Rasmus Larsen - Academia.edu (original) (raw)

Papers by Rasmus Larsen

Research paper thumbnail of ArgR and AhrC Are Both Required for Regulation of Arginine Metabolism in Lactococcus lactis

Journal of Bacteriology, 2004

The DNA binding proteins ArgR and AhrC are essential for regulation of arginine metabolism in Esc... more The DNA binding proteins ArgR and AhrC are essential for regulation of arginine metabolism in Escherichia coli and Bacillus subtilis, respectively. A unique property of these regulators is that they form hexameric protein complexes, mediating repression of arginine biosynthetic pathways as well as activation of arginine catabolic pathways. The gltS-argE operon of Lactococcus lactis encodes a putative glutamate or arginine transport protein and acetylornithine deacetylase, which catalyzes an important step in the arginine biosynthesis pathway. By random integration knockout screening we found that derepression mutants had ISS1 integrations in, among others, argR and ahrC. Single as well as double regulator deletion mutants were constructed from Lactococcus lactis subsp. cremoris MG1363. The three arginine biosynthetic operons argCJDBF, argGH, and gltS-argE were shown to be repressed by the products of argR and ahrC. Furthermore, the arginine catabolic arcABD1C1C2TD2 operon was activated by the product of ahrC but not by that of argR. Expression from the promoter of the argCJDBF operon reached similar levels in the single mutants and in the double mutant, suggesting that the regulators are interdependent and not able to complement each other. At the same time they also appear to have different functions, as only AhrC is involved in activation of arginine catabolism. This is the first study where two homologous arginine regulators are shown to be involved in arginine regulation in a prokaryote, representing an unusual mechanism of regulation.

Research paper thumbnail of A Food-Grade Cloning System for Industrial Strains of Lactococcus lactis

Applied and Environmental Microbiology, 2000

We have previously reported the construction of a food-grade cloning vector for Lactococcus using... more We have previously reported the construction of a food-grade cloning vector for Lactococcus using the ochre suppressor, supB, as the selective marker. This vector, pFG1, causes only a slight growth inhibition in the laboratory strain MG1363 but is unstable in the industrial strains tested. As supB suppresses both amber and ochre stop codons, which are present in 82% of all known lactococcal genes, this undesirable finding may result from the accumulation of elongated mistranslated polypeptides. Here, we report the development of a new food-grade cloning vector, pFG200, which is suitable for overexpressing a variety of genes in industrial strains of Lactococcus lactis. The vector uses an amber suppressor, supD, as selectable marker and consists entirely of Lactococcus DNA, with the exception of a small polylinker region. Using suppressible pyrimidine auxotrophs, selection and maintenance are efficient in any pyrimidine-free medium including milk. Importantly, the presence of this vector in a variety of industrial strains has no significant effect on the growth rate or the rate of acidification in milk, making this an ideal system for food-grade modification of industrially relevant L. lactis strains. The usefulness of this system is demonstrated by overexpressing the pepN gene in a number of industrial backgrounds.

Research paper thumbnail of A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data

BMC Genomics, 2005

2005). A Generally applicable validation scheme for the assessment of factors involved in reprodu... more 2005). A Generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC Genomics, 6(77), For guidance on citations see FAQs. c [not recorded] Version: [not recorded] Link(s) to article on publisher's website: http://dx.doi.org/

Research paper thumbnail of Probing Direct Interactions between CodY and the oppD Promoter of Lactococcus lactis

Journal of Bacteriology, 2005

CodY of Lactococcus lactis MG1363 is a transcriptional regulator that represses the expression of... more CodY of Lactococcus lactis MG1363 is a transcriptional regulator that represses the expression of several genes encoding proteins of the proteolytic system. These genes include pepN, pepC, opp-pepO1, and probably prtPM, pepX, and pepDA2, since the expression of the latter three genes relative to nitrogen availability is similar to that of the former. By means of in vitro DNA binding assays and DNase I footprinting techniques, we demonstrate that L. lactis CodY interacts directly with a region upstream of the promoter of its major target known so far, the opp system. Our results indicate that multiple molecules of CodY interact with this promoter and that the amount of bound CodY molecules is affected by the presence of branched-chain amino acids and not by GTP. Addition of these amino acids strongly affects the extent of the region protected by CodY in DNase I footprints. Random and site-directed mutagenesis of the upstream region of oppD yielded variants that were derepressed in a medium with an excess of nitrogen sources. Binding studies revealed the importance of specific bases in the promoter region required for recognition by CodY.

Research paper thumbnail of Fusion of stereo vision and Time-Of-Flight imaging for improved 3D estimation

International Journal of Intelligent Systems Technologies and Applications, 2008

In this paper the fusion of two 3D estimation techniques is suggested: Stereo vision and Time-of-... more In this paper the fusion of two 3D estimation techniques is suggested: Stereo vision and Time-of-Flight (TOF) imaging. By converting the TOF-depth measurements to stereo disparities the correspondence between images from a fast TOF-camera and standard high resolution camera pair are found so the TOF depth measurements can be linked to the image pairs. Also in the same framework a method is developed to initialize and constrain a hierarchical stereo matching algorithm. It is shown that in this way higher spatial resolution is obtained than by only using the TOF camera and higher quality dense stereo disparity maps are the results of this sensor fusion.

