Journal: Cell metabolism

Article Title: Mice Under Caloric Restriction Self-Impose a Temporal Restriction of Food Intake as Revealed by an Automated Feeder System

doi: 10.1016/j.cmet.2017.06.007

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Critical Commercial Assays Automated Feeder System Phenome Technologies and Actimetrics http://actimetrics.com/products/clocklab/clocklab-feeder-control/ Dustless Precision Pellets®, Rodent, Grain-Based BioServ F0175 Precision Xtra Blood Glucose & Ketone Monitoring System Abbott Diabetes Care 98814-65 Precision Xtra Blood Glucose test strips Abbott Diabetes Care 99878-BX Standard polycarbonate mouse cages with running wheels Actimetrics http://actimetrics.com/products/clocklab/running-wheel-cages/ Deposited Data Raw data files for feeding and wheel-running activity This paper http://dx.doi.org/10.17632/hxwwyycjy7.1 Raw mouse body weight data & blood glucose levels This paper http://dx.doi.org/10.17632/hxwwyycjy7.1 Experimental Models: Cell Lines Experimental Models: Organisms/Strains C57BL/6J, male Mouse Breeding Core, Wakeland lab, UT Southwestern Medical Center Oligonucleotides Recombinant DNA Software and Algorithms ggplot2 R package CRAN https://cran.r-project.org/web/packages/ggplot2/index.html Prism (version 7.0a) GraphPad Software https://www.graphpad.com/scientific-software/prism/ ClockLab USB Data Collection Program (version 3.15) Actimetrics http://actimetrics.com/downloads/clocklab/ ClockLab Analysis (version 6.0.34 –stand alone and version 2.72 – Matlab based) Actimetrics http://actimetrics.com/downloads/clocklab/ ClockLab Chamber Control Actimetrics http://actimetrics.com/downloads/clocklab/ Other Open in a separate window KEY RESOURCES TABLE

Techniques: Virus, Recombinant, Activity Assay, Software, Control

Journal: Cell host & microbe

Article Title: Gut Microbiota Produced Tryptamine Activates an Epithelial G-protein Coupled Receptor to Increase Colonic Secretion

doi: 10.1016/j.chom.2018.05.004

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial Strains Bacteroides thetaiotaomicron VPI-5482 ATCC ATCC 29148 Bacteroides thetaiotaomicron VPI-5482 pNBU2 This work N/A Bacteroides thetaiotaomicron VPI-5482 pNBU2:: trpD This work N/A Chemicals, Peptides, and Recombinant Proteins Ca 2+ Mg free PBS Corning 21-040-CV Gentle cell dissociation media Stem cell technologies Cat# 7174 Bovine Serum Albumin Sigma Life Science Cas# 9048-46-8 DMEM-F/12 media Life technologies Cat# 11330-032 IntestiCultTM organoid growth media Stem cell technologies Cat# 6000 Matrigel Corning Cat# 356231 Calcein green Invitrogen Cat# C3100MP Tryptamine hydrochloride Aldrich Cas# 343-92-2 GR-113808 Tocris Bioscience Cas# 144625-51-4 Ondansetron Sigma-Aldrich Cas# 99614-01-04 Forskolin Sigma-Aldrich Cas# 66575-29-9 Erythromycin Sigma Life Science Cas# 114-07-8 Gentamycin Sigma Life Science Cas# 1405-41-0 Methanol Sigma-Aldrich Cas# 67-56-1 Methylcellulose Sigma-Aldrich Cas#9004-67-5 Carmine red Sigma-Aldrich Cas# 1390-65-4 5-Nitro-2-(3-phenylpropylamino) benzoic acid Sigma-Aldrich Cas# 107254-86-4 Amiloride hdrochloride Sigma-Aldrich Cas# 2016-88-8 CH-223191 Tocris Cat# 3858 Tetrodotoxin EMD Biosciences Inc. Cat# 554412 Critical Commercial Assays cAMP Direct Immunoassay Detection Kit Abcam Cat# ab138880 Experimental Models: Organisms/Strains GF and HM mice Taconic Farms Swiss Webster 5-HT 4 R −/− and WT mice Compan et al.,2004 129/Sv Recombinant DNA pNBU2 Whitaker et al.2017 N/A Primers sequence 5-HT 4 R Forward: 5′-AGTTCCAACGAGGGTTTCAGG-3′ Reverse: 5′-CAGCAGGTTGCCCAAGATG-3′ Bhattarai et al. 2017 N/A Turicibacter Forward: 5′-GCGCGCAGGTGGTTAATTAAGTCT-3′ Reverse: 5′-TCAGTGTCAGTTGCAGACCAGGAA-3′ This work N/A Universal Forward: 5′-AGAGTTTGATCCTGGCTCAG-3′ Reverse: 5′-GACGGGCGGTGWGTRCA-3′ Bhattarai and Kashyap, 2016 N/A Software and Algorithms ImageJ NIH Version 1.50i GraphPad PRISM GraphPad Software Version 7.0a Acquire and Analyze Physiologic instruments Version 2.0 Leica Application Suite X Leica N/A Other Synergy MXplate reader BiotTek Gen5 1.09 Confocal live cell microscopy Leica Microsystems DMi8 Ussing Chamber Physiologic Instruments Cat# P2300 Voltage-clamp amplifier Physiologic Instruments Version VCC MC8 LC-MS/MS Waters N/A Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, Sequencing, Software, Microscopy

Journal: Cell host & microbe

Article Title: Gut Microbiota Produced Tryptamine Activates an Epithelial G-protein Coupled Receptor to Increase Colonic Secretion

doi: 10.1016/j.chom.2018.05.004

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial Strains Bacteroides thetaiotaomicron VPI-5482 ATCC ATCC 29148 Bacteroides thetaiotaomicron VPI-5482 pNBU2 This work N/A Bacteroides thetaiotaomicron VPI-5482 pNBU2:: trpD This work N/A Chemicals, Peptides, and Recombinant Proteins Ca 2+ Mg free PBS Corning 21-040-CV Gentle cell dissociation media Stem cell technologies Cat# 7174 Bovine Serum Albumin Sigma Life Science Cas# 9048-46-8 DMEM-F/12 media Life technologies Cat# 11330-032 IntestiCultTM organoid growth media Stem cell technologies Cat# 6000 Matrigel Corning Cat# 356231 Calcein green Invitrogen Cat# C3100MP Tryptamine hydrochloride Aldrich Cas# 343-92-2 GR-113808 Tocris Bioscience Cas# 144625-51-4 Ondansetron Sigma-Aldrich Cas# 99614-01-04 Forskolin Sigma-Aldrich Cas# 66575-29-9 Erythromycin Sigma Life Science Cas# 114-07-8 Gentamycin Sigma Life Science Cas# 1405-41-0 Methanol Sigma-Aldrich Cas# 67-56-1 Methylcellulose Sigma-Aldrich Cas#9004-67-5 Carmine red Sigma-Aldrich Cas# 1390-65-4 5-Nitro-2-(3-phenylpropylamino) benzoic acid Sigma-Aldrich Cas# 107254-86-4 Amiloride hdrochloride Sigma-Aldrich Cas# 2016-88-8 CH-223191 Tocris Cat# 3858 Tetrodotoxin EMD Biosciences Inc. Cat# 554412 Critical Commercial Assays cAMP Direct Immunoassay Detection Kit Abcam Cat# ab138880 Experimental Models: Organisms/Strains GF and HM mice Taconic Farms Swiss Webster 5-HT 4 R −/− and WT mice Compan et al.,2004 129/Sv Recombinant DNA pNBU2 Whitaker et al.2017 N/A Primers sequence 5-HT 4 R Forward: 5′-AGTTCCAACGAGGGTTTCAGG-3′ Reverse: 5′-CAGCAGGTTGCCCAAGATG-3′ Bhattarai et al. 2017 N/A Turicibacter Forward: 5′-GCGCGCAGGTGGTTAATTAAGTCT-3′ Reverse: 5′-TCAGTGTCAGTTGCAGACCAGGAA-3′ This work N/A Universal Forward: 5′-AGAGTTTGATCCTGGCTCAG-3′ Reverse: 5′-GACGGGCGGTGWGTRCA-3′ Bhattarai and Kashyap, 2016 N/A Software and Algorithms ImageJ NIH Version 1.50i GraphPad PRISM GraphPad Software Version 7.0a Acquire and Analyze Physiologic instruments Version 2.0 Leica Application Suite X Leica N/A Other Synergy MXplate reader BiotTek Gen5 1.09 Confocal live cell microscopy Leica Microsystems DMi8 Ussing Chamber Physiologic Instruments Cat# P2300 Voltage-clamp amplifier Physiologic Instruments Version VCC MC8 LC-MS/MS Waters N/A Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, Sequencing, Software, Microscopy

Journal: Cell host & microbe

Article Title: Gut Microbiota Produced Tryptamine Activates an Epithelial G-protein Coupled Receptor to Increase Colonic Secretion

doi: 10.1016/j.chom.2018.05.004

Figure Lengend Snippet: Colonization of GF mice with engineered B. thetaiotaomicron Trp D+ increases luminal conversion of tryptophan to tryptamine, without increasing circulating tryptamine and accelerates whole gut transit. Change in fecal (A–C) and serum (D–F) tryptophan, tryptamine and 5-HT concentrations following colonization of GF mice with either engineered B. thetaiotaomicron Trp D+ or B. thetaiotaomicron Trp D− empty vector control. Change in normalized pellet water content (G) and whole gut transit (H) in GF male mice colonized with B. thetaiotaomicron Trp D+ or Trp D−. Mean ± SEM, n=5, un-paired t-test and one-way ANOVA, *P < 0.05. See also Figure S7.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial Strains Bacteroides thetaiotaomicron VPI-5482 ATCC ATCC 29148 Bacteroides thetaiotaomicron VPI-5482 pNBU2 This work N/A Bacteroides thetaiotaomicron VPI-5482 pNBU2:: trpD This work N/A Chemicals, Peptides, and Recombinant Proteins Ca 2+ Mg free PBS Corning 21-040-CV Gentle cell dissociation media Stem cell technologies Cat# 7174 Bovine Serum Albumin Sigma Life Science Cas# 9048-46-8 DMEM-F/12 media Life technologies Cat# 11330-032 IntestiCultTM organoid growth media Stem cell technologies Cat# 6000 Matrigel Corning Cat# 356231 Calcein green Invitrogen Cat# C3100MP Tryptamine hydrochloride Aldrich Cas# 343-92-2 GR-113808 Tocris Bioscience Cas# 144625-51-4 Ondansetron Sigma-Aldrich Cas# 99614-01-04 Forskolin Sigma-Aldrich Cas# 66575-29-9 Erythromycin Sigma Life Science Cas# 114-07-8 Gentamycin Sigma Life Science Cas# 1405-41-0 Methanol Sigma-Aldrich Cas# 67-56-1 Methylcellulose Sigma-Aldrich Cas#9004-67-5 Carmine red Sigma-Aldrich Cas# 1390-65-4 5-Nitro-2-(3-phenylpropylamino) benzoic acid Sigma-Aldrich Cas# 107254-86-4 Amiloride hdrochloride Sigma-Aldrich Cas# 2016-88-8 CH-223191 Tocris Cat# 3858 Tetrodotoxin EMD Biosciences Inc. Cat# 554412 Critical Commercial Assays cAMP Direct Immunoassay Detection Kit Abcam Cat# ab138880 Experimental Models: Organisms/Strains GF and HM mice Taconic Farms Swiss Webster 5-HT 4 R −/− and WT mice Compan et al.,2004 129/Sv Recombinant DNA pNBU2 Whitaker et al.2017 N/A Primers sequence 5-HT 4 R Forward: 5′-AGTTCCAACGAGGGTTTCAGG-3′ Reverse: 5′-CAGCAGGTTGCCCAAGATG-3′ Bhattarai et al. 2017 N/A Turicibacter Forward: 5′-GCGCGCAGGTGGTTAATTAAGTCT-3′ Reverse: 5′-TCAGTGTCAGTTGCAGACCAGGAA-3′ This work N/A Universal Forward: 5′-AGAGTTTGATCCTGGCTCAG-3′ Reverse: 5′-GACGGGCGGTGWGTRCA-3′ Bhattarai and Kashyap, 2016 N/A Software and Algorithms ImageJ NIH Version 1.50i GraphPad PRISM GraphPad Software Version 7.0a Acquire and Analyze Physiologic instruments Version 2.0 Leica Application Suite X Leica N/A Other Synergy MXplate reader BiotTek Gen5 1.09 Confocal live cell microscopy Leica Microsystems DMi8 Ussing Chamber Physiologic Instruments Cat# P2300 Voltage-clamp amplifier Physiologic Instruments Version VCC MC8 LC-MS/MS Waters N/A Open in a separate window KEY RESOURCES TABLE

Techniques: Plasmid Preparation

Journal: Cell host & microbe

Article Title: Gut Microbiota Produced Tryptamine Activates an Epithelial G-protein Coupled Receptor to Increase Colonic Secretion

doi: 10.1016/j.chom.2018.05.004

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial Strains Bacteroides thetaiotaomicron VPI-5482 ATCC ATCC 29148 Bacteroides thetaiotaomicron VPI-5482 pNBU2 This work N/A Bacteroides thetaiotaomicron VPI-5482 pNBU2:: trpD This work N/A Chemicals, Peptides, and Recombinant Proteins Ca 2+ Mg free PBS Corning 21-040-CV Gentle cell dissociation media Stem cell technologies Cat# 7174 Bovine Serum Albumin Sigma Life Science Cas# 9048-46-8 DMEM-F/12 media Life technologies Cat# 11330-032 IntestiCultTM organoid growth media Stem cell technologies Cat# 6000 Matrigel Corning Cat# 356231 Calcein green Invitrogen Cat# C3100MP Tryptamine hydrochloride Aldrich Cas# 343-92-2 GR-113808 Tocris Bioscience Cas# 144625-51-4 Ondansetron Sigma-Aldrich Cas# 99614-01-04 Forskolin Sigma-Aldrich Cas# 66575-29-9 Erythromycin Sigma Life Science Cas# 114-07-8 Gentamycin Sigma Life Science Cas# 1405-41-0 Methanol Sigma-Aldrich Cas# 67-56-1 Methylcellulose Sigma-Aldrich Cas#9004-67-5 Carmine red Sigma-Aldrich Cas# 1390-65-4 5-Nitro-2-(3-phenylpropylamino) benzoic acid Sigma-Aldrich Cas# 107254-86-4 Amiloride hdrochloride Sigma-Aldrich Cas# 2016-88-8 CH-223191 Tocris Cat# 3858 Tetrodotoxin EMD Biosciences Inc. Cat# 554412 Critical Commercial Assays cAMP Direct Immunoassay Detection Kit Abcam Cat# ab138880 Experimental Models: Organisms/Strains GF and HM mice Taconic Farms Swiss Webster 5-HT 4 R −/− and WT mice Compan et al.,2004 129/Sv Recombinant DNA pNBU2 Whitaker et al.2017 N/A Primers sequence 5-HT 4 R Forward: 5′-AGTTCCAACGAGGGTTTCAGG-3′ Reverse: 5′-CAGCAGGTTGCCCAAGATG-3′ Bhattarai et al. 2017 N/A Turicibacter Forward: 5′-GCGCGCAGGTGGTTAATTAAGTCT-3′ Reverse: 5′-TCAGTGTCAGTTGCAGACCAGGAA-3′ This work N/A Universal Forward: 5′-AGAGTTTGATCCTGGCTCAG-3′ Reverse: 5′-GACGGGCGGTGWGTRCA-3′ Bhattarai and Kashyap, 2016 N/A Software and Algorithms ImageJ NIH Version 1.50i GraphPad PRISM GraphPad Software Version 7.0a Acquire and Analyze Physiologic instruments Version 2.0 Leica Application Suite X Leica N/A Other Synergy MXplate reader BiotTek Gen5 1.09 Confocal live cell microscopy Leica Microsystems DMi8 Ussing Chamber Physiologic Instruments Cat# P2300 Voltage-clamp amplifier Physiologic Instruments Version VCC MC8 LC-MS/MS Waters N/A Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, Sequencing, Software, Microscopy