Studies
What is a Study?Filters
Provided with genomic data over different pH values we have the opportunity to study the similarity of gene expression profiles and cluster groups of very simlar gene expression profiles. Via PCA we can furthermore study dynamic similarity and compe genes that are possible co-regulators or anti-regulators in the clostridial metabolism.
Submitter: Sebastian Curth
Investigation: The effect of pH upon the metabolic shift in Cl...
Assays: Identification of dynamically similar transcript profiles
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.
Submitter: Praveen kumar Sappa
Investigation: Identification of targets of the essential RNas...
Assays: Transcritome data_Identification of targets of the essential RNase Y of ...
Thiel BA, Worodria W, Nalukwago S, Nsereko M, Sanyu I, Rejani L, Zawedde J, Canaday DH, Stein CM, Chervenak KA, Malone LL, Kiyemba R, Silver RF, Johnson JL, Mayanja-Kizza H, Boom WH. Immune cells in bronchoalveolar lavage fluid of Ugandan adults who resist versus those who develop latent Mycobacterium tuberculosis infection. PLoS One. 2021 Apr 9;16(4):e0249477. doi: 10.1371/journal.pone.0249477. PMID: 33836031; PMCID: PMC8034721.
Abstract: ...
Submitter: Dikshant Pradhan
Investigation: IMPAcTB
Assays: Flow Cytometry Processing – Data Attached, Flow Cytometry – Data Linked, Patient Visit – Metadata, Tissue Collection - Metadata
Emmanouil Angelidakis, Sophia Chen, Shun Zhang, Zhengpeng Wan, Roger D. Kamm, Sarah E. Shelton
Link to Paper: https://doi.org/10.1002/adhm.202202984
A bidirectional association exists between metastatic dissemination and the hypercoagulable state associated with many types of cancer. As such, clinical studies have provided evidence that markers associated with elevated levels of coagulation and fibrinolysis correlate with decreased patient survival. However, ...
Submitter: Charles Demurjian
Investigation: MetNet
Assays: Cancer Cell Extravasation Analysis - Data Linked, Clot Modeling Analysis - Data Linked, Device Imaging - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Microfluidic Device Creation - Metadata, Permeability Analysis - Data Linked
Computational prediction of physicochemical and advanced descriptors related to ADME-Tox and PAINS assessment. Potential correlations of the computed descriptors with experimentally determined anti-parasitic activities and correlations between experimentally determined levels of target protein inhibition (PTR1, DHFR) with the anti-parasitic activity were also studied.
Location: UiB Date: 8-20 June 2017 Compounds tested: WY-14,643 (PPAR alpha agonist), GW501516 (PPAR beta agonist) No. of test groups: 5 (Control 1: DMSO/saline/PEG, WY-14.643 High (40 mg/kg), WY-14.643 Low (4.0 mg/kg), GW501516 High (4.0 mg/kg), GW501516 Low (0.4 mg/kg)) No. of fish per group: 22
Aim: *To investigate effects on lipid metabolism in Atlantic cod ( Gadus morhua) mediated by peroxisome proliferator-activated receptors (Ppars) by in vivo exposure to two mammalian PPAR agonists.
Submitter: Marta Eide
Investigation: 1 hidden item
Assays: In vivo II - GW and WY Biometric data, Proteomics data, RNA sequencing, Targeted lipidomics, Untargeted lipidomics
Aim: To investigate whether Atlantic cod that feed close to aquatic breeding facilities are affected by chlorpyrifos-methyl. Feeding experiment with chlorpyrifos-methyl, an organophosphorous pesticide detected in plant based salmon feed. Based on previous experiments using salmon.
Doses: 0, 0.5, 5.0, 25 mg/kg) chlorpyrifos-methyl. Duration: 30 days Set-up: Three tanks per treatment (12 in total)
Samples include: Liver, plasma, bile, brain. Analysis include:
- Have RNAseq and metabolomics from 36 ...
Submitter: Marta Eide
Investigation: 1 hidden item
Assays: Chemical analyses, EROD activity, Fish biometrics in vivo Nord, Metabolomics, Plasma parameters, Transcriptomics
Submitter: Daniel Hönicke
Investigation: Altering the expression pattern in Clostridium ...
Assays: Transcriptional analyses of a thioredoxin (trxB, encoded by CAC1548) kno...
HSD11B1 was inhibited in human subcutaneous and omental adipose tissue, and the effect on oxygenated adrogen metabolism was studied.
Submitter: Jurgen Haanstra
Investigation: Metabolism of HepG2 liver cancer cells
Assays: Inhibition experiment for the effect of SSZ on HepG2 metabolism
Initial rate kinetics for the purified Caulinobacter crescentus Weimberg pathway enzymes, including substrate dependence, and product inhibition.
Submitter: Jacky Snoep
Investigation: Caulobacter crescentus Weimberg pathway
sbgn model of signalling
Originally submitted to PLaSMo on 2012-03-05 11:53:41
Submitter: BioData SynthSys
Investigation: Beaton, Martin
Assays: Insulin-like growth factor signaling - PLM_62, version 1
Lauren Baugh, Brittany A. Goods, Juan S. Gnecco, Yunbeen Bae, Michael Retchin, Constantine N. Tzouanas, Megan Loring, Keith Isaacson, Alex K. Shalek, Douglas Lauffenburger, Linda Griffith
https://www.medrxiv.org/content/10.1101/2022.01.29.22269829v1
Endometriosis is a debilitating gynecological disorder affecting approximately 10% of the female population. Despite its prevalence, robust methods to classify and treat endometriosis remain elusive. Changes ...
Submitter: Charles Demurjian
Investigation: Endometriosis
Assays: All Metadata, DNA Extraction - Metadata, Immunohistochemistry - Data Linked, Linear Mixed Model - Data Linked, Mass Spectrometry Proteomics - Data Linked, Mass Spectrometry Proteomics Analysis - Data Linked, Patient Visit - Metadata, Single Cell Expression Matrix Analysis - Data Linked, Single Cell Sequencing - Data Linked, Tissue Collection - Metadata
This study includes the single snRNA-seq in whole adult murine hearts from an inbred (C57BL/6NRj) and an outbred (Fzt:DU) mouse strain in comparison to publicly available scRNA-seq data of the tabula muris project.
Submitter: Anne-Marie Galow
Investigation: 1 hidden item
Assays: integrative cluster analysis of single cell and single nuclei data
Haosheng Feng, Shao-Xiong Lennon Luo, Robert G Croy, John M. Essigmann, Timothy M. Swager
https://doi.org/10.1039/D2DT03848J
Cu(I) from tetrakis(acetonitrile)copper(I) hexafluorophosphate ([Cu(MeCN)4]PF6) was complexed with five structurally related phosphines containing N-heterocycles. The interactions between the resulting complexes and some N-nitrosamines were studied using X-ray crystallography as well as emission spectroscopy. Upon complexation, three ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: Absorption and Emission Spectroscopy - Data Linked, Absorption and Emission Spectroscopy Analysis - Data Linked, Chemical Synthesis - Metadata, Crystallography - Data Linked, Electron Paramagnetic Resonance - Data Linked, High Resolution Mass Spectra - Data Linked, High Resolution Mass Spectra Analysis - Data Linked, Nuclear Magnetic Resonance Spectroscopy - Data Linked, Nuclear Magnetic Resonance Spectroscopy Analysis - Data Linked, X-ray Photoelectron Spectroscopy - Data Linked
Submitter: Dawie van Niekerk
Investigation: Glucose metabolism in Plasmodium falciparum inf...
Investigation files _I_01_LabTrials
Investigation files _I_02_FieldTrials
Investigation files _I_03_Omics
Investigation files _I_T21_SXPsysbio
Submitter: Nikolay Zenkin
Investigation: Wetlab approach to transcription fidelity
Assays: Kinetics of misincorporation and proofreading by bacterial RNA polymerase
test test
Submitter: Holger Janssen
Investigation: Systems Biology of Clostridium acetobutylicum -...
Assays: test
How do the fluxes of rubidium (potassium) change during potassium starvation.
Submitter: Falko Krause
Investigation: K+ Starvation in Saccharomyces cerevisiae
Assays: Ammonium fluxes, Potassium fluxes, Proton fluxes
How does the flux of potassium, hydrogen change during potassium uptake? Which ions are involved in maintaining the required charge balance?
Submitter: Falko Krause
Investigation: Potassium uptake in Saccharomyces cerevisiae
Assays: Additional fluxes, Potassium fluxes, Proton fluxes
Measure binding of reactants to Gre2p by ITC (isothermal titration calorimetry).
Submitter: Gudrun Gygli
Investigation: Workflow for characterization of enzymes under ...
Assays: Analysis of data from ITC experiments (binding), Binding of HK to Gre2p (ITC-BIND), Binding of NADP+ to Gre2p in HEPES Buffer (ITC-BIND), Binding of NADP+ to Gre2p in KPi Buffer (ITC-BIND), Binding of NADP+ to Gre2p in PBS Buffer (ITC-BIND), Binding of NADPH to Gre2p in HEPES Buffer (ITC-BIND), Binding of NADPH to Gre2p in KPi Buffer (ITC-BIND), Binding of NADPH to Gre2p in PBS Buffer (ITC-BIND), Binding of NADPH to Gre2p in Tween-KPi Buffer (ITC-BIND), Binding of NDK to Gre2p (ITC-BIND)
Measure kinetics of reactants by Gre2p with ITC (isothermal titration calorimetry).
Submitter: Gudrun Gygli
Investigation: Workflow for characterization of enzymes under ...
Assays: Analysis of data from ITC experiments (kinetics), Kinetics of the reaction of NDK and NADPH with Gre2p (ITC-MIM) in HEPES ..., Kinetics of the reaction of NDK and NADPH with Gre2p (ITC-MIM) in KPi bu..., Kinetics of the reaction of NDK and NADPH with Gre2p (ITC-MIM) in PBS bu..., Kinetics of the reaction of NDK and NADPH with Gre2p (ITC-MIM) in Tween-..., Kinetics of the reaction of NDK and NADPH with Gre2p (ITC-rSIM) in 3 buf...
The output of the initial model of redox metabolism will be compared to experimental flux and metabolite data. Deviations between model and experiment will be prioritized together with WP2. We will apply Metabolic Control Analysis (Fell 1992 PMID: 1530563) to diagnose which enzymes control the deviating metabolite concentrations and/or rates. When the agreement between model and experiment is sufficient we will first link it to the existing model of trypanosome glycolysis and repeat the same ...
Submitter: Jurgen Haanstra
Investigation: Dynamic modelling of redox metabolism and gene ...
Assays: No Assays