262 results on '"Francke, C."'
Search Results
2. Relaxation and Trapping In Reaction Centers of the Green Sulfur Bacterium Prosthecochloris Aestuarii
- Author
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Neerken, S., Permentier, H. P., Aschenbrücker, J., Ma, Y-Z., Francke, C., Schmidt, K. A., Gillbro, T., Aartsma, T. J., Amesz, J., and Garab, G., editor
- Published
- 1998
- Full Text
- View/download PDF
3. Electron Transfer in Reaction Centers from Green Sulfur Bacteria
- Author
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Schmidt, K. A., Permentier, H. P., de Wijn, R., Neerken, S., Franken, E. M., Francke, C., Hager-Braun, C., Aartsma, T. J., Amesz, J., and Garab, G., editor
- Published
- 1998
- Full Text
- View/download PDF
4. Seismic deformation analysis of Tuttle Creek Dam
- Author
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Stark, Timothy D., Beaty, Michael H., Byrne, Peter M., Castro, Gonzalo, Walberg, Francke C., Perlea, Vlad G., Axtell, Paul J., Dillon, John C., Empson, William B., and Mathews, David L.
- Subjects
Seismology -- Research ,Geodynamics -- Research ,Dam failures -- Research -- United States ,Deformations (Mechanics) -- Research ,Earth sciences - Abstract
To facilitate the design of seismic remediation for Tuttle Creek Dam in east central Kansas, a seismic finite difference analysis of the dam was performed using the software FLAC and the UBCSAND and UBCTOT soil constitutive models. The FLAC software has a key advantage because it can use calibrated site-specific constitutive models. Earlier deformation analyses using a hyperbolic constitutive model for the foundation fine-grained materials did not properly represent the modulus and strength reduction and predicted extremely large permanent deformations. Cyclic triaxial laboratory tests using high-quality samples and in situ vane shear tests were used to calibrate the FLAC constitutive model herein. The resulting FLAC analysis of the unremediated dam predicted an upstream slope toe deformation of about 0.6 m, a crest settlement of about 0.6 m, and a downstream slope toe deformation of about 1.5 m using the design ground motion. Based on the estimated permanent deformations and other factors, it was decided that the anticipated upstream slope and crest deformations were tolerable and only the downstream slope had to be remediated to protect the downstream seepage control system. Key words: earthquakes, liquefaction, numerical analysis, shear strength, post-liquefaction, slope stability. Resume : Dans le but d'assister la conception de la rehabilitation sismique du barrage de Tuttle Creek dans le centre est du Kansas, une analyse sismique du barrage par difference finie a ete realisee a l'aide du logiciel FLAC et des modeles constitutifs de sols UBCSAND et UBCTOT. Le logiciel FLAC est avantageux puisqu'il peut utiliser des modeles constitutifs calibres pour un site specifique. Des analyses anterieures faites avec un modele constitutif hyperbolique pour des materiaux fins de fondation n' a pas pu representer adequatement la reduction du module et de la resistance et a predit des deformations permanentes extremement grandes. Pour la presente etude, des essais triaxiaux cycliques en laboratoire avec des echantillons de qualite elevee et des essais scissometriques in situ ont ete utilises pour calibrer le modele constitutif de FLAC. L'analyse par FLAC du barrage non rehabilite a predit une deformation du pied de la pente en amont d' environ 0,6 m, un tassement de la crete d'environ 0,6 m, et une deformation du pied de la pente en aval d'environ 1,5 m, et ce, en utilisant les mouvements du sol de conception. Base sur les deformations permanentes estimees et d'autres facteurs, il a ete decide que les deformations anticipees sur la pente en amont et sur la crete sont tolerables et que seulement la pente en aval doit etre rehabilitee afin de proteger le systeme de controle des exfiltrations en aval. Mots-cles : seismes, liquefaction, analyse numerique, resistance au cisaillement, post-liquefaction, stabilite de pente. [Traduit par la Redaction], Introduction Tuttle Creek Dam, located on the Big Blue River in the Kansas River Basin, is part of a system that provides a comprehensive plan for flood control and other [...]
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- 2012
- Full Text
- View/download PDF
5. Liquefaction subsurface investigation for Milford Dam
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Stark, Timothy D., Lewis, Justin R., Castro, Gonzalo, Walberg, Francke C., and Mathews, David L.
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Dams -- Research -- United States ,Soil liquefaction -- Research ,Soil structure -- Research ,Earth sciences - Abstract
The US Army Corps of Engineers (USACE) completed a liquefaction potential analysis as part of the seismic evaluation of Milford Dam in 1986. This paper uses data from the 1986 study to compare fines content data from in situ frozen and standard penetration test (SPT) samples that suggest fines content can be overestimated by 1-10% by SPT samples in stratified sand deposits. This result may have implications for liquefaction assessments because split-spoon samples may overestimate the actual fines content, resulting in a liquefiable deposit being classified as nonliquefiable. In addition, the paper evaluates the effectiveness of ground freezing on maintaining in situ soil structure and aging of the foundation sands at Milford Dam. Key words: soil mechanics, liquefaction, shear strength, cone penetration test, standard penetration test, seismic stability., Introduction Milford Dam is a US Army Corps of Engineers (USACE), Kansas City District (KCD) project, located on the Republican River in east central Kansas. The site is 6.5 km [...]
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- 2011
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6. Aggregation of 8,12-diethyl farnesyl bacteriochlorophyll c at low temperature
- Author
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Dudkowiak, A., Francke, C., and Amesz, J.
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- 1995
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7. SNS-DC-SQUIDs and flux transformers for integrated magnetometers in flip-chip technique
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Meyer, B., Hollkott, J., Francke, C., Wunderlich, R., and Muller, J.
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Superconducting quantum interference devices -- Research ,Josephson junction -- Research ,Plasma etching -- Methods ,Business ,Electronics ,Electronics and electrical industries - Abstract
SNS-direct current-superconducting quantum interference devices (DC-SQUIDs) with a step-and-gap geometry are fabricated by preparing YBCO/Ag/YBCO-Josephson junctions across steps in MgO substrates. An additional etching process is employed to remove the unwanted shunt resistance on top of the YBCO films. Transverse electromagnetic examinations show that this approach improves the DC-SQUIDs' normal resistance without any reduction of the critical current.
- Published
- 1995
8. Metabolic signal transduction in space and time. Facts, figures and principles: SL10-061
- Author
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Westerhoff, H. V., Bakker, B. M., Brady, N., Bruggeman, F., Blom, J., Francke, C., Peletier, M., Kholodenko, B. N., Reijenga, K. A., and Snoep, J. L.
- Published
- 2003
9. Energy Transfer in the Photosynthetic Antenna System of the Purple Non-Sulfur Bacterium Rhodopseudomonas Cryptolactis
- Author
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Kramer, H., primary, Deinum, G., additional, Gardiner, A. T., additional, Cogdell, R. J., additional, Francke, C., additional, Aartsma, T. J., additional, and Amesz, J, additional
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- 1995
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10. Spectral Properties of Monomeric Bacteriochlorophyll C in Nematic Liquid Crystal
- Author
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Dudkowiak, A., primary, Francke, C., additional, Planner, A., additional, Cegielski, R., additional, Hanyż, I., additional, Amesz, J., additional, and Frąckowiak, D., additional
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- 1995
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11. The plasticity of prokaryotic regulatory elements
- Author
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Siezen, R.J., Francke, C., Hijum, S.A.F.T. van, Overmars, L., Siezen, R.J., Francke, C., Hijum, S.A.F.T. van, and Overmars, L.
- Abstract
Radboud University, 31 mei 2017, Promotor : Siezen, R.J. Co-promotores : Francke, C., Hijum, S.A.F.T. van, Contains fulltext : 169268.pdf (publisher's version ) (Open Access)
- Published
- 2017
12. Development of an NGS data analysis strategy to identify the microbial population present in mushroom compost
- Author
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Francke, C., Lamers, W.L., Bongers, J., Klijn, N., Horst, C. van der, and Lokman, B.C.
- Published
- 2016
13. Jet Grouting and Safety of Tuttle Creek Dam
- Author
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Francke C. Walberg, David L. Mathews, John C. Dillon, Timothy D. Stark, Glen M. Bellew, and Paul J. Axtell
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Engineering ,Jet (fluid) ,business.industry ,High pressure ,Fracture (geology) ,Geotechnical engineering ,Building and Construction ,Cement slurry ,Geotechnical Engineering and Engineering Geology ,business ,Civil and Structural Engineering - Abstract
Jet grouting has increasingly become a ground improvement technology used to address seepage concerns and provide strength improvement to soils underlying dams. The technique of jet grouting uses high pressure/volume jet fluids to erode existing soil, evacuate some or most of the soil, and mix the remaining cuttings with cement slurry to form soilcrete. While considered a useful technology, this paper discusses some of the problems that can develop while jet grouting in or below a dam with an operational reservoir and seepage condition. Jet grouting experience at Tuttle Creek Dam indicates concerns with respect to ground fracture; spoil return, column diameter consistency, and homogeneity of resulting soilcrete. Recommendations are presented to increase monitoring of downhole parameters during jet grouting to better understand the downhole pressures and soil response during jet grouting.
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- 2012
14. Seismic deformation analysis of Tuttle Creek Dam
- Author
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Peter M. Byrne, Paul J. Axtell, Francke C. Walberg, Timothy D. Stark, John C. Dillon, William B. Empson, David L. Mathews, Michael Beaty, Vlad Perlea, and Gonzalo Castro
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Slope stability ,Finite difference analysis ,Geotechnical engineering ,Geotechnical Engineering and Engineering Geology ,Geology ,Civil and Structural Engineering - Abstract
To facilitate the design of seismic remediation for Tuttle Creek Dam in east central Kansas, a seismic finite difference analysis of the dam was performed using the software FLAC and the UBCSAND and UBCTOT soil constitutive models. The FLAC software has a key advantage because it can use calibrated site-specific constitutive models. Earlier deformation analyses using a hyperbolic constitutive model for the foundation fine-grained materials did not properly represent the modulus and strength reduction and predicted extremely large permanent deformations. Cyclic triaxial laboratory tests using high-quality samples and in situ vane shear tests were used to calibrate the FLAC constitutive model herein. The resulting FLAC analysis of the unremediated dam predicted an upstream slope toe deformation of about 0.6 m, a crest settlement of about 0.6 m, and a downstream slope toe deformation of about 1.5 m using the design ground motion. Based on the estimated permanent deformations and other factors, it was decided that the anticipated upstream slope and crest deformations were tolerable and only the downstream slope had to be remediated to protect the downstream seepage control system.
- Published
- 2012
15. Liquefaction subsurface investigation for Milford Dam
- Author
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Francke C. Walberg, Timothy D. Stark, David L. Mathews, Gonzalo Castro, and Justin R. Lewis
- Subjects
Engineering ,business.industry ,Forensic engineering ,Liquefaction ,Geotechnical engineering ,Standard penetration test ,Potential analysis ,Geotechnical Engineering and Engineering Geology ,business ,Civil and Structural Engineering - Abstract
The US Army Corps of Engineers (USACE) completed a liquefaction potential analysis as part of the seismic evaluation of Milford Dam in 1986. This paper uses data from the 1986 study to compare fine...
- Published
- 2011
16. Soil Inclusions in Jet Grout Columns
- Author
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John C. Dillon, Francke C. Walberg, Timothy D. Stark, William B. Empson, Joseph E. Topi, Justin R. Lewis, and Paul J. Axtell
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Break-Up ,Grout ,Building and Construction ,engineering.material ,Geotechnical Engineering and Engineering Geology ,Permeability (earth sciences) ,High pressure ,Soil water ,Test program ,Slurry ,engineering ,Geotechnical engineering ,Roof ,Geology ,Civil and Structural Engineering - Abstract
Jet grouting has increasingly become one of the ground improvement technologies used to address seepage concerns and to provide strength improvement of soils. The technique of jet grouting uses high pressure/velocity jet fluids to erode the existing soil and then to mix the cuttings with cement slurry to form soilcrete. Excess slurry or spoil is ejected to the surface. If the native soil is not completely mixed with slurry, the resulting columns will have soil inclusions which can reduce the strength of the column and/or increase the permeability of the column. A jet grout test program at Tuttle Creek Dam shows that the completed large diameter columns contain perhaps 40 to 50% or more of native soil that was not broken up and mixed during the jet grout process. The test program included excavation of full-scale columns to a depth of 35 ft (10.7 m) for visual inspection and testing. Additionally, six of the columns were cut or sectioned to investigate the interior of the columns. The observed inclusions include significant amounts of both fine grained (silts and clays) and coarse grained (fine sands and sands) soils. Evidence suggests at least two explanations: (1) fine grained soils can be difficult to erode and break up into small enough particles that can be ejected to the surface, especially if at low natural water content, and (2) when large diameter columns are being excavated, the excavated roof of the cylindrical cavity may be unstable and may collapse. With this roof instability large slabs of material can break off, fall into the slurry and escape the cutting and mixing action of the rotating jets. This paper describes the Tuttle Creek Dam test program, inclusions observed in the completed columns, and suggests potential causes of the inclusions.
- Published
- 2009
17. Rock mechanics activities at the Waste Isolation Pilot Plant
- Author
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Francke, C., primary and Saeb, S., additional
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- 1996
- Full Text
- View/download PDF
18. A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites
- Author
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Overmars, L., Siezen, R.J., Francke, C., Overmars, L., Siezen, R.J., and Francke, C.
- Abstract
Contains fulltext : 154712.PDF (publisher's version ) (Open Access), The identification of translation initiation sites (TISs) constitutes an important aspect of sequence-based genome analysis. An erroneous TIS annotation can impair the identification of regulatory elements and N-terminal signal peptides, and also may flaw the determination of descent, for any particular gene. We have formulated a reference-free method to score the TIS annotation quality. The method is based on a comparison of the observed and expected distribution of all TISs in a particular genome given prior gene-calling. We have assessed the TIS annotations for all available NCBI RefSeq microbial genomes and found that approximately 87% is of appropriate quality, whereas 13% needs substantial improvement. We have analyzed a number of factors that could affect TIS annotation quality such as GC-content, taxonomy, the fraction of genes with a Shine-Dalgarno sequence and the year of publication. The analysis showed that only the first factor has a clear effect. We have then formulated a straightforward Principle Component Analysis-based TIS identification strategy to self-organize and score potential TISs. The strategy is independent of reference data and a priori calculations. A representative set of 277 genomes was subjected to the analysis and we found a clear increase in TIS annotation quality for the genomes with a low quality score. The PCA-based annotation was also compared with annotation with the current tool of reference, Prodigal. The comparison for the model genome of Escherichia coli K12 showed that both methods supplement each other and that prediction agreement can be used as an indicator of a correct TIS annotation. Importantly, the data suggest that the addition of a PCA-based strategy to a Prodigal prediction can be used to 'flag' TIS annotations for re-evaluation and in addition can be used to evaluate a given annotation in case a Prodigal annotation is lacking.
