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- Praveen Kumar Sappa
I am PhD student at Prof.Uwe Voelker lab in Department of Functional Genomics. My area of research is microbial functional genomics in particular analysing the whole transcriptome(by microarray and other molecular biolology methods) of B.subtilis under various stress conditions.
I use QconCAT strategy for absolute quantification of carbon metabolic enzymes via MRM(multiple reaction monitoring) by LC-MS/MS.
I also perofrm experiments for understanding of dynamics of SigmaB network for modelling.
SEEK ID: https://fairdomhub.org/people/284
Location:
Germany
Expertise: bacterial physiology, Bacillus subtilis, Proteomics, Molecular Biology, Microbiology
Tools: analysis of functional genomics data, Cell culture, Molecular biology techniques (RNA/DNA/Protein), Mass spectrometry (LC-MS/MS), Enzyme assay, Microarray analysis, Proteomics, Transcriptomics
ORCID: Not specified
Related items
- Projects (1)
- Institutions (1)
- Investigations (3)
- Studies (6+1)
- Assays (8)
- Strains (4)
- Data files (15+4)
- SOPs (5+1)
- Publications (5)
- Presentations (1+1)
BaCell-SysMO 2
Modelling carbon core metabolism in Bacillus subtilis – Exploring the contribution of protein complexes in core carbon and nitrogen metabolism.
Bacillus subtilis is a prime model organism for systems biology approaches because it is one of the most advanced models for functional genomics. Furthermore, comprehensive information on cell and molecular biology, physiology and genetics is available and the European Bacillus community (BACELL) has a well-established reputation for applying
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Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=53
Organisms: Bacillus subtilis
The aim of the study is to assess the global function of RNase Y in RNA processing and degradation in Bacillus subtilis. To this end we constructed a strain allowing controlled depletion of RNase Y and used microarrays to analyze the transcriptome in response to the expression level of RNase Y.
Snapshots: No snapshots
The objective of this project is an integrated understanding the metabolic, proteomic and genetic network that controls the transition from growth to glucose starvation. This transition is a fundamental ecophysiological response that serves as a scientific model for environmental signal integration and is pivotal for industrial fermentations of Bacillus that occur predominantly under nutrient starvation.
Keywords:
Glucose starvation, Transcriptomics, Proteomics, Metabolomics,Bacillus subtilis,
Snapshots: No snapshots
Studies: B. subtilis Transcription Factor Competition, Batchfermentation exp-starv01_090204, Biphase Batch Fermentation(2009/02/04), Controlled sigmaB induction in shake flask, Transition to starvation in shake flask
Assays: 2D-gelbased analysis of intracellular proteins, Absolute quantification of proteins by the AQUA-technology, B. subtilis Transcription Factor Competition - theoretical interpretation, B. subtilis Transcription Factor Competition - theoretical interpretation, Fermentation-BM5_SysMo, Gene expression(Transcriptome), IPTG induction of sigmaB in BSA115, IPTG induction of sigmaB in BSA115, Relative quantification of proteins by metabolic labeling, Stressosome activation dynamics, metabolome-LCMS
Bacillus subtilis was subjected to various stress conditions like high temperature(57°C), low temperature(16°C), high osmalarity(1.2M NaCl). The above mentioned stress conditions are again split into two different types as 'continuous stress condition' and 'sudden shock'. All the conditions were then done in biological triplicates.
Transcriptome for these samples was then analysed with Nimblegen Tiling array.
Snapshots: No snapshots
Studies: Transcriptome analysis of glucose starvation in B. subtilis, Transcriptome of continuously stressed B. subtilis, Transcriptome of shocked B. subtilis cells
Assays: Tiling Array analysis of glucose strarved B. subtilis cells, Tiling Array analysis of shocked B. subtilis cells, Tiling array analysis of continuous growth stress conditions in SMM
The aim of the study is to assess the global function of RNase Y in RNA processing and degradation in Bacillus subtilis. To this end we constructed a strain allowing controlled depletion of RNase Y and used microarrays to analyze the transcriptome in response to the expression level of RNase Y.
Person responsible: Ulrike Mäder
Snapshots: No snapshots
The main aim of this experiment is to actively grow B.subtilis in presense of glucose until high optical density in an aerobic fermentor and then, at a definite point of the growth, the glucose supply is shut down which leads to complete glucose exhaustion in the media. Simultaneusly samples for transcriptomics, intra and extracellular metabolomics, intra and extracellular proteomics are harvested through out the experiment.
Person responsible: Praveen Kumar Sappa
Snapshots: No snapshots
Investigation: The transition from growing to non-growing Baci...
Assays: No Assays
The main aim of this experiment is to actively grow B.subtilis in presense of glucose until high optical density in an aerobic fermentor and then, at a definite point of the growth, the glucose supply is shut down which leads to complete glucose exhaustion in the media. Simultaneusly samples for transcriptomics, intra and extracellular metabolomics, intra and extracellular proteomics are harvested through out the experiment.
Person responsible: Praveen Kumar Sappa
Snapshots: No snapshots
Investigation: The transition from growing to non-growing Baci...
Assays: 2D-gelbased analysis of intracellular proteins, Absolute quantification of proteins by the AQUA-technology, Fermentation-BM5_SysMo, Gene expression(Transcriptome), Relative quantification of proteins by metabolic labeling, metabolome-LCMS
Growth of B.subtilis in shakeflask at 57°C; 16°C, 37°C(Control) and 1,2M NaCl in SMM.
Person responsible: Praveen Kumar Sappa
Snapshots: No snapshots
Transcriptome analysis for the samples harvested from Chemostat cultivated samples.
Contributor: Praveen Kumar Sappa
Assay type: Transcriptomics
Technology type: Microarray
Snapshots: No snapshots
Investigation: Multiomics study of Bacillus subtilis under osm...
Study: B. subtilis_SysMo2_Chemostat_growthrate-salt
Organisms: No organisms
SOPs: RNA isolation and quality check by Agilent bioa..., SOP for cDNA labelling and Microarray hybridizaton
Data files: 1 hidden item
Absolute quantification of proteins using heavy labeled QconCAT as an internal standard and quantifying the native proteins in the complex sample via scheduled Multiple Reaction Monitoring(MRM) .
Contributor: Praveen Kumar Sappa
Assay type: Proteomics
Technology type: Liquid Chromatography Mass Spectrometry
Snapshots: No snapshots
Investigation: Multiomics study of Bacillus subtilis under osm...
Study: B. subtilis_SysMo2_Chemostat_growthrate-salt
Organisms: Bacillus subtilis : 168 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: 1 hidden item
Contributor: Praveen Kumar Sappa
Assay type: Transcriptomics
Technology type: Custom Array
Snapshots: No snapshots
Investigation: Identification of targets of the essential RNas...
Study: Identification of targets of the essential RNas...
Organisms: Bacillus subtilis : 168 Trp+ (wild-type / tryptophan prototroph)
SOPs: RNA isolation and quality check by Agilent bioa..., SOP for cDNA labelling and Microarray hybridizaton
Data files: Trancriptome data - RNA processing in Bacillus ...
Contributor: Praveen Kumar Sappa
Assay type: Glucose Pulse
Technology type: Technology Type
Snapshots: No snapshots
Investigation: The transition from growing to non-growing Baci...
Study: Batchfermentation exp-starv01_090204
Organisms: Bacillus subtilis (batch)
SOPs: 1 hidden item
Data files: Batchfermentation_Exp-Starv01_Fermentationdetai..., batchfermentation exp-starv01 transcriptome_Mic..., batchfermentation exp-starv01 transcriptome_Mic...
B. subtilis was grown in SMM media with glucose as carbon source and the samples for RNA were harvested OD578nm- 1.0). The stress conditions that were applied over here are growthat 57°C, 16°C, 1.2M Nacl and 37°C(control).
All the samples were analysed for transcriptome as biological triplicates.
Contributor: Praveen Kumar Sappa
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Redefining the Complete Transcriptome of Bacill...
Study: Transcriptome of continuously stressed B. subtilis
Organisms: Bacillus subtilis : 168 Trp+ (wild-type / tryptophan prototroph)
SOPs: No SOPs
Data files: Continuous growth_16°C_SMM_Growth curve, Continuous growth_57°C_SMM_Growth curve, Contious growth_1.2M NaCl_SMM_Transcritome_Nimb..., Contious growth_16°C_SMM_Transcritome_Nimblegen, Contious growth_57°C_SMM_Transcritome_Nimblegen, Contiuous growth_37°C_SMM(control)_Growth curve., The condition-dependent transcriptome of Bacill...
Contributor: Praveen Kumar Sappa
Assay type: Transcriptomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Redefining the Complete Transcriptome of Bacill...
Study: Transcriptome of shocked B. subtilis cells
Organisms: Bacillus subtilis : 168 Trp+ (wild-type / tryptophan prototroph) (batch)
SOPs: No SOPs
Data files: The condition-dependent transcriptome of Bacill...
B. subtilis was grown in M9 media with glucose as carbon source and the samples were harvested during exponential phase (OD600nm- 0.4), early stationary phase(OD600nm- 1.3), late stationary phase(OD600nm- 1.0).
All the samples were analysed for transcriptome as biological triplicates.
Contributor: Praveen Kumar Sappa
Assay type: Transcriptomics
Technology type: Microarray
Snapshots: No snapshots
Investigation: Redefining the Complete Transcriptome of Bacill...
Study: Transcriptome analysis of glucose starvation in...
Organisms: Bacillus subtilis : 168 Trp+ (wild-type / tryptophan prototroph) (batch)
SOPs: SOP for cultivation of B.Subtilis, Total RNA isolation from B.Subtilis
Data files: M9_shake_flask_exp_trans_stat_transcriptome_nim..., The condition-dependent transcriptome of Bacill...
Contributor: Praveen Kumar Sappa
Assay type: Transcriptomics
Technology type: Custom Array
Snapshots: No snapshots
Investigation: The transition from growing to non-growing Baci...
Study: Batchfermentation exp-starv01_090204
Organisms: Bacillus subtilis
SOPs: RNA isolation and quality check by Agilent bioa..., SOP for cDNA labelling and Microarray hybridizaton
Data files: batchfermentation exp-starv01 transcriptome_Mic..., batchfermentation exp-starv01 transcriptome_Mic...
Contributor: Praveen Kumar Sappa
Provider Name: Not specified
Provider's strain ID: 168 Trp+
Organism: Bacillus subtilis
Genotypes: wild-type
Phenotypes: tryptophan prototroph
Comment: Trp+ derivative of B. subtilis 168 wild type.
Contributor: Praveen Kumar Sappa
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Bacillus subtilis
Genotypes: + trpC;rsbU19aa rsbU; PB 28::PSPAC SigB promoter;rsbX::spc rsbX;ctc::lacZ ctc
Phenotypes: wild-type
Comment: Not specified
Contributor: Praveen Kumar Sappa
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Bacillus subtilis
Genotypes: + trp;mutation by insertion spoIVCB (sigK)
Phenotypes: tryptophan autotroph; non-sporulating
Comment: Not specified
Contributor: Praveen Kumar Sappa
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Bacillus subtilis
Genotypes: wild-type
Phenotypes: wild-type
Comment: Not specified
Creator: Praveen Kumar Sappa
Contributor: The JERM Harvester
Investigations: The transition from growing to non-growing Baci...
Studies: Batchfermentation exp-starv01_090204
Assays: Fermentation-BM5_SysMo, Gene expression(Transcriptome)
Array hybridisation was done at Roche Nimblegen Inc. It cannot be displayed over here.
Creator: Praveen Kumar Sappa
Contributor: Praveen Kumar Sappa
Investigations: The transition from growing to non-growing Baci...
Studies: Batchfermentation exp-starv01_090204
Assays: Fermentation-BM5_SysMo, Gene expression(Transcriptome)
Creator: Praveen Kumar Sappa
Contributor: Praveen Kumar Sappa
Investigations: The transition from growing to non-growing Baci...
Studies: Batchfermentation exp-starv01_090204
Assays: Fermentation-BM5_SysMo
Recent studies revealed the unsuspected complexity of the bacterial transcriptome but its systematic analysis across many diverse conditions remains a challenge. Here we report the condition-dependent transcriptome of the prototype strain B. subtilis 168 across 104 conditions reflecting the bacterium's life-styles. This data set composed of 269 tiling array hybridizations allowed to observe ~85% of the annotated CDSs expressed in the higher 30% in at least one hybridization and thus provide an
...
Creators: Leif Steil, Ulrike Mäder, Colin Harwood, Rick Lewis, Ruben Mars, Priyanka Nannapaneni, Praveen Kumar Sappa, Joerg Stuelke, Jan Maarten Van Dijl, Michael Hecker, Uwe Voelker
Contributor: Leif Steil
Investigations: Redefining the Complete Transcriptome of Bacill...
Studies: Transcriptome analysis of glucose starvation in..., Transcriptome of continuously stressed B. subtilis, Transcriptome of shocked B. subtilis cells
Assays: Tiling Array analysis of glucose strarved B. su..., Tiling Array analysis of shocked B. subtilis cells, Tiling array analysis of continuous growth stre...
Creators: Ulrike Mäder, Joerg Stuelke, Praveen Kumar Sappa, Martin Lehnik-Habrink, Marc Schaffer
Contributor: Praveen Kumar Sappa
B. subtilis was grown in M9 media with glucose as carbon source and the samples for RNA were harvested at OD600nm- 0.4 , 1.3 and 1.0 ). Culture was done at 37°C and samples at OD600nm- 0.4(Exponential), OD600nm- 1.3 (Early stationary), OD600nm-1.0(Late Stationary). All the samples were analysed for transcriptome as biological triplicates.
Creator: Praveen Kumar Sappa
Contributor: Praveen Kumar Sappa
Creator: Praveen Kumar Sappa
Contributor: Praveen Kumar Sappa
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Isolation of total RNA from Bacillus Subtilis using phenol-chloroform extraction method by maintaining cryogenec conditions initailly to prevent RNA degradation. Quality of the obtained RNA is then tested with Agilent Bioanalyser before proceeding for gene expression analysis.
Creator: Praveen Kumar Sappa
Contributor: Praveen Kumar Sappa
SOP for ß-Galactosidase assay.
Creator: Praveen Kumar Sappa
Contributor: Praveen Kumar Sappa
Investigations: The transition from growing to non-growing Baci...
SOP for shake flask cultivation of B.Subtilis in Bacell-Sysmo
Creator: Praveen Kumar Sappa
Contributor: Praveen Kumar Sappa
Investigations: Redefining the Complete Transcriptome of Bacill..., The transition from growing to non-growing Baci...
Studies: Controlled sigmaB induction in shake flask, Transcriptome analysis of glucose starvation in...
Assays: IPTG induction of sigmaB in BSA115, Tiling Array analysis of glucose strarved B. su...
The reverse transcriptase synthesizes DNA, which complements the mRNA template
(complementary DNA, cDNA). Cy3/Cy5-dCTP are incorporated into cDNA during Reverse transcription. The obtained Cy3/Cy5 cDNA are then competitively hybridised onto Agilent microarray slide and subsequently scanned.
Creator: Praveen Kumar Sappa
Contributor: Praveen Kumar Sappa
Investigations: Identification of targets of the essential RNas..., Multiomics study of Bacillus subtilis under osm..., The transition from growing to non-growing Baci...
Studies: B. subtilis_SysMo2_Chemostat_growthrate-salt, Batchfermentation exp-starv01_090204, Identification of targets of the essential RNas...
Assays: Gene expression(Transcriptome), Transcriptome data for chemostat cultivated sam..., Transcritome data_Identification of targets of ...
Cells were harvested from culture keeping the cells cold to quench the physiological condition of RNA and the cells were mechanically disrupted. RNA was isolated from the cells by conventional acid-phenol method and the quality was checked by Agilent bioanalyser.
Creator: Praveen Kumar Sappa
Contributor: Praveen Kumar Sappa
Investigations: Identification of targets of the essential RNas..., Multiomics study of Bacillus subtilis under osm..., The transition from growing to non-growing Baci...
Studies: B. subtilis_SysMo2_Chemostat_growthrate-salt, Batchfermentation exp-starv01_090204, Identification of targets of the essential RNas...
Assays: Gene expression(Transcriptome), Transcriptome data for chemostat cultivated sam..., Transcritome data_Identification of targets of ...
Abstract (Expand)
Authors: Sandra Maass, Praveen Kumar Sappa, Uwe Voelker, Michael Hecker, Sievers Susanne,Zühlke Daniela,Kuzinski Judith,Muntel Jan,Hessling Bernd,Bernhardt Jörg,Sietmann Rabea,Becher Dörte
Date Published: 11th Mar 2011
Journal: Anal. Chem.
PubMed ID: 21395229
Citation:
Abstract (Expand)
Authors: Ulrike Mäder, Colin Harwood, Michael Hecker, Jan Maarten Van Dijl, van der Ploeg René,Homuth Georg,Schaffer Marc,Denham Emma L,Monteferrante Carmine G,Miethke Marcus,Marahiel Mohamed A,Winter Theresa,Antelmann Haike
Date Published: 30th Mar 2011
Journal: PLoS ONE
PubMed ID: 21479178
Citation:
Abstract (Expand)
Authors: Maike Bartholomae, Uwe Voelker, Gerald Seidel, Wolfgang Hillen, Wünsche Andrea,Hammer Elke,Burkovski Andreas
Date Published: 20th Apr 2012
Journal: The FEBS journal
PubMed ID: 22512862
Citation:
Abstract (Expand)
Authors: Ulf Liebal, Praveen Kumar Sappa, Thomas Millat, Leif Steil, Uwe Voelker, Olaf Wolkenhauer, Homuth Georg
Date Published: 2012
Journal: Mol. BioSyst.
DOI: 10.1039/C2MB25031D
Citation:
Abstract (Expand)
Authors: Ulrike Mäder, Colin Harwood, Rick Lewis, Ruben Mars, Priyanka Nannapaneni, Praveen Kumar Sappa, Leif Steil, Joerg Stuelke, Jan Maarten Van Dijl, Michael Hecker, Uwe Voelker, Nicolas Pierre,Dervyn Etienne,Rochat Tatiana,Leduc Aurélie,Pigeonneau Nathalie,Bidnenko Elena,Marchadier Elodie,Hoebeke Mark,Aymerich Stéphane,Becher Dörte,Bisicchia Paola,Botella Eric,Delumeau Olivier,Doherty Geoff,Denham Emma L,Fogg Mark J,Fromion Vincent,Goelzer Anne,Hansen Annette,Härtig Elisabeth,Homuth Georg,Jarmer Hanne,Jules Matthieu,Klipp Edda,Le Chat Ludovic,Lecointe François,Liebermeister Wolfram,March Anika,Noone David,Pohl Susanne,Rinn Bernd,Rügheimer Frank,Samson Franck,Schaffer Marc,Schwikowski Benno,Wiegert Thomas,Devine Kevin M,Wilkinson Anthony J,Bessières Philippe,Noirot Philippe
Date Published: 3rd Mar 2012
Journal: Science
PubMed ID: 22383849
Citation: