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- Jan-Willem Veening
The Veening lab is interested in phenotypic bi-stability in Streptococcus pneumoniae and its importance in virulence of this human pathogen.
SEEK ID: https://fairdomhub.org/people/342
Location:
Netherlands
Expertise: Medical microbiology, Streptococcus pneumoniae, Molecular microbiology, Bacterial Cell Biology, Bacillus subtilis, Single Cell analysis, Molecular Biology, Genetics, Microbiology
Tools: Molecular biology techniques (RNA/DNA/Protein), Fluorecence based reporter gene analyses/single cell analyses, Transcriptomics, Genetic modification, Genetics, Biochemistry, Microbiology
ORCID: Not specified
Related items
- Projects (1)
- Institutions (1)
- Investigations (3)
- Studies (4+1)
- Assays (4)
- Strains (2)
- Data files (24)
- Publications (22)
Bistable switches are the key elements of the regulatory networks governing cell development, differentiation and life-strategy decisions. Transcriptional noise is a main determinant that causes switching between different states in bistable systems. By using the human pathogen Streptococcus pneumoniae as a model bacterium, we will investigate how transcriptional fidelity and processivity influence (noisy) gene expression and participate in bistability. To study this question, we will use both
...
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=163
Organisms: Streptococcus pneumoniae
Snapshots: No snapshots
A key insight, emerging from discussions and data between the projects PIs, was the importance of switching rates in bistable systems.
While the existence of multiple steady states in bistable systems can be described by universal models (that do not differ between
different systems), switching rates from one stable state to another depend on the molecular details of the system under consideration.
Snapshots: No snapshots
Studies: No Studies
Assays: No Assays
Handling and manipulation of S. pneumoniae using molecular, cell biological and genetic tools.
Snapshots: No snapshots
Studies: Automated time-lapse microscopy, Chromosome segregation in S. pneumoniae, Investigation of bacterial transcription fidelity and processivity, The role of transcription factor GreA in transcription fidelity and proc...
Assays: Kinetics of misincorporation and proofreading by bacterial RNA polymerase, Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae usin..., ParB-GFP ChIP on chip, RNA-Seq
Person responsible: Jan-Willem Veening
Snapshots: No snapshots
Investigation: Chromosome segregation and cell division in Str...
For cells to accurately read out the genomic content, high fidelity during transcription is required. This is mainly established by the accuracy of the active centre of RNA polymerase (RNAP). Based on in vitro experiments with Escherichia coli RNAP it was also suggested that proofreading of transcription via RNA hydrolysis by RNAP may contribute to overall fidelity and processivity. RNAP’s intrinsic cleavage activity is stimulated by the highly conserved Gre factors suggesting that Gre factors
...
Person responsible: Jan-Willem Veening
Snapshots: No snapshots
Investigation: Wetlab approach to transcription fidelity
Assays: RNA-Seq
During the last few years scientists became increasingly aware that average data obtained from microbial population based experiments are not representative of the behavior, status or phenotype of single cells. Due to this new insight the number of single cell studies rises continuously (for recent reviews see (1,2,3)). However, many of the single cell techniques applied do not allow monitoring the development and behavior of one specific single cell in time (e.g. flow cytometry or standard
...
Person responsible: Jan-Willem Veening
Snapshots: No snapshots
Here we develop a set of new tools for S. pneumoniae and as a case study we show that S. pneumoniaea SMC is recruited to oriC by ParB and promotes chromosome segregation.
Person responsible: Jan-Willem Veening
Snapshots: No snapshots
Investigation: Wetlab approach to transcription fidelity
Assays: ParB-GFP ChIP on chip
Contributor: Jan-Willem Veening
Assay type: Experimental Assay Type
Technology type: Next generation sequencing
Snapshots: No snapshots
Investigation: Chromosome segregation and cell division in Str...
Study: Genome wide marker frequency analysis on new st...
Organisms: No organisms
SOPs: No SOPs
Data files: DCI15, MK453, MK454, Whole genome marker frequency analysis on strai..., Whole genome marker frequency analysis on strai..., Whole genome marker frequency analysis on strai...
Cells were grown to mid-exponential phase (OD600nm ~0.2) in GM17 medium at 37°C (with 0.15 mM ZnSO4 where relevant) and 84 ml of culture was mixed by inverting with 8.4 ml of fixing solution (50 mM Tris pH 8.0, 100 mM NaCl, 0.5 mM EGTA, 1 mM EDTA, 30% (v/v) formaldehyde) and incubated at room temperature for 30 min. Cells were disrupted and crosslinked DNA was sheared by sonication. Antibodies coupled to magnetic beads were used to pull down cross-linked complexes. DNA was purified, amplified,
...
