, G. Vaaje-Kolstad, M. Sørlie, B. Synstad, G. Vriend, K.M. Vårum, V.G.H.
Eijsink; Proc. Natl. Acad. Sci. USA 103(2006) 18089-18094.
2005
Enzymatic hydrolysis of Atlantic cod (Gadus morhua L.) viscera; Aspmo, S.I., Horn, S.J., Eijsink, V.G.H., Process Biochem. 40 (2005) 1957-1966.
Degradation of chitosans with Chitinase B from Serratia marcescens; production of chito-
oligosaccharides and insight in enzyme processivity; A. Sørbotten, S.J. Horn, V.G.H. Eijsink, K.M.
Vårum; FEBS J. 272 (2005) 1523-1534.
Plasmid p256 from Lactobacillus plantarum represents a new type of replicon in lactic acid bacteria and contains a toxin-antitoxin plasmid maintenance system; E. Sørvig, M. Skaugen, K. Naterstad, V.G.H. Eijsink, L. Axelsson; Microbiology 151 (2005) 421-431.
Crystal structure and binding properties of the chitin-binding protein from Serratia marcescens; G.
Vaaje-Kolstad, D.R. Houston, V.G.H. Eijsink, D.M.F. van Aalten; J. Biol. Chem. 280 (2005) 11313- 11319.
Development and application of a model for chitosan hydrolysis by a family 18 chitinase; P. Sikorski, B.T. Stokke, A. Sørbotten, K.M. Vårum, S.J. Horn, V.G.H. Eijsink; Biopolymers 77 (2005) 273-285.
Overexpression and characterisation of a new chitinase from Trichoderma atroviride strain P1; I. A.
Hoell, S. S. Klemsdal, G. Vaaje-Kolstad, S. J. Horn, V.G.H. Eijsink, Biochim. Biophys. Acta 1748 (2005) 180-190.
Characterization of a new bacteriocin operon in Sakacin P- producing lactobacillus sakei showing strong translational coupling between the bacteriocin and immunity genes; G. Mathiesen, K. Hühne, K.
Naterstad, L. Kröckel, L. Axelsson, V.G.H. Eijsink; Appl. Environm. Microbiol. 71 (2005) 3565-3574.
B. van den Burg, S. Gåseidnes, T.V. Borchert, V.G.H. Eijsink; Directed Evolution of Enzyme Stability;
Biomolecular Engineering 22 (2005) 21-30.
High-level, inducible gene expression in Lactobacillus sakei and L. plantarum using optimized
expression vectors; E. Sørvig; G. Mathiesen, K. Naterstad, V.G.H. Eijsink, L. Axelsson; Microbiology 151 (2005) 2439-2449.
Hydrolysates from atlantic cod (Gadus morhua L.) viscera as components of microbial growth media.
S.I. Aspmo, S.J. Horn, V.G.H. Eijsink; Process Biochem. 40 (2005) 3714-3722.
Use of hydrolysates from Atlantic cod (Gadus morhua L.) viscera as a complex nitrogen source for lactic acid bacteria. S.I. Aspmo, S.J. Horn, V.G.H. Eijsink; FEMS Microbiol. Lett. 248(2005) 65-68.
Growth of Lactobacillus plantarum in media containing hydrolysates of fish viscera. S.J. Horn, S.I.
Aspmo, V.G.H. Eijsink; J. Appl. Microbiol. 99 (2005) 1082-1089.
UMB::IKBM::The Protein Engineering and Proteomics Group
The non-catalytic chitin-binding protein CBP21 from Serratia marcescens is essential for chitin degradation. G. Vaaje-Kolstad, S.J. Horn, D.M.F. Van Aalten, B. Synstad, V.G.H. Eijsink. J. Biol.
Chem. 280 (2005) 28492-28497
Bacterial lessons in sausage making. V.G.H. Eijsink, L: Axelsson, Nature Biotechnol. 23 (2005) 1494-1495.
2004
Structure of the D142N mutant of the family 18 chitinase ChiB from Serratia marcescens and its complex with allosamidin; G. Vaaje-Kolstad D.R. Houston, F.V. Rao, M.G. Peter, B. Synstad, D.M.F.
van Aalten, V.G.H. Eijsink; Biochim. Biophys. Acta 1696 (2004) 103-111.
