Journal: bioRxiv

Article Title: Branched-chain keto acids promote an immune-suppressive and neurodegenerative microenvironment in leptomeningeal disease

doi: 10.1101/2023.12.18.572239

Figure Lengend Snippet: A. Tail suspension scoring for control PBS-injected mice vs. A20-injected lymphoma LMD mice. B. Grip strength assessing fore limb function for control PBS injected mice vs. A20 injected lymphoma LMD mice. C. Manifestation of kyphosis and loss of grooming in control PBS-injected mice vs. A20 injected lymphoma LMD mice. D. Kaplan-Meier analysis for probability of survival in control PBS injected mice vs. A20 injected lymphoma LMD mice. The p-value was calculated using the Log-Rank (Mantel-Cox) test. E. Images show a healthy, transparent pia membrane in the healthy control animals (green arrow) and a lack of this membrane in the LMD animals. LMD animals show significant tumor deposits instead (blue arrow). F. Immunofluorescent images of microtubule-associated protein 2 (MAP2, red) and DAPI (blue) in the brain hippocampus of LMD-lymphoma model. The top images show low magnification (scale bar is 400 μm), and the bottom images show high magnification of outlined areas. The scale bar is 400 μ m. Staining was repeated on four sections from different mice. G. Quantification of BCKA levels in brains of control and LMD-lymphoma model. Levels are calculated as ng/μg tissue using mass spectrometry. Data represent mean ± SEM (panels A, B, and G). Statistical significance was assessed using the Student’s t-test. Statistical tests were two-sided. ****P < 0.0001, ns = not significant.

Article Snippet: The murine lymphoma A20 cell line was purchased from ATCC.

Techniques: Suspension, Control, Injection, Membrane, Staining, Mass Spectrometry

Journal: bioRxiv

Article Title: Branched-chain keto acids promote an immune-suppressive and neurodegenerative microenvironment in leptomeningeal disease

doi: 10.1101/2023.12.18.572239

Figure Lengend Snippet: A. Schematic illustration for the in vivo experimental strategy showing the four LMD (A20 cell line injected) groups (left) and the timeline of tumor injections and the administered therapy (right). B. Kaplan Meier graph showing the progression-free survival for all mice. Progression was diagnosed in mice who scored a two or higher in any neurological assessment (motor function, tail suspension, kyphosis). The p-value was calculated using the Log-Rank (Mantel-Cox) test. C. Kaplan Meier graph showing the overall survival for all mice. The p-value was calculated using the Log-Rank (Mantel-Cox) test. D. Individual graphs showing the individual scores for each neurological assessment at endpoint (or last assessment before death), top. Individual graphs showing the number of days until mice displayed a score of 2+ for each assessment, paralysis or death, bottom. E. Immunofluorescent images of microtubule-associated protein 2 (MAP2, red) and DAPI (blue) in the brain hippocampus of the lymphoma LMD model. The left images show low magnification (scale bar is 400 μm), and the right images show high magnification of outlined areas. Staining was repeated on four sections from different mice. Data represent mean ± SE (D). Statistical significance was assessed using the Log-rank test (B, C) and Student t-test (D). *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001, ns = not significant.

Article Snippet: The murine lymphoma A20 cell line was purchased from ATCC.

Techniques: In Vivo, Injection, Suspension, Staining

Journal: The Journal of Cell Biology

Article Title: β-Arrestin–Dependent Endocytosis of Proteinase-Activated Receptor 2 Is Required for Intracellular Targeting of Activated Erk1/2

doi:

Figure Lengend Snippet: PAR2-mediated activation of ERK1/2. (a) KNRK-PAR2+ARR-GFP cells (•) and KNRK-PAR2+ARR 319-418 -GFP cells (○) and hBRIE cells (□) were incubated with 50 nM trypsin for 0–60 min at 37°C, and ERK activity was measured using the MBP assay. (b–d) Western blots using antibodies to pERK1/2. (b) KNRK-PAR2+ARR-GFP cells (•), KNRK-PAR2 cells (⋄), and KNRK-PAR2+ARR 319-418 -GFP cells (○) were incubated with 50 nM trypsin. (c) hBRIE cells (□), hBRIE+ARR-GFP (⋄), and hBRIE+ARR 319-418 -GFP (♦) were incubated with 50 nM trypsin for 0–30 min at 37°C. (d) KNRK-PAR2+ARR-GFP cells (•) and KNRK-PAR2+ARR 319-418 -GFP cells (○) were incubated 50 μM AP for 0–30 min at 37°C. * P < 0.05 compared with cells expressing PAR2 alone or PAR2 plus ARR-GFP cells, n = 4.