Research paper thumbnail of ArgR and AhrC Are Both Required for Regulation of Arginine Metabolism in Lactococcus lactis

Journal of Bacteriology, 2004

The DNA binding proteins ArgR and AhrC are essential for regulation of arginine metabolism in Esc... more The DNA binding proteins ArgR and AhrC are essential for regulation of arginine metabolism in Escherichia coli and Bacillus subtilis, respectively. A unique property of these regulators is that they form hexameric protein complexes, mediating repression of arginine biosynthetic pathways as well as activation of arginine catabolic pathways. The gltS-argE operon of Lactococcus lactis encodes a putative glutamate or arginine transport protein and acetylornithine deacetylase, which catalyzes an important step in the arginine biosynthesis pathway. By random integration knockout screening we found that derepression mutants had ISS1 integrations in, among others, argR and ahrC. Single as well as double regulator deletion mutants were constructed from Lactococcus lactis subsp. cremoris MG1363. The three arginine biosynthetic operons argCJDBF, argGH, and gltS-argE were shown to be repressed by the products of argR and ahrC. Furthermore, the arginine catabolic arcABD1C1C2TD2 operon was activated by the product of ahrC but not by that of argR. Expression from the promoter of the argCJDBF operon reached similar levels in the single mutants and in the double mutant, suggesting that the regulators are interdependent and not able to complement each other. At the same time they also appear to have different functions, as only AhrC is involved in activation of arginine catabolism. This is the first study where two homologous arginine regulators are shown to be involved in arginine regulation in a prokaryote, representing an unusual mechanism of regulation.

Research paper thumbnail of A Food-Grade Cloning System for Industrial Strains of Lactococcus lactis

Applied and Environmental Microbiology, 2000

We have previously reported the construction of a food-grade cloning vector for Lactococcus using... more We have previously reported the construction of a food-grade cloning vector for Lactococcus using the ochre suppressor, supB, as the selective marker. This vector, pFG1, causes only a slight growth inhibition in the laboratory strain MG1363 but is unstable in the industrial strains tested. As supB suppresses both amber and ochre stop codons, which are present in 82% of all known lactococcal genes, this undesirable finding may result from the accumulation of elongated mistranslated polypeptides. Here, we report the development of a new food-grade cloning vector, pFG200, which is suitable for overexpressing a variety of genes in industrial strains of Lactococcus lactis. The vector uses an amber suppressor, supD, as selectable marker and consists entirely of Lactococcus DNA, with the exception of a small polylinker region. Using suppressible pyrimidine auxotrophs, selection and maintenance are efficient in any pyrimidine-free medium including milk. Importantly, the presence of this vector in a variety of industrial strains has no significant effect on the growth rate or the rate of acidification in milk, making this an ideal system for food-grade modification of industrially relevant L. lactis strains. The usefulness of this system is demonstrated by overexpressing the pepN gene in a number of industrial backgrounds.

Research paper thumbnail of A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data

BMC Genomics, 2005

2005). A Generally applicable validation scheme for the assessment of factors involved in reprodu... more 2005). A Generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC Genomics, 6(77), For guidance on citations see FAQs. c [not recorded] Version: [not recorded] Link(s) to article on publisher's website: http://dx.doi.org/

Research paper thumbnail of Probing Direct Interactions between CodY and the oppD Promoter of Lactococcus lactis

Journal of Bacteriology, 2005

CodY of Lactococcus lactis MG1363 is a transcriptional regulator that represses the expression of... more CodY of Lactococcus lactis MG1363 is a transcriptional regulator that represses the expression of several genes encoding proteins of the proteolytic system. These genes include pepN, pepC, opp-pepO1, and probably prtPM, pepX, and pepDA2, since the expression of the latter three genes relative to nitrogen availability is similar to that of the former. By means of in vitro DNA binding assays and DNase I footprinting techniques, we demonstrate that L. lactis CodY interacts directly with a region upstream of the promoter of its major target known so far, the opp system. Our results indicate that multiple molecules of CodY interact with this promoter and that the amount of bound CodY molecules is affected by the presence of branched-chain amino acids and not by GTP. Addition of these amino acids strongly affects the extent of the region protected by CodY in DNase I footprints. Random and site-directed mutagenesis of the upstream region of oppD yielded variants that were derepressed in a medium with an excess of nitrogen sources. Binding studies revealed the importance of specific bases in the promoter region required for recognition by CodY.

Research paper thumbnail of Fusion of stereo vision and Time-Of-Flight imaging for improved 3D estimation

International Journal of Intelligent Systems Technologies and Applications, 2008

In this paper the fusion of two 3D estimation techniques is suggested: Stereo vision and Time-of-... more In this paper the fusion of two 3D estimation techniques is suggested: Stereo vision and Time-of-Flight (TOF) imaging. By converting the TOF-depth measurements to stereo disparities the correspondence between images from a fast TOF-camera and standard high resolution camera pair are found so the TOF depth measurements can be linked to the image pairs. Also in the same framework a method is developed to initialize and constrain a hierarchical stereo matching algorithm. It is shown that in this way higher spatial resolution is obtained than by only using the TOF camera and higher quality dense stereo disparity maps are the results of this sensor fusion.