Interactions of a family 18 chitinase with the designed inhibitor HM508 and its degradation product, chitobiono-delta-lactone; G. Vaaje-Kolstad, A. Vasella, M.G. Peter, C. Netter, D.R. Houston, B.
Westereng, B. Synstad, V.G.H. Eijsink, D.M.F. van Aalten; J. Biol. Chem. 279 (2004) 3612-3619.
Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase; B. Synstad, S. Gåseidnes, D.M.F. van Aalten, G. Vriend, J.E.Nielsen, V.G.H. Eijsink; Eur. J.
Biochem. 271 (2004) 253-262.
A reliable reducing end assay for chito-oligosaccharides; S.J. Horn, V.G.H. Eijsink; Carbohydrate Polymers 56 (2004) 35-39.
Use of bacteriocin promoters for gene expression in Lactobacillus plantarum C11; G. Mathiesen, H.M.
Namløs, P.A. Risøen, L. Axelsson, V.G.H. Eijsink; Journal of Applied Microbiology 96 (2004) 819- 827.
Transcriptional control of bacteriocin production by malt isolate Lactobacillus sakei 5; A.. Vaughan, J.
O’ Mahony, V.G.H. Eijsink , M. O’ Connell-Motherway, D. van Sinderen; FEMS Microbiol Lett. 235 (2004) 377-384.
High-level gene expression in Lactobacillus plantarum using a pheromone-regulated bacteriocin promoter; G. Mathiesen, E. Sørvig, J. Blatny, K. Naterstad, L. Axelsson, V.G.H. Eijsink; Letters Appl.
Microbiol. 39 (2004) 137-143.
123I-Labeled Chitinase as Specific Radioligand for In Vivo Detection of Fungal Infections in Mice; R.
Siaens, V.G.H. Eijsink, R. Dierckx, G. Slegers; J. of Nuclear Medicine 45 (2004) 1209-1216.
Rational engineering of enzyme stability; V.G.H. Eijsink, S. Gåseidnes, B. Synstad, A. Bjørk, R.
Sirevåg, B. Van den Burg, G. Vriend, G.; J. Biotechnol. 113 (2004) 105-120.
Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface; A. Bjørk, B. Dalhus, D. Mantzilas, R. Sirevåg, V.G.H. Eijsink; J.
Mol. Biol. 341 (2004) 1215-1226.
Structure-based optimization of a family 18 chitinase cyclic dipeptide inhibitor; D.R. Houston, B.
Synstad, V.G.H. Eijsink, I. Eggleston, D.M.F. van Aalten; J. Med. Chem. 47 (2004) 5713-5720.
2003
Rational engineering of the stability and the catalytic performance of enzymes; S. Gåseidnes, B.
Synstad, J.E. Nielsen, V.G.H. Eijsink; J. Molecular Catalysis, B: Enzymatic 21 (2003) 3-8.
A network of salt bridges contributes to the pH-dependent stability and oligomerization state of a tetrameric malate dehydrogenase; A. Bjørk, D. Mantzilas, R. Sirevåg, V.G.H. Eijsink; FEBS letters 553 (2003) 423-426.
Stabilization of a chitinase from Serratia marcescens by Gly -> Ala and Xxx -> Pro mutations; S.
UMB::IKBM::The Protein Engineering and Proteomics Group
Gåseidnes, B. Synstad, X. Jia, H. Kjellesvik, G. Vriend, V.G.H. Eijsink; Protein Engineering 16 (2003) 841-846.
Stabilization of a Tetrameric Malate Dehydrogenase by Introduction of a Disulfide Bridge at the Dimer- Dimer Interface; A. Bjørk, B. Dalhus, D. Mantzilas, V.G.H. Eijsink, R. Sirevåg; J. Mol. Biol. 334 (2003) 811-821.
Genetic dissection of a composite bacteriocin locus from malt isolate Lactobacillus sakei 5; A.
Vaughan, V.G.H. Eijsink, D. van Sinderen; Appl. Environm. Microbiol. 69 (2003) 7194-7203.
Construction of vectors for inducible gene expression in Lactobacillus sakei and L. plantarum; E.
Sørvig, S. Grönqvist, K. Naterstad, G. Mathiesen, V.G.H. Eijsink, L. Axelsson; FEMS Microbiol. Lett.
229 (2003) 119-126.
2002
Psammaplin A, a chitinase inhibitor isolated from Fijian Marine Sponge Aplysinella rhax; J.N.
Tabudravu, V.G.H. Eijsink, G.W. Gooday, M. Jaspars, D. Komander, M. Legg, B. Synstad, D.M.F. van Aalten; Bioorg. Med. Chem. 10 (2002) 1123-1128.
Crystal structure of the D140N mutant of chitinase B from Serratia marcescens at 1.45 Å resolution; G.
Kolstad, B. Synstad, V.G.H. Eijsink, D.M.F. Van Aalten,; Acta Crystallog. D58 (2002) 377-379.
The effect of modifying surface charge on the catalytic activity of a thermolysin-like protease; A. De Kreij, B. Van den Burg, G. Venema, G. Vriend, V.G.H. Eijsink, J.E. Nielsen; J. Biol. Chem. 277 (2002) 15432-15438
Production of class II bacteriocins by lactic acid bacteria; an example of biological warfare and communication; V.G.H. Eijsink, L. Axelsson, D.B. Diep, L.S. Håvarstein, H. Holo, I.F. Nes; Antonie van Leeuwenhoek 81 (2002) 639-654.
High resolution structures of a chitinase complexed with natural product cyclopentapeptide inhibitors – mimicry of carbohydrate substrate; D. Houston, K. Shiomi, N. Arai, S. Omura, M.G. Peter, A. Turberg, B. Synstad, V.G.H. Eijsink, D.M.F.van Aalten; Proc. Natl. Acad. Sci. USA 99 (2002) 9127-9132.
Selection of mutations for increased protein stability; B. van den Burg, V.G.H. Eijsink; Curr. Opinion Biotechnol. 13 (2002) 333-337.
Mutational analysis of the role of tryptophane residues in an antimicrobial peptide; G. Fimland, V. G.H.
Eijsink, Jon Nissen-Meyer; Biochemistry 41 (2002) 9508-9515.
Comparative studies of immunity proteins of pediocin-like bacteriocins; G. Fimland, V.G.H. Eijsink, J.
Nissen-Meyer; Microbiology 148 (2002) 3661-3670.
The cyclic dipeptide CI-4 inhibits family 18 chitinases by structural mimicry of a reaction intermediate;
D. Houston, I. Eggleston, B. Synstad, V.G.H. Eijsink, D.M.F. van Aalten; Biochem. J. 368 (2002) 23- 27.
Synthesis of pseudosugar analogues of chitotriose; G. Thiele, A. Rottmann, A. Germer, E. Kleinpeter, K.-D. Spindler, B. Synstad, V. G. H. Eijsink, M. G. Peter; J. Carbohydrate Chem. 21 (2002) 471-489.
Highlights before 2002
Structural determinants of the thermostability of thermolysin-like proteases; V.G.H. Eijsink, O.R.
Veltman, W. Aukema, G. Vriend, G. Venema; Nature Struct. Biol. 2 (1995) 374-379
Induction of bacteriocin production in Lactobacillus sake by a secreted peptide; V.G.H. Eijsink, M.B.
Brurberg, P.J. Middelhoven, I.F. Nes; J. Bacteriol. 178 (1996) 2232-2237
Comparative studies of chitinases A and B from Serratia marcescens; M.B. Brurberg, I.F. Nes, V.G.H.
UMB::IKBM::The Protein Engineering and Proteomics Group
Eijsink; Microbiology 142 (1996) 1581-1589.
Extreme stabilization of a thermolysin-like protease by an engineered disulfide bond; J. Mansfeld, G.
Vriend, B.W. Dijkstra, O.R. Veltman, B. van den Burg, G. Venema, R. Ulbrich-Hofman, V.G.H. Eijsink;
J. Biol. Chem. 272 (1997) 11152-11156.
Pheromone-induced production of anti-microbial peptides in Lactobacillus; M.B. Brurberg, I.F. Nes, V.G.H. Eijsink; Mol. Microbiol. 26 (1997) 347-360.