Contributor: Jan-Willem Veening
Assay type: Transcriptomics
Technology type: ChIP-on-chip
Snapshots: No snapshots
Investigation: Wetlab approach to transcription fidelity
Study: Chromosome segregation in S. pneumoniae
Organisms: Streptococcus pneumoniae : D39 (wild-type / wild-type) (batch)
SOPs: No SOPs
Data files: ChIP-chip ParB-GFP
S.pneumoniae D39 cells (wild type and delta greA) were grown in C+Y medium and cells were harvested for total RNA isolation at mid-exponential growth (OD600nm 0.3 for wt, 0.25 for delta greA). Total RNA was isolated as described before (Kloosterman et al 2006).
The total RNA samples were examined by capillary electrophoresis.
dephosphorylated with antarctic phosphatase followed by treatment with polynucleotide kinase (PNK).
Afterwards, samples were poly(A)-tailed using poly(A) polymerase. Then a
...
Contributor: Jan-Willem Veening
Assay type: Transcriptomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Wetlab approach to transcription fidelity
Study: The role of transcription factor GreA in transc...
Organisms: No organisms
SOPs: No SOPs
Data files: RNA-seq delta greA, RNA-seq wild type
1. Preparation of B. subtilis cultures
Inoculate cells from -80°C stocks in 10 ml time-lapse microscopy (TLM) medium (62 mM K2HPO4 , 44mM KH2PO4, 15 mM (NH4)2SO4, 6.5 mM sodium citrate, 0.8 mM MgSO4, 0.02 % casamino acids, 27.8 mM glucose, 0.1 mM L-tryptophan, the pH was set to 7 using a KOH solution) supplemented with antibiotics, if necessary.
Grow the cells overnight in a shake flask (30°C, 225 rpm).
The following morning, dilute the cells 1:10 in pre-warmed chemically defined medium (CDM) (62
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Contributor: Jan-Willem Veening
Assay type: Experimental Assay Type
Technology type: Imaging
Snapshots: No snapshots
Investigation: Wetlab approach to transcription fidelity
Study: Automated time-lapse microscopy
Organisms: Streptococcus pneumoniae
SOPs: No SOPs
Data files: No Data files
Contributor: Jan-Willem Veening
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Bacillus subtilis
Genotypes: wild-type
Phenotypes: wild-type
Comment: Not specified
Contributor: Jan-Willem Veening
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Streptococcus pneumoniae
Genotypes: wild-type
Phenotypes: wild-type
Comment: Not specified
Creator: Jan-Willem Veening
Contributor: Jan-Willem Veening
Investigations: Chromosome segregation and cell division in Str...
Creator: Jan-Willem Veening
Contributor: Jan-Willem Veening
Investigations: Chromosome segregation and cell division in Str...
Creator: Jan-Willem Veening
Contributor: Jan-Willem Veening
Investigations: Chromosome segregation and cell division in Str...
Strain MK423 was grown under the same conditions as used when growing cells for microscopy analysis; cells of OD600 = 0.4 were diluted 100-fold in C+Y medium with 0.1 mM ZnCl2 and incubated for 2.5 hours until OD600 = 0.15. Cells were then harvested by centrifugation for 5 min at 6500 x g at 4°C. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega) as described previously (Slager et al. 2014 Cell). Fragmentation was performed using Covaris instrument, and libraries
...
Creator: Jan-Willem Veening
Contributor: Jan-Willem Veening
Investigations: Chromosome segregation and cell division in Str...
Strain MK422 was grown under the same conditions as used when growing cells for microscopy analysis; cells of OD600 = 0.4 were diluted 100-fold in C+Y medium with 0.1 mM ZnCl2 and incubated for 2.5 hours until OD600 = 0.15. Cells were then harvested by centrifugation for 5 min at 6500 x g at 4°C. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega) as described previously (Slager et al. 2014 Cell). Fragmentation was performed using Covaris instrument, and libraries
...
Creator: Jan-Willem Veening
Contributor: Jan-Willem Veening
Investigations: Chromosome segregation and cell division in Str...
