Journal: eLife

Article Title: Recruitment of clathrin to intracellular membranes is sufficient for vesicle formation

doi: 10.7554/eLife.78929

Figure Lengend Snippet:

Article Snippet: Recombinant DNA reagent , CD8-dCherry-FRB , , RRID: Addgene_100739 , .

Techniques: Triple Knockout, Recombinant, Modification, Plasmid Preparation, Mutagenesis

Journal: Cell host & microbe

Article Title: An early-life microbiota metabolite protects against obesity by regulating intestinal lipid metabolism.

doi: 10.1016/j.chom.2023.09.002

Figure Lengend Snippet: Figure 2. Ligilactobacillus murinus protects against adiposity during early-life consumption of an HF diet (A) Heatmap showing differential abundance of the 5 most abundant families in the small intestine microbiota of mice after 5 weeks of treatment. (B) Relative abundance of the genus Lactobacillus in the small intestine microbiota as determined by 16S rRNA sequencing. (C) The abundance of L. murinus in the small intestine as determined by qPCR. (D and E) (D) Weight gain and (E) abdominal fat of mice given an HF diet and LDP alone or gavaged with a penicillin resistant strain of L. murinus (L. murinus PenR) after 5 weeks. (F) A schematic representation of the gnotobiotic experiment. (G) Lactobacillus abundance (colony-forming unit [CFU]/gram) in small intestine (SI) after 5 weeks on an HF. Dotted line indicates limit of detection for Lacto- bacillus species in this experiment. (H and I) (H) Weight gain and (I) abdominal fat (g) of mice after 5 weeks. Each dot represents one animal. Bars represent geometric mean. (A) n = 5 mice/group; (B) n = 9 mice/group; (C) n = 7–8 mice/group; (D and E) n = 12 mice/group; (G and H) n = 8 mice/group. Data representative of two in- dependent cohorts. *p < 0.05; **p < 0.01; ***p < 0.005; ****p < 0.001 using an unpaired two-tailed Student’s t test.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-PPAR-g Santa Cruz Biotechnology Cat #: sc-7273, RRID:AB_628115 Goat anti-mouse IgG Alexa Fluor 488 Thermo Fisher Scientific Cat #: A-11001, RRID:AB_2534069 Bacterial and virus strains Ligilactobacillus murinus This study CS010 Muribaculum intestinale DSMZ YL27 Clostridium clostridioforme DSMZ YL32 Clostridium sporogenes DSMZ B-CC-163-3B Streptococcus daniellae ERD01G DSMZ ERD01G Staphylococcus xylosus 33-ERD13C DSMZ 33-ERD13C Escherichia coli Mt1B1 DSMZ Mt1B1 Ligilactobacillus murinus PenR This study CS052 Ligilactobacillus murinus DSMZ M-6244-3B Lacticaseibacillus rhamnosus ATCC Cat #: 53103 Lactobacillus acidophilus ATCC Scav; Cat #: 4356 Bifidobacterium longum subsp animalis DSMZ YL2 Chemicals, peptides, and recombinant proteins Difco Lactobacilli MRS agar Becton Dickinson Cat #: 288210 Difco Lactobacilli MRS broth Becton Dickinson Cat #: 288130 Penicillin V potassium salt Sigma Cat #: P1382 D-(+)-3-phenyllactic acid Sigma Cat #: 376906 Difco LB broth Becton Dickinson Cat #: 244620 Difco Brain Heart Infustion agar Becton Dickinson Cat #: 241830 Bacto Yeast Extract Becton Dickinson Cat #: 212750 Bacto Tryptic soy broth Becton Dickinson Cat #: 211825 Dipotassium hydrogen phosphate Fisher Chemicals Cat #: P288 Hemin Sigma Cat #: 51280 D(+)-Glucose Acros Organics Cat #: 41095 Sodium carbonate Fisher Chemicals Cat #: 5263 (L) – cysteine Sigma Cat #: 168149 Menadione Sigma Cat #: 47775 Heat-Inactivated Fetal Bovine Serum Gibco Cat #: 16140-071 RPMI 1640 Medium Gibco Cat #: 11875093 Recombinant Mouse IFN-gamma Protein R&D Systems Cat #: 485-MI-100 Penicillin-Streptomycin Gibco Cat #: 15140122 ITS Liquid Media Supplement Sigma Cat #: I3146 Minimal Essential Media Gibco Cat #: 11095-080 Glutamax Gibco Cat #: 35050-061 Nonessential amino acids Gibco Cat #: 11140-050 Sodium pyruvate Gibco Cat #: 11360070 Trypsin-EDTA (0.05%) Gibco Cat #: 25300054 Primocin InvivoGen Cat #: ant-pm-1 Dithiothreitol Acros Organics Cat #: 16568 EDTA Sigma Cat #: E5134 EGTA Sigma Cat #: E3889 (Continued on next page) e1 Cell Host & Microbe 31, 1604–1619.e1–e10, October 11, 2023