Engineering an enzyme to resist boiling; B. van den Burg, G. Vriend, O.R. Veltman, G. Venema, V.G.H. Eijsink; Proc. Natl. Acad. Sci. USA, 95 (1998) 2056-2060
Early steps in the unfolding of thermolysin-like proteases; G. Vriend, H.J.C. Berendsen, B. van den Burg, G. Venema, V.G.H. Eijsink; J. Biol. Chem. 273 (1998) 35074-35077
Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9 Å resolution; D.M.F. van Aalten, B. Synstad, M.B. Brurberg, E. Hough, B. Riise, V.G.H. Eijsink, R.K. Wierenga; Proc. Natl.
Acad. Sci. USA 97 (2000) 5842-5847.
Functional analysis of promoters involved in quorum-sensing based regulation of bacteriocin
production in Lactobacillus sake; P.A. Risøen, M.B. Brurberg, V.G.H. Eijsink, I.F. Nes; Mol. Microbiol.
37 (2000) 619-628.
Structural insights into the catalytic mechanism of a family 18 exochitinase; D.M.F. Van Aalten, D.
Komander, B. Synstad, S. Gåseidnes, M.G. Peter, V.G.H. Eijsink; Proc. Natl. Acad. Sci. USA 98 (2001) 8979-8984
UMB::IKBM::The Protein Engineering and Proteomics Group
Education
The PEP group has the responsibility for courses:
KJB201, Laboratory Course in Biochemistry, 5 ECTS (norsk) KJB210, Experimental and Applied Biochemistry, 10 ECTS (norsk)
In addition, the PEP group contributes to courses:
BIN210, Introduction to Bioinformatics, 10 ECTS (norsk) KJB310, Protein Chemistry, 10 ECTS (norsk)
KJB320, Proteomics I, 5 ECTS (norsk) KJB420, Proteomics II, 10 ECTS (norsk)
We also provide several interesting master projects! Read more (in Norwegian)
[Biologikurs-Cappelen] Se på foredraget Vincent holdt 22. mai for lærere i videregående skolen i anledning lansering av boken BIOS Biologi 2.
UMB::IKBM::The Protein Engineering and Proteomics Group
Contents
1 Procedures (internal) 2 Procedures (external) 3 Bioinformatics
4 Software 5 Enzymes/Chitin 6 Literature
7 Journals/News/Books 8 "Communities"
9 Norske biotekrelaterte 10 Blogs
11 Organizations/other groups 12 Other useful information
Procedures (internal)
http://pep.umb.no/wiki/
Procedures (external)
http://www.openwetware.org/wiki/Protocols
http://www.bio.com/protocolstools/allDisciplines.jhtml http://www.protocol-online.org/
http://folk.uio.no/oddsg/metodebok/
http://www.imbv.uio.no/mol/protocol/
http://www.worthington-biochem.com/
http://www.roche-applied-science.com/LabFAQs/
http://www.neb.uk.com/tools/index.aspx?req=doubledigest - Optimal cutting conditions when doing a double cut..
Bioinformatics
http://www.ncbi.nlm.nih.gov/
http://www.ebi.ac.uk/services/
http://www.ensembl.org/index.html http://umber.sbs.man.ac.uk/dbbrowser/
http://www.ebi.ac.uk/InterProScan/
http://www.genome.ad.jp/
http://www.informatics.jax.org/
http://www.tigr.org/
http://genome.ucsc.edu/
http://srs.sanger.ac.uk/srs/
http://au.expasy.org/spdbv
http://swissmodel.expasy.org//SWISS-MODEL.html
http://www.bizon.org/ - "Biozon is a unified biological resource on DNA sequences, proteins, complexes and cellular pathways."
http://proteas.uio.no/emboss/ - "A collection of bioinformatics tools."
http://www.rcsb.org/pdb/ - "Provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease."
http://www.sanger.ac.uk/Software/Pfam/index.shtml - "Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families."
http://seq.yeastgenome.org/vectordb/ - A database of vectors
http://prospector.ucsf.edu/ - MS? this includes MS-calculators for everything you need http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=propt - "Protein structure Prediction"
http://www.cbs.dtu.dk - A myriad of useful tools (Incl. GenomeAtlas.) http://www.roche-applied-science.com/LabFAQs/ Lab FAQ(Roche)
http://www.bio.com/protocolstools/browsdesc.jhtml BioProtocol http://www.esabweb.org/ Esab
http://www.geneious.com/ - "Geneious puts core bioinformatics functions within the reach of all
UMB::IKBM::The Protein Engineering and Proteomics Group
molecular biologists and biochemists in an application that is as easy to use as email."
Software
http://www.acaclone.com/ - pDRAW32: "Freeware DNA cloning, sequence analysis and plasmid/DNA plotting software."
http://www.mbio.ncsu.edu/BioEdit/page2.html - BioEdit: "Sequence alignment editor and sequence analysis program."
http://www.biocenter.helsinki.fi/bi/Programs/fastpcr.htm - FastPCR: "In silico PCR."
http://pymol.sourceforge.net/ - PyMol: "Real-time visualization and rapid generation of high- quality molecular graphics and animations."
-http://www.pymolwiki.org/index.php/Main_Page - "Wiki for Pymol, hvis man skulle lure på noe."
http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ - ClustalX: "A multiple sequence alignment program."
http://www.ysbl.york.ac.uk/~emsley/coot/ - Coot: "A tool for crystallographic model building, model completion and validation."
http://wishart.biology.ualberta.ca/PlasMapper/ - Plasmapper: "Lager fancy bilder av plasmidene dine, litt mer muligheter til layout enn pDRAW."
http://salilab.org/modeller/ - Modeller: "programvarepakke for comparative modelling av proteiner"
Enzymes/Chitin
http://afmb.cnrs-mrs.fr/CAZY/index.html - "Describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds."
http://callisto.si.usherb.ca/~rbrzezin/index.html - "The purpose of this page is to present up- to-date information about the hydrolytic enzymes acting on chitosan and derivatives."
http://www.euchis.org/index2.html European Chitin Society http://www.genis.is/ Genis
http://www.glycobiology.org/ The Society for Glycobiology
http://kibt.chembio.ntnu.no/nobipol/ NOrwegian BIoPOlymer Laboratory http://kibt.chembio.ntnu.no/euchis02 EUCHIS'02
Literature
http://scholar.google.com/ - "Stand on the shoulders of giants."
http://pubcrawler.gen.tcd.ie - " It goes to the library - you go to the pub(TM)"
http://www.ebi.ac.uk/Rebholz-srv/ebimed/index.jsp - "Combines Information Retrieval and Extraction from Medline."
http://www.scirus.com/ - "Search engine that fetches only scientific websites."
http://portal.isiknowledge.com/portal.cgi/ - "ISI Web of Knowledge"
Journals/News/Books
http://www.pnas.org/ - "Proceedings of the National Academy of Sciences"
http://www.jbc.org/ - "Journal of Biological Chemistry"
http://www.sciencemag.org/ - Science http://www.nature.com/nature/ - Nature
http://www.nature.com/nbt/ - Nature Biotechnology http://www.cell.com/ - Cell
http://arstechnica.com/journals/science.ars - "Nobel Intent is Ars Technica’s science-centric journal."
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books - "A free online collection of several biomedical books, searchable, with illustrations/pictures."
"Communities"
http://www.bioforge.net/ - "Biological Invention for Open Society"
http://www.bio.net/bionet/ - "A set of electronic communication forums."
http://www.siphs.com/ - "A peer enabled search engine and online reference for the life sciences research community."
http://openwetware.org/ - "An effort to promote the sharing of information, and wisdom among researchers and groups who are working in biology & biological engineering."
http://www.biotech-talk.com/ - "A place for people from all around the world to discuss issues related to biotechnology at both technical and speculative levels."
http://www.orkut.com/ - "Orkut makes it easy to find people who share your hobbies and interests."
Norske biotekrelaterte
http://www.norbiobase.no/ - "A major aim of NorBioBase is to showcase the strong growth of biotechnological innovation in Norway"
http://www.scandinavianlifescience.org/ - "A comprehensive database presenting the power of the
UMB::IKBM::The Protein Engineering and Proteomics Group
http://www.biotekforum.no/ - "The Association is an independent member organization with purpose to promote development of Norwegian biotechnological trade and research."
http://www.medcoast.org/ - "MedCoast Scandinavia aims to establish the Göteborg Oslo (GO) Region as one of the leading bioregions in Europe where world-class researchers, a well-developed health service and excellent working conditions form an attractive environment for investors within the biotechnological and healthcare sector."
http://www.bion.no/ - "Bioteknologinemnda er en høringsinstans for norske myndigheter i forbindelse med saker som vedrører moderne bioteknologi. Bioteknologinemnda skal bidra med informasjon til publikum og forvaltningen, og fremme debatt omkring de etiske og samfunnsmessige konsekvensene ved bruk av moderne bioteknologi."
http://www.forskning.no/ - "En nettavis om norsk og internasjonal forskning."
Blogs
http://biosingularity.wordpress.com/ - "Biosingularity"
http://bioboom.blogspot.com/ - "BioBoom"
http://www.paraschopra.com/blog/biohacking.php - "BioHacking"
Organizations/other groups
http://www.cambia.org/ - "An international, independent non-profit research institute pioneering Biological Open Source (BiOS) and Informatics to support Patent Transparency."
http://sciencecommons.org/ - "We work to encourage scientific innovation by making it easier for scientists, universities, and enterprises to share scientific literature, data, and materials."
http://www.forskningsradet.no/ - "Forskningsrådet er et strategisk organ som peker ut satsingsområder, tildeler forskningsmidler og vurderer forskningen som utføres."
http://www.forskerforbundet.no/ - "Landets største og ledende fag- og interesseorganisasjon for ansatte i forskning, høyere utdanning og kulturminnevern."
http://www.esabweb.org/ - "European Federation of Biotechnology - Section on Applied Biocatalysis"
http://www.glycobiology.org/ - "A nonprofit scholarly society devoted to the pursuit of knowledge of glycan structures and functions, and to the sharing of that knowledge among scientists worldwide."
http://www.euchis.org/ - "Encourage basic and applied scientific studies of all aspects of chitin, including chitosan and derivatives of chitin and chitosan, and related enzymes."
http://www.biotech.ntnu.no/nobipol/ - "...main focus on the science and technologies of marine polysaccharides."
http://bioorganisk.umb.no/ - "Our research interests are in the intersection between chemistry and biology. Especially, we have a focus on ligand-enzyme interactions."
Other useful information
http://en.wikipedia.org/wiki/Main_Page Online Wiki Encyclopedia http://www.howstuffworks.com How stuff works
http://en.wikipedia.org/wiki/Functional_group Functional groups in organic chemistry
UMB::IKBM::The Protein Engineering and Proteomics Group
HVA FORSKER VI PÅ ? - På norsk
En introduksjon om kitin, rekeskall, kitololigosakkarider (CHOS), anvendelser, astma og malaria.
En artikkel om kitinforskningen vår fra forskning.no.
CBP21 omtalt for et bredt vitenskapelig pulikum i NBS-Nytt – se side 20-21 (2005) Oppslag om våre funn om betydningen av enzym prosessivitet(2006)
Våre funn rundt prosessivitet omtalt i NBS-Nytt – se side 30-32
En populærvitenskapelig artikkel om hvordan kitinforskningen hjelper oss til å utvikle enzymteknologi for produskjon av bioetanol (2006).
Frø i dag, tiger på tanken i morgen (vår 2007) Biomasse, bioetanol og bioteknologi (vår 2007)
Fra tre til tank via sopp (sommer 2007 – om samarbeid mellom PEP og Skog og landskap)
UMB::IKBM::The Protein Engineering and Proteomics Group
Masteroppgaver
Masteroppgaver i PEP 2009-2011
(hoveddokument, skriv ut dette hvis du er interessert i masteroppgave hos oss)
Kort oversikt over temaer.