- Published
- 2015
19. CiVi: circular genome visualization with unique features to analyze sequence elements
- Author
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Overmars, L., Hijum, S.A. van, Siezen, R.J., Francke, C., Overmars, L., Hijum, S.A. van, Siezen, R.J., and Francke, C.
- Abstract
Item does not contain fulltext, We have developed CiVi, a user-friendly web-based tool to create custom circular maps to aid the analysis of microbial genomes and sequence elements. Sequence related data such as gene-name, COG class, PFAM domain, GC%, and subcellular location can be comprehensively viewed. Quantitative gene-related data (e.g. expression ratios or read counts) as well as predicted sequence elements (e.g. regulatory sequences) can be uploaded and visualized. CiVi accommodates the analysis of genomic elements by allowing a visual interpretation in the context of: (i) their genome-wide distribution, (ii) provided experimental data and (iii) the local orientation and location with respect to neighboring genes. CiVi thus enables both experts and non-experts to conveniently integrate public genome data with the results of genome analyses in circular genome maps suitable for publication. CONTACT: L.Overmars@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. AVAILABILITY AND IMPLEMENTATION: CiVi is freely available at http://civi.cmbi.ru.nl.
- Published
- 2015
20. Concomitant induction of a Balbiani ring and a giant secretory protein in Chironomus salivary glands
- Author
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Edström, J. -E., Rydlander, L., and Francke, C.
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- 1980
- Full Text
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21. Soil Improvement for Seismic Retrofit of Tuttle Creek Dam
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David L. Mathews, Michael Beaty, Peter J. Nicholson, Francke C. Walberg, Paul J. Axtell, Glen M. Bellew, Peter M. Byrne, Timothy D. Stark, Gonzalo Castro, William B. Empson, John C. Dillon, and Joseph E. Topi
- Subjects
Jet (fluid) ,Constructability ,Deformation (mechanics) ,Slope stability ,Transverse shear ,Foundation (engineering) ,Shear wall ,Seismic retrofit ,Geotechnical engineering ,Geology - Abstract
This paper discusses the seismic retrofit of Tuttle Creek Dam near Manhattan, Kansas. Seismic analyses, construction, and stabilization techniques are presented. Constructability and dam safety issues, along with results of refined seismic deformation analyses, led to cancellation of the jet grouted upstream slope stabilization and cutoff wall. Downstream slope stabilization was to be accomplished by jet grouting or jet-assisted soil mixing, but ultimately was accomplished using self-hardening cement-bentonite slurry to construct transverse shear walls to reinforce the liquefiable foundation sands. A total of 351 transverse shear walls were constructed along the downstream toe by primarily clam shell equipment. Typical shear walls are 13.7 m long, 1.2 m wide, and extend 18.9 m deep or about 6.1 m into the foundation sands. The walls are spaced at 4.3m on center along the downstream toe for a replacement ratio of about 29%.
- Published
- 2013
22. COMBat : visualizing co-occurrence of annotation terms
- Author
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van Brakel, R.B.J., Fiers, M.W.E.J., Francke, C., Westenberg, M.A., Wetering, van de, H.M.M., Roerdink, J., Kennedy, J., Algorithms, Geometry and Applications, and Visualization
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Matrix (mathematics) ,Identification (information) ,Annotation ,Biological data ,Computer science ,Data mining ,Construct (python library) ,computer.software_genre ,Row and column spaces ,Column (database) ,computer ,Visualization - Abstract
We propose a visual analysis approach that employs a matrix-based visualization technique to explore relations between annotation terms in biological data sets. Our flexible framework provides various ways to form combinations of data elements, which results in a co-occurrence matrix. Each cell in this matrix stores a list of items associated with the combination of the corresponding row and column element. By re-arranging the rows and columns of this matrix, and color-coding the cell contents, patterns become visible. Our prototype tool COMBat allows users to construct a new matrix on the fly by selecting subsets of items of interest, or filtering out uninteresting ones, and it provides various additional interaction techniques. We illustrate our approach with a few case studies concerning the identification of functional links between the presence of particular genes or genomic sequences and particular cellular processes.
- Published
- 2013
23. Zur pathologischen Anatomie und Therapie der habituellen Schultergelenksluxationen
- Author
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Francke, C.
- Published
- 1898
- Full Text
- View/download PDF
24. Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs
- Author
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Wels, M., Overmars, L., Francke, C., Kleerebezem, M., and Siezen, R.J.
- Subjects
Chemical and physical biology [NCMLS 7] ,comparative genomics ,Microbiology ,Microbiologie ,regulon ,escherichia-coli ,identification ,ctsr ,transcriptional regulation ,Host-Microbe Interactomics ,bacteria ,bacillus-subtilis ,negative regulator ,discovery ,VLAG - Abstract
Contains fulltext : 119522.pdf (Publisher’s version ) (Open Access) Gene regulatory networks can be reconstructed by combining transcriptome data from many different experiments to elucidate relations between the activity of certain transcription factors and the genes they control. To obtain insight in the regulatory network of Lactobacillus plantarum, microarray transcriptome data from more than 70 different experimental conditions were combined and the expression profiles of the transcriptional units (TUs) were compared. The TUs that displayed correlated expression were used to identify putative cis-regulatory elements by searching the upstream regions of the TUs for conserved motifs. Predicted motifs were extended and refined by searching for motifs in the upstream regions of additional TUs with correlated expression. In this way, cis-acting elements were identified for 41 regulons consisting of at least four TUs (correlation > 0.7). This set of regulons included the known regulons of CtsR and LexA, but also several novel ones encompassing genes with coherent biological functions. Visualization of the regulons and their connections revealed a highly interconnected regulatory network. This network contains several subnetworks that encompass genes of correlated biological function, such as sugar and energy metabolism, nitrogen metabolism and stress response. 01 mei 2011
- Published
- 2011
25. Modeling Erosion of an Unlined Spillway Chute Cut in Rock
- Author
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Vlad Perlea, David L. Mathews, and Francke C. Walberg
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Hydrology ,geography ,Spillway ,geography.geographical_feature_category ,Ingenieurwissenschaften (620) ,Erosion ,Geotechnical engineering ,Escarpment ,Specific model ,Oil shale ,Geology - Abstract
Discharges up to 1700 m 3 /s that lasted 21 days caused extensive erosion of the spillway chute excavated in rock at Tuttle Creek Lake, Kansas. Nearly 300 000 m 3 of shale and limestone were eroded from the unlined chute resulting in a series of escarpments ranging in height from 1.20 to about 8 m. An empirical mathematical model, similar to a US Department of Agriculture model was developed for geologic conditions at Tuttle Creek Lake. This site specific model was used to evaluate the extent of erosion anticipated for future events and, based on this evaluation, to design the spillway repair. The model provides conservative results since it was conceived in such a manner as to over predict erosion. Initial attempts to generalize its use provided questionable results, but similar site specific procedures may be used in other locations for future events.
