Publications from Biomolecular Regulation Group

Total publications from unit:

2019

1.

Simon Riis, Britt Christensen, Birgitte Nellemann, Andreas Ruch Moller, Anna Sofie Husted, Steen B. Pedersen, Thue W. Schwartz, Jens Otto Lunde Jorgensen and Niels Jessen. (2019) Molecular adaptations in human subcutaneous adipose tissue after ten weeks of endurance exercise training in healthy males Journal of Applied Physiology 126(3):569-577.

2.

Steen Pedersen, Thilde Bagger Terkelsen, Mette Eriksen, Magnus Krarup Hauge, Casper Carstens Lund, Kim Sneppen and Namiko Mitarai. (2019) Fast Translation within the First 45 Codons Decreases mRNA Stability and Increases Premature Transcription Termination in E. coli Journal of Molecular Biology 431(6):1088-1097.

2018

3.

Rasmus Skytte Eriksen, Sine Lo Svenningsen, Kim Sneppen and Namiko Mitarai. (2018) A growing microcolony can survive and support persistent propagation of virulent phages Proceedings of the National Academy of Sciences USA (PNAS) 115(2):337-342.

4.

Michael Askvad Sørensen, Annaleigh Ohrt Fehler and Sine Lo Svenningsen. (2018) Transfer RNA instability as a stress response in Escherichia coli RNA Biology 15:586-593.

5.

Ryan William Paerl, John Sundh, Demeng Tan, Sine Lo Svenningsen, Samuel Hylander, Jarone Pinhassi, Anders F. Andersson and Lasse Riemann. (2018) Prevalent reliance of bacterioplankton on exogenous vitamin B1 and precursor availability Proceedings of the National Academy of Sciences of the United States of America 115(44):E10447-E10456.

6.

Sine Lo Svenningsen. (2018) Small RNA-Based Regulation of Bacterial Quorum Sensing and Biofilm Formation Microbiology Spectrum 6(4):337-342.

7.

Thomas Prossliner, Kristoffer Skovbo Winther, Michael Askvad Sørensen and Kenn Gerdes. (2018) Ribosome Hibernation Annual Review of Genetics 52:321-348.

2017

8.

Alexander Harms, Cinzia Fino, Michael Askvad Sørensen, Szabolcs Semsey and Kenn Gerdes. (2017) Prophages and growth dynamics confound experimental results with antibiotic-tolerant persister cells mBio 8(6):586-593.

9.

Thomas Søndergaard Stenum, Michael Askvad Sørensen and Sine Lo Svenningsen. (2017) Quantification of the abundance and charging levels of transfer RNAs in Escherichia coli Journal of Visualized Experiments 126:586-593.

10.

Vaibhhav Sinha, Akshit Goyal, Sine Lo Svenningsen, Szabolcs Semsey and Sandeep Krishna. (2017) In silico evolution of lysis-lysogeny strategies reproduces observed lysogeny propensities in temperate bacteriophages Frontiers in Microbiology 8:586-593.

11.

Mark K Nøhr, Natalia Bobba, Bjørn Richelsen, Sten Lund and Steen B Pedersen. (2017) Inflammation Downregulates UCP1 Expression in Brown Adipocytes Potentially via SIRT1 and DBC1 Interaction International Journal of Molecular Sciences (CD-ROM) 18(5):1088-1097.

12.

Mette Eriksen, Kim Sneppen, Steen Pedersen and Namiko Mitarai. (2017) Occlusion of the ribosome binding site connects the translational initiation frequency, mRNA stability and premature transcription termination Frontiers in Microbiology 8(5):1088-1097.

13.

Sine Lo Svenningsen, Mette Kongstad, Thomas Søndergaard Stenum, Ana Josefa Muñoz Gomez and Michael Askvad Sørensen. (2017) Transfer RNA is highly unstable during early amino acid starvation in Escherichia coli Nucleic Acids Research 45(2):793-804.

2016

14.

Chengzhe Tian, Mohammad Roghanian, Mikkel Girke Jørgensen, Kim Sneppen, Michael Askvad Sørensen, Kenn Gerdes and Namiko Mitarai. (2016) Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Encoded mRNases Journal of Bacteriology 198(14):1918-1926.

2015

15.

Szabolcs Semsey, Christopher Campion, Abdu Mohamed and Sine Lo Svenningsen. (2015) How long can bacteriophage ? change its mind? Bacteriophage 5(1):e1012930.

16.

Sabine Hansen, Sandeep Krishna, Szabolcs Semsey and Sine Lo Svenningsen. (2015) Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades Scientific Reports 5(1):e1012930.

17.

Demeng Tan, Sine Lo Svenningsen and Mathias Middelboe. (2015) Quorum sensing determines the choice of antiphage defense strategy in Vibrio anguillarum mBio 6(3):e1012930.

2014

18.

Rebecca Bolt Ettlinger, Michael Askvad Sørensen and Lene Broeng Oddershede. (2014) Force spectroscopy of DNA and RNA Nucleic Acid Nanotechnology 198(14):1918-1926.