Article Snippet: Kirsten murine sarcoma virus–transformed rat kidney epithelial cells (KNRK) were from the American Type Tissue Culture Collection (ATCC CRL 1569).

Techniques: Activation Assay, Incubation, Activity Assay, Western Blot, Expressing

Journal: The Journal of Cell Biology

Article Title: β-Arrestin–Dependent Endocytosis of Proteinase-Activated Receptor 2 Is Required for Intracellular Targeting of Activated Erk1/2

doi:

Figure Lengend Snippet: PAR2-mediated Ca 2+ mobilization in KNRK-PAR2 cells and KNRK-PAR2δ(ST363/6A) cells. (a) Concentration-response analysis for KNRK-PAR2 (•) and KNRK-PAR2 (δST363/6A) (▴) cells. (b–d) Each line shows [Ca 2+ ] i for individual KNRK-PAR2 cells (left) and KNRK-PAR2(δST363/6A) cells (right). (b) Note that the response to trypsin is prolonged in KNRK-PAR2(δST363/6A) cells. (c) Homologous desensitization in cells pretreated with 10 μM AP for 5 min before addition of 10 nM trypsin. (d) Heterologous desensitization in cells pretreated with 1 μM PDB for 20 min before addition of 10 nM trypsin. Note that KNRK-PAR2(δST363/6A) cells are resistant to desensitization.

Article Snippet: Kirsten murine sarcoma virus–transformed rat kidney epithelial cells (KNRK) were from the American Type Tissue Culture Collection (ATCC CRL 1569).

Techniques: Concentration Assay

Journal: The Journal of Cell Biology

Article Title: β-Arrestin–Dependent Endocytosis of Proteinase-Activated Receptor 2 Is Required for Intracellular Targeting of Activated Erk1/2

doi:

Figure Lengend Snippet: Agonist-induced PAR2 internalization. (a) Kinetics of PAR2 endocytosis in KNRK-PAR2+ARR-GFP cells (•), KNRK-PAR2 cells (⋄) KNRK-PAR2+ ARR 319-418 -GFP cells (○), KNRK-PAR2(δST363/6A) cells (▴), and hBRIE cells (□). Cells were incubated with 50 μM AP for 0–30 min at 37°C and endocytosis was determined by measuring surface Flag immunoreactivity by flow cytometry. * P < 0.05 compared with cells expressing PAR2 alone or PAR2 plus ARR-GFP cells, n = 3. (b–d) Localization of PAR2 and β-arrestin by immunofluorescence and confocal microscopy. KNRK-PAR2+ARR-GFP cells (b), KNRK-PAR2(δST363/6A)+ ARR-GFP cells (c), or KNRK-PAR2(δST363/6A) (d) were incubated with 50 nM trypsin for 0–30 min at 37°C. PAR2 was localized by immunofluorescence and β-arrestin was detected using GFP (b and c) or by immunofluorescence (d). The same cells are shown in each row and the images in the right panel are formed by superimposition of the images from the other two panels in the same row. Representative of two experiments. In KNRK-PAR2+ARR-GFP cells, note redistribution of β-arrestin to the plasma membrane at 5 min (arrowheads) and to endosomes at 30 min (arrows), where it colocalizes with PAR2. In KNRK-PAR2(δST363/6A)+ARR-GFP cells and in KNRK-PAR2(δST363/6A), note that PAR2 remains at the plasma membrane (arrowheads) and β-arrestin remains in the cytosol (arrows) with no colocalization. Bar, 10 μm.

Article Snippet: Kirsten murine sarcoma virus–transformed rat kidney epithelial cells (KNRK) were from the American Type Tissue Culture Collection (ATCC CRL 1569).

Techniques: Incubation, Flow Cytometry, Expressing, Immunofluorescence, Confocal Microscopy, Clinical Proteomics, Membrane

Journal: The Journal of Cell Biology

Article Title: β-Arrestin–Dependent Endocytosis of Proteinase-Activated Receptor 2 Is Required for Intracellular Targeting of Activated Erk1/2

doi:

Figure Lengend Snippet: (a) PAR2-mediated ERK1/2 activity. KNRK-PAR2 (⋄) and KNRK-PAR2(δST363/6A) (▴) cells were treated with 50 nM trypsin for 0–30 min, and ERK activity was measured using the MBP assay. (b) Activation of ERK1/2. KNRK-PAR2(δST363/6A) (▴), KNRK-PAR2 (δST363/6A)+ARR-GFP (▵), and KNRK-PAR2 (δST363/6A)+ARR 319-418 -GFP (♦) cells were treated with 50 nM trypsin for 0–30 min and phosphorylation was assessed using antibodies to pERK1/2. * P < 0.05 compared with KNRK-PAR2 cells, n = 3.

Article Snippet: Kirsten murine sarcoma virus–transformed rat kidney epithelial cells (KNRK) were from the American Type Tissue Culture Collection (ATCC CRL 1569).

Techniques: Activity Assay, Activation Assay, Phospho-proteomics

Journal: The Journal of Cell Biology

Article Title: β-Arrestin–Dependent Endocytosis of Proteinase-Activated Receptor 2 Is Required for Intracellular Targeting of Activated Erk1/2

doi:

Figure Lengend Snippet: Mechanism of PAR2-mediated activation of ERK1/2. (a) KNRK-PAR2, hBRIE, KNRK-PAR2+ARR 319-418 , and KNRK-PAR2(δST363/6A) cells were untreated (control, con), or incubated with 100 nM GF109203X (GFX), 20 nM LY379196 (LY), 100 ng/ml PTX, 10 μM genistein (GEN), 20 μM tyrphostin 25 (TP), or were cotransfected with N17ras. Cells were incubated with 50 nM trypsin for 5 min. * P < 0.05 compared with untreated cells, n = 4. (b–f) Analysis of KNRK-PAR2 and KNRK-PAR2(δST363/6A) cells by immunoprecipitation (IP) and Western blotting (WB). Cells were incubated with 50 nM trypsin for 5 min. Extracts were immunoprecipitated with antibodies to PYK2 (b), Shc (c and d), and src (e–g). Blots were probed for phosphotyrosine (b–e), PYK2 (f), and src (g).

Article Snippet: Kirsten murine sarcoma virus–transformed rat kidney epithelial cells (KNRK) were from the American Type Tissue Culture Collection (ATCC CRL 1569).

Techniques: Activation Assay, Control, Incubation, Immunoprecipitation, Western Blot

Journal: The Journal of Cell Biology

Article Title: β-Arrestin–Dependent Endocytosis of Proteinase-Activated Receptor 2 Is Required for Intracellular Targeting of Activated Erk1/2

doi:

Figure Lengend Snippet: Nuclear translocation of ERK1/2. (a–d) Subcellular fractionation of activated ERK1/2. KNRK-PAR2+ARR-GFP cells (•), KNRK-PAR2+ ARR 319-418 -GFP cells (○), or PAR2(δST363/6A) cells (s) were incubated with 50 nM trypsin for 0–30 min at 37°C, and pERK was determined in the cytosolic (a) and nuclear (b) fractions ( n = 3). hBRIE cells were incubated with 50 nM trypsin (□) or 10% serum (♦), and pERK was determined in the cytosolic (c) and nuclear (d) fractions. (e) KNRK-PAR2 and KNRK-PAR2(δST363/6A) cells, transiently transfected with ERK2-GFP, were incubated with 50 nM trypsin at 37°C, and translocation of ERK2-GFP was observed by confocal imaging. Representative of eight experiments. In KNRK-PAR2 cells, note that ERK2-GFP remains cytosolic but, in KNRK-PAR2(δST363/6A) cells, it redistributes to the nucleus. (f and g) Proliferative responses to AP and serum. KNRK-PAR2 (f, □) and KNRK-PAR2(δST363/6A) cells (f, ▪) or hBRIE cells (g) were incubated with 50 μM AP or 20% FCS for 24 h, and incorporation of [ 3 H]thymidine and cell number were measured. * P < 0.05 compared with untreated cells or KNRK-PAR2 cells, n = 3.

Article Snippet: Kirsten murine sarcoma virus–transformed rat kidney epithelial cells (KNRK) were from the American Type Tissue Culture Collection (ATCC CRL 1569).

Techniques: Translocation Assay, Fractionation, Incubation, Transfection, Imaging

Journal: The Journal of Cell Biology

Article Title: β-Arrestin–Dependent Endocytosis of Proteinase-Activated Receptor 2 Is Required for Intracellular Targeting of Activated Erk1/2

doi:

Figure Lengend Snippet: Trypsin induced association of β-arrestin and raf-1. (a and b) Localization of β-arrestin and raf-1 by immunofluorescence and confocal microscopy. KNRK-PAR2+ARR-GFP cells (a) or KNRK-PAR2(δST363/6A)+ ARR-GFP cells (b) were incubated with 50 nM trypsin for 0 or 5 min at 37°C. β-Arrestin was localized using GFP and raf-1 was localized by immunofluorescence. The same cells are shown in each row and the images in the right panel are formed by superimposition of images from the other two panels in the same row. Representative of two experiments. In KNRK-PAR2+ARR-GFP cells, note the redistribution of β-arrestin and raf-1 from the cytosol at 0 min (arrows) to the plasma membrane at 5 min (arrowheads), where they colocalize. In KNRK-PAR2 (δST363/6A)+ARR-GFP cells, note that β-arrestins remain in the cytosol (arrows) and raf-1 redistributes to the plasma membrane at 5 min (arrowheads). (c–f) Coimmunoprecipitation of raf-1 and β-arrestin. Cells were incubated with 50 nM trypsin for 0–30 min at 37°C, lysed, immunoprecipitated (IP) using antibodies to GFP or β-arrestin-1/2, and analyzed by Western blotting (WB) with a raf-1 antibody. (c) In KNRK-PAR2 cells, but not in KNRK-PAR2(δST363/6A) cells, β-arrestin and raf-1 coprecipitated. (d) Similarly, in KNRK-PAR2+ARR-GFP cells but not KNRK-PAR2(δST363/6A)+ARR-GFP cells ARR-GFP and raf-1 coprecipitated with antibodies to GFP. (e) In KNRK-PAR2+ARR 319-418 -GFP cells, endogenous β-arrestin and raf-1 coprecipitated, but ARR 319-418 and raf-1 did not coprecipitate. (f) In hBRIE+ARR-GFP cells, ARR-GFP and raf-1 coprecipitated. Bars, 10 μm.

Article Snippet: Kirsten murine sarcoma virus–transformed rat kidney epithelial cells (KNRK) were from the American Type Tissue Culture Collection (ATCC CRL 1569).

Techniques: Immunofluorescence, Confocal Microscopy, Incubation, Clinical Proteomics, Membrane, Immunoprecipitation, Western Blot

Journal: The Journal of Cell Biology

Article Title: β-Arrestin–Dependent Endocytosis of Proteinase-Activated Receptor 2 Is Required for Intracellular Targeting of Activated Erk1/2

doi:

Figure Lengend Snippet: Gel filtration analysis of an ERK signaling complex. KNRK-PAR2 (a and b), KNRK-PAR2(δST363/6A) cells (c and d), or hBRIE cells (e and f), or KNRK-PAR2+ARR 319-418 -GFP cells (g) were untreated (a, c, and e) or incubated with 50 μM AP (b, d, f, and g) for 5 min. Cell lysates were fractionated on a S300 Sephacryl column. The presence of pERK, raf-1, β-arrestin-1, and PAR2 in each fraction was determined by Western blotting (inset). PAR2 was detected using HA.11 antibody in KNRK cells and 2N antibody in hBRIE cells. Results are expressed as a percentage of the total protein for each partition coefficient (σ) ( n = 3). The bracketed columns represent regions where proteins coeluted. Representative Western blots are shown of fractions containing the complex in KNRK-PAR2 cells (★, σ = 0.34), hBRIE cells (⋆, σ = 0.31–34), and in KNRK-PAR2+ARR 319-418 -GFP (*, σ = 0.45). (h) The Stoke's radii of the four molecular mass standards and the complex in KNRK-PAR2 cells (★, ∼6.2), hBRIE cells (⋆, ∼6.2–6.6), and KNRK-PAR2+ARR 319-418 -GFP (*, ∼5 nm) are graphed as a function of the error function complement of σ.

Article Snippet: Kirsten murine sarcoma virus–transformed rat kidney epithelial cells (KNRK) were from the American Type Tissue Culture Collection (ATCC CRL 1569).

Techniques: Filtration, Incubation, Western Blot

Journal: The Journal of Cell Biology

Article Title: β-Arrestin–Dependent Endocytosis of Proteinase-Activated Receptor 2 Is Required for Intracellular Targeting of Activated Erk1/2

doi:

Figure Lengend Snippet: Coprecipitation of components of the β-arrestin–containing signaling complex. (a) Fractions from the gel filtration columns of AP-stimulated KNRK-PAR2 cells at partition coefficients 0.31–0.34 were pooled, concentrated, and immunoprecipitated with pERK or β-arrestin-1/2 antibodies. Western blots were probed for PAR2 using the HA.11 antibody, β-arrestin-1, raf-1, and pERK. (b) Fractions from the gel filtration columns of AP-stimulated hBRIE cells at partition coefficients 0.31–0.34 were similarly processed, immunoprecipitated with a β-arrestin-1/2 antibody, and blotted with antibodies to pERK and raf-1.

Article Snippet: Kirsten murine sarcoma virus–transformed rat kidney epithelial cells (KNRK) were from the American Type Tissue Culture Collection (ATCC CRL 1569).

Techniques: Filtration, Immunoprecipitation, Western Blot

Journal: Journal of the American Chemical Society

Article Title: Chemoselective Installation of Amine Bonds on Proteins through Aza-Michael Ligation

doi: 10.1021/jacs.7b10702

Figure Lengend Snippet: Assessment of the biological activity of Recombumin and C2Am protein after chemical modification. (a) Biacore SPR analysis of Recombumin-Cys34, blue, and Recombumin-NHBn34, red, n = 3 replicates. (b) Fast protein liquid chromatography analysis utilizing a HiPrep S FF (GE Healthcare)–affinity column comparing C2Am-Cys, black, and C2Am-NHBn, red. (c) Flow cytometry plots obtained by fluorescence activated cell sorting (FACS) of C2Am-Cys (top) and C2Am-NHBn (bottom) labeling viable (green), apoptotic (blue) and necrotic (red) EL4 cells. Cell populations (%) for C2Am-Cys95; C2Am-NHBn95:33 ± 1%; 34 ± 1% (viable), 36 ± 4%; 34 ± 1% (apoptotic), 31 ± 6%; 32 ± 1% (necrotic). Apoptotic/viable MFI ratios (C2Am-Cys95; C2Am-NHBn95): 35 ± 1%; 87 ± 11%. Necrotic/viable MFI ratios (C2Am-Cys95; C2Am-NHBn95): 98 ± 4%; 411 ± 32%. MFI-median fluorescence intensity at 660 nm. Data is mean ± s.d., n = 3 replicates, 2 independent experiments.

Article Snippet: Murine lymphoma (EL4) cells (ATCC, Piscataway, NJ) were propagated in RPMI 1640 media (Sigma) supplemented with 10% fetal calf serum (FCS) and 2 mM l -glutamine (Sigma).

Techniques: Activity Assay, Modification, Fast Protein Liquid Chromatography, Affinity Column, Flow Cytometry, Fluorescence, FACS, Labeling

Journal:

Article Title: Molecular Characterization of the phaEC Hm Genes, Required for Biosynthesis of Poly(3-Hydroxybutyrate) in the Extremely Halophilic Archaeon Haloarcula marismortui ▿

doi: 10.1128/AEM.00953-07

Figure Lengend Snippet: Strains and plasmids used in this study

Article Snippet: To confirm this, we knocked out the phaEC Hh genes from H. hispanica ATCC 33960 (see Materials and Methods) and thus generated a phaEC -deleted strain named H. hispanica PHB-1.

Techniques: Plasmid Preparation, Mutagenesis, Expressing, Knock-Out