- Published
- 2010
26. The identification of response regulator-specific binding sites reveals new roles of two-component systems in Bacillus cereus and closely related low-GC Gram-positives
- Author
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Been, M.W.H.J. de, Bart, M.J., Abee, T., Siezen, R.J., and Francke, C.
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fnr transcription ,staphylococcus-aureus ,transcriptional activator ,comparative genomics ,gene-expression ,Levensmiddelenmicrobiologie ,Metabolism, transport and motion [NCMLS 2] ,abc transporter ,histidine kinases ,Food Microbiology ,multiple sequence alignment ,lactobacillus-plantarum ,signal-transduction systems ,VLAG - Abstract
Contains fulltext : 70735.pdf (Publisher’s version ) (Closed access) In bacteria, environmental challenges are often translated into a transcriptional response via the cognate response regulators (RRs) of specialized two-component systems (TCSs). A phylogenetic footprinting/shadowing approach was designed and used to identify many novel RR-specific operators for species of the Bacillus cereus group and related Gram-positives. Analysis of the operator sequences revealed characteristic traits for each RR subfamily. For instance, operators related to the largest subfamily (OmpR) typically consisted of direct repeats (e.g. TTAAGA-N5-TTAAGA), whereas operators related to the second largest family (NarL) consisted of inverted repeats (e.g. ATGACA-N2-TGTCAT). This difference indicates a fundamentally different organization of the bound RR dimers between the two subfamilies. Moreover, the identification of the specific operator motifs allowed relating several RRs to a minimal regulon and thereby to a characteristic transcriptional response. Mostly, these regulons comprised genes encoding transport systems, suggesting a direct coupling of stimulus perception to the transport of target compounds. New biological roles could be attributed to various TCSs, including roles in cytochrome c biogenesis (HssRS), transport of carbohydrates, peptides and/or amino acids (YkoGH, LytSR), and resistance to toxic ions (LiaSR), antimicrobial peptides (BceRS) and beta-lactam antibiotics (BacRS, YcbLM). As more and more bacterial genome sequences are becoming available, the use of comparative analyses such as the approach applied in this study will further increase our knowledge of bacterial signal transduction mechanisms and provide directions for the assessment of their role in bacterial performance and survival strategies.
- Published
- 2008
27. Subarachnoïdale bloedingen
- Author
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Vermeulen, M., Roos, Y. B. W. E. M., Francke, C. L., Limburg, M., Amsterdam Neuroscience, Neurology, and Amsterdam Cardiovascular Sciences
- Published
- 2006
28. Pathologie, oorzaken en diagnostiek van hersenbloedingen
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Roos, Y. B. W. E. M., Vermeulen, M., Francke, C. L., Limburg, M., Amsterdam Cardiovascular Sciences, Amsterdam Neuroscience, and Neurology
- Published
- 2006
29. Secundaire preventie na een TIA of herseninfarct
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Boiten, J., Peters, R. J. G., Francke, C. L., Limburg, M., and Cardiology
- Published
- 2006
30. MGcV: the microbial genomic context viewer for comparative genome analysis
- Author
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Overmars, L., Kerkhoven, R., Siezen, R.J., Francke, C., Overmars, L., Kerkhoven, R., Siezen, R.J., and Francke, C.
- Abstract
Contains fulltext : 117085.pdf (publisher's version ) (Open Access), BACKGROUND: Conserved gene context is used in many types of comparative genome analyses. It is used to provide leads on gene function, to guide the discovery of regulatory sequences, but also to aid in the reconstruction of metabolic networks. We present the Microbial Genomic context Viewer (MGcV), an interactive, web-based application tailored to strengthen the practice of manual comparative genome context analysis for bacteria. RESULTS: MGcV is a versatile, easy-to-use tool that renders a visualization of the genomic context of any set of selected genes, genes within a phylogenetic tree, genomic segments, or regulatory elements. It is tailored to facilitate laborious tasks such as the interactive annotation of gene function, the discovery of regulatory elements, or the sequence-based reconstruction of gene regulatory networks. We illustrate that MGcV can be used in gene function annotation by visually integrating information on prokaryotic genes, like their annotation as available from NCBI with other annotation data such as Pfam domains, sub-cellular location predictions and gene-sequence characteristics such as GC content. We also illustrate the usefulness of the interactive features that allow the graphical selection of genes to facilitate data gathering (e.g. upstream regions, ID's or annotation), in the analysis and reconstruction of transcription regulation. Moreover, putative regulatory elements and their corresponding scores or data from RNA-seq and microarray experiments can be uploaded, visualized and interpreted in (ranked-) comparative context maps. The ranked maps allow the interpretation of predicted regulatory elements and experimental data in light of each other. CONCLUSION: MGcV advances the manual comparative analysis of genes and regulatory elements by providing fast and flexible integration of gene related data combined with straightforward data retrieval. MGcV is available at http://mgcv.cmbi.ru.nl.
- Published
- 2013
31. Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate specific hidden Markov models
- Author
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Khayatt, B., Overmars, L., Siezen, R.J., Francke, C., Khayatt, B., Overmars, L., Siezen, R.J., and Francke, C.
- Abstract
Contains fulltext : 118146.pdf (publisher's version ) (Open Access), There is a growing interest in the Non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) of microbes, fungi and plants because they can produce bioactive peptides such as antibiotics. The ability to identify the substrate specificity of the enzyme's adenylation (A) and acyl-transferase (AT) domains is essential to rationally deduce or engineer new products. We here report on a Hidden Markov Model (HMM)-based ensemble method to predict the substrate specificity at high quality. We collected a new reference set of experimentally validated sequences. An initial classification based on alignment and Neighbor Joining was performed in line with most of the previously published prediction methods. We then created and tested single substrate specific HMMs and found that their use improved the correct identification significantly for A as well as for AT domains. A major advantage of the use of HMMs is that it abolishes the dependency on multiple sequence alignment and residue selection that is hampering the alignment-based clustering methods. Using our models we obtained a high prediction quality for the substrate specificity of the A domains similar to two recently published tools that make use of HMMs or Support Vector Machines (NRPSsp and NRPS predictor2, respectively). Moreover, replacement of the single substrate specific HMMs by ensembles of models caused a clear increase in prediction quality. We argue that the superiority of the ensemble over the single model is caused by the way substrate specificity evolves for the studied systems. It is likely that this also holds true for other protein domains. The ensemble predictor has been implemented in a simple web-based tool that is available at http://www.cmbi.ru.nl/NRPS-PKS-substrate-predictor/.
- Published
- 2013
32. Flux control of the bacterial phosphoenolpyruvate: glucose phosphotransferase system and the effect of diffusion
- Author
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Francke, C., Westerhoff, H.V., Blom, J.G., Peletier, M.A., Molecular Cell Physiology, Center for Analysis, Scientific Computing & Appl., and Applied Analysis
- Abstract
We analyzed the role of diffusion and cell size on the flux control properties of the glucose-PTS of Escherichia coli, in silicon cells under various metabolic conditions. To our surprise, the influence of the concentration of phosphoryl-donor PEP on the distribution of control was small. We found for cells of bacterial size that PTS-flux control was mainly located in processes taking place in the membrane and that diffusion hardly controlled the flux (< 2.8 %). Enlargement of the cells shifted the control from membrane to cytoplasm and from process rates to diffusion rates, the latter now having a total control of about 38 %. In the presence of glucose, nearly all diffusion flux control resided in the component that links the cytoplasmic processes to those in the membrane.
- Published
- 2002
33. Why the phosphotransferase system of Escherichia coli escapes the diffusion limitation of signal transduction, transport and metabolism that confronts mammalian cells
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Francke, C., Postma, P.W., Westerhoff, H.V., Blom, J.G., Peletier, M.A., Center for Analysis, Scientific Computing & Appl., and Applied Analysis
- Published
- 2002
34. Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli.
- Author
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Groot Kormelink, T., Koenders, E., Hagemeijer, Y., Overmars, L., Siezen, R.J., Vos, W.M. de, Francke, C., Groot Kormelink, T., Koenders, E., Hagemeijer, Y., Overmars, L., Siezen, R.J., Vos, W.M. de, and Francke, C.
- Abstract
Contains fulltext : 110622.pdf (publisher's version ) (Open Access), BACKGROUND: The assimilation of nitrogen in bacteria is achieved through only a few metabolic conversions between alpha-ketoglutarate, glutamate and glutamine. The enzymes that catalyze these conversions are glutamine synthetase, glutaminase, glutamate dehydrogenase and glutamine alpha-ketoglutarate aminotransferase. In low-GC Gram-positive bacteria the transcriptional control over the levels of the related enzymes is mediated by four regulators: GlnR, TnrA, GltC and CodY. We have analyzed the genomes of all species belonging to the taxonomic families Bacillaceae, Listeriaceae, Staphylococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae to determine the diversity in central nitrogen metabolism and reconstructed the regulation by GlnR. RESULTS: Although we observed a substantial difference in the extent of central nitrogen metabolism in the various species, the basic GlnR regulon was remarkably constant and appeared not affected by the presence or absence of the other three main regulators. We found a conserved regulatory association of GlnR with glutamine synthetase (glnRA operon), and the transport of ammonium (amtB-glnK) and glutamine/glutamate (i.e. via glnQHMP, glnPHQ, gltT, alsT). In addition less-conserved associations were found with, for instance, glutamate dehydrogenase in Streptococcaceae, purine catabolism and the reduction of nitrite in Bacillaceae, and aspartate/asparagine deamination in Lactobacillaceae. CONCLUSIONS: Our analyses imply GlnR-mediated regulation in constraining the import of ammonia/amino-containing compounds and the production of intracellular ammonia under conditions of high nitrogen availability. Such a role fits with the intrinsic need for tight control of ammonia levels to limit futile cycling.
- Published
- 2012
35. Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome.
- Author
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Siezen, R.J., Francke, C., Renckens, B.A., Boekhorst, J., Wels, M.W., Kleerebezem, M., Hijum, S.A.F.T. van, Siezen, R.J., Francke, C., Renckens, B.A., Boekhorst, J., Wels, M.W., Kleerebezem, M., and Hijum, S.A.F.T. van
- Abstract
01 januari 2012, Item does not contain fulltext, There is growing interest in the beneficial effects of Lactobacillus plantarum on human health. The genome of L. plantarum WCFS1, first sequenced in 2001, was resequenced using Solexa technology. We identified 116 nucleotide corrections and improved function prediction for nearly 1,200 proteins, with a focus on metabolic functions and cell surface-associated proteins.
- Published
- 2012
36. Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria.
- Author
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Liu, M., Prakash, C., Nauta, A., Siezen, R.J., Francke, C., Liu, M., Prakash, C., Nauta, A., Siezen, R.J., and Francke, C.
- Abstract
01 juli 2012, Item does not contain fulltext, Sulfuric volatile compounds derived from cysteine and methionine provide many dairy products with a characteristic odor and taste. To better understand and control the environmental dependencies of sulfuric volatile compound formation by the dairy starter bacteria, we have used the available genome sequence and experimental information to systematically evaluate the presence of the key enzymes and to reconstruct the general modes of transcription regulation for the corresponding genes. The genomic organization of the key genes is suggestive of a subdivision of the reaction network into five modules, where we observed distinct differences in the modular composition between the families Lactobacillaceae, Enterococcaceae, and Leuconostocaceae, on the one hand, and the family Streptococcaceae, on the other. These differences are mirrored by the way in which transcription regulation of the genes is structured in these families. In the Lactobacillaceae, Enterococcaceae, and Leuconostocaceae, the main shared mode of transcription regulation is methionine (Met) T-box-mediated regulation. In addition, the gene metK, encoding S-adenosylmethionine (SAM) synthetase, is controlled via the S(MK) box (SAM). The S(MK) box is also found upstream of metK in species of the family Streptococcaceae. However, the transcription control of the other modules is mediated via three different LysR-family regulators, MetR/MtaR (methionine), CmbR (O-acetyl[homo]serine), and HomR (O-acetylhomoserine). Redefinition of the associated DNA-binding motifs helped to identify/disentangle the related regulons, which appeared to perfectly match the proposed subdivision of the reaction network.
- Published
- 2012
37. Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli
- Author
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Groot Kormelink, T. (author), Koenders, E. (author), Hagemeijer, Y. (author), Overmars, L. (author), Siezen, R.J. (author), De Vos, W.M. (author), Francke, C. (author), Groot Kormelink, T. (author), Koenders, E. (author), Hagemeijer, Y. (author), Overmars, L. (author), Siezen, R.J. (author), De Vos, W.M. (author), and Francke, C. (author)
- Abstract
Background: The assimilation of nitrogen in bacteria is achieved through only a few metabolic conversions between alpha-ketoglutarate, glutamate and glutamine. The enzymes that catalyze these conversions are glutamine synthetase, glutaminase, glutamate dehydrogenase and glutamine alpha-ketoglutarate aminotransferase. In low-GC Gram-positive bacteria the transcriptional control over the levels of the related enzymes is mediated by four regulators: GlnR, TnrA, GltC and CodY. We have analyzed the genomes of all species belonging to the taxonomic families Bacillaceae, Listeriaceae, Staphylococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae to determine the diversity in central nitrogen metabolism and reconstructed the regulation by GlnR. Results: Although we observed a substantial difference in the extent of central nitrogen metabolism in the various species, the basic GlnR regulon was remarkably constant and appeared not affected by the presence or absence of the other three main regulators. We found a conserved regulatory association of GlnR with glutamine synthetase (glnRA operon), and the transport of ammonium (amtB-glnK) and glutamine/glutamate (i.e. via glnQHMP, glnPHQ, gltT, alsT). In addition less-conserved associations were found with, for instance, glutamate dehydrogenase in Streptococcaceae, purine catabolism and the reduction of nitrite in Bacillaceae, and aspartate/asparagine deamination in Lactobacillaceae. Conclusions: Our analyses imply GlnR-mediated regulation in constraining the import of ammonia/amino-containing compounds and the production of intracellular ammonia under conditions of high nitrogen availability. Such a role fits with the intrinsic need for tight control of ammonia levels to limit futile cycling., Applied Sciences
- Published
- 2012
- Full Text
- View/download PDF
38. Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli
- Author
-
Kormelink, T.G., Koenders, E., Hagemeijer, Y., Overmars, L., Siezen, R.J., de Vos, W.M., Francke, C., Kormelink, T.G., Koenders, E., Hagemeijer, Y., Overmars, L., Siezen, R.J., de Vos, W.M., and Francke, C.
- Abstract
BACKGROUND: The assimilation of nitrogen in bacteria is achieved through only a few metabolic conversions between alpha-ketoglutarate, glutamate and glutamine. The enzymes that catalyze these conversions are glutamine synthetase, glutaminase, glutamate dehydrogenase and glutamine alpha-ketoglutarate aminotransferase. In low-GC Gram-positive bacteria the transcriptional control over the levels of the related enzymes is mediated by four regulators: GlnR, TnrA, GltC and CodY. We have analyzed the genomes of all species belonging to the taxonomic families Bacillaceae, Listeriaceae, Staphylococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae to determine the diversity in central nitrogen metabolism and reconstructed the regulation by GlnR. RESULTS: Although we observed a substantial difference in the extent of central nitrogen metabolism in the various species, the basic GlnR regulon was remarkably constant and appeared not affected by the presence or absence of the other three main regulators. We found a conserved regulatory association of GlnR with glutamine synthetase (glnRA operon), and the transport of ammonium (amtB-glnK) and glutamine/glutamate (i.e. via glnQHMP, glnPHQ, gltT, alsT). In addition less-conserved associations were found with, for instance, glutamate dehydrogenase in Streptococcaceae, purine catabolism and the reduction of nitrite in Bacillaceae, and aspartate/asparagine deamination in Lactobacillaceae. CONCLUSIONS: Our analyses imply GlnR-mediated regulation in constraining the import of ammonia/amino-containing compounds and the production of intracellular ammonia under conditions of high nitrogen availability. Such a role fits with the intrinsic need for tight control of ammonia levels to limit futile cycling
- Published
- 2012
39. Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs.
- Author
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Wels, M.W., Overmars, L., Francke, C., Kleerebezem, M., Siezen, R.J., Wels, M.W., Overmars, L., Francke, C., Kleerebezem, M., and Siezen, R.J.
- Abstract
01 mei 2011, Contains fulltext : 119522.pdf (publisher's version ) (Open Access), Gene regulatory networks can be reconstructed by combining transcriptome data from many different experiments to elucidate relations between the activity of certain transcription factors and the genes they control. To obtain insight in the regulatory network of Lactobacillus plantarum, microarray transcriptome data from more than 70 different experimental conditions were combined and the expression profiles of the transcriptional units (TUs) were compared. The TUs that displayed correlated expression were used to identify putative cis-regulatory elements by searching the upstream regions of the TUs for conserved motifs. Predicted motifs were extended and refined by searching for motifs in the upstream regions of additional TUs with correlated expression. In this way, cis-acting elements were identified for 41 regulons consisting of at least four TUs (correlation > 0.7). This set of regulons included the known regulons of CtsR and LexA, but also several novel ones encompassing genes with coherent biological functions. Visualization of the regulons and their connections revealed a highly interconnected regulatory network. This network contains several subnetworks that encompass genes of correlated biological function, such as sugar and energy metabolism, nitrogen metabolism and stress response.
- Published
- 2011
40. Novel sigmaB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases.
- Author
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Been, M.W.H.J. de, Francke, C., Siezen, R.J., Abee, T., Been, M.W.H.J. de, Francke, C., Siezen, R.J., and Abee, T.
- Abstract
1 januari 2011, Item does not contain fulltext, A common bacterial strategy to cope with stressful conditions is the activation of alternative sigma factors that control specific regulons enabling targeted responses. In the human pathogen Bacillus cereus, activation of the major stress-responsive sigma factor sigma(B) is controlled by a signalling route that involves the multi-sensor hybrid histidine kinase RsbK. RsbK-type kinases are not restricted to the B. cereus group, but occur in a wide variety of other bacterial species, including members of the the low-GC Gram-positive genera Geobacillus and Paenibacillus as well as the high-GC actinobacteria. Genome context and protein sequence analyses of 118 RsbK homologues revealed extreme variability in N-terminal sensory as well as C-terminal regulatory domains and suggested that RsbK-type kinases are subject to complex fine-tuning systems, including sensitization and desensitization via methylation and demethylation within the helical domain preceding the H-box. The RsbK-mediated stress-responsive sigma factor activation mechanism that has evolved in B. cereus and the other species differs markedly from the extensively studied and highly conserved RsbRST-mediated sigma(B) activation route found in Bacillus subtilis and other low-GC Gram-positive bacteria. Implications for future research on sigma factor control mechanisms are presented and current knowledge gaps are briefly discussed.
- Published
- 2011
41. Comparative analyses imply that the enigmatic Sigma factor 54 is a central controller of the bacterial exterior.
- Author
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Francke, C., Groot Kormelink, T., Hagemeijer, Y., Overmars, L., Sluijter, V., Moezelaar, R., Siezen, R.J., Francke, C., Groot Kormelink, T., Hagemeijer, Y., Overmars, L., Sluijter, V., Moezelaar, R., and Siezen, R.J.
- Abstract
Contains fulltext : 95738.pdf (publisher's version ) (Open Access), BACKGROUND: Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. Until now it has remained obscure whether these phenomena and the control by Sigma-54 share an underlying theme. RESULTS: We have uncovered the commonality by performing a range of comparative genome analyses. A) The presence of Sigma-54 and its associated activators was determined for all sequenced prokaryotes. We observed a phylum-dependent distribution that is suggestive of an evolutionary relationship between Sigma-54 and lipopolysaccharide and flagellar biosynthesis. B) All Sigma-54 activators were identified and annotated. The relation with phosphotransfer-mediated signaling (TCS and PTS) and the transport and assimilation of carboxylates and nitrogen containing metabolites was substantiated. C) The function annotations, that were represented within the genomic context of all genes encoding Sigma-54, its activators and its promoters, were analyzed for intra-phylum representation and inter-phylum conservation. Promoters were localized using a straightforward scoring strategy that was formulated to identify similar motifs. We found clear highly-represented and conserved genetic associations with genes that concern the transport and biosynthesis of the metabolic intermediates of exopolysaccharides, flagella, lipids, lipopolysaccharides, lipoproteins and peptidoglycan. CONCLUSION: Our analyses directly implicate Sigma-54 as a central player in the control over the processes that involve the physical interaction of an organism with its environment like in the colonization of a host (virulence) or the formation of biofilm.
- Published
- 2011
42. Clostridial spore germination versus bacilli: genome mining and current insights.
- Author
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Xiao, Y., Francke, C., Abee, T., Wells-Bennik, M.H., Xiao, Y., Francke, C., Abee, T., and Wells-Bennik, M.H.
- Abstract
1 april 2011, Item does not contain fulltext, Bacilli and clostridia share the characteristic of forming metabolically inactive endospores. Spores are highly resistant to adverse environmental conditions including heat, and their ubiquitous presence in nature makes them inevitable contaminants of foods and food ingredients. Spores can germinate under favourable conditions, and the following outgrowth can lead to food spoilage and foodborne illness. Germination of spores has been best studied in Bacillus species, but the process of spore germination is less well understood in anaerobic clostridia. This paper describes a genome mining approach focusing on the genes related to spore germination of clostridia. To this end, 12 representative sequenced Bacillus genomes and 24 Clostridium genomes were analyzed for the distribution of known and putative germination-related genes and their homologues. Overall, the number of ger operons encoding germinant receptors is lower in clostridia than in bacilli, and some Clostridium species are predicted to produce cortex-lytic enzymes that are different from the ones encountered in bacilli. The in silico germination model constructed for clostridia was linked to recently obtained experimental data for selected germination determinants, mainly in Clostridium perfringens. Similarities and differences between germination mechanisms of bacilli and clostridia will be discussed.
- Published
- 2011
43. Isolation of highly heat-resistant Listeria monocytogenes variants by use of a kinetic modeling-based sampling scheme.
- Author
-
Boeijen, I.K. Van, Francke, C., Moezelaar, R., Abee, T., Zwietering, M.H., Boeijen, I.K. Van, Francke, C., Moezelaar, R., Abee, T., and Zwietering, M.H.
- Abstract
1 april 2011, Item does not contain fulltext, Stable high-hydrostatic-pressure (HHP)-resistant Listeria monocytogenes LO28 variants were previously isolated and characterized. These HHP variants were also more resistant to heat. In addition, nonlinear heat inactivation kinetics pointed toward the existence of heat-resistant variants, although these could not be isolated so far. In this study, we used kinetic modeling of inactivation curves of two isolated HHP variants and their wild type, and this revealed that the probability of finding resistant variants should depend on the nature of the inactivation treatment and the time of exposure. At specific heat and HHP conditions, resistant LO28 and EGDe variants were indeed isolated. Resistant LO28 variants were even isolated after a heat inactivation at 72 degrees C in milk, and these variants showed high resistance to standard pasteurization conditions. The increased resistance of part of the isolated LO28 and EGDe variants was due to mutations in their ctsR genes. For the variants whose ctsR genes and upstream regions were not altered, the mechanisms leading to increased resistance remain to be elucidated. This research showed the strength of kinetic modeling in unraveling the causes of nonlinear inactivation and facilitating the isolation of heat-resistant L. monocytogenes variants.
- Published
- 2011
44. Novel SigB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases
- Author
-
de Been, M.W.H.J., Francke, C., Siezen, R.J., Abee, T., de Been, M.W.H.J., Francke, C., Siezen, R.J., and Abee, T.
- Abstract
A common bacterial strategy to cope with stressful conditions is the activation of alternative sigma factors that control specific regulons enabling targeted responses. In the human pathogen Bacillus cereus, activation of the major stress-responsive sigma factor sB is controlled by a signalling route that involves the multi-sensor hybrid histidine kinase RsbK. RsbK-type kinases are not restricted to the B. cereus group, but occur in a wide variety of other bacterial species, including members of the the low-GC Gram-positive genera Geobacillus and Paenibacillus as well as the high-GC actinobacteria. Genome context and protein sequence analyses of 118 RsbK homologues revealed extreme variability in N-terminal sensory as well as C-terminal regulatory domains and suggested that RsbK-type kinases are subject to complex fine-tuning systems, including sensitization and desensitization via methylation and demethylation within the helical domain preceding the H-box. The RsbK-mediated stress-responsive sigma factor activation mechanism that has evolved in B. cereus and the other species differs markedly from the extensively studied and highly conserved RsbRST-mediated sB activation route found in Bacillus subtilis and other low-GC Gram-positive bacteria. Implications for future research on sigma factor control mechanisms are presented and current knowledge gaps are briefly discussed.
- Published
- 2011
45. Isolation of highly heat-resistant Listeria monocytogenes variants by use of a kinetic modeling-based sampling scheme
- Author
-
van Boeijen, K.H., Francke, C., Moezelaar, H.R., Abee, T., Zwietering, M.H., van Boeijen, K.H., Francke, C., Moezelaar, H.R., Abee, T., and Zwietering, M.H.
- Abstract
Stable high-hydrostatic-pressure (HHP)-resistant Listeria monocytogenes LO28 variants were previously isolated and characterized. These HHP variants were also more resistant to heat. In addition, nonlinear heat inactivation kinetics pointed toward the existence of heat-resistant variants, although these could not be isolated so far. In this study, we used kinetic modeling of inactivation curves of two isolated HHP variants and their wild type, and this revealed that the probability of finding resistant variants should depend on the nature of the inactivation treatment and the time of exposure. At specific heat and HHP conditions, resistant LO28 and EGDe variants were indeed isolated. Resistant LO28 variants were even isolated after a heat inactivation at 72°C in milk, and these variants showed high resistance to standard pasteurization conditions. The increased resistance of part of the isolated LO28 and EGDe variants was due to mutations in their ctsR genes. For the variants whose ctsR genes and upstream regions were not altered, the mechanisms leading to increased resistance remain to be elucidated. This research showed the strength of kinetic modeling in unraveling the causes of nonlinear inactivation and facilitating the isolation of heat-resistant L. monocytogenes variants
- Published
- 2011
46. Complete genome sequence of the probiotic Lactobacillus casei strain BL23.
- Author
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Maze, A., Boel, G., Zuniga, M., Bourand, A., Loux, V., Yebra, M.J., Monedero, V., Correia, K., Jacques, N., Beaufils, S., Poncet, S., Joyet, P., Milohanic, E., Casaregola, S., Auffray, Y., Perez-Martinez, G., Gibrat, J.F., Zagorec, M., Francke, C., Hartke, A., Deutscher, J., Maze, A., Boel, G., Zuniga, M., Bourand, A., Loux, V., Yebra, M.J., Monedero, V., Correia, K., Jacques, N., Beaufils, S., Poncet, S., Joyet, P., Milohanic, E., Casaregola, S., Auffray, Y., Perez-Martinez, G., Gibrat, J.F., Zagorec, M., Francke, C., Hartke, A., and Deutscher, J.
- Abstract
01 mei 2010, Contains fulltext : 89754.pdf (publisher's version ) (Open Access), The entire genome of Lactobacillus casei BL23, a strain with probiotic properties, has been sequenced. The genomes of BL23 and the industrially used probiotic strain Shirota YIT 9029 (Yakult) seem to be very similar.
- Published
- 2010
47. Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus.
- Author
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Beekwilder, J.P., Marcozzi, D., Vecchi, S., Vos, R., Janssen, P., Francke, C., Hylckama Vlieg, J.E. van, Hall, R.D., Beekwilder, J.P., Marcozzi, D., Vecchi, S., Vos, R., Janssen, P., Francke, C., Hylckama Vlieg, J.E. van, and Hall, R.D.
- Abstract
Contains fulltext : 80035.pdf (publisher's version ) (Closed access), Lactobacilli are known to use plant materials as a food source. Many such materials are rich in rhamnose-containing polyphenols, and thus it can be anticipated that lactobacilli will contain rhamnosidases. Therefore, genome sequences of food-grade lactobacilli were screened for putative rhamnosidases. In the genome of Lactobacillus plantarum, two putative rhamnosidase genes (ram1(Lp) and ram2(Lp)) were identified, while in Lactobacillus acidophilus, one rhamnosidase gene was found (ramA(La)). Gene products from all three genes were produced after introduction into Escherichia coli and were then tested for their enzymatic properties. Ram1(Lp), Ram2(Lp), and RamA(La) were able to efficiently hydrolyze rutin and other rutinosides, while RamA(La) was, in addition, able to cleave naringin, a neohesperidoside. Subsequently, the potential application of Lactobacillus rhamnosidases in food processing was investigated using a single matrix, tomato pulp. Recombinant Ram1(Lp) and RamA(La) enzymes were shown to remove the rhamnose from rutinosides in this material, but efficient conversion required adjustment of the tomato pulp to pH 6. The potential of Ram1(Lp) for fermentation of plant flavonoids was further investigated by expression in the food-grade bacterium Lactococcus lactis. This system was used for fermentation of tomato pulp, with the aim of improving the bioavailability of flavonoids in processed tomato products. While import of flavonoids into L. lactis appeared to be a limiting factor, rhamnose removal was confirmed, indicating that rhamnosidase-producing bacteria may find commercial application, depending on the technological properties of the strains and enzymes.
- Published
- 2009
48. Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus.
- Author
-
Beekwilder, M.J., Marcozzi, D., Vecchi, S., de Vos, C.H., Janssen, P., Francke, C., van Hylckama Vlieg, J.E.T., Hall, R.D., Beekwilder, M.J., Marcozzi, D., Vecchi, S., de Vos, C.H., Janssen, P., Francke, C., van Hylckama Vlieg, J.E.T., and Hall, R.D.
- Abstract
Lactobacilli are known to use plant materials as a food source. Many such materials are rich in rhamnose-containing polyphenols, and thus it can be anticipated that lactobacilli will contain rhamnosidases. Therefore, genome sequences of food-grade lactobacilli were screened for putative rhamnosidases. In the genome of Lactobacillus plantarum, two putative rhamnosidase genes (ram1Lp and ram2Lp) were identified, while in Lactobacillus acidophilus, one rhamnosidase gene was found (ramALa). Gene products from all three genes were produced after introduction into Escherichia coli and were then tested for their enzymatic properties. Ram1Lp, Ram2Lp, and RamALa were able to efficiently hydrolyze rutin and other rutinosides, while RamALa was, in addition, able to cleave naringin, a neohesperidoside. Subsequently, the potential application of Lactobacillus rhamnosidases in food processing was investigated using a single matrix, tomato pulp. Recombinant Ram1Lp and RamALa enzymes were shown to remove the rhamnose from rutinosides in this material, but efficient conversion required adjustment of the tomato pulp to pH 6. The potential of Ram1Lp for fermentation of plant flavonoids was further investigated by expression in the food-grade bacterium Lactococcus lactis. This system was used for fermentation of tomato pulp, with the aim of improving the bioavailability of flavonoids in processed tomato products. While import of flavonoids into L. lactis appeared to be a limiting factor, rhamnose removal was confirmed, indicating that rhamnosidase-producing bacteria may find commercial application, depending on the technological properties of the strains and enzymes
- Published
- 2009
49. An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters.
- Author
-
Sanders, M.W.W., Kormelink, T.G., Kleerebezem, M., Siezen, R.J., Francke, C., Sanders, M.W.W., Kormelink, T.G., Kleerebezem, M., Siezen, R.J., and Francke, C.
- Abstract
Contains fulltext : 69761.pdf ( ) (Open Access), BACKGROUND: T-box anti-termination is an elegant and sensitive mechanism by which many bacteria maintain constant levels of amino acid-charged tRNAs. The amino acid specificity of the regulatory element is related to a so-called specifier codon and can in principle be used to guide the functional annotation of the genes controlled via the T-box anti-termination mechanism. RESULTS: Hidden Markov Models were defined to search the T-box regulatory element and were applied to all completed prokaryotic genomes. The vast majority of the genes found downstream of the retrieved elements encoded functionalities related to transport and synthesis of amino acids and the charging of tRNA. This is completely in line with findings reported in literature and with the proposed biological role of the regulatory element. For several species, the functional annotation of a large number of genes encoding proteins involved in amino acid transport could be improved significantly on basis of the amino acid specificity of the identified T-boxes. In addition, these annotations could be extrapolated to a larger number of orthologous systems in other species. Analysis of T-box distribution confirmed that the element is restricted predominantly to species of the phylum Firmicutes. Furthermore, it appeared that the distribution was highly species specific and that in the case of amino acid transport some boxes seemed to "pop-up" only recently. CONCLUSION: We have demonstrated that the identification of the molecular specificity of a regulatory element can be of great help in solving notoriously difficult annotation issues, e.g. by defining the substrate specificity of genes encoding amino acid transporters on basis of the amino acid specificity of the regulatory T-box. Furthermore, our analysis of the species-dependency of the occurrence of specific T-boxes indicated that these regulatory elements propagate in a semi-independent way from the genes that they control.
- Published
- 2008
50. LocateP: genome-scale subcellular-location predictor for bacterial proteins
- Author
-
Zhou, M., Boekhorst, J., Francke, C., Siezen, R.J., Zhou, M., Boekhorst, J., Francke, C., and Siezen, R.J.
- Abstract
Contains fulltext : 69477.pdf ( ) (Open Access), BACKGROUND: In the past decades, various protein subcellular-location (SCL) predictors have been developed. Most of these predictors, like TMHMM 2.0, SignalP 3.0, PrediSi and Phobius, aim at the identification of one or a few SCLs, whereas others such as CELLO and Psortb.v.2.0 aim at a broader classification. Although these tools and pipelines can achieve a high precision in the accurate prediction of signal peptides and transmembrane helices, they have a much lower accuracy when other sequence characteristics are concerned. For instance, it proved notoriously difficult to identify the fate of proteins carrying a putative type I signal peptidase (SPIase) cleavage site, as many of those proteins are retained in the cell membrane as N-terminally anchored membrane proteins. Moreover, most of the SCL classifiers are based on the classification of the Swiss-Prot database and consequently inherited the inconsistency of that SCL classification. As accurate and detailed SCL prediction on a genome scale is highly desired by experimental researchers, we decided to construct a new SCL prediction pipeline: LocateP. RESULTS: LocateP combines many of the existing high-precision SCL identifiers with our own newly developed identifiers for specific SCLs. The LocateP pipeline was designed such that it mimics protein targeting and secretion processes. It distinguishes 7 different SCLs within Gram-positive bacteria: intracellular, multi-transmembrane, N-terminally membrane anchored, C-terminally membrane anchored, lipid-anchored, LPxTG-type cell-wall anchored, and secreted/released proteins. Moreover, it distinguishes pathways for Sec- or Tat-dependent secretion and alternative secretion of bacteriocin-like proteins. The pipeline was tested on data sets extracted from literature, including experimental proteomics studies. The tests showed that LocateP performs as well as, or even slightly better than other SCL predictors for some locations and outperforms current tools especially wher
- Published
- 2008
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