Strain MK350 was grown under the same conditions as used when growing cells for microscopy analysis; cells of OD600 = 0.4 were diluted 100-fold in C+Y medium with 0.1 mM ZnCl2 and incubated for 2.5 hours until OD600 = 0.15. Cells were then harvested by centrifugation for 5 min at 6500 x g at 4°C. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega) as described previously (Slager et al. 2014 Cell). Fragmentation was performed using Covaris instrument, and libraries
...
Creator: Jan-Willem Veening
Contributor: Jan-Willem Veening
Investigations: Chromosome segregation and cell division in Str...
WT 110901_SN865_B_L006_R1_GQC-28-
ATCACG.fastq.gz
100 19.624.852 1,29
llumina fastq format
4 lines for each sequence:
1- Unique identifier, with the following format:
@<machine_id>:<lane>:<tile>:<x_coord>:<y_coord>#<index>/<read_#>
2- Sequence (A, T, C ,G or N (undetermined) only)
3- Orientation (always forward without mapping)
4- Quality value for each base, corresponding to a Phred-like score encoded in ASCII format, with an
offset of of 33 (e.g. “J” gives a value of 41)
...
Creator: Jan-Willem Veening
Contributor: Jan-Willem Veening
Investigations: Wetlab approach to transcription fidelity
Studies: The role of transcription factor GreA in transc...
Assays: RNA-Seq
See wild type sample.
Creator: Jan-Willem Veening
Contributor: Jan-Willem Veening
Investigations: Wetlab approach to transcription fidelity
Studies: The role of transcription factor GreA in transc...
Assays: RNA-Seq
S. pneumoniae RNA-Seq
Barcodes:
HPUra 1: CAGATC
HPUra 2: ACTTGA
Kanamycin: AGTCAA
Creator: Jan-Willem Veening
Contributor: Jan-Willem Veening
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
S. pneumoniae RNA-Seq
Barcodes:
Control 1: CAGATC
Control 2: ACTTGA
Creator: Jan-Willem Veening
Contributor: Jan-Willem Veening
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract (Expand)
Authors: None
Date Published: 24th Sep 2014
Journal: Nucleic Acids Res
PubMed ID: 25245949
Citation:
Abstract (Expand)
Authors: Yulia Yuzenkova, Pamela Gamba, Sulman Shafeeq, Oscar Kuipers, Nikolay Zenkin, Jan-Willem Veening, Herber M.,Attaiech L.,Klumpp S.
Date Published: 6th Sep 2014
Journal: Nucleic Acids Res
PubMed ID: 25190458
Citation:
Abstract (Expand)
Authors: Oscar Kuipers, Jan-Willem Veening, Overkamp W.,Beilharz K.,Detert Oude Weme R.,Solopova A.,Karsens H.,Kovacs A.,Kok J.
Date Published: 16th Aug 2013
Journal: Appl Environ Microbiol
PubMed ID: 23956387
Citation:
Abstract (Expand)
Authors: Johannes Berg, Kolar Michal,Meier Jörn,Mustonen Ville,Lässig Michael
Date Published: 21st Nov 2012
Journal: BMC Syst Biol
PubMed ID: 23171476
Citation:
Abstract (Expand)
Authors: None
Date Published: 4th Oct 2012
Journal: Environ. Microbiol.
PubMed ID: 23033921
Citation:
Abstract (Expand)
Authors: Yulia Yuzenkova, Nikolay Zenkin, Roghanian Mohammad
Date Published: 10th Jul 2012
Journal: Transcription
PubMed ID: 22771945
Citation:
Abstract (Expand)
Authors: None
Date Published: 28th Apr 2012
Journal: J. Mol. Evol.
PubMed ID: 22544085
Citation:
Abstract (Expand)
Authors: Jan-Willem Veening, Beilharz Katrin,Nováková Linda,Fadda Daniela,Branny Pavel,Massidda Orietta
Date Published: 21st Mar 2012
Journal: Proceedings of the National Academy of Sciences of the United States of America
PubMed ID: 22431591
Citation:
Abstract (Expand)
Authors: Johannes Berg, Perfeito Lilia,Ghozzi Stéphane,Schnetz Karin,Lässig Michael
Date Published: 21st Jul 2011
Journal: PLoS Genet.
PubMed ID: 21814515
Citation:
Abstract (Expand)
Authors: Nikolay Zenkin, Castro-Roa Daniel
Date Published: 3rd Jan 2012
Journal: Nucleic acids research
PubMed ID: 22210860
Citation: