Host Monitoring of Quorum Sensing During Pseudomonas aeruginosa Infection
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Citations
De novo design of an intercellular signaling toolbox for multi-channel cell-cell communication and biological computation.
Aryl hydrocarbon receptor (AHR) functions: Balancing opposing processes including inflammatory reactions
How the AHR Became Important in Intestinal Homeostasis—A Diurnal FICZ/AHR/CYP1A1 Feedback Controls Both Immunity and Immunopathology
Manipulation of epithelial integrity and mucosal immunity by host and microbiota-derived metabolites.
References
A new mathematical model for relative quantification in real-time RT-PCR.
limma powers differential expression analyses for RNA-sequencing and microarray studies
Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.
Comparative Protein Structure Modeling Using MODELLER
QUORUM SENSING: Cell-to-Cell Communication in Bacteria
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Frequently Asked Questions (13)
Q2. What is the first step in molecular docking?
The first step in molecular docking via Maestro11v0 is to set up the receptor grid defining shape and properties of the receptor binding site, important for scoring the ligand poses in a later step.
Q3. What is the use of a hierarchical filter?
Glide docking methodologies use a series of hierarchical filters searching for possible ligand positions in the receptor binding-site.
Q4. What software was used to extract the microarray image data?
Microarray image data were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.
Q5. What was the procedure used to analyze the microarrays?
Scanning of microarrays was performed with either 3 μm resolution (8x60K) or extended dynamic range (XDR) and 5 µm resolution (4x44K) using a G2565CA high-resolution laser microarray scanner (Agilent Technologies).
Q6. What was the procedure used to determine luciferase activity?
cells were harvested in reporter lysis buffer (Promega) and lysates were used to determine luciferase activity using Luciferase Assay System (Promega) according to manufacturer’s instructions.
Q7. What was the procedure for resuspended cells?
The cells were pelleted, and following lysis of red blood cells and another wash with medium, the cells were resuspended in Fc block and subsequently stained for flow cytometry (FACS).
Q8. What is the effect of LaCl3 on AhR activity?
(B-E) Shiner et al (80) reported that apoptosis induced by 3-o-C12-L-HSL can be blocked by Lanthanum chloride (LaCl3), leaving its immunomodulatory properties unaffected.
Q9. How many experiments were performed to determine the P value?
To compute P values, depending on sample distribution and variation, different tests were performed, as described in figure legends.
Q10. what is danio rerio egl-9 family member 4?
1.12 3.22E-03A_15_P596492 Unknown 1.01 1.90E-06gnb3aref|Danio rerio guanine nucleotide binding protein (G protein), beta polypeptide 3a (gnb3a), mRNA [NM_001002437] 0.99 8.50E-03egln3ref|Danio rerio egl-9 family hypoxiainducible factor 3 (egln3), mRNA [NM_213310] 0.98 5.26E-04nos1apaens|nitric oxide synthase 1 (neuronal) adaptor protein a [Source:ZFIN;Acc:ZDB-GENE-0810241] [ENSDART00000148997] 0.95 1.59E-02ndrg4ref|Danio rerio NDRG family member 4 (ndrg4), mRNA [NM_001045173] 0.91 1.57E-02ponzr3ref|Danio rerio plac8 onzin related protein 3 (ponzr3), mRNA [NM_001327984] 0.91 3.84E-02myhz1.2ref|Danio rerio myosin, heavy polypeptide 1.2, skeletal muscle (myhz1.2), mRNA [NM_001161446] 0.91 9.44E-04slc13a2ref|Danio rerio solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2 (slc13a2), mRNA [NM_213452] 0.88 1.69E-04hpdaref|Danio rerio 4-hydroxyphenylpyruvate dioxygenase a (hpda), mRNA [NM_201167] 0.87 2.01E-03pck1ref|Danio rerio phosphoenolpyruvate carboxykinase 1 (soluble) (pck1), mRNA [NM_214751] 0.84 5.14E-04NP13318914tc|GB|XM_001919200.1|XP_001919235. 1 hypothetical protein [NP13318914] 0.83 2.61E-03ampd1ref|Danio rerio adenosine monophosphate deaminase 1 (isoform M) (ampd1), mRNA [NM_200893] 0.83 4.55E-03exoc1ref|Danio rerio exocyst complex component 1 (exoc1), mRNA [NM_199597] 0.83 1.65E-02bcl6abref|Danio rerio B cell CLL/lymphoma 6ab (bcl6ab), mRNA [NM_001100074]
Q11. What was the method used for the quantification of total RNA?
Quality control and quantification of total RNA was analysed using an Agilent 2100 Bioanalyzer (Agilent Technologies) and a NanoDrop 1000 UV-Vis spectrophotometer (Thermo Fisher Scientific).
Q12. What is the luciferase activity of hepatocytic (?
(B,C) Luciferase activity of hepatocytic (Hepa-1c1c7) luciferase AhR reporter upon 4h stimulation with 1-HP (50 µM) in the presence or absence of different concentrations of QS molecules.
Q13. What is the docking pose for each of the investigated ligands?
(E) Best docking pose for each of the investigated ligands as 2D-interaction plot (green dashed: hydrogen donor, red dashed: hydrogen acceptor, orange: hydrophobic interactions (plots drawn by LigandScout 4.1).