Techniques: Sequencing, Two Tailed Test

Journal: Frontiers in Molecular Biosciences

Article Title: An Integrated Computational and Experimental Approach to Identifying Inhibitors for SARS-CoV-2 3CL Protease

doi: 10.3389/fmolb.2021.661424

Figure Lengend Snippet: The overview of the proposed workflow to discover new inhibitors of 3CLpro SARS– CoV– 2 .

Article Snippet: In each experimental group, 30 μL of 15 nM purified recombinant 3CLpro (BPS Bioscience Inc., CA) and 10 μL of 500 μM prepared inhibitor solution in 5% aqueous DMSO was added into a black 96-well plate (Nunc U96).

Techniques:

Journal: Frontiers in Molecular Biosciences

Article Title: An Integrated Computational and Experimental Approach to Identifying Inhibitors for SARS-CoV-2 3CL Protease

doi: 10.3389/fmolb.2021.661424

Figure Lengend Snippet: Enzyme activities (A,B) and IC 50 curve (C,D) of newly identified inhibitors, PMPT and CPSQPA. 3CLpro and inhibitors were incubated at 25°C with slow shaking for 2 h, with fluorescence recorded every 3 min (A,B) . The slope of each curve corresponded to the enzyme activity. Relative enzyme activities were calculated as ratio of compound-treated groups and positive control (no inhibitor) to determine IC 50 . Data analysis and curve fitting were conducted using the program Graphpad.

Article Snippet: In each experimental group, 30 μL of 15 nM purified recombinant 3CLpro (BPS Bioscience Inc., CA) and 10 μL of 500 μM prepared inhibitor solution in 5% aqueous DMSO was added into a black 96-well plate (Nunc U96).

Techniques: Incubation, Fluorescence, Activity Assay, Positive Control

Journal: Frontiers in Molecular Biosciences

Article Title: An Integrated Computational and Experimental Approach to Identifying Inhibitors for SARS-CoV-2 3CL Protease

doi: 10.3389/fmolb.2021.661424

Figure Lengend Snippet: Docking conformations of newly identified 3CLpro SARS– CoV– 2 inhibitors: (A,B) PMPT; (C,D) CPSQPA. 3CLpro was modified from the 6LU7 structure by removing the ligand and water. Protein is colored in yellow. Compounds are colored in sky blue. Amino acid residues interacting with the ligands are labeled. Surface of the protein is displayed and colored in gray (B,D) . Hydrogen bonds between PMPT and 3CLpro are shown as black lines (A) . As CPSQPA likely has a net charge of -1 (sulfonamide p K a ’s generally are in the range of 5.0–7.0), the anionic form was docked into the protein (C,D) . S1′, S1, S2, S3, and S4 are the sub-pockets for binding.

Article Snippet: In each experimental group, 30 μL of 15 nM purified recombinant 3CLpro (BPS Bioscience Inc., CA) and 10 μL of 500 μM prepared inhibitor solution in 5% aqueous DMSO was added into a black 96-well plate (Nunc U96).

Techniques: Modification, Labeling, Binding Assay