19.

Sine Lo Svenningsen and Szabolcs Semsey. (2014) Commitment to lysogeny is preceded by a prolonged period of sensitivity to the late lytic regulator Q in bacteriophage ? Journal of Bacteriology 196(20):3582-3588.

2013

20.

Namiko Mitarai and Steen Pedersen. (2013) Control of ribosome traffic by position-dependent choice of synonymous codons Physical Biology 10(5):1088-1097.

21.

Mette Eriksen, Peter Horvath, Michael Askvad Sørensen, Szabolcs Semsey, Lene Broeng Oddershede and Liselotte Jauffred Pedersen. (2013) A novel complex Journal of Nanomaterials 2013(14):1918-1926.

22.

Nina Molin Høyland-Kroghsbo, Rasmus Baadsgaard Mærkedahl and Sine Svenningsen. (2013) A quorum-sensing-induced bacteriophage defense mechanism mBio 4(1):1-9.

23.

Stefan Klumpp, Matthew Scott, Steen Pedersen and Terence Hwa. (2013) Molecular crowding limits translation and cell growth Proceedings of the National Academy of Sciences of the United States of America 110(42):16754-16759.

2012

24.

Jesper Tholstrup Hansen, Lene Broeng Oddershede and Michael Askvad Sørensen. (2012) mRNA pseudoknot structures can act as ribosomal roadblocks Nucleic Acids Research 40(1):303-313.

2011

25.

Brian K Hammer and Sine Lo Svenningsen. (2011) Small RNA target genes and regulatory connections in the Vibrio cholerae quorum sensing system Quorum sensing 407(1):35-44.

26.

Kristian Moss Bendtsen, Janos Erdossy, Zsolt Csiszovski, Sine Lo Svenningsen, Kim Sneppen, Sandeep Krishna and Szabolcs Semsey. (2011) Direct and indirect effects in the regulation of overlapping promoters Nucleic Acids Research 39(16):6879-6885.

27.

Margit Pedersen, Søren Nissen, Namiko Mitarai, Sine Lo Svenningsen, Kim Sneppen and Steen Pedersen. (2011) The functional half-life of an mRNA depends on the ribosome spacing in an early coding region Journal of Molecular Biology 407(1):35-44.

2010

28.

Kim Sneppen, Steen Pedersen, Sandeep Krishna, Ian Burwell Dodd and Szabolcs Semsey. (2010) Economy of operon formation Microbe 1(4):e00177-10.

29.

Kimberly C. Tu, Tao Long, Sine Lo Svenningsen, Ned S. Wingreen and Bonnie L. Bassler. (2010) Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi qourum-sensing response Molecular Cell 37(4):567-579.

2009

30.

Sine L Svenningsen, Kimberly C Tu and Bonnie L Bassler. (2009) Gene dosage compensation calibrates four regulatory RNAs to control Vibrio cholerae quorum sensing EMBO Journal 28(4):429-39.

2008

31.

Sine L. Svenningsen. (2008) Small RNA control of cell-to-cell communication in Vibrio harveyi and Vibrio cholerae small RNA control of quorum sensing Evolution from Cellular to Social Scales 28(4):429-39.

32.

Kimberly C. Tu, Christopher M. Waters, Sine L. Svenningsen and Bonnie L. Bassler. (2008) A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics in Vibrio harveyi Molecular Microbiology 70(4):896-907.

33.

Namiko Mitarai, Kim Sneppen and Steen Pedersen. (2008) Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization Journal of Molecular Biology 382(1):236-245.

34.

Sine Lo Svenningsen. (2008) A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics inVibrio harveyi Molecular Microbiology 70(4):896-907.

35.

Sine Lo Svenningsen. (2008) A negative feedback loop involving small RNAs accelerates Vibrio cholerae'stransition out of quorum-sensing mode Genes & Development 22(2):226-38.

2007

36.

Morten Ejby, Michael A Sørensen and Steen Pedersen. (2007) Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination. Proceedings of the National Academy of Science of the United States of America 104(49):19410-5.

37.

Thomas Møller Hansen, S Nader S Reihani, Lene B Oddershede and Michael A Sørensen. (2007) Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting. Proceedings of the National Academy of Science of the United States of America 104(14):5830-5.

2005

38.

K. A. Dittmar, Michael Askvad Sørensen, J. Elf, M. Ehrenberg and Tao Pan. (2005) Selective charging of tRNA isoacceptors induced by amino-acid starvation EMBO Reports 6(2):151–157.

39.

Michael Askvad Sørensen, J. Elf, E. Bouakaz, T. Tenson, S. Sanyal, G. R. Björk and M. Ehrenberg. (2005) Over Expression of a tRNALeu Isoacceptor Changes Charging Pattern of Leucine tRNAs and Reveals New Codon Reading Journal of Molecular Biology 354(1):16-24.

40.

Sine Lo Svenningsen, Nina Constantino, Donald L Court and Sankar Adhya. (2005) On the role of Cro in lambda prophage induction Proceedings of the National Academy of Science of the United States of America 102(12):4465-4469.

2003

41.

A.M. Sanden, I. Prytz, I. Tubelekas, C. Forsberg, H. Le, A. Hektor, P. Neubauer, Z. Pragai, C. Harwood, A. Ward, A. Picon, J.T. de Mattos, P. Postma, A. Farewell, T. Nystrøm, S. Reeh, Steen Pedersen and G. Larsson. (2003) Limiting factors in Escherichia colifed-batch production of recombinant proteins Biotechnology and Bioengineering (Print) 104:158-166.

42.

Kristoffer Torbjørn Bæk, Sine Lo Svenningsen, Harvey Eisen, Kim Sneppen and Stanley Brown. (2003) Single-cell Analysis of Lambda Immunity Regulation Journal of Molecular Biology 334(3):363-372.

2002

43.

Esben Selmer Buhl, Niels Jessen, Rasmus Pold, Thomas Ledet, Allan Flyvbjerg, Steen B Pedersen, Oluf Pedersen, Ole Schmitz and Sten Lund. (2002) Long-term AICAR administration reduces metabolic disturbances and lowers blood pressure in rats displaying features of the insulin resistance syndrome Diabetes 51(7):2199-206.

2001

44.

M.A. Sørensen. (2001) Charging Levels of Four tRNA Species in Escherichia coli Rel+ and REL- Strains during Amino Acid Starvation: A Simple Model for the Effect of ppGpp on Translational Accuracy Journal of Molecular Biology 307(3):785-798.

2000

45.

Steen Pedersen. (2000) Thermodynamics of heat-shock response. Physical Review Letters 51(7):Phys Rev Lett; 84: 3005-8..

1998

46.

M.A. Sørensen, J. Fricke and Steen Pedersen. (1998) Ribosomal Protein S1 required for translation of most, if not all, natural mRNAs in Escherichia coli in vivo Journal of Molecular Biology 51(280):561-569.

47.

Malene Kappen Krüger and M.A. Sørensen. (1998) Aminoacylation of hypomodified tRNAGlu in vivo Journal of Molecular Biology 284(3):609-620.

48.

Malene Kappen Krüger, Steen Pedersen, T.G. Hagervall and M.A. Sørensen. (1998) The modification of the wobble base of tRNAGlu modulates the translation rate of glutamic acid codons in vivo J. Mol. Biol. 51(284):609-620.

1994

49.

C.G. Jensen, S. Brown and Steen Pedersen. (1994) Effect of 4.5S RNA Depletion on Escherichia coli Protein Synthesis and Secretion Journal of Bacteriology 236:2502-2506.

50.

M.A. Sørensen, K.F. Jensen and Steen Pedersen. (1994) High Concentrations of ppGpp Decrease the RNA Chain Growth Rate. Implications for Protein Synthesis and Translation Fidelity During Amino Acid Starvation in Escherichia coli Journal of Molecular Biology 51:441-454.

51.

Michael Askvad Sørensen, Kaj Frank Jensen and Steen Pedersen. (1994) High concentrations of ppGpp decrease the RNA chain growth rate: implications for protein synthesis and translational fidelity during amino acid starvation in Escherichia coli Journal of Molecular Biology 236:441-454.

1993

52.

J. Vind, M.A. Sørensen, M.D. Rasmussen and Steen Pedersen. (1993) Synthesis of proteins in Escherichia coli is limited by the concentration of free ribosomes Journal of Molecular Biology 240:678-688.

53.

M.D. Rasmussen, M.A. Sørensen and Steen Pedersen. (1993) Isolation and characterization of mutants with impaired regulation of rpsA, the gene encoding ribosomal protein S1 of Escherichia coli Molecular Genetics and Genomics 240:23-28.

1992

54.

U. Vogel, M.A. Sørensen, Steen Pedersen, Kaj Frank Jensen and M. Kilstrup. (1992) Decreasing transcription elongation rate in Escherichia coli exposed to amino acid starvation Molecular Microbiology 6(15):2191-2200.

1991

55.

M.A. Sørensen and Steen Pedersen. (1991) Cysteine, Even in Low Concentrations, Induces Transient Amino Acid Starvation in Escherichia coli J. Bacteriol. 6:5244-46.

56.

M.A. Sørensen and Steen Pedersen. (1991) Absolute in vivo translation rates of individual codons in Escherichia coli: The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate Journal of Molecular Biology 222(2):265-280.

57.

Ulla Vogel, Steen Pedersen and Kaj Frank Jensen. (1991) An unusual correlation between ppGpp pool size and rate of ribosome synthesis during partial pyrimidine starvation of Escherichia coli Journal of Bacteriology 173(3):1168-1174.

1989

58.

Michael Askvad Sørensen, C G Kurland and Steen Pedersen. (1989) Codon usage determines translation rate in Escherichia coli Journal of Molecular Biology 207(2):365-77.

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