Eksempel på noen konkrete forslag til masteroppgaver Karakterisering av Kitobiase
Hovedoppgave melkesyrebakterier
Vi kan også formidle masteroppgaver hos våre samarbeidspartnere på Ås, f eks. ved Bioforsk: functional genomics of plant-pathogen interactions
Nofima-Mat: functional genomics of food microbes; proteomics Og vi har kontakter i flere miljøer i Oslo.
Interessert? Send en mail til Vincent Eijsink eller ta en tur opp til oss i 3. etasje i Biotekbygget for en uformell prat.
UMB::IKBM::The Protein Engineering and Proteomics Group
Enzymatic processing of carbohydrate polymers to fermentable sugars is one of the key bottle-necks in the production of second generation bioethanol. Through our years of experience with enzymatic degradation of chitin, we are in a good position to contribute to solving this bottle-neck.
When it comes to the enzymatic processing step, we are clearly leading in Norway, and we are reasonably competitive internationally. Several breakthrough findings in chitin- enzymology have given us some competitive advantage in the field and some new ideas that are currently being pursued. We are collaborating with Norwegian industry. We supply industry with enzyme competence related to process development for bioethanol production. Our efforts are part of a larger effort on the university campus to combine and exploit the competence in areas such as forestry,
biotechnology, biodiversity, economics and plant science for the benefit of sustainable production of biomass-based energy.
Dampeksplosjonsanlegg!!
Currently we have three focus areas Lignocellulose and biotehanol Barley
Fish
MORE INFORMATION
We and others have written several publications that provide general insight into bioethanol as well as into the possible contributions of the PEP group. These texts are written for a broad public in Norwegian. See:
Fra tre til tank (høsten 2006)
Frø i dag, tiger på tanken i morgen (vår 2007) Biomasse, bioetanol og bioteknologi (vår 2007)
Fra tre til tank via sopp (sommer 2007 – om samarbeid mellom PEP og Skog og landskap)
If you want to know more about the difference between first- and second generation bioethanol and about the potential social and environmental implications of this difference, you may take a look at ”The biofuels conundrum”, an editorial in Science, published in April 2007.
You may find a recent 20 minute lecture from Vincent on the topic here, in Norwegian (”Biomasse, bioetanol og bioteknologi”). Please do not hesitate to contact vincent.eijsink[AT]umb.no if you want to know more.
We use a Steam Explosion Unit to pretreat the biomass
UMB::IKBM::The Protein Engineering and Proteomics Group
OBS Norwegians: For norsk-talende lesere. Nedenfor vil dere finne flere linker til norske tekster, inklusive populærvitenskapelige tekster.
In the PEP group we are not only interested in fundamental knowledge on how enzymes work, we are also interested in applying enzyme technology in practice. Take a look at a recent poster, where we advertise for our activities in the field.
UMB::IKBM::The Protein Engineering and Proteomics Group
Feil: Ingen tilgang (local): "Bilde:Gustav_feirer.jpg"
UMB::IKBM::The Protein Engineering and Proteomics Group
Surprise party!!
UMB::IKBM::The Protein Engineering and Proteomics Group
UMB::IKBM::The Protein Engineering and Proteomics Group
Berit Bjugan Aam
Researcher
Department of Chemistry, Biotechnology and Food Science Norwegian University of Life Sciences
Phone: (+47) 6496 5862 Fax: (+47) 6496 5901 Mail: [email protected]
Postal address:
IKBM, UMB PB 5003
Chr. M. Falsensvei 1 N-1432 Ås
Norway
UMB::IKBM::The Protein Engineering and Proteomics Group
Links
Lactic acid bacteria
Henrik Zakariassen
PhD-student
Department of Chemistry, Biotechnology and Food Science Norwegian University of Life Sciences
Phone: (+47) 6496 Fax: (+47) 6496 5901 Mail:
UMB::IKBM::The Protein Engineering and Proteomics Group
Bowling 2008
Gustav "the champ" on his way
Liv Annette was the winner of the first round
UMB::IKBM::The Protein Engineering and Proteomics Group
Bjørge
UMB::IKBM::The Protein Engineering and Proteomics Group
Geir, very consentrated...
UMB::IKBM::The Protein Engineering and Proteomics Group
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Bioteknologi – fra gener til bærekraftige industrielle
prosesser
Vincent Eijsink
Universitet for Miljø- og Biovitenskap, Institutt for Kjemi, Bioteknologi og Matvitenskap
http://www.umb.no/ikbm/ http://pep.umb.no
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Forskningsfokus:
Bioaktive komponenter:
syntese/rensing, karaktersering, anvendelse
Mat & Helse
Molekylær mikrobiologi og bakteriell genetikk;
miljømikrobiologi samspillet mellom bakterier og
mennesker
Biologisk
prosessteknologi, fra yoghurt, ost og pølser til bioethanol
Institutt for Kjemi, Bioteknologi og Matvitenskap
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
www.umb.no
”Protein Engineering and Proteomics”
gruppe ved IKBM
Å finne, karakterisere, forstå, forbedre (”engineere”) og anvende enzymer
Grunnleggende studier og anvendelser av melkesyrebakterier
pep.umb.no
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Innhold i foredraget
Innledende merknader om bioteknologi og genteknologi
Eksempel fra UMB: melkesyrebakterier
Enzymer og enzymers fortreffelighet – bedre utnyttelse av biologiske råstoffer
Hvordan blir kunnskap om enzymer til?
Hvordan får man tak i nyttige enzymer?
Hvordan kan enzymer utnyttes?
Biodrivstoff
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Bioteknologi / biologisk prosessteknologi er
”gammel”
Genteknologi gir muligheter for nye prosesser og
produkter OG er et ekstremt viktig verktøy i det meste av moderne biologisk forskning
Genteknologi muliggjør raske framskritt mht å oppnå ny kunnskap og mht utvikling av ny
(bærekraftig) teknologi
Bioteknologi / Genteknologi
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Genteknologi, gener og genmodifisert mat
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Genteknologi, gener og bærekraft
Production of 7-Amino-cephalosporanic acid (7-ACA)
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Melkesyrebakterier
Eksempler: Lactococcus &
Lactobacillus
Vi spiser dem hver dag
De bor i våre kropper og de er Generally Regarded As Safe
De gjør mye bra for oss – i maten, og i kroppen
Noen er ”probiotiske”
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Krigen i naturen....
.... gir oss nye konserveringsmidler som er naturlige og
som oppfattes som 100 % trygge. Genteknologi må ofte
til for å forstå og for å utnytte.
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Melkesyrebakterier - nye muligheter...
Kan vi bruke melkesyrebakterier som in situ cellefabrikk?
Vaksinering via yoghurt vi spiser?
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Et plasmid for GMO melkesyrebakterier
Anchor sequence
pLp_0373sOFAcwa1 8622 bp
0373
s p p K
sp pR
O FA
c w a 1
pUC (G EM )
2 56rep E ry
Sørger for at proteinet setter seg fast på
bakteriens utside
Sørger for at
proteinet blir skilt ut
av bakterie Proteinet som vi vil
produsere
R R R
R
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Leting etter gode signaler for sekresjon
0 5 10 15 20 25 30 35 40
SPs fused to NucA U/ml OD
600Lp_3050
Lp_2145
M6
Lp_0373 Lp_0600
Lp_3093
Lp_2578
Lp_2940 Usp45
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Rekombinant L.
plantarum gitt til mus med kreft
Secreted OFA
Cell wallAnchored OFA
Secreted Hsp Wild type -27
Intracellular OFA
(Data fra Mouldy Sioud, Radiumhospitalet)
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
Bekjempelse av kroniske
tarmsykdommer
Institutt for kjemi, bioteknologi og matvitenskap
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UNIVERSITETET FOR MILJ Ø - OG BIOVITENSKAP
www.umb.no
Enzymers
fortreffelighet Katalyserer kjemiske reaksjoner under naturlige betingelser
Er meget presise; ingen bi-produkter
Ingen behov for bruk av forurensende kjemikalier, lave energibehov
Kan katalysere prosesser som vi ikke har kjemisk teknologi til
Essensiell for bedre utnyttelse av fornybare råstoffer
ChiA ChiB ChiC1 ChiC2
Signal sequence Catalytic domain
Fn3-like domain Chitin-binding domain
FnIII
CBM5 Cat
FnIII Cat
Cat CBM12
